@article {pmid40673184, year = {2025}, author = {Standeven, FJ and Dahlquist-Axe, G and Hendy, J and Fiddyment, S and Holst, M and McGrath, K and Collins, M and Mundorff, A and Radini, A and Wagner, J and Meehan, CJ and Tedder, A and Speller, CF}, title = {An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research.}, journal = {Data in brief}, volume = {61}, number = {}, pages = {111770}, pmid = {40673184}, issn = {2352-3409}, abstract = {Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used including the skeletons' historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological science topics such as diet, disease, and antimicrobial resistance (AMR).}, }
@article {pmid40671036, year = {2025}, author = {Williams, MP and Huber, CD}, title = {The genomic footprints of migration: how ancient DNA reveals our history of mobility.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {206}, pmid = {40671036}, issn = {1474-760X}, support = {R35GM146886//National Institute of Health/ ; R35GM146886//National Institute of Health/ ; }, mesh = {Humans ; *DNA, Ancient/analysis ; *Human Migration ; *Genetics, Population/methods ; *Genome, Human ; *Genomics/methods ; }, abstract = {Ancient DNA has emerged as a powerful tool for studying human migration through the detection of admixture signatures. Here, we present the theoretical principles and methodologies for admixture analysis, with an emphasis on f-statistics and qpAdm. We review case studies from the literature demonstrating how these methods uncover patterns of human mobility, and discuss challenges related to data quality, demographic complexity, and sample representativeness on admixture and migration inferences. Finally, we highlight promising advancements in admixture analysis and underscore the importance of integrating genetic, archaeological, and historical data to achieve a more interdisciplinary and nuanced reconstruction of human history.}, }
@article {pmid40663601, year = {2025}, author = {Perretti, S and Santos, P and Vizzari, MT and Tassani, E and Benazzo, A and Ghirotto, S and Barbujani, G}, title = {Inference of human pigmentation from ancient DNA by genotype likelihoods.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {29}, pages = {e2502158122}, doi = {10.1073/pnas.2502158122}, pmid = {40663601}, issn = {1091-6490}, support = {2020HJXCK9//Italian Ministry of University (MUR) PRIN 2020/ ; 2020TACEZR//Italian Ministry of University (MUR) PRIN 2020/ ; P20228M8ZN//Italian Ministry of University (PRIN) 2022-PNRR/ ; }, mesh = {Humans ; *DNA, Ancient/analysis ; Genotype ; *Skin Pigmentation/genetics ; *Hair Color/genetics ; Eye Color/genetics ; Likelihood Functions ; *Pigmentation/genetics ; }, abstract = {Light eyes, hair, and skins probably evolved several times as Homo sapiens dispersed from Africa. In areas with lower UV radiation, light pigmentation alleles increased in frequency because of their adaptive advantage and of other contingent factors such as migration and drift. However, the tempo and mode of their spread is not known. Phenotypic inference from ancient DNA is complicated, both because these traits are polygenic and because of low sequence depth. We evaluated the effects of the latter by randomly removing reads in three high-coverage ancient samples, the Paleolithic Ust'-Ishim from Russia, the Mesolithic SF12 from Sweden, and the Neolithic I5077 from current Croatia. We could thus compare three approaches to pigmentation inference, concluding that for suboptimal levels of coverage (<8×), a probabilistic method estimating genotype likelihoods leads to the most robust predictions. We then applied that protocol to 348 ancient genomes from Eurasia, describing how skin, eye, and hair color evolved over the past 45,000 y. The shift toward lighter pigmentations turned out to be all but linear in time and place, and slower than expected, with half of the individuals showing dark or intermediate skin colors well into the Bronze and Iron ages. We also observed a peak of light eye pigmentation in Mesolithic times, and an accelerated change during the spread of Neolithic farmers over Western Eurasia, although localized processes of gene flow and admixture, or lack thereof, also played a significant role.}, }
@article {pmid40662803, year = {2025}, author = {Yılmaz, MA and Ceylan, AA and Kaynar, G and Çiçek, AE}, title = {LYCEUM: learning to call copy number variants on low-coverage ancient genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {Supplement_1}, pages = {i285-i293}, doi = {10.1093/bioinformatics/btaf244}, pmid = {40662803}, issn = {1367-4811}, mesh = {*DNA Copy Number Variations ; Humans ; *Machine Learning ; *DNA, Ancient/analysis ; *Software ; Algorithms ; Genome, Human ; }, abstract = {MOTIVATION: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes crucial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient DNA (aDNA) samples poses substantial challenges due to several factors: (i) aDNA is often highly degraded; (ii) contamination from microbial DNA and DNA from closely related species introduces additional noise into sequencing data; and finally, (iii) the typically low-coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, which are optimized for high-coverage read-depth signals, underperform under such conditions.<br><br>RESULTS: To address these limitations, we introduce LYCEUM, the first machine learning-based CNV caller for aDNA. To overcome challenges related to data quality and scarcity, we employ a two-step training strategy. First, the model is pre-trained on whole genome sequencing data from the 1000 Genomes Project, teaching it CNV-calling capabilities similar to conventional methods. Next, the model is fine-tuned using high-confidence CNV calls derived from only a few existing high-coverage aDNA samples. During this stage, the model adapts to making CNV calls based on the downsampled read depth signals of the same aDNA samples. LYCEUM achieves accurate detection of CNVs even in typically low-coverage ancient genomes. We also observe that the segmental deletion calls made by LYCEUM show correlation with the demographic history of the samples and exhibit patterns of negative selection inline with natural selection.<br><br>LYCEUM is available at https://github.com/ciceklab/LYCEUM.}, }
@article {pmid40655309, year = {2025}, author = {De Jonge, C and Dubois, N and Ladd, SN and Deng, L and Gajendra, N and Haghipour, N and Schubert, CJ and Lever, M}, title = {Holocene environmental change in Rotsee and its impact on sedimentary carbon storage.}, journal = {Journal of paleolimnology}, volume = {73}, number = {4}, pages = {311-327}, pmid = {40655309}, issn = {0921-2728}, abstract = {To assess the long-term impact of climate change and human influence on lakes and their sedimentary carbon storage, paleo-environmental approaches using well-dated lake sediment cores can be employed. Here, we reconstruct carbon mass accumulation rates for organic and inorganic carbon since 13 ka BP in Rotsee, a perialpine lake near the Swiss Alps, using a 12-m sediment core. A multiproxy approach (XRF, carbon and nitrogen isotopes, organic macromolecule chemical compositions, aDNA) was used to explore changes in the lake system that affect sedimentary carbon storage. The Early Holocene (11.8-7 cal ka BP) was characterized by a mixed phytoplankton and watershed-derived provenance of organic matter, and the deposition of inorganic and organic sedimentary carbon. Warming during the Holocene Thermal Maximum (9.8-8.8 cal ka BP) increased sedimentary carbon storage. In the Mid- to Late Holocene (7-1 cal ka BP), the sedimentary record indicates an increased influx of allochthonous, vascular plant-derived organic matter, and low production or conservation of phytoplankton-derived carbon. Organic carbon storage increased, while inorganic carbon became negligible. Larger deforestation events, potentially during Neolithic times (around 4 ka BP), but especially during Roman times (2 ka BP), coincided with further increased organic carbon MARs. Recent sediments, influenced by eutrophication in the last century, show higher carbon accumulation rates compared to earlier Holocene periods. Rotsee serves as a case study of how climate warming and human land use changes have influenced lake development and sedimentary carbon6 storage, with broader implications for understanding carbon dynamics in high altitude lakes and their future carbon balance.}, }
@article {pmid40644297, year = {2025}, author = {Wang, K}, title = {Q&amp;A with Ke Wang.}, journal = {Cell reports}, volume = {44}, number = {7}, pages = {115968}, doi = {10.1016/j.celrep.2025.115968}, pmid = {40644297}, issn = {2211-1247}, abstract = {In this interview, Dr. Jorge Santos discusses with Dr. Ke Wang her research focusing on the evolutionary history of human ancient populations through the study of ancient DNA and sociocultural innovations. Dr. Wang recently published in Cell Reports on the prehistoric population interactions and dynamics along the Yellow River Bend of China.}, }
@article {pmid40640605, year = {2025}, author = {Bundell, S and Petrić Howe, N}, title = {Ancient DNA reveals farming led to more human diseases.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-025-02179-5}, pmid = {40640605}, issn = {1476-4687}, }
@article {pmid40635430, year = {2025}, author = {Campbell, MA and Ward, I and Blyth, A and Allentoft, ME}, title = {Using sedimentary ancient DNA in coastal and marine contexts to explore past human-environmental interactions in Australia.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1930}, pages = {20240032}, pmid = {40635430}, issn = {1471-2970}, mesh = {Australia ; *Geologic Sediments/chemistry/analysis ; *DNA, Ancient/analysis ; Humans ; *Ecosystem ; Biodiversity ; Oceans and Seas ; }, abstract = {Over the 65 000 years of human occupation in Australia, sea levels have fluctuated significantly, notably rising from -120 m around 21 000 years ago, submerging vast areas of the continental shelf. Current coastal ecosystems stabilized about 5000 years ago, leaving many early cultural landscapes underwater, complicating the study of ancient human activity. Sedimentary ancient DNA (sedaDNA) analysis, a powerful tool for monitoring ecological changes and human-environment interactions, has recently gained attention but its exploration is still in its early stages in Australia. This approach holds great potential for investigating shifts in resource and land-use changes, the introduction of non-native species and distinguishing between human and natural impacts on biodiversity. Despite challenges with DNA preservation due to Australia's harsh climate, organic-rich coastal and marine sediments may provide favourable conditions for sedaDNA. We review case studies across Australia, showcasing how sedaDNA offers valuable insights into past coastal ecologies and can contribute to developing a sustainable biocultural landscape.This article is part of the theme issue 'Shifting seas: understanding deep-time human impacts on marine ecosystems'.}, }
@article {pmid40635429, year = {2025}, author = {Zampirolo, G and McCarthy, ML and Živaljević, I and Penezić, K and Vuković, S and Mladenović, T and Marković, D and Marković, N and Radmanović, D and Orton, D and Tange Olsen, M and Pedersen, MW}, title = {Continuous mitochondrial diversity of Danube sturgeon species over millennia: insights from ancient DNA.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {380}, number = {1930}, pages = {20240034}, pmid = {40635429}, issn = {1471-2970}, support = {//Horizon 2020 Framework Programme/ ; //Carlsberg Semper Ardens Accelerate fellowship/ ; //Danmarks Grundforskningsfond/ ; //H2020 Marie Sk&#x142;odowska-Curie Actions/ ; //Carlsbergfondet/ ; }, mesh = {Animals ; *Fishes/genetics/classification ; *DNA, Ancient/analysis ; *DNA, Mitochondrial/genetics/analysis ; *Genetic Variation ; }, abstract = {Sturgeons, an iconic group of large fishes inhabiting marine and freshwater ecosystems, have historically had significant economic and cultural value, particularly prized for their meat and roe (caviar). Furthermore, sturgeons play a vital ecological role as mesopredators of prey fish and invertebrates. In the Danube basin, the European (Acipenser sturio) and fringebarbel or ship sturgeon (Acipenser nudiventris) are locally extinct, while beluga (Huso huso), Russian (Acipenser gueldenstaedtii), stellate (Acipenser stellatus) and sterlet (Acipenser ruthenus) sturgeon have significantly declined since the nineteenth century owing to overfishing, habitat loss and pollution. Archaeological evidence suggests that sturgeon exploitation along the Danube began as early as 11.6 thousand years before the present. This study explores the genetic landscape of Danube sturgeons over the past approximately 10 000 years using ancient DNA (aDNA) from archaeological specimens. Despite challenges posed by limited sample size, phylogenetic analyses of mitochondrial genomes and the D-loop reveal high genetic diversity within beluga, Russian and ship sturgeon populations. In addition, shared haplotypes between modern and historical specimens of both beluga and Russian sturgeons suggest genetic continuity within each species over time. This study provides, to our knowledge, the first high-coverage sequencing of ancient sturgeon mitogenomes establishing the foundation for future aDNA research.This article is part of the theme issue 'Shifting seas: understanding deep-time human impacts on marine ecosystems'.}, }
@article {pmid40634615, year = {2025}, author = {Green, DR and Uno, KT and Miller, ER and Feibel, CS and Aoron, EE and Beck, CC and Grossman, A and Kirera, FM and Kirinya, MM and Leakey, LN and Liutkus-Pierce, C and Manthi, FK and Ndiema, EK and Nengo, IO and Nyete, C and Rowan, J and Russo, GA and Sanders, WJ and Smiley, TM and Princehouse, P and Vitek, NS and Cleland, TP}, title = {Eighteen million years of diverse enamel proteomes from the East African Rift.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40634615}, issn = {1476-4687}, abstract = {Research into the palaeobiology of extinct taxa through ancient DNA and proteomics has been mostly limited to Plio-Pleistocene fossils[1-9], due to molecular breakdown over time, which is exacerbated in tropical settings[1-3]. Here we sample small proteomes from the interior enamel of fossils at palaeontological sites from the Pleistocene to the Oligocene in the Turkana Basin, Kenya, which has produced a rich record of Cenozoic mammalian evolution[10]. Through a mass-spectrometry-based proteomic workflow, and using criteria to locate diagenetiforms derived from enamel, we recover fragments of enamelin, ameloblastin, matrix metalloprotease-20 and dentin matrix acidic phosphoprotein 1 from an Early Miocene rhinocerotid and several proboscideans collected from the sites of Buluk (16 million years ago; Ma) and Loperot (18 Ma). Diagenetiform counts decline in progressively older fossils, and we observe variability in Early Miocene preservation across sites. Phylogenetic analyses reveal the contribution of these sequences to the systematic placement of extinct taxa, although we caution that this approach must account for sparse fragments, uncertainty in fragment identification and possible sequence diagenesis. We identify likely modifications that support the ancient age of these proteins, and some of the oldest examples of advanced glycation end-products yet known. The discovery of protein sequences within dense enamel tissues in one of the persistently warmest regions on Earth promises the discovery of much older proteomes that will aid in the study of the palaeobiology and evolutionary relationships of extinct taxa.}, }
@article {pmid40611166, year = {2025}, author = {Davidson, R and Roca-Rada, X and Ravishankar, S and Taufik, L and Haarkötter, C and Collen, E and Williams, MP and Webb, P and Mahmud, MI and Djami, ENI and Purnomo, GA and Santos, C and Malgosa, A and Manzanilla, LR and Silva, AM and Tereso, S and Matos, V and Carvalho, PC and Fernandes, T and Maurer, AF and Teixeira, JC and Tobler, R and Fehren-Schmitz, L and Llamas, B}, title = {Optimized in-solution enrichment of over a million ancient human SNPs.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {190}, pmid = {40611166}, issn = {1474-760X}, support = {PTDC/HAR-ARQ/6273/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; UIDB/00283/2020//Foundation for Science and Technology, Portugal/ ; FPU 20/01967//Ministerio de Universidades/ ; DE190101069//Australian Research Council/ ; CE170100015//Australian Research Council/ ; }, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *DNA, Ancient/analysis ; High-Throughput Nucleotide Sequencing/methods ; Gene Library ; Sequence Analysis, DNA/methods ; Genome, Human ; }, abstract = {BACKGROUND: In-solution hybridization enrichment of genetic markers is a method of choice in paleogenomic studies, where the DNA of interest is generally heavily fragmented and contaminated with environmental DNA, and where the retrieval of genetic data comparable between individuals is challenging. Here, we benchmark the commercial "Twist Ancient DNA" reagent from Twist Biosciences using sequencing libraries from ancient human samples of diverse demographic origin with low to high endogenous DNA content (0.1-44%). For each library, we tested one and two rounds of enrichment and assessed performance compared to deep shotgun sequencing.<br><br>RESULTS: We find that the "Twist Ancient DNA" assay provides robust enrichment of approximately 1.2M target SNPs without introducing allelic bias that may interfere with downstream population genetics analyses. Additionally, we show that pooling up to 4 sequencing libraries and performing two rounds of enrichment is both reliable and cost-effective for libraries with less than 27% endogenous DNA content. Above 38% endogenous content, a maximum of one round of enrichment is recommended for cost-effectiveness and to preserve library complexity.<br><br>CONCLUSIONS: In conclusion, we provide researchers in the field of human paleogenomics with a comprehensive understanding of the strengths and limitations of different sequencing and enrichment strategies, and our results offer practical guidance for optimizing experimental protocols.}, }
@article {pmid40609663, year = {2025}, author = {Muschick, M and Rüber, L and Matschiner, M}, title = {Museomics reveals the phylogenetic position of an enigmatic vertebrate family (Lophiiformes: Lophichthyidae).}, journal = {Molecular phylogenetics and evolution}, volume = {211}, number = {}, pages = {108406}, doi = {10.1016/j.ympev.2025.108406}, pmid = {40609663}, issn = {1095-9513}, abstract = {Lophichthys boschmai, the only member of the family Lophichthyidae, is an elusive lophiiform fish whose phylogenetic associations are debated. This family is among the last two vertebrate families lacking DNA sequence data, primarily due to the species' rarity, lack of fresh material and challenges associated with sequencing formalin-treated museum specimens. In this study, we provide mitochondrial and nuclear DNA sequences obtained from two museum specimens of Lophichthys boschmai. Employing ancient DNA techniques, we successfully extracted and analyzed the degraded and fragmented DNA. Our findings, derived from both mitochondrial genomes and nuclear ultra-conserved elements (UCE), reveal the Lophichthyidae as sister lineage to Tathicarpidae within the Antennarioidei. This study showcases the use of whole-genome "shotgun" sequencing data from formalin-fixed museum specimens in the context of an available UCE dataset. Given the enhanced versatility in data reusability this approach offers, we suggest it should be a favored approach when studying rare specimens.}, }
@article {pmid40608932, year = {2025}, author = {Liu, JH and Ruan, QJ and Ge, JY and Huang, YJ and Zhang, XL and Liu, J and Li, SF and Shen, H and Wang, Y and Stidham, TA and Deng, CL and Li, SH and Han, F and Jin, YS and O'Gorman, K and Li, B and Dennell, R and Gao, X}, title = {300,000-year-old wooden tools from Gantangqing, southwest China.}, journal = {Science (New York, N.Y.)}, volume = {389}, number = {6755}, pages = {78-83}, doi = {10.1126/science.adr8540}, pmid = {40608932}, issn = {1095-9203}, mesh = {China ; Animals ; Archaeology ; *Fossils ; Hominidae ; Wood ; Bone and Bones ; History, Ancient ; }, abstract = {Evidence of Early and Middle Pleistocene wooden implements is exceptionally rare, and existing evidence has been found only in Africa and western Eurasia. We report an assemblage of 35 wooden implements from the site of Gantangqing in southwestern China, which was found associated with stone tools, antler billets (soft hammers), and cut-marked bones and is dated from ~361,000 to ~250,000 years at a 95% confidence interval. The wooden implements include digging sticks and small, complete, hand-held pointed tools. The sophistication of many of these tools offsets the seemingly "primitive" aspects of stone tool assemblages in the East Asian Early Paleolithic. This discovery suggests that wooden implements might have played an important role in hominin survival and adaptation in Middle Pleistocene East Asia.}, }
@article {pmid40604287, year = {2025}, author = {Zeng, TC and Vyazov, LA and Kim, A and Flegontov, P and Sirak, K and Maier, R and Lazaridis, I and Akbari, A and Frachetti, M and Tishkin, AA and Ryabogina, NE and Agapov, SA and Agapov, DS and Alekseev, AN and Boeskorov, GG and Derevianko, AP and Dyakonov, VM and Enshin, DN and Fribus, AV and Frolov, YV and Grushin, SP and Khokhlov, AA and Kiryushin, KY and Kiryushin, YF and Kitov, EP and Kosintsev, P and Kovtun, IV and Makarov, NP and Morozov, VV and Nikolaev, EN and Rykun, MP and Savenkova, TM and Shchelchkova, MV and Shirokov, V and Skochina, SN and Sherstobitova, OS and Slepchenko, SM and Solodovnikov, KN and Solovyova, EN and Stepanov, AD and Timoshchenko, AA and Vdovin, AS and Vybornov, AV and Balanovska, EV and Dryomov, S and Hellenthal, G and Kidd, K and Krause, J and Starikovskaya, E and Sukernik, R and Tatarinova, T and Thomas, MG and Zhabagin, M and Callan, K and Cheronet, O and Fernandes, D and Keating, D and Candilio, F and Iliev, L and Kearns, A and Özdoğan, KT and Mah, M and Micco, A and Michel, M and Olalde, I and Zalzala, F and Mallick, S and Rohland, N and Pinhasi, R and Narasimhan, VM and Reich, D}, title = {Ancient DNA reveals the prehistory of the Uralic and Yeniseian peoples.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40604287}, issn = {1476-4687}, abstract = {The North Eurasian forest and forest-steppe zones have sustained millennia of sociocultural connections among northern peoples, but much of their history is poorly understood. In particular, the genomic formation of populations that speak Uralic and Yeniseian languages today is unknown. Here, by generating genome-wide data for 180 ancient individuals spanning this region, we show that the Early-to-Mid-Holocene hunter-gatherers harboured a continuous gradient of ancestry from fully European-related in the Baltic, to fully East Asian-related in the Transbaikal. Contemporaneous groups in Northeast Siberia were off-gradient and descended from a population that was the primary source for Native Americans, which then mixed with populations of Inland East Asia and the Amur River Basin to produce two populations whose expansion coincided with the collapse of pre-Bronze Age population structure. Ancestry from the first population, Cis-Baikal Late Neolithic-Bronze Age (Cisbaikal_LNBA), is associated with Yeniseian-speaking groups and those that admixed with them, and ancestry from the second, Yakutia Late Neolithic-Bronze Age (Yakutia_LNBA), is associated with migrations of prehistoric Uralic speakers. We show that Yakutia_LNBA first dispersed westwards from the Lena River Basin around 4,000 years ago into the Altai-Sayan region and into West Siberian communities associated with Seima-Turbino metallurgy-a suite of advanced bronze casting techniques that expanded explosively from the Altai[1]. The 16 Seima-Turbino period individuals were diverse in their ancestry, also harbouring DNA from Indo-Iranian-associated pastoralists and from a range of hunter-gatherer groups. Thus, both cultural transmission and migration were key to the Seima-Turbino phenomenon, which was involved in the initial spread of early Uralic-speaking communities.}, }
@article {pmid40603668, year = {2025}, author = {}, title = {Ancient DNA helps trace stinky Roman fish sauce to its source.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40603668}, issn = {1476-4687}, }
@article {pmid40598853, year = {2025}, author = {Fan, GY and Tian-Ge, J and Zhu, Y}, title = {Decoding the Han paternal legacy: a Y chromosomal genealogy of Xuzhou as the cradle of the Han civilization.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {}, number = {}, pages = {}, doi = {10.1127/anthranz/1857}, pmid = {40598853}, issn = {0003-5548}, abstract = {Xuzhou, hailed as the Oriental Athens, holds a pivotal position in the development of Han Chinese culture. This study delves into the genetic makeup of the Xuzhou Han population utilizing Y-chromosomal markers, aiming to enrich population genetics and forensic science research. We analyzed 638 unrelated males from Pei County, Xuzhou, through the SureID[®] PathFinder Plus Kit. The pairwise genetic relationships were compared between the Xuzhou Han and 52 other Chinese population. We employed the k-nearest neighbor algorithm for Y-SNP haplogroup prediction and Linear Discriminant Analysis (LDA) for category forecasting. Most Y-STR loci exhibited high polymorphism, with the exception of DYS645. The Xuzhou Han population showcased a haplotype diversity of 0.9997 and a discrimination capacity of 0.9708. Genetic similarities were detected among Han populations across the nation, with the Xuzhou Han revealing a prevalence of Y haplogroups O2a2 and O2a1. Comparisons of haplogroup distributions across 55 contemporary Chinese ethnic groups and ancient DNA from 59 archaeological sites unveiled the widespread presence of the O2 haplogroup before the Han Dynasty. Our research also underscores the Y chromosomal genealogy continuity of the O2 population in northern China from the Neolithic to modern times. Meanwhile, LDA hints a long history of integration between Jiangsu Han groups. Nevertheless, the Xuzhou Han still exhibited an extremely high O2a2 ratio, reflecting the rapid expansion of this patrilineal familys population base throughout history. Our study is not only expected to have a positive impact on the reconstruction of the local patrilineal history, but also defined forensic applications and deepens the understanding of Han Chinese culture through the lens of paternal genetics.}, }
@article {pmid40597195, year = {2025}, author = {Sun, L and Ma, H and Wang, R and Wu, Z and Qiu, L and Chen, H and Wang, CC}, title = {The demic expansion of Yangshao culture inferred from ancient human genomes.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {186}, pmid = {40597195}, issn = {1741-7007}, mesh = {Humans ; China ; *Genome, Human ; *Human Migration/history ; *DNA, Ancient/analysis ; Archaeology ; }, abstract = {BACKGROUND: Originating from the middle Yellow River, Yangshao culture is one of the most influential archaeological cultures in Neolithic China. It has long been debated whether there was a genetic substructure between the core Yangshao sites and those representing regional variants of the Yangshao culture, such as the Qinwangzhai culture. The excavated human remains from the burials at the Zhanmatun site, which belonged to the Qinwangzhai culture, present ideal material for inferring the population dynamics accompanying the cultural expansion.<br><br>RESULTS: In this study, we analyzed genome-wide data from 12 human remains obtained from the Zhanmatun site. The results indicated that Zhanmatun individuals were genetically homogeneous with all published Yangshao culture-related individuals from the core region of Yangshao and its periphery as well as Late Dawenkou culture-related Xixiahou people in the east, with no tracts of genetic influence from Neolithic Southern East Asian in the south.<br><br>CONCLUSIONS: Our findings support a demic diffusion model for Yangshao culture expansion, where human migration, rather than mere cultural diffusion, played a dominant role in spreading Yangshao-related ancestry across northern China.}, }
@article {pmid40590317, year = {2025}, author = {Champney, TH and Smith, HF and Hildebrandt, S and Cornwall, J}, title = {Human, Animal, or Mineral? Ethical Considerations for Studies of Fossilized Hominin Remains.}, journal = {American journal of biological anthropology}, volume = {187}, number = {3}, pages = {e70085}, pmid = {40590317}, issn = {2692-7691}, mesh = {*Fossils ; Humans ; *Hominidae ; Animals ; *Paleontology/ethics ; }, abstract = {Ethical considerations around research and education with modern human subjects, use of human tissue, and studies involving humans are ubiquitous within the global scientific community. This commentary explores considerations around how and whether these types of ethical considerations may apply to hominin fossils. While some might propose that the age of a fossil could be the basis for decisions around their ethical handling, it may be that characteristics or behaviors of the hominins are a more appropriate measure to determine their ethical status. These types of ethical considerations have recently been examined in other historical human tissues, such as mummies and ancient DNA, with these ethical explorations being driven by a recognition of evolving ethical perspectives around the world. Thus, there is both the precedent and stimulus for the paleoanthropology community to revisit current ethical practices within the profession. Doing so would help identify and establish standards that are reflective of global perspectives around the contemporary ethical management of hominin fossils, and potentially assist in aligning these practices with other disciplines that work with both hominin fossils and human tissues.}, }
@article {pmid40578321, year = {2025}, author = {Li, R and Zang, Y and Liu, Z and Yang, J and Wang, N and Liu, J and Wu, E and Wu, R and Sun, H}, title = {clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/gpbjnl/qzaf055}, pmid = {40578321}, issn = {2210-3244}, abstract = {The detection of identity-by-descent (IBD) segments is widely used to infer relatedness in many fields, including forensics and ancient DNA analysis. However, existing methods are often ineffective for poor-quality DNA samples. Here, we propose a method, clusIBD, which can robustly detect IBD segments using unphased genetic data with a high rate of genotype error. We evaluated and compared the performance of clusIBD with that of IBIS, TRUFFLE, and IBDseq using simulated data, artificial poor-quality materials, and ancient DNA samples. The results show that clusIBD outperforms these tools and could be used for kinship inference in fields such as ancient DNA analysis and criminal investigation. ClusIBD is publicly available at GitHub (https://github.com/Ryan620/clusIBD/) and BioCode (https://ngdc.cncb.ac.cn/biocode/tool/BT007882).}, }
@article {pmid40568545, year = {2025}, author = {Turvey, ST and Ortiz, A and Granger, M and Brace, S and Henriksen, RA and Yang, Q and Nguyễn, TA and Buck, LT and Ma, H and Hansford, JP and Booth, T and Chatterjee, HJ and Fan, P and Chen, X}, title = {Morphometric characterization of Holocene mandibles expands the ecological baseline for understanding gibbon extinction dynamics.}, journal = {Royal Society open science}, volume = {12}, number = {6}, pages = {242065}, pmid = {40568545}, issn = {2054-5703}, abstract = {Human activities have driven biodiversity loss for millennia, and conservation of 'refugee species' that survive as remnant populations requires insights from historical baselines. However, reconstructing the past distribution and ecology of such species is challenging due to data limitations with specimen-based archives. Here, we assess the taxonomic identity of two gibbon mandibles from the Wumingshan Neolithic site in Guangxi, China. Although ancient DNA extraction was unsuccessful, a suite of linear and geometric morphometric analyses using dental and mandibular characters reveals that these mandibles fall within or close to variation shown by extant Chinese Nomascus gibbons and can be assigned to the cao vit gibbon N. nasutus. This is now one of the world's rarest mammals, with a surviving population of 74 individuals in one site. Comparative assessment of bioclimatic, abiotic and anthropogenic parameters for Wumingshan and other sites where N. nasutus historically occurred reveals the species was formerly a landscape generalist but is now restricted to a high-elevation refugium with reduced human pressures. Our multidisciplinary analyses provide a new baseline on niche requirements and vulnerability for N. nasutus with implications for population management, demonstrating the importance of integrating environmental archives into conservation planning.}, }
@article {pmid40565531, year = {2025}, author = {Zhu, Y and Hou, X and Zhao, J and Xiao, B and Song, S and Zou, X and Liu, S and Hofreiter, M and Lai, X}, title = {Revisiting Aurochs Haplogroup C: Paleogenomic Perspectives from Northeastern China.}, journal = {Genes}, volume = {16}, number = {6}, pages = {}, pmid = {40565531}, issn = {2073-4425}, support = {41972001//National Natural Science Foundation of China/ ; 2016-2041//the "PPP" project jointly funded by China Scholarship Council and DAAD, Germany, funded by German Academic Exchange Service/ ; }, mesh = {Animals ; *Haplotypes/genetics ; China ; Cattle/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; Fossils ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; }, abstract = {BACKGROUND/OBJECTIVES: Aurochs (Bos primigenius), one of the earliest and largest herbivores domesticated by humans, were widely distributed in Eurasia and North Africa during the Pleistocene and Holocene. Studies of aurochs in China have focused mainly on the Northeastern region. Previous studies have suggested that haplogroup C is a haplogroup unique to China, but recent studies have shown that this is not the case. We have compiled all data on haplogroup C to revisit the classification of the aurochs haplogroup C.<br><br>METHODS: In this study, we obtained 13 nearly complete mitochondrial genomes from Late Pleistocene to early Holocene bovine samples from Northeastern China through fossil sample collection, ancient DNA extraction, library construction, and high-throughput sequencing. Based on the acquired ancient DNA data and in combination with previously published bovine data, the phylogenetic status, lineage divergence time, and population dynamics of aurochs in Northeastern China were analyzed.<br><br>RESULTS: Phylogenetic analyses and divergence time estimations suggest that the current definition of haplogroup C is overly inclusive, necessitating a refined reclassification of this haplogroup. We also estimated the population dynamics of aurochs in Northeastern China using Bayesian skyline plots found that the maternal effective population size of the aurochs increased significantly during Marine Isotope Stage 5 (MIS5), but began to decrease in the second half of MIS3 before they eventually became extinct.<br><br>CONCLUSIONS: Our results provide new molecular evidence on the phylogenetic status, divergence time, and population dynamics of aurochs in Northeastern China.}, }
@article {pmid40564233, year = {2025}, author = {Katanyuphan, Y and Krajaejun, P and Wattanapituksakul, A and Surat, W}, title = {The First Report of Rhino DNA in Thailand: A Possible Extinct Indian Javan Subspecies, Rhinoceros sondaicus inermis.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/ani15121678}, pmid = {40564233}, issn = {2076-2615}, support = {B4301-00121-65//Kasetsart University, Bangkok, Thailand/ ; N42A650275//the National Research Council of Thailand (NRCT)/ ; }, abstract = {The Javan rhino is a critically endangered species that has become extinct in several Asian countries, including Thailand. There are three Javan rhino subspecies: Rhinoceros sondaicus sondaicus, R. s. annamiticus, and R. s. inermis, and the first two subspecies existed in Thailand decades ago. However, no genetic study on Thai rhinos has been reported. In this study, we amplified a partial D-loop region of two ancient rhino specimens dated to approximately 100 years before present, from southwest Thailand. Then, we constructed phylogenetic trees and a haplotype network based on the D-loop sequences of the Thai rhinos and 39 Javan, Sumatran, and Indian rhinos from the GenBank database. The ancient Thai rhino DNA belonged to Javan rhinos and was clearly separated from R. s. annamiticus and R. s. sondaicus. The nucleotide differences among the ancient Thai, R. s. annamiticus, and R. s. sondaicus rhino DNA were 5.14-8.30%, similar to those between two white rhino subspecies. Moreover, species delimitation analyses confirmed that the ancient Thai rhinos should belong to another Javan rhino subspecies, possibly the extinct Indian Javan rhino. This is the first report of rhino DNA from Thailand and possibly the Indian Javan rhino DNA, which could be used for evolutionary studies.}, }
@article {pmid40559445, year = {2025}, author = {Rbbani, G and Siriyappagouder, P and Murshed, R and Joshi, R and Nedoluzhko, A and Galindo-Villegas, J and Fernandes, JMO}, title = {Optimization of Nile Tilapia Artificial Breeding Using Human Chorionic Gonadotropin (hCG) Hormone.}, journal = {Methods and protocols}, volume = {8}, number = {3}, pages = {}, pmid = {40559445}, issn = {2409-9279}, support = {683210, 101081935/ERC_/European Research Council/International ; 250548, 310103, 311799//Research Council of Norway/ ; 817992//EU H2020/ ; }, abstract = {Nile tilapia (Oreochromis niloticus) is the most widely farmed tilapia species globally, making it one of the most important aquaculture species. To meet increasing demand, hatcheries occasionally use artificial breeding techniques such as hormonal induction to synchronize breeding. Despite the common use of human chorionic gonadotropin (hCG) in fish breeding, no detailed protocol has been established specifically for Nile tilapia. The objective of this study is to establish an effective hCG-induced artificial breeding protocol for gene editing and aquaculture production, optimizing fertilization, hatching, and survival rates. We employed a single intramuscular injection of 2 IU/g hCG to induce ovulation. The protocol achieved an average fertilization rate of 88.3% and a larval survival rate of 90.5%, demonstrating its potential for obtaining high-quality embryos for functional studies and enhancing reproductive performance on a commercial scale.}, }
@article {pmid40556972, year = {2025}, author = {Andreeva, TV and Soshkina, AD and Kunizheva, SS and Manakhov, AD and Pezhemsky, DV and Rogaev, EI}, title = {Great Bolgar's historical genetics: a genomic study of individuals from burials close to the Greek Chamber in the 14th century.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {29}, number = {3}, pages = {423-432}, doi = {10.18699/vjgb-25-45}, pmid = {40556972}, issn = {2500-0462}, abstract = {Bolgar was one of the most significant mediaeval cities in Eastern Europe. Before the Mongol conquest, it served as a major administrative centre of Volga Bulgaria, and after 1236, it temporarily functioned as the capital of the Golden Horde. Historical, archaeological, and paleoanthropological evidence indicates a mixed population of this city during the 13th-15th centuries; however, the contributions of exact ethnic groups into its genetic structure remain unclear. To date, there are no genetic data for this medieval group. For the first time, using massive parallel sequencing methods, we determined whole-genome sequences for three individuals from Bolgar who were buried in the early 14th century close to the so-called "Greek Chamber". The average coverage of the studied genomes ranged from x0.5 to x1.5. We identified the genetic sex of the people (two men and one woman), and performed a population genetic analysis. The authenticity of the DNA studied and the low level of contamination were confirmed, and the mitochondrial DNA haplogroups of all three individuals as well as the Y-chromosome haplogroups of two male individuals were determined. We used more than 2.7 thousand DNA samples from representatives of ancient and modern populations that had been previously published to perform a comparative population-genetic analysis. Whole-genome data analysis employing uniparental markers (mitochondrial DNA and Y chromosome) and autosomal markers revealed genetic heterogeneity in this population. Based on PCA and f4- statistics analysis, a genetic connection was identified between one of the individuals (female) and modern Finno-Ugric peoples of the Volga-Ural region. Genomic analysis of the other two individuals suggests their Armenian origin and indicates migrant influx from the Caucasus or Anatolia. The results align well with archaeological and paleoanthropological findings and significantly enhance them by reconstructing the contributions of the indigenous population to the formation of the mediaeval Bolgar population structure.}, }
@article {pmid40555717, year = {2025}, author = {Szécsényi-Nagy, A and Virag, C and Jakab, K and Rohland, N and Ringbauer, H and Anders, A and Raczky, P and Hajdu, T and Kiss, K and Szeniczey, T and Évinger, S and Keszi, T and M Virág, Z and Cheronet, O and Mallick, S and Akbari, A and Pinhasi, R and Reich, D and Siklósi, Z}, title = {Ancient DNA reveals diverse community organizations in the 5th millennium BCE Carpathian Basin.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5318}, pmid = {40555717}, issn = {2041-1723}, mesh = {Humans ; *DNA, Ancient/analysis ; Haplotypes ; *Genetics, Population ; History, Ancient ; Genome, Human ; Male ; Genetic Variation ; }, abstract = {Little is known about the genetic connection system and community organization of Late Neolithic and Early Copper Age populations of the Carpathian Basin. Here, we present a comprehensive genetic investigation of these populations, leveraging whole genome data from 125 individuals. Using population genetics, kinship analyses and the study of networks of identity-by-descent haplotype segment sharing, we elucidate the social and genetic dynamics of these communities between 4800-3900 calibrated years BCE. Despite changes in settlement patterns, burial practices, and material culture, we document a high degree of genetic continuity. While one set of individuals from a large community cemetery is genetically diverse, another site is more homogenous and closed, with numerous consanguineous relationships and evidence of patrilineality and patrilocality. In this work, we document important differences in kinship systems in contemporaneous Early Copper Age communities using similar material culture and living only about 100 km apart.}, }
@article {pmid40534706, year = {2025}, author = {Skinner, L and Felix, M and Rodrigues, CL and Iñiguez, AM}, title = {Genotyping specimens of human lice from a centenary entomological collection.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {7}, number = {}, pages = {100276}, pmid = {40534706}, issn = {2667-114X}, abstract = {Pediculus humanus has been infesting humans since their origin. This obligatory hematophagous and monoxenic parasite has co-evolved with its hosts, carrying genetic information that reflects this long evolutionary history. The ecotypes of P. humanus are divided into six phylogenetic clades (A-F) with distinct geographical distributions. Paleoparasitological studies have revealed a high lice infestation rate in mummies from various chronological periods and cultures worldwide. In this study, we conducted a paleogenetic analysis of head lice specimens from the Entomological Collection of Oswaldo Cruz Institute, collected in Suriname in 1941, to investigate the P. humanus mitochondrial haplotypes that were circulating in that population at that time. Ancient DNA was extracted from adult lice specimens, and paleogenetic analysis was performed using PCR-Sanger sequencing targeting the mitochondrial cytochrome b (cytb) gene. Our results identified sequences belonging to the cosmopolitan clade A, specifically the haplotype A17. A17 is the second largest cosmopolitan haplotype within clade A, with representatives found across all continents, but never found in South America. In 1941, Suriname, as part of the Kingdom of the Netherlands, experienced various socio-political changes and movements of populations due to World War II. This finding reflects both the colonial activities of that time and the global conflicts influencing human migrations. Specimens housed in collections for many decades often exhibit degraded DNA due to preservation techniques being inappropriate for molecular studies, posing challenges for genetic analysis. Our findings highlight the importance of biological collections as valuable repositories of genetic information that can shed light on the past distributions and interactions of parasitic species.}, }
@article {pmid40527453, year = {2025}, author = {Manin, A and Debruyne, R and Lin, A and Lebrasseur, O and Dimopoulos, EA and González Venanzi, L and Charlton, S and Scarsbrook, L and Hogan, A and Linderholm, A and Boyko, AR and Joncour, P and Berón, M and González, P and Castro, JC and Cornero, S and Cantarutti, G and López Mendoza, P and Martínez, I and Mendoza España, V and Pavlovic, D and Prates, L and Prevosti, F and Rogan, J and Oyaneder, A and Power, X and deFrance, S and Wylde, M and Gutierrez, B and Grouard, S and Freiwald, C and Awe, JJ and Ebert, CE and Hoggarth, JA and Equihua, JC and Pereira, G and Parker, H and Lefèvre, C and Goepfert, N and Ostrander, E and Larson, G and Frantz, L and Hitte, C and Ollivier, M}, title = {Ancient dog mitogenomes support the dual dispersal of dogs and agriculture into South America.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2049}, pages = {20242443}, pmid = {40527453}, issn = {1471-2954}, support = {//Natural Environment Research Council/ ; //R&#xe9;gion Bretagne/ ; //Mus&#xe9;um National d'Histoire Naturelle/ ; //the Intramural Program of the National Human Genome Research Institute of the U.S, National Institute of Health/ ; }, mesh = {Animals ; Dogs/genetics ; *Genome, Mitochondrial ; South America ; *Agriculture ; Phylogeny ; *Animal Distribution ; Archaeology ; }, abstract = {Archaeological and palaeogenomic data show that dogs were the only domestic animals introduced during the early peopling of the Americas. Hunter-gatherer groups spread quickly towards the south of the continent, but it is unclear when dogs reached Central and South America. To address this issue, we generated and analysed 70 complete mitochondrial genomes from archaeological and modern dogs ranging from Central Mexico to Central Chile and Argentina, revealing the dynamics of dog populations. Our results demonstrate that pre-contact Central and South American dogs are all assigned to a specific clade that diverged after dogs entered North America. Specifically, the divergence time between North, Central and South American dog clades is consistent with the spread of agriculture and the adoption of maize in South America between 7000 and 5000 years ago. An isolation-by-distance best characterizes how dogs expanded into South America. We identify the arrival of new lineages of dogs in post-contact South America, likely of European origin, and their legacy in modern village dogs. Interestingly, the pre-contact Mesoamerican maternal origin of the Chihuahua has persisted in some modern individuals.}, }
@article {pmid40499537, year = {2025}, author = {Añorve-Garibay, V and Huerta-Sanchez, E and Sohail, M and Ortega-Del Vecchyo, D}, title = {Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples.}, journal = {American journal of human genetics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajhg.2025.05.009}, pmid = {40499537}, issn = {1537-6605}, abstract = {The prediction of phenotypes from ancient humans has gained interest due to its potential to investigate the evolution of complex traits. These predictions are commonly performed using polygenic scores computed with DNA information from ancient humans along with genome-wide association study (GWAS) data from present-day humans. However, numerous evolutionary processes could impact these phenotypic predictions. In this work, we investigate how natural selection shapes the temporal dynamics of variants with an effect on the trait and how these changes impact phenotypic predictions for ancient individuals using polygenic scores. We find that stabilizing selection accelerates the loss of large-effect alleles contributing to trait variation. Conversely, directional selection accelerates the loss of small- and large-effect alleles that drive individuals farther away from the optimal phenotypic value. These phenomena result in specific shared genetic variation patterns between ancient and modern populations that hamper the accuracy of polygenic scores to predict phenotypes. Our results assume perfectly estimated effect sizes at the causal loci of complex traits segregating in a GWAS performed in the present and, therefore, provide a putatively loose upper bound on the polygenic score portability to predict traits in the past. Furthermore, we show how natural selection could impact the predictive accuracy of ancient polygenic scores for two widely studied traits: height and body mass index. Our results emphasize the importance of considering decreases on the reliability of polygenic scores to perform phenotypic predictions in ancient individuals due to allele frequency changes driving the loss of alleles via natural selection.}, }
@article {pmid40497055, year = {2025}, author = {Wu, X and Liu, P and Yan, F and Jin, R and Zhong, C and Wang, L and Chen, K and Yang, F and Nie, L and Liang, J and Zhou, Y and Ding, B}, title = {Ancient genomes reveal the genetic structure and population interaction in the Central Plains of China during the Eastern Zhou Period.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1602625}, pmid = {40497055}, issn = {1664-302X}, abstract = {The Eastern Zhou period (770-256 BCE) was a transformative era in ancient China, marked by intensified social stratification, frequent warfare, and increased population movements. The Western Guo State, as an important vassal state during the Western Zhou period, migrated eastward with King Ping of Zhou and was eventually conquered by the Jin State. Due to limited genomic data, the genetic history of the Guo State population remains unclear. The Shangshihe cemetery, located in Yima City, Henan Province, is hypothesized to be associated with the Guo State and provides an opportunity to understand the genetic dynamics of this period. In our study, we successfully obtained 13 ancient genomes from the Shangshihe cemetery. Our findings suggest notable maternal and paternal genetic diversity within the Shangshihe population, although this observation is limited by the small sample size. Population genomic analysis shows that the Shangshihe individuals are predominantly of Yellow River Basin-related ancestry, with minor contributions from Southern East Asian-related and Eurasian Steppe-related sources. This genetic profile reflects extensive interactions between the Central Plains and surrounding populations during the Eastern Zhou period. Additionally, while distinct Y-chromosome haplogroups were observed among individuals with different burial orientations, autosomal analysis did not detect significant genetic differentiation, indicating overall genetic homogeneity within the population. These results not only elucidate the genetic characteristics of the Guo State population but also provide a new genetic perspective on the population dynamics and cultural exchanges in the Central Plains during the Eastern Zhou period.}, }
@article {pmid40493646, year = {2025}, author = {Ledger, ML and Murchie, TJ and Dickson, Z and Kuch, M and Haddow, SD and Knüsel, CJ and Stein, GJ and Pearson, MP and Ballantyne, R and Knight, M and Deforce, K and Carroll, M and Rice, C and Franconi, T and Šarkić, N and Redžič, S and Rowan, E and Cahill, N and Poblome, J and Palma, MF and Brückner, H and Mitchell, PD and Poinar, H}, title = {Sedimentary ancient DNA as part of a multimethod paleoparasitology approach reveals temporal trends in human parasitic burden in the Roman period.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {6}, pages = {e0013135}, pmid = {40493646}, issn = {1935-2735}, mesh = {Humans ; *DNA, Ancient/analysis ; Animals ; *Geologic Sediments/parasitology ; Enzyme-Linked Immunosorbent Assay ; *Parasitic Diseases/history/parasitology/epidemiology ; *Parasites/genetics/isolation &amp; purification/classification ; History, Ancient ; Roman World ; Feces/parasitology ; Paleopathology/methods ; Microscopy ; Helminths/genetics/isolation &amp; purification/classification ; DNA, Protozoan/genetics ; High-Throughput Nucleotide Sequencing ; Parasitology/methods ; Trichuris/genetics/isolation &amp; purification ; }, abstract = {The detection of parasite infections in past populations has classically relied on microscopic analysis of sediment samples and coprolites. In recent years, additional methods have been integrated into paleoparasitology such as enzyme-linked immunosorbent assay (ELISA) and ancient DNA (aDNA). The aim of this study was to evaluate a multimethod approach for paleoparasitology using microscopy, ELISA, and sedimentary ancient DNA (sedaDNA) with a parasite-specific targeted capture approach and high-throughput sequencing. Using 26 samples dating from c. 6400 BCE to 1500 CE that were previously analyzed with microscopy and ELISA, we aimed to more accurately detect and reconstruct parasite diversity in the Roman Empire and compare this diversity to earlier and later time periods to explore temporal changes in parasite diversity. Microscopy was found to be the most effective technique for identifying the eggs of helminths, with 8 taxa identified. ELISA was the most sensitive for detecting protozoa that cause diarrhea (notably Giardia duodenalis). Parasite DNA was recovered from 9 samples, with no parasite DNA recovered from any pre-Roman sites. Sedimentary DNA analysis identified whipworm at a site where only roundworm was visible on microscopy, and also revealed that the whipworm eggs at another site came from two different species (Trichuris trichiura and Trichuris muris). Our results show that a multimethod approach provides the most comprehensive reconstruction of parasite diversity in past populations. In the pre-Roman period, taxonomic diversity included a mixed spectrum of zoonotic parasites, together with whipworm, which is spread by ineffective sanitation. We see a marked change during the Roman and medieval periods with an increasing dominance of parasites transmitted by ineffective sanitation, especially roundworm, whipworm and protozoa that cause diarrheal illness.}, }
@article {pmid40490443, year = {2025}, author = {Noda, M and Kishida, T and Kitagawa, H and Fukuyama, I and Nishikawa, K}, title = {Ancient DNA integrates fossil and modern giant salamander taxonomy.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18642}, pmid = {40490443}, issn = {2045-2322}, support = {JPMJSP2110//JST SPRING/ ; 23K23956//Japan Society for the Promotion of Science/ ; JPMEERF20204002//the Environment Research and Technology Development Fund of the Environmental Restoration and Conservation Agency of Japan/ ; }, mesh = {Animals ; *Fossils ; *Caudata/genetics/classification ; *DNA, Ancient/analysis ; *DNA, Mitochondrial/genetics ; Phylogeny ; Japan ; }, abstract = {The genus Andrias includes the largest extant salamanders, and is comprised of one Japanese species A. japonicus and four Chinese species. The fossil record of the giant salamander is incomplete and modern giant salamanders are not differentiated osteologically among species, making it difficult to identify bones at the species level. In this study, we re-examined a fossil series of giant salamander discovered from a cave on Shikoku Island, Japan. We obtained ancient DNA from the fossil and confirmed that the partial sequence of mitochondrial DNA was identical to that of extant A. japonicus. These remains were dated to the Late Pleistocene, however, the result of carbon-14 dating in this study estimated the age as more recent, approximately 3,500-4,100 years ago. Currently, there is a small population of A. japonicus in Shikoku, but it is far removed from the fossil discovery area. Our findings suggest that wild A. japonicus in western Shikoku may have been extirpated very recently.}, }
@article {pmid40476363, year = {2025}, author = {Cheng, X and Steinrücken, M}, title = {diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkaf123}, pmid = {40476363}, issn = {2160-1836}, abstract = {Whole-genome time-series allele frequency data are becoming more prevalent as ancient DNA (aDNA) sequences and data from evolve-and-resequence (E&amp;R) experiments are generated at a rapid pace. Such data presents unprecedented opportunities to elucidate the dynamics of genetic variation under selection. However, despite many methods to infer parameters of selection models from allele frequency trajectories available in the literature, few provide user-friendly implementations for large-scale empirical applications. Here, we present diplo-locus, an open-source Python package that provides functionality to simulate and perform inference from time-series data under the Wright-Fisher diffusion with general diploid selection. The package includes Python modules as well as command-line tools and is available at: https://github.com/steinrue/diplo_locus.}, }
@article {pmid40475634, year = {2025}, author = {Brand, CM and Capra, JA}, title = {A catalog of ancient proxies for modern genetic variants.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.19.654975}, pmid = {40475634}, issn = {2692-8205}, abstract = {The ability to observe the genomes of past human populations using ancient DNA provides an extraordinary perspective on many fundamental questions in human genetics, including understanding the evolutionary history of variants that underlie human disease and other phenotypes. However, ancient DNA is often damaged and degraded, yielding low-coverage of most nucleotides. Further, many publicly available genotypes for ancient humans are limited to ∼1.23 million specific loci. Thus, variants of interest often fall outside these specific positions, limiting the ability of ancient DNA to shed light on many loci. Here, we address this challenge by quantifying linkage disequilibrium (LD) between modern variants and ancient genotyped variants (AGVs) to generate a catalog enabling rapid identification of proxy variants. We identified 260,732,675 pairs of AGVs and modern variants with a minimum LD threshold hold of R [2] ≥ 0.2. Even at R [2] ≥ 0.9, ≥ 60% of common variants were linked to an AGV in non-African ancestry groups, as were 34% of common variants in Africans. We evaluated the accuracy of the genotypes inferred from proxy variants in two high-coverage ancient genomes finding that > 90% of genotypes were correctly predicted, even in a 45,000 year old individual. We also find that AGVs are significantly older than expected and that many likely are evolving neutrally. We integrate these results in a database that researchers can easily query to identify ancient proxy variants if their variant of interest is not directly genotyped in ancient humans.}, }
@article {pmid40468069, year = {2025}, author = {Wang, J and Yan, S and Li, Z and Zan, J and Zhao, Y and Zhao, J and Chen, K and Wang, X and Ji, T and Zhang, C and Yang, T and Zhang, T and Qiao, R and Guo, M and Rao, Z and Zhang, J and Wang, G and Ran, Z and Duan, C and Zhang, F and Song, Y and Wu, X and Mace, R and Sun, B and Pang, Y and Huang, Y and Zhang, H and Ning, C}, title = {Ancient DNA reveals a two-clanned matrilineal community in Neolithic China.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40468069}, issn = {1476-4687}, abstract = {Studies of ancient DNA from cemeteries provide valuable insights into early human societies, and have strongly indicated patrilocality[1-10]. Here, we analysed ancient DNA alongside archaeological contexts and multiple stable isotopic data from 60 individuals in 2 separate cemeteries at the Fujia archaeological site in eastern China, dating between 2750 and 2500 BCE. Our findings suggest the existence of an early-described matrilineal community in the Neolithic period, characterized by high endogamy and a population practicing millet agriculture near the coast. Evidence of intermarriage between individuals in the two cemeteries and the presence of both primary and secondary burials, organized strictly according to maternal clans, underscore a strong sense of social cohesion and identity at Fujia. Bayesian modelling of radiocarbon dates indicates that the two cemeteries were used for approximately 250 years, implying a stable matrilineal lineage spanning at least 10 generations. This study contributes to the ongoing debate in anthropology and archaeology[11], not only suggesting the existence of a matrilineal society in early human history but also revealing a pair of Neolithic cemeteries organized around two matrilineal clans, furthering our understanding of the early evolution of human societies through kinship systems.}, }
@article {pmid40467681, year = {2025}, author = {Bonczarowska, JH and Wysocka, J and Drupka, B and da Silva, NA and Krause-Kyora, B and Krzepkowski, M}, title = {The outcasts, the sick, and the undead: atypical burials of the late medieval to modern greater Poland.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19608}, pmid = {40467681}, issn = {2045-2322}, support = {EXC 2167 - 390884018//International Max Planck Research School for Evolutionary Biology in Ploen, Germany and the Precision Medicine in Chronic Inflammation (PMI) Cluster/ ; CRC 1266 - 290391021//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Past burial practices can provide insights into the social status of the inhumed and inform us of how the individuals were perceived by their community. Atypical or "deviant" burials may indicate that the deceased was considered an outcast, either due to disease, different provenance, criminal activity, or religious beliefs. To explore the importance of atypical burial practices in medieval and modern Poland, an interdisciplinary study was conducted on three Polish cemeteries (Dzwonowo, Skoki, and Wągrowiec) dating to the 14th -18th centuries CE. Twelve individuals were examined using archaeological evidence, anthropological analysis, and ancient DNA (aDNA) analysis. This study aimed to determine the underlying reasons behind the atypical nature of the burials (i.e., whether the individuals were outsiders, outcasts, relatives, or victims of infectious disease) and shed light on the complex interplay between health, social status, and community perception in medieval and modern Poland. The results revealed that a non-adult male and a middle-aged female, who were holding hands in a double burial in Skoki, possibly died from the plague. Yersinia pestis DNA was recovered from the non-adult individual, making it the third confirmed case of plague in Poland. Using the nonmetric skeletal traits, archaeological assemblage, and aDNA analysis, we identified several individuals as likely "outsiders" in the community. The results of this study expand our knowledge of past societal structures and cultural responses to disease as well as provide crucial context for interpreting burial patterns elsewhere in Europe.}, }
@article {pmid40465848, year = {2025}, author = {Wang, R and Zhu, L and Ma, H and Song, M and Ma, G and Wang, B and Fu, L and Hao, J and Fu, G and Wang, J and Wang, Q and Zhu, K and Yang, X and Xu, Y and Tao, L and He, H and Li, S and Jiang, J and Zhang, W and Wang, CC and Cong, B}, title = {Genetic formation of Neolithic Hongshan people and demic expansion of Hongshan culture inferred from ancient human genomes.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaf139}, pmid = {40465848}, issn = {1537-1719}, abstract = {The Hongshan culture, situated at the crossroads of northern and northeast China, represented one of the earliest complex societies in Neolithic East Asia. The remains of Hongshan culture have been found in an area stretching from today's Inner Mongolia Autonomous Region to Liaoning Province, covering an area of over 200,000 square kilometers. However, the question of how Hongshan culture occupied such a vast geographical location, following either the demic diffusion (i.e., genetic interaction accompanied by cultural expansion) or cultural diffusion model (i.e., local groups adopting new culture without receiving genetic influence), remains unanswered due to a lack of ancient genomes. Here, we report genome-wide data from 19 individuals associated with the Hongshan culture, from the Zhengjiagou site in Hebei Province, the westernmost and southernmost Hongshan culture-related site discovered to date. We co-analyzed our newly generated Hebei Hongshan genomes with previously published 3 Hongshan culture-related genomes from the Banlashan site in Liaoning Province, located in the core region of Hongshan culture and about 473 km away from the Zhengjiagou site. Our genetic results revealed strong genetic links between the Hebei Hongshan and Liaoning Hongshan people, supporting the demic diffusion of the Hongshan culture. Both Liaoning and Hebei Hongshan people harboured Ancient Northeast Asian-related (possibly related to the local earlier Zhaobaogou culture) and Neolithic Yangshao culture-related millet farmer ancestries. Interestingly, our ancestral modelling suggested that Yangshao culture-related ancestry in the Hongshan people was more likely introduced by middle Neolithic Dawenkou culture-related farmers from Shandong, who carried about 40% of an early Neolithic Shandong hunter-gatherer-related lineage and 60% of a Yangshao culture-related lineage. Our findings highlight a complex interconnected gene pool among the West Liao River, the Central Plain, and Shandong during the middle Neolithic period.}, }
@article {pmid40461538, year = {2025}, author = {Santana, J and Del Pino Curbelo, M and Iriarte, E and Morales, J and Caro, JL and Fregel, R and Hagenblad, J and García González, R and Rodríguez Rodríguez, A}, title = {Climate, biogeography, and human resilience in the demographic history of the Canary Islands during the Amazigh period.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19485}, pmid = {40461538}, issn = {2045-2322}, support = {851733//H2020 European Research Council/ ; RTI2018-101923-J-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {Humans ; Spain ; *Climate ; Climate Change ; Population Dynamics ; History, Medieval ; History, Ancient ; History, 15th Century ; Radiometric Dating ; Agriculture ; Islands ; Demography ; }, abstract = {This study explores the dynamic interplay between biogeography, climate variability, and human agency in shaping the population trajectories of Amazigh communities in the Canary Islands (1st to fifteenth centuries cal CE). Using radiocarbon dating as a proxy for population size, this research suggests potential links between demographic trends and environmental factors, highlighting how climatic phases influence agricultural productivity and settlement patterns. Favorable conditions during the Roman Warm Period (RWP) facilitated population expansion, whereas climatic stress during positive phases of the North Atlantic oscillation (NAO) (700-800 cal CE) led to significant demographic declines, particularly on smaller and more arid islands. Larger and ecologically more diverse islands, such as Gran Canaria and Tenerife, showed resilience due to their ecological diversity, agricultural innovations, and food security strategies, which supported sustained growth even during challenging periods such as the Early Medieval Climate Anomaly (MCA, 800-1150 cal CE). From 1150 to 1350 cal CE, cooler sea surface temperatures and a prevailing negative NAO phase increased marine productivity, enabling demographic recovery across islands. However, the arrival of Europeans in the fourteenth-fifteenth centuries introduced external disruptions, including slave raids, novel pathogens, and land seizures, leading to societal collapse. Overall, this study highlights the critical role of environmental diversity and agricultural adaptability in supporting human populations through climatic change and offers valuable perspectives on the relationships among climate, biogeography and human societies.}, }
@article {pmid40460935, year = {2025}, author = {Qi, B and Dou, H and Liu, W and Bennett, A and Rao, H and Yang, Y}, title = {Differentiating goose eggshells through proteomics: A case study from Xitou, North China.}, journal = {Journal of proteomics}, volume = {}, number = {}, pages = {105467}, doi = {10.1016/j.jprot.2025.105467}, pmid = {40460935}, issn = {1876-7737}, abstract = {Eggshells are significant cultural symbols linked to funeral customs and social development. Identifying their species is crucial in archaeological research. However, their small fragment size makes eggshells difficult to accurately identify using traditional methods. Recent mass spectrometry advances have significantly enhanced eggshell species identification in archaeological research, but their success remains limited. For example, Anser cygnoides and Anser anser eggshells cannot yet be reliably distinguished. This paleoproteomic study uses Zooarchaeology by Mass Spectrometry and Liquid Chromatography-Tandem Mass Spectrometry to identify by proteotyping the species of eggshells from the Xitou site in China. We established a series of peptide markers and amino acid variants to distinguish A. cygnoides from A. anser, and with this method attribute three Xitou eggshell specimens to the graylag goose. Carbon isotope analysis and shell thickness measurements were conducted to understand the domestication of the geese associated with these eggshells. The isotope results indicate that these geese primarily ate C3 plants, and shell thickness results suggest they were possibly domesticated. These findings firstly provide direct molecular evidence of possibly domesticated graylag geese in China and offer new insights into poultry domestication and cultural practices. SIGNIFICANCE: Combing ZooMS and LC-MS/MS analysis, we have identified novel peptide markers to distinguish the eggshells of swan goose (Anser cygnoides) from those of graylag goose (Anser anser). Using a series of ZooMS markers and amino acid variations, the eggshells from Xitou site (north China) were identified to be derived from graylag goose. Further eggshells thickness and isotope analysis show that these geese were likely domesticated and primarily fed on C3 plants, offering valuable insights into early geese farming and sustainable practices during the Western Zhou period. Furthermore, the discovery of eggs as burial items highlights the important role that geese played in ancient Chinese culture and rituals.}, }
@article {pmid40447800, year = {2025}, author = {Bythell-Douglas, R and van Twest, S and Abbouche, L and Dunn, E and Coulthard, RJ and Briggs, DC and Murphy, V and Zhang, X and Tan, W and Henrikus, SS and Qian, D and Wu, Y and Wolf, J and Rigoreau, L and Shakeel, S and Chapman, KL and McDonald, NQ and Deans, AJ}, title = {Structural basis of Fanconi anemia pathway activation by FANCM.}, journal = {The EMBO journal}, volume = {}, number = {}, pages = {}, pmid = {40447800}, issn = {1460-2075}, support = {GNT1181110//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; CC2068/WT_/Wellcome Trust/United Kingdom ; }, abstract = {FANCM is crucial in genome maintenance, functioning in the Fanconi anemia (FA) pathway, alternative lengthening of telomeres (ALT), and replication fork protection. FANCM recognizes branched DNA structures and promotes their remodeling through ATP-dependent branch migration. The protein has emerged as a promising therapeutic target due to synthetic lethal interactions with BRCA1, SMARCAL1, and RAD52, and in ALT-positive cancers. Here we present crystal structures of FANCM's N-terminal ATP-dependent translocase domain (2.2 Å) and C-terminal FAAP24-bound region (2.4 Å), both complexed with branched DNA. Through structural analysis, biochemical reconstitution, and cellular studies, we demonstrate that FANCM employs two distinct mechanisms: an ATP-dependent branch migration activity essential for DNA damage survival, and a branched DNA-binding mode that enhances FANCD2-FANCI monoubiquitination through FA core complex interaction. The N-terminal translocase domain specifically recognizes DNA junctions through multiple key elements, while the C-terminal FAAP24-binding domain engages adjacent double-stranded DNA. Our results reveal how FANCM evolved from an ancient DNA repair motor into a sophisticated sensor that couples DNA damage recognition to selective pathway activation, providing a structural framework for developing targeted therapeutics.}, }
@article {pmid40444660, year = {2025}, author = {Lopez-Valdivia, I and Vallebueno-Estrada, M and Rangarajan, H and Swarts, K and Benz, BF and Blake, M and Sidhu, JS and Perez-Limon, S and Sawers, RJH and Schneider, H and Lynch, JP}, title = {In silico analysis of the evolution of root phenotypes during maize domestication in Neolithic soils of Tehuacán.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70245}, pmid = {40444660}, issn = {1469-8137}, support = {847548//European Union's Framework Programme for Research and Innovation Horizon 2020/ ; 602757//Foundation for Food and Agriculture Research/ ; //Social Sciences and Humanities Research Council of Canada/ ; 0091490//National Science Foundation/ ; PEN04732//United States Department of Agriculture-National Institiute of Food and Agriculture/ ; }, abstract = {Roots are essential for plant adaptation to changing environments, yet the role of roots in crop domestication remains unclear. This study examined the evolution of root phenotypes from teosinte to maize, a transition resulting in reduced nodal root number (NRN), multiseriate cortical sclerenchyma (MCS), and increased seminal root number (SRN). We reconstructed the root phenotypes of maize and teosinte, as well as the environments of the Tehuacán Valley over the last 18 000 yr using a combination of ancient DNA, paleobotany, and functional-structural modeling. Our models reveal that increasing Holocene atmospheric CO2 concentrations favored the appearance of reduced NRN and MCS between 12 000 and 8000 yr before present (yrBP), promoting deeper root systems. The advent of irrigation by 6000 yrBP switched nitrogen distribution from topsoil to subsoil domains, a change that increased the utility of reduced NRN and MCS. Comparison of allelic frequencies among ancient samples ranging from 5500 to 500 yrBP suggests that increased SRN may have appeared c. 3500 yrBP, coinciding with a period of increased human population, agricultural intensification, and soil degradation. Our results suggest that root phenotypes that enhance plant performance under nitrogen stress are important for maize adaptation to changing agricultural practices in the Tehuacán Valley.}, }
@article {pmid40441135, year = {2025}, author = {Murray, M and Nakamura, S and Fuentes, M and Canizales, R and Talavera, O and Varela, S and Madrid, Z and Carbajal, C and Ogawa, M and Yoneda, M and Cassidy, LM and Gakuhari, T and Nakagome, S}, title = {Ancient genomes reveal demographic trajectories during the Classic Maya period.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.05.002}, pmid = {40441135}, issn = {1879-0445}, abstract = {Copán was a major capital at the southeasternmost extreme of the Classic Maya civilization, serving as a crossroads connecting Central and South America. In 426/427 CE, the city witnessed the establishment of a royal dynasty, which endured for approximately 400 years. Despite extensive historical and archaeological records, there remains limited information regarding the genetic profile of people who resided in Copán. Here, we present genomes from seven Classic Copán individuals, including a potential member of the ruling dynasty and an accompanying sacrificial burial. Our analysis shows that the population associated with the Classic Copán culture forms a genetic cluster with the Late Archaic population from Belize, as well as with the Terminal Classic Maya from Chichén Itzá, the Colonial Maya from Campeche, and present-day Maya, all from Mexico. Using Late Archaic Belize as a source of local ancestry, we identify an influx of ancestry associated with highland Mexican populations from the Early-to-Middle Classic period onward, underscoring the role of gene flow in the formation of the Classic Maya state. Estimates of effective population size suggest a decline at the end of the Classic period, when Classic Maya civilization experienced widespread destabilization and collapse.}, }
@article {pmid40440428, year = {2025}, author = {Lopopolo, M and Avanzi, C and Duchene, S and Luisi, P and de Flamingh, A and Ponce-Soto, GY and Tressieres, G and Neumeyer, S and Lemoine, F and Nelson, EA and Iraeta-Orbegozo, M and Cybulski, JS and Mitchell, J and Marks, VT and Adams, LB and Lindo, J and DeGiorgio, M and Ortiz, N and Wiens, C and Hiebert, J and Bonifaz, A and Montes de Oca, G and Paredes-Solis, V and Franco-Paredes, C and Vera-Cabrera, L and Pereira Brunelli, JG and Jackson, M and Spencer, JS and Salgado, CG and Han, XY and Pearce, CM and Warren, AK and Rosa, PS and de Finardi, AJ and Belone, AFF and Ferreira, C and Suffys, PN and Fontes, ANB and Vasconcellos, SEG and Schaub, R and Couppié, P and Drak Alsibai, K and Hernández-Castro, R and Silva Miranda, M and Estrada-Garcia, I and Jurado-Santacruz, F and Orlando, L and Schroeder, H and Quintana-Murci, L and Del Papa, M and Lahiri, R and Malhi, RS and Rasmussen, S and Rascovan, N}, title = {Pre-European contact leprosy in the Americas and its current persistence.}, journal = {Science (New York, N.Y.)}, volume = {}, number = {}, pages = {eadu7144}, doi = {10.1126/science.adu7144}, pmid = {40440428}, issn = {1095-9203}, abstract = {Leprosy, primarily caused by Mycobacterium leprae, is considered a disease introduced into the Americas during European colonization. However, the recent discovery of a second pathogen causing leprosy, M. lepromatosis, mainly found in the Americas, challenges this view. Here, we show that M. lepromatosis infected humans in the Americas before European contact. By screening 389 ancient and 408 contemporary samples, we have expanded the genetic data available for the species. Phylogenetic analyses revealed distinct human-infecting clades of M. lepromatosis, with one dominating North America since colonial times. The presence of millennia-old strains in North and South America indicates M. lepromatosis may have been widespread during the Late Holocene, demonstrating M. lepromatosis leprosy has a long-standing history in the Americas before European arrival.}, }
@article {pmid40440389, year = {2025}, author = {Sidhu, RK and Mas Fiol, G and Lê-Bury, P and Demeure, CE and Bougit, E and Beau, R and Balière, C and Kwasiborski, A and Caro, V and Klunk, J and Salkeld, DJ and Carmichael, A and Varlık, N and Poinar, D and Earn, DJD and Bolker, BM and Dushoff, J and Golding, GB and Rascovan, N and Dussurget, O and Holmes, EC and Pizarro-Cerdá, J and Poinar, HN}, title = {Attenuation of virulence in Yersinia pestis across three plague pandemics.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6750}, pages = {eadt3880}, doi = {10.1126/science.adt3880}, pmid = {40440389}, issn = {1095-9203}, mesh = {*Yersinia pestis/pathogenicity/genetics ; *Plague/epidemiology/microbiology/mortality ; Animals ; Mice ; Virulence/genetics ; *Pandemics ; *Bacterial Proteins/genetics ; Humans ; Plasmids/genetics ; *Pore Forming Cytotoxic Proteins/genetics ; *Plasminogen Activators/genetics ; Rodentia/microbiology ; Gene Deletion ; Female ; Disease Models, Animal ; }, abstract = {Yersinia pestis has spilled over from wild rodent reservoirs to commensal rodents and humans, causing three historically recorded pandemics. Depletion in the copy number of the plasmid-encoded virulence gene pla occurred in later-dated strains of the first and second pandemics, yet the biological relevance of the pla deletion has been difficult to test. We identified modern Y. pestis strains that independently acquired the same pla depletion as ancient strains and herein show that excision of pla from the multicopy pPCP1 plasmid is accompanied by the integration of a separate full pPCP1 harboring pla into the single-copy pCD1 plasmid, reducing pla dosage. Moreover, we demonstrate that this depletion decreases the mortality of mice in models of bubonic plague but not in the pneumonic and septicemic forms of the disease. We hypothesize that pla depletion may have been selectively advantageous in bubonic plague, owing to rodent fragmentation after pandemic-induced mortality.}, }
@article {pmid40439179, year = {2025}, author = {Zhang, M and Wang, C and Zheng, Y and Ni, X and Hu, S and Zhuang, L and Guo, M and Dai, Q and Cao, P and Ren, L and Dong, G and Yang, R and Liu, F and Feng, X and Hou, H and Wang, H and Wang, W and Zhang, L and Bennett, EA and Fu, Q}, title = {Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Gray Wolves (Canis lupus).}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.13005}, pmid = {40439179}, issn = {1749-4877}, support = {41925009//National Natural Science Foundation of China/ ; 41625005//National Natural Science Foundation of China/ ; 2022YFE0203800//National Key R&amp;D Program of China/ ; 2024RS-CXTD-74//Science and Technology Innovation Team of Shaanxi Province/ ; YSBR-019//Ministry of Finance of the People's Republic of China/ ; }, abstract = {The gray wolf (Canis lupus) is the only wild ancestor of dogs (Canis lupus familiaris) and serves a crucial role in understanding the highly controversial issue of dog origins. Recently, ancient DNA studies on gray wolves from different regions of the Eurasian continent have achieved significant breakthroughs, providing important clues about the dog origins. As one of the potential origin areas for dogs, East Asia has seen some research on ancient dogs; however, reports related to gray wolves remain limited. In this study, we sequenced seven new mitogenomes of ancient gray wolves from Northern China, integrating them with 497 ancient and modern canid mitogenomes from published data. Our results reveal the following: (1) East Asian gray wolves have maintained high genetic diversity from ancient times to the present; (2) multiple haplogroup A gray wolves from Northern China support the hypothesis that Northeastern Eurasia is a core region for dog origins; (3) a deep gray wolf lineage in East Asia has been identified in this study; (4) different mitogenomes concentrated at the Jinchankou site indicate that admixture may have frequently occurred in the northeastern edge of the Tibetan Plateau. These findings enhance our understanding of the maternal genetic history of gray wolves in East Asia.}, }
@article {pmid40435234, year = {2025}, author = {Krettek, KL and Casas-Vargas, A and Mas-Sandoval, A and Alvis, LA and Reiter, E and Madero, JM and Urban, M and Vargas, JCN and Usaquén, W and Cuenca, JVR and Posth, C}, title = {A 6000-year-long genomic transect from the Bogotá Altiplano reveals multiple genetic shifts in the demographic history of Colombia.}, journal = {Science advances}, volume = {11}, number = {22}, pages = {eads6284}, pmid = {40435234}, issn = {2375-2548}, mesh = {Colombia ; Humans ; *Genomics/methods ; *Genetics, Population ; *Genome, Human ; *Indians, South American/genetics ; Phylogeny ; }, abstract = {Genetic studies on Native American populations have transformed our understanding of the demographic history of the Americas. However, a region that has not been investigated through ancient genomics so far is Colombia, the entry point into South America. Here, we report genome-wide data of 21 individuals from the Bogotá Altiplano in Colombia between 6000 and 500 years ago. We reveal that preceramic hunter-gatherers represent a previously unknown basal lineage that derives from the initial South American radiation. These hunter-gatherers do not carry differential affinity to ancient North American groups nor contribute genetically to ancient or present-day South American populations. By 2000 years ago, the local genetic ancestry is replaced by populations from Central America associated with the Herrera ceramic complex and survives through the Muisca period despite major cultural changes. These ancient Altiplano individuals show higher affinities to Chibchan speakers from the Isthmus of Panama than to Indigenous Colombians, suggesting a dilution of the Chibchan-related ancestry through subsequent dispersal events.}, }
@article {pmid40431178, year = {2025}, author = {Ekram, MA and Wuchter, C and Bijaksana, S and Grice, K and Russell, J and Stevenson, J and Vogel, H and Coolen, MJL}, title = {A Quaternary Sedimentary Ancient DNA (sedaDNA) Record of Fungal-Terrestrial Ecosystem Dynamics in a Tropical Biodiversity Hotspot (Lake Towuti, Sulawesi, Indonesia).}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051005}, pmid = {40431178}, issn = {2076-2607}, abstract = {Short-term observations suggest that environmental changes affect the diversity and composition of soil fungi, significantly influencing forest resilience, plant diversity, and soil processes. However, time-series experiments should be supplemented with geobiological archives to capture the long-term effects of environmental changes on fungi-soil-plant interactions, particularly in undersampled, floristically diverse tropical forests. We recently conducted trnL-P6 amplicon sequencing to generate a sedimentary ancient DNA (sedaDNA) record of the regional catchment vegetation of the tropical waterbody Lake Towuti (Sulawesi, Indonesia), spanning over one million years (Myr) of the lake's developmental history. In this study, we performed 18SV9 amplicon sequencing to create a parallel paleofungal record to (a) infer the composition, origins, and functional guilds of paleofungal community members and (b) determine the extent to which downcore changes in fungal community composition reflect the late Pleistocene evolution of the Lake Towuti catchment. We identified at least 52 members of Ascomycota (predominantly Dothiodeomycetes, Eurotiomycetes, and Leotiomycetes) and 12 members of Basidiomycota (primarily Agaricales and Polyporales). Spearman correlation analysis of the relative changes in fungal community composition, geochemical parameters, and paleovegetation assemblages revealed that the overwhelming majority consisted of soil organic matter and wood-decaying saprobes, except for a necrotrophic phytopathogenic association between Mycosphaerellaceae (Cadophora) and wetland herbs (Alocasia) in more-than-1-Myr-old silts and peats deposited in a pre-lake landscape, dominated by small rivers, wetlands, and peat swamps. During the lacustrine stage, vegetation that used to grow on ultramafic catchment soils during extended periods of inferred drying showed associations with dark septate endophytes (Ploettnerulaceae and Didymellaceae) that can produce large quantities of siderophores to solubilize mineral-bound ferrous iron, releasing bioavailable ferrous iron needed for several processes in plants, including photosynthesis. Our study showed that sedaDNA metabarcoding paired with the analysis of geochemical parameters yielded plausible insights into fungal-plant-soil interactions, and inferred changes in the paleohydrology and catchment evolution of tropical Lake Towuti, spanning more than one Myr of deposition.}, }
@article {pmid40426041, year = {2025}, author = {Zabel, S and Breitling, S and Posth, C and Nieselt, K}, title = {A probabilistic approach to visualize the effect of missing data on PCA in ancient human genomics.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {537}, pmid = {40426041}, issn = {1471-2164}, support = {16DHBKI086//Federal Ministry of Education and Research, Germany/ ; W73/2022//Leibniz ScienceCampus "Geogenomic Archaeology Campus T&#xfc;bingen (GACT)"/ ; }, mesh = {Humans ; *Genomics/methods ; *DNA, Ancient/analysis ; *Principal Component Analysis ; *Genome, Human ; Genotype ; Genetics, Population ; Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Principal Component Analysis (PCA) is widely used in population genetics to visualize genetic relationships and population structures. In ancient genomics, genotype information may in parts remain unresolved due to the low abundance and degraded quality of ancient DNA. While methods like SmartPCA allow the projection of ancient samples despite missing data, they do not quantify projection uncertainty. The reliability of PCA projections for often very sparse ancient genotype samples is not well understood. Ignoring this uncertainty may lead to overconfident conclusions about the observed genetic relationships and population structure.<br><br>RESULTS: This study systematically investigates the impact of missing loci on PCA projections using both simulated and real ancient human genotype data. Through extensive simulations with high-coverage ancient samples, we demonstrate that increasing levels of missing data can lead to less accurate SmartPCA projections, highlighting the importance of considering uncertainty when interpreting PCA results from ancient samples. To address this, we developed a probabilistic framework to quantify the uncertainty in PCA projections due to missing data. By applying our methodology to modern and ancient West Eurasian genotype samples from the Allen Ancient DNA Resource database, we could show a high concordance between our predicted projection and empirically derived distributions. Applying this framework to real-world data, we demonstrate its utility in predicting and visualizing embedding uncertainties for ancient samples of varying SNP coverages.<br><br>CONCLUSION: Our results emphasize the importance of accounting for projection uncertainty in ancient population studies. We therefore make our probabilistic model available through TrustPCA, a user-friendly web tool that provides researchers with uncertainty estimates alongside PCA projections, facilitating data exploration in ancient human genomic studies and enhancing transparency in data quality reporting.}, }
@article {pmid40411280, year = {2025}, author = {Grasso, G and Debruyne, R and Adamo, M and Rué, O and Lejzerowicz, F and Bittner, L and Bianciotto, V and Marmeisse, R}, title = {Ancient Microbiomes as Mirrored by DNA Extracted From Century-Old Herbarium Plants and Associated Soil.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14122}, doi = {10.1111/1755-0998.14122}, pmid = {40411280}, issn = {1755-0998}, support = {//Sorbonne Universit&#xe9;/ ; //Universit&#xe0; Italo Francese/ ; //Universit&#xe0; degli Studi di Torino/ ; ATM2021//Mus&#xe9;um National d'Histoire Naturelle/ ; //CNR: Short-Term Mobility (2023) program/ ; }, abstract = {Numerous specimens stored in natural history collections have been involuntarily preserved together with their associated microbiomes. We propose exploiting century-old soils occasionally found on the roots of herbarium plants to assess the diversity of ancient soil microbial communities originally associated with these plants. We extracted total DNA and sequenced libraries produced from rhizospheric soils and roots of four plants preserved in herbaria for more than 120 years in order to characterise the preservation and taxonomic diversity that can be recovered in such contexts. Extracted DNA displayed typical features of ancient DNA, with cytosine deamination at the ends of fragments predominantly shorter than 50 bp. When compared to extant microbiomes, herbarium microbial communities clustered with soil communities and were distinct from communities from other environments. Herbarium communities also displayed biodiversity features and assembly rules typical of soil and plant-associated ones. Soil communities were richer than root-associated ones with which they shared most taxa. Regarding community turnover, we detected collection site, soil versus root and plant species effects. Eukaryotic taxa that displayed a higher abundance in roots were mostly plant pathogens that were not identified among soil-enriched ones. Conservation of these biodiversity features and assembly rules in herbarium-associated microbial communities indicates that herbarium-extracted DNA might reflect the composition of the original plant-associated microbial communities and that preservation in herbaria seemingly did not dramatically alter these characteristics. Using this approach, it should be possible to investigate historical soils and herbarium plant roots to explore the diversity and temporal dynamics of soil microbial communities.}, }
@article {pmid40403731, year = {2025}, author = {Zhang, Y and Wang, J and Yi, C and Su, Y and Yin, Z and Zhang, S and Jin, L and Stoneking, M and Yang, J and Wang, K and Huang, H and Li, J and Fan, S}, title = {An ancient regulatory variant of ACSF3 influences the coevolution of increased human height and basal metabolic rate via metabolic homeostasis.}, journal = {Cell genomics}, volume = {}, number = {}, pages = {100855}, doi = {10.1016/j.xgen.2025.100855}, pmid = {40403731}, issn = {2666-979X}, abstract = {Anatomically modern humans (AMHs) exhibit a significant increase in basal metabolic rate (BMR) and height compared to non-human apes. This study investigates the genetic basis underlying these traits. Our analyses reveal a strong genetic correlation between height and BMR. A regulatory mutation, rs34590044-A, was found to be associated with the increased height and BMR in AMHs. rs34590044-A upregulates the expression of ACSF3 by increasing its enhancer activity, leading to increased body length and BMR in mice fed essential amino acids which are characteristic of meat-based diets. In the British population, rs34590044-A has been under positive selection over the past 20,000 years, with a particularly strong signal in the last 5,000 years, as also evidenced by ancient DNA analysis. These results suggest that the emergence of rs34590044-A may have facilitated the adaptation to a meat-enriched diet in AMHs, with increased height and BMR as consequences of this dietary shift.}, }
@article {pmid40392844, year = {2025}, author = {Andrews, AJ and Eriksen, EF and Star, B and Præbel, K and Di Natale, A and Malca, E and Onar, V and Aniceti, V and Carenti, G and Piquès, G and Nielsen, SV and Persson, P and Piattoni, F and Fontani, F and Atmore, LM and Kersten, O and Tinti, F and Cilli, E and Cariani, A}, title = {Ancient DNA suggests a historical demographic decline and genetic erosion in the Atlantic bluefin tuna.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {21}, pages = {e2409302122}, doi = {10.1073/pnas.2409302122}, pmid = {40392844}, issn = {1091-6490}, support = {813383//EU Horizion 2020/ ; }, mesh = {Animals ; *Tuna/genetics ; *DNA, Ancient/analysis ; Genetic Variation ; Population Dynamics ; Atlantic Ocean ; Conservation of Natural Resources ; }, abstract = {Overexploitation has depleted fish stocks during the past century; nonetheless, its genomic consequences remain poorly understood for most species. Characterizing the spatiotemporal patterns of these consequences may provide baseline estimates of past diversity and productivity to aid management targets, help predict future dynamics, and facilitate the identification of evolutionary factors limiting fish population recovery. Here, we evaluate human impacts on the evolution of the iconic Atlantic bluefin tuna (Thunnus thynnus), one of the longest and most intensely exploited marine fishes, with a tremendous cultural and economic importance. We sequenced whole genomes from modern (n = 49) and ancient (n = 41) specimens dating up to 5,000 y ago, uncovering several findings. First, we identify temporally stable patterns of population admixture, as bluefin tuna caught off Norway and in the eastern Mediterranean share a greater degree of ancestry with Gulf of Mexico bluefin tuna than western and central Mediterranean bluefin tuna. This suggests that Atlantic spawning areas are important mixing grounds for the genetic diversity of Mediterranean bluefin tuna. We model effective population size to show that Mediterranean bluefin tuna began to undergo a demographic decline by the year 1900 to an extent not observed across the previous millennia. Coinciding with this, we found that heterozygosity and nucleotide diversity were significantly lower in modern (2013 to 2020) than ancient (pre-1941) Mediterranean bluefin tuna, suggesting that bluefin tuna underwent a genetic bottleneck. With this work, we show how ancient DNA provides unique perspectives on ecological complexity with the potential to inform the management and conservation of fishes.}, }
@article {pmid40392669, year = {2025}, author = {Letsch, H and Greve, C and Hundsdoerfer, AK and Irisarri, I and Moore, JM and Espeland, M and Wanke, S and Arifin, U and Blom, MPK and Corrales, C and Donath, A and Fritz, U and Köhler, G and Kück, P and Lemer, S and Mengual, X and Salas, NM and Meusemann, K and Palandačić, A and Printzen, C and Sigwart, JD and Silva-Brandão, KL and Simões, M and Stange, M and Suh, A and Szucsich, N and Tilic, E and Töpfer, T and Böhne, A and Janke, A and Pauls, S}, title = {Type genomics: a Framework for integrating Genomic Data into Biodiversity and Taxonomic research.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syaf040}, pmid = {40392669}, issn = {1076-836X}, abstract = {Name-bearing type specimens have a fundamental role in characterising biodiversity, as these objects represent the physical link between a scientific name and the biological organism. Type specimens are usually deposited in natural history collections, which provide key infrastructure for research on essential biological structures and processes, while preserving records of biodiversity for future generations. Modern systematics increasingly depends on genetic and genomic data to differentiate and characterise species. While the results of genome sequencing are often connected to a physical voucher specimen, they are rarely derived from the ultimate taxonomic reference for a species, i.e., the name-bearing type specimens. This is a known but under-appreciated problem for ensuring the replicability of findings, especially those that affect the interpretation of biodiversity distributions and phylogenetic relationships. Destructive sampling of museum specimens, particularly of type material, often carries a high risk of sequencing failure, and thus the cost of damage to the specimen may outweigh the resulting benefit. Both taxonomic work and genome sequencing require specialist skills and there are often communication gaps between the respective experts. A new, harmonised approach, maximising information extraction while minimising risk to type specimens, is a critical step forward toward linking disciplines across biodiversity research and promoting a better taxonomic and systematic understanding of eukaryotic diversity. The genetic make-up of a type specimen is a fundamental part of its biological information, which can and should be made freely and digitally available through type genomics. Here we describe guidelines for the use of nomenclatural types in genome sequencing approaches considering different kinds of types in different stages of preservation and different data types.}, }
@article {pmid40390081, year = {2025}, author = {Beneker, O and Molinaro, L and Guellil, M and Sasso, S and Kabral, H and Bonucci, B and Gaens, N and D'Atanasio, E and Mezzavilla, M and Delbrassine, H and Braet, L and Lambert, B and Deckers, P and Biagini, SA and Hui, R and Becelaere, S and Geypen, J and Hoebreckx, M and Berk, B and Driesen, P and Pijpelink, A and van Damme, P and Vanhoutte, S and De Winter, N and Saag, L and Pagani, L and Tambets, K and Scheib, CL and Larmuseau, MHD and Kivisild, T}, title = {Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {127}, pmid = {40390081}, issn = {1474-760X}, support = {G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; S003422N//Fonds Wetenschappelijk Onderzoek/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek/ ; ZKD6488 C24M/19/075//KU Leuven/ ; ZKD6488 C24M/19/075//KU Leuven/ ; ZKD6488 C24M/19/075//KU Leuven/ ; PRG1027//Estonian Research Council/ ; PRG1027//Estonian Research Council/ ; PRG1027//Estonian Research Council/ ; PRG1027//Estonian Research Council/ ; PRG1027//Estonian Research Council/ ; 10.55776/ESP162//Austrian Science Fund/ ; TK215//Estonian Ministry of Education and Research/ ; TK215//Estonian Ministry of Education and Research/ ; TK215//Estonian Ministry of Education and Research/ ; TK215//Estonian Ministry of Education and Research/ ; 885137/ERC_/European Research Council/International ; CZ.02.01.01/00/22_008/0004593//Czech Ministry of Education, Youth and Sports/ ; 3M220588//Agentschap Onroerend Erfgoed/ ; }, mesh = {Humans ; History, Medieval ; *Urbanization/history ; Belgium ; Genetic Variation ; Genetics, Population ; Genomics ; Plague/epidemiology/history/genetics ; Genome, Human ; }, abstract = {BACKGROUND: Processes shaping the formation of the present-day population structure in highly urbanized Northern Europe are still poorly understood. Gaps remain in our understanding of when and how currently observable regional differences emerged and what impact city growth, migration, and disease pandemics during and after the Middle Ages had on these processes.<br><br>RESULTS: We perform low-coverage sequencing of the genomes of 338 individuals spanning the eighth to the eighteenth centuries in the city of Sint-Truiden in Flanders, in the northern part of Belgium. The early/high medieval Sint-Truiden population was more heterogeneous, having received migrants from Scotland or Ireland, and displayed less genetic relatedness than observed today between individuals in present-day Flanders. We find differences in gene variants associated with high vitamin D blood levels between individuals with Gaulish or Germanic ancestry. Although we find evidence of a Yersinia pestis infection in 5 of the 58 late medieval burials, we were unable to detect a major population-scale impact of the second plague pandemic on genetic diversity or on the elevated differentiation of immunity genes.<br><br>CONCLUSIONS: This study reveals that the genetic homogenization process in a medieval city population in the Low Countries was protracted for centuries. Over time, the Sint-Truiden population became more similar to the current population of the surrounding Limburg province, likely as a result of reduced long-distance migration after the high medieval period, and the continuous process of local admixture of Germanic and Gaulish ancestries which formed the genetic cline observable today in the Low Countries.}, }
@article {pmid40383374, year = {2025}, author = {Chen, Y and Xu, Y and Zhu, K and Wang, CC}, title = {ADGAP: a user-friendly online Ancient DNA Database and Genome Analysis Platform.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2025.05.006}, pmid = {40383374}, issn = {1673-8527}, }
@article {pmid40374632, year = {2025}, author = {Schreiber, L and Ribeiro, S and Jackson, R and Kvorning, AB and Nota, K and O'Regan, M and Pearce, C and Seersholm, F and Seidenkrantz, MS and Zimmermann, HH and Lorenzen, ED}, title = {Holocene shifts in marine mammal distributions around Northern Greenland revealed by sedimentary ancient DNA.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4543}, pmid = {40374632}, issn = {2041-1723}, mesh = {Animals ; Greenland ; *Geologic Sediments/chemistry ; *Mammals/genetics/physiology ; Fossils ; *DNA, Ancient/analysis ; Ecosystem ; Climate Change ; Ice Cover ; Arctic Regions ; *Aquatic Organisms/genetics ; Temperature ; }, abstract = {Arctic marine ecosystems have undergone notable reconfigurations in response to Holocene climate and environmental changes. Yet our understanding of how marine mammal occurrence was impacted remains limited, due to their relative scarcity in the fossil record. We reconstruct the occurrence of marine mammals across the past 12,000 years through detections based on sedimentary ancient DNA from four marine sediment cores collected around Northern Greenland, and integrate the findings with local and regional environmental proxy records. Our findings indicate a close association between marine mammals at densities detectable in marine sediments and the deglaciation of high Arctic marine environments at the onset of the Holocene. Further, we identify air temperature and changes in sea ice cover as significant drivers of community change across time. Several marine mammals are detected in the sediments earlier than in the fossil record, for some species by several thousand years. During the Early-to-Mid Holocene, a period of warmer climate, we record northward distribution shifts of temperate and low-arctic marine mammal species. Our findings provide unique, long-term baseline data on the occurrence of marine mammals around Northern Greenland, enabling insights into past community dynamics and the effects of Holocene climatic shifts on the region's marine ecosystems.}, }
@article {pmid40368150, year = {2025}, author = {Mascarenhas, S and Hodgins, HP and Doxey, AC}, title = {Widespread occurrence of botulinum and tetanus neurotoxin genes in ancient DNA.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {}, number = {}, pages = {108405}, doi = {10.1016/j.toxicon.2025.108405}, pmid = {40368150}, issn = {1879-3150}, abstract = {BACKGROUND: Ancient DNA collected from archaeological specimens not only provides a window into ancient human genetic diversity but also contains a rich mixture of associated microbial DNA including potential pathogens. In recent work, we identified C. tetani and tetanus neurotoxin (TeNT) genes in ancient DNA datasets collected from human archaeological specimens. However, the reasons underlying the occurrence of these toxin genes and the extent to which other toxin genes are present in ancient DNA is unclear.<br><br>METHODS: Here, we performed a large-scale analysis of 6,435 ancient DNA (aDNA) sequencing datasets including human and non-human sources, searching for 49 clostridial neurotoxin types and subtypes, as well as 3 additional unrelated toxins.<br><br>RESULTS: Our search identified a total of 105 ancient DNA datasets (1.6%) containing significant matches to one or more neurotoxin genes. Consistent with our earlier work, TeNT genes were most common, found in 50 ancient DNA datasets. In addition, we identified sequences encoding diverse botulinum neurotoxins including BoNT/C (40 samples), BoNT/D (6 samples), BoNT/B (4 samples), BoNT/E (1 sample), and the Enterococcus-associated BoNT/En (10 samples). TeNT genes were detected in a broad range of ancient samples including human and animal (horse, wild bear, chimpanzee, gorilla, dog) remains, whereas the largest diversity of toxins was detected in aDNA from Egyptian mummies. Phylogenetic and sequence analysis of the identified matches revealed close identity to modern forms of these toxins. Damage analysis revealed several toxin genes with hallmarks of ancient DNA associated damage, indicative of an ancient origin.<br><br>CONCLUSIONS: Our work reveals that clostridial neurotoxin genes occur frequently in aDNA samples, including human and animal-associated toxin variants. We conclude that the frequent association of these genes with aDNA likely reflects a strong ecological association of pathogenic clostridia with decaying human and animal remains and possible post-mortem colonization of these samples.}, }
@article {pmid40367347, year = {2025}, author = {Liu, L and Zhu, S and Gu, Y and Tao, S and Krock, B and Wang, C and Shi, X and Yan, Q and Pan, X and Chen, J and Lin, S and Luo, Z}, title = {Holocene and contemporary marine dinoflagellate community patterns predict expansion of generalist dinoflagellate blooms in warming oceans.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf095}, pmid = {40367347}, issn = {1751-7370}, abstract = {Existing data and models suggest increasing prominence of dinoflagellates and their blooms in future warmer ocean but supporting long-term data are sparse. Here, we used 18S rRNA gene sequencing to investigate sedimentary ancient dinoflagellate communities in northern South China Sea and compared them with contemporary dinoflagellate data from global oceans (TARA Oceans data) and 40 years of dinoflagellate bloom records in China. We found a continuous warming (by ~4.3°C in mean annual sea surface temperature) from 12 to 4.3 kiloyears before present (kyr BP), which caused an initial increase in the relative abundance and diversity of dinoflagellates, followed by a decrease reaching the lowest value, probably due to thermal stress. However, dinoflagellates flourished again after 4.3 kyr BP, coinciding with a rapid increase in human activities. Further analyses indicated that warming and environmental changes during the Holocene favored dinoflagellate generalists over specialists. These generalists have also been abundant throughout contemporary low- and mid-latitude regions, whereas specialists were more abundant at higher latitudes. The predominant generalist genera Noctiluca, Gymnodinium, and Prorocentrum in core sediment corresponded to taxa responsible for most dinoflagellate blooms in the contemporary China Seas over the past 40 years. The success of generalists during warmer periods suggests that dinoflagellate blooms are likely to expand geographically rather than simply shift toward high latitudes under global warming. Moreover, the homogenization of dinoflagellate communities resulting from generalist expansion may significantly reduce the complexity of marine plankton interactions and compromise ecosystem services under global warming.}, }
@article {pmid40360796, year = {2025}, author = {Amjadi, MA and Özdemir, YC and Ramezani, M and Jakab, K and Megyes, M and Bibak, A and Salehi, Z and Hayatmehar, Z and Taheri, MH and Moradi, H and Zargari, P and Hasanpour, A and Jahani, V and Sharifi, AM and Egyed, B and Mende, BG and Tavallaie, M and Szécsényi-Nagy, A}, title = {Ancient DNA indicates 3,000 years of genetic continuity in the Northern Iranian Plateau, from the Copper Age to the Sassanid Empire.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16530}, pmid = {40360796}, issn = {2045-2322}, mesh = {Iran ; *DNA, Ancient/analysis ; Humans ; History, Ancient ; *Genetics, Population ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Archaeology ; }, abstract = {In this study, we present new ancient DNA data from prehistoric and historic populations of the Iranian Plateau. By analysing 50 samples from nine archaeological sites across Iran, we report 23 newly sequenced mitogenomes and 13 nuclear genomes, spanning 4700 BCE to 1300 CE. We integrate an extensive reference sample set of previously published ancient DNA datasets from Western and South-Central Asia, enhancing our understanding of genetic continuity and diversity within ancient Iranian populations. A new Early Chalcolithic sample, predating all other Chalcolithic genomes from Iran, demonstrates mostly Early Neolithic Iranian genetic ancestry. This finding reflects long-term cultural and biological continuity in and around the Zagros area, alongside evidence of some western genetic influence. Our sample selection prioritizes northern Iran, with a particular focus on the Achaemenid, Parthian, and Sassanid periods (355 BCE-460 CE). The genetic profiles of historical samples from this region position them as intermediates on an east-west genetic cline across the Persian Plateau. They also exhibit strong connections to local and South-Central Asian Bronze Age populations, underscoring enduring genetic connections across these regions. Diachronic analyses of uniparental lineages on the Iranian Plateau further highlight population stability from prehistoric to modern times.}, }
@article {pmid40352621, year = {2025}, author = {Bro-Jørgensen, MH and Ahlgren, H and Glykou, A and Ruiz-Puerta, EJ and Lõugas, L and Gotfredsen, AB and Olsen, MT and Lidén, K}, title = {The Evolutionary History of the Extinct Baltic Sea Harp Seal Population.}, journal = {Ecology and evolution}, volume = {15}, number = {5}, pages = {e71322}, pmid = {40352621}, issn = {2045-7758}, abstract = {The now-extinct harp seal population that inhabited the Baltic Sea from the Mesolithic to the Iron Age is an enigma. It occurred outside the species' contemporary Arctic range, likely deviated from typical harp seal migratory behaviour, and experienced body size reductions and dramatic population fluctuations leading up to its extinction. Here we use ancient DNA analyses to shed more light on the evolutionary history of the Baltic Sea harp seal population, including its origin, timing of colonisation, diversity and factors contributing to its demise. We generated 49 ancient Baltic and eight ancient Arctic harp seal mitogenomes, which we analysed together with 53 contemporary Arctic harp seal mitogenomes. We detected limited phylogeographic resolution among ancient and contemporary populations, which we interpret as a late Pleistocene range expansion from a common refugial population with subsequent gene flow. Ancient Baltic harp seals were significantly genetically differentiated from contemporary harp seal populations and retained their own genetic composition throughout time. The genetic diversity of Baltic harp seals decreased over time, yet was comparable to that of contemporary populations. This suggests that Baltic harp seals formed a distinct breeding population, which may occasionally have received immigrants from the Arctic but was itself confined in the Baltic Sea until the end. We hypothesise that loss of genetic diversity and the ultimate extinction of the Baltic harp seal population was a consequence of population fluctuations caused by climatic change, reduced salinity and biological productivity, and periodic intense human harvest.}, }
@article {pmid40349970, year = {2025}, author = {Domingo, P and Prieto, P and Pons, L}, title = {A plague like no other Beyond the buboes in Thucydides' account of the plague of Athens.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2025.05.001}, pmid = {40349970}, issn = {1469-0691}, abstract = {BACKGROUND: The Athens Plague (430-427 BCE) was a devastating outbreak during the Peloponnesian War, described in detail by Thucydides. Although there is ongoing discussion, the specific cause of the epidemic remains undetermined.<br><br>OBJECTIVES: This review reexamines the Athenian plague through historical and microbiological lenses, reassessing diagnostic hypotheses and proposing the plausibility of an ancient pneumonic strain ofYersinia pestis.<br><br>SOURCES: We analyzed Thucydides' original account alongside interdisciplinary literature from classical studies, paleopathology, epidemiology, and microbiology. We gathered sources from PubMed, JSTOR, Google Scholar, and the Perseus Digital Library, covering works from 1634 to 2024.<br><br>CONTENT: The clinical progression described by Thucydides-fever, conjunctivitis, bloody cough, gastrointestinal symptoms, rash, and high mortality-is compared to the presentations of typhoid fever, smallpox, epidemic typhus, measles, and plague. This review considers archaeological and paleogenomic findings, including controversial evidence of Salmonella enterica and the evolutionary history of Y. pestis. Special emphasis is placed on early strains of Y. pestis that lacked flea-borne virulence factors but may have caused pneumonic forms transmitted between humans.<br><br>IMPLICATIONS: The epidemic's significant demographic, political, and social impacts highlight the broader consequences of infectious diseases in ancient history. This review emphasizes the necessity of employing a multidisciplinary approach in historical epidemiology and advocates for reassessing pneumonic plague as a likely contributor to the outbreak that occurred in Athens.}, }
@article {pmid40341774, year = {2025}, author = {Ralf, A and Zandstra, D and van Wersch, B and Köksal, Z and Larmuseau, MHD and Rosa, A and Jobling, MA and D'Amato, ME and Courts, C and Gysi, M and Haas, C and Flores, R and Neis, M and Wetton, JH and Kiesler, K and Ameur, A and Azonbakin, S and Bôžiková, A and Choma, A and De Ungria, MC and Corradini, B and Cruz, C and Dunkelmann, B and Ferri, G and Fleckhaus, J and Fragou, D and Gaens, N and Gonçalves, R and Havaš Auguštin, D and Helm, K and Hölzl-Müller, P and Kaliszan, M and Kasu, M and Kovatsi, L and Lesaoana, M and Mizuno, N and Neuhuber, F and Nováčková, J and Ňuňuková, A and Pamjav, H and Parson, W and Ramankulov, Y and Rangel Villalobos, H and Rębała, K and Rootsi, S and Salvador, J and Šarac, J and Steffen, CR and Stenzl, V and Török, T and Villems, R and Watahiki, H and Zhabagin, M and Schneider, PM and Kayser, M}, title = {UYSD: a novel data repository accessible via public website for worldwide population frequencies of Y-SNP haplogroups.}, journal = {European journal of human genetics : EJHG}, volume = {}, number = {}, pages = {}, pmid = {40341774}, issn = {1476-5438}, support = {101080117//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PRG1071//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1071//Eesti Teadusagentuur (Estonian Research Council)/ ; }, abstract = {For decades, there has been scientific interest in the variation and geographic distribution of paternal lineages associated with the human Y chromosome. However, the relevant data have been dispersed across numerous publications, making it difficult to consolidate. Additionally, understanding the relationships between different variants, and the tools used to analyze them, have evolved over time, further complicating efforts to harmonize this information. The Universal Y-SNP Database (UYSD) marks a substantial advancement by providing a comprehensive and accessible platform for Y-SNP and haplogroup data from populations around the world. UYSD harmonizes diverse datasets into a unified repository, facilitating the exploration of global Y-chromosomal variation. The platform handles data generated with both high- and low-throughput technology and is compatible with the automated analysis software tool, Yleaf v3. Key functionalities include the ability to: i) visualize haplogroup distributions on an interactive world map, ii) estimate haplogroup frequencies in geographic regions with sparse data through interpolation, and iii) display detailed phylogenetic trees of Y-chromosomal haplogroups. Currently, UYSD encompasses data from over 6,600 males across 27 populations. This dataset largely aligns with known global Y-haplogroup patterns, but also reveals unexplored finer-scale geographic variations. While the present dataset is largely European-centered, UYSD is designed for ongoing expansion by the scientific community, aiming to include more global data and higher-resolution population sequencing data. The platform thus offers valuable insights into human genetic diversity and migration patterns, serving several fields of research such as: human population genetics, genetic anthropology, ancient DNA analysis and forensic genetics.}, }
@article {pmid40333974, year = {2025}, author = {von Hippel, B and Stoof-Leichsenring, KR and Çabuk, U and Liu, S and Melles, M and Herzschuh, U}, title = {Postglacial bioweathering, soil nutrient cycling, and podzolization from palaeometagenomics of plants, fungi, and bacteria.}, journal = {Science advances}, volume = {11}, number = {19}, pages = {eadj5527}, pmid = {40333974}, issn = {2375-2548}, mesh = {*Soil/chemistry ; *Fungi/genetics/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/genetics ; *Plants/metabolism/genetics ; *Ice Cover ; Geologic Sediments/microbiology ; *Nutrients/metabolism ; DNA, Ancient/analysis ; }, abstract = {Warming-induced glacier retreat exposes bare rocks and glacial sediments, facilitating the establishment of soils. The dynamic interplay between climate, vegetation cover, and soil formation is poorly understood as time-series data are lacking. Here, we present postglacial soil formation during the past 23,000 years inferred from ancient DNA shotgun analyses of Lake Lama sediments targeting plants, soil-associated fungi, and bacteria showing postmortem damage signatures that verify their ancient origin. In the Late Glacial, we reveal basaltic weathering with high abundances of lichens, carbon, and arsenic cyclers, shifting to mycorrhizae domination and N cycling in the Holocene. We reconstruct podzolization starting with spruce forest migration in the Holocene, resulting in soil acidification and increased iron cycling. Our reconstruction of soil formation also contributes basic knowledge for the design of carbon-capture strategies using basalt weathering.}, }
@article {pmid40309111, year = {2025}, author = {Zhang, X and Zhang, F}, title = {Island ancient genomes reveal dynamic populations interactions in the northern China.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1584315}, pmid = {40309111}, issn = {1664-302X}, abstract = {The Longshan period (2500-1900 BC) was a transformative era in central China, marked by the emergence of complex social structures and early state formation. While human mobility likely played a role in these developments, the scale and nature of migration during this period remain poorly understood. Previous ancient DNA studies on Longshan culture populations have focused on individuals from inland Shandong, with no ancient DNA data available from island populations. In this study, we present the first ancient DNA analysis from individuals associated with the Longshan and subsequent Yueshi cultures on the Tuoji Island. Our findings indicate that, despite the widespread cultural influence of the inland Longshan culture in Shandong, the genetic ancestry of the Tuoji Island individuals primarily reflects connections to the preceding Dawenkou culture, with additional ancestry linked to the coastal regions of southern China. This suggests an earlier population movement into Tuoji Island before the Longshan period. However, during the Longshan period, the spread of Longshan cultural materials on Tuoji Island appears to represent the diffusion of ideas rather than significant population admixture from the inland. Additionally, our study shows genetic continuity of Longshan and Yueshi cultures in Tuoji Island highlighting the dynamic nature of coastal migration, as the Tuoji Island populations exhibit more genetic influence from coastal regions than from the inland. In contrast, inland populations during the Longshan period show no significant genetic influx from neighboring regions. This study not only advances our understanding of the prehistoric populations in Neolithic China but also provides new insights into patterns of migration and cultural exchange during this critical period.}, }
@article {pmid40307544, year = {2025}, author = {Pinotti, T and Adler, MA and Mermejo, R and Bitz-Thorsen, J and McColl, H and Scorrano, G and Feizabadifarahani, M and Gandy, D and Boulanger, M and Gaunitz, C and Stenderup, J and Ramsøe, A and Korneliussen, T and Demeter, F and Santos, FR and Vinner, L and Sikora, M and Meltzer, DJ and Moreno-Mayar, JV and Quanchello, C and Willerslev, E}, title = {Picuris Pueblo oral history and genomics reveal continuity in US Southwest.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40307544}, issn = {1476-4687}, abstract = {Indigenous groups often encounter significant challenges when asserting ancestral claims and cultural affiliations based on oral histories, particularly in the USA where such narratives have historically been undervalued. Although ancient DNA offers a tool to complement traditional knowledge and address gaps in oral history, longstanding disregard for Indigenous sovereignty and beliefs has understandably led many Indigenous communities to distrust DNA studies[1-4]. Earlier research often focused on repatriation claims[5-7], whereas more recent work has increasingly moved towards enhancing Tribal histories[8,9]. Here we present a collaborative study initiated by a federally recognized Native American tribe, the sovereign nation of Picuris Pueblo in the Northern Rio Grande region of New Mexico, USA, to address gaps in traditional knowledge and further their understanding of their population history and ancestry. We generated genomes from 16 ancient Picuris individuals and 13 present-day members of Picuris Pueblo, providing genomic data spanning the last millennium. We show genetic continuity between ancient and present-day Picuris, and more broadly with Ancestral Puebloans from Pueblo Bonito in Chaco Canyon[10], 275 km to the west. This suggests a firm spatiotemporal link among these Puebloan populations of the North American Southwest. Furthermore, we see no evidence of population decline before European arrival[11-13], and no Athabascan ancestry in individuals predating 1500 CE, challenging earlier migration hypotheses[14-16]. This work prioritizes Indigenous control of genetic data and brings together oral tradition, archaeology, ethnography and genetics.}, }
@article {pmid40296056, year = {2025}, author = {Oteo-Garcia, G and Silva, M and Foody, MGB and Yau, B and Fichera, A and Alapont, L and Justeau, P and Rodrigues, S and Monteiro, R and Gandini, F and Rovira Gomar, ML and Ribera I Lacomba, A and Pascual Beneyto, J and Mattiangeli, V and Bradley, DG and Edwards, CJ and Pala, M and Richards, MB}, title = {Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {108}, pmid = {40296056}, issn = {1474-760X}, support = {N&#xb0;101034324//European Union's Horizon 2020 research and innovation programme/ ; 205072/WT_/Wellcome Trust/United Kingdom ; 205072/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Africa, Northern ; Spain ; *Genome, Human ; History, Medieval ; *Gene Flow ; DNA, Ancient/analysis ; Genetics, Population ; Black People/genetics ; }, abstract = {BACKGROUND: The Islamic influence on the Iberian Peninsula left an enduring cultural and linguistic legacy. However, the demographic impact is less well understood. This study aims to explore the dynamics of gene flow and population structure in eastern Iberia from the early to late medieval period through ancient DNA.<br><br>RESULTS: Our comprehensive genomic analysis uncovers gene flow from various Mediterranean regions into Iberia before the Islamic period, supporting a pre-existing pan-Mediterranean homogenization phenomenon during the Roman Empire. North African ancestry is present but sporadic in late antiquity genomes but becomes consolidated during the Islamic period. We uncover one of the earliest dated Islamic burials in Spain, which shows high levels of consanguinity. For the first time, we also demonstrate the persistence of North African ancestry in a Christian cemetery until the seventeenth century, in addition to evidence of slave trafficking from&#xa0;North Africa.<br><br>CONCLUSIONS: This study reveals the complex interaction between political events and cultural shifts that influenced the population of eastern Iberia. It highlights the existence of a slave trade, underscores the low impact of the Reconquista in the genetic landscape, and shows the lasting impact of post-medieval events, such as the Expulsion of the Moriscos in 1609 CE, on the region's genetic and cultural landscape, through mass population displacement and replacement.}, }
@article {pmid40287785, year = {2025}, author = {Bai, F and He, W and Gao, Y and Ping, WJ and Fu, QM}, title = {Ancient genomes revealed the genetic history and interaction of prehistoric populations in the Ngari region of the western Tibetan Plateau.}, journal = {Yi chuan = Hereditas}, volume = {47}, number = {5}, pages = {501-512}, doi = {10.16288/j.yczz.24-368}, pmid = {40287785}, issn = {0253-9772}, mesh = {Humans ; Tibet ; Archaeology ; *Genetics, Population ; Human Migration/history ; *DNA, Ancient/analysis ; *Genome, Human ; *Asian People/genetics ; History, Ancient ; }, abstract = {The Ngari Prefecture is located in the western part of the Tibetan Plateau. Despite its high altitude and harsh natural environment, it occupies a strategic position adjacent to northern Nepal, India, and Ladakh. As a crossroads connecting the Tibetan Plateau, Xinjiang Autonomous Region, Central Asia, and South Asia, it likely played an important role in early human migration. Archaeological studies in recent years have revealed that even before the establishment of the Tubo Dynasty in the seventh century, the Ngari region maintained extensive cultural connections with Kashmir, Nepal, Xinjiang, and other regions. Furthermore, its subsistence economy reflected strong interactions between Ngari and northern South Asia. Recent paleogenetic studies have demonstrated that the genetic components of the ancient population in the Ngari region originated from the southern part of the plateau, with multiple population expansions occurring from south to west. These studies have also confirmed that alongside cultural exchanges, the Ngari region began experiencing complex genetic interactions with ancient populations from neighboring Central and South Asia at least 2,300 years ago. In this review, we integrate findings from paleogenetics, archaeology, archaeobotany, and zooarchaeology in the Ngari region to systematically examine the genetic origins of the ancient western plateau population and analyze both intraregional cultural-genetic interactions within the Tibetan Plateau and those between Ngari populations and external groups. This synthesis provides important insights for understanding the complex relationships between ancient population movements and interactions in the western Tibetan Plateau, as well as the transformation patterns of regional archaeological cultures and subsistence economies.}, }
@article {pmid40280921, year = {2025}, author = {Garcés-Pastor, S and Heintzman, PD and Zetter, S and Lammers, Y and Yoccoz, NG and Theurillat, JP and Schwörer, C and Tribsch, A and Walsh, K and Vannière, B and Wangensteen, OS and Heiri, O and Coissac, E and Lavergne, S and van Vugt, L and Rey, F and Giguet-Covex, C and Ficetola, GF and Karger, DN and Pellissier, L and Schabetsberger, R and Haas, JN and Strasser, M and Koinig, KA and Goslar, T and Szidat, S and ,  and Brown, AG and Tinner, W and Alsos, IG}, title = {Wild and domesticated animal abundance is associated with greater late-Holocene alpine plant diversity.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3924}, pmid = {40280921}, issn = {2041-1723}, support = {819192//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; KAW 2021.0048//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; KAW 2022.0033//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LCF/BQ/PI24/12040011//"la Caixa" Foundation (Caixa Foundation)/ ; FP7/2007-2013//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; }, mesh = {Animals ; *Biodiversity ; *Animals, Domestic ; *Plants/genetics/classification ; Cattle ; Ecosystem ; *Animals, Wild ; Sheep ; Goats ; Europe ; Geologic Sediments ; Climate Change ; Herbivory ; }, abstract = {In the face of human land use and climate dynamics, it is essential to know the key drivers of plant species diversity in montane regions. However, the relative roles of climate and ungulates in alpine ecosystem change is an open question. Neither observational data nor traditional palaeoecological data have the power to resolve this issue over decadal to centennial timescales, but sedimentary ancient DNA (sedaDNA) does. Here we record 603 plant taxa, as well as 5 wild, and 6 domesticated mammals from 14 lake sediment records over the last 14,000 years in the European Alps. Sheep were the first domesticated animals detected (at 5.8 ka), with cattle appearing at the early Bronze Age (4.2 ka) and goats arriving later (3.5 ka). While sheep had an impact similar to wild ungulates, cattle have been associated with increased plant diversity over the last 2 ka by promoting the diversity of forbs and graminoids. Modelling of the sedaDNA data revealed a significantly larger effect of cattle and wild ungulates than temperature on plant diversity. Our findings highlight the significant alteration of alpine vegetation and the entire ecosystem in the Alps by wild and domesticated herbivores. This study has immediate implications for the maintenance and management of high plant species diversity in the face of ongoing anthropogenic changes in the land use of montane regions.}, }
@article {pmid40272380, year = {2025}, author = {Boucher, RD and Godfrey, LV and Fehren-Schmitz, L and Koch, PL}, title = {Examination of Fe and Cu Isotope Variation in Great Apes Using an Optimized Protocol.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {39}, number = {14}, pages = {e10051}, doi = {10.1002/rcm.10051}, pmid = {40272380}, issn = {1097-0231}, support = {//Leakey Foundation/ ; 2216033//National Science Foundation/ ; }, mesh = {Animals ; Female ; Pan troglodytes ; Male ; *Copper/analysis ; *Iron Isotopes/analysis ; Pan paniscus ; Bone and Bones/chemistry ; Mass Spectrometry/methods ; }, abstract = {RATIONALE: Iron deficiency plagues reproductive-aged women across the world, and blood loss during menstruation is proposed as the driving force. To assess if other factors related to reproduction influence Fe and Cu isotope variation in females, we measured Fe and Cu isotope compositions in the bones of chimpanzees and bonobos.<br><br>METHODS: To do this, we optimize the protocol for isolating Fe and Cu (and Zn) from phosphate-rich skeletal materials for further analysis via MC-ICP-MS. Then, we address possible Fe and Cu variation sources in non-menstruating apes (n&#x2009;=&#x2009;26, of which the sex of 10 was obtained by DNA analysis).<br><br>RESULTS: The optimized method reduced acid volume by ~14%, and sample preparation time by ~37.5%. We did not find significant sex differences in &#x3b4;[56]Fe values (&#x394;[56]Fef-m&#x2009;=&#x2009;0.13&#x2030;) or &#x3b4;[65]Cu values (&#x394;[65]Cuf-m&#x2009;=&#x2009;0.33&#x2030;).<br><br>CONCLUSION: Given the similar &#x394;[56]Fef-m values between non-menstruating apes and humans, reproductive investment, instead of menstruation alone, is a key factor that drives Fe deficiency in reproductive-aged women and is important to consider with proxies of iron status. Our optimized protocol provides an effective method for exploring iron status in other mammalian species.}, }
@article {pmid40272075, year = {2025}, author = {Wooldridge, TB and Wang, MS and Saremi, NF and Kapp, JD and Moon, KL and Heintzman, PD and Dumbacher, JP and Alagona, PS and Long, B and Shapiro, B}, title = {Genomic data from the extinct California brown bear suggests a source population for reintroduction to California.}, journal = {The Journal of heredity}, volume = {}, number = {}, pages = {}, doi = {10.1093/jhered/esaf018}, pmid = {40272075}, issn = {1465-7333}, abstract = {California brown bears, also known as California grizzlies or golden bears, are an extinct group that once thrived in North America's western coastal habitats. Despite being common in the region as recently as the early 19th century, intense poisoning, trapping, and hunting led to their extinction by 1924. Today, California is emerging as a candidate for brown bear reintroduction as a component of larger ecosystem restoration efforts. Questions remain, however, about whether living brown bears are suitable proxies for the bears that once inhabited California. While recent work suggests that brown bears from California were similar in size and overall diet to brown bears living today in continental North America, the a) extent to which California bears were genetically differentiated from other populations, and b) what this means for proposed reintroductions, remain outstanding questions. We generated genomes from two of the last living California brown bears and compared them to genomes from living brown bears. Genomic estimates of divergence time combined with radiocarbon dating points towards brown bears arriving recently to California, having diverged within the last 10,000 years from a common ancestor with brown bears found today in Yellowstone National Park, Wyoming. This timeline, the overall genetic similarity between the California and Yellowstone populations, and the strong pattern of isolation-by-distance we observe all suggest that no closer living relatives are likely to be found. If genetic background is to be a consideration for reintroduction efforts in California, brown bears from Yellowstone might serve as a source population.}, }
@article {pmid40269306, year = {2025}, author = {Callaway, E}, title = {Ancient DNA reveals Phoenicians' surprising genetic ancestry.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40269306}, issn = {1476-4687}, }
@article {pmid40269169, year = {2025}, author = {Ringbauer, H and Salman-Minkov, A and Regev, D and Olalde, I and Peled, T and Sineo, L and Falsone, G and van Dommelen, P and Mittnik, A and Lazaridis, I and Pettener, D and Bofill, M and Mezquida, A and Costa, B and Jiménez, H and Smith, P and Vai, S and Modi, A and Shaus, A and Callan, K and Curtis, E and Kearns, A and Lawson, AM and Mah, M and Micco, A and Oppenheimer, J and Qiu, L and Stewardson, K and Workman, JN and Márquez-Grant, N and Sáez Romero, AM and Lavado Florido, ML and Jiménez-Arenas, JM and Toro Moyano, IJ and Viguera, E and Padilla, JS and Chamizo, SL and Marques-Bonet, T and Lizano, E and Riaza, AR and Olivieri, F and Toti, P and Giuliana, V and Barash, A and Carmel, L and Boaretto, E and Faerman, M and Lucci, M and La Pastina, F and Nava, A and Genchi, F and Del Vais, C and Lauria, G and Meli, F and Sconzo, P and Catalano, G and Cilli, E and Fariselli, AC and Fontani, F and Luiselli, D and Culleton, BJ and Mallick, S and Rohland, N and Nigro, L and Coppa, A and Caramelli, D and Pinhasi, R and Lalueza-Fox, C and Gronau, I and Reich, D}, title = {Punic people were genetically diverse with almost no Levantine ancestors.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40269169}, issn = {1476-4687}, abstract = {The maritime Phoenician civilization from the Levant transformed the entire Mediterranean during the first millennium BCE[1-3]. However, the extent of human movement between the Levantine Phoenician homeland and Phoenician-Punic settlements in the central and western Mediterranean has been unclear in the absence of comprehensive ancient DNA studies. Here, we generated genome-wide data for 210 individuals, including 196 from 14 sites traditionally identified as Phoenician and Punic in the Levant, North Africa, Iberia, Sicily, Sardinia and Ibiza, and an early Iron Age individual from Algeria. Levantine Phoenicians made little genetic contribution to Punic settlements in the central and western Mediterranean between the sixth and second centuries BCE, despite abundant archaeological evidence of cultural, historical, linguistic and religious links[4]. Instead, these inheritors of Levantine Phoenician culture derived most of their ancestry from a genetic profile similar to that of Sicily and the Aegean. Much of the remaining ancestry originated from North Africa, reflecting the growing influence of Carthage[5]. However, this was a minority contributor of ancestry in all of the sampled sites, including in Carthage itself. Different Punic sites across the central and western Mediterranean show similar patterns of high genetic diversity. We also detect genetic relationships across the Mediterranean, reflecting shared demographic processes that shaped the Punic world.}, }
@article {pmid40269167, year = {2025}, author = {Feng, C and Chen, B and Hofer, J and Shi, Y and Jiang, M and Song, B and Cheng, H and Lu, L and Wang, L and Howard, A and Bendahmane, A and Fouchal, A and Moreau, C and Sawada, C and LeSignor, C and Zhang, C and Vikeli, E and Tsanakas, G and Zhao, H and Cheema, J and Barclay, JE and Hou, J and Sayers, L and Wingen, L and Vigouroux, M and Vickers, M and Ambrose, M and Dalmais, M and Higuera-Poveda, P and Li, P and Yuan, Q and Spanner, R and Horler, R and Wouters, R and Chundakkad, S and Wu, T and Zhao, X and Li, X and Sun, Y and Huang, Z and Wu, Z and Deng, XW and Steuernagel, B and Domoney, C and Ellis, N and Chayut, N and Cheng, S}, title = {Genomic and genetic insights into Mendel's pea genes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40269167}, issn = {1476-4687}, abstract = {Mendel[1] studied in detail seven pairs of contrasting traits in pea (Pisum sativum), establishing the foundational principles of genetic inheritance. Here we investigate the genetic architecture that underlies these traits and uncover previously undescribed alleles for the four characterized Mendelian genes[2-7], including a rare revertant of Mendel's white-flowered a allele. Primarily, we focus on the three remaining uncharacterized traits and find that (1) an approximately 100-kb genomic deletion upstream of the Chlorophyll synthase (ChlG) gene disrupts chlorophyll biosynthesis through the generation of intergenic transcriptional fusion products, conferring the yellow pod phenotype of gp mutants; (2) a MYB gene with an upstream Ogre element insertion and a CLE peptide-encoding gene with an in-frame premature stop codon explain the v and p alleles, which disrupt secondary cell wall thickening and lignification, resulting in the parchmentless, edible-pod phenotype; and (3) a 5-bp exonic deletion in a CIK-like co-receptor kinase gene, in combination with a genetic modifier locus, is associated with the fasciated stem (fa) phenotype. Furthermore, we characterize genes and alleles associated with diverse agronomic traits, such as axil ring anthocyanin pigmentation, seed size and the 'semi-leafless' form. This study establishes a foundation for fundamental research, education in biology and genetics, and pea breeding practices.}, }
@article {pmid40236176, year = {2025}, author = {Xu, J and Zavala, EI and Moorjani, P}, title = {sedimix : A workflow for the analysis of hominin nuclear DNA sequences from sediments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.28.640818}, pmid = {40236176}, issn = {2692-8205}, abstract = {SUMMARY: Sediment DNA--the ability to extract DNA from archaeological sediments-- is an exciting new frontier in ancient DNA research, offering the potential to study individuals at a given archaeological site without destructive sampling. In recent years, several studies have demonstrated the promise of this approach by recovering hominin DNA from prehistoric sediments, including those dating back to the Middle or Late Pleistocene. However, a lack of open-source workflows for analysis of hominin sediment DNA samples poses a challenge for data processing and reproducibility of findings across studies. Here we introduce a snakemake workflow, sedimix , for processing genomic sequences from archaeological sediment DNA samples to identify hominin sequences and generate relevant summary statistics to assess the reliability of the pipeline. By performing simulations and comparing to published studies, we show that sedimix has high sensitivity and precision. sedimix offers a reliable and adaptable framework to aid in the analysis of sediment DNA datasets and improve reproducibility across studies.<br><br>sedimix is available as an open-source software with the associated code and user manual available at https://github.com/jierui-cell/sedimix Contact: Jierui Xu (jierui.xu@berkeley.edu) Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid40129172, year = {2025}, author = {De Cahsan, B and Sandoval Velasco, M and Westbury, MV and Duchêne, DA and Strander Sinding, MH and Morales, HE and Kalthoff, DC and Barnes, I and Brace, S and Portela Miguez, R and Roca, AL and Greenwood, AD and Johnson, RN and Lott, MJ and Gilbert, MTP}, title = {Road to Extinction? Past and Present Population Structure and Genomic Diversity in the Koala.}, journal = {Molecular biology and evolution}, volume = {42}, number = {4}, pages = {}, doi = {10.1093/molbev/msaf057}, pmid = {40129172}, issn = {1537-1719}, abstract = {Koalas are arboreal herbivorous marsupials, endemic to Australia. During the late 1800s and early 1900s, the number of koalas declined dramatically due to hunting for their furs. In addition, anthropogenic activities have further decimated their available habitat, and decreased population numbers. Here, we utilize 37 historic and 25 modern genomes sampled from across their historic and present geographic range, to gain insights into how their population structure and genetic diversity have changed across time; assess the genetic consequences of the period of intense hunting, and the current genetic status of this iconic Australian species. Our analyses reveal how genome-wide heterozygosity has decreased through time and unveil previously uncharacterized mitochondrial haplotypes and nuclear genotypes in the historic dataset, which are absent from today's koala populations.}, }
@article {pmid40217095, year = {2025}, author = {Barnes, I}, title = {A tour de force of ancient DNA analysis.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {40217095}, issn = {1471-0064}, }
@article {pmid40216956, year = {2025}, author = {}, title = {Mystery of medieval manuscripts revealed by ancient DNA.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40216956}, issn = {1476-4687}, }
@article {pmid40214271, year = {2025}, author = {Gersak, ZM and Zupanic-Pajnic, I and Podovsovnik, E and Salapura, V}, title = {Computed tomography differentiation of compact and cancellous bone tissue in short and sesamoid bones.}, journal = {Radiology and oncology}, volume = {}, number = {}, pages = {}, pmid = {40214271}, issn = {1581-3207}, abstract = {BACKGROUND: Selecting the most suitable skeletal remains for genetic analysis is challenging due to the variable DNA yield across different bone types and within individual bones. Compact bone typically preserves DNA longer, whereas cancellous bones, such as those in the hands and feet, often contain higher DNA quantities. This study aimed to incorporate dual-source computed tomography (DSCT), a technique frequently utilized for assessing bone density in living subjects, into targeted DNA sampling for dry, skeletonized remains by mapping compact and cancellous regions within six small skeletal elements.<br><br>MATERIALS AND METHODS: A total of 137 bones were analysed using an imaging protocol specifically adapted to highlight the skeletal structure of small bones. This tailored protocol involved meticulous calibration of imaging parameters. Anatomical landmarks for six distinct elements were identified, and regions of interest were selected for bone density measurement in Hounsfield units (HU).<br><br>RESULTS: Among 461 assessed regions, 312 (68%) were classified as compact bone, and 149 (32%) as cancellous bone. Given the abnormal distribution of data, statistical differences were evaluated using 95% confidence intervals, with significance indicated by non-overlapping intervals. The analysis revealed statistically significant differences between compact and cancellous bone, as well as within each type across different bones.<br><br>CONCLUSIONS: DSCT proved effective in mapping the internal structure of six small skeletal elements in dry, skeletonized remains, underscoring significant intra-bone variability in density. The findings illustrate DSCT's substantial potential for enhancing DNA sampling in forensic and paleogenetic studies, setting the stage for future research advancements.}, }
@article {pmid40206852, year = {2025}, author = {Lévêque, &#xc9; and Teasdale, MD and Fiddyment, S and Bro-Jørgensen, MH and Spindler, L and Macleod, R and Bougard, F and Tange Olsen, M and Collins, M}, title = {Hiding in plain sight: the biomolecular identification of pinniped use in medieval manuscripts.}, journal = {Royal Society open science}, volume = {12}, number = {4}, pages = {241090}, pmid = {40206852}, issn = {2054-5703}, abstract = {The survival of medieval manuscripts in their original bindings remains a rare occurrence. Taking advantage of the diversity of bindings in Cistercian libraries such as Clairvaux and its daughter abbeys during the twelfth and thirteenth centuries, this study focuses on the biocodicological analysis of medieval manuscript bindings, with particular emphasis on the use of sealskins. Using innovative methods such as electrostatic zooarchaeology by mass spectrometry (eZooMS) and ancient DNA (aDNA) analysis, this research identifies the animal species and origin of the leather used in these bindings as predominantly pinniped (seal) species. In particular, the collagen-based eZooMS technique facilitated the classification of seven chemises into the pinniped clade, although species identification remained elusive, except in one additional case where a bearded seal (Erignathus barbatus) was definitively identified. aDNA analysis was instrumental in verifying the origin of the sealskins, with four samples identified as harbour seals and a single sample as a harp seal and sourced to (contemporary) populations in Scandinavia, Scotland and Iceland or Greenland. This geographical inference supports the notion of a robust medieval trade network that went well beyond local sourcing, linking the Cistercians to wider economic circuits that included fur trade with the Norse. The study, therefore, highlights the use of an unexpected skin (seal) from an unexpected source (the northwestern Atlantic). The widespread use of sealskins in Cistercian libraries such as Clairvaux and its daughter abbeys during the twelfth and thirteenth centuries hints at broader trade networks that brought, for example, walrus ivory from the far north into continental Europe. This integration of the biological sciences into the study of historical manuscripts not only provides a clearer picture of the material culture of medieval Europe, but also illustrates the extensive trade networks that Cistercian monasteries were part of, challenging previous assumptions about local resource use in manuscript production.}, }
@article {pmid40203146, year = {2025}, author = {Anaïs, A and Yaxal, PG and Amélie, C and Philippe, C and Nicolás, R}, title = {An ancient Epstein-Barr virus genome recovered from a museum penis gourd from Papua.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaf189}, pmid = {40203146}, issn = {1537-6613}, abstract = {Ancient DNA provides a unique opportunity to study the history and spread of infectious diseases. Here, we analyzed 21 samples from a collection of 20th-century penis gourds (koteka) from Papua New Guinea housed at the Musée du quai Branly - Jacques Chirac in Paris. Despite the presence of environmental species, we identified human-associated bacteria and, notably, an Epstein-Barr Virus (EBV) genome at high coverage. Phylogenetic analysis placed this strain within a Papua New Guinea-Indonesian cluster. These findings highlight museum collections as valuable reservoirs of genetic data, offering historical insights into the evolution and spread of human pathogens.}, }
@article {pmid40202701, year = {2025}, author = {More, KD and Lebrasseur, O and Garrido, JL and Seguin-Orlando, A and Discamps, E and Estrada, O and Tonasso-Calvière, L and Chauvey, L and Tressières, G and Schiavinato, S and Gibert, M and Padula, H and Chiavazza, H and Fernández, PM and Guardia, NM and Borges, C and Bertani, S and Contreras-Mancilla, J and Allccarima-Crisóstomo, D and Fhon, M and Barrey, E and Charliquart, L and Robbe, E and de Noblet, T and Zhumatayev, R and Shakenov, S and Vila, E and Berthon, R and Mashkour, M and Khazaeli, R and Nikgoftar, A and Vahdati, AA and Kosintsev, P and Houle, JL and Bayarsaikhan, J and Wilczynski, J and Moskal-Del Hoyo, M and Nowak, M and Taylor, W and Bălășescu, A and Dobrescu, R and Benecke, N and Arbuckle, B and Steadman, S and McMahon, G and Šikanjić, PR and Buric, M and Vukičević, TT and Alvarez, N and Castel, JC and Boudadi-Maligne, M and Star, B and Post-Melbye, JR and Rødsrud, CL and Stanton, DWG and Charlton, S and Mullin, VE and Daly, KG and Burgos, NS and Pablos, A and Dalen, L and Bradley, DG and Frantz, L and Larson, G and Orlando, L}, title = {Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14112}, doi = {10.1111/1755-0998.14112}, pmid = {40202701}, issn = {1755-0998}, support = {101032990-PALEOQINOA//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 101062645-ZEPHYRUS//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 895107-ARAUCANA//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 897931-PALEOS//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; CoproDNA//CNRS Zone Atelier PYGAR/ ; ANR-17-CE27-0004//Agence Nationale de la Recherche (ANR)/ ; //Knut and Alice Wallenberg Foundation/ ; 101071707//European Research Council (ERC)/ ; 101117101//European Research Council (ERC)/ ; 681605//European Research Council (ERC)/ ; 949330//European Research Council (ERC)/ ; 101054984//European Research Council (ERC)/ ; MCIN/AEI/10.13039/501100011033//Fondo Social Europeo and Agencia Estatal de Investigaci&#xf3;n/ ; RYC2020-029656-I//Fondo Social Europeo and Agencia Estatal de Investigaci&#xf3;n/ ; CENIEH//Centro Nacional de Investigaci&#xf3;n sobre la Evoluci&#xf3;n Humana/ ; SciLifeLab//Science for Life Laboratory/ ; 2021-00625//Swedish Research Council/ ; CAGT//Universit&#xe9; de Toulouse/ ; SBPLY/24/180801/000019//Junta de Comunidades de Castilla la Mancha/ ; AnimalFarmIRP//Centre National de la Recherche Scientifique/ ; }, abstract = {In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.}, }
@article {pmid40199243, year = {2025}, author = {Mathieson, I}, title = {Iain Mathieson.}, journal = {Current biology : CB}, volume = {35}, number = {7}, pages = {R240-R241}, doi = {10.1016/j.cub.2025.03.005}, pmid = {40199243}, issn = {1879-0445}, mesh = {Humans ; *Biological Evolution ; *DNA, Ancient/analysis ; History, 21st Century ; History, 20th Century ; }, abstract = {Interview with Iain Mathieson, who studies ancient DNA and its relevance to recent human evolution at the University of Pennsylvania.}, }
@article {pmid40196638, year = {2025}, author = {Olalde, I and Altena, E and Bourgeois, Q and Fokkens, H and Amkreutz, L and Deguilloux, MF and Fichera, A and Flas, D and Gandini, F and Kegler, JF and Kootker, LM and Leijnse, K and Kooijmans, LL and Lauwerier, R and Miller, R and Molthof, H and Noiret, P and Raemaekers, DCM and Rivollat, M and Smits, L and Stewart, JR and Ten Anscher, T and Toussaint, M and Callan, K and Cheronet, O and Frost, T and Iliev, L and Mah, M and Micco, A and Oppenheimer, J and Patterson, I and Qiu, L and Soos, G and Workman, JN and Edwards, CJ and Lazaridis, I and Mallick, S and Patterson, N and Rohland, N and Richards, MB and Pinhasi, R and Haak, W and Pala, M and Reich, D}, title = {Long-term hunter-gatherer continuity in the Rhine-Meuse region was disrupted by local formation of expansive Bell Beaker groups.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.24.644985}, pmid = {40196638}, issn = {2692-8205}, abstract = {The first phase of the ancient DNA revolution painted a broad-brush picture of European Holocene prehistory, whereby 6500-4000 BCE, farmers descending from western Anatolians mixed with local hunter-gatherers resulting in 70-100% ancestry turnover, then 3000-2500 BCE people associated with the Corded Ware complex spread steppe ancestry into north-central Europe. We document an exception to this pattern in the wider Rhine-Meuse area in communities in the wetlands, riverine areas, and coastal areas of the western and central Netherlands, Belgium and western Germany, where we assembled genome-wide data for 109 people 8500-1700 BCE. Here, a distinctive population with high hunter-gatherer ancestry (∼50%) persisted up to three thousand years later than in continental European regions, reflecting limited incorporation of females of Early European Farmer ancestry into local communities. In the western Netherlands, the arrival of the Corded Ware complex was also exceptional: lowland individuals from settlements adopting Corded Ware pottery had hardly any steppe ancestry, despite a characteristic early Corded Ware Y-chromosome. The limited influx may reflect the unique ecology of the region's river-dominated landscapes, which were not amenable to wholesale adoption of the early Neolithic type of farming introduced by Linearbandkeramik, making it possible for previously established groups to thrive, and creating a persistent but permeable boundary that allowed transfer of ideas and low-level gene flow. This changed with the formation-through-mixture of Bell Beaker using populations ∼2500 BCE by fusion of local Rhine-Meuse people (9-17%) and Corded Ware associated migrants of both sexes. Their expansion from the Rhine-Meuse region then had a disruptive impact across a much wider part of northwest Europe, including Britain where its arrival was the main source of a 90-100% replacement of local Neolithic peoples.}, }
@article {pmid40196503, year = {2025}, author = {Tabin, D and Patterson, N and Mah, M and Reich, D}, title = {Addendum to Ancient DNA data from Mengzi Ren, a Late Pleistocene individual from Southeast Asia, cannot be reliably used in population genetic analysis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.24.645126}, pmid = {40196503}, issn = {2692-8205}, abstract = {In addition to the issues pointed out in Tabin et al [1] , the MZR data from Zhang et. al 2022 [2] are suggestive of high levels of contamination from a source similar to modern Han Chinese, the majority population in the country where MZR was sequenced. In fact, MZR can be modeled entirely as Han-related ancestry and noise. These results raise further concerns about the veracity of the MZR data and thus the paper's historical conclusions.}, }
@article {pmid40189540, year = {2025}, author = {Li, H and Wang, B and Yang, X and Yang, X and He, H and Wang, R and Wang, CC}, title = {Ancient genomes shed light on the genetic history of the Iron Age to historical central Xinjiang, northwest China.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {93}, pmid = {40189540}, issn = {1741-7007}, mesh = {China ; Humans ; *DNA, Ancient/analysis ; *Genome, Human ; *Genetics, Population ; History, Ancient ; Human Migration ; }, abstract = {BACKGROUND: The genetic profile of the population in Xinjiang, northwest China, has been shaped by interregional movement and admixture since the Bronze Age. However, the detailed and intraregional population history of Xinjiang, especially central Xinjiang, has been unsolved due to uneven sample distribution.<br><br>RESULTS: Here, we reported the ancient genomes from 8 individuals between the Iron Age and the&#xa0;historical period in central Xinjiang. We observed an east-west admixed ancestry profile and a&#xa0;degree of genetic continuity between the Iron Age and historical central Xinjiang individuals. Furthermore, these central Xinjiang individuals harboured ancestry related to ancient farmers of the Yellow River. We also identified a temporal change of the Yellow River farmers-related ancestry in central Xinjiang, showing an increase the Yelllow River affinity from Iron Age to Historical Era.<br><br>CONCLUSIONS: The finding indicated that the genetic structure of the central Xinjiang population since the Iron Age could have resulted from immigration from northern China, which was&#xa0;attributed to geopolitical factors. Hence, our results indicated that the geopolitical change with the deepening of Central Plains' management has influenced the genetic profile of central Xinjiang.}, }
@article {pmid40179167, year = {2025}, author = {Curry, A}, title = {Ancient DNA illuminates 'green Sahara' dwellers.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6742}, pages = {18}, doi = {10.1126/science.adx9095}, pmid = {40179167}, issn = {1095-9203}, mesh = {*DNA, Ancient/analysis ; Humans ; History, Ancient ; }, abstract = {Skeletons from an ancient, lush interlude offer genetic peek at a lost population.}, }
@article {pmid40175742, year = {2025}, author = {Prendergast, M}, title = {Rare ancient DNA from Sahara opens a window on the region's verdant past.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40175742}, issn = {1476-4687}, }
@article {pmid40175549, year = {2025}, author = {Salem, N and van de Loosdrecht, MS and Sümer, AP and Vai, S and Hübner, A and Peter, B and Bianco, RA and Lari, M and Modi, A and Al-Faloos, MFM and Turjman, M and Bouzouggar, A and Tafuri, MA and Manzi, G and Rotunno, R and Prüfer, K and Ringbauer, H and Caramelli, D and di Lernia, S and Krause, J}, title = {Ancient DNA from the Green Sahara reveals ancestral North African lineage.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40175549}, issn = {1476-4687}, abstract = {Although it is one of the most arid regions today, the Sahara Desert was a green savannah during the African Humid Period (AHP) between 14,500 and 5,000 years before present, with water bodies promoting human occupation and the spread of pastoralism in the middle Holocene epoch[1]. DNA rarely preserves well in this region, limiting knowledge of the Sahara's genetic history and demographic past. Here we report ancient genomic data from the Central Sahara, obtained from two approximately 7,000-year-old Pastoral Neolithic female individuals buried in the Takarkori rock shelter in southwestern Libya. The majority of Takarkori individuals' ancestry stems from a previously unknown North African genetic lineage that diverged from sub-Saharan African lineages around the same time as present-day humans outside Africa and remained isolated throughout most of its existence. Both Takarkori individuals are closely related to ancestry first documented in 15,000-year-old foragers from Taforalt Cave, Morocco[2], associated with the Iberomaurusian lithic industry and predating the AHP. Takarkori and Iberomaurusian-associated individuals are equally distantly related to sub-Saharan lineages, suggesting limited gene flow from sub-Saharan to Northern Africa during the AHP. In contrast to Taforalt individuals, who have half the Neanderthal admixture of non-Africans, Takarkori shows ten times less Neanderthal ancestry than Levantine farmers, yet significantly more than contemporary sub-Saharan genomes. Our findings suggest that pastoralism spread through cultural diffusion into a deeply divergent, isolated North African lineage that had probably been widespread in Northern Africa during the late Pleistocene epoch.}, }
@article {pmid40174641, year = {2025}, author = {He, T and Zhang, X and Zhang, X}, title = {Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.03.057}, pmid = {40174641}, issn = {2090-1224}, abstract = {INTRODUCTION: In the last two decades, outbreaks of pathogenic viruses have led to significant human mortality and economic repercussions. Despite extensive investigations into tracing these viruses in terrestrial environments, their origins remain enigmatic.<br><br>OBJECTIVES: The Earth's biosphere encompasses both sunlight-dependent terrestrial and surface ocean ecosystems, as well as the sunlight-independent deep-sea ecosystem. However, the traceability of human pathogenic viruses in the deep sea has not been thoroughly explored. This study aimed to investigate the presence of human pathogenic viruses in the deep sea.<br><br>METHODS: In this study, we performed a viral metagenomic analysis using a global deep-sea sediment virome 2.0 dataset which contained 159 deep-sea sediment samples with geologic ages from 2,500 to 7,750 years.<br><br>RESULTS: A total of 554,664 viral operational taxonomic units (vOTUs) were identified and further obtained 2,254 potential pathogenic viruses of vertebrates. Among them, 23 vOTUs exhibited high homology with 12 species of human pathogenic viruses which belonged to 4 viral families. Notably, variola virus, the first human pathogenic virus eradicated from humans and now only found in laboratories, was discovered in the ancient deep-sea sediments. The evolution analysis showed that these DNA viruses might represent the ancestors or variants of human pathogenic viruses, suggesting that the deep sea could be a crucial reservoir for human pathogenic viruses.<br><br>CONCLUSION: Our findings present all the ancient pathogenic DNA viruses of humans found in the deep sea for the first time, highlighting the source of the future epidemics. It is imperative to implement the stringent virus monitoring and management measures for human activities in marine environments to address the emerging challenges of marine biosecurity and promote sustainable use of oceans.}, }
@article {pmid40167159, year = {2025}, author = {Qiu, Y and Liu, L and Huang, M and Ruan, D and Ding, R and Zhang, Z and Zheng, E and Wang, S and Deng, S and Meng, X and Cheng, X and Shi, J and Yang, Y and Zhou, F and Huang, S and Yang, H and Li, Z and Cai, G and Wu, Z and Yang, J}, title = {Origins, Dispersal, and Impact: Bidirectional Introgression Between Chinese and European Pig Populations.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2416573}, doi = {10.1002/advs.202416573}, pmid = {40167159}, issn = {2198-3844}, support = {2023YFD1300201//National Key Research and Development Program of China/ ; 2022B0202090002//key Technologies R&amp;D Program of Guangdong Province/ ; 2024A1515010967//Natural Science Foundation of Guangdong Province/ ; 2019BT02N630//Local Innovative and Research Teams Project of Guangdong Province/ ; SL2023A04J00485//Young Scholars "Qihang" Program/ ; }, abstract = {Human mediated intra-continental exchange of genetic material among domesticated organisms has never been restricted to a single direction. The introduction of pig breeds between China and Europe aims to enhance economically important traits in local populations. However, the reciprocal introgression pattern, specifically the role of introgressed genes and structural variations (SVs), remains underexplored. A global collection of whole-genome resequencing data is utilized from 418 pigs to generate comprehensive dataset, including single-nucleotide polymorphisms (SNPs) as well as SVs. The analysis reveals incomplete linkage disequilibrium between SVs and adjacent SNPs, highlighting the limitations of conventional SNP-based analyses in capturing the genetic effects of SVs. By examining both population-level SNPs and SVs, bidirectional introgression between Chinese and European pig populations is characterized. It is identified 3558 bidirectional introgressed genomic segments and 30 SVs, with haplotypes at BMP2, which are associated with improved body size. The origin and allele frequency trajectory of the BMP2 segment are further validated using ancient genomes, suggesting that the body size-enhancing haplotype likely originated from ancient European populations and has since maintained a relatively high allele frequency. Overall, the results highlight the significant role of bidirectional introgression in shaping the genetic composition and phenotypic traits in modern pig breeds.}, }
@article {pmid40163762, year = {2025}, author = {Martin, N and Thibeault, A and Varadzinová, L and Usai, D and Ambrose, SH and Antoine, D and Brukner Havelková, P and Honegger, M and Irish, JD and Jesse, F and Maréchal, L and Osypińska, M and Osypiński, P and Santos, F and Vanderesse, N and Varadzin, L and Whiting, RJ and Zanolli, C and Velemínský, P and Crevecoeur, I}, title = {Enamel-dentine junction morphology reveals population replacement and mobility in the late prehistoric Middle Nile Valley.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {15}, pages = {e2419122122}, doi = {10.1073/pnas.2419122122}, pmid = {40163762}, issn = {1091-6490}, support = {IRP ABASC//Centre National de la Recherche Scientifique (CNRS)/ ; project NeoNile//French governement - University of Bordeaux IdEx "Investments for the Future" program / GPR "Human Past"/ ; ANR-14-CE31//Agence Nationale de la Recherche (ANR)/ ; 23-06488S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky (GA&#x10c;R)/ ; Cooperatio program//Filozofick&#xe1; Fakulta, Univerzita Karlova v Praze (Faculty of Arts, Charles University)/ ; DKRVO 2024-2028/7.I.a 7.I.b National Museum 00023272//Ministerstvo Kultury (Ministry of Culture)/ ; UMO-2020/37/B/HS3/00519//Narodowe Centrum Nauki (NCN)/ ; }, mesh = {Humans ; *Dental Enamel ; History, Ancient ; *Dentin ; Population Dynamics/history ; Fossils ; Sudan ; Human Migration/history ; X-Ray Microtomography ; }, abstract = {Transitions from foraging to food-production represent a worldwide turning point in recent human history. In the Middle Nile Valley this cultural shift occurred between the sixth and beginning of the fifth millennium BCE. Significant craniodental morphological differences remain inadequately tested by biometric analyses of ancestry and may reflect population origins or diet change between the last hunter-fisher-gatherers (Mesolithic) and first food-producers (Neolithic). Moreover, with no ancient DNA data for this region and very few morphological studies including large samples of Mesolithic individuals, the late prehistoric population history of the Nile Valley remains unclear. Here, we present enamel-dentine junction (EDJ) morphological analyses (based on X-ray microtomography) and biological affinities for 88 individuals spanning 14,000 y from Sudan and southern Egypt. Significant EDJ morphological differences between the last foragers and first food-producers suggest major biological discontinuity at the Neolithic transition. Nevertheless, the persistence of the earlier forager population in the Sudanese Eastern Sahara indicates settlement and population replacement mainly along the Nile. We also present biological evidence of interaction and mobility between these contemporaneous populations during the middle Holocene in the region. It supports the phylogenetic value of EDJ morphology for investigating population affinities at a microevolutionary scale. These results yield insights into the deep population history of the Nile Valley. They provide firm evidence for population replacement and migration toward the region at the onset of the Neolithic transition, attesting that these key changes were not solely triggered by cultural diffusion and diet change.}, }
@article {pmid40148574, year = {2025}, author = {Raghavan, M}, title = {The genesis of paleogenetics.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {40148574}, issn = {1471-0064}, }
@article {pmid40141254, year = {2025}, author = {Rayner, T and Mundy, JEA and Bilham, LJ and Moreau, C and Lawson, DM and Domoney, C and Wang, TL}, title = {A Suite of Pea (Pisum sativum L.) Near-Isolines: Genetic Resources and Molecular Tools to Breed for Seed Carbohydrate and Protein Quality in Legumes.}, journal = {International journal of molecular sciences}, volume = {26}, number = {6}, pages = {}, pmid = {40141254}, issn = {1422-0067}, support = {BB/J004561/1, BBS/E/J/000PR9799, BB/H009787/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; LK09126, IF0147, CH0103, CH0111//Department for Environment Food and Rural Affairs/ ; }, mesh = {*Pisum sativum/genetics/metabolism ; *Seeds/genetics/metabolism ; Mutation ; Phenotype ; Plant Proteins/genetics/metabolism ; Plant Breeding/methods ; Starch/metabolism ; }, abstract = {In recent years there has been a resurgent interest in plant products as substitutes for animal-derived food products, in which legumes, including peas, feature highly. Here, we report on a set of Pisum sativum L. (pea) near-isolines, comprising 24 unique mutants at five loci, where the impact of the mutations on the corresponding enzymes of the starch pathway confers a wrinkled-seeded phenotype. Together with a set of round-seeded mutants impacted at a sixth locus, all 27 mutants show variation for starch composition and protein content. The mutations have been mapped onto three-dimensional protein models to examine potential effects on the corresponding enzyme structures and their activities, and to guide targeted mutagenesis. The mutant lines represent a unique suite of alleles for rapid introduction into elite pea varieties to create new materials for the food and feed markets and industrial applications.}, }
@article {pmid40132550, year = {2025}, author = {Tabin, D and Patterson, N and Mah, M and Reich, D}, title = {Concerns about ancient DNA sequences reported from a Late Pleistocene individual from Southeast Asia.}, journal = {Current biology : CB}, volume = {35}, number = {6}, pages = {R212-R213}, doi = {10.1016/j.cub.2024.10.012}, pmid = {40132550}, issn = {1879-0445}, mesh = {*DNA, Ancient/analysis ; Asia, Southeastern ; Humans ; Fossils ; Female ; Sequence Analysis, DNA ; Animals ; Genetics, Population ; Caves ; }, abstract = {In a 2022 Current Biology paper, Zhang et al.[1] reported DNA sequences from an approximately 14-thousand-year-old female skeleton from Red Deer Cave referred to as 'Mengzi Ren' (MZR). MZR's data are the first DNA sequences reported from pre-Holocene Southeast Asia, revealing genetic affinities dissimilar to all previously published ancient DNA data. Here, we show extremely high error rates, an abnormal error distribution and evidence of contamination by modern human sequences in the published DNA sequences of MZR. Even ignoring these issues, we fail to replicate key population genetic findings of Zhang et al.[1], namely that Native Americans are equally related to MZR and ancient Northeast Asians. These results raise concerns regarding the paper's conclusions about population history, such as the claim that there was "an express northward expansion of AMHs starting in southern East Asia through the coastal line of China … eventually crossing the Bering Strait and reaching the Americas," and also about the general usability of the published sequences.}, }
@article {pmid40106345, year = {2025}, author = {Günther, T and Chisausky, J and Galindo-Pellicena, &#xc1;M and Iriarte, E and Cortes Gardyn, O and Eusebi, PG and García-González, R and Ureña, I and Moreno-García, M and Alday, A and Rojo, M and Pérez, A and Tejedor Rodríguez, C and García Martínez de Lagrán, I and Arsuaga, JL and Carretero, JM and Götherström, A and Smith, C and Valdiosera, C}, title = {The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {40106345}, issn = {2050-084X}, support = {2017-05267//Vetenskapsr&#xe5;det/ ; RYC2018-025223-I//Ram&#xf3;n y Cajal/ ; BGS220-461AA-69201//Beatriz Galindo Fellowship/ ; PID2021-122355NB-C31//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; A way of making Europe//European Regional Development Fund/ ; }, mesh = {Animals ; Cattle/genetics ; *Hybridization, Genetic ; *Gene Flow ; Spain ; Female ; Genomics/methods ; Male ; History, Ancient ; Genome ; Archaeology ; }, abstract = {Cattle (Bos taurus) play an important role in the life of humans in the Iberian Peninsula not just as a food source but also in cultural events. When domestic cattle were first introduced to Iberia, wild aurochs (Bos primigenius) were still present, leaving ample opportunity for mating (whether intended by farmers or not). Using a temporal bioarchaeological dataset covering eight millennia, we trace gene flow between the two groups. Our results show frequent hybridisation during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry in domestic cattle remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (~20%) continues into modern Western European breeds including Iberian cattle selected for aggressiveness and fighting ability. This study illuminates the genomic impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.}, }
@article {pmid40090872, year = {2025}, author = {Rhodes, C and Price, R and Willetts, C and Swall, J and Combs, LG and Seashols-Williams, S}, title = {Improved DNA recovery and STR profile development from weathered Bos taurus bones using demineralized bone slices.}, journal = {Journal of forensic sciences}, volume = {}, number = {}, pages = {}, doi = {10.1111/1556-4029.70023}, pmid = {40090872}, issn = {1556-4029}, support = {//Forensic Sciences Foundation/ ; 15PNIJ-23-GG-01944-RESS//National Institute of Justice/ ; }, abstract = {Current processing techniques for harvesting DNA from osseous elements are destructive, and success rates vary widely. When skeletal elements are homogenized into a fine powder, endogenous DNA may be subjected to fragmentation, and the likelihood of introducing co-purified inhibitory substances to the sample increases. While a limited number of articles in the relevant literature have challenged the status quo of pulverization, powdering hard tissue samples before DNA isolation continues to be standard practice in the forensic and ancient DNA communities. In this work, we have developed and optimized an alternative front-end processing method for demineralizing and slicing cortical bone using aged and weathered bovine skeletal samples as a model for degraded human bone. Additionally, this study evaluated the enzymatic digestion of demineralized bone slices using collagenase I as a powder-free alternative for cell isolation. The efficacy of pulverization, demineralized slices, and collagenase-digested demineralized slices was assessed via DNA quantitation and STR profile data. The combined treatment incorporating collagenase digestion of demineralized slices did not improve the recovery of endogenous DNA yields or STR profile development; however, profiles developed from demineralized slices retained a significantly greater percentage of expected alleles and higher peak heights than samples processed with conventional powdering and organic chemistry extraction. By eliminating pulverization of bone and employing modified silica-based extraction chemistry, the susceptibility to inhibitory and competitive effects from native and foreign components often found in degraded skeletal remains can be minimized when utilizing total demineralization of small fragments with subsequent slicing before lysis.}, }
@article {pmid40078674, year = {2023}, author = {Odenbaugh, J}, title = {Philosophy and ethics of de-extinction.}, journal = {Cambridge prisms. Extinction}, volume = {1}, number = {}, pages = {e7}, pmid = {40078674}, issn = {2755-0958}, abstract = {In this essay, we explore the philosophical and ethical issues concerning de-extinction. First, we will characterize what de-extinction is. This requires clarification of the process of extinction. Second, we consider whether de-extinction is even possible. There are a variety of arguments involving the nature of species that purport to show that once they have disappeared they cannot be resurrected. Third, we examine whether de-extinction is morally permissible. There are arguments that suggest we are obligated to do it based on restorative justice and biodiversity conservation. There are other arguments that conclude we are not permitted to do so based on considerations of animal welfare, hubris and the allocation of conservation resources.}, }
@article {pmid40075538, year = {2025}, author = {Borba, VH and Gurjão, L and Martin, C and Dufour, B and Le Bailly, M and Iñiguez, AM}, title = {Capillariid diversity in archaeological material from the New and the Old World: clustering and artificial intelligence approaches.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {104}, pmid = {40075538}, issn = {1756-3305}, support = {23038000059/2015-61//Coordination for the Improvement of Higher Education Personnel (CAPES)/ ; 33387UA, 88887.508110/2020-00, 465 88887.694725/2022-00//COFECUB/ ; 315634/2021-9//National Council for Scientific and Technological Development (CNPq)/ ; E-26/201.069/2021, E-461 26/210.131/2023//Carlos Chagas Filho Foundation for Research Support of the State of Rio de Janeiro (FAPERJ)/ ; }, mesh = {Animals ; *Archaeology ; *Artificial Intelligence ; Brazil ; Europe ; Humans ; Nematoda/classification/isolation &amp; purification ; Biodiversity ; Cluster Analysis ; History, Ancient ; Feces/parasitology ; }, abstract = {BACKGROUND: Capillariid nematode eggs have been reported in archaeological material in both the New and the Old World, mainly in Europe and South America. They have been found in various types of samples, as coprolites, sediments from latrines, pits, or burial. Modern parasitological records show that around 300 species of capillariids have been described in all vertebrate taxa, including humans, making it a very diversified group. The main proposal of this work is to characterize and identify capillariid eggs found in archaeological sites from Europe and Brazil.<br><br>METHODS: A total of 39 samples of archeological sites from Europe, deposited in the paleoparasitological collection of the University Marie &amp; Louis Pasteur, Besan&#xe7;on, France was analyzed. In addition, 80 coprolites from the pre-Colombian archaeological site Gruta do Gentio II, Brazil, deposited in the Paleogenetic Laboratory at Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, were evaluated. Samples were treated according to the protocols of each laboratory and then analyzed under light microscopy. Capillariid eggs were classified according to length, width, plugs, and eggshell sizes, and statistical analysis of the morphometric dataset was performed. Using a reference dataset of specimens provided by both Institutional Collections, three approaches to species identification were applied: discriminant analysis, hierarchical clustering, and artificial intelligence/machine learning.<br><br>RESULTS: A total of 10 samples from Europe and 4 from Brazil were positive for capillariid eggs, showing 13 different morphotypes. As European samples were mainly collected from latrines and pits, parasite-host information was absent, and consequently, species identification was impaired. In contrast, the availability of host information rendered the identification of capillariid species for the Brazilian coprolites. The new methodology indicates capillariid species identified on various samples, resulting in the presence of Capillaria exigua (Dujardin, 1845) in feline coprolite, Baruscapillaria resecta (Dujardin, 1845) in opossum, and Aonchotheca bovis (Schnyder, 1906) in bovid, in the Brazilian site, while in European sites, Capillaria venusta (Freitas e Mendon&#xe7;a, 1958), Aonchotheca myoxinitelae (Diesing, 1851), Eucoleus madjerdae (Bernard, 1964), and Baruscapillaria spiculata (Freitas, 1933) were found.<br><br>CONCLUSIONS: The study provides new results by applying innovative methodologies for parasite identification and gaining insights into the past host (human or animal)/parasite relationships.}, }
@article {pmid40075199, year = {2025}, author = {Callaway, E}, title = {Ancient DNA shows Stone Age Europeans voyaged by sea to Africa.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40075199}, issn = {1476-4687}, }
@article {pmid40074896, year = {2025}, author = {Lipson, M and Ringbauer, H and Lucarini, G and Aouadi, N and Aoudia, L and Belhouchet, L and Cheronet, O and Dahmani, AR and Genchi, F and La Pastina, F and Lucci, M and de Lumley, H and Mansouri, N and Nava, A and Touj, F and Mallick, S and Rohland, N and Coppa, A and Pinhasi, R and Reich, D}, title = {High continuity of forager ancestry in the Neolithic period of the eastern Maghreb.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40074896}, issn = {1476-4687}, abstract = {Ancient DNA from the Mediterranean region has revealed long-range connections and population transformations associated with the spread of food-producing economies[1-6]. However, in contrast to Europe, genetic data from this key transition in northern Africa are limited, and have only been available from the far western Maghreb (Morocco)[1-3]. Here we present genome-wide data for nine individuals from the Later Stone Age through the Neolithic period from Algeria and Tunisia. The earliest individuals cluster with pre-Neolithic people of the western Maghreb (around 15,000-7,600 years before present (BP)), showing that this 'Maghrebi' ancestry profile had a substantial geographic and temporal extent. At least one individual from Djebba (Tunisia), dating to around 8,000 years BP, harboured ancestry from European hunter-gatherers, probably reflecting movement in the Early Holocene across the Strait of Sicily. Later Neolithic people from the eastern Maghreb retained largely local forager ancestry, together with smaller contributions from European farmers (by around 7,000 years BP) and Levantine groups (by around 6,800 years BP), and were thus far less impacted by external gene flow than were populations in other parts of the Neolithic Mediterranean.}, }
@article {pmid40059317, year = {2025}, author = {Yang, Q and Sun, Y and Duan, S and Nie, S and Liu, C and Deng, H and Wang, M and He, G}, title = {High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/gpbjnl/qzaf022}, pmid = {40059317}, issn = {2210-3244}, abstract = {Large-scale international and regional human genomic and pangenomic resources derived from population-scale biobanks and ancient DNA sequences have provided significant insights into human evolution and the genetic determinants of complex diseases and traits. Despite these advances, challenges persist in optimizing the integration of phasing tools, merging haplotype reference panels (HRPs), developing imputation algorithms, and fully exploiting the diverse applications of post-imputation data. This review comprehensively summarizes the advancements, applications, limitations, and future directions of HRPs in human genomics research. Recent progress in the reconstruction of HRPs, based on over 830,000 human whole-genome sequences, has been synthesized, highlighting the broad spectrum of human genetic diversity captured. Additionally, we recapitulate advancements in fifty-six HRPs for global and regional populations. The evaluation of imputation accuracy indicated that Beagle and GLIMPSE are the most effective tools for phasing and imputing data from genotyping arrays and low-coverage sequencing, respectively. A critical strategy for selecting an appropriate HRP involves matching the population background of target groups with HRP reference populations and considering multi-ancestry or homogeneous genetic structures. The necessity of a single, integrative, high-quality HRP that captures haplotype structures and genetic diversity across various genetic variation types from globally representative populations is emphasized to support both modern and ancient genomic research and advance human precision medicine.}, }
@article {pmid40052334, year = {2025}, author = {Lu, Y and Dong, Y and Zhang, M and Mao, L}, title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14095}, doi = {10.1111/1755-0998.14095}, pmid = {40052334}, issn = {1755-0998}, support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; }, abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.}, }
@article {pmid40052289, year = {2025}, author = {Berg, AA and Askew, M and Seersholm, FV and Verry, AJF and Hoelzel, AR and Welch, A and Greig, K and Walter, R and Knapp, M and Barlow, A and Paijmans, JLA and Waters, JM and Bunce, M and McDonald, K and O'Connor, S and Hall, B and Koch, PL and Baroni, C and Salvatore, MC and Faulkner, P and Ho, SYW and Rawlence, NJ and de Bruyn, M}, title = {Postglacial Recolonization of the Southern Ocean by Elephant Seals Occurred From Multiple Glacial Refugia.}, journal = {Global change biology}, volume = {31}, number = {3}, pages = {e70101}, doi = {10.1111/gcb.70101}, pmid = {40052289}, issn = {1365-2486}, support = {//Office of Polar Programs, U.S. National Science Foundation./ ; FT200100464//Australian Research Council Future Fellowship/ ; }, mesh = {*Seals, Earless/physiology ; Animals ; *Refugium ; *Climate Change ; Australia ; Antarctic Regions ; New Zealand ; Fossils ; Phylogeny ; Oceans and Seas ; }, abstract = {The Southern Ocean is warming more rapidly than other parts of our planet. How this region's endemic biodiversity will respond to such changes can be illuminated by studying past events through genetic analyses of time-series data sets, including historic and fossil remains. Archaeological and subfossil remains show that the southern elephant seal (Mirounga leonina) was common along the coasts of Australia and New Zealand in the recent past. This species is now mostly confined to sub-Antarctic islands and the southern tip of South America. We analyzed ancient seal samples from Australia (Tasmania), New Zealand and the Antarctic mainland to examine how southern elephant seals have responded to a changing climate and anthropogenic pressures during the Holocene. Our analyses show that these seals formed part of a broader Australasian lineage, comprising seals from all sampled locations from the south Pacific sector of the Southern Ocean. Our study demonstrates that southern elephant seal populations have dynamically altered both range and population sizes under climatic and human pressures over surprisingly short evolutionary timeframes for such a large, long-lived mammal.}, }
@article {pmid40045199, year = {2025}, author = {Nedoluzhko, A and Vergasova, E and Sharko, F and Agapitova, N and Kharitonov, D and Sukhanova, X and Pushkina, O and Pankova, S and Slobodova, N and Boulygina, E and Plotnikov, N and Kim, A and Uchaneva, E and Pogodina, N and Ilinskaya, A and Rakitko, A and Chugunov, K and Ilinsky, V}, title = {Ancient DNA analysis of elite nomadic warrior from Chinge-Tey I funerary commemorative complex in the "Valley of the Kings", Tuva.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {220}, pmid = {40045199}, issn = {1471-2164}, mesh = {Humans ; *DNA, Ancient/analysis ; *Archaeology ; Russia ; DNA, Mitochondrial/genetics ; Transients and Migrants/history ; History, Ancient ; }, abstract = {BACKGROUND: In the I[st] millennium BC bearers of the Scythian-type nomadic cultures inhabited the steppes of Eurasia, from Northern China to the Carpathians. According to archaeological data, the origin of nomadic life style and economy can be traced to the eastern part of this steppe "corridor", primarily to the territory of the present-day Republic of Tuva in Russia. Here, in the Turan-Uyuk Basin, also known as the "Valley of the Kings", some of the earliest known Scythian-type archaeological sites called Arzhan-1, Arzhan-2, Chinge-Tey I, Tunnug 1 were studied. Each of them is a large-scale funerary commemorative complex with burials of tribal nomadic leaders, surrounded by graves of supposed members of their families or associates. All these people belonged to the societies which are associated with the earliest nomadic cultures in Asia. Representatives of similar cultures will later be known and described as the Scythians/the Saka in Assyrian, Achaemenid, and Greek sources. Arzhan 2 and Chinge-Tey I elite level sites as well as ordinary pastoralist burials of the early-Scythian period in Tuva are attributed to the Aldy-Bel archaeological culture of the Early Iron Age (8th- 6th century BC). Taking the first step to shed light on the genetic origin of Aldy-Bel elites, we carried out a comparative genome-wide analysis of an elite level person buried in grave 9 at Chinge-Tey I (7th- 6th centuries BC) and two published earlier genomes of individuals, whose burials (graves 14 and 22) accompanied the 'royal couple' (grave 5) at Arzhan-2. This study aims also at checking a hypothesis of genetic kinship between human individuals buried in the large-scale burial complexes of the "Valley of the Kings" and brings up the issue of possible dynastic connections of local elites, buried under different kurgans of the valley.<br><br>RESULTS: First, ancient DNA analysis of an elite nomadic warrior from Chinge-Tey I has been carried out, thus a third wide-genome dataset for Aldy-Bel culture- one of the earliest nomadic cultures in Asia, is presented in this study. Second, we undertook a comparative analysis of genome-wide data of three mentioned Aldy-Bel culture representatives and individuals of the other Bronze and Early Iron Age population groups of Asia to estimate their possible genetic connections. Then, kinship analysis was undertaken for these three Aldy-Bel culture individuals. Finally, mitochondrial and Y-chromosome haplogroups of Chinge-Tey princely person were compared to those of other Aldy-Bel culture representatives and to individuals of subsequent Scythian-type Uyuk-Sagly culture in Tuva.<br><br>CONCLUSION: (1) Generating the third wide-genome of the enabled us to undertake its comparison with two other genomes of Aldy-Bel culture representatives (Arzhan-2, graves 14 and 22) and with other Bronze and Early Iron Age population groups in Asia to trace the origin and genetic connection of Aldy-Bel population, representing one of the earliest Scythian-type nomadic group. (2) The results obtained show that the princely individual from Chinge-Tey I and two 'king's associates' from Arzhan-2 were genetically close to nomads of simultaneous Tasmola culture in Eastern and Central Kazakhstan and pastoralists buried in the Early Iron Age cemeteries of present-day Xinjiang (first of all, Abusanteer archaeological site). Aldy-Bel culture representatives appeared also close to individuals of the Middle Bronze Age Okunevo culture in the Minusinsk Basin. Besides, Aldy-Bel pastoralists turned out genetically close to nomads of the subsequent Uyuk-Sagly culture in Mongolia (5th -&#x2009;3rd centuries BC). (3) Ancient DNA kinship analyses, undertaken for three Aldy-Bel culture individuals pointed out to the absence of their tribe kinship. (4) On the other hand, Chinge-Tey warrior's mitochondrial haplogroup G was previously described in two (graves 14 and 5) individuals from Arzhan-2, including a female individual from the "royal" tomb 5. This result provided a possibility of maternal kinship among this so called 'queen' from Arzhan-2 and the princely person from Chinge-Tey I. This possibility supported a hypothesis of their family ties suggested on archaeological materials. Y-chromosome haplogroup Q1b1, revealed for the princely person, was widely distributed among local people of Aldy-Bel and subsequent Uyuk-Sagly cultures.}, }
@article {pmid40040400, year = {2025}, author = {Moosa, T and Ewuoso, C}, title = {Ancient DNA research may be conducted in the absence of consent from descendant communities.}, journal = {Indian journal of medical ethics}, volume = {X}, number = {1}, pages = {16-23}, doi = {10.20529/IJME.2024.081}, pmid = {40040400}, issn = {0975-5691}, mesh = {Humans ; *Informed Consent/ethics/standards ; *DNA, Ancient/analysis ; Genetic Research/ethics ; Ethics, Research ; Africa ; Morals ; Archaeology/ethics ; }, abstract = {BACKGROUND: Ancient deoxyribonucleic acid (aDNA) research studies the genomes of human ancestors. Since the archaeological remains that carry this aDNA are often those of the non-living ancestors of living humans, one less explored question is whether aDNA research ought to be permissible in the absence of informed consent of descendant communities. We interrogate this question.<br><br>METHOD: To address this question, this paper is a primarily conceptual paper that draws on moral norms arising from pre-existing - albeit competing - formulations of harmony in African moral philosophy. This methodological approach is not uncommon and has been accepted as a valid research method.<br><br>RESULT: The paper's methodological approach yields the conclusion that it is ethically permissible to conduct aDNA research on human archaeological remains in the absence of informed consent from descendant communities or individuals. Although we justify the ethical permissibility of conducting research without consent, we also emphasise the importance of consultation with descendant communities - where they are known - and the researchers' responsibility to share benefits with them before, during, and after aDNA research.<br><br>CONCLUSION: The sort of aDNA research that this paper considers permissible is that which is likely to enhance harmonious relationships in relevant ways. aDNA research is advancing rapidly and in proportion to technological advances. To ensure that aDNA research in a more technologically advanced world is undertaken in ethically permissible ways, global research guidelines would be required. Future studies can focus on articulating such guidelines.}, }
@article {pmid40027244, year = {2025}, author = {David, O and Vidal, M and Gorczyńska, A and Penaud, A and Pailler, Y and Nicolas, C and Debruyne, R and Martin, N and Goor, M and Garcia-Ladieu, P and Goubert, E and Stéphan, P and Ollivier, M and Barloy-Hubler, F}, title = {New coastal records in northern Brittany (Plouescat, NW France): Sedimentological, palynological and paleogenomic data over the last 7.3 ka BP.}, journal = {Data in brief}, volume = {59}, number = {}, pages = {111361}, pmid = {40027244}, issn = {2352-3409}, abstract = {The multidisciplinary approach conducted on the coastal cores ANE-C3 and PADMé (48°38'54.5114"N; 4°10'21.3848"W; Kerallé watershed, NW Brittany, NW France) revealed paleoenvironmental trajectories under both relative sea level rise and anthropogenic dynamics during Middle to Late Holocene, in the research paper: "From a coastal plain to an anthropized fluvial valley (NW Brittany, France): 7.3 kyr of paleoenvironmental evolution from sedimentological, palynological and paleogenomic perspectives" [1]. This additional article presents all the ANE-C3 and PADMé cores dataset discussed in [1] including sedimentological (XRF, grain size), palynological (pollen assemblages) and paleogenomic (plant and mammal sedimentary ancient DNA or sedaDNA) data. For the sedimentological data, the documents included here comprise high-resolution photographs and normalization of XRF-counts. A special emphasis was placed on characterising the modern pollinic signal in different sub-environments (i.e., salt marsh, coastal meadow, field) of the studied area. This was done to identify anthropogenic pollen indicators specific to this coastal zone, and, ultimately to detect more precisely the pollinic signature of human disturbances in the fossil record. Finally, this paper provides additional information on the methodologies developed, with a particular emphasis on sedaDNA analysis.}, }
@article {pmid40022192, year = {2025}, author = {da Silva, NA and Özer, O and Haller-Caskie, M and Chen, YR and Kolbe, D and Schade-Lindig, S and Wahl, J and Berszin, C and Francken, M and Görner, I and Schierhold, K and Pechtl, J and Grupe, G and Rinne, C and Müller, J and Lenz, TL and Nebel, A and Krause-Kyora, B}, title = {Admixture as a source for HLA variation in Neolithic European farming communities.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {43}, pmid = {40022192}, issn = {1474-760X}, support = {290391021 (CRC 1266 project)//Deutsche Forschungsgemeinschaft/ ; 390870439 (Clusters of Excellence ROOTS - EXC 2150)//Deutsche Forschungsgemeinschaft/ ; 437857095//Deutsche Forschungsgemeinschaft/ ; 400993799 (RTG 2501)//Deutsche Forschungsgemeinschaft/ ; 390884018 (Precision Medicine in Chronic Inflammation - EXC 2167)//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Haplotypes ; Male ; Gene Frequency ; HLA Antigens/genetics ; Female ; Farmers ; Agriculture ; Germany ; Genetic Variation ; Human Migration ; Genetics, Population ; Chromosomes, Human, Y/genetics ; }, abstract = {BACKGROUND: The northern European Neolithic is characterized by two major demographic events: immigration of early farmers from Anatolia at 7500 years before present, and their admixture with local western hunter-gatherers forming late farmers, from around 6200 years before present. The influence of this admixture event on variation in the immune-relevant human leukocyte antigen (HLA) region is understudied.<br><br>RESULTS: We analyzed genome-wide data of 125 individuals from seven archeological early farmer and late farmer sites located in present-day Germany. The late farmer group studied here is associated with the Wartberg culture, from around 5500-4800&#xa0;years before present. We note that late farmers resulted from sex-biased admixture from male western hunter-gatherers. In addition, we observe Y-chromosome haplogroup I as the dominant lineage in late farmers, with site-specific sub-lineages. We analyze true HLA genotypes from 135 Neolithic individuals, the majority of which were produced in this study. We observe significant shifts in HLA allele frequencies from early farmers to late farmers, likely due to admixture with western hunter-gatherers. Especially for the haplotype DQB1*04:01-DRB1*08:01, there is evidence for a western hunter-gatherer origin. The HLA diversity increased from early farmers to late farmers. However, it is considerably lower than in modern populations.<br><br>CONCLUSIONS: Both early farmers and late farmers exhibit a relatively narrow HLA allele spectrum compared to today. This coincides with sparse traces of pathogen DNA, potentially indicating a lower pathogen pressure at the time.}, }
@article {pmid40006948, year = {2025}, author = {Antoneli, F and Peter, CM and Briones, MRS}, title = {Statistical Distributions of Genome Assemblies Reveal Random Effects in Ancient Viral DNA Reconstructions.}, journal = {Viruses}, volume = {17}, number = {2}, pages = {}, pmid = {40006948}, issn = {1999-4915}, support = {20/08943-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP, Brazil)/ ; 311154/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq, Brazil)/ ; }, mesh = {*DNA, Ancient/analysis ; *Genome, Viral ; *DNA, Viral/genetics ; Humans ; Animals ; Neanderthals/genetics/virology ; Sequence Analysis, DNA/methods ; Signal-To-Noise Ratio ; Viruses/genetics/classification/isolation &amp; purification ; }, abstract = {Ancient human viruses have been detected in ancient DNA (aDNA) samples of both Anatomically Modern Humans and Neanderthals. Reconstructing genomes from aDNA using reference mapping presents numerous problems due to the unique nature of ancient samples, their degraded state, smaller read sizes and the limitations of current methodologies. The spurious alignments of reads to reference sequences (mapping) are a main source of false positives in aDNA assemblies and the assessment of signal-to-noise ratios is essential to differentiate bona fide reconstructions from random, noisy assemblies. Here, we analyzed the statistical distributions of viral genome assemblies, ancient and modern, and their respective random "mock" controls used to evaluate the signal-to-noise ratio. We tested if differences between real and random assemblies could be detected from their statistical distributions. Our analysis shows that the coverage distributions of (1) real viral aDNA assemblies of adenovirus (ADV), herpesvirus (HSV) and papillomavirus (HPV) do not follow power laws nor log-normal laws, (2) (ADV) and control aDNA assemblies are well approximated by log-normal laws, (3) negative control parvovirus B19 (real and random) follow a power law with infinite variance and (4) the mapDamage negative control with non-ancient DNA (modern ADV) and the mapDamage positive control (human mtDNA) are well approximated by the negative binomial distribution, consistent with the Lander-Waterman model. Our results show that the tails of the distributions of aDNA and their controls reveal the weight of random effects and can differentiate spurious assemblies, or false positives, from bona fide assemblies.}, }
@article {pmid39993190, year = {2025}, author = {Gnecchi-Ruscone, GA and Rácz, Z and Liccardo, S and Lee, J and Huang, Y and Traverso, L and Radzevičiūtė, R and Hajnal, Z and Szécsényi-Nagy, A and Gyuris, B and Mateovics-László, O and Bernert, Z and Szeniczey, T and Hajdu, T and Mészáros, B and Bálint, M and Mende, BG and Miller, B and Samashev, Z and Childebayeva, A and Djansugurova, L and Geary, P and Ringbauer, H and Vida, T and Jeong, C and Pohl, W and Krause, J and Hofmanová, Z}, title = {Ancient genomes reveal trans-Eurasian connections between the European Huns and the Xiongnu Empire.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {9}, pages = {e2418485122}, doi = {10.1073/pnas.2418485122}, pmid = {39993190}, issn = {1091-6490}, mesh = {Humans ; Europe ; *Genome, Human ; *Archaeology ; History, Ancient ; *DNA, Ancient/analysis ; Human Migration/history ; }, abstract = {The Huns appeared in Europe in the 370s, establishing an Empire that reshaped West Eurasian history. Yet until today their origins remain a matter of extensive debate. Traditional theories link them to the Xiongnu, the founders of the first nomadic empire of the Mongolian steppe. The Xiongnu empire dissolved, however, ~300 y before the Huns appeared in Europe, and there is little archaeological and historical evidence of Huns in the steppe during this time gap. Furthermore, despite the rich 5th to 6th centuries current era (CE) archaeological record of the Carpathian Basin, the cultural elements of connections with the steppe are limited to few findings and even fewer solitary eastern-type burials. In this study, we coanalyze archaeological evidence with 35 newly sequenced and published genomic data for a total of 370 individuals-from 5th to 6th century CE contexts in the Carpathian Basin including 10 Hun-period eastern-type burials, 2nd to 5th century sites across Central Asia and 2nd c. before current era (BCE) to 1st c. CE Xiongnu period sites across the Mongolian steppe. We find no evidence for the presence of a large eastern/steppe descent community among the Hun- and post-Hun-period Carpathian Basin population. We also observe a high genetic diversity among the eastern-type burials that recapitulates the variability observed across the Eurasian Steppe. This suggests a mixed origin of the incoming steppe conquerors. Nevertheless, long-shared genomic tracts provide compelling evidence of genetic lineages directly connecting some individuals of the highest Xiongnu-period elite with 5th to 6th century CE Carpathian Basin individuals, showing that some European Huns descended from them.}, }
@article {pmid39987348, year = {2025}, author = {Qiao, X and Shi, J and Xu, H and Liu, K and Pu, Y and Xue, X and Zheng, W and Guo, Y and Ma, H and Wang, CC and Bitsue, HK and Xu, X and Wang, S and Zhao, J and Guo, X and Hou, X and Wang, X and Peng, L and Qiu, Z and Su, B and Tang, W and He, Y and Guo, J and Yang, Z}, title = {Genetic diversity and dietary adaptations of the Central Plains Han Chinese population in East Asia.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {291}, pmid = {39987348}, issn = {2399-3642}, support = {32370664//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32070579//National Natural Science Foundation of China (National Science Foundation of China)/ ; 222300420067//Natural Science Foundation of Henan Province (Henan Province Natural Science Foundation)/ ; }, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *Asian People/genetics ; *Genetic Variation ; Diet ; China/epidemiology ; Whole Genome Sequencing ; Adaptation, Physiological/genetics ; Genome, Human ; Asia, Eastern ; Male ; East Asian People ; Fatty Acid Desaturases ; }, abstract = {The Central Plains Han Chinese (CPHC) is the typical agricultural population of East Asia. Investigating the genome of the CPHC is crucial to understanding the genetic structure and adaptation of the modern humans in East Asia. Here, we perform whole genome sequencing of 492 CPHC individuals and obtained 22.65 million SNPs, 4.26 million INDELs and 41,959 SVs. We found the CPHC has a higher level of genetic diversity and the glycolipid metabolic genes show strong selection signals, e.g. LONP2, FADS2, FGF21 and SLC19A2. Ancient DNA analyses suggest that the domestication of crops, which drove the emergence of the candidate mutations. Notably, East Asian-specific SVs, e.g., DEL_21699 (LINC01749) and DEL_38406 (FAM102A) may be associated with the high prevalence of esophageal squamous carcinoma and primary angle-closure glaucoma. Our results provide an important genetic resource and show that dietary adaptations play an important role in phenotypic evolution in East Asian populations.}, }
@article {pmid39980208, year = {2025}, author = {Holman, LE and Zampirolo, G and Gyllencreutz, R and Scourse, J and Frøslev, T and Carøe, C and Gopalakrishnan, S and Pedersen, MW and Bohmann, K}, title = {Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14086}, doi = {10.1111/1755-0998.14086}, pmid = {39980208}, issn = {1755-0998}, support = {856488//H2020 European Research Council/ ; }, abstract = {The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.}, }
@article {pmid39979344, year = {2025}, author = {Plascencia, AG and Jakobsson, M and Sánchez-Quinto, F}, title = {Ancient DNA HLA typing reveals significant shifts in frequency in Europe since the Neolithic.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6161}, pmid = {39979344}, issn = {2045-2322}, mesh = {Humans ; *DNA, Ancient/analysis ; Europe ; *Gene Frequency ; *Histocompatibility Testing/methods ; HLA Antigens/genetics ; Alleles ; Evolution, Molecular ; Genome, Human ; }, abstract = {Computational HLA typing has surged as a cost-effective strategy to uncover questions regarding the evolution of the HLA system, enabling immunogenic characterization from ancient DNA (aDNA) data. Nevertheless, it remains to be seen whether these methods are suitable for analyzing aDNA generated without target-enrichment. To investigate this, we evaluated the performance of five HLA typing tools using present-day data with simulated profiles typical of aDNA, as well as from high-coverage aDNA genomes downsampled at different read depths. We found that characterization of Class I genes at the first field resolution is feasible at read depths as low as 2x, where it retains an accuracy of ≈ 80%. Next, we used this insight to characterize HLA evolution in Europe from 154 ancient genomes by detecting allele frequency changes throughout distinct prehistoric European populations. We observed important shifts in alleles associated with infectious and autoimmune diseases, most of which are found by contrasting the HLA landscape of Neolithic Farmers to that of present-day. Interestingly, several of these observations are in line with findings that have been previously reported by target-enrichment-based studies. Our results highlight the feasibility of applying HLA typing on shotgun aDNA data to examine the evolution of this loci during important transitions.}, }
@article {pmid39975133, year = {2025}, author = {Smith, SP and Smith, OS and Mostafavi, H and Peng, D and Berg, JJ and Edge, MD and Harpak, A}, title = {A Litmus Test for Confounding in Polygenic Scores.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.01.635985}, pmid = {39975133}, issn = {2692-8205}, abstract = {Polygenic scores (PGSs) are being rapidly adopted for trait prediction in the clinic and beyond. PGSs are often thought of as capturing the direct genetic effect of one's genotype on their phenotype. However, because PGSs are constructed from population-level associations, they are influenced by factors other than direct genetic effects, including stratification, assortative mating, and dynastic effects ("SAD effects"). Our interpretation and application of PGSs may hinge on the relative impact of SAD effects, since they may often be environmentally or culturally mediated. We developed a method that estimates the proportion of variance in a PGS (in a given sample) that is driven by direct effects, SAD effects, and their covariance. We leverage a comparison of a PGS of interest based on a standard GWAS with a PGS based on a sibling GWAS-which is largely immune to SAD effects-to quantify the relative contribution of each type of effect to variance in the PGS of interest. Our method, Partitioning Genetic Scores Using Siblings (PGSUS, pron. "Pegasus"), breaks down variance components further by axes of genetic ancestry, allowing for a nuanced interpretation of SAD effects. In particular, PGSUS can detect stratification along major axes of ancestry as well as SAD variance that is "isotropic" with respect to axes of ancestry. Applying PGSUS, we found evidence of stratification in PGSs constructed using large meta-analyses of height and educational attainment as well as in a range of PGSs constructed using the UK Biobank. In some instances, a given PGS appears to be stratified along a major axis of ancestry in one prediction sample but not in another (for example, in comparisons of prediction in samples from different countries, or in ancient DNA vs. contemporary samples). Finally, we show that different approaches for adjustment for population structure in GWASs have distinct advantages with respect to mitigation of ancestry-axis-specific and isotropic SAD variance in PGS. Our study illustrates how family-based designs can be combined with standard population-based designs to guide the interpretation and application of genomic predictors.}, }
@article {pmid39967865, year = {2025}, author = {Oras, E and de Groot, J and Björkstén, U}, title = {The "biomolecular humanities"? New challenges and perspectives.}, journal = {iScience}, volume = {28}, number = {2}, pages = {111679}, pmid = {39967865}, issn = {2589-0042}, abstract = {Biomolecular humanities is a developing transdisciplinary research area in which we see natural sciences and humanities increasingly integrated and conceived of as data production and scientific discovery entities on an equal basis. This umbrella term allows us to think generatively about how humanities and natural sciences are providing study material, methodologies, theoretical conceptualizations, analytical results, and synergetic interpretations together, for and about each other.}, }
@article {pmid39962096, year = {2025}, author = {Parker, LD and West, CF and Tatum, KH and Etnier, M and Bethke, B and Reedy, K and Shellikoff, N and Hofman, CA}, title = {Polar bears and expanding sea ice in the Mid Holocene Aleutian Islands, Alaska.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5767}, pmid = {39962096}, issn = {2045-2322}, support = {2139044//National Science Foundation, United States/ ; 2139044//National Science Foundation, United States/ ; 2139044//National Science Foundation, United States/ ; 2139044//National Science Foundation, United States/ ; }, mesh = {Animals ; *Ursidae ; Alaska ; *Ice Cover ; Climate Change ; Archaeology ; Islands ; Humans ; }, abstract = {The archaeological record offers the opportunity to infer the effects of regional climatic shifts on species distributions and human-animal interactions. In Alaska's temperate Aleutian Islands, the archaeological record suggests that the Neoglacial climate phase (ca. 4700 - 2500 rcyr BP) was significantly colder and the region likely supported sea ice and ice-dependent animals. Previous analyses have identified polar bear (Ursus maritimus) remains in archaeological sites in Unalaska Bay, which have been used to infer bear range expansion and significant climate changes during this period. However, morphological similarities between polar and brown (Ursus arctos) bears make it difficult to distinguish between the two species, and the presence of bear material in Unalaska Bay could be the result of long-distance travel or trade rather than local harvest. Here, we applied zooarchaeological methods to address potential morphological and size differences, to age the bears, and to interpret human use of the bears. Our results suggest that the small assemblage is likely composed of both brown and polar bear remains, but that morphological analyses alone are insufficient to definitively reconstruct bear distributions in this context. Bear age profiles and butchery patterns suggest that the animals were harvested locally and the extension of sea ice in the Neoglacial phase likely facilitated their presence around Unalaska Island. Future analyses that use ancient DNA, collagen fingerprinting, and stable isotopes to determine the species, sex, number of individuals, and relationships to modern populations will be necessary to illuminate regional bear population dynamics in the Neoglacial.}, }
@article {pmid39953642, year = {2025}, author = {Abood, S and Oota, H}, title = {Human dispersal into East Eurasia: ancient genome insights and the need for research on physiological adaptations.}, journal = {Journal of physiological anthropology}, volume = {44}, number = {1}, pages = {5}, pmid = {39953642}, issn = {1880-6805}, mesh = {Humans ; *Human Migration ; Animals ; *Adaptation, Physiological/genetics ; Genome, Human/genetics ; Neanderthals/genetics ; Anthropology, Physical ; Biological Evolution ; }, abstract = {Humans have long pondered their genesis. The answer to the great question of where Homo sapiens come from has evolved in conjunction with biotechnologies that have allowed us to more brightly illuminate our distant past. The "Multiregional Evolution" model was once the hegemonic theory of Homo sapiens origins, but in the last 30 years, it has been supplanted by the "Out of Africa" model. Here, we review the major findings that have resulted in this paradigmatic shift. These include hominin brain expansion, classical insight from the mitochondrial genome (mtDNA) regarding the timing of the divergence point between Africans and non-Africans, and next-generation sequencing (NGS) of the Neanderthal and Denisovan genomes. These findings largely bolstered the "Out of Africa" model, although they also revealed a small degree of introgression of the Neanderthal and Denisovan genomes into those of non-African Homo sapiens. We also review paleogenomic studies for which migration route, north or south, early migrants to East Eurasia most likely traversed. Whichever route was taken, the migrants moved to higher latitudes, which necessitated adaptation for lower light conditions, colder clines, and pro-adipogenic mechanisms to counteract food scarcity. Further genetic and epigenetic investigations of these physiological adaptations constitute an integral aspect of the story of human origins and human migration to East Asia.}, }
@article {pmid39934375, year = {2025}, author = {Wang, R and Liu, W and Wu, Y and Ma, H and Lv, J and He, H and Qiu, L and Chen, H and Zhao, Y and Sun, B and Wang, CC}, title = {East and West admixture in eastern China of Tang Dynasty inferred from ancient human genomes.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {219}, pmid = {39934375}, issn = {2399-3642}, mesh = {Humans ; China ; *Genome, Human ; *DNA, Ancient/analysis ; *Polymorphism, Single Nucleotide ; DNA, Mitochondrial/genetics ; Haplotypes ; Asian People/genetics ; Genetics, Population ; Male ; Chromosomes, Human, Y/genetics ; History, Ancient ; Human Migration/history ; }, abstract = {The ancestry composition and Sinicisation process of the descendants of the immigrants of Hu people living in ancient China are largely unknown due to the lack of genetic evidence. Tang Dynasty people in Fudamen cemetery () excavated from Shandong province in eastern China are believed to be related to the descendants of Hu people, as some of the individuals with the surnames An (). The genetic origin of the Fudamen population requires genetic clarification using ancient DNA data. Here we successfully obtain genome-wide SNP data for 17 Tang dynasty individuals from Fudamen cemetery. Based on autosomal data, although all Fudamen individuals show high levels of middle reaches of Yellow River-related ancestry as previously published historical period Shandong populations, 2 Fudamen individuals require ~5% Western Eurasian/Central Asian-related ancestry to describe their ancestry composition best. To the best of our knowledge, it is the first evidence of such ancestry in Shandong, the eastern part of today's China. Moreover, the admixture pattern is also reflected by the presence of both west and east Eurasian-specific mtDNA and Y chromosomal haplogroups in Fudamen people. The estimated admixture time is also consistent with periods when Sogdians and other non-Han populations were active in ancient China. These genomic findings suggest that intermarriage with Han Chinese involved the Sinicization process of the Hu people.}, }
@article {pmid39919708, year = {2025}, author = {Fortes-Lima, CA and Diallo, MY and Janoušek, V and Černý, V and Schlebusch, CM}, title = {Population history and admixture of the Fulani people from the Sahel.}, journal = {American journal of human genetics}, volume = {112}, number = {2}, pages = {261-275}, doi = {10.1016/j.ajhg.2024.12.015}, pmid = {39919708}, issn = {1537-6605}, mesh = {Humans ; *Genetics, Population ; *Black People/genetics ; Africa South of the Sahara ; Genome, Human ; Ethnicity/genetics ; Genetic Variation ; Central African People ; East African People ; West African People ; }, abstract = {The Fulani people, one of the most important pastoralist groups in sub-Saharan Africa, are still largely underrepresented in population genomic research. They speak a Niger-Congo language called Fulfulde or Pulaar and live in scattered locations across the Sahel/Savannah belt, from the Atlantic Ocean to Lake Chad. According to historical records, their ancestors spread from Futa Toro in the Middle Senegal Valley to Futa-Jallon in Guinea and then eastward into the Sahel belt over the past 1,500 years. However, the earlier history of this traditionally pastoral population has not been well studied. To uncover the genetic structure and ancestry of this widespread population, we gathered genome-wide genotype data from 460 individuals across 18 local Fulani populations, along with comparative data from both modern and ancient worldwide populations. This represents a comprehensive geographically wide-scaled genome-wide study of the Fulani. We revealed a genetic component closely associated with all local Fulani populations, suggesting a shared ancestral component possibly linked to the beginning of African pastoralism in the Green Sahara. Comparison to ancient DNA results also identified the presence of an ancient Iberomaurusian-associated component across all Fulani groups, providing additional insights into their deep genetic history. Additionally, our genetic data indicate a later Fulani expansion from the western to the eastern Sahel, characterized by a clinal pattern and admixture with several other African populations north of the equator.}, }
@article {pmid39920258, year = {2025}, author = {Eriksen, EF and Andrews, AJ and Nielsen, SV and Persson, P and Malca, E and Onar, V and Aniceti, V and Piquès, G and Piattoni, F and Fontani, F and Wiech, M and Ferter, K and Kersten, O and Ferrari, G and Cariani, A and Tinti, F and Cilli, E and Atmore, LM and Star, B}, title = {Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA.}, journal = {Heredity}, volume = {}, number = {}, pages = {}, pmid = {39920258}, issn = {1365-2540}, support = {813383//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 951649//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; NA20OAR4320472//United States Department of Commerce | NOAA | National Marine Fisheries Service, National Oceanic and Atmospheric Administration (NOAA Fisheries)/ ; }, abstract = {Mitonuclear discordance between species is readily documented in marine fishes. Such discordance may either be the result of past natural phenomena or the result of recent introgression from previously seperated species after shifts in their spatial distributions. Using ancient DNA spanning five millennia, we here investigate the long-term presence of Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) -like mitochondrial (MT) genomes in Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance and age structure. Comparing ancient (n = 130) and modern (n = 78) Atlantic bluefin MT genomes from most of its range, we detect no significant spatial or temporal population structure, which implies ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify discordant MT haplotypes in ancient specimens up to 5000 years old and find that the frequency of these haplotypes has remained similar through time. We therefore conclude that MT discordance in the Atlantic bluefin tuna is not driven by recent introgression. Our observations provide oldest example of directly observed MT discordance in the marine environment, highlighting the utility of ancient DNA to obtain insights in the long-term persistence of such phenomena.}, }
@article {pmid39912442, year = {2025}, author = {Gilardet, A and Lord, E and García, GO and Xenikoudakis, G and Douka, K and Wooller, MJ and Rowe, T and Martin, MD and Le Moullec, M and Anisimov, M and Heintzman, PD and Dalén, L}, title = {A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14077}, doi = {10.1111/1755-0998.14077}, pmid = {39912442}, issn = {1755-0998}, support = {325589//Norges Forskningsr&#xe5;d/ ; 2021-00625//Vetenskapsr&#xe5;det/ ; KAW 2021.0048//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2022.0033//Knut och Alice Wallenbergs Stiftelse/ ; 715069 (FINDER)/ERC_/European Research Council/International ; PrimiGenomes 101054984/ERC_/European Research Council/International ; OPP 2310505//Office of Polar Programs/ ; }, abstract = {Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancient DNA laboratories and have even been automated on robotic platforms. Robots offer a solution for high-throughput screening but the costs, as well as necessity for trained technicians and engineers, can be prohibitive for some laboratories. Here, we present a high-throughput alternative to robot-based ancient DNA extraction using a 96-column plate. When compared to routine single MinElute columns, we retrieved highly similar endogenous DNA contents, an important metric in ancient DNA screening. Mitogenomes with a coverage depth greater than 0.1× could be generated and allowed for taxonomic assignment. However, average fragment lengths, DNA damage and library complexities significantly differed between methods but these differences became nonsignificant after modification of our library purification protocol. Our high-throughput extraction method allows generation of 96 extracts within approximately 4 hours of laboratory work while bringing the cost down by ~39% compared to using single columns. Additionally, we formally demonstrate that the addition of Tween-20 during the elution step results in higher complexity libraries, thereby enabling higher genome coverage for the same sequencing effort.}, }
@article {pmid39910300, year = {2025}, author = {Lazaridis, I and Patterson, N and Anthony, D and Vyazov, L and Fournier, R and Ringbauer, H and Olalde, I and Khokhlov, AA and Kitov, EP and Shishlina, NI and Ailincăi, SC and Agapov, DS and Agapov, SA and Batieva, E and Bauyrzhan, B and Bereczki, Z and Buzhilova, A and Changmai, P and Chizhevsky, AA and Ciobanu, I and Constantinescu, M and Csányi, M and Dani, J and Dashkovskiy, PK and Évinger, S and Faifert, A and Flegontov, P and Frînculeasa, A and Frînculeasa, MN and Hajdu, T and Higham, T and Jarosz, P and Jelínek, P and Khartanovich, VI and Kirginekov, EN and Kiss, V and Kitova, A and Kiyashko, AV and Koledin, J and Korolev, A and Kosintsev, P and Kulcsár, G and Kuznetsov, P and Magomedov, R and Mamedov, AM and Melis, E and Moiseyev, V and Molnár, E and Monge, J and Negrea, O and Nikolaeva, NA and Novak, M and Ochir-Goryaeva, M and Pálfi, G and Popovici, S and Rykun, MP and Savenkova, TM and Semibratov, VP and Seregin, NN and Šefčáková, A and Mussayeva, RS and Shingiray, I and Shirokov, VN and Simalcsik, A and Sirak, K and Solodovnikov, KN and Tárnoki, J and Tishkin, AA and Trifonov, V and Vasilyev, S and Akbari, A and Brielle, ES and Callan, K and Candilio, F and Cheronet, O and Curtis, E and Flegontova, O and Iliev, L and Kearns, A and Keating, D and Lawson, AM and Mah, M and Micco, A and Michel, M and Oppenheimer, J and Qiu, L and Workman, JN and Zalzala, F and Szécsényi-Nagy, A and Palamara, PF and Mallick, S and Rohland, N and Pinhasi, R and Reich, D}, title = {The genetic origin of the Indo-Europeans.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39910300}, issn = {1476-4687}, abstract = {The Yamnaya archaeological complex appeared around 3300 BC across the steppes north of the Black and Caspian Seas, and by 3000 BC it reached its maximal extent, ranging from Hungary in the west to Kazakhstan in the east. To localize Yamnaya origins among the preceding Eneolithic people, we assembled ancient DNA from 435 individuals, demonstrating three genetic clines. A Caucasus-lower Volga (CLV) cline suffused with Caucasus hunter-gatherer[1] ancestry extended between a Caucasus Neolithic southern end and a northern end at Berezhnovka along the lower Volga river. Bidirectional gene flow created intermediate populations, such as the north Caucasus Maikop people, and those at Remontnoye on the steppe. The Volga cline was formed as CLV people mixed with upriver populations of Eastern hunter-gatherer[2] ancestry, creating hypervariable groups, including one at Khvalynsk. The Dnipro cline was formed when CLV people moved west, mixing with people with Ukraine Neolithic hunter-gatherer ancestry[3] along the Dnipro and Don rivers to establish Serednii Stih groups, from whom Yamnaya ancestors formed around 4000 BC and grew rapidly after 3750-3350 BC. The CLV people contributed around four-fifths of the ancestry of the Yamnaya and, entering Anatolia, probably from the east, at least one-tenth of the ancestry of Bronze Age central Anatolians, who spoke Hittite[4,5]. We therefore propose that the final unity of the speakers of 'proto-Indo-Anatolian', the language ancestral to both Anatolian and Indo-European people, occurred in CLV people some time between 4400 BC and 4000 BC.}, }
@article {pmid39910371, year = {2025}, author = {Callaway, E}, title = {How one language family took over the world: ancient DNA traces its spread.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39910371}, issn = {1476-4687}, }
@article {pmid39902286, year = {2024}, author = {Gurjão, L and Brito, L and Dias, O and Neto, J and Iñiguez, AM}, title = {Integrating paleoparasitological, paleogenetic, and archaeological data to understand the paleoecological scenario of pre-Columbian archaeological site Gruta do Gentio II, Brazil.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1505059}, pmid = {39902286}, issn = {1664-302X}, abstract = {Paleoparasitology and paleogenetics is the study parasites in ancient remains from latrines, mummified individuals, and coprolites, that is fossilized or desiccated feces. Paleoparasitological studies in Brazil began with analyses of coprolites from the Gruta do Gentio II (GGII) archaeological site, the oldest site related to the Una ceramist tradition (12,000 to 410 BP), Brazil. The GGII archaeological site contained numerous human burials, lithics, and cultural artifacts such as basketry, ceremonial ornaments, and unique pottery of the Una tradition. Coprolites of GGII were submitted to paleoparasitological, and paleogenetic analyses for parasite identification and coprolite origin. In addition, the archaeological characterization of the GGII site was integrated into paleo analyses for proposing a paleoecological scenario. Five taxa of parasites, including Ancylostomidae, Echinostoma sp., Spirometra sp., and Trichostrongylus sp., and three different morphotypes of Capillariidae were recognized in multiple coprolites that were distributed heterogeneously in several stratigraphical layers. The origin of coprolites was genetically defined as five species of mammals, humans, felines as Panthera onca and Leopardus pardalis, and marsupials as Didelphis albiventris and Philander opossum. This is the first study in Brazil that identified both, parasites and species of animals in Pleistocene/Holocene producers of coprolites with geographical and temporal information. The integration of paleoparasitology, paleogenetics, and archaeology is essential to propose paleoecological scenarios from the past of Brazil.}, }
@article {pmid39895972, year = {2024}, author = {Benítez-Burraco, A}, title = {How (and why) languages became more complex as we evolved more prosocial: the human self-domestication view.}, journal = {Frontiers in psychology}, volume = {15}, number = {}, pages = {1499994}, pmid = {39895972}, issn = {1664-1078}, abstract = {This paper aims to re-examine the problem of the emergence of present-day languages from the specific perspective of the self-domestication account of human evolution. According to this view, our species went through an evolutionary process that parallels the changes experienced by domesticated mammals. Relying on evidence of diverse kind (from paleogenetic to clinical), the paper argues that our self-domestication might have potentiated the cognitive and behavioral features of the human phenotype with an impact on language acquisition and use. Specifically, it might have facilitated the creation of the cultural niche that favors the complexification of languages via a cultural mechanism. The paper further proposes a model of language complexification in the past under the effects of human self-domestication, including the complexification of the structural aspects of language (grammar, prosody, and semantics) and the potentiation of its functional properties (pragmatics). The paper concludes with some suggestions for any future research aimed to test and improve this view.}, }
@article {pmid39881595, year = {2025}, author = {Piffer, D}, title = {Directional Selection and Evolution of Polygenic Traits in Eastern Eurasia: Insights from Ancient DNA.}, journal = {Twin research and human genetics : the official journal of the International Society for Twin Studies}, volume = {}, number = {}, pages = {1-20}, doi = {10.1017/thg.2024.49}, pmid = {39881595}, issn = {1832-4274}, abstract = {This study explores directional selection on physical and psychosocial phenotypes in Eastern Eurasian populations, utilizing a dataset of 1245 ancient genomes. By analyzing polygenic scores (PGS) for traits including height, educational attainment (EA), IQ, autism, schizophrenia, and others, we observed significant temporal trends spanning the Holocene era. The results suggest positive selection for cognitive-related traits such as IQ, EA and autism spectrum disorder (ASD), alongside negative selection for anxiety and depression. The results for height were mixed and showed nonlinear relationships with Years Before Present (BP). These trends were partially mediated by genetic components linked to distinct ancestral populations. Regression models incorporating admixture, geography, and temporal variables were used to account for biases in population composition over time. Latitude showed a positive effect on ASD PGS, EA and height, while it had a negative effect on skin pigmentation scores. Additionally, latitude exhibited significant nonlinear effects on multiple phenotypes. The observed patterns highlight the influence of climate-mediated selection pressures on trait evolution. Spline regression revealed that several polygenic scores had nonlinear relationships with years BP. The findings provide evidence for complex evolutionary dynamics, with distinct selective pressures shaping phenotypic diversity across different timescales and environments.}, }
@article {pmid39875364, year = {2025}, author = {Liu, Y and Lisovski, S and Courtin, J and Stoof-Leichsenring, KR and Herzschuh, U}, title = {Plant interactions associated with a directional shift in the richness range size relationship during the Glacial-Holocene transition in the Arctic.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1128}, pmid = {39875364}, issn = {2041-1723}, support = {202106620011//China Scholarship Council (CSC)/ ; }, mesh = {Arctic Regions ; Siberia ; *Biodiversity ; Alaska ; *Lakes ; *Plants ; Tundra ; Ecosystem ; Geologic Sediments ; Ice Cover ; }, abstract = {A nearly ubiquitous negative relationship between taxonomic richness and mean range-size (average area of taxa) is observed across space. However, the complexity of the mechanism limits its applicability for conservation or range prediction. We explore whether the relationship holds over time, and whether plant speciation, environmental heterogeneity, or plant interactions are major factors of the relationship within northeast Siberia and Alaska. By analysing sedimentary ancient DNA from seven lakes, we reconstruct plant richness, biotic environmental heterogeneity, and mean range-size over the last 30,000 years. We find positive richness to range-size relationships during the glacial period, shifting to negative during the interglacial period. Our results indicate neither speciation nor environmental heterogeneity is the principal driver. Network analyses show more positive interactions during the glacial period, which may contribute to positive richness to range-size relationships. Conversely, in the interglacial environment, negative interactions may result in negative relationships. Our findings suggest potential susceptibility to invasion but conservation advantages in far northern tundra given their positive interactions.}, }
@article {pmid39868711, year = {2024}, author = {Ollivier, M}, title = {[Thousands of years of human-dog relationship].}, journal = {Biologie aujourd'hui}, volume = {218}, number = {3-4}, pages = {115-127}, doi = {10.1051/jbio/2024011}, pmid = {39868711}, issn = {2105-0686}, mesh = {Humans ; Animals ; Dogs ; *Biological Evolution ; Europe ; }, abstract = {During recent years, much progress has been made in understanding the origin and evolution of the dog. Thanks to the collaboration between zooarchaeology, genomics and paleogenetics, researchers were able to hypothesize scenarios regarding the origins of the canine lineages present in Europe at the end of the Pleistocene and the beginning of the Holocene. Research has also shown a correlation between human and canine migration across time and space, highlighting a strong relationship between man and his best friend. This proximity between the two species is also illustrated by the adaptation of this species to anthropogenic selective pressures, particularly in parallel with cultural transitions. Although the history of this species still requires much exploration to be fully understood, these results provide new theoretical bases for understanding the interplay between humans and dogs.}, }
@article {pmid39868174, year = {2025}, author = {Malomane, DK and Williams, MP and Huber, CD and Mangul, S and Abedalthagafi, M and Chiang, CWK}, title = {Patterns of population structure and genetic variation within the Saudi Arabian population.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.10.632500}, pmid = {39868174}, issn = {2692-8205}, abstract = {The Arabian Peninsula is considered the initial site of historic human migration out of Africa. The modern-day indigenous Arabians are believed to be the descendants who remained from the ancient split of the migrants into Eurasia. Here, we investigated how the population history and cultural practices such as endogamy have shaped the genetic variation of the Saudi Arabians. We genotyped 3,352 individuals and identified twelve genetic sub-clusters that corresponded to the geographical distribution of different tribal regions, differentiated by distinct components of ancestry based on comparisons to modern and ancient DNA references. These sub-clusters also showed variation across ranges of the genome covered in runs of homozygosity, as well as differences in population size changes over time. Using 25,488,981 variants found in whole genome sequencing data (WGS) from 302 individuals, we found that the Saudi tend to show proportionally more deleterious alleles than neutral alleles when compared to Africans/African Americans from gnomAD (e.g. a 13% increase of deleterious alleles annotated by AlphaMissense between 0.5 -5% frequency in Saudi, compared to 7% decrease of the benign alleles; P < 0.001). Saudi sub-clusters with greater inbreeding and lower effective population sizes showed greater enrichment of deleterious alleles as well. Additionally, we found that approximately 10% of the variants discovered in our WGS data are not observed in gnomAD; these variants are also enriched with deleterious annotations. To accelerate studying the population-enriched deleterious alleles and their health consequences in this population, we made available the allele frequency estimates of 25,488,981 variants discovered in our samples. Taken together, our results suggest that Saudi's population history impacts its pattern of genetic variation with potential consequences to the population health. It further highlights the need to sequence diverse and unique populations so to provide a foundation on which to interpret medical-and pharmaco-genomic findings from these populations.}, }
@article {pmid39858625, year = {2025}, author = {Jeromelj, T and Leskovar, T and Zupanič Pajnič, I}, title = {The Impact of Storage Conditions on DNA Preservation in Human Skeletal Remains: A Comparison of Freshly Excavated Samples and Those Stored for 12 Years in a Museum Depot.}, journal = {Genes}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/genes16010078}, pmid = {39858625}, issn = {2073-4425}, support = {J3-3080//The Slovenian Research and Innovation Agency/ ; }, mesh = {Humans ; *Specimen Handling/methods ; *Museums ; *DNA, Ancient/analysis ; Body Remains ; Bone and Bones/chemistry ; Humidity ; Archaeology/methods ; Preservation, Biological/methods ; Temperature ; }, abstract = {Background: As the field of ancient DNA research continues to evolve and produce significant discoveries, it is important to address the crucial limitations it still faces. Under conducive conditions, DNA can persist for thousands of years within human skeletal remains, but, as excavation occurs, the environment abruptly changes, often leading to the loss of DNA and valuable genetic information. Proper storage procedures are needed to mediate DNA degradation and maintain sample integrity. This study aimed to investigate the impact of long-term storage under unregulated temperatures and humidity conditions on DNA preservation in human skeletal remains. Methods: To achieve this, archaeological petrous bones were used for DNA recovery. The DNA yield and degree of DNA degradation were compared for samples originating from historically and geographically equivalent archaeological sites, which differed in times of excavation and, consequently, in storage durations and conditions. DNA yield and the degree of DNA degradation were determined using real time PCR. Results: A significant reduction in the DNA yield and a borderline significant increase in the degree of DNA degradation were detected for samples stored at unregulated conditions for approximately 12 years. Conclusions: Our results show the imperative need for adhering to scientific recommendations regarding the optimal temperature and humidity in the long-term storage of human skeletal material.}, }
@article {pmid39858570, year = {2024}, author = {Haarkötter, C and Roca-Rada, X and Saiz, M and Vinueza-Espinosa, DC and Gálvez, X and Medina-Lozano, MI and Díaz-Ruiz, D and Álvarez, JC and Llamas, B and Lorente, JA and Austin, J}, title = {Exploring the Potential of Genome-Wide Hybridization Capture Enrichment for Forensic DNA Profiling of Degraded Bones.}, journal = {Genes}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/genes16010023}, pmid = {39858570}, issn = {2073-4425}, support = {FPU 20/01967 and EST 23/0110//Ministerio de Universidades (Spain)/ ; PTDC/HAR-ARQ/6273/2020//FCT - Foundation for Science and Technology/ ; }, mesh = {Humans ; *Bone and Bones/chemistry ; *DNA Fingerprinting/methods ; *Forensic Genetics/methods ; *DNA, Ancient/analysis ; Microsatellite Repeats/genetics ; Nucleic Acid Hybridization/methods ; Genome, Human ; Body Remains ; }, abstract = {UNLABELLED: In many human rights and criminal contexts, skeletal remains are often the only available samples, and they present a significant challenge for forensic DNA profiling due to DNA degradation. Ancient DNA methods, particularly capture hybridization enrichment, have been proposed for dealing with severely degraded bones, given their capacity to yield results in ancient remains.<br><br>BACKGROUND/OBJECTIVES: This paper aims to test the efficacy of genome-wide capture enrichment on degraded forensic human remains compared to autosomal STRs analysis.<br><br>METHODS: Six highly degraded human bones from the Spanish Civil War (1936-1939) were quantified with Quantifiler[&#x2122;] Trio and amplified with GlobalFiler[&#x2122;]. Independently, partially UDG-treated double-stranded DNA libraries were generated and shotgun sequenced to screen for endogenous human DNA content. Subsequently, libraries were enriched with the Twist Bioscience "Twist Ancient DNA" reagent enrichment kit, which had not been previously tested for forensic purposes.<br><br>RESULTS: The results show that the samples behave similarly with both approaches (well-preserved samples yield good results). However, capture enrichment provides some new relevant insights, suggesting that its implementation in current NGS forensic platforms could be beneficial.<br><br>CONCLUSIONS: Shotgun results show that the analyzed samples exhibit the same characteristics as ancient DNA samples in terms of DNA fragmentation and molecular damage, which may enhance the value of this approach when authenticating the endogenous DNA of forensic samples.}, }
@article {pmid39856224, year = {2025}, author = {Heinrich, F and Simianer, H and Bölling, J and Röckelein, H and Roos, C and Reimer, C and Schmitt, AO}, title = {Genomic analysis of three medieval parchments from German monasteries.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3156}, pmid = {39856224}, issn = {2045-2322}, mesh = {Animals ; Cattle/genetics ; Germany ; *DNA, Ancient/analysis ; History, Medieval ; *DNA, Mitochondrial/genetics ; *Polymorphism, Single Nucleotide ; *Haplotypes ; *Genomics/methods ; Phylogeny ; }, abstract = {In the last two decades there has been growing interest in the analysis of ancient DNA obtained from the parchment used in historic documents. The genetic insight that this data provides makes collections of historic documents an invaluable source for studying the development and spread of historical livestock populations. Additionally, the biological data may provide new information for the historical analysis that could be used to determine the provenance as well as the authenticity of these documents. In this study, we extracted DNA from three medieval parchments that were written in German monasteries in the twelfth century. The source animal of the parchments could be identified as cattle and we compared their genome sequences with those of modern populations that are part of the 1000 Bull Genomes Project. The three animals were found to carry mtDNA haplogroup T3 and show a closer genetic relationship to other historic animals than to modern breeds. We further identified 39 haplotypes and 132 SNPs variants, which are rare (< 0.1) or even non-existent in modern breeds. Finally, the genetic distances between the parchment samples show a putative association with the dates when the documents were written, indicating the usefulness of genetic analysis for provenance research.}, }
@article {pmid39854269, year = {2025}, author = {Huang, Y and Carmi, S and Ringbauer, H}, title = {Estimating effective population size trajectories from time-series identity-by-descent segments.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyae212}, pmid = {39854269}, issn = {1943-2631}, support = {//Max Planck Society/ ; }, abstract = {Long, identical haplotypes shared between pairs of individuals, known as identity-by-descent (IBD) segments, result from recently shared co-ancestry. Various methods have been developed to utilize IBD sharing for demographic inference in contemporary DNA data. Recent methodological advances have extended the screening for IBD segments to ancient DNA (aDNA) data, making demographic inference based on IBD also possible for aDNA. However, aDNA data typically have varying sampling times, but most demographic inference methods for modern data assume that sampling is contemporaneous. Here, we present Ttne (Time-Transect Ne), which models time-transect sampling to infer recent effective population size trajectories. Using simulations, we show that utilizing IBD sharing in time series increased resolution to infer recent fluctuations in effective population sizes compared with methods that only use contemporaneous samples. To account for IBD detection errors common in empirical analyses, we implemented an approach to estimate and model IBD detection errors. Finally, we applied Ttne to two aDNA time transects: individuals associated with the Copper Age Corded Ware Culture and Medieval England. In both cases, we found evidence of a growing population, a signal consistent with archaeological records.}, }
@article {pmid39850751, year = {2025}, author = {Shen, W and Kruse, S and Liu, S and Stoof-Leichsenring, K and Kühn, I and Li, W and Cao, X and Zhang, ZR and Zeng, CX and Yang, JB and Li, DZ and Herzschuh, U}, title = {Post-Glacial Vegetation Trajectories on the Eastern Tibetan Plateau Reflect Millennial-Scale Migration Lags in Complex Mountain Terrain Based on Sedimentary Ancient DNA and Dynamic Dispersal Modeling.}, journal = {Ecology and evolution}, volume = {15}, number = {1}, pages = {e70862}, pmid = {39850751}, issn = {2045-7758}, abstract = {Mountains with complex terrain and steep environmental gradients are biodiversity hotspots such as the eastern Tibetan Plateau (TP). However, it is generally assumed that mountain terrain plays a secondary role in plant species assembly on a millennial time-scale compared to climate change. Here, we investigate plant richness and community changes during the last 18,000 years at two sites: Lake Naleng and Lake Ximen on the eastern TP with similar elevation and climatic conditions but contrasting terrain. We applied plant DNA metabarcoding to lake sediments leveraging a new regional reference database for taxa identification. Furthermore, we developed a simplified species dispersal model named SMARC. This was used to simulate species migration along river valleys in response to past climate change at the taxonomic resolution of the sedimentary ancient DNA (sedaDNA) approach. Statistical analyses, including ordination-based ecological trajectory analysis, yielded a significant match between sedaDNA and simulated results at single taxon and community levels including certain site-specific differences. Steep terrain downstream of Lake Naleng enhances connectivity to glacial lowland refugia during postglacial warming. In contrast, gentle terrain over long distances implies weak connectivity to the lowland and thus resulted in a strong migration lag at Lake Ximen. Likewise, terrain differences among our sites defined the different connectivity to alpine refugia during late-Holocene cooling. Our consistent proxy- and model-based results, for the first time, indicate that dispersal related migration lags in complex mountain terrain lead to uneven vegetation trajectories at sites with similar climatic conditions mainly because of differences in connectivity to refugia. Ultimately our results indicate that connectivity to refugia is a first-order factor for species migration in addition to elevation-related climatic conditions shaping the postglacial vegetation trajectory in mountainous terrain. This has hitherto largely been ignored when forecasting mountain vegetation responses to climate change and related risk assessment.}, }
@article {pmid39848961, year = {2025}, author = {Mazières, S and Condemi, S and El Nemer, W and Chiaroni, J}, title = {Rapid change in red cell blood group systems after the main Out of Africa of Homo sapiens.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1597}, pmid = {39848961}, issn = {2045-2322}, support = {ANR-20-CE03-0002//Agence Nationale de la Recherche/ ; }, mesh = {Humans ; Animals ; *Blood Group Antigens/genetics ; *Neanderthals/genetics ; *Genetic Variation ; Haplotypes ; Phylogeny ; Erythrocytes ; Alleles ; Africa ; }, abstract = {Despite the advances in paleogenomics, red cell blood group systems in ancient human populations remain scarcely known. Pioneer attempts showed that Neandertal and Denisova, two archaic hominid populations inhabiting Eurasia, expressed blood groups currently found in sub-Saharans and a rare "rhesus", part of which is found in Oceanians. Herein we fully pictured the blood group genetic diversity of 22 Homo sapiens and 14 Neandertals from Eurasia living between 120,000 and 20,000 years before present (yBP). From the ABO, Rh, Kell, Duffy, Kidd, MNS, Diego, H, secretor and Indian systems, we noted that the blood group allele diversity in the Neandertals remained unchanged since 120,000 yBP, while H. sapiens conquered Eurasia with blood group alleles presently exclusive to non-African populations, suggesting they may have differentiated right after the Out of Africa, between 70,000 and 45,000 yBP. Notably, Ust'Ishim possessed unknown alleles that may illustrate the lost genetic heritage of the early Eurasians. Lastly, Neandertals shared a unique Rh haplotype from which we updated the current RHD phylogeny. The contribution of this study is twofold. It enlightens the expansion patterns of H sapiens and recalls the anthropological effectiveness of genetic polymorphisms currently being surveyed for transfusion safety and pregnancy monitoring.}, }
@article {pmid39835499, year = {2025}, author = {Fleskes, RE and Gilmore, JK and Oubré, LS and Ofunniyin, AA and Cabana, GS and Schurr, TG}, title = {Immersive Videography of Ancient DNA Extraction for Community Engagement and Educational Initiatives by the Anson Street African Burial Ground Project.}, journal = {American journal of biological anthropology}, volume = {186}, number = {1}, pages = {e25055}, pmid = {39835499}, issn = {2692-7691}, support = {//College of Charleston/ ; //The City of Charleston/ ; NGS-52378R-18//National Geographic Society/ ; NGS-54324E-18//National Geographic Society/ ; }, mesh = {Humans ; *DNA, Ancient/analysis ; Video Recording ; Burial ; Community Participation/methods ; Archaeology/methods ; Africa ; }, abstract = {OBJECTIVE: Community engagement is an increasingly important component of ancient DNA (aDNA) research, especially when it involves archeological individuals connected to contemporary descendants or other invested communities. However, effectively explaining methods to non-specialist audiences can be challenging due to the intricacies of aDNA laboratory work. To overcome this challenge, the Anson Street African Burial Ground (ASABG) Project employed a GoPro camera to visually document the process of aDNA extraction for use in community engagement and education events.<br><br>METHODS: A GoPro Hero 6 camera enclosed in a decontaminated underwater case was used to film multiple rounds of aDNA extractions from first- and third-person perspectives. The raw footage was edited into long (13-minute) and short (5-minute) format videos to summarize the steps of aDNA extraction for different educational aims.<br><br>RESULTS: The videos were used at community engagement events, as well as in classrooms and other educational venues for students of different age groups. General feedback from the community was solicited at the events. We found that the use of videographic methods increased the transparency and accessibility of the aDNA research conducted by the ASABG Project team.<br><br>DISCUSSION: Providing a visual guide to the often destructive nature of aDNA testing served as an important step in the continuing practice of informed (dynamic) consent with the descendant community. Future initiatives could expand these visualization efforts by illustrating other steps in the aDNA testing process, such as library preparation or sequencing, or incorporating approaches such as live streaming to foster trust and expand public science literacy.}, }
@article {pmid39824823, year = {2025}, author = {Gelabert, P and Oberreiter, V and Straus, LG and Morales, MRG and Sawyer, S and Marín-Arroyo, AB and Geiling, JM and Exler, F and Brueck, F and Franz, S and Cano, FT and Szedlacsek, S and Zelger, E and Hämmerle, M and Zagorc, B and Llanos-Lizcano, A and Cheronet, O and Tejero, JM and Rattei, T and Kraemer, SM and Pinhasi, R}, title = {Author Correction: A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {779}, doi = {10.1038/s41467-025-56198-x}, pmid = {39824823}, issn = {2041-1723}, }
@article {pmid39823473, year = {2025}, author = {Bettisworth, B and Psonis, N and Poulakakis, N and Pavlidis, P and Stamatakis, A}, title = {Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaf006}, pmid = {39823473}, issn = {1537-1719}, abstract = {A common problem when analyzing ancient DNA (aDNA) data is to identify the species which corresponds to the recovered aDNA sequence(s). The standard approach is to deploy sequence similarity based tools, such as BLAST. However, as aDNA reads may frequently stem from unsampled taxa due to extinction, it is likely that there is no exact match in any database. As a consequence, these tools may not be able to accurately place such reads in a phylogenetic context. Phylogenetic placement is a technique where a read is placed onto a specific branch of a phylogenetic reference tree, which allows for a substantially finer resolution when identifying reads. Prior applications of phylogenetic placement has deployed only on data from extant sources. Therefore, it is unclear how the aDNA damage affects phylogenetic placement's applicability to aDNA data. To investigate how aDNA damage affects placement accuracy, we re-implemented a statistical model of aDNA damage. We deploy this model, along with a modified version of the existing assessment pipeline PEWO, to seven empirical datasets with four leading tools: APPLES, EPA-NG, pplacer, and RAPPAS. We explore the aDNA damage parameter space via a grid search in order to identify the aDNA damage factors that exhibit the largest impact on placement accuracy. We find that the frequency of DNA backbone nicks (and consequently read length) has the, by far, largest impact on aDNA read placement accuracy, and that other factors, such as misincorporations, have a negligible effect on overall placement accuracy.}, }
@article {pmid39814885, year = {2025}, author = {Wang, K and Tobias, B and Pany-Kucera, D and Berner, M and Eggers, S and Gnecchi-Ruscone, GA and Zlámalová, D and Gretzinger, J and Ingrová, P and Rohrlach, AB and Tuke, J and Traverso, L and Klostermann, P and Koger, R and Friedrich, R and Wiltschke-Schrotta, K and Kirchengast, S and Liccardo, S and Wabnitz, S and Vida, T and Geary, PJ and Daim, F and Pohl, W and Krause, J and Hofmanová, Z}, title = {Ancient DNA reveals reproductive barrier despite shared Avar-period culture.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39814885}, issn = {1476-4687}, abstract = {After a long-distance migration, Avars with Eastern Asian ancestry arrived in Eastern Central Europe in 567 to 568 CE and encountered groups with very different European ancestry[1,2]. We used ancient genome-wide data of 722 individuals and fine-grained interdisciplinary analysis of large seventh- to eighth-century CE neighbouring cemeteries south of Vienna (Austria) to address the centuries-long impact of this encounter[1,2]. We found that even 200 years after immigration, the ancestry at one site (Leobersdorf) remained dominantly East Asian-like, whereas the other site (Mödling) shows local, European-like ancestry. These two nearby sites show little biological relatedness, despite sharing a distinctive late-Avar culture[3,4]. We reconstructed six-generation pedigrees at both sites including up to 450 closely related individuals, allowing per-generation demographic profiling of the communities. Despite different ancestry, these pedigrees together with large networks of distant relatedness show absence of consanguinity, patrilineal pattern with female exogamy, multiple reproductive partnerships (for example, levirate) and direct correlation of biological connectivity with archaeological markers of social status. The generation-long genetic barrier was maintained by systematically choosing partners with similar ancestry from other sites in the Avar realm. Leobersdorf had more biological connections with the Avar heartlands than with Mödling, which is instead linked to another site from the Vienna Basin with European-like ancestry. Mobility between sites was mostly due to female exogamy pointing to different marriage networks as the main driver of the maintenance of the genetic barrier.}, }
@article {pmid39809323, year = {2025}, author = {Boast, AP and Wood, JR and Cooper, J and Bolstridge, N and Perry, GLW and Wilmshurst, JM}, title = {DNA and spores from coprolites reveal that colourful truffle-like fungi endemic to New Zealand were consumed by extinct moa (Dinornithiformes).}, journal = {Biology letters}, volume = {21}, number = {1}, pages = {20240440}, pmid = {39809323}, issn = {1744-957X}, support = {//University of Auckland/ ; //Linnean Society of NSW/ ; //Ornithological Society of New Zealand/ ; //Royal Society Te Ap&#x101;rangi/ ; //New Zealand Ministry of Business, Innovation and Employment's Science and Innovation Group/ ; }, mesh = {Animals ; New Zealand ; *Spores, Fungal ; DNA, Fungal/genetics ; Extinction, Biological ; Feces/microbiology ; Ascomycota/genetics/physiology ; }, abstract = {Mycovores (animals that consume fungi) are important for fungal spore dispersal, including ectomycorrhizal (ECM) fungi symbiotic with forest-forming trees. As such, fungi and their symbionts may be impacted by mycovore extinction. New Zealand (NZ) has a diversity of unusual, colourful, endemic sequestrate (truffle-like) fungi, most of which are ECM. As NZ lacks native land mammals (except bats), and sequestrate fungi are typically drab and mammal-dispersed, NZ's sequestrate fungi are hypothesized to be adapted for bird dispersal. However, there is little direct evidence for this hypothesis, as 41% of NZ's native land bird species became extinct since initial human settlement in the thirteenth century. Here, we report ancient DNA and spores from the inside of two coprolites of NZ's extinct, endemic upland moa (Megalapteryx didinus) that reveal consumption and likely dispersal of ECM fungi, including at least one colourful sequestrate species. Contemporary data from NZ show that birds rarely consume fungi and that the introduced mammals preferentially consume exotic fungi. NZ's endemic sequestrate fungi could therefore be dispersal limited compared with fungi that co-evolved with mammalian dispersers. NZ's fungal communities may thus be undergoing a gradual species turnover following avian mycovore extinction and the establishment of mammalian mycovores, potentially affecting forest resilience and facilitating invasion by exotic tree taxa.}, }
@article {pmid39803566, year = {2025}, author = {Szécsényi-Nagy, A and Virag, C and Jakab, K and Rohland, N and Ringbauer, H and Anders, A and Raczky, P and Hajdu, T and Kiss, K and Szeniczey, T and Évinger, S and Keszi, T and Virág, ZM and Cheronet, O and Mallick, S and Akbari, A and Pinhasi, R and Reich, D and Siklósi, Z}, title = {Ancient DNA reveals diverse community organizations in the 5th millennium BCE Carpathian Basin.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.02.631136}, pmid = {39803566}, issn = {2692-8205}, abstract = {We present a comprehensive genetic investigation of Late Neolithic (LN) and Early Copper Age (ECA) populations living in the Carpathian Basin, leveraging whole genome data from 125 previously unreported individuals. Using population genetics, kinship analyses and the study of networks of identity-by-descent haplotype segment sharing, we elucidate the social and genetic dynamics of these communities between 4800-3900 cal BCE. Despite changes in settlement patterns, burial practices, and material culture, we document a high degree of genetic continuity. While one set of individuals we analyzed from a large community cemetery was genetically diverse, another site was more homogenous and closed, with numerous consanguineous relationships and evidence of patrilineality and patrilocality. These results document radically different kinship systems in contemporaneous ECA communities using similar material culture and living only about 100 km apart.}, }
@article {pmid39794407, year = {2025}, author = {Weber, GW and Šimková, PG and Fernandes, DM and Cheronet, O and Úry, E and Wilfing, H and Matiasek, K and Llano-Lizcano, A and Gelabert, P and Trinks, I and Douka, K and Ladstätter, S and Higham, T and Steskal, M and Pinhasi, R}, title = {The cranium from the Octagon in Ephesos.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {943}, pmid = {39794407}, issn = {2045-2322}, support = {369300//University of Vienna HEAS/ ; 369300//University of Vienna HEAS/ ; 369300//University of Vienna HEAS/ ; 369300//University of Vienna HEAS/ ; BE547005//University of Vienna/ ; }, mesh = {Humans ; Male ; *Skull/anatomy &amp; histology ; Turkey ; Child ; Adolescent ; Archaeology ; Femur/anatomy &amp; histology ; }, abstract = {During excavations in 1929, a well-preserved skeleton was discovered in a sarcophagus in the Octagon at Ephesos (Turkey). For the following century, archaeologists have speculated about the identity of this obviously notable person. Repeated claim is that the remains could represent Arsinoë IV, daughter of Ptolemy XII, and younger (half-)sister of Cleopatra VII. To address these questions we undertook state-of-the-art morphological, genetic and dating analyses of the cranium and further analyses of bone samples from a femur and a rib of the skeleton found in the same tomb. We confirm based on genetic analyses from the cranium and the femur that they derive from the same person. [14]C-dating of the cranium provides a most likely time range between 205-36 BC. The connection with Arsinoë IV can be excluded because we confirmed that the individual is a male. The cranium represents an 11-14-year-old boy who suffered from significant developmental disturbances. Genetics suggest an ancestry from the Italian peninsula or Sardinia. The fate of the body of Arsinoë IV, who reportedly was killed in 41 BC in Ephesos, remains open. In contrast, investigations regarding the fate and social background of the boy from the Octagon can now proceed free of speculation.}, }
@article {pmid39791298, year = {2025}, author = {Sheng, GL and Zheng, MM and Xiao, B and Yuan, JX}, title = {Progress on ancient DNA investigation of Late Quaternary mammals in China.}, journal = {Yi chuan = Hereditas}, volume = {47}, number = {1}, pages = {46-57}, doi = {10.16288/j.yczz.24-193}, pmid = {39791298}, issn = {0253-9772}, mesh = {*DNA, Ancient/analysis ; Animals ; China ; *Mammals/genetics ; Humans ; Evolution, Molecular ; Phylogeny ; Fossils ; }, abstract = {It has been more than 40 years since the beginning of exploring the genetic composition of ancient organisms from the perspective of ancient DNA. In the recent 20 years, with the development and application of high-throughput sequencing technology platforms and the improved efficiency of retrieving highly fragmented DNA molecules, ancient DNA research moved forward to a brand-new era of deep-time paleogenomics. It not only solved many controversial phylogenetic problems, enriched the migration and evolution details of various organisms including humans, but also launched exploration of the molecular responses to climate changes in terms of "whole genomic-big data-multi-species" level. Moreover, it expanded the sample age from no more than 100,000 years to the Early Pleistocene, ~2 million years ago. Recently, Chinese scientists have made many influential breakthroughs in evolution and migration integration of East Asian populations and thus filled an important gap in the evolutionary process of modern human. Compared to the situation in human paleogenomic studies, less attention has been paid to the study of ancient DNA from vertebrates remains. In this review, we introduce a series of advances in ancient DNA investigations of large mammals in Late Quaternary in China, summarize the research breakthroughs in revealing the systematic evolutionary relationship between ancient and extant groups, gene flow, and molecular responses of mammalian populations to climate change, and explore the opportunities and key challenges in the field of mammalian paleogenomics.}, }
@article {pmid39791297, year = {2025}, author = {Zhang, DX and Dai, SR and Cui, YQ}, title = {The migration and evolutionary mechanisms of northern Asian populations from the perspective of ancient genomics.}, journal = {Yi chuan = Hereditas}, volume = {47}, number = {1}, pages = {34-45}, doi = {10.16288/j.yczz.24-196}, pmid = {39791297}, issn = {0253-9772}, mesh = {Humans ; *Human Migration ; *Genomics/methods ; *DNA, Ancient/analysis ; Genetics, Population ; Asian People/genetics ; Evolution, Molecular ; China ; }, abstract = {The northern part of Asia, including Siberia, the Mongolian Plateau, and northern China, is not only a crossroads for population exchange on the Eurasian continent but also an important bridge connecting the American continent. This region holds a unique and irreplaceable significance in exploring the origins of humanity, tracking human migration routes, and elucidating evolutionary mechanisms. Despite the limited number of samples unearthed, varying preservation conditions, and constraints of technical means, our understanding of the interactions among populations in northern Asia is still in its infancy. However, the development of high-throughput sequencing technology and its advancement in ancient DNA research have provided us with a new perspective for delving into the genetic history of ancient populations from a molecular level. In this review, we synthesize the changes in the genetic structure of ancient populations in different stages of northern Asia, aiming to reveal the patterns of interaction among ancient populations in this region, the evolutionary process of their genetic structure, and their genetic contributions to modern populations. It will also discuss the adaptive strategies of humans in response to extreme natural conditions. This will not only deepen our understanding of the origins and migration processes of humanity but also provide a solid foundation for studying the evolutionary mechanisms and adaptive strategies of humans under environmental selective pressures.}, }
@article {pmid39791296, year = {2025}, author = {Ping, WJ and Xue, JY and Fu, QM}, title = {Ancient DNA elucidates the migration and evolutionary history of northern and southern populations in East Asia.}, journal = {Yi chuan = Hereditas}, volume = {47}, number = {1}, pages = {18-33}, doi = {10.16288/j.yczz.24-224}, pmid = {39791296}, issn = {0253-9772}, mesh = {Humans ; *DNA, Ancient/analysis ; *Human Migration ; Asia, Eastern ; Genetics, Population ; Asian People/genetics ; Gene Flow ; Genome, Human ; Evolution, Molecular ; China ; }, abstract = {Over the past decade, the continuous development of ancient genomic technology and research has significantly advanced our understanding of human history. Since 2017, large-scale studies of ancient human genomes in East Asia, particularly in China, have emerged, resulting in a wealth of ancient genomic data from various time periods and locations, which has provided new insights into the genetic history of East Asian populations over tens of thousands of years. Especially since 2022, there emerged a series of new research progresses in the genetic histories of the northern and southern Chinese populations within the past 10,000 years. However, there is currently no systematic review focused on these recent ancient genomic studies in East Asia. Therefore, this article emphasizes the study of ancient human genomes in China and systematically reviews the genetic patterns and migration history of populations in East Asia since the Late Paleolithic. Existing research indicates that by at least 19,000 years ago, there was a north-south differentiation among ancient East Asian populations, leading to different genetic lineages divided by the Qinling-Huaihe line. Gene flow and interactions between northern and southern East Asians began in the Early Neolithic and were further strengthened from the Mid-Neolithic. By the historical period, northern East Asian ancestry played a profound role in the genetic components of southern populations, shaping the genetic structure of present-day Chinese populations. Throughout this process, ancient populations in northern and southern China also engaged in extensive interactions through coastal and inland routes with populations from surrounding regions, including Siberia, Japan, Korea, Southeast Asia, and Pacific islands, playing a crucial role in the formation of different linguistic groups. These studies have charted the evolutionary and interaction history of East Asian populations over tens of thousands of years; yet, many unresolved mysteries remain. Further exploration is needed through ancient genomic data from additional time periods and broader geographic areas to facilitate a more comprehensive and detailed investigation, thereby advancing related scientific questions.}, }
@article {pmid39789608, year = {2025}, author = {Koptekin, D and Yapar, E and Vural, KB and Sağlıcan, E and Altınışık, NE and Malaspinas, AS and Alkan, C and Somel, M}, title = {Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {6}, pmid = {39789608}, issn = {1474-760X}, mesh = {Humans ; *Algorithms ; DNA, Ancient/analysis ; Genomics/methods ; Genome, Human ; Software ; }, abstract = {We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sites and graph alignment effectively remove reference bias, but only starting from raw read files. We next study approaches to overcome postmortem damage: trimming, rescaling, and our newly developed algorithm, bamRefine (github.com/etkayapar/bamRefine and zenodo.org/records/14234666), masking reads only at positions possibly affected by PMD. We propose graph alignment coupled with bamRefine as a simple strategy to minimize data loss and bias, and urge the community to publish FASTQ files.}, }
@article {pmid39788103, year = {2025}, author = {Kun, E and Sohail, M and Narasimhan, VM}, title = {The trait-specific timing of accelerated genomic change in the human lineage.}, journal = {Cell genomics}, volume = {5}, number = {1}, pages = {100740}, doi = {10.1016/j.xgen.2024.100740}, pmid = {39788103}, issn = {2666-979X}, mesh = {Humans ; Animals ; *Genome-Wide Association Study ; Neanderthals/genetics ; Evolution, Molecular ; Genome, Human/genetics ; Macaca mulatta/genetics ; Phenotype ; Genomics/methods ; Epigenesis, Genetic ; }, abstract = {Humans exhibit distinct characteristics compared to our primate and ancient hominin ancestors. To investigate genomic bursts in the evolution of these traits, we use two complementary approaches to examine enrichment among genome-wide association study loci spanning diseases and AI-based image-derived brain, heart, and skeletal tissue phenotypes with genomic regions reflecting four evolutionary divergence points. These regions cover epigenetic differences among humans and rhesus macaques, human accelerated regions (HARs), ancient selective sweeps, and Neanderthal-introgressed alleles. Skeletal traits such as pelvic width and limb proportions showed enrichment in evolutionary annotations that mirror morphological changes in the primate fossil record. Additionally, we observe enrichment of loci associated with the longitudinal fasciculus in human-gained epigenetic elements since macaques, the visual cortex in HARs, and the thalamus proper in Neanderthal-introgressed alleles, implying that associated cognitive functions such as language processing, decision-making, sensory signaling, and motor control are enriched at different evolutionary depths.}, }
@article {pmid39783862, year = {2025}, author = {Lubbe, P and Rawlence, NJ and Dussex, N and Kardialsky, O and Knapp, M}, title = {Plio-Pleistocene Environmental Changes Drove the Settlement of Aotearoa New Zealand by Australian Open-Habitat Bird Lineages.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17648}, doi = {10.1111/mec.17648}, pmid = {39783862}, issn = {1365-294X}, support = {16-UOO-096//Marsden Fund/ ; 14-UOO-007//Royal Society Te Ap&#x101;rangi/ ; }, abstract = {In a changing environment, vacant niches can be filled either by adaptation of local taxa or range-expanding invading species. The relative tempo of these patterns is of key interest in the modern age of climate change. Aotearoa New Zealand has been a hotspot of biogeographic research for decades due to its long-term isolation and dramatic geological history. An island with high levels of faunal endemicity, it is a system well suited to studying the relative effects of in situ evolution versus dispersal in determining faunal assemblages, while its turbulent climate and geological history provide valuable insights into the evolutionary impacts of environmental changes. Such investigations are of urgent importance given predicted climate change and human impacts rapidly affecting environments globally. Here, we analyse the divergence dates of nearly all endemic Aotearoa New Zealand bird species from their overseas relatives to assess the role of environmental changes in driving speciation and colonisation, with special regard to cooling climate during the Pliocene and Pleistocene. We uncover a wave of colonisation events by Australian open-habitat adapted species since the Pliocene that peaked at the beginning of the Pleistocene. Furthermore, we highlight an even distribution of divergence dates in forest-adapted taxa through time, consistent with millions of years of extensive forest cover. Finally, we note parallels to the modern-day establishment of new bird populations from Australia and suggest this is largely influenced by anthropogenic land-use patterns. This research contributes to the growing body of work recognising the long-lasting impacts of Pleistocene climate change on Aotearoa New Zealand's avifauna, and reinforces biological invasions as a key evolutionary response to changing environmental conditions.}, }
@article {pmid39780098, year = {2025}, author = {Pla-Díaz, M and Akgül, G and Molak, M and du Plessis, L and Panagiotopoulou, H and Doan, K and Bogdanowicz, W and Dąbrowski, P and Oziembłowski, M and Kwiatkowska, B and Szczurowski, J and Grzelak, J and Arora, N and Majander, K and González-Candelas, F and Schuenemann, VJ}, title = {Insights into Treponema pallidum genomics from modern and ancient genomes using a novel mapping strategy.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {7}, pmid = {39780098}, issn = {1741-7007}, mesh = {*Treponema pallidum/genetics ; *Genome, Bacterial ; *Phylogeny ; *Genomics/methods ; Humans ; }, abstract = {BACKGROUND: Treponemal diseases are a significant global health risk, presenting challenges to public health and severe consequences to individuals if left untreated. Despite numerous genomic studies on Treponema pallidum and the known possible biases introduced by the choice of the reference genome used for mapping, few investigations have addressed how these biases affect phylogenetic and evolutionary analysis of these bacteria. In this study, we ascertain the importance of selecting an appropriate genomic reference on phylogenetic and evolutionary analyses of T. pallidum.<br><br>RESULTS: We designed a multiple-reference-based (MRB) mapping strategy using four different reference genomes and compared it to traditional single-reference mapping. To conduct this comparison, we created a genomic dataset comprising 77 modern and ancient genomes from the three subspecies of T. pallidum, including a newly sequenced seventeenth century genome (35X mean coverage) of a syphilis-causing strain (designated as W86). Our findings show that recombination detection was consistent across different references, but the choice of reference significantly affected ancient genome reconstruction and phylogenetic inferences. The high-coverage W86 genome introduced in this study also provided a new calibration point for Bayesian molecular clock dating, improving the reconstruction of the evolutionary history of treponemal diseases. Additionally, we identified novel recombination events, positive selection targets, and refined dating estimates for key events in the species' history.<br><br>CONCLUSIONS: This study highlights the importance of considering methodological implications and reference genome bias in high-throughput sequencing-based whole-genome analysis of T. pallidum, especially of ancient or low-coverage samples, contributing to a deeper understanding of the treponemal pathogen and its subspecies.}, }
@article {pmid39776197, year = {2025}, author = {Cuesta-Aguirre, DR and Amor-Jimenez, C and Malgosa, A and Santos, C}, title = {A Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14061}, doi = {10.1111/1755-0998.14061}, pmid = {39776197}, issn = {1755-0998}, support = {Ref. 2017 SGR 1630; 2021 SGR 00186//Generalitat de Catalunya/ ; //European Social Fund Plus/ ; //Departament d'Innovaci&#xf3;, Universitats i Empresa, Generalitat de Catalunya/ ; Ref. PGC2018-096666-B-100//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2020 FI_B1 00641//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, abstract = {Mitochondrial DNA (mtDNA) analysis is crucial for understanding human population structure and genetic diversity. However, post-mortem DNA damage poses challenges, that make analysis difficult. DNA preservation is affected by environmental conditions which, among other factors, complicates the differentiation of endogenous variants from artefacts in ancient mtDNA mix profiles. This study aims to develop a molecular damage profile for ancient mtDNA that can become a useful tool in analysing mtDNA from ancient remains. A dataset of 427 whole genomes or capture of mtDNA sequences from individuals representing different historical periods and climatic regions was compiled from the ENA database. Present-day and UDG-treated ancient samples were also included and used to establish levels of damaged reads. Results indicated that samples from cold regions exhibited the lowest percentage of damaged reads, followed by arid, cold, tropical and temperate regions, with significant differences observed between cold and temperate regions. A global damage profile was generated, identifying 2933 positions (25% of the positions considered) with damage in more than 23.8% of the samples analysed, deemed as damage hotspots. Notably, 2856 of these hotspots had never been reported as damage or mutational hotspots, or heteroplasmic positions. Damage hotspot frequency by position was slightly higher in the non-coding region compared with the coding region. In conclusion, this study provides a molecular damage profile for ancient mtDNA analysis that is expected to be a valuable tool in the interpretation of mtDNA variation in ancient samples.}, }
@article {pmid39772917, year = {2025}, author = {Kishida, T and Sawada, K and Namigata, S and Takabatake, T and Suzuki, M and Takezoe, N and Yamamoto, T and Nakanishi, T and Kitagawa, H}, title = {Hidden population turnover of small odontocetes in the northwestern North Pacific during the Holocene.}, journal = {Biology letters}, volume = {21}, number = {1}, pages = {20240525}, pmid = {39772917}, issn = {1744-957X}, support = {23K23956//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *DNA, Mitochondrial/genetics ; Dolphins ; Pacific Ocean ; Japan ; Porpoises/physiology ; Fossils ; Population Dynamics ; Radiometric Dating ; }, abstract = {Despite numerous studies on the rise and fall of terrestrial megafauna in the late Quaternary, knowledge about marine megafauna from this period remains limited. In this study, we performed radiocarbon dating and partial mitochondrial DNA sequencing from the skeletal remains of three species of small odontocetes (Pacific white-sided dolphins, Dall's porpoises and harbour porpoises) excavated from prehistoric archaeological sites around the Japanese shore dating back to 8500-1000 years ago (ya). Pacific white-sided dolphins that habituated the eastern coast of Hokkaido around 2000 ya belonged to different maternal groups than those from over 5000 ya and today. Furthermore, the species composition excavated from eastern Hokkaido sites varies between 5000 and 2000 ya. These findings suggest two significant population turnovers of small odontocetes on the east coast of Hokkaido, a transitional zone between the coastal area of East Asia and the offshore North Pacific. Notably, the first turnover, occurring between 5000 and 2000 ya, represents the oldest evidence of local population turnovers of marine megafauna during the late Quaternary.}, }
@article {pmid39765596, year = {2024}, author = {Anaya, G and Garrido, JM and Riquelme, JA and Martínez, RM and Membrillo, A and Caro, JA and Pajuelo, A and Ruiz, A and Martín de la Cruz, JC and Molina, A}, title = {Ancient DNA Reveals the Earliest Evidence of Sheep Flocks During the Late Fourth and Third Millennia BC in Southern Iberia.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {24}, pages = {}, pmid = {39765596}, issn = {2076-2615}, abstract = {The Spanish Merino is the most significant sheep breed globally due to its economic and cultural importance in human history. It has also had a substantial influence on the development of other Merino and Merino-derived breeds. Historical sources indicate that crossbreeding to produce finer, higher-quality wool was already taking place in the south of the Iberian Peninsula during the Roman era. This evidence suggests that individuals with a racial pattern very similar to that of the modern Merino may have already existed on the peninsula. The presence of the skeletal remains of these animals at various human settlements dated to the late fourth and third millennia BC could provide insights into the genomics of these ancestral sheep. This study analyses ancient DNA extracted from nine skeletal remains from three archaeological sites in Southern Iberia, dated to the third millennium BC. The samples were sequenced and aligned with the ovine genome. The genetic distances observed among the samples indicate a closer relationship between several animals from the Marinaleda (Seville) and Grañena Baja (Jaén) sites. The study of the slaughter/death age profiles identified at La Minilla (La Rambla, Córdoba) suggests an approach centred on meat exploitation, while the data from Marinaleda (Seville) and Grañena Baja (Jaén) indicate the potential exploitation of secondary resources. A review of the composition of these small ruminant herds could provide insights into the type of secondary resource exploitation that may have been prioritised. Our aim is to investigate the presence of distinct production systems, differentiating between those aimed primarily at meat use and those focused on secondary products. This is the first approach to exploring the genetic evidence for sheep livestock related to its productive use during this period and in this geographical area.}, }
@article {pmid39762943, year = {2025}, author = {Swiel, Y and Kelso, J and Peyrégne, S}, title = {Resolving the source of branch length variation in the Y chromosome phylogeny.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {4}, pmid = {39762943}, issn = {1474-760X}, mesh = {*Chromosomes, Human, Y/genetics ; Humans ; *Phylogeny ; Animals ; *Evolution, Molecular ; Genetic Variation ; Neanderthals/genetics ; Male ; }, abstract = {BACKGROUND: Genetic variation in the non-recombining part of the human Y chromosome has provided important insight into the paternal history of human populations. However, a significant and yet unexplained branch length variation of Y chromosome lineages has been observed, notably amongst those that are highly diverged from the human reference Y chromosome. Understanding the origin of this variation, which has previously been attributed to changes in generation time, mutation rate, or efficacy of selection, is important for accurately reconstructing human evolutionary and demographic history.<br><br>RESULTS: Here, we analyze Y chromosomes from present-day and ancient modern humans, as well as Neandertals, and show that branch length variation amongst human Y chromosomes cannot solely be explained by differences in demographic or biological processes. Instead, reference bias results in mutations being missed on Y chromosomes that are highly diverged from the reference used for alignment. We show that masking fast-evolving, highly divergent regions of the human Y chromosome mitigates the effect of this bias and enables more accurate determination of branch lengths in the Y chromosome phylogeny.<br><br>CONCLUSION: We show that our approach allows us to estimate the age of ancient samples from Y chromosome sequence data and provide updated estimates for the time to the most recent common ancestor using the portion of the Y chromosome where the effect of reference bias is minimized.}, }
@article {pmid39755798, year = {2025}, author = {Llanos-Lizcano, A and Hämmerle, M and Sperduti, A and Sawyer, S and Zagorc, B and Özdoğan, KT and Guellil, M and Cheronet, O and Kuhlwilm, M and Pinhasi, R and Gelabert, P}, title = {Intra-individual variability in ancient plasmodium DNA recovery highlights need for enhanced sampling.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {757}, pmid = {39755798}, issn = {2045-2322}, support = {P-36433//Austrian Science Fund (FWF)/ ; FW547002//Austrian Science Fund (FWF)/ ; ISID_2019//Infravec/ ; 10.47379/VRG20001//Vienna Science and Technology Fund/ ; }, mesh = {Humans ; *Plasmodium falciparum/genetics ; *DNA, Ancient/analysis ; *DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; Malaria, Falciparum/parasitology ; Genetic Variation ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Malaria has been a leading cause of death in human populations for centuries and remains a major public health challenge in African countries, especially affecting children. Among the five Plasmodium species infecting humans, Plasmodium falciparum is the most lethal. Ancient DNA research has provided key insights into the origins, evolution, and virulence of pathogens that affect humans. However, extensive screening of ancient skeletal remains for Plasmodium DNA has shown that such genomic material is rare, with no studies so far addressing potential intra-individual variability. Consequently, the pool of ancient mitochondrial DNA (mtDNA) or genomic sequences for P. falciparum is extremely limited, with fewer than 20 ancient sequences available for genetic analysis, and no complete P. falciparum mtDNA from Classical antiquity published to date. To investigate intra-individual diversity and genetic origins of P. falciparum from the Roman period, we generated 39 sequencing libraries from multiple teeth and two from the femur of a Roman malaria-infected individual. The results revealed considerable variability in P. falciparum recovery across different dental samples within the individual, while the femur samples showed no preservation of Plasmodium DNA. The reconstructed 43-fold P. falciparum mtDNA genome supports the hypothesis of an Indian origin for European P. falciparum and suggests mtDNA continuity in Europe over the past 2000 years.}, }
@article {pmid39755464, year = {2024}, author = {Chen, S and Xia, H and Chen, F}, title = {Paleogenomic research reintroduces extinct East Asian aurochs to our sights.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2024.12.028}, pmid = {39755464}, issn = {2095-9281}, }
@article {pmid39747910, year = {2025}, author = {Gelabert, P and Oberreiter, V and Straus, LG and Morales, MRG and Sawyer, S and Marín-Arroyo, AB and Geiling, JM and Exler, F and Brueck, F and Franz, S and Cano, FT and Szedlacsek, S and Zelger, E and Hämmerle, M and Zagorc, B and Llanos-Lizcano, A and Cheronet, O and Tejero, JM and Rattei, T and Kraemer, SM and Pinhasi, R}, title = {A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {107}, pmid = {39747910}, issn = {2041-1723}, mesh = {Spain ; Humans ; *DNA, Ancient/analysis ; Animals ; *Caves ; *Fossils ; *Neanderthals/genetics ; Archaeology ; Phylogeny ; Carnivora/genetics ; DNA, Mitochondrial/genetics ; Geologic Sediments ; History, Ancient ; }, abstract = {Caves are primary sites for studying human and animal subsistence patterns and genetic ancestry throughout the Palaeolithic. Iberia served as a critical human and animal refugium in Europe during the Last Glacial Maximum (LGM), 26.5 to 19 thousand years before the present (cal kya). Therefore, it is a key location for understanding human and animal population dynamics during this event. We recover and analyse sedimentary ancient DNA (sedaDNA) data from the lower archaeological stratigraphic sequence of El Mirón Cave (Cantabria, Spain), encompassing the (1) Late Mousterian period, associated with Neanderthals, and (2) the Gravettian (c. 31.5 cal kya), Solutrean (c. 24.5-22 cal kya), and Initial Magdalenian (d. 21-20.5 cal kya) periods, associated with anatomically modern humans. We identify 28 animal taxa including humans. Fifteen of these taxa had not been identified from the archaeozoological (i.e., faunal) record, including the presence of hyenas in the Magdalenian. Additionally, we provide phylogenetic analyses on 70 sedaDNA mtDNA genomes of fauna including the densest Iberian Pleistocene sampling of C. lupus. Finally, we recover three human mtDNA sequences from the Solutrean levels. These sequences, along with published data, suggest mtDNA haplogroup continuity in Iberia throughout the Solutrean/Last Glacial Maximum period.}, }
@article {pmid39723543, year = {2024}, author = {Atmore, LM and van der Jagt, I and Boilard, A and Häberle, S and Blevis, R and Dierickx, K and Quinlan, LM and Orton, DC and Hufthammer, AK and Barrett, JH and Star, B}, title = {The Once and Future Fish: Assessing a Millennium of Atlantic Herring Exploitation Through Mixed-Stock Analysis and Ancient DNA.}, journal = {Global change biology}, volume = {30}, number = {12}, pages = {e70010}, pmid = {39723543}, issn = {1365-2486}, support = {951649//H2020 European Research Council/ ; 813383//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, mesh = {*DNA, Ancient/analysis ; Animals ; *Fishes/genetics ; *Polymorphism, Single Nucleotide ; *Fisheries ; Archaeology ; Europe ; }, abstract = {Small pelagic fish support profitable fisheries and are important for food security around the world. Yet, their sustainable management can be hindered by the indiscriminate impacts of simultaneous exploitation of fish from multiple distinct biological populations over extended periods of time. The quantification of such impacts is greatly facilitated by recently developed molecular tools-including diagnostic single nucleotide polymorphism (SNP) panels for mixed-stock analysis (MSA)-that can accurately detect the population identity of individual fish. However, the biological relevance of such tools over longer periods of time remains unknown. Here, we demonstrate that diagnostic SNP panels designed for contemporary MSA in Atlantic herring have a millennium-long biological relevance and applicability. We assign the population identity of ancient Atlantic herring specimens-obtained through famously profitable historic fisheries-up to 1300 years old from eight archaeological sites across Europe. Analyzing contemporary and ancient whole-genome data, we obtain evidence for the long-term mixed-stock exploitation of Atlantic herring. Despite such mixed-stock exploitation, we exclusively identify autumn-spawning herring amongst these archaeological remains, indicative of a specific biological availability or cultural preference for certain herring ecotypes in the past. Moreover, our results show that herring demographic patterns were relatively stable until the dramatic disruptions and stock collapses during the 20th century. We find small but significant reductions in genetic diversity over time, indicating long-term evolutionary consequences from 20th-century stock declines. The long-term applicability of diagnostic SNP panels underscores their biological relevance and cost-effective application for the genetic monitoring of herring stocks and highlights the utility of ancient DNA to obtain insights in herring ecology and population dynamics.}, }
@article {pmid39723349, year = {2025}, author = {Brandl, M and Martinez, MM and Hauzenberger, C and Filzmoser, P and Milić, B and Horejs, B}, title = {Unveiling Neolithic Economic Behavior: A Novel Approach to Chert Procurement at Çukuriçi Höyük, Western Anatolia.}, journal = {Journal of archaeological method and theory}, volume = {32}, number = {1}, pages = {16}, pmid = {39723349}, issn = {1573-7764}, abstract = {UNLABELLED: The expansion of the Neolithic way of life triggered the most profound changes in peoples' socioeconomic behaviors, including how critical resources for everyday life were managed. Recent research spearheaded by ancient DNA analysis has greatly contributed to our understanding of the main direction of Neolithisation spreading from western Anatolia into central Europe. Due to the diverse processes involved in Neolithisation, which resulted in a high diversity of regional and local phenomena, the underlying mechanisms of these developments are still largely unexplored. One of these mechanisms is economic behavior and resource management. Neolithic economic behavior is the result of social processes involving the physical actions of the procurement, processing, use, discard, and distribution of raw materials as well as finished products for utilitarian needs and to create and maintain social relations. Within this continuum, the key for tracing meaningful behavioral patterns is the identification of raw material procurement. Since stone tools are among the most ubiquitous and stable finds at Neolithic sites, they are ideally suited for this endeavor. Here, we present the results of a case study from the Neolithic site of Çukuriçi Höyük in western Anatolia tracing lithic raw material procurement. We employ a novel approach using geochemical provenance analyses coupled with quantitative technological and econometric methods. The key finding of this diachronic study covering almost 700 years revealed patterns of socioeconomic dynamics undetectable through conventional analytical approaches. We demonstrate that technological concepts fluctuate over time and are subject to innovations, whereas raw material procurement remains a stable element.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10816-024-09681-6.}, }
@article {pmid39715432, year = {2025}, author = {Quilter, J and Harkins, K and Fanco Jordan, R and Marsh, E and Prieto, G and Verano, J and LeBlanc, S and Broomandkhoshbacht, N and Krigbaum, J and Fehren-Schmitz, L}, title = {Family relations of Moche elite burials on the North Coast of Peru (~500 CE): Analyses of the Señora de Cao and relatives.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {1}, pages = {e2416321121}, pmid = {39715432}, issn = {1091-6490}, support = {NGS- HJ-142R-17//National Geographic Society (NGS)/ ; NGS-52945R-19//National Geographic Society (NGS)/ ; NGS-7844-05//National Geographic Society (NGS)/ ; NGS-7961-05//National Geographic Society (NGS)/ ; }, mesh = {Peru ; Humans ; *Burial/history ; Male ; *Archaeology ; Female ; Family Relations ; History, Medieval ; Family ; History, Ancient ; }, abstract = {The Moche archaeological culture flourished along Peru's North Coast between the 4th and 10th centuries CE and was characterized by a complex social hierarchy dominated by political and religious elites. Previous archaeological evidence suggests kinship was a key factor in maintaining political authority within Moche society. To test this hypothesis, we applied archaeological, genetic, and isotopic methods to examine familial relationships between six individuals, including the prominent Señora de Cao (~500 CE), buried together in a pyramid-like, painted temple, Huaca Cao Viejo, in the Chicama Valley, Peru. Our findings reveal that all six individuals were biologically related, with varying degrees of kinship. The Señora de Cao was interred with a sacrificed juvenile, identified as a possible niece, and at least one, and potentially two siblings and a grandparent in separate tombs nearby. One of the male siblings was accompanied in death by his sacrificed son. Isotopic analysis indicates that while most individuals had diets rich in maize and animal protein and spent their childhoods in or near the Chicama Valley, the sacrificed juvenile accompanying the Señora had a distinct diet and geographic origin. These results demonstrate that Moche elites were interred with family members, including some raised far from their parental homes. This supports the hypothesis that kinship was central to transmitting status and authority. Moreover, sacrificing family members to accompany deceased elites underscores the significance of ritual sacrifice in reinforcing familial ties and linking the deceased to both ancestors and the divine.}, }
@article {pmid39705165, year = {2024}, author = {Patin, E and Quintana-Murci, L}, title = {Tracing the Evolution of Human Immunity Through Ancient DNA.}, journal = {Annual review of immunology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-immunol-082323-024638}, pmid = {39705165}, issn = {1545-3278}, abstract = {Infections have imposed strong selection pressures throughout human evolution, making the study of natural selection's effects on immunity genes highly complementary to disease-focused research. This review discusses how ancient DNA studies, which have revolutionized evolutionary genetics, increase our understanding of the evolution of human immunity. These studies have shown that interbreeding between modern humans and Neanderthals or Denisovans has influenced present-day immune responses, particularly to viruses. Additionally, ancient genomics enables the tracking of how human immunity has evolved across cultural transitions, highlighting strong selection since the Bronze Age in Europe (<4,500 years) and potential genetic adaptations to epidemics raging during the Middle Ages and the European colonization of the Americas. Furthermore, ancient genomic studies suggest that the genetic risk for noninfectious immune disorders has gradually increased over millennia because alleles associated with increased risk for autoimmunity and inflammation once conferred resistance to infections. The challenge now is to extend these findings to diverse, non-European populations and to provide a more global understanding of the evolution of human immunity.}, }
@article {pmid39703808, year = {2024}, author = {Veselka, B and Reich, D and Capuzzo, G and Olalde, I and Callan, K and Zalzala, F and Altena, E and Goffette, Q and Ringbauer, H and van der Velde, H and Polet, C and Toussaint, M and Snoeck, C and Cattelain, L}, title = {Assembling Ancestors: the manipulation of Neolithic and Gallo-Roman skeletal remains from Pommerœul, Belgium.}, journal = {Antiquity}, volume = {98}, number = {402}, pages = {1576-1591}, pmid = {39703808}, issn = {0003-598X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; }, abstract = {The ancient cemetery of Pommerœul, Belgium, was classified as Gallo-Roman in the 1970s', yielding 76 cremation graves and one inhumation. However, subsequent radiocarbon analyses dated the inhumation to the Late Neolithic (4[th]-3[rd] millennium calBC). We report osteoarchaeological analysis indicating that the inhumation was composed of bones from multiple individuals, afterwards buried as "one". Ancient DNA analyses also finds evidence of multiple individuals and revealed another surprise: the cranium is post-Neolithic and genetically related to a pair of siblings from another Belgian Gallo-Roman site. This composite burial may have been created in Late Neolithic times, with Gallo-Romans adding the cranium, or alternatively the burial may have been fully assembled in the Gallo-Roman periods. This exceptional burial documents unexpected burial practices for both prehistoric and Roman times.}, }
@article {pmid39701966, year = {2024}, author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L}, title = {Unraveling the ancient fungal DNA from the Iceman gut.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1225}, pmid = {39701966}, issn = {1471-2164}, mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; }, abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).<br><br>METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.<br><br>RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.<br><br>CONCLUSION: We suggest that &#xd6;tzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.}, }
@article {pmid39698825, year = {2024}, author = {Shastry, V and Berg, JJ}, title = {Allele ages provide limited information about the strength of negative selection.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyae211}, pmid = {39698825}, issn = {1943-2631}, abstract = {For many problems in population genetics, it is useful to characterize the distribution of fitness effects (DFE) of de novo mutations among a certain class of sites. A DFE is typically estimated by fitting an observed site frequency spectrum (SFS) to an expected SFS given a hypothesized distribution of selection coefficients and demographic history. The development of tools to infer gene trees from haplotype alignments, along with ancient DNA resources, provides us with additional information about the frequency trajectories of segregating mutations. Here, we ask how useful this additional information is for learning about the DFE, using the joint distribution on allele frequency and age to summarize information about the trajectory. To this end, we introduce an accurate and efficient numerical method for computing the density on the age of a segregating variant found at a given sample frequency, given the strength of selection and an arbitrarily complex population size history. We then use this framework to show that the unconditional age distribution of negatively selected alleles is very closely approximated by re-weighting the neutral age distribution in terms of the negatively selected SFS, suggesting that allele ages provide little information about the DFE beyond that already contained in the present day frequency. To confirm this prediction, we extended the standard Poisson Random Field (PRF) method to incorporate the joint distribution of frequency and age in estimating selection coefficients, and test its performance using simulations. We find that when the full SFS is observed and the true allele ages are known, including ages in the estimation provides only small increases in the accuracy of estimated selection coefficients. However, if only sites with frequencies above a certain threshold are observed, then the true ages can provide substantial information about the selection coefficients, especially when the selection coefficient is large. When ages are estimated from haplotype data using state-of-the-art tools, uncertainty about the age abrogates most of the additional information in the fully observed SFS case, while the neutral prior assumed in these tools when estimating ages induces a downward bias in the case of the thresholded SFS.}, }
@article {pmid39697594, year = {2024}, author = {Wang, B and Hao, D and Xu, Y and Zhu, K and Wang, R and Yang, X and Shen, Q and Xu, M and Bai, T and Ma, H and Zheng, J and Wang, X and Zou, X and Zhou, H and Mao, X and Tang, J and Peng, Y and Tao, L and He, H and Chen, H and Guo, J and Ji, Z and Liu, Y and Wen, S and Jin, L and Zhang, Q and Wang, CC}, title = {Population expansion from central plain to northern coastal China inferred from ancient human genomes.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111405}, pmid = {39697594}, issn = {2589-0042}, abstract = {The population history of the northern coastal Chinese is largely unknown due to the lack of ancient human genomes from the Neolithic to historical periods. In this study, we reported 14 newly generated ancient genomes from Linzi, one of China's densely populated and economically prosperous cities from the Zhou to Han Dynasties. The ancient samples in this study were dated to the Warring States period to the Eastern Han Dynasty (∼2,000 BP). We found the samples derived all their ancestry from Late Bronze Age to Iron Age Middle Yellow River farmers rather than local Neolithic populations. They were genetically homogeneous with present-day Han Chinese of Shandong, suggesting 2,000 years of genetic stability. Our results highlight the role of the eastward migration of Yellow River farmers in the Central Plain to northern coastal China in forming the present-day genetic structure of Han Chinese.}, }
@article {pmid39697469, year = {2024}, author = {Owsley, DW and Bruwelheide, KS and Harney, &#xc9; and Mallick, S and Rohland, N and Olalde, I and Barca, KG and Ramsey, AJ and Hull-Walski, DA and Kelso, WM and May, JE and Broomandkhoshbacht, N and Ferry, M and Lawson, AM and Michel, M and Oppenheimer, J and Stewardson, K and Zalzala, F and Simon, VE and Givens, DM and Lavin, MD and Reich, DE}, title = {Historical and Archaeogenomic Identification of High-Status Englishmen at Jamestown, Virginia.}, journal = {Antiquity}, volume = {98}, number = {400}, pages = {1040-1054}, pmid = {39697469}, issn = {0003-598X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; }, abstract = {Ancient DNA (aDNA) data are reported for two human skeletons buried within the chancel of the 1608-1616 church at the North American colonial settlement of Jamestown, Virginia. The men are suspected kinsmen of the colony's first Governor, Thomas West, 3[rd] Baron De La Warr based on archaeological, osteological, and documentary evidence. Genomic analyses of these men, Sir Ferdinando Wenman and Captain William West, identify a shared mitochondrial haplogroup, H10e, inferring maternal relatedness. In this unusual case, aDNA prompted further historical research that led to the discovery of illegitimacy, an aspect of identity omitted, likely intentionally, from genealogical records.}, }
@article {pmid39694065, year = {2024}, author = {Barquera, R and Sitter, TL and Kirkpatrick, CL and Ramirez, DA and Kocher, A and Spyrou, MA and Couoh, LR and Talavera-González, JA and Castro, M and von Hunnius, T and Guevara, EK and Hamilton, WD and Roberts, P and Scott, E and Fabra, M and Da Peña, GV and Pacheco, A and Rodriguez, M and Aspillaga, E and Tiliakou, A and Nelson, EA and Giffin, KL and Bianco, RA and Rohrlach, AB and de Los Ángeles García Martínez, M and Ballesteros Solís, FA and Sajantila, A and Saunders, SR and Nores, R and Herbig, A and Krause, J and Bos, KI}, title = {Ancient genomes reveal a deep history of treponemal disease in the Americas.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-024-08515-5}, pmid = {39694065}, issn = {1476-4687}, abstract = {Human treponemal infections are caused by a family of closely related Treponema pallidum that give rise to the diseases yaws, bejel, pinta and, most famously, syphilis[1]. Debates on both a common origin for these pathogens and the history of syphilis itself has weighed evidence for the "Columbian hypothesis"[2], which argues for an American origin, against that for the "pre-Columbian hypothesis"[3], which argues for presence of the disease in Eurasia in the Medieval period and possibly earlier. While molecular data has provided a genetic basis for distinction of the typed subspecies[4], deep evolution of the complex has remained unresolved due to limitations in the conclusions that can be drawn from the sparse paleogenomic data currently available. Here we explore this evolutionary history through analyses of five pre- and peri-contact ancient treponemal genomes from the Americas that represent ancient relatives of the T. pallidum pallidum (syphilis), T. pallidum pertenue (yaws) and T. pallidum endemicum (bejel) lineages. Our data indicate unexplored diversity and an emergence of T. pallidum that post-dates human occupation in the Americas. Together these results support an American origin for all T. pallidum characterized at the genomic level, both modern and ancient.}, }
@article {pmid39689706, year = {2025}, author = {Donegan, MA and Kahn, AK and Becker, N and Castillo Siri, A and Campos, PE and Boyer, K and Colwell, A and Briand, M and Almeida, RPP and Rieux, A}, title = {Century-old herbarium specimen provides insights into Pierce's disease of grapevines emergence in the Americas.}, journal = {Current biology : CB}, volume = {35}, number = {1}, pages = {145-153.e4}, doi = {10.1016/j.cub.2024.11.029}, pmid = {39689706}, issn = {1879-0445}, mesh = {*Vitis/microbiology/genetics ; *Plant Diseases/microbiology ; *Phylogeny ; *Xylella/genetics/pathogenicity ; Genome, Fungal ; }, abstract = {Fossils and other preserved specimens are integral for informing timing and evolutionary history in every biological system. By isolating a plant pathogen genome from herbarium-preserved diseased grapevine material from 1906 (Herb_1906), we were able to answer questions about an enigmatic system. The emergence of Pierce's disease (PD) of grapevine has shaped viticultural production in North America; yet, there are uncertainties about the geographic origin of the pathogen (Xylella fastidiosa subsp. fastidiosa, Xff) and the timing and route of its introduction. We produced a high-quality, de novo genome assembly of this historical plant pathogen and confirmed degradation patterns unique to ancient DNA. Due to the inclusion of the Herb_1906 sample, we were able to generate a significant temporal signal in the genomic data. This allowed us to build a time-calibrated phylogeny, where we estimate the introduction of Xff into the US between 1734 and 1741 CE, an earlier time frame than previously inferred. In a large collection of >300 Xff genomes, the Herb_1906 sample was genetically most similar to a small population from Northern California but not basal to the entire Xff California clade. Based on phylogenetic placement and a phylogeographic reconstruction, our data support a single introduction of Xff into the Southeastern US from Central America, with multiple subsequent introductions into California.}, }
@article {pmid39677618, year = {2024}, author = {Yediay, FE and Kroonen, G and Sabatini, S and Frei, KM and Frank, AB and Pinotti, T and Wigman, A and Thorsø, R and Vimala, T and McColl, H and Moutafi, I and Altinkaya, I and Ramsøe, A and Gaunitz, C and Renaud, G and Martin, AM and Demeter, F and Scorrano, G and Canci, A and Fischer, P and Duyar, I and Serhal, C and Varzari, A and Türkteki, M and O'Shea, J and Rahmstorf, L and Polat, G and Atamtürk, D and Vinner, L and Omura, S and Matsumura, K and Cao, J and Valeur Seersholm, F and Morillo Leon, JM and Voutsaki, S and Orgeolet, R and Burke, B and Herrmann, NP and Recchia, G and Corazza, S and Borgna, E and Sampò, MC and Trucco, F and Pando, AP and Schjellerup Jørkov, ML and Courtaud, P and Peake, R and Bao, JFG and Parditka, G and Stenderup, J and Sjögren, KG and Staring, J and Olsen, L and Deyneko, IV and Pálfi, G and Aldana, PML and Burns, B and Paja, L and Mühlenbock, C and Cavazzuti, C and Cazzella, A and Lagia, A and Lambrinoudakis, V and Kolonas, L and Rambach, J and Sava, E and Agulnikov, S and Castañeda Fernández, V and Broné, M and Peña Romo, V and Molina González, F and Cámara Serrano, JA and Jiménez Brobeil, S and Nájera Molino, T and Rodríguez Ariza, MO and Galán Saulnier, C and González Martín, A and Cauwe, N and Mordant, C and Roscio, M and Staniaszek, L and Tafuri, MA and Yıldırım, T and Salzani, L and Sand Korneliussen, T and Moreno-Mayar, JV and Allentoft, ME and Sikora, M and Nielsen, R and Kristiansen, K and Willerslev, E}, title = {Ancient genomics support deep divergence between Eastern and Western Mediterranean Indo-European languages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39677618}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM153400/GM/NIGMS NIH HHS/United States ; }, abstract = {The Indo-European languages are among the most widely spoken in the world, yet their early diversification remains contentious[1-5]. It is widely accepted that the spread of this language family across Europe from the 5th millennium BP correlates with the expansion and diversification of steppe-related genetic ancestry from the onset of the Bronze Age[6,7]. However, multiple steppe-derived populations co-existed in Europe during this period, and it remains unclear how these populations diverged and which provided the demographic channels for the ancestral forms of the Italic, Celtic, Greek, and Armenian languages[8,9]. To investigate the ancestral histories of Indo-European-speaking groups in Southern Europe, we sequenced genomes from 314 ancient individuals from the Mediterranean and surrounding regions, spanning from 5,200 BP to 2,100 BP, and co-analysed these with published genome data. We additionally conducted strontium isotope analyses on 224 of these individuals. We find a deep east-west divide of steppe ancestry in Southern Europe during the Bronze Age. Specifically, we show that the arrival of steppe ancestry in Spain, France, and Italy was mediated by Bell Beaker (BB) populations of Western Europe, likely contributing to the emergence of the Italic and Celtic languages. In contrast, Armenian and Greek populations acquired steppe ancestry directly from Yamnaya groups of Eastern Europe. These results are consistent with the linguistic Italo-Celtic[10,11] and Graeco-Armenian[1,12,13] hypotheses accounting for the origins of most Mediterranean Indo-European languages of Classical Antiquity. Our findings thus align with specific linguistic divergence models for the Indo-European language family while contradicting others. This underlines the power of ancient DNA in uncovering prehistoric diversifications of human populations and language communities.}, }
@article {pmid39674265, year = {2024}, author = {Ravishankar, S and Perez, V and Davidson, R and Roca-Rada, X and Lan, D and Souilmi, Y and Llamas, B}, title = {Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39674265}, issn = {1477-4054}, support = {CE170100015//Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage/ ; GA204260//NHMRC SYNERGY/ ; //Australian Government Research Training Program Scholarship/ ; //Portuguese National Funds/ ; }, mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Sequence Analysis, DNA/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Workflow ; DNA Contamination ; }, abstract = {Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.}, }
@article {pmid39672950, year = {2024}, author = {Tournebize, R and Chikhi, L}, title = {Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {39672950}, issn = {2397-334X}, support = {ANR-10-LABX-25-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-25-01//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Genomic and ancient DNA data have revolutionized palaeoanthropology and our vision of human evolution, with indisputable landmarks like the sequencing of Neanderthal and Denisovan genomes. Yet, using genetic data to identify, date and quantify evolutionary events-such as ancient bottlenecks or admixture-is not straightforward, as inferences may depend on model assumptions. In the last two decades, the idea that Neanderthals and members of the Homo sapiens lineage interbred has gained momentum. From the status of unlikely theory, it has reached consensus among human evolutionary biologists. This theory is mainly supported by statistical approaches that depend on demographic models minimizing or ignoring population structure, despite its widespread occurrence and the fact that, when ignored, population structure can lead to the inference of spurious demographic events. We simulated genomic data under a structured and admixture-free model of human evolution, and found that all the tested admixture approaches identified long Neanderthal fragments in our simulated genomes and an admixture event that never took place. We also observed that several published admixture models failed to predict important empirical diversity or admixture statistics, and that we could identify several scenarios from our structured model that better predicted these statistics jointly. Using a simulated time series of ancient DNA, the structured scenarios could also predict the trajectory of the empirical D statistics. Our results suggest that models accounting for population structure are fundamental to improve our understanding of human evolution, and that admixture between Neanderthals and H. sapiens needs to be re-evaluated in the light of structured models. Beyond the Neanderthal case, we argue that ancient hybridization events, which are increasingly documented in many species, including with other hominins, may also benefit from such re-evaluation.}, }
@article {pmid39666807, year = {2024}, author = {Curry, A}, title = {Study reveals kinship among first modern humans in Europe.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6727}, pages = {1207}, doi = {10.1126/science.adv2424}, pmid = {39666807}, issn = {1095-9203}, mesh = {Humans ; Czech Republic ; *DNA, Ancient/analysis ; History, Ancient ; *Human Migration/history ; Pedigree ; Female ; Neanderthals/genetics ; Animals ; }, abstract = {Ancient DNA links people across hundreds of kilometers.}, }
@article {pmid39660047, year = {2024}, author = {Klapper, M and Stallforth, P}, title = {Accessing microbial natural products of the past.}, journal = {microLife}, volume = {5}, number = {}, pages = {uqae023}, pmid = {39660047}, issn = {2633-6693}, abstract = {Microbial natural products-low molecular weight compounds biosynthesized by microorganisms-form the foundation of important modern therapeutics, including antibiotics, immunomodulators, and anti-cancer agents. This perspective discusses and contrasts two emerging approaches for uncovering natural products of the past. On the one hand, ancestral sequence reconstruction allows recreating biosynthetic pathways that date back hundreds of millions of years. On the other hand, sequencing and de novo assembly of ancient DNA reveals the biosynthetic potential of ancient microbial communities up to 100 000 years. Together, these approaches unveil an otherwise hidden reservoir of functional and structural molecular diversity. They also offer new opportunities to study the biological function and evolution of these molecules within an archaeological context.}, }
@article {pmid39658639, year = {2024}, author = {Bergström, A and Fellows Yates, JA and Warinner, C}, title = {Ancient DNA data hold insights into past organisms and ecosystems - handle them with more care.}, journal = {Nature}, volume = {636}, number = {8042}, pages = {296-298}, pmid = {39658639}, issn = {1476-4687}, }
@article {pmid39658338, year = {2024}, author = {Simeone, CA and McNulty, MT and Gupta, Y and Genovese, G and Sampson, MG and Sanna-Cherchi, S and Friedman, DJ and Pollak, MR}, title = {The APOL1 p.N264K variant is co-inherited with the G2 kidney disease risk variant through a proximity recombination event.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkae290}, pmid = {39658338}, issn = {2160-1836}, abstract = {Black Americans are three to four times more likely to develop nondiabetic kidney disease than other populations. Exclusively found in people of recent African (AFR) ancestry, risk variants in Apolipoprotein L1 (APOL1) termed G1 and G2 contribute significantly to this increased susceptibility. Our group and others showed that a missense variant in APOL1, rs73885316 (p.N264K, "M1"), is remarkably protective against APOL1 kidney disease when co-inherited with the G2 risk allele. Since the distance between the M1 and G2 variants is only 367 base pairs, we initially suspected that two independent mutation events occurred to create non-risk M1-G0 and M1-G2 haplotypes. Here, we examined APOL1 haplotypes in individuals of AFR ancestry from the 1000 Genomes Project, the Nephrotic Syndrome Study Network (NEPTUNE), and an ancient individual from the Allen Ancient Genome Diversity Project to determine how the M1-G2 haplotype arose. We demonstrate that M1 most likely first appeared on a non-risk G0 haplotype, and that a subsequent recombination event bypassed strong recombination hotspots flanking APOL1 and occurred between p.N388Y389del on a G2 haplotype and M1 on a G0 haplotype to create the M1-G2 haplotype. Observing a recombination event within a small region between clinically relevant loci emphasizes the importance of studying the entire haplotype repertoire of a disease gene and the impact of haplotype backgrounds in disease susceptibility.}, }
@article {pmid39638089, year = {2024}, author = {Wang, L and Wang, Y and Sun, B and Zhang, D and Liang, G and Ma, P and Zhang, H and Li, C and Hu, X and Zhang, Q and Cui, Y}, title = {Ancient DNA reveals genetic exchange in the Hehuang valley in the context of demic diffusion during the Han dynasty.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.11.013}, pmid = {39638089}, issn = {1673-8527}, }
@article {pmid39637852, year = {2025}, author = {Ramos-Madrigal, J and Fritz, GJ and Schroeder, B and Smith, B and Sánchez-Barreiro, F and Carøe, C and Runge, AKW and Boer, S and McGrath, K and Vieira, FG and Liu, S and da Fonseca, RR and Guo, C and Zhang, G and Petersen, B and Sicheritz-Pontén, T and Gopalakrishnan, S and Gilbert, MTP and Wales, N}, title = {The genomic origin of early maize in eastern North America.}, journal = {Cell}, volume = {188}, number = {1}, pages = {33-43.e16}, doi = {10.1016/j.cell.2024.11.003}, pmid = {39637852}, issn = {1097-4172}, mesh = {*Zea mays/genetics ; *Genome, Plant ; North America ; Domestication ; Genomics ; Phylogeny ; Mexico ; Amylose/metabolism ; }, abstract = {Indigenous maize varieties from eastern North America have played an outsized role in breeding programs, yet their early origins are not fully understood. We generated paleogenomic data to reconstruct how maize first reached this region and how it was selected during the process. Genomic ancestry analyses reveal recurrent movements northward from different parts of Mexico, likely culminating in at least two dispersals from the US Southwest across the Great Plains to the Ozarks and beyond. We find that 1,000-year-old Ozark specimens carry a highly differentiated wx1 gene, which is involved in the synthesis of amylose, highlighting repeated selective pressures on the starch metabolic pathway throughout maize's domestication. This population shows a close affinity with the lineage that ultimately became the Northern Flints, a major contributor to modern commercial maize.}, }
@article {pmid39620136, year = {2024}, author = {Ellegaard, MR and Ebenesersdóttir, SS and Moore, KHS and Petersén, A and Vågene, &#xc5;J and Bieker, VC and Denham, SD and Cavalleri, GL and Gilbert, E and Werge, T and Hansen, TF and Kockum, I and Alfredsson, L and Olsson, T and Hovig, E and Gilbert, MTP and Stefánsson, K and Stenøien, HK and Helgason, A and Martin, MD}, title = {Corroborating written history with ancient DNA: The case of the Well-man described in an Old Norse saga.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111076}, pmid = {39620136}, issn = {2589-0042}, abstract = {The potential of ancient DNA analyses to provide independent sources of information about events in the historical record remains to be demonstrated. Here we apply palaeogenomic analysis to human remains excavated from a medieval well at the ruins of Sverresborg Castle in central Norway. In Sverris Saga, the Old Norse saga of King Sverre Sigurdsson, one passage details a 1197-CE raid on the castle and mentions a dead man thrown into the well. Radiocarbon dating supports that these are that individual's remains. We sequenced the Well-man's nuclear genome to 3.4× and compared it to Scandinavian populations, revealing he was closely related to inhabitants of southern Norway. This was surprising because King Sverre's defeated army was assumed to be recruited from parts of central Norway, whereas the raiders were from the south. The findings also indicate that the unique genetic drift seen in present-day southern Norwegians already existed 800 years ago.}, }
@article {pmid39613690, year = {2025}, author = {Gaul, E and Spyrou, MA}, title = {Historical plague pandemics: perspectives from ancient DNA.}, journal = {Trends in microbiology}, volume = {33}, number = {1}, pages = {7-10}, doi = {10.1016/j.tim.2024.10.008}, pmid = {39613690}, issn = {1878-4380}, mesh = {*Plague/history/microbiology/epidemiology ; *Yersinia pestis/genetics ; *DNA, Ancient/analysis ; Humans ; *Pandemics/history ; Evolution, Molecular ; Animals ; DNA, Bacterial/genetics ; History, Ancient ; }, abstract = {Ancient DNA research has provided important insights into the evolutionary history of Yersinia pestis during the historical plague pandemics. Future work should prioritise a more diversified approach to sampling, to ensure a broader understanding of the factors underlying pandemic onset, spread, and impact across different regions and hosts.}, }
@article {pmid39612613, year = {2024}, author = {Ferrando-Bernal, M and Brand, CM and Capra, JA}, title = {Inferring human phenotypes using ancient DNA: from molecules to populations.}, journal = {Current opinion in genetics &amp; development}, volume = {90}, number = {}, pages = {102283}, doi = {10.1016/j.gde.2024.102283}, pmid = {39612613}, issn = {1879-0380}, abstract = {The increasing availability of ancient DNA (aDNA) from human groups across space and time has yielded deep insights into the movements of our species. However, given the challenges of mapping from genotype to phenotype, aDNA has revealed less about the phenotypes of ancient individuals. In this review, we highlight recent advances in inferring ancient phenotypes - from the molecular to population scale - with a focus on applications enabled by new machine learning approaches. The genetic architecture of complex traits across human groups suggests that the prediction of individual-level complex traits, like behavior or disease risk, is often challenging across the relevant evolutionary distances. Thus, we propose an approach that integrates predictions of molecular phenotypes, whose mechanisms are more conserved, with nongenetic data.}, }
@article {pmid39606698, year = {2024}, author = {Zagorc, B and Blanz, M and Gelabert, P and Sawyer, S and Oberreiter, V and Cheronet, O and Chen, HS and Carić, M and Visković, E and Olalde, I and Ivanova-Bieg, M and Novak, M and Reich, D and Pinhasi, R}, title = {Bioarchaeological Perspectives on Late Antiquity in Dalmatia: Paleogenetic, Dietary, and Population Studies of the Hvar - Radošević burial site.}, journal = {Archaeological and anthropological sciences}, volume = {16}, number = {9}, pages = {150}, pmid = {39606698}, issn = {1866-9557}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {Late Antiquity Dalmatia was a time and place of political unrest in the Roman Empire that influenced the lives of those in that region. The Late Antique burial site of Hvar - Radošević, spanning the 3[rd] to 5[th] centuries CE, is located on the Croatian Dalmatian island of Hvar. Given the time frame and location on a busy marine trade route, the study of this burial site offers us a glimpse into the lives of the Late Antique population living on this island. It comprises 33 individuals, with 17 buried within a confined grave tomb and the remaining individuals buried in separate locations in the tomb's proximity. The study aims to provide a new perspective on the lives of people on the island during those times by studying ancestry, population structure, possible differences within the buried population, dietary habits, and general health. The genetic analysis of the ancestral origins of the individuals buried at Hvar - Radošević revealed a diverse population reflective of the era's genetic variability. The identification of genetic outliers suggests a range of ancestries from distinct regions of the Roman Empire, possibly linked to trade routes associated with the Late Antique port in ancient Hvar. Stable isotope ratio analysis (δ[13]C and δ[15]N) indicated a diet mainly consisting of C3 plants, with minimal consumption of marine foods. High childhood mortality rates, physiological stress markers, and dental diseases suggest a low quality of life in the population. Assessment of kinship and dietary patterns revealed no discernible distinctions between individuals buried within the tomb and those buried outside, indicative of an absence of differential burial practices based on social status and familial ties among this specific buried population.}, }
@article {pmid39592000, year = {2024}, author = {Martínez-García, L and Pulido, A and Ferrari, G and Hufthammer, AK and Vedeler, M and Hirons, A and Kneale, C and Barrett, JH and Star, B}, title = {Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2035}, pages = {20242019}, pmid = {39592000}, issn = {1471-2954}, support = {//European Union's Horizon 2020 Research and Innovation Programme under the Marie Sk&#x142;odowska-Curie grant agreement, SeaChanges/ ; //Research Council of Norway projects 'FOODIMPACT'/ ; //4-OCEANS Synergy grant agreement/ ; }, mesh = {*Gadus morhua/genetics ; *DNA, Ancient/analysis ; Norway ; Animals ; History, Medieval ; Carbon Isotopes/analysis ; Fisheries ; Nitrogen Isotopes/analysis ; Archaeology ; History, 17th Century ; }, abstract = {Marine resources have been important for the survival and economic development of coastal human communities across northern Europe for millennia. Knowledge of the origin of such historic resources can provide key insights into fishing practices and the spatial extent of trade networks. Here, we combine ancient DNA and stable isotopes (δ[13]C, δ[15]N, non-exchangeable δ[2]H and δ[34]S) to investigate the geographical origin of archaeological cod remains in Oslo from the eleventh to seventeenth centuries CE. Our findings provide genetic evidence that Atlantic cod was obtained from different geographical populations, including a variety of distant-water populations like northern Norway and possibly Iceland. Evidence for such long-distance cod trade is already observed from the eleventh century, contrasting with archaeological and historical evidence from Britain and other areas of Continental Europe around the North and Baltic Seas, where such trade increased during the thirteenth to fourteenth centuries. The genomic assignments of specimens to different populations coincide with significantly different δ[13]C values between those same specimens, indicating that multiple Atlantic cod populations living in different environments were exploited. This research provides novel information about the exploitation timeline of specific Atlantic cod stocks and highlights the utility of combining ancient DNA (aDNA) methods and stable isotope analysis to describe the development of medieval and post-medieval marine fisheries.}, }
@article {pmid39586186, year = {2025}, author = {Zavala, EI and Rohlfs, RV and Moorjani, P}, title = {Benchmarking for genotyping and imputation using degraded DNA for forensic applications across diverse populations.}, journal = {Forensic science international. Genetics}, volume = {75}, number = {}, pages = {103177}, doi = {10.1016/j.fsigen.2024.103177}, pmid = {39586186}, issn = {1878-0326}, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *Benchmarking ; *Genotyping Techniques/standards/methods ; *High-Throughput Nucleotide Sequencing ; *DNA Degradation, Necrotic ; *Genotype ; Genetics, Population ; DNA Fingerprinting/methods ; Sequence Analysis, DNA ; Forensic Genetics/methods ; Software ; DNA/genetics ; }, abstract = {Advancements in sequencing and laboratory technologies have enabled forensic genetic analysis on increasingly low quality and degraded DNA samples. However, existing computational methods applied to genotyping and imputation for generating DNA profiles from degraded DNA have not been tested for forensic applications. Here we simulated sequencing data of varying qualities-coverage, fragment lengths, and deamination patterns-from forty individuals of diverse genetic ancestries. We used this dataset to test the performance of commonly used genotype and imputation methods (SAMtools, GATK, ATLAS, Beagle, and GLIMPSE) on five different SNP panels (MPS-plex, FORCE, two extended kinship panels, and the Human Origins array) that are used for forensic and population genetics applications. For genome mapping and variant calling with degraded DNA, we find use of parameters and methods (such as ATLAS) developed for ancient DNA analysis provides a marked improvement over conventional standards used for next generation sequencing analysis. We find that ATLAS outperforms GATK and SAMtools, achieving over 90 % genotyping accuracy for the four largest SNP panels with coverages greater than 10X. For lower coverages, decreased concordance rates are correlated with increased rates of heterozygosity. Genotype refinement and imputation improve the accuracy at lower coverages by leveraging population reference data. For all five SNP panels, we find that using a population reference panel representative of worldwide populations (e.g., the 1000 Genomes Project) results in increased genotype accuracies across genetic ancestries, compared to ancestry-matched population reference panels. Importantly, we find that the low SNP density of commonly used forensics SNP panels can impact the reliability and performance of genotype refinement and imputation. This highlights a critical trade-off between enhancing privacy by using panels with fewer SNPs and maintaining the effectiveness of genomic tools. We provide benchmarks and recommendations for analyzing degraded DNA from diverse populations with widely used genomic methods in forensic casework.}, }
@article {pmid39584937, year = {2024}, author = {Bragazzi, NL and Lehr, T}, title = {Big Epidemiology: The Birth, Life, Death, and Resurgence of Diseases on a Global Timescale.}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {5}, number = {4}, pages = {669-691}, pmid = {39584937}, issn = {2673-3986}, abstract = {Big Epidemiology represents an innovative framework that extends the interdisciplinary approach of Big History to understand disease patterns, causes, and effects across human history on a global scale. This comprehensive methodology integrates epidemiology, genetics, environmental science, sociology, history, and data science to address contemporary and future public health challenges through a broad historical and societal lens. The foundational research agenda involves mapping the historical occurrence of diseases and their impact on societies over time, utilizing archeological findings, biological data, and historical records. By analyzing skeletal remains, ancient DNA, and artifacts, researchers can trace the origins and spread of diseases, such as Yersinia pestis in the Black Death. Historical documents, including chronicles and medical treatises, provide contextual narratives and quantitative data on past disease outbreaks, societal responses, and disruptions. Modern genetic studies reveal the evolution and migration patterns of pathogens and human adaptations to diseases, offering insights into co-evolutionary dynamics. This integrative approach allows for temporal and spatial mapping of disease patterns, linking them to social upheavals, population changes, and economic transformations. Big Epidemiology also examines the roles of environmental changes and socioeconomic factors in disease emergence and re-emergence, incorporating climate science, urban development, and economic history to inform public health strategies. The framework reviews historical and contemporary policy responses to pandemics, aiming to enhance future global health governance. By addressing ethical, legal, and societal implications, Big Epidemiology seeks to ensure responsible and effective epidemiological research and interventions. This approach aims to profoundly impact how we understand, prevent, and respond to diseases, leveraging historical perspectives to enrich modern scientific inquiry and global public health strategies.}, }
@article {pmid39577594, year = {2024}, author = {Majewski, W and Szczuciński, W and Pawłowska, J and Szymczak-Żyła, M and Lubecki, L and Niedzielski, P}, title = {Environmental degradation and recovery after termination of whaling in sub-Antarctic fjord, South Georgia.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177536}, doi = {10.1016/j.scitotenv.2024.177536}, pmid = {39577594}, issn = {1879-1026}, mesh = {Antarctic Regions ; *Estuaries ; *Geologic Sediments/chemistry ; *Environmental Monitoring ; Ecosystem ; Water Pollutants, Chemical/analysis ; }, abstract = {Polar ecosystems are considered very fragile, however, due to the short observation record it is hard to assess the recovery processes of the coastal and fjord environments after a major disturbance. Here, we provide a unique case study from South Georgia (sub-Antarctic), an area seriously affected by the whaling industry. The study focuses on King Edward Cove, serving as a sheltered harbor for the former whaling station at Grytviken, as well as other parts of Cumberland Bay considered to represent generally pristine areas. We studied [210]Pb dated sediment cores, which were subjected to analysis of sediment geochemical composition, concentrations of anthropogenic organic markers and biomarkers, foraminiferal assemblage changes, as well as sedimentary ancient DNA. Three distinct phases have been identified. The oldest one, predating ca. 1970, recorded the whaling period, and was characterized by anoxic conditions, high organic carbon content, contamination with heavy metals, organic markers, distinct DNA signature and lack of foraminiferal microfossils. It took only a few years to establish a new ecosystem with a fully developed foraminiferal assemblage and decreased contamination characteristic for the middle phase (ca. 1970-2000). Ancient DNA suggests macro-zoobenthic recovery being delayed by a several years in comparison to benthic foraminifera. In the youngest period, around Cumberland Bay, the increase of iceberg rafted debris from rapidly retreating tidewater glaciers was noted, while the improved oxygen availability in bottom waters in King Edward Cove can be likely ascribed to frequent water mixing due to increasing traffic of large cruise vessels. The recorded pace of ecosystem recovery from major anthropogenic disturbance appears similar to that observed in the temperate fjords from the Northern Hemisphere, however, the effects of new anthropogenic threat and the ongoing climate change are already resulting in the new ecosystem disturbance.}, }
@article {pmid39567978, year = {2024}, author = {Ravasini, F and Kabral, H and Solnik, A and de Gennaro, L and Montinaro, F and Hui, R and Delpino, C and Finocchi, S and Giroldini, P and Mei, O and Beck De Lotto, MA and Cilli, E and Hajiesmaeil, M and Pistacchia, L and Risi, F and Giacometti, C and Scheib, CL and Tambets, K and Metspalu, M and Cruciani, F and D'Atanasio, E and Trombetta, B}, title = {The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {292}, pmid = {39567978}, issn = {1474-760X}, mesh = {Italy ; Humans ; History, Ancient ; *Roman World/history ; DNA, Ancient/analysis ; Genome, Human ; Ethnicity/genetics ; Genetics, Population ; Genomics ; }, abstract = {BACKGROUND: The Italic Iron Age is characterized by the presence of various ethnic groups partially examined from a genomic perspective. To explore the evolution of Iron Age Italic populations and the genetic impact of Romanization, we focus on the Picenes, one of the most fascinating pre-Roman civilizations, who flourished on the Middle Adriatic side of Central Italy between the 9[th] and the 3[rd] century BCE, until the Roman colonization.<br><br>RESULTS: More than 50 samples are reported, spanning more than 1000&#xa0;years of history from the Iron Age to Late Antiquity. Despite cultural diversity, our analysis reveals no major differences between the Picenes and other coeval populations, suggesting a shared genetic history of the Central Italian Iron Age ethnic groups. Nevertheless, a slight genetic differentiation between populations along the Adriatic and Tyrrhenian coasts can be observed, possibly due to different population dynamics in the two sides of Italy and/or genetic contacts across the Adriatic Sea. Additionally, we identify several individuals with ancestries deviating from their general population. Lastly, in our Late Antiquity site, we observe a drastic change in the genetic landscape of the Middle Adriatic region, indicating a relevant influx from the Near East, possibly as a consequence of Romanization.<br><br>CONCLUSIONS: Our findings, consistently with archeological hypotheses, suggest genetic interactions across the Adriatic Sea during the Bronze/Iron Age and a high level of individual mobility typical of cosmopolitan societies. Finally, we highlight the role of the Roman Empire in shaping genetic and phenotypic changes that greatly impact the Italian peninsula.}, }
@article {pmid39567925, year = {2024}, author = {Lv, M and Ma, H and Wang, R and Li, H and Zhang, X and Zhang, W and Zeng, Y and Qin, Z and Zhai, H and Lou, Y and Lin, Y and Tao, L and He, H and Yang, X and Zhu, K and Zhou, Y and Wang, CC}, title = {Ancient genomes from the Tang Dynasty capital reveal the genetic legacy of trans-Eurasian communication at the eastern end of Silk Road.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {267}, pmid = {39567925}, issn = {1741-7007}, mesh = {Humans ; China ; *Genome, Human ; DNA, Ancient/analysis ; History, Ancient ; Asian People/genetics ; Gene Flow ; Genetic Variation ; Human Migration/history ; }, abstract = {BACKGROUND: Ancient Chang'an in the Tang Dynasty (618-907 AD) was one of the world's largest and most populated cities and acted as the eastern end of the world-famous Silk Road. However, little is known about the genetics of Chang'an people and whether the Western Regions-related gene flows have been prevalent in this cosmopolitan city.<br><br>RESULTS: Here, we present seven genomes from Xingfulindai (XFLD) sites dating to the Tang Dynasty in Chang'an. We observed that four of seven XFLD individuals (XFLD_1) were genetically homogenous with the Late Neolithic Wadian, Pingliangtai, and Haojiatai populations from the middle reaches of the Yellow River Basin (YR_LN), with no genetic influence from the Western Eurasian or other non-Yellow River-related lineages. The remaining three XFLD individuals were a mixture of YR_LN-related ancestry and&#x2009;~&#x2009;3-15% Western Eurasian-related ancestry. Mixtures of XFLD_1 and Western Eurasian-related ancestry drove the main gradient of genetic variation in northern and central Shaanxi Province today.<br><br>CONCLUSIONS: Our study underlined the widespread distribution of the YR_LN-related ancestry alongside the Silk Road within the territory of China during the historical era and provided direct evidence of trans-Eurasian communication in Chang'an from a genetic perspective.}, }
@article {pmid39567757, year = {2025}, author = {Mathov, Y and Nissim-Rafinia, M and Leibson, C and Galun, N and Marques-Bonet, T and Kandel, A and Liebergal, M and Meshorer, E and Carmel, L}, title = {Inferring DNA methylation in non-skeletal tissues of ancient specimens.}, journal = {Nature ecology &amp; evolution}, volume = {9}, number = {1}, pages = {153-165}, pmid = {39567757}, issn = {2397-334X}, support = {R01 HG010898/HG/NHGRI NIH HHS/United States ; 61739//John Templeton Foundation (JTF)/ ; }, mesh = {*DNA Methylation ; Humans ; *DNA, Ancient/analysis ; Algorithms ; Animals ; Fossils ; }, abstract = {Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes.}, }
@article {pmid39532856, year = {2024}, author = {Pandey, D and Harris, M and Garud, NR and Narasimhan, VM}, title = {Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9772}, pmid = {39532856}, issn = {2041-1723}, mesh = {*DNA, Ancient/analysis ; *Selection, Genetic ; Humans ; Europe ; *Genetic Drift ; *Gene Frequency ; Haplotypes/genetics ; Animals ; Lactase/genetics ; Genetics, Population/methods ; Evolution, Molecular ; Genotype ; }, abstract = {Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture.}, }
@article {pmid39515325, year = {2024}, author = {Pilli, E and Vai, S and Moses, VC and Morelli, S and Lari, M and Modi, A and Diroma, MA and Amoretti, V and Zuchtriegel, G and Osanna, M and Kennett, DJ and George, RJ and Krigbaum, J and Rohland, N and Mallick, S and Caramelli, D and Reich, D and Mittnik, A}, title = {Ancient DNA challenges prevailing interpretations of the Pompeii plaster casts.}, journal = {Current biology : CB}, volume = {34}, number = {22}, pages = {5307-5318.e7}, pmid = {39515325}, issn = {1879-0445}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient/analysis ; Male ; Female ; History, Ancient ; Archaeology ; Roman World/history ; Adult ; }, abstract = {The eruption of Somma-Vesuvius in 79 CE buried several nearby Roman towns, killing the inhabitants and burying under pumice lapilli and ash deposits a unique set of civil and private buildings, monuments, sculptures, paintings, and mosaics that provide a rich picture of life in the empire. The eruption also preserved the forms of many of the dying as the ash compacted around their bodies. Although the soft tissue decayed, the outlines of the bodies remained and were recovered by excavators centuries later by filling the cavities with plaster. From skeletal material embedded in the casts, we generated genome-wide ancient DNA and strontium isotopic data to characterize the genetic relationships, sex, ancestry, and mobility of five individuals. We show that the individuals' sexes and family relationships do not match traditional interpretations, exemplifying how modern assumptions about gendered behaviors may not be reliable lenses through which to view data from the past. For example, an adult wearing a golden bracelet with a child on their lap-often interpreted as mother and child-is genetically an adult male biologically unrelated to the child. Similarly, a pair of individuals who were thought to have died in an embrace-often interpreted as sisters-included at least one genetic male. All Pompeiians with genome-wide data consistently derive their ancestry largely from recent immigrants from the eastern Mediterranean, as has also been seen in contemporaneous ancient genomes from the city of Rome, underscoring the cosmopolitanism of the Roman Empire in this period.}, }
@article {pmid39514086, year = {2024}, author = {Geršak, &#x17d;M and Golob, A and Kravanja, P and Concato, M and Leskovar, T and Pajnič, IZ}, title = {Patellae as a source of DNA in forensic and archaeological analysis.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {39514086}, issn = {1437-1596}, support = {J3-3080//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, abstract = {Analysing genetic material from skeletonised human remains has become valuable in forensic and archaeological contexts. While the petrous bone is often preferred for DNA extraction, its availability is not guaranteed, and because of destructive sampling, it is not frequently used in forensic cases. This study explores the potential of patellae as an alternative source of bone material for genetic investigations. Forty-five patellae were sampled from a post-World War II mass grave and an archaeological Christian cemetery dated from the 13th to 19th centuries. A full demineralisation extraction method was used to obtain the DNA, and real-time PCR quantification was used to determine the quantity and quality of DNA. To evaluate the suitability of patellae for forensic and archaeological analyses, short tandem repeat (STR) typing was performed using the ESI17 Fast PCR amplification kit (Promega). To explore the difference in DNA yield, DNA degradation and STR typing success between the post-World War II and archaeological patellae, statistical analysis was performed. The results revealed significantly higher DNA yield and STR typing success in WWII patellae and higher degradation of DNA in archaeological patellae, highlighting the impact of environmental exposure time on genetic material preservation. Almost all WWII patellae achieved a high success rate in STR typing with full profiles generated. More than half of the archaeological patellae showed high STR typing performance and highly informative partial profiles were obtained, indicating the suitability of patellae not only for forensic purposes but also for archaeological genetic analyses.}, }
@article {pmid39509486, year = {2024}, author = {Chandrashekhar, V}, title = {India looks to ancient DNA to track migrations.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6722}, pages = {607}, doi = {10.1126/science.adu4090}, pmid = {39509486}, issn = {1095-9203}, mesh = {Humans ; Bone and Bones ; *DNA, Ancient/analysis ; *Human Migration/history ; India ; *South Asian People/history ; }, abstract = {Findings from analyses of human bones could be politically sensitive.}, }
@article {pmid39500721, year = {2024}, author = {Hong, JH and Fujita, H and Kim, J and Shin, DH}, title = {Cost-effectiveness and other considerations for different research techniques applied in ancient DNA analysis.}, journal = {Anatomy &amp; cell biology}, volume = {}, number = {}, pages = {}, doi = {10.5115/acb.24.125}, pmid = {39500721}, issn = {2093-3665}, abstract = {Ancient DNA (aDNA) analysis has developed rapidly since it first emerged in the 1980s, becoming an almost indispensable tool in anthropological and archaeological sciences. Earlier aDNA study was based on the polymerase chain reaction (PCR) technique, with which, unfortunately, modern DNA contamination and other authenticity issues were often incurred. These technical hurdles were soon overcome by application of advancements in the forms of the next generation sequencing (NGS) technique and others. However, since NGS requires money, time, and, in the case of large projects, manpower as well, genetic analysis of some ancient samples considered to be insignificant is commonly delayed or, in the worst cases, neglected entirely. We acknowledge that as a diagnostic tool in aDNA analysis, PCR is less accurate than NGS and more easily affected by modern DNA contamination; but it also has advantages, such as simplicity, time-saving, and greater ease of interpretation, among others. The role of PCR in aDNA analysis, then, should be reconsidered.}, }
@article {pmid39493412, year = {2024}, author = {Sedig, J and Snow, M and Searcy, M and Diaz, JLP and LeBlanc, S and Ramos, F and Eccles, L and Reich, D}, title = {High levels of consanguinity in a child from Paquimé, Chihuahua, Mexico.}, journal = {Antiquity}, volume = {98}, number = {400}, pages = {1023-1039}, pmid = {39493412}, issn = {0003-598X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {This study reports results from the ancient DNA analysis of a unique child burial at Paquimé, northern Chihuahua, Mexico. Located between Mesoamerican and Ancestral Puebloan groups, Paquimé (also known as Casas Grandes) was a vibrant multicultural centre during the 13th-14th centuries AD. Archaeologists have long debated Paquimé's social organization. Our analysis of Burial 23-8 has revealed that this child, placed under the centre post of an important room, had parents who were close genetic relatives. We argue that this child's consanguinity and special depositional context resulted from an elite family's practice of aggrandizing social status.}, }
@article {pmid39481771, year = {2025}, author = {Brambilla, L and Ibarra, DA and Barboza, MC and Bresso, EG and Rosano, G and Pérez, G and Straccia, P and Scian, RD and Brun, LR}, title = {Mitochondrial genome of Neuryurus rudis (Xenarthra, Cingulata); contribution to phylogeny and origin of glyptodonts.}, journal = {Gene}, volume = {936}, number = {}, pages = {149059}, doi = {10.1016/j.gene.2024.149059}, pmid = {39481771}, issn = {1879-0038}, mesh = {*Phylogeny ; Animals ; *Genome, Mitochondrial ; Evolution, Molecular ; Xenarthra/genetics/classification ; Fossils ; DNA, Mitochondrial/genetics ; Armadillos/genetics ; }, abstract = {The remarkable glyptodonts have sparked the interest of evolutionary biologists since the 19th century, in their attempts to elucidate the phylogenetic relationships among the various species of these armored giants and their relationship with other xenarthrans. In recent years, the molecular analysis of the first glyptodont has included them within the cingulates, as a special group of armadillos that lost the mobility of the bands of their armor during their evolutionary history. In this research, we obtained the mitochondrial DNA sequence of the elusive and poorly known glyptodont Neuryurus rudis, inferring its phylogenetic position with respect to the glyptodont Doedicurus sp. and extant armadillos. This study reaffirms glyptodonts as a subgroup of cingulates, with Neuryurus and Doedicurus sharing a common ancestor from the late Oligocene or early Miocene and traces the group's origin back to an armadillo ancestor in the Eocene.}, }
@article {pmid39478221, year = {2024}, author = {Ghalichi, A and Reinhold, S and Rohrlach, AB and Kalmykov, AA and Childebayeva, A and Yu, H and Aron, F and Semerau, L and Bastert-Lamprichs, K and Belinskiy, AB and Berezina, NY and Berezin, YB and Broomandkhoshbacht, N and Buzhilova, AP and Erlikh, VR and Fehren-Schmitz, L and Gambashidze, I and Kantorovich, AR and Kolesnichenko, KB and Lordkipanidze, D and Magomedov, RG and Malek-Custodis, K and Mariaschk, D and Maslov, VE and Mkrtchyan, L and Nagler, A and Fazeli Nashli, H and Ochir, M and Piotrovskiy, YY and Saribekyan, M and Sheremetev, AG and Stöllner, T and Thomalsky, J and Vardanyan, B and Posth, C and Krause, J and Warinner, C and Hansen, S and Haak, W}, title = {The rise and transformation of Bronze Age pastoralists in the Caucasus.}, journal = {Nature}, volume = {635}, number = {8040}, pages = {917-925}, pmid = {39478221}, issn = {1476-4687}, mesh = {*Agriculture/history ; *Archaeology ; Eastern European People/genetics ; *Farmers/history ; *Gene Flow ; *Genetics, Population ; *Genome, Human/genetics ; Genomics ; Georgia (Republic)/ethnology ; *Grassland ; History, Ancient ; Human Migration/history ; Hunting/history ; Russia/ethnology ; West Asian People/genetics ; }, abstract = {The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age[1] and the birthplace of the earliest steppe pastoralist societies[2]. Yet, despite this region having a large influence on the subsequent development of Europe and Asia, questions remain regarding its hunter-gatherer past and its formation of expansionist mobile steppe societies[3-5]. Here we present new genome-wide data for 131 individuals from 38 archaeological sites spanning 6,000 years. We find a strong genetic differentiation between populations north and south of the Caucasus mountains during the Mesolithic, with Eastern hunter-gatherer ancestry[4,6] in the north, and a distinct Caucasus hunter-gatherer ancestry[7] with increasing East Anatolian farmer admixture in the south. During the subsequent Eneolithic period, we observe the formation of the characteristic West Eurasian steppe ancestry and heightened interaction between the mountain and steppe regions, facilitated by technological developments of the Maykop cultural complex[8]. By contrast, the peak of pastoralist activities and territorial expansions during the Early and Middle Bronze Age is characterized by long-term genetic stability. The Late Bronze Age marks another period of gene flow from multiple distinct sources that coincides with a decline of steppe cultures, followed by a transformation and absorption of the steppe ancestry into highland populations.}, }
@article {pmid39478147, year = {2024}, author = {Yavuz, OE and Oxilia, G and Silvestrini, S and Tassoni, L and Reiter, E and Drucker, DG and Talamo, S and Fontana, F and Benazzi, S and Posth, C}, title = {Biomolecular analysis of the Epigravettian human remains from Riparo Tagliente in northern Italy.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1415}, pmid = {39478147}, issn = {2399-3642}, mesh = {Italy ; Humans ; *Radiometric Dating ; Fossils ; Male ; Body Remains/chemistry ; Femur/chemistry/metabolism ; }, abstract = {The Epigravettian human remains from Riparo Tagliente in northern Italy represent some of the earliest evidence of human occupation in the southern Alpine slopes after the Last Glacial Maximum. Genomic analyses of the 17,000-year-old Tagliente 2 mandible revealed the oldest presence of a genetic profile with affinities to the Near East in the Italian peninsula, which later became the most widespread hunter-gatherer ancestry across Europe. However, a comparable biomolecular characterization of the Tagliente 1 burial remains unavailable, preventing us from defining its biological relationships with Tagliente 2. Here, we apply paleogenomic, isotopic, and radiocarbon dating analyses on a femur fragment of Tagliente 1 and compare the reconstructed data with previously reported results from Tagliente 2. Despite their different isotopic signatures and non-overlapping radiocarbon dates, we reveal that the two human remains belong to the same male individual. We determine that the distinct isotopic values can be explained by different dietary practices during lifetime, whereas the non-overlapping radiocarbon dates can be caused by minimal radiocarbon contamination, possibly deriving from chemical treatments for conservation purposes. These findings highlight the importance of interdisciplinary biomolecular studies in offering new perspectives on the Palaeolithic fossil record and addressing long-standing bioarchaeological questions.}, }
@article {pmid39468234, year = {2024}, author = {Słowakiewicz, M and Borkowski, A and Perri, E and Działak, P and Tagliasacchi, E and Gradziński, M and Kele, S and Reuning, L and Kibblewhite, T and Whitaker, F and Reid, RP and Tucker, ME}, title = {Biofilms in modern CaCO3-supersaturated freshwater environments reveal viral proxies.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25889}, pmid = {39468234}, issn = {2045-2322}, support = {2019/35/B/ST10/02190//Narodowe Centrum Nauki/ ; PLG/2023/016421//Akademia G&#xf3;rniczo-Hutnicza im. Stanislawa Staszica/ ; PLG/2023/016421//Akademia G&#xf3;rniczo-Hutnicza im. Stanislawa Staszica/ ; }, mesh = {*Biofilms/growth &amp; development ; *Fresh Water/microbiology/virology ; *Calcium Carbonate/metabolism/chemistry ; Geologic Sediments/microbiology/virology ; Viruses/genetics/metabolism ; Principal Component Analysis ; Metagenomics/methods ; }, abstract = {Biofilms are mucilaginous-organic layers produced by microbial activity including viruses. Growing biofilms form microbial mats which enhance sediment stability by binding particles with extracellular polymeric substances and promoting growth through nutrient cycling and organic matter accumulation. They preferentially develop at the sediment-water interface of both marine and non-marine environments, and upon the growing surfaces of modern tufa and travertine. In this context, however, little is known about the factors, environmental or anthropogenic, which affect viral communities in freshwater spring settings. To explore this issue, geochemical and metagenomic data were subjected to multidimensional analyses (Principal Component Analysis, Classical Multidimensional Scaling, Partial Least Squares analysis and cluster analysis based on beta-diversity), and these show that viral composition is specific and dependent on environment. Indeed, waters precipitating tufa and travertine do vary in their geochemistry with their viruses showing distinct variability between sites. These differences between virus groups allow the formulation of a viral proxy, based on the Caudoviricetes/Megaviricetes ratio established on the most abundant groups of viruses. This ratio may be potentially used in analysing ancient DNA preserved in carbonate formations as an additional source of information on the microbiological community during sedimentation.}, }
@article {pmid39440313, year = {2024}, author = {Malyarchuk, BA}, title = {Genetic aspects of lactase deficiency in indigenous populations of Siberia.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {28}, number = {6}, pages = {650-658}, doi = {10.18699/vjgb-24-72}, pmid = {39440313}, issn = {2500-0462}, abstract = {The ability to metabolize lactose in adulthood is associated with the persistence of lactase enzyme activity. In European populations, lactase persistence is determined mainly by the presence of the rs4988235-T variant in the MCM6 gene, which increases the expression of the LCT gene, encoding lactase. The highest rates of lactase persistence are characteristic of Europeans, and the lowest rates are found in East Asian populations. Analysis of published data on the distribution of the hypolactasia-associated variant rs4988235-C in the populations of Central Asia and Siberia showed that the frequency of this variant increases in the northeastern direction. The frequency of this allele is 87 % in Central Asia, 90.6 % in Southern Siberia, and 92.9 % in Northeastern Siberia. Consequently, the ability of the population to metabolize lactose decreases in the same geographical direction. The analysis of paleogenomic data has shown that the higher frequency of the rs4988235-T allele in populations of Central Asia and Southern Siberia is associated with the eastward spread of ancient populations of the Eastern European steppes, starting from the Bronze Age. The results of polymorphism analysis of exons and adjacent introns of the MCM6 and LCT genes in indigenous populations of Siberia indicate the possibility that polymorphic variants may potentially be related to lactose metabolism exist in East Asian populations. In East Asian populations, including Siberian ethnic groups, a ~26.5 thousand nucleotide pairs long region of the MCM6 gene, including a combination of the rs4988285-A, rs2070069-G, rs3087353-T, and rs2070068-A alleles, was found. The rs4988285 and rs2070069 loci are located in the enhancer region that regulates the activity of the LCT gene. Analysis of paleogenomic sequences showed that the genomes of Denisovans and Neanderthals are characterized by the above combination of alleles of the MCM6 gene. Thus, the haplotype discovered appears to be archaic. It could have been inherited from a common ancestor of modern humans, Neanderthals, and Denisovans, or it could have been acquired by hybridization with Denisovans or Neanderthals. The data obtained indicate a possible functional significance of archaic variants of the MCM6 gene.}, }
@article {pmid39438503, year = {2024}, author = {Feinauer, IS and Lord, E and von Seth, J and Xenikoudakis, G and Ersmark, E and Dalén, L and Meleg, IN}, title = {Heterochronous mitogenomes shed light on the Holocene history of the Scandinavian brown bear.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24917}, pmid = {39438503}, issn = {2045-2322}, mesh = {*Ursidae/genetics ; Animals ; Scandinavian and Nordic Countries ; *Genome, Mitochondrial ; *Haplotypes ; *Genetic Variation ; *Phylogeny ; Female ; DNA, Mitochondrial/genetics ; Genetics, Population ; }, abstract = {Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears' mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears.}, }
@article {pmid39437846, year = {2024}, author = {Kaptan, D and Atağ, G and Vural, KB and Morell Miranda, P and Akbaba, A and Yüncü, E and Buluktaev, A and Abazari, MF and Yorulmaz, S and Kazancı, DD and Küçükakdağ Doğu, A and Çakan, YG and Özbal, R and Gerritsen, F and De Cupere, B and Duru, R and Umurtak, G and Arbuckle, BS and Baird, D and Çevik, &#xd6; and Bıçakçı, E and Gündem, CY and Pişkin, E and Hachem, L and Canpolat, K and Fakhari, Z and Ochir-Goryaeva, M and Kukanova, V and Valipour, HR and Hoseinzadeh, J and Küçük Baloğlu, F and Götherström, A and Hadjisterkotis, E and Grange, T and Geigl, EM and Togan, &#x130;Z and Günther, T and Somel, M and Özer, F}, title = {The Population History of Domestic Sheep Revealed by Paleogenomes.}, journal = {Molecular biology and evolution}, volume = {41}, number = {10}, pages = {}, pmid = {39437846}, issn = {1537-1719}, support = {772390/ERC_/European Research Council/International ; //University Paris Diderot/ ; DGE20111123014//Fondation pour la Recherche M&#xe9;dicale/ ; 11015901//R&#xe9;gion Ile-de-France/ ; 2017-05267//Swedish Research Council Vetenskapsr&#xe5;det/ ; F20-0274//Helge Ax:son Johnson Stiftelse/ ; 075-15-2019-1879//Government of Russian Federation/ ; BCS-0530699//National Science Foundation/ ; }, mesh = {Animals ; *Sheep, Domestic/genetics ; *Domestication ; Sheep/genetics ; Genome ; DNA, Ancient/analysis ; Europe ; }, abstract = {Sheep was one of the first domesticated animals in Neolithic West Eurasia. The zooarchaeological record suggests that domestication first took place in Southwest Asia, although much remains unresolved about the precise location(s) and timing(s) of earliest domestication, or the post-domestication history of sheep. Here, we present 24 new partial sheep paleogenomes, including a 13,000-year-old Epipaleolithic Central Anatolian wild sheep, as well as 14 domestic sheep from Neolithic Anatolia, two from Neolithic Iran, two from Neolithic Iberia, three from Neolithic France, and one each from Late Neolithic/Bronze Age Baltic and South Russia, in addition to five present-day Central Anatolian Mouflons and two present-day Cyprian Mouflons. We find that Neolithic European, as well as domestic sheep breeds, are genetically closer to the Anatolian Epipaleolithic sheep and the present-day Anatolian and Cyprian Mouflon than to the Iranian Mouflon. This supports a Central Anatolian source for domestication, presenting strong evidence for a domestication event in SW Asia outside the Fertile Crescent, although we cannot rule out multiple domestication events also within the Neolithic Fertile Crescent. We further find evidence for multiple admixture and replacement events, including one that parallels the Pontic Steppe-related ancestry expansion in Europe, as well as a post-Bronze Age event that appears to have further spread Asia-related alleles across global sheep breeds. Our findings mark the dynamism of past domestic sheep populations in their potential for dispersal and admixture, sometimes being paralleled by their shepherds and in other cases not.}, }
@article {pmid39432055, year = {2025}, author = {Zhao, L and Henriksen, RA and Ramsøe, A and Nielsen, R and Korneliussen, TS}, title = {Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14029}, pmid = {39432055}, issn = {1755-0998}, support = {CF19-0712//Carlsberg Foundation/ ; CF20-0071//Carlsberg Foundation/ ; R302-2018-2155//Lundbeck Foundation/ ; }, mesh = {*DNA, Ancient/analysis ; DNA Damage ; Sequence Analysis, DNA/methods ; Likelihood Functions ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Humans ; }, abstract = {One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.}, }
@article {pmid39429655, year = {2024}, author = {Farhud, DD and Azari, M and Rahbar, M}, title = {Tuberculosis in Human Bones from 4000 Years Ago, Iran.}, journal = {Iranian journal of public health}, volume = {53}, number = {9}, pages = {2103-2112}, pmid = {39429655}, issn = {2251-6093}, abstract = {BACKGROUND: Tuberculosis is caused by a bacterium called Mycobacterium tuberculosis, which is a contagious and infectious disease; in the first stage, it destroys the lungs and in the next stage other body organs, such as the spine and long bones. This disease is transmitted through an infected person and due to the weakness of the immune system, the infection intensifies. Tuberculosis has two stages: low activity and high activity. In this article, we have discussed the signs of tuberculosis destruction with high intensity on the bones of prehistory human remains.<br><br>METHODS: The examples of our research are related to human remains from the ancient cemetery of 4000 years ago from Sagezabad region of Qazvin Province of Iran. That period of history coincides with the Iron Age 2 and 3 in the region. People inside the Sagezabad cemetery were very near to early urban (the late rural) society.<br><br>RESULTS: By matching the form of bone destruction with international atlases for tuberculosis, we have reached a satisfactory result in this article. Due to the strong penetration of the infection into the bones, destruction in the remains was high, so it has simplified the diagnosis for us.<br><br>CONCLUSION: We found tuberculosis among the bones. This common ancient disease existed even among Neanderthals.}, }
@article {pmid39415996, year = {2024}, author = {Rubin, J and van Waaij, J and Kraft, L and Sirén, J and Sackett, PW and Renaud, G}, title = {SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39415996}, issn = {2692-8205}, support = {R01 HG010485/HG/NHGRI NIH HHS/United States ; U01 HG010961/HG/NHGRI NIH HHS/United States ; U41 HG010972/HG/NHGRI NIH HHS/United States ; }, abstract = {Aligning DNA sequences retrieved from fossils or other paleontological artifacts, referred to as ancient DNA, is particularly challenging due to the short sequence length and chemical damage which creates a specific pattern of substitution (C→T and G→A) in addition to the heightened divergence between the sample and the reference genome thus exacerbating reference bias. This bias can be mitigated by aligning to pangenome graphs to incorporate documented organismic variation, but this approach still suffers from substitution patterns due to chemical damage. We introduce a novel methodology introducing the RYmer index, a variant of the commonly-used minimizer index which represents purines (A,G) and pyrimidines (C,T) as R and Y respectively. This creates an indexing scheme robust to the aforementioned chemical damage. We implemented SAFARI, an ancient DNA damage-aware version of the pangenome aligner vg giraffe which uses RYmers to rescue alignments containing deaminated seeds. We show that our approach produces more correct alignments from ancient DNA sequences than current approaches while maintaining a tolerable rate of spurious alignments. In addition, we demonstrate that our algorithm improves the estimate of the rate of ancient DNA damage, especially for highly damaged samples. Crucially, we show that this improved alignment can directly translate into better insights gained from the data by showcasing its integration with a number of extant pangenome tools.}, }
@article {pmid39408629, year = {2024}, author = {Herbert, A}, title = {A Compendium of G-Flipon Biological Functions That Have Experimental Validation.}, journal = {International journal of molecular sciences}, volume = {25}, number = {19}, pages = {}, pmid = {39408629}, issn = {1422-0067}, mesh = {*G-Quadruplexes ; Animals ; Humans ; Transcription Factors/metabolism/genetics ; DNA/metabolism/genetics ; RNA, Untranslated/genetics/metabolism ; DNA Repair ; Caenorhabditis elegans/genetics/metabolism ; }, abstract = {As with all new fields of discovery, work on the biological role of G-quadruplexes (GQs) has produced a number of results that at first glance are quite baffling, sometimes because they do not fit well together, but mostly because they are different from commonly held expectations. Like other classes of flipons, those that form G-quadruplexes have a repeat sequence motif that enables the fold. The canonical DNA motif (G3N1-7)3G3, where N is any nucleotide and G is guanine, is a feature that is under active selection in avian and mammalian genomes. The involvement of G-flipons in genome maintenance traces back to the invertebrate Caenorhabditis elegans and to ancient DNA repair pathways. The role of GQs in transcription is supported by the observation that yeast Rap1 protein binds both B-DNA, in a sequence-specific manner, and GQs, in a structure-specific manner, through the same helix. Other sequence-specific transcription factors (TFs) also engage both conformations to actuate cellular transactions. Noncoding RNAs can also modulate GQ formation in a sequence-specific manner and engage the same cellular machinery as localized by TFs, linking the ancient RNA world with the modern protein world. The coevolution of noncoding RNAs and sequence-specific proteins is supported by studies of early embryonic development, where the transient formation of G-quadruplexes coordinates the epigenetic specification of cell fate.}, }
@article {pmid39395415, year = {2024}, author = {de Flamingh, A and Gnoske, TP and Kerbis Peterhans, JC and Simeonovski, VA and Gitahi, N and Mwebi, O and Agwanda, BR and Catchen, JM and Roca, AL and Malhi, RS}, title = {Compacted hair in broken teeth reveals dietary prey of historic lions.}, journal = {Current biology : CB}, volume = {34}, number = {21}, pages = {5104-5111.e4}, doi = {10.1016/j.cub.2024.09.029}, pmid = {39395415}, issn = {1879-0445}, mesh = {Animals ; *Lions/genetics ; *Hair/chemistry ; Kenya ; Predatory Behavior ; Tooth/chemistry ; Diet/veterinary ; Phylogeny ; }, abstract = {With recent advances, nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA[1] and from specimens that are more than a million years old.[2] DNA analysis from hair is a well-established approach[3] widely used in forensic science[4] and wildlife conservation.[5] Hair samples can be effectively decontaminated[6] and can be used to identify the mammalian species from which the hair was shed.[7][,][8] We aimed to use advances optimized for degraded DNA to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo lions that lived during the 1890s in Kenya (see description of samples in the STAR Methods and Patterson[9] and Kerbis Peterhans and Gnoske[10] for background on the Tsavo "man-eaters"). Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest, and zebra as prey and also identified hair that originated from lion. DNA preservation allowed for analyses of complete mitogenome profiles of zebra, giraffe, and lion. Giraffe mitogenomes are phylogeographically partitioned, and we found that the lions ate at least two individuals that belong to a subspecies of Masai giraffe (Giraffa tippelskirchi tippelskirchi) typically found in southeast Kenya. The lion mitogenome from a hair sample was identical to the Tsavo lion endogenous mitogenome and most closely matched other East African lions from Kenya and Tanzania. Our approach enables a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for extinct populations and species.}, }
@article {pmid39390557, year = {2024}, author = {Sawyer, S and Gelabert, P and Yakir, B and Llanos-Lizcano, A and Sperduti, A and Bondioli, L and Cheronet, O and Neugebauer-Maresch, C and Teschler-Nicola, M and Novak, M and Pap, I and Szikossy, I and Hajdu, T and Moiseyev, V and Gromov, A and Zariņa, G and Meshorer, E and Carmel, L and Pinhasi, R}, title = {Improved detection of methylation in ancient DNA.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {261}, pmid = {39390557}, issn = {1474-760X}, mesh = {*DNA Methylation ; *DNA, Ancient/analysis ; Humans ; *Sulfites ; Sequence Analysis, DNA/methods ; }, abstract = {Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.}, }
@article {pmid39383567, year = {2025}, author = {Wu, Y and Ma, Q and Han, B and Shen, Y and Wen, S}, title = {Familial hypodontia in bronze age Northwest China (1046-771BC).}, journal = {Archives of oral biology}, volume = {169}, number = {}, pages = {106104}, doi = {10.1016/j.archoralbio.2024.106104}, pmid = {39383567}, issn = {1879-1506}, mesh = {Humans ; China/epidemiology ; *Anodontia/genetics/epidemiology ; Male ; History, Ancient ; Female ; DNA, Ancient/analysis ; Cemeteries ; Prevalence ; }, abstract = {OBJECTIVE: This research aimed to report hypodontia cases in a Middle Bronze Age high-tier cemetery in China and test the possible hereditary behind hypodontia by performing kinship tests on those individuals.<br><br>DESIGN: In this study, dental anomalies were observed on a human skeletal sample (n = 45) uncovered from Yaoheyuan, China. Ancient DNA analysis was subsequently employed on a subsample of the Yaoheyuan individuals (n = 15), including individuals observed hypodontia and individuals randomly sampled from the cemetery for preliminary investigation on the cemetery demography. Kinship estimation tests (READ, TKGWV2, KIN, and F3 test) were subsequently employed.<br><br>RESULTS: The Yaoheyuan elite population had a prevalence (n = 7, 15&#x202f;%) of tooth agenesis in either the maxilla or mandible, with one to two teeth missing. All missing teeth were incisors, except for one individual missing maxillary second molar. Preliminary ancient DNA results indicate that several kinship groups existed among interred individuals, including those with hypodontia, indicating the hereditary origin of these cases.<br><br>CONCLUSIONS: The prevalence of hypodontia observed on site is high compared to that in both modern East Asian populations and archaeological samples in the Chinese population. The preliminary kinship analysis suggests a case of familial hypodontia. Ancient DNA analysis should be thoroughly conducted in future studies to understand the genetic markers contributing to those hypodontia cases among the Yaoheyuan individuals.}, }
@article {pmid39357284, year = {2024}, author = {Fuchs, J and García-Tabernero, A and Rosas, A and Camus, H and Metz, L and Slimak, L and Zanolli, C}, title = {The dentition of a new adult Neanderthal individual from Grotte Mandrin, France.}, journal = {Journal of human evolution}, volume = {196}, number = {}, pages = {103599}, doi = {10.1016/j.jhevol.2024.103599}, pmid = {39357284}, issn = {1095-8606}, mesh = {*Neanderthals/anatomy &amp; histology/genetics ; Animals ; France ; *Fossils/anatomy &amp; histology ; Male ; Tooth/anatomy &amp; histology ; Dentition ; X-Ray Microtomography ; }, abstract = {Grotte Mandrin is located in the middle Rhône River Valley, in Mediterranean France, and has yielded 11 Pleistocene archeological and paleoanthropological layers (ranging from the oldest layer J to the youngest layer B) dating from Marine Isotope Stage (MIS) 5 to MIS 3. We report here the nearly complete dentition of an adult Neanderthal individual, nicknamed 'Thorin,' associated to the last phase of the Post-Neronian II, in layer B2 (∼44.50-42.25 ka). A previous paleogenetic analysis revealed that Thorin is a male individual and that he shows a deep genetic divergence with other penecontemporaneous Neanderthals from western Europe that possibly occurred ∼105 ka. The 31 teeth of Thorin (including two distomolars) are described and analyzed using microcomputed tomography imaging and are compared with other Neanderthals and modern humans. Based on direct observation and measurements on the fossil remains, and using microtomographic imaging, tooth wear, nonmetric characters, crown dimensions, and dental tissue proportions were investigated, and the shape of the enamel-dentine junction of the M[2], M2, and M3 was analyzed by geometric morphometrics. Our results indicate that Thorin's teeth show dental characteristics typical of MIS 5-3 Neanderthals. It is also the first time that the presence of two distomolars is reported in a Neanderthal individual, a trait that is rare among modern human populations. Combined with the genetic peculiarities of this individual, the results of the present study imply either a process of morphological convergence among the latest Neanderthal groups or an underestimation of the genetic variability of recent Neanderthal groups.}, }
@article {pmid39345259, year = {2024}, author = {Wu, X and Ding, B and Nie, L and Zhong, C and Liu, P and Liang, J and Wang, L and Gao, X and Wei, J and Zhou, Y}, title = {Genomic insights into the complex demographic history and inbreeding phenomena during Zhou Dynasty on the Central Plains of China.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1471740}, pmid = {39345259}, issn = {1664-302X}, abstract = {In the Central Plains of China during the Zhou Dynasty (1046-256 BCE), the social hierarchy gradually solidified, accompanied by frequent wars and the phenomena of multicultural and multi-ethnic integration. These social phenomena collectively influenced the population's genetic structure at that time. However, our understanding of the genetic history of this period remains largely unknown owing to limited ancient DNA studies. In this study, we successfully obtained 11 ancient genomes from the Guanzhuang site during the Zhou Dynasty on the central plain of China. Our findings revealed remarkable genetic continuity with the Neolithic populations of the Yellow River Basin and emphasized genetic diversity through the analysis of uniparental genetic markers. Population structure analysis further confirmed the genetic similarity between the Guanzhuang population and ancient populations of the Yellow River Basin and indicated genetic exchanges with ancient populations from surrounding regions. Intriguingly, signs of inbreeding within the Guanzhuang community cast doubt on the stringent enforcement of the contemporary marital regulations against consanguineous marriages within the same surname or clan. These revelations significantly enhance our insight into the complex interplay of ancient demography and societal organization, concurrently presenting a genetic perspective to view the complex evolution of Chinese civilization's multiethnic.}, }
@article {pmid39343094, year = {2024}, author = {Wei, X and Zhang, M and Min, R and Jiang, Z and Xue, J and Zhu, Z and Yuan, H and Li, X and Zhao, D and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Wu, X and Hu, C and Ma, M and Liu, X and Wan, Y and Yang, F and Zhou, R and Kang, L and Dong, G and Ping, W and Wang, T and Miao, B and Bai, F and Zheng, Y and Liu, Y and Yang, MA and Wang, W and Bennett, EA and Fu, Q}, title = {Neolithic to Bronze Age human maternal genetic history in Yunnan, China.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.09.013}, pmid = {39343094}, issn = {1673-8527}, abstract = {Yunnan in southwest China is a geographically and ethnically complex region at the intersection of southern China and Southeast Asia, and a focal point for human migrations. To clarify its maternal genetic history, we generated 152 complete mitogenomes from 17 Yunnan archaeological sites. Our results reveal distinct genetic histories segregated by geographical regions. Maternal lineages of ancient populations from northwestern and northern Yunnan exhibit closer affinities with past and present-day populations from northern East Asia and Xizang, providing important genetic evidence for the migration and interaction of populations along the Tibetan-Yi corridor since the Neolithic. Between 5500 and 1800 years ago, central Yunnan populations maintained their internal genetic relationships, including a 7000-year-old basal lineage of the rare and widely dispersed haplogroup M61. At the Xingyi site, changes in mitochondrial DNA haplogroups occurred between the Late Neolithic and Bronze Age, with haplogroups shifting from those predominant in the Yellow River region to those predominant in coastal southern China. These results highlight the high diversity of Yunnan populations during the Neolithic to Bronze Age.}, }
@article {pmid39333293, year = {2024}, author = {Petrova, TV and Panitsina, VA and Bodrov, SY and Abramson, NI}, title = {The mitochondrial genome of the critically endangered enigmatic Kazakhstani endemic Selevinia betpakdalaensis (Rodentia: Gliridae) and its phylogenetic relationships with other dormouse species.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22259}, pmid = {39333293}, issn = {2045-2322}, support = {075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Animals ; *Phylogeny ; *Genome, Mitochondrial ; Endangered Species ; Rodentia/genetics/classification ; }, abstract = {Dormice (family Gliridae) are an ancient group of rodents. It was fully dominant in the Oligocene and Early Miocene, and its current diversity is represented by a few extant species. A Kazakhstani endemic, the desert dormouse Selevinia betpakdalaensis is one of the most enigmatic dormouse species. Lack of genetic data has not allowed Selevinia to be included in previous molecular phylogenetic analyses. In the current study, we report the first genetic data on S. betpakdalaensis as well as mitochondrial genomes of Myomimus roachi and Glirulus japonicus (retrieved from museum specimens) and a mitogenome of Graphiurus murinus (assembled from SRA data). The assembled mitochondrial genomes were combined with available mitochondrial data from GenBank to reconstruct the mitochondrial phylogeny of Gliridae. Taking into account a distortion of the phylogeny as a result of an analysis of the saturated third codon position, we obtained for the first time a resolved phylogeny of the family. The first split within Gliridae was estimated as an average of 34.6 Mya, whereas divergence time of subfamilies Graphiurinae and Glirinae was assessed at 32.67 Mya. The phylogenetic analysis confirmed the relationship (previously shown based on cranial and mandibular morphology) between Selevinia and the Myomimus.}, }
@article {pmid39326418, year = {2024}, author = {Liu, Y and Miao, B and Li, W and Hu, X and Bai, F and Abuduresule, Y and Liu, Y and Zheng, Z and Wang, W and Chen, Z and Zhu, S and Feng, X and Cao, P and Ping, W and Yang, R and Dai, Q and Liu, F and Tian, C and Yang, Y and Fu, Q}, title = {Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history.}, journal = {Cell}, volume = {187}, number = {21}, pages = {5891-5900.e8}, doi = {10.1016/j.cell.2024.08.008}, pmid = {39326418}, issn = {1097-4172}, mesh = {Humans ; *Cheese/microbiology ; *Lactobacillus/genetics ; Kefir/microbiology ; History, Ancient ; Phylogeny ; China ; Biological Evolution ; Fermentation ; Asia, Eastern ; }, abstract = {Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.}, }
@article {pmid39322456, year = {2024}, author = {Hou, J and Guan, X and Xia, X and Lyu, Y and Liu, X and Mazei, Y and Xie, P and Chang, F and Zhang, X and Chen, J and Li, X and Zhang, F and Jin, L and Luo, X and Sinding, MS and Sun, X and Achilli, A and Migliore, NR and Zhang, D and Lenstra, JA and Han, J and Fu, Q and Liu, X and Zhang, X and Chen, N and Lei, C and Zhang, H}, title = {Evolution and legacy of East Asian aurochs.}, journal = {Science bulletin}, volume = {69}, number = {21}, pages = {3425-3433}, doi = {10.1016/j.scib.2024.09.016}, pmid = {39322456}, issn = {2095-9281}, mesh = {Animals ; Cattle/genetics ; Asia, Eastern ; Biological Evolution ; Evolution, Molecular ; Gene Flow ; Genetic Variation/genetics ; Genome, Mitochondrial/genetics ; *Phylogeny ; Phylogeography ; *Ruminants/genetics ; Extinction, Biological ; }, abstract = {Aurochs (Bos primigenius), once widely distributed in Afro-Eurasia, became extinct in the early 1600 s. However, their phylogeography and relative contributions to domestic cattle remain unknown. In this study, we analyzed 16 genomes of ancient aurochs and three mitogenomes of ancient bison (Bison priscus) excavated in East Asia, dating from 43,000 to 3,590 years ago. These newly generated data with previously published genomic information on aurochs as well as ancient/extant domestic cattle worldwide through genome analysis. Our findings revealed significant genetic divergence between East Asian aurochs and their European, Near Eastern, and African counterparts on the basis of both mitochondrial and nuclear genomic data. Furthermore, we identified evidence of gene flow from East Asian aurochs into ancient and present-day taurine cattle, suggesting their potential role in facilitating the environmental adaptation of domestic cattle.}, }
@article {pmid39314480, year = {2024}, author = {Akbari, A and Barton, AR and Gazal, S and Li, Z and Kariminejad, M and Perry, A and Zeng, Y and Mittnik, A and Patterson, N and Mah, M and Zhou, X and Price, AL and Lander, ES and Pinhasi, R and Rohland, N and Mallick, S and Reich, D}, title = {Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39314480}, issn = {2692-8205}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, abstract = {We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ~0% to ~20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1; a rise from ~0% to ~8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ~2% to ~9% from ~5500 to ~3000 years ago before dropping to ~3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the "Thrifty Gene" hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.}, }
@article {pmid39305897, year = {2024}, author = {Zampirolo, G and Holman, LE and Sawafuji, R and Ptáková, M and Kovačiková, L and Šída, P and Pokorný, P and Pedersen, MW and Walls, M}, title = {Tracing early pastoralism in Central Europe using sedimentary ancient DNA.}, journal = {Current biology : CB}, volume = {34}, number = {20}, pages = {4650-4661.e4}, doi = {10.1016/j.cub.2024.08.047}, pmid = {39305897}, issn = {1879-0445}, mesh = {*DNA, Ancient/analysis ; Animals ; *Archaeology ; Forests ; Sheep/genetics ; Microbiota/genetics ; Agriculture/history ; Geologic Sediments/analysis ; Europe ; }, abstract = {Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5-6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1-3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the "Anthropocene."}, }
@article {pmid39302159, year = {2024}, author = {Leppälä, K and da Silva Coelho, FA and Richter, M and Albert, VA and Lindqvist, C}, title = {Five-leaf Generalizations of the D-statistic Reveal the Directionality of Admixture.}, journal = {Molecular biology and evolution}, volume = {41}, number = {11}, pages = {}, pmid = {39302159}, issn = {1537-1719}, mesh = {*Models, Genetic ; Polymorphism, Single Nucleotide ; Hybridization, Genetic ; Animals ; Phylogeny ; Genetic Introgression ; Alleles ; }, abstract = {Over the past 15 years, the D-statistic, a four-taxon test for organismal admixture (hybridization, or introgression) which incorporates single nucleotide polymorphism data with allelic patterns ABBA and BABA, has seen considerable use. This statistic seeks to discern significant deviation from either a given species tree assumption, or from the balanced incomplete lineage sorting that could otherwise defy this species tree. However, while the D-statistic can successfully discriminate admixture from incomplete lineage sorting, it is not a simple matter to determine the directionality of admixture using only four-leaf tree models. As such, methods have been developed that use five leaves to evaluate admixture. Among these, the DFOIL method ("FOIL", a mnemonic for "First-Outer-Inner-Last"), which tests allelic patterns on the "symmetric" tree S=(((1,2),(3,4)),5), succeeds in finding admixture direction for many five-taxon examples. However, DFOIL does not make full use of all symmetry, nor can DFOIL function properly when ancient samples are included because of the reliance on singleton patterns (such as BAAAA and ABAAA). Here, we take inspiration from DFOIL to develop a new and completely general family of five-leaf admixture tests, dubbed Δ-statistics, that can either incorporate or exclude the singleton allelic patterns depending on individual taxon and age sampling choices. We describe two new shapes that are also fully testable, namely the "asymmetric" tree A=((((1,2),3),4),5) and the "quasisymmetric" tree Q=(((1,2),3),(4,5)), which can considerably supplement the "symmetric" S=(((1,2),(3,4)),5) model used by DFOIL. We demonstrate the consistency of Δ-statistics under various simulated scenarios, and provide empirical examples using data from black, brown and polar bears, the latter also including two ancient polar bear samples from previous studies. Recently, DFOIL and one of these ancient samples was used to argue for a dominant polar bear → brown bear introgression direction. However, we find, using both this ancient polar bear and our own, that by far the strongest signal using both DFOIL and Δ-statistics on tree S is actually bidirectional gene flow of indistinguishable direction. Further experiments on trees A and Q instead highlight what were likely two phases of admixture: one with stronger brown bear → polar bear introgression in ancient times, and a more recent phase with predominant polar bear → brown bear directionality.}, }
@article {pmid39300260, year = {2024}, author = {Gretzinger, J and Gibbon, VE and Penske, SE and Sealy, JC and Rohrlach, AB and Salazar-García, DC and Krause, J and Schiffels, S}, title = {9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter.}, journal = {Nature ecology &amp; evolution}, volume = {8}, number = {11}, pages = {2121-2134}, pmid = {39300260}, issn = {2397-334X}, mesh = {Humans ; South Africa ; *DNA, Ancient/analysis ; Genetic Variation ; }, abstract = {Southern Africa has one of the longest records of fossil hominins and harbours the largest human genetic diversity in the world. Yet, despite its relevance for human origins and spread around the globe, the formation and processes of its gene pool in the past are still largely unknown. Here, we present a time transect of genome-wide sequences from nine individuals recovered from a single site in South Africa, Oakhurst Rockshelter. Spanning the whole Holocene, the ancient DNA of these individuals allows us to reconstruct the demographic trajectories of the indigenous San population and their ancestors during the last 10,000 years. We show that, in contrast to most regions around the world, the population history of southernmost Africa was not characterized by several waves of migration, replacement and admixture but by long-lasting genetic continuity from the early Holocene to the end of the Later Stone Age. Although the advent of pastoralism and farming substantially transformed the gene pool in most parts of southern Africa after 1,300 BP, we demonstrate using allele-frequency and identity-by-descent segment-based methods that the ‡Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers, a pattern obscured by recent, extensive non-Southern African admixture. Yet, some southern San in South Africa still preserve this ancient, Pleistocene-derived genetic signature, extending the period of genetic continuity until today.}, }
@article {pmid39294129, year = {2024}, author = {Bozzi, D and Neuenschwander, S and Cruz Dávalos, DI and Sousa da Mota, B and Schroeder, H and Moreno-Mayar, JV and Allentoft, ME and Malaspinas, AS}, title = {Towards predicting the geographical origin of ancient samples with metagenomic data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21794}, pmid = {39294129}, issn = {2045-2322}, mesh = {Humans ; *DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome ; Geography ; Microbiota/genetics ; }, abstract = {Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.}, }
@article {pmid39292210, year = {2024}, author = {Atağ, G and Waldman, S and Carmi, S and Somel, M}, title = {An explanation for the sister repulsion phenomenon in Patterson's f-statistics.}, journal = {Genetics}, volume = {228}, number = {3}, pages = {}, pmid = {39292210}, issn = {1943-2631}, support = {772390//H2020 ERC Consolidator/ ; 952317//H2020-WIDESPREAD-05-2020 TWINNING/ ; //Scientific and Technological Research Council of Turkey (T&#xdc;B&#x130;TAK)/ ; }, mesh = {Humans ; *Models, Genetic ; *Gene Flow ; *Gene Frequency ; Genetics, Population ; Genome, Human ; Greece ; }, abstract = {Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f3- and f4-statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behavior of f-statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbors, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern "sister repulsion". We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity toward Bronze Age Greece rather than each other. This is observed both using f3- and f4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using principal components analysis or multidimensional scaling on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculate f3- and f4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from 1 region can create sister repulsion in f-statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, multidimensional scaling analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f-statistics.}, }
@article {pmid39291130, year = {2024}, author = {Song, G and Wang, Y and Ruan, Q and Cai, DE}, title = {The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) from Jartai Pass Site in Xinjiang, China, and its phylogenetic relationships.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {9}, number = {9}, pages = {1232-1236}, pmid = {39291130}, issn = {2380-2359}, abstract = {The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) coded as NJ26S from Jartai Pass Site was obtained by high throughput sequencing. The damage pattern demonstrated the authenticity and reliability of the ancient DNA data. The length of the mitogenome was 16,357 bp, which contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition of the mitochondrial genome is 28.17% A, 25.01% T, 11.89% G, 19.72% C, and 15.21% missing data with an AT composition of 53.18%. A maximum-likelihood phylogenetic tree was recovered including other roe deer sequences under the TIM2 + I + G4 model. This study presents molecular evidence indicating the presence of Capreolus pygargus in the Xinjiang Uygur Autonomous Region in China more than 3,000 years ago.}, }
@article {pmid39280844, year = {2024}, author = {Modina, SA and Kusliy, MA and Malikov, DG and Molodtseva, AS}, title = {Phylogeography of the woolly mammoth (Mammuthus primigenius) in the Minusinsk Depression of southern Siberia in the Late Pleistocene.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {28}, number = {5}, pages = {571-577}, doi = {10.18699/vjgb-24-63}, pmid = {39280844}, issn = {2500-0462}, abstract = {To date, a number of studies have been published on the phylogenetics of woolly mammoths (Mammuthus primigenius), ranging from analyses of parts of the mitochondrial genome to studies of complete nuclear genomes. However, until recently nothing was known about the genetic diversity of woolly mammoths in southern Siberia, in the Minusinsk Depression in particular. Within the framework of this effort, libraries for high-throughput sequencing of seven bone samples of woolly mammoths were obtained, two-round enrichment using biotinylated probes of modern mtDNA of Elephas maximus immobilised on magnetic microspheres and sequencing with subsequent bioinformatic analysis were carried out. Phylogenetic reconstructions showed the presence of all studied mammoths in clade I, which expanded its range. The assignment of mammoth mitotypes in the Minusinsk Depression to different clusters within clade I may indicate a sufficiently high diversity of their gene pool. Phylogeographic reconstructions revealed a genetic proximity of mitochondrial lineages of Late Pleistocene mammoths of the Minusinsk Depression and other regions of eastern Siberia and estimated their divergence time in the range of 100-150 thousand years ago, which indicates active migrations of woolly mammoths over vast territories of eastern Siberia in the late Middle Pleistoceneearly Late Pleistocene.}, }
@article {pmid39279684, year = {2024}, author = {Pan, J and Liu, X and Baca, M and Calvière-Tonasso, L and Schiavinato, S and Chauvey, L and Tressières, G and Perdereau, A and Aury, JM and Oliveira, PH and Wincker, P and Abdykanova, A and Arsuaga, JL and Bayarsaikhan, J and Belinskiy, AB and Carbonell, E and Davoudi, H and Lira Garrido, J and Gilbert, AS and Hermes, T and Warinner, C and Kalmykov, AA and Lordkipanidze, D and Mackiewicz, P and Mohaseb, AF and Richter, K and Sayfullaev, N and Shapiro, B and Shnaider, S and Southon, J and Stefaniak, K and Summers, GD and van Asperen, EN and Vanishvili, N and Hill, EA and Kuznetsov, P and Reinhold, S and Hansen, S and Mashkour, M and Berthon, R and Taylor, WTT and Houle, JL and Hekkala, E and Popović, D and Orlando, L}, title = {Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses.}, journal = {Molecular ecology}, volume = {33}, number = {19}, pages = {e17527}, doi = {10.1111/mec.17527}, pmid = {39279684}, issn = {1365-294X}, support = {101027750//European Union's Horizon 2020 research and innovation programme/ ; 101062645//European Union's Horizon 2020 research and innovation programme/ ; //Agricultural Science and Technology Innovation Program (ASTIP-05)/ ; //CNRS and University Paul Sabatier (AnimalFarm IRP)/ ; //Spanish Ministerio de Educaci&#xf3;n, Cultura y Deporte (Archaeological Projects Abroad 2017)/ ; //Wroclaw Centre of Biotechnology programme ('The Leading National Research Center [KNOW]')/ ; 681605//HORIZON EUROPE European Research Council/ ; 834616//HORIZON EUROPE European Research Council/ ; 101071707//HORIZON EUROPE European Research Council/ ; ANR-10-INBS-09//Agence Nationale pour la Recherche/ ; 19-78-10053//Russian Science Foundation/ ; 22-18-00194//Russian Science Foundation/ ; }, mesh = {Animals ; *Equidae/genetics ; *Genetics, Population ; Mongolia ; Genome/genetics ; Phylogeny ; Fossils ; Horses/genetics ; Adaptation, Physiological/genetics ; }, abstract = {The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome-wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4-kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown.}, }
@article {pmid39278943, year = {2024}, author = {Sun, Y and Lorenzen, ED and Westbury, MV}, title = {Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {826}, pmid = {39278943}, issn = {1471-2164}, support = {37352//Villum Fonden/ ; 9064-00025B//Danmarks Frie Forskningsfond/ ; }, mesh = {*Ursidae/genetics ; Animals ; Arctic Regions ; *Alleles ; *Genome ; Adaptation, Physiological/genetics ; Evolution, Molecular ; Selection, Genetic ; }, abstract = {The polar bear (Ursus maritimus) occupies a relatively narrow ecological niche, with many traits adapted for cold temperatures, movement across snow, ice and open water, and for consuming highly lipid-dense prey species. The divergence of polar bears from brown bears (Ursus arctos) and their adaptation to their Arctic lifestyle is a well-known example of rapid evolution. Previous research investigating whole genomes uncovered twelve key genes that are highly differentiated between polar and brown bears, show signatures of selection in the polar bear lineage, and are associated with polar bear adaptation to the Arctic environment. Further research suggested fixed derived alleles in these genes arose from selection on both standing variation and de novo mutations in the evolution of polar bears. Here, we reevaluate these findings based on a larger and geographically more representative dataset of 119 polar bears and 135 brown bears, and assess the timing of derived allele fixation in polar bears by incorporating the genomes of two Late Pleistocene individuals (aged 130-100,000 years old and 100-70,000 years old). In contrast with previous results, we found no evidence of derived alleles fixed in present-day polar bears within the key genes arising from de novo mutation. Most derived alleles fixed in present-day polar bears were also fixed in the Late Pleistocene polar bears, suggesting selection occurred prior to 70,000 years ago. However, some derived alleles fixed in present-day polar bears were not fixed in the two Late Pleistocene polar bears, including at sites within APOB, LYST, and TTN. These three genes are associated with cardiovascular function, metabolism, and pigmentation, suggesting selection may have acted on different loci at different times.}, }
@article {pmid39268685, year = {2024}, author = {Scheib, CL and Hui, R and Rose, AK and D'Atanasio, E and Inskip, SA and Dittmar, J and Cessford, C and Griffith, SJ and Solnik, A and Wiseman, R and Neil, B and Biers, T and Harknett, SJ and Sasso, S and Biagini, SA and Runfeldt, G and Duhig, C and Evans, C and Metspalu, M and Millett, MJ and O'Connell, TC and Robb, JE and Kivisild, T}, title = {Low Genetic Impact of the Roman Occupation of Britain in Rural Communities.}, journal = {Molecular biology and evolution}, volume = {41}, number = {9}, pages = {}, pmid = {39268685}, issn = {1537-1719}, support = {2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; //St John's College, Cambridge/ ; 2014-2020.4.01.15-0012//European Regional Development Fund/ ; PRG243//Estonian Research Council/ ; 2014-2020.4.01.16-0030//European Union through the European Regional Development Fund/ ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; United Kingdom ; *Human Migration ; *Rural Population ; History, Ancient ; DNA, Ancient/analysis ; Genetics, Population ; }, abstract = {The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored. Here, using genome-wide data from 52 ancient individuals from eight sites in Cambridgeshire covering the period of Roman occupation, we show low levels of genetic ancestry differentiation between Romano-British sites and indications of larger populations than in the Bronze Age and Neolithic. We find no evidence of long-distance migration from elsewhere in the Empire, though we do find one case of possible temporary mobility within a family unit during the Late Romano-British period. We also show that the present-day patterns of genetic ancestry composition in Britain emerged after the Roman period.}, }
@article {pmid39262445, year = {2023}, author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, &#xc5;J and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA}, title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {926}, pmid = {39262445}, issn = {2046-1402}, support = {T32 GM139782/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; }, abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.<br><br>METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.<br><br>RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.<br><br>CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.}, }
@article {pmid39261697, year = {2024}, author = {Thompson, B and Petrić Howe, N}, title = {Ancient DNA debunks Rapa Nui 'ecological suicide' theory.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-024-02963-9}, pmid = {39261697}, issn = {1476-4687}, }
@article {pmid39261696, year = {2024}, author = {Callaway, E}, title = {Famed Pacific island's population 'crash' debunked by ancient DNA.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39261696}, issn = {1476-4687}, }
@article {pmid39261607, year = {2024}, author = {Schiffels, S and Nägele, K}, title = {Rapa Nui's population history rewritten using ancient DNA.}, journal = {Nature}, volume = {633}, number = {8029}, pages = {290-291}, pmid = {39261607}, issn = {1476-4687}, mesh = {Humans ; *DNA, Ancient/analysis ; *Genetics, Population/history ; History, Ancient ; Reproducibility of Results ; Polynesia ; Colonialism/history ; }, }
@article {pmid39261501, year = {2024}, author = {Canesin, LEC and Vilaça, ST and Oliveira, RRM and Al-Ajli, F and Tracey, A and Sims, Y and Formenti, G and Fedrigo, O and Banhos, A and Sanaiotti, TM and Farias, IP and Jarvis, ED and Oliveira, G and Hrbek, T and Solferini, V and Aleixo, A}, title = {A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19925}, pmid = {39261501}, issn = {2045-2322}, support = {316531/2023-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 316532/2023-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 309243/2023-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *Genome ; *Eagles/genetics ; Female ; DNA Transposable Elements/genetics ; Phylogeny ; Evolution, Molecular ; Retroelements/genetics ; Genomics/methods ; }, abstract = {The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.}, }
@article {pmid39235046, year = {2024}, author = {de la Fuente Castro, C and Cortés, C and Raghavan, M and Castillo, D and Castro, M and Verdugo, RA and Moraga, M}, title = {The Genomic and Cultural Diversity of the Inka Qhapaq Hucha Ceremony in Chile and Argentina.}, journal = {Genome biology and evolution}, volume = {16}, number = {9}, pages = {}, pmid = {39235046}, issn = {1759-6653}, support = {1181889//ANID-FONDECYT/ ; //American Association of University Women/ ; //University of Chicago/ ; }, mesh = {Humans ; Argentina ; Chile ; *Genome, Human ; Genetic Variation ; Cultural Diversity ; Ceremonial Behavior ; Indians, South American/genetics ; Genomics ; }, abstract = {The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.}, }
@article {pmid39233501, year = {2024}, author = {Pavlova, SV and Romanenko, SA and Matveevsky, SN and Kuksin, AN and Dvoyashov, IA and Kovalskaya, YM and Proskuryakova, AA and Serdyukova, NA and Petrova, TV}, title = {Supernumerary Chromosomes Enhance Karyotypic Diversification of Narrow-Headed Voles of the Subgenus Stenocranius (Rodentia, Mammalia).}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {342}, number = {8}, pages = {538-556}, doi = {10.1002/jez.b.23273}, pmid = {39233501}, issn = {1552-5015}, support = {//This study was supported by Russian Science Foundation (Grant 22-24-00513)./ ; }, mesh = {Animals ; *Arvicolinae/genetics ; *Karyotype ; Male ; Siberia ; Mongolia ; Female ; Chromosomes, Mammalian/genetics ; DNA, Ribosomal/genetics ; Karyotyping ; }, abstract = {The subgenus Stenocranius contains two cryptic species: Lasiopodomys gregalis (subdivided into three allopatrically distributed and genetically well-isolated lineages A, B, and C) and Lasiopodomys raddei. To identify karyotype characteristics of this poorly studied cryptic species complex, we used comparative cytogenetic analysis of 138 individuals from 41 localities in South Siberia and Mongolia. A detailed description of the L. raddei karyotype and of the L. gregalis lineage С karyotype is presented for the first time. The A chromosome complement of all examined narrow-headed voles consisted of 2n = 36 and a fundamental number of autosomal arms (FNa) of 50. Between species, patterns of differential staining were similar, though additional C-heterochromatic blocks were found in L. gregalis lineages; Ag-positive nucleolar organizers and ribosomal DNA (rDNA) clusters are located on eight and nine acrocentric pairs, respectively. No B chromosomes (Bs) were found in the Early Pleistocene relic L. raddei, while one to five small heterochromatic acrocentric Bs were detected in all L. gregalis lineages; the number and frequency of Bs varied considerably within lineages, but no intraindividual variation was observed. In both species, telomeric repeats were visualized at termini of all chromosomes, including Bs. The number and localization of rDNA clusters on Bs varied among B-carriers. Immunodetection of several meiotic proteins indicated that meio-Bs are transcriptionally inactive and have a pattern of meiotic behavior similar to that of sex chromosomes (some homology of Bs to sex chromosomes is supposed). The nature, mechanisms of inheritance and stability of Bs in L. gregalis require further investigation.}, }
@article {pmid39222521, year = {2024}, author = {Garcia-Heras, J}, title = {The Discovery of Common Chromosome Aneuploidies with Medical Implications Through Innovative Analysis of Ancient DNA (aDNA).}, journal = {Journal of the Association of Genetic Technologists}, volume = {50}, number = {3}, pages = {96-99}, pmid = {39222521}, issn = {1523-7834}, abstract = {Two recent studies that re-examined through novel approaches previous shotgun sequencing data from prehistoric/historic Europeans uncovered several autosomal and sex chromosome aneuploidies (Anastasiadou et al., 2024; Rohrlach et al., 2024). These disorders, which are common in contemporary humans, were trisomies 18 and 21, Klinefelter syndrome (47,XXY), 47,XYY syndrome, and mosaic Turner syndrome X/XX. These discoveries about prehistoric/historic occurrence of constitutional chromosomal syndromes with high clinical significance in modern medical genetics are an important breakthrough. They contribute to a more comprehensive genetic delineation of past human populations and give impetus to perform more historic/prehistoric studies to discover other contemporary genetic disorders. A molecular profiling of ancient DNA (aDNA) from human remains added to anthropological and archaeological data may also give a broader picture of the social and historical contexts of individuals who were affected by genetic diseases. These advances in the detection of chromosome aneuploidies and previous discoveries of current monogenic syndromes in archaic hominins also highlight the possibility of detecting other genetic diseases of present-day occurrence in our ancestors. As a result, it might be feasible to delineate the evolutionary history of modern genetic diseases, establishing a timeline of their emergence, patterns of mutations, putative mechanisms of selection, and genomic mechanisms involved.}, }
@article {pmid39215552, year = {2024}, author = {Laval, G and Patin, E and Quintana-Murci, L and Kerner, G}, title = {Deep estimation of the intensity and timing of natural selection from ancient genomes.}, journal = {Molecular ecology resources}, volume = {24}, number = {8}, pages = {e14015}, doi = {10.1111/1755-0998.14015}, pmid = {39215552}, issn = {1755-0998}, mesh = {*Selection, Genetic ; Humans ; *DNA, Ancient/analysis ; Gene Frequency ; Europe ; Computer Simulation ; Genotype ; Neural Networks, Computer ; }, abstract = {Leveraging past allele frequencies has proven to be key for identifying the impact of natural selection across time. However, this approach suffers from imprecise estimations of the intensity (s) and timing (T) of selection, particularly when ancient samples are scarce in specific epochs. Here, we aimed to bypass the computation of allele frequencies across arbitrarily defined past epochs and refine the estimations of selection parameters by implementing convolutional neural networks (CNNs) algorithms that directly use ancient genotypes sampled across time. Using computer simulations, we first show that genotype-based CNNs consistently outperform an approximate Bayesian computation (ABC) approach based on past allele frequency trajectories, regardless of the selection model assumed and the number of available ancient genotypes. When applying this method to empirical data from modern and ancient Europeans, we replicated the reported increased number of selection events in post-Neolithic Europe, independently of the continental subregion studied. Furthermore, we substantially refined the ABC-based estimations of s and T for a set of positively and negatively selected variants, including iconic cases of positive selection and experimentally validated disease-risk variants. Our CNN predictions support a history of recent positive and negative selection targeting variants associated with host defence against pathogens, aligning with previous work that highlights the significant impact of infectious diseases, such as tuberculosis, in Europe. These findings collectively demonstrate that detecting the footprints of natural selection on ancient genomes is crucial for unravelling the history of severe human diseases.}, }
@article {pmid39191285, year = {2024}, author = {Arzelier, A and De Belvalet, H and Pemonge, MH and Garberi, P and Binder, D and Duday, H and Deguilloux, MF and Pruvost, M}, title = {Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2029}, pages = {rspb20241215}, pmid = {39191285}, issn = {1471-2954}, support = {DFG-HA-5407/4-1//Deutsche Forschungsgemeinschaft/ ; ANR22-CE27-0012, ANR15-CE27-0001, ANR17-FRAL-0010//Agence Nationale de la Recherche/ ; }, mesh = {*DNA, Ancient/analysis ; France ; Humans ; *Burial/history ; *Archaeology ; Male ; Bayes Theorem ; Female ; History, Ancient ; }, abstract = {The Aven de la Boucle (Corconne, Gard, southern France) is a karst shaft used as a collective burial between 3600 and 2800 cal BCE. The site encompasses the skeletal remains of approximately 75 individuals comprising a large majority of adult individuals, represented by scattered and commingled remains. To date, few studies have explored the potential of ancient DNA to tackle the documentation of Neolithic collective burials, and the funerary selection rules within such structures remain largely debated. In this study, we combine genomic analysis of 37 individuals with archaeo-anthropological data and Bayesian modelling of radiocarbon dates. Through this multidisciplinary approach, we aim to characterize the identity of the deceased and their relationships, as well as untangle the genetic diversity and funerary dynamics of this community. Genomic results identify 76% of male Neolithic individuals, suggesting a marked sex-biased selection. Available data emphasize the importance of biological relatedness and a male-mediated transmission of social status, as the affiliation to a specific male-lineage appears as a preponderant selection factor. The genomic results argue in favour of 'continuous' deposits between 3600 and 2800 BCE, carried out by the same community, despite cultural changes reflected by the ceramic material.}, }
@article {pmid39169089, year = {2024}, author = {Oberreiter, V and Gelabert, P and Brück, F and Franz, S and Zelger, E and Szedlacsek, S and Cheronet, O and Cano, FT and Exler, F and Zagorc, B and Karavanić, I and Banda, M and Gasparyan, B and Straus, LG and Gonzalez Morales, MR and Kappelman, J and Stahlschmidt, M and Rattei, T and Kraemer, SM and Sawyer, S and Pinhasi, R}, title = {Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19388}, pmid = {39169089}, issn = {2045-2322}, support = {1111111//Research Platform MINERVA, University of Vienna/ ; M 3108/FWF_/Austrian Science Fund FWF/Austria ; CA19141-8d068698//COST iNEAL STSM Grant/ ; No. 101042570//European Research Council (ERC) MicroStratDNA project/ ; M3108-G//Austrian Science Fund/ ; NECEM, HRZZ-IP-2019-04-6649//Hrvatska Zaklada za Znanost/ ; }, mesh = {*DNA, Ancient/analysis ; *Geologic Sediments ; Humans ; Animals ; Archaeology/methods ; Fossils ; High-Throughput Nucleotide Sequencing/methods ; Hominidae/genetics ; Europe ; Africa ; }, abstract = {In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.}, }
@article {pmid39165395, year = {2024}, author = {Armbrecht, L and Bolch, CJS and Paine, B and Cooper, A and McMinn, A and Woodward, C and Hallegraeff, G}, title = {Recovering sedimentary ancient DNA of harmful dinoflagellates accumulated over the last 9000 years off Eastern Tasmania, Australia.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae098}, pmid = {39165395}, issn = {2730-6151}, abstract = {Harmful algal blooms (HABs) have had significant adverse impacts on the seafood industry along the Tasmanian east coast over the past 4 decades. To investigate the history of regional HABs, we performed analyses of sedimentary ancient DNA (sedaDNA) in coastal sediments up to ~9000 years old collected inshore and offshore of Maria Island, Tasmania. We used metagenomic shotgun sequencing and a hybridisation capture array ("HABbaits1") to target three harmful dinoflagellate genera, Alexandrium, Gymnodinium, and Noctiluca. Bioinformatic and DNA damage analyses verified the authenticity of the sedaDNA sequences. Our results show that dinoflagellates of Alexandrium genera have been present off eastern Tasmania during the last ~8300 years, and we sporadically detected and unambiguously verified sequences of Gymnodinium catenatum that were present offshore up to ~7600 years ago. We also recovered sedaDNA of the fragile, soft-bodied Noctiluca scintillans with increased relative abundance since 2010, consistent with plankton surveys. This study enabled us to identify challenges of sedaDNA sequence validation (in particular for G. catenatum, a microreticulate gymnodinoid species) and provided guidance for the development of tools to monitor past and present HAB species and improvement of future HAB event predictions.}, }
@article {pmid39159385, year = {2024}, author = {Tian, Y and Koncz, I and Defant, S and Giostra, C and Vyas, DN and Sołtysiak, A and Pejrani Baricco, L and Fetner, R and Posth, C and Brandt, G and Bedini, E and Modi, A and Lari, M and Vai, S and Francalacci, P and Fernandes, R and Steinhof, A and Pohl, W and Caramelli, D and Krause, J and Izdebski, A and Geary, PJ and Veeramah, KR}, title = {The role of emerging elites in the formation and development of communities after the fall of the Roman Empire.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {36}, pages = {e2317868121}, pmid = {39159385}, issn = {1091-6490}, support = {856453//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; 426551838//Deutsche Forschungsgemeinschaft (DFG)/ ; 2018/31/G/HS3/01159//Narodowe Centrum Nauki (NCN)/ ; }, mesh = {Humans ; *Archaeology ; *Roman World/history ; Italy ; History, Medieval ; Human Migration/history ; History, Ancient ; }, abstract = {Elites played a pivotal role in the formation of post-Roman Europe on both macro- and microlevels during the Early Medieval period. History and archaeology have long focused on their description and identification based on written sources or through their archaeological record. We provide a different perspective on this topic by integrating paleogenomic, archaeological, and isotopic data to gain insights into the role of one such elite group in a Langobard period community near Collegno, Italy dated to the 6-8th centuries CE. Our analysis of 28 newly sequenced genomes together with 24 previously published ones combined with isotope (Sr, C, N) measurements revealed that this community was established by and organized around a network of biologically and socially related individuals likely composed of multiple elite families that over time developed into a single extended pedigree. The community also included individuals with diverse genetic ancestries, maintaining its diversity by integrating newcomers and groups in later stages of its existence. This study highlights how shifts in political power and migration impacted the formation and development of a small rural community within a key region of the former Western Roman Empire after its dissolution and the emergence of a new kingdom. Furthermore, it suggests that Early Medieval elites had the capacity to incorporate individuals from varied backgrounds and that these elites were the result of (political) agency rather than belonging to biologically homogeneous groups.}, }
@article {pmid39158588, year = {2024}, author = {Van Emmenis, L}, title = {Sarah Gaffen: I thrive on turning my vision for the lab into reality.}, journal = {The Journal of experimental medicine}, volume = {221}, number = {9}, pages = {}, pmid = {39158588}, issn = {1540-9538}, mesh = {Humans ; History, 20th Century ; History, 21st Century ; *Interleukin-17/metabolism ; Autoimmunity ; }, abstract = {Sarah Gaffen, PhD, is a professor of medicine and rheumatology and holds the Gerald P. Rodnan endowed chair at the University of Pittsburgh. Her lab explores the biological function of IL-17 and its receptor in the context of fungal host defense and autoimmunity. We spoke to Sarah about where her interest in cytokines began, the importance of saying no in your career, and her interest in paleogenetics.}, }
@article {pmid39151011, year = {2024}, author = {Rathmann, H and Vizzari, MT and Beier, J and Bailey, SE and Ghirotto, S and Harvati, K}, title = {Human population dynamics in Upper Paleolithic Europe inferred from fossil dental phenotypes.}, journal = {Science advances}, volume = {10}, number = {33}, pages = {eadn8129}, pmid = {39151011}, issn = {2375-2548}, mesh = {Humans ; *Fossils ; Europe ; *Phenotype ; *Tooth/anatomy &amp; histology ; *Population Dynamics ; Bayes Theorem ; Archaeology ; }, abstract = {Despite extensive archaeological research, our knowledge of the human population history of Upper Paleolithic Europe remains limited, primarily due to the scarce availability and poor molecular preservation of fossil remains. As teeth dominate the fossil record and preserve genetic signatures in their morphology, we compiled a large dataset of 450 dentitions dating between ~47 and 7 thousand years ago (ka), outnumbering existing skeletal and paleogenetic datasets. We tested a range of competing demographic scenarios using a coalescent-based machine learning Approximate Bayesian Computation (ABC) framework that we modified for use with phenotypic data. Mostly in agreement with but also challenging some of the hitherto available evidence, we identified a population turnover in western Europe at ~28 ka, isolates in western and eastern refugia between ~28 and 14.7 ka, and bottlenecks during the Last Glacial Maximum. Methodologically, this study marks the pioneering application of ABC to skeletal phenotypes, paving the way for exciting future research avenues.}, }
@article {pmid39149515, year = {2024}, author = {Rbbani, G and Murshed, R and Siriyappagouder, P and Sharko, F and Nedoluzhko, A and Joshi, R and Galindo-Villegas, J and Raeymaekers, JAM and Fernandes, JMO}, title = {Embryonic temperature has long-term effects on muscle circRNA expression and somatic growth in Nile tilapia.}, journal = {Frontiers in cell and developmental biology}, volume = {12}, number = {}, pages = {1369758}, pmid = {39149515}, issn = {2296-634X}, abstract = {Embryonic temperature has a lasting impact on muscle phenotype in vertebrates, involving complex molecular mechanisms that encompass both protein-coding and non-coding genes. Circular RNAs (circRNAs) are a class of regulatory RNAs that play important roles in various biological processes, but the effect of variable thermal conditions on the circRNA transcriptome and its long-term impact on muscle growth plasticity remains largely unexplored. To fill this knowledge gap, we performed a transcriptomic analysis of circRNAs in fast muscle of Nile tilapia (Oreochromis niloticus) subjected to different embryonic temperatures (24°C, 28°C and 32°C) and then reared at a common temperature (28°C) for 4 months. Nile tilapia embryos exhibited faster development and subsequently higher long-term growth at 32°C compared to those reared at 28°C and 24°C. Next-generation sequencing data revealed a total of 5,141 unique circRNAs across all temperature groups, of which 1,604, 1,531, and 1,169 circRNAs were exclusively found in the 24°C, 28°C and 32°C groups, respectively. Among them, circNexn exhibited a 1.7-fold (log2) upregulation in the 24°C group and a 1.3-fold (log2) upregulation in the 32°C group when compared to the 28°C group. Conversely, circTTN and circTTN_b were downregulated in the 24°C groups compared to their 28°C and 32°C counterparts. Furthermore, these differentially expressed circRNAs were found to have multiple interactions with myomiRs, highlighting their potential as promising candidates for further investigation in the context of muscle growth plasticity. Taken together, our findings provide new insights into the molecular mechanisms that may underlie muscle growth plasticity in response to thermal variation in fish, with important implications in the context of climate change, fisheries and aquaculture.}, }
@article {pmid39146937, year = {2024}, author = {Du, P and Zhu, K and Wang, M and Sun, Z and Tan, J and Sun, B and Sun, B and Wang, P and He, G and Xiong, J and Huang, Z and Meng, H and Sun, C and Xie, S and Wang, B and Ge, D and Ma, Y and Sheng, P and Ren, X and Tao, Y and Xu, Y and Qin, X and Allen, E and Zhang, B and Chang, X and Wang, K and Bao, H and Yu, Y and Wang, L and Ma, X and Du, Z and Guo, J and Yang, X and Wang, R and Ma, H and Li, D and Pan, Y and Li, B and Zhang, Y and Zheng, X and Han, S and Jin, L and Chen, G and Li, H and Wang, CC and Wen, S}, title = {Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic.}, journal = {Current biology : CB}, volume = {34}, number = {17}, pages = {3996-4006.e11}, doi = {10.1016/j.cub.2024.07.063}, pmid = {39146937}, issn = {1879-0445}, mesh = {Humans ; China ; *Genome, Human ; History, Ancient ; DNA, Ancient/analysis ; Human Migration/history ; Rivers ; Genetics, Population ; Archaeology ; Genetic Variation ; Genomics ; }, abstract = {The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities.}, }
@article {pmid39140291, year = {2024}, author = {de la Fuente, J}, title = {Catastrophic selection: the other side of the coin.}, journal = {Annals of medicine}, volume = {56}, number = {1}, pages = {2391014}, pmid = {39140291}, issn = {1365-2060}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Peptides/pharmacology ; Machine Learning ; Drug Resistance, Bacterial ; Proteomics/methods ; }, abstract = {Recently, a machine learning molecular de-extinction paleoproteomic approach was used to recover inactivated antimicrobial peptides to overcome the challenges posed by antibiotic-resistant pathogens. The authors showed the possibility of identifying lost molecules with antibacterial capacity, but the other side of the coin associated with catastrophic selection should be considered for the development of new pharmaceuticals.}, }
@article {pmid39136992, year = {2024}, author = {Skovrind, M and Louis, M and Ferguson, SH and Glazov, DM and Litovka, DI and Loseto, L and Meschersky, IG and Miller, MM and Petr, M and Postma, L and Rozhnov, VV and Scott, M and Westbury, MV and Szpak, P and Friesen, TM and Lorenzen, ED}, title = {Elucidating the sustainability of 700 y of Inuvialuit beluga whale hunting in the Mackenzie River Delta, Northwest Territories, Canada.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {34}, pages = {e2405993121}, pmid = {39136992}, issn = {1091-6490}, support = {37352//Villum Fonden YIP+/ ; 9064-00025B//Independent research fund, Sapre Aude/ ; CF23-1061//Carlsberg Foundation Semper Ardens Accelerate/ ; 435-2012-0641//Canadian Government | Social Sciences and Humanities Research Council of Canada (SSHRC)/ ; 61914//Polar Continental Shelf Program/ ; 62816//Polar Continental Shelf Program/ ; 000//Aurora Research Institute (ARI)/ ; }, mesh = {Animals ; *Beluga Whale/genetics ; Northwest Territories ; Female ; Male ; Hunting ; Nitrogen Isotopes/analysis ; Carbon Isotopes/analysis ; DNA, Mitochondrial/genetics ; Inuit ; }, abstract = {Beluga whales play a critical role in the subsistence economies and cultural heritage of Indigenous communities across the Arctic, yet the effects of Indigenous hunting on beluga whales remain unknown. Here, we integrate paleogenomics, genetic simulations, and stable δ[13]C and δ[15]N isotope analysis to investigate 700 y of beluga subsistence hunting in the Mackenzie Delta area of northwestern Canada. Genetic identification of the zooarchaeological remains, which is based on radiocarbon dating, span three time periods (1290 to 1440 CE; 1450 to 1650 CE; 1800 to 1870 CE), indicates shifts across time in the sex ratio of the harvested belugas. The equal number of females and males harvested in 1450 to 1650 CE versus more males harvested in the two other time periods may reflect changes in hunting practices or temporal shifts in beluga availability. We find temporal shifts and sex-based differences in δ[13]C of the harvested belugas across time, suggesting historical adaptability in the foraging ecology of the whales. We uncovered distinct mitochondrial diversity unique to the Mackenzie Delta belugas, but found no changes in nuclear genomic diversity nor any substructuring across time. Our findings indicate the genomic stability and continuity of the Mackenzie Delta beluga population across the 700 y surveyed, indicating the impact of Inuvialuit subsistence harvests on the genetic diversity of contemporary beluga individuals has been negligible.}, }
@article {pmid39135339, year = {2024}, author = {Tseng, YH and Kuo, LY and Borokini, I and Fawcett, S}, title = {The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae.}, journal = {American journal of botany}, volume = {111}, number = {8}, pages = {e16388}, doi = {10.1002/ajb2.16388}, pmid = {39135339}, issn = {1537-2197}, mesh = {*Hybridization, Genetic ; *Ferns/genetics/classification ; *Genetic Speciation ; *Phylogeny ; Polyploidy ; }, abstract = {PREMISE: Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape.<br><br>METHODS: By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework.<br><br>RESULTS: We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other.<br><br>CONCLUSIONS: The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.}, }
@article {pmid39135108, year = {2024}, author = {Alaçamlı, E and Naidoo, T and Güler, MN and Sağlıcan, E and Aktürk, &#x15e; and Mapelli, I and Vural, KB and Somel, M and Malmström, H and Günther, T}, title = {READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {216}, pmid = {39135108}, issn = {1474-760X}, support = {P21-0266//Riksbankens Jubileumsfond/ ; 772390//HORIZON EUROPE European Research Council/ ; }, mesh = {Humans ; *DNA, Ancient/analysis ; *Software ; *Archaeology/methods ; Genomics/methods ; Pedigree ; }, abstract = {The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.}, }
@article {pmid39114968, year = {2024}, author = {Moriano, J and Leonardi, O and Vitriolo, A and Testa, G and Boeckx, C}, title = {A multi-layered integrative analysis reveals a cholesterol metabolic program in outer radial glia with implications for human brain evolution.}, journal = {Development (Cambridge, England)}, volume = {151}, number = {16}, pages = {}, pmid = {39114968}, issn = {1477-9129}, support = {2021-SGR-313; FI-SDUR 2020//Generalitat de Catalunya/ ; PID2019-107042GB-I00//Ministerio de Ciencia e Innovacion/ ; 2021-SGR-313//Generalitat de Catalunya/ ; PID2019-107042GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; //University of Barcelona/ ; }, mesh = {Humans ; *Cholesterol/metabolism ; *Brain/metabolism ; *Ependymoglial Cells/metabolism/cytology ; *Gene Regulatory Networks ; Biological Evolution ; Neurogenesis/genetics ; Neural Stem Cells/metabolism/cytology ; Gene Expression Regulation, Developmental ; Kruppel-Like Factor 6/metabolism/genetics ; }, abstract = {The definition of molecular and cellular mechanisms contributing to brain ontogenetic trajectories is essential to investigate the evolution of our species. Yet their functional dissection at an appropriate level of granularity remains challenging. Capitalizing on recent efforts that have extensively profiled neural stem cells from the developing human cortex, we develop an integrative computational framework to perform trajectory inference and gene regulatory network reconstruction, (pseudo)time-informed non-negative matrix factorization for learning the dynamics of gene expression programs, and paleogenomic analysis for a higher-resolution mapping of derived regulatory variants in our species in comparison with our closest relatives. We provide evidence for cell type-specific regulation of gene expression programs during indirect neurogenesis. In particular, our analysis uncovers a key role for a cholesterol program in outer radial glia, regulated by zinc-finger transcription factor KLF6. A cartography of the regulatory landscape impacted by Homo sapiens-derived variants reveals signals of selection clustering around regulatory regions associated with GLI3, a well-known regulator of radial glial cell cycle, and impacting KLF6 regulation. Our study contributes to the evidence of significant changes in metabolic pathways in recent human brain evolution.}, }
@article {pmid39114174, year = {2024}, author = {Civáň, P and Fricano, A and Russell, J and Pont, C and Özkan, H and Kilian, B and Brown, TA}, title = {Genetic erosion in domesticated barley and a hypothesis of a North African centre of diversity.}, journal = {Ecology and evolution}, volume = {14}, number = {8}, pages = {e70068}, pmid = {39114174}, issn = {2045-7758}, abstract = {Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process affected genetic diversity. We set out to revisit this question by integrating public DNA sequencing data from ancient barley and wide collections of extant wild and domesticated accessions. Using two previously overlooked approaches - analyses of chloroplast genomes and genome-wide proportions of private variants - we found that the barley cultivated six millennia ago was genetically unique and more diverse when compared to extant landraces and cultivars. Moreover, the chloroplast genomes revealed a link between the ancient barley, an obscure wild genotype from north-eastern Libya, and a distinct population of barley cultivated in Ethiopia/Eritrea. Based on these results, we hypothesize past existence of a wider North African population that included both wild and cultivated types and suffered from genetic erosion in the past six millennia, likely due to a rapid desertification that ended the Holocene African humid period. Besides providing clues about the origin of Ethiopian landraces, the hypothesis explains the post-domestication loss of diversity observed in barley. Analyses of additional samples will be necessary to resolve the history of African barley and its contribution to the extant cultivated gene pool.}, }
@article {pmid39113775, year = {2024}, author = {Furness, LH and Kersten, O and Boilard, A and Keith-Diagne, L and Brito, C and Barrett, JH and Kitchener, A and Sabin, R and Lavery, S and Plön, S and Star, B}, title = {Population structure of Dugong dugon across the Indo-Pacific revealed by historical mitogenomes.}, journal = {Royal Society open science}, volume = {11}, number = {8}, pages = {240599}, pmid = {39113775}, issn = {2054-5703}, abstract = {Sirenia, an iconic marine taxon with a tropical and subtropical worldwide distribution, face an uncertain future. All species are designated 'Vulnerable' to extinction by the IUCN. Nonetheless, a comprehensive understanding of geographic structuring across the global range is lacking, impeding our ability to highlight particularly vulnerable populations for conservation priority. Here, we use ancient DNA to investigate dugong (Dugong dugon) population structure, analysing 56 mitogenomes from specimens comprising the known historical range. Our results reveal geographically structured and distinct monophyletic clades characterized by contrasting evolutionary histories. We observe deep-rooted and divergent lineages in the East (Indo-Pacific) and obtain new evidence for the relatively recent dispersal of dugongs into the western Indian Ocean. All populations are significantly differentiated from each other with western populations having approximately 10-fold lower levels of genetic variation than eastern Indo-Pacific populations. Additionally, we find a significant temporal loss of genetic diversity in western Indian Ocean dugongs since the mid-twentieth century, as well as a decline in population size beginning approximately 1000 years ago. Our results add to the growing body of evidence that dugong populations are becoming ever more susceptible to ongoing human action and global climate change.}, }
@article {pmid39105137, year = {2024}, author = {de Vos, JM and Streiff, SJR and Bachelier, JB and Epitawalage, N and Maurin, O and Forest, F and Baker, WJ}, title = {Phylogenomics of the pantropical Connaraceae: revised infrafamilial classification and the evolution of heterostyly.}, journal = {Plant systematics and evolution = Entwicklungsgeschichte und Systematik der Pflanzen}, volume = {310}, number = {4}, pages = {29}, pmid = {39105137}, issn = {0378-2697}, abstract = {UNLABELLED: Connaraceae is a pantropical family of about 200 species containing lianas and small trees with remarkably diverse floral polymorphisms, including distyly, tristyly, homostyly, and dioecy. To date, relationships within the family have not been investigated using a targeted molecular phylogenetic treatment, severely limiting systematic understanding and reconstruction of trait evolution. Accordingly, their last infrafamilial classification was based only on morphological data. Here, we used phylogenomic data obtained using the Angiosperms353 nuclear target sequence capture probes, sampling all tribes and almost all genera, entirely from herbarium specimens, to revise infrafamilial classification and investigate the evolution of heterostyly. The backbone of the resulting molecular phylogenetic tree is almost entirely resolved. Connaraceae consists of two clades, one containing only the African genus Manotes (4 or 5 species), which we newly recognize at the subfamily level. Vegetative and reproductive synapomorphies are proposed for Manotoideae. Within Connaroideae, Connareae is expanded to include the former Jollydoreae. The backbone of Cnestideae, which contains more than half of the Connaraceae species, remains incompletely resolved. Reconstructions of reproductive system evolution are presented that tentatively support tristyly as the ancestral state for the family, with multiple parallel losses, in agreement with previous hypotheses, plus possible re-gains. However, the great diversity of stylar polymorphisms and their phylogenetic lability preclude a definitive answer. Overall, this study reinforces the usefulness of herbarium phylogenomics, and unlocks the reproductive diversity of Connaraceae as a model system for the evolution of complex biological phenomena.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00606-024-01909-y.}, }
@article {pmid39098141, year = {2024}, author = {Golob, A and Kravanja, P and Concato, M and Leskovar, T and Zupanič Pajnič, I}, title = {Searching for alternative high DNA-yielding bone types for DNA analysis of aged skeletal remains.}, journal = {Forensic science international}, volume = {362}, number = {}, pages = {112184}, doi = {10.1016/j.forsciint.2024.112184}, pmid = {39098141}, issn = {1872-6283}, mesh = {Humans ; *Microsatellite Repeats ; *DNA Fingerprinting/methods ; Male ; *Real-Time Polymerase Chain Reaction ; *DNA/analysis/isolation &amp; purification ; Adult ; Middle Aged ; Female ; Body Remains ; DNA Degradation, Necrotic ; Aged ; Femur/chemistry/anatomy &amp; histology ; History, Medieval ; Bone and Bones/chemistry ; Petrous Bone/chemistry/anatomy &amp; histology ; Aged, 80 and over ; Forensic Anthropology/methods ; Young Adult ; Calcaneus/anatomy &amp; histology ; }, abstract = {The petrous bone contains significantly higher amounts of DNA than any other human bone. Because of highly destructive sampling and because it is not always part of the recovered remains, the need for alternative sources of DNA is important. To identify additional optimal bone types, petrous bones were compared to femurs, tali, and calcanei sampled from 66 adult skeletons from two distinct modern-era Christian cemeteries. An extraction method employing full demineralization was used to obtain DNA, real-time PCR quantification to ascertain DNA quantity and degradation, and a commercial forensic short tandem repeats (STR) PCR amplification kit to determine genetic profiles. Statistical analysis was performed to explore the differences in DNA yield, DNA degradation, and success of STR amplification. A systematic studies exploring intra-skeletal variability in DNA preservation including various excavation sites differing by time period and geographical position are rare, and the second part of the investigation was based on a comparison of both archaeological sites, which allowed us to compare the effect of different post-mortem intervals and environmental conditions on DNA preservation. The older burial site in Črnomelj was active between the 13th and 18th century, whereas the more recent Polje burial was in use from the 16th to 19th century, creating different temporal and geographical environments. Results for the Črnomelj burial site revealed that the petrous bone outperformed all other bone types studied, except the calcaneus. At the Polje archeological site calcanei, tali, and femurs yielded the same STR typing success as petrous bones. The results obtained highlight the importance of careful bone sample selection for DNA analysis of aged skeletal remains. In addition to petrous bones, calcanei were found to be an alternative source of DNA when older burial sites are investigated. When more recent burial sites are processed, calcanei, tali, and femurs should be sampled besides petrous bones, not only because they exhibited good performance, but also because of easier sampling and easier grinding in the case of trabecular bones. This study contributes valuable insights into the potential use of various skeletal types as a source of DNA for investigation of aged skeletal remains, and it offers practical implications for forensic and archaeological investigations.}, }
@article {pmid39091721, year = {2024}, author = {Gyuris, B and Vyazov, L and Türk, A and Flegontov, P and Szeifert, B and Langó, P and Mende, BG and Csáky, V and Chizhevskiy, AA and Gazimzyanov, IR and Khokhlov, AA and Kolonskikh, AG and Matveeva, NP and Ruslanova, RR and Rykun, MP and Sitdikov, A and Volkova, EV and Botalov, SG and Bugrov, DG and Grudochko, IV and Komar, O and Krasnoperov, AA and Poshekhonova, OE and Chikunova, I and Sungatov, F and Stashenkov, DA and Zubov, S and Zelenkov, AS and Ringbauer, H and Cheronet, O and Pinhasi, R and Akbari, A and Rohland, N and Mallick, S and Reich, D and Szécsényi-Nagy, A}, title = {Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39091721}, issn = {2692-8205}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, abstract = {During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.}, }
@article {pmid39088604, year = {2024}, author = {Kukutai, T and Black, A}, title = {CARE-ing for Indigenous nonhuman genomic data - rethinking our approach.}, journal = {Science (New York, N.Y.)}, volume = {385}, number = {6708}, pages = {eadr2493}, doi = {10.1126/science.adr2493}, pmid = {39088604}, issn = {1095-9203}, mesh = {Animals ; Biological Evolution ; *Birds/genetics ; DNA, Ancient/analysis ; *Fossils ; *Genome ; *Genomics/ethics ; New Zealand ; Sequence Analysis, DNA ; }, abstract = {Earlier this year, an international group of scientists published a paper in ScienceAdvances on the draft genome of the little bush moa (Anomalopteryx didiformis), one of about nine species of extinct flightless birds endemic to Aotearoa (New Zealand). The genome was sequenced from the ancient DNA of a "poorly provenanced" fossil bone acquired by the Royal Ontario Museum. It held important clues about the moa's evolutionary history and aspects of its biology.}, }
@article {pmid39086419, year = {2024}, author = {Farhud, DD and Azari, M and Rahbar, M}, title = {Tracking of Infectious Diseases and Deadly Injuries through Signs Observed in Excavated Human Skeletons of 2000 BC/Iron Age in Iran.}, journal = {Iranian journal of public health}, volume = {53}, number = {7}, pages = {1598-1611}, pmid = {39086419}, issn = {2251-6093}, abstract = {BACKGROUND: Throughout history, many wars have occurred for various reasons, and many empires and kings have fallen or many people killed by wars. Wars were not always due to the conquest of the country. in the Iron Age, societies were governed by tribes at the head of the tribe, and war was only for to seize property, slaves, and food. Our research area is the same period as the Medes Kingdom, which included the union of small, large tribes, wars between tribes existed in that period, and their signs can be seen on the remains of the people of that period.<br><br>METHODS: Our research is related to human remains from Sagezabad cemetery, Qazvin plain, which dates back to 2000 BC (Iron Age 2 and 3) in Iran.<br><br>RESULTS: The blows on the remains were very serious and caused death. We have discussed how to kill by "considering the injured body".<br><br>CONCLUSION: Our investigation of how people were killed in war based on injury marks and bullet holes in bones, and simulating those injuries to body tissues and organs also, people who had bone cuts from the war and survived and had bone repair and died due to lack of nutrients and infection were also discussed.}, }
@article {pmid39080329, year = {2024}, author = {Boggi, B and Sharpen, JDA and Taylor, G and Drosou, K}, title = {A novel integrated extraction protocol for multi-omic studies in heavily degraded samples.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17477}, pmid = {39080329}, issn = {2045-2322}, mesh = {Animals ; Brain/metabolism ; DNA/isolation &amp; purification ; Genomics/methods ; Lipids/analysis ; Metabolomics/methods ; *Multiomics/methods ; Proteins/isolation &amp; purification/metabolism ; Proteomics/methods ; Swine ; }, abstract = {The combination of multi-omic techniques, such as genomics, transcriptomics, proteomics, metabolomics and epigenomics, has revolutionised studies in medical research. These techniques are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence of protocols that integrate all four biomolecules in a single extraction process. Here, we demonstrate for the first time a minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yields of all four biomolecules. This integrated protocol is key to facilitating the preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics.}, }
@article {pmid39078618, year = {2024}, author = {Vaughn, AH and Nielsen, R}, title = {Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA.}, journal = {Molecular biology and evolution}, volume = {41}, number = {8}, pages = {}, pmid = {39078618}, issn = {1537-1719}, mesh = {*Selection, Genetic ; Humans ; *DNA, Ancient/analysis ; *Models, Genetic ; *Gene Frequency ; Likelihood Functions ; Markov Chains ; Algorithms ; Evolution, Molecular ; Alleles ; Computer Simulation ; }, abstract = {We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.}, }
@article {pmid39078610, year = {2024}, author = {Nagel, AA and Flouri, T and Yang, Z and Rannala, B}, title = {Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences.}, journal = {Systematic biology}, volume = {73}, number = {6}, pages = {964-978}, pmid = {39078610}, issn = {1076-836X}, support = {R01 GM123306/GM/NIGMS NIH HHS/United States ; BB/T003502/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 2036201//National Science Foundation Graduate Research/ ; GM123306/NH/NIH HHS/United States ; }, mesh = {*DNA, Ancient/analysis ; Animals ; *Bayes Theorem ; *Phylogeny ; *Classification/methods ; *Mammoths/genetics/classification ; Elephants/genetics/classification ; Models, Genetic ; Computer Simulation ; }, abstract = {Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of nucleotide substitutions) are reduced relative to contemporary samples. This can be accounted for by incorporating sample ages into phylogenetic analyses. Existing methods that use tip (sample) dates infer gene trees rather than species trees, which can lead to incorrect or biased inferences of the species tree. Methods using a multispecies coalescent (MSC) model overcome these issues. We developed an MSC model with tip dates and implemented it in the program BPP. The method performed well for a range of biologically realistic scenarios, estimating calibrated divergence times and mutation rates precisely. Simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples. Incorrectly treating ancient samples as contemporary in analyzing simulated data, mimicking a common practice of empirical analyses, led to large systematic biases in model parameters, including divergence times. Two genomic datasets of mammoths and elephants were analyzed, demonstrating the method's empirical utility.}, }
@article {pmid39067763, year = {2024}, author = {Bragazzi, NL and Del Rio, D and Mayer, EA and Mena, P}, title = {We Are What, When, And How We Eat: The Evolutionary Impact of Dietary Shifts on Physical and Cognitive Development, Health, and Disease.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {15}, number = {9}, pages = {100280}, pmid = {39067763}, issn = {2156-5376}, mesh = {Humans ; *Diet ; *Biological Evolution ; *Cognition ; *Feeding Behavior ; Animals ; }, abstract = {"We are what, when, and how we eat": the evolution of human dietary habits mirrors the evolution of humans themselves. Key developments in human history, such as the advent of stone tool technology, the shift to a meat-based diet, control of fire, advancements in cooking and fermentation techniques, and the domestication of plants and animals, have significantly influenced human anatomical, physiological, social, cognitive, and behavioral changes. Advancements in scientific methods, such as the analysis of microfossils like starch granules, plant-derived phytoliths, and coprolites, have yielded unprecedented insights into past diets. Nonetheless, the isolation of ancient food matrices remains analytically challenging. Future technological breakthroughs and a more comprehensive integration of paleogenomics, paleoproteomics, paleoglycomics, and paleometabolomics will enable a more nuanced understanding of early human ancestors' diets, which holds the potential to guide contemporary dietary recommendations and tackle modern health challenges, with far-reaching implications for human well-being, and ecological impact on the planet.}, }
@article {pmid39050717, year = {2024}, author = {Monnereau, A and Ughi, A and Orecchioni, P and Hagan, R and Talbot, HM and Nikita, E and Hamilton, D and Le Roux, P and Molinari, A and Carver, M and Craig, OE and Speller, CF and Alexander, MM and Wales, N}, title = {Multi-proxy bioarchaeological analysis of skeletal remains shows genetic discontinuity in a Medieval Sicilian community.}, journal = {Royal Society open science}, volume = {11}, number = {7}, pages = {240436}, pmid = {39050717}, issn = {2054-5703}, abstract = {The medieval period in Sicily was turbulent, involving successive regime changes, from Byzantine (Greek Christian), Aghlabid (Sunni Muslim), Fatimid (Shī'a Muslim), to Normans and Swabians (Latin Christian). To shed new light on the local implications of regime changes, we conducted a multidisciplinary analysis of 27 individuals buried in adjacent Muslim and Christian cemeteries at the site of Segesta, western Sicily. By combining radiocarbon dating, genome-wide sequencing, stable and radiogenic isotopic data, and archaeological records, we uncover genetic differences between the two communities but find evidence of continuity in other aspects of life. Historical and archaeological evidence shows a Muslim community was present by the 12th century during Norman governance, with the Christian settlement appearing in the 13th century under Swabian governance. A Bayesian analysis of radiocarbon dates from the burials finds the abandonment of the Muslim cemetery likely occurred after the establishment of the Christian cemetery, indicating that individuals of both faiths were present in the area in the first half of the 13th century. The biomolecular results suggest the Christians remained genetically distinct from the Muslim community at Segesta while following a substantially similar diet. This study demonstrates that medieval regime changes had major impacts beyond the political core, leading to demographic changes while economic systems persisted and new social relationships emerged.}, }
@article {pmid39044634, year = {2024}, author = {Rivera Rosas, DE and Geraldi, NR and Glud, RN and Oguri, K and Haond, SA and Duarte, CM}, title = {A sedimentary DNA record of the Atacama Trench reveals biodiversity changes in the most productive marine ecosystem.}, journal = {Global change biology}, volume = {30}, number = {7}, pages = {e17412}, doi = {10.1111/gcb.17412}, pmid = {39044634}, issn = {1365-2486}, support = {JP20H02013//Japan Society for the Promotion of Science/ ; 669947//ERC Advanced Grant "Benthic diagenesis and microbiology of hadal trenches"/ ; DNRF145//Danmarks Grundforskningsfond/ ; //King Abdullah University of Science and Technology/ ; }, mesh = {*Geologic Sediments/analysis ; *Biodiversity ; *DNA, Environmental/analysis ; *RNA, Ribosomal, 18S/genetics ; *Ecosystem ; Chile ; Animals ; DNA Barcoding, Taxonomic ; Eukaryota/genetics ; Aquatic Organisms/genetics ; }, abstract = {The hadopelagic environment remains highly understudied due to the inherent difficulties in sampling at these depths. The use of sediment environmental DNA (eDNA) can overcome some of these restrictions as settled and preserved DNA represent an archive of the biological communities. We use sediment eDNA to assess changes in the community within one of the world's most productive open-ocean ecosystems: the Atacama Trench. The ecosystems around the Atacama Trench have been intensively fished and are affected by climate oscillations, but the understanding of potential impacts on the marine community is limited. We sampled five sites using sediment cores at water depths from 2400 to ~8000 m. The chronologies of the sedimentary record were determined using [210]Pbex. Environmental DNA was extracted from core slices and metabarcoding was used to identify the eukaryote community using two separate primer pairs for different sections of the 18S rRNA gene (V9 and V7) effectively targeting pelagic taxa. The reconstructed communities were similar among markers and mainly composed of chordates and members of the Chromista kingdom. Alpha diversity was estimated for all sites in intervals of 15 years (from 1842 to 2018), showing a severe drop in biodiversity from 1970 to 1985 that aligns with one of the strongest known El Niño events and extensive fishing efforts during the time. We find a direct impact of sea surface temperature on the community composition over time. Fish and cnidarian read abundance was examined separately to determine whether fishing had a direct impact, but no direct relation was found. These results demonstrate that sediment eDNA can be a valuable emerging tool providing insight in historical perspectives on ecosystem developments. This study constitutes an important step toward an improved understanding of the importance of environmental and anthropogenic drivers in affecting open and deep ocean communities.}, }
@article {pmid39028337, year = {2024}, author = {Çubukcu, H and Kılınç, GM}, title = {Evaluation of genotype imputation using Glimpse tools on low coverage ancient DNA.}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {35}, number = {3}, pages = {461-473}, pmid = {39028337}, issn = {1432-1777}, mesh = {Humans ; *DNA, Ancient/analysis ; *Genome, Human ; *Polymorphism, Single Nucleotide ; *Genotype ; Genetics, Population/methods ; Software ; Genomics/methods ; }, abstract = {Ancient DNA provides a unique frame for directly studying human population genetics in time and space. Still, since most of the ancient genomic data is low coverage, analysis is confronted with a low number of SNPs, genotype uncertainties, and reference-bias. Here, we for the first time benchmark the two distinct versions of Glimpse tools on 120 ancient human genomes from Eurasia including those largely from previously under-evaluated regions and compare the performance of genotype imputation with de facto analysis approaches for low coverage genomic data analysis. We further investigate the impact of two distinct reference panels on imputation accuracy for low coverage genomic data. We compute accuracy statistics and perform PCA and f4-statistics to explore the behaviour of genotype imputation on low coverage data regarding (i)two versions of Glimpse, (ii)two reference panels, (iii)four post-imputation filters and coverages, as well as (iv)data type and geographical origin of the samples on the analyses. Our results reveal that even for 0.1X coverage ancient human genomes, genotype imputation using Glimpse-v2 is suitable. Additionally, using the 1000 Genomes merged with Human Genome Diversity Panel improves the accuracy of imputation for the rare variants with low MAF, which might be important not only for ancient genomics but also for modern human genomic studies based on low coverage data and for haplotype-based analysis. Most importantly, we reveal that genotype imputation of low coverage ancient human genomes reduces the genetic affinity of the samples towards human reference genome. Through solving one of the most challenging biases in data analysis, so-called reference bias, genotype imputation using Glimpse v2 is promising for low coverage ancient human genomic data analysis and for rare-variant-based and haplotype-based analysis.}, }
@article {pmid39026955, year = {2024}, author = {Worth, JRP and Kikuchi, S and Kanetani, S and Takahashi, D and Aizawa, M and Marchuk, EA and Choi, HJ and Polezhaeva, MA and Sheiko, VV and Ueno, S}, title = {Chloroplast genome-based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11584}, pmid = {39026955}, issn = {2045-7758}, abstract = {The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.}, }
@article {pmid39018301, year = {2024}, author = {Del Papa, M and De Los Reyes, M and Poiré, DG and Rascovan, N and Jofré, G and Delgado, M}, title = {Anthropic cut marks in extinct megafauna bones from the Pampean region (Argentina) at the last glacial maximum.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0304956}, pmid = {39018301}, issn = {1932-6203}, mesh = {*Fossils ; Animals ; Argentina ; *Bone and Bones/anatomy &amp; histology ; Humans ; *Extinction, Biological ; Xenarthra/anatomy &amp; histology ; Paleontology ; Archaeology ; }, abstract = {The initial peopling of South America is a topic of intense archaeological debate. Among the most contentious issues remain the nature of the human-megafauna interaction and the possible role of humans, along with climatic change, in the extinction of several megamammal genera at the end of the Pleistocene. In this study, we present the analysis of fossil remains with cutmarks belonging to a specimen of Neosclerocalyptus (Xenarthra, Glyptodontidae), found on the banks of the Reconquista River, northeast of the Pampean region (Argentina), whose AMS 14C dating corresponds to the Last Glacial Maximum (21,090-20,811 cal YBP). Paleoenvironmental reconstructions, stratigraphic descriptions, absolute chronological dating of bone materials, and deposits suggest a relatively rapid burial event of the bone assemblage in a semi-dry climate during a wet season. Quantitative and qualitative analyses of the cut marks, reconstruction of butchering sequences, and assessments of the possible agents involved in the observed bone surface modifications indicate anthropic activities. Our results provide new elements for discussing the earliest peopling of southern South America and specifically for the interaction between humans and local megafauna in the Pampean region during the Last Glacial Maximum.}, }
@article {pmid39013011, year = {2024}, author = {Williams, MP and Flegontov, P and Maier, R and Huber, CD}, title = {Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA.}, journal = {Genetics}, volume = {228}, number = {1}, pages = {}, pmid = {39013011}, issn = {1943-2631}, support = {R35GM146886//National Institute of Health/ ; CZ.10.03.01/00/22_003/0000003//European Union/ ; R35 GM146886/GM/NIGMS NIH HHS/United States ; CZ.10.03.01/00/22_003/0000003//European Union Operational Programme/ ; 61220//John Templeton Foundation/ ; 21-27624S//Czech Science Foundation/ ; LL2103//Czech Ministry of Education, Youth and Sports/ ; }, mesh = {*DNA, Ancient/analysis ; Humans ; *Models, Genetic ; Genetics, Population/methods ; Gene Flow ; Polymorphism, Single Nucleotide ; Genome, Human ; Evolution, Molecular ; }, abstract = {Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches-firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes-and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudohaploidization. We observe that population differentiation is the primary factor driving qpAdm performance. Notably, while complex gene flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible among a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations.}, }
@article {pmid39009303, year = {2024}, author = {Shen, Q and Wu, Z and Zan, J and Yang, X and Guo, J and Ji, Z and Wang, B and Liu, Y and Mao, X and Wang, X and Zou, X and Zhou, H and Peng, Y and Ma, H and He, H and Bai, T and Xu, M and Wen, S and Jin, L and Zhang, Q and Wang, CC}, title = {Ancient genomes illuminate the demographic history of Shandong over the past two millennia.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.07.008}, pmid = {39009303}, issn = {1673-8527}, abstract = {Shandong province, located in the Lower Yellow River, is one of the birthplaces of ancient Chinese civilization. However, the comprehensive genetic histories of this region have remained largely unknown until now due to a lack of ancient human genomes. Here, we present 21 ancient genomes from Shandong dating from the Warring States period to the Jin-Yuan Dynasties. Unlike the early Neolithic samples from Shandong, the historical samples are most closely related to post-Late Neolithic populations of the Middle Yellow River Basin, suggesting a population turnover in Shandong from the Neolithic Age to the Historical era. In addition, we detect a close genetic affinity between the historical samples in Shandong and present-day Han Chinese, showing long-term genetic stability in Han Chinese at least since the Warring States period.}, }
@article {pmid39009302, year = {2024}, author = {Yu, Y and Yang, X and Liu, D and Du, P and Meng, H and Huang, Z and Xiong, J and Ding, Y and Ren, X and Allen, E and Wang, H and Han, S and Jin, L and Wang, CC and Wen, S}, title = {Ancient genomic analysis of a Chinese hereditary elite from the Northern and Southern Dynasties.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.07.009}, pmid = {39009302}, issn = {1673-8527}, abstract = {China's Northern and Southern Dynasties period (3rd-6th centuries AD) marked a significant era of ethnic integration in northern China. However, previous ancient DNA studies have primarily focused on northern ethnic groups, with limited research on the genetic formation of the hereditary elite family, especially considering their abundant archaeological record and clear material identity. In this study, we obtained the ancient genome of a hereditary elite family, Gao Bin (, 503 AD-572 AD), at 0.6473-fold coverage with 475,132 single-nucleotide polymorphisms (SNPs) on the 1240k panel. His mitochondrial haplogroup belonged to Z4 and Y-haplogroup to O1a1a2b-F2444∗. The genetic profile of Gao Bin was most similar to that of the northern Han Chinese. He could be modeled as deriving all his ancestry from Late Neolithic to Iron Age Yellow River farmers without influence from Northeast Asia, Korea, or the Mongolian Plateau. Our study sheds light on the genetic formation of hereditary elite families in the context of the Southern and Northern Dynasties ethnic integration.}, }
@article {pmid39002897, year = {2024}, author = {Du, S and Chen, J and Li, J and Qian, W and Wu, S and Peng, Q and Liu, Y and Pan, T and Li, Y and Hadi, SS and Tan, J and Yuan, Z and Wang, J and Tang, K and Wang, Z and Wen, Y and Dong, X and Zhou, W and Ruiz-Linares, A and Shi, Y and Jin, L and Liu, F and Zhang, M and Wang, S}, title = {A multi-ancestry GWAS meta-analysis of facial features and its application in predicting archaic human features.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.07.005}, pmid = {39002897}, issn = {1673-8527}, abstract = {Facial morphology, a complex trait influenced by genetics, holds great significance in evolutionary research. However, due to limited fossil evidence, the facial characteristics of Neanderthals and Denisovans have remained largely unknown. In this study, we conducted a large-scale multi-ethnic meta-analysis of the genome-wide association study (GWAS), including 9674 East Asians and 10,115 Europeans, quantitatively assessing 78 facial traits using 3D facial images. We identified 71 genomic loci associated with facial features, including 21 novel loci. We developed a facial polygenic score (FPS) that enables the prediction of facial features based on genetic information. Interestingly, the distribution of FPSs among populations from diverse continental groups exhibited relevant correlations with observed facial features. Furthermore, we applied the FPS to predict the facial traits of seven Neanderthals and one Denisovan using ancient DNA and aligned predictions with the fossil records. Our results suggested that Neanderthals and Denisovans likely shared similar facial features, such as a wider but shorter nose and a wider endocanthion distance. The decreased mouth width was characterized specifically in Denisovans. The integration of genomic data and facial trait analysis provides valuable insights into the evolutionary history and adaptive changes in human facial morphology.}, }
@article {pmid38996487, year = {2024}, author = {Sandoval-Velasco, M and Dudchenko, O and Rodríguez, JA and Pérez Estrada, C and Dehasque, M and Fontsere, C and Mak, SST and Khan, R and Contessoto, VG and Oliveira Junior, AB and Kalluchi, A and Zubillaga Herrera, BJ and Jeong, J and Roy, RP and Christopher, I and Weisz, D and Omer, AD and Batra, SS and Shamim, MS and Durand, NC and O'Connell, B and Roca, AL and Plikus, MV and Kusliy, MA and Romanenko, SA and Lemskaya, NA and Serdyukova, NA and Modina, SA and Perelman, PL and Kizilova, EA and Baiborodin, SI and Rubtsov, NB and Machol, G and Rath, K and Mahajan, R and Kaur, P and Gnirke, A and Garcia-Treviño, I and Coke, R and Flanagan, JP and Pletch, K and Ruiz-Herrera, A and Plotnikov, V and Pavlov, IS and Pavlova, NI and Protopopov, AV and Di Pierro, M and Graphodatsky, AS and Lander, ES and Rowley, MJ and Wolynes, PG and Onuchic, JN and Dalén, L and Marti-Renom, MA and Gilbert, MTP and Aiden, EL}, title = {Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.}, journal = {Cell}, volume = {187}, number = {14}, pages = {3541-3562.e51}, doi = {10.1016/j.cell.2024.06.002}, pmid = {38996487}, issn = {1097-4172}, support = {R35 GM146852/GM/NIGMS NIH HHS/United States ; R35 GM147467/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Mammoths/genetics ; *Genome/genetics ; Female ; *Skin ; Elephants/genetics ; Chromatin/genetics ; Fossils ; DNA, Ancient/analysis ; Mice ; Humans ; X Chromosome/genetics ; }, abstract = {Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.}, }
@article {pmid38996465, year = {2024}, author = {Sawchuk, EA and Sirak, KA and Manthi, FK and Ndiema, EK and Ogola, CA and Prendergast, ME and Reich, D and Aluvaala, E and Ayodo, G and Badji, L and Bird, N and Black, W and Fregel, R and Gachihi, N and Gibbon, VE and Gidna, A and Goldstein, ST and Hamad, R and Hassan, HY and Hayes, VM and Hellenthal, G and Kebede, S and Kurewa, A and Kusimba, C and Kyazike, E and Lane, PJ and MacEachern, S and Massilani, D and Mbua, E and Morris, AG and Mutinda, C and M'Mbogori, FN and Reynolds, AW and Tishkoff, S and Vilar, M and Yimer, G}, title = {Charting a landmark-driven path forward for population genetics and ancient DNA research in Africa.}, journal = {American journal of human genetics}, volume = {111}, number = {7}, pages = {1243-1251}, pmid = {38996465}, issn = {1537-6605}, mesh = {Humans ; *DNA, Ancient/analysis ; *Genetics, Population ; Africa ; Genomics ; Black People/genetics ; }, abstract = {Population history-focused DNA and ancient DNA (aDNA) research in Africa has dramatically increased in the past decade, enabling increasingly fine-scale investigations into the continent's past. However, while international interest in human genomics research in Africa grows, major structural barriers limit the ability of African scholars to lead and engage in such research and impede local communities from partnering with researchers and benefitting from research outcomes. Because conversations about research on African people and their past are often held outside Africa and exclude African voices, an important step for African DNA and aDNA research is moving these conversations to the continent. In May 2023 we held the DNAirobi workshop in Nairobi, Kenya and here we synthesize what emerged most prominently in our discussions. We propose an ideal vision for population history-focused DNA and aDNA research in Africa in ten years' time and acknowledge that to realize this future, we need to chart a path connecting a series of "landmarks" that represent points of consensus in our discussions. These include effective communication across multiple audiences, reframed relationships and capacity building, and action toward structural changes that support science and beyond. We concluded there is no single path to creating an equitable and self-sustaining research ecosystem, but rather many possible routes linking these landmarks. Here we share our diverse perspectives as geneticists, anthropologists, archaeologists, museum curators, and educators to articulate challenges and opportunities for African DNA and aDNA research and share an initial map toward a more inclusive and equitable future.}, }
@article {pmid38993187, year = {2023}, author = {Meng, XY and Wang, QL and Shi, MJ and Zhang, HY}, title = {Historical Pathogen-Driven Selection May Contribute to Contemporary Ethnic Difference in Bladder Cancer Susceptibility.}, journal = {Bladder cancer (Amsterdam, Netherlands)}, volume = {9}, number = {3}, pages = {211-216}, pmid = {38993187}, issn = {2352-3735}, abstract = {BACKGROUND: The rationale for ethnic differences in bladder cancer (BCa) susceptibility is an important open question. In this study, we raised the hypothesis that the APOBEC3-rs1014971 variant associated with BCa risk and APOBEC-mutagenesis probably contribute to ethnic differences.<br><br>METHODS: We calculated the ethnicity-stratified 5-year age-adjusted incidence rates of BCa using the US SEER database. We performed somatic mutational-signature analyses and compared the APOBEC-related mutational contribution across BCa tumors in patients of different ethnicities. We analyzed the allele frequency distribution of APOBEC3-related rs1014971 in contemporary populations of different ethnicities and in ancient human genomes. We also analyzed the natural selection profiles and ages of the investigated SNPs.<br><br>RESULTS: We validated the ethnic difference in BCa risk using US SEER data, revealing Caucasians to be at >2-fold greater risk than Asians / Pacific islanders. In contemporary populations, we observed a coherent ethnic distribution in terms not only of the allele frequency of APOBEC3-related rs1014971, but also the mutational contribution of APOBEC-mediated mutagenesis in BCa tumors. Population genetics and ancient genome analyses further suggested that the diverse ethnic distribution of rs1014971 could be rooted in human evolution.<br><br>CONCLUSIONS: It is possible that APOBEC3-related rs1014971 is involved in the different BCa incidence across ethnic groups, and this difference is potentially derived from human evolution. Our findings suggested an evolutionary link between contemporary population-level variations in malignancy susceptibility and pathogen-driven selection in the past, not unlike previously reported cases of certain autoimmune and metabolic disorders.}, }
@article {pmid38987254, year = {2024}, author = {Bergström, A}, title = {Improving data archiving practices in ancient genomics.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {754}, pmid = {38987254}, issn = {2052-4463}, mesh = {*Genomics ; Humans ; *DNA, Ancient/analysis ; Animals ; Metadata ; }, abstract = {Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.}, }
@article {pmid38986104, year = {2024}, author = {Jordan, B}, title = {[Ancient DNA speaks].}, journal = {Medecine sciences : M/S}, volume = {40}, number = {6-7}, pages = {563-565}, doi = {10.1051/medsci/2024070}, pmid = {38986104}, issn = {1958-5381}, mesh = {Humans ; *DNA, Ancient/analysis ; Sequence Analysis, DNA/methods ; Pedigree ; }, abstract = {Many human DNA sequences have been obtained from ancient remains dating back from several millennia. However, these have low coverage and may contain many errors; this has limited their usefulness for many analyses, in particular the search for Identical By Descent (IBD) segments that is very powerful for detection of kinship. A new method, using imputation from database data and sophisticated statistical analysis, proves able to detect IBD segments (and thus parenthood) in low-quality DNA sequences from individuals linked only by sixth degree parenthood, opening a whole new field of investigation using ancient DNA.}, }
@article {pmid38981530, year = {2024}, author = {Goldstein, ST and Mueller, NG and Janzen, A and Ogola, C and Dal Martello, R and Fernandes, R and Li, S and Iminjili, V and Juengst, S and Odera Otwani, A and Sawchuk, EA and Wang, K and Ndiema, E and Boivin, N}, title = {Early agriculture and crop transitions at Kakapel Rockshelter in the Lake Victoria region of eastern Africa.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2026}, pages = {20232747}, pmid = {38981530}, issn = {1471-2954}, support = {//Max-Planck-Institut f&#xfc;r Menschheitsgeschichte/ ; }, mesh = {*Crops, Agricultural ; Kenya ; *Archaeology ; *Agriculture ; Animals ; Radiometric Dating ; Africa, Eastern ; }, abstract = {The histories of African crops remain poorly understood despite their contemporary importance. Integration of crops from western, eastern and northern Africa probably first occurred in the Great Lakes Region of eastern Africa; however, little is known about when and how these agricultural systems coalesced. This article presents archaeobotanical analyses from an approximately 9000-year archaeological sequence at Kakapel Rockshelter in western Kenya, comprising the largest and most extensively dated archaeobotanical record from the interior of equatorial eastern Africa. Direct radiocarbon dates on carbonized seeds document the presence of the West African crop cowpea (Vigna unguiculata (L.) Walp) approximately 2300 years ago, synchronic with the earliest date for domesticated cattle (Bos taurus). Peas (Pisum sativum L. or Pisum abyssinicum A. Braun) and sorghum (Sorghum bicolor (L.) Moench) from the northeast and eastern African finger millet (Eleusine coracana (L.) Gaertn.) are incorporated later, by at least 1000 years ago. Combined with ancient DNA evidence from Kakapel and the surrounding region, these data support a scenario in which the use of diverse domesticated species in eastern Africa changed over time rather than arriving and being maintained as a single package. Findings highlight the importance of local heterogeneity in shaping the spread of food production in sub-Saharan Africa.}, }
@article {pmid38976766, year = {2024}, author = {Souilmi, Y and Wasef, S and Williams, MP and Conroy, G and Bar, I and Bover, P and Dann, J and Heiniger, H and Llamas, B and Ogbourne, S and Archer, M and Ballard, JWO and Reed, E and Tobler, R and Koungoulos, L and Walshe, K and Wright, JL and Balme, J and O'Connor, S and Cooper, A and Mitchell, KJ}, title = {Ancient genomes reveal over two thousand years of dingo population structure.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {30}, pages = {e2407584121}, pmid = {38976766}, issn = {1091-6490}, support = {CE170100015//Department of Education and Training | Australian Research Council (ARC)/ ; DP210101960//Department of Education and Training | Australian Research Council (ARC)/ ; FL140100260//Department of Education and Training | Australian Research Council (ARC)/ ; 2021/GNT2011277//DHAC | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Animals ; Australia ; *Genome ; Dogs/genetics ; Wolves/genetics ; DNA, Ancient/analysis ; Genetics, Population ; }, abstract = {Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.}, }
@article {pmid38969261, year = {2024}, author = {Wang, M and Chen, H and Luo, L and Huang, Y and Duan, S and Yuan, H and Tang, R and Liu, C and He, G}, title = {Forensic investigative genetic genealogy: expanding pedigree tracing and genetic inquiry in the genomic era.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2024.06.016}, pmid = {38969261}, issn = {1673-8527}, abstract = {Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descent to understand kinship, migration patterns, and population dynamics. Within forensic science, forensic investigative genetic genealogy (FIGG) has gained prominence by leveraging next-generation sequencing technologies and population-specific genomic resources, opening new investigative avenues. In this review, we synthesize current knowledge, underscore recent advancements, and discuss the growing role of FIGG in forensic genomics. FIGG has been pivotal in revitalizing dormant inquiries and offering new genetic leads in numerous cold cases. Its effectiveness relies on the extensive single-nucleotide polymorphism profiles contributed by individuals from diverse populations to specialized genomic databases. Advances in computational genomics and the growth of human genomic databases have spurred a profound shift in the application of genetic genealogy across forensics, anthropology, and ancient DNA studies. As the field progresses, FIGG is evolving from a nascent practice into a more sophisticated and specialized discipline, shaping the future of forensic investigations.}, }
@article {pmid38965340, year = {2024}, author = {Gibbon, VE and Thompson, JC and Alves, S}, title = {Informed proxy consent for ancient DNA research.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {815}, pmid = {38965340}, issn = {2399-3642}, mesh = {Humans ; *Informed Consent ; *DNA, Ancient/analysis ; }, abstract = {We argue for implementation of informed proxy or relational autonomy consent in human aDNA research, where the deceased may be represented by living people the research affects. Embracing the underlying principles and process of informed proxy consent has the potential to transform research by (1) enriching outcomes by learning from and collaborating with interested and affected persons; (2) empowering people potentially impacted by research to stipulate evidence for information flow; (3) guarding researchers against actual or perceived violations by providing a common set of guidelines; and (4) highlighting the essential nature of long-term consultation and community partnerships to research outcome success.}, }
@article {pmid38963678, year = {2024}, author = {Coppola Bove, L and Kirkpatrick, CL and Vigil-Escalera Guirado, A and Botella López, MC and Bos, KI}, title = {A morphological and molecular approach to investigating infectious disease in early medieval Iberia: The necropolis of La Olmeda (Palencia, Spain).}, journal = {American journal of biological anthropology}, volume = {185}, number = {1}, pages = {e24994}, doi = {10.1002/ajpa.24994}, pmid = {38963678}, issn = {2692-7691}, support = {//Erasmus+ Traineeship Program Scholarship/ ; //Junta de Andaluc&#xed;a and SEPIE/ ; 756-2023-0246//Social Sciences and Humanities Research Council of Canada Postdoctoral Fellowship/ ; 805268/ERC_/European Research Council/International ; }, mesh = {Humans ; Male ; History, Medieval ; Spain ; Female ; Adult ; Middle Aged ; *Malaria/history ; Young Adult ; Adolescent ; Child ; DNA, Ancient/analysis ; Child, Preschool ; Infant ; Bone and Bones/pathology/microbiology ; Communicable Diseases/history ; Paleopathology ; Brucellosis/history ; Tuberculosis/history ; }, abstract = {OBJECTIVE: Here we investigate infectious diseases that potentially contribute to osteological lesions in individuals from the early medieval necropolis of La Olmeda (6th-11th c. CE) in North Iberia.<br><br>MATERIALS AND METHODS: We studied a minimum number of 268 individuals (33 adult females; 38 adult males, 77 unknown/indeterminate sex; and 120 non-adults), including articulated and commingled remains. Individuals with differential diagnoses suggesting chronic systemic infectious diseases were sampled and bioinformatically screened for ancient pathogen DNA.<br><br>RESULTS: Five non-adults (and no adults) presented skeletal evidence of chronic systemic infectious disease (1.87% of the population; 4.67% of non-adults). The preferred diagnoses for these individuals included tuberculosis, brucellosis, and malaria. Ancient DNA fragments assigned to the malaria-causing pathogen, Plasmodium spp., were identified in three of the five individuals. Observed pathology includes lesions generally consistent with malaria; however, additional lesions in two of the individuals may represent hitherto unknown variation in the skeletal manifestation of this disease or co-infection with tuberculosis or brucellosis. Additionally, spondylolysis was observed in one individual with skeletal lesions suggestive of infectious disease.<br><br>CONCLUSIONS: This study sheds light on the pathological landscape in Iberia during a time of great social, demographic, and environmental change. Genetic evidence challenges the hypothesis that malaria was absent from early medieval Iberia and demonstrates the value of combining osteological and archaeogenetic methods. Additionally, all of the preferred infectious diagnoses for the individuals included in this study (malaria, tuberculosis, and brucellosis) could have contributed to the febrile cases described in historical sources from this time.}, }
@article {pmid38960861, year = {2024}, author = {Dolenz, S and van der Valk, T and Jin, C and Oppenheimer, J and Sharif, MB and Orlando, L and Shapiro, B and Dalén, L and Heintzman, PD}, title = {Unravelling reference bias in ancient DNA datasets.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {7}, pages = {}, pmid = {38960861}, issn = {1367-4811}, support = {2021.0048//Knut and Alice Wallenberg Foundation/ ; }, mesh = {*DNA, Ancient/analysis ; Humans ; *Sequence Analysis, DNA/methods ; Software ; Animals ; Sequence Alignment/methods ; Computational Biology/methods ; Algorithms ; }, abstract = {MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.<br><br>RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.<br><br>AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).}, }
@article {pmid38957694, year = {2024}, author = {Mousavi-Derazmahalleh, M and Haue, N and Kanstrup, M and Laursen, JT and Lukehurst, SS and Kveiborg, J and Allentoft, ME}, title = {Far away from home? Ancient DNA shows the presence of bicolored shrew (Crocidura leucodon) in Bronze Age Denmark.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11680}, pmid = {38957694}, issn = {2045-7758}, abstract = {An excavation of an Early Iron Age village near Aalborg in Denmark uncovered the jaws and skull fragments from a small mammal that were morphologically identified to the genus Crocidura (white-toothed shrews). Three Crocidura species are known from prehistoric continental Europe but none of them are distributed in Scandinavia, which is why this surprising finding warranted further analyses. The bone was radiocarbon-dated to 2840-2750 calibrated years before present (cal. BP), corresponding to the Late Bronze Age and hence earlier than the Iron Age archeological context in which it was found. Using highly optimized ancient DNA protocols, we extracted DNA from one tooth and shotgun-sequenced the sample to reconstruct a near-complete mitochondrial reference genome (17,317 bp, 32.6× coverage). Phylogenetic analyses determined this specimen as a bicolored shrew (Crocidura leucodon) but with a phylogenetic position basal to the clade of known sequences from this species. The confirmation of Crocidura presence in Denmark by the Late Bronze Age sheds new light on the prehistoric natural history of Scandinavia. We discuss the implications of this finding from both zoo-archeological and ecological perspectives. Furthermore, the mitochondrial genome reconstructed in this study offers a valuable resource for future research exploring the genetic makeup and evolutionary history of Eurasian shrew populations.}, }
@article {pmid38957308, year = {2024}, author = {Çokoğlu, SS and Koptekin, D and Fidan, FR and Somel, M}, title = {Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise.}, journal = {Evolutionary applications}, volume = {17}, number = {7}, pages = {e13743}, pmid = {38957308}, issn = {1752-4571}, abstract = {The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.}, }
@article {pmid38948161, year = {2024}, author = {Özdoğan, KT and Gelabert, P and Hammers, N and Altınışık, NE and de Groot, A and Plets, G}, title = {Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past.}, journal = {Archaeological and anthropological sciences}, volume = {16}, number = {7}, pages = {108}, pmid = {38948161}, issn = {1866-9557}, abstract = {Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evolutionary history of a few species. However, its application in archaeology has been limited and primarily focused on humans. This article argues that sedaDNA holds significant potential in addressing key archaeological questions concerning the origins, lifestyles, and environments of past human populations. Our aim is to facilitate the integration of sedaDNA into the standard workflows in archaeology as a transformative tool, thereby unleashing its full potential for studying the human past. Ultimately, we not only underscore the challenges inherent in the sedaDNA field but also provide a research agenda for essential enhancements needed for implementing sedaDNA into the archaeological workflow.}, }
@article {pmid38946459, year = {2024}, author = {Özkan, M and Gürün, K and Yüncü, E and Vural, KB and Atağ, G and Akbaba, A and Fidan, FR and Sağlıcan, E and Altınışık, EN and Koptekin, D and Pawłowska, K and Hodder, I and Adcock, SE and Arbuckle, BS and Steadman, SR and McMahon, G and Erdal, YS and Bilgin, CC and Togan, &#x130; and Geigl, EM and Götherström, A and Grange, T and Özer, F and Somel, M}, title = {The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus).}, journal = {Molecular ecology}, volume = {33}, number = {14}, pages = {e17440}, doi = {10.1111/mec.17440}, pmid = {38946459}, issn = {1365-294X}, support = {772390//European Research Council Consolidator Grant H2020/ ; 952317//European Commission Horizon 2020 TWINNING Programme/ ; 117Z991//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; }, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Haplotypes/genetics ; *Phylogeny ; *Gene Flow ; Equidae/genetics ; Genome, Mitochondrial ; Extinction, Biological ; Fossils ; Genetics, Population ; Genetic Variation ; }, abstract = {We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present-day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid-first millennium BCE, a possible sign of its eventual demise.}, }
@article {pmid38942016, year = {2024}, author = {Dehasque, M and Morales, HE and Díez-Del-Molino, D and Pečnerová, P and Chacón-Duque, JC and Kanellidou, F and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Nikolskiy, P and Danilov, GK and Giannì, M and van der Sluis, L and Higham, T and Heintzman, PD and Oskolkov, N and Gilbert, MTP and Götherström, A and van der Valk, T and Vartanyan, S and Dalén, L}, title = {Temporal dynamics of woolly mammoth genome erosion prior to extinction.}, journal = {Cell}, volume = {187}, number = {14}, pages = {3531-3540.e13}, doi = {10.1016/j.cell.2024.05.033}, pmid = {38942016}, issn = {1097-4172}, mesh = {Animals ; *Mammoths/genetics ; *Extinction, Biological ; *Genome/genetics ; *Mutation ; Siberia ; Phylogeny ; Evolution, Molecular ; Time Factors ; }, abstract = {A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.}, }
@article {pmid38932149, year = {2024}, author = {Ferreira, RC and Alves, GV and Ramon, M and Antoneli, F and Briones, MRS}, title = {Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data.}, journal = {Viruses}, volume = {16}, number = {6}, pages = {}, pmid = {38932149}, issn = {1999-4915}, support = {20/08943-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; }, mesh = {Animals ; *Neanderthals/genetics/virology ; *Genome, Viral ; *DNA, Ancient/analysis ; Evolution, Molecular ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; Humans ; Phylogeny ; DNA Viruses/genetics/classification/isolation &amp; purification ; Fossils/virology ; }, abstract = {DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10[-5] to 10[-8] substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.}, }
@article {pmid38929847, year = {2024}, author = {Puga, M and Serrano, JG and García, EL and González Carracedo, MA and Jiménez-Canino, R and Pino-Yanes, M and Karlsson, R and Sullivan, PF and Fregel, R}, title = {El Hierro Genome Study: A Genomic and Health Study in an Isolated Canary Island Population.}, journal = {Journal of personalized medicine}, volume = {14}, number = {6}, pages = {}, pmid = {38929847}, issn = {2075-4426}, support = {D0886501//Swedish Research Council/ ; PID2021-123080NB-I00//Spanish Ministry of Science, Innovation, and Universities/ ; RYC-2015-17205//Spanish Ministry of Science, Innovation, and Universities/ ; }, abstract = {El Hierro is the smallest and westernmost island of the Canary Islands, whose population derives from an admixture of different ancestral components and that has been subjected to genetic isolation. We established the "El Hierro Genome Study" to characterize the health status and the genetic composition of ~10% of the current population of the island, accounting for a total of 1054 participants. Detailed demographic and clinical data and a blood sample for DNA extraction were obtained from each participant. Genomic genotyping was performed with the Global Screening Array (Illumina). The genetic composition of El Hierro was analyzed in a subset of 416 unrelated individuals by characterizing the mitochondrial DNA (mtDNA) and Y-chromosome haplogroups and performing principal component analyses (PCAs). In order to explore signatures of isolation, runs of homozygosity (ROHs) were also estimated. Among the participants, high blood pressure, hypercholesterolemia, and diabetes were the most prevalent conditions. The most common mtDNA haplogroups observed were of North African indigenous origin, while the Y-chromosome ones were mainly European. The PCA showed that the El Hierro population clusters near 1000 Genomes' European population but with a shift toward African populations. Moreover, the ROH analysis revealed some individuals with an important portion of their genomes with ROHs exceeding 400 Mb. Overall, these results confirmed that the "El Hierro Genome" cohort offers an opportunity to study the genetic basis of several diseases in an unexplored isolated population.}, }
@article {pmid38927726, year = {2024}, author = {Zhu, S and Zhang, N and Zhang, J and Shao, X and Guo, Y and Cai, D}, title = {Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China.}, journal = {Genes}, volume = {15}, number = {6}, pages = {}, pmid = {38927726}, issn = {2073-4425}, support = {NO.17ZDA221//Major Project of the National Social Science Foundation of China/ ; NO.2020YFC1521606//National Key Research and Development Program of China/ ; NO. 2022M722460//Project funded by China Postdoctoral Science Foundation/ ; NO. 2022CXTD17//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Horses/genetics ; *Genome, Mitochondrial/genetics ; China ; *DNA, Ancient/analysis ; *Haplotypes ; DNA, Mitochondrial/genetics ; Phylogeny ; History, Ancient ; High-Throughput Nucleotide Sequencing ; Domestication ; }, abstract = {This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.}, }
@article {pmid38927608, year = {2024}, author = {Di Stefano, B and Zupanič Pajnič, I and Concato, M and Bertoglio, B and Calvano, MG and Sorçaburu Ciglieri, S and Bosetti, A and Grignani, P and Addoum, Y and Vetrini, R and Introna, F and Bonin, S and Previderè, C and Fattorini, P}, title = {Evaluation of a New DNA Extraction Method on Challenging Bone Samples Recovered from a WWII Mass Grave.}, journal = {Genes}, volume = {15}, number = {6}, pages = {}, pmid = {38927608}, issn = {2073-4425}, support = {no available//Comunit&#xe0; di Lussino, Trieste, Italy/ ; }, mesh = {Humans ; *Bone and Bones/chemistry ; World War II ; DNA Fingerprinting/methods ; Forensic Genetics/methods ; Microsatellite Repeats/genetics ; DNA/genetics/isolation &amp; purification ; DNA, Ancient/analysis ; }, abstract = {Bones and teeth represent a common finding in ancient DNA studies and in forensic casework, even after a long burial. Genetic typing is the gold standard for the personal identification of skeletal remains, but there are two main factors involved in the successful DNA typing of such samples: (1) the set-up of an efficient DNA extraction method; (2) the identification of the most suitable skeletal element for the downstream genetic analyses. In this paper, a protocol based on the processing of 0.5 g of bone powder decalcified using Na2EDTA proved to be suitable for a semi-automated DNA extraction workflow using the Maxwell[®] FSC DNA IQ™ Casework Kit (Promega, Madison, WI, USA). The performance of this method in terms of DNA recovery and quality was compared with a full demineralisation extraction protocol based on Qiagen technology and kits. No statistically significant differences were scored according to the DNA recovery and DNA degradation index (p-values ≥ 0.176; r ≥ 0.907). This new DNA extraction protocol was applied to 88 bone samples (41 femurs, 19 petrous bones, 12 metacarpals and 16 molars) allegedly belonging to 27 World War II Italian soldiers found in a mass grave on the isle of Cres (Croatia). The results of the qPCR performed by the Quantifiler Human DNA Quantification kit showed values above the lowest Limit of Quantification (lLOQ; 23 pg/µL) for all petrous bones, whereas other bone types showed, in most cases, lower amounts of DNA. Replicate STR-CE analyses showed successful typing (that is, >12 markers) in all tests on the petrous bones, followed by the metacarpals (83.3%), femurs (52.2%) and teeth (20.0%). Full profiles (22/22 autosomal markers) were achieved mainly in the petrous bones (84.2%), followed by the metacarpals (41.7%). Stochastic amplification artefacts such as drop-outs or drop-ins occurred with a frequency of 1.9% in the petrous bones, whereas they were higher when the DNA recovered from other bone elements was amplified (up to 13.9% in the femurs). Overall, the results of this study confirm that petrous bone outperforms other bone elements in terms of the quantity and quality of the recovered DNA; for this reason, if available, it should always be preferred for genetic testing. In addition, our results highlight the need for accurate planning of the DVI operation, which should be carried out by a multi-disciplinary team, and the tricky issue of identifying other suitable skeletal elements for genetic testing. Overall, the results presented in this paper support the need to adopt preanalytical strategies positively related to the successful genetic testing of aged skeletal remains in order to reduce costs and the time of analysis.}, }
@article {pmid38926415, year = {2024}, author = {Austin, RM and Honap, TP and Mann, AE and Hübner, A and DeGaglia, CMS and Warinner, C and Zuckerman, MK and Hofman, CA}, title = {Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14720}, pmid = {38926415}, issn = {2045-2322}, support = {Pre-doctoral Fellowship//Smithsonian Institution, National Museum of Natural History, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; }, mesh = {*Dental Calculus/microbiology/history ; Humans ; *Metagenomics/methods ; *Paleopathology/methods ; *Tuberculosis/diagnosis/microbiology ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Male ; Treponema pallidum/genetics/isolation &amp; purification ; Syphilis/diagnosis/microbiology/history ; Female ; Adult ; Metagenome/genetics ; Middle Aged ; }, abstract = {Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution's Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of Treponema pallidum subsp. pallidum and Mycobacterium tuberculosis complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of T. p. pallidum DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections.}, }
@article {pmid38916350, year = {2024}, author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G}, title = {Exploring antimicrobial resistance determinants in the Neanderthal microbiome.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0266223}, pmid = {38916350}, issn = {2165-0497}, support = {20/2022-ECR-II//Indian Council of Medical Research (ICMR)/ ; }, mesh = {Animals ; *Microbiota/genetics/drug effects ; *Neanderthals/genetics/microbiology ; *DNA, Ancient/analysis ; *Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; Feces/microbiology ; Metagenome ; Drug Resistance, Microbial/genetics ; Europe ; Fossils/microbiology ; }, abstract = {UNLABELLED: This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history.<br><br>IMPORTANCE: The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.}, }
@article {pmid38913897, year = {2024}, author = {Sasso, S and Saag, L and Spros, R and Beneker, O and Molinaro, L and Biagini, SA and Lehouck, A and Van De Vijver, K and Hui, R and D'Atanasio, E and Kushniarevich, A and Kabral, H and Metspalu, E and Guellil, M and Ali, MQA and Geypen, J and Hoebreckx, M and Berk, B and De Winter, N and Driesen, P and Pijpelink, A and Van Damme, P and Scheib, CL and Deschepper, E and Deckers, P and Snoeck, C and Dewilde, M and Ervynck, A and Tambets, K and Larmuseau, MHD and Kivisild, T}, title = {Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {27}, pages = {e2406734121}, pmid = {38913897}, issn = {1091-6490}, support = {NA//agentschap Onroerend Erfgoed Archeologie syntheseproject/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; STG/18/021//KU Leuven start-up grant/ ; ZKD6488 C24M/19/075//KU Leuven BOF-C24/ ; NA//EWI-Vlaanderen citizien science project "MamaMito"/ ; PRG1027//Estonian Research fundation grant/ ; NA//Sapienza University Rome fellowship/ ; }, mesh = {Humans ; History, Medieval ; *Pedigree ; Belgium ; Burial/history ; Genetics, Population/methods ; Female ; Male ; DNA, Ancient/analysis ; England ; Human Migration ; Archaeology ; Netherlands ; Genome, Human ; }, abstract = {The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.}, }
@article {pmid38912151, year = {2024}, author = {Farhud, DD and Azari, M and Rahbar, M}, title = {Oral Infections in Ancient Human Skulls in 2000 BC/Iron Age, Iran.}, journal = {Iranian journal of public health}, volume = {53}, number = {5}, pages = {1115-1127}, pmid = {38912151}, issn = {2251-6093}, abstract = {BACKGROUND: Oral infections have been seen in humans since ancient times. Excessive penetration of this infection can cause human death. Most of these infections are gum cysts and abscesses. The cyst creates large hard lumps in the gums, which is causes loose, and protruding teeth and abscesses, causing cavities in the jawbone and teeth. In this article, we have discussed for this infectious disease in 4000 - year - old ancient humans from Qazvin Province, Iran. The bone remains of our research are related to Sagezabad ancient cemetery in Qazvin plain.<br><br>METHODS: We tried to use reliable international atlases to get detailed information about ancient oral infections. The bones were extracted from the 2019 excavation of the Ghara Tappe area of Sagezabad for the Iron Age 2[nd] and 3[rd] Qazvin plains of Iran. This cemetery belongs to the period of the Medes Kingdom (pre - Achaemenian kingdom) in Iran.<br><br>RESULTS: We have discussed one of the ancient cemeteries with a large number of ancient populations. In this cemetery, there are signs of war and infectious diseases on the bones, which can be clearly seen. We have specially mentioned the abscess as the cause of oral infection from Sagezabad cemetery.<br><br>CONCLUSION: Oral infection existed in Iran since 2000 BC. Of course, this infection was common in ancient times and even Paleolithic period, like Homo Heidelbergensis.}, }
@article {pmid38903121, year = {2024}, author = {Bougiouri, K and Aninta, SG and Charlton, S and Harris, A and Carmagnini, A and Piličiauskienė, G and Feuerborn, TR and Scarsbrook, L and Tabadda, K and Blaževičius, P and Parker, HG and Gopalakrishnan, S and Larson, G and Ostrander, EA and Irving-Pease, EK and Frantz, LAF and Racimo, F}, title = {Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38903121}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R[2]>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.}, }
@article {pmid38891676, year = {2024}, author = {Abdelmanova, AA and Deniskova, TE and Kharzinova, VR and Chinarov, RY and Boronetskaya, OI and Sölkner, J and Brem, G and Ai, H and Huang, L and Trukhachev, VI and Zinovieva, NA}, title = {Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {11}, pages = {}, pmid = {38891676}, issn = {2076-2615}, support = {23-46-00014//Russian Science Foundation/ ; }, abstract = {The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people's pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775-1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs.}, }
@article {pmid38886480, year = {2024}, author = {Laffranchi, Z and Zingale, S and Indra, L and Coia, V and Salazar García, DC and Paladin, A and Kaeser, MA and Delley, G and Szidat, S and Lösch, S and Zink, A and Milella, M}, title = {Geographic origin, ancestry, and death circumstances at the Cornaux/Les Sauges Iron Age bridge, Switzerland.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {12180}, pmid = {38886480}, issn = {2045-2322}, support = {10531FL_197103 / 1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; Funding Decree n.9/2021//Autonomous Province of Bolzano-Alto Adige - Department of Innovation, Research, University and Museums/ ; CIDEGENT/2019/061//Generalitat Valenciana/ ; }, mesh = {Humans ; Switzerland ; Male ; History, Ancient ; Adult ; Female ; *Archaeology ; Fossils ; Bone and Bones ; Radiometric Dating ; }, abstract = {Cornaux/Les Sauges (Switzerland, Late Iron Age) revealed remnants of a wooden bridge, artifacts, and human and animal skeletal remains. The relationship between the collapsed structure and the skeletal material, whether it indicates a potential accident or cultural practices, remains elusive. We evaluate the most plausible scenario for Cornaux based on osteological, taphonomic, isotopic, and paleogenomic analysis of the recovered individuals. The latter amount to at least 20 individuals, mostly adult males. Perimortem lesions include only blunt force traumas. Radiocarbon data fall between the 3rd and 1st c. BCE, although in some cases predating available dendrochronological estimates from the bridge. Isotopic data highlight five to eight nonlocals. No close genetic relatedness links the analyzed skeletons. Paleogenomic results, the first for Iron Age Switzerland, point to a genetic affinity with other Central and Western European Iron Age groups. The type of skeletal lesions supports an accidental event as the more plausible explanation. Radiocarbon data and the demographic structure of the sample may suggest a sequence of different events possibly including executions and/or sacrifices. Isotopic and paleogenomic data, while not favoring one scenario over the other, do support earlier interpretations of the last centuries BCE in Europe as a dynamic period from a biocultural perspective.}, }
@article {pmid38885310, year = {2024}, author = {Wang, M and Huang, Y and Liu, K and Wang, Z and Zhang, M and Yuan, H and Duan, S and Wei, L and Yao, H and Sun, Q and Zhong, J and Tang, R and Chen, J and Sun, Y and Li, X and Su, H and Yang, Q and Hu, L and Yun, L and Yang, J and Nie, S and Cai, Y and Yan, J and Zhou, K and Wang, C and ,  and Zhu, B and Liu, C and He, G}, title = {Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage.}, journal = {Molecular biology and evolution}, volume = {41}, number = {7}, pages = {}, pmid = {38885310}, issn = {1537-1719}, support = {82202078//National Natural Science Foundation of China/ ; 23&amp;ZD203//Major Project of the National Social Science Foundation of China/ ; }, mesh = {Humans ; *Human Migration ; China ; Male ; *Chromosomes, Human, Y/genetics ; DNA, Ancient/analysis ; Paternal Inheritance ; Phylogeny ; East Asian People ; }, abstract = {Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations.}, }
@article {pmid38883810, year = {2024}, author = {Pathak, AK and Simonian, H and Ibrahim, IAA and Hrechdakian, P and Behar, DM and Ayub, Q and Arsanov, P and Metspalu, E and Yepiskoposyan, L and Rootsi, S and Endicott, P and Villems, R and Sahakyan, H}, title = {Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection.}, journal = {iScience}, volume = {27}, number = {6}, pages = {110016}, pmid = {38883810}, issn = {2589-0042}, abstract = {West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.}, }
@article {pmid38881417, year = {2024}, author = {Green, MH}, title = {The Pandemic Arc: Expanded Narratives in the History of Global Health.}, journal = {Journal of the history of medicine and allied sciences}, volume = {79}, number = {4}, pages = {345-362}, doi = {10.1093/jhmas/jrae008}, pmid = {38881417}, issn = {1468-4373}, mesh = {Humans ; *Global Health/history ; *Pandemics/history ; History, 20th Century ; History, 19th Century ; History, 21st Century ; COVID-19/epidemiology/history ; History, 18th Century ; SARS-CoV-2 ; }, abstract = {Using the examples of plague, smallpox, and HIV/AIDS, the present essay argues for the benefits of incorporating the evolutionary histories of pathogens, beyond visible epidemic spikes within human populations, into our understanding of what pandemics actually are as epidemiological phenomena. The pandemic arc - which takes the pathogen as the defining "actor" in a pandemic, from emergence to local proliferation to globalization - offers a framework capable of bringing together disparate aspects not only of the manifestations of disease but also of human involvement in the pandemic process. Pathogens may differ, but there are common patterns in disease emergence and proliferation that distinguish those diseases that become pandemic, dispersed through human communities regionally or globally. The same methods of genomic analysis that allow tracking the evolutionary development of a modern pathogen such as SARS-CoV-2 also allow us to trace pandemics into the past. Reconstruction of these pandemic arcs brings new elements of these stories into view, recovering the experiences of regions and populations hitherto overlooked by Eurocentric narratives. This expanded global history of infectious diseases, in turn, lays a groundwork for reconceiving what ambitions a truly global health might aim for.}, }
@article {pmid38871872, year = {2024}, author = {Callaway, E}, title = {Ancient DNA from Maya ruins tells story of ritual human sacrifices.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {38871872}, issn = {1476-4687}, }
@article {pmid38870299, year = {2024}, author = {Curry, A}, title = {Sacrificed Maya boys tied to myth of 'Hero Twins'.}, journal = {Science (New York, N.Y.)}, volume = {384}, number = {6701}, pages = {1160-1161}, doi = {10.1126/science.adr0288}, pmid = {38870299}, issn = {1095-9203}, mesh = {Female ; Humans ; Male ; *DNA, Ancient ; History, Ancient ; *Twins/history ; Child ; *Ceremonial Behavior ; *Civilization/history ; }, abstract = {Ancient DNA shows continuity between living and ancient Maya communities.}, }
@article {pmid38845985, year = {2024}, author = {Tejero, JM and Cheronet, O and Gelabert, P and Zagorc, B and Álvarez-Fernández, E and Arias, P and Averbouh, A and Bar-Oz, G and Barzilai, O and Belfer-Cohen, A and Bosch, MD and Brück, F and Cueto, M and Dockner, M and Fullola, JM and Gárate, D and Giannakoulis, M and González, C and Jakeli, N and Mangado, X and Meshveliani, T and Neruda, P and Nigst, P and Ontañón, R and Shemer, M and Šimková, PG and Tapia, J and Sánchez de la Torre, M and Schwab, C and Weber, G and Pinhasi, R}, title = {Cervidae antlers exploited to manufacture prehistoric tools and hunting implements as a reliable source of ancient DNA.}, journal = {Heliyon}, volume = {10}, number = {11}, pages = {e31858}, pmid = {38845985}, issn = {2405-8440}, abstract = {Antler is one of the primary animal raw materials exploited for technical purposes by the hunter-gatherer groups of the Eurasian Upper Palaeolithic (UP) all over the ecological range of deers, and beyond. It was exhaustively employed to produce one of the most critical tools for the survival of the UP societies: hunting weapons. However, antler implements can be made from diverse deer taxa, with different ecological requirements and ethological behaviours. Identifying the antler's origin at a taxonomic level is thus essential in improving our knowledge of humans' functional, practical and symbolic choices, as well as the human-animal interface during Prehistoric times. Nevertheless, palaeogenetics analyses have focused mainly on bone and teeth, with genetic studies of antler generally focused on modern deer conservation. Here we present the results of the first whole mitochondrial genome ancient DNA (aDNA) analysis by means of in-solution hybridisation capture of antlers from pre-Holocene archaeological contexts. We analysed a set of 50 Palaeolithic and Neolithic (c. 34-8ka) antler and osseous objects from South-Western Europe, Central Europe, South-Western Asia and the Caucasus. We successfully obtained aDNA, allowing us to identify the exploited taxa and demonstrate the archaeological relevance of those finds. Moreover, as most of the antlers were sampled using a minimally-invasive method, further analyses (morphometric, technical, genetic, radiometric and more) remain possible on these objects.}, }
@article {pmid38830089, year = {2024}, author = {Fordham, DA and Brown, SC and Canteri, E and Austin, JJ and Lomolino, MV and Haythorne, S and Armstrong, E and Bocherens, H and Manica, A and Rey-Iglesia, A and Rahbek, C and Nogués-Bravo, D and Lorenzen, ED}, title = {52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {24}, pages = {e2316419121}, pmid = {38830089}, issn = {1091-6490}, support = {DP180102392//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {Animals ; *Extinction, Biological ; *Perissodactyla ; *Population Dynamics ; *Fossils ; Ecosystem ; DNA, Ancient/analysis ; Paleontology ; }, abstract = {The extinction of the woolly rhinoceros (Coelodonta antiquitatis) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.}, }
@article {pmid38813936, year = {2024}, author = {Arsuaga, JL and Martínez, I and Gracia-Téllez, A and Carretero, JM and Esquivel, A and García, N and Lorenzo, C and Quam, R and Aramburu, A and Sala, N and Trueba, J}, title = {How the Sima de los Huesos was won.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2225-2245}, doi = {10.1002/ar.25509}, pmid = {38813936}, issn = {1932-8494}, support = {PID2021-122355NB-C31 supported by MCIN/AEI/10.1303//Government of Spain/ ; //C&#xe1;tedra de Otoac&#xfa;stica Evolutiva y Paleoantropolog&#xed;a (HM Hospitales-Universidad de Alcal&#xe1;)/ ; EPU-INV-UAH/2022/006//Universidad de Alcal&#xe1;/ ; }, mesh = {Humans ; *Fossils ; Animals ; *Biological Evolution ; Female ; Male ; Hominidae/anatomy &amp; histology ; Spain ; }, abstract = {Although the first discovery of a human fossil in the Sima de los Huesos took place in 1976, systematic excavations did not begin there until 1984. Since then, this site has been continuously excavated in month-long camps. The site is dated by different radiometric techniques to between 430,000 and 300,000 years ago. Until the 2023 campaign, just over 7000 human fossils have been recovered, constituting the largest collection of fossils prior to Homo sapiens ever discovered. The fossils correspond to a minimum of 29 individuals of both sexes and different ages at death, from preadolescents to a specimen of advanced age. Comparative anatomy and ancient DNA studies both suggest that this is a population closely related to Homo neanderthalensis. The great variety and extraordinary quality of the fossils recovered have allowed us to carry out a series of investigations that have greatly increased our knowledge about the evolution of Homo in the Middle Pleistocene. Among the most important discoveries, it has been possible to establish body size and proportions, the confirmation that the origin of the accumulation of human fossils was of an anthropic nature, that those past humans took care of disabled individuals and who were capable of having an oral language almost as complex and efficient as that of our own species.}, }
@article {pmid38806487, year = {2024}, author = {Bagnasco, G and Marzullo, M and Cattaneo, C and Biehler-Gomez, L and Mazzarelli, D and Ricciardi, V and Müller, W and Coppa, A and McLaughlin, R and Motta, L and Prato, O and Schmidt, F and Gaveriaux, F and Marras, GB and Millet, MA and Madgwick, R and Ballantyne, R and Makarewicz, CA and Trentacoste, A and Reimer, P and Mattiangeli, V and Bradley, DG and Malone, C and Esposito, C and Breslin, EM and Stoddart, S}, title = {Bioarchaeology aids the cultural understanding of six characters in search of their agency (Tarquinia, ninth-seventh century BC, central Italy).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11895}, pmid = {38806487}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Italy ; Humans ; *Archaeology ; History, Ancient ; Male ; DNA, Ancient/analysis ; Female ; }, abstract = {Etruria contained one of the great early urban civilisations in the Italian peninsula during the first millennium BC, much studied from a cultural, humanities-based, perspective, but relatively little with scientific data, and rarely in combination. We have addressed the unusual location of twenty inhumations found in the sacred heart of the Etruscan city of Tarquinia, focusing on six of these as illustrative, contrasting with the typical contemporary cremations found in cemeteries on the edge of the city. The cultural evidence suggests that the six skeletons were also distinctive in their ritualization and memorialisation. Focusing on the six, as a representative sample, the scientific evidence of osteoarchaeology, isotopic compositions, and ancient DNA has established that these appear to show mobility, diversity and violence through an integrated bioarchaeological approach. The combination of multiple lines of evidence makes major strides towards a deeper understanding of the role of these extraordinary individuals in the life of the early city of Etruria.}, }
@article {pmid38798346, year = {2024}, author = {Fine, AG and Steinrücken, M}, title = {A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38798346}, issn = {2692-8205}, support = {R01 GM146051/GM/NIGMS NIH HHS/United States ; }, abstract = {Detecting and quantifying the strength of selection is a main objective in population genetics. Since selection acts over multiple generations, many approaches have been developed to detect and quantify selection using genetic data sampled at multiple points in time. Such time series genetic data is commonly analyzed using Hidden Markov Models, but in most cases, under the assumption of additive selection. However, many examples of genetic variation exhibiting non-additive mechanisms exist, making it critical to develop methods that can characterize selection in more general scenarios. Thus, we extend a previously introduced expectation-maximization algorithm for the inference of additive selection coefficients to the case of general diploid selection, in which the heterozygote and homozygote fitness are parameterized independently. We furthermore introduce a framework to identify bespoke modes of diploid selection from given data, as well as a procedure for aggregating data across linked loci to increase power and robustness. Using extensive simulation studies, we find that our method accurately and efficiently estimates selection coefficients for different modes of diploid selection across a wide range of scenarios; however, power to classify the mode of selection is low unless selection is very strong. We apply our method to ancient DNA samples from Great Britain in the last 4,450 years, and detect evidence for selection in six genomic regions, including the well-characterized LCT locus. Our work is the first genome-wide scan characterizing signals of general diploid selection.}, }
@article {pmid38796876, year = {2024}, author = {Psonis, N and Vassou, D and Nafplioti, A and Tabakaki, E and Pavlidis, P and Stamatakis, A and Poulakakis, N}, title = {Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes.}, journal = {Forensic science international. Genetics}, volume = {71}, number = {}, pages = {103060}, doi = {10.1016/j.fsigen.2024.103060}, pmid = {38796876}, issn = {1878-0326}, mesh = {Humans ; *DNA, Ancient/analysis ; *World War II ; Male ; Greece ; *DNA Fingerprinting ; Skull ; Genome, Human ; Forensic Anthropology ; Whole Genome Sequencing ; }, abstract = {In the Battle of Crete during the World War II occupation of Greece, the German forces faced substantial civilian resistance. To retribute the numerous German losses, a series of mass executions took place in numerous places in Crete; a common practice reported from Greece and elsewhere. In Adele, a village in the regional unit of Rethymnon, 18 male civilians were executed and buried in a burial pit at the Sarakina site. In this study, the first one conducted for a conflict that occurred in Greece, we identified for humanitarian purposes the 18 skulls of the Sarakina victims, following a request from the local community of Adele. The molecular identification of historical human remains via ancient DNA approaches and low coverage whole genome sequencing has only recently been introduced. Here, we performed genome skimming on the living relatives of the victims, as well as high throughput historical DNA analysis on the skulls to infer the kinship degrees among the victims via genetic relatedness analyses. We also conducted targeted anthropological analysis to successfully complete the identification of all Sarakina victims. We demonstrate that our methodological approach constitutes a potentially highly informative forensic tool to identify war victims. It can hence be applied to analogous studies on degraded DNA, thus, paving the path for systematic war victim identification in Greece and beyond.}, }
@article {pmid38795367, year = {2024}, author = {Larsson, MNA and Morell Miranda, P and Pan, L and Başak Vural, K and Kaptan, D and Rodrigues Soares, AE and Kivikero, H and Kantanen, J and Somel, M and Özer, F and Johansson, AM and Storå, J and Günther, T}, title = {Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.}, journal = {Genome biology and evolution}, volume = {16}, number = {6}, pages = {}, pmid = {38795367}, issn = {1759-6653}, support = {2017-05267//Vetenskapsr&#xe5;det/ ; P21-0266//Riksbankens Jubileumsfond/ ; CTS 18:129//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; //Knut and Alice Wallenberg Foundation/ ; //National Academic Infrastructure for Supercomputing in Sweden/ ; //Swedish National Infrastructure for Computing/ ; }, mesh = {Animals ; *Genome ; Sheep/genetics ; Genetic Variation ; Sheep, Domestic/genetics ; DNA, Ancient/analysis ; }, abstract = {Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.}, }
@article {pmid38781957, year = {2024}, author = {Bai, F and Liu, Y and Wangdue, S and Wang, T and He, W and Xi, L and Tsho, Y and Tsering, T and Cao, P and Dai, Q and Liu, F and Feng, X and Zhang, M and Ran, J and Ping, W and Payon, D and Mao, X and Tong, Y and Tsring, T and Chen, Z and Fu, Q}, title = {Ancient genomes revealed the complex human interactions of the ancient western Tibetans.}, journal = {Current biology : CB}, volume = {34}, number = {12}, pages = {2594-2605.e7}, doi = {10.1016/j.cub.2024.04.068}, pmid = {38781957}, issn = {1879-0445}, mesh = {Humans ; *DNA, Ancient/analysis ; East Asian People/genetics ; Genetics, Population ; *Genome, Human ; *Human Migration/history ; Tibet ; }, abstract = {The western Tibetan Plateau is the crossroad between the Tibetan Plateau, Central Asia, and South Asia, and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500-300 years before present (BP) in the Ngari prefecture. The ancient western Tibetan Plateau populations share the majority of their genetic components with the southern Tibetan Plateau populations and have maintained genetic continuity since 3,500 BP while maintaining interactions with populations within and outside the Tibetan Plateau. Within the Tibetan Plateau, the ancient western Tibetan Plateau populations were influenced by the additional expansion from the south to the southwest plateau before 1,800 BP. Outside the Tibetan Plateau, the western Tibetan Plateau populations interacted with both South and Central Asian populations at least 2,000 years ago, and the South Asian-related genetic influence, despite being very limited, was from the Indus Valley Civilization (IVC) migrants in Central Asia instead of the IVC populations from the Indus Valley. In light of the new genetic data, our study revealed the complex population interconnections across and within the Tibetan Plateau.}, }
@article {pmid38781323, year = {2024}, author = {Edwards, SV and Cloutier, A and Cockburn, G and Driver, R and Grayson, P and Katoh, K and Baldwin, MW and Sackton, TB and Baker, AJ}, title = {A nuclear genome assembly of an extinct flightless bird, the little bush moa.}, journal = {Science advances}, volume = {10}, number = {21}, pages = {eadj6823}, doi = {10.1126/sciadv.adj6823}, pmid = {38781323}, issn = {2375-2548}, mesh = {Animals ; *Birds/genetics ; *Genome ; *Extinction, Biological ; Cell Nucleus/genetics ; Phylogeny ; Fossils ; Genome, Mitochondrial ; Flight, Animal ; New Zealand ; Male ; DNA Transposable Elements/genetics ; Genomics/methods ; }, abstract = {We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.}, }
@article {pmid38769390, year = {2024}, author = {Borbély, N and Dudás, D and Tapasztó, A and Dudás-Boda, E and Csáky, V and Szeifert, B and Mende, BG and Egyed, B and Szécsényi-Nagy, A and Pamjav, H}, title = {Phylogenetic insights into the genetic legacies of Hungarian-speaking communities in the Carpathian Basin.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11480}, pmid = {38769390}, issn = {2045-2322}, support = {FK 127938//Hungarian National Research, Development, and Innovation Office/ ; }, mesh = {Humans ; *Phylogeny ; *Chromosomes, Human, Y/genetics ; Hungary ; *Genome, Mitochondrial ; Male ; Genetics, Population ; Female ; DNA, Mitochondrial/genetics ; DNA, Ancient/analysis ; Microsatellite Repeats/genetics ; Haplotypes ; }, abstract = {This study focuses on exploring the uniparental genetic lineages of Hungarian-speaking minorities residing in rural villages of Baranja (Croatia) and the Zobor region (Slovakia). We aimed to identify ancestral lineages by examining genetic markers distributed across the entire mitogenome and on the Y-chromosome. This allowed us to discern disparities in regional genetic structures within these communities. By integrating our newly acquired genetic data from a total of 168 participants with pre-existing Eurasian and ancient DNA datasets, our goal was to enrich the understanding of the genetic history trajectories of Carpathian Basin populations. Our findings suggest that while population-based analyses may not be sufficiently robust to detect fine-scale uniparental genetic patterns with the sample sizes at hand, phylogenetic analysis of well-characterized Y-chromosomal Short Tandem Repeat (STR) data and entire mitogenome sequences did uncover multiple lineage ties to far-flung regions and eras. While the predominant portions of both paternal and maternal DNA align with the East-Central European spectrum, rarer subhaplogroups and lineages have unveiled ancient ties to both prehistoric and historic populations spanning Europe and Eastern Eurasia. This research augments the expansive field of phylogenetics, offering critical perspectives on the genetic constitution and heritage of the communities in East-Central Europe.}, }
@article {pmid38756579, year = {2024}, author = {Wang, Z and Wang, M and Hu, L and He, G and Nie, S}, title = {Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives.}, journal = {Heliyon}, volume = {10}, number = {9}, pages = {e30067}, pmid = {38756579}, issn = {2405-8440}, abstract = {Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.}, }
@article {pmid38754423, year = {2024}, author = {Yuan, J and Hu, J and Liu, W and Chen, S and Zhang, F and Wang, S and Zhang, Z and Wang, L and Xiao, B and Li, F and Hofreiter, M and Lai, X and Westbury, MV and Sheng, G}, title = {Camelus knoblochi genome reveals the complex evolutionary history of Old World camels.}, journal = {Current biology : CB}, volume = {34}, number = {11}, pages = {2502-2508.e5}, doi = {10.1016/j.cub.2024.04.050}, pmid = {38754423}, issn = {1879-0445}, mesh = {Animals ; *Camelus/genetics ; *Phylogeny ; Genome ; Biological Evolution ; }, abstract = {Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.[1][,][2] Although many remains have been unearthed,[3][,][4][,][5] we know neither whether the prevalent hybridization observed between extant Camelus species[2][,][6][,][7] also occurred between extinct lineages and the ancestors of extant Camelus species nor why some populations became extinct while others survived. To investigate these questions, we generated paleogenomic and stable isotope data from an extinct two-humped camel species, Camelus knoblochi. We find that in the mitochondrial phylogeny, all C. knoblochi form a paraphyletic group that nests within the diversity of modern, wild two-humped camels (Camelus ferus). In contrast, they are clearly distinguished from both wild and domesticated (Camelus bactrianus) two-humped camels on the nuclear level. Moreover, the divergence pattern of the three camel species approximates a trifurcation, because the most common topology is only slightly more frequent than the two other possible topologies. This mito-nuclear phylogenetic discordance likely arose due to interspecific gene flow between all three species, suggesting that interspecific hybridization is not exclusive to modern camels but a recurrent phenomenon throughout the evolutionary history of the genus Camelus. These results suggest that the genomic complexity of Old World camels' evolutionary history is underestimated when considering data from only modern species. Finally, we find that C. knoblochi populations began declining prior to the last glacial maximum and, by integrating palaeoecological evidence and stable isotope data, suggest that this was likely due to failure to adapt to a changing environment.}, }
@article {pmid38750053, year = {2024}, author = {Cabrera, VM}, title = {New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11150}, pmid = {38750053}, issn = {2045-2322}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *DNA, Ancient/analysis ; *Phylogeography ; Spain ; Phylogeny ; Genetics, Population ; Indigenous Peoples/genetics ; Archaeology ; Human Migration ; History, Ancient ; High-Throughput Nucleotide Sequencing ; }, abstract = {Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.}, }
@article {pmid38745401, year = {2024}, author = {Ekram, MA and Campbell, M and Kose, SH and Plet, C and Hamilton, R and Bijaksana, S and Grice, K and Russell, J and Stevenson, J and Vogel, H and Coolen, MJL}, title = {A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia).}, journal = {Geobiology}, volume = {22}, number = {3}, pages = {e12599}, doi = {10.1111/gbi.12599}, pmid = {38745401}, issn = {1472-4669}, support = {DP15102587//Australian Research Council/ ; //International Continental Scientific Drilling Program (ICDP)/ ; //U.S. National Science Foundation (NSF)/ ; 200021_153053/SNSF_/Swiss National Science Foundation/Switzerland ; //PT Vale Indonesia/ ; //Ministry of Research, Education, and Higher Technology of Indonesia (RISTEK)/ ; //Brown University/ ; //The Institute for Geoscience Research (TIGeR)/ ; //Research Office at Curtin University (ROC)/ ; }, mesh = {*Lakes/chemistry ; *Geologic Sediments ; Indonesia ; *DNA, Ancient/analysis ; Plants ; Tropical Climate ; Ecosystem ; DNA, Plant/genetics ; }, abstract = {Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.}, }
@article {pmid38742634, year = {2024}, author = {Harris, KD and Greenbaum, G}, title = {DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data.}, journal = {Nucleic acids research}, volume = {52}, number = {W1}, pages = {W54-W60}, pmid = {38742634}, issn = {1362-4962}, mesh = {Humans ; *DNA, Ancient/analysis ; *Software ; Genomics/methods ; Genome, Human ; Genotype ; User-Computer Interface ; Genetics, Population/methods ; }, abstract = {The ability to sequence ancient genomes has revolutionized the way we study evolutionary history by providing access to the most important aspect of evolution-time. Until recently, studying human demography, ecology, biology, and history using population genomic inference relied on contemporary genomic datasets. Over the past decade, the availability of human ancient DNA (aDNA) has increased rapidly, almost doubling every year, opening the way for spatiotemporal studies of ancient human populations. However, the multidimensionality of aDNA, with genotypes having temporal, spatial and genomic coordinates, and integrating multiple sources of data, poses a challenge for developing meta-analyses pipelines. To address this challenge, we developed a publicly-available interactive tool, DORA, which integrates multiple data types, genomic and non-genomic, in a unified interface. This web-based tool enables browsing sample metadata alongside additional layers of information, such as population structure, climatic data, and unpublished samples. Users can perform analyses on genotypes of these samples, or export sample subsets for external analyses. DORA integrates analyses and visualizations in a single intuitive interface, resolving the technical issues of combining datasets from different sources and formats, and allowing researchers to focus on the scientific questions that can be addressed through analysis of aDNA datasets.}, }
@article {pmid38739117, year = {2024}, author = {Dahlquist-Axe, G and Standeven, FJ and Speller, CF and Tedder, A and Meehan, CJ}, title = {Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes.}, journal = {Microbial genomics}, volume = {10}, number = {5}, pages = {}, pmid = {38739117}, issn = {2057-5858}, mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; *Anti-Bacterial Agents/pharmacology ; History, Ancient ; Diet ; Bacteria/genetics/classification/drug effects ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; History, Medieval ; History, 17th Century ; History, 18th Century ; History, 16th Century ; }, abstract = {The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.}, }
@article {pmid38703773, year = {2024}, author = {Urban, C and Blom, AA and Avanzi, C and Walker-Meikle, K and Warren, AK and White-Iribhogbe, K and Turle, R and Marter, P and Dawson-Hobbis, H and Roffey, S and Inskip, SA and Schuenemann, VJ}, title = {Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host.}, journal = {Current biology : CB}, volume = {34}, number = {10}, pages = {2221-2230.e8}, doi = {10.1016/j.cub.2024.04.006}, pmid = {38703773}, issn = {1879-0445}, mesh = {Animals ; *Mycobacterium leprae/genetics/isolation &amp; purification ; *Sciuridae/microbiology ; *Leprosy/microbiology/history ; Humans ; *Genome, Bacterial ; *Phylogeny ; England ; DNA, Ancient/analysis ; Archaeology ; History, Medieval ; }, abstract = {Leprosy, one of the oldest recorded diseases in human history, remains prevalent in Asia, Africa, and South America, with over 200,000 cases every year.[1][,][2] Although ancient DNA (aDNA) approaches on the major causative agent, Mycobacterium leprae, have elucidated the disease's evolutionary history,[3][,][4][,][5] the role of animal hosts and interspecies transmission in the past remains unexplored. Research has uncovered relationships between medieval strains isolated from archaeological human remains and modern animal hosts such as the red squirrel in England.[6][,][7] However, the time frame, distribution, and direction of transmissions remains unknown. Here, we studied 25 human and 12 squirrel samples from two archaeological sites in Winchester, a medieval English city well known for its leprosarium and connections to the fur trade. We reconstructed four medieval M. leprae genomes, including one from a red squirrel, at a 2.2-fold average coverage. Our analysis revealed a phylogenetic placement of all strains on branch 3 as well as a close relationship between the squirrel strain and one newly reconstructed medieval human strain. In particular, the medieval squirrel strain is more closely related to some medieval human strains from Winchester than to modern red squirrel strains from England, indicating a yet-undetected circulation of M. leprae in non-human hosts in the Middle Ages. Our study represents the first One Health approach for M. leprae in archaeology, which is centered around a medieval animal host strain, and highlights the future capability of such approaches to understand the disease's zoonotic past and current potential.}, }
@article {pmid38691462, year = {2024}, author = {Zhu, K and He, H and Tao, L and Ma, H and Yang, X and Wang, R and Guo, J and Wang, CC}, title = {Protocol for a comprehensive pipeline to study ancient human genomes.}, journal = {STAR protocols}, volume = {5}, number = {2}, pages = {102985}, pmid = {38691462}, issn = {2666-1667}, mesh = {Humans ; *Genome, Human/genetics ; *DNA, Ancient/analysis ; *Genomics/methods ; Sequence Analysis, DNA/methods ; Gene Library ; Genetics, Population/methods ; }, abstract = {Ancient genomics has revolutionized our understanding of human evolution and migration history in recent years. Here, we present a protocol to prepare samples for ancient genomics research. We describe steps for releasing DNA from human remains, DNA library construction, hybridization capture, quantification, and sequencing. We then detail procedures for mapping sequence reads and population genetics analysis. This protocol also outlines challenges in extracting ancient DNA samples and authenticating ancient DNA to uncover the genetic history and diversity of ancient populations. For complete details on the use and execution of this protocol, please refer to Tao et al.[1].}, }
@article {pmid38676702, year = {2024}, author = {Aktürk, &#x15e; and Mapelli, I and Güler, MN and Gürün, K and Katırcıoğlu, B and Vural, KB and Sağlıcan, E and Çetin, M and Yaka, R and Sürer, E and Atağ, G and Çokoğlu, SS and Sevkar, A and Altınışık, NE and Koptekin, D and Somel, M}, title = {Benchmarking kinship estimation tools for ancient genomes using pedigree simulations.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13960}, doi = {10.1111/1755-0998.13960}, pmid = {38676702}, issn = {1755-0998}, mesh = {*Pedigree ; *Benchmarking/methods ; *Polymorphism, Single Nucleotide ; Humans ; Gene Frequency ; DNA, Ancient/analysis ; Computer Simulation ; Genetics, Population/methods ; Computational Biology/methods ; }, abstract = {There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.}, }
@article {pmid38671208, year = {2024}, author = {Taurozzi, AJ and Rüther, PL and Patramanis, I and Koenig, C and Sinclair Paterson, R and Madupe, PP and Harking, FS and Welker, F and Mackie, M and Ramos-Madrigal, J and Olsen, JV and Cappellini, E}, title = {Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel.}, journal = {Nature protocols}, volume = {19}, number = {7}, pages = {2085-2116}, pmid = {38671208}, issn = {1750-2799}, support = {17649//Villum Fonden (Villum Foundation)/ ; 722606//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 861389//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101021361//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 948365//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PROTEIOS (DNRF128)//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, mesh = {*Phylogeny ; *Dental Enamel/chemistry/metabolism ; *Proteomics/methods ; Animals ; Humans ; Paleontology/methods ; Mass Spectrometry/methods ; Fossils ; }, abstract = {In temperate and subtropical regions, ancient proteins are reported to survive up to about 2 million years, far beyond the known limits of ancient DNA preservation in the same areas. Accordingly, their amino acid sequences currently represent the only source of genetic information available to pursue phylogenetic inference involving species that went extinct too long ago to be amenable for ancient DNA analysis. Here we present a complete workflow, including sample preparation, mass spectrometric data acquisition and computational analysis, to recover and interpret million-year-old dental enamel protein sequences. During sample preparation, the proteolytic digestion step, usually an integral part of conventional bottom-up proteomics, is omitted to increase the recovery of the randomly degraded peptides spontaneously generated by extensive diagenetic hydrolysis of ancient proteins over geological time. Similarly, we describe other solutions we have adopted to (1) authenticate the endogenous origin of the protein traces we identify, (2) detect and validate amino acid variation in the ancient protein sequences and (3) attempt phylogenetic inference. Sample preparation and data acquisition can be completed in 3-4 working days, while subsequent data analysis usually takes 2-5 days. The workflow described requires basic expertise in ancient biomolecules analysis, mass spectrometry-based proteomics and molecular phylogeny. Finally, we describe the limits of this approach and its potential for the reconstruction of evolutionary relationships in paleontology and paleoanthropology.}, }
@article {pmid38659893, year = {2024}, author = {Lazaridis, I and Patterson, N and Anthony, D and Vyazov, L and Fournier, R and Ringbauer, H and Olalde, I and Khokhlov, AA and Kitov, EP and Shishlina, NI and Ailincăi, SC and Agapov, DS and Agapov, SA and Batieva, E and Bauyrzhan, B and Bereczki, Z and Buzhilova, A and Changmai, P and Chizhevsky, AA and Ciobanu, I and Constantinescu, M and Csányi, M and Dani, J and Dashkovskiy, PK and Évinger, S and Faifert, A and Flegontov, PN and Frînculeasa, A and Frînculeasa, MN and Hajdu, T and Higham, T and Jarosz, P and Jelínek, P and Khartanovich, VI and Kirginekov, EN and Kiss, V and Kitova, A and Kiyashko, AV and Koledin, J and Korolev, A and Kosintsev, P and Kulcsár, G and Kuznetsov, P and Magomedov, R and Malikovich, MA and Melis, E and Moiseyev, V and Molnár, E and Monge, J and Negrea, O and Nikolaeva, NA and Novak, M and Ochir-Goryaeva, M and Pálfi, G and Popovici, S and Rykun, MP and Savenkova, TM and Semibratov, VP and Seregin, NN and Šefčáková, A and Serikovna, MR and Shingiray, I and Shirokov, VN and Simalcsik, A and Sirak, K and Solodovnikov, KN and Tárnoki, J and Tishkin, AA and Trifonov, V and Vasilyev, S and Akbari, A and Brielle, ES and Callan, K and Candilio, F and Cheronet, O and Curtis, E and Flegontova, O and Iliev, L and Kearns, A and Keating, D and Lawson, AM and Mah, M and Micco, A and Michel, M and Oppenheimer, J and Qiu, L and Noah Workman, J and Zalzala, F and Szécsényi-Nagy, A and Palamara, PF and Mallick, S and Rohland, N and Pinhasi, R and Reich, D}, title = {The Genetic Origin of the Indo-Europeans.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38659893}, issn = {2692-8205}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, abstract = {The Yamnaya archaeological complex appeared around 3300BCE across the steppes north of the Black and Caspian Seas, and by 3000BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize the ancestral and geographical origins of the Yamnaya among the diverse Eneolithic people that preceded them, we studied ancient DNA data from 428 individuals of which 299 are reported for the first time, demonstrating three previously unknown Eneolithic genetic clines. First, a "Caucasus-Lower Volga" (CLV) Cline suffused with Caucasus hunter-gatherer (CHG) ancestry extended between a Caucasus Neolithic southern end in Neolithic Armenia, and a steppe northern end in Berezhnovka in the Lower Volga. Bidirectional gene flow across the CLV cline created admixed intermediate populations in both the north Caucasus, such as the Maikop people, and on the steppe, such as those at the site of Remontnoye north of the Manych depression. CLV people also helped form two major riverine clines by admixing with distinct groups of European hunter-gatherers. A "Volga Cline" was formed as Lower Volga people mixed with upriver populations that had more Eastern hunter-gatherer (EHG) ancestry, creating genetically hyper-variable populations as at Khvalynsk in the Middle Volga. A "Dnipro Cline" was formed as CLV people bearing both Caucasus Neolithic and Lower Volga ancestry moved west and acquired Ukraine Neolithic hunter-gatherer (UNHG) ancestry to establish the population of the Serednii Stih culture from which the direct ancestors of the Yamnaya themselves were formed around 4000BCE. This population grew rapidly after 3750-3350BCE, precipitating the expansion of people of the Yamnaya culture who totally displaced previous groups on the Volga and further east, while admixing with more sedentary groups in the west. CLV cline people with Lower Volga ancestry contributed four fifths of the ancestry of the Yamnaya, but also, entering Anatolia from the east, contributed at least a tenth of the ancestry of Bronze Age Central Anatolians, where the Hittite language, related to the Indo-European languages spread by the Yamnaya, was spoken. We thus propose that the final unity of the speakers of the "Proto-Indo-Anatolian" ancestral language of both Anatolian and Indo-European languages can be traced to CLV cline people sometime between 4400-4000 BCE.}, }
@article {pmid38658749, year = {2024}, author = {Gnecchi-Ruscone, GA and Rácz, Z and Samu, L and Szeniczey, T and Faragó, N and Knipper, C and Friedrich, R and Zlámalová, D and Traverso, L and Liccardo, S and Wabnitz, S and Popli, D and Wang, K and Radzeviciute, R and Gulyás, B and Koncz, I and Balogh, C and Lezsák, GM and Mácsai, V and Bunbury, MME and Spekker, O and le Roux, P and Szécsényi-Nagy, A and Mende, BG and Colleran, H and Hajdu, T and Geary, P and Pohl, W and Vida, T and Krause, J and Hofmanová, Z}, title = {Network of large pedigrees reveals social practices of Avar communities.}, journal = {Nature}, volume = {629}, number = {8011}, pages = {376-383}, pmid = {38658749}, issn = {1476-4687}, mesh = {Adult ; Female ; Humans ; Male ; *Archaeology/methods ; Asia/ethnology ; Cemeteries/history ; Consanguinity ; *DNA, Ancient/analysis ; Europe/ethnology ; *Family Characteristics/ethnology/history ; Genomics ; *Grassland ; History, Medieval ; *Pedigree ; Politics ; Adolescent ; Young Adult ; }, abstract = {From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years[1]. Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies[2]. Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment.}, }
@article {pmid38658715, year = {2024}, author = {Cassidy, LM}, title = {Ancient DNA traces family lines and political shifts in the Avar empire.}, journal = {Nature}, volume = {629}, number = {8011}, pages = {287-288}, pmid = {38658715}, issn = {1476-4687}, mesh = {*DNA, Ancient/analysis ; Humans ; *Politics ; History, Ancient ; Female ; }, }
@article {pmid38642939, year = {2024}, author = {Zhu, S and Chen, Z and Hu, S and Wang, W and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Ping, W and Fu, Q}, title = {Corrigendum to "Ancient DNA traces a Chinese 5400-year-old cat specimen as leopard cat (Prionailurus bengalensis)" [Journal of Genetics and Genomics (2022) 49, 1076-1079].}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {51}, number = {4}, pages = {466}, doi = {10.1016/j.jgg.2024.03.002}, pmid = {38642939}, issn = {1673-8527}, }
@article {pmid38640342, year = {2024}, author = {Lin, Q and Zhang, K and Giguet-Covex, C and Arnaud, F and McGowan, S and Gielly, L and Capo, E and Huang, S and Ficetola, GF and Shen, J and Dearing, JA and Meadows, ME}, title = {Transient social-ecological dynamics reveal signals of decoupling in a highly disturbed Anthropocene landscape.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {17}, pages = {e2321303121}, pmid = {38640342}, issn = {1091-6490}, support = {2022YFF0801101//MOST | National Key Research and Development Program of China (NKPs)/ ; 42230507//MOST | National Natural Science Foundation of China (NSFC)/ ; 42361144717//MOST | National Natural Science Foundation of China (NSFC)/ ; 42111530229//MOST | National Natural Science Foundation of China (NSFC)/ ; BK20201099//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; }, mesh = {*Ecosystem ; *Rivers ; Eutrophication ; Conservation of Natural Resources/methods ; }, abstract = {Understanding the transient dynamics of interlinked social-ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended historical timeline. Our approach leverages multidecadal rates of change in socioeconomic data, paleoenvironmental, and cutting-edge sedimentary ancient DNA records from China's Yangtze River Delta, one of the most densely populated and intensively modified landscapes on Earth. Our analysis reveals two significant social-ecological transitions characterized by contrasting interactions and feedback spanning several centuries. Initially, the regional SES exhibited a loosely connected and ecologically sustainable regime. Nevertheless, starting in the 1950s, an increasingly interconnected regime emerged, ultimately resulting in the crossing of tipping points and an unprecedented acceleration in soil erosion, water eutrophication, and ecosystem degradation. Remarkably, the second transition occurring around the 2000s, featured a notable decoupling of socioeconomic development from ecoenvironmental degradation. This decoupling phenomenon signifies a more desirable reconfiguration of the regional SES, furnishing essential insights not only for the Yangtze River Basin but also for regions worldwide grappling with similar sustainability challenges. Our extensive multidecadal empirical investigation underscores the value of coevolutionary approaches in understanding and addressing social-ecological system dynamics.}, }
@article {pmid38636619, year = {2024}, author = {Sun, Z and Pan, L and Tian, A and Chen, P}, title = {Critically-ill COVID-19 susceptibility gene CCR3 shows natural selection in sub-Saharan Africans.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {121}, number = {}, pages = {105594}, doi = {10.1016/j.meegid.2024.105594}, pmid = {38636619}, issn = {1567-7257}, mesh = {Humans ; Africa South of the Sahara/epidemiology ; Black People/genetics ; *COVID-19/genetics/virology/epidemiology ; *Critical Illness ; Gene Frequency ; *Genetic Predisposition to Disease ; Haplotypes ; Mendelian Randomization Analysis ; *Polymorphism, Single Nucleotide ; *Receptors, CCR3/genetics ; *SARS-CoV-2/genetics ; *Selection, Genetic ; Sub-Saharan African People ; }, abstract = {The prevalence of COVID-19 critical illness varies across ethnicities, with recent studies suggesting that genetic factors may contribute to this variation. The aim of this study was to investigate natural selection signals of genes associated with critically-ill COVID-19 in sub-Saharan Africans. Severe COVID-19 SNPs were obtained from the HGI website. Selection signals were assessed in 661 sub-Sahara Africans from 1000 Genomes Project using integrated haplotype score (iHS), cross-population extended haplotype homozygosity (XP-EHH), and fixation index (Fst). Allele frequency trajectory analysis of ancient DNA samples were used to validate the existing of selection in sub-Sahara Africans. We also used Mendelian randomization to decipher the correlation between natural selection and critically-ill COVID-19. We identified that CCR3 exhibited significant natural selection signals in sub-Sahara Africans. Within the CCR3 gene, rs17217831-A showed both high iHS (Standardized iHS = 2) and high XP-EHH (Standardized XP-EHH = 2.5) in sub-Sahara Africans. Allele frequency trajectory of CCR3 rs17217831-A revealed natural selection occurring in the recent 1,500 years. Natural selection resulted in increased CCR3 expression in sub-Sahara Africans. Mendelian Randomization provided evidence that increased blood CCR3 expression and eosinophil counts lowered the risk of critically ill COVID-19. Our findings suggest that sub-Saharan Africans are resistant to critically ill COVID-19 due to natural selection and identify CCR3 as a potential novel therapeutic target.}, }
@article {pmid38626302, year = {2024}, author = {Ghimire, P and Palacios, C and Trimble, J and Lamichhaney, S}, title = {Museum genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {7}, pages = {}, doi = {10.1093/g3journal/jkae081}, pmid = {38626302}, issn = {2160-1836}, support = {//Kent State University/ ; }, mesh = {*Museums ; Animals ; *Genomics/methods ; *Phylogeny ; *Birds/genetics/classification ; Biological Evolution ; Genome ; Evolution, Molecular ; Genetic Variation ; }, abstract = {The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia spp.) and examine their genetic composition and taxonomic status and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences; however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollynecks are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspecies Ciconia episcopus neglecta and Ciconia episcopus episcopus, suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds.}, }
@article {pmid38623594, year = {2024}, author = {Meijer, H}, title = {Janus faced: The co-evolution of war and peace in the human species.}, journal = {Evolutionary anthropology}, volume = {33}, number = {3}, pages = {e22027}, doi = {10.1002/evan.22027}, pmid = {38623594}, issn = {1520-6505}, mesh = {Humans ; Animals ; *Warfare ; Cultural Evolution ; Biological Evolution ; Social Behavior ; Cooperative Behavior ; Hominidae/physiology ; Violence ; }, abstract = {The human species presents a paradox. No other species possesses the propensity to carry out coalitionary lethal attacks on adult conspecifics coupled with the inclination to establish peaceful relations with genetically unrelated groups. What explains this seemingly contradictory feature? Existing perspectives, the "deep roots" and "shallow roots" of war theses, fail to capture the plasticity of human intergroup behaviors, spanning from peaceful cooperation to warfare. By contrast, this article argues that peace and war have both deep roots, and they co-evolved through an incremental process over several million years. On the one hand, humans inherited the propensity for coalitionary lethal violence from their chimpanzee-like ancestor. Specifically, having first inherited the skills to engage in cooperative hunting, they gradually repurposed such capacity to execute coalitionary killings of adult conspecifics and subsequently enhanced it through tech`nological innovations like the use of weapons. On the other hand, they underwent a process of cumulative cultural evolution and, subsequently, of self-domestication which led to heightened cooperative communication and increased prosocial behavior within and between groups. The combination of these two biocultural evolutionary processes-coupled with feedback loop effects between self-domestication and Pleistocene environmental variability-considerably broadened the human intergroup behavioral repertoire, thereby producing the distinctive combination of conflictual and peaceful intergroup relations that characterizes our species. To substantiate this argument, the article synthesizes and integrates the findings from a variety of disciplines, leveraging evidence from evolutionary anthropology, primatology, archeology, paleo-genetics, and paleo-climatology.}, }
@article {pmid38617445, year = {2024}, author = {Zhang, J and Li, X and Li, L and Chen, A and Zhang, S}, title = {Y-STR analysis of highly degraded DNA from skeletal remains over 70 years old.}, journal = {Forensic sciences research}, volume = {9}, number = {2}, pages = {owae020}, pmid = {38617445}, issn = {2471-1411}, abstract = {The goal of the following study is to clarify whether the skeletal remains over 70 years old from missing persons and their alleged relatives shared identical Y-STR loci. Nowadays, advances in ancient DNA extraction techniques and approaches of using multiple different Y-STRs have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Given the ages and conditions of the skeletal remains, ancient DNA extraction methods can be used to maximize the probability of DNA recovery. Considering that information about distant relatives is more relevant for long-term missing persons and alleged family members are male, Y-STR loci analysis is considered the most appropriate and informative approach for determining paternal lineage relationship. In this study, Y-STR genotypes obtained from these alleged relatives were identical to each other and to the alleles of missing persons' consensus profiles at more than 22 loci examined, whilst not being found in Y-STR population database from Y-Chromosome STR Haplotype Reference Database. Therefore, Missing Person No.7 and Missing Person No.18 have a patrilineal relationship with reference samples from Family1 and Family2, respectively. In addition, the fact that Y-STR haplotypes obtained from skeletal remains of missing persons and reference samples are not found in the Han Chinese people from East Asian demonstrates its rarity and further supports a paternal lineage relationship amongst them.}, }
@article {pmid38614080, year = {2024}, author = {Hempel, E and Faith, JT and Preick, M and de Jager, D and Barish, S and Hartmann, S and Grau, JH and Moodley, Y and Gedman, G and Pirovich, KM and Bibi, F and Kalthoff, DC and Bocklandt, S and Lamm, B and Dalén, L and Westbury, MV and Hofreiter, M}, title = {Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size.}, journal = {Current biology : CB}, volume = {34}, number = {9}, pages = {2020-2029.e6}, doi = {10.1016/j.cub.2024.03.051}, pmid = {38614080}, issn = {1879-0445}, mesh = {*Extinction, Biological ; Animals ; *Antelopes/genetics/physiology ; *Population Density ; Genetic Variation ; Gene Flow ; Adaptation, Physiological/genetics ; Ecosystem ; Genome ; }, abstract = {Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.[1][,][2][,][3][,][4][,][5][,][6] Moreover, small population size may promote gene flow with congeners and outbreeding depression.[7][,][8][,][9][,][10][,][11][,][12][,][13] Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,[14][,][15] populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.[16][,][17][,][18] However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species' unique traits.}, }
@article {pmid38612593, year = {2024}, author = {Ferreira, RC and Rodrigues, CR and Broach, JR and Briones, MRS}, title = {Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, pmid = {38612593}, issn = {1422-0067}, support = {20/08943-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; }, mesh = {Humans ; Animals ; *Neanderthals/genetics ; *Genome, Mitochondrial ; Mutation ; *Alzheimer Disease ; Nucleotides ; }, abstract = {The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.}, }
@article {pmid38601034, year = {2024}, author = {Abbona, CC and Lebrasseur, O and Prevosti, FJ and Peralta, E and González Venanzi, L and Frantz, L and Larson, G and Gil, AF and Neme, GA}, title = {Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities.}, journal = {Royal Society open science}, volume = {11}, number = {4}, pages = {231835}, pmid = {38601034}, issn = {2054-5703}, abstract = {The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ[13]Ccol and δ[15]N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca. Previous morphological identifications suggested that it belonged to the genus Lycalopex, but our results conclusively demonstrate that the individual belongs to the extinct fox species Dusicyon avus. This finding expands Dusicyon avus' known geographical distribution to Patagonia's northern extremity. Furthermore, statistical predictions based on genetic divergence undermine the hypothesis that hybridization between Canis and Dusicyon, facilitated by the introduction of domestic dogs, played a role in the extinction of Dusicyon species. On the other hand, our findings indicate that a Dusicyon avus individual shared a similar diet and was probably buried alongside humans, suggesting a close relationship between the two species during their lives and deaths.}, }
@article {pmid38589385, year = {2024}, author = {Mills, KK and Hildebrandt, KPB and Everson, KM and Horstmann, L and Misarti, N and Olson, LE}, title = {Ancient DNA indicates a century of overhunting did not reduce genetic diversity in Pacific Walruses (Odobenus rosmarus divergens).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8257}, pmid = {38589385}, issn = {2045-2322}, support = {Walrus Adaptability and Long-term Responses; Using multi-proxy data to project Sustainability, Award #1263848//National Science Foundation/ ; OIA-1826801//National Science Foundation/ ; }, mesh = {Animals ; *Walruses/genetics ; DNA, Ancient ; *Caniformia ; Ecosystem ; Genetic Variation ; }, abstract = {Pacific Walruses (Odobenus rosmarus divergens [Illiger 1815]) are gregarious marine mammals considered to be sentinels of the Arctic because of their dependence on sea ice for feeding, molting, and parturition. Like many other marine mammal species, their population sizes were decimated by historical overhunting in the nineteenth and twentieth centuries. Although they have since been protected from nearly all commercial hunting pressure, they now face rapidly accelerating habitat loss as global warming reduces the extent of summer sea ice in the Arctic. To investigate how genetic variation was impacted by overhunting, we obtained mitochondrial DNA sequences from historic Pacific Walrus samples in Alaska that predate the period of overhunting, as well as from extant populations. We found that genetic variation was unchanged over this period, suggesting Pacific Walruses are resilient to genetic attrition in response to reduced population size, and that this may be related to their high vagility and lack of population structure. Although Pacific Walruses will almost certainly continue to decline in number as the planet warms and summer sea ice is further reduced, they may be less susceptible to the ratcheting effects of inbreeding that typically accompany shrinking populations.}, }
@article {pmid38586998, year = {2024}, author = {Brack, J and Biran, M and Amitai, R}, title = {Plague and the Mongol conquest of Baghdad (1258)? A reevaluation of the sources.}, journal = {Medical history}, volume = {}, number = {}, pages = {1-19}, doi = {10.1017/mdh.2023.38}, pmid = {38586998}, issn = {2048-8343}, abstract = {This paper reexamines the sources used by N. Fancy and M.H. Green in "Plague and the Fall of Baghdad (1258)" (Medical History, 65/2 (2021), 157-177). Fancy and Green argued that the Arabic and Persian descriptions of the Mongol sieges in Iran and Iraq, and in particular, in the conquest of Baghdad in 1258, indicate that the besieged fortresses and cities were struck by Plague after the Mongol sieges were lifted. This, they suggested, is part of a recurrent pattern of the outbreak of Plague transmitted by the Mongol expansion across Eurasia. Fancy and Green concluded that the primary sources substantiate the theory driven by recent paleogenetic studies indicating that the Mongol conquests of the thirteenth century set the stage for the massive pandemic of the mid-fourteenth century. The link between the Plague outbreak and the Mongol siege of Baghdad relies on three near-contemporaneous historical accounts. However, our re-examination of the sources shows that the main text (in Persian) has been significantly misunderstood, and that the two other texts (in Syriac and Arabic) have been mis-contextualized, and thus not understood properly. They do not support the authors' claim regarding Plague epidemic in Baghdad in 1258, nor do other contemporary and later Arabic texts from Syria and Egypt adduced by them, which we re-examine in detail here. We conclude that there is no evidence for the appearance of Plague during or immediately after the Mongol conquests in the Middle East, certainly not for its transmission by the Mongols.}, }
@article {pmid38583481, year = {2024}, author = {Alsos, IG and Boussange, V and Rijal, DP and Beaulieu, M and Brown, AG and Herzschuh, U and Svenning, JC and Pellissier, L}, title = {Using ancient sedimentary DNA to forecast ecosystem trajectories under climate change.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1902}, pages = {20230017}, pmid = {38583481}, issn = {1471-2970}, mesh = {Animals ; *Ecosystem ; *DNA, Ancient ; Climate Change ; Biodiversity ; Pollen ; Mammals ; }, abstract = {Ecosystem response to climate change is complex. In order to forecast ecosystem dynamics, we need high-quality data on changes in past species abundance that can inform process-based models. Sedimentary ancient DNA (sedaDNA) has revolutionised our ability to document past ecosystems' dynamics. It provides time series of increased taxonomic resolution compared to microfossils (pollen, spores), and can often give species-level information, especially for past vascular plant and mammal abundances. Time series are much richer in information than contemporary spatial distribution information, which have been traditionally used to train models for predicting biodiversity and ecosystem responses to climate change. Here, we outline the potential contribution of sedaDNA to forecast ecosystem changes. We showcase how species-level time series may allow quantification of the effect of biotic interactions in ecosystem dynamics, and be used to estimate dispersal rates when a dense network of sites is available. By combining palaeo-time series, process-based models, and inverse modelling, we can recover the biotic and abiotic processes underlying ecosystem dynamics, which are traditionally very challenging to characterise. Dynamic models informed by sedaDNA can further be used to extrapolate beyond current dynamics and provide robust forecasts of ecosystem responses to future climate change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.}, }
@article {pmid38567866, year = {2024}, author = {Miles, LS and Waterman, H and Ayoub, NA and Garb, JE and Haney, RA and Rosenberg, MS and Krabbenhoft, TJ and Verrelli, BC}, title = {Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider.}, journal = {The Journal of heredity}, volume = {115}, number = {3}, pages = {241-252}, doi = {10.1093/jhered/esae018}, pmid = {38567866}, issn = {1465-7333}, support = {//Virginia Commonwealth University/ ; //University at Buffalo/ ; }, mesh = {Animals ; *Black Widow Spider/genetics ; *Gene Duplication ; *Evolution, Molecular ; *Genome ; Chromosomes/genetics ; Phylogeny ; Transcriptome ; Spiders/genetics ; Biological Evolution ; Molecular Sequence Annotation ; Selection, Genetic ; }, abstract = {Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.}, }
@article {pmid38559769, year = {2024}, author = {Bellini, G and Schrieber, K and Kirleis, W and Erfmeier, A}, title = {Exploring the complex pre-adaptations of invasive plants to anthropogenic disturbance: a call for integration of archaeobotanical approaches.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1307364}, pmid = {38559769}, issn = {1664-462X}, abstract = {Pre-adaptation to anthropogenic disturbance is broadly considered key for plant invasion success. Nevertheless, empirical evidence remains scarce and fragmentary, given the multifaceted nature of anthropogenic disturbance itself and the complexity of other evolutionary forces shaping the (epi)-genomes of recent native and invasive plant populations. Here, we review and critically revisit the existing theory and empirical evidence in the field of evolutionary ecology and highlight novel integrative research avenues that work at the interface with archaeology to solve open questions. The approaches suggested so far focus on contemporary plant populations, although their genomes have rapidly changed since their initial introduction in response to numerous selective and stochastic forces. We elaborate that a role of pre-adaptation to anthropogenic disturbance in plant invasion success should thus additionally be validated based on the analyses of archaeobotanical remains. Such materials, in the light of detailed knowledge on past human societies could highlight fine-scale differences in the type and timing of past disturbances. We propose a combination of archaeobotanical, ancient DNA and morphometric analyses of plant macro- and microremains to assess past community composition, and species' functional traits to unravel the timing of adaptation processes, their drivers and their long-term consequences for invasive species. Although such methodologies have proven to be feasible for numerous crop plants, they have not been yet applied to wild invasive species, which opens a wide array of insights into their evolution.}, }
@article {pmid38552628, year = {2024}, author = {Du, P and Zhu, K and Qiao, H and Zhang, J and Meng, H and Huang, Z and Yu, Y and Xie, S and Allen, E and Xiong, J and Zhang, B and Chang, X and Ren, X and Xu, Y and Zhou, Q and Han, S and Jin, L and Wei, P and Wang, CC and Wen, S}, title = {Ancient genome of the Chinese Emperor Wu of Northern Zhou.}, journal = {Current biology : CB}, volume = {34}, number = {7}, pages = {1587-1595.e5}, doi = {10.1016/j.cub.2024.02.059}, pmid = {38552628}, issn = {1879-0445}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Asian People/genetics ; Genome ; Polymorphism, Single Nucleotide ; China ; Genetics, Population ; }, abstract = {Emperor Wu (, Wudi) of the Xianbei-led Northern Zhou dynasty, named Yuwen Yong (, 543-578 CE), was a highly influential emperor who reformed the system of regional troops, pacified the Turks, and unified the northern part of the country. His genetic profile and physical characteristics, including his appearance and potential diseases, have garnered significant interest from the academic community and the public. In this study, we have successfully generated a 0.343×-coverage genome of Wudi with 1,011,419 single-nucleotide polymorphisms (SNPs) on the 1240k panel. By analyzing pigmentation-relevant SNPs and conducting cranial CT-based facial reconstruction, we have determined that Wudi possessed a typical East or Northeast Asian appearance. Furthermore, pathogenic SNPs suggest Wudi faced an increased susceptibility to certain diseases, such as stroke. Wudi shared the closest genetic relationship with ancient Khitan and Heishui Mohe samples and modern Daur and Mongolian populations but also showed additional affinity with Yellow River (YR) farmers. We estimated that Wudi derived 61% of his ancestry from ancient Northeast Asians (ANAs) and nearly one-third from YR farmer-related groups. This can likely be attributed to continuous intermarriage between Xianbei royal families, and local Han aristocrats.[1][,][2] Furthermore, our study has revealed genetic diversities among available ancient Xianbei individuals from different regions, suggesting that the formation of the Xianbei was a dynamic process influenced by admixture with surrounding populations.}, }
@article {pmid38552260, year = {2024}, author = {Rmoutilová, R and Brůžek, J and Gómez-Olivencia, A and Madelaine, S and Couture-Veschambre, C and Holliday, T and Maureille, B}, title = {Sex estimation of the adult Neandertal Regourdou 1 (Montignac, France): Implications for sexing human fossil remains.}, journal = {Journal of human evolution}, volume = {189}, number = {}, pages = {103470}, doi = {10.1016/j.jhevol.2023.103470}, pmid = {38552260}, issn = {1095-8606}, mesh = {Animals ; Humans ; Male ; *Neanderthals/anatomy &amp; histology ; Fossils ; Genomics ; Paleontology ; *Hominidae ; France ; }, abstract = {Sex is a biological trait fundamental to the study of hominin fossils. Among the many questions that can be addressed are those related to taxonomy, biological variability, sexual dimorphism, paleoobstetrics, funerary selection, and paleodemography. While new methodologies such as paleogenomics or paleoproteomics can be used to determine sex, they have not been systematically applied to Pleistocene human remains due to their destructive nature. Therefore, we estimated sex from the coxal bone of the newly discovered pelvic remains of the Regourdou 1 Neandertal (Southwest France, MIS 5) based on morphological and metric data employing two methods that have been recently revised and shown to be reliable in multiple studies. Both methods calculate posterior probabilities of the estimate. The right coxal bone of Regourdou 1 was partially reconstructed providing additional traits for sex estimation. These methods were cross validated on 14 sufficiently preserved coxal bones of specimens from the Neandertal lineage. Our results show that the Regourdou 1 individual, whose postcranial skeleton is not robust, is a male, and that previous sex attributions of comparative Neandertal specimens are largely in agreement with those obtained here. Our results encourage additional morphological research of fossil hominins in order to develop a set of methods that are applicable, reliable, and reproducible.}, }
@article {pmid38552017, year = {2024}, author = {Boilard, A and Walker, SJ and Lødøen, TK and Henriksen, M and Takken Beijersbergen, LM and Star, B and Robu, M and Tøssebro, C and Albrektsen, CM and Soleng, Y and Aksnes, S and Jørgensen, R and Hufthammer, AK and van Kolfschoten, T and Lauritzen, SE and Boessenkool, S}, title = {Ancient DNA and osteological analyses of a unique paleo-archive reveal Early Holocene faunal expansion into the Scandinavian Arctic.}, journal = {Science advances}, volume = {10}, number = {13}, pages = {eadk3032}, pmid = {38552017}, issn = {2375-2548}, mesh = {Arctic Regions ; Climate ; *DNA, Ancient ; *Ecosystem ; Norway ; }, abstract = {Paleo-archives are essential for our understanding of species responses to climate warming, yet such archives are extremely rare in the Arctic. Here, we combine morphological analyses and bulk-bone metabarcoding to investigate a unique chronology of bone deposits sealed in the high-latitude Storsteinhola cave system (68°50' N 16°22' E) in Norway. This deposit dates to a period of climate warming from the end of the Late Glacial [~13 thousand calibrated years before the present (ka cal B.P.)] to the Holocene thermal maximum (~5.6 ka cal B.P.). Paleogenetic analyses allow us to exploit the 1000s of morphologically unidentifiable bone fragments resulting in a high-resolution sequence with 40 different taxa, including species not previously found here. Our record reveals borealization in both the marine and terrestrial environments above the Arctic Circle as a naturally recurring phenomenon in past periods of warming, providing fundamental insights into the ecosystem-wide responses that are ongoing today.}, }
@article {pmid38533900, year = {2024}, author = {Jackson, I and Woodman, P and Dowd, M and Fibiger, L and Cassidy, LM}, title = {Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts.}, journal = {Molecular biology and evolution}, volume = {41}, number = {3}, pages = {}, pmid = {38533900}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; IRCLA/2022/126//Wellcome Trust Institutional Strategic Support Fund/ ; 18/CRT/6214//Science Foundation Ireland Centre for Research Training in Genomics Data Science/ ; }, mesh = {Humans ; Phylogeny ; *Streptococcus mutans/genetics ; Genomics ; Metagenome ; *Microbiota ; }, abstract = {Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.}, }
@article {pmid38530148, year = {2024}, author = {Yaka, R and Maja Krzewińska,  and Lagerholm, VK and Linderholm, A and Özer, F and Somel, M and Götherström, A}, title = {Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.}, journal = {BioTechniques}, volume = {76}, number = {5}, pages = {216-223}, doi = {10.2144/btn-2023-0107}, pmid = {38530148}, issn = {1940-9818}, support = {STF 7909//EMBO (short-term fellowship)/ ; 772390//ERC (consolidator grant)/ ; 117Z229//TUBITAK of Turkey/ ; NAISS 2023/22-504, NAISS 2023/23-262//Uppsala Multidisciplinary Center for Advanced Computational Science/ ; }, mesh = {*DNA, Ancient/analysis/isolation &amp; purification ; Humans ; *Genome, Human/genetics ; Gene Library ; Sequence Analysis, DNA/methods ; Silicon Dioxide/chemistry ; }, abstract = {Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.}, }
@article {pmid38526010, year = {2024}, author = {Gill, H and Lee, J and Jeong, C}, title = {Reconstructing the Genetic Relationship between Ancient and Present-Day Siberian Populations.}, journal = {Genome biology and evolution}, volume = {16}, number = {4}, pages = {}, pmid = {38526010}, issn = {1759-6653}, support = {RS-2023-00212640//National Research Foundation of Korea/ ; }, mesh = {Humans ; Siberia ; *Genome, Human ; *Genetics, Population ; *North Asian People ; }, abstract = {Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here, we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 yr ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history.}, }
@article {pmid38517967, year = {2024}, author = {Pryor, AJE and Ameen, C and Liddiard, R and Baker, G and Kanne, KS and Milton, JA and Standish, CD and Hambach, B and Orlando, L and Chauvey, L and Schiavinato, S and Calvière-Tonasso, L and Tressières, G and Wagner, S and Southon, J and Shapiro, B and Pipe, A and Creighton, OH and Outram, AK}, title = {Isotopic biographies reveal horse rearing and trading networks in medieval London.}, journal = {Science advances}, volume = {10}, number = {12}, pages = {eadj5782}, pmid = {38517967}, issn = {2375-2548}, mesh = {Humans ; Middle Aged ; Male ; Female ; Horses ; Animals ; London ; *Commerce ; *Bone and Bones/chemistry ; Oxygen Isotopes/analysis ; Strontium Isotopes/analysis ; Internationality ; }, abstract = {This paper reports a high-resolution isotopic study of medieval horse mobility, revealing their origins and in-life mobility both regionally and internationally. The animals were found in an unusual horse cemetery site found within the City of Westminster, London, England. Enamel strontium, oxygen, and carbon isotope analysis of 15 individuals provides information about likely place of birth, diet, and mobility during the first approximately 5 years of life. Results show that at least seven horses originated outside of Britain in relatively cold climates, potentially in Scandinavia or the Western Alps. Ancient DNA sexing data indicate no consistent sex-specific mobility patterning, although three of the five females came from exceptionally highly radiogenic regions. Another female with low mobility is suggested to be a sedentary broodmare. Our results provide direct and unprecedented evidence for a variety of horse movement and trading practices in the Middle Ages and highlight the importance of international trade in securing high-quality horses for medieval London elites.}, }
@article {pmid38507661, year = {2024}, author = {Zhang, M and Song, Y and Wang, C and Sun, G and Zhuang, L and Guo, M and Ren, L and Wangdue, S and Dong, G and Dai, Q and Cao, P and Yang, R and Liu, F and Feng, X and Bennett, EA and Zhang, X and Chen, X and Wang, F and Luan, F and Dong, W and Lu, G and Hao, D and Hou, H and Wang, H and Qiao, H and Wang, Z and Hu, X and He, W and Xi, L and Wang, W and Shao, J and Sun, Z and Yue, L and Ding, Y and Tashi, N and Tsho, Y and Tong, Y and Yang, Y and Zhu, S and Miao, B and Wang, W and Zhang, L and Hu, S and Ni, X and Fu, Q}, title = {Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs.}, journal = {Molecular biology and evolution}, volume = {41}, number = {4}, pages = {}, pmid = {38507661}, issn = {1537-1719}, support = {41925009//National Natural Science Foundation of China/ ; 2022YFE0203800//National Key R&amp;D Program of China/ ; 2024RS-CXTD-74//Science and Technology Innovation Team of Shaanxi Province/ ; XDB26000000//Chinese Academy of Sciences/ ; //Ministry of Finance of the People's/ ; YSBR-019//Republic of China/ ; //new Cornerstone Science Foundation/ ; }, mesh = {Animals ; Dogs ; Animals, Domestic/genetics ; Asia, Eastern ; DNA, Mitochondrial/genetics ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Mammals/genetics ; Phylogeny ; }, abstract = {Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.}, }
@article {pmid38486065, year = {2024}, author = {Garrido Marques, A and Rubinacci, S and Malaspinas, AS and Delaneau, O and Sousa da Mota, B}, title = {Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6227}, pmid = {38486065}, issn = {2045-2322}, support = {679330/ERC_/European Research Council/International ; 679330/ERC_/European Research Council/International ; 679330/ERC_/European Research Council/International ; }, mesh = {*DNA, Ancient ; Genotype ; *Genome ; Genome-Wide Association Study/methods ; Polymorphism, Single Nucleotide ; }, abstract = {Low-coverage imputation is becoming ever more present in ancient DNA (aDNA) studies. Imputation pipelines commonly used for present-day genomes have been shown to yield accurate results when applied to ancient genomes. However, post-mortem damage (PMD), in the form of C-to-T substitutions at the reads termini, and contamination with DNA from closely related species can potentially affect imputation performance in aDNA. In this study, we evaluated imputation performance (i) when using a genotype caller designed for aDNA, ATLAS, compared to bcftools, and (ii) when contamination is present. We evaluated imputation performance with principal component analyses and by calculating imputation error rates. With a particular focus on differently imputed sites, we found that using ATLAS prior to imputation substantially improved imputed genotypes for a very damaged ancient genome (42% PMD). Trimming the ends of the sequencing reads led to similar improvements in imputation accuracy. For the remaining genomes, ATLAS brought limited gains. Finally, to examine the effect of contamination on imputation, we added various amounts of reads from two present-day genomes to a previously downsampled high-coverage ancient genome. We observed that imputation accuracy drastically decreased for contamination rates above 5%. In conclusion, we recommend (i) accounting for PMD by either trimming sequencing reads or using a genotype caller such as ATLAS before imputing highly damaged genomes and (ii) only imputing genomes containing up to 5% of contamination.}, }
@article {pmid38466119, year = {2024}, author = {Poyraz, L and Colbran, LL and Mathieson, I}, title = {Predicting Functional Consequences of Recent Natural Selection in Britain.}, journal = {Molecular biology and evolution}, volume = {41}, number = {3}, pages = {}, pmid = {38466119}, issn = {1537-1719}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; R35GM133708/GM/NIGMS NIH HHS/United States ; grant T32HG009495/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; United Kingdom ; *Selection, Genetic ; Genome ; Genotype ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; }, abstract = {Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are noncoding, so we expect that a large proportion of the phenotypic effects of selection will also act through noncoding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation [JTI]) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4,500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (false discovery rate [FDR] < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-single nucleotide polymorphism (SNP) selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally, we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.}, }
@article {pmid38462159, year = {2024}, author = {Ahlawat, B and Kumar, L and Ambekar, A and Singh Sehrawat, J and Rawat, YS and Rai, N}, title = {Ancient mitogenomes suggest complex maternal history of one of the oldest settlements of western India.}, journal = {Mitochondrion}, volume = {76}, number = {}, pages = {101871}, doi = {10.1016/j.mito.2024.101871}, pmid = {38462159}, issn = {1872-8278}, mesh = {Humans ; India ; *Genome, Mitochondrial ; DNA, Ancient/analysis ; History, Medieval ; Human Migration ; Archaeology ; Female ; DNA, Mitochondrial/genetics ; Haplotypes ; History, Ancient ; }, abstract = {The ancient township of Vadnagar tells a story of a long chain of cultural diversity and exchange. Vadnagar has been continuously habituated and shows a presence of rich cultural amalgamation and continuous momentary sequences between the 2th century BCE and present-day. Seven cultural periods developed a complex and enriched settlement at Vadnagar in spatio-temporality. Although archaeological studies done on this oldest settlement suggested a rich cultural heritage, the genetic studies to pinpoint the genetic ancestry was lacking till date. In our current study we have for the first time reconstructed the complete mitogenomes of medieval individuals of the Vadnagar archaeological site in Gujarat. The study aimed to investigate the cosmopolitan nature of the present population as well as the migratory pattern and the inflow of different groups through trade, cultural and religious practices. Our analysis suggests heterogeneous nature of the medieval population of Vadnagar with presence of deeply rooted local ancestral components as well as central Asian genetic ancestry. This Central Asian component associated with mitochondrial haplotype U2e was not shared with any individual from India, but rather with individuals from the Bronze Age of Tajikistan and with an earlier age of coalescence. In summary, we propose that the medieval site of Vadnagar in western India was rich in cultural and genetic aspects, with both local and western Eurasian components.}, }
@article {pmid38458749, year = {2024}, author = {Geier, A and Trost, J and Wang, K and Schmid, C and Krawczyk, M and Schiffels, S}, title = {PNPLA3 fatty liver allele was fixed in Neanderthals and segregates neutrally in humans.}, journal = {Gut}, volume = {73}, number = {6}, pages = {1008-1014}, doi = {10.1136/gutjnl-2023-331594}, pmid = {38458749}, issn = {1468-3288}, support = {851511/ERC_/European Research Council/International ; }, mesh = {Animals ; Humans ; *Acyltransferases/genetics ; *Alleles ; DNA, Ancient/analysis ; *Fatty Liver/genetics ; Gene Frequency ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genotype ; *Neanderthals/genetics ; *Phospholipases A2, Calcium-Independent/genetics ; }, abstract = {OBJECTIVE: Fat deposition is modulated by environmental factors and genetic predisposition. Genome-wide association studies identified PNPLA3 p.I148M (rs738409) as a common variant that increases risk of developing liver steatosis. When and how this variant evolved in humans has not been studied to date.<br><br>DESIGN: Here we analyse ancient DNA to track the history of this allele throughout human history. In total, 6444 published ancient (modern humans, Neanderthal, Denisovan) and 3943 published present day genomes were used for analysis after extracting genotype calls for PNPLA3 p.I148M. To quantify changes through time, logistic and, by grouping individuals according to geography and age, linear regression analyses were performed.<br><br>RESULTS: We find that archaic human individuals (Neanderthal, Denisovan) exclusively carried a fixed PNPLA3 risk allele, whereas allele frequencies in modern human populations range from very low in Africa to >50% in Mesoamerica. Over the last 15&#x2009;000 years, distributions of ancestral and derived alleles roughly match the present day distribution. Logistic regression analyses did not yield signals of natural selection during the last 10&#x2009;000 years.<br><br>CONCLUSION: Archaic human individuals exclusively carried a fixed PNPLA3 allele associated with fatty liver, whereas allele frequencies in modern human populations are variable even in the oldest samples. Our observation might underscore the advantage of fat storage in cold climate and particularly for Neanderthal under ice age conditions. The absent signals of natural selection during modern human history does not support the thrifty gene hypothesis in case of PNPLA3 p.I148M.}, }
@article {pmid38453993, year = {2024}, author = {Bergfeldt, N and Kırdök, E and Oskolkov, N and Mirabello, C and Unneberg, P and Malmström, H and Fraser, M and Sanchez-Quinto, F and Jorgensen, R and Skar, B and Lidén, K and Jakobsson, M and Storå, J and Götherström, A}, title = {Identification of microbial pathogens in Neolithic Scandinavian humans.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5630}, pmid = {38453993}, issn = {2045-2322}, support = {2017-02503//Vetenskapsr&#xe5;det/ ; 2019-00849//Vetenskapsr&#xe5;det/ ; P21-0266//Riksbankens Jubileumsfond/ ; P19.0740:1//Riksbankens Jubileumsfond/ ; }, mesh = {Humans ; Agriculture ; *DNA, Mitochondrial/genetics ; Europe ; History, Ancient ; *Yersinia/classification/isolation &amp; purification ; *Microbiota ; }, abstract = {With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.}, }
@article {pmid38452965, year = {2024}, author = {Galaktionov, KV and Gonchar, A and Postanogova, D and Miroliubov, A and Bodrov, SY}, title = {Parvatrema spp. (Digenea, Gymnophallidae) with parthenogenetic metacercariae: diversity, distribution and host specificity in the palaearctic.}, journal = {International journal for parasitology}, volume = {54}, number = {7}, pages = {333-355}, doi = {10.1016/j.ijpara.2024.02.002}, pmid = {38452965}, issn = {1879-0135}, mesh = {Animals ; Biodiversity ; Birds/parasitology ; Bivalvia/parasitology ; *Host Specificity ; *Metacercariae/physiology/genetics/growth &amp; development ; Parthenogenesis ; Phylogeny ; *Trematoda/genetics/physiology/classification/growth &amp; development ; *Trematode Infections/parasitology/veterinary/transmission ; }, abstract = {There are several species of gymnophallid digeneans in the genus Parvatrema that are unique in developing metacercariae that reproduce by parthenogenesis in the second intermediate host. Transmission of these digeneans takes place in coastal ecosystems of the North Pacific and North Atlantic seas. The first intermediate hosts are bivalves, the second ones are gastropods, and the definitive hosts are migratory birds. We integrated data accumulated over 25 years of research and differentiated a complex of five closely related species. They differ in the molluscan second intermediate hosts, distribution ranges, and life cycles patterns. The type I life cycle includes two generations of parthenogenetic metacercariae, followed by development of metacercariae which are invasive for the definitive host. In the type II life cycle, the number of generations of parthenogenetic metacercariae is unlimited, and they can also produce cercariae. These cercariae emerge into the environment and can infect new individuals of the second intermediate host. We conclude that the type I life cycle is a derived option that has evolved as a better fit to transmission in the unstable conditions in the intertidal zone. Another evolutionary trend in Parvatrema is transition from inhabiting the extrapallial space of the gastropod second intermediate host to endoparasitism in its mantle and internal organs. rDNA sequence analysis highlighted that Parvatrema spp. with parthenogenetic metacercariae form a monophyletic clade and suggested the Pacific origin of the group, with two transfers to the North Atlantic and colonisation of new second intermediate host species. Apparently the group formed in the late Pliocene-Pleistocene and diversified as a result of recurrent isolation in inshore refugia during glacial periods. We argue that parthenogenetic metacercariae in Parvatrema may serve as a model for early digenean evolution, demonstrating the first steps of adopting the molluscan first intermediate host and becoming tissue parasites.}, }
@article {pmid38447923, year = {2024}, author = {Mokrousov, I}, title = {Origin and dispersal of the Mycobacterium tuberculosis Haarlem genotype: Clues from its phylogeographic landscape and human migration.}, journal = {Molecular phylogenetics and evolution}, volume = {195}, number = {}, pages = {108045}, doi = {10.1016/j.ympev.2024.108045}, pmid = {38447923}, issn = {1095-9513}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Phylogeny ; *Tuberculosis/microbiology ; Human Migration ; Genotype ; }, abstract = {The Haarlem family belongs to the Euro-American phylogenetic lineage of Mycobacterium tuberculosis and is one of the globally spread genotypes of this important human pathogen. In spite of the sporadic observations on drug resistance and peculiar virulence profile, Haarlem remains in the shade of other M. tuberculosis genotypes. I analyzed genotyping data of the Haarlem genotype in light of its pathogenic properties and relevant human migration, to gain insight into its origin, evolutionary history, and current spread. Central Europe is marked with a very high prevalence of both major Haarlem subclades ancestral H3/SIT50 and derived H1, jointly making 33-41% in Czechia, Austria, and Hungary. There is a declining gradient of Haarlem beyond central Europe with 10-18% in Italy, France, Belgium, 10-13% in the Balkan countries and Turkey. Placing the available genetic diversity and ancient DNA data within the historical context, I hypothesize that M. tuberculosis Haarlem genotype likely originated in Central Europe and its primary long-term circulation occurred within the area of the former Austria/Austria-Hungary Empire in the 14th-19th centuries. The genotype is not highly transmissible and its spread was driven by long-term human migration. The European colonial expansion (when accompanied by a sufficient volume of migration) was a vehicle of its secondary dissemination. I conclude that human migration and its lack thereof (but not strain pathobiology) was a major driving force that shaped the population structure of this global lineage of M. tuberculosis. At the same time, Haarlem strains appear over-represented in some ethnic groups which warrants in-depth experimental research.}, }
@article {pmid38446809, year = {2024}, author = {MacRoberts, RA and Liberato, M and Roca-Rada, X and Valente, MJ and Relvado, C and Matos Fernandes, T and Barrocas Dias, C and Llamas, B and Vasconcelos Vilar, H and Schöne, BR and Ribeiro, S and Santos, JF and Teixeira, JC and Maurer, AF}, title = {Shrouded in history: Unveiling the ways of life of an early Muslim population in Santarém, Portugal (8th- 10th century AD).}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0299958}, pmid = {38446809}, issn = {1932-6203}, mesh = {Humans ; Adult ; Female ; Male ; Portugal ; *Islam ; *Strontium Isotopes ; Carbon ; }, abstract = {In around 716 AD, the city of Santarém, Portugal, was conquered by the Berber and Arab armies that swept the Iberian Peninsula and went on to rule the region until the 12th century. Archaeological excavations in 2007/08 discovered an Islamic necropolis (Avenida 5 de Outubro #2-8) that appears to contain the remains of an early Muslim population in Santarém (8th- 10th century). In this study, skeletal material from 58 adult individuals was analysed for stable carbon (δ13Ccol; δ13Cap), nitrogen (δ15N) and sulphur (δ34S) isotope ratios in bones, and stable oxygen (δ18O), carbon (δ13Cen) and radiogenic strontium (87Sr/86Sr) isotopes in tooth enamel. The results of this study revealed a dietary pattern of predominantly C3-plant and domestic C3-fed herbivore consumption during adulthood (δ13Ccol and δ15N, respectively) but a higher proportion of C4-plant input during childhood (δ13Cen) for some individuals-interpreted as possible childhood consumption of millet porridge, a common practice in North Africa-in those with unorthodox burial types (Groups 1 and 2) that was not practiced in the individuals with canonical burials (Group 3). In this first mobility study of a medieval Muslim population in Portugal, δ18ODW values revealed greater heterogeneity in Groups 1 and 2, consistent with diverse origins, some in more humid regions than Santarém when compared to regional precipitation δ18O data, contrasting the more homogenous Group 3, consistent with the local precipitation δ18O range. Ancient DNA analysis conducted on three individuals revealed maternal (mtDNA) and paternal (Y-chromosome) lineages compatible with a North African origin for (at least) some of the individuals. Additionally, mobility of females in this population was higher than males, potentially resulting from a patrilocal social system, practiced in Berber and Arab communities. These results serve to offer a more detailed insight into the ancestry and cultural practices of early Muslim populations in Iberia.}, }
@article {pmid38440408, year = {2024}, author = {Eisenhofer, R and Wright, S and Weyrich, L}, title = {Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16770}, pmid = {38440408}, issn = {2167-8359}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Benchmarking ; Genes, rRNA ; Dental Calculus ; *Microbiota ; DNA, Ancient ; }, abstract = {The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.}, }
@article {pmid38428387, year = {2024}, author = {Bennett, EA and Fu, Q}, title = {Ancient genomes and the evolutionary path of modern humans.}, journal = {Cell}, volume = {187}, number = {5}, pages = {1042-1046}, doi = {10.1016/j.cell.2024.01.047}, pmid = {38428387}, issn = {1097-4172}, mesh = {Animals ; Humans ; *Biological Evolution ; *DNA, Ancient ; Genome, Human ; *Hominidae/genetics ; }, abstract = {Growing evidence from archaic and early modern human genomes brings new insights to the emergence of modern humans. We recount recent information collected from ancient DNA studies that inform us about the evolutionary pathway to modern humanity. These findings point to both individual- and population-level advantages underlying modern human expansion.}, }
@article {pmid38423916, year = {2024}, author = {Meiri, M and Bar-Oz, G}, title = {Unraveling the diversity and cultural heritage of fruit crops through paleogenomics.}, journal = {Trends in genetics : TIG}, volume = {40}, number = {5}, pages = {398-409}, pmid = {38423916}, issn = {0168-9525}, mesh = {*Crops, Agricultural/genetics ; *Fruit/genetics ; Genomics/methods ; Domestication ; Plant Breeding/methods ; Genetic Variation ; Genome, Plant/genetics ; Vitis/genetics ; Solanum lycopersicum/genetics ; Phoeniceae/genetics ; }, abstract = {Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.}, }
@article {pmid38418841, year = {2024}, author = {Huang, J and Chen, J and Shi, M and Zheng, J and Chen, M and Wu, L and Zhu, H and Zheng, Y and Wu, Q and Wu, F}, title = {Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4867}, pmid = {38418841}, issn = {2045-2322}, support = {2018KJCX023//Forestry Science and Technology Innovation Project of Guangdong province/ ; 2021B1212040015//Guangdong Provincial Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products/ ; QD202122//school-level projects of Hanshan Normal University/ ; QD202123//school-level projects of Hanshan Normal University/ ; 060302052305//the program for scientific research start-up funds of Guangdong Ocean University/ ; }, mesh = {*Genome, Plant ; China ; Repetitive Sequences, Nucleic Acid ; *Malpighiales ; Evolution, Molecular ; Phylogeny ; }, abstract = {Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is primarily distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semi-cultivated tree species with ornamental, edible, and medicinal value, exhibiting significant development potential. In this study, we present the whole-genome sequencing of B. ramiflora, employing a combination of PacBio SMRT and Illumina HiSeq 2500 sequencing techniques. The assembled genome size was 975.8 Mb, with a contig N50 of 509.33 kb and the longest contig measuring 7.74 Mb. The genome comprises approximately 73.47% highly repetitive sequences, of which 52.1% are long terminal repeat-retrotransposon sequences. A total of 29,172 protein-coding genes were predicted, of which 25,980 (89.06%) have been annotated, Additionally, 3452 non-coding RNAs were identified. Comparative genomic analysis revealed a close relationship between B. ramiflora and the Euphorbiaceae family, with both being sister groups that diverged approximately 59.9 million years ago. During the evolutionary process, B. ramiflora exhibited positive selection in 278 candidate genes. Synonymous substitution rate and collinearity analysis demonstrated that B. ramiflora underwent a single ancient genome-wide triploidization event, without recent genome-wide duplication events. This high-quality B. ramiflora genome provides a valuable resource for basic research and tree improvement programs focusing on the Phyllanthaceae family.}, }
@article {pmid38417515, year = {2024}, author = {Thomson-Laing, G and Howarth, JD and Atalah, J and Vandergoes, MJ and Li, X and Pearman, JK and Fitzsimons, S and Moy, C and Moody, A and Shepherd, C and McKay, N and Wood, SA}, title = {Sedimentary ancient DNA reveals the impact of anthropogenic land use disturbance and ecological shifts on fish community structure in small lowland lake.}, journal = {The Science of the total environment}, volume = {922}, number = {}, pages = {171266}, doi = {10.1016/j.scitotenv.2024.171266}, pmid = {38417515}, issn = {1879-1026}, mesh = {Animals ; Humans ; *DNA, Ancient ; *Lakes ; Biodiversity ; DNA ; Fishes ; Ruminants ; Ecosystem ; }, abstract = {Freshwater fish biodiversity and abundance are decreasing globally. The drivers of decline are primarily anthropogenic; however, the causative links between disturbances and fish community change are complex and challenging to investigate. We used a suite of sedimentary DNA methods (droplet digital PCR and metabarcoding) and traditional paleolimnological approaches, including pollen and trace metal analysis, ITRAX X-ray fluorescence and hyperspectral core scanning to explore changes in fish abundance and drivers over 1390 years in a small lake. This period captured a disturbance trajectory from pre-human settlement through subsistence living to intensive agriculture. Generalized additive mixed models explored the relationships between catchment inputs, internal drivers, and fish community structure. Fish community composition distinctly shifted around 1350 CE, with the decline of a sensitive Galaxias species concomitant with early land use changes. Total fish abundance significantly declined around 1950 CE related to increases in ruminant bacterial DNA (a proxy for ruminant abundance) and cadmium flux (a proxy for phosphate fertilizers), implicating land use intensification as a key driver. Concurrent shifts in phytoplankton and zooplankton suggested that fish communities were likely impacted by food web dynamics. This study highlights the potential of sedDNA to elucidate the long-term disturbance impacts on biological communities in lakes.}, }
@article {pmid38417441, year = {2024}, author = {Martiniano, R and Haber, M and Almarri, MA and Mattiangeli, V and Kuijpers, MCM and Chamel, B and Breslin, EM and Littleton, J and Almahari, S and Aloraifi, F and Bradley, DG and Lombard, P and Durbin, R}, title = {Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria.}, journal = {Cell genomics}, volume = {4}, number = {3}, pages = {100507}, pmid = {38417441}, issn = {2666-979X}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 205072/WT_/Wellcome Trust/United Kingdom ; 207492/WT_/Wellcome Trust/United Kingdom ; 205072/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Arabs/genetics ; Bahrain ; *DNA, Ancient ; *Genetics, Population ; *Genome, Human ; }, abstract = {The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.}, }
@article {pmid38415845, year = {2024}, author = {Emery, MV and Bolhofner, K and Spake, L and Ghafoor, S and Versoza, CJ and Rawls, EM and Winingear, S and Buikstra, JE and Loreille, O and Fulginiti, LC and Stone, AC}, title = {Targeted enrichment of whole-genome SNPs from highly burned skeletal remains.}, journal = {Journal of forensic sciences}, volume = {69}, number = {5}, pages = {1558-1577}, doi = {10.1111/1556-4029.15482}, pmid = {38415845}, issn = {1556-4029}, support = {2016-DN-BX-0158//National Institute of Justice/ ; }, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *High-Throughput Nucleotide Sequencing ; *Tooth/chemistry ; *Burns/genetics ; *Body Remains ; *Fires ; *Bone and Bones/chemistry ; Sequence Analysis, DNA ; Genome, Human ; DNA/isolation &amp; purification ; DNA Degradation, Necrotic ; Male ; Female ; }, abstract = {Genetic assessment of highly incinerated and/or degraded human skeletal material is a persistent challenge in forensic DNA analysis, including identifying victims of mass disasters. Few studies have investigated the impact of thermal degradation on whole-genome single-nucleotide polymorphism (SNP) quality and quantity using next-generation sequencing (NGS). We present whole-genome SNP data obtained from the bones and teeth of 27 fire victims using two DNA extraction techniques. Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform. Raw reads were processed using the EAGER (Efficient Ancient Genome Reconstruction) pipeline, and the SNPs filtered and called using FreeBayes and GATK (v. 3.8). Mixed-effects modeling of the data suggest that SNP variability and preservation is predominantly determined by skeletal element and burn category, and not by extraction type. Whole-genome SNP data suggest that selecting long bones, hand and foot bones, and teeth subjected to temperatures <350°C are the most likely sources for higher genomic DNA yields. Furthermore, we observed an inverse correlation between the number of captured SNPs and the extent to which samples were burned, as well as a significant decrease in the total number of SNPs measured for samples subjected to temperatures >350°C. Our data complement previous analyses of burned human remains that compare extraction methods for downstream forensic applications and support the idea of adopting a modified Dabney extraction technique when traditional forensic methods fail to produce DNA yields sufficient for genetic identification.}, }
@article {pmid38412309, year = {2024}, author = {McComish, BJ and Charleston, MA and Parks, M and Baroni, C and Salvatore, MC and Li, R and Zhang, G and Millar, CD and Holland, BR and Lambert, DM}, title = {Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time.}, journal = {Genome biology and evolution}, volume = {16}, number = {3}, pages = {}, pmid = {38412309}, issn = {1759-6653}, support = {RGP0036/2011//Human Frontier Science Program/ ; 2157200//Australian Research Council Linkage/ ; //Australia-India Strategic Research Fund/ ; //Griffith University/ ; //University of Tasmania/ ; PNRA-4.2/2004//Italian National Program on Antarctic Research/ ; //Antarctica New Zealand/ ; }, mesh = {Humans ; *Genome ; *Genetics, Population ; Mutation ; Microsatellite Repeats ; Polymorphism, Genetic ; }, abstract = {Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over 2 timescales: one based on Adélie penguin samples dating to ∼46.5 ka and the other dating to the diversification of chordates aged more than 500 Ma. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long timescales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.}, }
@article {pmid38407438, year = {2024}, author = {Shao, W and Wang, J and Zhang, Y and Zhang, C and Chen, J and Chen, Y and Fei, Z and Ma, Z and Sun, X and Jiao, C}, title = {The jet-like chromatin structure defines active secondary metabolism in fungi.}, journal = {Nucleic acids research}, volume = {52}, number = {9}, pages = {4906-4921}, pmid = {38407438}, issn = {1362-4962}, support = {2022YFD1400100//National Key Research and Development Program of China/ ; U21A20219//National Natural Science Foundation of China/ ; CARS-03-29//Earmarked Fund for China Agriculture Research System/ ; //National Excellent Young Scientists (overseas) Fund of NSFC/ ; }, mesh = {Acetylation ; *Chromatin/metabolism/genetics ; *Chromosomes, Fungal/genetics/metabolism ; Fungal Proteins/metabolism/genetics ; *Fusarium/genetics/metabolism ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Histone Acetyltransferases/metabolism/genetics ; Histones/metabolism/genetics ; Multigene Family ; *Secondary Metabolism/genetics ; Transcription, Genetic ; }, abstract = {Eukaryotic genomes are spatially organized within the nucleus in a nonrandom manner. However, fungal genome arrangement and its function in development and adaptation remain largely unexplored. Here, we show that the high-order chromosome structure of Fusarium graminearum is sculpted by both H3K27me3 modification and ancient genome rearrangements. Active secondary metabolic gene clusters form a structure resembling chromatin jets. We demonstrate that these jet-like domains, which can propagate symmetrically for 54 kb, are prevalent in the genome and correlate with active gene transcription and histone acetylation. Deletion of GCN5, which encodes a core and functionally conserved histone acetyltransferase, blocks the formation of the domains. Insertion of an exogenous gene within the jet-like domain significantly augments its transcription. These findings uncover an interesting link between alterations in chromatin structure and the activation of fungal secondary metabolism, which could be a general mechanism for fungi to rapidly respond to environmental cues, and highlight the utility of leveraging three-dimensional genome organization in improving gene transcription in eukaryotes.}, }
@article {pmid38378781, year = {2024}, author = {Rohrlach, AB and Rivollat, M and de-Miguel-Ibáñez, P and Moilanen, U and Liira, AM and Teixeira, JC and Roca-Rada, X and Armendáriz-Martija, J and Boyadzhiev, K and Boyadzhiev, Y and Llamas, B and Tiliakou, A and Mötsch, A and Tuke, J and Prevedorou, EA and Polychronakou-Sgouritsa, N and Buikstra, J and Onkamo, P and Stockhammer, PW and Heyne, HO and Lemke, JR and Risch, R and Schiffels, S and Krause, J and Haak, W and Prüfer, K}, title = {Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1294}, pmid = {38378781}, issn = {2041-1723}, support = {771234//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Pregnancy ; Female ; Humans ; *Down Syndrome/genetics ; Trisomy/genetics ; Trisomy 18 Syndrome/genetics ; *Chromosome Disorders/genetics ; DNA, Ancient ; Trisomy 13 Syndrome ; }, abstract = {Aneuploidies, and in particular, trisomies represent the most common genetic aberrations observed in human genetics today. To explore the presence of trisomies in historic and prehistoric populations we screen nearly 10,000 ancient human individuals for the presence of three copies of any of the target autosomes. We find clear genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome), and all cases are present in infant or perinatal burials. We perform comparative osteological examinations of the skeletal remains and find overlapping skeletal markers, many of which are consistent with these syndromes. Interestingly, three cases of trisomy 21, and the case of trisomy 18 were detected in two contemporaneous sites in early Iron Age Spain (800-400 BCE), potentially suggesting a higher frequency of burials of trisomy carriers in those societies. Notably, the care with which the burials were conducted, and the items found with these individuals indicate that ancient societies likely acknowledged these individuals with trisomy 18 and 21 as members of their communities, from the perspective of burial practice.}, }
@article {pmid38365253, year = {2024}, author = {Buchwald, SZ and Herzschuh, U and Nürnberg, D and Harms, L and Stoof-Leichsenring, KR}, title = {Plankton community changes during the last 124 000 years in the subarctic Bering Sea derived from sedimentary ancient DNA.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365253}, issn = {1751-7370}, support = {03G0672A//German Ministry of Education and Research/ ; }, mesh = {Plankton/genetics ; DNA, Ancient ; Oceans and Seas ; Phytoplankton/genetics ; *Diatoms/genetics ; *Cyanobacteria/genetics ; Carbon ; Ecosystem ; }, abstract = {Current global warming results in rising sea-water temperatures, and the loss of sea ice in Arctic and subarctic oceans impacts the community composition of primary producers with cascading effects on the food web and potentially on carbon export rates. This study analyzes metagenomic shotgun and diatom rbcL amplicon sequencing data from sedimentary ancient DNA of the subarctic western Bering Sea that records phyto- and zooplankton community changes over the last glacial-interglacial cycles, including the last interglacial period (Eemian). Our data show that interglacial and glacial plankton communities differ, with distinct Eemian and Holocene plankton communities. The generally warm Holocene period is dominated by picosized cyanobacteria and bacteria-feeding heterotrophic protists, while the Eemian period is dominated by eukaryotic picosized chlorophytes and Triparmaceae. By contrast, the glacial period is characterized by microsized phototrophic protists, including sea ice-associated diatoms in the family Bacillariaceae and co-occurring diatom-feeding crustaceous zooplankton. Our deep-time record of plankton community changes reveals a long-term decrease in phytoplankton cell size coeval with increasing temperatures, resembling community changes in the currently warming Bering Sea. The phytoplankton community in the warmer-than-present Eemian period is distinct from modern communities and limits the use of the Eemian as an analog for future climate scenarios. However, under enhanced future warming, the expected shift toward the dominance of small-sized phytoplankton and heterotrophic protists might result in an increased productivity, whereas the community's potential of carbon export will be decreased, thereby weakening the subarctic Bering Sea's function as an effective carbon sink.}, }
@article {pmid38363870, year = {2024}, author = {Simon, A and Coop, G}, title = {The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {9}, pages = {e2312377121}, pmid = {38363870}, issn = {1091-6490}, support = {R35 GM136290/GM/NIGMS NIH HHS/United States ; R35 GM136290/GF/NIH HHS/United States ; }, mesh = {Humans ; *Gene Flow ; *Selection, Genetic ; DNA, Ancient ; Gene Frequency ; Genetic Drift ; Genetics, Population ; }, abstract = {Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.}, }
@article {pmid38362924, year = {2024}, author = {Taylor, GM and White-Iribhogbe, K and Cole, G and Ashby, D and Stewart, GR and Dawson-Hobbis, H}, title = {Bioarchaeological investigation of individuals with suspected multibacillary leprosy from the mediaeval leprosarium of St Mary Magdalen, Winchester, Hampshire, UK.}, journal = {Journal of medical microbiology}, volume = {73}, number = {2}, pages = {}, doi = {10.1099/jmm.0.001806}, pmid = {38362924}, issn = {1473-5644}, mesh = {Adult ; Child ; Humans ; Male ; Female ; Adolescent ; X-Ray Microtomography ; *Leprosy/microbiology ; Mycobacterium leprae/genetics ; DNA, Bacterial/genetics ; *Leprosy, Multibacillary ; United Kingdom ; }, abstract = {Introduction. We have examined four burials from the St Mary Magdalen mediaeval leprosarium cemetery in Winchester, Hampshire, UK. One (Sk.8) was a male child, two (Sk.45 and Sk.52) were adolescent females and the fourth (Sk.512) was an adult male. The cemetery was in use between the 10th and 12th centuries. All showed skeletal lesions of leprosy. Additionally, one of the two females (Sk.45) had lesions suggestive of multi-cystic tuberculosis and the second (Sk.52) of leprogenic odontodysplasia (LO), a rare malformation of the roots of the permanent maxillary incisors.Gap statement. Relatively little is known of the manifestations of lepromatous leprosy (LL) in younger individuals from the archaeological record.Aims and Methodology. To address this, we have used ancient DNA testing and osteological examination of the individuals, supplemented with X-ray and microcomputed tomography (micro-CT) scan as necessary to assess the disease status.Results and Conclusions. The presence of Mycobacterium leprae DNA was confirmed in both females, and genotyping showed SNP type 3I-1 strains but with a clear genotypic variation. We could not confirm Mycobacterium tuberculosis complex DNA in the female individual SK.45. High levels of M. leprae DNA were found within the pulp cavities of four maxillary teeth from the male child (Sk.8) with LO, consistent with the theory that the replication of M. leprae in alveolar bone may interfere with root formation at key stages of development. We report our biomolecular findings in these individuals and review the evidence this site has contributed to our knowledge of mediaeval leprosy.}, }
@article {pmid38354185, year = {2024}, author = {Laffranchi, Z and Zingale, S and Tecchiati, U and Amato, A and Coia, V and Paladin, A and Salzani, L and Thompson, SR and Bersani, M and Dori, I and Szidat, S and Lösch, S and Ryan-Despraz, J and Arenz, G and Zink, A and Milella, M}, title = {"Until death do us part". A multidisciplinary study on human- Animal co- burials from the Late Iron Age necropolis of Seminario Vescovile in Verona (Northern Italy, 3rd-1st c. BCE).}, journal = {PloS one}, volume = {19}, number = {2}, pages = {e0293434}, pmid = {38354185}, issn = {1932-6203}, mesh = {Humans ; Animals ; Horses ; Dogs ; *Body Remains ; *Burial/methods ; Italy ; Anthropology ; Culture ; Archaeology ; }, abstract = {Animal remains are a common find in prehistoric and protohistoric funerary contexts. While taphonomic and osteological data provide insights about the proximate (depositional) factors responsible for these findings, the ultimate cultural causes leading to this observed mortuary behavior are obscured by the opacity of the archaeological record and the lack of written sources. Here, we apply an interdisciplinary suite of analytical approaches (zooarchaeological, anthropological, archaeological, paleogenetic, and isotopic) to explore the funerary deposition of animal remains and the nature of joint human-animal burials at Seminario Vescovile (Verona, Northern Italy 3rd-1st c. BCE). This context, culturally attributed to the Cenomane culture, features 161 inhumations, of which only 16 included animal remains in the form of full skeletons, isolated skeletal parts, or food offerings. Of these, four are of particular interest as they contain either horses (Equus caballus) or dogs (Canis lupus familiaris)-animals that did not play a dietary role. Analyses show no demographic, dietary, funerary similarities, or genetic relatedness between individuals buried with animals. Isotopic data from two analyzed dogs suggest differing management strategies for these animals, possibly linked to economic and/or ritual factors. Overall, our results point to the unsuitability of simple, straightforward explanations for the observed funerary variability. At the same time, they connect the evidence from Seminario Vescovile with documented Transalpine cultural traditions possibly influenced by local and Roman customs.}, }
@article {pmid38350445, year = {2024}, author = {Laine, J and Mak, SST and Martins, NFG and Chen, X and Gilbert, MTP and Jones, FC and Pedersen, MW and Romundset, A and Foote, AD}, title = {Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation.}, journal = {Current biology : CB}, volume = {34}, number = {5}, pages = {1142-1147.e6}, doi = {10.1016/j.cub.2024.01.056}, pmid = {38350445}, issn = {1879-0445}, mesh = {Animals ; *Ecosystem ; Adaptation, Physiological/genetics ; *Smegmamorpha/genetics ; Retrospective Studies ; Lakes ; }, abstract = {Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms[1][,][2][,][3] and to thereby potentially provide an understanding of the evolutionary histories of past populations.[4][,][5] To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.[6][,][7] Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies[1][,][2][,][3] to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)[8] were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches[9][,][10][,][11] and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.}, }
@article {pmid38348756, year = {2024}, author = {Vincenti, G and Molinaro, L and Sajjadi, SMS and Moradi, H and Pagani, L and Fabbri, PF}, title = {Female biased adult sex ratio in the Bronze Age cemetery of Shahr-i Sokhta (Iran) as an indicator of long distance trade and matrilocality.}, journal = {American journal of biological anthropology}, volume = {183}, number = {4}, pages = {e24911}, doi = {10.1002/ajpa.24911}, pmid = {38348756}, issn = {2692-7691}, support = {//Ministero degli Affari Esteri e della Cooperazione Internazionale/ ; //University of Salento/ ; }, mesh = {Adult ; Male ; Middle Aged ; Humans ; Female ; Iran ; *Cemeteries ; Sex Ratio ; Middle East ; Anthropology ; *Polygonaceae ; }, abstract = {OBJECTIVES: This paper starts from the unusual observation of the overrepresentation of females among adults in the cemetery of Bronze Age Shahr-i Sokhta (Seistan, Iran) and explores the post marital residence pattern. By integrating taphonomical (skeletal preservation), anthropological (sex ratio [SR], sexual dimorphism, stress indicators, age at death), archeological (long distance trade indicators, habitation floor area, social role of women), and ancient DNA (heterozygosity levels in X chromosomes) data we test the hypothesis of post marital matrilocality in the site.<br><br>METHODS: We computed the SR (pelvis-based sex determination) in a random unpublished adult sample from the cemetery of Shahr-i Sokhta and in two samples previously published by other authors. We used comparative data on SR from: a large Supra Regional multi-chronological sample of sites, n&#x2009;=&#x2009;47, with 8808 adult sexed individuals, from Southern Europe, Egypt, Middle East, Southern Russia; a Regional Bronze Age sample of sites (n&#x2009;=&#x2009;10) from Bactria Margiana and Indus Valley with 1324 adult sexed individuals. We estimated the heterozygosity levels in X chromosomes compared with the rest of the autosomes on the assumption that in a matrilocal society females should show lower variability than men.<br><br>RESULTS: Adult SR in a sample (n&#x2009;=&#x2009;549) from Shahr-i Sokhta is 70.5, the overrepresentation of females is shared with Regional Bronze Age sites from Bactria Margiana (SR&#x2009;=&#x2009;72.09) and Indus Valley (SR&#x2009;=&#x2009;67.54). On the contrary, in a larger Supra Regional multi-chronological sample of sites, mean SR ranges between 112.7 (Bronze Age) and 163.1 (Middle Ages). Taphonomical and anthropological indicators do not explain the overrepresentation of female skeletons. Archeological indicators suggest a high social status of women and that the society was devoted to long range trade activities. heterozygosity levels in X chromosomes are in agreement with a matrilocal society.<br><br>CONCLUSIONS: Indicators suggest that Bronze Age Shahr-&#xec; Sokhta was a matrilocal society and that long distance trade was an important economic factor producing an overrepresentation of adult female skeletons in the cemetery.}, }
@article {pmid38341426, year = {2024}, author = {Mallick, S and Micco, A and Mah, M and Ringbauer, H and Lazaridis, I and Olalde, I and Patterson, N and Reich, D}, title = {The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {182}, pmid = {38341426}, issn = {2052-4463}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; *Genome, Human ; *Genomics ; Paleontology ; }, abstract = {More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.}, }
@article {pmid38308451, year = {2024}, author = {Navarro-Romero, MT and Muñoz, ML and Krause-Kyora, B and Cervini-Silva, J and Alcalá-Castañeda, E and David, RE}, title = {Bioanthropological analysis of human remains from the archaic and classic period discovered in Puyil cave, Mexico.}, journal = {American journal of biological anthropology}, volume = {184}, number = {2}, pages = {e24903}, doi = {10.1002/ajpa.24903}, pmid = {38308451}, issn = {2692-7691}, support = {2015-Marzo 2016-290936//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 2014_Primer Periodo-380118//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {Humans ; Mexico ; *Caves ; *DNA, Mitochondrial/genetics ; *Body Remains/chemistry/anatomy &amp; histology ; Radiometric Dating ; Male ; History, Ancient ; Female ; Anthropology, Physical ; Archaeology ; }, abstract = {OBJECTIVES: Determine the geographic place of origin and maternal lineage of prehistoric human skeletal remains discovered in Puyil Cave, Tabasco State, Mexico, located in a region currently populated by Olmec, Zoque and Maya populations.<br><br>MATERIALS AND METHODS: All specimens were radiocarbon ([14]C) dated (beta analytic), had dental modifications classified, and had an analysis of 13 homologous reference points conducted to evaluate artificial cranial deformation (ACD). Following DNA purification, hypervariable region I (HVR-1) of the mitogenome was amplified and Sanger sequenced. Finally, Next Generation Sequencing (NGS) was performed for total DNA. Mitochondrial DNA (mtDNA) variants and haplogroups were determined using BioEdit 7.2 and IGV software and confirmed with MITOMASTER and WebHome softwares.<br><br>RESULTS: Radiocarbon dating ([14]C) demonstrated that the inhabitants of Puyil Cave lived during the Archaic and Classic Periods and displayed tabular oblique and tabular mimetic ACD. These pre-Hispanic remains exhibited five mtDNA lineages: A, A2, C1, C1c and D4. Network analysis revealed a close genetic affinity between pre-Hispanic Puyil Cave inhabitants and contemporary Maya subpopulations from Mexico and Guatemala, as well as individuals from Bolivia, Brazil, the Dominican Republic, and China.<br><br>CONCLUSIONS: Our results elucidate the dispersal of pre-Hispanic Olmec and Maya ancestors and suggest that ACD practices are closely related to Olmec and Maya practices. Additionally, we conclude that ACD has likely been practiced in the region since the Middle-Archaic Period.}, }
@article {pmid38302698, year = {2024}, author = {Petrić Howe, N and Bundell, S}, title = {Ancient DNA solves the mystery of who made a set of stone tools.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-024-00290-7}, pmid = {38302698}, issn = {1476-4687}, }
@article {pmid38288729, year = {2024}, author = {Antonio, ML and Weiß, CL and Gao, Z and Sawyer, S and Oberreiter, V and Moots, HM and Spence, JP and Cheronet, O and Zagorc, B and Praxmarer, E and Özdoğan, KT and Demetz, L and Gelabert, P and Fernandes, D and Lucci, M and Alihodžić, T and Amrani, S and Avetisyan, P and Baillif-Ducros, C and Bedić, &#x17d; and Bertrand, A and Bilić, M and Bondioli, L and Borówka, P and Botte, E and Burmaz, J and Bužanić, D and Candilio, F and Cvetko, M and De Angelis, D and Drnić, I and Elschek, K and Fantar, M and Gaspari, A and Gasperetti, G and Genchi, F and Golubović, S and Hukeľová, Z and Jankauskas, R and Vučković, KJ and Jeremić, G and Kaić, I and Kazek, K and Khachatryan, H and Khudaverdyan, A and Kirchengast, S and Korać, M and Kozlowski, V and Krošláková, M and Kušan Špalj, D and La Pastina, F and Laguardia, M and Legrand, S and Leleković, T and Leskovar, T and Lorkiewicz, W and Los, D and Silva, AM and Masaryk, R and Matijević, V and Cherifi, YMS and Meyer, N and Mikić, I and Miladinović-Radmilović, N and Milošević Zakić, B and Nacouzi, L and Natuniewicz-Sekuła, M and Nava, A and Neugebauer-Maresch, C and Nováček, J and Osterholtz, A and Paige, J and Paraman, L and Pieri, D and Pieta, K and Pop-Lazić, S and Ruttkay, M and Sanader, M and Sołtysiak, A and Sperduti, A and Stankovic Pesterac, T and Teschler-Nicola, M and Teul, I and Tončinić, D and Trapp, J and Vulović, D and Waliszewski, T and Walter, D and Živanović, M and Filah, MEM and Čaušević-Bully, M and Šlaus, M and Borić, D and Novak, M and Coppa, A and Pinhasi, R and Pritchard, JK}, title = {Stable population structure in Europe since the Iron Age, despite high mobility.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {38288729}, issn = {2050-084X}, support = {M 3108/FWF_/Austrian Science Fund FWF/Austria ; R01 HG011432/HG/NHGRI NIH HHS/United States ; HG011432/NH/NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; *Genome, Human ; Europe ; France ; Genetics, Population ; Population Dynamics ; Human Migration ; }, abstract = {Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000-3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire's mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history.}, }
@article {pmid38287404, year = {2024}, author = {Lei, H and Li, J and Zhao, B and Kou, SH and Xiao, F and Chen, T and Wang, SM}, title = {Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {5}, pmid = {38287404}, issn = {1479-7364}, support = {2019YFE0198800//National Key Research-Development Program of China/ ; 2021R52020//Ten-Thousand Talents Plan of Zhejiang Province/ ; 085/2017/A2//Macau Science and Technology Development Fund/ ; 0077/2019/AMJ//Macau Science and Technology Development Fund/ ; 0032/2022/A1//Macau Science and Technology Development Fund/ ; SRG2017-00097-FHS//University of Macau/ ; MYRG2019-00018-FHS//University of Macau/ ; MYRG2020-00094-FHS//University of Macau/ ; FHSIG/SW/0007/2020P, MOE Frontiers Science Center for Precision Oncology pilot grant and a startup fund//Faculdade de Ci&#xea;ncias da Sa&#xfa;de, Universidade de Macau/ ; }, mesh = {Humans ; *DNA Mismatch Repair/genetics ; Phylogeny ; *Neoplastic Syndromes, Hereditary ; Germ-Line Mutation/genetics ; Germ Cells ; *Brain Neoplasms ; *Colorectal Neoplasms ; }, abstract = {BACKGROUND: Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs.<br><br>METHODS: We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis.<br><br>RESULTS: Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100&#xa0;years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000&#xa0;years with similar quantitative patterns.<br><br>CONCLUSION: Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.}, }
@article {pmid38284317, year = {2024}, author = {Śledziński, &#x141;J and Zamerska, A and Jędrychowska-Dańska, K and Strózik, T and Wasiak, T and Płoszaj, T and Witas, P and Witas, HW and Borowiec, M and Agier, J}, title = {Suggested mechanism of CCR5Δ32, CCR2-64I and SDF 1-3'A allele frequency change in Polish and Lithuanian gene pools from the perspective of passing time.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {81}, number = {3}, pages = {261-280}, doi = {10.1127/anthranz/2024/1637}, pmid = {38284317}, issn = {0003-5548}, mesh = {Humans ; Lithuania ; *Receptors, CCR5/genetics ; *Receptors, CCR2/genetics ; Poland ; *Gene Frequency ; *Chemokine CXCL12/genetics ; Haplotypes ; DNA, Mitochondrial/genetics ; Polymorphism, Genetic ; }, abstract = {The study aimed to determine the frequency of the alleles associated with hereditary immune response in 16 historical populations and assess which evolutionary forces may have contributed to the observed frequency fluctuation. The analysed polymorphic sites are located in three genes - CCR5, CCR2 and SDF 1 (CXCL12). Protein products are involved in the innate immune response and are also involved in various types of infections, autoimmune diseases and tumours. The frequency of the alleles found in the DNA of the studied individuals was determined by the Sanger methodology and was compared with the data obtained for modern populations. To confirm the authenticity of the obtained results, mtDNA HVRI haplotypes of all the studied samples were obtained and compared with the genetic database of the laboratory personnel who came into contact with the studied material. Based on the variability of allele frequency, advanced biostatistical analysis was used to distinguish the effect of natural selection from genetic drift, i.e. the forces operating on the polymorphic sites studied. All procedures were performed according to the guidelines for working with ancient DNA to avoid contamination with modern DNA molecules. 681 samples from 39 archaeological sites in Poland and Lithuania dated to the 40[th] century BC and the 19[th] century were studied. The biostatistical analysis showed that the fluctuations in the frequency of CCR5Δ32 in the analysed time interval could be mainly the effect of genetic drift. Nevertheless, for CCR2-64I and SDF 1-3'A, the results confirm the suggestion of negative selection as the mechanism involved. Since all the polymorphic sites encode the elements of innate immune response that are indirectly associated with the process of an HPV infection and the development of cervical cancer, the human papillomavirus may be a good candidate for a selection coefficient affecting the frequency of CCR2-64I and SDF 1-3'A. However, for CCR5Δ32, selection was not detected despite its proven role in the molecular mechanism involved in the response to an HPV infection. The presented work seems to be the first in which the problem of the pattern of CCR5Δ32, CCR2-64I and SDF 1-3'A frequency fluctuations in a temporal perspective was discussed, proposing HPV as a factor influencing the occurrence of the CCR2 and SDF1 alleles.}, }
@article {pmid38279681, year = {2024}, author = {Kellner, FL and Le Moullec, M and Ellegaard, MR and Rosvold, J and Peeters, B and Burnett, HA and Pedersen, &#xc5;&#xd8; and Brealey, JC and Dussex, N and Bieker, VC and Hansen, BB and Martin, MD}, title = {A palaeogenomic investigation of overharvest implications in an endemic wild reindeer subspecies.}, journal = {Molecular ecology}, volume = {33}, number = {5}, pages = {e17274}, doi = {10.1111/mec.17274}, pmid = {38279681}, issn = {1365-294X}, support = {14/137//Svalbard Environmental Protection Fund/ ; 15/105//Svalbard Environmental Protection Fund/ ; 223257//Norwegian Research Council/ ; 276080//Norwegian Research Council/ ; 325589//Norwegian Research Council/ ; 235652//Arctic Field Grant/ ; 246054//Arctic Field Grant/ ; 257173//Arctic Field Grant/ ; }, mesh = {Animals ; *Reindeer/genetics ; Animals, Wild ; Gene Frequency ; Genetic Drift ; Svalbard ; }, abstract = {Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20th centuries. Here, we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90) to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.}, }
@article {pmid38273870, year = {2024}, author = {Wurst, C and Maixner, F and Paladin, A and Mussauer, A and Valverde, G and Narula, J and Thompson, R and Zink, A}, title = {Genetic Predisposition of Atherosclerotic Cardiovascular Disease in Ancient Human Remains.}, journal = {Annals of global health}, volume = {90}, number = {1}, pages = {6}, pmid = {38273870}, issn = {2214-9996}, mesh = {Humans ; *Cardiovascular Diseases ; Genome-Wide Association Study ; Body Remains ; *Atherosclerosis/genetics ; Genetic Predisposition to Disease ; Risk Factors ; Risk Assessment ; }, abstract = {BACKGROUND: Several computed tomographic studies have shown the presence of atherosclerosis in ancient human remains. However, while it is important to understand the development of atherosclerotic cardiovascular disease (ASCVD), genetic data concerning the prevalence of the disease-associated single nucleotide polymorphisms (SNPs) in our ancestors are scarce.<br><br>OBJECTIVE: For a better understanding of the role of genetics in the evolution of ASCVD, we applied an enrichment capture sequencing approach to mummified human remains from different geographic regions and time periods.<br><br>METHODS: Twenty-two mummified individuals were analyzed for their genetic predisposition of ASCVD. Next-generation sequencing methods were applied to ancient DNA (aDNA) samples, including a novel enrichment approach specifically designed to capture SNPs associated with ASCVD in genome-wide association studies of modern humans.<br><br>FINDINGS: Five out of 22 ancient individuals passed all filter steps for calculating a weighted polygenic risk score (PRS) based on 87 SNPs in 56 genes. PRSs were correlated to scores obtained from contemporary people from around the world and cover their complete range. The genetic results of the ancient individuals reflect their phenotypic results, given that the only two mummies showing calcified atherosclerotic arterial plaques on computed tomography scans are the ones exhibiting the highest calculated PRSs.<br><br>CONCLUSIONS: These data show that alleles associated with ASCVD have been widespread for at least 5,000 years. Despite some limitations due to the nature of aDNA, our approach has the potential to lead to a better understanding of the interaction between environmental and genetic influences on the development of ASCVD.}, }
@article {pmid38267579, year = {2024}, author = {Majander, K and Pla-Díaz, M and du Plessis, L and Arora, N and Filippini, J and Pezo-Lanfranco, L and Eggers, S and González-Candelas, F and Schuenemann, VJ}, title = {Redefining the treponemal history through pre-Columbian genomes from Brazil.}, journal = {Nature}, volume = {627}, number = {8002}, pages = {182-188}, pmid = {38267579}, issn = {1476-4687}, mesh = {Humans ; Brazil/epidemiology/ethnology ; Europe/epidemiology ; *Evolution, Molecular ; *Genome, Bacterial/genetics ; History, 15th Century ; History, Ancient ; Syphilis/epidemiology/history/microbiology/transmission ; *Treponema pallidum/classification/genetics/isolation &amp; purification ; *Treponemal Infections/epidemiology/history/microbiology/transmission ; }, abstract = {The origins of treponemal diseases have long remained unknown, especially considering the sudden onset of the first syphilis epidemic in the late 15th century in Europe and its hypothesized arrival from the Americas with Columbus' expeditions[1,2]. Recently, ancient DNA evidence has revealed various treponemal infections circulating in early modern Europe and colonial-era Mexico[3-6]. However, there has been to our knowledge no genomic evidence of treponematosis recovered from either the Americas or the Old World that can be reliably dated to the time before the first trans-Atlantic contacts. Here, we present treponemal genomes from nearly 2,000-year-old human remains from Brazil. We reconstruct four ancient genomes of a prehistoric treponemal pathogen, most closely related to the bejel-causing agent Treponema pallidum endemicum. Contradicting the modern day geographical niche of bejel in the arid regions of the world, the results call into question the previous palaeopathological characterization of treponeme subspecies and showcase their adaptive potential. A high-coverage genome is used to improve molecular clock date estimations, placing the divergence of modern T. pallidum subspecies firmly in pre-Columbian times. Overall, our study demonstrates the opportunities within archaeogenetics to uncover key events in pathogen evolution and emergence, paving the way to new hypotheses on the origin and spread of treponematoses.}, }
@article {pmid38266614, year = {2024}, author = {Delezene, LK and Scott, JE and Irish, JD and Villaseñor, A and Skinner, MM and Hawks, J and Berger, LR}, title = {Sex-biased sampling may influence Homo naledi tooth size variation.}, journal = {Journal of human evolution}, volume = {187}, number = {}, pages = {103490}, doi = {10.1016/j.jhevol.2023.103490}, pmid = {38266614}, issn = {1095-8606}, mesh = {Humans ; Animals ; *Hominidae ; Fossils ; *Tooth ; Genetic Drift ; Molar ; Tooth, Deciduous ; }, abstract = {A frequent source of debate in paleoanthropology concerns the taxonomic unity of fossil assemblages, with many hominin samples exhibiting elevated levels of variation that can be interpreted as indicating the presence of multiple species. By contrast, the large assemblage of hominin fossils from the Rising Star cave system, assigned to Homo naledi, exhibits a remarkably low degree of variation for most skeletal elements. Many factors can contribute to low sample variation, including genetic drift, strong natural selection, biased sex ratios, and sampling of closely related individuals. In this study, we tested for potential sex-biased sampling in the Rising Star dental sample. We compared coefficients of variation for the H. naledi teeth to those for eight extant hominoid samples. We used a resampling procedure that generated samples from the extant taxa that matched the sample size of the fossil sample for each possible Rising Star dental sex ratio. We found that variation at four H. naledi tooth positions-I2, M1, P[4], M1-is so low that the possibility that one sex is represented by few or no individuals in the sample cannot be excluded. Additional evidence is needed to corroborate this inference, such as ancient DNA or enamel proteome data, and our study design does not address other potential factors that would account for low sample variation. Nevertheless, our results highlight the importance of considering the taphonomic history of a hominin assemblage and suggest that sex-biased sampling is a plausible explanation for the low level of phenotypic variation found in some aspects of the current H. naledi assemblage.}, }
@article {pmid38261973, year = {2024}, author = {Barouch, A and Mathov, Y and Meshorer, E and Yakir, B and Carmel, L}, title = {Reconstructing DNA methylation maps of ancient populations.}, journal = {Nucleic acids research}, volume = {52}, number = {4}, pages = {1602-1612}, pmid = {38261973}, issn = {1362-4962}, support = {2436/22//Israel Science Foundation/ ; 61739//John Templeton Foundation/ ; 1001584586//Israel Ministry of Innovation, Science &amp; Technology/ ; }, mesh = {Humans ; *DNA Methylation/genetics ; *DNA, Ancient ; Genome ; Genomics ; Sequence Analysis, DNA/methods ; Human Genetics ; }, abstract = {Studying premortem DNA methylation from ancient DNA (aDNA) provides a proxy for ancient gene activity patterns, and hence valuable information on evolutionary changes in gene regulation. Due to statistical limitations, current methods to reconstruct aDNA methylation maps are constrained to high-coverage shotgun samples, which comprise a small minority of available ancient samples. Most samples are sequenced using in-situ hybridization capture sequencing which targets a predefined set of genomic positions. Here, we develop methods to reconstruct aDNA methylation maps of samples that were not sequenced using high-coverage shotgun sequencing, by way of pooling together individuals to obtain a DNA methylation map that is characteristic of a population. We show that the resulting DNA methylation maps capture meaningful biological information and allow for the detection of differential methylation across populations. We offer guidelines on how to carry out comparative studies involving ancient populations, and how to control the rate of falsely discovered differentially methylated regions. The ability to reconstruct DNA methylation maps of past populations allows for the development of a whole new frontier in paleoepigenetic research, tracing DNA methylation changes throughout human history, using data from thousands of ancient samples.}, }
@article {pmid38257973, year = {2024}, author = {Bennasar-Figueras, A}, title = {The Natural and Clinical History of Plague: From the Ancient Pandemics to Modern Insights.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, pmid = {38257973}, issn = {2076-2607}, abstract = {The human pathogen Yersinia pestis is responsible for bubonic, septicemic, and pneumonic plague. A deeply comprehensive overview of its historical context, bacteriological characteristics, genomic analysis based on ancient DNA (aDNA) and modern strains, and its impact on historical and actual human populations, is explored. The results from multiple studies have been synthesized to investigate the origins of plague, its transmission, and effects on different populations. Additionally, molecular interactions of Y. pestis, from its evolutionary origins to its adaptation to flea-born transmission, and its impact on human and wild populations are considered. The characteristic combinations of aDNA patterns, which plays a decisive role in the reconstruction and analysis of ancient genomes, are reviewed. Bioinformatics is fundamental in identifying specific Y. pestis lineages, and automated pipelines are among the valuable tools in implementing such studies. Plague, which remains among human history's most lethal infectious diseases, but also other zoonotic diseases, requires the continuous investigation of plague topics. This can be achieved by improving molecular and genetic screening of animal populations, identifying ecological and social determinants of outbreaks, increasing interdisciplinary collaborations among scientists and public healthcare providers, and continued research into the characterization, diagnosis, and treatment of these diseases.}, }
@article {pmid38247180, year = {2024}, author = {Zhang, M and Wang, CH and Zheng, YX and Jiangzuo, QG and Hou, YM and Cao, P and Dai, QY and Yang, RW and Liu, F and Feng, XT and Mo, LH and Fu, QM}, title = {Ancient DNA unravels species identification from Laosicheng site, Hunan Province, China, and provides insights into maternal genetic history of East Asian leopards.}, journal = {Zoological research}, volume = {45}, number = {1}, pages = {226-229}, pmid = {38247180}, issn = {2095-8137}, mesh = {Animals ; China ; *DNA, Ancient ; *Panthera/genetics ; Asia, Eastern ; }, }
@article {pmid38238372, year = {2024}, author = {Kırdök, E and Kashuba, N and Damlien, H and Manninen, MA and Nordqvist, B and Kjellström, A and Jakobsson, M and Lindberg, AM and Storå, J and Persson, P and Andersson, B and Aravena, A and Götherström, A}, title = {Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22125}, pmid = {38238372}, issn = {2045-2322}, support = {2019-3-AP3-3729//Mersin University BAP project/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; project no. 2019-00849//The Swedish Research Council/ ; }, mesh = {Animals ; Humans ; Dysbiosis/genetics ; Metagenome ; *Microbiota/genetics ; Oral Health ; *Periodontitis/genetics ; }, abstract = {Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.}, }
@article {pmid38233869, year = {2024}, author = {Budaeva, N and Agne, S and Ribeiro, PA and Straube, N and Preick, M and Hofreiter, M}, title = {Wide-spread dispersal in a deep-sea brooding polychaete: the role of natural history collections in assessing the distribution in quill worms (Onuphidae, Annelida).}, journal = {Frontiers in zoology}, volume = {21}, number = {1}, pages = {1}, pmid = {38233869}, issn = {1742-9994}, support = {351649567//Deutsche Forschungsgemeinschaft/ ; 25-17-70184238//Norwegian Biodiversity Information Centre/ ; PRODEEP//FP7 People: Marie-Curie Actions/ ; SFRH/BPD/69232/2010//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {BACKGROUND: Modern integrative taxonomy-based annelid species descriptions are detailed combining morphological data and, since the last decades, also molecular information. Historic species descriptions are often comparatively brief lacking such detail. Adoptions of species names from western literature in the past led to the assumption of cosmopolitan ranges for many species, which, in many cases, were later found to include cryptic or pseudocryptic lineages with subtle morphological differences. Natural history collections and databases can aid in assessing the geographic ranges of species but depend on correct species identification. Obtaining DNA sequence information from wet-collection museum specimens of marine annelids is often impeded by the use of formaldehyde and/or long-term storage in ethanol resulting in DNA degradation and cross-linking.<br><br>RESULTS: The application of ancient DNA&#xa0;extraction methodology in combination with single-stranded DNA library preparation and target gene capture resulted in successful sequencing of a 110-year-old collection specimen of quill worms. Furthermore, a 40-year-old specimen of quill worms was successfully sequenced using a standard extraction protocol for modern samples, PCR and Sanger sequencing. Our study presents the first molecular analysis of Hyalinoecia species including the previously known species Hyalinoecia robusta, H. tubicloa, H. artifex, and H. longibranchiata, and a potentially undescribed species from equatorial western Africa morphologically indistinguishable from H. tubicola. The study also investigates the distribution of these five Hyalinoecia species. Reassessing the distribution of H. robusta reveals a geographical range covering both the Atlantic and the Indian Oceans as indicated by molecular data obtained from recent and historical specimens.<br><br>CONCLUSION: Our results represent an example of a very wide geographical distribution of a brooding deep-sea annelid with a&#xa0;complex reproduction strategy and seemingly very limited dispersal capacity of its offspring, and highlights the importance of molecular information from museum specimens for integrative annelid taxonomy and biogeography.}, }
@article {pmid38227345, year = {2024}, author = {Grasso, G and Bianciotto, V and Marmeisse, R}, title = {Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities.}, journal = {Microbial biotechnology}, volume = {17}, number = {1}, pages = {e14390}, pmid = {38227345}, issn = {1751-7915}, support = {//Alliance Sorbonne Universit&#xe9;/ ; ATM 2021//Mus&#xe9;um National d'Histoire Naturelle/ ; Bando Da Vinci 2022//Universit&#xe0; Italo Francese/ ; }, mesh = {Humans ; *Microbiota ; DNA ; Microbial Consortia ; }, abstract = {By deciphering information encoded in degraded ancient DNA extracted from up to million-years-old samples, molecular paleomicrobiology enables to objectively retrace the temporal evolution of microbial species and communities. Assembly of full-length genomes of ancient pathogen lineages allows not only to follow historical epidemics in space and time but also to identify the acquisition of genetic features that represent landmarks in the evolution of the host-microbe interaction. Analysis of microbial community DNA extracted from essentially human paleo-artefacts (paleofeces, dental calculi) evaluates the relative contribution of diet, lifestyle and geography on the taxonomic and functional diversity of these guilds in which have been identified species that may have gone extinct in today's human microbiome. As for non-host-associated environmental samples, such as stratified sediment cores, analysis of their DNA illustrates how and at which pace microbial communities are affected by local or widespread environmental disturbance. Description of pre-disturbance microbial diversity patterns can aid in evaluating the relevance and effectiveness of remediation policies. We finally discuss how recent achievements in paleomicrobiology could contribute to microbial biotechnology in the fields of medical microbiology and food science to trace the domestication of microorganisms used in food processing or to illustrate the historic evolution of food processing microbial consortia.}, }
@article {pmid38216764, year = {2024}, author = {Wong, C}, title = {Ancient DNA reveals first known case of sex-development disorder.}, journal = {Nature}, volume = {625}, number = {7996}, pages = {639}, pmid = {38216764}, issn = {1476-4687}, mesh = {Humans ; *Disorders of Sex Development/genetics/history ; *DNA, Ancient/analysis ; Turner Syndrome/genetics/history ; History, Ancient ; }, }
@article {pmid38213708, year = {2023}, author = {Borodko, DD and Zhenilo, SV and Sharko, FS}, title = {Search for differentially methylated regions in ancient and modern genomes.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {27}, number = {7}, pages = {820-828}, doi = {10.18699/VJGB-23-95}, pmid = {38213708}, issn = {2500-0462}, abstract = {Currently, active research is focused on investigating the mechanisms that regulate the development of various pathologies and their evolutionary dynamics. Epigenetic mechanisms, such as DNA methylation, play a significant role in evolutionary processes, as their changes have a faster impact on the phenotype compared to mutagenesis. In this study, we attempted to develop an algorithm for identifying differentially methylated regions associated with metabolic syndrome, which have undergone methylation changes in humans during the transition from a hunter-gatherer to a sedentary lifestyle. The application of existing whole-genome bisulfite sequencing methods is limited for ancient samples due to their low quality and fragmentation, and the approach to obtaining DNA methylation profiles differs significantly between ancient hunter-gatherer samples and modern tissues. In this study, we validated DamMet, an algorithm for reconstructing ancient methylomes. Application of DamMet to Neanderthal and Denisovan genomes showed a moderate level of correlation with previously published methylation profiles and demonstrated an underestimation of methylation levels in the reconstructed profiles by an average of 15-20 %. Additionally, we developed a new Python-based algorithm that allows for the comparison of methylomes in ancient and modern samples, despite the absence of methylation profiles in modern bone tissue within the context of obesity. This analysis involves a two-step data processing approach, where the first step involves the identification and filtration of tissue-specific methylation regions, and the second step focuses on the direct search for differentially methylated regions in specific areas associated with the researcher's target condition. By applying this algorithm to test data, we identified 38 differentially methylated regions associated with obesity, the majority of which were located in promoter regions. The pipeline demonstrated sufficient efficiency in detecting these regions. These results confirm the feasibility of reconstructing DNA methylation profiles in ancient samples and comparing them with modern methylomes. Furthermore, possibilities for further methodological development and the implementation of a new step for studying differentially methylated positions associated with evolutionary processes are discussed.}, }
@article {pmid38212558, year = {2024}, author = {Anastasiadou, K and Silva, M and Booth, T and Speidel, L and Audsley, T and Barrington, C and Buckberry, J and Fernandes, D and Ford, B and Gibson, M and Gilardet, A and Glocke, I and Keefe, K and Kelly, M and Masters, M and McCabe, J and McIntyre, L and Ponce, P and Rowland, S and Ruiz Ventura, J and Swali, P and Tait, F and Walker, D and Webb, H and Williams, M and Witkin, A and Holst, M and Loe, L and Armit, I and Schulting, R and Skoglund, P}, title = {Detection of chromosomal aneuploidy in ancient genomes.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {14}, pmid = {38212558}, issn = {2399-3642}, support = {/WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Male ; Humans ; *Klinefelter Syndrome/diagnosis/genetics ; DNA, Ancient ; Aneuploidy ; *Down Syndrome ; Sex Chromosomes ; }, abstract = {Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes (~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.}, }
@article {pmid38207026, year = {2024}, author = {Curry, A}, title = {Ancient DNA ties modern diseases to ancestry.}, journal = {Science (New York, N.Y.)}, volume = {383}, number = {6679}, pages = {138-139}, doi = {10.1126/science.adn9644}, pmid = {38207026}, issn = {1095-9203}, mesh = {Humans ; *DNA, Ancient ; Europe/epidemiology ; Genome, Human ; *Multiple Sclerosis/epidemiology/genetics/history ; }, abstract = {Among Europeans, risk of multiple sclerosis rises with genes from Bronze Age Yamnaya herders.}, }
@article {pmid38200339, year = {2024}, author = {Reardon, S}, title = {Ancient DNA reveals origins of multiple sclerosis in Europe.}, journal = {Nature}, volume = {625}, number = {7995}, pages = {431-432}, pmid = {38200339}, issn = {1476-4687}, mesh = {Humans ; Archaeology ; *DNA, Ancient/analysis ; Europe ; *Multiple Sclerosis/genetics/history ; }, }
@article {pmid38200296, year = {2024}, author = {Barrie, W and Yang, Y and Irving-Pease, EK and Attfield, KE and Scorrano, G and Jensen, LT and Armen, AP and Dimopoulos, EA and Stern, A and Refoyo-Martinez, A and Pearson, A and Ramsøe, A and Gaunitz, C and Demeter, F and Jørkov, MLS and Møller, SB and Springborg, B and Klassen, L and Hyldgård, IM and Wickmann, N and Vinner, L and Korneliussen, TS and Allentoft, ME and Sikora, M and Kristiansen, K and Rodriguez, S and Nielsen, R and Iversen, AKN and Lawson, DJ and Fugger, L and Willerslev, E}, title = {Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations.}, journal = {Nature}, volume = {625}, number = {7994}, pages = {321-328}, pmid = {38200296}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_UU_00036/3/MRC_/Medical Research Council/United Kingdom ; R01 GM138634/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Datasets as Topic ; Diet/ethnology/history ; Europe/ethnology ; *Genetic Predisposition to Disease/history ; Genetics, Medical ; *Genome, Human ; *Grassland ; History, 15th Century ; History, Ancient ; History, Medieval ; Human Migration/history ; Life Style/ethnology/history ; *Multiple Sclerosis/genetics/history/immunology ; Neurodegenerative Diseases/genetics/history/immunology ; Population Density ; }, abstract = {Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated[1]. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age[2], along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment.}, }
@article {pmid38200208, year = {2024}, author = {Scaggion, C and Marinato, M and Dal Sasso, G and Nodari, L and Saupe, T and Aneli, S and Pagani, L and Scheib, CL and Rigo, M and Artioli, G}, title = {A fresh perspective on infrared spectroscopy as a prescreening method for molecular and stable isotopes analyses on ancient human bones.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1028}, pmid = {38200208}, issn = {2045-2322}, support = {Ph.D. scholarship//Fondazione Cassa di Risparmio di Padova e Rovigo/ ; scholarship//Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali/ ; }, mesh = {Humans ; Spectrophotometry, Infrared ; *Archaeology ; *Burial ; Chromosome Mapping ; DNA, Ancient ; Isotopes ; }, abstract = {Following the development of modern genome sequencing technologies, the investigation of museum osteological finds is increasingly informative and popular. Viable protocols to help preserve these collections from exceedingly invasive analyses, would allow greater access to the specimens for scientific research. The main aim of this work is to survey skeletal tissues, specifically petrous bones and roots of teeth, using infrared spectroscopy as a prescreening method to assess the bone quality for molecular analyses. This approach could overcome the major problem of identifying useful genetic material in archaeological bone collections without resorting to demanding, time consuming and expensive laboratory studies. A minimally invasive sampling of archaeological bones was developed and bone structural and compositional changes were examined, linking isotopic and genetic data to infrared spectra. The predictive model based on Infrared parameters is effective in determining the occurrence of ancient DNA (aDNA); however, the quality/quantity of aDNA cannot be determined because of the influence of environmental and local factors experienced by the examined bones during the burial period.}, }
@article {pmid38194921, year = {2024}, author = {Bellwood, P}, title = {Archaeogenetics: Tracing ancient migrations from the Yellow River.}, journal = {Current biology : CB}, volume = {34}, number = {1}, pages = {R18-R20}, doi = {10.1016/j.cub.2023.11.024}, pmid = {38194921}, issn = {1879-0445}, mesh = {Humans ; *Rivers ; Asia, Eastern ; China ; *DNA, Ancient ; Language ; }, abstract = {Migration from the Yellow River homeland of Sino-Tibetan languages and people has impacted humans in East Asia for more than 6,000 years. A new study of ancient DNA from southwest China reveals an important component of this migration history.}, }
@article {pmid38189170, year = {2024}, author = {Lammers, Y and Taberlet, P and Coissac, E and Elliott, LD and Merkel, MF and Pitelkova, I and ,  and ,  and Alsos, IG}, title = {Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA.}, journal = {Molecular ecology resources}, volume = {24}, number = {3}, pages = {e13926}, doi = {10.1111/1755-0998.13926}, pmid = {38189170}, issn = {1755-0998}, support = {226134/F50//Norges Forskningsr&#xe5;d/ ; 250963/F20//Norges Forskningsr&#xe5;d/ ; 255415//Norges Forskningsr&#xe5;d/ ; 14-14//Norwegian Biodiversity Information Centre/ ; 70184209//Norwegian Biodiversity Information Centre/ ; 819192//H2020 European Research Council/ ; ANR-10-INBS-09-08//France G&#xe9;nomique/ ; }, mesh = {*DNA, Environmental ; Genetics, Population ; Phylogeography ; DNA, Ancient/analysis ; Multiplex Polymerase Chain Reaction ; Genetic Variation ; }, abstract = {Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages in present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primer sets to target these. Initial multiplex PCR testing resulted in a final set of 38 primer sets. These primer sets were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primer sets could be recovered from the sedaDNA data. For each sample on average 28.1 primer sets, representing 34.15 sequence variants, were recovered. All sediment samples were dominated by a single lineage, except three Alpine samples which had co-occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present-day phylogeographical studies may overlook past genetic patterns. Multiplexing primer is a promising tool for generating population-level genetic information from sedaDNA. The relatively simple method, combined with high sensitivity, provides a scalable method which will allow researchers to track populations through time and space using environmental DNA.}, }
@article {pmid38179684, year = {2024}, author = {Hipp, AL and Lazic, D}, title = {Ancient tree genomes for old questions.}, journal = {Molecular ecology}, volume = {33}, number = {3}, pages = {e17259}, doi = {10.1111/mec.17259}, pmid = {38179684}, issn = {1365-294X}, support = {2129281//Division of Environmental Biology/ ; }, mesh = {*Trees/genetics ; Genomics ; Paleontology ; Wood ; Ecology ; *Quercus/genetics ; }, abstract = {Most foundational work on the evolution and migration of plant species relies on genomic data from contemporary samples. Ancient plant samples can give us access to allele sequences and distributions on the landscape dating back to the mid Holocene or earlier (Gugerli et al., 2005). Nuclear DNA from ancient wood, however, has been mostly inaccessible until now. In a From the Cover article in this issue of Molecular Ecology, Wagner et al. (2023) present the first resequenced nuclear genomes from ancient oak wood, including two samples dated to the 15th century and one that dates to more than 3500 years ago. These ancient tree genomes open the possibility for investigating species adaptation, migration, divergence, and hybridisation in the deep past. They pave the way for what we hope will be a new era in the use of paleogenomics to study Holocene tree histories.}, }
@article {pmid38177452, year = {2024}, author = {Barrie, W and Irving-Pease, EK and Willerslev, E and Iversen, AKN and Fugger, L}, title = {Ancient DNA reveals evolutionary origins of autoimmune diseases.}, journal = {Nature reviews. Immunology}, volume = {24}, number = {2}, pages = {85-86}, pmid = {38177452}, issn = {1474-1741}, mesh = {Humans ; *DNA, Ancient ; Biological Evolution ; Evolution, Molecular ; *Autoimmune Diseases/genetics ; }, }
@article {pmid38177408, year = {2024}, author = {Sharko, FS and Boulygina, ES and Tsygankova, SV and Slobodova, NV and Rastorguev, SM and Krasivskaya, AA and Belinsky, AB and Härke, H and Kadieva, AA and Demidenko, SV and Malashev, VY and Shvedchikova, TY and Dobrovolskaya, MV and Reshetova, IK and Korobov, DS and Nedoluzhko, AV}, title = {Koban culture genome-wide and archeological data open the bridge between Bronze and Iron Ages in the North Caucasus.}, journal = {European journal of human genetics : EJHG}, volume = {32}, number = {11}, pages = {1483-1491}, pmid = {38177408}, issn = {1476-5438}, mesh = {Humans ; *DNA, Ancient/analysis ; Female ; Male ; *Genome, Human ; Archaeology ; History, Ancient ; White People/genetics ; Polymorphism, Single Nucleotide ; Russia ; }, abstract = {The North Caucasus played a key role during the ancient colonization of Eurasia and the formation of its cultural and genetic ancestry. Previous archeogenetic studies described a relative genetic and cultural continuity of ancient Caucasus societies, since the Eneolithic period. The Koban culture, which formed in the Late Bronze Age on the North Caucasian highlands, is considered as a cultural "bridge" between the ancient and modern autochthonous peoples of the Caucasus. Here, we discuss the place of this archeological culture and its representatives in the genetic orbit of Caucasian cultures using genome-wide SNP data from five individuals of the Koban culture and one individual of the early Alanic culture as well as previously published genomic data of ancient and modern North Caucasus individuals. Ancient DNA analysis shows that an ancient individual from Klin-Yar III, who was previously described as male, was in fact a female. Additional studies on well-preserved ancient human specimens are necessary to determine the level of local mobility and kinship between individuals in ancient societies of North Caucasus. Further studies with a larger sample size will allow us gain a deeper understanding of this topic.}, }
@article {pmid38173222, year = {2024}, author = {Caduff, M and Eckel, R and Leuenberger, C and Wegmann, D}, title = {Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.}, journal = {Molecular ecology resources}, volume = {24}, number = {3}, pages = {e13913}, doi = {10.1111/1755-0998.13913}, pmid = {38173222}, issn = {1755-0998}, support = {310030_200420//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {Humans ; Bayes Theorem ; *Sex Chromosomes/genetics ; *Genomics ; Genetic Testing ; Karyotype ; }, abstract = {The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non-model organisms.}, }
@article {pmid38167834, year = {2024}, author = {Yang, S and Sun, X and Jin, L and Zhang, M}, title = {Inferring language dispersal patterns with velocity field estimation.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {190}, pmid = {38167834}, issn = {2041-1723}, support = {T2122007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32070577//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Cultural Evolution ; Phylogeny ; Language ; Phylogeography ; Agriculture ; }, abstract = {Reconstructing the spatial evolution of languages can deepen our understanding of the demic diffusion and cultural spread. However, the phylogeographic approach that is frequently used to infer language dispersal patterns has limitations, primarily because the phylogenetic tree cannot fully explain the language evolution induced by the horizontal contact among languages, such as borrowing and areal diffusion. Here, we introduce the language velocity field estimation, which does not rely on the phylogenetic tree, to infer language dispersal trajectories and centre. Its effectiveness and robustness are verified through both simulated and empirical validations. Using language velocity field estimation, we infer the dispersal patterns of four agricultural language families and groups, encompassing approximately 700 language samples. Our results show that the dispersal trajectories of these languages are primarily compatible with population movement routes inferred from ancient DNA and archaeological materials, and their dispersal centres are geographically proximate to ancient homelands of agricultural or Neolithic cultures. Our findings highlight that the agricultural languages dispersed alongside the demic diffusions and cultural spreads during the past 10,000 years. We expect that language velocity field estimation could aid the spatial analysis of language evolution and further branch out into the studies of demographic and cultural dynamics.}, }
@article {pmid38150503, year = {2024}, author = {Srigyan, M and Schubert, BW and Bushell, M and Santos, SHD and Figueiró, HV and Sacco, S and Eizirik, E and Shapiro, B}, title = {Mitogenomic analysis of a late Pleistocene jaguar from North America.}, journal = {The Journal of heredity}, volume = {115}, number = {4}, pages = {424-431}, pmid = {38150503}, issn = {1465-7333}, support = {OPP-2131589//NSF/ ; }, mesh = {Animals ; *Panthera/genetics/classification ; *Genome, Mitochondrial ; *Phylogeny ; *Fossils ; Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; North America ; Georgia ; Evolution, Molecular ; Genetic Variation ; }, abstract = {The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.}, }
@article {pmid38150491, year = {2024}, author = {de Flamingh, A and Gnoske, TP and Rivera-Colón, AG and Simeonovski, VA and Kerbis Peterhans, JC and Yamaguchi, N and Witt, KE and Catchen, J and Roca, AL and Malhi, RS}, title = {Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction.}, journal = {The Journal of heredity}, volume = {115}, number = {2}, pages = {155-165}, doi = {10.1093/jhered/esad081}, pmid = {38150491}, issn = {1465-7333}, support = {1645087//National Science Fund/ ; }, mesh = {Animals ; *Lions/genetics ; Genomics ; South Africa ; Genome ; Population Dynamics ; }, abstract = {Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "black-maned lions" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate Cape lion genome characteristics, population dynamics, and genetic distinctiveness prior to their extinction. We generated genomic data from 2 historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, and illustrates how alternative knowledge systems, for example, Indigenous perspectives, could potentially further inform interpretations of species histories.}, }
@article {pmid38132343, year = {2023}, author = {Panitsina, VA and Bodrov, SY and Boulygina, ES and Slobodova, NV and Kosintsev, PA and Abramson, NI}, title = {In Search of the Elusive North: Evolutionary History of the Arctic Fox (Vulpes lagopus) in the Palearctic from the Late Pleistocene to the Recent Inferred from Mitogenomic Data.}, journal = {Biology}, volume = {12}, number = {12}, pages = {}, pmid = {38132343}, issn = {2079-7737}, support = {075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 122031100282-2//State research theme/ ; 20-29-01038//Russian Foundation for Basic Research/ ; }, abstract = {Despite the high level of interest, the population history of arctic foxes during the Late Pleistocene and Holocene remains poorly understood. Here we aimed to fill gaps in the demographic and colonization history of the arctic fox by analyzing new ancient DNA data from fossil specimens aged from 50 to 1 thousand years from the Northern and Polar Urals, historic DNA from museum specimens from the Novaya Zemlya Archipelago and the Taymyr Peninsula and supplementing these data by previously published sequences of recent and extinct arctic foxes from other regions. This dataset was used for reconstruction of a time-calibrated phylogeny and a temporal haplotype network covering four time intervals: Late Pleistocene (ranging from 30 to 13 thousand years bp), Holocene (ranging from 4 to 1 thousand years bp), historical (approximately 150 years), and modern. Our results revealed that Late Pleistocene specimens showed no genetic similarity to either modern or historical specimens, thus supporting the earlier hypothesis on local extinction rather than habitat tracking.}, }
@article {pmid38131007, year = {2023}, author = {Lien, A and Legori, LP and Kraft, L and Sackett, PW and Renaud, G}, title = {Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1260486}, pmid = {38131007}, issn = {2673-7647}, abstract = {Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient DNA molecules, therefore the reads often contain some portion of the sequencing adaptors. It is crucial to remove those adaptors, as they can interfere with downstream analysis. Furthermore, overlapping portions when DNA has been read forward and backward (paired-end) can be merged to correct sequencing errors and improve read quality. Several tools have been developed for adapter trimming and read merging, however, no one has attempted to evaluate their accuracy and evaluate their potential impact on downstream analyses. Through the simulation of sequencing data, seven commonly used tools were analyzed in their ability to reconstruct ancient DNA sequences through read merging. The analyzed tools exhibit notable differences in their abilities to correct sequence errors and identify the correct read overlap, but the most substantial difference is observed in their ability to calculate quality scores for merged bases. Selecting the most appropriate tool for a given project depends on several factors, although some tools such as fastp have some shortcomings, whereas others like leeHom outperform the other tools in most aspects. While the choice of tool did not result in a measurable difference when analyzing population genetics using principal component analysis, it is important to note that downstream analyses that are sensitive to wrongly merged reads or that rely on quality scores can be significantly impacted by the choice of tool.}, }
@article {pmid38123640, year = {2024}, author = {Ringbauer, H and Huang, Y and Akbari, A and Mallick, S and Olalde, I and Patterson, N and Reich, D}, title = {Accurate detection of identity-by-descent segments in human ancient DNA.}, journal = {Nature genetics}, volume = {56}, number = {1}, pages = {143-151}, pmid = {38123640}, issn = {1546-1718}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; Genotype ; *Genome, Human/genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Long DNA segments shared between two individuals, known as identity-by-descent (IBD), reveal recent genealogical connections. Here we introduce ancIBD, a method for identifying IBD segments in ancient human DNA (aDNA) using a hidden Markov model and imputed genotype probabilities. We demonstrate that ancIBD accurately identifies IBD segments >8 cM for aDNA data with an average depth of >0.25× for whole-genome sequencing or >1× for 1240k single nucleotide polymorphism capture data. Applying ancIBD to 4,248 ancient Eurasian individuals, we identify relatives up to the sixth degree and genealogical connections between archaeological groups. Notably, we reveal long IBD sharing between Corded Ware and Yamnaya groups, indicating that the Yamnaya herders of the Pontic-Caspian Steppe and the Steppe-related ancestry in various European Corded Ware groups share substantial co-ancestry within only a few hundred years. These results show that detecting IBD segments can generate powerful insights into the growing aDNA record, both on a small scale relevant to life stories and on a large scale relevant to major cultural-historical events.}, }
@article {pmid38118448, year = {2024}, author = {Silva, M and Booth, T and Moore, J and Anastasiadou, K and Walker, D and Gilardet, A and Barrington, C and Kelly, M and Williams, M and Henderson, M and Smith, A and Bowsher, D and Montgomery, J and Skoglund, P}, title = {An individual with Sarmatian-related ancestry in Roman Britain.}, journal = {Current biology : CB}, volume = {34}, number = {1}, pages = {204-212.e6}, doi = {10.1016/j.cub.2023.11.049}, pmid = {38118448}, issn = {1879-0445}, mesh = {Humans ; United Kingdom ; Iran ; *Isotopes ; *Roman World/history ; }, abstract = {In the second century CE the Roman Empire had increasing contact with Sarmatians, nomadic Iranian speakers occupying an area stretching from the Pontic-Caspian steppe to the Carpathian mountains, both in the Caucasus and in the Danubian borders of the empire.[1][,][2][,][3] In 175 CE, following their defeat in the Marcomannic Wars, emperor Marcus Aurelius drafted Sarmatian cavalry into Roman legions and deployed 5,500 Sarmatian soldiers to Britain, as recorded by contemporary historian Cassius Dio.[4][,][5] Little is known about where the Sarmatian cavalry were stationed, and no individuals connected with this historically attested event have been identified to date, leaving its impact on Britain largely unknown. Here we document Caucasus- and Sarmatian-related ancestry in the whole genome of a Roman-period individual (126-228 calibrated [cal.] CE)-an outlier without traceable ancestry related to local populations in Britain-recovered from a farmstead site in present-day Cambridgeshire, UK. Stable isotopes support a life history of mobility during childhood. Although several scenarios are possible, the historical deployment of Sarmatians to Britain provides a parsimonious explanation for this individual's extraordinary life history. Regardless of the factors behind his migrations, these results highlight how long-range mobility facilitated by the Roman Empire impacted provincial locations outside of urban centers.}, }
@article {pmid38096384, year = {2023}, author = {Fiddaman, SR and Dimopoulos, EA and Lebrasseur, O and du Plessis, L and Vrancken, B and Charlton, S and Haruda, AF and Tabbada, K and Flammer, PG and Dascalu, S and Marković, N and Li, H and Franklin, G and Symmons, R and Baron, H and Daróczi-Szabó, L and Shaymuratova, DN and Askeyev, IV and Putelat, O and Sana, M and Davoudi, H and Fathi, H and Mucheshi, AS and Vahdati, AA and Zhang, L and Foster, A and Sykes, N and Baumberg, GC and Bulatović, J and Askeyev, AO and Askeyev, OV and Mashkour, M and Pybus, OG and Nair, V and Larson, G and Smith, AL and Frantz, LAF}, title = {Ancient chicken remains reveal the origins of virulence in Marek's disease virus.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6676}, pages = {1276-1281}, doi = {10.1126/science.adg2238}, pmid = {38096384}, issn = {1095-9203}, support = {ERC-2019-STG-853272-PALAEOFARM/ERC_/European Research Council/International ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Chickens/virology ; *Herpesvirus 2, Gallid/classification/genetics/pathogenicity ; Lymphoma/virology ; *Marek Disease/history/virology ; Virulence/genetics ; Phylogeny ; }, abstract = {The pronounced growth in livestock populations since the 1950s has altered the epidemiological and evolutionary trajectory of their associated pathogens. For example, Marek's disease virus (MDV), which causes lymphoid tumors in chickens, has experienced a marked increase in virulence over the past century. Today, MDV infections kill >90% of unvaccinated birds, and controlling it costs more than US$1 billion annually. By sequencing MDV genomes derived from archeological chickens, we demonstrate that it has been circulating for at least 1000 years. We functionally tested the Meq oncogene, one of 49 viral genes positively selected in modern strains, demonstrating that ancient MDV was likely incapable of driving tumor formation. Our results demonstrate the power of ancient DNA approaches to trace the molecular basis of virulence in economically relevant pathogens.}, }
@article {pmid38087919, year = {2023}, author = {Pilowsky, JA and Brown, SC and Llamas, B and van Loenen, AL and Kowalczyk, R and Hofman-Kamińska, E and Manaseryan, NH and Rusu, V and Križnar, M and Rahbek, C and Fordham, DA}, title = {Millennial processes of population decline, range contraction and near extinction of the European bison.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2013}, pages = {20231095}, pmid = {38087919}, issn = {1471-2954}, mesh = {Animals ; Humans ; *Bison/genetics ; Europe ; Fossils ; Human Activities ; Hunting ; }, abstract = {European bison (Bison bonasus) were widespread throughout Europe during the late Pleistocene. However, the contributions of environmental change and humans to their near extinction have never been resolved. Using process-explicit models, fossils and ancient DNA, we disentangle the combinations of threatening processes that drove population declines and regional extinctions of European bison through space and across time. We show that the population size of European bison declined abruptly at the termination of the Pleistocene in response to rapid environmental change, hunting by humans and their interaction. Human activities prevented populations of European bison from rebounding in the Holocene, despite improved environmental conditions. Hunting caused range loss in the north and east of its distribution, while land use change was responsible for losses in the west and south. Advances in hunting technologies from 1500 CE were needed to simulate low abundances observed in 1870 CE. While our findings show that humans were an important driver of the extinction of the European bison in the wild, vast areas of its range vanished during the Pleistocene-Holocene transition because of post-glacial environmental change. These areas of its former range have been climatically unsuitable for millennia and should not be considered in reintroduction efforts.}, }
@article {pmid38081999, year = {2024}, author = {Cox, SL and Nicklisch, N and Francken, M and Wahl, J and Meller, H and Haak, W and Alt, KW and Rosenstock, E and Mathieson, I}, title = {Socio-cultural practices may have affected sex differences in stature in Early Neolithic Europe.}, journal = {Nature human behaviour}, volume = {8}, number = {2}, pages = {243-255}, pmid = {38081999}, issn = {2397-3374}, support = {Al 287/7-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Al 287/7-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Me 3245/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Me 3245/1-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RO 4148/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BCS2123627//National Science Foundation (NSF)/ ; }, mesh = {Female ; Male ; Humans ; *Genetics, Population ; *Sex Characteristics ; DNA, Mitochondrial ; Europe ; Isotopes ; }, abstract = {The rules and structure of human culture impact health as much as genetics or environment. To study these relationships, we combine ancient DNA (n = 230), skeletal metrics (n = 391), palaeopathology (n = 606) and dietary stable isotopes (n = 873) to analyse stature variation in Early Neolithic Europeans from North Central, South Central, Balkan and Mediterranean regions. In North Central Europe, stable isotopes and linear enamel hypoplasias indicate high environmental stress across sexes, but female stature is low, despite polygenic scores identical to males, and suggests that cultural factors preferentially supported male recovery from stress. In Mediterranean populations, sexual dimorphism is reduced, indicating male vulnerability to stress and no strong cultural preference for males. Our analysis indicates that biological effects of sex-specific inequities can be linked to cultural influences at least as early as 7,000 yr ago, and culture, more than environment or genetics, drove height disparities in Early Neolithic Europe.}, }
@article {pmid38065079, year = {2023}, author = {Olalde, I and Carrión, P and Mikić, I and Rohland, N and Mallick, S and Lazaridis, I and Mah, M and Korać, M and Golubović, S and Petković, S and Miladinović-Radmilović, N and Vulović, D and Alihodžić, T and Ash, A and Baeta, M and Bartík, J and Bedić, &#x17d; and Bilić, M and Bonsall, C and Bunčić, M and Bužanić, D and Carić, M and Čataj, L and Cvetko, M and Drnić, I and Dugonjić, A and Đukić, A and Đukić, K and Farkaš, Z and Jelínek, P and Jovanovic, M and Kaić, I and Kalafatić, H and Krmpotić, M and Krznar, S and Leleković, T and M de Pancorbo, M and Matijević, V and Milošević Zakić, B and Osterholtz, AJ and Paige, JM and Tresić Pavičić, D and Premužić, Z and Rajić Šikanjić, P and Rapan Papeša, A and Paraman, L and Sanader, M and Radovanović, I and Roksandic, M and Šefčáková, A and Stefanović, S and Teschler-Nicola, M and Tončinić, D and Zagorc, B and Callan, K and Candilio, F and Cheronet, O and Fernandes, D and Kearns, A and Lawson, AM and Mandl, K and Wagner, A and Zalzala, F and Zettl, A and Tomanović, &#x17d; and Keckarević, D and Novak, M and Harper, K and McCormick, M and Pinhasi, R and Grbić, M and Lalueza-Fox, C and Reich, D}, title = {A genetic history of the Balkans from Roman frontier to Slavic migrations.}, journal = {Cell}, volume = {186}, number = {25}, pages = {5472-5485.e9}, pmid = {38065079}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Balkan Peninsula ; Europe ; *White People/genetics ; *Human Migration ; }, abstract = {The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1[st] millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between ∼250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that "barbarian" migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%-60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period.}, }
@article {pmid38060128, year = {2024}, author = {Grasso, G and Rotunno, S and Debruyne, R and Bittner, L and Miozzi, L and Marmeisse, R and Bianciotto, V}, title = {Identification of DNA Viruses in Ancient DNA from Herbarium Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {221-234}, pmid = {38060128}, issn = {1940-6029}, mesh = {*DNA, Ancient ; Sequence Analysis, DNA/methods ; Phylogeny ; *DNA Viruses ; Soil ; }, abstract = {Herbaria encompass millions of plant specimens, mostly collected in the nineteenth and twentieth centuries that can represent a key resource for investigating the history and evolution of phytopathogens. In the last years, the application of high-throughput sequencing technologies for the analysis of ancient nucleic acids has revolutionized the study of ancient pathogens including viruses, allowing the reconstruction of historical genomic viral sequences, improving phylogenetic based molecular dating, and providing essential insight into plant virus ecology. In this chapter, we describe a protocol to reconstruct ancient plant and soil viral sequences starting from highly fragmented ancient DNA extracted from herbarium plants and their associated rhizospheric soil. Following Illumina high-throughput sequencing, sequence data are de novo assembled, and DNA viral sequences are selected, according to their similarity with known viruses.}, }
@article {pmid38056335, year = {2024}, author = {Peng, K and Liu, X and Cheng, H and Xu, M and Liu, Y and Yang, H and Liu, P and Yang, S}, title = {Characterization of driving factors for the long-term succession of bloom-forming cyanobacterial genera in Lake Erhai, southwest China.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119729}, doi = {10.1016/j.jenvman.2023.119729}, pmid = {38056335}, issn = {1095-8630}, mesh = {China ; *Cyanobacteria ; Eutrophication ; Lakes/microbiology ; *Microcystis/genetics ; Nutrients ; }, abstract = {Cyanobacterial blooms pose a global environmental concern, with various genera contributing to their formation. The harmfulness of cyanobacterial blooms varies depending on the specific genus, yet the factors triggering their formation remain incompletely understood. This study conducted qPCR of sediment DNA in Lake Erhai to reconstruct the historical succession of three common bloom-forming cyanobacterial genera (i.e., Microcystis, Dolichospermum, and Aphanizomenon). The driving factors and their corresponding thresholds were identified, and human activities related to driving factors were evaluated. The results revealed two successions in the past century. The first succession transitioned from Aphanizomenon (1902-1978) to Microcystis and Dolichospermum (1978-1999), driven by TN:TP and TP. The second succession shifted from Microcystis and Dolichospermum (1978-1999) to Microcystis (1999-2010), driven by TP, TN:TP, and temperature. The thresholds of TP and TN:TP for the Microcystis bloom were 0.023 mg/L and 17, respectively. TN:TP was significantly influenced by domestic pollution and crop farming in both successions, while TP was significantly impacted by domestic pollution in the first succession and by pollution from crop and dairy farming in the second succession. These results shed light on the underlying mechanism responsible for the blooms of various cyanobacterial genera and could serve as a valuable reference for effectively preventing and controlling nutrient input in the watershed.}, }
@article {pmid38051947, year = {2023}, author = {Wroblewski, TH and Witt, KE and Lee, SB and Malhi, RS and Peede, D and Huerta-Sánchez, E and Villanea, FA and Claw, KG}, title = {Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications.}, journal = {Genome biology and evolution}, volume = {15}, number = {12}, pages = {}, pmid = {38051947}, issn = {1759-6653}, support = {1R35GM128946-01/NH/NIH HHS/United States ; R35 HG011319/HG/NHGRI NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; R35HG011319/HG/NHGRI NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Neanderthals/genetics ; Pharmacogenetics ; Genome, Human ; *Hominidae/genetics ; Biological Evolution ; }, abstract = {Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.}, }
@article {pmid38047074, year = {2023}, author = {Xiao, B and Rey-Lglesia, A and Yuan, J and Hu, J and Song, S and Hou, Y and Chen, X and Germonpré, M and Bao, L and Wang, S and Taogetongqimuge,  and Valentinovna, LL and Lister, AM and Lai, X and Sheng, G}, title = {Relationships of Late Pleistocene giant deer as revealed by Sinomegaceros mitogenomes from East Asia.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108406}, pmid = {38047074}, issn = {2589-0042}, abstract = {The giant deer, widespread in northern Eurasia during the Late Pleistocene, have been classified as western Megaloceros and eastern Sinomegaceros through morphological studies. While Megaloceros's evolutionary history has been unveiled through mitogenomes, Sinomegaceros remains molecularly unexplored. Herein, we generated mitogenomes of giant deer from East Asia. We find that, in contrast to the morphological differences between Megaloceros and Sinomegaceros, they are mixed in the mitochondrial phylogeny, and Siberian specimens suggest a range contact or overlap between these two groups. Meanwhile, one deep divergent clade and another surviving until 20.1 thousand years ago (ka) were detected in northeastern China, the latter implying this area as a potential refugium during the Last Glacial Maximum (LGM). Moreover, stable isotope analyses indicate correlations between climate-introduced vegetation changes and giant deer extinction. Our study demonstrates the genetic relationship between eastern and western giant deer and explores the promoters of their extirpation in northern East Asia.}, }
@article {pmid38047066, year = {2023}, author = {Fewlass, H and Zavala, EI and Fagault, Y and Tuna, T and Bard, E and Hublin, JJ and Hajdinjak, M and Wilczyński, J}, title = {Chronological and genetic analysis of an Upper Palaeolithic female infant burial from Borsuka Cave, Poland.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108283}, pmid = {38047066}, issn = {2589-0042}, abstract = {Six infant human teeth and 112 animal tooth pendants from Borsuka Cave were identified as the oldest burial in Poland. However, uncertainties around the dating and the association of the teeth to the pendants have precluded their association with an Upper Palaeolithic archaeological industry. Using <67 mg per tooth, we combined dating and genetic analyses of two human teeth and six herbivore tooth pendants to address these questions. Our interdisciplinary approach yielded informative results despite limited sampling material, and high levels of degradation and contamination. Our results confirm the Palaeolithic origin of the human remains and herbivore pendants, and permit us to identify the infant as female and discuss the association of the assemblage with different Palaeolithic industries. This study exemplifies the progress that has been made toward minimally destructive methods and the benefits of integrating methods to maximize data retrieval from precious but highly degraded and contaminated prehistoric material.}, }
@article {pmid38040695, year = {2023}, author = {Fournier, R and Tsangalidou, Z and Reich, D and Palamara, PF}, title = {Haplotype-based inference of recent effective population size in modern and ancient DNA samples.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7945}, pmid = {38040695}, issn = {2041-1723}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R21 HG010748/HG/NHGRI NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Haplotypes/genetics ; *DNA, Ancient ; Population Density ; *Genomics ; Linkage Disequilibrium ; Genetics, Population ; Polymorphism, Single Nucleotide ; }, abstract = {Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.}, }
@article {pmid38030719, year = {2024}, author = {Fortes-Lima, CA and Burgarella, C and Hammarén, R and Eriksson, A and Vicente, M and Jolly, C and Semo, A and Gunnink, H and Pacchiarotti, S and Mundeke, L and Matonda, I and Muluwa, JK and Coutros, P and Nyambe, TS and Cikomola, JC and Coetzee, V and de Castro, M and Ebbesen, P and Delanghe, J and Stoneking, M and Barham, L and Lombard, M and Meyer, A and Steyn, M and Malmström, H and Rocha, J and Soodyall, H and Pakendorf, B and Bostoen, K and Schlebusch, CM}, title = {The genetic legacy of the expansion of Bantu-speaking peoples in Africa.}, journal = {Nature}, volume = {625}, number = {7995}, pages = {540-547}, pmid = {38030719}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Africa, Western ; Datasets as Topic ; Democratic Republic of the Congo ; *DNA, Ancient/analysis ; *Emigration and Immigration/history ; Founder Effect ; Gene Flow/genetics ; Genetic Variation/genetics ; *Genetics, Population ; History, Ancient ; *Language/history ; Linguistics/history ; Zambia ; Geographic Mapping ; }, abstract = {The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent[1-7]. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals[8]. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods[9] and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies[10] and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.}, }
@article {pmid38014190, year = {2023}, author = {Williams, MP and Flegontov, P and Maier, R and Huber, CD}, title = {Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38014190}, issn = {2692-8205}, support = {R35 GM146886/GM/NIGMS NIH HHS/United States ; }, abstract = {Paleogenomics has expanded our knowledge of human evolutionary history. Since the 2020s, the study of ancient DNA has increased its focus on reconstructing the recent past. However, the accuracy of paleogenomic methods in answering questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation within the historical period remains an open question. We used two simulation approaches to evaluate the limitations and behavior of commonly used methods, qpAdm and the f3-statistic, on admixture inference. The first is based on branch-length data simulated from four simple demographic models of varying complexities and configurations. The second, an analysis of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We show that under conditions resembling historical populations, qpAdm can identify a small candidate set of true sources and populations closely related to them. However, in typical ancient DNA conditions, qpAdm is unable to further distinguish between them, limiting its utility for resolving fine-scaled hypotheses. Notably, we find that complex gene-flow histories generally lead to improvements in the performance of qpAdm and observe no bias in the estimation of admixture weights. We offer a heuristic for admixture inference that incorporates admixture weight estimate and P-values of qpAdm models, and f3-statistics to enhance the power to distinguish between multiple plausible candidates. Finally, we highlight the future potential of qpAdm through whole-genome branch-length f2-statistics, demonstrating the improved demographic inference that could be achieved with advancements in f-statistic estimations.}, }
@article {pmid38012935, year = {2023}, author = {Jäger, HY and Atz Zanotelli, D and Maixner, F and Nicklisch, N and Alt, KW and Meller, H and Pap, I and Szikossy, I and Pálfi, G and Zink, AR}, title = {Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {143S}, number = {}, pages = {102392}, doi = {10.1016/j.tube.2023.102392}, pmid = {38012935}, issn = {1873-281X}, support = {2014-2020_CALL-FESR 2017//European Regional Development Fund/ ; FESR1078//Research and Innovation_Autonomous Province Bolzano-South Tyrol_/ ; NKTIH K 125561//National Research Development and Innovation Office (Hungary)/ ; 57437987//Germany Academic Exchange Service/ ; }, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Body Remains ; *Tuberculosis/microbiology ; Bone and Bones ; DNA ; DNA, Ancient ; }, abstract = {Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of ancient pathogens remains challenging. Here, we present a first assessment of the intra-bone variability of metagenomic composition in human skeletal remains and its effect on the sampling success for Mycobacterium tuberculosis (MTB) and human endogenous DNA. For this purpose, four bone samples from published peer-reviewed studies with PCR-based evidence for ancient MTB DNA were selected. Two bone samples of a Neolithic individual from Halberstadt, Germany and two ribs of two 18th-century Hungarian church mummies were sampled at multiple locations for equal amounts, followed by DNA extraction and library construction. Shotgun sequencing data was generated for taxonomic profiling as well as quantitative and qualitative evaluation of MTB and human endogenous DNA. Despite low variance in microbial diversity within and across samples, intra-bone variability of up to 36.45- and 62.88-fold for authentic ancient MTB and human reads, respectively, was detected. This study demonstrates the variable sampling success for MTB and human endogenous DNA within single skeletal samples despite relatively consistent microbial composition and highlights how a multisampling approach can facilitate the detection of hotspots with highly concentrated pathogen and human endogenous DNA.}, }
@article {pmid38012931, year = {2023}, author = {Zink, A and Maixner, F and Jäger, HY and Szikossy, I and Pálfi, G and Pap, I}, title = {Tuberculosis in mummies - New findings, perspectives and limitations.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {143S}, number = {}, pages = {102371}, doi = {10.1016/j.tube.2023.102371}, pmid = {38012931}, issn = {1873-281X}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Body Remains ; *Mummies ; DNA, Bacterial/genetics/analysis ; *Tuberculosis/microbiology ; }, abstract = {The molecular analysis of ancient pathogen DNA represents a unique opportunity for the study of infectious diseases in ancient human remains. Among other diseases, paleogenetic studies have been successful in detecting tuberculous DNA in ancient human remains. In the beginning of ancient DNA (aDNA) studies, the presence of tuberculosis (TB) DNA was assessed using a PCR-based assay targeting specific regions of the Mycobacterium tuberculosis (MTB) complex, such as the repetitive element IS6110. The advent of high-throughput sequencing has enabled the reconstruction of full ancient TB genomes in the field of paleomicrobiology. However, despite the numerous paleopathological and PCR-based studies on the presence of tuberculosis in historic human remains, full genome wide reconstructions are still limited to well-preserved specimens with low environmental contamination and connected with extensive screening efforts. This has led to some controversies regarding the evolutionary history of its causative agent Mycobacterium tuberculosis. In this context, mummies have been shown to be a good source for the detection of MTB complex DNA due to a low exposure to environmental influences and the overall good state of preservation of hard and soft tissues in the human remains. Here, we present the major findings on the presence of TB infections in the 18th century naturally mummified human remains from Vác, Hungary and the current status of the detection of MTB complex DNA in mummified human remains. The future perspectives of detecting tuberculosis in mummies will be discussed in the light of methodological aspects, as well as ethical and curational challenges.}, }
@article {pmid38012918, year = {2023}, author = {Kharlamova, N and Ogarkov, O and Berdnikov, I and Berdnikova, N and Galeev, R and Mokrousov, I}, title = {Bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century orthodox cemeteries in Irkutsk, Eastern Siberia.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {143S}, number = {}, pages = {102368}, doi = {10.1016/j.tube.2023.102368}, pmid = {38012918}, issn = {1873-281X}, mesh = {Male ; Humans ; Female ; *Mycobacterium tuberculosis/genetics ; Siberia ; Body Remains ; Phylogeny ; Cemeteries ; *Tuberculosis/microbiology ; Genotype ; DNA ; }, abstract = {In this study, we tested the skeletal human remains from the 18th - early 19th century Orthodox cemeteries in Irkutsk, Eastern Siberia, for tuberculosis-associated morphological alterations and Mycobacterium tuberculosis DNA. The morphologically studied bone collection included 591 individuals of mainly Caucasian origin. The molecular methods (IS6110-PCR and spoligotyping) suggested that at least four individuals (out of 15 TB-suspected, DNA-tested) were positive for the presence of M. tuberculosis DNA. All of them were males (3 maturus, 1 maturus senilis). Two of them date back to the second and third quarters of the 18th century, another to the last quarter of the 18th century, and the last one to the second half of the 19th century. The combined molecular analysis cautiously suggested presence of different strains and at least some of them represented not the currently predominant in Siberia Beijing genotype (M. tuberculosis East-Asian lineage) but strains of European origin. In conclusion, this study presented bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century Orthodox cemeteries in Irkutsk, Eastern Siberia. The samples are not M. bovis and represent human M. tuberculosis sensu stricto. Their precise phylogenetic identity is elusive but evokes the European/Russian origin of at least some isolates.}, }
@article {pmid38006200, year = {2023}, author = {Houldcroft, CJ and Underdown, S}, title = {Infectious disease in the Pleistocene: Old friends or old foes?.}, journal = {American journal of biological anthropology}, volume = {182}, number = {4}, pages = {513-531}, doi = {10.1002/ajpa.24737}, pmid = {38006200}, issn = {2692-7691}, support = {//Oxford Brookes University/ ; }, mesh = {Animals ; Humans ; Friends ; *Hominidae ; *Communicable Diseases/epidemiology ; Genome ; DNA ; }, abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.}, }
@article {pmid38002979, year = {2023}, author = {Uricoechea Patiño, D and Collins, A and Romero García, OJ and Santos Vecino, G and Aristizábal Espinosa, P and Bernal Villegas, JE and Benavides Benitez, E and Vergara Muñoz, S and Briceño Balcázar, I}, title = {Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley.}, journal = {Genes}, volume = {14}, number = {11}, pages = {}, pmid = {38002979}, issn = {2073-4425}, support = {Convocatoria interna de 2013 (Internal Call of 2013) as per acta 809 de la comisi&#xf3;n de asuntos generales, proyecto MED-168-2013.//Universidad de La Sabana/ ; }, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Genetics, Population ; Mitochondria/genetics ; North America ; Human Migration ; }, abstract = {This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area.}, }
@article {pmid37993617, year = {2023}, author = {Izarraras-Gomez, A and Ortega-Del Vecchyo, D}, title = {Ancient DNA uncovers past migrations in California.}, journal = {Nature}, volume = {624}, number = {7990}, pages = {43-44}, pmid = {37993617}, issn = {1476-4687}, mesh = {*DNA, Ancient ; *Archaeology ; Human Migration ; California ; }, }
@article {pmid37992125, year = {2023}, author = {Di Santo, LN and Quilodrán, CS and Currat, M}, title = {Temporal Variation in Introgressed Segments' Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses.}, journal = {Molecular biology and evolution}, volume = {40}, number = {12}, pages = {}, pmid = {37992125}, issn = {1537-1719}, mesh = {Animals ; *Genomics ; Paleontology ; *Neanderthals/genetics ; Genome ; Biological Evolution ; }, abstract = {Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remain a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a 2-population system and described temporal neutral introgression patterns under a single- and 2-pulse admixture model. We computed 6 summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within genomes, as well as genome-wide introgression proportions and related measures. The first 2 statistics could confidently be used to infer interlineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.}, }
@article {pmid37971141, year = {2024}, author = {Pečnerová, P and Lord, E and Garcia-Erill, G and Hanghøj, K and Rasmussen, MS and Meisner, J and Liu, X and van der Valk, T and Santander, CG and Quinn, L and Lin, L and Liu, S and Carøe, C and Dalerum, F and Götherström, A and Måsviken, J and Vartanyan, S and Raundrup, K and Al-Chaer, A and Rasmussen, L and Hvilsom, C and Heide-Jørgensen, MP and Sinding, MS and Aastrup, P and Van Coeverden de Groot, PJ and Schmidt, NM and Albrechtsen, A and Dalén, L and Heller, R and Moltke, I and Siegismund, HR}, title = {Population genomics of the muskox' resilience in the near absence of genetic variation.}, journal = {Molecular ecology}, volume = {33}, number = {2}, pages = {e17205}, doi = {10.1111/mec.17205}, pmid = {37971141}, issn = {1365-294X}, support = {CF20-0539//Carlsbergfondet/ ; 8021-00344B//Danmarks Frie Forskningsfond/ ; }, mesh = {Humans ; Animals ; Infant, Newborn ; *Metagenomics ; *Resilience, Psychological ; Biological Evolution ; Genomics ; Ruminants/genetics ; Genetic Variation/genetics ; }, abstract = {Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.}, }
@article {pmid37955570, year = {2023}, author = {Harning, DJ and Sacco, S and Anamthawat-Jónsson, K and Ardenghi, N and Thordarson, T and Raberg, JH and Sepúlveda, J and Geirsdóttir, &#xc1; and Shapiro, B and Miller, GH}, title = {Delayed postglacial colonization of Betula in Iceland and the circum North Atlantic.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37955570}, issn = {2050-084X}, mesh = {*Betula ; Ecosystem ; Iceland ; Betulaceae ; Biodiversity ; DNA, Ancient ; *Tracheophyta ; }, abstract = {As the Arctic continues to warm, woody shrubs are expected to expand northward. This process, known as 'shrubification,' has important implications for regional biodiversity, food web structure, and high-latitude temperature amplification. While the future rate of shrubification remains poorly constrained, past records of plant immigration to newly deglaciated landscapes in the Arctic may serve as useful analogs. We provide one new postglacial Holocene sedimentary ancient DNA (sedaDNA) record of vascular plants from Iceland and place a second Iceland postglacial sedaDNA record on an improved geochronology; both show Salicaceae present shortly after deglaciation, whereas Betulaceae first appears more than 1000 y later. We find a similar pattern of delayed Betulaceae colonization in eight previously published postglacial sedaDNA records from across the glaciated circum North Atlantic. In nearly all cases, we find that Salicaceae colonizes earlier than Betulaceae and that Betulaceae colonization is increasingly delayed for locations farther from glacial-age woody plant refugia. These trends in Salicaceae and Betulaceae colonization are consistent with the plant families' environmental tolerances, species diversity, reproductive strategies, seed sizes, and soil preferences. As these reconstructions capture the efficiency of postglacial vascular plant migration during a past period of high-latitude warming, a similarly slow response of some woody shrubs to current warming in glaciated regions, and possibly non-glaciated tundra, may delay Arctic shrubification and future changes in the structure of tundra ecosystems and temperature amplification.}, }
@article {pmid37955431, year = {2024}, author = {Salado, I and Preick, M and Lupiáñez-Corpas, N and Fernández-Gil, A and Vilà, C and Hofreiter, M and Leonard, JA}, title = {Large variance in inbreeding within the Iberian wolf population.}, journal = {The Journal of heredity}, volume = {115}, number = {4}, pages = {349-359}, pmid = {37955431}, issn = {1465-7333}, support = {P18-FR-5099//Junta de Andaluc&#xed;a/ ; PCI2022-135098-2//WOLFNESS Biodiversa+ project/ ; FPU17/02584//Spanish Ministry of Universities/ ; //Asociaci&#xf3;n Apadrina La Ciencia-Ford Spain/ ; //Ford Motor Company Fund/ ; BES-2017-082260//Spanish Ministry of Economy, Industry, and Competitiveness/ ; }, mesh = {*Wolves/genetics ; Animals ; *Inbreeding ; *Genetics, Population ; Spain ; *Genetic Variation ; Gene Flow ; }, abstract = {The gray wolf (Canis lupus) population on the Iberian Peninsula was the largest in western and central Europe during most of the 20th century, with its size apparently never under a few hundred individuals. After partial legal protection in the 1970s in Spain, the northwest Iberian population increased to about 300 to 350 packs and then stabilized. In contrast to many current European wolf populations, which have been connected through gene flow, the Iberian wolf population has been isolated for decades. Here, we measured changes in genomic diversity and inbreeding through the last decades in a geographic context. We find that the level of genomic diversity in Iberian wolves is low compared with other Eurasian wolf populations. Despite population expansion in the last 50 years, some modern wolves had very high inbreeding, especially in the recently recolonized and historical edge areas. These individuals contrast with others with low inbreeding within the same population. The high variance in inbreeding despite population expansion seems associated with small-scale fragmentation of the range that is revealed by the genetic similarity between modern and historical samples from close localities despite being separated by decades, remaining differentiated from other individuals that are just over 100 km away, a small distance for a species with great dispersal capacity inhabiting a continuous range. This illustrates that, despite its demographically stable condition, the population would probably benefit from favoring connectivity within the population as well as genetic exchange with other European wolf populations to avoid excessive fragmentation and local inbreeding depression.}, }
@article {pmid37955259, year = {2023}, author = {}, title = {Neolithic Community Revealed Using Ancient DNA Data.}, journal = {American journal of medical genetics. Part A}, volume = {191}, number = {12}, pages = {2797-2798}, doi = {10.1002/ajmg.a.62840}, pmid = {37955259}, issn = {1552-4833}, mesh = {Humans ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Haplotypes ; Europe ; }, }
@article {pmid37953960, year = {2023}, author = {Coia, V and Paladin, A and Zingale, S and Wurst, C and Croze, M and Maixner, F and Zink, A}, title = {Ancestry and kinship in a Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108215}, pmid = {37953960}, issn = {2589-0042}, abstract = {In South Tyrol (Eastern Italian Alps), during Late Antiquity-Early Middle Ages, archeological records indicate cultural hybridization among alpine groups and peoples of various origin. Using paleogenomics, we reconstructed the ancestry of 20 individuals (4[th]-7[th] cent. AD) from a cemetery to analyze whether they had heterogeneous or homogeneous ancestry and to study their social organization. The results revealed a primary genetic ancestry from southern Europe and additional ancestries from south-western, western, and northern Europe, suggesting that cultural hybridization was accompanied by complex genetic admixture. Kinship analyses found no genetic relatedness between the only two individuals buried with grave goods. Instead, a father-son pair was discovered in one multiple grave, together with unrelated individuals and one possible non-local female. These genetic findings indicate the presence of a high social status familia, which is supported by the cultural materials and the proximity of the grave to the most sacred area of the church.}, }
@article {pmid37949985, year = {2023}, author = {Callaway, E}, title = {How to keep wildcats wild: ancient DNA offers fresh insights.}, journal = {Nature}, volume = {623}, number = {7987}, pages = {463-465}, pmid = {37949985}, issn = {1476-4687}, mesh = {Animals ; *Animals, Wild/genetics ; *Conservation of Natural Resources/methods ; *DNA, Ancient/analysis ; Scotland ; *Tigers/genetics ; Animals, Domestic/genetics ; *Endangered Species ; }, }
@article {pmid37935117, year = {2023}, author = {Jamieson, A and Carmagnini, A and Howard-McCombe, J and Doherty, S and Hirons, A and Dimopoulos, E and Lin, AT and Allen, R and Anderson-Whymark, H and Barnett, R and Batey, C and Beglane, F and Bowden, W and Bratten, J and De Cupere, B and Drew, E and Foley, NM and Fowler, T and Fox, A and Geigl, EM and Gotfredsen, AB and Grange, T and Griffiths, D and Groß, D and Haruda, A and Hjermind, J and Knapp, Z and Lebrasseur, O and Librado, P and Lyons, LA and Mainland, I and McDonnell, C and Muñoz-Fuentes, V and Nowak, C and O'Connor, T and Peters, J and Russo, IM and Ryan, H and Sheridan, A and Sinding, MS and Skoglund, P and Swali, P and Symmons, R and Thomas, G and Trolle Jensen, TZ and Kitchener, AC and Senn, H and Lawson, D and Driscoll, C and Murphy, WJ and Beaumont, M and Ottoni, C and Sykes, N and Larson, G and Frantz, L}, title = {Limited historical admixture between European wildcats and domestic cats.}, journal = {Current biology : CB}, volume = {33}, number = {21}, pages = {4751-4760.e14}, doi = {10.1016/j.cub.2023.08.031}, pmid = {37935117}, issn = {1879-0445}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Cats/genetics ; Animals ; Cattle ; Bees ; Sheep ; Swine ; *Hybridization, Genetic ; Chickens ; *Felis/genetics ; Europe ; Gene Flow ; }, abstract = {Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities.}, }
@article {pmid37935112, year = {2023}, author = {Schurr, TG and Shengelia, R and Shamoon-Pour, M and Chitanava, D and Laliashvili, S and Laliashvili, I and Kibret, R and Kume-Kangkolo, Y and Akhvlediani, I and Bitadze, L and Mathieson, I and Yardumian, A}, title = {Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus).}, journal = {Genome biology and evolution}, volume = {15}, number = {11}, pages = {}, pmid = {37935112}, issn = {1759-6653}, support = {BCS-1824826//National Science Foundation/ ; //University of Pennsylvania Museum of Archaeology and Anthropology/ ; //University of Pennsylvania Faculty Research Funds/ ; //Paul Carpenter Scholars Program/ ; //Bryn Athyn College Summer Research Funds/ ; }, mesh = {Humans ; Male ; Female ; *Genetics, Population ; Georgia (Republic) ; *Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Europe ; Haplotypes ; Genetic Variation ; }, abstract = {To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.}, }
@article {pmid37928683, year = {2023}, author = {Roche, K and Dalle, F and Capelli, N and Borne, R and Jouffroy-Bapicot, I and Valot, B and Grenouillet, F and Le Bailly, M}, title = {From modern-day parasitology to paleoparasitology: the elusive past record and evolution of Cryptosporidium.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1249884}, pmid = {37928683}, issn = {1664-302X}, abstract = {Recent efforts have been made to review the state of the art on a variety of questions and targets in paleoparasitology, including protozoan taxa. Meanwhile, these efforts seemed to let aside Cryptosporidium, and we then intended to review its paleoparasitological record to assess its past distribution and favored detection methods, and eventually highlight needed research trajectories. This review shows that contrary to other parasites, most of the positive results came from South-American sites and coprolites rather than sediment samples, highlighting the need to test this kind of material, notably in Europe where many negative results were reported in the published literature from sediment samples. Moreover, aDNA-based detections are nearly absent from the paleoparasitological record of this parasite, though punctually shown successful. With their potential to address the evolutionary history of Cryptosporidium species, notably through their 18S rRNA tree, aDNA-based approaches should be encouraged in the future. In sum, and though the limits of currently used methods and materials remain unclear, this review highlights the potential role of coprolites and aDNA for the study of Cryptosporidium species in the past and how this history shaped their current diversity and distribution, notably among human populations but also farm animals.}, }
@article {pmid37927550, year = {2023}, author = {Childebayeva, A and Zavala, EI}, title = {Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108066}, pmid = {37927550}, issn = {2589-0042}, abstract = {Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.}, }
@article {pmid37926832, year = {2023}, author = {Duitama González, C and Vicedomini, R and Lemane, T and Rascovan, N and Richard, H and Chikhi, R}, title = {decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {243}, pmid = {37926832}, issn = {2049-2618}, mesh = {Animals ; Humans ; *Metagenome ; *Metagenomics/methods ; }, abstract = {BACKGROUND: The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices.<br><br>RESULTS: We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker.<br><br>CONCLUSIONS: decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract.}, }
@article {pmid37923262, year = {2024}, author = {Fracasso, I and Zaccone, C and Oskolkov, N and Da Ros, L and Dinella, A and Belelli Marchesini, L and Buzzini, P and Sannino, C and Turchetti, B and Cesco, S and Le Roux, G and Tonon, G and Vernesi, C and Mimmo, T and Ventura, M and Borruso, L}, title = {Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168159}, doi = {10.1016/j.scitotenv.2023.168159}, pmid = {37923262}, issn = {1879-1026}, mesh = {Humans ; *Soil ; *DNA, Ancient ; Ecosystem ; Bacteria/genetics ; Metagenome ; Fungi/genetics ; }, abstract = {Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.}, }
@article {pmid37909055, year = {2023}, author = {Seeber, PA and Palmer, Z and Schmidt, A and Chagas, A and Kitagawa, K and Marinova-Wolff, E and Tafelmaier, Y and Epp, LS}, title = {The first European woolly rhinoceros mitogenomes, retrieved from cave hyena coprolites, suggest long-term phylogeographic differentiation.}, journal = {Biology letters}, volume = {19}, number = {11}, pages = {20230343}, pmid = {37909055}, issn = {1744-957X}, mesh = {Animals ; Phylogeny ; *Hyaenidae/genetics ; *Genome, Mitochondrial ; DNA ; Perissodactyla/genetics/metabolism ; Fossils ; }, abstract = {The woolly rhinoceros (Coelodonta antiquitatis) is an iconic species of the Eurasian Pleistocene megafauna, which was abundant in Eurasia in the Pleistocene until its demise beginning approximately 10 000 years ago. Despite the early recovery of several specimens from well-known European archaeological sites, including its type specimen (Blumenbach 1799), no genomes of European populations were available so far, and all available genomic data originated exclusively from Siberian populations. Using coprolites of cave hyenas (Crocuta crocuta spelea) recovered from Middle Palaeolithic layers of two caves in Germany (Bockstein-Loch and Hohlenstein-Stadel), we isolated and enriched predator and prey DNA to assemble the first European woolly rhinoceros mitogenomes, in addition to cave hyena mitogenomes. Both coprolite samples produced copious sequences assigned to C. crocuta (27% and 59% mitogenome coverage, respectively) and woolly rhinoceros (Coelodonta antiquitatis; 27% and 81% coverage, respectively). The sequences suggested considerable DNA degradation, which may limit the conclusions to be drawn; however, the mitogenomes of European woolly rhinoceros are genetically distinct from the Siberian woolly rhinoceros, and analyses of the more complete mitogenome suggest a split of the populations potentially coinciding with the earliest fossil records of woolly rhinoceros in Europe.}, }
@article {pmid37908771, year = {2023}, author = {Zhur, KV and Sharko, FS and Sedov, VV and Dobrovolskaya, MV and Volkov, VG and Maksimov, NG and Seslavine, AN and Makarov, NA and Prokhortchouk, EB}, title = {The Rurikids: The First Experience of Reconstructing the Genetic Portrait of the Ruling Family of Medieval Rus' Based on Paleogenomic Data.}, journal = {Acta naturae}, volume = {15}, number = {3}, pages = {50-65}, pmid = {37908771}, issn = {2075-8251}, abstract = {The Rurikids were the reigning house of Rus', its principalities and, ultimately the Tsardom of Russia, for seven centuries: from the IX to the end of the XVI century. According to the Primary Chronicle (the Tale of Bygone Years), the main chronicle of Rus', the Rurik dynasty was founded by the Varangian prince Rurik, invited to reign in Novgorod in 862, but still there is no direct genetic evidence of the origin of the early Rurikids. This research, for the first time, provides a genome-wide paleogenetic analysis of bone remains belonging to one of the Rurikids, Prince Dmitry Alexandrovich (?-1294), the son of the Grand Prince of Vladimir Alexander Yaroslavich Nevsky (1221-1263). It has been established that his Y chromosome belongs to the N1a haplogroup. Most of the modern Rurikids, according to their genealogies, belonging to the N1a haplogroup, have the most similar variants of Y chromosomes to each other, as well as to the Y chromosome of Prince Dmitry Alexandrovich. Genome-wide data of the medieval and modern Rurikids unequivocally indicates that they belong to the N1a haplogroup of the Y chromosome, starting at least from the XI century (since the time of Prince Yaroslav the Wise). All the other alleged Rurikids, both ancient and modern, being carriers of other haplogroups (R1a, I2a), possess high heterogeneity of the sequence of Y chromosomes, meaning that we cannot confirm their common ancestry. The most probable ancestors of Prince Dmitry Alexandrovich in the male line were the men who left the burial ground Bolshoy Oleny Island on the coast of the Kola Peninsula about 3,600 years ago. The reconstruction of the genome of Prince Dmitry Alexandrovich indicates the contribution of three ancestral components to his origin: (1) the early medieval population of the east of Scandinavia from the island of Oland, (2) representatives of the steppe nomadic peoples of the Eurasian steppes of the Iron Age or the early medieval population of central Europe (steppe nomads from the territory of Hungary), and (3) the ancient East-Eurasian component. Reliable statistics were also obtained when the Scandinavians were replaced with the Medieval Russian Slavic populations of the XI century. Thus, for the first time, we have shown the complex nature of interethnic interactions in the formation of the nobility of medieval Rus' on the example of the ancient Rurikid.}, }
@article {pmid37907573, year = {2023}, author = {Zedda, N and Meheux, K and Blöcher, J and Diekmann, Y and Gorelik, AV and Kalle, M and Klein, K and Titze, AL and Winkelbach, L and Naish, E and Brou, L and Valotteau, F and Le Brun-Ricalens, F and Burger, J and Brami, M}, title = {Biological and substitute parents in Beaker period adult-child graves.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18765}, pmid = {37907573}, issn = {2045-2322}, mesh = {Humans ; Adult ; Female ; *Archaeology ; *Burial/methods ; Europe ; Parents ; Adult Children ; }, abstract = {Joint inhumations of adults and children are an intriguing aspect of the shift from collective to single burial rites in third millennium BC Western Eurasia. Here, we revisit two exceptional Beaker period adult-child graves using ancient DNA: Altwies in Luxembourg and Dunstable Downs in Britain. Ancestry modelling and patterns of shared IBD segments between the individuals examined, and contemporary genomes from Central and Northwest Europe, highlight the continental connections of British Beakers. Although simultaneous burials may involve individuals with no social or biological ties, we present evidence that close blood relations played a role in shaping third millennium BC social systems and burial practices, for example a biological mother and her son buried together at Altwies. Extended family, such as a paternal aunt at Dunstable Downs, could also act as 'substitute parents' in the grave. Hypotheses are explored to explain such simultaneous inhumations. Whilst intercommunity violence, infectious disease and epidemics may be considered as explanations, they fail to account for both the specific, codified nature of this particular form of inhumation, and its pervasiveness, as evidenced by a representative sample of 131 adult-child graves from 88 sites across Eurasia, all dating to the third and second millennia BC.}, }
@article {pmid37905072, year = {2024}, author = {Cheng, X and Steinrücken, M}, title = {diplo-locus: A lightweight toolkit for inference and simulation of time-series genetic data under general diploid selection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37905072}, issn = {2692-8205}, support = {R01 GM146051/GM/NIGMS NIH HHS/United States ; }, abstract = {Whole-genome time-series allele frequency data are becoming more prevalent as ancient DNA (aDNA) sequences and data from evolve-and-resequence (E&amp;R) experiments are generated at a rapid pace. Such data presents unprecedented opportunities to elucidate the dynamics of genetic variation under selection. However, despite many methods to infer parameters of selection models from allele frequency trajectories available in the literature, few provide user-friendly implementations for large-scale empirical applications. Here, we present diplo-locus, an open-source Python package that provides functionality to simulate and perform inference from time-series data under the Wright-Fisher diffusion with general diploid selection. The package includes Python modules as well as command-line tools and is available at: https://github.com/steinrue/diplo_locus.}, }
@article {pmid37904954, year = {2023}, author = {Poyraz, L and Colbran, LL and Mathieson, I}, title = {Predicting functional consequences of recent natural selection in Britain.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37904954}, issn = {2692-8205}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; }, abstract = {Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are non-coding, so we expect that a large proportion of the phenotypic effects of selection will also act through non-coding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation; JTI) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (FDR < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-SNP selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.}, }
@article {pmid37900966, year = {2023}, author = {Papa, V and Galassi, FM and Varotto, E and Gori, A and Vaccarezza, M}, title = {The Evolution of Diagnostic Techniques in the Paleopathology of Tuberculosis: A Scoping Review.}, journal = {Pathogens &amp; immunity}, volume = {8}, number = {1}, pages = {93-116}, pmid = {37900966}, issn = {2469-2964}, abstract = {Tuberculosis (TB) is an ancient chronic infectious disease that remains a global health concern. In human remains, the most common and characteristic clinical signs are the skeletal modifications involving the spine, such as in Pott's disease. Diagnosing TB in ancient human remains is challenging. Therefore, in this systematic review, the authors investigated the studies assessing molecular diagnosis of Pott's disease in ancient human remains with the intention to survey the literature, map the evidence, and identify gaps and future perspectives on TB in paleopathology. Our systematic review offers a full contextualization of the history of Pott's disease in ancient times. Our search strategy was performed between August 2022 and March 2023. The authors initially identified 340 records, and 74 studies were finally included and assessed for qualitative analysis. Due to non-specific clinical signs associated with TB, how best to diagnose tuberculosis in human remains still represents a central point. Nevertheless, ancient DNA (aDNA) analysis, lipid biomarkers, and spoligotyping might be extremely useful tools in the study of TB in human remains. Moreover, we propose the extraction and study of immune response genes involved in innate and adaptive immunity versus Mycobacterium spp. as an innovative and vastly overlooked approach in TB paleopathology. Complementary methodologies should be integrated to provide the best approach to the study of TB in human remains.}, }
@article {pmid37895202, year = {2023}, author = {Uricoechea Patiño, D and Collins, A and García, OJR and Santos Vecino, G and Cuenca, JVR and Bernal, JE and Benavides Benítez, E and Vergara Muñoz, S and Briceño Balcázar, I}, title = {High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia.}, journal = {Genes}, volume = {14}, number = {10}, pages = {}, pmid = {37895202}, issn = {2073-4425}, mesh = {Humans ; Colombia ; *DNA, Mitochondrial/genetics/analysis ; *Genetic Variation/genetics ; Haplotypes/genetics ; Indians, South American ; Genetics, Population ; }, abstract = {The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia.}, }
@article {pmid37894136, year = {2023}, author = {Pusadkar, V and Azad, RK}, title = {Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894136}, issn = {2076-2607}, abstract = {Taxonomic profiling of ancient metagenomic samples is challenging due to the accumulation of specific damage patterns on DNA over time. Although a number of methods for metagenome profiling have been developed, most of them have been assessed on modern metagenomes or simulated metagenomes mimicking modern metagenomes. Further, a comparative assessment of metagenome profilers on simulated metagenomes representing a spectrum of degradation depth, from the extremity of ancient (most degraded) to current or modern (not degraded) metagenomes, has not yet been performed. To understand the strengths and weaknesses of different metagenome profilers, we performed their comprehensive evaluation on simulated metagenomes representing human dental calculus microbiome, with the level of DNA damage successively raised to mimic modern to ancient metagenomes. All classes of profilers, namely, DNA-to-DNA, DNA-to-protein, and DNA-to-marker comparison-based profilers were evaluated on metagenomes with varying levels of damage simulating deamination, fragmentation, and contamination. Our results revealed that, compared to deamination and fragmentation, human and environmental contamination of ancient DNA (with modern DNA) has the most pronounced effect on the performance of each profiler. Further, the DNA-to-DNA (e.g., Kraken2, Bracken) and DNA-to-marker (e.g., MetaPhlAn4) based profiling approaches showed complementary strengths, which can be leveraged to elevate the state-of-the-art of ancient metagenome profiling.}, }
@article {pmid37884848, year = {2023}, author = {}, title = {Ancient DNA reveals traces of elusive first humans in Europe.}, journal = {Nature}, volume = {623}, number = {7985}, pages = {11}, pmid = {37884848}, issn = {1476-4687}, mesh = {Animals ; Humans ; *DNA, Ancient ; *Hominidae ; Europe ; }, }
@article {pmid37876815, year = {2023}, author = {Duitama González, C and Rangavittal, S and Vicedomini, R and Chikhi, R and Richard, H}, title = {aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108057}, pmid = {37876815}, issn = {2589-0042}, abstract = {Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and therefore have limited use cases. We present a reference-free decontamination tool tailored for the removal of contaminant DNA of ancient oral sample called aKmerBroom. Our tool builds a Bloom filter of known ancient and modern oral k-mers, then scans an input set of ancient metagenomic reads using multiple passes to iteratively retain reads likely to be of oral origin. On synthetic data, aKmerBroom achieves over 89.53% sensitivity and 94.00% specificity. On real datasets, aKmerBroom shows higher read retainment (+60% on average) than other methods. We anticipate aKmerBroom will be a valuable tool for the processing of ancient oral samples as it will prevent contaminated datasets from being completely discarded in downstream analyses.}, }
@article {pmid37873879, year = {2023}, author = {Kim, AS and Kreiner, JM and Hernández, F and Bock, DG and Hodgins, KA and Rieseberg, LH}, title = {Temporal collections to study invasion biology.}, journal = {Molecular ecology}, volume = {32}, number = {24}, pages = {6729-6742}, doi = {10.1111/mec.17176}, pmid = {37873879}, issn = {1365-294X}, mesh = {*DNA/genetics ; *Museums ; Biology ; }, abstract = {Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.}, }
@article {pmid37872569, year = {2023}, author = {Pochon, Z and Bergfeldt, N and Kırdök, E and Vicente, M and Naidoo, T and van der Valk, T and Altınışık, NE and Krzewińska, M and Dalén, L and Götherström, A and Mirabello, C and Unneberg, P and Oskolkov, N}, title = {aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {242}, pmid = {37872569}, issn = {1474-760X}, mesh = {Workflow ; *Metagenome ; *Metagenomics ; Archaeology ; DNA, Ancient ; }, abstract = {Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.}, }
@article {pmid37852263, year = {2023}, author = {Tao, L and Yuan, H and Zhu, K and Liu, X and Guo, J and Min, R and He, H and Cao, D and Yang, X and Zhou, Z and Wang, R and Zhao, D and Ma, H and Chen, J and Zhao, J and Li, Y and He, Y and Suo, D and Zhang, R and Li, S and Li, L and Yang, F and Li, H and Zhang, L and Jin, L and Wang, CC}, title = {Ancient genomes reveal millet farming-related demic diffusion from the Yellow River into southwest China.}, journal = {Current biology : CB}, volume = {33}, number = {22}, pages = {4995-5002.e7}, doi = {10.1016/j.cub.2023.09.055}, pmid = {37852263}, issn = {1879-0445}, mesh = {Humans ; *Millets/genetics ; *Rivers ; Agriculture ; Genome ; Farms ; DNA, Ancient ; Human Migration ; }, abstract = {The study of southwest China is vital for understanding the dispersal and development of farming because of the coexistence of millet and rice in this region since the Neolithic period.[1][,][2] However, the process of the Neolithic transition in southwest China is largely unknown, mainly due to the lack of ancient DNA from the Neolithic period. Here, we report genome-wide data from 11 human samples from the Gaoshan and Haimenkou sites with mixed farming of millet and rice dating to between 4,500 and 3,000 years before present in southwest China. The two ancient groups derived approximately 90% of their ancestry from the Neolithic Yellow River farmers, suggesting a demic diffusion of millet farming to southwest China. We inferred their remaining ancestry to be derived from a Hòabìnhian-related hunter-gatherer lineage. We did not detect rice farmer-related ancestry in the two ancient groups, which indicates that they likely adopted rice farming without genetic assimilation. We, however, observed rice farmer-related ancestry in the formation of some present-day Tibeto-Burman populations. Our results suggested the occurrence of both demic and cultural diffusion in the development of Neolithic mixed farming in some parts of southwest China.}, }
@article {pmid37844237, year = {2023}, author = {Lucquin, A and Robson, HK and Oras, E and Lundy, J and Moretti, G and González Carretero, L and Dekker, J and Demirci, &#xd6; and Dolbunova, E and McLaughlin, TR and Piezonka, H and Talbot, HM and Adamczak, K and Czekaj-Zastawny, A and Groß, D and Gumiński, W and Hartz, S and Kabaciński, J and Koivisto, S and Linge, TE and Meyer, AK and Mökkönen, T and Philippsen, B and Piličiauskas, G and Visocka, V and Kriiska, A and Raemaekers, D and Meadows, J and Heron, C and Craig, OE}, title = {The impact of farming on prehistoric culinary practices throughout Northern Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {43}, pages = {e2310138120}, pmid = {37844237}, issn = {1091-6490}, mesh = {Animals ; Humans ; *Archaeology ; *Agriculture ; Europe ; Farms ; Farmers ; }, abstract = {To investigate changes in culinary practices associated with the arrival of farming, we analysed the organic residues of over 1,000 pottery vessels from hunter-gatherer-fisher and early agricultural sites across Northern Europe from the Lower Rhine Basin to the Northeastern Baltic. Here, pottery was widely used by hunter-gatherer-fishers prior to the introduction of domesticated animals and plants. Overall, there was surprising continuity in the way that hunter-gatherer-fishers and farmers used pottery. Both aquatic products and wild plants remained prevalent, a pattern repeated consistently across the study area. We argue that the rapid adaptation of farming communities to exploit coastal and lagoonal resources facilitated their northerly expansion, and in some cases, hunting, gathering, and fishing became the most dominant subsistence strategy. Nevertheless, dairy products frequently appear in pottery associated with the earliest farming groups often mixed with wild plants and fish. Interestingly, we also find compelling evidence of dairy products in hunter-gatherer-fisher Ertebølle pottery, which predates the arrival of domesticated animals. We propose that Ertebølle hunter-gatherer-fishers frequently acquired dairy products through exchange with adjacent farming communities prior to the transition. The continuity observed in pottery use across the transition to farming contrasts with the analysis of human remains which shows substantial demographic change through ancient DNA and, in some cases, a reduction in marine consumption through stable isotope analysis. We postulate that farmers acquired the knowledge and skills they needed to succeed from local hunter-gatherer-fishers but without substantial admixture.}, }
@article {pmid37836192, year = {2023}, author = {Papalini, S and Di Vittori, V and Pieri, A and Allegrezza, M and Frascarelli, G and Nanni, L and Bitocchi, E and Bellucci, E and Gioia, T and Pereira, LG and Susek, K and Tenaillon, M and Neumann, K and Papa, R}, title = {Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {19}, pages = {}, pmid = {37836192}, issn = {2223-7747}, support = {862862//European Union's Horizon 2020 research and innovation programme/ ; 20177RL4KL//Italian Government (MIUR)/ ; }, abstract = {Paleogenomics focuses on the recovery, manipulation, and analysis of ancient DNA (aDNA) from historical or long-dead organisms to reconstruct and analyze their genomes. The aDNA is commonly obtained from remains found in paleontological and archaeological sites, conserved in museums, and in other archival collections. Herbarium collections represent a great source of phenotypic and genotypic information, and their exploitation has allowed for inference and clarification of previously unsolved taxonomic and systematic relationships. Moreover, herbarium specimens offered a new source for studying phenological traits in plants and for disentangling biogeography and evolutionary scenarios of species. More recently, advances in molecular technologies went in parallel with the decreasing costs of next-generation sequencing (NGS) approaches, which paved the way to the utilization of aDNA for whole-genome studies. Although many studies have been carried out combining modern analytic techniques and ancient samples, such as herbarium specimens, this research field is still relatively unexplored due to the need for improving strategies for aDNA manipulation and exploitation from ancient samples. The higher susceptibility of aDNA to degradation and contamination during herbarium conservation and manipulation and the occurrence of biochemical postmortem damage can result in a more challenging reconstruction of the original DNA sequence. Here, we review the methodological approaches that have been developed for the exploitation of historical herbarium plant materials, such as best practices for aDNA extraction, amplification, and genotyping. We also focus on some strategies to overcome the main problems related to the utilization of herbarium specimens for their exploitation in plant evolutionary studies.}, }
@article {pmid37830773, year = {2023}, author = {Muschick, M and Jemmi, E and Lengacher, N and Hänsch, S and Wales, N and Kishe, MA and Mwaiko, S and Dieleman, J and Lever, MA and Salzburger, W and Verschuren, D and Seehausen, O}, title = {Ancient DNA is preserved in fish fossils from tropical lake sediments.}, journal = {Molecular ecology}, volume = {32}, number = {22}, pages = {5913-5931}, doi = {10.1111/mec.17159}, pmid = {37830773}, issn = {1365-294X}, support = {CRSII5_183566//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 324249//FP7 Ideas: European Research Council/ ; //Strategy pool of the Faculty of Natural Sciences of the University of Bern/ ; 11-97251-000-INP//MacArthur Foundation/ ; }, mesh = {Animals ; *Lakes ; Phylogeny ; Fossils ; DNA, Ancient ; *Cichlids/genetics ; }, abstract = {Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.}, }
@article {pmid37829208, year = {2022}, author = {Atağ, G and Vural, KB and Kaptan, D and Özkan, M and Koptekin, D and Sağlıcan, E and Doğramacı, S and Köz, M and Yılmaz, A and Söylev, A and Togan, &#x130; and Somel, M and Özer, F}, title = {MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes.}, journal = {Open research Europe}, volume = {2}, number = {}, pages = {100}, pmid = {37829208}, issn = {2732-5121}, abstract = {A major challenge in zooarchaeology is to morphologically distinguish closely related species' remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species' reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.3x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are difficult to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.}, }
@article {pmid37828091, year = {2023}, author = {Breglia, F and Bouby, L and Wales, N and Ivorra, S and Fiorentino, G}, title = {Disentangling the origins of viticulture in the western Mediterranean.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {17284}, pmid = {37828091}, issn = {2045-2322}, mesh = {Italy ; *Domestication ; *Vitis/genetics ; Archaeology ; Radiometric Dating ; }, abstract = {We present direct evidence of early grape domestication in southern Italy via a multidisciplinary study of pip assemblage from one site, shedding new light on the spread of viticulture in the western Mediterranean during the Bronze Age. This consist of 55 waterlogged pips from Grotta di Pertosa, a Middle Bronze Age settlement in the south of the Italian peninsula. Direct radiocarbon dating of pips was carried out, confirming the chronological consistency of the samples with their archaeological contexts (ca. 1450-1200 BCE). The extraordinary state of conservation of the sample allowed to perform geometric morphometric (GMM) and paleogenetic analyses (aDNA) at the same time. The combination of the two methods has irrefutably shown the presence of domestic grapevines, together with wild ones, in Southern Italy during the Middle/Late Bronze Age. The results converge towards an oriental origin of the domestic grapes, most likely arriving from the Aegean area through the Mycenaeans. A parent/offspring kinship was also recognised between a domestic/wild hybrid individual and a domestic clonal group. This data point out a little known aspect of the diffusion of the first viticulture in Italy, and therefore in the western Mediterranean, which involved the hybridization between imported domestic varieties with, likely local, wild vines.}, }
@article {pmid37821799, year = {2023}, author = {Reeves, IM and Totterdell, JA and Betty, EL and Donnelly, DM and George, A and Holmes, S and Moller, L and Stockin, KA and Wellard, R and White, C and Foote, AD}, title = {Ancestry testing of "Old Tom," a killer whale central to mutualistic interactions with human whalers.}, journal = {The Journal of heredity}, volume = {114}, number = {6}, pages = {598-611}, pmid = {37821799}, issn = {1465-7333}, support = {ERC-COG-101045346/ERC_/European Research Council/International ; }, mesh = {Animals ; Humans ; *Whale, Killer/genetics ; Australia ; Whales/genetics ; Base Sequence ; New Zealand ; }, abstract = {Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as "Old Tom," washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to other populations globally and whether their genetic descendants persist today remains unknown. We extracted and sequenced DNA from Old Tom using ancient DNA techniques. Genomic sequences were then compared with a global dataset of mitochondrial and nuclear genomes. Old Tom shared a most recent common ancestor with killer whales from Australasia, the North Atlantic, and the North Pacific, having the highest genetic similarity with contemporary New Zealand killer whales. However, much of the variation found in Old Tom's genome was not shared with these widespread populations, suggesting ancestral rather than ongoing gene flow. Our genetic comparisons also failed to find any clear descendants of Tom, raising the possibility of local extinction of this group. We integrated Traditional Custodian knowledge to recapture the events in Eden and recognize that Indigenous Australians initiated the relationship with the killer whales before European colonization and the advent of commercial whaling locally. This study rectifies discrepancies in local records and provides new insight into the origins of the killer whales in Eden and the history of Australasian killer whales.}, }
@article {pmid37819893, year = {2023}, author = {Reynoso-García, J and Santiago-Rodriguez, TM and Narganes-Storde, Y and Cano, RJ and Toranzos, GA}, title = {Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0292077}, pmid = {37819893}, issn = {1932-6203}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; R25 GM061151/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; Puerto Rico ; *Diet ; Ethnicity ; Fungi ; }, abstract = {Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifestyles. We also analyzed DNA sequences of putative phytopathogenic fungi, likely ingested during food consumption, to further support dietary habits. Our findings show that pre-Columbian Caribbean cultures had a diverse diet consisting of maize (Zea mays), sweet potato (Ipomoea batatas), chili peppers (Capsicum annuum), peanuts (Arachis spp.), papaya (Carica papaya), tomato (Solanum lycopersicum) and, very surprisingly cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris). Modelling of putative phytopathogenic fungi and plant interactions confirmed the potential consumption of these plants as well as edible fungi, particularly Ustilago spp., which suggest the consumption of maize and huitlacoche. These findings suggest that a variety of dietary, medicinal, and hallucinogenic plants likely played an important role in ancient human subsistence and societal customs. We compared our results with coprolites found in Mexico and the United States, as well as present-day faeces from Mexico, Peru, and the United States. The results suggest that the diet of pre-Columbian cultures resembled that of present-day hunter-gatherers, while agriculturalists exhibited a transitional state in dietary lifestyles between the pre-Columbian cultures and larger scale farmers and United States individuals. Our study highlights differences in dietary patterns related to human lifestyles and provides insight into the flora present in the pre-Columbian Caribbean area. Importantly, data from ancient fecal specimens demonstrate the importance of ancient DNA studies to better understand pre-Columbian populations.}, }
@article {pmid37819677, year = {2024}, author = {Marchi, N and Kapopoulou, A and Excoffier, L}, title = {Demogenomic inference from spatially and temporally heterogeneous samples.}, journal = {Molecular ecology resources}, volume = {24}, number = {1}, pages = {e13877}, doi = {10.1111/1755-0998.13877}, pmid = {37819677}, issn = {1755-0998}, support = {310030_188883/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Humans ; *Genetics, Population ; *Genome ; Genomics ; DNA, Ancient ; Models, Genetic ; }, abstract = {Modern and ancient genomes are not necessarily drawn from homogeneous populations, as they may have been collected from different places and at different times. This heterogeneous sampling can be an issue for demographic inferences and results in biased demographic parameters and incorrect model choice if not properly considered. When explicitly accounted for, it can result in very complex models and high data dimensionality that are difficult to analyse. In this paper, we formally study the impact of such spatial and temporal sampling heterogeneity on demographic inference, and we introduce a way to circumvent this problem. To deal with structured samples without increasing the dimensionality of the site frequency spectrum (SFS), we introduce a new structured approach to the existing program fastsimcoal2. We assess the efficiency and relevance of this methodological update with simulated and modern human genomic data. We particularly focus on spatial and temporal heterogeneities to evidence the interest of this new SFS-based approach, which can be especially useful when handling scattered and ancient DNA samples, as in conservation genetics or archaeogenetics.}, }
@article {pmid37819040, year = {2023}, author = {Quiroz-Morales, SE and Muriel-Millán, LF and Ponce-Soto, GY and González-Valdez, A and Castillo-Juárez, I and Servín-González, L and Soberón-Chávez, G}, title = {Pseudomonas aeruginosa strains belonging to phylogroup 3 frequently exhibit an atypical quorum sensing response: the case of MAZ105, a tomato rhizosphere isolate.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {10}, pages = {}, pmid = {37819040}, issn = {1465-2080}, mesh = {Animals ; Mice ; *Quorum Sensing/genetics ; Pseudomonas aeruginosa/metabolism ; *Solanum lycopersicum ; Rhizosphere ; Signal Transduction/genetics ; Virulence Factors/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; }, abstract = {Pseudomonas aeruginosa is a widespread γ-proteobacterium and an important opportunistic pathogen. The genetically diverse P. aeruginosa phylogroup 3 strains are characterized by producing the pore-forming ExlA toxin and by their lack of a type III secretion system. However, like all strains of this species, they produce several virulence-associated traits, such as elastase, rhamnolipids and pyocyanin, which are regulated by quorum sensing (QS). The P. aeruginosa QS response comprises three systems (Las, Rhl and Pqs, respectively) that hierarchically regulate these virulence factors. The Pqs QS system is composed of the PqsR transcriptional factor, which, coupled with the alkyl-quinolones HHQ or PQS, activates the transcription of the pqsABCDE operon. The products of the first four genes of this operon produce HHQ, which is then converted to PQS by PqsH, while PqsE forms a complex with RhlR and stabilizes it. In this study we report that mutations affecting the Pqs system are particularly common in phylogroup 3 strains. To better understand QS in phylogroup 3 strains we studied strain MAZ105 isolated from tomato rhizosphere and showed that it contains mutations in the central QS transcriptional regulator, LasR, and in the gene encoding the PqsA enzyme involved in the synthesis of PQS. However, it can still produce QS-regulated virulence factors and is virulent in Galleria mellonella and mildly pathogenic in the mouse abscess/necrosis model; our results show that this may be due to the expression of pqsE from a different PqsR-independent promoter than the pqsA promoter. Our results indicate that using anti-virulence therapy based on targeting the PQS system will not be effective against infections by P. aeruginosa phylogroup 3 strains.}, }
@article {pmid37810237, year = {2023}, author = {Gînguță, A and Kovács, B and Schütz, O and Tihanyi, B and Nyerki, E and Maár, K and Maróti, Z and Varga, GIB and Băcueț-Crișan, D and Keresztes, T and Török, T and Neparáczki, E}, title = {Genetic identification of members of the prominent Báthory aristocratic family.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107911}, pmid = {37810237}, issn = {2589-0042}, abstract = {The Báthory family was one of the most powerful noble families in the medieval Hungarian Kingdom. Their influence peaked during the Ottoman occupation of Hungary, when the only partially autonomous region of the country was Transylvania, under Turkish protectorate. Several members of the family became Princes of Transylvania, and one of them, István Báthory, was also the elected King of Poland. We hereby present the first genetic data about this extinct family. Archaeological excavations in Pericei, a settlement now part of Romania, revealed the former family chapel of the Báthory family. Through this work, two Báthory family members were successfully identified among the 13 skeletons found at the site. The presence of Y chromosome haplogroup R-S498 fits the historical account describing the family's German (Swabian) origins. Their genomic composition also indicates a family of Germanic origin that intermixed with medieval Hungarians.}, }
@article {pmid37810206, year = {2023}, author = {Menéndez, LP and Barbieri, C and López Cruz, IG and Schmelzle, T and Breidenstein, A and Barquera, R and Borzi, G and Schuenemann, VJ and Sánchez-Villagra, MR}, title = {On Roth's "human fossil" from Baradero, Buenos Aires Province, Argentina: morphological and genetic analysis.}, journal = {Swiss journal of palaeontology}, volume = {142}, number = {1}, pages = {26}, pmid = {37810206}, issn = {1664-2384}, abstract = {The "human fossil" from Baradero, Buenos Aires Province, Argentina, is a collection of skeleton parts first recovered by the paleontologist Santiago Roth and further studied by the anthropologist Rudolf Martin. By the end of the nineteenth century and beginning of the twentieth century it was considered one of the oldest human skeletons from South America's southern cone. Here, we present the results of an interdisciplinary approach to study and contextualize the ancient individual remains. We discuss the context of the finding by first compiling the available evidence associated with the historical information and any previous scientific publications on this individual. Then, we conducted an osteobiographical assessment, by which we evaluated the sex, age, and overall preservation of the skeleton based on morphological features. To obtain a 3D virtual reconstruction of the skull, we performed high resolution CT-scans on selected skull fragments and the mandible. This was followed by the extraction of bone tissue and tooth samples for radiocarbon and genetic analyses, which brought only limited results due to poor preservation and possible contamination. We estimate that the individual from Baradero is a middle-aged adult male. We conclude that the revision of foundational collections with current methodological tools brings new insights and clarifies long held assumptions on the significance of samples that were recovered when archaeology was not yet professionalized.}, }
@article {pmid37809321, year = {2023}, author = {Dillon, EM and Dunne, EM and Womack, TM and Kouvari, M and Larina, E and Claytor, JR and Ivkić, A and Juhn, M and Carmona, PSM and Robson, SV and Saha, A and Villafaña, JA and Zill, ME}, title = {Challenges and directions in analytical paleobiology.}, journal = {Paleobiology}, volume = {49}, number = {3}, pages = {377-393}, pmid = {37809321}, issn = {0094-8373}, support = {P 31592/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite-or even spurred by-this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.}, }
@article {pmid37808674, year = {2023}, author = {Tretmanis, JM and Jay, F and Avila-Árcos, MC and Huerta-Sanchez, E}, title = {Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37808674}, issn = {2692-8205}, support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; }, abstract = {Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing quality. We also develop a software tool that simulates aDNA taking into account the features of aDNA as well as the evolutionary history of the population. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (~ 400 generations in the past) as long as contamination and read depth are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resulting in the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations.}, }
@article {pmid37797036, year = {2023}, author = {Dalén, L and Heintzman, PD and Kapp, JD and Shapiro, B}, title = {Deep-time paleogenomics and the limits of DNA survival.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6666}, pages = {48-53}, pmid = {37797036}, issn = {1095-9203}, support = {/HHMI/Howard Hughes Medical Institute/United States ; 101054984/ERC_/European Research Council/International ; }, mesh = {Biodiversity ; DNA/genetics ; *DNA, Ancient ; *Genomics/methods ; Paleontology ; *Biological Evolution ; Animals ; }, abstract = {Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.}, }
@article {pmid37797028, year = {2023}, author = {Burbano, HA and Gutaker, RM}, title = {Ancient DNA genomics and the renaissance of herbaria.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6666}, pages = {59-63}, doi = {10.1126/science.adi1180}, pmid = {37797028}, issn = {1095-9203}, mesh = {*DNA, Ancient ; Genomics ; *Plants/genetics ; *Collections as Topic ; Conservation of Natural Resources ; Biological Evolution ; Adaptation, Biological/genetics ; Phenotype ; }, abstract = {Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.}, }
@article {pmid37797024, year = {2023}, author = {Ávila-Arcos, MC and Raghavan, M and Schlebusch, C}, title = {Going local with ancient DNA: A review of human histories from regional perspectives.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6666}, pages = {53-58}, doi = {10.1126/science.adh8140}, pmid = {37797024}, issn = {1095-9203}, support = {R35 GM143094/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Africa ; Americas ; Asia ; *DNA, Ancient ; Oceania ; *Demography/history ; *Social Structure ; *Health/history ; }, abstract = {Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.}, }
@article {pmid37797011, year = {2023}, author = {Curry, A}, title = {Family ties.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6666}, pages = {24-27}, doi = {10.1126/science.adl1577}, pmid = {37797011}, issn = {1095-9203}, abstract = {Giant family trees based on ancient DNA from thousands of people are revealing prehistoric politics and social structure.}, }
@article {pmid37767965, year = {2023}, author = {Grathwol, F and Roos, C and Zinner, D and Hume, B and Porcier, SM and Berthet, D and Cuisin, J and Merker, S and Ottoni, C and Van Neer, W and Dominy, NJ and Kopp, GH}, title = {Adulis and the transshipment of baboons during classical antiquity.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37767965}, issn = {2050-084X}, mesh = {Humans ; Animals ; *Papio ; Phylogeny ; Africa ; Egypt ; Geography ; }, abstract = {Adulis, located on the Red Sea coast in present-day Eritrea, was a bustling trading centre between the first and seventh centuries CE. Several classical geographers-Agatharchides of Cnidus, Pliny the Elder, Strabo-noted the value of Adulis to Greco-Roman Egypt, particularly as an emporium for living animals, including baboons (Papio spp.). Though fragmentary, these accounts predict the Adulite origins of mummified baboons in Ptolemaic catacombs, while inviting questions on the geoprovenance of older (Late Period) baboons recovered from Gabbanat el-Qurud ('Valley of the Monkeys'), Egypt. Dated to ca. 800-540 BCE, these animals could extend the antiquity of Egyptian-Adulite trade by as much as five centuries. Previously, Dominy et al. (2020) used stable isotope analysis to show that two New Kingdom specimens of Papio hamadryas originate from the Horn of Africa. Here, we report the complete mitochondrial genomes from a mummified baboon from Gabbanat el-Qurud and 14 museum specimens with known provenance together with published georeferenced mitochondrial sequence data. Phylogenetic assignment connects the mummified baboon to modern populations of P. hamadryas in Eritrea, Ethiopia, and eastern Sudan. This result, assuming geographical stability of phylogenetic clades, corroborates Greco-Roman historiographies by pointing toward present-day Eritrea, and by extension Adulis, as a source of baboons for Late Period Egyptians. It also establishes geographic continuity with baboons from the fabled Land of Punt (Dominy et al., 2020), giving weight to speculation that Punt and Adulis were essentially the same trading centres separated by a thousand years of history.}, }
@article {pmid37752842, year = {2023}, author = {Ruiz-Puerta, EJ and Keighley, X and Desjardins, SPA and Gotfredsen, AB and Pan, SE and Star, B and Boessenkool, S and Barrett, JH and McCarthy, ML and Andersen, LW and Born, EW and Howse, LR and Szpak, P and Pálsson, S and Malmquist, HJ and Rufolo, S and Jordan, PD and Olsen, MT}, title = {Holocene deglaciation drove rapid genetic diversification of Atlantic walrus.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2007}, pages = {20231349}, pmid = {37752842}, issn = {1471-2954}, abstract = {Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.}, }
@article {pmid37752477, year = {2023}, author = {Kroes, R and Winkel, Y and Breeuwer, JAJ and van Loon, EE and Loader, SP and Maclaine, JS and Verdonschot, PFM and van der Geest, HG}, title = {Phylogenetic analysis of museum specimens of houting Coregonus oxyrinchus shows the need for a revision of its extinct status.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {57}, pmid = {37752477}, issn = {2730-7182}, mesh = {Animals ; Phylogeny ; *Museums ; *Salmonidae/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {According to the IUCN Red List the anadromous houting Coregonus oxyrinchus is categorized as 'extinct'. However, this extinct status might be incorrect because taxonomic difference between C. oxyrinchus and the closely related C. lavaretus is based on a disputable morphological comparison. Also, phylogenetic studies on mtDNA only focused on recent obtained coregonids. We are the first to perform a mtDNA analysis on both historic and recent specimens, including the syntype specimen which was used for species description by Linnaeus originally. Two primer pairs for mitochondrial CytB and ND3 were used to extract sequences for phylogenetic analysis. Sequences from 14 out of 21 C. oxyrinchus museum specimens were successfully obtained and compared with sequences from recent obtained C. lavaretus. The sequences were combined with GenBank data from a previous phylogenetic study on houting to create a phylogenetic tree and two minimum spanning haplotype networks. Results show that C. oxyrinchus and C. lavaretus form a clade with limited genetic variation. Low bootstrap values also show weak support for geographical patterns in distribution of mitochondrial haplotypes. Statistical analysis of the haplotype networks also shows that historic and recent specimens are similar species. Our results suggest that C. oxyrinchus is a junior synonym of C. lavaretus. A definitive taxonomic revision could not be made because only CytB sequencing was successful for the syntype specimen. We discuss taxonomic consequences and the species-specific focus in nature conservation. We propose a shift in nature conservation to a more functional approach based on traits rather than species.}, }
@article {pmid37749660, year = {2023}, author = {Wegner, CE and Stahl, R and Velsko, I and Hübner, A and Fagernäs, Z and Warinner, C and Lehmann, R and Ritschel, T and Totsche, KU and Küsel, K}, title = {A glimpse of the paleome in endolithic microbial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {210}, pmid = {37749660}, issn = {2049-2618}, mesh = {*Genomics ; Paleontology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; }, abstract = {BACKGROUND: The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards.<br><br>RESULTS: By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25&#x2009;&#xd7;&#x2009;10[5] cells&#x2009;&#xd7;&#x2009;g[-1] rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past.<br><br>CONCLUSIONS: Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.}, }
@article {pmid37738339, year = {2023}, author = {Oliveira, S and Fehn, AM and Amorim, B and Stoneking, M and Rocha, J}, title = {Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry.}, journal = {Science advances}, volume = {9}, number = {38}, pages = {eadh3822}, pmid = {37738339}, issn = {2375-2548}, mesh = {Humans ; *Black People/genetics ; *DNA, Ancient ; Namibia ; }, abstract = {Ancient DNA studies reveal the genetic structure of Africa before the expansion of Bantu-speaking agriculturalists; however, the impact of now extinct hunter-gatherer and herder societies on the genetic makeup of present-day African groups remains elusive. Here, we uncover the genetic legacy of pre-Bantu populations from the Angolan Namib Desert, where we located small-scale groups associated with enigmatic forager traditions, as well as the last speakers of the Khoe-Kwadi family's Kwadi branch. By applying an ancestry decomposition approach to genome-wide data from these and other African populations, we reconstructed the fine-scale histories of contact emerging from the migration of Khoe-Kwadi-speaking pastoralists and identified a deeply divergent ancestry, which is exclusively shared between groups from the Angolan Namib and adjacent areas of Namibia. The unique genetic heritage of the Namib peoples shows how modern DNA research targeting understudied regions of high ethnolinguistic diversity can complement ancient DNA studies in probing the deep genetic structure of the African continent.}, }
@article {pmid37719142, year = {2023}, author = {Wang, K and Prüfer, K and Krause-Kyora, B and Childebayeva, A and Schuenemann, VJ and Coia, V and Maixner, F and Zink, A and Schiffels, S and Krause, J}, title = {High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry.}, journal = {Cell genomics}, volume = {3}, number = {9}, pages = {100377}, pmid = {37719142}, issn = {2666-979X}, abstract = {The Tyrolean Iceman is known as one of the oldest human glacier mummies, directly dated to 3350-3120 calibrated BCE. A previously published low-coverage genome provided novel insights into European prehistory, despite high present-day DNA contamination. Here, we generate a high-coverage genome with low contamination (15.3×) to gain further insights into the genetic history and phenotype of this individual. Contrary to previous studies, we found no detectable Steppe-related ancestry in the Iceman. Instead, he retained the highest Anatolian-farmer-related ancestry among contemporaneous European populations, indicating a rather isolated Alpine population with limited gene flow from hunter-gatherer-ancestry-related populations. Phenotypic analysis revealed that the Iceman likely had darker skin than present-day Europeans and carried risk alleles associated with male-pattern baldness, type 2 diabetes, and obesity-related metabolic syndrome. These results corroborate phenotypic observations of the preserved mummified body, such as high pigmentation of his skin and the absence of hair on his head.}, }
@article {pmid37717498, year = {2023}, author = {Díaz-Navarro, S and Haber Uriarte, M and García-González, R}, title = {Holes in the Head. Double cranial surgery on an individual from the Chalcolithic burial site of Camino del Molino (SE Spain).}, journal = {International journal of paleopathology}, volume = {43}, number = {}, pages = {22-30}, doi = {10.1016/j.ijpp.2023.09.003}, pmid = {37717498}, issn = {1879-9825}, mesh = {Adult ; Humans ; Female ; Spain ; *Skull/pathology ; *Trephining ; Burial/methods ; Europe ; }, abstract = {OBJECTIVE: This article analyses new prehistoric evidence of trepanation from a collective burial site in the south-eastern Iberian Peninsula.<br><br>MATERIALS: The trepanned individual was documented in the Chalcolithic burial site of Camino del Molino, where 1348 individuals (30.7 % non-adults and 69.3 % adults) were deposited in two contiguous funerary phases, making it a reference site for the knowledge of Recent Prehistoric populations.<br><br>METHODS: The individual has been sexed using traditional anthropological methods and ancient DNA. C14 dating has also been obtained. The lesion has been analysed macroscopically and microscopically using SEM.<br><br>RESULTS: The skull under study belonged to an adult female deposited in the second burial phase (2566-2239 years cal BCE). It exhibits in the anterior region of the right temporal fossa two contiguous and partially overlapping holes that correspond to two trepanations performed using the scraping technique.<br><br>CONCLUSIONS: It is a double cranial trepanation with signs of bone remodelling suggesting survival from surgery. No pathological signs were identified potentially associated with the intervention.<br><br>SIGNIFICANCE: This is the second case of surgical interventions in the geographical area of study and one of the few evidences of this practice in women during prehistoric times.<br><br>LIMITATIONS: So far only the articulated skeletons from this burial have been thoroughly analysed.<br><br>Further intensive review of skull collection is advised to learn more about these surgical interventions in Copper Age and to go deeper into the causes that motivated their execution.}, }
@article {pmid37712846, year = {2023}, author = {Davidson, R and Williams, MP and Roca-Rada, X and Kassadjikova, K and Tobler, R and Fehren-Schmitz, L and Llamas, B}, title = {Allelic bias when performing in-solution enrichment of ancient human DNA.}, journal = {Molecular ecology resources}, volume = {23}, number = {8}, pages = {1823-1840}, doi = {10.1111/1755-0998.13869}, pmid = {37712846}, issn = {1755-0998}, support = {DE190101069//Australian Research Council/ ; FT170100448//Australian Research Council/ ; 1515138//National Science Foundation/ ; }, abstract = {In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.}, }
@article {pmid37701515, year = {2022}, author = {Jaramillo-Valverde, L and Vásquez-Domínguez, A and Levano, KS and Castrejon-Cabanillas, R and Novoa-Bellota, P and Machacuay-Romero, M and Garcia-de-la-Guarda, R and Cano, RJ and Shady Solis, R and Guio, H}, title = {A mobile lab for ancient DNA extraction in Perug.}, journal = {Bioinformation}, volume = {18}, number = {12}, pages = {1114-1118}, pmid = {37701515}, issn = {0973-2063}, abstract = {We report the use of a mobile laboratory set up to extract ancient DNA (aDNA) from 34 human coprolites (fossilized faeces) samples. Our approach enabled the rapid genetic characterization of 5,000 years old archeological samples. It is useful for the on-site screening of museums and freshly excavated samples for DNA. This approach is accessible to other investigators as the mobile laboratory was set up using commercially available instruments.}, }
@article {pmid37699853, year = {2023}, author = {Chocholova, E and Roudnicky, P and Potesil, D and Fialova, D and Krystofova, K and Drozdova, E and Zdrahal, Z}, title = {Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus.}, journal = {Journal of proteome research}, volume = {22}, number = {10}, pages = {3311-3319}, pmid = {37699853}, issn = {1535-3907}, abstract = {Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.}, }
@article {pmid37683613, year = {2023}, author = {Sandoval-Velasco, M and Jagadeesan, A and Ramos-Madrigal, J and Ávila-Arcos, MC and Fortes-Lima, CA and Watson, J and Johannesdóttir, E and Cruz-Dávalos, DI and Gopalakrishnan, S and Moreno-Mayar, JV and Niemann, J and Renaud, G and Robson Brown, KA and Bennett, H and Pearson, A and Helgason, A and Gilbert, MTP and Schroeder, H}, title = {The ancestry and geographical origins of St Helena's liberated Africans.}, journal = {American journal of human genetics}, volume = {110}, number = {9}, pages = {1590-1599}, pmid = {37683613}, issn = {1537-6605}, mesh = {Humans ; Female ; Male ; *African People ; DNA, Ancient ; Black People/genetics ; *Enslaved Persons ; Genotype ; }, abstract = {The island of St Helena played a crucial role in the suppression of the transatlantic slave trade. Strategically located in the middle of the South Atlantic, it served as a staging post for the Royal Navy and reception point for enslaved Africans who had been "liberated" from slave ships intercepted by the British. In total, St Helena received approximately 27,000 liberated Africans between 1840 and 1867. Written sources suggest that the majority of these individuals came from West Central Africa, but their precise origins are unknown. Here, we report the results of ancient DNA analyses that we conducted as part of a wider effort to commemorate St Helena's liberated Africans and to restore knowledge of their lives and experiences. We generated partial genomes (0.1-0.5×) for 20 individuals whose remains had been recovered during archaeological excavations on the island. We compared their genomes with genotype data for over 3,000 present-day individuals from 90 populations across sub-Saharan Africa and conclude that the individuals most likely originated from different source populations within the general area between northern Angola and Gabon. We also find that the majority (17/20) of the individuals were male, supporting a well-documented sex bias in the latter phase of the transatlantic slave trade. The study expands our understanding of St Helena's liberated African community and illustrates how ancient DNA analyses can be used to investigate the origins and identities of individuals whose lives were bound up in the story of slavery and its abolition.}, }
@article {pmid37673908, year = {2023}, author = {Hodgins, HP and Chen, P and Lobb, B and Wei, X and Tremblay, BJM and Mansfield, MJ and Lee, VCY and Lee, PG and Coffin, J and Duggan, AT and Dolphin, AE and Renaud, G and Dong, M and Doxey, AC}, title = {Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5475}, pmid = {37673908}, issn = {2041-1723}, support = {R01 NS080833/NS/NINDS NIH HHS/United States ; R01 NS117626/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *DNA, Ancient ; Neurotoxins ; *Tetanus ; Phylogeny ; Clostridium ; Chile ; Mammals ; }, abstract = {The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals.}, }
@article {pmid37666338, year = {2023}, author = {Han, W and Zhang, E and Sun, W and Lin, Q and Meng, X and Ni, Z and Ning, D and Shen, J}, title = {Anthropogenic activities altering the ecosystem in Lake Yamzhog Yumco, southern Qinghai-Tibetan Plateau.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166715}, doi = {10.1016/j.scitotenv.2023.166715}, pmid = {37666338}, issn = {1879-1026}, mesh = {Humans ; *Ecosystem ; Tibet ; *Lakes ; Anthropogenic Effects ; Eutrophication ; China ; }, abstract = {Lakes on the Qinghai-Tibet Plateau (QTP) have been subject to multiple environmental pressures from rapid climate change and intensified human activity in recent decades. However, their ecological effects on the lake ecosystem remain largely unclear due to the lack of long-term monitoring data. This study presented the environmental and ecological changes of the lake Yamzhog Yumco (Southern QTP) over the past three decades based on multi-proxy analysis (geochemistry and sedaDNA) on a high-time resolution sediment core. The result showed that the lake exhibited a continuous eutrophication process from 2004 CE, which has accelerated since 2014 CE. The nutrient enrichment was mainly attributed to anthropogenic emissions from the catchment. The sedimentary ancient DNA (sedaDNA) metabarcoding data registered a sensitive response of aquatic communities to the additional nutrient supply. Eukaryotic algae and aquatic invertebrate communities exhibited similar temporal dynamics, characterized by the increase in eutrophic taxa and the decrease in oligotrophic taxa. Change points analysis suggested that lake ecosystems underwent a slight ecological shift in 2003 CE and an abrupt shift in 2012 CE driven by nutrient enrichment. Quantitative analysis revealed that nutrients and human activity accounted for 27.9 % and 21.7 % of the temporal variation in aquatic communities, whereas climate change only explained 6.9 % of the total variation. From a paleolimnological view, our study supported that regional human activity could distinctly alter the nutrient level and aquatic community structure of lake ecosystems in the QTP. Considering that anthropogenic disturbance will continuously increase, it is crucial to strengthen the field monitoring of the lakes on the plateau and make effective management measures to avoid irreversible ecological consequences.}, }
@article {pmid37652999, year = {2023}, author = {Sun, X and Liu, YC and Tiunov, MP and Gimranov, DO and Zhuang, Y and Han, Y and Driscoll, CA and Pang, Y and Li, C and Pan, Y and Velasco, MS and Gopalakrishnan, S and Yang, RZ and Li, BG and Jin, K and Xu, X and Uphyrkina, O and Huang, Y and Wu, XH and Gilbert, MTP and O'Brien, SJ and Yamaguchi, N and Luo, SJ}, title = {Ancient DNA reveals genetic admixture in China during tiger evolution.}, journal = {Nature ecology &amp; evolution}, volume = {7}, number = {11}, pages = {1914-1929}, pmid = {37652999}, issn = {2397-334X}, support = {NSFC32070598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18-04-00327//Russian Foundation for Basic Research (RFBR)/ ; }, mesh = {Animals ; *Tigers/genetics ; DNA, Ancient ; Phylogeny ; Russia ; China ; }, abstract = {The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.}, }
@article {pmid37652634, year = {2023}, author = {Beltrame, MO and Moviglia, GS and De Tommaso, D and Quintana, S}, title = {Gastrointestinal parasites of domestic sheep from Patagonia throughout historical times: A paleoparasitological approach.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {44}, number = {}, pages = {100915}, doi = {10.1016/j.vprsr.2023.100915}, pmid = {37652634}, issn = {2405-9390}, mesh = {Animals ; Sheep ; *Parasites ; Sheep, Domestic ; *Intestinal Diseases, Parasitic/veterinary ; *Fascioliasis/veterinary ; Argentina/epidemiology ; *Eimeria ; *Nematodirus ; *Sheep Diseases ; }, abstract = {Sheep husbandry in Patagonia, Argentina, started at the beginning of the 20th century from European settlers. Sanitary management is minimal, which has serious implications for the sheep health. Sheep can be infested by diverse parasites, with well over 150 species of internal and external parasites reported worldwide. Gastrointestinal parasitism is one of the most common and important infections in sheep concerning the health status, and is the cause of significant morbidity and mortality, which generates considerable production losses. The present work is the first paleoparasitological study of sheep coprolites from Patagonia throughout historical times. Fifty-seven coprolites from the 'Cueva Peligro' archaeological site (Patagonia, Argentina) were analyzed using the Lutz spontaneous sedimentation technique and the modified Faust flotation technique. Ancient DNA (aDNA) study was carried out in order to identify the zoological origin of coprolites. The results obtained from Cytb analysis confirmed the identity of the host as Ovis aries (domestic sheep). A total of 39 coprolites examined were positive for parasites by at least one of the studied methods. Thirty eight samples were positive by spontaneous sedimentation and 10 samples were positive by the modified Faust technique. The parasitic fauna found was Trichuris sp. (Trichinellida: Trichuridae), Nematodirus sp., Nematodirus spathiger (Strongylida, Trichostrongyloidea), two unidentified Strongylida-type egg morphotypes, Fasciola hepatica (Trematoda: Digenea) and coccidia oocysts of Eimeria spp. (Apicomplexa: Eimeriidae). The modified Faust technique provided satisfactory results in terms of sensitivity for the detection of Eimeria spp. The use of this methodology as a routine procedure enables the processing of ancient samples, in order to increase recoveries. These results show the importance of integrating different diagnostic approaches in order to optimize parasitic findings. The recorded parasite diversity appears to have not changed over the last 120 years. The study displayed the presence of different parasitic species which suggests potential exposure to parasitic diseases through the historical times, both for sheep and for other domestic and wild mammals from Patagonia. Also, suggests the presence of fasciolosis, a zoonotic disease that implies a potential risk for Patagonian populations in the past.}, }
@article {pmid37644833, year = {2023}, author = {Aoki, K and Takahata, N and Oota, H and Wakano, JY and Feldman, MW}, title = {Infectious diseases may have arrested the southward advance of microblades in Upper Palaeolithic East Asia.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2005}, pages = {20231262}, pmid = {37644833}, issn = {1471-2954}, mesh = {Humans ; *Archaeology ; Asia, Eastern ; *Communicable Diseases ; DNA, Ancient ; East Asian People ; }, abstract = {An unsolved archaeological puzzle of the East Asian Upper Palaeolithic is why the southward expansion of an innovative lithic technology represented by microblades stalled at the Qinling-Huaihe Line. It has been suggested that the southward migration of foragers with microblades stopped there, which is consistent with ancient DNA studies showing that populations to the north and south of this line had differentiated genetically by 19 000 years ago. Many infectious pathogens are believed to have been associated with hominins since the Palaeolithic, and zoonotic pathogens in particular are prevalent at lower latitudes, which may have produced a disease barrier. We propose a mathematical model to argue that mortality due to infectious diseases may have arrested the wave-of-advance of the technologically advantaged foragers from the north.}, }
@article {pmid37633281, year = {2023}, author = {Vyas, DN and Koncz, I and Modi, A and Mende, BG and Tian, Y and Francalacci, P and Lari, M and Vai, S and Straub, P and Gallina, Z and Szeniczey, T and Hajdu, T and Pejrani Baricco, L and Giostra, C and Radzevičiūtė, R and Hofmanová, Z and Évinger, S and Bernert, Z and Pohl, W and Caramelli, D and Vida, T and Geary, PJ and Veeramah, KR}, title = {Fine-scale sampling uncovers the complexity of migrations in 5th-6th century Pannonia.}, journal = {Current biology : CB}, volume = {33}, number = {18}, pages = {3951-3961.e11}, doi = {10.1016/j.cub.2023.07.063}, pmid = {37633281}, issn = {1879-0445}, mesh = {Humans ; Female ; *Archaeology ; *Cemeteries/history ; Culture ; Base Sequence ; Europe ; }, abstract = {As the collapse of the Western Roman Empire accelerated during the 4th and 5th centuries, arriving "barbarian" groups began to establish new communities in the border provinces of the declining (and eventually former) empire. This was a time of significant cultural and political change throughout not only these border regions but Europe as a whole.[1][,][2] To better understand post-Roman community formation in one of these key frontier zones after the collapse of the Hunnic movement, we generated new paleogenomic data for a set of 38 burials from a time series of three 5[th] century cemeteries[3][,][4][,][5] at Lake Balaton, Hungary. We utilized a comprehensive sampling approach to characterize these cemeteries along with data from 38 additional burials from a previously published mid-6th century site[6] and analyzed them alongside data from over 550 penecontemporaneous individuals.[7][,][8][,][9][,][10][,][11][,][12][,][13][,][14][,][15][,][16][,][17][,][18][,][19] The range of genetic diversity in all four of these local burial communities is extensive and wider ranging than penecontemporaneous Europeans sequenced to date. Despite many commonalities in burial customs and demography, we find that there were substantial differences in genetic ancestry between the sites. We detect evidence of northern European gene flow into the Lake Balaton region. Additionally, we observe a statistically significant association between dress artifacts and genetic ancestry among 5[th] century genetically female burials. Our analysis shows that the formation of early Medieval communities was a multifarious process even at a local level, consisting of genetically heterogeneous groups.}, }
@article {pmid37631973, year = {2023}, author = {Burk, RD and Mirabello, L and DeSalle, R}, title = {Distinguishing Genetic Drift from Selection in Papillomavirus Evolution.}, journal = {Viruses}, volume = {15}, number = {8}, pages = {}, pmid = {37631973}, issn = {1999-4915}, support = {P30 CA013330/CA/NCI NIH HHS/United States ; U01 CA238592/CA/NCI NIH HHS/United States ; U01 CA078527/CA/NCI NIH HHS/United States ; P30 AI124414/AI/NIAID NIH HHS/United States ; }, mesh = {Phylogeny ; *Papillomaviridae/genetics ; *Alphapapillomavirus ; Genetic Drift ; Codon Usage ; }, abstract = {Pervasive purifying selection on non-synonymous substitutions is a hallmark of papillomavirus genome history, but the role of selection on and the drift of non-coding DNA motifs on HPV diversification is poorly understood. In this study, more than a thousand complete genomes representing Alphapapillomavirus types, lineages, and SNP variants were examined phylogenetically and interrogated for the number and position of non-coding DNA sequence motifs using Principal Components Analyses, Ancestral State Reconstructions, and Phylogenetic Independent Contrasts. For anciently diverged Alphapapillomavirus types, composition of the four nucleotides (A, C, G, T), codon usage, trimer usage, and 13 established non-coding DNA sequence motifs revealed phylogenetic clusters consistent with genetic drift. Ancestral state reconstruction and Phylogenetic Independent Contrasts revealed ancient genome alterations, particularly for the CpG and APOBEC3 motifs. Each evolutionary analytical method we performed supports the unanticipated conclusion that genetic drift and different evolutionary drivers have structured Alphapapillomavirus genomes in distinct ways during successive epochs, even extending to differences in more recently formed variant lineages.}, }
@article {pmid37628575, year = {2023}, author = {Kusliy, MA and Yurlova, AA and Neumestova, AI and Vorobieva, NV and Gutorova, NV and Molodtseva, AS and Trifonov, VA and Popova, KO and Polosmak, NV and Molodin, VI and Vasiliev, SK and Semibratov, VP and Iderkhangai, TO and Kovalev, AA and Erdenebaatar, D and Graphodatsky, AS and Tishkin, AA}, title = {Genetic History of the Altai Breed Horses: From Ancient Times to Modernity.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628575}, issn = {2073-4425}, mesh = {Animals ; Horses/genetics ; Phylogeny ; *Hybridization, Genetic ; *DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Haplotypes/genetics ; }, abstract = {This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.}, }
@article {pmid37611212, year = {2023}, author = {van Waaij, J and Li, S and Garcia-Erill, G and Albrechtsen, A and Wiuf, C}, title = {Evaluation of population structure inferred by principal component analysis or the admixture model.}, journal = {Genetics}, volume = {225}, number = {2}, pages = {}, doi = {10.1093/genetics/iyad157}, pmid = {37611212}, issn = {1943-2631}, support = {8021-00360B//Independent Research Fund Denmark/ ; //China Scholarship Council/ ; }, abstract = {Principal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed that individuals belong to one of several possible populations or are admixed between these populations. We propose a new method to assess the statistical fit of PCA (interpreted as a model spanned by the top principal components) and to show that violations of the PCA assumptions affect the fit. Our method uses the chosen top principal components to predict the genotypes. By assessing the covariance (and the correlation) of the residuals (the differences between observed and predicted genotypes), we are able to detect violation of the model assumptions. Based on simulations and genome-wide human data, we show that our assessment of fit can be used to guide the interpretation of the data and to pinpoint individuals that are not well represented by the chosen principal components. Our method works equally on other similar models, such as the admixture model, where the mean of the data is represented by linear matrix decomposition.}, }
@article {pmid37608001, year = {2023}, author = {Arbøll, TP and Rasmussen, SL and de Jonge, N and Hansen, AH and Pertoldi, C and Nielsen, JL}, title = {Revealing the secrets of a 2900-year-old clay brick, discovering a time capsule of ancient DNA.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13092}, pmid = {37608001}, issn = {2045-2322}, mesh = {*Clay/chemistry ; *Construction Materials/history ; *DNA, Ancient/analysis/isolation &amp; purification ; History, Ancient ; Iraq ; Museums ; *Plants/classification/genetics ; Time Factors ; Archaeology/methods ; }, abstract = {The recent development of techniques to sequence ancient DNA has provided valuable insights into the civilisations that came before us. However, the full potential of these methods has yet to be realised. We extracted ancient DNA from a recently exposed fracture surface of a clay brick deriving from the palace of king Ashurnasirpal II (883-859 BCE) in Nimrud, Iraq. We detected 34 unique taxonomic groups of plants. With this research we have made the pioneering discovery that ancient DNA, effectively protected from contamination inside a mass of clay, can successfully be extracted from a 2900-year-old clay brick. We encourage future research into this subject, as the scientific prospects for this approach are substantial, potentially leading to a deeper understanding of ancient and lost civilisations.}, }
@article {pmid37604894, year = {2023}, author = {Utzeri, VJ and Cilli, E and Fontani, F and Zoboli, D and Orsini, M and Ribani, A and Latorre, A and Lissovsky, AA and Pillola, GL and Bovo, S and Gruppioni, G and Luiselli, D and Fontanesi, L}, title = {Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13635}, pmid = {37604894}, issn = {2045-2322}, mesh = {Animals ; *DNA, Ancient ; Phylogeny ; *Lagomorpha ; Biological Evolution ; Archaeology ; }, abstract = {Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.}, }
@article {pmid37589132, year = {2023}, author = {Essel, E}, title = {Releasing secrets bound to ancient remains with modern DNA extraction techniques: an interview with Elena Essel.}, journal = {BioTechniques}, volume = {75}, number = {2}, pages = {42-46}, doi = {10.2144/btn-2023-0067}, pmid = {37589132}, issn = {1940-9818}, mesh = {Humans ; Female ; *DNA, Ancient ; *Anthropology ; Body Remains ; Sequence Analysis, DNA ; Universities ; }, abstract = {Elena Essel (Msc) spoke to Ebony Torrington, Managing Editor of BioTechniques. Essel is a molecular biologist in Matthias Meyer's Advanced DNA Sequencing Techniques group at the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany). Essel studied biology at University of Erlangen-Nuremberg (Erlangen, Germany) for her bachelor's and in Martin-Luther-University Halle-Wittenberg (Halle an der Saale, Germany) for her master's. Essel worked in Meyer's group on DNA extraction of very degraded material for her master's thesis. Meyer is an expert in developing new cutting-edge methods for researching ancient DNA, with a focus on skeletal remains, and more recently on sediment remains. Essel now focusses on DNA sampling and extraction aspects of the pipeline at Meyer's lab for the ancient DNA workflow.}, }
@article {pmid37584528, year = {2023}, author = {Kambouris, ME and Patrinos, GP and Velegraki, A and Manoussopoulos, Y}, title = {Historical microbiology: researching past bioevents by integrating scholarship (re)sources with paleomicrobiology assets.}, journal = {Future microbiology}, volume = {18}, number = {}, pages = {681-693}, doi = {10.2217/fmb-2023-0031}, pmid = {37584528}, issn = {1746-0921}, mesh = {Humans ; *Paleopathology/methods ; *Fellowships and Scholarships ; Pandemics ; }, abstract = {The analysis of past epidemics and pandemics, either spontaneous or of human origin, may revise the physical history of microbiota and create a temporal context in our understanding regarding pathogen attributes like virulence, evolution, transmission and disease dynamics. The data of high-tech scientific methods seem reliable, but their interpretation may still be biased when tackling events of the distant past. Such endeavors should be adjusted to other cognitive resources including historical accounts reporting the events of interest and references in alien medical cultures and terminologies; the latter may contextualize them differently from current practices. Thus 'historical microbiology' emerges. Validating such resources requires utmost care, as these may be susceptible to different biases regarding the interpretation of facts and phenomena; biases partly due to methodological limitations.}, }
@article {pmid37582830, year = {2023}, author = {Serrano, JG and Ordóñez, AC and Santana, J and Sánchez-Cañadillas, E and Arnay, M and Rodríguez-Rodríguez, A and Morales, J and Velasco-Vázquez, J and Alberto-Barroso, V and Delgado-Darias, T and de Mercadal, MCC and Hernández, JC and Moreno-Benítez, MA and Pais, J and Ringbauer, H and Sikora, M and McColl, H and Pino-Yanes, M and Ferrer, MH and Bustamante, CD and Fregel, R}, title = {The genomic history of the indigenous people of the Canary Islands.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4641}, pmid = {37582830}, issn = {2041-1723}, mesh = {Humans ; Spain ; *Genetic Drift ; Africa, Northern ; *Genomics ; Indigenous Peoples ; Islands ; Genetic Variation ; Genetics, Population ; }, abstract = {The indigenous population of the Canary Islands, which colonized the archipelago around the 3[rd] century CE, provides both a window into the past of North Africa and a unique model to explore the effects of insularity. We generate genome-wide data from 40 individuals from the seven islands, dated between the 3[rd]-16[rd] centuries CE. Along with components already present in Moroccan Neolithic populations, the Canarian natives show signatures related to Bronze Age expansions in Eurasia and trans-Saharan migrations. The lack of gene flow between islands and constant or decreasing effective population sizes suggest that populations were isolated. While some island populations maintained relatively high genetic diversity, with the only detected bottleneck coinciding with the colonization time, other islands with fewer natural resources show the effects of insularity and isolation. Finally, consistent genetic differentiation between eastern and western islands points to a more complex colonization process than previously thought.}, }
@article {pmid37580949, year = {2024}, author = {Bretschneider, A and Mazanec, J and Wittmeier, P and Flux, AL and Schmidt, D and Hummel, S}, title = {X-chromosomal STRs in aDNA kinship analysis.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {81}, number = {2}, pages = {131-138}, doi = {10.1127/anthranz/2023/1714}, pmid = {37580949}, issn = {0003-5548}, mesh = {Humans ; *DNA, Ancient ; Haplotypes/genetics ; *DNA, Mitochondrial/genetics ; Germany ; Body Remains ; Microsatellite Repeats/genetics ; Chromosomes, Human, Y/genetics ; }, abstract = {The analysis of ancient DNA (aDNA) from human skeletal remains can provide useful insights when investigating archaeological finds. One popular application of aDNA is to examine genealogical relationships between individuals recovered at the same archaeological site. For the reconstruction of genealogical relationships, several genetic markers are commonly used: autosomal STRs, mitochondrial lineages (based on SNP-analysis) and Y-chromosomal haplotypes (based on Y-STR-analysis). In this paper, we present the additional opportunities that X-STRs provide in aDNA kinship reconstruction, especially in deficiency cases and for the examination of father-daughter relationships. Possible applications are demonstrated on a range of different kinship reconstructions: confirmation of half-siblingship in the Lichtenstein cave (Germany), exclusion of two potential father-daughter relationships in Goslar (Germany), investigation of three siblingships in Boilstädt (Germany) as well as the confirmation of a father-daughter relationship in Stolpe (Germany). This study shows that the analysis of X-STRs can contribute to the investigation of relationship constellations otherwise difficult to approach (e.g. father-daughter relationships) and that X-STRs are useful to support and complement autosomal STRs, mtDNA and Y-STR data.}, }
@article {pmid37567955, year = {2023}, author = {Kim, J and Rosenberg, NA}, title = {Record-matching of STR profiles with fragmentary genomic SNP data.}, journal = {European journal of human genetics : EJHG}, volume = {31}, number = {11}, pages = {1283-1290}, pmid = {37567955}, issn = {1476-5438}, support = {R01 HG005855/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *DNA Fingerprinting/methods ; Microsatellite Repeats ; Genotype ; Genomics ; DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {In many forensic settings, identity of a DNA sample is sought from poor-quality DNA, for which the typical STR loci tabulated in forensic databases are not possible to reliably genotype. Genome-wide SNPs, however, can potentially be genotyped from such samples via next-generation sequencing, so that queries can in principle compare SNP genotypes from DNA samples of interest to STR genotype profiles that represent proposed matches. We use genetic record-matching to evaluate the possibility of testing SNP profiles obtained from poor-quality DNA samples to identify exact and relatedness matches to STR profiles. Using simulations based on whole-genome sequences, we show that in some settings, similar match accuracies to those seen with full coverage of the genome are obtained by genetic record-matching for SNP data that represent 5-10% genomic coverage. Thus, if even a fraction of random genomic SNPs can be genotyped by next-generation sequencing, then the potential may exist to test the resulting genotype profiles for matches to profiles consisting exclusively of nonoverlapping STR loci. The result has implications in relation to criminal justice, mass disasters, missing-person cases, studies of ancient DNA, and genomic privacy.}, }
@article {pmid37562011, year = {2023}, author = {Gerber, D and Szeifert, B and Székely, O and Egyed, B and Gyuris, B and Giblin, JI and Horváth, A and Köhler, K and Kulcsár, G and Kustár, &#xc1; and Major, I and Molnár, M and Palcsu, L and Szeverényi, V and Fábián, S and Mende, BG and Bondár, M and Ari, E and Kiss, V and Szécsényi-Nagy, A}, title = {Interdisciplinary Analyses of Bronze Age Communities from Western Hungary Reveal Complex Population Histories.}, journal = {Molecular biology and evolution}, volume = {40}, number = {9}, pages = {}, pmid = {37562011}, issn = {1537-1719}, mesh = {Humans ; History, Ancient ; Hungary ; *Human Migration ; *Genome, Human ; Europe ; DNA, Ancient ; }, abstract = {In this study, we report 21 ancient shotgun genomes from present-day Western Hungary, from previously understudied Late Copper Age Baden, and Bronze Age Somogyvár-Vinkovci, Kisapostag, and Encrusted Pottery archeological cultures (3,530-1,620 cal Bce). Our results indicate the presence of high steppe ancestry in the Somogyvár-Vinkovci culture. They were then replaced by the Kisapostag group, who exhibit an outstandingly high (up to ∼47%) Mesolithic hunter-gatherer ancestry, despite this component being thought to be highly diluted by the time of the Early Bronze Age. The Kisapostag population contributed the genetic basis for the succeeding community of the Encrusted Pottery culture. We also found an elevated hunter-gatherer component in a local Baden culture-associated individual, but no connections were proven to the Bronze Age individuals. The hunter-gatherer ancestry in Kisapostag is likely derived from two main sources, one from a Funnelbeaker or Globular Amphora culture-related population and one from a previously unrecognized source in Eastern Europe. We show that this ancestry not only appeared in various groups in Bronze Age Central Europe but also made contributions to Baltic populations. The social structure of Kisapostag and Encrusted Pottery cultures is patrilocal, similarly to most contemporaneous groups. Furthermore, we developed new methods and method standards for computational analyses of ancient DNA, implemented to our newly developed and freely available bioinformatic package. By analyzing clinical traits, we found carriers of aneuploidy and inheritable genetic diseases. Finally, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin.}, }
@article {pmid37561011, year = {2023}, author = {Sánchez-Barreiro, F and De Cahsan, B and Westbury, MV and Sun, X and Margaryan, A and Fontsere, C and Bruford, MW and Russo, IM and Kalthoff, DC and Sicheritz-Pontén, T and Petersen, B and Dalén, L and Zhang, G and Marquès-Bonet, T and Gilbert, MTP and Moodley, Y}, title = {Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros.}, journal = {Molecular biology and evolution}, volume = {40}, number = {9}, pages = {}, pmid = {37561011}, issn = {1537-1719}, support = {R01 HG010898/HG/NHGRI NIH HHS/United States ; 681396/ERC_/European Research Council/International ; }, mesh = {Animals ; Africa, Eastern ; Africa South of the Sahara ; *Biological Evolution ; *Perissodactyla/genetics ; Endangered Species ; }, abstract = {The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.}, }
@article {pmid37559969, year = {2023}, author = {Ozga, AT and Ottoni, C}, title = {Dental calculus as a proxy for animal microbiomes.}, journal = {Quaternary international : the journal of the International Union for Quaternary Research}, volume = {653-654}, number = {}, pages = {47-52}, pmid = {37559969}, issn = {1040-6182}, abstract = {The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze all previously available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.}, }
@article {pmid37548135, year = {2023}, author = {Arencibia, V and Muñoz, M and Crespo, CM and Russo, MG and Vera, P and Lia, VV and García Guraieb, S and Goñi, RA and Avena, S and Puebla, A and Dejean, CB}, title = {Novel B2 mitogenomes from Continental southern Patagonia's Late Holocene: New insights into the peopling of the Southern Cone.}, journal = {American journal of biological anthropology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ajpa.24822}, pmid = {37548135}, issn = {2692-7691}, support = {PICT 2014-3012//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; //Fundaci&#xf3;n Cient&#xed;fica Felipe Fiorellino/ ; //Fundaci&#xf3;n de Historia Natural F&#xe9;lix Azara/ ; UBACyT 20020150200233BA//Universidad de Buenos Aires/ ; UBACyT 20020170200363BA//Universidad de Buenos Aires/ ; //CONICET/ ; }, abstract = {OBJECTIVES: The main aim of this study is to discuss the migratory processes and peopling dynamics that shaped the genetic variability of populations during the settlement of the Southern Cone, through the analysis of complete mitogenomes of individuals from southern Patagonia.<br><br>MATERIALS AND METHODS: Complete mitogenomes were sequenced through massively parallel sequencing from two late Holocene individuals (SAC 1-1-3 and SAC 1-1-4) buried in the same chenque at Salitroso Lake Basin (Santa Cruz province, Argentina). To evaluate matrilineal phylogenetic affinities with other haplotypes, maximum likelihood and Bayesian phylogenetic reconstructions were performed, as well as a haplotype median-joining network.<br><br>RESULTS: The mitogenomes were assigned to haplogroups B2 and B2b, exhibiting an average depth of 54X and 89X (&#x2265;1X coverage of 98.6% and 100%), and a high number of nucleotide differences among them. The phylogenetic analyses showed a relatively close relationship between the haplotype found in SAC 1-1-4 and those retrieved from a Middle Holocene individual from Laguna Chica (Buenos Aires province), and from a group of individuals from the Peruvian coast. For the SAC 1-1-3, no clear affiliations to any other haplotype were established.<br><br>DISCUSSION: The large divergence between the haplotypes presented in this study suggests either a highly variable founder gene pool, or a later enrichment by frequent biological contact with other populations. Our results underline the persistence of genetic signals related to the first waves of peopling in South America, suggesting that the regional settlement of the southern end of the continent has been much more complex than initially thought.}, }
@article {pmid37541241, year = {2023}, author = {Harney, &#xc9; and Sirak, K and Sedig, J and Micheletti, S and Curry, R and Ancona Esselmann, S and Reich, D}, title = {Ethical considerations when co-analyzing ancient DNA and data from private genetic databases.}, journal = {American journal of human genetics}, volume = {110}, number = {9}, pages = {1447-1453}, pmid = {37541241}, issn = {1537-6605}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; Reproducibility of Results ; *Communication ; DNA/genetics ; Databases, Genetic ; }, abstract = {Ancient DNA studies have begun to explore the possibility of identifying identical DNA segments shared between historical and living people. This research requires access to large genetic datasets to maximize the likelihood of identifying previously unknown, close genetic connections. Direct-to-consumer genetic testing companies, such as 23andMe, Inc., manage by far the largest and most diverse genetic databases that can be used for this purpose. It is therefore important to think carefully about guidelines for carrying out collaborations between researchers and such companies. Such collaborations require consideration of ethical issues, including policies for sharing ancient DNA datasets, and ensuring reproducibility of research findings when access to privately controlled genetic datasets is limited. At the same time, they introduce unique possibilities for returning results to the research participants whose data are analyzed, including those who are identified as close genetic relatives of historical individuals, thereby enabling ancient DNA research to contribute to the restoration of information about ancestral connections that were lost over time, which can be particularly meaningful for families and groups where such history has not been well documented. We explore these issues by describing our experience designing and carrying out a study searching for genetic connections between 18th- and 19th-century enslaved and free African Americans who labored at Catoctin Furnace, Maryland, and 23andMe research participants. We share our experience in the hope of helping future researchers navigate similar ethical considerations, recognizing that our perspective is part of a larger conversation about best ethical practices.}, }
@article {pmid37537290, year = {2023}, author = {Callaway, E}, title = {Ancient DNA reveals the living descendants of enslaved people through 23andMe.}, journal = {Nature}, volume = {620}, number = {7973}, pages = {251-252}, pmid = {37537290}, issn = {1476-4687}, mesh = {Humans ; *Black People/genetics/history ; *DNA, Ancient/analysis ; *Enslaved Persons/history ; *Genetic Testing ; *Genetics, Population ; Genome, Human ; *Genomics ; History, 18th Century ; History, 19th Century ; Mass Screening ; }, }
@article {pmid37535713, year = {2023}, author = {Jackson, FLC}, title = {Community-initiated genomics.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6657}, pages = {482-483}, doi = {10.1126/science.adj2380}, pmid = {37535713}, issn = {1095-9203}, mesh = {Humans ; *Black or African American/genetics ; *DNA, Ancient ; Metagenomics ; *Enslavement/history ; }, abstract = {Ancient DNA is used to connect enslaved African Americans to modern descendants.}, }
@article {pmid37531864, year = {2023}, author = {Klever, AM and Alexander, KA and Almeida, D and Anderson, MZ and Ball, RL and Beamer, G and Boggiatto, P and Buikstra, JE and Chandler, B and Claeys, TA and Concha, AE and Converse, PJ and Derbyshire, KM and Dobos, KM and Dupnik, KM and Endsley, JJ and Endsley, MA and Fennelly, K and Franco-Paredes, C and Hagge, DA and Hall-Stoodley, L and Hayes, D and Hirschfeld, K and Hofman, CA and Honda, JR and Hull, NM and Kramnik, I and Lacourciere, K and Lahiri, R and Lamont, EA and Larsen, MH and Lemaire, T and Lesellier, S and Lee, NR and Lowry, CA and Mahfooz, NS and McMichael, TM and Merling, MR and Miller, MA and Nagajyothi, JF and Nelson, E and Nuermberger, EL and Pena, MT and Perea, C and Podell, BK and Pyle, CJ and Quinn, FD and Rajaram, MVS and Mejia, OR and Rothoff, M and Sago, SA and Salvador, LCM and Simonson, AW and Spencer, JS and Sreevatsan, S and Subbian, S and Sunstrum, J and Tobin, DM and Vijayan, KKV and Wright, CTO and Robinson, RT}, title = {The Many Hosts of Mycobacteria 9 (MHM9): A conference report.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {142}, number = {}, pages = {102377}, pmid = {37531864}, issn = {1873-281X}, support = {R01 AI166304/AI/NIAID NIH HHS/United States ; R01 AI130236/AI/NIAID NIH HHS/United States ; K23 AI131913/AI/NIAID NIH HHS/United States ; R13 AI169929/AI/NIAID NIH HHS/United States ; R01 AI150765/AI/NIAID NIH HHS/United States ; R01 HL126066/HL/NHLBI NIH HHS/United States ; R01 AI125517/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Humans ; *Coinfection ; *Mycobacterium Infections, Nontuberculous/microbiology ; *Mycobacterium tuberculosis ; Nontuberculous Mycobacteria ; *Tuberculosis, Bovine ; }, abstract = {The Many Hosts of Mycobacteria (MHM) meeting series brings together basic scientists, clinicians and veterinarians to promote robust discussion and dissemination of recent advances in our knowledge of numerous mycobacterial diseases, including human and bovine tuberculosis (TB), nontuberculous mycobacteria (NTM) infection, Hansen's disease (leprosy), Buruli ulcer and Johne's disease. The 9th MHM conference (MHM9) was held in July 2022 at The Ohio State University (OSU) and centered around the theme of "Confounders of Mycobacterial Disease." Confounders can and often do drive the transmission of mycobacterial diseases, as well as impact surveillance and treatment outcomes. Various confounders were presented and discussed at MHM9 including those that originate from the host (comorbidities and coinfections) as well as those arising from the environment (e.g., zoonotic exposures), economic inequality (e.g. healthcare disparities), stigma (a confounder of leprosy and TB for millennia), and historical neglect (a confounder in Native American Nations). This conference report summarizes select talks given at MHM9 highlighting recent research advances, as well as talks regarding the historic and ongoing impact of TB and other infectious diseases on Native American Nations, including those in Southwestern Alaska where the regional TB incidence rate is among the highest in the Western hemisphere.}, }
@article {pmid37529780, year = {2023}, author = {Zhao, C and Han, B and Yi, G and Jin, S and Zhang, Z and Li, S}, title = {Editorial: Epigenomics implication for economic traits in domestic animals.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1252640}, doi = {10.3389/fgene.2023.1252640}, pmid = {37529780}, issn = {1664-8021}, }
@article {pmid37528780, year = {2023}, author = {Fesenko, DO and Aramova, OY and Vdovchenkov, EV and Ivanovsky, ID and Fesenko, OE and Polyakov, SA and Faleeva, TG and Filippova, MA and Florinskaya, VS and Kornienko, IV}, title = {[DNA Phenotyping of Remains from Elite Burials of the Khazar Period of Southern Russia].}, journal = {Molekuliarnaia biologiia}, volume = {57}, number = {4}, pages = {597-608}, pmid = {37528780}, issn = {0026-8984}, mesh = {Humans ; *Eye Color ; DNA/genetics ; Burial ; Russia ; *Blood Group Antigens ; }, abstract = {Ancient DNA analyses help to solve the problems related to the genogeographic origin and migration patterns of populations. The Khazar Khaganate is a subject of controversy among researchers. Its complex historical development, lack of a sufficient number of artistic and written sources, the disappearance of representatives of Khazar culture leaves open the question of the appearance of the Khazars. DNA phenotyping of bone remains from elite burials of the Khazar period of Southern Russia was carried out with respect to eye color, hair color, skin color, and AB0 blood groups. Eight out of 10 individuals had brown eyes, dark hair (to varying degrees), and a predominantly dark skin during their lifetime. Individuals from two burials had gray-blue eyes, and one individual had blond hair. The most probable AB0 blood group was identified in eight people, of which five blood group 0 (I) group, four had blood group A (II), and one had blood group B (III). The allele frequency distribution was assessed for ten population-specific autosomal markers and suggested high heterogeneity for the ethnogeographic origin of the Khazars examined. The results are evidence for ethnocultural, genetic, and phenotypic diversity of the Khazar Khaganate.}, }
@article {pmid37528222, year = {2023}, author = {Delsol, N and Stucky, BJ and Oswald, JA and Cobb, CR and Emery, KF and Guralnick, R}, title = {Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12444}, pmid = {37528222}, issn = {2045-2322}, mesh = {Humans ; Animals ; Cattle/genetics ; *DNA, Ancient ; Phylogeny ; Americas ; Europe ; Caribbean Region ; *DNA, Mitochondrial/genetics ; Haplotypes ; }, abstract = {Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries.}, }
@article {pmid37525572, year = {2023}, author = {Tamburrini, C and Dahinten, SL and Saihueque, RRR and Ávila-Arcos, MC and Parolin, ML}, title = {Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia.}, journal = {American journal of biological anthropology}, volume = {182}, number = {2}, pages = {161-176}, doi = {10.1002/ajpa.24821}, pmid = {37525572}, issn = {2692-7691}, mesh = {Humans ; *Genomics ; Argentina ; }, abstract = {Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective.}, }
@article {pmid37510218, year = {2023}, author = {Zhang, N and Shao, X and Guo, Y and Zhang, X and Zhou, Y and Yuan, J and Tang, Z and Hu, S and Minyaev, SS and Cai, D}, title = {Ancient Mitochondrial Genomes Provide New Clues to the Origin of Domestic Cattle in China.}, journal = {Genes}, volume = {14}, number = {7}, pages = {}, pmid = {37510218}, issn = {2073-4425}, mesh = {Animals ; Cattle/genetics ; *Genome, Mitochondrial ; Phylogeny ; Genetic Variation ; DNA, Ancient ; DNA, Mitochondrial/genetics ; China ; }, abstract = {Cattle are one of the six livestock species that have occupied an important place in Chinese history. Previous ancient DNA studies have indicated that Chinese taurine cattle (Bos taurus taurus) are exotic, but the exact route and diffusion by which they were introduced to China is unknown. In this study, we extracted the mitochondrial genomes of 34 cases of ancient taurine cattle (from the late Neolithic to Qin and Han dynasties) excavated from sites in northern China and the eastern Eurasian steppe, and successfully obtained 14 mitochondrial genome sequences. The results of ancient DNA analysis reveal that with cultural exchange and trade, there was close genetic exchange between domestic taurine cattle in different regions. The haplotypes shared by domestic cattle have genetic continuity, reflecting the strong cultural influence of the large capital city sites such as Taosi, Shimao and Erlitou on the surrounding areas. This study suggests that ancient northern Chinese taurine cattle may have accompanied the westward transmission of agricultural or painted pottery culture and thus had a maternal genetic contribution to modern Tibetan cattle.}, }
@article {pmid37503227, year = {2024}, author = {Simon, A and Coop, G}, title = {The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37503227}, issn = {2692-8205}, support = {R35 GM136290/GM/NIGMS NIH HHS/United States ; }, abstract = {Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.}, }
@article {pmid37499002, year = {2023}, author = {Heggarty, P and Anderson, C and Scarborough, M and King, B and Bouckaert, R and Jocz, L and Kümmel, MJ and Jügel, T and Irslinger, B and Pooth, R and Liljegren, H and Strand, RF and Haig, G and Macák, M and Kim, RI and Anonby, E and Pronk, T and Belyaev, O and Dewey-Findell, TK and Boutilier, M and Freiberg, C and Tegethoff, R and Serangeli, M and Liosis, N and Stroński, K and Schulte, K and Gupta, GK and Haak, W and Krause, J and Atkinson, QD and Greenhill, SJ and Kühnert, D and Gray, RD}, title = {Language trees with sampled ancestors support a hybrid model for the origin of Indo-European languages.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6656}, pages = {eabg0818}, doi = {10.1126/science.abg0818}, pmid = {37499002}, issn = {1095-9203}, mesh = {Bayes Theorem ; Europe ; Farms ; *Language/history ; Phylogeny ; }, abstract = {The origins of the Indo-European language family are hotly disputed. Bayesian phylogenetic analyses of core vocabulary have produced conflicting results, with some supporting a farming expansion out of Anatolia ~9000 years before present (yr B.P.), while others support a spread with horse-based pastoralism out of the Pontic-Caspian Steppe ~6000 yr B.P. Here we present an extensive database of Indo-European core vocabulary that eliminates past inconsistencies in cognate coding. Ancestry-enabled phylogenetic analysis of this dataset indicates that few ancient languages are direct ancestors of modern clades and produces a root age of ~8120 yr B.P. for the family. Although this date is not consistent with the Steppe hypothesis, it does not rule out an initial homeland south of the Caucasus, with a subsequent branch northward onto the steppe and then across Europe. We reconcile this hybrid hypothesis with recently published ancient DNA evidence from the steppe and the northern Fertile Crescent.}, }
@article {pmid37495791, year = {2023}, author = {Callaway, E}, title = {Seven generations of a prehistoric family mapped with ancient DNA.}, journal = {Nature}, volume = {620}, number = {7972}, pages = {19}, pmid = {37495791}, issn = {1476-4687}, mesh = {History, Ancient ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Human Migration ; }, }
@article {pmid37495780, year = {2023}, author = {}, title = {Family trees of a Neolithic community uncovered by ancient DNA.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37495780}, issn = {1476-4687}, }
@article {pmid37495691, year = {2023}, author = {Rivollat, M and Rohrlach, AB and Ringbauer, H and Childebayeva, A and Mendisco, F and Barquera, R and Szolek, A and Le Roy, M and Colleran, H and Tuke, J and Aron, F and Pemonge, MH and Späth, E and Télouk, P and Rey, L and Goude, G and Balter, V and Krause, J and Rottier, S and Deguilloux, MF and Haak, W}, title = {Extensive pedigrees reveal the social organization of a Neolithic community.}, journal = {Nature}, volume = {620}, number = {7974}, pages = {600-606}, pmid = {37495691}, issn = {1476-4687}, mesh = {Adult ; Child ; Female ; Humans ; Male ; Agriculture/history ; *Anthropology, Cultural ; Burial/history ; Fathers/history ; Fertility ; France ; History, Ancient ; Mortality/history ; *Pedigree ; Siblings ; Social Support/history ; Strontium Isotopes/analysis ; *Social Environment ; Mothers/history ; }, abstract = {Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations[1-4]. However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy 'les Noisats' (France), dated to the western European Neolithic around 4850-4500 BC. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality[5]. Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.}, }
@article {pmid37494435, year = {2023}, author = {Salazar, L and Burger, R and Forst, J and Barquera, R and Nesbitt, J and Calero, J and Washburn, E and Verano, J and Zhu, K and Sop, K and Kassadjikova, K and Ibarra Asencios, B and Davidson, R and Bradley, B and Krause, J and Fehren-Schmitz, L}, title = {Insights into the genetic histories and lifeways of Machu Picchu's occupants.}, journal = {Science advances}, volume = {9}, number = {30}, pages = {eadg3377}, pmid = {37494435}, issn = {2375-2548}, abstract = {Machu Picchu originally functioned as a palace within the estate of the Inca emperor Pachacuti between ~1420 and 1532 CE. Before this study, little was known about the people who lived and died there, where they came from or how they were related to the inhabitants of the Inca capital of Cusco. We generated genome-wide data for 34 individuals buried at Machu Picchu who are believed to have been retainers or attendants assigned to serve the Inca royal family, as well as 34 individuals from Cusco for comparative purposes. When the ancient DNA results are contextualized using historical and archaeological data, we conclude that the retainer population at Machu Picchu was highly heterogeneous with individuals exhibiting genetic ancestries associated with groups from throughout the Inca Empire and Amazonia. The results suggest a diverse retainer community at Machu Picchu in which people of different genetic backgrounds lived, reproduced, and were interred together.}, }
@article {pmid37491505, year = {2023}, author = {Barsch, E and Kowarik, K and Rodler, K and Hörweg, C and Reschreiter, H and Sattmann, H and Walochnik, J}, title = {First molecular data on the human roundworm Ascaris lumbricoides species complex from the Bronze and Iron Age in Hallstatt, Austria.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12055}, pmid = {37491505}, issn = {2045-2322}, mesh = {Animals ; Humans ; Ascaris lumbricoides/genetics ; Austria ; Ascaris/genetics ; *Ascariasis ; *Nematode Infections ; Trichuris/genetics ; Feces/parasitology ; Soil ; }, abstract = {Palaeoparasitological studies can provide valuable information on the emergence, distribution, and elimination of parasites during a particular time in the past. In the prehistoric salt mines of Hallstatt, located in the Austrian Alps, human faeces have been conserved in salt. The aim of this study was to recover ancient DNA of intestinal parasites from these coprolites. Altogether, 35 coprolites from the Hallstatt salt mines, dating back to the Bronze Age mining phase (1158-1063 BCE) and the Iron Age mining phase (750-662 BCE), respectively, were analysed by microscopy and molecular methods. In 91% of the coprolite samples, eggs of soil-transmitted helminths (STH), namely of Trichuris and/or Ascaris were detected by light microscopy. The Ascaris eggs were exceptionally well preserved. For further analysis, DNA was extracted from the palaeofaecal samples and species-specific primers targeting different genes were designed. While amplification of Trichuris DNA remained unsuccessful, sequence data of A. lumbricoides species complex were successfully obtained from 16 coprolites from three different genes, the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), the mitochondrial cytochrome B gene (cytB) and the mitochondrial NADH dehydrogenase subunit 1 gene (nadh1). Importantly, these included two Ascaris sequences from a coprolite from the Bronze Age, which to the best of our knowledge are the first molecular data of this genus from this period.}, }
@article {pmid37488251, year = {2023}, author = {Fontani, F and Boano, R and Cinti, A and Demarchi, B and Sandron, S and Rampelli, S and Candela, M and Traversari, M and Latorre, A and Iacovera, R and Abondio, P and Sarno, S and Mackie, M and Collins, M and Radini, A and Milani, C and Petrella, E and Giampalma, E and Minelli, A and Larocca, F and Cilli, E and Luiselli, D}, title = {Bioarchaeological and paleogenomic profiling of the unusual Neolithic burial from Grotta di Pietra Sant'Angelo (Calabria, Italy).}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11978}, pmid = {37488251}, issn = {2045-2322}, mesh = {Humans ; *Burial ; *Archaeology ; Body Remains ; Bone Matrix ; Italy ; }, abstract = {The Neolithic burial of Grotta di Pietra Sant'Angelo (CS) represents a unique archaeological finding for the prehistory of Southern Italy. The unusual placement of the inhumation at a rather high altitude and far from inhabited areas, the lack of funerary equipment and the prone deposition of the body find limited similarities in coeval Italian sites. These elements have prompted wider questions on mortuary customs during the prehistory of Southern Italy. This atypical case requires an interdisciplinary approach aimed to build an integrated bioarchaeological profile of the individual. The paleopathological investigation of the skeletal remains revealed the presence of numerous markers that could be associated with craft activities, suggesting possible interpretations of the individual's lifestyle. CT analyses, carried out on the maxillary bones, showed the presence of a peculiar type of dental wear, but also a good density of the bone matrix. Biomolecular and micromorphological analyses of dental calculus highlight the presence of a rich Neolithic-like oral microbiome, the composition of which is consistent with the presence pathologies. Finally, paleogenomic data obtained from the individual were compared with ancient and modern Mediterranean populations, including unpublished high-resolution genome-wide data for 20 modern inhabitants of the nearby village of San Lorenzo Bellizzi, which provided interesting insights into the biodemographic landscape of the Neolithic in Southern Italy.}, }
@article {pmid37485357, year = {2023}, author = {Ginja, C and Guimarães, S and da Fonseca, RR and Rasteiro, R and Rodríguez-Varela, R and Simões, LG and Sarmento, C and Belarte, MC and Kallala, N and Torres, JR and Sanmartí, J and Arruda, AM and Detry, C and Davis, S and Matos, J and Götherström, A and Pires, AE and Valenzuela-Lamas, S}, title = {Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle.}, journal = {iScience}, volume = {26}, number = {7}, pages = {107196}, pmid = {37485357}, issn = {2589-0042}, abstract = {The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.}, }
@article {pmid37474518, year = {2023}, author = {Campos, PE and Pruvost, O and Boyer, K and Chiroleu, F and Cao, TT and Gaudeul, M and Baider, C and Utteridge, TMA and Becker, N and Rieux, A and Gagnevin, L}, title = {Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4306}, pmid = {37474518}, issn = {2041-1723}, mesh = {Humans ; Phylogeny ; *Xanthomonas/genetics ; Genomics ; *Citrus/microbiology ; Plant Diseases/microbiology ; }, abstract = {Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).}, }
@article {pmid37465192, year = {2023}, author = {Malyarchuk, BA}, title = {The role of Beringia in human adaptation to Arctic conditions based on results of genomic studies of modern and ancient populations.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {27}, number = {4}, pages = {373-382}, doi = {10.18699/VJGB-23-45}, pmid = {37465192}, issn = {2500-0462}, abstract = {The results of studies in Quaternary geology, archeology, paleoanthropology and human genetics demonstrate that the ancestors of Native Americans arrived in mid-latitude North America mainly along the Pacific Northwest Coast, but had previously inhabited the Arctic and during the last glacial maximum were in a refugium in Beringia, a land bridge connecting Eurasia and North America. The gene pool of Native Americans is represented by unique haplogroups of mitochondrial DNA and the Y chromosome, the evolutionary age of which ranges from 13 to 22 thousand years. The results of a paleogenomic analysis also show that during the last glacial maximum Beringia was populated by human groups that had arisen as a result of interaction between the most ancient Upper Paleolithic populations of Northern Eurasia and newcomer groups from East Asia. Approximately 20 thousand years ago the Beringian populations began to form, and the duration of their existence in relative isolation is estimated at about 5 thousand years. Thus, the adaptation of the Beringians to the Arctic conditions could have taken several millennia. The adaptation of Amerindian ancestors to high latitudes and cold climates is supported by genomic data showing that adaptive genetic variants in Native Americans are associated with various metabolic pathways: melanin production processes in the skin, hair and eyes, the functioning of the cardiovascular system, energy metabolism and immune response characteristics. Meanwhile, the analysis of the existing hypotheses about the selection of some genetic variants in the Beringian ancestors of the Amerindians in connection with adaptation to the Arctic conditions (for example, in the FADS, ACTN3, EDAR genes) shows the ambiguity of the testing results, which may be due to the loss of some traces of the "Beringian" adaptation in the gene pools of modern Native Americans. The most optimal strategy for further research seems to be the search for adaptive variant.}, }
@article {pmid37463880, year = {2023}, author = {Louis, M and Korlević, P and Nykänen, M and Archer, F and Berrow, S and Brownlow, A and Lorenzen, ED and O'Brien, J and Post, K and Racimo, F and Rogan, E and Rosel, PE and Sinding, MS and van der Es, H and Wales, N and Fontaine, MC and Gaggiotti, OE and Foote, AD}, title = {Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4020}, pmid = {37463880}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Genetics, Population ; Genomics ; Paleontology ; *Bottle-Nosed Dolphin/genetics ; Ecosystem ; }, abstract = {Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.}, }
@article {pmid37463752, year = {2023}, author = {Mármol-Sánchez, E and Fromm, B and Oskolkov, N and Pochon, Z and Kalogeropoulos, P and Eriksson, E and Biryukova, I and Sekar, V and Ersmark, E and Andersson, B and Dalén, L and Friedländer, MR}, title = {Historical RNA expression profiles from the extinct Tasmanian tiger.}, journal = {Genome research}, volume = {33}, number = {8}, pages = {1299-1316}, pmid = {37463752}, issn = {1549-5469}, mesh = {Animals ; *Genomics/methods ; Phylogeny ; Extinction, Biological ; Paleontology ; *Marsupialia/genetics ; RNA/genetics ; }, abstract = {Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.}, }
@article {pmid37463654, year = {2023}, author = {Lin, H and Hu, J and Baleka, S and Yuan, J and Chen, X and Xiao, B and Song, S and Du, Z and Lai, X and Hofreiter, M and Sheng, G}, title = {A genetic glimpse of the Chinese straight-tusked elephants.}, journal = {Biology letters}, volume = {19}, number = {7}, pages = {20230078}, pmid = {37463654}, issn = {1744-957X}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; *Elephants/genetics ; Fossils ; Phylogeny ; Phylogeography ; }, abstract = {Straight-tusked elephants (genus: Palaeoloxodon) including their island dwarf forms are extinct enigmatic members of the Pleistocene megafauna and the most common Pleistocene elephants after the mammoths. Their taxonomic placement has been revised several times. Using palaeogenomic evidence, previous studies suggested that the European P. antiquus has a hybrid origin, but no molecular data have been retrieved from their Asian counterparts, leaving a gap in our knowledge of the global phylogeography and population dynamics of Palaeoloxodon. Here, we captured a high-quality complete mitogenome from a Pleistocene Elephantidae molar (CADG841) from Northern China, which was previously morphologically assigned to the genus Elephas (Asian elephant), and partial mitochondrial sequences (838 bp) of another Palaeoloxodon sp. specimen (CADG1074) from Northeastern China. We found that both Chinese specimens cluster with a 244 000-year-old P. antiquus (specimen name: WE) from Western Europe, suggesting that this clade may represent a population with a large spatial span across Eurasia. Based on the fossil record and the molecular dating of both the divergences of different Palaeoloxodon mitochondrial clades and previously determined hybridization events, we propose that this Eurasian-wide WE clade provides evidence for an earlier migration and/or another hybridization event that happened in the evolutionary history of straight-tusked elephants.}, }
@article {pmid37452091, year = {2023}, author = {Yang, C and Zhou, Y and Song, Y and Wu, D and Zeng, Y and Nie, L and Liu, P and Zhang, S and Chen, G and Xu, J and Zhou, H and Zhou, L and Qian, X and Liu, C and Tan, S and Zhou, C and Dai, W and Xu, M and Qi, Y and Wang, X and Guo, L and Fan, G and Wang, A and Deng, Y and Zhang, Y and Jin, J and He, Y and Guo, C and Guo, G and Zhou, Q and Xu, X and Yang, H and Wang, J and Xu, S and Mao, Y and Jin, X and Ruan, J and Zhang, G}, title = {The complete and fully-phased diploid genome of a male Han Chinese.}, journal = {Cell research}, volume = {33}, number = {10}, pages = {745-761}, pmid = {37452091}, issn = {1748-7838}, mesh = {Humans ; Male ; Asian People/genetics ; *Diploidy ; *East Asian People/ethnology/genetics ; *Genome, Human/genetics ; Genomics ; *Telomere/genetics ; }, abstract = {Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.}, }
@article {pmid37450551, year = {2023}, author = {Pryor, Y and Lindo, J}, title = {Deconstructing Eurocentrism in skin pigmentation research via the incorporation of diverse populations and theoretical perspectives.}, journal = {Evolutionary anthropology}, volume = {32}, number = {4}, pages = {195-205}, doi = {10.1002/evan.21993}, pmid = {37450551}, issn = {1520-6505}, support = {1926075//Division of Behavioral and Cognitive Sciences/ ; 1945046//Division of Behavioral and Cognitive Sciences/ ; //Ford Foundation Predoctoral Fellowship/ ; 21602//National Science Foundation Graduate Research Fellowship/ ; }, mesh = {Animals ; Humans ; *Skin Pigmentation ; Biological Evolution ; *Hominidae ; Genomics ; }, abstract = {The evolution of skin pigmentation has been shaped by numerous biological and cultural shifts throughout human history. Vitamin D is considered a driver of depigmentation evolution in humans, given the deleterious health effects associated with vitamin D deficiency, which is often shaped by cultural factors. New advancements in genomics and epigenomics have opened the door to a deeper exploration of skin pigmentation evolution in both contemporary and ancient populations. Data from ancient Europeans has offered great context to the spread of depigmentation alleles via the evaluation of migration events and cultural shifts that occurred during the Neolithic. However, novel insights can further be gained via the inclusion of diverse ancient and contemporary populations. Here we present on how potential biases and limitations in skin pigmentation research can be overcome with the integration of interdisciplinary data that includes both cultural and biological elements, which have shaped the evolutionary history of skin pigmentation in humans.}, }
@article {pmid37438988, year = {2025}, author = {Lewis, DA and Simpson, R and Hermes, A and Brown, A and Llamas, B}, title = {More than dirt: Sedimentary ancient DNA and Indigenous Australia.}, journal = {Molecular ecology resources}, volume = {25}, number = {2}, pages = {e13835}, doi = {10.1111/1755-0998.13835}, pmid = {37438988}, issn = {1755-0998}, support = {2011277//National Health and Medical Research Council/ ; 1137563//National Health and Medical Research Council/ ; }, mesh = {Humans ; Archaeology/methods ; Australia ; *DNA, Ancient/analysis ; *Geologic Sediments/chemistry ; *Indigenous Peoples/genetics ; }, abstract = {The rise of sedimentary ancient DNA (sedaDNA) studies has opened new possibilities for studying past environments. This groundbreaking area of genomics uses sediments to identify organisms, even in cases where macroscopic remains no longer exist. Managing this substrate in Indigenous Australian contexts, however, requires special considerations. Sediments and soils are often considered as waste by-products during archaeological and paleontological excavations and are not typically regulated by the same ethics guidelines utilised in mainstream 'western' research paradigms. Nevertheless, the product of sedaDNA work-genetic information from past fauna, flora, microbial communities and human ancestors-is likely to be of cultural significance and value for Indigenous peoples. This article offers an opinion on the responsibilities of researchers in Australia who engage in research related to this emerging field, particularly when it involves Indigenous communities. One aspect that deserves consideration in such research is the concept of benefit sharing. Benefit sharing refers to the practice of ensuring that the benefits that arise from research are shared equitably with the communities from which the research data were derived. This practice is particularly relevant in research that involves Indigenous communities, who may have unique cultural and spiritual connections to the research material. We argue that the integration of Traditional Knowledges into sedaDNA research would add enormous value to research and its outcomes by providing genomic outputs alongside and within the rich context of multimillennia oral histories.}, }
@article {pmid37438447, year = {2023}, author = {Tran, HL and Mai, HP and Le Thi, D and Thi, ND and Le Tung, L and Thanh, TP and Manh, HT and Mau, HN and Chu, HH and Hoang, H}, title = {The first maternal genetic study of hunter-gatherers from Vietnam.}, journal = {Molecular genetics and genomics : MGG}, volume = {298}, number = {5}, pages = {1225-1235}, pmid = {37438447}, issn = {1617-4623}, support = {DL0000.08/20-23//Vietnam Academy of Science and Technology/ ; }, mesh = {Humans ; Vietnam ; *Archaeology ; *DNA, Ancient/analysis ; Genome, Human ; }, abstract = {The current limitation of ancient DNA data from Vietnam led to the controversy surrounding the prehistory of people in this region. The combination of high heat and humidity damaged ancient bones that challenged the study of human evolution, especially when using DNA as study materials. So far, only 4 k years of history have been recorded despite the 65 k years of history of anatomically modern human occupations in Vietnam. Here we report, to our knowledge, the oldest mitogenomes of two hunter-gatherers from Vietnam. We extracted DNA from the femurs of two individuals aged 6.2 k cal BP from the Con Co Ngua (CCN) site in Thanh Hoa, Vietnam. This archeological site is the largest cemetery of the hunter-gatherer population in Southeast Asia (SEA) that was discovered, but their genetics have not been explored until the present. We indicated that the CCN haplotype belongs to a rare haplogroup that was not detected in any present-day Vietnamese individuals. Further matrilineal analysis on CCN mitogenomes showed a close relationship with ancient farmers and present-day populations in SEA. The mitogenomes of hunter-gatherers from Vietnam debate the "two layers" model of peopling history in SEA and provide an alternative solution for studying challenging ancient human samples from Vietnam.}, }
@article {pmid37433640, year = {2023}, author = {Weissensteiner, MH and Cremona, MA and Guiblet, WM and Stoler, N and Harris, RS and Cechova, M and Eckert, KA and Chiaromonte, F and Huang, YF and Makova, KD}, title = {Accurate sequencing of DNA motifs able to form alternative (non-B) structures.}, journal = {Genome research}, volume = {33}, number = {6}, pages = {907-922}, pmid = {37433640}, issn = {1549-5469}, support = {R01 GM136684/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Nucleotide Motifs ; *DNA, Z-Form ; Sequence Analysis, DNA ; DNA/genetics ; Base Composition ; High-Throughput Nucleotide Sequencing ; *Nanopores ; }, abstract = {Approximately 13% of the human genome at certain motifs have the potential to form noncanonical (non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular processes but also affect the activity of polymerases and helicases. Because sequencing technologies use these enzymes, they might possess increased errors at non-B structures. To evaluate this, we analyzed error rates, read depth, and base quality of Illumina, Pacific Biosciences (PacBio) HiFi, and Oxford Nanopore Technologies (ONT) sequencing at non-B motifs. All technologies showed altered sequencing success for most non-B motif types, although this could be owing to several factors, including structure formation, biased GC content, and the presence of homopolymers. Single-nucleotide mismatch errors had low biases in HiFi and ONT for all non-B motif types but were increased for G-quadruplexes and Z-DNA in all three technologies. Deletion errors were increased for all non-B types but Z-DNA in Illumina and HiFi, as well as only for G-quadruplexes in ONT. Insertion errors for non-B motifs were highly, moderately, and slightly elevated in Illumina, HiFi, and ONT, respectively. Additionally, we developed a probabilistic approach to determine the number of false positives at non-B motifs depending on sample size and variant frequency, and applied it to publicly available data sets (1000 Genomes, Simons Genome Diversity Project, and gnomAD). We conclude that elevated sequencing errors at non-B DNA motifs should be considered in low-read-depth studies (single-cell, ancient DNA, and pooled-sample population sequencing) and in scoring rare variants. Combining technologies should maximize sequencing accuracy in future studies of non-B DNA.}, }
@article {pmid37431939, year = {2023}, author = {Mizuno, F and Taniguchi, Y and Kondo, O and Hayashi, M and Kurosaki, K and Ueda, S}, title = {Diversity in matrilineages among the Jomon individuals of Japan.}, journal = {Annals of human biology}, volume = {50}, number = {1}, pages = {324-331}, doi = {10.1080/03014460.2023.2224060}, pmid = {37431939}, issn = {1464-5033}, mesh = {Humans ; Japan ; *Body Remains ; *Archaeology ; High-Throughput Nucleotide Sequencing ; Knowledge ; }, abstract = {BACKGROUND: The Jomon period of Japan is characterised by a unique combination of sedentary and hunting/gathering lifestyles, spanning for more than 10,000 years from the final Pleistocene to the Holocene. The transition from the preceding Palaeolithic period to the Jomon period is known to have begun with the appearance of pottery usage. However, knowledge of the genetic background of the Jomon people is still limited.<br><br>AIM: We aimed to determine the population-scale complete mitogenome sequences of the Initial Jomon human remains and compare the occurrence of mitochondrial haplogroups in the Jomon period from temporal and regional perspectives.<br><br>SUBJECTS AND METHODS: For human remains dated to 8200-8600&#x2009;cal BP, we determined their complete mitogenome sequences using target enrichment-coupled next-generation sequencing.<br><br>RESULTS: We successfully obtained the complete mitogenome sequences with high depth of coverage and high concordance on consensus sequences. These sequences differed by more than three bases each, except for two individuals having completely identical sequences. Co-existence of individuals with haplogroups N9b and M7a was first observed at the same archaeological site from the Initial Jomon period.<br><br>CONCLUSION: The genetic diversity within the population was not found to be low even in the Initial Jomon period.}, }
@article {pmid37423869, year = {2023}, author = {Bailey, E}, title = {Ancient DNA reveals an early adoption of horse culture by Native Americans.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {11}, pages = {808-809}, doi = {10.1016/j.tig.2023.06.010}, pmid = {37423869}, issn = {0168-9525}, mesh = {Animals ; Humans ; *American Indian or Alaska Native ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Horses/genetics ; }, abstract = {Native Americans of the Plains and Rocky Mountains are renowned for their horsemanship. Taylor et al. recently used ancient DNA and other bioarcheological approaches to document how horses dispersed throughout America and transformed Native American societies following their introduction by the Spanish in 1519, well before the arrival of European settlers.}, }
@article {pmid37422275, year = {2023}, author = {Ibrahim, J and Rechav, K and Boaretto, E and Weiner, S}, title = {Three dimensional structures of the inner and outer pig petrous bone using FIB-SEM: Implications for development and ancient DNA preservation.}, journal = {Journal of structural biology}, volume = {215}, number = {3}, pages = {107998}, doi = {10.1016/j.jsb.2023.107998}, pmid = {37422275}, issn = {1095-8657}, mesh = {Animals ; Swine ; *DNA, Ancient ; *Odonata ; Petrous Bone ; Collagen ; Minerals ; }, abstract = {We report on the 3D ultrastructure of the mineralized petrous bone of mature pig using focused ion beam - scanning electron microscopy (FIB-SEM). We divide the petrous bone into two zones based on the degree of mineralization; one zone close to the otic chamber has higher mineral density than the second zone further away from the otic chamber. The hypermineralization of the petrous bone results in the collagen D-banding being poorly revealed in the lower mineral density zone (LMD), and absent in the high mineral density zone (HMD). We therefore could not use D-banding to decipher the 3D structure of the collagen assembly. Instead we exploited the anisotropy option in the Dragonfly image processing software to visualize the less mineralized collagen fibrils and/or nanopores that surround the more mineralized zones known as tesselles. This approach therefore indirectly tracks the orientations of the collagen fibrils in the matrix itself. We show that the HMD bone has a structure similar to that of woven bone, and the LMD is composed of lamellar bone with a plywood-like structural motif. This agrees with the fact that the bone close to the otic chamber is fetal bone and is not remodeled. The lamellar structure of the bone further away from the otic chamber is consistent with modeling/remodeling. The absence of the less mineralized collagen fibrils and nanopores resulting from the confluence of the mineral tesselles may contribute to shielding DNA during diagenesis. We show that anisotropy evaluation of the less mineralized collagen fibrils could be a useful tool to analyze bone ultrastructures and in particular the directionality of collagen fibril bundles that make up the bone matrix.}, }
@article {pmid37395407, year = {2023}, author = {Brázda, V and Dobrovolná, M and Bohálová, N and Mergny, JL}, title = {G-quadruplexes in the evolution of hepatitis B virus.}, journal = {Nucleic acids research}, volume = {51}, number = {14}, pages = {7198-7204}, pmid = {37395407}, issn = {1362-4962}, mesh = {Humans ; *G-Quadruplexes ; Genome, Human ; Genomics ; *Hepatitis B virus/genetics ; Paleontology ; Biological Evolution ; }, abstract = {Hepatitis B virus (HBV) is one of the most dangerous human pathogenic viruses found in all corners of the world. Recent sequencing of ancient HBV viruses revealed that these viruses have accompanied humanity for several millenia. As G-quadruplexes are considered to be potential therapeutic targets in virology, we examined G-quadruplex-forming sequences (PQS) in modern and ancient HBV genomes. Our analyses showed the presence of PQS in all 232 tested HBV genomes, with a total number of 1258 motifs and an average frequency of 1.69 PQS per kbp. Notably, the PQS with the highest G4Hunter score in the reference genome is the most highly conserved. Interestingly, the density of PQS motifs is lower in ancient HBV genomes than in their modern counterparts (1.5 and 1.9/kb, respectively). This modern frequency of 1.90 is very close to the PQS frequency of the human genome (1.93) using identical parameters. This indicates that the PQS content in HBV increased over time to become closer to the PQS frequency in the human genome. No statistically significant differences were found between PQS densities in HBV lineages found in different continents. These results, which constitute the first paleogenomics analysis of G4 propensity, are in agreement with our hypothesis that, for viruses causing chronic infections, their PQS frequencies tend to converge evolutionarily with those of their hosts, as a kind of 'genetic camouflage' to both hijack host cell transcriptional regulatory systems and to avoid recognition as foreign material.}, }
@article {pmid37387654, year = {2023}, author = {Kerner, G and Quintana-Murci, L}, title = {[Paleogenomics and the evolution of the human immune system over the last ten millennia].}, journal = {Medecine sciences : M/S}, volume = {39}, number = {6-7}, pages = {496-499}, doi = {10.1051/medsci/2023070}, pmid = {37387654}, issn = {1958-5381}, mesh = {Humans ; *Genomics ; *Paleontology ; }, }
@article {pmid37380840, year = {2023}, author = {Lewis, D}, title = {Ancient-DNA researcher fired for 'serious misconduct' lands new role.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-023-02147-x}, pmid = {37380840}, issn = {1476-4687}, }
@article {pmid37372418, year = {2023}, author = {Bonfigli, A and Cesare, P and Volpe, AR and Colafarina, S and Forgione, A and Aloisi, M and Zarivi, O and Poma, AMG}, title = {Estimation of DNA Degradation in Archaeological Human Remains.}, journal = {Genes}, volume = {14}, number = {6}, pages = {}, pmid = {37372418}, issn = {2073-4425}, mesh = {Humans ; *DNA, Ancient ; Italy ; *Body Remains ; Bone and Bones ; DNA, Mitochondrial/genetics ; }, abstract = {The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained.}, }
@article {pmid37372367, year = {2023}, author = {Song, S and Xiao, B and Hu, J and Lin, H and Du, Z and Xiang, K and Pan, D and Hou, X and Yuan, J and Lai, X and Sheng, G}, title = {Ancient Mitogenomes Reveal Stable Genetic Continuity of the Holocene Serows.}, journal = {Genes}, volume = {14}, number = {6}, pages = {}, pmid = {37372367}, issn = {2073-4425}, mesh = {Humans ; Animals ; Phylogeny ; Bayes Theorem ; *Genome, Mitochondrial/genetics ; Ruminants ; Asia ; }, abstract = {As one of the remaining species of Caprinae only found in Asia, serows (Capricornis) and their classification and conservation have received increasing attention in recent years. However, their evolutionary history and population dynamics are not yet clear. To shed light on these topics, we report the first near-complete ancient mitochondrial genomes from two serow sub-fossils (CADG839 and CADG946) dating to 8860 ± 30 years and 2450 ± 30 years, and incorporate the newly obtained mitogenomes into the dataset of living serows (18 complete mitochondrial genomes drawn from National Center for Biotechnology Information, NCBI) to investigate their relationships and evolution. Phylogenetic results support four clades of serows that can be further divided into five subclades, indicating higher genetic diversity than previously thought. Notably, our two ancient samples do not form a separate branch but belong to Capricornis sumatraensis clade A together with modern individuals, which suggests genetic continuity between ancient and modern serows. Furthermore, our results suggest that the maternal divergences of serows occurred at the beginning of the Pleistocene. Bayesian estimation indicates that the first divergence among all serows happened approximately 2.37 Ma (95% highest posterior density, HPD: 2.74-2.02 Ma) when Japanese serow (Capricornis crispus) appeared, while the last divergence occurred within the Sumatran serow (C. sumatraensis clade A and B) around 0.37-0.25 Ma. Additionally, we found the effective maternal population size of C. sumatraensis increased around 225-160 and 90-50 ka, then remained stable since 50 ka. Overall, our study provides new insights into serow phylogeny and evolutionary history.}, }
@article {pmid37339987, year = {2023}, author = {Sousa da Mota, B and Rubinacci, S and Cruz Dávalos, DI and G Amorim, CE and Sikora, M and Johannsen, NN and Szmyt, MH and Włodarczak, P and Szczepanek, A and Przybyła, MM and Schroeder, H and Allentoft, ME and Willerslev, E and Malaspinas, AS and Delaneau, O}, title = {Imputation of ancient human genomes.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3660}, pmid = {37339987}, issn = {2041-1723}, support = {R35 GM142939/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Genotyping Techniques/methods ; *Genome, Human/genetics ; DNA, Ancient ; Genotype ; Genome-Wide Association Study/methods ; Polymorphism, Single Nucleotide ; }, abstract = {Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.}, }
@article {pmid37337956, year = {2023}, author = {Doan, K and Schnitzler, A and Preston, F and Griggo, C and Lang, G and Belhaoues, F and Blaise, E and Crégut-Bonnoure, E and Frère, S and Foucras, S and Gardeisen, A and Laurent, A and Müller, W and Picavet, R and Puissant, S and Yvinec, JH and Pilot, M}, title = {Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene.}, journal = {Molecular ecology}, volume = {32}, number = {16}, pages = {4627-4647}, doi = {10.1111/mec.17054}, pmid = {37337956}, issn = {1365-294X}, mesh = {Dogs ; Animals ; *Wolves/genetics ; Phylogeny ; Biological Evolution ; Phylogeography ; France ; Haplotypes/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.}, }
@article {pmid37330109, year = {2024}, author = {Yang, L and Zhang, X and Hu, Y and Zhu, P and Li, H and Peng, Z and Xiang, H and Zhou, X and Zhao, X}, title = {Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {51}, number = {1}, pages = {87-95}, doi = {10.1016/j.jgg.2023.06.002}, pmid = {37330109}, issn = {1673-8527}, mesh = {Sheep/genetics ; Animals ; Phylogeny ; *Genome, Mitochondrial/genetics ; Genetic Variation ; DNA, Mitochondrial/genetics ; Asia, Eastern ; China ; }, abstract = {Sheep have been one of the most important groups of animals since ancient times. However, the knowledge of their migration routes and genetic relationships is still poorly understood. To investigate sheep maternal migration histories alongside Eurasian communications routes, in this study, we obtain mitochondrial genomes (mitogenomes) from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429-3100 years before present (BP). By obtaining the mitogenomes from the sheep (4429-3556 BP) found in the Tongtian Cave site in Xinjiang, Altai region of northwest China, our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429-3556 BP. The combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern Asia. At least two migration events have taken place for sheep crossing Eurasia to China, one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 BP to 2500 BP. Overall, this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.}, }
@article {pmid37323114, year = {2023}, author = {Russo, MG and Arencibia, V and Emery, M and Bettera Marcat, G and Seldes, V and Mercolli, P and Soria, S and Maldonado, L and Kamenetzky, L and Avena, S and Dejean, C and Stone, AC}, title = {Ancient mitochondrial genome diversity in South America: Contributions from Quebrada del Toro, Northwestern Argentina.}, journal = {American journal of biological anthropology}, volume = {181}, number = {4}, pages = {597-610}, doi = {10.1002/ajpa.24795}, pmid = {37323114}, issn = {2692-7691}, mesh = {Humans ; Argentina ; *Genome, Mitochondrial/genetics ; Phylogeny ; Bayes Theorem ; DNA, Mitochondrial/genetics ; South America ; }, abstract = {OBJECTIVES: The objective of this study was to enhance our understanding of the population history in South America, specifically Northwestern Argentina, by analyzing complete ancient mitogenomes of individuals from the Ojo de Agua archeological site (970 BP) in Quebrada del Toro (Salta, Argentina).<br><br>MATERIALS AND METHODS: We analyzed teeth from four individuals from the site Ojo de Agua (970&#x2009;&#xb1;&#x2009;60 BP), located in Quebrada del Toro (Andean region of Northwestern Argentina). DNA extracts were converted to double-stranded DNA libraries and indexed using unique dual-indexing primer combinations. DNA libraries were then enriched for the complete mitochondrial genome, pooled at equimolar concentrations, and sequenced on an Illumina&#xae; MiSeq&#x2122; platform. Reads from high quality libraries were trimmed, merged, and then mapped to the revised Cambridge Reference Sequence. The aDNA damage patterns were assessed and contamination estimated. Finally, variants were called, filtered, and the consensus mitogenome was constructed and used for haplogroup assignment. We also compiled available mitogenome sequences from ancient and present-day populations from the Southcentral Andes and other surrounding regions in Argentina. Maximum Likelihood and Bayesian phylogenetic reconstructions were obtained using the generated dataset.<br><br>RESULTS: We successfully obtained the complete mitogenome sequence from one individual with an average depth coverage of 102X. We discovered a novel haplotype that was assigned to haplogroup D1. Phylogenetic reconstructions suggests that this haplotype falls within the sister branches of the D1j lineage, forming a well-supported clade. The estimate TMRCA of this clade that includes D1j and its sister branches ranged between 12,535 and 18,669&#x2009;ya.<br><br>DISCUSSION: The sequence analyzed in this study represents the first ancient mitogenome from within the valley region in Northwestern Argentina. We found that a representative of a lineage highly associated with D1j was already present approximately 1000 BP in the region. Our results agree with the proposed origin of D1j in other regions north of Patagonia and independent of the Pacific coast fast migratory route, contrary to what was originally hypothesized. This study highlights the lack of information regarding pre-Hispanic genetic diversity and contributes to the knowledge about the peopling process in South America.}, }
@article {pmid37317074, year = {2023}, author = {Sant'Anna, TB and Araujo, NM}, title = {Hepatitis B Virus Genotype D: An Overview of Molecular Epidemiology, Evolutionary History, and Clinical Characteristics.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317074}, issn = {2076-2607}, support = {E-26/210.450/2019//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {The hepatitis B virus (HBV) genotype D (HBV/D) is the most extensively distributed genotype worldwide with distinct molecular and epidemiological features. This report provides an up-to-date review on the history of HBV/D subgenotyping and misclassifications, along with large-scale analysis of over 1000 HBV/D complete genome sequences, with the aim of gaining a thorough understanding of the global prevalence and geographic distribution of HBV/D subgenotypes. We have additionally explored recent paleogenomic findings, which facilitated the detection of HBV/D genomes dating back to the late Iron Age and provided new perspectives on the origins of modern HBV/D strains. Finally, reports on distinct disease outcomes and responses to antiviral therapy among HBV/D subgenotypes are discussed, further highlighting the complexity of this genotype and the importance of HBV subgenotyping in the management and treatment of hepatitis B.}, }
@article {pmid37313847, year = {2023}, author = {Legendre, L and Rode, J and Germon, I and Pavie, M and Quiviger, C and Policarpo, M and Leclercq, J and Père, S and Fumey, J and Hyacinthe, C and Ornelas-García, P and Espinasa, L and Rétaux, S and Casane, D}, title = {Genetic identification and reiterated captures suggest that the Astyanax mexicanus El Pachón cavefish population is closed and declining.}, journal = {Zoological research}, volume = {44}, number = {4}, pages = {701-711}, pmid = {37313847}, issn = {2095-8137}, mesh = {Animals ; Biological Evolution ; *Caves ; Population Density ; *Fishes/genetics ; }, abstract = {The sizes of Astyanax mexicanus blind cavefish populations of North-East Mexico are demographic parameters of great importance for investigating a variety of ecological, evolutionary, and conservation issues. However, few estimates have been obtained. For these mobile animals living in an environment difficult to explore as a whole, methods based on capture-mark-recapture are appropriate, but their feasibility and interpretation of results depend on several assumptions that must be carefully examined. Here, we provide evidence that minimally invasive genetic identification from captures at different time intervals (three days and three years) can give insights into cavefish population size dynamics as well as other important demographic parameters of interest. We also provide tools to calibrate sampling and genotyping efforts necessary to reach a given level of precision. Our results suggest that the El Pachón cave population is currently very small, of an order of magnitude of a few hundreds of individuals, and is distributed in a relatively isolated area. The probable decline in population size in the El Pachón cave since the last census in 1971 raises serious conservation issues.}, }
@article {pmid37311857, year = {2023}, author = {de Sousa, AA and Beaudet, A and Calvey, T and Bardo, A and Benoit, J and Charvet, CJ and Dehay, C and Gómez-Robles, A and Gunz, P and Heuer, K and van den Heuvel, MP and Hurst, S and Lauters, P and Reed, D and Salagnon, M and Sherwood, CC and Ströckens, F and Tawane, M and Todorov, OS and Toro, R and Wei, Y}, title = {From fossils to mind.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {636}, pmid = {37311857}, issn = {2399-3642}, support = {P20 GM103653/GM/NIGMS NIH HHS/United States ; R01 AG067419/AG/NIA NIH HHS/United States ; R01 HG011641/HG/NHGRI NIH HHS/United States ; R24 NS092988/NS/NINDS NIH HHS/United States ; }, mesh = {*Fossils ; Phylogeny ; *Brain ; Archaeology ; Artifacts ; }, abstract = {Fossil endocasts record features of brains from the past: size, shape, vasculature, and gyrification. These data, alongside experimental and comparative evidence, are needed to resolve questions about brain energetics, cognitive specializations, and developmental plasticity. Through the application of interdisciplinary techniques to the fossil record, paleoneurology has been leading major innovations. Neuroimaging is shedding light on fossil brain organization and behaviors. Inferences about the development and physiology of the brains of extinct species can be experimentally investigated through brain organoids and transgenic models based on ancient DNA. Phylogenetic comparative methods integrate data across species and associate genotypes to phenotypes, and brains to behaviors. Meanwhile, fossil and archeological discoveries continuously contribute new knowledge. Through cooperation, the scientific community can accelerate knowledge acquisition. Sharing digitized museum collections improves the availability of rare fossils and artifacts. Comparative neuroanatomical data are available through online databases, along with tools for their measurement and analysis. In the context of these advances, the paleoneurological record provides ample opportunity for future research. Biomedical and ecological sciences can benefit from paleoneurology's approach to understanding the mind as well as its novel research pipelines that establish connections between neuroanatomy, genes and behavior.}, }
@article {pmid37291482, year = {2023}, author = {Chen, N and Nedoluzhko, A}, title = {Ancient DNA: the past for the future.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {309}, pmid = {37291482}, issn = {1471-2164}, mesh = {Animals ; *DNA, Ancient ; Sequence Analysis, DNA/methods ; *Plants/genetics ; Laboratories ; }, abstract = {The last decade has seen advancements in sequencing technologies and laboratory preparation protocols for ancient DNA (aDNA) that have rapidly been applied in multiple research areas thus enabling large-scale scientific research. Future research could also refine our understanding of the evolution of humans, non-human animals, plants, invertebrate specimens, and microorganisms.}, }
@article {pmid37286670, year = {2023}, author = {Humphrey, L and Bouzouggar, A}, title = {Ancient DNA reveals how farming spread into northwest Africa.}, journal = {Nature}, volume = {618}, number = {7965}, pages = {460-461}, pmid = {37286670}, issn = {1476-4687}, mesh = {History, Ancient ; *DNA, Ancient ; Africa ; *Anthropology ; Agriculture ; Archaeology ; }, }
@article {pmid37284851, year = {2023}, author = {Zupanič Pajnič, I and Leskovar, T and Črešnar, M}, title = {Eye and hair color prediction of an early medieval adult and subadult skeleton using massive parallel sequencing technology.}, journal = {International journal of legal medicine}, volume = {137}, number = {5}, pages = {1629-1638}, pmid = {37284851}, issn = {1437-1596}, support = {J3-3080//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, mesh = {Male ; Humans ; Adult ; Middle Aged ; Child ; *Eye Color/genetics ; *Hair Color/genetics ; Powders ; DNA/genetics ; Bone and Bones ; Polymorphism, Single Nucleotide ; }, abstract = {Phenotypic trait prediction in ancient DNA analysis can provide information about the external appearance of individuals from past human populations. Some studies predicting eye and hair color in ancient adult skeletons have been published, but not for ancient subadult skeletons, which are more prone to decay. In this study, eye and hair color were predicted for an early medieval adult skeleton and a subadult skeleton that was anthropologically characterized as a middle-aged man and a subadult of unknown sex about 6 years old. When processing the petrous bones, precautions were taken to prevent contamination with modern DNA. The MillMix tissue homogenizer was used for grinding, 0.5 g of bone powder was decalcified, and DNA was purified in Biorobot EZ1. The PowerQuant System was used for quantification and a customized version of the HIrisPlex panel for massive parallel sequencing (MPS) analysis. Library preparation and templating were performed on the HID Ion Chef Instrument and sequencing on the Ion GeneStudio S5 System. Up to 21 ng DNA/g of powder was obtained from ancient petrous bones. Clean negative controls and no matches with elimination database profiles confirmed no contamination issue. Brown eyes and dark brown or black hair were predicted for the adult skeleton and blue eyes and brown or dark brown hair for the subadult skeleton. The MPS analysis results obtained proved that it is possible to predict hair and eye color not only for an adult from the Early Middle Ages, but also for a subadult skeleton dating to this period.}, }
@article {pmid37269363, year = {2023}, author = {Garcia-Heras, J}, title = {The 2022 Nobel Prize in Physiology or Medicine.}, journal = {Journal of the Association of Genetic Technologists}, volume = {49}, number = {2}, pages = {56-67}, pmid = {37269363}, issn = {1523-7834}, abstract = {The Nobel Assembly at the Karolinska Institute awarded the 2022 Nobel Prize in Physiology or Medicine to Svante Pääbo (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany). This award acknowledged his discoveries about the genomes of extinct hominins (Neandertal man and the Denisovans), the molecular genetic insights of human origin and evolutionary history, and the understanding of phylogenetic relationships between archaic hominins and modern humans. The scientific advances included detection of Neandertal and Denisovan DNA carried by modern humans due to past admixture events, which in turn stimulated active research about the functional and phenotypic significance of such archaic ancestry on non-disease and disease phenotypic features in modern populations. In addition, comparative genomic studies started to delineate the genes and genetic regulation mechanisms that distinguish modern-day humans from the archaic hominins and our immediate ancestors, the anatomically modern humans. These breakthroughs allowed a more thorough understanding of ancestral and modern human population genetics, and propelled the take-off of human paleogenomics as a new scientific discipline in its own right.}, }
@article {pmid37268008, year = {2023}, author = {Guzmán-Solís, AA and Navarro, MA and Ávila-Arcos, MC and Blanco-Melo, D}, title = {A Glimpse into the Past: What Ancient Viral Genomes Reveal About Human History.}, journal = {Annual review of virology}, volume = {10}, number = {1}, pages = {49-75}, doi = {10.1146/annurev-virology-111821-123859}, pmid = {37268008}, issn = {2327-0578}, mesh = {Humans ; Genomics ; *Virus Diseases/genetics ; *Viruses/genetics ; Disease Outbreaks ; Genome, Viral ; }, abstract = {Humans have battled viruses for millennia. However, directly linking the symptomatology of disease outbreaks to specific viral pathogens was not possible until the twentieth century. With the advent of the genomic era and the development of advanced protocols for isolation, sequencing, and analysis of ancient nucleic acids from diverse human remains, the identification and characterization of ancient viruses became feasible. Recent studies have provided invaluable information about past epidemics and made it possible to examine assumptions and inferences on the origin and evolution of certain viral families. In parallel, the study of ancient viruses also uncovered their importance in the evolution of the human lineage and their key roles in shaping major events in human history. In this review, we describe the strategies used for the study of ancient viruses, along with their limitations, and provide a detailed account of what past viral infections have revealed about human history.}, }
@article {pmid37265549, year = {2022}, author = {Elalouf, JM and Palacio, P and Bon, C and Berthonaud, V and Maksud, F and Stafford, TW and Hitte, C}, title = {The genome and diet of a 35,000-year-old Canis lupus specimen from the Paleolithic painted cave, Chauvet-Pont d'Arc, France.}, journal = {Ecology and evolution}, volume = {12}, number = {8}, pages = {e9238}, pmid = {37265549}, issn = {2045-7758}, abstract = {The Chauvet-Pont-d'Arc Cave (Ardèche, France) contains some of the oldest Paleolithic paintings recorded to date, as well as thousands of bones of the extinct cave bear, and some remains and footprints of other animals. As part of the interdisciplinary research project devoted to this reference cave site, we analyzed a coprolite collected within the deep cave. AMS radiocarbon dating of bone fragments from the coprolite yielded an age of 30,450 ± 550 RC yr. BP (AAR-19656; 36,150-34,000 cal BP), similar to ages assigned to Paleolithic artwork and cave bear remains from the same cave sector. Using high-throughput shotgun DNA sequencing, we demonstrated a high abundance of canid DNA and lesser amounts of DNA from the extinct cave bear. We interpret the sample as feces from a canid that had consumed cave bear tissue. The high amount of canid DNA allowed us to reconstruct a complete canid mitochondrial genome sequence (average coverage: 83×) belonging to a deeply divergent clade of extinct mitochondrial wolf lineages that are most closely related to coeval (~35 ka) Belgian wolves. Analysis of the nuclear genome yielded a similar coverage for the X chromosome (2.4×) and the autosomes (range: 2.3-3.2×), indicating that the Chauvet canid was a female. Comparing the relationship of the nuclear genome of this specimen with that of a variety of canids, we found it more closely related to gray wolves' genomes than to other wild canid or dog genomes, especially wolf genomes from Europe and the Middle East. We conclude that the coprolite is feces from an animal within an extinct wolf lineage. The consumption of cave bear by this wolf likely explains its intrusion into the dark cave sectors and sheds new light on the paleoecology of a major cave site.}, }
@article {pmid37259901, year = {2023}, author = {Signore, AV and Morrison, PR and Brauner, CJ and Fago, A and Weber, RE and Campbell, KL}, title = {Evolution of an extreme hemoglobin phenotype contributed to the sub-Arctic specialization of extinct Steller's sea cows.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37259901}, issn = {2050-084X}, mesh = {Animals ; *Dugong ; Mammals ; Hemoglobins/genetics ; Climate ; Oxygen ; }, abstract = {The extinct Steller's sea cow (Hydrodamalis gigas; †1768) was a whale-sized marine mammal that manifested profound morphological specializations to exploit the harsh coastal climate of the North Pacific. Yet despite first-hand accounts of their biology, little is known regarding the physiological adjustments underlying their evolution to this environment. Here, the adult-expressed hemoglobin (Hb; α2β/δ2) of this sirenian is shown to harbor a fixed amino acid replacement at an otherwise invariant position (β/δ82Lys→Asn) that alters multiple aspects of Hb function. First, our functional characterization of recombinant sirenian Hb proteins demonstrates that the Hb-O2 affinity of this sub-Arctic species was less affected by temperature than those of living (sub)tropical sea cows. This phenotype presumably safeguarded O2 delivery to cool peripheral tissues and largely arises from a reduced intrinsic temperature sensitivity of the H. gigas protein. Additional experiments on H. gigas β/δ82Asn→Lys mutant Hb further reveal this exchange renders Steller's sea cow Hb unresponsive to the potent intraerythrocytic allosteric effector 2,3-diphosphoglycerate, a radical modification that is the first documented example of this phenotype among mammals. Notably, β/δ82Lys→Asn moreover underlies the secondary evolution of a reduced blood-O2 affinity phenotype that would have promoted heightened tissue and maternal/fetal O2 delivery. This conclusion is bolstered by analyses of two Steller's sea cow prenatal Hb proteins (Hb Gower I; ζ2ε2 and HbF; α2γ2) that suggest an exclusive embryonic stage expression pattern, and reveal uncommon replacements in H. gigas HbF (γ38Thr→Ile and γ101Glu→Asp) that increased Hb-O2 affinity relative to dugong HbF. Finally, the β/δ82Lys→Asn replacement of the adult/fetal protein is shown to increase protein solubility, which may have elevated red blood cell Hb content within both the adult and fetal circulations and contributed to meeting the elevated metabolic (thermoregulatory) requirements and fetal growth rates associated with this species cold adaptation.}, }
@article {pmid37252429, year = {2023}, author = {Furtwängler, A and Baumann, C and Majander, K and Wilkin, S and Tomoum, N and Rühli, F and Jaeggi, AV and Eppenberger, P and Bender, N and Schuenemann, VJ}, title = {The Mummy Explorer-a self-regulated open-access online teaching tool.}, journal = {Evolution, medicine, and public health}, volume = {11}, number = {1}, pages = {129-138}, pmid = {37252429}, issn = {2050-6201}, abstract = {BACKGROUND AND OBJECTIVES: Virtual teaching tools have gained increasing importance in recent years. In particular, the COVID-19 pandemic has reinforced the need for media-based and self-regulated tools. What is missing are tools that allow us to interlink highly interdisciplinary fields such as evolutionary medicine and, at the same time, allow us to adapt content to different lectures.<br><br>METHODOLOGY: We designed an interactive online teaching tool, namely, the Mummy Explorer, using open-access software (Google Web Designer), and we provided a freely downloadable template. We tested the tool on students and lecturers of evolutionary medicine using questionnaires and improved the tool according to their feedback.<br><br>RESULTS: The tool has a modular design and provides an overview of a virtual mummy excavation, including the subfields of palaeopathology, paleoradiology, cultural and ethnographic context, provenance studies, paleogenetics, and physiological analyses. The template allows lecturers to generate their own versions of the tool for any topic of interest by simply changing the text and pictures. Tests undertaken with students of evolutionary medicine showed that the tool was helpful during their studies. Lecturers commented that they appreciated having a similar tool in other fields.<br><br>CONCLUSIONS AND IMPLICATIONS: Mummy Explorer fills a gap in the virtual teaching landscape of highly interdisciplinary fields such as evolutionary medicine. It will be offered for free download and can be adapted to any educational topic. Translations into German and possibly other languages are in progress.}, }
@article {pmid37250315, year = {2023}, author = {Clavel, P and Louis, L and Sarkissian, C and Thèves, C and Gillet, C and Chauvey, L and Tressières, G and Schiavinato, S and Calvière-Tonasso, L and Telmon, N and Clavel, B and Jonvel, R and Tzortzis, S and Bouniol, L and Fémolant, JM and Klunk, J and Poinar, H and Signoli, M and Costedoat, C and Spyrou, MA and Seguin-Orlando, A and Orlando, L}, title = {Improving the extraction of ancient Yersinia pestis genomes from the dental pulp.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106787}, pmid = {37250315}, issn = {2589-0042}, abstract = {Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17[th] and 18[th] centuries Common Era.}, }
@article {pmid37239398, year = {2023}, author = {Buss, DL and Atmore, LM and Zicos, MH and Goodall-Copestake, WP and Brace, S and Archer, FI and Baker, CS and Barnes, I and Carroll, EL and Hart, T and Kitchener, AC and Sabin, R and Sremba, AL and Weir, CR and Jackson, JA}, title = {Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239398}, issn = {2073-4425}, mesh = {Animals ; *Fin Whale/genetics ; Whales/genetics ; Population Density ; Antarctic Regions ; }, abstract = {Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.}, }
@article {pmid37239354, year = {2023}, author = {Thomas, JT and Cavagnino, C and Kjelland, K and Anderson, E and Sturk-Andreaggi, K and Daniels-Higginbotham, J and Amory, C and Spatola, B and Moran, K and Parson, W and Marshall, C}, title = {Evaluating the Usefulness of Human DNA Quantification to Predict DNA Profiling Success of Historical Bone Samples.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239354}, issn = {2073-4425}, mesh = {Humans ; *DNA Fingerprinting/methods ; *Microsatellite Repeats/genetics ; Bone and Bones ; DNA, Mitochondrial/genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {This study assessed the usefulness of DNA quantification to predict the success of historical samples when analyzing SNPs, mtDNA, and STR targets. Thirty burials from six historical contexts were utilized, ranging in age from 80 to 800 years postmortem. Samples underwent library preparation and hybridization capture with two bait panels (FORCE and mitogenome), and STR typing (autosomal STR and Y-STR). All 30 samples generated small (~80 bp) autosomal DNA target qPCR results, despite mean mappable fragments ranging from 55-125 bp. The qPCR results were positively correlated with DNA profiling success. Samples with human DNA inputs as low as 100 pg resulted in ≥80% FORCE SNPs at 10X coverage. All 30 samples resulted in mitogenome coverage ≥100X despite low human DNA input (as low as 1 pg). With PowerPlex Fusion, ≥30 pg human DNA input resulted in >40% of auSTR loci. At least 59% of Y-STR loci were recovered with Y-target qPCR-based inputs of ≥24 pg. The results also indicate that human DNA quantity is a better predictor of success than the ratio of human to exogenous DNA. Accurate quantification with qPCR is feasible for historical bone samples, allowing for the screening of extracts to predict the success of DNA profiling.}, }
@article {pmid37237270, year = {2023}, author = {Nedoluzhko, A}, title = {Sea of opportunities: marine genomics in an era of global environmental change.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {286}, pmid = {37237270}, issn = {1471-2164}, mesh = {Oceans and Seas ; *Aquatic Organisms/genetics ; *Ecosystem ; Genomics ; Seawater ; }, abstract = {Overexploitation of natural resources and pollution of seas, acidification of the ocean, and rising temperatures all contribute to the destruction of marine habitats and, in 2015, the protection of the ocean became one of the UN Sustainable Development Goals (SDG 14: Life Below Water). This collection aims to highlight the molecular genetic changes currently happening in marine organisms.}, }
@article {pmid37224187, year = {2023}, author = {Gibbon, VE and Feris, L and Gretzinger, J and Smith, K and Hall, S and Penn, N and Mutsvangwa, TEM and Heale, M and Finaughty, DA and Karanja, YW and Esterhuyse, J and Kotze, D and Barnes, N and Gunston, G and May, J and Krause, J and Wilkinson, CM and Schiffels, S and Februarie, D and Alves, S and Sealy, JC}, title = {Confronting historical legacies of biological anthropology in South Africa-Restitution, redress and community-centered science: The Sutherland Nine.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0284785}, pmid = {37224187}, issn = {1932-6203}, mesh = {Humans ; South Africa ; *Anthropology ; *Archaeology ; Cemeteries ; DNA, Ancient ; }, abstract = {We describe a process of restitution of nine unethically acquired human skeletons to their families, together with attempts at redress. Between 1925-1927 C.E., the skeletonised remains of nine San or Khoekhoe people, eight of them known-in-life, were removed from their graves on the farm Kruisrivier, near Sutherland in the Northern Cape Province of South Africa. They were donated to the Anatomy Department at the University of Cape Town. This was done without the knowledge or permission of their families. The donor was a medical student who removed the remains from the labourers' cemetery on his family farm. Nearly 100 years later, the remains are being returned to their community, accompanied by a range of community-driven interdisciplinary historical, archaeological and analytical (osteobiographic, craniofacial, ancient DNA, stable isotope) studies to document, as far as possible, their lives and deaths. The restitution process began by contacting families living in the same area with the same surnames as the deceased. The restitution and redress process prioritises the descendant families' memories, wishes and desire to understand the situation, and learn more about their ancestors. The descendant families have described the process as helping them to reconnect with their ancestors. A richer appreciation of their ancestors' lives, gained in part from scientific analyses, culminating with reburial, is hoped to aid the descendant families and wider community in [re-]connecting with their heritage and culture, and contribute to restorative justice, reconciliation and healing while confronting a traumatic historical moment. While these nine individuals were exhumed as specimens, they will be reburied as people.}, }
@article {pmid37220274, year = {2023}, author = {Tobler, R and Souilmi, Y and Huber, CD and Bean, N and Turney, CSM and Grey, ST and Cooper, A}, title = {The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {22}, pages = {e2213061120}, pmid = {37220274}, issn = {1091-6490}, mesh = {Humans ; Animals ; Africa ; *Neanderthals ; Acclimatization ; Arabia ; Selection, Genetic ; }, abstract = {The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.}, }
@article {pmid37216609, year = {2023}, author = {Ciecierski, L and Stolarek, I and Figlerowicz, M}, title = {Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics.}, journal = {Nucleic acids research}, volume = {51}, number = {W1}, pages = {W269-W273}, pmid = {37216609}, issn = {1362-4962}, mesh = {Humans ; *Genomics/methods ; Software ; Human Genetics ; DNA, Ancient ; Databases, Genetic ; }, abstract = {Archeogenomics is a rapidly growing interdisciplinary research field driven by the development of techniques that enable the acquisition and analysis of ancient DNA (aDNA). Recent advances in aDNA studies have contributed significantly to increasing our understanding of the natural history of humans. One of the most significant challenges facing archeogenomics is the integration of highly heterogeneous genomic, archeological, and anthropological data and their comprehensive analysis, considering changes that occur in time and space. Only this complex approach can explain the relationship between past populations in the context of migration or cultural development. To address these challenges, we developed a Human AGEs web server. It focuses on creating comprehensive spatiotemporal visualizations of genomic, archeogenomic, and archeological information, which can be provided by the user or loaded from a graph database. The interactive map application at the center of Human AGEs can display multiple layers of data in various forms, such as bubble charts, pie charts, heatmaps, or tag clouds. These visualizations can be modified using various clustering, filtering, and styling options, and the map state can be exported to a high-resolution image or saved as a session file for later use. Human AGEs, along with their tutorial, are accessible at https://archeogenomics.eu/.}, }
@article {pmid37215481, year = {2023}, author = {Mármol-Sánchez, E and Heidemann, PL and Gredal, H and Cirera, S}, title = {MicroRNA profiling of cerebrospinal fluid from dogs with steroid responsive meningitis-arteritis and meningoencephalitis of unknown origin.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1144084}, pmid = {37215481}, issn = {2297-1769}, abstract = {INTRODUCTION: Non-infectious inflammatory diseases of the central nervous system in dogs, such as steroid responsive meningitis-arteritis (SRMA) and meningoencephalitis of unknown origin (MUO), represent a common clinical challenge that needs extensive and multimodal work-up to reach a presumptive diagnosis. Both diseases are presumably caused by dysregulations of the immune system, but further research is needed in order to understand the molecular mechanisms behind each disease and to optimize treatment.<br><br>METHODS: By next-generation sequencing and subsequent quantitative real-time PCR (qPCR) verification, we designed a prospective case-control pilot study to analyze the small RNA profiles of cerebrospinal fluid from dogs suffering from MUO (N = 5), dogs suffering from SRMA (N = 8), and healthy dogs (N = 5) presented for elective euthanasia used as the Control group.<br><br>RESULTS: Our results showed an overall enrichment in Y-RNA fragments across all samples, followed by microRNAs (miRNAs) and ribosomal RNAs as the major findings. Additional traces of short RNA reads mapped to long non-coding RNAs and protein-coding genes were also found. From the detected canine miRNAs, miR-21, miR-486, miR-148a, miR-99a, miR-191 and miR-92a were among the most abundant. Dogs with SRMA showed higher differences in miRNA abundance than dogs with MUO when compared to healthy dogs, and miR-142-3p was consistently detected as differentially upregulated in both diseases, although at a low concentration. Moreover, miR-405-5p and miR-503-5p showed different profiles between SRMA and MUO dogs. Subsequent qPCR analyses confirmed miR-142-5p, miR-191-5p and miR-92a-3p as significantly upregulated miRNAs in dogs with SRMA and/or MUO.<br><br>DISCUSSION: Cerebrospinal fluid is a challenging biological material to use for profiling miRNAs due to the low content of circulating RNAs. Despite this, we could confirm several miRNAs being differentially abundant when comparing healthy dogs and dogs with MUO and SRMA, respectively. The results of this study indicate a potential role of miRNAs in the underlying molecular mechanisms of these diseases and establish the basis for further studies.}, }
@article {pmid37212188, year = {2023}, author = {Bunce, M}, title = {It is time for ancient DNA to sweat the small stuff.}, journal = {Molecular ecology}, volume = {32}, number = {11}, pages = {2689-2691}, doi = {10.1111/mec.16970}, pmid = {37212188}, issn = {1365-294X}, mesh = {Animals ; *DNA, Ancient ; Sweat ; DNA/genetics ; Biological Evolution ; Birds/genetics ; *Mammoths/genetics ; Fossils ; Phylogeny ; }, abstract = {When one thinks of the field of ancient DNA it conjures images of extinct megafauna, from mammoths and woolly rhinos, through to the giant, flightless elephant bird (but hopefully not dinosaurs - despite the pervasive idea of 'dino DNA' from Jurassic park). These taxa have fascinating evolutionary histories, and their extinction stories need to be told. At the other end of the vertebrate scale, however, is the often neglected 'small stuff' - lizards, frogs, and other herpetofauna. But here's the rub - extracting DNA from the bones of this 'small stuff' is not only difficult, it often destroys the sample. In this issue, Scarsbrook et al. (2023) describe a new way to study the ancient (or historical) DNA of small vertebrates that is minimally destructive. The authors use the method to reconstruct the dynamic evolutionary history of New Zealand geckos and make new insights into how remnant populations should be managed. This work provides some key insights into New Zealand geckos but also opens up opportunities of biomolecular research on the smallest of vouchered vertebrate samples held within museum collections.}, }
@article {pmid37208611, year = {2023}, author = {Sharko, F and Rbbani, G and Siriyappagouder, P and Raeymaekers, JAM and Galindo-Villegas, J and Nedoluzhko, A and Fernandes, JMO}, title = {CircPrime: a web-based platform for design of specific circular RNA primers.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {205}, pmid = {37208611}, issn = {1471-2105}, support = {683210/ERC_/European Research Council/International ; }, mesh = {*RNA, Circular/genetics ; *RNA/genetics ; Sequence Analysis, RNA/methods ; Polymerase Chain Reaction ; Computational Biology/methods ; Internet ; }, abstract = {BACKGROUND: Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase chain reaction (PCR) cross-validation for circRNAs predicted by bioinformatic tools remains an essential part of any circRNA study before publication.<br><br>RESULTS: Here, we present the CircPrime web-based platform, providing a user-friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods.<br><br>CONCLUSIONS: User-friendly CircPrime web platform (http://circprime.elgene.net/) works with outputs of the most popular bioinformatic predictors of circRNAs to design specific circular RNA primers. CircPrime works with circRNA coordinates and any reference genome from the National Center for Biotechnology Information database).}, }
@article {pmid37207647, year = {2023}, author = {Fleskes, RE and Owsley, DW and Bruwelheide, KS and Barca, KG and Griffith, DR and Cabana, GS and Schurr, TG}, title = {Historical genomes elucidate European settlement and the African diaspora in Delaware.}, journal = {Current biology : CB}, volume = {33}, number = {11}, pages = {2350-2358.e7}, doi = {10.1016/j.cub.2023.04.069}, pmid = {37207647}, issn = {1879-0445}, mesh = {Adult ; Child ; Humans ; *Black People/genetics ; Delaware ; DNA, Mitochondrial/genetics ; Genetics, Population ; Haplotypes ; *Human Migration ; White ; Black or African American ; }, abstract = {The 17[th]-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.[1] The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.[2] European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.[3][,][4] To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.[5] Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17[th] and early 18[th] century North America.}, }
@article {pmid37187366, year = {2023}, author = {Wilke, T and Kehlmaier, C and Stelbrink, B and Albrecht, C and Bouchet, P}, title = {Historical DNA solves century-old mystery on sessility in freshwater gastropods.}, journal = {Molecular phylogenetics and evolution}, volume = {185}, number = {}, pages = {107813}, doi = {10.1016/j.ympev.2023.107813}, pmid = {37187366}, issn = {1095-9513}, mesh = {Animals ; Phylogeny ; *Fresh Water ; *Rivers ; DNA/genetics ; Snails/genetics ; }, abstract = {Extinction rates are increasing unabatedly but resources available for conservation action are limited. Therefore, some conservationists are pushing for ecology- and evolution-based conservation choices, prioritizing taxa with phylogenetic and trait-based originality. Extinction of original taxa may result in a disproportionate loss of evolutionary innovations and potentially prevent transformative changes in living systems. Here, we generated historical DNA data from an almost 120-year-old syntype of the enigmatic sessile snail Helicostoa sinensis from the Three Gorges region of the Yangtze River (PR China), using a next-generation sequencing protocol developed for ancient DNA. In a broader phylogenetic context, we assessed the phylogenetic and trait-based originality of this enigmatic taxon to solve the century-old puzzle of sessility in freshwater gastropods. Our multi-locus data confirm the phylogenetic and trait-based originality of H. sinensis. It is an ultra-rare, subfamily-level taxon (Helicostoinae stat. nov.) within the family Bithyniidae, which exhibits the evolutionary innovation of sessility. While we conservatively classify H. sinensis as "Critically Endangered", there is mounting evidence of the biological annihilation of this endemic species. Although rapidly rising extinction rates in invertebrates are increasingly recognized, the potential loss of originality in these "little things that run the world" has received little attention. We therefore call for comprehensive surveys of originality in invertebrates, particularly from extreme environments such as rapids of large rivers, as a basis for urgently needed ecology- and evolution-based conservation decisions.}, }
@article {pmid37167404, year = {2023}, author = {Llamas, B and Roca-Rada, X}, title = {Paleogenomic study of the Mexican past.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6645}, pages = {578-579}, doi = {10.1126/science.adh7902}, pmid = {37167404}, issn = {1095-9203}, mesh = {Humans ; *DNA, Ancient ; Mexico ; *North American People/genetics/history ; Anthropology ; Genomics ; Demography ; }, abstract = {Ancient DNA analysis of ancestral Mexicans reveals a complex demographic history.}, }
@article {pmid37163039, year = {2023}, author = {Pandey, D and Harris, M and Garud, NR and Narasimhan, VM}, title = {Understanding natural selection in Holocene Europe using multi-locus genotype identity scans.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37163039}, issn = {2692-8205}, support = {T32 GM008185/GM/NIGMS NIH HHS/United States ; T32 HG002536/HG/NHGRI NIH HHS/United States ; }, abstract = {Ancient DNA (aDNA) has been a revolutionary technology in understanding human history but has not been used extensively to study natural selection as large sample sizes to study allele frequency changes over time have thus far not been available. Here, we examined a time transect of 708 published samples over the past 7,000 years of European history using multi-locus genotype-based selection scans. As aDNA data is affected by high missingness, ascertainment bias, DNA damage, random allele calling, and is unphased, we first validated our selection scan, G12ancient, on simulated data resembling aDNA under a demographic model that captures broad features of the allele frequency spectrum of European genomes as well as positive controls that have been previously identified and functionally validated in modern European datasets on data from ancient individuals from time periods very close to the present time. We then applied our statistic to the aDNA time transect to detect and resolve the timing of natural selection occurring genome wide and found several candidates of selection across the different time periods that had not been picked up by selection scans using single SNP allele frequency approaches. In addition, enrichment analysis discovered multiple categories of complex traits that might be under adaptation across these periods. Our results demonstrate the utility of applying different types of selection scans to aDNA to uncover putative selection signals at loci in the ancient past that might have been masked in modern samples.}, }
@article {pmid37157914, year = {2023}, author = {Whitehouse, LS and Schrider, DR}, title = {Timesweeper: accurately identifying selective sweeps using population genomic time series.}, journal = {Genetics}, volume = {224}, number = {3}, pages = {}, pmid = {37157914}, issn = {1943-2631}, support = {R01 AI153523/AI/NIAID NIH HHS/United States ; R35 GM138286/GM/NIGMS NIH HHS/United States ; R35GM138286/GF/NIH HHS/United States ; }, mesh = {*Metagenomics ; Time Factors ; *Genetics, Population ; Polymorphism, Genetic ; Selection, Genetic ; }, abstract = {Despite decades of research, identifying selective sweeps, the genomic footprints of positive selection, remains a core problem in population genetics. Of the myriad methods that have been developed to tackle this task, few are designed to leverage the potential of genomic time-series data. This is because in most population genetic studies of natural populations, only a single period of time can be sampled. Recent advancements in sequencing technology, including improvements in extracting and sequencing ancient DNA, have made repeated samplings of a population possible, allowing for more direct analysis of recent evolutionary dynamics. Serial sampling of organisms with shorter generation times has also become more feasible due to improvements in the cost and throughput of sequencing. With these advances in mind, here we present Timesweeper, a fast and accurate convolutional neural network-based tool for identifying selective sweeps in data consisting of multiple genomic samplings of a population over time. Timesweeper analyzes population genomic time-series data by first simulating training data under a demographic model appropriate for the data of interest, training a one-dimensional convolutional neural network on said simulations, and inferring which polymorphisms in this serialized data set were the direct target of a completed or ongoing selective sweep. We show that Timesweeper is accurate under multiple simulated demographic and sampling scenarios, identifies selected variants with high resolution, and estimates selection coefficients more accurately than existing methods. In sum, we show that more accurate inferences about natural selection are possible when genomic time-series data are available; such data will continue to proliferate in coming years due to both the sequencing of ancient samples and repeated samplings of extant populations with faster generation times, as well as experimentally evolved populations where time-series data are often generated. Methodological advances such as Timesweeper thus have the potential to help resolve the controversy over the role of positive selection in the genome. We provide Timesweeper as a Python package for use by the community.}, }
@article {pmid37153511, year = {2023}, author = {Sharko, FS and Zhur, KV and Trifonov, VA and Prokhortchouk, EB}, title = {Distortion of Population Statistics due to the Use of Different Methodological Approaches to the Construction of Genomic DNA Libraries.}, journal = {Acta naturae}, volume = {15}, number = {1}, pages = {87-96}, pmid = {37153511}, issn = {2075-8251}, abstract = {Several different methods of DNA library preparation for paleogenetic studies are now available. However, the chemical reactions underlying each of them can affect the primary sequence of ancient DNA (aDNA) in the libraries and taint the results of a statistical analysis. In this paper, we compare the results of a sequencing of the aDNA libraries of a Bronze Age sample from burials of the Caucasian burial ground Klady, prepared using three different approaches: (1) shotgun sequencing, (2) strategies for selecting target genomic regions, and (3) strategies for selecting target genomic regions, including DNA pre-treatment with a mixture of uracil-DNA glycosylase (UDG) and endonuclease VIII. The impact of the studied approaches to genomic library preparation on the results of a secondary analysis of the statistical data, namely F4 statistics, ADMIXTURE, and principal component analysis (PCA), was analyzed. It was shown that preparation of genomic libraries without the use of UDG can result in distorted statistical data due to postmortem chemical modifications of the aDNA. This distortion can be alleviated by analyzing only the single nucleotide polymorphisms caused by transversions in the genome.}, }
@article {pmid37141673, year = {2023}, author = {Zupanič Pajnič, I and Leskovar, T and Zupanc, T and Podovšovnik, E}, title = {A fast and highly efficient automated DNA extraction method from small quantities of bone powder from aged bone samples.}, journal = {Forensic science international. Genetics}, volume = {65}, number = {}, pages = {102882}, doi = {10.1016/j.fsigen.2023.102882}, pmid = {37141673}, issn = {1878-0326}, mesh = {Humans ; Aged ; Powders ; Edetic Acid ; *DNA Fingerprinting/methods ; *Microsatellite Repeats ; DNA ; }, abstract = {An efficient extraction method is important for obtaining high-quality DNA from degraded aged bone samples. An automated full-demineralization method using the EDTA and DNA Investigator Kit (Qiagen) combined with Qiagen's biorobots was optimized in our laboratory in the past to extract the DNA from 500 mg of aged bone samples. The purpose of this research was to further improve the method with the aim of reducing the required sample material, shortening the extraction time, and achieving higher throughput. To process extremely small samples, the amount of bone powder was reduced to 75 mg, EDTA was replaced with reagents from the Bone DNA Extraction Kit (Promega), and decalcification was shortened from overnight to 2.5 h. Instead of 50 ml tubes, 2 ml tubes were used, which allows higher throughput. The DNA Investigator Kit (Qiagen) and EZ1 Advanced XL biorobot (Qiagen) was used for DNA purification. A comparison between both extraction methods was made on 29 Second World War bones and 22 archaeological bone samples. The differences between both methods were explored by measuring nuclear DNA yield and STR typing success. After cleaning the samples, 500 mg of bone powder was processed using EDTA, and 75 mg of powder from the same bone was processed using the Bone DNA Extraction Kit (Promega). DNA content and DNA degradation were determined using PowerQuant (Promega), and the PowerPlex ESI 17 Fast System (Promega) was used for STR typing. The results showed that the full-demineralization protocol using 500 mg of bone was efficient for Second World War and archaeological samples, and the partial-demineralization protocol using 75 mg of bone powder was only efficient for the Second World War bones. The improved extraction method-for which significantly lower amounts of bone powder can be used, the extraction process is faster, and higher throughput of bone samples is possible-is applicable for genetic identification of relatively well-preserved aged bone samples in routine forensic analyses.}, }
@article {pmid37141315, year = {2023}, author = {Klapper, M and Hübner, A and Ibrahim, A and Wasmuth, I and Borry, M and Haensch, VG and Zhang, S and Al-Jammal, WK and Suma, H and Fellows Yates, JA and Frangenberg, J and Velsko, IM and Chowdhury, S and Herbst, R and Bratovanov, EV and Dahse, HM and Horch, T and Hertweck, C and González Morales, MR and Straus, LG and Vilotijevic, I and Warinner, C and Stallforth, P}, title = {Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6645}, pages = {619-624}, doi = {10.1126/science.adf5300}, pmid = {37141315}, issn = {1095-9203}, mesh = {Animals ; Humans ; *Biological Products/metabolism ; *Genome, Bacterial ; *Hominidae/genetics ; Metagenome ; *Neanderthals/genetics ; *Furans/metabolism ; DNA, Ancient ; }, abstract = {Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. We investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans ranging from 100,000 years ago to the present and reconstructed 459 bacterial metagenome-assembled genomes. We identified a biosynthetic gene cluster shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites that we name "paleofurans." This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.}, }
@article {pmid37138779, year = {2023}, author = {Aqil, A and Gill, S and Gokcumen, O and Malhi, RS and Reese, EA and Smith, JL and Heaton, TT and Lindqvist, C}, title = {A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106581}, pmid = {37138779}, issn = {2589-0042}, abstract = {Many specifics of the population histories of the Indigenous peoples of North America remain contentious owing to a dearth of physical evidence. Only few ancient human genomes have been recovered from the Pacific Northwest Coast, a region increasingly supported as a coastal migration route for the initial peopling of the Americas. Here, we report paleogenomic data from the remains of a ∼3,000-year-old female individual from Southeast Alaska, named Tatóok yík yées sháawat (TYYS). Our results demonstrate at least 3,000 years of matrilineal genetic continuity in Southeast Alaska, and that TYYS is most closely related to ancient and present-day northern Pacific Northwest Coast Indigenous Americans. We find no evidence of Paleo-Inuit (represented by Saqqaq) ancestry in present-day or ancient Pacific Northwest peoples. Instead, our analyses suggest the Saqqaq genome harbors Northern Native American ancestry. This study sheds further light on the human population history of the northern Pacific Northwest Coast.}, }
@article {pmid37137206, year = {2023}, author = {Zupanič Pajnič, I and Geršak, &#x17d;M and Leskovar, T and Črešnar, M}, title = {Kinship analysis of 5th- to 6th-century skeletons of Romanized indigenous people from the Bled-Pristava archaeological site.}, journal = {Forensic science international. Genetics}, volume = {65}, number = {}, pages = {102886}, doi = {10.1016/j.fsigen.2023.102886}, pmid = {37137206}, issn = {1878-0326}, mesh = {Female ; Child ; Humans ; Male ; Middle Aged ; Powders ; *DNA Fingerprinting ; *DNA/genetics ; Bone and Bones ; Microsatellite Repeats ; Chromosomes, Human, Y ; Indigenous Peoples ; Haplotypes ; }, abstract = {The familial relationship between skeletons buried together in a shared grave is important for understanding the burial practices of past human populations. Four skeletons were excavated from the Late Antiquity part of the Bled-Pristava burial site in Slovenia, dated to the 5th to 6th century. They were anthropologically characterized as two adults (a middle-aged man and a young woman) and two non-adults (of unknown sex). Based on stratigraphy, the skeletons were considered to be buried simultaneously in one grave. Our aim was to determine whether the skeletons were related. Petrous bones and teeth were used for genetic analysis. Specific precautions were followed to prevent contamination of ancient DNA with contemporary DNA, and an elimination database was established. Bone powder was obtained using a MillMix tissue homogenizer. Prior to extracting the DNA using Biorobot EZ1, 0.5 g of powder was decalcified. The PowerQuant System was used for quantification, various autosomal kits for autosomal short tandem repeat (STR) typing, and the PowerPlex Y23 kit for Y-STR typing. All analyses were performed in duplicate. Up to 28 ng DNA/g of powder was extracted from the samples analyzed. Almost full autosomal STR profiles obtained from all four skeletons and almost full Y-STR haplotypes obtained from two male skeletons were compared, and the possibility of a familial relationship was evaluated. No amplification was obtained in the negative controls, and no match was found in the elimination database. Autosomal STR statistical calculations confirmed that the adult male was the father of two non-adult individuals and one young adult individual from the grave. The relationship between the males (father and son) was additionally confirmed by an identical Y-STR haplotype that belonged to the E1b1b haplogroup, and a combined likelihood ratio for autosomal and Y-STRs was calculated. Kinship analysis confirmed with high confidence (kinship probability greater than 99.9% was calculated for all three children) that all four skeletons belonged to the same family (a father, two daughters, and a son). Through genetic analysis, the burial of members of the same family in a shared grave was confirmed as a burial practice of the population living in the Bled area in Late Antiquity.}, }
@article {pmid37127762, year = {2023}, author = {Zupanič Pajnič, I and Leskovar, T and Črešnar, M}, title = {Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology.}, journal = {International journal of legal medicine}, volume = {137}, number = {4}, pages = {1007-1015}, pmid = {37127762}, issn = {1437-1596}, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *DNA Fingerprinting ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; DNA ; Skeleton ; Probability ; Sequence Analysis, DNA ; }, abstract = {In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 10[7] (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.}, }
@article {pmid37117261, year = {2023}, author = {Ferrando-Bernal, M}, title = {Ancient DNA suggests anaemia and low bone mineral density as the cause for porotic hyperostosis in ancient individuals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6968}, pmid = {37117261}, issn = {2045-2322}, mesh = {Humans ; Skull ; DNA, Ancient ; Paleopathology ; *Anemia/complications ; *Hyperostosis/genetics ; *Bone Diseases, Metabolic/complications ; }, abstract = {Porotic hyperostosis (PH) is a disease that had high prevalence during the Neolithic. Several hypotheses have been suggested to explain the origin of the disease, such as an iron deficiency diet, low B12 intake, malaria caused by Plasmodium spp., low haemoglobin levels or low vitamin D levels. None of these hypotheses have been tested genetically. Here, I calculated different genetic scores to test each hypothesis. Additionally, I calculated a genetic score of bone mineral density as it is a phenotype that seems to be selected in ancient Europeans. I apply these genetic scores on 80 ancient samples, 33 with diagnosed PH. The results seem to suggest anaemia and low bone mineral density as the main cause for this disease. Additionally, Neolithic individuals show the lowest genetic risk score for bone mineral density of all other periods tested here, which may explain the highest prevalence of the porotic hyperostosis during this age.}, }
@article {pmid37114314, year = {2022}, author = {Benítez-Burraco, A and Torres-Ruiz, R and Gelabert, P and Lalueza-Fox, C and Rodríguez-Perales, S and García-Bellido, P}, title = {Human-specific changes in two functional enhancers of FOXP2.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {68}, number = {11}, pages = {16-19}, doi = {10.14715/cmb/2022.68.11.3}, pmid = {37114314}, issn = {1165-158X}, mesh = {Humans ; *Forkhead Transcription Factors/genetics/metabolism ; }, abstract = {FOXP2 is a gene involved in language development and function. Neanderthals and humans share the same coding region of the gene, although the formers are thought to have exhibited less sophisticated language abilities. In this paper, we report on several human-specific changes in two functional enhancers of FOXP2. Two of these variants are located within the binding sites for the transcription factors POLR2A and SMARCC1, respectively. Interestingly, SMARCC1 is involved in brain development and vitamin D metabolism. We hypothesize that the human specific change in this position might have resulted in a different regulation pattern of FOXP2 expression in our species compared to extinct hominins, with a potential impact on our language abilities.}, }
@article {pmid37101579, year = {2023}, author = {Kowal, E and Weyrich, LS and Argüelles, JM and Bader, AC and Colwell, C and Cortez, AD and Davis, JL and Figueiro, G and Fox, K and Malhi, RS and Matisoo-Smith, E and Nayak, A and Nelson, EA and Nicholas, G and Nieves-Colón, MA and Russell, L and Ulm, S and Vergara-Silva, F and Villanea, FA and Wagner, JK and Yracheta, JM and Tsosie, KS}, title = {Community partnerships are fundamental to ethical ancient DNA research.}, journal = {HGG advances}, volume = {4}, number = {2}, pages = {100161}, pmid = {37101579}, issn = {2666-2477}, mesh = {Humans ; *DNA, Ancient ; *Ethics, Research ; Family ; Population Groups ; Research Personnel ; *Human Genetics/ethics ; Guidelines as Topic ; Stakeholder Participation ; Community-Institutional Relations ; }, abstract = {The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article "Ethics of DNA research on human remains: five globally applicable guidelines" published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of "scientific" and "community" concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines' authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on "ethical" grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research.}, }
@article {pmid37096383, year = {2023}, author = {da Silva Coelho, FA and Gill, S and Tomlin, CM and Papavassiliou, M and Farley, SD and Cook, JA and Sonsthagen, SA and Sage, GK and Heaton, TH and Talbot, SL and Lindqvist, C}, title = {Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska.}, journal = {Molecular ecology}, volume = {32}, number = {13}, pages = {3641-3656}, doi = {10.1111/mec.16960}, pmid = {37096383}, issn = {1365-294X}, mesh = {Animals ; *Ursidae/genetics ; Alaska ; Refugium ; *Genome, Mitochondrial ; North America ; }, abstract = {During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (Ursus americanus) and brown (U. arctos) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.}, }
@article {pmid37072186, year = {2023}, author = {Fernandes, DM and Sirak, KA and Cheronet, O and Novak, M and Brück, F and Zelger, E and Llanos-Lizcano, A and Wagner, A and Zettl, A and Mandl, K and Duffet Carlson, KS and Oberreiter, V and Özdoğan, KT and Sawyer, S and La Pastina, F and Borgia, E and Coppa, A and Dobeš, M and Velemínský, P and Reich, D and Bell, LS and Pinhasi, R}, title = {Density separation of petrous bone powders for optimized ancient DNA yields.}, journal = {Genome research}, volume = {33}, number = {4}, pages = {622-631}, pmid = {37072186}, issn = {1549-5469}, support = {M 3108/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; *DNA, Ancient ; *Petrous Bone ; Powders ; Plastics ; DNA/genetics ; }, abstract = {Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders before DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using nontoxic heavy liquid solutions, we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into eight density intervals (2.15 to 2.45 g/cm[3], in 0.05 increments). We found that the 2.30 to 2.35 g/cm[3] and 2.35 to 2.40 g/cm[3] intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and not reducing library complexity. Although small 0.05 g/cm[3] intervals may maximally optimize yields, a single separation to remove materials with a density above 2.40 g/cm[3] yielded up to 2.57-fold more endogenous DNA on average, which enables the simultaneous separation of samples that vary in preservation or in the type of material analyzed. While requiring no new ancient DNA laboratory equipment and fewer than 30 min of extra laboratory work, the implementation of density separation before DNA extraction can substantially boost endogenous DNA yields without decreasing library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments.}, }
@article {pmid37071008, year = {2023}, author = {Vassallo, A and Modi, A and Quagliariello, A and Bacci, G and Faddetta, T and Gallo, M and Provenzano, A and La Barbera, A and Lombardo, G and Maggini, V and Firenzuoli, F and Zaccaroni, M and Gallo, G and Caramelli, D and Aleo Nero, C and Baldi, F and Fani, R and Palumbo Piccionello, A and Pucciarelli, S and Puglia, AM and Sineo, L}, title = {Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy).}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0437422}, pmid = {37071008}, issn = {2165-0497}, mesh = {Animals ; Humans ; Sicily ; *Bacteria ; *Biodiversity ; Anti-Bacterial Agents ; Soil/chemistry ; }, abstract = {The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.}, }
@article {pmid37070964, year = {2023}, author = {Vallebueno-Estrada, M and Hernández-Robles, GG and González-Orozco, E and Lopez-Valdivia, I and Rosales Tham, T and Vásquez Sánchez, V and Swarts, K and Dillehay, TD and Vielle-Calzada, JP and Montiel, R}, title = {Domestication and lowland adaptation of coastal preceramic maize from Paredones, Peru.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37070964}, issn = {2050-084X}, mesh = {Peru ; *Domestication ; *Zea mays/genetics ; South America ; Mexico ; }, abstract = {Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating ~6700-5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by ~6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.}, }
@article {pmid37065506, year = {2023}, author = {Gancz, AS and Weyrich, LS}, title = {Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {109}, pmid = {37065506}, issn = {2046-1402}, mesh = {Humans ; *Noncommunicable Diseases/epidemiology ; *Microbiota/genetics ; *Diabetes Mellitus/epidemiology ; Diet ; Prevalence ; }, abstract = {Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.}, }
@article {pmid37068234, year = {2023}, author = {Cohen, P and Bacilieri, R and Ramos-Madrigal, J and Privman, E and Boaretto, E and Weber, A and Fuks, D and Weiss, E and Erickson-Gini, T and Bucking, S and Tepper, Y and Cvikel, D and Schmidt, J and Gilbert, MTP and Wales, N and Bar-Oz, G and Meiri, M}, title = {Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {17}, pages = {e2213563120}, pmid = {37068234}, issn = {1091-6490}, mesh = {History, Ancient ; *Vitis/genetics ; *Wine ; DNA, Ancient ; Archaeology ; Israel ; }, abstract = {Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.}, }
@article {pmid37066305, year = {2023}, author = {Mallick, S and Micco, A and Mah, M and Ringbauer, H and Lazaridis, I and Olalde, I and Patterson, N and Reich, D}, title = {The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37066305}, issn = {2692-8205}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, abstract = {More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases since it first was made available and crossed the threshold of >10,000 ancient individuals with genome-wide data at the end of 2022. This note is intended as a citable description of the AADR.}, }
@article {pmid37059363, year = {2023}, author = {Kattner, AA}, title = {When it doesn't run in the blood(vessels) - events involved in vascular disorders.}, journal = {Biomedical journal}, volume = {46}, number = {2}, pages = {100591}, pmid = {37059363}, issn = {2320-2890}, mesh = {Infant, Newborn ; Humans ; Male ; Child ; Follow-Up Studies ; *COVID-19 ; Vesicular Transport Proteins ; }, abstract = {In the current issue of the Biomedical Journal the underlying pathology of hemodynamic compromise in acute small subcortical infarction are elucidated. A follow-up study in patients with childhood Kawasaki disease is presented, as well as an insight into the gradually decreasing antigen expression in cases of acute myeloid leukemia. Furthermore this issue provides an exciting update concerning COVID-19 and the use of CRISPR-Cas, a review about computational approaches in the research of kidney stone formation, factors connected to central precocious puberty, and why a rock star of paleogenetics recently received a Nobel Prize. Additionally, this issue contains an article proposing the repurposing of the lung cancer drug Capmatinib, a study of how the gut microbiome develops in neonates, an impulse about the role of the transmembrane protein TMED3 in esophageal carcinoma, and the revelation about how competing endogenous RNA influences ischemic stroke. Lastly, genetic reasons for male infertility are discussed, as well as the relation between non-alcoholic fatty liver disease and chronic kidney disease.}, }
@article {pmid37057308, year = {2023}, author = {Ķimsis, J and Pokšāne, A and Kazarina, A and Vilcāne, A and Petersone-Gordina, E and Zayakin, P and Gerhards, G and Ranka, R}, title = {Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.}, journal = {Environmental microbiology reports}, volume = {15}, number = {5}, pages = {383-391}, pmid = {37057308}, issn = {1758-2229}, mesh = {Animals ; Humans ; Latvia ; *Microbiota/genetics ; DNA ; Burial ; }, abstract = {In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.}, }
@article {pmid37052272, year = {2023}, author = {Bader, AC and Carbaugh, AE and Davis, JL and Krupa, KL and Malhi, RS}, title = {Biological samples taken from Native American Ancestors are human remains under NAGPRA.}, journal = {American journal of biological anthropology}, volume = {181}, number = {4}, pages = {527-534}, doi = {10.1002/ajpa.24726}, pmid = {37052272}, issn = {2692-7691}, mesh = {Humans ; *American Indian or Alaska Native ; *Indians, North American ; United States ; *Human Body ; Funeral Rites ; *Culture ; *Human Rights/legislation &amp; jurisprudence ; }, abstract = {In the United States, the Native American Graves Protection and Repatriation Act (NAGPRA) provides a specific framework for the disposition of Native American Ancestral remains within its purview. However, samples such as a bone fragment, tooth, or other biological tissue taken from the remains of these Ancestors have been treated by institutions and researchers as independent of the individual from whom they were removed and used in destructive research such as paleogenomic and other archaeometric analyses without consultation, consent, and collaboration from Native American communities; are not cared for in keeping with the current best practices for Indigenous Ancestors; and are not likely to be repatriated to their communities. Here, we demonstrate that any biological samples removed from Ancestors who are covered under NAGPRA must also be handled according to the stipulations defined for "human remains" within the legislation. As such, we are not proposing a change to existing legislation, but rather best practices, specific to the context of the United States and NAGPRA, relating to the use of and care for biological samples taken from Native American Ancestors.}, }
@article {pmid37044651, year = {2023}, author = {Scarsbrook, L and Walton, K and Rawlence, NJ and Hitchmough, RA}, title = {Revision of the New Zealand gecko genus Hoplodactylus, with the description of a new species.}, journal = {Zootaxa}, volume = {5228}, number = {3}, pages = {267-291}, doi = {10.11646/zootaxa.5228.3.3}, pmid = {37044651}, issn = {1175-5334}, mesh = {Animals ; New Zealand ; *Lizards ; }, abstract = {The New Zealand endemic gecko genus Hoplodactylus is revised. Two species are recognized: Hoplodactylus duvaucelii (Duméril &amp; Bibron, 1836) from the North Island and some near-shore islands, and H. tohu n. sp., which was formerly widespread throughout the South Island but is presently restricted to some islands in the Cook Strait region. H. delcourti (Bauer &amp; Russell, 1986) is retained in Hoplodactylus sensu lato in the interest of taxonomic stability, pending further research, but is probably neither congeneric nor from New Zealand.}, }
@article {pmid37043523, year = {2023}, author = {Rümpler, F and Tessari, C and Gramzow, L and Gafert, C and Blohs, M and Theißen, G}, title = {The Origin of Floral Quartet Formation-Ancient Exon Duplications Shaped the Evolution of MIKC-type MADS-domain Transcription Factor Interactions.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37043523}, issn = {1537-1719}, mesh = {*Transcription Factors/metabolism ; Phylogeny ; *MADS Domain Proteins/genetics ; Genes, Plant ; Exons ; Plant Proteins/genetics ; Gene Expression Regulation, Plant ; }, abstract = {During development of flowering plants, some MIKC-type MADS-domain transcription factors (MTFs) exert their regulatory function as heterotetrameric complexes bound to two sites on the DNA of target genes. This way they constitute "floral quartets" or related "floral quartet-like complexes" (FQCs), involving a unique multimeric system of paralogous protein interactions. Tetramerization of MTFs is brought about mainly by interactions of keratin-like (K) domains. The K-domain associated with the more ancient DNA-binding MADS-domain during evolution in the stem group of extant streptophytes (charophyte green algae + land plants). However, whether this was sufficient for MTF tetramerization and FQC formation to occur, remains unknown. Here, we provide biophysical and bioinformatic data indicating that FQC formation likely originated in the stem group of land plants in a sublineage of MIKC-type genes termed MIKCC-type genes. In the stem group of this gene lineage, the duplication of the most downstream exon encoding the K-domain led to a C-terminal elongation of the second K-domain helix, thus, generating the tetramerization interface found in extant MIKCC-type proteins. In the stem group of the sister lineage of the MIKCC-type genes, termed MIKC*-type genes, the duplication of two other K-domain exons occurred, extending the K-domain at its N-terminal end. Our data indicate that this structural change prevents heterodimerization between MIKCC-type and MIKC*-type proteins. This way, two largely independent gene regulatory networks could be established, featuring MIKCC-type or MIKC*-type proteins, respectively, that control different aspects of plant development.}, }
@article {pmid37040705, year = {2023}, author = {Wegmann, D and Eckel, R}, title = {Human evolution: When admixture met selection.}, journal = {Current biology : CB}, volume = {33}, number = {7}, pages = {R259-R261}, doi = {10.1016/j.cub.2023.02.077}, pmid = {37040705}, issn = {1879-0445}, mesh = {Humans ; *DNA, Ancient ; *Biological Evolution ; }, abstract = {Admixture has been a major force during human evolution. Two new studies using ancient DNA now show how two key admixture events in the evolutionary history of Europeans altered their adaptive trajectories and facilitated rapid evolution.}, }
@article {pmid37002784, year = {2023}, author = {Honap, TP and Monroe, CR and Johnson, SJ and Jacobson, DK and Abin, CA and Austin, RM and Sandberg, P and Levine, M and Sankaranarayanan, K and Lewis, CM}, title = {Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era.}, journal = {American journal of biological anthropology}, volume = {182}, number = {4}, pages = {542-556}, doi = {10.1002/ajpa.24735}, pmid = {37002784}, issn = {2692-7691}, support = {NSF BCS-2045308//National Science Foundation/ ; }, mesh = {Humans ; *American Indian or Alaska Native ; Calculi/genetics ; Chloroflexi/genetics ; DNA, Bacterial/analysis ; *Metagenome/genetics ; Periodontitis/microbiology ; Treponema denticola/genetics ; *Mouth/microbiology ; }, abstract = {OBJECTIVES: Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA.<br><br>MATERIALS AND METHODS: Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450&#x2009;CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted.<br><br>RESULTS: Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains.<br><br>DISCUSSION: We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.}, }
@article {pmid39582673, year = {2023}, author = {Armit, I and Fischer, CE and Koon, H and Nicholls, R and Olalde, I and Rohland, N and Buckberry, J and Montgomery, J and Mason, P and Črešnar, M and Büster, L and Reich, D}, title = {Kinship practices in Early Iron Age southeast Europe: genetic and isotopic analysis of burials from the Dolge njive barrow cemetery, Dolenjska, Slovenia.}, journal = {Antiquity}, volume = {97}, number = {392}, pages = {403-418}, pmid = {39582673}, issn = {0003-598X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, abstract = {DNA analysis demonstrates that all seven individuals buried in an Early Iron Age barrow at Dolge njive, southeast Slovenia, are close biological relatives. Although group composition does not suggest strict adherence to a patrilineal or matrilineal kinship system, the funerary tradition appears highly gendered, with family links through both the male and female line being important in structuring communities. We explore the implications for our understandings of kinship and funerary practices in Early Iron Age southeast Europe.}, }
@article {pmid37002389, year = {2023}, author = {Callaway, E}, title = {Ancient DNA illuminates Swahili culture's origins.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37002389}, issn = {1476-4687}, }
@article {pmid36996223, year = {2023}, author = {Curry, A}, title = {'Persian princes' helped found early African trade power.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6639}, pages = {1284-1285}, doi = {10.1126/science.adi0093}, pmid = {36996223}, issn = {1095-9203}, abstract = {Ancient DNA reflects foreign influx to Swahili coast, but its culture is largely local.}, }
@article {pmid36994803, year = {2023}, author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F}, title = {Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis.}, journal = {Molecular ecology resources}, volume = {23}, number = {6}, pages = {1226-1240}, doi = {10.1111/1755-0998.13790}, pmid = {36994803}, issn = {1755-0998}, mesh = {Horses/genetics ; Animals ; *DNA, Ancient ; *Epistasis, Genetic ; DNA/genetics ; Biological Evolution ; Algorithms ; }, abstract = {Innovations in ancient DNA (aDNA) preparation and sequencing technologies have exponentially increased the quality and quantity of aDNA data extracted from ancient biological materials. The additional temporal component from the incoming aDNA data can provide improved power to address fundamental evolutionary questions like characterizing selection processes that shape the phenotypes and genotypes of contemporary populations or species. However, utilizing aDNA to study past selection processes still involves considerable hurdles like how to eliminate the confounding factor of genetic interactions in the inference of selection. To address this issue, we extend the approach of He et al., 2023 to infer temporally variable selection from the aDNA data in the form of genotype likelihoods with the flexibility of modelling linkage and epistasis in this work. Our posterior computation is carried out by a robust adaptive version of the particle marginal Metropolis-Hastings algorithm with a coerced acceptance rate. Our extension inherits the desirable features of He et al., 2023 such as modelling sample uncertainty resulting from the damage and fragmentation of aDNA molecules and reconstructing underlying gamete frequency trajectories of the population. We evaluate its performance through extensive simulations and show its utility with an application to the aDNA data from pigmentation loci in horses.}, }
@article {pmid36993413, year = {2023}, author = {Barton, AR and Santander, CG and Skoglund, P and Moltke, I and Reich, D and Mathieson, I}, title = {Insufficient evidence for natural selection associated with the Black Death.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36993413}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; R01 HG012287/HG/NHGRI NIH HHS/United States ; R35 GM133708/GM/NIGMS NIH HHS/United States ; }, abstract = {Klunk et al. analyzed ancient DNA data from individuals in London and Denmark before, during and after the Black Death [1], and argued that allele frequency changes at immune genes were too large to be produced by random genetic drift and thus must reflect natural selection. They also identified four specific variants that they claimed show evidence of selection including at ERAP2, for which they estimate a selection coefficient of 0.39-several times larger than any selection coefficient on a common human variant reported to date. Here we show that these claims are unsupported for four reasons. First, the signal of enrichment of large allele frequency changes in immune genes comparing people in London before and after the Black Death disappears after an appropriate randomization test is carried out: the P value increases by ten orders of magnitude and is no longer significant. Second, a technical error in the estimation of allele frequencies means that none of the four originally reported loci actually pass the filtering thresholds. Third, the filtering thresholds do not adequately correct for multiple testing. Finally, in the case of the ERAP2 variant rs2549794, which Klunk et al. show experimentally may be associated with a host interaction with Y. pestis, we find no evidence of significant frequency change either in the data that Klunk et al. report, or in published data spanning 2,000 years. While it remains plausible that immune genes were subject to natural selection during the Black Death, the magnitude of this selection and which specific genes may have been affected remains unknown.}, }
@article {pmid36991187, year = {2023}, author = {Brielle, ES and Fleisher, J and Wynne-Jones, S and Sirak, K and Broomandkhoshbacht, N and Callan, K and Curtis, E and Iliev, L and Lawson, AM and Oppenheimer, J and Qiu, L and Stewardson, K and Workman, JN and Zalzala, F and Ayodo, G and Gidna, AO and Kabiru, A and Kwekason, A and Mabulla, AZP and Manthi, FK and Ndiema, E and Ogola, C and Sawchuk, E and Al-Gazali, L and Ali, BR and Ben-Salem, S and Letellier, T and Pierron, D and Radimilahy, C and Rakotoarisoa, JA and Raaum, RL and Culleton, BJ and Mallick, S and Rohland, N and Patterson, N and Mwenje, MA and Ahmed, KB and Mohamed, MM and Williams, SR and Monge, J and Kusimba, S and Prendergast, ME and Reich, D and Kusimba, CM}, title = {Entwined African and Asian genetic roots of medieval peoples of the Swahili coast.}, journal = {Nature}, volume = {615}, number = {7954}, pages = {866-873}, pmid = {36991187}, issn = {1476-4687}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {DNA, Ancient/analysis ; Male ; *Genetics, Population ; History, 16th Century ; Arabs ; India/ethnology ; Mozambique ; Middle Eastern People ; *Asian/genetics ; History, Medieval ; Comoros ; Female ; History, 17th Century ; History, 15th Century ; Kenya ; Indian Ocean ; Arabia/ethnology ; Humans ; *African People/genetics ; Tanzania ; Persia/ethnology ; }, abstract = {The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people[1,2]. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast[3]. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia[4]. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.}, }
@article {pmid36980999, year = {2023}, author = {Toncheva, D and Marinova, M and Chobanov, T and Serbezov, D}, title = {Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980999}, issn = {2073-4425}, mesh = {Animals ; Humans ; Infant, Newborn ; *Neanderthals/genetics ; Rare Diseases/genetics ; *Hominidae/genetics ; Genome, Human ; DNA ; }, abstract = {Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.}, }
@article {pmid36980972, year = {2023}, author = {Sharko, F and Slobodova, N and Boulygina, E and Cheprasov, M and Gladysheva-Azgari, M and Tsygankova, S and Rastorguev, S and Novgorodov, G and Boeskorov, G and Grigorieva, L and Hwang, WS and Tikhonov, A and Nedoluzhko, A}, title = {Ancient DNA of the Don-Hares Assumes the Existence of Two Distinct Mitochondrial Clades in Northeast Asia.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980972}, issn = {2073-4425}, mesh = {Animals ; Female ; Cattle ; *Hares/genetics ; Phylogeny ; DNA, Ancient ; *Lagomorpha/genetics ; Asia ; }, abstract = {Paleoclimatic changes during the Pleistocene-Holocene transition is suggested as a main factor that led to species extinction, including the woolly mammoth (Mammuthus primigenius), Steller's sea cow (Hydrodamalis gigas) and the Don-hare (Lepus tanaiticus). These species inhabited the territory of Eurasia during the Holocene, but eventually went extinct. The Don-hare is an extinct species of the genus Lepus (Leporidae, Lagomorpha), which lived in the Late Pleistocene-Early Holocene in Eastern Europe and Northern Asia. For a long time, the Don-hare was considered a separate species, but at the same time, its species status was disputed, taking into account both morphological data and mitochondrial DNA. In this study, mitochondrial genomes of five Don-hares, whose remains were found on the territory of Northeastern Eurasia were reconstructed. Firstly, we confirm the phylogenetic proximity of the "young" specimens of Don-hare and mountain or white hare, and secondly, that samples older than 39 Kya form a completely distinct mitochondrial clade.}, }
@article {pmid36968599, year = {2023}, author = {Yu, HX and Ao, C and Wang, XP and Zhang, XP and Sun, J and Li, H and Liu, KJ and Wei, LH}, title = {The impacts of bronze age in the gene pool of Chinese: Insights from phylogeographics of Y-chromosomal haplogroup N1a2a-F1101.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1139722}, pmid = {36968599}, issn = {1664-8021}, abstract = {Objectives: Previous studies of archaeology and history suggested that the rise and prosperity of Bronze Age culture in East Asia had made essential contribution to the formation of early state and civilization in this region. However, the impacts in perspective of genetics remain ambiguous. Previous genetic researches indicated the Y-chromosome Q1a1a-M120 and N1a2a-F1101 may be the two most important paternal lineages among the Bronze Age people in ancient northwest China. Here, we investigated the 9,000-years history of haplogroup N1a2a-F1101 with revised phylogenetic tree and spatial autocorrelation analysis. Materials and Methods: In this study, 229 sequences of N1a2a-F1101 were analyzed. We developed a highly-revised phylogenetic tree with age estimates for N1a2a-F1101. In addition, we also explored the geographical distribution of sub-lineages of N1a2a-F1101, and spatial autocorrelation analysis was conducted for each sub-branch. Results: The initial differentiation location of N1a2a-F1101 and its most closely related branch, N1a2b-P43, a major lineage of Uralic-speaking populations in northern Eurasia, is likely the west part of northeast China. After ~4 thousand years of bottleneck effect period, haplgroup N1a2a-F1101 experienced continuous expansion during the Chalcolithic age (~ 4.5 kya to 4 kya) and Bronze age (~ 4 kya to 2.5 kya) in northern China. Ancient DNA evidence supported that this haplogroup is the lineage of ruling family of Zhou Dynasty (~ 3 kya-2.2 kya) of ancient China. Discussion: In general, we proposed that the Bronze Age people in the border area between the eastern Eurasian steppe and northern China not only played a key role in promoting the early state and civilization of China, but also left significant traces in the gene pool of Chinese people.}, }
@article {pmid36967935, year = {2023}, author = {Sen, A and Andersen, LW and Kjeldsen, KU and Michel, LN and Hong, WL and Choquet, M and Rasmussen, TL}, title = {The phylogeography and ecology of Oligobrachia frenulate species suggest a generalist chemosynthesis-based fauna in the arctic.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14232}, pmid = {36967935}, issn = {2405-8440}, abstract = {We used ancient DNA (aDNA) extraction methods to sequence museum voucher samples of Oligobrachia webbi, a frenulate siboglinid polychaete described from a northern Norwegian fjord over fifty years ago. Our sequencing results indicate a genetic match with the cryptic seep species, Oligobrachia haakonmosbiensis (99% pairwise identity for 574 bp mtCOI fragments). Due to its similarity with O. webbi, the identity of O. haakonmosbiensis has been a matter of debate since its description, which we have now resolved. Furthermore, our results demonstrate that chemosynthesis-based siboglinids, that constitute the bulk of the biomass at Arctic seeps are not seep specialists. Our data on sediment geochemistry and carbon and nitrogen content reveal reduced conditions in fjords/sounds, similar to those at seep systems. Accumulation and decomposition of both terrestrial and marine organic matter results in the buildup of methane and sulfide that apparently can sustain chemosymbiotic fauna. The occurrence of fjords and by extension, highly reducing habitats, could have led to Arctic chemosymbiotic species being relatively generalist with their habitat, as opposed to being seep or vent specialists. Our stable isotope analyses indicate the incorporation of photosynthetically derived carbon in some individuals, which aligns with experiments conducted on frenulates before the discovery of chemosynthesis that demonstrated their ability to take up organic molecules from the surrounding sediment. Since reduced gases in non-seep environments are ultimately sourced from photosynthetic processes, we suggest that the extreme seasonality of the Arctic has resulted in Arctic chemosymbiotic animals seasonally changing their degree of reliance on chemosynthetic partners. Overall, the role of chemosynthesis in Arctic benthos and marine ecosystems and links to photosynthesis may be complex, and more extensive than currently known.}, }
@article {pmid36966434, year = {2023}, author = {Hixson, KK and Fajardo, DA and Devitt, NP and Sena, JA and Costa, MA and Meng, Q and Boschiero, C and Zhao, PX and Baack, EJ and Paurus, VL and Davin, LB and Lewis, NG and Bell, CJ}, title = {Annotated genome sequence of a fast-growing diploid clone of red alder (Alnus rubra Bong.).}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {6}, pages = {}, pmid = {36966434}, issn = {2160-1836}, mesh = {*Alnus/metabolism ; Diploidy ; Plant Breeding ; Symbiosis ; Trees ; }, abstract = {Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen-fixing symbiosis and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation, and wood quality traits. We established that this clone is most likely diploid and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales and established some similarities with previous reports in this clade, suggesting a biased retention of certain gene functions in the vestiges of an ancient genome duplication when compared with more recent tandem duplications.}, }
@article {pmid36964154, year = {2023}, author = {Zimmermann, HH and Stoof-Leichsenring, KR and Dinkel, V and Harms, L and Schulte, L and Hütt, MT and Nürnberg, D and Tiedemann, R and Herzschuh, U}, title = {Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1650}, pmid = {36964154}, issn = {2041-1723}, mesh = {*Ecosystem ; *DNA, Ancient ; Ice Cover ; Climate ; Geologic Sediments ; Arctic Regions ; Oceans and Seas ; }, abstract = {Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.}, }
@article {pmid36963383, year = {2023}, author = {Davy, T and Ju, D and Mathieson, I and Skoglund, P}, title = {Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers.}, journal = {Current biology : CB}, volume = {33}, number = {7}, pages = {1365-1371.e3}, pmid = {36963383}, issn = {1879-0445}, support = {852558/ERC_/European Research Council/International ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; R35 GM133708/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; }, mesh = {Humans ; *Farmers ; Europe ; *DNA ; Alleles ; Selection, Genetic ; }, abstract = {Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.[1][,][2][,][3][,][4] Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10[-56]). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.}, }
@article {pmid36958333, year = {2023}, author = {Begg, TJA and Schmidt, A and Kocher, A and Larmuseau, MHD and Runfeldt, G and Maier, PA and Wilson, JD and Barquera, R and Maj, C and Szolek, A and Sager, M and Clayton, S and Peltzer, A and Hui, R and Ronge, J and Reiter, E and Freund, C and Burri, M and Aron, F and Tiliakou, A and Osborn, J and Behar, DM and Boecker, M and Brandt, G and Cleynen, I and Strassburg, C and Prüfer, K and Kühnert, D and Meredith, WR and Nöthen, MM and Attenborough, RD and Kivisild, T and Krause, J}, title = {Genomic analyses of hair from Ludwig van Beethoven.}, journal = {Current biology : CB}, volume = {33}, number = {8}, pages = {1431-1447.e22}, doi = {10.1016/j.cub.2023.02.041}, pmid = {36958333}, issn = {1879-0445}, mesh = {Male ; Humans ; Genetic Predisposition to Disease ; *Famous Persons ; *Deafness ; Genomics ; *Music ; Hair ; }, abstract = {Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.}, }
@article {pmid36951219, year = {2023}, author = {Kolbe, D and da Silva, NA and Dose, J and Torres, GG and Caliebe, A and Krause-Kyora, B and Nebel, A}, title = {Current allele distribution of the human longevity gene APOE in Europe can mainly be explained by ancient admixture.}, journal = {Aging cell}, volume = {22}, number = {5}, pages = {e13819}, pmid = {36951219}, issn = {1474-9726}, mesh = {Humans ; Infant, Newborn ; Alleles ; Gene Frequency/genetics ; *Longevity/genetics ; *Apolipoproteins E/genetics ; Europe ; }, abstract = {Variation in apolipoprotein E (APOE) has been shown to have the strongest genetic effect on human longevity. The aim of this study was to unravel the evolutionary history of the three major APOE alleles in Europe by analysing ancient samples up to 12,000 years old. We detected significant allele frequency shifts between populations and over time. Our analyses indicated that selection led to large frequency differences between the earliest European populations (i.e., hunter-gatherers vs. first farmers), possibly due to changes in diet/lifestyle. In contrast, the allele distributions in populations from ~4000 BCE onward can mainly be explained by admixture, suggesting that it also played an important role in shaping current APOE variation. In any case, the resulting allele frequencies strongly influence the predisposition for longevity today, likely as a consequence of past adaptations and demographic processes.}, }
@article {pmid36945531, year = {2023}, author = {Ringbauer, H and Huang, Y and Akbari, A and Mallick, S and Patterson, N and Reich, D}, title = {ancIBD - Screening for identity by descent segments in human ancient DNA.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36945531}, issn = {2692-8205}, abstract = {Long DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set ('1240k'). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.}, }
@article {pmid36933795, year = {2023}, author = {Zhang, G and Cui, C and Wangdue, S and Lu, H and Chen, H and Xi, L and He, W and Yuan, H and Tsring, T and Chen, Z and Yang, F and Tsering, T and Li, S and Tashi, N and Yang, T and Tong, Y and Wu, X and Li, L and He, Y and Cao, P and Dai, Q and Liu, F and Feng, X and Wang, T and Yang, R and Ping, W and Zhang, M and Gao, X and Liu, Y and Wang, W and Fu, Q}, title = {Maternal genetic history of ancient Tibetans over the past 4000 years.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {50}, number = {10}, pages = {765-775}, doi = {10.1016/j.jgg.2023.03.007}, pmid = {36933795}, issn = {1673-8527}, mesh = {Tibet ; Humans ; *Phylogeny ; *Haplotypes/genetics ; Female ; Genome, Mitochondrial/genetics ; DNA, Mitochondrial/genetics ; History, Ancient ; Asian People/genetics ; Genetics, Population ; Maternal Inheritance/genetics ; East Asian People ; }, abstract = {The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity. Here, we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet. The phylogeny of haplotypes M9a1a, M9a1b, D4g2, G2a'c, and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene. In addition, the connections between Tibetans and Northeastern Asians vary over the past 4000 years, with a stronger matrilineal connection between the two during 4000 BP-3000 BP, and a weakened connection after 3000 BP, that are coincident with climate change, followed by a reinforced connection after the Tubo period (1400 BP-1100 BP). Besides, an over 4000-year matrilineal continuity is observed in some of the maternal lineages. We also find the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations. Overall, the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that are dynamically shaped by geography, climate changes, as well as historical events.}, }
@article {pmid36930997, year = {2023}, author = {Schats, R}, title = {Developing an archaeology of malaria. A critical review of current approaches and a discussion on ways forward.}, journal = {International journal of paleopathology}, volume = {41}, number = {}, pages = {32-42}, doi = {10.1016/j.ijpp.2023.03.002}, pmid = {36930997}, issn = {1879-9825}, mesh = {Humans ; *Archaeology ; *Malaria/diagnosis/epidemiology ; Forecasting ; Prevalence ; }, abstract = {OBJECTIVE: This paper presents the current state of the art in the investigation of past malaria by providing an extensive review of previous studies and identifying research possibilities for the future.<br><br>MATERIALS: All previous research on the detection of malaria in human skeletal material using macroscopic and biomolecular approaches is considered.<br><br>METHODS: The approaches and methods used by scholars and the results they obtained are evaluated and the limitations discussed.<br><br>RESULTS: There is a link between malaria and porous lesions with significantly higher prevalence in malaria-endemic areas, however, they are not pathognomonic or specific for malaria. Malaria can be identified using biomolecular techniques, yet, to date there is no completely satisfactory method that is able to consistently diagnose the disease.<br><br>CONCLUSIONS: Using macroscopic and biomolecular techniques, malaria can be investigated in past populations and the impact of the disease studied. Yet, this is not a straightforward process and the use of multiple lines of evidence is necessary to obtain the best results.<br><br>SIGNIFICANCE: The extensive discussion on ways malaria can and cannot be identified in past populations and the suggestions for new approaches provide a steppingstone for future research into this debilitating, global disease.<br><br>LIMITATIONS: Malaria is a difficult disease to study archaeologically and successful identification depends on many intrinsic and extrinsic factors.<br><br>More large-scale spatial analyses of porous lesions as well as targeting different tissues or molecules for biomolecular identification may improve the archaeological understanding of malaria.}, }
@article {pmid36930529, year = {2023}, author = {de-Dios, T and Scheib, CL and Houldcroft, CJ}, title = {An Adagio for Viruses, Played Out on Ancient DNA.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36930529}, issn = {1759-6653}, mesh = {Humans ; *Genomics/methods ; DNA, Ancient ; Paleontology ; DNA ; *Viruses/genetics ; }, abstract = {Studies of ancient DNA have transformed our understanding of human evolution. Paleogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic, and pandemic pathogens. Viruses-and in particular those with single- or double-stranded DNA genomes-are an important part of the paleogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly evolving viruses which cause disease. In this review, we revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We look at how paleogenomics works for viral pathogens, such as the need for careful precautions against modern contamination and robust computational pipelines to identify and analyze authenticated viral sequences. We discuss the insights into virus evolution which have been gained through paleogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.}, }
@article {pmid36922577, year = {2023}, author = {Kerner, G and Choin, J and Quintana-Murci, L}, title = {Ancient DNA as a tool for medical research.}, journal = {Nature medicine}, volume = {29}, number = {5}, pages = {1048-1051}, pmid = {36922577}, issn = {1546-170X}, mesh = {*DNA, Ancient ; Fossils ; *Biomedical Research ; Sequence Analysis, DNA ; }, }
@article {pmid36919783, year = {2023}, author = {Motti, JMB and Pauro, M and Scabuzzo, C and García, A and Aldazábal, V and Vecchi, R and Bayón, C and Pastor, N and Demarchi, DA and Bravi, CM and Reich, D and Cabana, GS and Nores, R}, title = {Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization.}, journal = {American journal of biological anthropology}, volume = {181}, number = {2}, pages = {216-230}, doi = {10.1002/ajpa.24727}, pmid = {36919783}, issn = {2692-7691}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Humans ; Argentina ; Phylogeny ; *Genome, Mitochondrial/genetics ; Bayes Theorem ; South America ; }, abstract = {OBJECTIVE: This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes.<br><br>MATERIALS AND METHODS: We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723&#x2009;cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis.<br><br>RESULTS: We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000&#x2009;years BP.<br><br>DISCUSSION: The history of the human populations in the Southern Pampas is temporally deep, exhibiting long-term continuity of mitogenome lineages. Additionally, the identification of highly localized mtDNA clades accords with a model of relatively rapid initial colonization of South America by Indigenous communities, followed by more local patterns of limited gene flow and genetic drift in various South American regions, including the Pampas.}, }
@article {pmid36919199, year = {2023}, author = {Bellec, A and Sow, MD and Pont, C and Civan, P and Mardoc, E and Duchemin, W and Armisen, D and Huneau, C and Thévenin, J and Vernoud, V and Depège-Fargeix, N and Maunas, L and Escale, B and Dubreucq, B and Rogowsky, P and Bergès, H and Salse, J}, title = {Tracing 100 million years of grass genome evolutionary plasticity.}, journal = {The Plant journal : for cell and molecular biology}, volume = {114}, number = {6}, pages = {1243-1266}, doi = {10.1111/tpj.16185}, pmid = {36919199}, issn = {1365-313X}, support = {0001455 project SyntenyViewer//Institut Carnot Plant2Pro/ ; 'Pack Ambition Recherche Project' TransBl&#xe9;//ISITE CAP2025/ ; #23000816//R&#xe9;gion Auvergne-Rh&#xf4;ne-Alpes/ ; }, mesh = {*Poaceae/genetics ; *Genome, Plant/genetics ; Phylogeny ; Evolution, Molecular ; Edible Grain/genetics ; Polyploidy ; Gene Duplication ; }, abstract = {Grasses derive from a family of monocotyledonous plants that includes crops of major economic importance such as wheat, rice, sorghum and barley, sharing a common ancestor some 100 million years ago. The genomic attributes of plant adaptation remain obscure and the consequences of recurrent whole genome duplications (WGD) or polyploidization events, a major force in plant evolution, remain largely speculative. We conducted a comparative analysis of omics data from ten grass species to unveil structural (inversions, fusions, fissions, duplications, substitutions) and regulatory (expression and methylation) basis of genome plasticity, as possible attributes of plant long lasting evolution and adaptation. The present study demonstrates that diverged polyploid lineages sharing a common WGD event often present the same patterns of structural changes and evolutionary dynamics, but these patterns are difficult to generalize across independent WGD events as a result of non-WGD factors such as selection and domestication of crops. Polyploidy is unequivocally linked to the evolutionary success of grasses during the past 100 million years, although it remains difficult to attribute this success to particular genomic consequences of polyploidization, suggesting that polyploids harness the potential of genome duplication, at least partially, in lineage-specific ways. Overall, the present study clearly demonstrates that post-polyploidization reprogramming is more complex than traditionally reported in investigating single species and calls for a critical and comprehensive comparison across independently polyploidized lineages.}, }
@article {pmid36918761, year = {2023}, author = {Marsh, WA and Brace, S and Barnes, I}, title = {Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {111}, pmid = {36918761}, issn = {1471-2164}, mesh = {Humans ; *DNA, Ancient/analysis ; *Software ; Genotype ; Genome ; }, abstract = {BACKGROUND: The inference of biological relations between individuals is fundamental to understanding past human societies. Caregiving, resource sharing and sexual behaviours are often mediated by biological kinship and yet the identification and interpretation of kin relationships in prehistoric human groups is difficult. In recent years, the advent of archaeogenetic techniques have offered a fresh approach, and when combined with more traditional osteological and interpretive archaeological methods, allows for improved interpretation of the burial practices, cultural behaviours, and societal stratification in ancient societies. Although archaeogenetic techniques are developing at pace, questions remain as to their accuracy, particularly when applied to the low coverage datasets that results from the sequencing of DNA derived from highly degraded ancient material.<br><br>RESULTS: The performance of six of the most commonly used kinship identifcation software methods was explored at a range of low and ultra low genome coverages. An asymmetrical response was observed across packages, with decreased genome coverage resulting in differences in both direction and degree of change of calculated kinship scores and thus pairwise relatedness estimates are dependant on both package used and genome coverage. Methods reliant upon genotype likelihoods methods (lcMLkin, NGSrelate and NGSremix) show a decreased level of prediction at coverage below 1x, although were consistent in the particular relationships identified at these coverages when compared to the pseudohaploid reliant methods tested (READ, the Kennett 2017 method and TKGWV2.0). The three pseudohaploid methods show predictive potential at coverages as low as 0.05x, although the accuracy of the relationships identified is questionable given the increase in the number of relationships identifIed at the low coverage (type I errors).<br><br>CONCLUSION: Two pseudohaploid methods (READ and Kennett 2017) show relatively consistent inference of kin relationships at low coverage (0.5x), with READ only showing a significant performance drop off at ultralow coverages (<&#x2009;0.2x). More generally, our results reveal asymmetrical kinship classifications in some software packages even at high coverages, highlighting the importance of applying multiple methods to authenticate kin relationships in ancient material, along with the continuing need to develop laboratory methods that maximise data output for downstream analyses.}, }
@article {pmid36906188, year = {2023}, author = {Rbbani, G and Nedoluzhko, A and Siriyappagouder, P and Sharko, F and Galindo-Villegas, J and Raeymaekers, JAM and Joshi, R and Fernandes, JMO}, title = {The novel circular RNA CircMef2c is positively associated with muscle growth in Nile tilapia.}, journal = {Genomics}, volume = {115}, number = {3}, pages = {110598}, pmid = {36906188}, issn = {1089-8646}, support = {683210/ERC_/European Research Council/International ; }, mesh = {Animals ; RNA, Circular/genetics ; *Cichlids/genetics ; *MicroRNAs/metabolism ; RNA, Messenger/metabolism ; Muscles/metabolism ; Gene Regulatory Networks ; }, abstract = {Muscle growth in teleosts is a complex biological process orchestrated by numerous protein-coding genes and non-coding RNAs. A few recent studies suggest that circRNAs are involved in teleost myogenesis, but the molecular networks involved remain poorly understood. In this study, an integrative omics approach was used to determine myogenic circRNAs in Nile tilapia by quantifying and comparing the expression profile of mRNAs, miRNAs, and circRNAs in fast muscle from full-sib fish with distinct growth rates. There were 1947 mRNAs, 9 miRNAs, and 4 circRNAs differentially expressed between fast- and slow-growing individuals. These miRNAs can regulate myogenic genes and have binding sites for the novel circRNA circMef2c. Our data indicate that circMef2c may interact with three miRNAs and 65 differentially expressed mRNAs to form multiple competing endogenous RNA networks that regulate growth, thus providing novel insights into the role of circRNAs in the regulation of muscle growth in teleosts.}, }
@article {pmid36869137, year = {2023}, author = {Rifkin, RF and Vikram, S and Alcorta, J and Ramond, JB and Cowan, DA and Jakobsson, M and Schlebusch, CM and Lombard, M}, title = {Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {240}, pmid = {36869137}, issn = {2399-3642}, support = {NGS-371R-18//National Geographic Society/ ; }, mesh = {Humans ; Child ; *Rickettsia felis ; Africa, Southern ; DNA ; South Africa ; DNA, Ancient ; }, abstract = {The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.}, }
@article {pmid36862777, year = {2023}, author = {Curry, A}, title = {Ancient DNA upends European prehistory.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6635}, pages = {865-866}, doi = {10.1126/science.adh3912}, pmid = {36862777}, issn = {1095-9203}, mesh = {*Cultural Diversity ; *DNA, Ancient ; Europe ; Humans ; }, abstract = {Genes reveal striking diversity within similar ice age cultures.}, }
@article {pmid36855115, year = {2023}, author = {Nyerki, E and Kalmár, T and Schütz, O and Lima, RM and Neparáczki, E and Török, T and Maróti, Z}, title = {correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {38}, pmid = {36855115}, issn = {1474-760X}, mesh = {Humans ; *Genome, Human ; *Forensic Medicine ; Whole Genome Sequencing ; }, abstract = {Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×-11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data.}, }
@article {pmid39017120, year = {2023}, author = {Leonard, D}, title = {Quick Hits: A linguistic puzzle, ancient DNA, the origins of bipedalism, and much more in this month's Quick Hits.}, journal = {Scientific American}, volume = {328}, number = {3}, pages = {13}, doi = {10.1038/scientificamerican0323-13}, pmid = {39017120}, issn = {0036-8733}, }
@article {pmid36853456, year = {2023}, author = {Ayling, C}, title = {TA Cloning Approaches to Cloning DNA with Damaged Ends DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2633}, number = {}, pages = {55-64}, pmid = {36853456}, issn = {1940-6029}, mesh = {*DNA/genetics ; *DNA, Ancient ; DNA Damage ; Sonication ; Cloning, Molecular ; }, abstract = {DNA ends can become damaged for various reasons making them unsuitable for TA cloning techniques, the easiest and most common of the DNA cloning technologies. Examples of end-damaged DNA include ancient DNA and those produced by laboratory methods such as sonication. In this chapter, we discuss how to deal with end-damaged DNA prior to cloning with either the popular pGEM[®]-T Easy Vector Systems Kit and TOPO™ TA Cloning™ Kits.}, }
@article {pmid36853452, year = {2023}, author = {Mikić, A and Alomari, A and Gowers, DM}, title = {Classical Recombinant DNA Cloning.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2633}, number = {}, pages = {1-24}, pmid = {36853452}, issn = {1940-6029}, mesh = {*DNA, Recombinant ; *Escherichia coli/genetics ; Cloning, Molecular ; Polymerase Chain Reaction ; Genetic Vectors/genetics ; DNA Ligase ATP ; }, abstract = {Traditional molecular cloning involves a series of linked experimental steps performed with the overall goal of isolating ("cloning") a specific DNA sequence-often a gene. The main purpose of cloning is to study either that DNA sequence or the RNA or protein product it encodes. Building on key enzymatic discoveries in the late 1960s, gene cloning was pioneered in the early 1970s. Since then, DNA cloning and manipulation have been used in every area of biological and biomedical research, from molecular genetics, structural biology, and developmental biology to neurobiology, ancient DNA studies, and immunology. It is a versatile technique that can be applied to a variety of starting DNA types and lengths, including cDNAs, genes, gene fragments, chromosomal regions, or shorter fragments such as PCR products and functional control regions such as enhancers or promoters. The starting DNA can originate from any cell, tissue, or organism. In this chapter we will cover traditional ("classic") molecular cloning strategy. This comprises six linked stages in which (1) PCR is used to amplify a DNA region of interest that is then (2) digested with restriction enzymes, alongside a selected vector, to produce complementary ends crucial for the two molecules to be (3) ligated by an ATP-dependent DNA ligase, creating a recombinant DNA molecule. The recombinant DNA is then (4) introduced into competent bacterial cells by transformation and (5) grown on a selective agar media, followed by (6) colony-PCR for screening purposes. We provide a worked example to demonstrate the cloning of an average-size gene (in this case the 2 kb DNA ligase A gene) from E. coli into a common plasmid expression vector. We have included six color figures and two tables to depict the key stages of a classical molecular cloning protocol. If you are cloning a segment of DNA or a gene, remember that each DNA cloning experiment is unique in terms of sequence, length, and experimental purpose. However, the principles of traditional cloning covered in this chapter are the same for any DNA sequence; we have included a detailed notes section, so you should easily be able to transfer them to your own work. Some of the following chapters in this volume will cover other, more recently developed, cloning protocols.}, }
@article {pmid36847465, year = {2022}, author = {Hublin, JJ and Changeux, JP}, title = {Paleoanthropology of cognition: an overview on Hominins brain evolution.}, journal = {Comptes rendus biologies}, volume = {345}, number = {2}, pages = {57-75}, doi = {10.5802/crbiol.92}, pmid = {36847465}, issn = {1768-3238}, mesh = {Humans ; Animals ; *Hominidae ; Biological Evolution ; Brain ; Cognition/physiology ; Neurons ; Fossils ; }, abstract = {Recent advances in neurobiology, paleontology, and paleogenetics allow us to associate changes in brain size and organization with three main "moments" of increased behavioral complexity and, more speculatively, language development. First, Australopiths display a significant increase in brain size relative to the great apes and an incipient extension of postnatal brain development. However, their cortical organization remains essentially similar to that of apes. Second, over the last 2 My, with two notable exceptions, brain size increases dramatically, partly in relation to changes in body size. Differential enlargements and reorganizations of cortical areas lay the foundation for the "language-ready" brain and cumulative culture of later Homo species. Third, in Homo sapiens, brain size remains fairly stable over the last 300,000 years but an important cerebral reorganization takes place. It affects the frontal and temporal lobes, the parietal areas and the cerebellum and resulted in a more globular shape of the brain. These changes are associated, among others, with an increased development of long-distance-horizontal-connections. A few regulatory genetic events took place in the course of this hominization process with, in particular, enhanced neuronal proliferation and global brain connectivity.}, }
@article {pmid36847121, year = {2023}, author = {Salse, J}, title = {Translational research from models to crops: comparative genomics for plant breeding.}, journal = {Comptes rendus biologies}, volume = {345}, number = {4}, pages = {111-128}, doi = {10.5802/crbiol.103}, pmid = {36847121}, issn = {1768-3238}, mesh = {*Plant Breeding/methods ; *Translational Research, Biomedical ; Genomics/methods ; Crops, Agricultural/genetics ; Genotype ; Genome, Plant/genetics ; }, abstract = {The concept of translational research, which originated in the medical field in the 1980s, consists in improving the efficient transfer of research results obtained in a species (which can be considered as a model or pivot) to all the species for which these results are of interest for its improvement in Agriculture. In this context, comparative genomics is an important tool for translational research, effectively identifying genes controlling common functions between species. Editing and phenotyping tools must thus allow the functional validation of the gene conserved within the species for which the knowledge has been extrapolated, that is to say transferred, and the identification of the best alleles and associated genotypes for exploitation in current breeding programs.}, }
@article {pmid36845441, year = {2023}, author = {Boeckx, C}, title = {What made us "hunter-gatherers of words".}, journal = {Frontiers in neuroscience}, volume = {17}, number = {}, pages = {1080861}, pmid = {36845441}, issn = {1662-4548}, abstract = {This paper makes three interconnected claims: (i) the "human condition" cannot be captured by evolutionary narratives that reduce it to a recent 'cognitive modernity', nor by narratives that eliminates all cognitive differences between us and out closest extinct relatives, (ii) signals from paleogenomics, especially coming from deserts of introgression but also from signatures of positive selection, point to the importance of mutations that impact neurodevelopment, plausibly leading to temperamental differences, which may impact cultural evolutionary trajectories in specific ways, and (iii) these trajectories are expected to affect the language phenotypes, modifying what is being learned and how it is put to use. In particular, I hypothesize that these different trajectories influence the development of symbolic systems, the flexible ways in which symbols combine, and the size and configurations of the communities in which these systems are put to use.}, }
@article {pmid36841239, year = {2023}, author = {Eaton, K and Sidhu, RK and Klunk, J and Gamble, JA and Boldsen, JL and Carmichael, AG and Varlık, N and Duchene, S and Featherstone, L and Grimes, V and Golding, GB and DeWitte, SN and Holmes, EC and Poinar, HN}, title = {Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark.}, journal = {Current biology : CB}, volume = {33}, number = {6}, pages = {1147-1152.e5}, doi = {10.1016/j.cub.2023.01.064}, pmid = {36841239}, issn = {1879-0445}, mesh = {Humans ; *Yersinia pestis/genetics ; *Plague/epidemiology/microbiology ; Phylogeny ; Genome, Bacterial ; Denmark ; }, abstract = {The historical epidemiology of plague is controversial due to the scarcity and ambiguity of available data.[1][,][2] A common source of debate is the extent and pattern of plague re-emergence and local continuity in Europe during the 14th-18th century CE.[3] Despite having a uniquely long history of plague (∼5,000 years), Scandinavia is relatively underrepresented in the historical archives.[4][,][5] To better understand the historical epidemiology and evolutionary history of plague in this region, we performed in-depth (n = 298) longitudinal screening (800 years) for the plague bacterium Yersinia pestis (Y. pestis) across 13 archaeological sites in Denmark from 1000 to 1800 CE. Our genomic and phylogenetic data captured the emergence, continuity, and evolution of Y. pestis in this region over a period of 300 years (14th-17th century CE), for which the plague-positivity rate was 8.3% (3.3%-14.3% by site). Our phylogenetic analysis revealed that the Danish Y. pestis sequences were interspersed with those from other European countries, rather than forming a single cluster, indicative of the generation, spread, and replacement of bacterial variants through communities rather than their long-term local persistence. These results provide an epidemiological link between Y. pestis and the unknown pestilence that afflicted medieval and early modern Europe. They also demonstrate how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology and help pave the way for the next generation of historical disease research.}, }
@article {pmid36833406, year = {2023}, author = {Dalal, V and Pasupuleti, N and Chaubey, G and Rai, N and Shinde, V}, title = {Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833406}, issn = {2073-4425}, mesh = {Humans ; *DNA, Ancient ; *Evolution, Molecular ; *Human Migration ; }, abstract = {Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.}, }
@article {pmid36833230, year = {2023}, author = {Wiscovitch-Russo, RA and Santiago-Rodriguez, TM and Toranzos, GA}, title = {Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833230}, issn = {2073-4425}, mesh = {Animals ; Humans ; *Parasites ; *Parasitic Diseases/parasitology ; Paleopathology/methods ; Diet ; Life Style ; }, abstract = {Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.}, }
@article {pmid36824241, year = {2023}, author = {D Farhud, D}, title = {The 2022 Nobel Prize in Medicine for Paleogenomics Discovery the Genomes of Extinct Hominins and Human Evolution.}, journal = {Iranian journal of public health}, volume = {52}, number = {1}, pages = {i-iii}, pmid = {36824241}, issn = {2251-6093}, }
@article {pmid36822963, year = {2023}, author = {Lalueza-Fox, C}, title = {Across the North Sea and beyond.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {4}, pages = {240-241}, doi = {10.1016/j.tig.2023.01.006}, pmid = {36822963}, issn = {0168-9525}, mesh = {North Sea ; Humans ; Human Genetics ; *Genetics, Population ; Human Migration ; }, abstract = {Increasing numbers of ancient genomes from the Viking period retrieved across the North Sea regions are revealing a complex layer of genetic ancestries and a past cosmopolitanism that was triggered by different mobility patterns.}, }
@article {pmid36819665, year = {2023}, author = {Kerner, G and Neehus, AL and Philippot, Q and Bohlen, J and Rinchai, D and Kerrouche, N and Puel, A and Zhang, SY and Boisson-Dupuis, S and Abel, L and Casanova, JL and Patin, E and Laval, G and Quintana-Murci, L}, title = {Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe.}, journal = {Cell genomics}, volume = {3}, number = {2}, pages = {100248}, pmid = {36819665}, issn = {2666-979X}, abstract = {Ancient genomics can directly detect human genetic adaptation to environmental cues. However, it remains unclear how pathogens have exerted selective pressures on human genome diversity across different epochs and affected present-day inflammatory disease risk. Here, we use an ancestry-aware approximate Bayesian computation framework to estimate the nature, strength, and time of onset of selection acting on 2,879 ancient and modern European genomes from the last 10,000 years. We found that the bulk of genetic adaptation occurred after the start of the Bronze Age, <4,500 years ago, and was enriched in genes relating to host-pathogen interactions. Furthermore, we detected directional selection acting on specific leukocytic lineages and experimentally demonstrated that the strongest negatively selected candidate variant in immunity genes, lipopolysaccharide-binding protein (LBP) D283G, is hypomorphic. Finally, our analyses suggest that the risk of inflammatory disorders has increased in post-Neolithic Europeans, possibly because of antagonistic pleiotropy following genetic adaptation to pathogens.}, }
@article {pmid36812666, year = {2023}, author = {Bľandová, G and Patlevičová, A and Palkovičová, J and Pavlíková, &#x160; and Beňuš, R and Repiská, V and Baldovič, M}, title = {Pilot study of correlation of selected genetic factors with cribra orbitalia in individuals from a medieval population from Slovakia.}, journal = {International journal of paleopathology}, volume = {41}, number = {}, pages = {1-7}, doi = {10.1016/j.ijpp.2023.02.001}, pmid = {36812666}, issn = {1879-9825}, mesh = {Humans ; Pilot Projects ; Slovakia ; *Lactose Intolerance/genetics ; *Anemia ; Cemeteries ; }, abstract = {OBJECTIVE: The aim of this study is to investigate the potential genetic etiology of cribra orbitalia noted on human skeletal remains.<br><br>MATERIALS: We obtained and analyzed ancient DNA of 43 individuals with cribra orbitalia. The analyzed set represented medieval individuals from two cemeteries in western Slovakia, Castle Dev&#xed;n (11th-12th century AD) and C&#xed;fer-P&#xe1;c (8th-9th century AD).<br><br>METHODS: We performed a sequence analysis of 5 variants in 3 genes associated with anemia (HBB, G6PD, PKLR), which are the most common pathogenic variants in present day of European populations, and one variant MCM6:c.1917&#xa0;+&#xa0;326&#xa0;C>T (rs4988235) associated with lactose intolerance.<br><br>RESULTS: DNA variants associated with anemia were not found in the samples. The allele frequency of MCM6:c.1917&#xa0;+&#xa0;326&#xa0;C was 0.875. This frequency is higher but not statistically significant in individuals displaying cribra orbitalia compared to individuals without the lesion.<br><br>SIGNIFICANCE: This study seeks to expand our knowledge of the etiology of cribra orbitalia by exploring the potential association between the lesion and the presence of alleles linked to hereditary anemias and lactose intolerance.<br><br>LIMITATIONS: A relatively small set of individuals were analyzed, so an unequivocal conclusion cannot be drawn. Hence, although it is unlikely, a genetic form of anemia caused by rare variants cannot be ruled out.<br><br>Genetic research based on larger sample sizes and in more diverse geographical regions.}, }
@article {pmid36812179, year = {2023}, author = {Kalisher, R and Cradic, MS and Adams, MJ and Martin, MAS and Finkelstein, I}, title = {Cranial trephination and infectious disease in the Eastern Mediterranean: The evidence from two elite brothers from Late Bronze Megiddo, Israel.}, journal = {PloS one}, volume = {18}, number = {2}, pages = {e0281020}, pmid = {36812179}, issn = {1932-6203}, mesh = {Male ; Young Adult ; Humans ; History, Ancient ; Israel ; *Trephining ; Siblings ; DNA, Ancient ; *Communicable Diseases ; }, abstract = {Here we present the paleopathological profiles of two young adult males, identified as brothers through ancient DNA analysis, who were buried together beneath the floor of an elite early Late Bronze Age I (ca. 1550-1450 BC) domestic structure at the urban center of Megiddo (modern Israel). Both individuals displayed uncommon morphological variants related to developmental conditions, and each exhibited extensive bone remodeling consistent with chronic infectious disease. Additionally, one brother had a healed fracture of the nose, as well as a large square piece of bone cut from the frontal bone (cranial trephination). We consider the potential etiologies for the appearance of the skeletal anomalies and lesions. Based on the bioarchaeological context, we propose that a shared epigenetic landscape predisposed the brothers to acquiring an infectious disease and their elite status privileged them enough to endure it. We then contextualize these potential illnesses and disorders with the trephination procedure. The infrequency of trephination in the region indicates that only selected individuals could access such a procedure, and the severity of the pathological lesions suggests the procedure was possibly intended as curative to deteriorating health. Ultimately, both brothers were buried with the same rites as others in their community, thus demonstrating their continued integration in society even after death.}, }
@article {pmid36796758, year = {2023}, author = {Min-Shan Ko, A}, title = {The 2022 nobel prize in physiology or medicine awarded for the decoding of the complete ancient human genome.}, journal = {Biomedical journal}, volume = {46}, number = {2}, pages = {100584}, pmid = {36796758}, issn = {2320-2890}, mesh = {Male ; Humans ; *Nobel Prize ; DNA, Ancient ; Genome, Human/genetics ; *Medicine ; Germany ; }, abstract = {Since the publication of the first ancient DNA sequence in 1984, experimental methods used to recover ancient DNA have advanced greatly, illuminating previously unknown branches of the human family tree and opening up several promising new avenues for future studies of human evolution. The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, for his work on ancient DNA and human evolution. On his first day back at work, he was thrown in the pond as part of his institute's tradition of celebrating award winners.}, }
@article {pmid36790695, year = {2022}, author = {Rayo, E and Neukamm, J and Tomoum, N and Eppenberger, P and Breidenstein, A and Bouwman, AS and Schuenemann, VJ and Rühli, FJ}, title = {Metagenomic analysis of Ancient Egyptian canopic jars.}, journal = {American journal of biological anthropology}, volume = {179}, number = {2}, pages = {307-313}, pmid = {36790695}, issn = {2692-7691}, mesh = {Humans ; Egypt ; *DNA, Ancient ; *Mummies/pathology ; Lung ; Base Sequence ; }, abstract = {UNLABELLED: Ancient Egyptian remains have been of interest for anthropological research for decades. Despite many investigations, the ritual vessels for the internal organs removed during body preparation-liver, lungs, stomach, and intestines, of Egyptian mummies are rarely used for palaeopathological or medical investigations. These artifacts, commonly referred to as canopic jars, are the perfect combination of cultural and biological material and present an untapped resource for both Egyptological and medical fields. Nevertheless, technical challenges associated with this archeological material have prevented the application of current ancient DNA techniques for both the characterization of human and pathogenic DNA. We present shotgun-sequenced metagenomic profiles and ancient DNA degradation patterns from multiple canopic jars sampled from several European museum collections and enumerate current limitations and possible solutions for the future analysis of similar material. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars and the first associated metagenomic description of bacterial taxa in these funerary artifacts.<br><br>OBJECTIVES: In this study, our objectives were to characterize the metagenomic profile of the Ancient Egyptian funerary vessels known as canopic jars to retrieve endogenous ancient human DNA, reconstruct ancient microbial communities, and identify possible pathogens that could shed light on disease states of individuals from the past.<br><br>METHODS: We applied ancient DNA techniques on 140 canopic jars to extract DNA and generate whole-genome sequencing libraries for the analysis of both human and bacterial DNA. The samples were obtained from museum collections in Berlin (DE), Burgdorf (DE), Leiden (NE), Manchester (UK), Munich (DE), St. Gallen (CH), Turin (IT), and Zagreb (HR).<br><br>RESULTS: Here we describe the first isolated DNA from the Egyptian artifacts that hold human viscera. No previous work was ever conducted on such material, which led to the first characterization of human DNA from Ancient Egyptian canopic jars and the profiling of the complex bacterial composition of this highly degraded, challenging, organic material. However, the DNA recovered was not of enough quality to confidently characterize bacterial taxa associated with infectious diseases, nor exclusive bacterial members of the human microbiome.<br><br>DISCUSSION: In summary, we present the first genomic survey of the visceral content of Ancient Egyptian funerary artifacts and demonstrate the limitations of current molecular methods to analyze canopic jars, such as the incomplete history of the objects or the presence of uncharacterized compounds that can hamper the recovery of DNA. Our work highlights the main challenges and caveats when working with such complicated archeological material - and offers sampling recommendations for similarly complex future studies, such as incrementing the amount of starting material and sampling from the less exposed parts of the jar content. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars, and our results open new avenues in the study of neglected archeological artifacts.}, }
@article {pmid36790664, year = {2022}, author = {Vigeant, J and Ribot, I and Hélie, JF}, title = {Investigating individual migration life histories: An isotopic case study from 17th to 18th century Nouvelle France.}, journal = {American journal of biological anthropology}, volume = {177}, number = {2}, pages = {232-248}, doi = {10.1002/ajpa.24455}, pmid = {36790664}, issn = {2692-7691}, mesh = {Child ; Humans ; Male ; Adult ; *Diet/history ; Oxygen Isotopes/analysis ; *Cemeteries/history ; Europe ; France ; }, abstract = {OBJECTIVES: This isotopic study explores the mobility patterns of a growing urban population from Notre Dame's Catholic cemetery (1691-1796), located in Montreal (Canada). The site offers a unique opportunity to investigate early colonial settlement in Nouvelle France through individual life patterns.<br><br>MATERIALS AND METHODS: Stable oxygen isotopic compositions (&#x3b4;[18]O) were measured on the enamel of 32 individuals from the Notre Dame collection. Premolars and third molars were selected, as they reflected the &#x3b4;[18]O of the drinking water during childhood (2.5-5.5&#x2009;years) and pre-adulthood (9.5-15.5&#x2009;years). Firstly, premolars from three children (4-8&#x2009;years of age) allowed us to provide a mean &#x3b4;[18]O for the water consumed locally (22.7&#x2009;&#xb1;&#x2009;&#x2009;1.0 &#x2030; vs. VSMOW). Then, our &#x3b4;[18]O were compared with published data from various geographical regions in North America (Eastern Canada and the United States) and Europe (France and the British Isles) to highlight mobility patterns of each individual.<br><br>RESULTS: Forty-eight percent of our sample (14 out of 29 individuals) did not reflect any long-distance mobility, as all their &#x3b4;[18]O reflected Montreal's variation during their lifetime. The remaining (15 out of 29 individuals) experienced mobility within (n&#xa0;=&#xa0;8) and outside (n&#xa0;=&#xa0;7) North America and at different phases of their life (five at pre-adulthood, six at adulthood and four during both phases). Their migration patterns were analyzed according to age, sex, diet and possible ancestry in order to propose some "biographies."<br><br>DISCUSSION: This study highlights high population diversity in early colonial Montreal. Historians wrote that the city was growing, not only with the arrival of Europeans (e.g., young male workers, sailors), but also other groups (e.g., Indigenous people, slaves from North America). Additional analyses (e.g., ancient DNA) will be needed to explore further this phenomenon.}, }
@article {pmid36790637, year = {2023}, author = {Balentine, CM and Alfonso-Durruty, M and Reynolds, AW and Vilar, M and Morello, F and Román, MS and Springs, LC and Smith, RWA and Archer, SM and Mata-Míguez, J and Wing, N and Bolnick, DA}, title = {Evaluating population histories in Patagonia and Tierra del Fuego, Chile, using ancient mitochondrial and Y-chromosomal DNA.}, journal = {American journal of biological anthropology}, volume = {180}, number = {1}, pages = {144-161}, doi = {10.1002/ajpa.24638}, pmid = {36790637}, issn = {2692-7691}, mesh = {Humans ; Chile ; *Mitochondria/genetics ; *Archaeology ; Y Chromosome ; DNA, Ancient ; DNA, Mitochondrial/genetics ; }, abstract = {OBJECTIVES: This study aims to characterize the genetic histories of ancient hunter-gatherer groups in Fuego-Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y-chromosome data were generated to test three hypotheses. H0: All individuals were drawn from the same panmictic population; H1: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H2: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region.<br><br>METHODS: Ancient DNA was extracted from the teeth of 50 Fuegian-Patagonian individuals dating from 6,895&#x2009;cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y-chromosome variation was analyzed.<br><br>RESULTS: Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, FST comparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (p&#x2009;<&#x2009;0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000&#x2009;cal BP. Y-chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout.<br><br>DISCUSSION: These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego-Patagonia.}, }
@article {pmid36787794, year = {2023}, author = {Baca, M and Popović, D and Agadzhanyan, AK and Baca, K and Conard, NJ and Fewlass, H and Filek, T and Golubiński, M and Horáček, I and Knul, MV and Krajcarz, M and Krokhaleva, M and Lebreton, L and Lemanik, A and Maul, LC and Nagel, D and Noiret, P and Primault, J and Rekovets, L and Rhodes, SE and Royer, A and Serdyuk, NV and Soressi, M and Stewart, JR and Strukova, T and Talamo, S and Wilczyński, J and Nadachowski, A}, title = {Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1993}, pages = {20222238}, pmid = {36787794}, issn = {1471-2954}, mesh = {Animals ; *DNA, Ancient ; *Arvicolinae/genetics ; Bayes Theorem ; Phylogeny ; Population Dynamics ; DNA, Mitochondrial/genetics ; Genetic Variation ; }, abstract = {The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.}, }
@article {pmid36787792, year = {2022}, author = {Broccard, N and Silva, NM and Currat, M}, title = {Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe.}, journal = {American journal of biological anthropology}, volume = {177}, number = {1}, pages = {134-146}, pmid = {36787792}, issn = {2692-7691}, mesh = {*Mitochondria/genetics ; Europe ; *DNA, Mitochondrial/genetics ; Emigration and Immigration ; Biological Evolution ; DNA, Ancient ; }, abstract = {OBJECTIVES: The analysis of ancient mitochondrial DNA from osteological remains has challenged previous conclusions drawn from the analysis of mitochondrial DNA from present populations, notably by revealing an absence of genetic continuity between the Neolithic and modern populations in Central Europe. Our study investigates how to reconcile these contradictions at the mitochondrial level using a modeling approach.<br><br>MATERIALS AND METHODS: We used a spatially explicit computational framework to simulate ancient and modern DNA sequences under various evolutionary scenarios of post Neolithic demographic events and compared the genetic diversity of the simulated and observed mitochondrial sequences. We investigated which-if any-scenarios were able to reproduce statistics of genetic diversity similar to those observed, with a focus on the haplogroup N1a, associated with the spread of early Neolithic farmers.<br><br>RESULTS: Demographic fluctuations during the Neolithic transition or subsequent demographic collapses after this period, that is, due to epidemics such as plague, are not sufficient to explain the signal of population discontinuity detected on the mitochondrial DNA in Central Europe. Only a scenario involving a substantial genetic input due to the arrival of migrants after the Neolithic transition, possibly during the Bronze Age, is compatible with observed patterns of genetic diversity.<br><br>DISCUSSION: Our results corroborate paleogenomic studies, since out of the alternative hypotheses tested, the best one that was able to recover observed patterns of mitochondrial diversity in modern and ancient Central European populations was one were immigration of populations from the Pontic steppes during the Bronze Age was explicitly simulated.}, }
@article {pmid36778139, year = {2022}, author = {Fregel, R}, title = {The origin of the Carpathian Avar elites revealed.}, journal = {Cell genomics}, volume = {2}, number = {6}, pages = {100143}, pmid = {36778139}, issn = {2666-979X}, abstract = {In the sixth century, the Avar elites established themselves in the Carpathian Basin as evidenced today by the astounding archaeological sites with exquisite grave goods made of silver and gold. Recently reported in Cell, Gnecchi-Ruscone et al.[1] obtained paleogenomic evidence from Avar sites in Hungary, placing the Avar elites' origin in Mongolia and confirming their own historical claims.}, }
@article {pmid36776693, year = {2023}, author = {Hagymási, K}, title = {The Nobel prize in physiology and medicine - 2022.}, journal = {Structural chemistry}, volume = {34}, number = {2}, pages = {733-736}, pmid = {36776693}, issn = {1040-0400}, abstract = {The Nobel Assembly at Karolinska Institutet awarded the 2022 Nobel Prize in Physiology or Medicine to a Swedish geneticist, Svante Pääbo, for his discoveries concerning the genomes of extinct hominins and human evolution, for the sequencing of the genome of the Neanderthal, the discovery of a previously unknown hominin, Denisova, and the establishment of a new scientific discipline, paleogenomics.}, }
@article {pmid36762361, year = {2022}, author = {Riedel, A}, title = {Nine new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Sundaland.}, journal = {ZooKeys}, volume = {1124}, number = {}, pages = {109-130}, pmid = {36762361}, issn = {1313-2989}, abstract = {The DNA of Trigonopterus specimens from the Sundaland region stored between ten and 32 years in museums could be used for next-generation sequencing. The availability of their cox1 sequence allowed the description of the following nine new species: Trigonopterusgrimmi sp. nov., T.johorensis sp. nov., T.lambirensis sp. nov., T.linauensis sp. nov., T.microreticulatus Riedel, Trnka &amp; Wahab sp. nov., T.mulensis sp. nov., T.sarawakensis sp. nov., T.siamensis sp. nov., and T.singaporensis sp. nov. The alternative original spelling of the name T.tounensis Narakusumo &amp; Riedel is chosen to prevail over T.tounaensis Narakusumo &amp; Riedel. The new species represent the first country records of Trigonopterus for Brunei, Singapore, and Thailand. Thus, the genus´ known area of distribution in the Sundaland region is significantly extended. A key and a catalogue are provided to the Trigonopterus species from Borneo, W-Malaysia, Singapore, and Thailand.}, }
@article {pmid36760997, year = {2023}, author = {Chang, X and Pamjav, H and Zhabagin, M and Wen, S}, title = {Editorial: The genetic history of human populations along the ancient silk road.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1130104}, pmid = {36760997}, issn = {1664-8021}, }
@article {pmid36748324, year = {2024}, author = {Wagner, S and Seguin-Orlando, A and Leplé, JC and Leroy, T and Lalanne, C and Labadie, K and Aury, JM and Poirier, S and Wincker, P and Plomion, C and Kremer, A and Orlando, L}, title = {Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood.}, journal = {Molecular ecology}, volume = {33}, number = {3}, pages = {e16859}, pmid = {36748324}, issn = {1365-294X}, support = {339728/ERC_/European Research Council/International ; /ERC_/European Research Council/International ; }, mesh = {Humans ; *Wood ; *Quercus/genetics ; Ecosystem ; Forests ; Trees/genetics ; }, abstract = {Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.}, }
@article {pmid36747166, year = {2023}, author = {Sarhan, MS and Wurst, C and Tzankov, A and Bircher, AJ and Wittig, H and Briellmann, T and Augsburger, M and Hotz, G and Zink, A and Maixner, F}, title = {A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {9}, pmid = {36747166}, issn = {1741-7007}, mesh = {Humans ; Female ; Aged ; Nontuberculous Mycobacteria/genetics ; *Mycobacterium Infections, Nontuberculous/diagnosis/epidemiology/microbiology ; Switzerland ; *Syphilis ; Virulence ; }, abstract = {BACKGROUND: In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.<br><br>RESULTS: Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations.<br><br>CONCLUSIONS: The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.}, }
@article {pmid36721228, year = {2023}, author = {He, G and Wang, J and Yang, L and Duan, S and Sun, Q and Li, Y and Wu, J and Wu, W and Wang, Z and Liu, Y and Tang, R and Yang, J and Liu, C and Yuan, B and Wang, D and Xu, J and Wang, M}, title = {Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China.}, journal = {Human genomics}, volume = {17}, number = {1}, pages = {3}, pmid = {36721228}, issn = {1479-7364}, mesh = {Humans ; Haplotypes/genetics ; Alleles ; China ; *Asian People/genetics ; *Adaptation, Biological ; }, abstract = {BACKGROUND: Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized.<br><br>OBJECTIVES: To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling.<br><br>RESULTS: The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways.<br><br>CONCLUSIONS: Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.}, }
@article {pmid36714834, year = {2022}, author = {Velsko, IM and Semerau, L and Inskip, SA and García-Collado, MI and Ziesemer, K and Ruber, MS and Benítez de Lugo Enrich, L and Molero García, JM and Valle, DG and Peña Ruiz, AC and Salazar-García, DC and Hoogland, MLP and Warinner, C}, title = {Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology.}, journal = {PNAS nexus}, volume = {1}, number = {4}, pages = {pgac148}, pmid = {36714834}, issn = {2752-6542}, support = {MR/T022302/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.}, }
@article {pmid36712342, year = {2022}, author = {Brown, T and Rijal, DP and Heintzman, PD and Clarke, CL and Blankholm, HP and Høeg, HI and Lammers, Y and Bråthen, KA and Edwards, M and Alsos, IG}, title = {Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway.}, journal = {PNAS nexus}, volume = {1}, number = {5}, pages = {pgac209}, pmid = {36712342}, issn = {2752-6542}, abstract = {Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The large Mortensnes site complex (Ceavccageađgi, 70°N) has yielded the most comprehensive multiproxy record in the Arctic to date. The site saw occupation from the Pioneer period (c. 10,000 cal. years BP) with more intensive use from c. 4,200 to 2,000 cal. years BP and after 1,600 cal. years BP. Here, we combine on-site environmental archaeology with a near-site lake record of plant and animal sedaDNA. The rich animal sedaDNA data (42 taxa) and on-site faunal analyses reveal switches in human dietary composition from early-Holocene fish + marine mammals, to mixed marine + reindeer, then finally to marine + reindeer + domesticates (sheep, cattle, pigs), with highest reindeer concentrations in the last millennium. Archaeological evidence suggests these changes are not directly driven by climate or variation in population densities at the site or in the region, but rather are the result of changing socio-economic activities and culture, probably reflecting settlers' origins. This large settlement only had discernable effects on its hinterland in the last 3,600 years (grazing) and more markedly in the last 1,000 years through reindeer keeping/herding and, possibly domestic stock. Near-site sedaDNA can be linked to and validate the faunal record from archaeological excavations, demonstrating that environmental impacts can be assessed at a landscape scale.}, }
@article {pmid36691623, year = {2023}, author = {de March, CA and Matsunami, H and Abe, M and Cobb, M and Hoover, KC}, title = {Genetic and functional odorant receptor variation in the Homo lineage.}, journal = {iScience}, volume = {26}, number = {1}, pages = {105908}, pmid = {36691623}, issn = {2589-0042}, abstract = {Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.}, }
@article {pmid36672975, year = {2023}, author = {Danielewski, M and Żuraszek, J and Zielińska, A and Herzig, KH and Słomski, R and Walkowiak, J and Wielgus, K}, title = {Methodological Changes in the Field of Paleogenetics.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672975}, issn = {2073-4425}, mesh = {Sequence Analysis, DNA/methods ; *DNA, Ancient/analysis ; *High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound popularity of this budding field of science. Finally, a breakthrough was made with the development of next-generation sequencing (NGS) technologies and the update of DNA isolation protocols, through which even very fragmented aDNA samples could be used to sequence whole genomes. In this paper, we review the achievements made thus far and compare the methodologies utilized in this field of science, discussing their benefits and challenges.}, }
@article {pmid36672874, year = {2023}, author = {Borbély, N and Székely, O and Szeifert, B and Gerber, D and Máthé, I and Benkő, E and Mende, BG and Egyed, B and Pamjav, H and Szécsényi-Nagy, A}, title = {High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672874}, issn = {2073-4425}, mesh = {Humans ; Romania ; *Genetics, Population ; Phylogeny ; *Genome, Mitochondrial/genetics ; Chromosomes, Human, Y/genetics ; }, abstract = {Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.}, }
@article {pmid36672816, year = {2022}, author = {Salado, I and Preick, M and Lupiáñez-Corpas, N and Fernández-Gil, A and Vilà, C and Hofreiter, M and Leonard, JA}, title = {Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672816}, issn = {2073-4425}, mesh = {Humans ; Animals ; *Wolves/genetics ; Genetics, Population ; Population Growth ; Europe ; Genetic Variation/genetics ; }, abstract = {Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.}, }
@article {pmid36669262, year = {2023}, author = {Dzehverovic, M and Jusic, B and Pilav, A and Lukic, T and Cakar, J}, title = {Kinship analysis of skeletal remains from the Middle Ages.}, journal = {Forensic science international. Genetics}, volume = {63}, number = {}, pages = {102829}, doi = {10.1016/j.fsigen.2023.102829}, pmid = {36669262}, issn = {1878-0326}, mesh = {Humans ; Male ; *Body Remains ; Chromosomes, Human, Y ; *DNA Fingerprinting/methods ; Family ; Genetic Markers ; Haplotypes ; Microsatellite Repeats ; History, Medieval ; }, abstract = {Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry.}, }
@article {pmid36661852, year = {2023}, author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F}, title = {Estimating Temporally Variable Selection Intensity from Ancient DNA Data.}, journal = {Molecular biology and evolution}, volume = {40}, number = {3}, pages = {}, pmid = {36661852}, issn = {1537-1719}, mesh = {Animals ; Horses/genetics ; *DNA, Ancient ; Bayes Theorem ; Gene Frequency ; *DNA/genetics ; Time Factors ; Models, Genetic ; }, abstract = {Novel technologies for recovering DNA information from archaeological and historical specimens have made available an ever-increasing amount of temporally spaced genetic samples from natural populations. These genetic time series permit the direct assessment of patterns of temporal changes in allele frequencies and hold the promise of improving power for the inference of selection. Increased time resolution can further facilitate testing hypotheses regarding the drivers of past selection events such as the incidence of plant and animal domestication. However, studying past selection processes through ancient DNA (aDNA) still involves considerable obstacles such as postmortem damage, high fragmentation, low coverage, and small samples. To circumvent these challenges, we introduce a novel Bayesian framework for the inference of temporally variable selection based on genotype likelihoods instead of allele frequencies, thereby enabling us to model sample uncertainties resulting from the damage and fragmentation of aDNA molecules. Also, our approach permits the reconstruction of the underlying allele frequency trajectories of the population through time, which allows for a better understanding of the drivers of selection. We evaluate its performance through extensive simulations and demonstrate its utility with an application to the ancient horse samples genotyped at the loci for coat coloration. Our results reveal that incorporating sample uncertainties can further improve the inference of selection.}, }
@article {pmid36661298, year = {2023}, author = {Henriksen, RA and Zhao, L and Korneliussen, TS}, title = {NGSNGS: next-generation simulator for next-generation sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36661298}, issn = {1367-4811}, support = {R302-2018-2155//Lundbeck Foundation Centre for Disease Evolution/ ; //Carlsberg Foundation in 2019/ ; }, mesh = {*Software ; *Genome ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; DNA, Ancient ; Sequence Analysis, DNA/methods ; }, abstract = {SUMMARY: With the rapid expansion of the capabilities of the DNA sequencers throughout the different sequencing generations, the quantity of generated data has likewise increased. This evolution has also led to new bioinformatical methods, for which in silico data have become crucial when verifying the accuracy of a model or the robustness of a genomic analysis pipeline. Here, we present a multithreaded next-generation simulator for next-generation sequencing data (NGSNGS), which simulates reads faster than currently available methods and programs. NGSNGS can simulate reads with platform-specific characteristics based on nucleotide quality score profiles as well as including a post-mortem damage model which is relevant for simulating ancient DNA. The simulated sequences are sampled (with replacement) from a reference DNA genome, which can represent a haploid genome, polyploid assemblies or even population haplotypes and allows the user to simulate known variable sites directly. The program is implemented in a multithreading framework and is factors faster than currently available tools while extending their feature set and possible output formats.<br><br>The method and associated programs are released as open-source software, code and user manual are available at https://github.com/RAHenriksen/NGSNGS.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36656838, year = {2023}, author = {Wu, MY and Forcina, G and Low, GW and Sadanandan, KR and Gwee, CY and van Grouw, H and Wu, S and Edwards, SV and Baldwin, MW and Rheindt, FE}, title = {Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene.}, journal = {PLoS genetics}, volume = {19}, number = {1}, pages = {e1010551}, pmid = {36656838}, issn = {1553-7404}, mesh = {Animals ; *Chickens/genetics ; Gene Flow ; *Genome/genetics ; Genotype ; Phylogeny ; *Genetics, Population ; }, abstract = {Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20-50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.}, }
@article {pmid36653523, year = {2023}, author = {Nwosu, EC and Brauer, A and Monchamp, ME and Pinkerneil, S and Bartholomäus, A and Theuerkauf, M and Schmidt, JP and Stoof-Leichsenring, KR and Wietelmann, T and Kaiser, J and Wagner, D and Liebner, S}, title = {Early human impact on lake cyanobacteria revealed by a Holocene record of sedimentary ancient DNA.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {72}, pmid = {36653523}, issn = {2399-3642}, mesh = {Humans ; *DNA, Ancient ; Lakes/microbiology ; Anthropogenic Effects ; *Cyanobacteria/genetics ; Ecology ; }, abstract = {Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over the last centuries, yet we continue to lack information over longer timescales. Here, we apply high-resolution molecular analyses on sedimentary ancient DNA to reconstruct the history of cyanobacteria throughout the Holocene in a lake in north-eastern Germany. We find a substantial increase in cyanobacteria abundance coinciding with deforestation during the early Bronze Age around 4000 years ago, suggesting increased nutrient supply to the lake by local communities settling on the lakeshore. The next substantial human-driven increase in cyanobacteria abundance occurred only about a century ago due to intensified agricultural fertilisation which caused the dominance of potentially toxic taxa (e.g., Aphanizomenon). Our study provides evidence that humans began to locally impact lake ecology much earlier than previously assumed. Consequently, managing aquatic systems today requires awareness of the legacy of human influence dating back potentially several millennia.}, }
@article {pmid36650598, year = {2023}, author = {Popli, D and Peyrégne, S and Peter, BM}, title = {KIN: a method to infer relatedness from low-coverage ancient DNA.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {10}, pmid = {36650598}, issn = {1474-760X}, mesh = {Humans ; *DNA, Ancient ; *Inbreeding ; }, abstract = {Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness of a pair of individuals from the identical-by-descent segments they share. KIN accurately classifies up to 3rd-degree relatives using at least 0.05x sequence coverage and differentiates siblings from parent-child pairs. It incorporates additional models to adjust for contamination and detect inbreeding, which improves classification accuracy.}, }
@article {pmid36649412, year = {2023}, author = {Wang, X and Skourtanioti, E and Benz, M and Gresky, J and Ilgner, J and Lucas, M and Morsch, M and Peters, J and Pöllath, N and Ringbauer, H and le Roux, P and Schultz, M and Krause, J and Roberts, P and Stockhammer, PW}, title = {Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {4}, pages = {e2210611120}, pmid = {36649412}, issn = {1091-6490}, mesh = {Animals ; Humans ; History, Ancient ; Turkey ; Jordan ; *Domestication ; *Carbon ; Archaeology ; DNA ; }, abstract = {Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a "revolutionary" social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevalı Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevalı Çori together with newly generated radiocarbon dates. Our results are based on strontium ([87]Sr/[86]Sr), carbon, and oxygen (δ[18]O and δ[13]Ccarb) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevalı Çori. [87]Sr/[86]Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevalı Çori and Ba'ja demonstrate a diverse gene pool at Nevalı Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevalı Çori.}, }
@article {pmid36649410, year = {2023}, author = {Lewis, CM and Akinyi, MY and DeWitte, SN and Stone, AC}, title = {Ancient pathogens provide a window into health and well-being.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {4}, pages = {e2209476119}, pmid = {36649410}, issn = {1091-6490}, mesh = {Humans ; History, Ancient ; *Communicable Diseases ; Genome ; DNA, Ancient ; }, abstract = {This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.}, }
@article {pmid36646948, year = {2023}, author = {Skourtanioti, E and Ringbauer, H and Gnecchi Ruscone, GA and Bianco, RA and Burri, M and Freund, C and Furtwängler, A and Gomes Martins, NF and Knolle, F and Neumann, GU and Tiliakou, A and Agelarakis, A and Andreadaki-Vlazaki, M and Betancourt, P and Hallager, BP and Jones, OA and Kakavogianni, O and Kanta, A and Karkanas, P and Kataki, E and Kissas, K and Koehl, R and Kvapil, L and Maran, J and McGeorge, PJP and Papadimitriou, A and Papathanasiou, A and Papazoglou-Manioudaki, L and Paschalidis, K and Polychronakou-Sgouritsa, N and Preve, S and Prevedorou, EA and Price, G and Protopapadaki, E and Schmidt-Schultz, T and Schultz, M and Shelton, K and Wiener, MH and Krause, J and Jeong, C and Stockhammer, PW}, title = {Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean.}, journal = {Nature ecology &amp; evolution}, volume = {7}, number = {2}, pages = {290-303}, pmid = {36646948}, issn = {2397-334X}, mesh = {Humans ; *DNA, Ancient ; *Human Migration/history ; Europe ; Greece ; Genome ; }, abstract = {The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe's prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by 'eastern' gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries BC, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices.}, }
@article {pmid36641836, year = {2023}, author = {Barrenechea Angeles, I and Romero-Martínez, ML and Cavaliere, M and Varrella, S and Francescangeli, F and Piredda, R and Mazzocchi, MG and Montresor, M and Schirone, A and Delbono, I and Margiotta, F and Corinaldesi, C and Chiavarini, S and Montereali, MR and Rimauro, J and Parrella, L and Musco, L and Dell'Anno, A and Tangherlini, M and Pawlowski, J and Frontalini, F}, title = {Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites.}, journal = {Environment international}, volume = {172}, number = {}, pages = {107738}, doi = {10.1016/j.envint.2023.107738}, pmid = {36641836}, issn = {1873-6750}, mesh = {Humans ; Animals ; *Ecosystem ; *Biodiversity ; Biota ; Europe ; Human Activities ; Geologic Sediments ; }, abstract = {The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.}, }
@article {pmid36638796, year = {2023}, author = {Wang, K and Yu, H and Radzevičiūtė, R and Kiryushin, YF and Tishkin, AA and Frolov, YV and Stepanova, NF and Kiryushin, KY and Kungurov, AL and Shnaider, SV and Tur, SS and Tiunov, MP and Zubova, AV and Pevzner, M and Karimov, T and Buzhilova, A and Slon, V and Jeong, C and Krause, J and Posth, C}, title = {Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia.}, journal = {Current biology : CB}, volume = {33}, number = {3}, pages = {423-433.e5}, doi = {10.1016/j.cub.2022.11.062}, pmid = {36638796}, issn = {1879-0445}, mesh = {Humans ; History, Ancient ; Infant, Newborn ; *Gene Pool ; *Genome, Human ; Asia ; Russia ; Siberia ; Human Migration ; Genetics, Population ; }, abstract = {The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.}, }
@article {pmid36637197, year = {2023}, author = {Neuenschwander, S and Cruz Dávalos, DI and Anchieri, L and Sousa da Mota, B and Bozzi, D and Rubinacci, S and Delaneau, O and Rasmussen, S and Malaspinas, AS}, title = {Mapache: a flexible pipeline to map ancient DNA.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {2}, pages = {}, pmid = {36637197}, issn = {1367-4811}, support = {PCEGP3_181251//SNSF/ ; //Novo Nordisk Foundation/ ; }, mesh = {*Software ; *DNA, Ancient ; Genome ; Workflow ; }, abstract = {SUMMARY: We introduce mapache, a flexible, robust and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large datasets-such as reference panels and multiple extracts and libraries per sample - to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools.<br><br>Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). An extensive manual is provided at https://github.com/sneuensc/mapache/wiki.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36630487, year = {2023}, author = {Kehlmaier, C and Graciá, E and Ali, JR and Campbell, PD and Chapman, SD and Deepak, V and Ihlow, F and Jalil, NE and Pierre-Huyet, L and Samonds, KE and Vences, M and Fritz, U}, title = {Ancient DNA elucidates the lost world of western Indian Ocean giant tortoises and reveals a new extinct species from Madagascar.}, journal = {Science advances}, volume = {9}, number = {2}, pages = {eabq2574}, pmid = {36630487}, issn = {2375-2548}, abstract = {Before humans arrived, giant tortoises occurred on many western Indian Ocean islands. We combined ancient DNA, phylogenetic, ancestral range, and molecular clock analyses with radiocarbon and paleogeographic evidence to decipher their diversity and biogeography. Using a mitogenomic time tree, we propose that the ancestor of the extinct Mascarene tortoises spread from Africa in the Eocene to now-sunken islands northeast of Madagascar. From these islands, the Mascarenes were repeatedly colonized. Another out-of-Africa dispersal (latest Eocene/Oligocene) produced on Madagascar giant, large, and small tortoise species. Two giant and one large species disappeared c. 1000 to 600 years ago, the latter described here as new to science using nuclear and mitochondrial DNA. From Madagascar, the Granitic Seychelles were colonized (Early Pliocene) and from there, repeatedly Aldabra (Late Pleistocene). The Granitic Seychelles populations were eradicated and later reintroduced from Aldabra. Our results underline that integrating ancient DNA data into a multi-evidence framework substantially enhances the knowledge of the past diversity of island faunas.}, }
@article {pmid36625884, year = {2023}, author = {Xu, Y and Wang, N and Gao, S and Li, C and Ma, P and Yang, S and Jiang, H and Shi, S and Wu, Y and Zhang, Q and Cui, Y}, title = {Solving the two-decades-old murder case through joint application of ZooMS and ancient DNA approaches.}, journal = {International journal of legal medicine}, volume = {137}, number = {2}, pages = {319-327}, pmid = {36625884}, issn = {1437-1596}, support = {20210508040RQ//Jilin Scientific and Technological Development Program/ ; 20200201138JC//Jilin Scientific and Technological Development Program/ ; 715069-FINDER-ERC-2016-STG//H2020 European Research Council/ ; }, mesh = {Humans ; *DNA, Ancient ; Reproducibility of Results ; *DNA ; Mass Spectrometry ; Bone and Bones ; DNA Fingerprinting/methods ; }, abstract = {Bones are one of the most common biological types of evidence in forensic cases. Discriminating human bones from irrelevant species is important for the identification of victims; however, the highly degraded bones could be undiagnostic morphologically and difficult to analyze with standard DNA profiling approaches. The same challenge also exists in archaeological studies. Here, we present an initial study of an analytical strategy that involves zooarchaeology by mass spectrometry (ZooMS) and ancient DNA methods. Through the combined strategy, we managed to identify the only biological evidence of a two-decades-old murder case - a small piece of human bone out of 19 bone fragments - and confirmed the kinship between the victim and the putative parents through joint application of next-generation sequencing (NGS) and Sanger sequencing methods. ZooMS effectively screened out the target human bone while ancient DNA methods improve the DNA yields. The combined strategy in this case outperforms the standard DNA profiling approach with shorter time, less cost, as well as higher reliability for the genetic identification results. HIGHLIGHTS: • The first application of zooarchaeology by mass spectrometry technique in the forensic case for screening out human bones from bone fragment mixtures. • Application of ancient DNA technique to recover the highly degraded DNA sequence from the challenging sample that failed standard DNA profiling approaches. • A fast, sensitive, and low-cost strategy that combines the strengths of protein analysis and DNA analysis for kinship identification in forensic research.}, }
@article {pmid36625391, year = {2023}, author = {Straiton, J}, title = {Ancient DNA sequencing: telling the tale of human history and evolution.}, journal = {BioTechniques}, volume = {74}, number = {1}, pages = {5-7}, doi = {10.2144/btn-2022-0121}, pmid = {36625391}, issn = {1940-9818}, mesh = {Humans ; *DNA, Ancient ; Sequence Analysis, DNA ; Base Sequence ; }, abstract = {Standfirst: In the last decade, ancient DNA research has provided invaluable insights into the lives of ancient populations, adding detail and enriching the story of human evolution and development. [Formula: see text].}, }
@article {pmid36623185, year = {2023}, author = {Fleskes, RE and Cabana, GS and Gilmore, JK and Juarez, C and Karcher, E and Oubré, L and Mishoe, G and Ofunniyin, AA and Schurr, TG}, title = {Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {3}, pages = {e2201620120}, pmid = {36623185}, issn = {1091-6490}, support = {P2C HD044964/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Male ; *Black People/genetics ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Genomics ; Haplotypes/genetics ; South Carolina/ethnology ; Black or African American ; }, abstract = {In this study, we present the results of community-engaged ancient DNA research initiated after the remains of 36 African-descended individuals dating to the late 18th century were unearthed in the port city of Charleston, South Carolina. The Gullah Society of Charleston, along with other Charleston community members, initiated a collaborative genomic study of these ancestors of presumed enslaved status, in an effort to visibilize their histories. We generated 18 low-coverage genomes and 31 uniparental haplotypes to assess their genetic origins and interrelatedness. Our results indicate that they have predominantly West and West-Central African genomic ancestry, with one individual exhibiting some genomic affiliation with populations in the Americas. Most were assessed as genetic males, and no autosomal kin were identified among them. Overall, this study expands our understanding of the colonial histories of African descendant populations in the US South.}, }
@article {pmid36620416, year = {2023}, author = {Alfieri, JM and Johnson, T and Linderholm, A and Blackmon, H and Athrey, GN}, title = {Genomic investigation refutes record of most diverged avian hybrid.}, journal = {Ecology and evolution}, volume = {13}, number = {1}, pages = {e9689}, pmid = {36620416}, issn = {2045-7758}, support = {R35 GM138098/GM/NIGMS NIH HHS/United States ; }, abstract = {The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the "record" of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.}, }
@article {pmid36610858, year = {2023}, author = {Miao, B and Liu, Y and Yang, R and Feng, X and Liu, F and Cao, P and Dai, Q and Ping, W and Liu, Y and Fu, Q}, title = {Assessment of contaminants associated with gold-standard ancient DNA protocols.}, journal = {Science bulletin}, volume = {68}, number = {1}, pages = {5-9}, doi = {10.1016/j.scib.2022.12.027}, pmid = {36610858}, issn = {2095-9281}, mesh = {*DNA, Ancient ; Sequence Analysis, DNA/methods ; *Fossils ; }, }
@article {pmid36593352, year = {2023}, author = {Montag, A}, title = {[The history of skin color is the history of mankind!].}, journal = {Dermatologie (Heidelberg, Germany)}, volume = {74}, number = {2}, pages = {75-79}, pmid = {36593352}, issn = {2731-7013}, mesh = {Animals ; Humans ; *Hominidae/genetics ; Skin Pigmentation/genetics ; *Neanderthals ; Africa, Eastern ; Hair Color/genetics ; }, abstract = {In the early days of mankind, at a time when various other human species populated the earth coexisting with Homo sapiens, the genetic mixing of mankind had already begun. Today, paleogenetics-as a branch of human genetic research-can prove that individuals from the most diverse human species already produced offspring together long before our era. This intermixing was supported from the beginning by massive migratory movements that started in East Africa and led first Homo neanderthalensis and much later also Homo sapiens to as far as Europe-two human species of which we know today that they were lighter-skinned than their ancestors. The adaptation to life in different climatic zones led to development of specific characteristics, which, in addition to physique and physiognomy, also affect specific features of the skin and the integumentary system. The most striking feature among these is the skin color and all associated skin-specific characteristics. These characteristics ensure special protection, but can also be the origin for specific diseases. Any division of Homo sapiens into races has been scientifically refuted. Due to ongoing genetic mixing of mankind, skin color, hair color and all associated characteristics should always be considered individually.}, }
@article {pmid36582485, year = {2022}, author = {Zhu, K and Du, P and Li, J and Zhang, J and Hu, X and Meng, H and Chen, L and Zhou, B and Yang, X and Xiong, J and Allen, E and Ren, X and Ding, Y and Xu, Y and Chang, X and Yu, Y and Han, S and Dong, G and Wang, CC and Wen, S}, title = {Cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105636}, pmid = {36582485}, issn = {2589-0042}, abstract = {A high point of Tibetan Plateau (TP) civilization, the expansive Tubo Empire (618-842 AD) wielded great influence across ancient western China. However, whether the Tubo expansion was cultural or demic remains unclear due to sparse ancient DNA sampling. Here, we reported ten ancient genomes at 0.017- to 0.867-fold coverages from the Dulan site with typical Tubo archaeological culture dating to 1308-1130 BP. Nine individuals from three different grave types have close relationship with previously reported ancient highlanders from the southwestern Himalayas and modern core-Tibetan populations. A Dulan-related Tubo ancestry contributed overwhelmingly (95%-100%) to the formation of modern Tibetans. A genetic outlier with dominant Eurasian steppe-related ancestry suggesting a potential population movement into the Tubo-controlled regions from Central Asia. Together with archeological evidence from burial styles and customs, our study suggested the impact of the Tubo empire on the northeast edge of the TP involved both cultural and demic diffusion.}, }
@article {pmid36581666, year = {2022}, author = {Changmai, P and Pinhasi, R and Pietrusewsky, M and Stark, MT and Ikehara-Quebral, RM and Reich, D and Flegontov, P}, title = {Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st-3rd centuries CE.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22507}, pmid = {36581666}, issn = {2045-2322}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Genetics, Population ; *DNA, Ancient ; Cambodia ; South Asian People ; Asian People ; }, abstract = {Indian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40-50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78-234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations.}, }
@article {pmid36576953, year = {2022}, author = {Nägele, K and Rivollat, M and Yu, H and Wang, K}, title = {Ancient genomic research - From broad strokes to nuanced reconstructions of the past.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {193-230}, doi = {10.4436/JASS.10017}, pmid = {36576953}, issn = {2037-0644}, mesh = {Humans ; History, Ancient ; *Genomics ; *Archaeology ; DNA, Ancient ; }, abstract = {Ancient DNA (aDNA) studies have deployed genetic material from archaeological contexts to investigate human dispersals and interactions, corroborating some longstanding hypotheses and revealing new aspects of human history. After drawing the broad genomic strokes of human history, geneticists have discovered the exciting possibilities of applying this method to answer questions on a smaller scale. This review provides an overview of the commonly used methods, both in the laboratory and the analyses, and summarizes the current state of genomic research. It reviews human dispersals across the continents and additionally highlights some studies that integrated genomics to answer questions beyond biology to understand the cultural and societal traits of past societies. By shining a light from multiple angles, we gain a much better understanding of the real shape of the human past.}, }
@article {pmid36565457, year = {2022}, author = {Vallini, L and Pagani, L}, title = {The future of the Eurasian past: highlighting plotholes and pillars of human population movements in the Late Pleistocene.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {231-241}, doi = {10.4436/JASS.10013}, pmid = {36565457}, issn = {2037-0644}, mesh = {Humans ; Africa ; Italy ; *Population Dynamics ; }, abstract = {The major genetic divergences among non-Africans took place within a relatively short period of time, between 50 and 40 thousand years ago. These events shaped human diversity worldwide and set the basis for our current understanding of demographic history, patterns of adaptation and genetic burden across human populations. While the global picture appears already set, with the main human expansion Out of Africa inferred to have occurred between 60 and 70 thousand years ago and the main separation between contemporary East and West Eurasian to have taken place at around 40 thousand years ago, several finer details remain unresolved, including the whereabouts of such expansions and the dynamics of their interactions with archaic hominins and the interplay between environmental, cultural and demographic effectors. Here we review the major events that characterize human movements across and beyond Eurasia until the last glacial maximum and, at the end of each paragraph, spell out in italics the major questions that remain unsolved and that may provide major breakthroughs in the field in the upcoming years.}, }
@article {pmid36553640, year = {2022}, author = {Taufik, L and Teixeira, JC and Llamas, B and Sudoyo, H and Tobler, R and Purnomo, GA}, title = {Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects.}, journal = {Genes}, volume = {13}, number = {12}, pages = {}, pmid = {36553640}, issn = {2073-4425}, mesh = {Animals ; Humans ; *Hominidae/genetics ; Human Migration ; New Guinea ; Australia ; Phylogeography ; *Coleoptera ; }, abstract = {Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.}, }
@article {pmid36547255, year = {2022}, author = {van der Kuyl, AC}, title = {Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens.}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {3}, number = {4}, pages = {443-464}, pmid = {36547255}, issn = {2673-3986}, abstract = {Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.}, }
@article {pmid36537881, year = {2022}, author = {Muktupavela, RA and Petr, M and Ségurel, L and Korneliussen, T and Novembre, J and Racimo, F}, title = {Modeling the spatiotemporal spread of beneficial alleles using ancient genomes.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36537881}, issn = {2050-084X}, support = {R01 GM132383/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Alleles ; Gene Frequency ; *Selection, Genetic ; }, abstract = {Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.}, }
@article {pmid36531224, year = {2022}, author = {Xiang, H and Wang, Z and Yang, L and Zhang, X and Zhao, X}, title = {Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {1000123}, pmid = {36531224}, issn = {1664-8021}, abstract = {Ancient DNA is vitally important in evolutionary research, and obtaining authentic ancient DNA sequences is critical for a proper analysis. However, it is difficult to acquire amplicons accurately and efficiently from ancient DNA templates using current techniques. Here, we established a loop-primer-mediated amplification method (L-PCR) to obtain target ancient DNA sequences with high accuracy and efficiency. The method was tested using 66 ancient samples (including 27 pig bones or teeth and 39 chicken bones) and serially diluted modern animal DNA templates. Compared to nested PCR, L-PCR was proven to be more efficient and accurate and could obtain more amplicons from both ancient pig samples and chicken bones and detect as low as 10[-3] ng/μl modern pig template DNA. The efficiency was at least 100-fold that of the nested PCR. The results suggest that L-PCR is advantageous for obtaining authentic DNA sequences from poorly preserved or recalcitrant ancient specimens.}, }
@article {pmid36525814, year = {2023}, author = {Bardan, F and Higgins, D and Austin, JJ}, title = {A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage.}, journal = {Forensic science international. Genetics}, volume = {63}, number = {}, pages = {102822}, doi = {10.1016/j.fsigen.2022.102822}, pmid = {36525814}, issn = {1878-0326}, mesh = {Female ; Humans ; Male ; *Chromosomes, Human, Y/genetics ; *DNA Fingerprinting/methods ; DNA, Mitochondrial/genetics ; *Eye Color/genetics ; *Forensic Genetics/methods ; Hair ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; }, abstract = {Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.}, }
@article {pmid36525576, year = {2023}, author = {de Flamingh, A and Rivera-Colón, AG and Gnoske, TP and Kerbis Peterhans, JC and Catchen, J and Malhi, RS and Roca, AL}, title = {Numt Parser: Automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera.}, journal = {The Journal of heredity}, volume = {114}, number = {2}, pages = {120-130}, doi = {10.1093/jhered/esac065}, pmid = {36525576}, issn = {1465-7333}, mesh = {Animals ; Pseudogenes ; *Genome, Mitochondrial ; *Panthera/genetics ; Phylogeny ; Reproducibility of Results ; DNA, Mitochondrial/genetics ; Cell Nucleus/genetics ; Sequence Analysis, DNA ; }, abstract = {Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from 2 ancient Cape lions (Panthera leo), because mtDNA is often the marker of choice for ancient DNA studies and the genus Panthera is known to have numt pseudogenes. Numt Parser decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of Numt Parser to 2 other bioinformatic approaches that can be used to account for numt contamination. We found that Numt Parser outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. Numt Parser therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.}, }
@article {pmid36520391, year = {2023}, author = {Gorgé, O and Bennett, EA and Massilani, D and Daligault, J and Geigl, EM and Grange, T}, title = {Analysis of Ancient Microbial DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {103-131}, pmid = {36520391}, issn = {1940-6029}, mesh = {Animals ; Humans ; DNA, Ancient ; Body Remains ; *Hominidae/genetics ; DNA/genetics ; Genome, Microbial ; *Neanderthals/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.}, }
@article {pmid36518622, year = {2022}, author = {Anderson, LA}, title = {Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation.}, journal = {Ecology and evolution}, volume = {12}, number = {12}, pages = {e9518}, pmid = {36518622}, issn = {2045-7758}, abstract = {Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.}, }
@article {pmid36517229, year = {2022}, author = {Rohland, N and Mallick, S and Mah, M and Maier, R and Patterson, N and Reich, D}, title = {Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs.}, journal = {Genome research}, volume = {32}, number = {11-12}, pages = {2068-2078}, pmid = {36517229}, issn = {1549-5469}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Humans ; *DNA, Ancient/analysis ; Sequence Analysis, DNA ; *Polymorphism, Single Nucleotide ; DNA/genetics ; Gene Library ; }, abstract = {The strategy of in-solution enrichment for hundreds of thousands of single-nucleotide polymorphisms (SNPs) has been used to analyze >70% of individuals with genome-scale ancient DNA published to date. This approach makes it economical to study ancient samples with low proportions of human DNA and increases the rate of conversion of sampled remains into interpretable data. So far, nearly all such data have been generated using a set of bait sequences targeting about 1.24 million SNPs (the "1240k reagent"), but synthesis of the reagent has been cost-effective for only a few laboratories. In 2021, two companies, Daicel Arbor Biosciences and Twist Bioscience, made available assays that target the same core set of SNPs along with supplementary content. We test all three assays on a common set of 27 ancient DNA libraries and show that all three are effective at enriching many hundreds of thousands of SNPs. For all assays, one round of enrichment produces data that are as useful as two. In our testing, the "Twist Ancient DNA" assay produces the highest coverages, greatest uniformity on targeted positions, and almost no bias toward enriching one allele more than another relative to shotgun sequencing. We also identify hundreds of thousands of targeted SNPs for which there is minimal allelic bias when comparing 1240k data to either shotgun or Twist data. This facilitates coanalysis of the large data sets that have been generated using 1240k and Twist capture, as well as shotgun sequencing approaches.}, }
@article {pmid36516232, year = {2022}, author = {Söylev, A and Çokoglu, SS and Koptekin, D and Alkan, C and Somel, M}, title = {CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.}, journal = {PLoS computational biology}, volume = {18}, number = {12}, pages = {e1010788}, pmid = {36516232}, issn = {1553-7358}, mesh = {Humans ; *DNA Copy Number Variations/genetics ; Genotype ; *Genomics/methods ; Genome, Human/genetics ; Genetics, Population ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.}, }
@article {pmid36514938, year = {2023}, author = {Rannamäe, E and Saarma, U and Kantanen, J and Bläuer, A}, title = {Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds.}, journal = {Animal genetics}, volume = {54}, number = {2}, pages = {177-188}, doi = {10.1111/age.13281}, pmid = {36514938}, issn = {1365-2052}, support = {SA286499//Academy of Finland/ ; PRG29//Eesti Teadusagentuur/ ; PRG1209//Eesti Teadusagentuur/ ; }, mesh = {Animals ; *Goats/genetics ; Estonia ; Finland ; *Genetic Variation ; Haplotypes ; DNA, Mitochondrial/genetics ; Phylogeny ; }, abstract = {Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.}, }
@article {pmid36513080, year = {2023}, author = {Peltola, S and Majander, K and Makarov, N and Dobrovolskaya, M and Nordqvist, K and Salmela, E and Onkamo, P}, title = {Genetic admixture and language shift in the medieval Volga-Oka interfluve.}, journal = {Current biology : CB}, volume = {33}, number = {1}, pages = {174-182.e10}, doi = {10.1016/j.cub.2022.11.036}, pmid = {36513080}, issn = {1879-0445}, mesh = {Humans ; *White People ; Russia ; Language ; *Multilingualism ; }, abstract = {The Volga-Oka interfluve in northwestern Russia has an intriguing history of population influx and language shift during the Common Era. Today, most inhabitants of the region speak Russian, but until medieval times, northwestern Russia was inhabited by Uralic-speaking peoples.[1][,][2][,][3] A gradual shift to Slavic languages started in the second half of the first millennium with the expansion of Slavic tribes, which led to the foundation of the Kievan Rus' state in the late 9[th] century CE. The medieval Rus' was multicultural and multilingual-historical records suggest that its northern regions comprised Slavic and Uralic peoples ruled by Scandinavian settlers.[4][,][5][,][6] In the 10[th]-11[th] centuries, the introduction of Christianity and Cyrillic literature raised the prestige status of Slavic, driving a language shift from Uralic to Slavic.[3] This eventually led to the disappearance of the Uralic languages from northwestern Russia. Here, we study a 1,500-year time transect of 30 ancient genomes and stable isotope values from the Suzdal region in the Volga-Oka interfluve. We describe a previously unsampled local Iron Age population and a gradual genetic turnover in the following centuries. Our time transect captures the population shift associated with the spread of Slavic languages and illustrates the ethnically mixed state of medieval Suzdal principality, eventually leading to the formation of the admixed but fully Slavic-speaking population that inhabits the area today. We also observe genetic outliers that highlight the importance of the Suzdal region in medieval times as a hub of long-reaching contacts via trade and warfare.}, }
@article {pmid36510283, year = {2022}, author = {Bonczarowska, JH and Susat, J and Mühlemann, B and Jasch-Boley, I and Brather, S and Höke, B and Brather-Walter, S and Schoenenberg, V and Scheschkewitz, J and Graenert, G and Krausse, D and Francken, M and Jones, TC and Wahl, J and Nebel, A and Krause-Kyora, B}, title = {Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {250}, pmid = {36510283}, issn = {1474-760X}, support = {HHSN272201400008C/AI/NIAID NIH HHS/United States ; }, mesh = {Middle Aged ; Humans ; Phylogeny ; *Coinfection ; Mycobacterium leprae/genetics ; *Leprosy/epidemiology/history/microbiology ; DNA, Ancient ; }, abstract = {BACKGROUND: The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim "Mittelhofen," in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically.<br><br>RESULTS: Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK.<br><br>CONCLUSIONS: The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later.}, }
@article {pmid36494546, year = {2022}, author = {Forshaw, R}, title = {Dental calculus - oral health, forensic studies and archaeology: a review.}, journal = {British dental journal}, volume = {233}, number = {11}, pages = {961-967}, pmid = {36494546}, issn = {1476-5373}, mesh = {Humans ; Dental Calculus ; Oral Health ; Archaeology ; *Dental Plaque ; *Microbiota ; }, abstract = {Dental calculus is recognised as a secondary aetiological factor in periodontal disease, and being a prominent plaque retentive factor, it is routinely removed by the dental team to maintain oral health. Conversely, dental calculus can potentially be useful in forensic studies by supplying data that may be helpful in the identification of human remains and assist in determining the cause of death. During the last few decades, dental calculus has been increasingly recognised as an informative tool to understand ancient diet and health. As an archaeological deposit, it may contain non-dietary debris which permits the exploration of human behaviour and activities. While optical and scanning electron microscopy were the original analytical methods utilised to study microparticles entrapped within the calcified matrix, more recently, molecular approaches, including ancient DNA (aDNA) and protein analyses, have been applied. Oral bacteria, a major component of calculus, is the primary target of these aDNA studies. Such analyses can detect changes in the oral microbiota, including those that have reflected the shift from agriculture to industrialisation, as well as identifying markers for various systemic diseases.}, }
@article {pmid36493775, year = {2023}, author = {Koptekin, D and Yüncü, E and Rodríguez-Varela, R and Altınışık, NE and Psonis, N and Kashuba, N and Yorulmaz, S and George, R and Kazancı, DD and Kaptan, D and Gürün, K and Vural, KB and Gemici, HC and Vassou, D and Daskalaki, E and Karamurat, C and Lagerholm, VK and Erdal, &#xd6;D and Kırdök, E and Marangoni, A and Schachner, A and Üstündağ, H and Shengelia, R and Bitadze, L and Elashvili, M and Stravopodi, E and Özbaşaran, M and Duru, G and Nafplioti, A and Rose, CB and Gencer, T and Darbyshire, G and Gavashelishvili, A and Pitskhelauri, K and Çevik, &#xd6; and Vuruşkan, O and Kyparissi-Apostolika, N and Büyükkarakaya, AM and Oğuzhanoğlu, U and Günel, S and Tabakaki, E and Aliev, A and Ibrahimov, A and Shadlinski, V and Sampson, A and Kılınç, GM and Atakuman, &#xc7; and Stamatakis, A and Poulakakis, N and Erdal, YS and Pavlidis, P and Storå, J and Özer, F and Götherström, A and Somel, M}, title = {Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.}, journal = {Current biology : CB}, volume = {33}, number = {1}, pages = {41-57.e15}, pmid = {36493775}, issn = {1879-0445}, mesh = {Humans ; Male ; History, Ancient ; *Racial Groups ; Iran ; *Genome, Human ; Gene Flow ; Human Migration ; Genetics, Population ; }, abstract = {We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.}, }
@article {pmid36493597, year = {2023}, author = {Keeling, BA and Quam, R and Martínez, I and Arsuaga, JL and Maroto, J}, title = {Reassessment of the human mandible from Banyoles (Girona, Spain).}, journal = {Journal of human evolution}, volume = {174}, number = {}, pages = {103291}, doi = {10.1016/j.jhevol.2022.103291}, pmid = {36493597}, issn = {1095-8606}, mesh = {Animals ; Humans ; Spain ; Proteomics ; *Hominidae/anatomy &amp; histology ; Mandible/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; Fossils ; Biological Evolution ; }, abstract = {Since the discovery of a human mandible in 1887 near the present-day city of Banyoles, northeastern Spain, researchers have generally emphasized its archaic features, including the lack of chin structures, and suggested affinities with the Neandertals or European Middle Pleistocene (Chibanian) specimens. Uranium-series and electron spin resonance dating suggest the mandible dates to the Late Pleistocene (Tarantian), approximately ca. 45-66 ka. In this study, we reassessed the taxonomic affinities of the Banyoles mandible by comparing it to samples of Middle Pleistocene fossils from Africa and Europe, Neandertals, Early and Upper Paleolithic modern humans, and recent modern humans. We evaluated the frequencies and expressions of morphological features and performed a three-dimensional geometric morphometric analysis on a virtual reconstruction of Banyoles to capture overall mandibular shape. Our results revealed no derived Neandertal morphological features in Banyoles. While a principal component analysis based on Euclidean distances from the first two principal components clearly grouped Banyoles with both fossil and recent Homo sapiens individuals, an analysis of the Procrustes residuals demonstrated that Banyoles did not fit into any of the comparative groups. The lack of Neandertal features in Banyoles is surprising considering its Late Pleistocene age. A consideration of the Middle Pleistocene fossil record in Europe and southwest Asia suggests that Banyoles is unlikely to represent a late-surviving Middle Pleistocene population. The lack of chin structures also complicates an assignment to H. sapiens, although early fossil H. sapiens do show somewhat variable development of the chin structures. Thus, Banyoles represents a non-Neandertal Late Pleistocene European individual and highlights the continuing signal of diversity in the hominin fossil record. The present situation makes Banyoles a prime candidate for ancient DNA or proteomic analyses, which may shed additional light on its taxonomic affinities.}, }
@article {pmid36481947, year = {2022}, author = {Bundell, S}, title = {Record-breaking ancient DNA found in frozen soil.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-04398-6}, pmid = {36481947}, issn = {1476-4687}, }
@article {pmid36481704, year = {2023}, author = {Zhang, J and Shi, K and Paerl, HW and Rühland, KM and Yuan, Y and Wang, R and Chen, J and Ge, M and Zheng, L and Zhang, Z and Qin, B and Liu, J and Smol, JP}, title = {Ancient DNA reveals potentially toxic cyanobacteria increasing with climate change.}, journal = {Water research}, volume = {229}, number = {}, pages = {119435}, doi = {10.1016/j.watres.2022.119435}, pmid = {36481704}, issn = {1879-2448}, mesh = {Humans ; *DNA, Ancient ; Ecosystem ; Climate Change ; Eutrophication ; *Cyanobacteria/genetics ; Lakes/microbiology ; China ; }, abstract = {Cyanobacterial blooms in freshwater systems are a global threat to human and aquatic ecosystem health, exhibiting particularly harmful effects when toxin-producing taxa are present. While climatic change and nutrient over-enrichment control the global expansion of total cyanobacterial blooms, it remains unknown to what extent this expansion reflected cyanobacterial assemblage due to the scarcity of long-term monitoring data. Here we use high-throughput sequencing of sedimentary DNA to track ∼100 years of changes in cyanobacterial community in hyper-eutrophic Lake Taihu, China's third largest freshwater lake and the key water source for ∼30 million people. A steady increase in the abundance of Microcystis (as potential toxin producers) during the past thirty years was correlated with increasing temperatures and declining wind speeds, but not with temporal trends in lakewater nutrient concentrations, highlighting recent climate effects on potentially increasing toxin-producing taxa. The socio-environmental repercussions of these findings are worrisome as continued anthropogenic climate change may counteract nutrient amelioration efforts in this critical freshwater resource.}, }
@article {pmid36472532, year = {2022}, author = {Moraitou, M and Forsythe, A and Fellows Yates, JA and Brealey, JC and Warinner, C and Guschanski, K}, title = {Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species.}, journal = {Molecular biology and evolution}, volume = {39}, number = {12}, pages = {}, pmid = {36472532}, issn = {1537-1719}, mesh = {Animals ; Gorilla gorilla ; Phylogeny ; Dental Calculus ; *Hominidae ; *Microbiota/genetics ; }, abstract = {Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.}, }
@article {pmid36465121, year = {2022}, author = {Ma, X and Xu, S}, title = {Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105614}, pmid = {36465121}, issn = {2589-0042}, abstract = {Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such as SLC19A2, SLC35F3, and SLC35F4, were assumed to be underlying positive selection in East Asians, but the detailed mechanism remains unknown. Here, we analyzed genome data of 3,823 individuals representing 223 global populations and identified the adaptive haplotypes at thiamine genes. Interestingly, the putative adaptive haplotype at SLC35F4 was of Neanderthal ancestry, while that at SLC35F3 was also likely of archaic origins. Leveraging new methods and available ancient DNA data, we further demonstrated that the beneficial haplotypes reached a high frequency at least 10,000 years ago and are maintained persistently in present-day East Asians. We argue that pathogens, rather than agriculture developed ∼10,000 years ago in East Asia, were likely the initial driving force of the putative positive selection. Notably, the first American people did not carry the putative adaptive haplotype at SLC35F4.}, }
@article {pmid36463384, year = {2022}, author = {Wang, K and Bleasdale, M and Le Moyne, C and Freund, C and Krause, J and Boivin, N and Schiffels, S}, title = {4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20939}, pmid = {36463384}, issn = {2045-2322}, mesh = {Humans ; *DNA, Ancient ; Africa, Eastern ; *Hair ; Sudan ; Body Remains ; }, abstract = {Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.}, }
@article {pmid36455558, year = {2022}, author = {Waldman, S and Backenroth, D and Harney, &#xc9; and Flohr, S and Neff, NC and Buckley, GM and Fridman, H and Akbari, A and Rohland, N and Mallick, S and Olalde, I and Cooper, L and Lomes, A and Lipson, J and Cano Nistal, J and Yu, J and Barzilai, N and Peter, I and Atzmon, G and Ostrer, H and Lencz, T and Maruvka, YE and Lämmerhirt, M and Beider, A and Rutgers, LV and Renson, V and Prufer, KM and Schiffels, S and Ringbauer, H and Sczech, K and Carmi, S and Reich, D}, title = {Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14[th] century.}, journal = {Cell}, volume = {185}, number = {25}, pages = {4703-4716.e16}, pmid = {36455558}, issn = {1097-4172}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Jews/genetics ; *White People ; Genetics, Population ; Genome, Human ; }, abstract = {We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14[th] century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14[th] century and highlight late medieval genetic heterogeneity no longer present in modern AJ.}, }
@article {pmid36450657, year = {2023}, author = {Oh, CS and Kim, MJ and Kim, YS and Min, S and Oh, KT and Lee, SD and Shin, DH}, title = {Revealing Joseon period People's single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea.}, journal = {Anatomy &amp; cell biology}, volume = {56}, number = {1}, pages = {54-60}, pmid = {36450657}, issn = {2093-3665}, abstract = {Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.}, }
@article {pmid36437963, year = {2022}, author = {Charlier, P and Bourdin, V and Augias, A and Brun, L and Kenmogne, JB and Josue, E}, title = {Are museums the future of evolutionary medicine?.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {1043702}, pmid = {36437963}, issn = {1664-8021}, }
@article {pmid36437603, year = {2023}, author = {Jeunen, GJ and Dowle, E and Edgecombe, J and von Ammon, U and Gemmell, NJ and Cross, H}, title = {crabs-A software program to generate curated reference databases for metabarcoding sequencing data.}, journal = {Molecular ecology resources}, volume = {23}, number = {3}, pages = {725-738}, doi = {10.1111/1755-0998.13741}, pmid = {36437603}, issn = {1755-0998}, support = {CAWX1904//Ministry of Business, Innovation and Employment/ ; MFP-21-UOO-087//Royal Society Te Ap&#x101;rangi/ ; }, mesh = {Animals ; *Brachyura ; Reproducibility of Results ; DNA Barcoding, Taxonomic/methods ; Software ; Eukaryota ; }, abstract = {The measurement of biodiversity is an integral aspect of life science research. With the establishment of second- and third-generation sequencing technologies, an increasing amount of metabarcoding data is being generated as we seek to describe the extent and patterns of biodiversity in multiple contexts. The reliability and accuracy of taxonomically assigning metabarcoding sequencing data have been shown to be critically influenced by the quality and completeness of reference databases. Custom, curated, eukaryotic reference databases, however, are scarce, as are the software programs for generating them. Here, we present crabs (Creating Reference databases for Amplicon-Based Sequencing), a software package to create custom reference databases for metabarcoding studies. crabs includes tools to download sequences from multiple online repositories (i.e., NCBI, BOLD, EMBL, MitoFish), retrieve amplicon regions through in silico PCR analysis and pairwise global alignments, curate the database through multiple filtering parameters (e.g., dereplication, sequence length, sequence quality, unresolved taxonomy, inclusion/exclusion filter), export the reference database in multiple formats for immediate use in taxonomy assignment software, and investigate the reference database through implemented visualizations for diversity, primer efficiency, reference sequence length, database completeness and taxonomic resolution. crabs is a versatile tool for generating curated reference databases of user-specified genetic markers to aid taxonomy assignment from metabarcoding sequencing data. crabs can be installed via docker and is available for download as a conda package and via GitHub (https://github.com/gjeunen/reference_database_creator).}, }
@article {pmid36426357, year = {2022}, author = {Thuesen, NH and Klausen, MS and Gopalakrishnan, S and Trolle, T and Renaud, G}, title = {Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {987655}, pmid = {36426357}, issn = {1664-3224}, mesh = {Humans ; Sequence Analysis, DNA/methods ; Histocompatibility Testing/methods ; *High-Throughput Nucleotide Sequencing/methods ; *HLA-A Antigens/genetics ; Algorithms ; }, abstract = {Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype's typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools' robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA's typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype's typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high.}, }
@article {pmid36414613, year = {2022}, author = {Quagliariello, A and Modi, A and Innocenti, G and Zaro, V and Conati Barbaro, C and Ronchitelli, A and Boschin, F and Cavazzuti, C and Dellù, E and Radina, F and Sperduti, A and Bondioli, L and Ricci, S and Lognoli, M and Belcastro, MG and Mariotti, V and Caramelli, D and Mariotti Lippi, M and Cristiani, E and Martino, ME and Muntoni, IM and Lari, M}, title = {Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6927}, pmid = {36414613}, issn = {2041-1723}, mesh = {Humans ; *Agriculture ; *Microbiota ; Diet ; Farmers ; Italy ; }, abstract = {The human microbiome has recently become a valuable source of information about host life and health. To date little is known about how it may have evolved during key phases along our history, such as the Neolithic transition towards agriculture. Here, we shed light on the evolution experienced by the oral microbiome during this transition, comparing Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers that populated a same restricted area in Italy. We integrate the analysis of 76 dental calculus oral microbiomes with the dietary information derived from the identification of embedded plant remains. We detect a stronger deviation from the hunter-gatherer microbiome composition in the last part of the Neolithic, while to a lesser extent in the early phases of the transition. Our findings demonstrate that the introduction of agriculture affected host microbiome, supporting the hypothesis of a gradual transition within the investigated populations.}, }
@article {pmid36405775, year = {2022}, author = {Arzelier, A and Rivollat, M and De Belvalet, H and Pemonge, MH and Binder, D and Convertini, F and Duday, H and Gandelin, M and Guilaine, J and Haak, W and Deguilloux, MF and Pruvost, M}, title = {Neolithic genomic data from southern France showcase intensified interactions with hunter-gatherer communities.}, journal = {iScience}, volume = {25}, number = {11}, pages = {105387}, pmid = {36405775}, issn = {2589-0042}, abstract = {Archaeological research shows that the dispersal of the Neolithic took a more complex turn when reaching western Europe, painting a contrasted picture of interactions between autochthonous hunter-gatherers (HGs) and incoming farmers. In order to clarify the mode, the intensity, and the regional variability of biological exchanges implied in these processes, we report new palaeogenomic data from Occitanie, a key region in Southern France. Genomic data from 28 individuals originating from six sites spanning from c. 5,500 to c. 2,500 BCE allow us to characterize regional patterns of ancestries throughout the Neolithic period. Results highlight major differences between the Mediterranean and Continental Neolithic expansion routes regarding both migration and interaction processes. High proportions of HG ancestry in both Early and Late Neolithic groups in Southern France support multiple pulses of inter-group gene flow throughout time and space and confirm the need for regional studies to address the complexity of the processes involved.}, }
@article {pmid36400919, year = {2022}, author = {Scorrano, G and Nielsen, SH and Vetro, DL and Sawafuji, R and Mackie, M and Margaryan, A and Fotakis, AK and Martínez-Labarga, C and Fabbri, PF and Allentoft, ME and Carra, M and Martini, F and Rickards, O and Olsen, JV and Pedersen, MW and Cappellini, E and Sikora, M}, title = {Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1262}, pmid = {36400919}, issn = {2399-3642}, mesh = {Humans ; Animals ; *Proteomics ; Dental Calculus ; Diet ; Genomics ; *Microbiota/genetics ; }, abstract = {Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.}, }
@article {pmid36399972, year = {2023}, author = {Pilli, E and Morelli, S and Poggiali, B and Alladio, E}, title = {Biogeographical ancestry, variable selection, and PLS-DA method: a new panel to assess ancestry in forensic samples via MPS technology.}, journal = {Forensic science international. Genetics}, volume = {62}, number = {}, pages = {102806}, doi = {10.1016/j.fsigen.2022.102806}, pmid = {36399972}, issn = {1878-0326}, mesh = {Humans ; DNA/genetics ; *Forensic Genetics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Least-Squares Analysis ; Phylogeography ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; *Population Groups/genetics ; }, abstract = {As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry information obtained from DNA can provide investigative leads to identify the victims (missing/unidentified persons, crime/armed conflict/mass disaster victims) or trace their perpetrators when no matches were found with the reference profile or in the database. Recently, the advent of Massively Parallel Sequencing technologies associated with the possibility of harnessing high-throughput genetic data allowed us to investigate the associations between phenotypic and genomic variations in worldwide human populations and develop new BGA forensic tools capable of simultaneously analyzing up to millions of markers if for example the ancient DNA approach of hybridization capture was adopted to target SNPs of interest. In the present study, a selection of more than 3000 SNPs was performed to create a new BGA panel and the accuracy of the new panel to infer ancestry from unknown samples was evaluated by the PLS-DA method. Subsequently, the panel created was assessed using three variable selection techniques (Backward variable elimination, Genetic Algorithm and Regularized elimination procedure), and the best SNPs in terms of inferring bio-geographical ancestry at inter- and intra-continental level were selected to obtain panels to predict BGA with a reduced number of selected markers to be applied in routine forensic cases where PCR amplification is the best choice to target SNPs.}, }
@article {pmid36399550, year = {2022}, author = {Sugiyama, N and Sugiyama, S and Cagnato, C and France, CAM and Iriki, A and Hughes, KS and Singleton, RR and Thornton, E and Hofman, CA}, title = {Earliest evidence of primate captivity and translocation supports gift diplomacy between Teotihuacan and the Maya.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {47}, pages = {e2212431119}, pmid = {36399550}, issn = {1091-6490}, mesh = {Humans ; Animals ; *Diplomacy ; Ceremonial Behavior ; DNA, Ancient ; *Atelinae ; Mexico ; }, abstract = {A multimethod archaeometry study (zooarchaeological, isotopic, ancient DNA, paleobotanical, and radiocarbon dating) of a spider monkey sacrificed in the ceremonial center of Teotihuacan, Mexico (1 to 550 CE) is interpreted as a diplomatic gift exchange with neighboring Maya. Not only does this spider monkey provide the earliest known instance of primate translocation and captivity in Mesoamerica, it helps date incipient modes of interregional diplomacy between two major powers during Early Classic Mesoamerica: Teotihuacan and the Maya. Details of human-primate interaction include age at capture and transport (before ∼3 y of age), captive duration (over 2 y), anthropogenic diet (staple was maize, though secondary resources unique to anthropogenic diet including arrowroot and chili pepper were also found), context of sacrifice (tethered and associated with complete golden eagle and an array of other statecrafts), and general site context (including presence of Maya vessels and Maya-style murals). The timing of the spider monkey's sacrifice (250 to 300 CE) and its life history suggest a reconsideration of epigraphically attested militaristic involvement of Teotihuacan at certain Maya sites. We propose that a period of more multilateral and fluid ritual exchange with Maya dignitaries preceded the Teotihuacan state's eventual ascent to prominence.}, }
@article {pmid36377787, year = {2023}, author = {Ausmees, K and Nettelblad, C}, title = {Achieving improved accuracy for imputation of ancient DNA.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36377787}, issn = {1367-4811}, support = {2017-00453//Formas/ ; }, mesh = {Animals ; Dogs ; Humans ; *DNA, Ancient ; Genotype ; Haplotypes ; *Software ; Ethnicity ; }, abstract = {MOTIVATION: Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.<br><br>RESULTS: We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU.<br><br>The C++ code for prophaser is available in the GitHub repository https://github.com/scicompuu/prophaser.<br><br>SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.}, }
@article {pmid36375244, year = {2022}, author = {Harvati, K and Reyes-Centeno, H}, title = {Evolution of Homo in the Middle and Late Pleistocene.}, journal = {Journal of human evolution}, volume = {173}, number = {}, pages = {103279}, pmid = {36375244}, issn = {1095-8606}, mesh = {Animals ; Humans ; *Hominidae ; Phylogeny ; Biological Evolution ; Fossils ; *Neanderthals ; }, abstract = {The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.}, }
@article {pmid36373266, year = {2022}, author = {Gaughran, SJ and vonHoldt, B}, title = {Pleistocene parades of carnivores into North America.}, journal = {Molecular ecology}, volume = {31}, number = {24}, pages = {6387-6389}, doi = {10.1111/mec.16783}, pmid = {36373266}, issn = {1365-294X}, mesh = {Animals ; Humans ; *Carnivora/genetics ; Phylogeography ; *Ursidae/genetics ; Biological Evolution ; *Lions ; North America ; Phylogeny ; }, abstract = {The distribution and movement of species, broadly known as biogeography, is one of the fundamental subfields of ecology and evolutionary biology. However, significant mysteries remain about the processes that gave rise to the modern distribution of biodiversity across the globe. Over the last several decades, the genetic study of ancient and subfossil specimens has started to shed light on past migrations of some species, with a particular focus on humans and megafauna. In this issue of Molecular Ecology, Salis et al. (2021) use ancient mitogenomes and a new phylogeographic method to add an important new piece of evidence to the mystery of megafaunal migrations into North America during the Pleistocene. They found a striking synchronicity of brown bear (Ursus arctos) and lion (Panthera spp.) migrations across the Bering Land Bridge at several time points during the late Pleistocene, which highlights the lasting impact of sea level change on the prehistoric and modern dispersal of terrestrial carnivores across continents.}, }
@article {pmid36371979, year = {2022}, author = {Howarth, A and Drummond, B and Wasef, S and Matheson, CD}, title = {An assessment of DNA extraction methods from blood-stained soil in forensic science.}, journal = {Forensic science international}, volume = {341}, number = {}, pages = {111502}, doi = {10.1016/j.forsciint.2022.111502}, pmid = {36371979}, issn = {1872-6283}, mesh = {Humans ; *Soil ; Polymerase Chain Reaction/methods ; DNA/analysis ; Chloroform/analysis ; Povidone ; Endopeptidase K ; *Blood Stains ; Silicon Dioxide ; }, abstract = {In forensic crime scene investigations, biological fluids such as blood are commonly found in soil. However, the analysis of blood-stained soil can be challenging due to the presence of inhibitors which limit the effective extraction and amplification of the deoxyribonucleic acid (DNA) required to produce a reportable DNA profile. There are some extraction methods that have been applied to blood-stained soil in forensic science, but these have produced sporadic results. This research has taken a number of different extraction methods from the fields of ancient DNA and environmental DNA and broken them down into the individual steps of pre-treatment, incubation, separation and purification. These steps were assessed independently then combined into various extraction methods to determine the best technique that can effectively and reliably profile human DNA from blood-stained soil. Testing involved assessment of three extraction buffers, (cetyltrimethylammonium bromide, guanidine thiocyanate, and proteinase K), four pre-treatment methods, (polyvinylpyrrolidone, ethylenediaminetetraacetic acid, hydrochloric acid, and sodium hydroxide), three separation steps, (centrifugation, phenol chloroform, and chloroform) and four purification steps, (size exclusion chromatography, bind elute columns, isopropanol precipitation and silica magnetic beads). The most effective procedure was found to be a polyvinylpyrrolidone pre-treatment with a proteinase K extraction buffer followed by magnetic silica bead purification with or without centrifugation. However, centrifugation separation was found to be equally effective after the pre-treatment step as after the incubation step. Our results shows that most of the current forensic procedures would benefit from the addition of a pre-treatment step prior to processing through the automated DNA profiling pipeline.}, }
@article {pmid36360198, year = {2022}, author = {Boulygina, E and Sharko, F and Cheprasov, M and Gladysheva-Azgari, M and Slobodova, N and Tsygankova, S and Rastorguev, S and Grigorieva, L and Kopp, M and Fernandes, JMO and Novgorodov, G and Boeskorov, G and Protopopov, A and Hwang, WS and Tikhonov, A and Nedoluzhko, A}, title = {Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear (Ursus arctos) Population during the Holocene.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360198}, issn = {2073-4425}, mesh = {Animals ; *Ursidae/genetics ; DNA, Ancient ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; }, abstract = {Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.}, }
@article {pmid36348137, year = {2023}, author = {Kimsis, J and Petersone-Gordina, E and Poksane, A and Vilcāne, A and Moore, J and Gerhards, G and Ranka, R}, title = {Application of natural sciences methodology in archaeological study of Iron Age burials in Latvia: pilot study.}, journal = {Forensic science, medicine, and pathology}, volume = {19}, number = {1}, pages = {8-15}, pmid = {36348137}, issn = {1556-2891}, support = {lzp-2018/1-0395.//Latvijas Zin&#x101;tnes Padome/ ; }, mesh = {Humans ; Pilot Projects ; Latvia ; *Burial ; *DNA, Mitochondrial/genetics ; Cemeteries/history ; }, abstract = {Natural sciences provide several modern methodologies that could be successfully applied in archaeological studies. In this pilot study, archaeological human remains from two Iron Age cemeteries (7th-twelfth centuries AD), Lejasbitēni and Čunkāni-Dreņģeri, which are located in different regions of Latvia, were studied. We applied ancient DNA (aDNA) and tooth enamel peptide analysis to determine the biological sex of the individuals. In addition, aDNA analysis was used to perform mtDNA haplogroup analysis. In most cases, the results of aDNA analysis regarding the biological sex of individuals coincided with the gender assigned based on grave orientation and grave goods. The results of sex determination using peptide analysis in all four individuals for whom data were available matched the possible gender. Of the 17 samples that had sufficient DNA for sequencing, seven samples had enough reads to perform mtDNA haplogroup analysis. The H2a2a, I4a1, H2a2a1, and H16c mtDNA haplogroups were identified in the individuals from the Lejasbitēni cemetery, while the T2b and K1a + 150 mtDNA haplogroups were identified in the individuals from the Čunkāni-Dreņģeri cemetery. Overall, the obtained results demonstrated the feasibility of applying aDNA and tooth enamel peptide analysis for biological sex determination within archaeological studies. The availability of human aDNA data will be highly useful for investigating the demographic history and social structures in Iron Age Latvia.}, }
@article {pmid36344562, year = {2022}, author = {Miszkiewicz, JJ and Buckley, HR and Feldman, M and Kiko, L and Carlhoff, S and Naegele, K and Bertolini, E and Guimarães, NRD and Walker, MM and Powell, A and Posth, C and Kinaston, RL}, title = {Female bone physiology resilience in a past Polynesian Outlier community.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18857}, pmid = {36344562}, issn = {2045-2322}, support = {DE190100068//Australian Research Council/ ; ERC758967//European Research Council Starting Grant 'Waves'/ ; }, mesh = {Male ; Humans ; Female ; *Haversian System ; *Femur ; Bone and Bones ; Bone Remodeling ; Melanesia ; }, abstract = {Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in 69 individuals from ca. 440-150 BP Taumako in Solomon Islands, a remote 'Polynesian Outlier' island in Melanesia. We tested whether bone remodelling indicators differed between age groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-osteon (~ 8%) did not differ between the sexes. Our results indicate that, compared to males, localised femoral bone tissue of the Taumako females did not drastically decline with age, contrary to what is often observed in modern populations. However, our results match findings in other archaeological samples-a testament to past female bone physiology resilience, also now observed in the Pacific region.}, }
@article {pmid36329382, year = {2022}, author = {Lord, E and Marangoni, A and Baca, M and Popović, D and Goropashnaya, AV and Stewart, JR and Knul, MV and Noiret, P and Germonpré, M and Jimenez, EL and Abramson, NI and Vartanyan, S and Prost, S and Smirnov, NG and Kuzmina, EA and Olsen, RA and Fedorov, VB and Dalén, L}, title = {Population dynamics and demographic history of Eurasian collared lemmings.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {126}, pmid = {36329382}, issn = {2730-7182}, support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; P20 GM130443/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Ecosystem ; *Arvicolinae ; Population Dynamics ; Arctic Regions ; DNA, Ancient ; }, abstract = {BACKGROUND: Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.<br><br>RESULTS: Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.<br><br>CONCLUSIONS: This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.}, }
@article {pmid36322514, year = {2022}, author = {Campelo Dos Santos, AL and Owings, A and Sullasi, HSL and Gokcumen, O and DeGiorgio, M and Lindo, J}, title = {Genomic evidence for ancient human migration routes along South America's Atlantic coast.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1986}, pages = {20221078}, pmid = {36322514}, issn = {1471-2954}, support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; History, Ancient ; Animals ; *Human Migration ; Genomics ; Genome, Human ; *Neanderthals ; Brazil ; }, abstract = {An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.}, }
@article {pmid36322483, year = {2022}, author = {Hempel, E and Bibi, F and Faith, JT and Koepfli, KP and Klittich, AM and Duchêne, DA and Brink, JS and Kalthoff, DC and Dalén, L and Hofreiter, M and Westbury, MV}, title = {Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).}, journal = {Molecular biology and evolution}, volume = {39}, number = {12}, pages = {}, pmid = {36322483}, issn = {1537-1719}, mesh = {Animals ; Humans ; *Antelopes/genetics ; Biological Evolution ; Phylogeny ; Genome ; *Mustelidae/genetics ; }, abstract = {The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.}, }
@article {pmid36316157, year = {2022}, author = {Mathieson, I and Terhorst, J}, title = {Direct detection of natural selection in Bronze Age Britain.}, journal = {Genome research}, volume = {32}, number = {11-12}, pages = {2057-2067}, pmid = {36316157}, issn = {1549-5469}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; United Kingdom ; *Selection, Genetic ; Skin Pigmentation ; Genome, Human ; }, abstract = {We developed a novel method for efficiently estimating time-varying selection coefficients from genome-wide ancient DNA data. In simulations, our method accurately recovers selective trajectories and is robust to misspecification of population size. We applied it to a large data set of ancient and present-day human genomes from Britain and identified seven loci with genome-wide significant evidence of selection in the past 4500 yr. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength of selection on individual loci varied substantially over time, suggesting that cultural or environmental factors moderated the genetic response. Of 28 complex anthropometric and metabolic traits, skin pigmentation was the only one with significant evidence of polygenic selection, further underscoring the importance of phenotypes related to vitamin D. Our approach illustrates the power of ancient DNA to characterize selection in human populations and illuminates the recent evolutionary history of Britain.}, }
@article {pmid36300941, year = {2022}, author = {Nino Barreat, JG and Katzourakis, A}, title = {Evolutionary Analysis of Placental Orthologues Reveals Two Ancient DNA Virus Integrations.}, journal = {Journal of virology}, volume = {96}, number = {22}, pages = {e0093322}, pmid = {36300941}, issn = {1098-5514}, mesh = {Animals ; Female ; Humans ; Pregnancy ; *DNA, Ancient ; Eutheria ; *Evolution, Molecular ; Genome, Human ; *Mammals/genetics/virology ; Marsupialia ; Phylogeny ; Virus Integration ; *DNA Viruses/genetics ; }, abstract = {The genomes of eukaryotes preserve a vast diversity of ancient viruses in the form of endogenous viral elements (EVEs). Study of this genomic fossil record provides insights into the diversity, origin, and evolution of viruses across geological timescales. In particular, Mavericks have emerged as one of the oldest groups of endogenous viruses infecting vertebrates (≥419 million years [My]). They have been found in the genomes of fish, amphibians, birds, and nonavian reptiles but had been overlooked in mammals. Thus, their evolutionary history and the causes of their demise in mammals remain puzzling questions. Here, we conducted a detailed evolutionary study of two Maverick integrations found on human chromosomes 7 and 8. We performed a comparative analysis of the integrations and determined their orthology across placental mammals (Eutheria) via the syntenic arrangement of neighboring genes. The integrations were absent at the orthologous sites in the genomes of marsupials and monotremes. These observations allowed us to reconstruct a time-calibrated phylogeny and infer the age of their most recent common ancestor at 127 to 262 My. In addition, we estimate the age of the individual integrations at ~102 My, which represents the oldest nonretroviral EVEs found in the human genome. Our findings suggest that active Mavericks still existed in the ancestors of modern mammals ~172 My ago (Jurassic Period) and potentially to the end of the Early Cretaceous. We hypothesize that Mavericks could have gone extinct in mammals from the evolution of an antiviral defense system or from reduced opportunities for transmission in terrestrial hosts. IMPORTANCE The genomes of vertebrates preserve a large diversity of endogenous viral elements (remnants of ancient viruses that accumulate in host genomes over evolutionary time). Although retroviruses account for the vast majority of these elements, diverse DNA viruses have also been found and novel lineages are being described. Here, we analyzed two elements found in the human genome belonging to an ancient group of DNA viruses called Mavericks. We studied their evolutionary history, finding that the elements are shared between humans and many different species of placental mammals. These observations suggest that the elements inserted at least ~102 million years ago (Mya) in the most recent common ancestor of placentals. We further estimated the age of the viral ancestor at around 127 to 262 My. Our results provide evidence for some of the oldest viral integrations in the human genome and insights into the ancient interactions of viruses with the ancestors of modern-day mammals.}, }
@article {pmid36292743, year = {2022}, author = {Nedoluzhko, A and Orlova, SY and Kurnosov, DS and Orlov, AM and Galindo-Villegas, J and Rastorguev, SM}, title = {Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii).}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292743}, issn = {2073-4425}, mesh = {Animals ; *Adaptation, Physiological/genetics ; Pacific Ocean ; *Lakes ; Genomics ; }, abstract = {Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as "genomic islands of divergence". Moreover, the Tajima's D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait-osmoregulation.}, }
@article {pmid36292570, year = {2022}, author = {Hou, X and Zhao, J and Zhang, H and Preick, M and Hu, J and Xiao, B and Wang, L and Deng, M and Liu, S and Chang, F and Sheng, G and Lai, X and Hofreiter, M and Yuan, J}, title = {Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292570}, issn = {2073-4425}, mesh = {Animals ; *Bison/genetics ; Bayes Theorem ; *Genome, Mitochondrial/genetics ; Fossils ; Biological Evolution ; }, abstract = {Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.}, }
@article {pmid36289417, year = {2022}, author = {Thompson, B and Bundell, S}, title = {Ancient DNA reveals family of Neanderthals living in Siberian cave.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-03460-7}, pmid = {36289417}, issn = {1476-4687}, }
@article {pmid36282902, year = {2022}, author = {Atmore, LM and Martínez-García, L and Makowiecki, D and André, C and Lõugas, L and Barrett, JH and Star, B}, title = {Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {45}, pages = {e2208703119}, pmid = {36282902}, issn = {1091-6490}, mesh = {Animals ; Humans ; *Fisheries ; *DNA, Ancient ; Conservation of Natural Resources ; Population Dynamics ; Fishes/genetics ; Genomics ; Baltic States ; }, abstract = {The world's oceans are currently facing major stressors in the form of overexploitation and anthropogenic climate change. The Baltic Sea was home to the first "industrial" fishery ∼800 y ago targeting the Baltic herring, a species that is still economically and culturally important today. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. Here, we study long-term population dynamics of Baltic herring to evaluate the past impacts of humans on the marine environment. We combine modern whole-genome data with ancient DNA (aDNA) to identify the earliest-known long-distance herring trade in the region, illustrating that extensive fish trade began during the Viking Age. We further resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Øresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Øresund fishery had a negative impact on the western Baltic herring stock, the demographic shift to spring-spawning dominance did not occur until the 20th century. Instead, demographic reconstructions reveal population trajectories consistent with expected impacts of environmental change and historical reports on shifting fishing targets over time. This study illustrates the joint impact of climate change and human exploitation on marine species as well as the role historical ecology can play in conservation and management policies.}, }
@article {pmid36282813, year = {2022}, author = {Ibrahim, J and Brumfeld, V and Addadi, Y and Rubin, S and Weiner, S and Boaretto, E}, title = {The petrous bone contains high concentrations of osteocytes: One possible reason why ancient DNA is better preserved in this bone.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0269348}, pmid = {36282813}, issn = {1932-6203}, mesh = {Humans ; Swine ; Animals ; *Osteocytes/pathology ; *DNA, Ancient ; Petrous Bone/diagnostic imaging ; Bone and Bones ; DNA/genetics ; }, abstract = {The characterization of ancient DNA in fossil bones is providing invaluable information on the genetics of past human and other animal populations. These studies have been aided enormously by the discovery that ancient DNA is relatively well preserved in the petrous bone compared to most other bones. The reasons for this better preservation are however not well understood. Here we examine the hypothesis that one reason for better DNA preservation in the petrous bone is that fresh petrous bone contains more DNA than other bones. We therefore determined the concentrations of osteocyte cells occluded inside lacunae within the petrous bone and compared these concentrations to other bones from the domestic pig using high resolution microCT. We show that the concentrations of osteocyte lacunae in the inner layer of the pig petrous bone adjacent to the otic chamber are about three times higher (around 95,000 lacunae per mm3) than in the mastoid of the temporal bone (around 28,000 lacunae per mm3), as well as the cortical bone of the femur (around 27,000 lacunae per mm3). The sizes and shapes of the lacuna in the inner layer of the petrous bone are similar to those in the femur. We also show that the pig petrous bone lacunae do contain osteocytes using a histological stain for DNA. We therefore confirm and significantly expand upon previous observations of osteocytic lacuna concentrations in the petrous bone, supporting the notion that one possible reason for better preservation of ancient DNA in the petrous bone is that this bone initially contains at least three times more DNA than other bones. Thus during diagenesis more DNA is likely to be preserved in the petrous bone compared to other bones.}, }
@article {pmid36277234, year = {2022}, author = {Cessford, C and Neil, B}, title = {The people of the Cambridge Austin friars.}, journal = {Archaeological journal}, volume = {179}, number = {2}, pages = {383-444}, pmid = {36277234}, issn = {2373-2288}, support = {200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The Austin friars in Cambridge was an important religious institution between the late thirteenth and mid-sixteenth centuries. Excavations have revealed well-dated and contextualised burials associated with the friary, as well as a range of material culture. The burials have been subject to a wide range of analyses including osteology, palaeopathology, stable isotopes, ancient DNA and geometric morphometrics. Significantly the distinction between clothed and shrouded burials allows members of the Augustinian order and the laity to be identified. This represents the best-understood published group of burials from an Austin friars in the British Isles and emphasises the importance of nuanced interpretation, as burial at friaries was a structured and multi-local phenomenon. These burials and other material can be interpreted in terms of both mendicant ideals and anti-fraternal criticisms.}, }
@article {pmid36276948, year = {2022}, author = {Xu, B and Yang, G and Jiao, B and Zhu, H}, title = {Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {944933}, pmid = {36276948}, issn = {1664-8021}, abstract = {Background: The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication. Objective: We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication. Methods: First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient horses and sequences of lncRNA genes and the promoter regions of domestication-critical genes shared in modern horses, modern donkeys, and Przewalski horses to form two sample groups. Third, we used the LongTarget program to predict potential regulatory interactions between these lncRNAs and these domestication-critical genes and analyzed the differences between the regulation in ancient/modern horses and between horses/donkeys/Przewalski horses. Fourth, we performed functional enrichment analyses of genes that exhibit differences in epigenetic regulation. Results: First, genes associated with neural crest development and domestication syndrome are important targets of lncRNAs. Second, compared with undomesticated Przewalski horses, more lncRNAs participate in the epigenetic regulation in modern horses and donkeys, suggesting that domestication is linked to more epigenetic regulatory changes. Third, lncRNAs' potential target genes in modern horses are mainly involved in two functional areas: 1) the nervous system, behavior, and cognition, and 2) muscle, body size, cardiac function, and metabolism. Conclusion: Domestication is linked to substantial epigenetic regulatory changes. Genes associated with neural crest development and domestication syndrome underwent noticeable lncRNA-mediated epigenetic regulation changes during horse domestication.}, }
@article {pmid36261712, year = {2022}, author = {Enard, D}, title = {Ancient DNA reveals rapid natural selection during the Black Death.}, journal = {Nature}, volume = {611}, number = {7935}, pages = {237-238}, pmid = {36261712}, issn = {1476-4687}, mesh = {Humans ; *DNA, Ancient ; *Plague ; Selection, Genetic ; Evolution, Molecular ; }, }
@article {pmid36261521, year = {2022}, author = {Klunk, J and Vilgalys, TP and Demeure, CE and Cheng, X and Shiratori, M and Madej, J and Beau, R and Elli, D and Patino, MI and Redfern, R and DeWitte, SN and Gamble, JA and Boldsen, JL and Carmichael, A and Varlik, N and Eaton, K and Grenier, JC and Golding, GB and Devault, A and Rouillard, JM and Yotova, V and Sindeaux, R and Ye, CJ and Bikaran, M and Dumaine, A and Brinkworth, JF and Missiakas, D and Rouleau, GA and Steinrücken, M and Pizarro-Cerdá, J and Poinar, HN and Barreiro, LB}, title = {Evolution of immune genes is associated with the Black Death.}, journal = {Nature}, volume = {611}, number = {7935}, pages = {312-319}, pmid = {36261521}, issn = {1476-4687}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; F32 GM140568/GM/NIGMS NIH HHS/United States ; R01 GM146051/GM/NIGMS NIH HHS/United States ; R56 AI146556/AI/NIAID NIH HHS/United States ; R01 GM134376/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Aminopeptidases/genetics/immunology ; *DNA, Ancient ; *Plague/genetics/immunology/microbiology/mortality ; *Yersinia pestis/immunology/pathogenicity ; *Selection, Genetic/immunology ; Europe/epidemiology/ethnology ; *Immunity/genetics ; Datasets as Topic ; *Genetic Predisposition to Disease ; London/epidemiology ; Denmark/epidemiology ; }, abstract = {Infectious diseases are among the strongest selective pressures driving human evolution[1,2]. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis[3]. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population[4]. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.}, }
@article {pmid36259206, year = {2022}, author = {Martínez-García, L and Ferrari, G and Cuevas, A and Atmore, LM and López-Arias, B and Culling, M and Llorente-Rodríguez, L and Morales-Muñiz, A and Roselló-Izquierdo, E and Quirós, JA and Marlasca-Martín, R and Hänfling, B and Hutchinson, WF and Jakobsen, KS and Jentoft, S and Orton, D and Star, B and Barrett, JH}, title = {Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1985}, pages = {20221107}, pmid = {36259206}, issn = {1471-2954}, mesh = {Animals ; *DNA, Ancient ; Europe ; Fisheries ; *Gadus morhua/genetics ; Hunting ; Internationality ; }, abstract = {Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050-1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.}, }
@article {pmid36248846, year = {2022}, author = {Charlie-Silva, I and Feitosa, NM and Pontes, LG and Fernandes, BH and Nóbrega, RH and Gomes, JMM and Prata, MNL and Ferraris, FK and Melo, DC and Conde, G and Rodrigues, LF and Aracati, MF and Corrêa-Junior, JD and Manrique, WG and Superio, J and Garcez, AS and Conceição, K and Yoshimura, TM and Núñez, SC and Eto, SF and Fernandes, DC and Freitas, AZ and Ribeiro, MS and Nedoluzhko, A and Lopes-Ferreira, M and Borra, RC and Barcellos, LJG and Perez, AC and Malafaia, G and Cunha, TM and Belo, MAA and Galindo-Villegas, J}, title = {Plasma proteome responses in zebrafish following λ-carrageenan-Induced inflammation are mediated by PMN leukocytes and correlate highly with their human counterparts.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1019201}, pmid = {36248846}, issn = {1664-3224}, mesh = {Acute-Phase Proteins ; Animals ; Carrageenan/metabolism ; Glycosaminoglycans ; Humans ; Inflammation/chemically induced ; *Leukocytes ; Neutrophils/metabolism ; Plasma/metabolism ; *Proteome ; Proteomics ; *Zebrafish/metabolism ; }, abstract = {Regulation of inflammation is a critical process for maintaining physiological homeostasis. The λ-carrageenan (λ-CGN) is a mucopolysaccharide extracted from the cell wall of red algae (Chondrus crispus) capable of inducing acute intestinal inflammation, which is translated into the production of acute phase reactants secreted into the blood circulation. However, the associated mechanisms in vertebrates are not well understood. Here, we investigated the crucial factors behind the inflammatory milieu of λ-CGN-mediated inflammation administered at 0, 1.75, and 3.5% (v/w) by i.p. injection into the peritoneal cavity of adult zebrafish (ZF) (Danio rerio). We found that polymorphonuclear leukocytes (neutrophils) and lymphocytes infiltrating the ZF peritoneal cavity had short-term persistence. Nevertheless, they generate a strong pattern of inflammation that affects systemically and is enough to produce edema in the cavity. Consistent with these findings, cell infiltration, which causes notable tissue changes, resulted in the overexpression of several acute inflammatory markers at the protein level. Using reversed-phase high-performance liquid chromatography followed by a hybrid linear ion-trap mass spectrometry shotgun proteomic approach, we identified 2938 plasma proteins among the animals injected with PBS and 3.5% λ-CGN. First, the bioinformatic analysis revealed the composition of the plasma proteome. Interestingly, 72 commonly expressed proteins were recorded among the treated and control groups, but, surprisingly, 2830 novel proteins were differentially expressed exclusively in the λ-CGN-induced group. Furthermore, from the commonly expressed proteins, compared to the control group 62 proteins got a significant (p < 0.05) upregulation in the λ-CGN-treated group, while the remaining ten proteins were downregulated. Next, we obtained the major protein-protein interaction networks between hub protein clusters in the blood plasma of the λ-CGN induced group. Moreover, to understand the molecular underpinnings of these effects based on the unveiled protein sets, we performed a bioinformatic structural similarity analysis and generated overlapping 3D reconstructions between ZF and humans during acute inflammation. Biological pathway analysis pointed to the activation and abundance of diverse classical immune and acute phase reactants, several catalytic enzymes, and varied proteins supporting the immune response. Together, this information can be used for testing and finding novel pharmacological targets to treat human intestinal inflammatory diseases.}, }
@article {pmid36224018, year = {2022}, author = {Xu, Y and Allen, E and Wang, L and Wen, S}, title = {Identifying Human Remains from 20th Century Warfare: A State of the Field Essay.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {27}, number = {9}, pages = {271}, doi = {10.31083/j.fbl2709271}, pmid = {36224018}, issn = {2768-6698}, mesh = {Body Remains ; *DNA Fingerprinting/methods ; DNA, Ancient ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; Humans ; *Microsatellite Repeats ; }, abstract = {As we continually reflect on the wars of the 20th century, identification of the remains of victims takes an increasingly prominent position in ongoing research. Existing work on the identification of human remains from 20th century wars primarily covers the determination of phenotypic characteristics, kinship and geographic origins, supporting the establishment of genetic information databases. Compared with standard forensic methods, DNA analyses have revealed greater effectiveness. The process of DNA analysis includes DNA extraction, genetic marker testing and data analysis. Protocols from ancient DNA research can be applied to degraded remains, and next-generation sequencing (NGS) techniques can compensate for shortcomings in the most commonly-used PCR-capillary electrophoresis typing. As it stands, wide-ranging inter-governmental and inter-institutional collaboration is necessary in order to set up NGS-based public databases, and thereby promote the identification of human remains and archaeological forensics.}, }
@article {pmid36206720, year = {2022}, author = {Ter Schure, ATM and Bruch, AA and Kandel, AW and Gasparyan, B and Bussmann, RW and Brysting, AK and de Boer, HJ and Boessenkool, S}, title = {Sedimentary ancient DNA metabarcoding as a tool for assessing prehistoric plant use at the Upper Paleolithic cave site Aghitu-3, Armenia.}, journal = {Journal of human evolution}, volume = {172}, number = {}, pages = {103258}, doi = {10.1016/j.jhevol.2022.103258}, pmid = {36206720}, issn = {1095-8606}, mesh = {Humans ; Animals ; *DNA, Ancient ; Armenia ; DNA Barcoding, Taxonomic ; Charcoal ; Caves ; *Hominidae/genetics ; Archaeology/methods ; Plants/genetics ; }, abstract = {Current knowledge about Paleolithic human plant use is limited by the rare survival of identifiable plant remains as well as the availability of methods for plant detection and identification. By analyzing DNA preserved in cave sediments, we can identify organisms in the absence of any visible remains, opening up new ways to study details of past human behavior, including plant use. Aghitu-3 Cave contains a 15,000-yearlong record (from ∼39,000 to 24,000 cal BP) of Upper Paleolithic human settlement and environmental variability in the Armenian Highlands. Finds from this cave include stone artifacts, faunal remains, bone tools, shell beads, charcoal, and pollen, among others. We applied sedimentary ancient DNA (sedaDNA) metabarcoding to the Aghitu-3 sedimentary sequence and combined this with pollen data to obtain a temporal reconstruction of plant assemblages. Our results reveal a stratification of plant abundance and diversity where sedaDNA reflects periods of human occupation, showing higher diversity in layers with increased human activity. Low pollen concentrations combined with high sedaDNA abundance indicate plant remains may have been brought into the cave by animals or humans during the deposition of the lower two archaeological horizons. Most of the recovered plants are reported to be useful for food, flavor, medicine, and/or technical purposes, demonstrating the potential of the environment around Aghitu-3 Cave to support humans during the Upper Paleolithic. Moreover, we identified several specific plant taxa that strengthen previous findings about Upper Paleolithic plant use in this region (i.e., for medicine and the manufacturing and dyeing of textiles). This study represents the first application of plant sedaDNA analysis of cave sediments for the investigation of potential plant use by prehistoric humans.}, }
@article {pmid36203052, year = {2022}, author = {Seersholm, FV and Harmsen, H and Gotfredsen, AB and Madsen, CK and Jensen, JF and Hollesen, J and Meldgaard, M and Bunce, M and Hansen, AJ}, title = {Ancient DNA provides insights into 4,000 years of resource economy across Greenland.}, journal = {Nature human behaviour}, volume = {6}, number = {12}, pages = {1723-1730}, pmid = {36203052}, issn = {2397-3374}, mesh = {Animals ; *DNA, Ancient/analysis ; *Reindeer ; Greenland ; Archaeology ; }, abstract = {The success and failure of past cultures across the Arctic was tightly coupled to the ability of past peoples to exploit the full range of resources available to them. There is substantial evidence for the hunting of birds, caribou and seals in prehistoric Greenland. However, the extent to which these communities relied on fish and cetaceans is understudied because of taphonomic processes that affect how these taxa are presented in the archaeological record. To address this, we analyse DNA from bulk bone samples from 12 archaeological middens across Greenland covering the Palaeo-Inuit, Norse and Neo-Inuit culture. We identify an assemblage of 42 species, including nine fish species and five whale species, of which the bowhead whale (Balaena mysticetus) was the most commonly detected. Furthermore, we identify a new haplotype in caribou (Rangifer tarandus), suggesting the presence of a distinct lineage of (now extinct) dwarfed caribou in Greenland 3,000 years ago.}, }
@article {pmid36201580, year = {2022}, author = {Curry, A}, title = {Ancient DNA pioneer Svante Pääbo wins Nobel.}, journal = {Science (New York, N.Y.)}, volume = {378}, number = {6615}, pages = {12}, doi = {10.1126/science.adf1845}, pmid = {36201580}, issn = {1095-9203}, mesh = {Animals ; *DNA, Ancient ; *Hominidae/genetics ; Humans ; Nobel Prize ; }, abstract = {By sequencing ancient hominins' DNA, Pääbo explored "what makes us uniquely human".}, }
@article {pmid36195712, year = {2022}, author = {Graham, F}, title = {Daily briefing: Medicine Nobel for ancient DNA.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-03163-z}, pmid = {36195712}, issn = {1476-4687}, }
@article {pmid36191217, year = {2022}, author = {Reitsema, LJ and Mittnik, A and Kyle, B and Catalano, G and Fabbri, PF and Kazmi, ACS and Reinberger, KL and Sineo, L and Vassallo, S and Bernardos, R and Broomandkhoshbacht, N and Callan, K and Candilio, F and Cheronet, O and Curtis, E and Fernandes, D and Lari, M and Lawson, AM and Mah, M and Mallick, S and Mandl, K and Micco, A and Modi, A and Oppenheimer, J and Özdogan, KT and Rohland, N and Stewardson, K and Vai, S and Vergata, C and Workman, JN and Zalzala, F and Zaro, V and Achilli, A and Anagnostopoulos, A and Capelli, C and Constantinou, V and Lancioni, H and Olivieri, A and Papadopoulou, A and Psatha, N and Semino, O and Stamatoyannopoulos, J and Valliannou, I and Yannaki, E and Lazaridis, I and Patterson, N and Ringbauer, H and Caramelli, D and Pinhasi, R and Reich, D}, title = {The diverse genetic origins of a Classical period Greek army.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {41}, pages = {e2205272119}, pmid = {36191217}, issn = {1091-6490}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; n/a//Howard Hughes Medical Institute (HHMI)/ ; }, mesh = {*Archaeology/methods ; Europe ; Greece ; History, Ancient ; Humans ; *Military Personnel ; Warfare ; }, abstract = {Trade and colonization caused an unprecedented increase in Mediterranean human mobility in the first millennium BCE. Often seen as a dividing force, warfare is in fact another catalyst of culture contact. We provide insight into the demographic dynamics of ancient warfare by reporting genome-wide data from fifth-century soldiers who fought for the army of the Greek Sicilian colony of Himera, along with representatives of the civilian population, nearby indigenous settlements, and 96 present-day individuals from Italy and Greece. Unlike the rest of the sample, many soldiers had ancestral origins in northern Europe, the Steppe, and the Caucasus. Integrating genetic, archaeological, isotopic, and historical data, these results illustrate the significant role mercenaries played in ancient Greek armies and highlight how participation in war contributed to continental-scale human mobility in the Classical world.}, }
@article {pmid36190761, year = {2022}, author = {Daly, KG and Arbuckle, BS and Rossi, C and Mattiangeli, V and Lawlor, PA and Mashkour, M and Sauer, E and Lesur, J and Atici, L and Erek, CM and Bradley, DG}, title = {A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36190761}, issn = {2050-084X}, mesh = {Alleles ; Animals ; *Genomics ; *Goats/genetics ; Phylogeny ; Turkey ; }, abstract = {Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a ~14,000 year old 2.59 X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten 'Taurasian tur' likely survived Late Pleistocene climatic change in a Taurus Mountain refuge and its genomic fate is unknown.}, }
@article {pmid36184671, year = {2022}, author = {Armbrecht, L and Weber, ME and Raymo, ME and Peck, VL and Williams, T and Warnock, J and Kato, Y and Hernández-Almeida, I and Hoem, F and Reilly, B and Hemming, S and Bailey, I and Martos, YM and Gutjahr, M and Percuoco, V and Allen, C and Brachfeld, S and Cardillo, FG and Du, Z and Fauth, G and Fogwill, C and Garcia, M and Glüder, A and Guitard, M and Hwang, JH and Iizuka, M and Kenlee, B and O'Connell, S and Pérez, LF and Ronge, TA and Seki, O and Tauxe, L and Tripathi, S and Zheng, X}, title = {Ancient marine sediment DNA reveals diatom transition in Antarctica.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5787}, pmid = {36184671}, issn = {2041-1723}, mesh = {Antarctic Regions ; DNA, Ancient ; *Diatoms/genetics ; Ecosystem ; Eukaryota ; Geologic Sediments ; }, abstract = {Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sedaDNA damage analysis) metagenomic marine eukaryote sedaDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sedaDNA record of ~1 Mio. years and diatom and chlorophyte sedaDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising <10% of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sedaDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles.}, }
@article {pmid36182700, year = {2022}, author = {Gopalakrishnan, S and Ebenesersdóttir, SS and Lundstrøm, IKC and Turner-Walker, G and Moore, KHS and Luisi, P and Margaryan, A and Martin, MD and Ellegaard, MR and Magnússon, &#xd3;&#xde; and Sigurðsson, &#xc1; and Snorradóttir, S and Magnúsdóttir, DN and Laffoon, JE and van Dorp, L and Liu, X and Moltke, I and Ávila-Arcos, MC and Schraiber, JG and Rasmussen, S and Juan, D and Gelabert, P and de-Dios, T and Fotakis, AK and Iraeta-Orbegozo, M and Vågene, &#xc5;J and Denham, SD and Christophersen, A and Stenøien, HK and Vieira, FG and Liu, S and Günther, T and Kivisild, T and Moseng, OG and Skar, B and Cheung, C and Sandoval-Velasco, M and Wales, N and Schroeder, H and Campos, PF and Guðmundsdóttir, VB and Sicheritz-Ponten, T and Petersen, B and Halgunset, J and Gilbert, E and Cavalleri, GL and Hovig, E and Kockum, I and Olsson, T and Alfredsson, L and Hansen, TF and Werge, T and Willerslev, E and Balloux, F and Marques-Bonet, T and Lalueza-Fox, C and Nielsen, R and Stefánsson, K and Helgason, A and Gilbert, MTP}, title = {The population genomic legacy of the second plague pandemic.}, journal = {Current biology : CB}, volume = {32}, number = {21}, pages = {4743-4751.e6}, pmid = {36182700}, issn = {1879-0445}, mesh = {Humans ; *Plague/epidemiology/genetics ; Pandemics/history ; Metagenomics ; Genome, Bacterial ; Phylogeny ; }, abstract = {Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.[1] It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).[2] Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17[th]-19[th] century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.}, }
@article {pmid36178955, year = {2022}, author = {Dimopoulos, EA and Carmagnini, A and Velsko, IM and Warinner, C and Larson, G and Frantz, LAF and Irving-Pease, EK}, title = {HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.}, journal = {PLoS computational biology}, volume = {18}, number = {9}, pages = {e1010493}, pmid = {36178955}, issn = {1553-7358}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Bayes Theorem ; *DNA, Ancient ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Identification of specific species in metagenomic samples is critical for several key applications, yet many tools available require large computational power and are often prone to false positive identifications. Here we describe High-AccuracY and Scalable Taxonomic Assignment of MetagenomiC data (HAYSTAC), which can estimate the probability that a specific taxon is present in a metagenome. HAYSTAC provides a user-friendly tool to construct databases, based on publicly available genomes, that are used for competitive read mapping. It then uses a novel Bayesian framework to infer the abundance and statistical support for each species identification and provide per-read species classification. Unlike other methods, HAYSTAC is specifically designed to efficiently handle both ancient and modern DNA data, as well as incomplete reference databases, making it possible to run highly accurate hypothesis-driven analyses (i.e., assessing the presence of a specific species) on variably sized reference databases while dramatically improving processing speeds. We tested the performance and accuracy of HAYSTAC using simulated Illumina libraries, both with and without ancient DNA damage, and compared the results to other currently available methods (i.e., Kraken2/Bracken, KrakenUniq, MALT/HOPS, and Sigma). HAYSTAC identified fewer false positives than both Kraken2/Bracken, KrakenUniq and MALT in all simulations, and fewer than Sigma in simulations of ancient data. It uses less memory than Kraken2/Bracken, KrakenUniq as well as MALT both during database construction and sample analysis. Lastly, we used HAYSTAC to search for specific pathogens in two published ancient metagenomic datasets, demonstrating how it can be applied to empirical datasets. HAYSTAC is available from https://github.com/antonisdim/HAYSTAC.}, }
@article {pmid36174312, year = {2022}, author = {Hider, J and Duggan, AT and Klunk, J and Eaton, K and Long, GS and Karpinski, E and Giuffra, V and Ventura, L and Fornaciari, A and Fornaciari, G and Golding, GB and Prowse, TL and Poinar, HN}, title = {Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis.}, journal = {International journal of paleopathology}, volume = {39}, number = {}, pages = {20-34}, doi = {10.1016/j.ijpp.2022.08.002}, pmid = {36174312}, issn = {1879-9825}, mesh = {Humans ; *Brucella melitensis/genetics ; DNA, Ancient ; *Monks ; *Brucellosis ; Italy ; }, abstract = {OBJECTIVE: To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 [th] century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis.<br><br>METHODS: Shotgun sequencing data from was examined to determine the presence of Brucella DNA.<br><br>RESULTS: Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7-169), but for many the data quality was insufficient to withstand our identification and authentication criteria.<br><br>CONCLUSIONS: We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification.<br><br>SIGNIFICANCE: Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease.<br><br>LIMITATIONS: Study focuses on pathogen recovery in a single individual.<br><br>Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples.}, }
@article {pmid36170372, year = {2022}, author = {Alsos, IG and Rijal, DP and Ehrich, D and Karger, DN and Yoccoz, NG and Heintzman, PD and Brown, AG and Lammers, Y and Pellissier, L and Alm, T and Bråthen, KA and Coissac, E and Merkel, MKF and Alberti, A and Denoeud, F and Bakke, J and , }, title = {Postglacial species arrival and diversity buildup of northern ecosystems took millennia.}, journal = {Science advances}, volume = {8}, number = {39}, pages = {eabo7434}, pmid = {36170372}, issn = {2375-2548}, abstract = {What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival times were mainly predicted by adaptation to temperature, disturbance, and light. Major break points in ecological trait diversity were seen between 13.9 and 10.8 calibrated thousand years before the present (cal ka BP), as well as break point in functional diversity at 12.0 cal ka BP, shifting from a state of ecosystem buildup to a state where most habitat types and biotic ecosystem components were in place. Trait and functional diversity stabilized around 8 cal ka BP, after which both remained stable, although changes in climate took place and species inflow continued. Our ecosystem reconstruction indicates a millennial-scale time phase of formation to reach stable and resilient levels of diversity and functioning.}, }
@article {pmid36164432, year = {2022}, author = {Connah, K and Michael, B and Brassey, C}, title = {MiTiSegmenter: Software for high throughput segmentation and meshing of microCT data in microtiter plate arrays.}, journal = {MethodsX}, volume = {9}, number = {}, pages = {101849}, pmid = {36164432}, issn = {2215-0161}, abstract = {Lab-based microCT is a powerful means of visualising the internal structure of physical specimens deployed across the physical sciences, engineering and the arts. As its popularity has grown, demand for bulk digitisation of multiple samples within a single scan has increased. High throughput workflows can increase sample sizes and reduce scan time, yet downstream segmentation and meshing remain a bottleneck. We present MiTiSegmenter as a new tool for the bulk archiving of valuable zooarchaeological and palaeontological remains. We foresee MiTiSegmenter as particularly useful when incorporated into workflows that ultimately require the destructive testing of specimens, including sampling for ancient DNA and proteomics. The software may also play an important role in national museums' ongoing mass digitisation efforts, facilitating the high-speed archiving of specimen 3D morphology across extensive collections with very minimal user intervention or prior training. •We present MiTiSegmenter, a software package for semi-automated image processing and segmentation of array-based batch microCT data.•Implemented in Python, MiTiSegmenter expedites cropping, meshing and exporting samples within stacked microtiter plates, facilitating the rapid digitisation of hundreds-thousands of samples per scan.•We illustrate MiTiSegmenter's capabilities when applied to bulk archiving of valuable zooarchaeological and palaeontological remains.}, }
@article {pmid36161899, year = {2022}, author = {Alagöz, G and Molz, B and Eising, E and Schijven, D and Francks, C and Stein, JL and Fisher, SE}, title = {Using neuroimaging genomics to investigate the evolution of human brain structure.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2200638119}, pmid = {36161899}, issn = {1091-6490}, support = {MC_PC_17228/MRC_/Medical Research Council/United Kingdom ; MC_QA137853/MRC_/Medical Research Council/United Kingdom ; R01 DC016977/DC/NIDCD NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Brain/growth &amp; development/ultrastructure ; DNA, Ancient ; *Genomics/methods ; Humans ; *Neuroimaging/methods ; *Polymorphism, Single Nucleotide ; }, abstract = {Alterations in brain size and organization represent some of the most distinctive changes in the emergence of our species. Yet, there is limited understanding of how genetic factors contributed to altered neuroanatomy during human evolution. Here, we analyze neuroimaging and genetic data from up to 30,000 people in the UK Biobank and integrate with genomic annotations for different aspects of human evolution, including those based on ancient DNA and comparative genomics. We show that previously reported signals of recent polygenic selection for cortical anatomy are not replicable in a more ancestrally homogeneous sample. We then investigate relationships between evolutionary annotations and common genetic variants shaping cortical surface area and white-matter connectivity for each hemisphere. Our analyses identify single-nucleotide polymorphism heritability enrichment in human-gained regulatory elements that are active in early brain development, affecting surface areas of several parts of the cortex, including left-hemispheric speech-associated regions. We also detect heritability depletion in genomic regions with Neanderthal ancestry for connectivity of the uncinate fasciculus; this is a white-matter tract involved in memory, language, and socioemotional processing with relevance to neuropsychiatric disorders. Finally, we show that common genetic loci associated with left-hemispheric pars triangularis surface area overlap with a human-gained enhancer and affect regulation of ZIC4, a gene implicated in neurogenesis. This work demonstrates how genomic investigations of present-day neuroanatomical variation can help shed light on the complexities of our evolutionary past.}, }
@article {pmid36159977, year = {2022}, author = {Modi, A and Vizzari, MT and Catalano, G and Boscolo Agostini, R and Vai, S and Lari, M and Vergata, C and Zaro, V and Liccioli, L and Fedi, M and Barone, S and Nigro, L and Lancioni, H and Achilli, A and Sineo, L and Caramelli, D and Ghirotto, S}, title = {Genetic structure and differentiation from early bronze age in the mediterranean island of sicily: Insights from ancient mitochondrial genomes.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {945227}, pmid = {36159977}, issn = {1664-8021}, abstract = {Sicily is one of the main islands of the Mediterranean Sea, and it is characterized by a variety of archaeological records, material culture and traditions, reflecting the history of migrations and populations' interaction since its first colonization, during the Paleolithic. These deep and complex demographic and cultural dynamics should have affected the genomic landscape of Sicily at different levels; however, the relative impact of these migrations on the genomic structure and differentiation within the island remains largely unknown. The available Sicilian modern genetic data gave a picture of the current genetic structure, but the paucity of ancient data did not allow so far to make predictions about the level of historical variation. In this work, we sequenced and analyzed the complete mitochondrial genomes of 36 individuals from five different locations in Sicily, spanning from Early Bronze Age to Iron Age, and with different cultural backgrounds. The comparison with coeval groups from the Mediterranean Basin highlighted structured genetic variation in Sicily since Early Bronze Age, thus supporting a demic impact of the cultural transitions within the Island. Explicit model testing through Approximate Bayesian Computation allowed us to make predictions about the origin of Sicanians, one of the three indigenous peoples of Sicily, whose foreign origin from Spain, historically attributed, was not confirmed by our analysis of genetic data. Sicilian modern mitochondrial data show a different, more homogeneous, genetic composition, calling for a recent genetic replacement in the Island of pre-Iron Age populations, that should be further investigated.}, }
@article {pmid36152077, year = {2022}, author = {Yu, XE and Sun, C and Zou, YT and Li, JY and Ren, X and Li, H}, title = {Ancient DNA from Tubo Kingdom-related tombs in northeastern Tibetan Plateau revealed their genetic affinity to both Tibeto-Burman and Altaic populations.}, journal = {Molecular genetics and genomics : MGG}, volume = {297}, number = {6}, pages = {1755-1765}, pmid = {36152077}, issn = {1617-4623}, support = {2020YFE0201600//National Key Research and Development Program/ ; 18490750300//B&amp;R Joint Laboratory of Eurasian Anthropology/ ; 91731303//National Natural Science Foundation of China/ ; 31671297//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *DNA, Ancient ; *Genetics, Population ; Tibet ; Asian People/genetics ; Ethnicity ; Genetic Variation/genetics ; }, abstract = {The rise of the Tubo Kingdom is considered as the key period for the formation of modern groups on the Tibetan Plateau. The ethnic origin of the residents of the Tubo Kingdom is quite complex, and their genetic structure remains unclear. The tombs of the Tubo Kingdom period in Dulan County, Qinghai Province, dating back to the seventh century, are considered to be the remains left by Tubo conquerors or the Tuyuhun people dominated by the Tubo Kingdom. The human remains of these tombs are ideal materials for studying the population dynamics in the Tubo Kingdom. In this paper, we analyzed the genome-wide data of eight remains from these tombs by shotgun sequencing and multiplex PCR panels and compared the results with data of available ancient and modern populations across East Asia. Genetic continuity between ancient Dulan people with ancient Xianbei tribes in Northeast Asia, ancient settlers on the Tibetan Plateau, and modern Tibeto-Burman populations was found. Surprisingly, one out of eight individuals showed typical genetic features of populations from Central Asia. In summary, the genetic diversity of ancient Dulan people and their affiliations with other populations provide an example of the complex origin of the residents in the Tubo Kingdom and their long-distance connection with populations in a vast geographic region across ancient Asia.}, }
@article {pmid36144317, year = {2022}, author = {Bellanger, N and Dereeper, A and Koebnik, R}, title = {Clustered Regularly Interspaced Short Palindromic Repeats in Xanthomonas citri-Witnesses to a Global Expansion of a Bacterial Pathogen over Time.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144317}, issn = {2076-2607}, abstract = {Xanthomonas citri pv. citri, a Gram-negative bacterium, is the causal agent of citrus canker, a significant threat to citrus production. Understanding of global expansion of the pathogen and monitoring introduction into new regions are of interest for integrated disease management at the local and global level. Genetic diversity can be assessed using genomic approaches or information from partial gene sequences, satellite markers or clustered regularly interspaced short palindromic repeats (CRISPR). Here, we compared CRISPR loci from 355 strains of X. citri pv. citri, including a sample from ancient DNA, and generated the genealogy of the spoligotypes, i.e., the absence/presence patterns of CRISPR spacers. We identified 26 novel spoligotypes and constructed their likely evolutionary trajectory based on the whole-genome information. Moreover, we analyzed ~30 additional pathovars of X. citri and found that the oldest part of the CRISPR array was present in the ancestor of several pathovars of X. citri. This work presents a framework for further analyses of CRISPR loci and allows drawing conclusions about the global spread of the citrus canker pathogen, as exemplified by two introductions in West Africa.}, }
@article {pmid36139328, year = {2022}, author = {Horsburgh, KA and Gosling, AL and Cochrane, EE and Kirch, PV and Swift, JA and McCoy, MD}, title = {Origins of Polynesian Pigs Revealed by Mitochondrial Whole Genome Ancient DNA.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {18}, pages = {}, pmid = {36139328}, issn = {2076-2615}, support = {P17AP00233//U.S. National Center for Preservation Technology and Training/ ; }, abstract = {Domestic pigs (Sus scrofa) were first transported to Polynesia through a series of long-distance voyages ultimately linked to the Neolithic expansion of Austronesian-speaking people out of Asia. The descendants of the founding pigs belong to a rare mtDNA group referred to as the "Pacific Clade" that may have originated in peninsular or island Southeast Asia. We report the first whole genome mtDNA from domestic pigs from any of the remote islands of the Pacific. In this brief report, we describe the close link we discovered between ancient mtDNA from archaeological specimens from across Polynesia and from that of modern pigs in northern peninsular Southeast Asia, specifically southern China's Yunnan Province. More complete mtDNA coverage in commensal animals is necessary to improve our picture of the settlement of Polynesia (ca. 2800-700 years before the present) and specify the route, or routes, that pigs took from northern peninsular Southeast Asia.}, }
@article {pmid36131059, year = {2022}, author = {}, title = {Ancient DNA reveals details about early medieval migration into England.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {36131059}, issn = {1476-4687}, }
@article {pmid36131019, year = {2022}, author = {Gretzinger, J and Sayer, D and Justeau, P and Altena, E and Pala, M and Dulias, K and Edwards, CJ and Jodoin, S and Lacher, L and Sabin, S and Vågene, &#xc5;J and Haak, W and Ebenesersdóttir, SS and Moore, KHS and Radzeviciute, R and Schmidt, K and Brace, S and Bager, MA and Patterson, N and Papac, L and Broomandkhoshbacht, N and Callan, K and Harney, &#xc9; and Iliev, L and Lawson, AM and Michel, M and Stewardson, K and Zalzala, F and Rohland, N and Kappelhoff-Beckmann, S and Both, F and Winger, D and Neumann, D and Saalow, L and Krabath, S and Beckett, S and Van Twest, M and Faulkner, N and Read, C and Barton, T and Caruth, J and Hines, J and Krause-Kyora, B and Warnke, U and Schuenemann, VJ and Barnes, I and Dahlström, H and Clausen, JJ and Richardson, A and Popescu, E and Dodwell, N and Ladd, S and Phillips, T and Mortimer, R and Sayer, F and Swales, D and Stewart, A and Powlesland, D and Kenyon, R and Ladle, L and Peek, C and Grefen-Peters, S and Ponce, P and Daniels, R and Spall, C and Woolcock, J and Jones, AM and Roberts, AV and Symmons, R and Rawden, AC and Cooper, A and Bos, KI and Booth, T and Schroeder, H and Thomas, MG and Helgason, A and Richards, MB and Reich, D and Krause, J and Schiffels, S}, title = {The Anglo-Saxon migration and the formation of the early English gene pool.}, journal = {Nature}, volume = {610}, number = {7930}, pages = {112-119}, pmid = {36131019}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; 851511/ERC_/European Research Council/International ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; DNA, Ancient/analysis ; Denmark ; England ; Female ; France ; *Gene Pool ; Genetics, Population ; Genome, Human/genetics ; Germany ; History, Medieval ; *Human Migration/history ; Humans ; Language ; Male ; Population Dynamics ; Weapons/history ; }, abstract = {The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture[1]. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate[2-4]. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France[5,6].}, }
@article {pmid36124912, year = {2022}, author = {Wu, MY and Lau, CJ and Ng, EYX and Baveja, P and Gwee, CY and Sadanandan, K and Ferasyi, TR and Haminuddin,  and Ramadhan, R and Menner, JK and Rheindt, FE}, title = {Genomes From Historic DNA Unveil Massive Hidden Extinction and Terminal Endangerment in a Tropical Asian Songbird Radiation.}, journal = {Molecular biology and evolution}, volume = {39}, number = {9}, pages = {}, pmid = {36124912}, issn = {1537-1719}, mesh = {Animals ; DNA/genetics ; Extinction, Biological ; Genome ; Phylogeny ; *Songbirds/genetics ; }, abstract = {Quantifying the magnitude of the global extinction crisis is important but remains challenging, as many extinction events pass unnoticed owing to our limited taxonomic knowledge of the world's organisms. The increasing rarity of many taxa renders comprehensive sampling difficult, further compounding the problem. Vertebrate lineages such as birds, which are thought to be taxonomically well understood, are therefore used as indicator groups for mapping and quantifying global extinction. To test whether extinction patterns are adequately gauged in well-studied groups, we implemented ancient-DNA protocols and retrieved whole genomes from the historic DNA of museum specimens in a widely known songbird radiation of shamas (genus Copsychus) that is assumed to be of least conservation concern. We uncovered cryptic diversity and an unexpected degree of hidden extinction and terminal endangerment. Our analyses reveal that >40% of the phylogenetic diversity of this radiation is already either extinct in the wild or nearly so, including the two genomically most distinct members of this group (omissus and nigricauda), which have so far flown under the conservation radar as they have previously been considered subspecies. Comparing the genomes of modern samples with those from roughly a century ago, we also found a significant decrease in genetic diversity and a concomitant increase in homozygosity affecting various taxa, including small-island endemics that are extinct in the wild as well as subspecies that remain widespread across the continental scale. Our application of modern genomic approaches demonstrates elevated levels of allelic and taxonomic diversity loss in a songbird clade that has not been listed as globally threatened, highlighting the importance of ongoing reassessments of extinction incidence even across well-studied animal groups. Key words: extinction, introgression, white-rumped shama, conservation.}, }
@article {pmid36114431, year = {2022}, author = {Cole, G and Taylor, GM and Stewart, GR and Dawson-Hobbis, H}, title = {Ancient DNA confirmation of lepromatous leprosy in a skeleton with concurrent osteosarcoma, excavated from the leprosarium of St. Mary Magdalen in Winchester, Hants., UK.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {41}, number = {11}, pages = {1295-1304}, pmid = {36114431}, issn = {1435-4373}, mesh = {Bone and Bones ; DNA, Ancient ; Humans ; *Leprosy/diagnosis ; *Leprosy, Lepromatous/microbiology ; Male ; Mycobacterium leprae/genetics ; *Osteosarcoma/genetics ; United Kingdom ; }, abstract = {To establish a biological profile and disease aetiologies for one of four burials recovered during a Time Team dig at the St. Mary Magdalen leprosarium, Winchester, UK in AD 2000. Osteological techniques were applied to estimate age at death, biological sex, stature and pathology. Visual assessment of the material was supplemented by radiographic examination. Evidence for leprosy DNA was sought using ancient DNA (aDNA) analysis. The remains are those of a male individual excavated from a west-east aligned grave. The skeleton shows signs of two pathologies. Remodelling of the rhino-maxillary area and degenerative changes to small bones of the feet and reactive bone on the distal lower limbs suggest a multibacillary form of leprosy, whereas the right tibia and fibula show the presence of a primary neoplasm identified as an osteosarcoma. The aDNA study confirmed presence of Mycobacterium leprae in several skeletal elements, and the strain was genotyped to the 3I lineage, one of two main SNP types present in mediaeval Britain and ancestral to extant strains in America. This is a rare documentation of leprosy in association with a primary neoplasm.}, }
@article {pmid36108636, year = {2022}, author = {Arauna, LR and Bergstedt, J and Choin, J and Mendoza-Revilla, J and Harmant, C and Roux, M and Mas-Sandoval, A and Lémée, L and Colleran, H and François, A and Valentin, F and Cassar, O and Gessain, A and Quintana-Murci, L and Patin, E}, title = {The genomic landscape of contemporary western Remote Oceanians.}, journal = {Current biology : CB}, volume = {32}, number = {21}, pages = {4565-4575.e6}, doi = {10.1016/j.cub.2022.08.055}, pmid = {36108636}, issn = {1879-0445}, mesh = {Humans ; *Human Migration ; *DNA, Ancient ; Genomics ; Genome, Human ; Genetics, Population ; }, abstract = {The Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands ∼3,000 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity. Here, we report new genome-wide data for 1,433 contemporary ni-Vanuatu from 29 different islands, including 287 couples. We find that ni-Vanuatu derive their East Asian- and Papuan-related ancestry from the same source populations and descend from relatively synchronous, sex-biased admixture events that occurred ∼1,700-2,300 years ago, indicating a peopling history common to the whole archipelago. However, East Asian-related ancestry proportions differ markedly across islands, suggesting that the Papuan-related population turnover was geographically uneven. Furthermore, we detect Polynesian ancestry arriving ∼600-1,000 years ago to Central and South Vanuatu in both Polynesian-speaking and non-Polynesian-speaking populations. Last, we provide evidence for a tendency of spouses to carry similar genetic ancestry, when accounting for relatedness avoidance. The signal is not driven by strong genetic effects of specific loci or trait-associated variants, suggesting that it results instead from social assortative mating. Altogether, our findings provide an insight into both the genetic history of ni-Vanuatu populations and how sociocultural processes have shaped the diversity of their genomes.}, }
@article {pmid36097018, year = {2022}, author = {Low, YW and Rajaraman, S and Tomlin, CM and Ahmad, JA and Ardi, WH and Armstrong, K and Athen, P and Berhaman, A and Bone, RE and Cheek, M and Cho, NRW and Choo, LM and Cowie, ID and Crayn, D and Fleck, SJ and Ford, AJ and Forster, PI and Girmansyah, D and Goyder, DJ and Gray, B and Heatubun, CD and Ibrahim, A and Ibrahim, B and Jayasinghe, HD and Kalat, MA and Kathriarachchi, HS and Kintamani, E and Koh, SL and Lai, JTK and Lee, SML and Leong, PKF and Lim, WH and Lum, SKY and Mahyuni, R and McDonald, WJF and Metali, F and Mustaqim, WA and Naiki, A and Ngo, KM and Niissalo, M and Ranasinghe, S and Repin, R and Rustiami, H and Simbiak, VI and Sukri, RS and Sunarti, S and Trethowan, LA and Trias-Blasi, A and Vasconcelos, TNC and Wanma, JF and Widodo, P and Wijesundara, DSA and Worboys, S and Yap, JW and Yong, KT and Khew, GSW and Salojärvi, J and Michael, TP and Middleton, DJ and Burslem, DFRP and Lindqvist, C and Lucas, EJ and Albert, VA}, title = {Genomic insights into rapid speciation within the world's largest tree genus Syzygium.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5031}, pmid = {36097018}, issn = {2041-1723}, mesh = {Genetic Speciation ; Genomics ; Phylogeny ; *Syzygium/genetics ; *Trees ; }, abstract = {Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.}, }
@article {pmid36092944, year = {2022}, author = {Nedoluzhko, A and Sharko, F and Tsygankova, S and Boulygina, E and Slobodova, N and Teslyuk, A and Galindo-Villegas, J and Rastorguev, S}, title = {Intergeneric hybridization of two stickleback species leads to introgression of membrane-associated genes and invasive TE expansion.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {863547}, pmid = {36092944}, issn = {1664-8021}, abstract = {Interspecific hybridization has occurred relatively frequently during the evolution of vertebrates. This process usually abolishes reproductive isolation between the parental species. Moreover, it results in the exchange of genetic material and can lead to hybridogenic speciation. Hybridization between species has predominately been observed at the interspecific level, whereas intergeneric hybridization is rarer. Here, using whole-genome sequencing analysis, we describe clear and reliable signals of intergeneric introgression between the three-spined stickleback (Gasterosteus aculeatus) and its distant mostly freshwater relative the nine-spined stickleback (Pungitius pungitius) that inhabit northwestern Russia. Through comparative analysis, we demonstrate that such introgression phenomena apparently take place in the moderate-salinity White Sea basin, although it is not detected in Japanese sea stickleback populations. Bioinformatical analysis of the sites influenced by introgression showed that they are located near transposable elements, whereas those in protein-coding sequences are mostly found in membrane-associated and alternative splicing-related genes.}, }
@article {pmid36072661, year = {2022}, author = {Guarino-Vignon, P and Marchi, N and Chimènes, A and Monnereau, A and Kroll, S and Mashkour, M and Lhuillier, J and Bendezu-Sarmiento, J and Heyer, E and Bon, C}, title = {Genetic analysis of a bronze age individual from Ulug-depe (Turkmenistan).}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {884612}, pmid = {36072661}, issn = {1664-8021}, abstract = {The Oxus Civilisation (or Bactrio-Margian Archaeological Complex, BMAC) was the main archaeological culture of the Bronze Age in southern Central Asia. Paleogenetic analyses were previously conducted mainly on samples from the eastern part of BMAC. The population associated with BMAC descends from local Chalcolithic populations, with some outliers of steppe or South-Asian descent. Here, we present new genome-wide data for one individual from Ulug-depe (Turkmenistan), one of the main BMAC sites, located at the southwestern edge of the BMAC. We demonstrate that this individual genetically belongs to the BMAC cluster. Using this genome, we confirm that modern Indo-Iranian-speaking populations from Central Asia derive their ancestry from BMAC populations, with additional gene flow from the western and the Altai steppes in higher proportions among the Tajiks than the Yagnobi ethnic group.}, }
@article {pmid36071150, year = {2022}, author = {Richards, SM and Li, L and Breen, J and Hovhannisyan, N and Estrada, O and Gasparyan, B and Gilliham, M and Smith, A and Cooper, A and Zhang, H}, title = {Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15164}, pmid = {36071150}, issn = {2045-2322}, mesh = {Armenia ; Edible Grain/genetics ; *Genome, Chloroplast ; Millets ; *Panicum/genetics ; }, abstract = {Panicum miliaceum L. was domesticated in northern China at least 7000 years ago and was subsequentially adopted in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, where vast quantities archaeobotanical material were well preserved via desiccation. The rich botanical material found at Areni-1 includes P. miliaceum grains that were identified morphologically and[14]C dated to the medieval period (873 ± 36 CE and 1118 ± 35 CE). To investigate the demographic and evolutionary history of the Areni-1 millet, we used ancient DNA extraction, hybridization capture enrichment, and high throughput sequencing to assemble three chloroplast genomes from the medieval grains and then compared these sequences to 50 modern P. miliaceum chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity with domesticated accessions separated by a maximum of 5 SNPs and little inference on demography could be made. However, in phylogenies the chloroplast genomes separated into two clades, similar to what has been reported for nuclear DNA from P. miliaceum. The chloroplast genomes of two wild (undomesticated) accessions of P. miliaceum contained a relatively large number of variants, 11 SNPs, not found in the domesticated accessions. These results demonstrate that P. miliaceum grains from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.}, }
@article {pmid36066013, year = {2022}, author = {Flux, AL and Schultz, M and Hummel, S}, title = {Ancient DNA analysis from epoxy resin Biodur[®]-embedded bones.}, journal = {BioTechniques}, volume = {73}, number = {3}, pages = {113-122}, doi = {10.2144/btn-2022-0056}, pmid = {36066013}, issn = {1940-9818}, mesh = {DNA/analysis/genetics ; *DNA Fingerprinting/methods ; *DNA, Ancient ; Epoxy Resins ; Humans ; Microsatellite Repeats ; }, abstract = {For microscopic investigation, archaeological bone samples are often embedded in Biodur[®] epoxy resin. This study wants to test whether it is possible to extract DNA suitable for PCR amplification from this sample type. For eight individuals a set of samples - each consisting of a Biodur-embedded femur sample, a native femur sample and a control sample of different anatomical origin - were submitted to organic DNA extraction. The extraction success was tested by autosomal short tandem repeat amplification. Seven out of eight Biodur-embedded femur samples revealed successful amplification results. If Biodur-embedded bone material exists from earlier microscopic investigations, our results encourage the use of this sample type as a source for genetic research.}, }
@article {pmid36064759, year = {2022}, author = {Harvati, K and Ackermann, RR}, title = {Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {10}, pages = {1573-1585}, pmid = {36064759}, issn = {2397-334X}, mesh = {Animals ; DNA, Ancient ; Fossils ; *Hominidae/anatomy &amp; histology/genetics ; Humans ; Hybridization, Genetic ; Mammals/genetics ; *Neanderthals/genetics ; }, abstract = {Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.}, }
@article {pmid36052370, year = {2022}, author = {Le, MK and Smith, OS and Akbari, A and Harpak, A and Reich, D and Narasimhan, VM}, title = {1,000 ancient genomes uncover 10,000 years of natural selection in Europe.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36052370}, issn = {2692-8205}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; R35 GM151108/GM/NIGMS NIH HHS/United States ; }, abstract = {Ancient DNA has revolutionized our understanding of human population history. However, its potential to examine how rapid cultural evolution to new lifestyles may have driven biological adaptation has not been met, largely due to limited sample sizes. We assembled genome-wide data from 1,291 individuals from Europe over 10,000 years, providing a dataset that is large enough to resolve the timing of selection into the Neolithic, Bronze Age, and Historical periods. We identified 25 genetic loci with rapid changes in frequency during these periods, a majority of which were previously undetected. Signals specific to the Neolithic transition are associated with body weight, diet, and lipid metabolism-related phenotypes. They also include immune phenotypes, most notably a locus that confers immunity to Salmonella infection at a time when ancient Salmonella genomes have been shown to adapt to human hosts, thus providing a possible example of human-pathogen co-evolution. In the Bronze Age, selection signals are enriched near genes involved in pigmentation and immune-related traits, including at a key human protein interactor of SARS-CoV-2. Only in the Historical period do the selection candidates we detect largely mirror previously-reported signals, highlighting how the statistical power of previous studies was limited to the last few millennia. The Historical period also has multiple signals associated with vitamin D binding, providing evidence that lactase persistence may have been part of an oligogenic adaptation for efficient calcium uptake and challenging the theory that its adaptive value lies only in facilitating caloric supplementation during times of scarcity. Finally, we detect selection on complex traits in all three periods, including selection favoring variants that reduce body weight in the Neolithic. In the Historical period, we detect selection favoring variants that increase risk for cardiovascular disease plausibly reflecting selection for a more active inflammatory response that would have been adaptive in the face of increased infectious disease exposure. Our results provide an evolutionary rationale for the high prevalence of these deadly diseases in modern societies today and highlight the unique power of ancient DNA in elucidating biological change that accompanied the profound cultural transformations of recent human history.}, }
@article {pmid36050453, year = {2022}, author = {Gregory, MD and Berman, KF}, title = {Correction to: Echoes of ancient DNA in living modern humans affect risk for neuropsychiatric disease and brain structure and function of networks subserving higher-order cognition.}, journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology}, volume = {47}, number = {12}, pages = {2173}, doi = {10.1038/s41386-022-01439-6}, pmid = {36050453}, issn = {1740-634X}, }
@article {pmid36048257, year = {2022}, author = {Šuligoj, A and Mesesnel, S and Leskovar, T and Podovšovnik, E and Zupanič Pajnič, I}, title = {Comparison of DNA preservation between adult and non-adult ancient skeletons.}, journal = {International journal of legal medicine}, volume = {136}, number = {6}, pages = {1521-1539}, pmid = {36048257}, issn = {1437-1596}, support = {J3-3080//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, mesh = {*Body Remains ; Bone and Bones ; DNA ; *DNA Fingerprinting ; Female ; Humans ; Male ; Microsatellite Repeats ; }, abstract = {Studies evaluating DNA preservation in non-adults, or comparing preservation in adults and non-adults, are very rare. This study compares the preservation of DNA in the skeletal remains of adults and non-adults. It compares the quality and quantity of DNA recovered from different skeletal elements of adults and non-adults, and from non-adults of different age classes. In addition, the preservation of DNA in males and females is compared. Bone DNA preservation was estimated by measuring nuclear DNA concentration and its degradation, and through STR typing success. The study analyzed 29 adult skeletons and 23 non-adult skeletons from the Ljubljana-Polje archeological site, dating from the seventeenth to nineteenth century, and up to four skeletal elements (petrous bone, femur, calcaneus, and talus) were included. After full demineralization extraction, the PowerQuant System and the PowerPlex ESI 17 Fast System (Promega) were used for qPCR and STR typing, respectively. The results showed that, among the four bone types analyzed, only the petrous bone proved to be a suitable source of DNA for STR typing of non-adult skeletal remains, and DNA yield is even higher than in the adult petrous bone, which can be attributed to the higher DNA degradation observed in the adult petrous bone. In adult skeletons, petrous bones and tali produced high STR amplification success and low DNA yield was observed in adult femurs. The results of this study are applicable for the sampling strategy in routine forensic genetics cases for solving identification cases, including badly preserved non-adult and also adult skeletons.}, }
@article {pmid36048238, year = {2023}, author = {Gochi, L and Kawai, Y and Fujimoto, A}, title = {Comprehensive analysis of microsatellite polymorphisms in human populations.}, journal = {Human genetics}, volume = {142}, number = {1}, pages = {45-57}, pmid = {36048238}, issn = {1432-1203}, support = {18H02680//Japan Society for the Promotion of Science London/ ; 18H05511//MEXT KAKENHI/ ; JP21km0908001//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Genetics, Population ; *Genome ; Chromosome Mapping ; Polymorphism, Single Nucleotide ; Microsatellite Repeats/genetics ; }, abstract = {Microsatellites (MS) are tandem repeats of short units, and have been used for population genetics, individual identification, and medical genetics. However, studies of MS on a whole-genome level are limited, and genotyping methods for MS have yet to be established. Here, we analyzed approximately 8.5 million MS regions using a previously developed MS caller for short reads (MIVcall method) for three large publicly available human genome sequencing data sets: the Korean Personal Genome Project, Simons Genome Diversity Project, and Human Genome Diversity Project. Our analysis identified 253,114 polymorphic MS. A comparison among different populations suggests that MS in the coding region evolved by random genetic drift and natural selection. In an analysis of genetic structures, MS clearly revealed population structures as SNPs and detected clusters that were not found by SNPs in African and Oceanian populations. Based on the MS polymorphisms, we selected MS marker candidates for individual identification. Finally, we applied our method to a deep sequenced ancient DNA sample. This study provides a comprehensive picture of MS polymorphisms and application to human population studies.}, }
@article {pmid36046618, year = {2022}, author = {Behnamian, S and Esposito, U and Holland, G and Alshehab, G and Dobre, AM and Pirooznia, M and Brimacombe, CS and Elhaik, E}, title = {Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years.}, journal = {Cell reports methods}, volume = {2}, number = {8}, pages = {100270}, pmid = {36046618}, issn = {2667-2375}, support = {MR/R025126/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Radiometric Dating/methods ; *Genetic Techniques ; Skeleton ; Archaeology/methods ; }, abstract = {Radiocarbon dating is the gold standard in archeology to estimate the age of skeletons, a key to studying their origins. Many published ancient genomes lack reliable and direct dates, which results in obscure and contradictory reports. We developed the temporal population structure (TPS), a DNA-based dating method for genomes ranging from the Late Mesolithic to today, and applied it to 3,591 ancient and 1,307 modern Eurasians. TPS predictions aligned with the known dates and correctly accounted for kin relationships. TPS dating of poorly dated Eurasian samples resolved conflicting reports in the literature, as illustrated by one test case. We also demonstrated how TPS improved the ability to study phenotypic traits over time. TPS can be used when radiocarbon dating is unfeasible or uncertain or to develop alternative hypotheses for samples younger than 10,000 years ago, a limitation that may be resolved over time as ancient data accumulate.}, }
@article {pmid36044903, year = {2022}, author = {Brace, S and Diekmann, Y and Booth, T and Macleod, R and Timpson, A and Stephen, W and Emery, G and Cabot, S and Thomas, MG and Barnes, I}, title = {Genomes from a medieval mass burial show Ashkenazi-associated hereditary diseases pre-date the 12th century.}, journal = {Current biology : CB}, volume = {32}, number = {20}, pages = {4350-4359.e6}, pmid = {36044903}, issn = {1879-0445}, support = {100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Gene Frequency ; *Jews/genetics/history ; Alleles ; *Burial ; }, abstract = {We report genome sequence data from six individuals excavated from the base of a medieval well at a site in Norwich, UK. A revised radiocarbon analysis of the assemblage is consistent with these individuals being part of a historically attested episode of antisemitic violence on 6 February 1190 CE. We find that four of these individuals were closely related and all six have strong genetic affinities with modern Ashkenazi Jews. We identify four alleles associated with genetic disease in Ashkenazi Jewish populations and infer variation in pigmentation traits, including the presence of red hair. Simulations indicate that Ashkenazi-associated genetic disease alleles were already at appreciable frequencies, centuries earlier than previously hypothesized. These findings provide new insights into a significant historical crime, into Ashkenazi population history, and into the origins of genetic diseases associated with modern Jewish populations.}, }
@article {pmid36031712, year = {2022}, author = {Canteri, E and Brown, SC and Schmidt, NM and Heller, R and Nogués-Bravo, D and Fordham, DA}, title = {Spatiotemporal influences of climate and humans on muskox range dynamics over multiple millennia.}, journal = {Global change biology}, volume = {28}, number = {22}, pages = {6602-6617}, pmid = {36031712}, issn = {1365-2486}, mesh = {Animals ; Arctic Regions ; Climate Change ; *DNA, Ancient ; Fossils ; Humans ; *Ruminants ; }, abstract = {Processes leading to range contractions and population declines of Arctic megafauna during the late Pleistocene and early Holocene are uncertain, with intense debate on the roles of human hunting, climatic change, and their synergy. Obstacles to a resolution have included an overreliance on correlative rather than process-explicit approaches for inferring drivers of distributional and demographic change. Here, we disentangle the ecological mechanisms and threats that were integral in the decline and extinction of the muskox (Ovibos moschatus) in Eurasia and in its expansion in North America using process-explicit macroecological models. The approach integrates modern and fossil occurrence records, ancient DNA, spatiotemporal reconstructions of past climatic change, species-specific population ecology, and the growth and spread of anatomically modern humans. We show that accurately reconstructing inferences of past demographic changes for muskox over the last 21,000 years require high dispersal abilities, large maximum densities, and a small Allee effect. Analyses of validated process-explicit projections indicate that climatic change was the primary driver of muskox distribution shifts and demographic changes across its previously extensive (circumpolar) range, with populations responding negatively to rapid warming events. Regional analyses show that the range collapse and extinction of the muskox in Europe (~13,000 years ago) was likely caused by humans operating in synergy with climatic warming. In Canada and Greenland, climatic change and human activities probably combined to drive recent population sizes. The impact of past climatic change on the range and extinction dynamics of muskox during the Pleistocene-Holocene transition signals a vulnerability of this species to future increased warming. By better establishing the ecological processes that shaped the distribution of the muskox through space and time, we show that process-explicit macroecological models have important applications for the future conservation and management of this iconic species in a warming Arctic.}, }
@article {pmid36029689, year = {2022}, author = {Smith-Guzmán, NE}, title = {A paleoepidemiological approach to the challenging differential diagnosis of an isolated 1500-year-old anomalous molar from Panamá.}, journal = {International journal of paleopathology}, volume = {39}, number = {}, pages = {1-13}, doi = {10.1016/j.ijpp.2022.07.002}, pmid = {36029689}, issn = {1879-9825}, mesh = {Humans ; Diagnosis, Differential ; *Syphilis, Congenital ; Molar/diagnostic imaging ; Panama ; *Tooth Abnormalities ; }, abstract = {OBJECTIVE: This study seeks to quantify the presence and prevalence of specific genetic and infectious diseases in the pre-Colombian Panamanian population and uses these data to consider the plausibility of these diseases as causative factors in the development of an abnormal supernumerary cusp morphology in a 1500-year-old isolated molar recovered from Cerro Juan Díaz (Los Santos, Panama).<br><br>MATERIALS: 267 individuals from pre-Columbian sites throughout Panama.<br><br>METHODS: The anomalous tooth was analyzed through macroscopic, odontometric, and radiographic means. Tentative differential diagnosis was performed using inferences from paleopathological features of the broader regional population.<br><br>RESULTS: The regional sample showed evidence of treponemal infection and developmental anomalies in 10.1% and 10.9% of individuals, respectively.<br><br>CONCLUSIONS: While not able to rule out three potential genetic conditions, more evidence was found to support the differential diagnosis of congenital syphilis as the causative agent leading to the development of abnormal supernumerary cusps in the isolated molar.<br><br>SIGNIFICANCE: This study demonstrates how characterizing disease experience in the population can assist in differential diagnoses at the individual level and cautions against the assumption that any one lesion in isolation is unique to only one specific pathological condition.<br><br>LIMITATIONS: The timing discrepancy between clinical descriptions of congenital syphilis and genetic disorders, lack of knowledge on pathophysiological mechanisms of the former, poor preservation of Treponema pathogen ancient DNA, and deficiencies in modern public health data from Panama limit the differential diagnosis.<br><br>Inclusion and serious contemplation of genetic diseases in paleopathological differential diagnoses is necessary.}, }
@article {pmid36015403, year = {2022}, author = {Bosi, G and De Felice, S and Wilkinson, MJ and Allainguillaume, J and Arru, L and Nascimbene, J and Buldrini, F}, title = {Brassica and Sinapis Seeds in Medieval Archaeological Sites: An Example of Multiproxy Analysis for Their Identification and Ethnobotanical Interpretation.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {16}, pages = {}, pmid = {36015403}, issn = {2223-7747}, abstract = {The genus Brassica includes some of the most important vegetable and oil crops worldwide. Many Brassica seeds (which can show diagnostic characters useful for species identification) were recovered from two archaeological sites in northern Italy, dated from between the Middle Ages and the Renaissance. We tested the combined use of archaeobotanical keys, ancient DNA barcoding, and references to ancient herbarium specimens to address the issue of diagnostic uncertainty. An unequivocal conventional diagnosis was possible for much of the material recovered, with the samples dominated by five Brassica species and Sinapis. The analysis using ancient DNA was restricted to the seeds with a Brassica-type structure and deployed a variant of multiplexed tandem PCR. The quality of diagnosis strongly depended on the molecular locus used. Nevertheless, many seeds were diagnosed down to species level, in concordance with their morphological identification, using one primer set from the core barcode site (matK). The number of specimens found in the Renaissance herbaria was not high; Brassica nigra, which is of great ethnobotanical importance, was the most common taxon. Thus, the combined use of independent means of species identification is particularly important when studying the early use of closely related crops, such as Brassicaceae.}, }
@article {pmid36014039, year = {2022}, author = {Pérez, V and Liu, Y and Hengst, MB and Weyrich, LS}, title = {A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014039}, issn = {2076-2607}, support = {1211515//FONDECYT/ ; 1201692//FONDECYT/ ; 1181773//FONDECYT/ ; 74190093//ANID-International Postdoctoral Research fellowship-ANID/ ; FT180100407//Australian Research Council Future Fellowship/ ; }, abstract = {High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol−chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.}, }
@article {pmid36012483, year = {2022}, author = {Sá, L and Almeida, M and Azonbakin, S and Matos, E and Franco-Duarte, R and Gómez-Carballa, A and Salas, A and Laleye, A and Rosa, A and Brehm, A and Richards, MB and Soares, P and Rito, T}, title = {Phylogeography of Sub-Saharan Mitochondrial Lineages Outside Africa Highlights the Roles of the Holocene Climate Changes and the Atlantic Slave Trade.}, journal = {International journal of molecular sciences}, volume = {23}, number = {16}, pages = {}, pmid = {36012483}, issn = {1422-0067}, support = {PTDC/SOC-ANT/30316/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UIDB/04050/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, mesh = {Africa South of the Sahara ; Climate Change ; DNA, Ancient ; *DNA, Mitochondrial/genetics ; *Enslaved Persons ; Humans ; Phylogeny ; Phylogeography ; }, abstract = {Despite the importance of ancient DNA for understanding human prehistoric dispersals, poor survival means that data remain sparse for many areas in the tropics, including in Africa. In such instances, analysis of contemporary genomes remains invaluable. One promising approach is founder analysis, which identifies and dates migration events in non-recombining systems. However, it has yet to be fully exploited as its application remains controversial. Here, we test the approach by evaluating the age of sub-Saharan mitogenome lineages sampled outside Africa. The analysis confirms that such lineages in the Americas date to recent centuries-the time of the Atlantic slave trade-thereby validating the approach. By contrast, in North Africa, Southwestern Asia and Europe, roughly half of the dispersal signal dates to the early Holocene, during the "greening" of the Sahara. We elaborate these results by showing that the main source regions for the two main dispersal episodes are distinct. For the recent dispersal, the major source was West Africa, but with two exceptions: South America, where the fraction from Southern Africa was greater, and Southwest Asia, where Eastern Africa was the primary source. These observations show the potential of founder analysis as both a supplement and complement to ancient DNA studies.}, }
@article {pmid36011343, year = {2022}, author = {Zupanič Pajnič, I and Zupanc, T and Leskovar, T and Črešnar, M and Fattorini, P}, title = {Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach.}, journal = {Genes}, volume = {13}, number = {8}, pages = {}, pmid = {36011343}, issn = {2073-4425}, mesh = {Aged ; *Body Remains ; DNA/genetics ; DNA, Ancient ; *Eye Color/genetics ; *Hair Color/genetics ; Humans ; Polymerase Chain Reaction ; World War II ; }, abstract = {To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.}, }
@article {pmid36009790, year = {2022}, author = {Churchill, SE and Keys, K and Ross, AH}, title = {Midfacial Morphology and Neandertal-Modern Human Interbreeding.}, journal = {Biology}, volume = {11}, number = {8}, pages = {}, pmid = {36009790}, issn = {2079-7737}, abstract = {Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes. The results of canonical variates analysis and hierarchical cluster analysis suggest important affinities in facial morphology between both Middle and Upper Paleolithic early modern humans of the Near East with Neandertals, highlighting the importance of this region for interbreeding between the two lineages.}, }
@article {pmid36008480, year = {2022}, author = {Modzelewski, AJ and Gan Chong, J and Wang, T and He, L}, title = {Mammalian genome innovation through transposon domestication.}, journal = {Nature cell biology}, volume = {24}, number = {9}, pages = {1332-1340}, pmid = {36008480}, issn = {1476-4679}, support = {R21 OD027053/OD/NIH HHS/United States ; U41 HG010972/HG/NHGRI NIH HHS/United States ; R01 HD106809/HD/NICHD NIH HHS/United States ; R01 NS120287/NS/NINDS NIH HHS/United States ; U01 CA200060/CA/NCI NIH HHS/United States ; K99 HD096108/HD/NICHD NIH HHS/United States ; R00 HD096108/HD/NICHD NIH HHS/United States ; U24 ES026699/ES/NIEHS NIH HHS/United States ; R01 CA139067/CA/NCI NIH HHS/United States ; U01 HG009391/HG/NHGRI NIH HHS/United States ; U24 HG012070/HG/NHGRI NIH HHS/United States ; R01 HG007175/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM114414/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *DNA Transposable Elements/genetics ; *Domestication ; Evolution, Molecular ; Mammals ; }, abstract = {Since the discovery of transposons, their sheer abundance in host genomes has puzzled many. While historically viewed as largely harmless 'parasitic' DNAs during evolution, transposons are not a mere record of ancient genome invasion. Instead, nearly every element of transposon biology has been integrated into host biology. Here we review how host genome sequences introduced by transposon activities provide raw material for genome innovation and document the distinct evolutionary path of each species.}, }
@article {pmid36008437, year = {2022}, author = {Slon, V and Clark, JL and Friesem, DE and Orbach, M and Porat, N and Meyer, M and Kandel, AW and Shimelmitz, R}, title = {Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {14528}, pmid = {36008437}, issn = {2045-2322}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaeology ; Biological Evolution ; Caves ; *DNA, Ancient ; Fossils ; Humans ; *Hyaenidae ; Infant, Newborn ; Israel ; }, abstract = {Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA-information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts.}, }
@article {pmid36007054, year = {2022}, author = {Lazaridis, I and Alpaslan-Roodenberg, S and Acar, A and Açıkkol, A and Agelarakis, A and Aghikyan, L and Akyüz, U and Andreeva, D and Andrijašević, G and Antonović, D and Armit, I and Atmaca, A and Avetisyan, P and Aytek, A&#x130; and Bacvarov, K and Badalyan, R and Bakardzhiev, S and Balen, J and Bejko, L and Bernardos, R and Bertsatos, A and Biber, H and Bilir, A and Bodružić, M and Bonogofsky, M and Bonsall, C and Borić, D and Borovinić, N and Bravo Morante, G and Buttinger, K and Callan, K and Candilio, F and Carić, M and Cheronet, O and Chohadzhiev, S and Chovalopoulou, ME and Chryssoulaki, S and Ciobanu, I and Čondić, N and Constantinescu, M and Cristiani, E and Culleton, BJ and Curtis, E and Davis, J and Demcenco, TI and Dergachev, V and Derin, Z and Deskaj, S and Devejyan, S and Djordjević, V and Duffett Carlson, KS and Eccles, LR and Elenski, N and Engin, A and Erdoğan, N and Erir-Pazarcı, S and Fernandes, DM and Ferry, M and Freilich, S and Frînculeasa, A and Galaty, ML and Gamarra, B and Gasparyan, B and Gaydarska, B and Genç, E and Gültekin, T and Gündüz, S and Hajdu, T and Heyd, V and Hobosyan, S and Hovhannisyan, N and Iliev, I and Iliev, L and Iliev, S and İvgin, &#x130; and Janković, I and Jovanova, L and Karkanas, P and Kavaz-Kındığılı, B and Kaya, EH and Keating, D and Kennett, DJ and Deniz Kesici, S and Khudaverdyan, A and Kiss, K and Kılıç, S and Klostermann, P and Kostak Boca Negra Valdes, S and Kovačević, S and Krenz-Niedbała, M and Krznarić Škrivanko, M and Kurti, R and Kuzman, P and Lawson, AM and Lazar, C and Leshtakov, K and Levy, TE and Liritzis, I and Lorentz, KO and Łukasik, S and Mah, M and Mallick, S and Mandl, K and Martirosyan-Olshansky, K and Matthews, R and Matthews, W and McSweeney, K and Melikyan, V and Micco, A and Michel, M and Milašinović, L and Mittnik, A and Monge, JM and Nekhrizov, G and Nicholls, R and Nikitin, AG and Nikolov, V and Novak, M and Olalde, I and Oppenheimer, J and Osterholtz, A and Özdemir, C and Özdoğan, KT and Öztürk, N and Papadimitriou, N and Papakonstantinou, N and Papathanasiou, A and Paraman, L and Paskary, EG and Patterson, N and Petrakiev, I and Petrosyan, L and Petrova, V and Philippa-Touchais, A and Piliposyan, A and Pocuca Kuzman, N and Potrebica, H and Preda-Bălănică, B and Premužić, Z and Price, TD and Qiu, L and Radović, S and Raeuf Aziz, K and Rajić Šikanjić, P and Rasheed Raheem, K and Razumov, S and Richardson, A and Roodenberg, J and Ruka, R and Russeva, V and Şahin, M and Şarbak, A and Savaş, E and Schattke, C and Schepartz, L and Selçuk, T and Sevim-Erol, A and Shamoon-Pour, M and Shephard, HM and Sideris, A and Simalcsik, A and Simonyan, H and Sinika, V and Sirak, K and Sirbu, G and Šlaus, M and Soficaru, A and Söğüt, B and Sołtysiak, A and Sönmez-Sözer, &#xc7; and Stathi, M and Steskal, M and Stewardson, K and Stocker, S and Suata-Alpaslan, F and Suvorov, A and Szécsényi-Nagy, A and Szeniczey, T and Telnov, N and Temov, S and Todorova, N and Tota, U and Touchais, G and Triantaphyllou, S and Türker, A and Ugarković, M and Valchev, T and Veljanovska, F and Videvski, Z and Virag, C and Wagner, A and Walsh, S and Włodarczak, P and Workman, JN and Yardumian, A and Yarovoy, E and Yavuz, AY and Yılmaz, H and Zalzala, F and Zettl, A and Zhang, Z and Çavuşoğlu, R and Rohland, N and Pinhasi, R and Reich, D and Davtyan, R}, title = {Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6609}, pages = {982-987}, pmid = {36007054}, issn = {1095-9203}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Archaeology ; Armenia ; Cyprus ; DNA, Ancient ; *Farmers/history ; *Gene Flow ; History, Ancient ; *Human Migration/history ; Mesopotamia ; }, abstract = {We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.}, }
@article {pmid36007048, year = {2022}, author = {Curry, A}, title = {Ancient DNA from the Near East probes a cradle of civilization.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6609}, pages = {908-909}, doi = {10.1126/science.ade5539}, pmid = {36007048}, issn = {1095-9203}, mesh = {*Civilization/history ; *DNA, Ancient ; *Farms/history ; History, Ancient ; Humans ; *Language/history ; Middle East ; }, abstract = {Studies seek clues to origins of farming, early languages.}, }
@article {pmid36007032, year = {2022}, author = {Arbuckle, BS and Schwandt, Z}, title = {Ancient genomes and West Eurasian history.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6609}, pages = {922-923}, doi = {10.1126/science.add9059}, pmid = {36007032}, issn = {1095-9203}, mesh = {Asia ; DNA, Ancient ; Europe ; *Genome, Human ; History, Ancient ; Humans ; *Sequence Analysis, DNA ; }, abstract = {Storytelling with ancient DNA reveals challenges and potential for writing new histories.}, }
@article {pmid36006373, year = {2022}, author = {Dai, SS and Sulaiman, X and Isakova, J and Xu, WF and Abdulloevich, NT and Afanasevna, ME and Ibrohimovich, KB and Chen, X and Yang, WK and Wang, MS and Shen, QK and Yang, XY and Yao, YG and Aldashev, AA and Saidov, A and Chen, W and Cheng, LF and Peng, MS and Zhang, YP}, title = {The Genetic Echo of the Tarim Mummies in Modern Central Asians.}, journal = {Molecular biology and evolution}, volume = {39}, number = {9}, pages = {}, pmid = {36006373}, issn = {1537-1719}, mesh = {Asian People/genetics ; *DNA, Ancient ; Ethnicity ; Gene Flow ; Genetics, Population ; Humans ; *Mummies ; }, abstract = {The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians. We found that the major ancestry of present-day Tajik populations can be traced back to the admixture of the Bronze Age Bactria-Margiana Archaeological Complex and Andronovo-related populations. Highland Tajik populations further received additional gene flow from the Tarim mummies, an isolated ancient North Eurasian-related population. The West Eurasian ancestry of Kyrgyz is mainly derived from Historical Era populations in Xinjiang of China. Furthermore, the recent admixture signals detected in both Tajik and Kyrgyz are ascribed to the expansions of Eastern Steppe nomadic pastoralists during the Historical Era.}, }
@article {pmid35998599, year = {2022}, author = {Schuenemann, VJ}, title = {Ancient DNA: Pathogens caught in the Minoan labyrinth.}, journal = {Current biology : CB}, volume = {32}, number = {16}, pages = {R886-R889}, doi = {10.1016/j.cub.2022.07.032}, pmid = {35998599}, issn = {1879-0445}, mesh = {Biological Evolution ; DNA, Ancient ; Genomics ; History, Ancient ; Humans ; *Plague ; *Typhoid Fever ; }, abstract = {Ancient DNA methodologies enable research on past prevalence and evolutionary history of pathogens. A new study found plague and typhoid fever-causing bacteria in Minoan Crete, showcasing both the potential and the limitations of the growing field of ancient pathogen genomics.}, }
@article {pmid35991555, year = {2022}, author = {Collen, EJ and Johar, AS and Teixeira, JC and Llamas, B}, title = {The immunogenetic impact of European colonization in the Americas.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {918227}, pmid = {35991555}, issn = {1664-8021}, abstract = {The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.}, }
@article {pmid35960716, year = {2022}, author = {Illanes, G and Fariello, MI and Spangenberg, L and Mordecki, E and Naya, H}, title = {Testing the existence of an unadmixed ancestor from a specific population t generations ago.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0271097}, pmid = {35960716}, issn = {1932-6203}, mesh = {*Genetics, Population ; Genome, Human ; Humans ; *Polymorphism, Single Nucleotide ; Uruguay ; }, abstract = {The ancestry of each locus of the genome can be estimated (local ancestry) based on sequencing or genotyping information together with reference panels of ancestral source populations. The length of those ancestry-specific genomic segments are commonly used to understand migration waves and admixture events. In short time scales, it is often of interest to determine the existence of the most recent unadmixed ancestor from a specific population t generations ago. We built a hypothesis test to determine if an individual has an ancestor belonging to a target ancestral population t generations ago based on these lengths of the ancestry-specific segments at an individual level. We applied this test on a data set that includes 20 Uruguayan admixed individuals to estimate for each one how many generations ago the most recent indigenous ancestor lived. As this method tests each individual separately, it is particularly suited to small sample sizes, such as our study or ancient genome samples.}, }
@article {pmid35951485, year = {2023}, author = {Walton, K and Scarsbrook, L and Mitchell, KJ and Verry, AJF and Marshall, BA and Rawlence, NJ and Spencer, HG}, title = {Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {118-130}, pmid = {35951485}, issn = {1755-0998}, mesh = {Animals ; Phylogeny ; New Zealand ; Phylogeography ; *Gastropoda/genetics ; Mollusca/genetics ; DNA ; }, abstract = {Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here, we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: (1) The Three Kings Islands; (2) the Auckland, Chatham and Antipodes Islands; and (3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our nonreliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.}, }
@article {pmid35944486, year = {2022}, author = {Wang, R and Wang, CC}, title = {Human genetics: The dual origin of Three Kingdoms period Koreans.}, journal = {Current biology : CB}, volume = {32}, number = {15}, pages = {R844-R847}, doi = {10.1016/j.cub.2022.06.044}, pmid = {35944486}, issn = {1879-0445}, mesh = {*Asian People/genetics ; *DNA, Ancient ; Genetics, Population ; Genome ; History, Ancient ; Humans ; Republic of Korea ; }, abstract = {The genetic history of Koreans remains poorly understood due to a lack of ancient DNA. A new paleo-genomic study shows that population stratification in 4[th]-5[th] century South Korean populations was linked to a varied proportion of indigenous Jomon-related ancestry, which does not survive in present-day Koreans.}, }
@article {pmid35943423, year = {2022}, author = {Scott, CB and Cárdenas, A and Mah, M and Narasimhan, VM and Rohland, N and Toth, LT and Voolstra, CR and Reich, D and Matz, MV}, title = {Millennia-old coral holobiont DNA provides insight into future adaptive trajectories.}, journal = {Molecular ecology}, volume = {31}, number = {19}, pages = {4979-4990}, pmid = {35943423}, issn = {1365-294X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; DNA, Ancient ; *Dinoflagellida/genetics ; Ecosystem ; Genome ; }, abstract = {Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we utilized aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE to 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence aDNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.}, }
@article {pmid35937837, year = {2022}, author = {Lu, Y and Shi, C and Jin, X and He, J and Yin, Z}, title = {Domestication of farmed fish via the attenuation of stress responses mediated by the hypothalamus-pituitary-inter-renal endocrine axis.}, journal = {Frontiers in endocrinology}, volume = {13}, number = {}, pages = {923475}, pmid = {35937837}, issn = {1664-2392}, mesh = {Animals ; *Domestication ; Genomics ; Humans ; Hypothalamo-Hypophyseal System ; Hypothalamus ; *Pituitary-Adrenal System ; }, abstract = {Human-directed domestication of terrestrial animals traditionally requires thousands of years for breeding. The most prominent behavioral features of domesticated animals include reduced aggression and enhanced tameness relative to their wild forebears, and such behaviors improve the social tolerance of domestic animals toward both humans and crowds of their own species. These behavioral responses are primarily mediated by the hypothalamic-pituitary-adrenal (inter-renal in fish) (HPA/I) endocrine axis, which is involved in the rapid conversion of neuronal-derived perceptual information into hormonal signals. Over recent decades, growing evidence implicating the attenuation of the HPA/I axis during the domestication of animals have been identified through comprehensive genomic analyses of the paleogenomic datasets of wild progenitors and their domestic congeners. Compared with that of terrestrial animals, domestication of most farmed fish species remains at early stages. The present review focuses on the application of HPI signaling attenuation to accelerate the domestication and genetic breeding of farmed fish. We anticipate that deeper understanding of HPI signaling and its implementation in the domestication of farmed fish will benefit genetic breeding to meet the global demands of the aquaculture industry.}, }
@article {pmid35933511, year = {2022}, author = {Petrou, EL and Kopperl, R and Lepofsky, D and Rodrigues, AT and Yang, D and Moss, ML and Speller, CF and Hauser, L}, title = {Ancient DNA reveals phenological diversity of Coast Salish herring harvests over multiple centuries.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13512}, pmid = {35933511}, issn = {2045-2322}, mesh = {Animals ; *DNA, Ancient ; Fisheries ; *Fishes/genetics ; Food Chain ; Seafood ; }, abstract = {Phenological diversity in food resources prolongs foraging opportunities for consumers and buffers them against environmental disturbances. Such diversity is particularly important in forage fish such as Pacific herring (Clupea pallasii), which are foundational to coastal food webs and fisheries. While the importance of phenological diversity is well-known from contemporary studies, the extent to which different populations contribute to fisheries over long time scales is mostly unknown. In this study, we investigated the relative contributions of genetically and phenologically distinct herring populations to Indigenous Peoples' food systems over multiple centuries, using ancient DNA extracted from archaeological herring bones. These bones were excavated from two Coast Salish archaeological sites (Burton Acres Shell Midden and Bay Street Shell Midden) in the Puget Sound region, USA. Using genetic stock identification from seven nuclear DNA markers, we showed that catches at the two sites in central Puget Sound were dominated by January-February and March-April spawners, which are the contemporary spawning groups in the vicinity of the sites. However, May spawners were detected in the older Burton Acres assemblage (dated to 910-685 cal BP), and a mixed stock analysis indicated that catches at this site consisted of multiple populations. These results suggest that Coast Salish ancestors used a portfolio of herring populations and benefited from the ecological resource wave created by different spawning groups of herring. This study of ancient DNA allowed us to glimpse into Indigenous traditional food and management systems, and it enabled us to investigate long-term patterns of biodiversity in an ecologically important forage fish species.}, }
@article {pmid35923939, year = {2022}, author = {Royle, TCA and Guiry, EJ and Zhang, H and Clark, LT and Missal, SM and Rabinow, SA and James, M and Yang, DY}, title = {Documenting the short-tailed albatross (Phoebastria albatrus) clades historically present in British Columbia, Canada, through ancient DNA analysis of archaeological specimens.}, journal = {Ecology and evolution}, volume = {12}, number = {8}, pages = {e9116}, pmid = {35923939}, issn = {2045-7758}, abstract = {The short-tailed albatross (Phoebastria albatrus) is a threatened seabird whose present-day range encompasses much of the North Pacific. Within this species, there are two genetic clades (Clades 1 and 2) that have distinctive morphologies and foraging ecologies. Due to a global population collapse in the late 19th and early 20th centuries, the frequency of these clades among the short-tailed albatross population that historically foraged off British Columbia, Canada, is unclear. To document the species' historical genetic structure in British Columbia, we applied ancient DNA (aDNA) analysis to 51 archaeological short-tailed albatross specimens from the Yuquot site (Borden site number: DjSp-1) that span the past four millennia. We obtained a 141 bp cytochrome b sequence from 43 of the 51 (84.3%) analyzed specimens. Analyses of these sequences indicate 40 of the specimens belong to Clade 1, while 2 belong to Clade 2. We also identified a single specimen with a novel cytochrome b haplotype. Our results indicate that during the past four millennia most of the short-tailed albatrosses foraging near Yuquot belonged to Clade 1, while individuals from other lineages made more limited use of the area. Comparisons with the results of previous aDNA analyses of archaeological albatrosses from Japanese sites suggest the distribution of Clades 1 and 2 differed. While both albatross clades foraged extensively in the Northwest Pacific, Clade 1 albatrosses appear to have foraged along the west coast of Vancouver Island to a greater extent. Due to their differing distributions, these clades may be exposed to different threats.}, }
@article {pmid35922549, year = {2023}, author = {Gregory, MD and Berman, KF}, title = {Echoes of ancient DNA in living modern humans affect risk for neuropsychiatric disease and brain structure and function of networks subserving higher-order cognition.}, journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology}, volume = {48}, number = {1}, pages = {236-237}, pmid = {35922549}, issn = {1740-634X}, support = {ZIA MH002942/ImNIH/Intramural NIH HHS/United States ; ZIA MH002652/ImNIH/Intramural NIH HHS/United States ; ZIA MH002717/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; *Cognition ; Brain ; }, }
@article {pmid35921988, year = {2022}, author = {Zhu, S and Chen, Z and Hu, S and Wang, W and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Ping, W and Fu, Q}, title = {Ancient DNA traces a Chinese 5400-year-old cat specimen as leopard cat (Prionailurus bengalensis).}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {49}, number = {11}, pages = {1076-1079}, doi = {10.1016/j.jgg.2022.07.005}, pmid = {35921988}, issn = {1673-8527}, mesh = {*DNA, Ancient ; *Genetic Variation ; China ; }, }
@article {pmid35915153, year = {2022}, author = {Padró, J and De Panis, DN and Luisi, P and Dopazo, H and Szajnman, S and Hasson, E and Soto, IM}, title = {Ortholog genes from cactophilic Drosophila provide insight into human adaptation to hallucinogenic cacti.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13180}, pmid = {35915153}, issn = {2045-2322}, support = {R01 GM090087/GM/NIGMS NIH HHS/United States ; 1R01GM090087/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; *Alkaloids ; Animals ; *Cactaceae/chemistry ; Drosophila/genetics ; Genomics ; Hallucinogens ; Humans ; }, abstract = {Cultural transformations of lifestyles and dietary practices have been key drivers of human evolution. However, while most of the evidence of genomic adaptations is related to the hunter-gatherer transition to agricultural societies, little is known on the influence of other major cultural manifestations. Shamanism is considered the oldest religion that predominated throughout most of human prehistory and still prevails in many indigenous populations. Several lines of evidence from ethno-archeological studies have demonstrated the continuity and importance of psychoactive plants in South American cultures. However, despite the well-known importance of secondary metabolites in human health, little is known about its role in the evolution of ethnic differences. Herein, we identified candidate genes of adaptation to hallucinogenic cactus in Native Andean populations with a long history of shamanic practices. We used genome-wide expression data from the cactophilic fly Drosophila buzzatii exposed to a hallucinogenic columnar cactus, also consumed by humans, to identify ortholog genes exhibiting adaptive footprints of alkaloid tolerance. Genomic analyses in human populations revealed a suite of ortholog genes evolving under recent positive selection in indigenous populations of the Central Andes. Our results provide evidence of selection in genetic variants related to alkaloids toxicity, xenobiotic metabolism, and neuronal plasticity in Aymara and Quechua populations, suggesting a possible process of gene-culture coevolution driven by religious practices.}, }
@article {pmid35914369, year = {2022}, author = {Doniec, A and Januła, M and Grzmil, P and Kupiec, T}, title = {Assessing the utility of quantitative and qualitative metrics in the DNA quantification process of skeletal remains for autosomal and Y-chromosome STR amplification purposes.}, journal = {Forensic science international. Genetics}, volume = {60}, number = {}, pages = {102751}, doi = {10.1016/j.fsigen.2022.102751}, pmid = {35914369}, issn = {1878-0326}, mesh = {*Body Remains ; DNA/analysis/genetics ; DNA Fingerprinting ; Humans ; *Microsatellite Repeats ; Real-Time Polymerase Chain Reaction ; Y Chromosome/chemistry ; }, abstract = {In historical cases, ancient DNA investigations and missing persons identification, teeth or bone samples are often the only and almost always the best biological material available for DNA typing. On the other hand, DNA obtained from bone material may be characterized by a high degradation index (DI) or its low content, or DNA tests cannot be repeated due to bone piece size limitation. That is often the effect of the environment in which the material was placed and the time during which exposure to unfavorable environmental factors took place. Therefore, it is very important to use appropriate procedures related to STR analysis. For our study, we selected 80 challenging bone samples. The amount of DNA was compared in qPCR using Quantifiler™ Trio DNA Quantification Kit and Investigator® Quantiplex® Pro RGQ. All qPCR results were confirmed by PCR-CE. The results of DNA concentrations and the assigned degradation index (DI) differed significantly within analyzed samples (~10%). Additionally, the Y-chromosome DI also differed from the autosomal DI in the samples. The difference in degradation indexes could explain the lower Y-chromosome amplification success rate compared to autosomal e.g. during human identification process. The results indicate that performing two DNA quantifications with the use of two different kits (primers sets) allows for a much more precise evaluation of the DNA quality and quantity in the isolate. We suggest that at least one of two suggested DNA concentration measurements should be based on an additional determination of the Y chromosome degradation index. Altogether, it allows for rational isolate management, especially when the volume is limited and the sample is unique.}, }
@article {pmid39635427, year = {2022}, author = {Tiesler, V and Sedig, J and Nakatsuka, N and Mallick, S and Lazaridis, I and Bernardos, R and Broomandkhoshacht, N and Oppenheimer, J and Lawson, AM and Stewardson, K and Rohland, N and Kennett, DJ and Price, TD and Reich, D}, title = {Life and death in early colonial Campeche: new insights from ancient DNA.}, journal = {Antiquity}, volume = {96}, number = {388}, pages = {937-954}, pmid = {39635427}, issn = {0003-598X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; }, }
@article {pmid35907246, year = {2022}, author = {Pérez-Escobar, OA and Tusso, S and Przelomska, NAS and Wu, S and Ryan, P and Nesbitt, M and Silber, MV and Preick, M and Fei, Z and Hofreiter, M and Chomicki, G and Renner, SS}, title = {Genome Sequencing of up to 6,000-Year-Old Citrullus Seeds Reveals Use of a Bitter-Fleshed Species Prior to Watermelon Domestication.}, journal = {Molecular biology and evolution}, volume = {39}, number = {8}, pages = {}, pmid = {35907246}, issn = {1537-1719}, mesh = {Chromosome Mapping ; *Citrullus/genetics ; Domestication ; Genomics ; Seeds/genetics ; }, abstract = {Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-year-old seeds from Libya and Sudan, and from worldwide herbarium collections made between 1824 and 2019, and analyzed these data together with resequenced genomes from important germplasm collections for a total of 131 accessions. Phylogenomic and population-genomic analyses reveal that (1) much of the nuclear genome of both ancient seeds is traceable to West African seed-use "egusi-type" watermelon (Citrullus mucosospermus) rather than domesticated pulp-use watermelon (Citrullus lanatus ssp. vulgaris); (2) the 6,000-year-old watermelon likely had bitter pulp and greenish-white flesh as today found in C. mucosospermus, given alleles in the bitterness regulators ClBT and in the red color marker LYCB; and (3) both ancient genomes showed admixture from C. mucosospermus, C. lanatus ssp. cordophanus, C. lanatus ssp. vulgaris, and even South African Citrullus amarus, and evident introgression between the Libyan seed (UMB-6) and populations of C. lanatus. An unexpected new insight is that Citrullus appears to have initially been collected or cultivated for its seeds, not its flesh, consistent with seed damage patterns induced by human teeth in the oldest Libyan material.}, }
@article {pmid35903348, year = {2022}, author = {Erven, JAM and Çakirlar, C and Bradley, DG and Raemaekers, DCM and Madsen, O}, title = {Imputation of Ancient Whole Genome Sus scrofa DNA Introduces Biases Toward Main Population Components in the Reference Panel.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {872486}, pmid = {35903348}, issn = {1664-8021}, abstract = {Sequencing ancient DNA to high coverage is often limited by sample quality and cost. Imputing missing genotypes can potentially increase information content and quality of ancient data, but requires different computational approaches than modern DNA imputation. Ancient imputation beyond humans has not been investigated. In this study we report results of a systematic evaluation of imputation of three whole genome ancient Sus scrofa samples from the Early and Late Neolithic (∼7,100-4,500 BP), to test the utility of imputation. We show how issues like genetic architecture and, reference panel divergence, composition and size affect imputation accuracy. We evaluate a variety of imputation methods, including Beagle5, GLIMPSE, and Impute5 with varying filters, pipelines, and variant calling methods. We achieved genotype concordance in most cases reaching above 90%; with the highest being 98% with ∼2,000,000 variants recovered using GLIMPSE. Despite this high concordance the sources of diversity present in the genotypes called in the original high coverage genomes were not equally imputed leading to biases in downstream analyses; a trend toward genotypes most common in the reference panel is observed. This demonstrates that the current reference panel does not possess the full diversity needed for accurate imputation of ancient Sus, due to missing variations from Near Eastern and Mesolithic wild boar. Imputation of ancient Sus scrofa holds potential but should be approached with caution due to these biases, and suggests that there is no universal approach for imputation of non-human ancient species.}, }
@article {pmid35882233, year = {2022}, author = {Neumann, GU and Skourtanioti, E and Burri, M and Nelson, EA and Michel, M and Hiss, AN and McGeorge, PJP and Betancourt, PP and Spyrou, MA and Krause, J and Stockhammer, PW}, title = {Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete.}, journal = {Current biology : CB}, volume = {32}, number = {16}, pages = {3641-3649.e8}, doi = {10.1016/j.cub.2022.06.094}, pmid = {35882233}, issn = {1879-0445}, mesh = {Genome, Bacterial ; Greece ; Humans ; Phylogeny ; *Salmonella enterica/genetics ; *Yersinia pestis/genetics ; }, abstract = {During the late 3[rd] millennium BCE, the Eastern Mediterranean and Near East witnessed societal changes in many regions, which are usually explained with a combination of social and climatic factors.[1-4] However, recent archaeogenetic research forces us to rethink models regarding the role of infectious diseases in past societal trajectories.[5] The plague bacterium Yersinia pestis, which was involved in some of the most destructive historical pandemics,[5-8] circulated across Eurasia at least from the onset of the 3[rd] millennium BCE,[9-13] but the challenging preservation of ancient DNA in warmer climates has restricted the identification of Y. pestis from this period to temperate climatic regions. As such, evidence from culturally prominent regions such as the Eastern Mediterranean is currently lacking. Here, we present genetic evidence for the presence of Y. pestis and Salmonella enterica, the causative agent of typhoid/enteric fever, from this period of transformation in Crete, detected at the cave site Hagios Charalambos. We reconstructed one Y. pestis genome that forms part of a now-extinct lineage of Y. pestis strains from the Late Neolithic and Bronze Age that were likely not yet adapted for transmission via fleas. Furthermore, we reconstructed two ancient S. enterica genomes from the Para C lineage, which cluster with contemporary strains that were likely not yet fully host adapted to humans. The occurrence of these two virulent pathogens at the end of the Early Minoan period in Crete emphasizes the necessity to re-introduce infectious diseases as an additional factor possibly contributing to the transformation of early complex societies in the Aegean and beyond.}, }
@article {pmid35876520, year = {2022}, author = {Gibert, JM}, title = {[Small scale evolution].}, journal = {Biologie aujourd'hui}, volume = {216}, number = {1-2}, pages = {41-47}, doi = {10.1051/jbio/2022008}, pmid = {35876520}, issn = {2105-0686}, mesh = {Animals ; Beak/anatomy &amp; histology ; Biological Evolution ; Cats ; Evolution, Molecular ; *Finches/anatomy &amp; histology/genetics ; Genetic Variation ; Mutation ; Phenotype ; *Selection, Genetic ; }, abstract = {Small-scale evolution or microevolution concerns evolution at the intra-specific level or between closely related species. At the intra-specific level, it allows the analysis of the evolutionary forces at work: mutation, genetic drift, migration and selection. Moreover, because of the short evolutionary time, it is easier to identify the genetic basis of observed phenotypic differences. Most studies focus on current populations but more and more analyses are performed on ancient DNA. This provides important information for tracing the history of populations and also allows the reconstruction of phenotypes of individuals that disappeared several thousand years ago. In this short review, I present studies showing how pre-zygotic or post-zygotic barriers involved in species formation are set up using the example of the geographical barrier due to the formation of the Isthmus of Panama and that of the heterochromatin divergence in Drosophilidae. I also describe the different approaches that have been used to identify the genetic basis of well known phenotypic variations: candidate gene approach (about melanism in felines), QTL mapping (variation in the number of lateral bone plates in sticklebacks), association study (pigmentation in the Asian ladybird). Finally, I illustrate the key impact of natural selection with the iconic example of the evolution of the beak of Galapagos finches, and the role of certain developmental genes in its morphological diversification.}, }
@article {pmid35874301, year = {2022}, author = {Silvestrini, S and Romandini, M and Marciani, G and Arrighi, S and Carrera, L and Fiorini, A and López-García, JM and Lugli, F and Ranaldo, F and Slon, V and Tassoni, L and Higgins, OA and Bortolini, E and Curci, A and Meyer, M and Meyer, MC and Oxilia, G and Zerboni, A and Benazzi, S and Spinapolice, EE}, title = {Integrated multidisciplinary ecological analysis from the Uluzzian settlement at the Uluzzo C Rock Shelter, south-eastern Italy.}, journal = {Journal of quaternary science}, volume = {37}, number = {2}, pages = {235-256}, pmid = {35874301}, issn = {0267-8179}, abstract = {The Middle to Upper Palaeolithic transition, between 50 000 and 40 000 years ago, is a period of important ecological and cultural changes. In this framework, the Rock Shelter of Uluzzo C (Apulia, southern Italy) represents an important site due to Late Mousterian and Uluzzian evidence preserved in its stratigraphic sequence. Here, we present the results of a multidisciplinary analysis performed on the materials collected between 2016 and 2018 from the Uluzzian stratigraphic units (SUs) 3, 15 and 17. The analysis involved lithic technology, use-wear, zooarchaeology, ancient DNA of sediments and palaeoproteomics, completed by quartz single-grain optically stimulated luminescence dating of the cave sediments. The lithic assemblage is characterized by a volumetric production and a debitage with no or little management of the convexities (by using the bipolar technique), with the objective to produce bladelets and flakelets. The zooarchaeological study found evidence of butchery activity and of the possible exploitation of marine resources, while drawing a picture of a patchy landscape, composed of open forests and dry open environments surrounding the shelter. Ancient mitochondrial DNA from two mammalian taxa were recovered from the sediments. Preliminary zooarchaeology by mass spectrometry results are consistent with ancient DNA and zooarchaeological taxonomic information, while further palaeoproteomics investigations are ongoing. Our new data from the re-discovery of the Uluzzo C Rock Shelter represent an important contribution to better understand the meaning of the Uluzzian in the context of the Middle/Upper Palaeolithic transition in south-eastern Italy.}, }
@article {pmid35868268, year = {2022}, author = {Liu, Y and Bennett, EA and Fu, Q}, title = {Evolving ancient DNA techniques and the future of human history.}, journal = {Cell}, volume = {185}, number = {15}, pages = {2632-2635}, doi = {10.1016/j.cell.2022.06.009}, pmid = {35868268}, issn = {1097-4172}, mesh = {*DNA, Ancient ; *Genome, Human ; History, Ancient ; Humans ; }, abstract = {Ancient DNA (aDNA) techniques applied to human genomics have significantly advanced in the past decade, enabling large-scale aDNA research, sometimes independent of human remains. This commentary reviews the major milestones of aDNA techniques and explores future directions to expand the scope of aDNA research and insights into present-day human health.}, }
@article {pmid35857780, year = {2022}, author = {Gòdia, M and Brogaard, L and Mármol-Sánchez, E and Langhorn, R and Nordang Kieler, I and Jan Reezigt, B and Nikolic Nielsen, L and Rem Jessen, L and Cirera, S}, title = {Urinary microRNAome in healthy cats and cats with pyelonephritis or other urological conditions.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0270067}, pmid = {35857780}, issn = {1932-6203}, mesh = {Animals ; Biomarkers/urine ; Case-Control Studies ; Cats ; Humans ; *MicroRNAs/metabolism ; *Pyelonephritis/diagnosis/genetics/veterinary ; *Renal Insufficiency, Chronic ; }, abstract = {MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression at the post-transcriptional level. miRNAs have been found in urine and have shown diagnostic potential in human nephropathies. Here, we aimed to characterize, for the first time, the feline urinary miRNAome and explore the use of urinary miRNA profiles as non-invasive biomarkers for feline pyelonephritis (PN). Thirty-eight cats were included in a prospective case-control study and classified in five groups: healthy Control cats (n = 11), cats with PN (n = 10), cats with subclinical bacteriuria or cystitis (SB/C, n = 5), cats with ureteral obstruction (n = 7) and cats with chronic kidney disease (n = 5). By small RNA sequencing we identified 212 miRNAs in cat urine, including annotated (n = 137) and putative novel (n = 75) miRNAs. The 15 most highly abundant urinary miRNAs accounted for nearly 71% of all detected miRNAs, most of which were previously identified in feline kidney. Ninety-nine differentially abundant (DA) miRNAs were identified when comparing Control cats to cats with urological conditions and 102 DA miRNAs when comparing PN to other urological conditions. Tissue clustering analysis revealed that the majority of urine samples clustered close to kidney, which confirm the likely cellular origin of the secreted urinary miRNAs. Relevant DA miRNAs were verified by quantitative real-time PCR (qPCR). Eighteen miRNAs discriminated Control cats from cats with a urological condition. Of those, seven miRNAs were DA by both RNAseq and qPCR methods between Control and PN cats (miR-125b-5p, miR-27a-3p, miR-21-5p, miR-27b-3p, miR-125a-5p, miR-17-5p and miR-23a-3p) or DA between Control and SB/C cats (miR-125b-5p). Six additional miRNAs (miR-30b-5p, miR-30c, miR-30e-5p, miR-27a-3p, miR-27b-39 and miR-222) relevant for discriminating PN from other urological conditions were identified by qPCR alone (n = 4) or by both methods (n = 2) (P<0.05). This panel of 13 miRNAs has potential as non-invasive urinary biomarkers for diagnostic of PN and other urological conditions in cats.}, }
@article {pmid35839766, year = {2022}, author = {Zhang, X and Ji, X and Li, C and Yang, T and Huang, J and Zhao, Y and Wu, Y and Ma, S and Pang, Y and Huang, Y and He, Y and Su, B}, title = {A Late Pleistocene human genome from Southwest China.}, journal = {Current biology : CB}, volume = {32}, number = {14}, pages = {3095-3109.e5}, doi = {10.1016/j.cub.2022.06.016}, pmid = {35839766}, issn = {1879-0445}, mesh = {Animals ; China ; *Deer ; Fossils ; Genome, Human ; *Hominidae ; Humans ; }, abstract = {Southern East Asia is the dispersal center regarding the prehistoric settlement and migrations of modern humans in Asia-Pacific regions. However, the settlement pattern and population structure of paleolithic humans in this region remain elusive, and ancient DNA can provide direct information. Here, we sequenced the genome of a Late Pleistocene hominin (MZR), dated ∼14.0 thousand years ago from Red Deer Cave located in Southwest China, which was previously reported possessing mosaic features of modern and archaic hominins. MZR is the first Late Pleistocene genome from southern East Asia. Our results indicate that MZR is a modern human who represents an early diversified lineage in East Asia. The mtDNA of MZR belongs to an extinct basal lineage of the M9 haplogroup, reflecting a rich matrilineal diversity in southern East Asia during the Late Pleistocene. Combined with the published data, we detected clear genetic stratification in ancient southern populations of East/Southeast Asia and some degree of south-versus-north divergency during the Late Pleistocene, and MZR was identified as a southern East Asian who exhibits genetic continuity to present day populations. Markedly, MZR is linked deeply to the East Asian ancestry that contributed to First Americans.}, }
@article {pmid35835776, year = {2022}, author = {Askari, Z and Ruehli, F and Bouwman, A and Shariati, V and Naddaf, SR and Otranto, D and Mas-Coma, S and Rezaeian, M and Boenke, N and Stöllner, T and Aali, A and Mobedi, I and Mowlavi, G}, title = {Genomic palaeoparasitology traced the occurrence of Taenia asiatica in ancient Iran (Sassanid Empire, 2th cent. CE-6th cent. CE).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {12045}, pmid = {35835776}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient ; Genomics ; *Helminths/genetics ; History, Ancient ; Humans ; Iran ; *Taenia/genetics ; }, abstract = {Palaeoparasitology investigates parasitological infections in animals and humans of past distance by examining biological remains. Palaeofaeces (or coprolites) are biological remains that provide valuable information on the disease, diet, and population movements in ancient times. Today, advances in detecting ancient DNA have cast light on dark corners that microscopy could never reach. The archaeological site of the Chehrabad salt mine of Achaemenid (550-330 BC) and Sassanid (third-seventh century AD) provides remains of various biotic and abiotic samples, including animal coprolites, for multidisciplinary studies. In the present work, we investigated coprolites for helminth eggs and larvae by microscopy and traced their biological agents' DNA by Next Generation Sequencing. Our results revealed various helminths, including Taenia asiatica, the species introduced in the 1990s. Implementing advanced modern molecular techniques like NGS gives a paramount view of pathogenic agents in space and time.}, }
@article {pmid35818010, year = {2022}, author = {Estrada, O and Richards, SM and Breen, J}, title = {Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2512}, number = {}, pages = {261-267}, doi = {10.1007/978-1-0716-2429-6_15}, pmid = {35818010}, issn = {1940-6029}, mesh = {DNA, Plant/genetics ; Genomics/methods ; *Museums ; *Plants/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Plant DNA preserved in ancient specimens has recently gained importance as a tool in comparative genomics, allowing the investigation of evolutionary processes in plant genomes through time. However, recovering the genomic information contained in such specimens is challenging owing to the presence of secondary substances that limit DNA retrieval. In this chapter, we provide a DNA extraction protocol optimized for the recovery of DNA from degraded plant materials. The protocol is based on a commercially available DNA extraction kit that does not require handling of hazardous reagents.}, }
@article {pmid35779768, year = {2022}, author = {Psonis, N and Vardinoyannis, K and Poulakakis, N}, title = {High-throughput degraded DNA sequencing of subfossil shells of a critically endangered stenoendemic land snail in the Aegean.}, journal = {Molecular phylogenetics and evolution}, volume = {175}, number = {}, pages = {107561}, doi = {10.1016/j.ympev.2022.107561}, pmid = {35779768}, issn = {1095-9513}, mesh = {Animals ; DNA/genetics ; Endangered Species ; *High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Sequence Analysis, DNA/methods ; *Snails/genetics ; }, abstract = {High-throughput sequencing has enabled the comprehensive genetic exploration of biological diversity, especially by using natural history collections to study hard-to-find, threatened or even extinct-in-the-wild taxa. Mollusk shells are under-exploited as a source for DNA-based approaches, despite their apparent advantages in the field of conservation genetics. More particularly, degraded DNA techniques combined with high-throughput sequencing have never been used to gain insights about the DNA preservation in land snail subfossil or historical shells. Here, we applied degraded DNA analysis on two historical shells of Levantina rechingeri, a stenoendemic Critically Endangered species that has never been found alive, in order to explore the patterns of DNA preservation on land snail shells originating from the eastern Mediterranean, as well as to infer its molecular phylogenetic placement. Our results showed that centuries to decades-old DNA from an empty shell collected in an Aegean island exhibits characteristic post-mortem damage patterns similar to those observed in ancient DNA from eastern Mediterranean terrestrial animals, setting a precedent for future museomics studies on taxa distributed in areas with similar climate. Finally, genome skimming of the empty shell allowed high coverage of multiple nuclear and mitochondrial loci, enabling the phylogenetic placement of the focal taxon, the re-evaluation of its taxonomic classification, and the revealing of a new Aegean land snail lineage, Aristena genus novum. This approach is a non-invasive way to sample DNA from threatened land snail species and suitable to study the evolutionary history of taxa with cryptic ecology, stenoendemics, or extinct-in-the-wild, as well as old museum specimens.}, }
@article {pmid35774991, year = {2022}, author = {Marinček, P and Wagner, ND and Tomasello, S}, title = {Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?.}, journal = {Applications in plant sciences}, volume = {10}, number = {3}, pages = {e11477}, pmid = {35774991}, issn = {2168-0450}, abstract = {PREMISE: Herbaria harbor a tremendous number of plant specimens that are rarely used for molecular systematic studies, largely due to the difficulty in extracting sufficient amounts of high-quality DNA from the preserved plant material.<br><br>METHODS: We compared the standard Qiagen DNeasy Plant Mini Kit and a specific protocol for extracting ancient DNA (aDNA) (the N-phenacylthiazolium bromide and dithiothreitol [PTB-DTT] extraction method) from two different plant genera (Xanthium and Salix). The included herbarium materials covered about two centuries of plant collections. To analyze the success of DNA extraction using each method, a subset of samples was subjected to a standard library preparation as well as target-enrichment approaches.<br><br>RESULTS: The PTB-DTT method produced a higher DNA yield of better quality than the Qiagen kit; however, extracts from the Qiagen kit over a certain DNA yield and quality threshold produced comparable sequencing results. The sequencing resulted in high proportions of endogenous reads. We were able to successfully sequence 200-year-old samples.<br><br>DISCUSSION: This method comparison revealed that, for younger specimens, DNA extraction using a standard kit might be sufficient. For old and precious herbarium specimens, aDNA extraction methods are better suited to meet the requirements for next-generation sequencing.}, }
@article {pmid35771911, year = {2022}, author = {Liu, YC and Hunter-Anderson, R and Cheronet, O and Eakin, J and Camacho, F and Pietrusewsky, M and Rohland, N and Ioannidis, A and Athens, JS and Douglas, MT and Ikehara-Quebral, RM and Bernardos, R and Culleton, BJ and Mah, M and Adamski, N and Broomandkhoshbacht, N and Callan, K and Lawson, AM and Mandl, K and Michel, M and Oppenheimer, J and Stewardson, K and Zalzala, F and Kidd, K and Kidd, J and Schurr, TG and Auckland, K and Hill, AVS and Mentzer, AJ and Quinto-Cortés, CD and Robson, K and Kennett, DJ and Patterson, N and Bustamante, CD and Moreno-Estrada, A and Spriggs, M and Vilar, M and Lipson, M and Pinhasi, R and Reich, D}, title = {Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6601}, pages = {72-79}, pmid = {35771911}, issn = {1095-9203}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Asian People/genetics ; Child ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Female ; History, Ancient ; *Human Migration/history ; Humans ; Male ; Micronesia ; Oceania ; }, abstract = {Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain-related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up.}, }
@article {pmid35771611, year = {2022}, author = {Liu, X and Orlando, L}, title = {mapDATAge: a ShinyR package to chart ancient DNA data through space and time.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {16}, pages = {3992-3994}, pmid = {35771611}, issn = {1367-4811}, support = {101027750//Marie Curie Intra-European Fellowship programme/ ; 681605//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {*Software ; *DNA, Ancient ; }, abstract = {SUMMARY: Ancient DNA datasets are increasingly difficult to visualize for users lacking computational experience. Here, we describe mapDATAge, which aims to provide user-friendly automated modules for the interactive mapping of allele, haplogroup and/or ancestry distributions through space and time. mapDATAge enhances collaborative data sharing while assisting the assessment and reporting of spatiotemporal patterns of genetic changes.<br><br>mapDATAge is a Shiny R application designed for exploring spatiotemporal patterns in ancient DNA data through a graphical user interface. It is freely available under GNU Public License in Github: https://github.com/xuefenfei712/mapDATAge.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid39439471, year = {2024}, author = {Verry, AJF and Lubbe, P and Mitchell, KJ and Rawlence, NJ}, title = {Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions.}, journal = {Journal of the Royal Society of New Zealand}, volume = {54}, number = {1}, pages = {75-97}, pmid = {39439471}, issn = {1175-8899}, abstract = {Thirty years ago, DNA sequences were obtained from an extinct Aotearoa New Zealand animal for the first time. Since then, ancient DNA research has provided many - often unexpected - insights into the origins of New Zealand's terrestrial and marine vertebrate fauna. Because recent human activities in New Zealand have caused the decline or extinction of many endemic plant, bird, reptile, and marine mammal species, ancient DNA has been instrumental in reconstructing their identities and origins. However, most ancient DNA studies focusing on New Zealand species have been restricted to vertebrates, with small sample sizes, and/or relatively few genetic markers. This has limited their power to infer fine-scale biogeographic patterns, including (pre)historic distributions and range-shifts driven by past climate and environmental change. Recently, 'next-generation' methodological and technological advances have broadened the range of hypotheses that can feasibly be tested with ancient DNA. These advances represent an exciting opportunity for further exploring New Zealand biogeography using ancient DNA, but their promise has not yet been fully realised. In this review, we summarise the last 30 years of ancient DNA research into New Zealand faunal biogeography and highlight key objectives, challenges, and possibilities for the next 30 years and beyond.}, }
@article {pmid35751552, year = {2022}, author = {,  and Nijman, IJ and Rosen, BD and Bardou, P and Faraut, T and Cumer, T and Daly, KG and Zheng, Z and Cai, Y and Asadollahpour, H and Kul, B&#xc7; and Zhang, WY and E, G and Ayin, A and Baird, H and Bakhtin, M and Bâlteanu, VA and Barfield, D and Berger, B and Blichfeldt, T and Boink, G and Bugiwati, SRA and Cai, Z and Carolan, S and Clark, E and Cubric-Curik, V and Dagong, MIA and Dorji, T and Drew, L and Guo, J and Hallsson, J and Horvat, S and Kantanen, J and Kawaguchi, F and Kazymbet, P and Khayatzadeh, N and Kim, N and Shah, MK and Liao, Y and Martínez, A and Masangkay, JS and Masaoka, M and Mazza, R and McEwan, J and Milanesi, M and Omar, FM and Nomura, Y and Ouchene-Khelifi, NA and Pereira, F and Sahana, G and Salavati, M and Sasazaki, S and Da Silva, A and Simčič, M and Sölkner, J and Sutherland, A and Tigchelaar, J and Zhang, H and ,  and Ajmone-Marsan, P and Bradley, DG and Colli, L and Drögemüller, C and Jiang, Y and Lei, C and Mannen, H and Pompanon, F and Tosser-Klopp, G and Lenstra, JA}, title = {Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions.}, journal = {Molecular ecology}, volume = {31}, number = {16}, pages = {4364-4380}, doi = {10.1111/mec.16579}, pmid = {35751552}, issn = {1365-294X}, support = {BBS/OS/GC/000012F/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Genetic Variation ; Goats/genetics ; Haplotypes/genetics ; Phylogeny ; Y Chromosome/genetics ; }, abstract = {By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range.}, }
@article {pmid35749392, year = {2022}, author = {Toncheva, D and Marinova, M and Borovska, P and Serbezov, D}, title = {Spatio-temporal dynamics of pathogenic variants associated with monogenic disorders reconstructed with ancient DNA.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0269628}, pmid = {35749392}, issn = {1932-6203}, mesh = {DNA, Ancient ; Gene Frequency ; Genotype ; Humans ; *Phenylketonurias ; *Symporters ; }, abstract = {Genetic disease burden in ancient communities has barely been evaluated despite an ever expanding body of ancient genomes becoming available. In this study, we inspect 2729 publicly available ancient genomes (100 BP-52000 BP) for the presence of pathogenic variants in 32643 disease-associated loci. We base our subsequent analyses on 19 variants in seven genes-PAH, EDAR, F11, HBB, LRRK2, SLC12A6 and MAOA, associated with monogenic diseases and with well-established pathogenic impact in contemporary populations. We determine 230 homozygote genotypes of these variants in the screened 2729 ancient DNA samples. Eleven of these are in the PAH gene (126 ancient samples in total), a gene associated with the condition phenylketonuria in modern populations. The variants examined seem to show varying dynamics over the last 10000 years, some exhibiting a single upsurge in frequency and subsequently disappearing, while others maintain high frequency levels (compared to contemporary population frequencies) over long time periods. The geographic distribution and age of the ancient DNA samples with established pathogenic variants suggests multiple independent origin of these variants. Comparison of estimates of the geographic prevalence of these variants from ancient and contemporary data show discontinuity in their prevalence and supports their recurrent emergence. The oldest samples in which a variant is established might give an indication of their age and place origin, and an EDAR gene pathogenic variant was established in a sample estimated to be 33210-32480 calBCE. Knowledge about the historical prevalence of variants causing monogenic disorders provides insight on their emergence, dynamics and spread.}, }
@article {pmid35746807, year = {2022}, author = {Nishimura, L and Fujito, N and Sugimoto, R and Inoue, I}, title = {Detection of Ancient Viruses and Long-Term Viral Evolution.}, journal = {Viruses}, volume = {14}, number = {6}, pages = {}, pmid = {35746807}, issn = {1999-4915}, mesh = {*COVID-19 ; DNA, Ancient ; Evolution, Molecular ; Genome, Viral ; Humans ; *Viruses/genetics ; }, abstract = {The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.}, }
@article {pmid35734848, year = {2022}, author = {Saldías, E and Valdebenito, G and Zamora, L and Bastías, B and Flores, C and Vila, B and Vinueza, D and Tornero, C and Malgosa, A and Becker, E}, title = {Multidisciplinary analysis of a mummy from the War of the Pacific.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {79}, number = {4}, pages = {451-465}, doi = {10.1127/anthranz/2022/1543}, pmid = {35734848}, issn = {0003-5548}, mesh = {Adult ; Archaeology ; Humans ; Male ; *Mummies ; Peru ; Tomography, X-Ray Computed ; *Wounds, Gunshot ; }, abstract = {The War of the Pacific (1879-1884) was a big scale war between Chile against the alliance of Peru and Bolivia. One of the most important battles, the "Batalla del Campo de la Alianza" was situated in the desert near Tacna, Peru. The conditions of this environment favored the conservation of the dead soldiers after many years. Decades ago, the Natural History Museum of Concepción in Chile, received a naturally mummified individual of a probably Chilean soldier as a donation; its uncertain context was never studied nor confirmed. Considering this, our investigation analyzed this body under exploratory methods, ballistic analysis, archaeological contrast, [14]C radiocarbon dating, ancient DNA, and isotopic analysis to reconstruct the biological profile of this mummy. The results indicated that the mummy belongs to an adult man between 33-39 years of age (> 1.50 m) and has a perimortem wound in the left flank of the abdomen. CT scan and X-rays revealed the presence of a bullet (Comblain II or Gras) hosted near the L2 vertebra. It is possible that the individual died of bleeding from a gunshot wound done by a long-distance firearm projectile from an inferior level, whose trajectory was from left to right, with slight inclination towards the top, and without a projectile exit. Other analyses confirmed the historical context and suggests the Chilean origin of the mummy. Despite the passage of time and other factors, it was possible to reconstruct the death of this individual thanks to technology and approaches from different disciplines.}, }
@article {pmid35732180, year = {2022}, author = {Gelabert, P and Blazyte, A and Chang, Y and Fernandes, DM and Jeon, S and Hong, JG and Yoon, J and Ko, Y and Oberreiter, V and Cheronet, O and Özdoğan, KT and Sawyer, S and Yang, S and Greytak, EM and Choi, H and Kim, J and Kim, JI and Jeong, C and Bae, K and Bhak, J and Pinhasi, R}, title = {Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea.}, journal = {Current biology : CB}, volume = {32}, number = {15}, pages = {3232-3244.e6}, doi = {10.1016/j.cub.2022.06.004}, pmid = {35732180}, issn = {1879-0445}, mesh = {Archaeology ; *Asian People/genetics ; *Ethnicity ; Genome ; History, Ancient ; Humans ; Polymorphism, Single Nucleotide ; }, abstract = {The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small number of ancient genomes are available. Here, we report the first paleogenomic data from the Korean Three Kingdoms period, a crucial point in the cultural and historic formation of Korea. These data comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th century CE and are best modeled as an admixture between a northern China Bronze Age genetic source and a source of Jomon-related ancestry that shares similarities with the present-day genomes from Japan. The observed substructure and proportion of Jomon-related ancestry suggest the presence of two genetic groups within the population and diversity among the Gaya population. We could not correlate the genomic differences between these two groups with either social status or sex. All the ancient individuals' genomic profiles, including phenotypically relevant SNPs associated with hair and eye color, facial morphology, and myopia, imply strong genetic and phenotypic continuity with modern Koreans for the last 1,700 years.}, }
@article {pmid35731946, year = {2022}, author = {Översti, S and Palo, JU}, title = {Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages.}, journal = {Genome biology and evolution}, volume = {14}, number = {7}, pages = {}, pmid = {35731946}, issn = {1759-6653}, mesh = {Bayes Theorem ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Evolution, Molecular ; Fossils ; Genetic Variation ; Haplotypes ; Humans ; Phylogeny ; }, abstract = {Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.}, }
@article {pmid35729698, year = {2022}, author = {Zheng, ZQ and Fu, QM and Liu, YC}, title = {Exploration of adaptation, evolution and domestication of fermentation microorganisms by applying ancient DNA technology.}, journal = {Yi chuan = Hereditas}, volume = {44}, number = {5}, pages = {414-423}, doi = {10.16288/j.yczz.22-057}, pmid = {35729698}, issn = {0253-9772}, mesh = {*DNA, Ancient ; Domestication ; Fermentation ; *Fermented Foods ; Humans ; Technology ; }, abstract = {Fermentation production is the most primitive application of microorganisms by humans, which is of great significance in human history. However, due to the lack of molecular evidence, the history of human fermentation production and the evolution and domestication of fermentation microorganisms remain to be further investigated. Taking wine and fermented dairy, the two most common types of fermented foods as examples, we introduce the archaeology evidence of fermented foods and the evolution and domestication of fermented microorganisms, introduce the research status of paleomicrobiology and fermented paleomicroorganisms, and explore the feasibility and challenges of the research of ancient fermented microorganisms applying microbial ancient DNA technology, as well as the application potential of ancient DNA capture technology in this field.}, }
@article {pmid35729694, year = {2022}, author = {Ping, WJ and Liu, YC and Fu, QM}, title = {Exploring the evolution of archaic humans through sedimentary ancient DNA.}, journal = {Yi chuan = Hereditas}, volume = {44}, number = {5}, pages = {362-369}, doi = {10.16288/j.yczz.22-032}, pmid = {35729694}, issn = {0253-9772}, mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Genome, Human ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; }, abstract = {Recent success in the retrieval of nuclear DNA of ancient humans and animals from cave sediments paves the way for genome-wide studies of past populations directly from sediments. In three studies, nuclear genomes of different species were obtained from the sediments of multiple archeological caves and their genetic histories were revealed, including an unknown population replacement of Neanderthals from Estatuas cave in Spain, which was recovered using a new DNA capture approach. By extending sediments as a source of DNA beyond fossils, this breakthrough is of particular significance to the field of ancient human genomics, which brings about more possibilities for exploring the history of past population migration, evolution and adaptation within larger time-scales and geographical areas where no fossil remains exist. Here, we mainly review the significance of the technical advances in retrieving ancient nuclear DNA from sediments and present new insights into the genetic history of Neanderthals revealed by this technique. By combining ancient genomes retrieved from fossils and additional mitochondrial DNA extracted from sediments of archaeological sites, we may begin investigating diverse archaic populations and examine their genetic relationships, movements and replacements in detail.}, }
@article {pmid35719876, year = {2022}, author = {Rodrigues Soares, AE and Boroffka, N and Schröder, O and Sverchkov, L and Benecke, N and Günther, T}, title = {Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.}, journal = {Royal Society open science}, volume = {9}, number = {6}, pages = {220104}, pmid = {35719876}, issn = {2054-5703}, abstract = {Central Asia has been an important region connecting the different parts of Eurasia throughout history and prehistory, with large states developing in this region during the Iron Age. Archaeogenomics is a powerful addition to the zooarchaeological toolkit for understanding the relation of these societies to animals. Here, we present the genetic identification of a goitered gazelle specimen (Gazella subgutturosa) at the site Gazimulla-Tepa, in modern-day Uzbekistan, supporting hunting of the species in the region during the Iron Age. The sample was directly radiocarbon dated to 2724-2439 calBP. A phylogenetic analysis of the mitochondrial genome places the individual into the modern variation of G. subgutturosa. Our data do represent both the first ancient DNA and the first nuclear DNA sequences of this species. The lack of genomic resources available for this gazelle and related species prevented us from performing a more in-depth analysis of the nuclear sequences generated. Therefore, we are making our sequence data available to the research community to facilitate other research of this nowadays threatened species which has been subject to human hunting for several millennia across its entire range on the Asian continent.}, }
@article {pmid35715597, year = {2022}, author = {Graham, F}, title = {Daily briefing: Ancient DNA traces origin of Black Death.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-01703-1}, pmid = {35715597}, issn = {1476-4687}, }
@article {pmid35710940, year = {2022}, author = {Long, GS and Klunk, J and Duggan, AT and Tapson, M and Giuffra, V and Gazzè, L and Fornaciari, A and Duchene, S and Fornaciari, G and Clermont, O and Denamur, E and Golding, GB and Poinar, H}, title = {A 16[th] century Escherichia coli draft genome associated with an opportunistic bile infection.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {599}, pmid = {35710940}, issn = {2399-3642}, mesh = {Animals ; Bile ; Escherichia coli/genetics ; *Escherichia coli Infections/genetics/microbiology ; Genome, Bacterial ; Mice ; *Opportunistic Infections ; }, abstract = {Escherichia coli - one of the most characterized bacteria and a major public health concern - remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16[th] century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past.}, }
@article {pmid35709264, year = {2022}, author = {Gibbons, A}, title = {Ancient DNA reveals Black Death source.}, journal = {Science (New York, N.Y.)}, volume = {376}, number = {6599}, pages = {1254-1255}, doi = {10.1126/science.add4865}, pmid = {35709264}, issn = {1095-9203}, mesh = {Burial/history ; DNA, Ancient ; *Epidemics/history ; History, Medieval ; Humans ; Kyrgyzstan/epidemiology ; *Plague/epidemiology/history ; *Yersinia pestis/isolation &amp; purification ; }, abstract = {Graves in Kyrgyzstan hold early victims of plague that swept medieval Europe.}, }
@article {pmid35705867, year = {2022}, author = {Callaway, E}, title = {Ancient DNA traces origin of Black Death.}, journal = {Nature}, volume = {606}, number = {7915}, pages = {635-636}, pmid = {35705867}, issn = {1476-4687}, mesh = {*DNA, Ancient ; *DNA, Bacterial ; History, Medieval ; Humans ; *Plague/epidemiology/genetics/history/microbiology ; }, }
@article {pmid35705810, year = {2022}, author = {Spyrou, MA and Musralina, L and Gnecchi Ruscone, GA and Kocher, A and Borbone, PG and Khartanovich, VI and Buzhilova, A and Djansugurova, L and Bos, KI and Kühnert, D and Haak, W and Slavin, P and Krause, J}, title = {The source of the Black Death in fourteenth-century central Eurasia.}, journal = {Nature}, volume = {606}, number = {7915}, pages = {718-724}, pmid = {35705810}, issn = {1476-4687}, support = {771234/ERC_/European Research Council/International ; }, mesh = {Archaeology ; Cemeteries ; DNA, Ancient/analysis ; DNA, Bacterial/analysis ; History, Medieval ; Humans ; Kyrgyzstan/epidemiology ; Pandemics/history ; Phylogeny ; *Plague/epidemiology/history/microbiology ; *Yersinia pestis/classification/pathogenicity ; }, abstract = {The origin of the medieval Black Death pandemic (AD 1346-1353) has been a topic of continuous investigation because of the pandemic's extensive demographic impact and long-lasting consequences[1,2]. Until now, the most debated archaeological evidence potentially associated with the pandemic's initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan[1,3-9]. These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338-1339 state 'pestilence' as the cause of death for the buried individuals[9]. Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic's emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia.}, }
@article {pmid35700547, year = {2022}, author = {Curto, A and Fernandes, T}, title = {Clubfoot and its implications for the locomotion of a medieval skeleton from Estremoz, Portugal.}, journal = {International journal of paleopathology}, volume = {38}, number = {}, pages = {13-17}, doi = {10.1016/j.ijpp.2022.05.004}, pmid = {35700547}, issn = {1879-9825}, mesh = {Adult ; *Clubfoot ; Foot ; Humans ; Locomotion ; Male ; *Metatarsal Bones ; Middle Aged ; Portugal ; }, abstract = {OBJECTIVE: This study describes foot bone anomalies and the degenerative changes associated with locomotion adaptations.<br><br>MATERIALS: An adult male (approximately 29-46 years old) from Estremoz, Portugal (13th-15th century).<br><br>METHODS: The skeletal anomalies observed in this skeleton were described and measurements were compared between both sides of the individual and with the mean of the adult males from the same collection.<br><br>RESULTS: The most anomalous bones are the right medial cuneiform and metatarsals. Degenerative changes are more severe on the left lower limb and right upper limb.<br><br>CONCLUSIONS: This skeleton represents a unilateral case of talipes varus of the right foot, with the metatarsals being more affected while previously published cases show more severe anomalies of the hindfoot. The degenerative changes observed in the skeleton suggest that both legs and arms, aided by crutches, were used for locomotion.<br><br>SIGNIFICANCE: This case shows that club foot skeletal anomalies are variable and the pattern of bony changes throughout the body can reveal locomotion adaptations.<br><br>LIMITATIONS: The possibility of a genetic cause cannot be assessed due to the absence of paleogenomic data.<br><br>Since the anomalies found in this case are different than those previously published, we recommend care when analysing foot bones.}, }
@article {pmid35698034, year = {2022}, author = {Kutschera, VE and Kierczak, M and van der Valk, T and von Seth, J and Dussex, N and Lord, E and Dehasque, M and Stanton, DWG and Khoonsari, PE and Nystedt, B and Dalén, L and Díez-Del-Molino, D}, title = {GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {228}, pmid = {35698034}, issn = {1471-2105}, support = {17:109//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 19:257//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 796877//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 2017-04647//Vetenskapsr&#xe5;det/ ; 2018-05973//Vetenskapsr&#xe5;det/ ; 2015-676//Svenska Forskningsr&#xe5;det Formas/ ; P2SKP3_165031/SNSF_/Swiss National Science Foundation/Switzerland ; P300PA_177845/SNSF_/Swiss National Science Foundation/Switzerland ; National Bioinformatics Infrastructure Sweden at SciLifeLab//Knut och Alice Wallenbergs Stiftelse/ ; }, mesh = {Animals ; *Computational Biology ; Endangered Species ; *Genome ; Genomics ; Reproducibility of Results ; Software ; }, abstract = {BACKGROUND: Many wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.<br><br>RESULTS: Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode).<br><br>CONCLUSIONS: GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.}, }
@article {pmid35695771, year = {2022}, author = {Huang, Y and Ringbauer, H}, title = {hapCon: estimating contamination of ancient genomes by copying from reference haplotypes.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {15}, pages = {3768-3777}, pmid = {35695771}, issn = {1367-4811}, support = {//Max Planck Society/ ; }, mesh = {Male ; Humans ; Haplotypes ; Sequence Analysis, DNA/methods ; *Genome ; *Software ; DNA, Ancient ; }, abstract = {MOTIVATION: Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1× average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1× and below) remains a challenging task for existing approaches.<br><br>RESULTS: We present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&amp;Stephens haplotype copying model for haploid X chromosomes, with mismatches modeled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1&#xd7; for SNP capture data (1240k) and 0.02&#xd7; for whole genome sequencing data, substantially extending the coverage limit of previous male X chromosome-based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25-30% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as &#x223c;45&#xa0;000 and various global ancestries.<br><br>We make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid35692842, year = {2022}, author = {Xue, J and Wang, W and Shao, J and Dai, X and Sun, Z and Gardner, JD and Chen, L and Guo, X and Di, N and Pei, X and Wu, X and Zhang, G and Cui, C and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Ping, W and Zhang, L and He, N and Fu, Q}, title = {Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {909267}, pmid = {35692842}, issn = {1664-8021}, abstract = {Shimao City is considered an important political and religious center during the Late Neolithic Longshan period of the Middle Yellow River basin. The genetic history and population dynamics among the Shimao and other ancient populations, especially the Taosi-related populations, remain unknown. Here, we sequenced 172 complete mitochondrial genomes, ranging from the Yangshao to Longshan period, from individuals related to the Shimao culture in northern Shaanxi Province and Taosi culture in southern Shanxi Province, Middle Yellow River basin. Our results show that the populations inhabiting Shimao City had close genetic connections with an earlier population in the Middle Neolithic Yangshao period of northern Shaanxi Province, revealing a mostly local origin for the Shimao Society. In addition, among the populations in other regions of the Yellow River basin, the Shimao-related populations had the closest maternal affinity with the contemporaneous Taosi populations from the Longshan period. The Shimao-related populations also shared more affinity with present-day northern Han populations than with the minorities and southern Han in China. Our study provides a new perspective on the genetic origins and structure of the Shimao people and the population dynamics in the Middle Yellow River basin during the Neolithic period.}, }
@article {pmid35687599, year = {2022}, author = {Poma, A and Cesare, P and Bonfigli, A and Volpe, AR and Colafarina, S and Vecchiotti, G and Forgione, A and Zarivi, O}, title = {A qPCR-duplex assay for sex determination in ancient DNA.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0269913}, pmid = {35687599}, issn = {1932-6203}, mesh = {Amelogenin/genetics ; DNA/analysis/genetics ; *DNA, Ancient ; Humans ; Male ; Real-Time Polymerase Chain Reaction ; *Sex Determination Analysis/methods ; }, abstract = {Molecular biology techniques are increasingly being used in sex identification of skeletal remains when traditional anthropometric analyzes are not successful in identifying sex of remains that are incomplete, fragmented and /or of immature individuals. In the present work, we investigated the possibility of determining sex by using the qPCR-duplex method for both ancient and modern DNA samples. This method involves the co-amplification of two genes in a single reaction system and the subsequent analysis of the fusion curves; the gene sequences used for the construction of suitable primers are those of steroid sulfatase (STS) and testis specific protein Y-linked 1 (TSPY) genes which turned out to be two sensitive markers as they have a detection limit of 60 pg and 20 pg respectively on modern DNA. The validity of the method was verified on modern DNA in which gender was identified in all the samples with 100% accuracy; thus, allowing for the same results as the classic method with amelogenin, but in a faster and more immediate way, as it allows for sex determination solely by analyzing the denaturation curves without having to perform an electrophoretic run. The proposed molecular technique proves to be sensitive and precise even on degraded DNA, in fact on 9 archaeological finds dating from the VII-XII century in which sex had been identified through anthropometric analysis, it confirmed the sex of 8 out of 9 finds correctly.}, }
@article {pmid35681049, year = {2022}, author = {Schulte, L and Meucci, S and Stoof-Leichsenring, KR and Heitkam, T and Schmidt, N and von Hippel, B and Andreev, AA and Diekmann, B and Biskaborn, BK and Wagner, B and Melles, M and Pestryakova, LA and Alsos, IG and Clarke, C and Krutovsky, KV and Herzschuh, U}, title = {Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {570}, pmid = {35681049}, issn = {2399-3642}, mesh = {DNA, Ancient ; Ecosystem ; *Larix/genetics ; Siberia ; Trees ; }, abstract = {Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate.}, }
@article {pmid35671731, year = {2022}, author = {Choin, J and Quintana-Murci, L}, title = {Paleogenomics: The demographic past of prehistoric Europeans.}, journal = {Current biology : CB}, volume = {32}, number = {11}, pages = {R535-R538}, doi = {10.1016/j.cub.2022.04.081}, pmid = {35671731}, issn = {1879-0445}, mesh = {DNA, Ancient ; Demography ; Europe ; *Genome, Human ; *Genomics ; History, Ancient ; Humans ; Paleontology ; }, abstract = {Ancient DNA provides answers to long-standing debates about past human history. New work using demographic modeling on ancient genomes documents the nature and timing of the demographic processes - population size changes, divergences and admixture - that took place in prehistoric Europe.}, }
@article {pmid35652762, year = {2022}, author = {Nagler, M and Podmirseg, SM and Ascher-Jenull, J and Sint, D and Traugott, M}, title = {Why eDNA fractions need consideration in biomonitoring.}, journal = {Molecular ecology resources}, volume = {22}, number = {7}, pages = {2458-2470}, pmid = {35652762}, issn = {1755-0998}, support = {I 3808/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Biodiversity ; Biological Monitoring ; DNA Barcoding, Taxonomic ; *DNA, Environmental ; Environmental Monitoring ; }, abstract = {The analysis of environmental DNA (eDNA) is revolutionizing the monitoring of biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists of an extracellular and intracellular fraction, each characterized by particular properties that determine the retrievable information on when and where organisms live or have been living. Here, we review the fractions of eDNA, describe how to obtain them from environmental samples and present a four-scenario concept that aims at enhancing spatial and temporal resolution of eDNA-based monitoring. Importantly, we highlight how the appropriate choice of eDNA fractions precludes misinterpretation of eDNA-based biodiversity data. Finally, future avenues of research towards eDNA fraction-specific analyses are outlined to unravel the full potential of eDNA-based studies targeting micro- and macro-organisms.}, }
@article {pmid39759958, year = {2022}, author = {Anthony, DW and Khokhlov, AA and Agapov, SA and Agapov, DS and Schulting, R and Olalde, I and Reich, D}, title = {The Eneolithic cemetery at Khvalynsk on the Volga River.}, journal = {Praehistorische Zeitschrift}, volume = {97}, number = {1}, pages = {22-67}, pmid = {39759958}, issn = {1613-0804}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {The genetically attested migrations of the third millennium BC have made the origins and nature of the Yamnaya culture a question of broad relevance across northern Eurasia. But none of the key archaeological sites most important for understanding the evolution of Yamnaya culture is published in western languages. These key sites include the fifth-millennium BC Khvalynsk cemetery in the middle Volga steppes. When the first part of the Eneolithic cemetery (Khvalynsk I) was discovered in 1977-79, the graves displayed many material and ritual traits that were quickly recognized as similar and probably ancestral to Yamnaya customs, but without the Yamnaya kurgans. With the discovery of a second burial plot (Khvalynsk II) 120m to the south in 1987-88, Khvalynsk became the largest excavated Eneolithic cemetery in the Don-Volga-Ural steppes (201 recorded graves), dated about 4500-4300 BCE. It has the largest copper assemblage of the fifth millennium BC in the steppes (373 objects) and the largest assemblage of sacrificed domesticated animals (at least 106 sheep-goat, 29 cattle, and 16 horses); and it produced four polished stone maces from well-documented grave contexts. The human skeletons have been sampled extensively for ancient DNA, the basis for an analysis of family relationships. This report compiles information from the relevant Russian-language publications and from the archaeologists who excavated the site, two of whom are co-authors, about the history of excavations, radiocarbon dates, copper finds, domesticated animal sacrifices, polished stone maces, genetic and skeletal studies, and relationships with other steppe cultures as well as agricultural cultures of the North Caucasus (Svobodnoe-Meshoko) and southeastern Europe (Varna and Cucuteni-Tripol'ye B1). Khvalynsk is described as a coalescent culture, integrating and combining northern and southern elements, a hybrid that can be recognized genetically, in cranio-facial types, in exchanged artifacts, and in social segments within the cemetery. Stone maces symbolized the unification and integration of socially defined segments at Khvalynsk.}, }
@article {pmid35635751, year = {2022}, author = {Chintalapati, M and Patterson, N and Moorjani, P}, title = {The spatiotemporal patterns of major human admixture events during the European Holocene.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35635751}, issn = {2050-084X}, support = {R35 GM142978/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeology ; DNA, Ancient ; Europe ; *Genome, Human ; *Human Migration ; Humans ; Iran ; }, abstract = {Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES (Distribution of Ancestry Tracts of Evolutionary Signals) that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on~1100 ancient genomes from sixteen regions in Europe and west Asia, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry across Europe. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of Steppe pastoralism. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.}, }
@article {pmid35627311, year = {2022}, author = {Abondio, P and Cilli, E and Luiselli, D}, title = {Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods.}, journal = {Genes}, volume = {13}, number = {5}, pages = {}, pmid = {35627311}, issn = {2073-4425}, mesh = {*Genome ; Haplotypes/genetics ; Linkage Disequilibrium ; *Selection, Genetic ; Whole Genome Sequencing ; }, abstract = {Signatures of positive selection in the genome are a characteristic mark of adaptation that can reveal an ongoing, recent, or ancient response to environmental change throughout the evolution of a population. New sources of food, climate conditions, and exposure to pathogens are only some of the possible sources of selective pressure, and the rise of advantageous genetic variants is a crucial determinant of survival and reproduction. In this context, the ability to detect these signatures of selection may pinpoint genetic variants that are responsible for a significant change in gene regulation, gene expression, or protein synthesis, structure, and function. This review focuses on statistical methods that take advantage of linkage disequilibrium and haplotype determination to reveal signatures of positive selection in whole-genome sequencing data, showing that they emerge from different descriptions of the same underlying event. Moreover, considerations are provided around the application of these statistics to different species, their suitability for ancient DNA, and the usefulness of discovering variants under selection for biomedicine and public health in an evolutionary medicine framework.}, }
@article {pmid35618734, year = {2022}, author = {Scorrano, G and Viva, S and Pinotti, T and Fabbri, PF and Rickards, O and Macciardi, F}, title = {Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6468}, pmid = {35618734}, issn = {2045-2322}, mesh = {Archaeology ; Body Remains ; *DNA, Ancient ; *Exanthema ; Humans ; Italy ; }, abstract = {The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius' eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian' genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.}, }
@article {pmid35617951, year = {2022}, author = {Maróti, Z and Neparáczki, E and Schütz, O and Maár, K and Varga, GIB and Kovács, B and Kalmár, T and Nyerki, E and Nagy, I and Latinovics, D and Tihanyi, B and Marcsik, A and Pálfi, G and Bernert, Z and Gallina, Z and Horváth, C and Varga, S and Költő, L and Raskó, I and Nagy, PL and Balogh, C and Zink, A and Maixner, F and Götherström, A and George, R and Szalontai, C and Szenthe, G and Gáll, E and Kiss, AP and Gulyás, B and Kovacsóczy, BN and Gál, SS and Tomka, P and Török, T}, title = {The genetic origin of Huns, Avars, and conquering Hungarians.}, journal = {Current biology : CB}, volume = {32}, number = {13}, pages = {2858-2870.e7}, doi = {10.1016/j.cub.2022.04.093}, pmid = {35617951}, issn = {1879-0445}, mesh = {Asian People ; *Gene Pool ; *Genetics, Population ; Haplotypes ; Humans ; Hungary ; }, abstract = {Huns, Avars, and conquering Hungarians were migration-period nomadic tribal confederations that arrived in three successive waves in the Carpathian Basin between the 5[th] and 9[th] centuries. Based on the historical data, each of these groups are thought to have arrived from Asia, although their exact origin and relation to other ancient and modern populations have been debated. Recently, hundreds of ancient genomes were analyzed from Central Asia, Mongolia, and China, from which we aimed to identify putative source populations for the above-mentioned groups. In this study, we have sequenced 9 Hun, 143 Avar, and 113 Hungarian conquest period samples and identified three core populations, representing immigrants from each period with no recent European ancestry. Our results reveal that this "immigrant core" of both Huns and Avars likely originated in present day Mongolia, and their origin can be traced back to Xiongnus (Asian Huns), as suggested by several historians. On the other hand, the "immigrant core" of the conquering Hungarians derived from an earlier admixture of Mansis, early Sarmatians, and descendants of late Xiongnus. We have also shown that a common "proto-Ugric" gene pool appeared in the Bronze Age from the admixture of Mezhovskaya and Nganasan people, supporting genetic and linguistic data. In addition, we detected shared Hun-related ancestry in numerous Avar and Hungarian conquest period genetic outliers, indicating a genetic link between these successive nomadic groups. Aside from the immigrant core groups, we identified that the majority of the individuals from each period were local residents harboring "native European" ancestry.}, }
@article {pmid35609205, year = {2022}, author = {Demarchi, B and Stiller, J and Grealy, A and Mackie, M and Deng, Y and Gilbert, T and Clarke, J and Legendre, LJ and Boano, R and Sicheritz-Pontén, T and Magee, J and Zhang, G and Bunce, M and Collins, MJ and Miller, G}, title = {Ancient proteins resolve controversy over the identity of Genyornis eggshell.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {43}, pages = {e2109326119}, pmid = {35609205}, issn = {1091-6490}, mesh = {Animals ; Humans ; Phylogeny ; *Egg Shell ; *Birds/genetics ; DNA/genetics ; Biological Evolution ; Fossils ; DNA, Ancient ; }, abstract = {The realization that ancient biomolecules are preserved in "fossil" samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia's indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.}, }
@article {pmid35588742, year = {2022}, author = {Ariano, B and Mattiangeli, V and Breslin, EM and Parkinson, EW and McLaughlin, TR and Thompson, JE and Power, RK and Stock, JT and Mercieca-Spiteri, B and Stoddart, S and Malone, C and Gopalakrishnan, S and Cassidy, LM and Bradley, DG}, title = {Ancient Maltese genomes and the genetic geography of Neolithic Europe.}, journal = {Current biology : CB}, volume = {32}, number = {12}, pages = {2668-2680.e6}, pmid = {35588742}, issn = {1879-0445}, support = {/WT_/Wellcome Trust/United Kingdom ; 205072/WT_/Wellcome Trust/United Kingdom ; 205072/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Agriculture ; *Archaeology ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Europe ; *Genome, Human ; Geography ; History, Ancient ; Human Migration ; Humans ; }, abstract = {Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans.}, }
@article {pmid35578825, year = {2022}, author = {Childebayeva, A and Rohrlach, AB and Barquera, R and Rivollat, M and Aron, F and Szolek, A and Kohlbacher, O and Nicklisch, N and Alt, KW and Gronenborn, D and Meller, H and Friederich, S and Prüfer, K and Deguilloux, MF and Krause, J and Haak, W}, title = {Population Genetics and Signatures of Selection in Early Neolithic European Farmers.}, journal = {Molecular biology and evolution}, volume = {39}, number = {6}, pages = {}, pmid = {35578825}, issn = {1537-1719}, mesh = {Agriculture ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Europe ; *Farmers ; Genetics, Population ; History, Ancient ; *Human Migration ; Humans ; }, abstract = {Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia.}, }
@article {pmid35573598, year = {2022}, author = {Zhang, X and Yang, L and Zhao, X and Xiang, H}, title = {The complete mitochondrial genome of an ancient cattle (Bos taurus) from Taosi site, China, and its phylogenetic assessment.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {7}, number = {5}, pages = {804-806}, pmid = {35573598}, issn = {2380-2359}, abstract = {The complete mitochondrial genome (mitogenome) of one 4000-years-old cattle from Taosi site was determined by high throughput sequencing. The mitogenome was 16,336 bp in length and contained 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The protein-coding genes had two types of start codons (ATG and ATA) and three types of stop codons (TAA, TAG, and AGA). The overall base composition of the genome was 33%-A, 27%-T, 26%-C, 14%-G. The matrilineal genealogical analysis based on mitogenome revealed that the 4000-years-old cattle from Taosi site was domestic taurine cattle. In this study, we not only reported a complete mitogenome for a 4000-years-old bovine remain from the middle Yellow River region but also provided the mitogenomic evidence for the close phylogenetic relationship between the early taurine cattle in Northern China and modern domestic cattle.}, }
@article {pmid35571044, year = {2022}, author = {Sehrawat, JS and Agrawal, S and Sankhyan, D and Singh, M and Kumar, S and Prakash, S and Rajpal, R and Chaubey, G and Thangaraj, K and Rai, N}, title = {Pinpointing the Geographic Origin of 165-Year-Old Human Skeletal Remains Found in Punjab, India: Evidence From Mitochondrial DNA and Stable Isotope Analysis.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {813934}, pmid = {35571044}, issn = {1664-8021}, abstract = {In 2014, 157 years after the Sepoy Mutiny of 1857, several unidentified human skeletons were discovered in an abandoned well at Ajnala, Punjab. The most prevailing hypothesis suggested them as Indian soldiers who mutinied during the Indian uprising of 1857. However, there is an intense debate on their geographic affinity. Therefore, to pinpoint their area of origin, we have successfully isolated DNA from cementum-rich material of 50 good-quality random teeth samples and analyzed mtDNA haplogroups. In addition to that, we analyzed 85 individuals for oxygen isotopes (δ[18]O values). The mtDNA haplogroup distribution and clustering pattern rejected the local ancestry and indicated their genetic link with the populations living east of Punjab. In addition, the oxygen isotope analysis (δ[18]O values) from archaeological skeletal remains corroborated the molecular data and suggested the closest possible geographical affinity of these skeletal remains toward the eastern part of India, largely covering the Gangetic plain region. The data generated from this study are expected to expand our understanding of the ancestry and population affinity of martyr soldiers.}, }
@article {pmid35563041, year = {2022}, author = {Heraclides, A and Fernández-Domínguez, E}, title = {Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods.}, journal = {International journal of molecular sciences}, volume = {23}, number = {9}, pages = {}, pmid = {35563041}, issn = {1422-0067}, mesh = {DNA, Ancient ; *DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {Retrieving high-quality endogenous ancient DNA (aDNA) poses several challenges, including low molecular copy number, high rates of fragmentation, damage at read termini, and potential presence of exogenous contaminant DNA. All these factors complicate a reliable reconstruction of consensus aDNA sequences in reads from high-throughput sequencing platforms. Here, we report findings from a thorough evaluation of two alternative tools (ANGSD and schmutzi) aimed at overcoming these issues and constructing high-quality ancient mitogenomes. Raw genomic data (BAM/FASTQ) from a total of 17 previously published whole ancient human genomes ranging from the 14th to the 7th millennium BCE were retrieved and mitochondrial consensus sequences were reconstructed using different quality filters, with their accuracy measured and compared. Moreover, the influence of different sequence parameters (number of reads, sequenced bases, mean coverage, and rate of deamination and contamination) as predictors of derived sequence quality was evaluated. Complete mitogenomes were successfully reconstructed for all ancient samples, and for the majority of them, filtering substantially improved mtDNA consensus calling and haplogroup prediction. Overall, the schmutzi pipeline, which estimates and takes into consideration exogenous contamination, appeared to have the edge over the much faster and user-friendly alternative method (ANGSD) in moderate to high coverage samples (>1,000,000 reads). ANGSD, however, through its read termini trimming filter, showed better capabilities in calling the consensus sequence from low-quality samples. Among all the predictors of overall sample quality examined, the strongest correlation was found for the available number of sequence reads and bases. In the process, we report a previously unassigned haplogroup (U3b) for an Early Chalcolithic individual from Southern Anatolia/Northern Levant.}, }
@article {pmid35559028, year = {2022}, author = {Ávila-Arcos, MC and de la Fuente Castro, C and Nieves-Colón, MA and Raghavan, M}, title = {Recommendations for Sustainable Ancient DNA Research in the Global South: Voices From a New Generation of Paleogenomicists.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {880170}, pmid = {35559028}, issn = {1664-8021}, support = {R35 GM143094/GM/NIGMS NIH HHS/United States ; }, abstract = {Paleogenomics - the study of ancient genomes - has made significant contributions, especially to our understanding of the evolutionary history of humans. This knowledge influx has been a direct result of the coupling of next-generation sequencing with improved methods for DNA recovery and analysis of ancient samples. The appeal of ancient DNA studies in the popular media coupled with the trend for such work to be published in "high impact" journals has driven the amassing of ancestral human remains from global collections, often with limited to no engagement or involvement of local researchers and communities. This practice in the paleogenomics literature has led to limited representation of researchers from the Global South at the research design and subsequent stages. Additionally, Indigenous and descendant communities are often alienated from popular and academic narratives that both involve and impact them, sometimes adversely. While some countries have safeguards against 'helicopter science', such as federally regulated measures to protect their biocultural heritage, there is variable oversight in others with regard to sampling and exportation of human remains for destructive research, and differing requirements for accountability or consultation with local researchers and communities. These disparities reveal stark contrasts and gaps in regional policies that lend themselves to persistent colonial practices. While essential critiques and conversations in this sphere are taking place, these are primarily guided through the lens of US-based heritage legislation such as the Native American Graves and Protection Act (NAGPRA). In this article, we aim to expand the scope of ongoing conversations by taking into account diverse regional contexts and challenges drawing from our own research experiences in the field of paleogenomics. We emphasize that true collaborations involve knowledge sharing, capacity building, mutual respect, and equitable participation, all of which take time and the implementation of sustainable research methods; amass-and-publish strategy is simply incompatible with this ethos.}, }
@article {pmid35557944, year = {2022}, author = {Buisan, R and Moriano, J and Andirkó, A and Boeckx, C}, title = {A Brain Region-Specific Expression Profile for Genes Within Large Introgression Deserts and Under Positive Selection in Homo sapiens.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {824740}, pmid = {35557944}, issn = {2296-634X}, abstract = {Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of "archaic" haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions and the specific expression trajectories of genes within them, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, in particular the cerebellum, the striatum and the mediodorsal nucleus of the thalamus show the most divergent transcriptomic profiles when considering genes within large introgression deserts and under positive selection.}, }
@article {pmid35552521, year = {2022}, author = {Callaway, E}, title = {Ancient DNA maps 'dawn of farming'.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {35552521}, issn = {1476-4687}, }
@article {pmid35550934, year = {2022}, author = {Rath, K and Käßner, A and Melisch, C and Powers, N and Tichomirowa, M and Nagy, M and Friedrich, R and Riege, J and Rothe, J}, title = {Genetic and isotope analysis of a triple burial from medieval St. Peter's cemetery in Cölln/Berlin.}, journal = {Forensic science international. Genetics}, volume = {59}, number = {}, pages = {102718}, doi = {10.1016/j.fsigen.2022.102718}, pmid = {35550934}, issn = {1878-0326}, mesh = {Berlin ; *Burial/history ; *Cemeteries/history ; History, Medieval ; Humans ; Isotopes ; Male ; White People ; }, abstract = {The German capital Berlin originates from the two medieval settlements Berlin and Cölln on either side of the river Spree. Whereas Berlin is world famous, there is very little awareness of former Cölln. From 2007-2009, during excavations of the earliest cemetery of this forgotten medieval town; 3,126 graves were discovered containing the remains of 3,717 individuals. Amongst those graves was an unusual triple burial. This grave was exceptional due to the relative postures of the skeletons and their extensive facial injuries. Here we present genetic and isotope data for this grave. Genetic results confirmed all of them as biological male individuals and ruled out their biological kinship. Combining genetic ancestry information with strontium isotope data we furthermore determined that two of the men most likely originated from the Berlin-Brandenburg region, whereas a more distant origin of the third individual can be debated.}, }
@article {pmid35543411, year = {2022}, author = {Cai, D and Zhu, S and Gong, M and Zhang, N and Wen, J and Liang, Q and Sun, W and Shao, X and Guo, Y and Cai, Y and Zheng, Z and Zhang, W and Hu, S and Wang, X and Tian, H and Li, Y and Liu, W and Yang, M and Yang, J and Wu, D and Orlando, L and Jiang, Y}, title = {Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35543411}, issn = {2050-084X}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Equidae/genetics ; *Fossils ; Genome ; Genomics ; Horses/genetics ; Phylogeny ; }, abstract = {The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3-2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species' chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.}, }
@article {pmid35538842, year = {2022}, author = {Verry, AJF and Mitchell, KJ and Rawlence, NJ}, title = {Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa (Emeus crassus).}, journal = {Biology letters}, volume = {18}, number = {5}, pages = {20220013}, pmid = {35538842}, issn = {1744-957X}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Ecosystem ; *Genetic Variation ; Haplotypes ; Phylogeny ; Phylogeography ; *Refugium ; }, abstract = {Cycles of glacial expansion and contraction throughout the Pleistocene drove increases and decreases, respectively, in the geographical range and population size of many animal species. Genetic data have revealed that during glacial maxima the distribution of many Eurasian animals was restricted to small refugial areas, from which species expanded to reoccupy parts of their former range as the climate warmed. It has been suggested that the extinct eastern moa (Emeus crassus)-a large, flightless bird from New Zealand-behaved analogously during glacial maxima, possibly surviving only in a restricted area of lowland habitat in the southern South Island of New Zealand during the Last Glacial Maximum (LGM). However, previous studies have lacked the power and geographical sampling to explicitly test this hypothesis using genetic data. Here we analyse 46 ancient mitochondrial genomes from Late Pleistocene and Holocene bones of the eastern moa from across their post-LGM distribution. Our results are consistent with a post-LGM increase in the population size and genetic diversity of eastern moa. We also demonstrate that genetic diversity was higher in eastern moa from the southern extent of their range, supporting the hypothesis that they expanded from a single glacial refugium following the LGM.}, }
@article {pmid35537469, year = {2022}, author = {Fleskes, RE and Bader, AC and Tsosie, KS and Wagner, JK and Claw, KG and Garrison, NA}, title = {Ethical Guidance in Human Paleogenomics: New and Ongoing Perspectives.}, journal = {Annual review of genomics and human genetics}, volume = {23}, number = {}, pages = {627-652}, pmid = {35537469}, issn = {1545-293X}, support = {R35 HG011319/HG/NHGRI NIH HHS/United States ; }, mesh = {DNA, Ancient ; *Genomics ; Humans ; Informed Consent ; *Paleontology ; Research Personnel ; }, abstract = {Over the past two decades, the study of ancient genomes from Ancestral humans, or human paleogenomic research, has expanded rapidly in both scale and scope. Ethical discourse has subsequently emerged to address issues of social responsibility and scientific robusticity in conducting research. Here, we highlight and contextualize the primary sources of professional ethical guidance aimed at paleogenomic researchers. We describe the tension among existing guidelines, while addressing core issues such as consent, destructive research methods, and data access and management. Currently, there is a dissonance between guidelines that focus on scientific outcomes and those that hold scientists accountable to stakeholder communities,such as descendants. Thus, we provide additional tools to navigate the complexities of ancient DNA research while centering engagement with stakeholder communities in the scientific process.}, }
@article {pmid35537455, year = {2022}, author = {Segawa, T and Yonezawa, T and Mori, H and Kohno, A and Kudo, Y and Akiyoshi, A and Wu, J and Tokanai, F and Sakamoto, M and Kohno, N and Nishihara, H}, title = {Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan.}, journal = {Current biology : CB}, volume = {32}, number = {11}, pages = {2494-2504.e5}, doi = {10.1016/j.cub.2022.04.034}, pmid = {35537455}, issn = {1879-0445}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genomics ; Japan ; Paleontology ; Phylogeny ; *Wolves/anatomy &amp; histology/genetics ; }, abstract = {Little is known about the spatiotemporal dynamics of gray wolves in the Pleistocene across low-latitude regions of Eurasia. In Japan, a small-bodied endemic subspecies of Japanese wolves existed and went extinct in the early 1900s. The fossil record indicates that a giant wolf, which reached 70 cm in body height, inhabited Japan during the Pleistocene, but its evolutionary relationship, if any, with the Japanese wolf remains uncertain. Here, to reveal the genetic origin of the Japanese wolf, we analyzed ancient DNA from remains (recovered in Japan) of one Pleistocene wolf that lived 35,000 years ago and one Holocene wolf from 5,000 years ago. The analysis of the mitochondrial DNA revealed that the Pleistocene wolf was not part of the Japanese wolf clade but rather an earlier-diverging lineage. The analysis of the nuclear DNA of the Holocene Japanese wolf revealed that it was an admixture of the Japanese Pleistocene wolf and continental wolf lineages. These findings suggest that the Japanese wolf originated via waves of colonization of multiple Pleistocene wolf populations at 57-35 and 37-14 ka, respectively, followed by interpopulation hybridization.}, }
@article {pmid35526849, year = {2022}, author = {Malyarchuk, AB and Andreeva, TV and Kuznetsova, IL and Kunizheva, SS and Protasova, MS and Uralsky, LI and Tyazhelova, TV and Gusev, FE and Manakhov, AD and Rogaev, EI}, title = {Genomics of Ancient Pathogens: First Advances and Prospects.}, journal = {Biochemistry. Biokhimiia}, volume = {87}, number = {3}, pages = {242-258}, pmid = {35526849}, issn = {1608-3040}, mesh = {DNA, Ancient ; *Genomics/methods ; History, Ancient ; Humans ; Mycobacterium leprae/genetics ; Paleontology ; *Yersinia pestis/genetics ; }, abstract = {Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today's world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.}, }
@article {pmid35506242, year = {2022}, author = {Martínez-García, L and Ferrari, G and Hufthammer, AK and Jakobsen, KS and Jentoft, S and Barrett, JH and Star, B}, title = {Ancient DNA reveals a southern presence of the Northeast Arctic cod during the Holocene.}, journal = {Biology letters}, volume = {18}, number = {5}, pages = {20220021}, pmid = {35506242}, issn = {1744-957X}, mesh = {Animals ; Climate Change ; *DNA, Ancient ; Fishes ; *Gadus morhua/genetics ; Temperature ; }, abstract = {Climate change has been implicated in an increased number of distributional shifts of marine species during the last century. Nonetheless, it is unclear whether earlier climatic fluctuations had similar impacts. We use ancient DNA to investigate the long-term spawning distribution of the Northeast Arctic cod (skrei) which performs yearly migrations from the Barents Sea towards spawning grounds along the Norwegian coast. The distribution of these spawning grounds has shifted northwards during the last century, which is thought to be associated with food availability and warming temperatures. We genetically identify skrei specimens from Ruskeneset in west Norway, an archaeological site located south of their current spawning range. Remarkably, [14]C analyses date these specimens to the late Holocene, when temperatures were warmer than present-day conditions. Our results either suggest that temperature is not the only driver influencing the spawning distribution of Atlantic cod, or could be indicative of uncertainty in palaeoclimate reconstructions in this region. Regardless, our findings highlight the utility of aDNA to reconstruct the historical distribution of economically important fish populations and reveal the complexity of long-term ecological interactions in the marine environment.}, }
@article {pmid35506233, year = {2022}, author = {Yarlagadda, K and Zachwieja, AJ and de Flamingh, A and Phungviwatnikul, T and Rivera-Colón, AG and Roseman, C and Shackelford, L and Swanson, KS and Malhi, RS}, title = {Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1974}, pages = {20220052}, pmid = {35506233}, issn = {1471-2954}, mesh = {Animals ; Diet ; Dogs ; Feces ; India ; *Microbiota ; South Africa ; }, abstract = {Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome.}, }
@article {pmid35501689, year = {2022}, author = {Corrochano-Fraile, A and Davie, A and Carboni, S and Bekaert, M}, title = {Evidence of multiple genome duplication events in Mytilus evolution.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {340}, pmid = {35501689}, issn = {1471-2164}, mesh = {Animals ; Gene Duplication ; Genome ; Genomics ; *Mytilidae/genetics ; *Mytilus/genetics ; }, abstract = {BACKGROUND: Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia.<br><br>RESULTS: Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences.<br><br>CONCLUSIONS: The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises.}, }
@article {pmid35494246, year = {2022}, author = {Yu, H and van de Loosdrecht, MS and Mannino, MA and Talamo, S and Rohrlach, AB and Childebayeva, A and Villalba-Mouco, V and Aron, F and Brandt, G and Burri, M and Freund, C and Radzeviciute, R and Stahl, R and Wissgott, A and Fewlass, H and Tagliacozzo, A and Piperno, M and Tusa, S and Collina, C and Schimmenti, V and Di Salvo, R and Prüfer, K and Posth, C and Hublin, JJ and Gronenborn, D and Binder, D and Jeong, C and Haak, W and Krause, J}, title = {Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily.}, journal = {iScience}, volume = {25}, number = {5}, pages = {104244}, pmid = {35494246}, issn = {2589-0042}, abstract = {Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700-4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell'Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition.}, }
@article {pmid35482488, year = {2022}, author = {Ausmees, K and Sanchez-Quinto, F and Jakobsson, M and Nettelblad, C}, title = {An empirical evaluation of genotype imputation of ancient DNA.}, journal = {G3 (Bethesda, Md.)}, volume = {12}, number = {6}, pages = {}, pmid = {35482488}, issn = {2160-1836}, mesh = {Alleles ; *DNA, Ancient ; Gene Frequency ; *Genotype ; Humans ; Software ; }, abstract = {With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.}, }
@article {pmid35476992, year = {2022}, author = {Kędzior, M and Garcia, AK and Li, M and Taton, A and Adam, ZR and Young, JN and Kaçar, B}, title = {Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time.}, journal = {Cell reports}, volume = {39}, number = {4}, pages = {110726}, doi = {10.1016/j.celrep.2022.110726}, pmid = {35476992}, issn = {2211-1247}, support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria/genetics ; Carbon Isotopes ; *Ribulose-Bisphosphate Carboxylase/chemistry/genetics ; }, abstract = {The earliest geochemical indicators of microbes-and the enzymes that powered them-extend back ∼3.8 Ga on Earth. Paleobiologists often attempt to understand these indicators by assuming that the behaviors of extant microbes and enzymes are uniform with those of their predecessors. This consistency in behavior seems at odds with our understanding of the inherent variability of living systems. Here, we examine whether a uniformitarian assumption for an enzyme thought to generate carbon isotope indicators of biological activity, RuBisCO, can be corroborated by independently studying the history of changes recorded within RuBisCO's genetic sequences. We resurrected a Precambrian-age RuBisCO by engineering its ancient DNA inside a cyanobacterium genome and measured the engineered organism's fitness and carbon-isotope-discrimination profile. Results indicate that Precambrian uniformitarian assumptions may be warranted but with important caveats. Experimental studies illuminating early innovations are crucial to explore the molecular foundations of life's earliest traces.}, }
@article {pmid35456493, year = {2022}, author = {Dehasque, M and Pečnerová, P and Kempe Lagerholm, V and Ersmark, E and Danilov, GK and Mortensen, P and Vartanyan, S and Dalén, L}, title = {Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.}, journal = {Genes}, volume = {13}, number = {4}, pages = {}, pmid = {35456493}, issn = {2073-4425}, mesh = {Bone and Bones ; DNA/genetics ; *DNA, Ancient ; *Silicon Dioxide ; Uracil ; }, abstract = {Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/µL (as compared to 0.3 U/µL) of ancient DNA extracts.}, }
@article {pmid35456371, year = {2022}, author = {Gînguță, A and Kovács, B and Tihanyi, B and Maár, K and Schütz, O and Maróti, Z and Varga, GIB and Kiss, AP and Stanciu, I and Török, T and Neparáczki, E}, title = {Maternal Lineages of Gepids from Transylvania.}, journal = {Genes}, volume = {13}, number = {4}, pages = {}, pmid = {35456371}, issn = {2073-4425}, mesh = {Archaeology ; Cemeteries ; *Gene Pool ; *Genetics, Population ; Humans ; White People ; }, abstract = {According to the written historical sources, the Gepids were a Germanic tribe that settled in the Carpathian Basin during the Migration Period. They were allies of the Huns, and an independent Gepid Kingdom arose after the collapse of the Hun Empire. In this period, the Carpathian Basin was characterized by so-called row-grave cemeteries. Due to the scarcity of historical and archaeological data, we have a poor knowledge of the origin and composition of these barbarian populations, and this is still a subject of debate. To better understand the genetic legacy of migration period societies, we obtained 46 full mitogenome sequences from three Gepid cemeteries located in Transylvania, Romania. The studied samples represent the Classical Gepidic period and illustrate the genetic make-up of this group from the late 5th and early 6th centuries AD, which is characterized by cultural markers associated with the Gepid culture in Transylvania. The genetic structure of the Gepid people is explored for the first time, providing new insights into the genetic makeup of this archaic group. The retrieved genetic data showed mainly the presence of Northwestern European mitochondrial ancient lineages in the Gepid group and all population genetic analyses reiterated the same genetic structure, showing that early ancient mitogenomes from Europe were the major contributors to the Gepid maternal genetic pool.}, }
@article {pmid35446704, year = {2022}, author = {Lopez-Valdivia, I and Perkins, AC and Schneider, HM and Vallebueno-Estrada, M and Burridge, JD and González-Orozco, E and Montufar, A and Montiel, R and Lynch, JP and Vielle-Calzada, JP}, title = {Gradual domestication of root traits in the earliest maize from Tehuacán.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {17}, pages = {e2110245119}, pmid = {35446704}, issn = {1091-6490}, mesh = {*Domestication ; Mexico ; Phenotype ; *Zea mays/genetics ; }, abstract = {Efforts to understand the phenotypic transition that gave rise to maize from teosinte have mainly focused on the analysis of aerial organs, with little insights into possible domestication traits affecting the root system. Archeological excavations in San Marcos cave (Tehuacán, Mexico) yielded two well-preserved 5,300 to 4,970 calibrated y B.P. specimens (SM3 and SM11) corresponding to root stalks composed of at least five nodes with multiple nodal roots and, in case, a complete embryonic root system. To characterize in detail their architecture and anatomy, we used laser ablation tomography to reconstruct a three-dimensional segment of their nodal roots and a scutellar node, revealing exquisite preservation of the inner tissue and cell organization and providing reliable morphometric parameters for cellular characteristics of the stele and cortex. Whereas SM3 showed multiple cortical sclerenchyma typical of extant maize, the scutellar node of the SM11 embryonic root system completely lacked seminal roots, an attribute found in extant teosinte and in two specific maize mutants: root with undetectable meristem1 (rum1) and rootless concerning crown and seminal roots (rtcs). Ancient DNA sequences of SM10—a third San Marcos specimen of equivalent age to SM3 and SM11—revealed the presence of mutations in the transcribed sequence of both genes, offering the possibility for some of these mutations to be involved in the lack of seminal roots of the ancient specimens. Our results indicate that the root system of the earliest maize from Tehuacán resembled teosinte in traits important for maize drought adaptation.}, }
@article {pmid35446690, year = {2022}, author = {Rivollat, M and Thomas, A and Ghesquière, E and Rohrlach, AB and Späth, E and Pemonge, MH and Haak, W and Chambon, P and Deguilloux, MF}, title = {Ancient DNA gives new insights into a Norman Neolithic monumental cemetery dedicated to male elites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {18}, pages = {e2120786119}, pmid = {35446690}, issn = {1091-6490}, mesh = {Archaeology ; Burial/history ; *Cemeteries ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Female ; Genomics ; History, Ancient ; Humans ; Male ; }, abstract = {The Middle Neolithic in western Europe is characterized by monumental funerary structures, known as megaliths, along the Atlantic façade. The first manifestations of this phenomenon occurred in modern-day France with the long mounds of the Cerny culture. Here, we present genome-wide data from the fifth-millennium BCE site of Fleury-sur-Orne in Normandy (France), famous for its impressively long monuments built for selected individuals. The site encompasses 32 monuments of variable sizes, containing the burials of 19 individuals from the Neolithic period. To address who was buried at the site, we generated genome-wide data for 14 individuals, of whom 13 are males, completing previously published data [M. Rivollat et al., Sci. Adv. 6, eaaz5344 (2020)]. Population genetic and Y chromosome analyses show that the Fleury-sur-Orne group fits within western European Neolithic genetic diversity and that the arrival of a new group is detected after 4,000 calibrated BCE. The results of analyzing uniparentally inherited markers and an overall low number of long runs of homozygosity suggest a patrilineal group practicing female exogamy. We find two pairs of individuals to be father and son, buried together in the same monument/grave. No other biological relationship can link monuments together, suggesting that each monument was dedicated to a genetically independent lineage. The combined data and documented father–son line of descent suggest a male-mediated transmission of sociopolitical authority. However, a single female buried with an arrowhead, otherwise considered a symbol of power of the male elite of the Cerny culture, questions a strictly biological sex bias in the burial rites of this otherwise “masculine” monumental cemetery.}, }
@article {pmid35445261, year = {2022}, author = {Vallini, L and Marciani, G and Aneli, S and Bortolini, E and Benazzi, S and Pievani, T and Pagani, L}, title = {Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa.}, journal = {Genome biology and evolution}, volume = {14}, number = {4}, pages = {}, pmid = {35445261}, issn = {1759-6653}, mesh = {Africa ; Animals ; Anthropology, Cultural ; Europe ; Genetics, Population ; Humans ; *Neanderthals/genetics ; Siberia ; }, abstract = {The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.}, }
@article {pmid35440148, year = {2022}, author = {Brand, CM and Colbran, LL and Capra, JA}, title = {Predicting Archaic Hominin Phenotypes from Genomic Data.}, journal = {Annual review of genomics and human genetics}, volume = {23}, number = {}, pages = {591-612}, pmid = {35440148}, issn = {1545-293X}, support = {R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient ; Genome, Human ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Phenotype ; }, abstract = {Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes.}, }
@article {pmid35413261, year = {2022}, author = {Schlebusch, CM}, title = {Genomics: Testing the limits of de-extinction.}, journal = {Current biology : CB}, volume = {32}, number = {7}, pages = {R324-R327}, doi = {10.1016/j.cub.2022.03.023}, pmid = {35413261}, issn = {1879-0445}, mesh = {DNA, Ancient ; *Extinction, Biological ; Genome ; *Genomics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Resurrecting extinct species through de-extinction by genome editing requires full and unbiased information from the extinct species' genome. A new study establishes a framework to assess how much of an extinct species genome can be recovered by ancient DNA sequencing and which factors influence recovery.}, }
@article {pmid35412864, year = {2022}, author = {Andrades Valtueña, A and Neumann, GU and Spyrou, MA and Musralina, L and Aron, F and Beisenov, A and Belinskiy, AB and Bos, KI and Buzhilova, A and Conrad, M and Djansugurova, LB and Dobeš, M and Ernée, M and Fernández-Eraso, J and Frohlich, B and Furmanek, M and Hałuszko, A and Hansen, S and Harney, &#xc9; and Hiss, AN and Hübner, A and Key, FM and Khussainova, E and Kitov, E and Kitova, AO and Knipper, C and Kühnert, D and Lalueza-Fox, C and Littleton, J and Massy, K and Mittnik, A and Mujika-Alustiza, JA and Olalde, I and Papac, L and Penske, S and Peška, J and Pinhasi, R and Reich, D and Reinhold, S and Stahl, R and Stäuble, H and Tukhbatova, RI and Vasilyev, S and Veselovskaya, E and Warinner, C and Stockhammer, PW and Haak, W and Krause, J and Herbig, A}, title = {Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {17}, pages = {e2116722119}, pmid = {35412864}, issn = {1091-6490}, mesh = {Animal Husbandry/history ; Animals ; DNA, Ancient ; Genetic Variation ; *Genome, Bacterial ; History, Ancient ; Human Migration/history ; Humans ; Phylogeny ; *Plague/epidemiology/history/microbiology ; *Yersinia pestis/classification/genetics/isolation &amp; purification ; }, abstract = {The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology.}, }
@article {pmid35402880, year = {2022}, author = {Fischer, CE and Pemonge, MH and Ducoussau, I and Arzelier, A and Rivollat, M and Santos, F and Barrand Emam, H and Bertaud, A and Beylier, A and Ciesielski, E and Dedet, B and Desenne, S and Duday, H and Chenal, F and Gailledrat, E and Goepfert, S and Gorgé, O and Gorgues, A and Kuhnle, G and Lambach, F and Lefort, A and Mauduit, A and Maziere, F and Oudry, S and Paresys, C and Pinard, E and Plouin, S and Richard, I and Roth-Zehner, M and Roure, R and Thevenet, C and Thomas, Y and Rottier, S and Deguilloux, MF and Pruvost, M}, title = {Origin and mobility of Iron Age Gaulish groups in present-day France revealed through archaeogenomics.}, journal = {iScience}, volume = {25}, number = {4}, pages = {104094}, pmid = {35402880}, issn = {2589-0042}, abstract = {The Iron Age period occupies an important place in French history because the Gauls are regularly presented as the direct ancestors of the extant French population. We documented here the genomic diversity of Iron Age communities originating from six French regions. The 49 acquired genomes permitted us to highlight an absence of discontinuity between Bronze Age and Iron Age groups in France, lending support to a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. Genomic analyses revealed strong genetic homogeneity among the regional groups associated with distinct archaeological cultures. This genomic homogenization appears to be linked to individuals' mobility between regions and gene flow with neighbouring groups from England and Spain. Thus, the results globally support a common genomic legacy for the Iron Age population of modern-day France that could be linked to recurrent gene flow between culturally differentiated communities.}, }
@article {pmid35398984, year = {2022}, author = {Suchan, T and Chauvey, L and Poullet, M and Tonasso-Calvière, L and Schiavinato, S and Clavel, P and Clavel, B and Lepetz, S and Seguin-Orlando, A and Orlando, L}, title = {Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA.}, journal = {Molecular ecology resources}, volume = {22}, number = {6}, pages = {2262-2274}, doi = {10.1111/1755-0998.13619}, pmid = {35398984}, issn = {1755-0998}, support = {//University Paul Sabatier IDEX Chaire d'Excellence (OURASI)/ ; //CNRS Programme de Recherche Conjoint (PRC)/ ; //CNRS International Research Project (IRP AMADEUS)/ ; 681605//European Union's Horizon 2020 Research and Innovation Programme/ ; 797449//Marie Sk&#x142;odowska-Curie/ ; //European Research Council (ERC)/ ; }, mesh = {Animals ; *Cytosine ; DNA Damage ; DNA Methylation ; *DNA, Ancient ; Equidae/genetics ; Horses/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER-treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st-17th century CE), including horses, donkeys and their first-generation mule hybrids. We found that USER-treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on-target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey-specific and horse-specific alleles in mule capture sequence data, due to the combined effects of USER-treatment, probe sets and reference bias. Our work demonstrates that while USER-treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.}, }
@article {pmid35389750, year = {2022}, author = {Marciniak, S and Bergey, CM and Silva, AM and Hałuszko, A and Furmanek, M and Veselka, B and Velemínský, P and Vercellotti, G and Wahl, J and Zariņa, G and Longhi, C and Kolář, J and Garrido-Pena, R and Flores-Fernández, R and Herrero-Corral, AM and Simalcsik, A and Müller, W and Sheridan, A and Miliauskienė, &#x17d; and Jankauskas, R and Moiseyev, V and Köhler, K and Király, &#xc1; and Gamarra, B and Cheronet, O and Szeverényi, V and Kiss, V and Szeniczey, T and Kiss, K and Zoffmann, ZK and Koós, J and Hellebrandt, M and Maier, RM and Domboróczki, L and Virag, C and Novak, M and Reich, D and Hajdu, T and von Cramon-Taubadel, N and Pinhasi, R and Perry, GH}, title = {An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {15}, pages = {e2106743119}, pmid = {35389750}, issn = {1091-6490}, support = {R01 GM115656/GM/NIGMS NIH HHS/United States ; }, mesh = {Adult ; *Agriculture/history ; *Body Height/genetics ; Child ; DNA, Ancient ; Europe ; *Farmers/history ; Genetic Variation ; Genomics ; *Health/history ; History, Ancient ; Humans ; Paleopathology ; *Skeleton/anatomy &amp; histology ; }, abstract = {Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.}, }
@article {pmid35383854, year = {2022}, author = {Di, D and Simon Thomas, J and Currat, M and Nunes, JM and Sanchez-Mazas, A}, title = {Challenging Ancient DNA Results About Putative HLA Protection or Susceptibility to Yersinia pestis.}, journal = {Molecular biology and evolution}, volume = {39}, number = {4}, pages = {}, pmid = {35383854}, issn = {1537-1719}, mesh = {DNA ; DNA, Ancient ; Europe ; *Genetic Predisposition to Disease ; *HLA Antigens/genetics ; Histocompatibility Antigens Class II ; Humans ; *Plague/genetics ; Yersinia pestis ; }, abstract = {In a recent article, Immel et al. (Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, et al. 2021. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol. 38:4059-4076) extracted DNA from 36 individuals dead from plague in Ellwangen, Southern Germany, during the 16th century. By comparing their human leukocyte antigen (HLA) genotypes with those of 50 present-day Ellwangen inhabitants, the authors reported a significant decrease of HLA-B*51:01 and HLA-C*06:02 and a significant increase of HLA-DRB1*13:01/13:02 frequencies from ancient to modern populations. After comparing these frequencies with a larger sample of 8,862 modern Germans and performing simulations of natural selection, they concluded that these changes had been driven by natural selection. In an attempt to provide more evidence on such stimulating results, we explored the HLA frequency patterns over all of Europe, we predicted binding affinities of HLA-B/C/DRB1 alleles to 106,515 Yersinia pestis-derived peptides, and we performed forward simulations of HLA genetic profiles under neutrality. Our analyses do not sustain the conclusions of HLA protection or susceptibility to plague based on ancient DNA.}, }
@article {pmid35382600, year = {2022}, author = {Barrett, JH and Khamaiko, N and Ferrari, G and Cuevas, A and Kneale, C and Hufthammer, AK and Pálsdóttir, AH and Star, B}, title = {Walruses on the Dnieper: new evidence for the intercontinental trade of Greenlandic ivory in the Middle Ages.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1972}, pages = {20212773}, pmid = {35382600}, issn = {1471-2954}, mesh = {Animals ; Archaeology ; *DNA, Ancient ; Geography ; Russia ; *Walruses/genetics ; }, abstract = {Mediaeval walrus hunting in Iceland and Greenland-driven by Western European demand for ivory and walrus hide ropes-has been identified as an important pre-modern example of ecological globalization. By contrast, the main origin of walrus ivory destined for eastern European markets, and then onward trade to Asia, is assumed to have been Arctic Russia. Here, we investigate the geographical origin of nine twelfth-century CE walrus specimens discovered in Kyiv, Ukraine-combining archaeological typology (based on chaîne opératoire assessment), ancient DNA (aDNA) and stable isotope analysis. We show that five of seven specimens tested using aDNA can be genetically assigned to a western Greenland origin. Moreover, six of the Kyiv rostra had been sculpted in a way typical of Greenlandic imports to Western Europe, and seven are tentatively consistent with a Greenland origin based on stable isotope analysis. Our results suggest that demand for the products of Norse Greenland's walrus hunt stretched not only to Western Europe but included Ukraine and, by implication given linked trade routes, also Russia, Byzantium and Asia. These observations illuminate the surprising scale of mediaeval ecological globalization and help explain the pressure this process exerted on distant wildlife populations and those who harvested them.}, }
@article {pmid35366416, year = {2022}, author = {Gnecchi-Ruscone, GA and Szécsényi-Nagy, A and Koncz, I and Csiky, G and Rácz, Z and Rohrlach, AB and Brandt, G and Rohland, N and Csáky, V and Cheronet, O and Szeifert, B and Rácz, T&#xc1; and Benedek, A and Bernert, Z and Berta, N and Czifra, S and Dani, J and Farkas, Z and Hága, T and Hajdu, T and Jászberényi, M and Kisjuhász, V and Kolozsi, B and Major, P and Marcsik, A and Kovacsóczy, BN and Balogh, C and Lezsák, GM and Ódor, JG and Szelekovszky, M and Szeniczey, T and Tárnoki, J and Tóth, Z and Tutkovics, EK and Mende, BG and Geary, P and Pohl, W and Vida, T and Pinhasi, R and Reich, D and Hofmanová, Z and Jeong, C and Krause, J}, title = {Ancient genomes reveal origin and rapid trans-Eurasian migration of 7[th] century Avar elites.}, journal = {Cell}, volume = {185}, number = {8}, pages = {1402-1413.e21}, pmid = {35366416}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Asian People/genetics ; *DNA, Ancient ; *Genetics, Population ; Genome ; History, Ancient ; Human Migration/history ; Humans ; Sulfur ; }, abstract = {The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar's empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population.}, }
@article {pmid35359699, year = {2022}, author = {Molodtseva, AS and Makunin, AI and Salomashkina, VV and Kichigin, IG and Vorobieva, NV and Vasiliev, SK and Shunkov, MV and Tishkin, AA and Grushin, SP and Anijalg, P and Tammeleht, E and Keis, M and Boeskorov, GG and Mamaev, N and Okhlopkov, IM and Kryukov, AP and Lyapunova, EA and Kholodova, MV and Seryodkin, IV and Saarma, U and Trifonov, VA and Graphodatsky, AS}, title = {Phylogeography of ancient and modern brown bears from eastern Eurasia.}, journal = {Biological journal of the Linnean Society. Linnean Society of London}, volume = {135}, number = {4}, pages = {722-733}, pmid = {35359699}, issn = {0024-4066}, support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The brown bear (Ursus arctos) is an iconic carnivoran species of the Northern Hemisphere. Its population history has been studied extensively using mitochondrial markers, which demonstrated signatures of multiple waves of migration, arguably connected with glaciation periods. Among Eurasian brown bears, Siberian populations remain understudied. We have sequenced complete mitochondrial genomes of four ancient (~4.5-40 kya) bears from South Siberia and 19 modern bears from South Siberia and the Russian Far East. Reconstruction of phylogenetic relationships between haplotypes and evaluation of modern population structure have demonstrated that all the studied samples belong to the most widespread Eurasian clade 3. One of the ancient haplotypes takes a basal position relative to the whole of clade 3; the second is basal to the haplogroup 3a (the most common subclade), and two others belong to clades 3a1 and 3b. Modern Siberian bears retain at least some of this diversity; apart from the most common haplogroup 3a, we demonstrate the presence of clade 3b, which was previously found mainly in mainland Eurasia and Northern Japan. Our findings highlight the importance of South Siberia as a refugium for northern Eurasian brown bears and further corroborate the hypothesis of several waves of migration in the Pleistocene.}, }
@article {pmid35356467, year = {2022}, author = {Arizmendi Cárdenas, YO and Neuenschwander, S and Malaspinas, AS}, title = {Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e12784}, pmid = {35356467}, issn = {2167-8359}, mesh = {Humans ; *DNA, Viral/genetics ; DNA, Ancient ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; Benchmarking ; High-Throughput Nucleotide Sequencing/methods ; *Viruses/genetics ; }, abstract = {Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.}, }
@article {pmid35356424, year = {2022}, author = {Xiong, J and Du, P and Chen, G and Tao, Y and Zhou, B and Yang, Y and Wang, H and Yu, Y and Chang, X and Allen, E and Sun, C and Zhou, J and Zou, Y and Xu, Y and Meng, H and Tan, J and Li, H and Wen, S}, title = {Sex-Biased Population Admixture Mediated Subsistence Strategy Transition of Heishuiguo People in Han Dynasty Hexi Corridor.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {827277}, pmid = {35356424}, issn = {1664-8021}, abstract = {The Hexi Corridor was an important arena for culture exchange and human migration between ancient China and Central and Western Asia. During the Han Dynasty (202 BCE-220 CE), subsistence strategy along the corridor shifted from pastoralism to a mixed pastoralist-agriculturalist economy. Yet the drivers of this transition remain poorly understood. In this study, we analyze the Y-chromosome and mtDNA of 31 Han Dynasty individuals from the Heishuiguo site, located in the center of the Hexi Corridor. A high-resolution analysis of 485 Y-SNPs and mitogenomes was performed, with the Heishuiguo population classified into Early Han and Late Han groups. It is revealed that (1) when dissecting genetic lineages, the Yellow River Basin origin haplogroups (i.e., Oα-M117, Oβ-F46, Oγ-IMS-JST002611, and O2-P164+, M134-) reached relatively high frequencies for the paternal gene pools, while haplogroups of north East Asian origin (e.g., D4 and D5) dominated on the maternal side; (2) in interpopulation comparison using PCA and Fst heatmap, the Heishuiguo population shifted from Southern-Northern Han cline to Northern-Northwestern Han/Hui cline with time, indicating genetic admixture between Yellow River immigrants and natives. By comparison, in maternal mtDNA views, the Heishuiguo population was closely clustered with certain Mongolic-speaking and Northwestern Han populations and exhibited genetic continuity through the Han Dynasty, which suggests that Heishuiguo females originated from local or neighboring regions. Therefore, a sex-biased admixture pattern is observed in the Heishuiguo population. Additionally, genetic contour maps also reveal the same male-dominated migration from the East to Hexi Corridor during the Han Dynasty. This is also consistent with historical records, especially excavated bamboo slips. Combining historical records, archeological findings, stable isotope analysis, and paleoenvironmental studies, our uniparental genetic investigation on the Heishuiguo population reveals how male-dominated migration accompanied with lifestyle adjustments brought by these eastern groups may be the main factor affecting the subsistence strategy transition along the Han Dynasty Hexi Corridor.}, }
@article {pmid35342764, year = {2022}, author = {Kim, K and Kim, DH and Kim, KY}, title = {Mitochondrial Haplogroup Classification of Ancient DNA Samples Using Haplotracker.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {5344418}, pmid = {35342764}, issn = {2314-6141}, mesh = {*DNA, Ancient ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Humans ; Mitochondria/genetics ; }, abstract = {Mitochondrial DNA haplogroup classification is used to study maternal lineage of ancient human populations. The haplogrouping of ancient DNA is not easy because the DNA is usually found in small pieces in limited quantities. We have developed Haplotracker, a straightforward and efficient high-resolution haplogroup classification tool optimized specifically for ancient DNA samples. Haplotracker offers a user-friendly input interface for multiple mitochondrial DNA sequence fragments in a sample. It provides accurate haplogroup classification with full-length mitochondrial genome sequences and provides high-resolution haplogroup predictions for some fragmented control region sequences using a novel algorithm built on Phylotree mtDNA Build 17 (Phylotree) and our haplotype database (n = 118,869). Its performance for accuracy was demonstrated to be high through haplogroup classification using 8,216 Phylotree full-length and control region mitochondrial DNA sequences compared with HaploGrep 2, one of the most accurate current haplogroup classifiers. Haplotracker provides a novel haplogroup tracking solution for fragmented sequences to track subhaplogroups or verify the haplogroups efficiently. Using Haplotracker, we classified mitochondrial haplogroups to the final subhaplogroup level in nine ancient DNA samples extracted from human skeletal remains found in 2,000-year-old elite Xiongnu cemetery in Northeast Mongolia. Haplotracker can be freely accessed at https://haplotracker.cau.ac.kr.}, }
@article {pmid35336803, year = {2022}, author = {Horsburgh, KA and Beckett, DB and Gosling, AL}, title = {Maternal Relationships among Ancient and Modern Southern African Sheep: Newly Discovered Mitochondrial Haplogroups.}, journal = {Biology}, volume = {11}, number = {3}, pages = {}, pmid = {35336803}, issn = {2079-7737}, support = {N/A//Fry Undergraduate Award, Southern Methodist University/ ; N/A//University of Otago Research Grant/ ; }, abstract = {We investigated the genetic diversity and historic relationships among southern African sheep as well as the relationships between them and sheep outside the continent by sourcing both archaeological and modern sheep samples. Archaeological sheep samples derived from the site Die Kelders 1, near Cape Town, date to approximately 1500 years ago. The modern samples were taken as ear snips from Damara, Namaqua Afrikaner, and Ronderib Afrikaner sheep on a farm in Prieska in the Northern Cape. Illumina sequencing libraries were constructed for both ancient and modern specimens. Ancient specimens were enriched for the mitochondrial genome using an in-solution hybridization protocol and modern specimens were subjected to shotgun sequencing. Sequences were mapped to the Ovis aries reference genome, assigned to haplogroups and subhaplogroups, and used to calculate a phylogenetic tree using previously published, geographically dispersed mitochondrial genome sheep sequences. Genetic diversity statistics show that southern African sheep have lower diversity than sheep in other regions. Phylogenetic analysis reveals that many modern southern African sheep are likely descended from prehistoric indigenous sheep populations and not from sheep imported from Europe during the historic period.}, }
@article {pmid35324275, year = {2022}, author = {Gibbons, A}, title = {Southern roots for the Maya-and the maize that fed them.}, journal = {Science (New York, N.Y.)}, volume = {375}, number = {6587}, pages = {1325}, doi = {10.1126/science.abq1704}, pmid = {35324275}, issn = {1095-9203}, abstract = {Migrants from the south may have helped spread early farming in Central America, ancient DNA suggests.}, }
@article {pmid35318319, year = {2022}, author = {Kennett, DJ and Lipson, M and Prufer, KM and Mora-Marín, D and George, RJ and Rohland, N and Robinson, M and Trask, WR and Edgar, HHJ and Hill, EC and Ray, EE and Lynch, P and Moes, E and O'Donnell, L and Harper, TK and Kate, EJ and Ramos, J and Morris, J and Gutierrez, SM and Ryan, TM and Culleton, BJ and Awe, JJ and Reich, D}, title = {South-to-north migration preceded the advent of intensive farming in the Maya region.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1530}, pmid = {35318319}, issn = {2041-1723}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Agriculture ; Central America ; Colombia ; *DNA, Ancient ; Forests ; Humans ; }, abstract = {The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.}, }
@article {pmid35312358, year = {2022}, author = {Severson, AL and Byrd, BF and Mallott, EK and Owings, AC and DeGiorgio, M and de Flamingh, A and Nijmeh, C and Arellano, MV and Leventhal, A and Rosenberg, NA and Malhi, RS}, title = {Ancient and modern genomics of the Ohlone Indigenous population of California.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {13}, pages = {e2111533119}, pmid = {35312358}, issn = {1091-6490}, support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeology ; DNA, Ancient ; Genetics, Population ; *Genomics ; History, Ancient ; Humans ; *Indigenous Peoples ; Linguistics ; San Francisco ; }, abstract = {SignificanceCalifornia supports a high cultural and linguistic diversity of Indigenous peoples. In a partnership of researchers with the Muwekma Ohlone tribe, we studied genomes of eight present-day tribal members and 12 ancient individuals from two archaeological sites in the San Francisco Bay Area, spanning ∼2,000 y. We find that compared to genomes of Indigenous individuals from throughout the Americas, the 12 ancient individuals are most genetically similar to ancient individuals from Southern California, and that despite spanning a large time period, they share distinctive ancestry. This ancestry is also shared with present-day tribal members, providing evidence of genetic continuity between past and present Indigenous individuals in the region, in contrast to some popular reconstructions based on archaeological and linguistic information.}, }
@article {pmid35307645, year = {2022}, author = {Fu, M and Li, Y}, title = {The origin and domestication history of domestic horses and the domestication characteristics of breeds.}, journal = {Yi chuan = Hereditas}, volume = {44}, number = {3}, pages = {216-229}, doi = {10.16288/j.yczz.21-260}, pmid = {35307645}, issn = {0253-9772}, mesh = {Animals ; Animals, Domestic/genetics ; *Breeding ; DNA, Mitochondrial/genetics ; *Domestication ; *Horses/genetics ; Phylogeny ; }, abstract = {The horse (Equus caballus) was domesticated thousands of years after dog, cattle, pig, sheep, and goat. Importantly, it represents the domestic animal that mostly impacted the development of human civilization. Its excellent loading and moving ability prompted the changes from fixed farming mode into mobile sharing mode. Accordingly, its domestication history deserves considerable attention. So far, many issues have long been controversial, due to the extinction of the closest wild relatives and the dramatic reduction of genetic diversity. With the continuous development of sequencing technology and the utilization of ancient samples, we got more clues to the origin and domestication process. In this review, we summarize 1) current progresses on the domestication history revealed by nuclear genes, mtDNA, Y chromosome, and ancient DNA, 2) the characteristics of population structure and diversification among modern breeds, 3) the genetic basis of important phenotypes, such as coat color, speed, and body size. The overall aim of the review is to provide in-depth insights into the studies of horse domestication, the preservation and utilization of genetic resources, the direction of breeding improvement, and the development of modern horse industry in future.}, }
@article {pmid35306727, year = {2023}, author = {Scarsbrook, L and Verry, AJF and Walton, K and Hitchmough, RA and Rawlence, NJ}, title = {Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus.}, journal = {Molecular ecology}, volume = {32}, number = {11}, pages = {2964-2984}, doi = {10.1111/mec.16434}, pmid = {35306727}, issn = {1365-294X}, mesh = {Animals ; Phylogeography ; Phylogeny ; New Zealand ; DNA, Ancient ; *Genome, Mitochondrial/genetics ; X-Ray Microtomography ; DNA/genetics ; *Lizards/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied this method to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator-free island and mainland sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historical/archival (1898-2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post-extraction micro-computed tomography reconstructions. All "large gecko" specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographical structuring within Hoplodactylus spp. highlighted the impacts of Late Cenozoic biogeographical barriers, including the opening and closure of Pliocene marine straits, fluctuations in the size and suitability of glacial refugia, and eustatic sea-level change. Recent mainland extinction obscured these signals from the modern tissue-derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.}, }
@article {pmid35306671, year = {2022}, author = {Schwörer, C and Leunda, M and Alvarez, N and Gugerli, F and Sperisen, C}, title = {The untapped potential of macrofossils in ancient plant DNA research.}, journal = {The New phytologist}, volume = {235}, number = {2}, pages = {391-401}, pmid = {35306671}, issn = {1469-8137}, mesh = {Animals ; *DNA, Ancient ; DNA, Plant/genetics ; Lakes ; *Permafrost ; Plants/genetics ; }, abstract = {The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.}, }
@article {pmid35294015, year = {2022}, author = {Biddanda, A and Steinrücken, M and Novembre, J}, title = {Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples.}, journal = {Genetics}, volume = {221}, number = {1}, pages = {}, pmid = {35294015}, issn = {1943-2631}, support = {R01 HG007089/HG/NHGRI NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; T32 GM07197/GF/NIH HHS/United States ; }, mesh = {Archaeology/*methods ; Genetics, Population/*methods ; Genotype ; Haplotypes ; Humans ; Linkage Disequilibrium ; Population Density ; }, abstract = {Archeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the nonrandom association of genetic variants at different loci (i.e. linkage disequilibrium). This may be in part because basic properties of linkage disequilibrium in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: (1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; (2) The product of the linkage disequilibrium coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and (3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.}, }
@article {pmid35288946, year = {2022}, author = {Her, C and Rezaei, HR and Hughes, S and Naderi, S and Duffraisse, M and Mashkour, M and Naghash, HR and Bălășescu, A and Luikart, G and Jordan, S and Özüt, D and Kence, A and Bruford, MW and Tresset, A and Vigne, JD and Taberlet, P and Hänni, C and Pompanon, F}, title = {Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros.}, journal = {Animal genetics}, volume = {53}, number = {3}, pages = {452-459}, doi = {10.1111/age.13191}, pmid = {35288946}, issn = {1365-2052}, support = {ANR 05-GANI-004-02//Project Chronobos/ ; }, mesh = {Animals ; Cytochromes b/genetics ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes ; Phylogeny ; Sheep/genetics ; *Sheep, Domestic/genetics ; Turkey ; }, abstract = {We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).}, }
@article {pmid35288565, year = {2022}, author = {Zhou, BF and Yuan, S and Crowl, AA and Liang, YY and Shi, Y and Chen, XY and An, QQ and Kang, M and Manos, PS and Wang, B}, title = {Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1320}, pmid = {35288565}, issn = {2041-1723}, mesh = {Ecosystem ; Forests ; *Genome, Plastid/genetics ; Phylogeny ; *Quercus ; }, abstract = {Northern Hemisphere forests changed drastically in the early Eocene with the diversification of the oak family (Fagaceae). Cooling climates over the next 20 million years fostered the spread of temperate biomes that became increasingly dominated by oaks and their chestnut relatives. Here we use phylogenomic analyses of nuclear and plastid genomes to investigate the timing and pattern of major macroevolutionary events and ancient genome-wide signatures of hybridization across Fagaceae. Innovation related to seed dispersal is implicated in triggering waves of continental radiations beginning with the rapid diversification of major lineages and resulting in unparalleled transformation of forest dynamics within 15 million years following the K-Pg extinction. We detect introgression at multiple time scales, including ancient events predating the origination of genus-level diversity. As oak lineages moved into newly available temperate habitats in the early Miocene, secondary contact between previously isolated species occurred. This resulted in adaptive introgression, which may have further amplified the diversification of white oaks across Eurasia.}, }
@article {pmid35279516, year = {2022}, author = {Lorentz, KO and Kamel, G and Lemmers, SAM and Miyauchi, Y and Çubukçu, E and Alpagut, A and Büyükkarakaya, AM}, title = {Synchrotron Radiation Fourier Transform Infrared (SR-FTIR) spectroscopy in exploring ancient human hair from Roman period Juliopolis: Preservation status and alterations of organic compounds.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {274}, number = {}, pages = {121026}, doi = {10.1016/j.saa.2022.121026}, pmid = {35279516}, issn = {1873-3557}, mesh = {Archaeology/methods ; *Body Remains ; Fourier Analysis ; Hair/chemistry ; Humans ; Organic Chemicals ; Spectroscopy, Fourier Transform Infrared/methods ; *Synchrotrons ; }, abstract = {We explore the preservation status and alterations of organic compounds in Roman period human hairstrandsfrom a specific individual (M196) excavated at Juliopolis (JP). How do these organic compounds present in this c. 2000-year-old human hair compare to those present in modern hair? Alterations to organic compounds in archaeological human hair are caused by biological degradative processes dependent on multifactorial processes acting on the hair since the deposition of a body in a mortuary context. We investigate the type of organic compounds present using Synchrotron Radiation Fourier Transform Infrared (SR-FTIR). Juliopolis (Iuliopolis) is an ancient multiperiod city, located in the Çayırhan district of Nallıhan, northwest of Ankara. The Juliopolis necropolis from which M196 was recovered was in use throughout the Hellenistic, Roman, and Byzantine periods, and yielded over 700 tombs with numerous human remains. One tomb (M196) contained human remains of exceptional preservation status, including substantial amounts of hair. Human hair from archaeological contexts is not only extremely rare, but importantly, has high analytical value, with potential for analysis of diet, geographical origins, ancient DNA, metal exposure, and other aspects of life in a time-resolved manner. These data make significant contributions to the life history of the individual (osteobiography), as well as contribute towards key archaeological questions. As these analyses are in their majority destructive, prior evaluation of the preservation of sufficient amounts of the organic compounds on which many such analyses rely upon is crucial, to avoid unnecessary loss of precious ancient samples. The results of our SR-FTIR analyses at SESAME synchrotron show that keratin in the JP M196 is more degraded in comparison to the modern reference sample. However, the results also point to clear potential for further analyses with techniques relying on organic compound preservation, such as C and N isotopic analyses for diet, and aDNA.}, }
@article {pmid35271794, year = {2022}, author = {Lin, J and Duchêne, D and Carøe, C and Smith, O and Ciucani, MM and Niemann, J and Richmond, D and Greenwood, AD and MacPhee, R and Zhang, G and Gopalakrishnan, S and Gilbert, MTP}, title = {Probing the genomic limits of de-extinction in the Christmas Island rat.}, journal = {Current biology : CB}, volume = {32}, number = {7}, pages = {1650-1656.e3}, pmid = {35271794}, issn = {1879-0445}, mesh = {Animals ; Australia ; Biological Evolution ; Extinction, Biological ; *Genome ; *Genomics ; Norway ; Phylogeny ; Rats ; }, abstract = {Three principal methods are under discussion as possible pathways to "true" de-extinction; i.e., back-breeding, cloning, and genetic engineering.[1,2] Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.[3-5] We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species.}, }
@article {pmid35263821, year = {2022}, author = {Zavala, EI and Aximu-Petri, A and Richter, J and Nickel, B and Vernot, B and Meyer, M}, title = {Quantifying and reducing cross-contamination in single- and multiplex hybridization capture of ancient DNA.}, journal = {Molecular ecology resources}, volume = {22}, number = {6}, pages = {2196-2207}, doi = {10.1111/1755-0998.13607}, pmid = {35263821}, issn = {1755-0998}, support = {//Max-Planck-Gesellschaft/ ; }, mesh = {*DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; *Genomics ; Nucleic Acid Hybridization/methods ; Sequence Analysis, DNA/methods ; }, abstract = {The use of hybridization capture has enabled a massive upscaling in sample sizes for ancient DNA studies, allowing the analysis of hundreds of skeletal remains or sediments in single studies. Nevertheless, demands in throughput continue to grow, and hybridization capture has become a limiting step in sample preparation due to the large consumption of reagents, consumables and time. Here, we explored the possibility of improving the economics of sample preparation via multiplex capture, that is, the hybridization capture of pools of double-indexed ancient DNA libraries. We demonstrate that this strategy is feasible, at least for small genomic targets such as mitochondrial DNA, if the annealing temperature is increased and PCR cycles are limited in post-capture amplification to avoid index swapping by jumping PCR, which manifests as cross-contamination in resulting sequence data. We also show that the reamplification of double-indexed libraries to PCR plateau before or after hybridization capture can sporadically lead to small, but detectable cross-contamination even if libraries are amplified in separate reactions. We provide protocols for both manual capture and automated capture in 384-well format that are compatible with single- and multiplex capture and effectively suppress cross-contamination and artefact formation. Last, we provide a simple computational method for quantifying cross-contamination due to index swapping in double-indexed libraries, which we recommend using for routine quality checks in studies that are sensitive to cross-contamination.}, }
@article {pmid35256608, year = {2022}, author = {Vågene, &#xc5;J and Honap, TP and Harkins, KM and Rosenberg, MS and Giffin, K and Cárdenas-Arroyo, F and Leguizamón, LP and Arnett, J and Buikstra, JE and Herbig, A and Krause, J and Stone, AC and Bos, KI}, title = {Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {1195}, pmid = {35256608}, issn = {2041-1723}, mesh = {Animals ; *Caniformia/genetics ; DNA, Ancient ; Humans ; *Mycobacterium/genetics ; *Mycobacterium tuberculosis/genetics ; Racial Groups ; South America/epidemiology ; *Tuberculosis/epidemiology/microbiology ; }, abstract = {Previous ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal access to marine resources- a scenario incompatible with TB transmission directly from infected pinnipeds or their tissues. In this study, we investigate the causative agent of TB in ten pre-colonial, non-coastal individuals from South America. We reconstruct M. pinnipedii genomes (10- to 15-fold mean coverage) from three contemporaneous individuals from inland Peru and Colombia, demonstrating the widespread dissemination of M. pinnipedii beyond the coast, either through human-to-human and/or animal-mediated routes. Overall, our study suggests that TB transmission in the pre-colonial era Americas involved a more complex transmission pathway than simple pinniped-to-human transfer.}, }
@article {pmid35240033, year = {2022}, author = {Hong, JH and Oh, CS and Kim, S and Kang, IU and Shin, DH}, title = {Genetic analysis of mitochondrial DNA from ancient Equus caballus bones found at archaeological site of Joseon dynasty period capital area.}, journal = {Animal bioscience}, volume = {35}, number = {8}, pages = {1141-1150}, pmid = {35240033}, issn = {2765-0189}, support = {//Ministry of Education/ ; 2019S1A5C2A01083578//National Research Foundation of Korea/ ; 2020R1I1A1A01073501//National Research Foundation of Korea/ ; }, abstract = {OBJECTIVE: To understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea.<br><br>METHODS: We extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by polymerase chain reaction. Cloning and sequencing were conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software.<br><br>RESULTS: By means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia.<br><br>CONCLUSION: The horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseonperiod horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.}, }
@article {pmid35238427, year = {2022}, author = {Nores, R and Tavella, MP and Fabra, M and Demarchi, DA}, title = {Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre-Hispanic populations from Central Argentina.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {34}, number = {7}, pages = {e23733}, doi = {10.1002/ajhb.23733}, pmid = {35238427}, issn = {1520-6300}, mesh = {Argentina ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Humans ; *Indians, South American/genetics ; }, abstract = {OBJECTIVES: The study of the ancient populations of Central Argentina has a crucial importance for our understanding of the evolutionary processes in the Southern Cone of South America, given its geographic position as a crossroads. Therefore, the aim of this study is to evaluate the temporal and geographical patterns of genetic variation among the groups that inhabited the current territory of Córdoba Province during the Middle and Late Holocene.<br><br>METHODS: We analyzed the mitochondrial haplogroups of 74 individuals and 46 Hypervariable Region I (HVR-I) sequences, both novel and previously reported, from archeological populations of the eastern Plains and western Sierras regions of the province of C&#xf3;rdoba. The HVR-I sequences were also compared with other ancient groups from Argentina and with present-day populations from Central Argentina by pairwise distance analysis and identification of shared haplotypes.<br><br>RESULTS: Significant differences in haplogroup and haplotype distributions between the two geographical regions were found. Sierras showed genetic affinities with certain ancient populations of Northwestern Argentina, while Plains resembled its neighbors from Santiago del Estero Province and the Pampas region. We did not observe genetic differences among the pre 1200 and post 1200 yBP temporal subsets of individuals defined by the emergence of horticulture, considering both geographical samples jointly.<br><br>CONCLUSIONS: The observed patterns of geographical heterogeneity could indicate the existence of biologically distinct populations inhabiting the mountainous region and the eastern plains of C&#xf3;rdoba Province in pre-Hispanic times. Maternal lineages analyses support a scenario of local evolution with great temporal depth in Central Argentina, with continuity until the present.}, }
@article {pmid37332506, year = {2022}, author = {Fagernäs, Z and Salazar-García, DC and Haber Uriarte, M and Avilés Fernández, A and Henry, AG and Lomba Maurandi, J and Ozga, AT and Velsko, IM and Warinner, C}, title = {Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation.}, journal = {FEMS microbes}, volume = {3}, number = {}, pages = {xtac006}, pmid = {37332506}, issn = {2633-6685}, abstract = {The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.}, }
@article {pmid35210171, year = {2022}, author = {Jäger, HY and Maixner, F and Pap, I and Szikossy, I and Pálfi, G and Zink, AR}, title = {Metagenomic analysis reveals mixed Mycobacterium tuberculosis infection in a 18th century Hungarian midwife.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {137}, number = {}, pages = {102181}, doi = {10.1016/j.tube.2022.102181}, pmid = {35210171}, issn = {1873-281X}, mesh = {Female ; Humans ; *Coinfection/microbiology ; DNA, Bacterial/genetics/analysis ; Hungary ; *Midwifery ; *Mycobacterium tuberculosis/genetics ; Phylogeny ; *Tuberculosis/diagnosis/history ; History, 18th Century ; Metagenome ; }, abstract = {The Vác Mummy Collection comprises 265 well documented mummified individuals from the late 16th to the early 18th century that were discovered in 1994 inside a crypt in Vác, Hungary. This collection offers a unique opportunity to study the relationship between humans and pathogens in the pre-antibiotic era, as previous studies have shown a high proportion of tuberculosis (TB) infections among the individuals. In this study, we recovered ancient DNA with shotgun sequencing from a rib bone sample of a 18th century midwife. This individual is part of the collection and shows clear skeletal changes that are associated with tuberculosis and syphilis. To provide molecular proof, we applied a metagenomic approach to screen for ancient pathogen DNA. While we were unsuccessful to recover any ancient Treponema pallidum DNA, we retrieved high coverage ancient TB DNA and identified a mixed infection with two distinct TB strains by detailed single-nucleotide polymorphism and phylogenetic analysis. Thereby, we have obtained comprehensive results demonstrating the long-time prevalence of mixed infections with the sublineages L4.1.2.1/Haarlem and L4.10/PGG3 within the local community in preindustrial Hungary and put them in context of sociohistorical factors.}, }
@article {pmid35208912, year = {2022}, author = {Reynoso-García, J and Narganes-Storde, Y and Santiago-Rodriguez, TM and Toranzos, GA}, title = {Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208912}, issn = {2076-2607}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; 5R25GM061151-20/NH/NIH HHS/United States ; }, abstract = {Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found in Mexico and Ötzi, the Iceman's large intestine. Stool mycobiome samples from extant populations in Peru and urban cultures from the United States were also included. The ancient Puerto Rican cultures exhibited a lower fungal diversity in comparison to the extant populations. Dissimilarity distances showed that the Huecoid gut mycobiome resembled that from ancient Mexico. Fungal genera including Aspergillus spp., Penicillium spp., Rasamsonia spp., Byssochlamys spp., Talaromyces spp., Blastomyces spp., Monascus spp., and Penicilliopsis spp. were differentially abundant in the ancient and extant populations. Despite cultural differences, certain fungal taxa were present in all samples. These results suggest that culture and diet may impact the gut mycobiome and emphasize that modern lifestyles could be associated with the alteration of gut mycobiome diversity. The present study presents data on ancient and extant human gut mycobiomes in terms of lifestyle, ethnicity, and diet in the Americas.}, }
@article {pmid35205247, year = {2022}, author = {Loreille, O and Tillmar, A and Brandhagen, MD and Otterstatter, L and Irwin, JA}, title = {Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family.}, journal = {Genes}, volume = {13}, number = {2}, pages = {}, pmid = {35205247}, issn = {2073-4425}, mesh = {DNA, Mitochondrial/analysis/genetics ; Famous Persons ; Female ; *Genome, Mitochondrial ; Hair/chemistry ; Heteroplasmy ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Polymorphism, Single Nucleotide ; Russia ; }, abstract = {This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome sequences of Tsar Nicholas II and his wife, Tsarina Alexandra, made these samples ideal to assess this DNA extraction protocol and evaluate the types of genetic information that can be recovered by sequencing ultrashort fragments. Using this method, the mtGenome of the Tsarina's lineage was identified in hairs that were concealed in a pendant made by Karl Fabergé for Alexandra Feodorovna Romanov. In addition, to determine if the lock originated from more than one individual, two hairs from the locket were extracted independently and converted into Illumina libraries for shotgun sequencing on a NextSeq 500 platform. From these data, autosomal SNPs were analyzed to assess relatedness. The results indicated that the two hairs came from a single individual. Genetic testing of hairs that were found in the second artifact, a framed photograph of Louise of Hesse-Kassel, Queen of Denmark and maternal grandmother of Tsar Nicholas II, revealed that the hair belonged to a woman who shared Tsar Nicholas' maternal lineage, including the well-known point heteroplasmy at position 16169.}, }
@article {pmid35205223, year = {2022}, author = {Niiranen, L and Leciej, D and Edlund, H and Bernhardsson, C and Fraser, M and Quinto, FS and Herzig, KH and Jakobsson, M and Walkowiak, J and Thalmann, O}, title = {Epigenomic Modifications in Modern and Ancient Genomes.}, journal = {Genes}, volume = {13}, number = {2}, pages = {}, pmid = {35205223}, issn = {2073-4425}, mesh = {Animals ; DNA Methylation/genetics ; *DNA, Ancient ; Epigenesis, Genetic/genetics ; *Epigenomics ; Genome/genetics ; }, abstract = {Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.}, }
@article {pmid35197631, year = {2022}, author = {Lipson, M and Sawchuk, EA and Thompson, JC and Oppenheimer, J and Tryon, CA and Ranhorn, KL and de Luna, KM and Sirak, KA and Olalde, I and Ambrose, SH and Arthur, JW and Arthur, KJW and Ayodo, G and Bertacchi, A and Cerezo-Román, JI and Culleton, BJ and Curtis, MC and Davis, J and Gidna, AO and Hanson, A and Kaliba, P and Katongo, M and Kwekason, A and Laird, MF and Lewis, J and Mabulla, AZP and Mapemba, F and Morris, A and Mudenda, G and Mwafulirwa, R and Mwangomba, D and Ndiema, E and Ogola, C and Schilt, F and Willoughby, PR and Wright, DK and Zipkin, A and Pinhasi, R and Kennett, DJ and Manthi, FK and Rohland, N and Patterson, N and Reich, D and Prendergast, ME}, title = {Ancient DNA and deep population structure in sub-Saharan African foragers.}, journal = {Nature}, volume = {603}, number = {7900}, pages = {290-296}, pmid = {35197631}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Africa South of the Sahara ; Archaeology ; *Black People/genetics/history ; *DNA, Ancient/analysis ; Gene Flow/genetics ; *Genetics, Population ; Genome, Human/genetics ; History, Ancient ; Humans ; }, abstract = {Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa[1-4]. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations[3,5]. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.}, }
@article {pmid35197586, year = {2022}, author = {}, title = {Ancient DNA illuminates how humans travelled and interacted in Stone Age Africa.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {35197586}, issn = {1476-4687}, }
@article {pmid35183376, year = {2022}, author = {Cuenca-Cambronero, M and Courtney-Mustaphi, CJ and Greenway, R and Heiri, O and Hudson, CM and King, L and Lemmen, KD and Moosmann, M and Muschick, M and Ngoepe, N and Seehausen, O and Matthews, B}, title = {An integrative paleolimnological approach for studying evolutionary processes.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {6}, pages = {488-496}, doi = {10.1016/j.tree.2022.01.007}, pmid = {35183376}, issn = {1872-8383}, mesh = {*Biological Evolution ; *Ecosystem ; }, abstract = {The field of paleolimnology has made tremendous progress in reconstructing past biotic and abiotic environmental conditions of aquatic ecosystems based on sediment records. This, together with the rapid development of molecular technologies, provides new opportunities for studying evolutionary processes affecting lacustrine communities over multicentennial to millennial timescales. From an evolutionary perspective, such analyses provide important insights into the chronology of past environmental conditions, the dynamics of phenotypic evolution, and species diversification. Here, we review recent advances in paleolimnological, paleogenetic, and molecular approaches and highlight how their integrative use can help us better understand the ecological and evolutionary responses of species and communities to environmental change.}, }
@article {pmid35178874, year = {2022}, author = {Jiménez-Mena, B and Flávio, H and Henriques, R and Manuzzi, A and Ramos, M and Meldrup, D and Edson, J and Pálsson, S and Ásta Ólafsdóttir, G and Ovenden, JR and Nielsen, EE}, title = {Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits.}, journal = {Molecular ecology resources}, volume = {22}, number = {5}, pages = {2105-2119}, pmid = {35178874}, issn = {1755-0998}, support = {"CODSTORY"//The Icelandic Research Fund/ ; "SDPAS//Innovationsfonden: Udvikling af den danske laksebestand - st&#xf8;rre populationer, genetiske ressourcer og rekreativt fiskeri"/ ; 6108-00583//The Danish Council for Independent Research Grant DFF/ ; DP170102043//Australian Research Grant/ ; }, mesh = {Animals ; DNA/genetics ; Genetics, Population ; Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Fishes ; }, abstract = {Targeted sequencing is an increasingly popular next-generation sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits.}, }
@article {pmid35176104, year = {2022}, author = {Rauf, S and Austin, JJ and Higgins, D and Khan, MR}, title = {Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel.}, journal = {PloS one}, volume = {17}, number = {2}, pages = {e0264125}, pmid = {35176104}, issn = {1932-6203}, mesh = {Chromosomes, Human, Y/*genetics ; DNA Fingerprinting/*methods ; Ethnicity/*genetics ; Female ; *Forensic Genetics ; Geography ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Pakistan ; *Phenotype ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; *Sex Determination Processes ; }, abstract = {Massively parallel sequencing following hybridisation enrichment provides new opportunities to obtain genetic data for various types of forensic testing and has proven successful on modern as well as degraded and ancient DNA. A customisable forensic intelligence panel that targeted 124 SNP markers (67 ancestry informative markers, 23 phenotype markers from the HIrisplex panel, and 35 Y-chromosome SNPs) was used to examine biogeographic ancestry, phenotype and sex and Y-lineage in samples from different ethnic populations of Pakistan including Pothwari, Gilgit, Baloach, Pathan, Kashmiri and Siraiki. Targeted sequencing and computational data analysis pipeline allowed filtering of variants across the targeted loci. Study samples showed an admixture between East Asian and European ancestry. Eye colour was predicted accurately based on the highest p-value giving overall prediction accuracy of 92.8%. Predictions were consistent with reported hair colour for all samples, using the combined highest p-value approach and step-wise model incorporating probability thresholds for light or dark shade. Y-SNPs were successfully recovered only from male samples which indicates the ability of this method to identify biological sex and allow inference of Y-haplogroup. Our results demonstrate practicality of using hybridisation enrichment and MPS to aid in human intelligence gathering and will open many insights into forensic research in South Asia.}, }
@article {pmid35171192, year = {2022}, author = {Antkowiak, PL and Koch, J and Rzepka, P and Nguyen, BH and Strauss, K and Stark, WJ and Grass, RN}, title = {Anhydrous calcium phosphate crystals stabilize DNA for dry storage.}, journal = {Chemical communications (Cambridge, England)}, volume = {58}, number = {19}, pages = {3174-3177}, doi = {10.1039/d2cc00414c}, pmid = {35171192}, issn = {1364-548X}, mesh = {Biocompatible Materials/*chemistry ; Calcium Phosphates/*chemistry ; DNA/*chemistry ; Materials Testing ; }, abstract = {The resilience of ancient DNA (aDNA) in bone gives rise to the preservation of synthetic DNA with bioinorganic materials such as calcium phosphate (CaP). Accelerated aging experiments at elevated temperature and humidity displayed a positive effect of co-precipitated, crystalline dicalcium phosphate on the stability of synthetic DNA in contrast to amorphous CaP. Quantitative PXRD in combination with SEM and EDX measurements revealed distinct CaP phase transformations of calcium phosphate dihydrate (brushite) to anhydrous dicalcium phosphate (monetite) influencing DNA stability.}, }
@article {pmid35167699, year = {2022}, author = {Oh, CS and Seo, M and Lee, HJ and Kim, MJ and Lim, DS and Shin, DH}, title = {GENETIC ANALYSIS OF ANCIENT CLONORCHIS SINENSIS EGGS ATTAINED FROM GORYEONG MUMMY OF JOSEON DYNASTY PERIOD.}, journal = {The Journal of parasitology}, volume = {108}, number = {1}, pages = {70-78}, doi = {10.1645/21-49}, pmid = {35167699}, issn = {1937-2345}, mesh = {Animals ; Clonorchiasis/*history/parasitology ; Clonorchis sinensis/classification/*genetics ; DNA, Helminth/chemistry/genetics ; History, Ancient ; Mummies/*parasitology ; Ovum ; Phylogeny ; Republic of Korea ; }, abstract = {Although Clonorchis sinensis is a parasite that still infects many people in East Asia, its genetics remain largely unknown. We conducted ancient DNA analysis of C. sinensis eggs obtained from a Joseon period mummy newly discovered in South Korea. Clonorchis sinensis DNA was amplified for internal transcribed spacer 1, cytochrome c oxidase subunit 1, and NADH dehydrogenase subunit 2 and 5 genes. The results of BLAST/NCBI showed that the consensus sequences were 98.24 to 100% identical to the modern and ancient C. sinensis sequences reported from Korea, China, Japan, and other Asian countries. Our report helps to fill in the genetic profile of ancient C. sinensis strains that infected East Asian people hundreds of years ago.}, }
@article {pmid35145268, year = {2022}, author = {Izdebski, A and Guzowski, P and Poniat, R and Masci, L and Palli, J and Vignola, C and Bauch, M and Cocozza, C and Fernandes, R and Ljungqvist, FC and Newfield, T and Seim, A and Abel-Schaad, D and Alba-Sánchez, F and Björkman, L and Brauer, A and Brown, A and Czerwiński, S and Ejarque, A and Fiłoc, M and Florenzano, A and Fredh, ED and Fyfe, R and Jasiunas, N and Kołaczek, P and Kouli, K and Kozáková, R and Kupryjanowicz, M and Lagerås, P and Lamentowicz, M and Lindbladh, M and López-Sáez, JA and Luelmo-Lautenschlaeger, R and Marcisz, K and Mazier, F and Mensing, S and Mercuri, AM and Milecka, K and Miras, Y and Noryśkiewicz, AM and Novenko, E and Obremska, M and Panajiotidis, S and Papadopoulou, ML and Pędziszewska, A and Pérez-Díaz, S and Piovesan, G and Pluskowski, A and Pokorny, P and Poska, A and Reitalu, T and Rösch, M and Sadori, L and Sá Ferreira, C and Sebag, D and Słowiński, M and Stančikaitė, M and Stivrins, N and Tunno, I and Veski, S and Wacnik, A and Masi, A}, title = {Palaeoecological data indicates land-use changes across Europe linked to spatial heterogeneity in mortality during the Black Death pandemic.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {3}, pages = {297-306}, pmid = {35145268}, issn = {2397-334X}, mesh = {Animals ; DNA, Ancient ; Europe/epidemiology ; Humans ; Pandemics/history ; *Plague/epidemiology/history/microbiology ; *Yersinia pestis/genetics ; }, abstract = {The Black Death (1347-1352 CE) is the most renowned pandemic in human history, believed by many to have killed half of Europe's population. However, despite advances in ancient DNA research that conclusively identified the pandemic's causative agent (bacterium Yersinia pestis), our knowledge of the Black Death remains limited, based primarily on qualitative remarks in medieval written sources available for some areas of Western Europe. Here, we remedy this situation by applying a pioneering new approach, 'big data palaeoecology', which, starting from palynological data, evaluates the scale of the Black Death's mortality on a regional scale across Europe. We collected pollen data on landscape change from 261 radiocarbon-dated coring sites (lakes and wetlands) located across 19 modern-day European countries. We used two independent methods of analysis to evaluate whether the changes we see in the landscape at the time of the Black Death agree with the hypothesis that a large portion of the population, upwards of half, died within a few years in the 21 historical regions we studied. While we can confirm that the Black Death had a devastating impact in some regions, we found that it had negligible or no impact in others. These inter-regional differences in the Black Death's mortality across Europe demonstrate the significance of cultural, ecological, economic, societal and climatic factors that mediated the dissemination and impact of the disease. The complex interplay of these factors, along with the historical ecology of plague, should be a focus of future research on historical pandemics.}, }
@article {pmid35131896, year = {2022}, author = {Dulias, K and Foody, MGB and Justeau, P and Silva, M and Martiniano, R and Oteo-García, G and Fichera, A and Rodrigues, S and Gandini, F and Meynert, A and Donnelly, K and Aitman, TJ and ,  and Chamberlain, A and Lelong, O and Kozikowski, G and Powlesland, D and Waddington, C and Mattiangeli, V and Bradley, DG and Bryk, J and Soares, P and Wilson, JF and Wilson, G and Moore, H and Pala, M and Edwards, CJ and Richards, MB}, title = {Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {8}, pages = {}, pmid = {35131896}, issn = {1091-6490}, support = {MC_PC_15080/MRC_/Medical Research Council/United Kingdom ; G0901467/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; G0802729/MRC_/Medical Research Council/United Kingdom ; G0400116/MRC_/Medical Research Council/United Kingdom ; 205072/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; England ; Europe ; Female ; Fossils ; Gene Pool ; Genome, Human/genetics ; Genomics ; Haplotypes ; History, Ancient ; History, Medieval ; Human Migration/*history ; Humans ; Ireland ; Male ; Paternal Inheritance/*genetics ; Scotland ; }, abstract = {Orkney was a major cultural center during the Neolithic, 3800 to 2500 BC. Farming flourished, permanent stone settlements and chambered tombs were constructed, and long-range contacts were sustained. From ∼3200 BC, the number, density, and extravagance of settlements increased, and new ceremonial monuments and ceramic styles, possibly originating in Orkney, spread across Britain and Ireland. By ∼2800 BC, this phenomenon was waning, although Neolithic traditions persisted to at least 2500 BC. Unlike elsewhere in Britain, there is little material evidence to suggest a Beaker presence, suggesting that Orkney may have developed along an insular trajectory during the second millennium BC. We tested this by comparing new genomic evidence from 22 Bronze Age and 3 Iron Age burials in northwest Orkney with Neolithic burials from across the archipelago. We identified signals of inward migration on a scale unsuspected from the archaeological record: As elsewhere in Bronze Age Britain, much of the population displayed significant genome-wide ancestry deriving ultimately from the Pontic-Caspian Steppe. However, uniquely in northern and central Europe, most of the male lineages were inherited from the local Neolithic. This suggests that some male descendants of Neolithic Orkney may have remained distinct well into the Bronze Age, although there are signs that this had dwindled by the Iron Age. Furthermore, although the majority of mitochondrial DNA lineages evidently arrived afresh with the Bronze Age, we also find evidence for continuity in the female line of descent from Mesolithic Britain into the Bronze Age and even to the present day.}, }
@article {pmid35119923, year = {2022}, author = {Le Duc, D and Velluva, A and Cassatt-Johnstone, M and Olsen, RA and Baleka, S and Lin, CC and Lemke, JR and Southon, JR and Burdin, A and Wang, MS and Grunewald, S and Rosendahl, W and Joger, U and Rutschmann, S and Hildebrandt, TB and Fritsch, G and Estes, JA and Kelso, J and Dalén, L and Hofreiter, M and Shapiro, B and Schöneberg, T}, title = {Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.}, journal = {Science advances}, volume = {8}, number = {5}, pages = {eabl6496}, pmid = {35119923}, issn = {2375-2548}, mesh = {Animals ; Cattle ; *Dugong ; Female ; Mammals ; Mice ; Phenotype ; }, abstract = {Steller's sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller's descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller's sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold aquatic (or marine) environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse models cause ichthyosis, a skin disease characterized by a thick, hyperkeratotic epidermis that recapitulates Steller's sea cows' reportedly bark-like skin. We also found that Steller's sea cows' abundance was continuously declining for tens of thousands of years before their description, implying that environmental changes also contributed to their extinction.}, }
@article {pmid35119154, year = {2022}, author = {Kearns, AM and Campana, MG and Slikas, B and Berry, L and Saitoh, T and Cibois, A and Fleischer, RC}, title = {Conservation genomics and systematics of a near-extinct island radiation.}, journal = {Molecular ecology}, volume = {31}, number = {7}, pages = {1995-2012}, doi = {10.1111/mec.16382}, pmid = {35119154}, issn = {1365-294X}, mesh = {Animals ; Conservation of Natural Resources ; *DNA, Mitochondrial/genetics ; Endangered Species ; Genetic Variation/genetics ; *Genomics ; Geography ; Inbreeding ; Phylogeny ; }, abstract = {Conservation benefits from incorporating genomics to explore the impacts of population declines, inbreeding, loss of genetic variation and hybridization. Here we use the near-extinct Mariana Islands reedwarbler radiation to showcase how ancient DNA approaches can allow insights into the population dynamics of extinct species and threatened populations for which historical museum specimens or material with low DNA yield (e.g., scats, feathers) are the only sources for DNA. Despite their having paraphyletic mitochondrial DNA (mtDNA), nuclear single nucleotide polymorphisms (SNPs) support the distinctiveness of critically endangered Acrocephalus hiwae and the other three species in the radiation that went extinct between the 1960s and 1990s. Two extinct species, A. yamashinae and A. luscinius, were deeply divergent from each other and from a third less differentiated lineage containing A. hiwae and extinct A. nijoi. Both mtDNA and SNPs suggest that the two isolated populations of A. hiwae from Saipan and Alamagan Islands are sufficiently distinct to warrant subspecies recognition and separate conservation management. We detected no significant differences in genetic diversity or inbreeding between Saipan and Alamagan, nor strong signatures of geographical structuring within either island. However, the implications of possible signatures of inbreeding in both Saipan and Alamagan, and long-term population declines in A. hiwae that pre-date modern anthropogenic threats require further study with denser population sampling. Our study highlights the value that conservation genomics studies of island radiations have as windows onto the possible future for the world's biota as climate change and habitat destruction increasingly fragment their ranges and contribute to rapid declines in population abundances.}, }
@article {pmid35109894, year = {2022}, author = {Guellil, M and Keller, M and Dittmar, JM and Inskip, SA and Cessford, C and Solnik, A and Kivisild, T and Metspalu, M and Robb, JE and Scheib, CL}, title = {An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {22}, pmid = {35109894}, issn = {1474-760X}, support = {/WT_/Wellcome Trust/United Kingdom ; 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Child ; *Haemophilus Vaccines ; Haemophilus influenzae/genetics ; Humans ; Infant ; Phylogeny ; *Plague ; Serogroup ; }, abstract = {BACKGROUND: The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen's evolutionary history, and no genomes dating prior to 1940 were available.<br><br>RESULTS: We describe a Hib genome isolated from a 6-year-old Anglo-Saxon plague victim, from approximately 540 to 550&#x2009;CE, Edix Hill, England, showing signs of invasive infection on its skeleton. We find that the genome clusters in phylogenetic division II with Hib strain NCTC8468, which also caused invasive disease. While the virulence profile of our genome was distinct, its genomic similarity to NCTC8468 points to mostly clonal evolution of the clade since the 6th century. We also reconstruct a partial Yersinia pestis genome, which is likely identical to a published first plague pandemic genome of Edix Hill.<br><br>CONCLUSIONS: Our study presents the earliest genomic evidence for H. influenzae, points to the potential presence of larger genomic diversity in the phylogenetic division II serotype b clade in the past, and allows the first insights into the evolutionary history of this major human pathogen. The identification of both plague and Hib opens questions on the effect of plague in immunocompromised individuals already affected by infectious diseases.}, }
@article {pmid35098251, year = {2021}, author = {Westbury, MV and Barnett, R and Sandoval-Velasco, M and Gower, G and Vieira, FG and de Manuel, M and Hansen, AJ and Yamaguchi, N and Werdelin, L and Marques-Bonet, T and Gilbert, MTP and Lorenzen, ED}, title = {A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives.}, journal = {Open research Europe}, volume = {1}, number = {}, pages = {25}, pmid = {35098251}, issn = {2732-5121}, abstract = {Background: The evolutionary relationships of Felidae during their Early-Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths. Methods: Here, we sequenced a draft nuclear genome of Smilodon populator, dated to 13,182 ± 90 cal BP, making this the oldest palaeogenome from South America to date, a region known to be problematic for ancient DNA preservation. We analysed this genome, together with genomes from other extinct and extant cats to investigate their phylogenetic relationships. Results: We confirm a deep divergence (~20.65 Ma) within sabre-toothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae. Conclusions: Given that some species traditionally assigned to Pseudaelurus originated in the Early Miocene ~20 Ma, this indicates that some species of Pseudaelurus may be younger than the lineages they purportedly gave rise to, further supporting the hypothesis that Pseudaelurus was paraphyletic.}, }
@article {pmid35090588, year = {2022}, author = {Plassais, J and vonHoldt, BM and Parker, HG and Carmagnini, A and Dubos, N and Papa, I and Bevant, K and Derrien, T and Hennelly, LM and Whitaker, DT and Harris, AC and Hogan, AN and Huson, HJ and Zaibert, VF and Linderholm, A and Haile, J and Fest, T and Habib, B and Sacks, BN and Benecke, N and Outram, AK and Sablin, MV and Germonpré, M and Larson, G and Frantz, L and Ostrander, EA}, title = {Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids.}, journal = {Current biology : CB}, volume = {32}, number = {4}, pages = {889-897.e9}, pmid = {35090588}, issn = {1879-0445}, support = {/WT_/Wellcome Trust/United Kingdom ; Z99 HG999999/ImNIH/Intramural NIH HHS/United States ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Animals ; Body Size/genetics ; Breeding ; *Canidae/genetics ; Humans ; *Wolves/genetics ; }, abstract = {Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.[1] Although dogs of variable size are found in the archeological record,[2-4] the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.[5] Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFβ signaling, and skeletal formation.[6-10] Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.[8] The identification of a functional mutation associated with IGF1 has thus far proven elusive.[6][,][10][,][11] Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.}, }
@article {pmid35084493, year = {2022}, author = {Martiniano, R and De Sanctis, B and Hallast, P and Durbin, R}, title = {Placing Ancient DNA Sequences into Reference Phylogenies.}, journal = {Molecular biology and evolution}, volume = {39}, number = {2}, pages = {}, pmid = {35084493}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; WT207492/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Base Sequence ; *Chromosomes, Human, Y ; *DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Haplotypes ; Humans ; Likelihood Functions ; Male ; *Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.}, }
@article {pmid35060661, year = {2022}, author = {Nieves-Colón, MA}, title = {Anthropological genetic insights on Caribbean population history.}, journal = {Evolutionary anthropology}, volume = {31}, number = {3}, pages = {118-137}, doi = {10.1002/evan.21935}, pmid = {35060661}, issn = {1520-6505}, mesh = {Anthropology ; Caribbean Region ; *DNA, Mitochondrial/genetics ; Genetic Variation ; *Genetics, Population ; Humans ; West Indies ; }, abstract = {As the last American region settled by humans, yet the first to experience European colonization, the Caribbean islands have a complex history characterized by continuous migration, admixture, and demographic change. In the last 20 years, genetics research has transformed our understanding of Caribbean population history and revisited major debates in Caribbean anthropology, such as those surrounding the first peopling of the Antilles and the relationship between ancient Indigenous communities and present-day islanders. Genetics studies have also contributed novel perspectives for understanding pivotal events in Caribbean post-contact history such as European colonization, the Atlantic Slave Trade, and the Asian Indenture system. Here, I discuss the last 20 years of Caribbean genetics research and emphasize the importance of integrating genetics with interdisciplinary historic, archaeological, and anthropological approaches. Such interdisciplinary research is essential for investigating the dynamic history of the Caribbean and characterizing its impact on the biocultural diversity of present-day Caribbean peoples.}, }
@article {pmid35058955, year = {2021}, author = {Yu, N and Sun, H and Yang, J and Li, R}, title = {The Diesel Tree Sindora glabra Genome Provides Insights Into the Evolution of Oleoresin Biosynthesis.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {794830}, pmid = {35058955}, issn = {1664-462X}, abstract = {Sindora glabra is an economically important tree that produces abundant oleoresin in the trunk. Here, we present a high-quality chromosome-scale assembly of S. glabra genome by combining Illumina HiSeq, Pacific Biosciences sequencing, and Hi-C technologies. The size of S. glabra genome was 1.11 Gb, with a contig N50 of 1.27 Mb and 31,944 predicted genes. This is the first sequenced genome of the subfamily Caesalpinioideae. As a sister taxon to Papilionoideae, S. glabra underwent an ancient genome triplication shared by core eudicots and further whole-genome duplication shared by early-legume in the last 73.3 million years. S. glabra harbors specific genes and expanded genes largely involved in stress responses and biosynthesis of secondary metabolites. Moreover, 59 terpene backbone biosynthesis genes and 64 terpene synthase genes were identified, which together with co-expressed transcription factors could contribute to the diversity and specificity of terpene compounds and high terpene content in S. glabra stem. In addition, 63 disease resistance NBS-LRR genes were found to be unique in S. glabra genome and their expression levels were correlated with the accumulation of terpene profiles, suggesting potential defense function of terpenes in S. glabra. These together provide new resources for understanding genome evolution and oleoresin production.}, }
@article {pmid35052476, year = {2022}, author = {De Angelis, F and Romboni, M and Veltre, V and Catalano, P and Martínez-Labarga, C and Gazzaniga, V and Rickards, O}, title = {First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First-Third Centuries AD).}, journal = {Genes}, volume = {13}, number = {1}, pages = {}, pmid = {35052476}, issn = {2073-4425}, mesh = {Adolescent ; Bacteria/*classification/genetics/isolation &amp; purification ; Bone and Bones/*metabolism/*microbiology ; Child ; Child, Preschool ; DNA, Ancient/*analysis/isolation &amp; purification ; Female ; Genome, Human ; Genomics/*methods ; Humans ; Infant ; Male ; Paleopathology ; Rome ; Whole Genome Sequencing ; }, abstract = {This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first-third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops.}, }
@article {pmid35052469, year = {2022}, author = {Zavala, EI and Thomas, JT and Sturk-Andreaggi, K and Daniels-Higginbotham, J and Meyers, KK and Barrit-Ross, S and Aximu-Petri, A and Richter, J and Nickel, B and Berg, GE and McMahon, TP and Meyer, M and Marshall, C}, title = {Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns.}, journal = {Genes}, volume = {13}, number = {1}, pages = {}, pmid = {35052469}, issn = {2073-4425}, mesh = {Body Remains/*metabolism ; DNA Fingerprinting/*methods ; DNA, Ancient/*analysis/isolation &amp; purification ; *Forensic Genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Korean War ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; World War II ; }, abstract = {The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains.}, }
@article {pmid35052455, year = {2022}, author = {Deng, MX and Xiao, B and Yuan, JX and Hu, JM and Kim, KS and Westbury, MV and Lai, XL and Sheng, GL}, title = {Ancient Mitogenomes Suggest Stable Mitochondrial Clades of the Siberian Roe Deer.}, journal = {Genes}, volume = {13}, number = {1}, pages = {}, pmid = {35052455}, issn = {2073-4425}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/analysis/*genetics ; Deer/*genetics ; *Evolution, Molecular ; Fossils ; *Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {The roe deer (Capreolus spp.) has been present in China since the early Pleistocene. Despite abundant fossils available for detailed morphological analyses, little is known about the phylogenetic relationships of the fossil individuals to contemporary roe deer. We generated near-complete mitochondrial genomes for four roe deer remains from Northeastern China to explore the genetic connection of the ancient roe deer to the extant populations and to investigate the evolutionary history and population dynamics of this species. Phylogenetic analyses indicated the four ancient samples fall into three out of four different haplogroups of the Siberian roe deer. Haplogroup C, distributed throughout Eurasia, have existed in Northeastern China since at least the Late Pleistocene, while haplogroup A and D, found in the east of Lake Baikal, emerged in Northeastern China after the Mid Holocene. The Bayesian estimation suggested that the first split within the Siberian roe deer occurred approximately 0.34 million years ago (Ma). Moreover, Bayesian skyline plot analyses suggested that the Siberian roe deer had a population increase between 325 and 225 thousand years ago (Kya) and suffered a transient decline between 50 and 18 Kya. This study provides novel insights into the evolutionary history and population dynamics of the roe deer.}, }
@article {pmid35049133, year = {2022}, author = {Capo, E and Monchamp, ME and Coolen, MJL and Domaizon, I and Armbrecht, L and Bertilsson, S}, title = {Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential.}, journal = {Environmental microbiology}, volume = {24}, number = {5}, pages = {2201-2209}, pmid = {35049133}, issn = {1462-2920}, mesh = {Biodiversity ; DNA ; *Ecosystem ; Geologic Sediments/microbiology ; Humans ; Lakes/microbiology ; *Microbiota/genetics ; }, abstract = {In-depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo-genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human-induced global changes.}, }
@article {pmid35038748, year = {2022}, author = {Aneli, S and Saupe, T and Montinaro, F and Solnik, A and Molinaro, L and Scaggion, C and Carrara, N and Raveane, A and Kivisild, T and Metspalu, M and Scheib, CL and Pagani, L}, title = {The Genetic Origin of Daunians and the Pan-Mediterranean Southern Italian Iron Age Context.}, journal = {Molecular biology and evolution}, volume = {39}, number = {2}, pages = {}, pmid = {35038748}, issn = {1537-1719}, mesh = {*DNA, Mitochondrial/genetics ; Europe ; Italy ; }, abstract = {The geographical location and shape of Apulia, a narrow land stretching out in the sea at the South of Italy, made this region a Mediterranean crossroads connecting Western Europe and the Balkans. Such movements culminated at the beginning of the Iron Age with the Iapygian civilization which consisted of three cultures: Peucetians, Messapians, and Daunians. Among them, the Daunians left a peculiar cultural heritage, with one-of-a-kind stelae and pottery, but, despite the extensive archaeological literature, their origin has been lost to time. In order to shed light on this and to provide a genetic picture of Iron Age Southern Italy, we collected and sequenced human remains from three archaeological sites geographically located in Northern Apulia (the area historically inhabited by Daunians) and radiocarbon dated between 1157 and 275 calBCE. We find that Iron Age Apulian samples are still distant from the genetic variability of modern-day Apulians, they show a degree of genetic heterogeneity comparable with the cosmopolitan Republican and Imperial Roman civilization, even though a few kilometers and centuries separate them, and they are well inserted into the Iron Age Pan-Mediterranean genetic landscape. Our study provides for the first time a window on the genetic make-up of pre-Roman Apulia, whose increasing connectivity within the Mediterranean landscape, would have contributed to laying the foundation for modern genetic variability. In this light, the genetic profile of Daunians may be compatible with an at least partial autochthonous origin, with plausible contributions from the Balkan peninsula.}, }
@article {pmid35037474, year = {2022}, author = {Rayo, E and Ferrari, G and Neukamm, J and Akgül, G and Breidenstein, AM and Cooke, M and Phillips, C and Bouwman, AS and Rühli, FJ and Schuenemann, VJ}, title = {Non-destructive extraction of DNA from preserved tissues in medical collections.}, journal = {BioTechniques}, volume = {72}, number = {2}, pages = {60-64}, doi = {10.2144/btn-2021-0014}, pmid = {35037474}, issn = {1940-9818}, mesh = {*DNA/genetics ; Fixatives ; Humans ; *Preservation, Biological/methods ; Retrospective Studies ; Sequence Analysis, DNA/methods ; }, abstract = {Museum specimens and histologically fixed material are valuable samples for the study of historical soft tissues and represent a possible pathogen-specific source for retrospective molecular investigations. However, current methods for molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology, thus damaging the sample, and conserving the material for future investigations. Here the authors present the first tests of a non-destructive alternative that facilitates genetic analysis of fixed wet tissues while avoiding tissue damage. The authors extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. The results show that human historical DNA can be retrieved from the fixative material of medical specimens and provide new options for sampling valuable collections.}, }
@article {pmid35016010, year = {2022}, author = {Murchie, TJ and Karpinski, E and Eaton, K and Duggan, AT and Baleka, S and Zazula, G and MacPhee, RDE and Froese, D and Poinar, HN}, title = {Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments.}, journal = {Current biology : CB}, volume = {32}, number = {4}, pages = {851-860.e7}, doi = {10.1016/j.cub.2021.12.023}, pmid = {35016010}, issn = {1879-0445}, mesh = {Animals ; DNA, Ancient ; *DNA, Environmental ; DNA, Mitochondrial/genetics ; Ecosystem ; Fossils ; *Genome, Mitochondrial ; Horses/genetics ; *Mammoths/genetics ; *Permafrost ; Phylogeny ; }, abstract = {Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.[1] In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.[2] Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia[3]-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.[4][,][5] However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,[6-12] in paleodietary reconstructions,[13-19] and facilitated genomic reconstructions from cave contexts.[8][,][20-22] Murchie et al.[6][,][23] used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.[24] Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 40,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.}, }
@article {pmid35003706, year = {2021}, author = {Oliva, A and Tobler, R and Llamas, B and Souilmi, Y}, title = {Additional evaluations show that specific BWA-aln settings still outperform BWA-mem for ancient DNA data alignment.}, journal = {Ecology and evolution}, volume = {11}, number = {24}, pages = {18743-18748}, pmid = {35003706}, issn = {2045-7758}, abstract = {Xu et al. (2021) recently recommended a new parameterization of BWA-mem as a superior alternative to the widely-used BWA-aln algorithm to map ancient DNA sequencing data. Here, we compare the BWA-mem parameterization recommended by Xu et al. with the best-performing alignment methods determined in the recent benchmarks of Oliva and colleagues (2021), demonstrating that BWA-aln is still the gold-standard for ancient DNA read alignment .}, }
@article {pmid34988402, year = {2022}, author = {Baleka, S and Varela, L and Tambusso, PS and Paijmans, JLA and Mothé, D and Stafford, TW and Fariña, RA and Hofreiter, M}, title = {Revisiting proboscidean phylogeny and evolution through total evidence and palaeogenetic analyses including Notiomastodon ancient DNA.}, journal = {iScience}, volume = {25}, number = {1}, pages = {103559}, pmid = {34988402}, issn = {2589-0042}, abstract = {The extinct Gomphotheriidae is the only proboscidean family that colonized South America. The phylogenetic position of the endemic taxa has been through several revisions using morphological comparisons. Morphological studies are enhanced by paleogenetic analyses, a powerful tool to resolve phylogenetic relationships; however, ancient DNA (aDNA) preservation decreases in warmer regions. Despite the poor preservation conditions for aDNA in humid, sub-tropical climates, we recovered ∼3,000 bp of mtDNA of Notiomastodon platensis from the Arroyo del Vizcaíno site, Uruguay. Our calibrated phylogeny places Notiomastodon as a sister taxon to Elephantidae, with a divergence time of ∼13.5 Ma. Additionally, a total evidence analysis combining morphological and paleogenetic data shows that the three most diverse clades within Proboscidea diverged during the early Miocene, coinciding with the formation of a land passage between Africa and Eurasia. Our results are a further step toward aDNA analyses on Pleistocene samples from subtropical regions and provide a framework for proboscidean evolution.}, }
@article {pmid34988387, year = {2021}, author = {Sarhan, MS and Lehmkuhl, A and Straub, R and Tett, A and Wieland, G and Francken, M and Zink, A and Maixner, F}, title = {Ancient DNA diffuses from human bones to cave stones.}, journal = {iScience}, volume = {24}, number = {12}, pages = {103397}, pmid = {34988387}, issn = {2589-0042}, abstract = {Recent studies have demonstrated the potential to recover ancient human mitochondrial DNA and nuclear DNA from cave sediments. However, the source of such sedimentary ancient DNA is still under discussion. Here we report the case of a Bronze Age human skeleton, found in a limestone cave, which was covered with layers of calcite stone deposits. By analyzing samples representing bones and stone deposits from this cave, we were able to: i) reconstruct the full human mitochondrial genome from the bones and the stones (same haplotype); ii) determine the sex of the individual; iii) reconstruct six ancient bacterial and archaeal genomes; and finally iv) demonstrate better ancient DNA preservation in the stones than in the bones. Thereby, we demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource.}, }
@article {pmid34969841, year = {2022}, author = {Massilani, D and Morley, MW and Mentzer, SM and Aldeias, V and Vernot, B and Miller, C and Stahlschmidt, M and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Conard, NJ and Wurz, S and Henshilwood, CS and Vasquez, J and Essel, E and Nagel, S and Richter, J and Nickel, B and Roberts, RG and Pääbo, S and Slon, V and Goldberg, P and Meyer, M}, title = {Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {1}, pages = {}, pmid = {34969841}, issn = {1091-6490}, mesh = {Animals ; *Caves ; *DNA, Ancient ; *Fossils ; Hominidae/*genetics ; Neanderthals/*genetics ; }, abstract = {Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.}, }
@article {pmid34963129, year = {2022}, author = {Pedersen, MW and Antunes, C and De Cahsan, B and Moreno-Mayar, JV and Sikora, M and Vinner, L and Mann, D and Klimov, PB and Black, S and Michieli, CT and Braig, HR and Perotti, MA}, title = {Ancient Human Genomes and Environmental DNA from the Cement Attaching 2,000-Year-Old Head Lice Nits.}, journal = {Molecular biology and evolution}, volume = {39}, number = {2}, pages = {}, pmid = {34963129}, issn = {1537-1719}, support = {BB/N001400/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N001443/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *DNA, Environmental ; Genome, Human ; Genome-Wide Association Study ; Humans ; Infant, Newborn ; *Pediculus/genetics ; Skull ; }, abstract = {Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500-2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.}, }
@article {pmid34951605, year = {2021}, author = {Anagnostou, P and Capocasa, M and Brisighelli, F and Battaggia, C and Destro Bisol, G}, title = {The emerging complexity of Open Science: assessing Intelligent Data Openness in Genomic Anthropology and Human Genomics.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {99}, number = {}, pages = {135-152}, doi = {10.4436/JASS.99016}, pmid = {34951605}, issn = {2037-0644}, abstract = {In recent decades, the scientific community has become aware of the importance of science being effectively open in order to speed up scientific and technological progress. In this context, the achievement of a robust, effective and responsible form of data sharing is now widely acknowledged as a fundamental part of the research process. The production and resolution of human genomic data has steadily increased in recent years, mainly due to technological advances and decreasing costs of DNA genotyping and sequencing. There is, however, a downside to this process due to the huge increase in the complexity of the data and related metadata. This means it is advisable to go beyond traditional forms of sharing analysis, which have focused on data availability only. Here we present a pilot study that aims to complement a survey on the availability of data related to peer-reviewed publications with an analysis of their findability, accessibility, useability and assessability (according to the "intelligent data openness" scheme). Sharing rates in genomic anthropology (73.0%) were found to be higher than human genomics (32.4%), but lower than closely related research fields (from 96.8% to 79.2% for paleogenetics and evolutionary genetics, respectively). We discuss the privacy and methodological issues that could be linked to this finding. Comparisons of sharing rates across a wide range of disciplines has suggested that the idea of human genomics as a forerunner for the open data movement should be questioned. Finally, both in genomic anthropology and human genomics, findability and useability were found to be compliant with the expectations of an intelligent data openness, whereas only a minor part of studies met the need to make the data completely assessable.}, }
@article {pmid34947853, year = {2021}, author = {Haarkötter, C and Saiz, M and Gálvez, X and Medina-Lozano, MI and Álvarez, JC and Lorente, JA}, title = {Usefulness of Microbiome for Forensic Geolocation: A Review.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {34947853}, issn = {2075-1729}, abstract = {Forensic microbiomics is a promising tool for crime investigation. Geolocation, which connects an individual to a certain place or location by microbiota, has been fairly well studied in the literature, and several applications have been found. The aim of this review is to highlight the main findings in this field, including the current sample storage, DNA extraction, sequencing and data analysis techniques that are being used, and its potential applications in human trafficking and ancient DNA studies. Second, the challenges and limitations of forensic microbiomics and geolocation are emphasised, providing recommendations for the establishment of this tool in the forensic science community.}, }
@article {pmid34946894, year = {2021}, author = {Bondareva, O and Genelt-Yanovskiy, E and Petrova, T and Bodrov, S and Smorkatcheva, A and Abramson, N}, title = {Signatures of Adaptation in Mitochondrial Genomes of Palearctic Subterranean Voles (Arvicolinae, Rodentia).}, journal = {Genes}, volume = {12}, number = {12}, pages = {}, pmid = {34946894}, issn = {2073-4425}, mesh = {*Adaptation, Physiological ; Animals ; Arvicolinae/*genetics ; Computational Biology/methods ; Cytochromes b/*genetics ; Databases, Genetic ; *Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondrial Proton-Translocating ATPases/*genetics ; Phylogeny ; }, abstract = {This study evaluates signatures of selection in the evolution of the mitochondrial DNA of voles, subfamily Arvicolinae, during the colonization of subterranean environments. The comparative sequence analysis of mitochondrial protein-coding genes of eight subterranean vole species (Prometheomys schaposchnikowi, three species of the genus Ellobius: Ellobius talpinus, Ellobius fuscocapillus and Ellobius lutescens, two species of the genus Terricola: Terricola subterraneus and Terricola daghestanicus, Lasiopodomys mandarinus, and Hyperacrius fertilis) and their closest aboveground relatives was applied using codon-substitution models. The highest number of selection signatures was detected in genes ATP8 and CYTB. The relaxation of selection was observed in most mitochondrial DNA protein-coding genes for subterranean species. The largest amount of relaxed genes is discovered in mole voles (genus Ellobius). The number of selection signatures was found to be independent of the evolutionary age of the lineage but fits the degree of specialization to the subterranean niche. The common trends of selective pressures were observed among the evolutionary ancient and highly specialized subterranean rodent families and phylogenetically young lineages of voles. It suggests that the signatures of adaptation in individual mitochondrial protein-coding genes associated with the colonization of the subterranean niche may appear within a rather short evolutionary timespan.}, }
@article {pmid34943238, year = {2021}, author = {White, AE and de-Dios, T and Carrión, P and Bonora, GL and Llovera, L and Cilli, E and Lizano, E and Khabdulina, MK and Tleugabulov, DT and Olalde, I and Marquès-Bonet, T and Balloux, F and Pettener, D and van Dorp, L and Luiselli, D and Lalueza-Fox, C}, title = {Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome.}, journal = {Biology}, volume = {10}, number = {12}, pages = {}, pmid = {34943238}, issn = {2079-7737}, support = {grant agreement No. 864203//European Union Horizon 2020/ ; PGC2018-0955931-B-100//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; Grant number AP09261134//Ministry of the Education and Science of the Republic of Kazakhstan/ ; BFU2017-86471-P//MINECO, Spain/ ; GRC 2017 SGR 880//Departament d'Economia i Coneixement de la Generalitat de Catalunya/ ; }, abstract = {The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.}, }
@article {pmid34937939, year = {2022}, author = {Fowler, C and Olalde, I and Cummings, V and Armit, I and Büster, L and Cuthbert, S and Rohland, N and Cheronet, O and Pinhasi, R and Reich, D}, title = {A high-resolution picture of kinship practices in an Early Neolithic tomb.}, journal = {Nature}, volume = {601}, number = {7894}, pages = {584-587}, pmid = {34937939}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; Archaeology ; *Burial ; Child ; *DNA, Ancient ; Female ; Humans ; Male ; Mothers ; Pedigree ; }, abstract = {To explore kinship practices at chambered tombs in Early Neolithic Britain, here we combined archaeological and genetic analyses of 35 individuals who lived about 5,700 years ago and were entombed at Hazleton North long cairn[1]. Twenty-seven individuals are part of the first extended pedigree reconstructed from ancient DNA, a five-generation family whose many interrelationships provide statistical power to document kinship practices that were invisible without direct genetic data. Patrilineal descent was key in determining who was buried in the tomb, as all 15 intergenerational transmissions were through men. The presence of women who had reproduced with lineage men and the absence of adult lineage daughters suggest virilocal burial and female exogamy. We demonstrate that one male progenitor reproduced with four women: the descendants of two of those women were buried in the same half of the tomb over all generations. This suggests that maternal sub-lineages were grouped into branches whose distinctiveness was recognized during the construction of the tomb. Four men descended from non-lineage fathers and mothers who also reproduced with lineage male individuals, suggesting that some men adopted the children of their reproductive partners by other men into their patriline. Eight individuals were not close biological relatives of the main lineage, raising the possibility that kinship also encompassed social bonds independent of biological relatedness.}, }
@article {pmid34937536, year = {2021}, author = {Andreeva, T and Manakhov, A and Kunizheva, S and Rogaev, E}, title = {Genetic Evidence of Authenticity of a Hair Shaft Relic from the Portrait of Tsesarevich Alexei, Son of the Last Russian Emperor.}, journal = {Biochemistry. Biokhimiia}, volume = {86}, number = {12}, pages = {1572-1578}, doi = {10.1134/S0006297921120063}, pmid = {34937536}, issn = {1608-3040}, mesh = {DNA, Mitochondrial/*genetics ; *Forensic Anthropology ; *Forensic Genetics ; *Hair ; *High-Throughput Nucleotide Sequencing ; Humans ; Russia ; }, abstract = {To determine the value of an art piece, authenticity of the artwork must be verified. We demonstrate here a genetic approach to determine origin of a historic relic in the museum piece. We tested two hair shafts of unknown origin framed into a watercolor portrait of Tsesarevich Alexei Romanov, son of the last Russian Tzar Nicholas II, which is a unique item kept in the State Historical Museum. Genetic identification of the hair shafts was performed by analysis of mitochondrial DNA (mtDNA) markers using both massive parallel genomic sequencing and multiplex targeted PCR, followed by Sanger sequencing. In previous works, we reconstructed the complete mtDNA sequence inherited to Alexei Romanov through the Queen Victoria lineage [Rogaev et al. (2009) Proc. Natl. Acad. Sci. USA, 106, 5258-5263]. DNA extracts were obtained from the two thin hair shafts and used for comparative genetic analysis. Despite the very low quantity and quality of the DNA templates retrieved from the historical single hair shaft specimen, informative mtDNA sequences were determined. The mtDNA haplotype in the hair shafts corresponds to the mtDNA haplotype of Tsarevich Alexei, his sisters, and his mother, Empress Alexandra Feodorovna. This haplotype remains unique in the currently available mtDNA databases. Our results reveal that the hair relic from the portrait is associated with the family of the last Russian Emperor Nicholas II. The study is an example of first application of the genetic methodology for verification of the value of museum artwork items.}, }
@article {pmid34937535, year = {2021}, author = {Zhur, KV and Trifonov, VA and Prokhortchouk, EB}, title = {Progress and Prospects in Epigenetic Studies of Ancient DNA.}, journal = {Biochemistry. Biokhimiia}, volume = {86}, number = {12}, pages = {1563-1571}, doi = {10.1134/S0006297921120051}, pmid = {34937535}, issn = {1608-3040}, mesh = {Animals ; *DNA Methylation ; *DNA, Ancient ; *Epigenesis, Genetic ; Epigenomics/trends ; *Evolution, Molecular ; Human Migration ; Humans ; Neanderthals/*genetics ; }, abstract = {Development of technologies for high-throughput whole-genome sequencing and improvement of sample preparation techniques made it possible to study ancient DNA (aDNA) from archaeological samples over a million year old. The studies of aDNA have shed light on the history of human migration, replacement of populations, interbreeding of Cro-Magnons with Neanderthals and Denisovans, evolution of human pathogens, etc. Equally important is the possibility to investigate epigenetic modifications of ancient genomes, which has allowed to obtain previously inaccessible information on gene expression, nucleosome positioning, and DNA methylation. Analysis of methylation status of certain genomic sites can predict an individual's age at death and reconstruct some phenotypic features, as it was done for the Denisovan genome, and even to elucidate unfavorable environmental factors that had affected this archaic individual. In this review, we discuss current progress in epigenetic studies of aDNA, including methodological approaches and promising research directions in this field.}, }
@article {pmid34933781, year = {2022}, author = {Bianciotto, V and Selosse, MA and Martos, F and Marmeisse, R}, title = {Herbaria preserve plant microbiota responses to environmental changes.}, journal = {Trends in plant science}, volume = {27}, number = {2}, pages = {120-123}, doi = {10.1016/j.tplants.2021.11.012}, pmid = {34933781}, issn = {1878-4372}, mesh = {*Microbiota ; *Plants ; }, abstract = {Interaction between plants and their microbiota is a central theme to understand adaptation of plants to their environment. Considering herbaria as repositories of holobionts that preserved traces of ancient plant-associated microbial communities, we propose to explore these historical collections to evaluate the impact of long-lasting global changes on plant-microbiota interactions.}, }
@article {pmid34932923, year = {2021}, author = {Renom, P and de-Dios, T and Civit, S and Llovera, L and Sánchez-Gracia, A and Lizano, E and Rando, JC and Marquès-Bonet, T and Kergoat, GJ and Casanovas-Vilar, I and Lalueza-Fox, C}, title = {Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives.}, journal = {Biology letters}, volume = {17}, number = {12}, pages = {20210533}, pmid = {34932923}, issn = {1744-957X}, mesh = {Animals ; Islands ; *Phylogeny ; Rats ; Spain ; }, abstract = {Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, †Canariomys bravoi and †Canariomys tamarani, endemic to Tenerife and Gran Canaria, respectively, disappeared soon after human settlement. The highly derived morphological features of these insular endemic rodents hamper the reconstruction of their evolutionary histories. We have retrieved partial nuclear and mitochondrial data from †C. bravoi and used this information to explore its evolutionary affinities. The resulting dated phylogeny confidently places †C. bravoi within the African grass rat clade (Arvicanthis niloticus). The estimated divergence time, 650 000 years ago (95% higher posterior densities: 373 000-944 000), points toward an island colonization during the Günz-Mindel interglacial stage. †Canariomys bravoi ancestors would have reached the island via passive rafting and then underwent a yearly increase of mean body mass calculated between 0.0015 g and 0.0023 g; this corresponds to fast evolutionary rates (in darwins (d), ranging from 7.09 d to 2.78 d) that are well above those observed for non-insular mammals.}, }
@article {pmid34931883, year = {2021}, author = {Der Sarkissian, C and Velsko, IM and Fotakis, AK and Vågene, &#xc5;J and Hübner, A and Fellows Yates, JA}, title = {Ancient Metagenomic Studies: Considerations for the Wider Scientific Community.}, journal = {mSystems}, volume = {6}, number = {6}, pages = {e0131521}, pmid = {34931883}, issn = {2379-5077}, support = {Paleobiotechnology//Werner Siemens-Stiftung/ ; CEH - DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; CF18-1109//Carlsbergfondet (Carlsberg Foundation)/ ; //Centre National de la Recherche Scientifique (CNRS)/ ; 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; ERC-2015-StG 678901-FoodTransforms//EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC)/ ; //Max-Planck-Gesellschaft (MPG)/ ; }, abstract = {Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions &amp; Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.}, }
@article {pmid34927609, year = {2021}, author = {Parker, CE and Bos, KI and Haak, W and Krause, J}, title = {Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {177}, pages = {}, doi = {10.3791/63250}, pmid = {34927609}, issn = {1940-087X}, mesh = {*Archaeology/methods ; Bone and Bones/chemistry ; DNA/genetics ; *DNA, Ancient/analysis ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {The methods presented here seek to maximize the chances for the recovery of human DNA from ancient archaeological remains while limiting input sample material. This was done by targeting anatomical sampling locations previously determined to yield the highest amounts of ancient DNA (aDNA) in a comparative analysis of DNA recovery across the skeleton. Prior research has suggested that these protocols maximize the chances for the successful recovery of ancient human and pathogen DNA from archaeological remains. DNA yields were previously assessed by Parker et al. 2020 in a broad survey of aDNA preservation across multiple skeletal elements from 11 individuals recovered from the medieval (radiocarbon dated to a period of circa (ca.) 1040-1400 CE, calibrated 2-sigma range) graveyard at Krakauer Berg, an abandoned medieval settlement near Peißen Germany. These eight sampling spots, which span five skeletal elements (pars petrosa, permanent molars, thoracic vertebra, distal phalanx, and talus) successfully yielded high-quality ancient human DNA, where yields were significantly greater than the overall average across all elements and individuals. Yields were adequate for use in most common downstream population genetic analyses. Our results support the preferential use of these anatomical sampling locations for most studies involving the analyses of ancient human DNA from archaeological remains. Implementation of these methods will help to minimize the destruction of precious archaeological specimens.}, }
@article {pmid34906355, year = {2022}, author = {Liu, X and Zhang, Y and Liu, W and Li, Y and Pan, J and Pu, Y and Han, J and Orlando, L and Ma, Y and Jiang, L}, title = {A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses.}, journal = {Current biology : CB}, volume = {32}, number = {2}, pages = {480-487.e6}, pmid = {34906355}, issn = {1879-0445}, mesh = {Animals ; Body Size/genetics ; Genome ; Horses/genetics ; Mice ; Mutation ; *Nucleotides ; *Polymorphism, Single Nucleotide ; T-Box Domain Proteins/genetics ; Transcription Factors/genetics ; }, abstract = {Chinese ponies are endemic to the mountainous areas of southwestern China and were first reported in the archaeological record at the Royal Tomb of Zhongshan King, Mancheng, dated to approximately ∼2,100 YBP.[1] Previous work has started uncovering the genetic basis of size variation in western ponies and horses, revealing a limited number of loci, including HMGA2,[2]LCORL/NCAPG,[3]ZFAT, and LASP1.[4,5] Whether the same genetic pathways also drive the small body size of Chinese ponies, which show striking anatomical differences to Shetland ponies,[6] remains unclear.[2,7] To test this, we combined whole-genome sequences of 187 horses across China. Statistical analyses revealed top association between genetic variation at the T-box transcription factor 3 (TBX3) and the body size. Fine-scale analysis across an extended population of 189 ponies and 574 horses narrowed down the association to one A/G SNP at an enhancer region upstream of the TBX3 (ECA8:20,644,555, p = 2.34e-39). Luciferase assays confirmed the single-nucleotide G mutation upregulating TBX3 expression, and enhancer-knockout mice exhibited shorter limbs than wild-type littermates (p < 0.01). Re-analysis of ancient DNA data showed that the G allele, which is most frequent in modern horses, first occurred some ∼2,300 years ago and rose in frequency since. This supports selection for larger size in Asia from approximately the beginning of the Chinese Empire. Overall, this study characterized the causal regulatory mutation underlying small body size in Chinese ponies and revealed size as one of the main selection targets of past Chinese breeders.}, }
@article {pmid34902603, year = {2022}, author = {Zhang, M and Liu, Y and Li, Z and Lü, P and Gardner, JD and Ye, M and Wang, J and Yang, M and Shao, J and Wang, W and Dai, Q and Cao, P and Yang, R and Liu, F and Feng, X and Zhang, L and Li, E and Shi, Y and Chen, Z and Zhu, S and Zhai, W and Deng, T and Duan, Z and Bennett, EA and Hu, S and Fu, Q}, title = {Ancient DNA reveals the maternal genetic history of East Asian domestic pigs.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {49}, number = {6}, pages = {537-546}, doi = {10.1016/j.jgg.2021.11.014}, pmid = {34902603}, issn = {1673-8527}, mesh = {Animals ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Sus scrofa/genetics ; Swine/genetics ; }, abstract = {Zoo-archaeological and genetic evidence suggest that pigs were domesticated independently in Central China and Eastern Anatolia along with the development of agricultural communities and civilizations. However, the genetic history of domestic pigs, especially in China, has not been fully explored. In this study, we generate 42 complete mitochondrial DNA sequences from ∼7500- to 2750-year-old individuals from the Yellow River basin. Our results show that the maternal genetic continuity of East Asian domestic pigs dates back to at least the Early to Middle Neolithic. In contrast, the Near Eastern ancestry in European domestic pigs saw a near-complete genomic replacement by the European wild boar. The majority of East Asian domestic pigs share close haplotypes, and the most recent common ancestor of most branches dates back to less than 20,000 years before present, inferred using new substitution rates of whole mitogenomes or combined protein-coding regions. Two major population expansion events of East Asian domestic pigs coincided with changes in climate, widespread adoption of introduced crops, and the development of agrarian societies. These findings add to our understanding of the maternal genetic composition and help to complete the picture of domestic pig evolutionary history in East Asia.}, }
@article {pmid34893875, year = {2022}, author = {Garg, KM and Chattopadhyay, B and Cros, E and Tomassi, S and Benedick, S and Edwards, DP and Rheindt, FE}, title = {Island Biogeography Revisited: Museomics Reveals Affinities of Shelf Island Birds Determined by Bathymetry and Paleo-Rivers, Not by Distance to Mainland.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, pmid = {34893875}, issn = {1537-1719}, mesh = {Animals ; Genome ; Islands ; Phylogeny ; Population Dynamics ; *Rivers ; *Songbirds/genetics ; }, abstract = {Island biogeography is one of the most powerful subdisciplines of ecology: its mathematical predictions that island size and distance to mainland determine diversity have withstood the test of time. A key question is whether these predictions follow at a population-genomic level. Using rigorous ancient-DNA protocols, we retrieved approximately 1,000 genomic markers from approximately 100 historic specimens of two Southeast Asian songbird complexes from across the Sunda Shelf archipelago collected 1893-1957. We show that the genetic affinities of populations on small shelf islands defy the predictions of geographic distance and appear governed by Earth-historic factors including the position of terrestrial barriers (paleo-rivers) and persistence of corridors (Quaternary land bridges). Our analyses suggest that classic island-biogeographic predictors may not hold well for population-genomic dynamics on the thousands of shelf islands across the globe, which are exposed to dynamic changes in land distribution during Quaternary climate change.}, }
@article {pmid34887902, year = {2021}, author = {Zhang, X and Yang, L and Hou, L and Li, H and Xiang, H and Zhao, X}, title = {Ancient Mitogenomes Reveal the Domestication and Distribution of Cattle During the Longshan Culture Period in North China.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {759827}, pmid = {34887902}, issn = {1664-8021}, abstract = {Cattle, as an important tool for agricultural production in ancient China, have a complex history of domestication and distribution in China. Although it is generally accepted that ancient Chinese taurine cattle originated from the Near East, the explanation regarding their spread through China and whether or not this spread was associated with native aurochs during ancient times are still unclear. In this study, we obtained three nearly complete mitochondrial genomes (mitogenomes) from bovine remains dating back ca. 4,000 years at the Taosi and Guchengzhai sites in North China. For the first time at the mitogenome level, phylogenetic analyses confirmed the approximately 4,000-year-old bovines from North China as taurine cattle. All ancient cattle from both sites belonged to the T3 haplogroup, suggesting their origin from the Near East. The high affinity between ancient samples and southern Chinese taurine cattle indicated that ancient Chinese cattle had a genetic contribution to the taurine cattle of South China. A rapid decrease in the female effective population size ca. 4.65 thousand years ago (kya) and a steep increase ca. 1.99 kya occurred in Chinese taurine cattle. Overall, these results provide increasing evidence of the origin of cattle in the middle Yellow River region of China.}, }
@article {pmid34883299, year = {2022}, author = {Haas, C and Körner, C and Sulzer, A and Kratzer, A}, title = {19th century family saga re-told by DNA recovered from postcard stamps.}, journal = {Forensic science international}, volume = {330}, number = {}, pages = {111129}, doi = {10.1016/j.forsciint.2021.111129}, pmid = {34883299}, issn = {1872-6283}, mesh = {Child ; Chromosomes, Human, Y ; DNA ; *DNA Fingerprinting ; DNA, Ancient ; Family ; Humans ; Male ; *Microsatellite Repeats ; }, abstract = {Old postcards with stamps might help unravelling historical family stories and relationships. By employing ancient DNA recovered from world war I postage stamps, we disprove a family saga of an illegitimate child born in 1887. We developed a protocol to collect DNA from saliva, trapped and protected on the backside of postage stamps glued on postcards. With replicate STR analyses we were able to assemble almost full autosomal and Y-STR profiles of three male, deceased family members. The illegitimate child turned out to be a legitimate child of a later married couple.}, }
@article {pmid34880234, year = {2021}, author = {Murchie, TJ and Monteath, AJ and Mahony, ME and Long, GS and Cocker, S and Sadoway, T and Karpinski, E and Zazula, G and MacPhee, RDE and Froese, D and Poinar, HN}, title = {Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {7120}, pmid = {34880234}, issn = {2041-1723}, mesh = {Animals ; Canada ; Climate Change ; *DNA, Ancient ; *DNA, Environmental ; Ecosystem ; Equidae/genetics ; Fossils ; Horses/genetics ; Human Activities ; Mammoths/*genetics ; Metagenome ; Plants/genetics ; Yukon Territory ; }, abstract = {The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.}, }
@article {pmid34850636, year = {2022}, author = {Smith, RW and Non, AL}, title = {Assessing the achievements and uncertain future of paleoepigenomics.}, journal = {Epigenomics}, volume = {14}, number = {4}, pages = {167-173}, doi = {10.2217/epi-2021-0382}, pmid = {34850636}, issn = {1750-192X}, mesh = {*DNA Methylation ; Epigenesis, Genetic ; *Epigenomics ; Humans ; }, }
@article {pmid34848867, year = {2021}, author = {Tsosie, KS and Bader, AC and Fox, K and Bolnick, DA and Garrison, NA and Smith, RWA}, title = {Ancient-DNA researchers write their own rules.}, journal = {Nature}, volume = {600}, number = {7887}, pages = {37}, doi = {10.1038/d41586-021-03542-y}, pmid = {34848867}, issn = {1476-4687}, mesh = {*DNA, Ancient ; Ethics, Research ; Humans ; *Research Personnel ; Writing ; }, }
@article {pmid34848866, year = {2021}, author = {Somel, M and Altınışık, NE and Özer, F and Ávila-Arcos, MC}, title = {Collaborate equitably in ancient DNA research and beyond.}, journal = {Nature}, volume = {600}, number = {7887}, pages = {37}, doi = {10.1038/d41586-021-03541-z}, pmid = {34848866}, issn = {1476-4687}, mesh = {*DNA, Ancient ; }, }
@article {pmid34832510, year = {2021}, author = {Raele, DA and Panzarino, G and Sarcinelli, G and Cafiero, MA and Maria Tunzi, A and Dellù, E}, title = {Genetic Evidence of the Black Death in the Abbey of San Leonardo (Apulia Region, Italy): Tracing the Cause of Death in Two Individuals Buried with Coins.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {34832510}, issn = {2076-0817}, abstract = {The Abbey of San Leonardo in Siponto (Apulia, Southern Italy) was an important religious and medical center during the Middle Ages. It was a crossroads for pilgrims heading along the Via Francigena to the Sanctuary of Monte Sant'Angelo and for merchants passing through the harbor of Manfredonia. A recent excavation of Soprintendenza Archeologica della Puglia investigated a portion of the related cemetery, confirming its chronology to be between the end of the 13th and beginning of the 14th century. Two single graves preserved individuals accompanied by numerous coins dating back to the 14th century, hidden in clothes and in a bag tied to the waist. The human remains of the individuals were analyzed in the Laboratorio di Antropologia Fisica of Soprintendenza ABAP della città metropolitana di Bari. Three teeth from each individual were collected and sent to the Istituto Zooprofilattico Sperimentale di Puglia e Basilicata to study infectious diseases such as malaria, plague, tuberculosis, epidemic typhus and Maltese fever (Brucellosis), potentially related to the lack of inspection of the bodies during burial procedures. DNA extracted from six collected teeth and two additional unrelated human teeth (negative controls) were analyzed using PCR to verify the presence of human DNA (β-globulin) and of pathogens such as Plasmodium spp., Yersinia pestis, Mycobacterium spp., Rickettsia spp. and Brucella spp. The nucleotide sequence of the amplicon was determined to confirm the results. Human DNA was successfully amplified from all eight dental extracts and two different genes of Y. pestis were amplified and sequenced in 4 out of the 6 teeth. Molecular analyses ascertained that the individuals buried in San Leonardo were victims of the Black Death (1347-1353) and the data confirmed the lack of inspection of the corpses despite the presence of numerous coins. This study represents molecular evidence, for the first time, of Southern Italy's involvement in the second wave of the plague pandemic.}, }
@article {pmid34824815, year = {2021}, author = {Baca, M and Popović, D and Lemanik, A and Fewlass, H and Talamo, S and Zima, J and Ridush, B and Popov, V and Nadachowski, A}, title = {The Tien Shan vole (Microtus ilaeus; Rodentia: Cricetidae) as a new species in the Late Pleistocene of Europe.}, journal = {Ecology and evolution}, volume = {11}, number = {22}, pages = {16113-16125}, pmid = {34824815}, issn = {2045-7758}, abstract = {Grey voles (subgenus Microtus) represent a complex of at least seven closely related and partly cryptic species. The range of these species extends from the Atlantic to the Altai Mountains, but most of them occur east of the Black Sea. Using ancient DNA analyses of the Late Pleistocene specimens, we identified a new mtDNA lineage of grey voles in Europe. Phylogenetic analysis of mitochondrial DNA cytochrome b sequences from 23 voles from three caves, namely, Emine-Bair-Khosar (Crimea, Ukraine), Cave 16 (Bulgaria), and Bacho Kiro (Bulgaria), showed that 14 specimens form a previously unrecognized lineage, sister to the Tien Shan vole. The average sequence divergence of this lineage and the extant Tien Shan vole was 4.8%, which is similar to the divergence of grey vole forms, which are considered distinct species or being on the verge of speciation; M. arvalis and M. obscurus or M. mystacinus and M. rossiaemeridionalis. We estimated the time to the most recent common ancestor of the grey voles to be 0.66 Ma, which is over twice the recent estimates, while the divergence of the extant Tien Shan vole and the new lineage to be 0.29 Ma. Our discovery suggests that grey voles may have been more diversified in the past and that their ranges may have differed substantially from current ones. It also underlines the utility of ancient DNA to decipher the evolutionary history of voles.}, }
@article {pmid34805800, year = {2021}, author = {Ning, C and Zhang, F and Cao, Y and Qin, L and Hudson, MJ and Gao, S and Ma, P and Li, W and Zhu, S and Li, C and Li, T and Xu, Y and Li, C and Robbeets, M and Zhang, H and Cui, Y}, title = {Ancient genome analyses shed light on kinship organization and mating practice of Late Neolithic society in China.}, journal = {iScience}, volume = {24}, number = {11}, pages = {103352}, pmid = {34805800}, issn = {2589-0042}, abstract = {Anthropology began in the late nineteenth century with an emphasis on kinship as a key factor in human evolution. From the 1960s, archaeologists attempted increasingly sophisticated ways of reconstructing prehistoric kinship but ancient DNA analysis has transformed the field, making it possible, to directly examine kin relations from human skeletal remains. Here, we retrieved genomic data from four Late Neolithic individuals in central China associated with the Late Neolithic Longshan culture. We provide direct evidence of consanguineous mating in ancient China, revealing inbreeding among the Longshan populations. By combining ancient genomic data with anthropological and archaeological evidence, we further show that Longshan society household was built based on the extended beyond the nuclear family, coinciding with intensified social complexity during the Longshan period, perhaps showing the transformation of large communities through a new role of genetic kinship-based extended family units.}, }
@article {pmid34791203, year = {2022}, author = {Moreno-Mayar, JV}, title = {FrAnTK: a Frequency-based Analysis ToolKit for efficient exploration of allele sharing patterns in present-day and ancient genomic datasets.}, journal = {G3 (Bethesda, Md.)}, volume = {12}, number = {1}, pages = {}, pmid = {34791203}, issn = {2160-1836}, mesh = {Alleles ; Computational Biology ; *Genomics ; *Software ; }, abstract = {Present-day and ancient population genomic studies from different study organisms have rapidly become accessible to diverse research groups worldwide. Unfortunately, as datasets and analyses become more complex, researchers with less computational experience often miss their chance to analyze their own data. We introduce FrAnTK, a user-friendly toolkit for computation and visualization of allele frequency-based statistics in ancient and present-day genome variation datasets. We provide fast, memory-efficient tools that allow the user to go from sequencing data to complex exploratory analyses and visual representations with minimal data manipulation. Its simple usage and low computational requirements make FrAnTK ideal for users that are less familiar with computer programming carrying out large-scale population studies.}, }
@article {pmid34784770, year = {2021}, author = {Zhang, H and Sun, Y and Zeng, Q and Crowe, SA and Luo, H}, title = {Snowball Earth, population bottleneck and Prochlorococcus evolution.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1963}, pages = {20211956}, pmid = {34784770}, issn = {1471-2954}, mesh = {Earth, Planet ; Genome, Bacterial ; Oceans and Seas ; Phylogeny ; *Prochlorococcus/genetics/metabolism ; Seawater/chemistry ; }, abstract = {Prochlorococcus are the most abundant photosynthetic organisms in the modern ocean. A massive DNA loss event occurred in their early evolutionary history, leading to highly reduced genomes in nearly all lineages, as well as enhanced efficiency in both nutrient uptake and light absorption. The environmental landscape that shaped this ancient genome reduction, however, remained unknown. Through careful molecular clock analyses, we established that this Prochlorococcus genome reduction occurred during the Neoproterozoic Snowball Earth climate catastrophe. The lethally low temperature and exceedingly dim light during the Snowball Earth event would have inhibited Prochlorococcus growth and proliferation, and caused severe population bottlenecks. These bottlenecks are recorded as an excess of deleterious mutations accumulated across genomic regions and inherited by descendant lineages. Prochlorococcus adaptation to extreme environmental conditions during Snowball Earth intervals can be inferred by tracing the evolutionary paths of genes that encode key metabolic potential. Key metabolic innovation includes modified lipopolysaccharide structure, strengthened peptidoglycan biosynthesis, the replacement of a sophisticated circadian clock with an hourglass-like mechanism that resets daily for dim light adaption and the adoption of ammonia diffusion as an efficient membrane transporter-independent mode of nitrogen acquisition. In this way, the Neoproterozoic Snowball Earth event may have altered the physiological characters of Prochlorococcus, shaping their ecologically vital role as the most abundant primary producers in the modern oceans.}, }
@article {pmid34783162, year = {2022}, author = {Lyu, W and Dai, X and Beaumont, M and Yu, F and He, Z}, title = {Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data.}, journal = {Molecular ecology resources}, volume = {22}, number = {4}, pages = {1362-1379}, doi = {10.1111/1755-0998.13553}, pmid = {34783162}, issn = {1755-0998}, mesh = {Animals ; Bayes Theorem ; *Chickens/genetics ; *DNA, Ancient ; Evolution, Molecular ; Gene Frequency ; Models, Genetic ; Selection, Genetic ; }, abstract = {With the rapid growth of the number of sequenced ancient genomes, there has been increasing interest in using this new information to study past and present adaptation. Such an additional temporal component has the promise of providing improved power for the estimation of natural selection. Over the last decade, statistical approaches for the detection and quantification of natural selection from ancient DNA (aDNA) data have been developed. However, most of the existing methods do not allow us to estimate the timing of natural selection along with its strength, which is key to understanding the evolution and persistence of organismal diversity. Additionally, most methods ignore the fact that natural populations are almost always structured, which can result in an overestimation of the effect of natural selection. To address these issues, we introduce a novel Bayesian framework for the inference of natural selection and gene migration from aDNA data with Markov chain Monte Carlo techniques, co-estimating both timing and strength of natural selection and gene migration. Such an advance enables us to infer drivers of natural selection and gene migration by correlating genetic evolution with potential causes such as the changes in the ecological context in which an organism has evolved. The performance of our procedure is evaluated through extensive simulations, with its utility shown with an application to ancient chicken samples.}, }
@article {pmid34779123, year = {2022}, author = {Ferrari, G and Atmore, LM and Jentoft, S and Jakobsen, KS and Makowiecki, D and Barrett, JH and Star, B}, title = {An accurate assignment test for extremely low-coverage whole-genome sequence data.}, journal = {Molecular ecology resources}, volume = {22}, number = {4}, pages = {1330-1344}, doi = {10.1111/1755-0998.13551}, pmid = {34779123}, issn = {1755-0998}, support = {221734/O30//The Aqua Genome Project/ ; 262777//Catching the Past/ ; 813383//Marie Sk&#x142;odowska-Curie/ ; }, mesh = {Animals ; *Butterflies/genetics ; Ecotype ; *Gadus morhua/genetics ; Genome/genetics ; Haplotypes ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/methods ; }, abstract = {Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.}, }
@article {pmid34764978, year = {2021}, author = {Piro, M}, title = {Aspects of Molecular Genetics in Dromedary Camel.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {723181}, pmid = {34764978}, issn = {1664-8021}, abstract = {Dromedary camels are unique in their morphological and physiological characteristics and are capable of providing milk and meat even under extreme environmental conditions. Like other species, the dromedary camel has also benefitted from the development of the molecular genetics to increase the knowledge about different aspect in camel genetics (genetic variation, molecular marker, parentage control, gene of interest, whole genome, dating…etc.). In this paper we review the different molecular genetic technics used in this particular species and future prospects. Dromedary genetic studies started in the end of the 1980s with phenotypic evaluation and the attempts to highlight the protein and biochemical diversity. In the 2000s, with the development of molecular markers such as microsatellites, genetic diversity of different types in several countries were estimated and microsatellites were also used for parentage control. In terms of genetic characterization, microsatellites revealed a defined global structure, differentiating East African and South Arabian dromedaries from North African, North Arabian, and South Asian individuals, respectively. Also, mitochondrialDNA sequence analysis of ancient DNA proved to be crucial in resolving domestication processes in dromedaries. Ancient and modern DNA revealed dynamics of domestication and cross-continental dispersion of the dromedary. Nuclear SNPs, single nucleotide polymorphisms changes that occur approximately each 1000 bps in the mammalian genome were also applied in some studies in dromedary. These markers are a very useful alternative to microsatellites and have been employed in some studies on genetic diversity and relevant phenotypic traits in livestock. Finally, thanks to the use of Next Generation Sequencing (NGS) the whole-genome assemblies of the dromedary (Camelus dromedarius) and a work to establish the organization of the dromedary genome at chromosome level were recently published.}, }
@article {pmid36755065, year = {2021}, author = {Armbrecht, L and Eisenhofer, R and Utge, J and Sibert, EC and Rocha, F and Ward, R and Pierella Karlusich, JJ and Tirichine, L and Norris, R and Summers, M and Bowler, C}, title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {66}, pmid = {36755065}, issn = {2730-6151}, abstract = {Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.}, }
@article {pmid34748674, year = {2022}, author = {Salis, AT and Bray, SCE and Lee, MSY and Heiniger, H and Barnett, R and Burns, JA and Doronichev, V and Fedje, D and Golovanova, L and Harington, CR and Hockett, B and Kosintsev, P and Lai, X and Mackie, Q and Vasiliev, S and Weinstock, J and Yamaguchi, N and Meachen, JA and Cooper, A and Mitchell, KJ}, title = {Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge.}, journal = {Molecular ecology}, volume = {31}, number = {24}, pages = {6407-6421}, doi = {10.1111/mec.16267}, pmid = {34748674}, issn = {1365-294X}, mesh = {Humans ; Horses/genetics ; Animals ; *Ursidae/genetics ; *Lions ; Phylogeny ; DNA, Mitochondrial/genetics ; North America ; }, abstract = {The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.}, }
@article {pmid34745073, year = {2021}, author = {Urban, C and Blom, AA and Pfrengle, S and Walker-Meikle, K and Stone, AC and Inskip, SA and Schuenemann, VJ}, title = {One Health Approaches to Trace Mycobacterium leprae's Zoonotic Potential Through Time.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {762263}, pmid = {34745073}, issn = {1664-302X}, abstract = {Hansen's disease (leprosy), mainly caused by infection with Mycobacterium leprae, has accompanied humanity for thousands of years. Although currently rare in Europe, there are over 200,000 new infections annually in South East Asia, Africa, and South America. Over the years many disciplines - palaeopathology, ancient DNA and other ancient biomolecules, and history - have contributed to a better understanding of leprosy's past, in particular its history in medieval Europe. We discuss their contributions and potential, especially in relation to the role of inter-species transmission, an unexplored phenomenon in the disease's history. Here, we explore the potential of interdisciplinary approaches that understand disease as a biosocial phenomenon, which is a product of both infection with M. leprae and social behaviours that facilitate transmission and spread. Genetic evidence of M. leprae isolated from archaeological remains combined with systematic zooarchaeological and historical analysis would not only identify when and in what direction transmission occurred, but also key social behaviours and motivations that brought species together. In our opinion, this combination is crucial to understand the disease's zoonotic past and current potential.}, }
@article {pmid34738712, year = {2022}, author = {Fordham, DA and Brown, SC and Akçakaya, HR and Brook, BW and Haythorne, S and Manica, A and Shoemaker, KT and Austin, JJ and Blonder, B and Pilowsky, JA and Rahbek, C and Nogues-Bravo, D}, title = {Process-explicit models reveal pathway to extinction for woolly mammoth using pattern-oriented validation.}, journal = {Ecology letters}, volume = {25}, number = {1}, pages = {125-137}, doi = {10.1111/ele.13911}, pmid = {34738712}, issn = {1461-0248}, support = {DP180102392//Australian Research Council/ ; FT140101192//Australian Research Council/ ; DNRF96//Danish Research Foundation/ ; }, mesh = {Animals ; Anthropogenic Effects ; Climate ; Extinction, Biological ; Fossils ; Humans ; *Mammoths/genetics ; }, abstract = {Pathways to extinction start long before the death of the last individual. However, causes of early stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.}, }
@article {pmid34735939, year = {2022}, author = {Emery, MV and Bolhofner, K and Ghafoor, S and Winingear, S and Buikstra, JE and Fulginiti, LC and Stone, AC}, title = {Whole mitochondrial genomes assembled from thermally altered forensic bones and teeth.}, journal = {Forensic science international. Genetics}, volume = {56}, number = {}, pages = {102610}, doi = {10.1016/j.fsigen.2021.102610}, pmid = {34735939}, issn = {1878-0326}, mesh = {DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; *Tooth ; }, abstract = {The recovery and analysis of genetic material obtained from thermally altered human bones and teeth are increasingly important to forensic investigations, especially in cases where soft-tissue identification is no longer possible. Although little is known about how these fire-related processes affect DNA degradation over time, next-generation sequencing technology in combination with traditional osteobiographical applications may provide us clues to these questions. In this study, we compare whole mitochondrial genome data generated using two different DNA extraction methods from 27 thermally altered samples obtained from fire victims (Maricopa County, Arizona) . DNA extracts were converted to double-stranded DNA libraries and enriched for whole mitochondrial DNA (mtDNA) using synthetic biotinylated RNA baits, then sequenced on an Illumina MiSeq. We processed the mitochondrial data using an in-house computational pipeline (MitoPipe1.0) composed of ancient DNA and modern genomics applications, then compared the resulting information across the two extraction types and five burn categories. Our analysis shows that DNA fragmentation increases with temperature, but that the acute insult from fire combined with the lack of water is insufficient to produce 5' and 3' terminal deamination characteristic of ancient DNA. Our data also suggest an acute and significant point of DNA degradation between 350 °C and 550 °C, and that the likelihood of generating high quality mtDNA haplogroup calls decreases significantly at temperatures > 550 °C. This research is part of a concerted effort to understand how fire affects our ability to generate genetic profiles suitable for forensic identification purposes.}, }
@article {pmid34731404, year = {2022}, author = {Oh, CS and Hong, JH and Chai, JY and Song, MK and Jang, HJ and Seo, M and Shin, DH}, title = {Ancient DNA of Metagonimus yokogawai Recovered from Joseon Period Human Remains Newly Discovered at Goryeong County in South Korea.}, journal = {Acta parasitologica}, volume = {67}, number = {1}, pages = {539-545}, pmid = {34731404}, issn = {1896-1851}, support = {2019S1A5C2A01083578//ministry of education/ ; 2020R1A2C1010708//ministry of science and ict (kr)/ ; }, mesh = {Animals ; Body Remains ; DNA, Ancient ; *Heterophyidae/genetics ; Humans ; Phylogeny ; Republic of Korea ; *Trematode Infections/parasitology ; }, abstract = {PURPOSE: Metagonimiasis, commonly seen in East Asian countries, is a parasitic disorder caused by definitive hosts' ingestion of undercooked freshwater fishes. Recently, genetic analysis has proved 28S rRNA and cytochrome c oxidase subunit I (COI) mtDNA gene to be a successful marker differentiating species of the genus Metagonimus. In the present study, using specimens from the newly discovered Joseon Dynasty human remains of Goryeong, we obtained updated genetic data on genus Metagonimus, which was also prevalent during the Joseon period.<br><br>METHODS: The ancient DNA (aDNA) was retrieved from the coprolite sample of the seventeenth century, half-mummified individual discovered at Goryeong Country, South Korea. Cloning and sequencing were performed on PCR-amplified amplicons for M. yokogawai 28S rRNA and COI mtDNA gene. The consensus sequences were used for species identification and phylogenetic analysis using NCBI/BLAST and MEGA X software.<br><br>RESULTS: Based on the COI mtDNA gene region, the Goryeong sequence was confirmed as belonging to M. yokogawai, as it was shown to form a separate cluster with other M. yokogawai taxa that are distinct also from M. takahashii and M. miyatai.<br><br>CONCLUSION: In a series of our genetic analyses on genus Metagonimus using samples retrieved from Joseon-period cases, aDNA sequences of genus Metagonimus revealed in South Korea thus far are those of M. yokogawai, but not of M. miyatai or M. takahashii yet.}, }
@article {pmid34721545, year = {2021}, author = {Wang, L and Sheng, G and Preick, M and Hu, S and Deng, T and Taron, UH and Barlow, A and Hu, J and Xiao, B and Sun, G and Song, S and Hou, X and Lai, X and Hofreiter, M and Yuan, J}, title = {Ancient Mitogenomes Provide New Insights into the Origin and Early Introduction of Chinese Domestic Donkeys.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {759831}, pmid = {34721545}, issn = {1664-8021}, abstract = {Both molecular data and archaeological evidence strongly support an African origin for the domestic donkey. Recent genetic studies further suggest that there were two distinct maternal lineages involved in its initial domestication. However, the exact introduction time and the dispersal process of domestic donkeys into ancient China are still unresolved. To address these questions, we retrieved three near-complete mitochondrial genomes from donkey specimens excavated from Gaoling County, Shaanxi Province, and Linxia Basin, Gansu Province, China, dated at 2,349-2,301, 469-311, and 2,160-2,004 cal. BP, respectively. Maximum-likelihood and Bayesian phylogenetic analyses reveal that the two older samples fall into the two different main lineages (i.e., clade Ⅰ and clade Ⅱ) of the domestic donkey, suggesting that the two donkey maternal lineages had been introduced into Midwestern China at least at the opening of Silk Road (approximately the first century BC). Bayesian analysis shows that the split of the two donkey maternal lineages is dated at 0.323 Ma (95% CI: 0.583-0.191 Ma) using root-tip dating calibrations based on near-complete mitogenomes, supporting the hypothesis that modern domestic donkeys go back to at least two independent domestication events. Moreover, Bayesian skyline plot analyses indicate an apparent female population increase between 5,000 and 2,500 years ago for clade I followed by a stable population size to the present day. In contrast, clade II keeps a relatively stable population size over the past 5,000 years. Overall, our study provides new insights into the early domestication history of Chinese domestic donkeys.}, }
@article {pmid34712923, year = {2021}, author = {Sinding, MS and Ciucani, MM and Ramos-Madrigal, J and Carmagnini, A and Rasmussen, JA and Feng, S and Chen, G and Vieira, FG and Mattiangeli, V and Ganjoo, RK and Larson, G and Sicheritz-Pontén, T and Petersen, B and Frantz, L and Gilbert, MTP and Bradley, DG}, title = {Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos.}, journal = {iScience}, volume = {24}, number = {11}, pages = {103226}, pmid = {34712923}, issn = {2589-0042}, abstract = {The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.}, }
@article {pmid34711884, year = {2021}, author = {Fernandes, DM and Cheronet, O and Gelabert, P and Pinhasi, R}, title = {TKGWV2: an ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21262}, pmid = {34711884}, issn = {2045-2322}, mesh = {Algorithms ; *Alleles ; Computational Biology/methods ; *DNA, Ancient ; Databases, Genetic ; Genetic Variation ; *Genome, Human ; *Genomics/methods ; Humans ; Models, Genetic ; Polymorphism, Single Nucleotide ; }, abstract = {Estimation of genetically related individuals is playing an increasingly important role in the ancient DNA field. In recent years, the numbers of sequenced individuals from single sites have been increasing, reflecting a growing interest in understanding the familial and social organisation of ancient populations. Although a few different methods have been specifically developed for ancient DNA, namely to tackle issues such as low-coverage homozygous data, they require a 0.1-1× minimum average genomic coverage per analysed pair of individuals. Here we present an updated version of a method that enables estimates of 1st and 2nd-degrees of relatedness with as little as 0.026× average coverage, or around 18,000 SNPs from 1.3 million aligned reads per sample with average length of 62 bp-four times less data than 0.1× coverage at similar read lengths. By using simulated data to estimate false positive error rates, we further show that a threshold even as low as 0.012×, or around 4000 SNPs from 600,000 reads, will always show 1st-degree relationships as related. Lastly, by applying this method to published data, we are able to identify previously undocumented relationships using individuals that had been excluded from prior kinship analysis due to their very low coverage. This methodological improvement has the potential to enable relatedness estimation on ancient whole genome shotgun data during routine low-coverage screening, and therefore improve project management when decisions need to be made on which individuals are to be further sequenced.}, }
@article {pmid34705496, year = {2021}, author = {Moltke, I and Korneliussen, TS and Seguin-Orlando, A and Moreno-Mayar, JV and LaPointe, E and Billeck, W and Willerslev, E}, title = {Identifying a living great-grandson of the Lakota Sioux leader Tatanka Iyotake (Sitting Bull).}, journal = {Science advances}, volume = {7}, number = {44}, pages = {eabh2013}, pmid = {34705496}, issn = {2375-2548}, abstract = {A great-grandson of the legendary Lakota Sioux leader Sitting Bull (Tatanka Iyotake), Ernie LaPointe, wished to have their familial relationship confirmed via genetic analysis, in part, to help settle concerns over Sitting Bull’s final resting place. To address Ernie LaPointe’s claim of family relationship, we obtained minor amounts of genomic data from a small piece of hair from Sitting Bull’s scalp lock, which was repatriated in 2007. We then compared these data to genome-wide data from LaPointe and other Lakota Sioux using a new probabilistic approach and concluded that Ernie LaPointe is Sitting Bull’s great-grandson. To our knowledge, this is the first published example of a familial relationship between contemporary and a historical individual that has been confirmed using such limited amounts of ancient DNA across such distant relatives. Hence, this study opens the possibility for broadening genealogical research, even when only minor amounts of ancient genetic material are accessible.}, }
@article {pmid34702906, year = {2021}, author = {Iadarola, B and Lavezzari, D and Modi, A and Degli Esposti, C and Beltrami, C and Rossato, M and Zaro, V and Napione, E and Latella, L and Lari, M and Caramelli, D and Salviati, A and Delledonne, M}, title = {Whole-exome sequencing of the mummified remains of Cangrande della Scala (1291-1329 CE) indicates the first known case of late-onset Pompe disease.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21070}, pmid = {34702906}, issn = {2045-2322}, mesh = {*DNA, Ancient ; Glycogen Storage Disease Type II/*genetics/history ; History, Medieval ; Humans ; Male ; *Mummies ; *Exome Sequencing ; }, abstract = {Mummified remains of relevant historical figures are nowadays an important source of information to retrace data concerning their private life and health, especially when historical archives are not available. Next-generation-sequencing was proved to be a valuable tool to unravel the characteristics of these individuals through their genetic heritage. Using the strictest criteria currently available for the validation of ancient DNA sequences, whole-genome and whole-exome sequencing were generated from the mummy remains of an Italian nobleman died almost 700 years ago, Cangrande della Scala. While its genome sequencing could not yield sufficient coverage for in depth investigation, exome sequencing could overcome the limitations of this approach to achieve significantly high coverage on coding regions, thus allowing to perform the first extensive exome analysis of a mummy genome. Similar to a standard "clinical exome analysis" conducted on modern DNA, an in-depth variant annotation, high-quality filtering and interpretation was performed, leading to the identification of a genotype associated with late-onset Pompe disease (glycogen storage disease type II). This genetic diagnosis was concordant with the limited clinical history available for Cangrande della Scala, who likely represents the earliest known case of this autosomal recessive metabolic disorder.}, }
@article {pmid34672750, year = {2021}, author = {Gibbons, A}, title = {Ancient DNA reveals long-sought homeland of modern horses.}, journal = {Science (New York, N.Y.)}, volume = {374}, number = {6566}, pages = {384-385}, doi = {10.1126/science.acx9390}, pmid = {34672750}, issn = {1095-9203}, mesh = {Animals ; *Animals, Domestic ; *DNA, Ancient ; *Domestication ; History, Ancient ; *Horses ; Mongolia ; }, }
@article {pmid34672105, year = {2022}, author = {O'Grady, CJ and Dhandapani, V and Colbourne, JK and Frisch, D}, title = {Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs.}, journal = {Molecular ecology resources}, volume = {22}, number = {3}, pages = {946-961}, doi = {10.1111/1755-0998.13524}, pmid = {34672105}, issn = {1755-0998}, support = {//Midlands Integrative Biosciences Training Partnership/ ; 658714//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; NBAF998//NERC Biomolecular Analysis Facility/ ; }, mesh = {Animals ; *Daphnia/genetics ; *Ecosystem ; Genomics/methods ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing ; }, abstract = {Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100-year-old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.}, }
@article {pmid34671385, year = {2021}, author = {Zhu, K and Du, P and Xiong, J and Ren, X and Sun, C and Tao, Y and Ding, Y and Xu, Y and Meng, H and Wang, CC and Wen, SQ}, title = {Comparative Performance of the MGISEQ-2000 and Illumina X-Ten Sequencing Platforms for Paleogenomics.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {745508}, pmid = {34671385}, issn = {1664-8021}, abstract = {The MGISEQ-2000 sequencer is widely used in various omics studies, but the performance of this platform for paleogenomics has not been evaluated. We here compare the performance of MGISEQ-2000 with the Illumina X-Ten on ancient human DNA using four samples from 1750BCE to 60CE. We found there were only slight differences between the two platforms in most parameters (duplication rate, sequencing bias, θ, δS, and λ). MGISEQ-2000 performed well on endogenous rate and library complexity although X-Ten had a higher average base quality and lower error rate. Our results suggest that MGISEQ-2000 and X-Ten have comparable performance, and MGISEQ-2000 can be an alternative platform for paleogenomics sequencing.}, }
@article {pmid34671160, year = {2021}, author = {Alpaslan-Roodenberg, S and Anthony, D and Babiker, H and Bánffy, E and Booth, T and Capone, P and Deshpande-Mukherjee, A and Eisenmann, S and Fehren-Schmitz, L and Frachetti, M and Fujita, R and Frieman, CJ and Fu, Q and Gibbon, V and Haak, W and Hajdinjak, M and Hofmann, KP and Holguin, B and Inomata, T and Kanzawa-Kiriyama, H and Keegan, W and Kelso, J and Krause, J and Kumaresan, G and Kusimba, C and Kusimba, S and Lalueza-Fox, C and Llamas, B and MacEachern, S and Mallick, S and Matsumura, H and Morales-Arce, AY and Matuzeviciute, GM and Mushrif-Tripathy, V and Nakatsuka, N and Nores, R and Ogola, C and Okumura, M and Patterson, N and Pinhasi, R and Prasad, SPR and Prendergast, ME and Punzo, JL and Reich, D and Sawafuji, R and Sawchuk, E and Schiffels, S and Sedig, J and Shnaider, S and Sirak, K and Skoglund, P and Slon, V and Snow, M and Soressi, M and Spriggs, M and Stockhammer, PW and Szécsényi-Nagy, A and Thangaraj, K and Tiesler, V and Tobler, R and Wang, CC and Warinner, C and Yasawardene, S and Zahir, M}, title = {Ethics of DNA research on human remains: five globally applicable guidelines.}, journal = {Nature}, volume = {599}, number = {7883}, pages = {41-46}, pmid = {34671160}, issn = {1476-4687}, support = {T32 GM007753/GM/NIGMS NIH HHS/United States ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {American Indian or Alaska Native ; Anthropology/ethics ; Archaeology/ethics ; *Cadaver ; Community-Institutional Relations ; DNA, Ancient/*analysis ; *Guidelines as Topic ; Human Genetics/*ethics ; Humans ; Indigenous Peoples ; *Internationality ; Molecular Biology/*ethics ; Stakeholder Participation ; Translations ; }, abstract = {We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.}, }
@article {pmid34671077, year = {2021}, author = {Andrews, AJ and Puncher, GN and Bernal-Casasola, D and Di Natale, A and Massari, F and Onar, V and Toker, NY and Hanke, A and Pavey, SA and Savojardo, C and Martelli, PL and Casadio, R and Cilli, E and Morales-Muñiz, A and Mantovani, B and Tinti, F and Cariani, A}, title = {Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {20744}, pmid = {34671077}, issn = {2045-2322}, mesh = {Animals ; Anthropogenic Effects ; Conservation of Natural Resources/methods ; DNA, Ancient/*chemistry ; Genetic Variation/*genetics ; Genotype ; Mediterranean Sea ; Tuna/*genetics ; }, abstract = {Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009-2012) specimens with archival (1911-1926) and archaeological (2nd century BCE-15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.}, }
@article {pmid34663498, year = {2021}, author = {Calvignac-Spencer, S and Düx, A and Gogarten, JF and Patrono, LV}, title = {Molecular archeology of human viruses.}, journal = {Advances in virus research}, volume = {111}, number = {}, pages = {31-61}, doi = {10.1016/bs.aivir.2021.07.002}, pmid = {34663498}, issn = {1557-8399}, mesh = {*Archaeology ; Genomics ; Humans ; *Viruses/genetics ; }, abstract = {The evolution of human-virus associations is usually reconstructed from contemporary patterns of genomic diversity. An intriguing, though still rarely implemented, alternative is to search for the genetic material of viruses in archeological and medical archive specimens to document evolution as it happened. In this chapter, we present lessons from ancient DNA research and incorporate insights from virology to explore the potential range of applications and likely limitations of archeovirological approaches. We also highlight the numerous questions archeovirology will hopefully allow us to tackle in the near future, and the main expected roadblocks to these avenues of research.}, }
@article {pmid34659342, year = {2021}, author = {Bini, C and Cilli, E and Sarno, S and Traversari, M and Fontani, F and Boattini, A and Pelotti, S and Luiselli, D}, title = {Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {720640}, pmid = {34659342}, issn = {1664-8021}, abstract = {Roccapelago (MO) is a small village located in the Northern Central Apennines, with a population of 31 inhabitants (2014). In 2010, more than 400 individuals dated between the end of the 16th and the 18th century, many of which partially mummified, were discovered in the crypt of the church. This small village, because of its geographical location and surrounding environment, seems to possess the characteristics of a genetic isolate, useful for population genetics and genealogical analyses. Thus, a diachronic study of DNA aimed at investigating the structure and dynamics of the population of Roccapelago over the about 4 centuries, was conducted by analyzing ancient and modern inhabitants of the village. The 14 modern samples were selected by considering both the founder surnames of the village, identified thanks to the study of parish registers, and the grandparent's criterion. From 25 ancient mummies, morphologically assigned to male individuals, the petrous bone, that harbors high DNA amounts, was selected for the DNA extraction. The quantification and qualitative assessment of total human male DNA were evaluated by a real-time PCR assay using the Quantifiler Trio DNA Quantification Kit and multiplex PCR of 27 Y-chromosome short tandem repeat (Y-STR) markers included in the Yfiler Plus PCR Amplification Kit, with seven rapidly mutating Y-STR loci for improving discrimination of male lineages, was performed to genotype the samples. Y-STRs were analyzed according to the criteria of ancient DNA (aDNA) analysis to ensure that authentic DNA typing results were obtained from these ancient samples. The molecular analysis showed the usefulness of the Y chromosome to identify historically relevant remains and discover patterns of relatedness in communities moving from anthropology to genetic genealogy and forensics.}, }
@article {pmid34656830, year = {2022}, author = {Wurst, C and Maixner, F and Castella, V and Cipollini, G and Hotz, G and Zink, A}, title = {The Lady from Basel's Barfüsserkirche - Molecular confirmation of the Mummy's identity through mitochondrial DNA of living relatives spanning 22 generations.}, journal = {Forensic science international. Genetics}, volume = {56}, number = {}, pages = {102604}, doi = {10.1016/j.fsigen.2021.102604}, pmid = {34656830}, issn = {1878-0326}, mesh = {DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Haplotypes ; Humans ; *Mummies ; Sequence Analysis, DNA ; }, abstract = {The identity of the mummified Lady from the Barfüsser Church in Basel, Switzerland has been unsolved for decades, despite the prominent location of the burial place in front of the choir screen. A recent multidisciplinary research approach came up with a possible candidate, Anna Catharina Bischoff who died in Basel in 1787 with an age of 69 years (1719-1787). To verify the identity of the mummy, genealogists of the Citizen Science Basel discovered three living individuals of the maternal lineage of two different family branches, separated from Anna Catharina Bischoff by up to 22 generations. In this study we compare the ancient mitochondrial DNA of the mummy recovered from a premolar to the mitochondrial DNA of these three candidates. Initially the mitochondrial hypervariable regions I and II of the living individuals were screened using the Sanger sequencing method. This was followed by a mitochondrial capture approach and next generation sequencing to enrich for the whole mitochondrial genome of the mummy and one living person. A full mitochondrial genome has been recovered of both individuals sharing an identical haplotype. The sequence was assigned to the mitochondrial haplogroup U5a1+!16192 including two private mutations 10006G and 16293C. Only by using an interdisciplinary approach combining ancient DNA analysis and genealogy a maternal lineage of a non-noble family spanning 22 generations could be confirmed.}, }
@article {pmid34655517, year = {2021}, author = {Ciucani, MM and Jensen, JK and Sinding, MS and Smith, O and Lucenti, SB and Rosengren, E and Rook, L and Tuveri, C and Arca, M and Cappellini, E and Galaverni, M and Randi, E and Guo, C and Zhang, G and Sicheritz-Pontén, T and Dalén, L and Gilbert, MTP and Gopalakrishnan, S}, title = {Evolutionary history of the extinct Sardinian dhole.}, journal = {Current biology : CB}, volume = {31}, number = {24}, pages = {5571-5579.e6}, doi = {10.1016/j.cub.2021.09.059}, pmid = {34655517}, issn = {1879-0445}, support = {681396/ERC_/European Research Council/International ; }, mesh = {Animals ; Biological Evolution ; *Canidae/genetics ; Dogs ; Gene Flow ; Genome ; Phylogeny ; }, abstract = {The Sardinian dhole (Cynotherium sardous)[1] was an iconic and unique canid species that was endemic to Sardinia and Corsica until it became extinct at the end of the Late Pleistocene.[2-5] Given its peculiar dental morphology, small body size, and high level of endemism, several extant canids have been proposed as possible relatives of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor.[3][,][6-9] Morphometric analyses[3][,][6][,][8-12] have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca-21,100-year-old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found that it represents a separate taxon from all other living canids from Eurasia, Africa, and North America, and that the Sardinian dhole lineage diverged from the Asian dhole ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, which ended approximately 500-300 ka, when the land bridge between Sardinia and mainland Italy was already broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids-probably a result of the long-term isolation-that could have contributed to the subsequent extinction of the Sardinian dhole.}, }
@article {pmid34643070, year = {2021}, author = {Boubli, JP and Janiak, MC and Porter, LM and de la Torre, S and Cortés-Ortiz, L and Da Silva, MNF and Rylands, AB and Nash, S and Bertuol, F and Byrne, H and Silva, FE and Rohe, F and de Vries, D and Beck, RMD and Ruiz-Gartzia, I and Kuderna, LFK and Marques-Bonet, T and Hrbek, T and Farias, IP and Van Heteren, AH and Roos, C}, title = {Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum.}, journal = {Zoological research}, volume = {42}, number = {6}, pages = {761-771}, pmid = {34643070}, issn = {2095-8137}, mesh = {Animal Distribution ; Animals ; Brazil ; Callitrichinae/*classification/*genetics ; DNA, Mitochondrial/*genetics ; *Phylogeny ; Species Specificity ; }, abstract = {The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimões-Amazonas rivers. However, reconciling this new biological evidence with current taxonomy, i.e., two subspecies, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris (Lönnberg, 1940), was problematic given the uncertainty as to whether Spix's pygmy marmoset (Cebuella pygmaea pygmaea) was collected north or south of the Napo and Solimões-Amazonas rivers, making it unclear to which of the two newly revealed species the name pygmaea would apply. Here, we present the first molecular data from Spix's type specimen of Cebuella pygmaea, as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality (Tabatinga) on both sides of the river. With these data, we can confirm the correct names of the two species identified, i.e., C. pygmaea for animals north of the Napo and Solimões-Amazonas rivers and C. niveiventris for animals south of these two rivers. Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to re-evaluate the geographical distribution for the two Cebuella species. We dated the split of these two species to 2.54 million years ago. We discuss additional, more recent, subdivisions within each lineage, as well as potential contact zones between the two species in the headwaters of these rivers.}, }
@article {pmid34630530, year = {2021}, author = {Ning, C and Zheng, HX and Zhang, F and Wu, S and Li, C and Zhao, Y and Xu, Y and Wei, D and Wu, Y and Gao, S and Jin, L and Cui, Y}, title = {Ancient Mitochondrial Genomes Reveal Extensive Genetic Influence of the Steppe Pastoralists in Western Xinjiang.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {740167}, pmid = {34630530}, issn = {1664-8021}, abstract = {The population prehistory of Xinjiang has been a hot topic among geneticists, linguists, and archaeologists. Current ancient DNA studies in Xinjiang exclusively suggest an admixture model for the populations in Xinjiang since the early Bronze Age. However, almost all of these studies focused on the northern and eastern parts of Xinjiang; the prehistoric demographic processes that occurred in western Xinjiang have been seldomly reported. By analyzing complete mitochondrial sequences from the Xiabandi (XBD) cemetery (3,500-3,300 BP), the up-to-date earliest cemetery excavated in western Xinjiang, we show that all the XBD mitochondrial sequences fall within two different West Eurasian mitochondrial DNA (mtDNA) pools, indicating that the migrants into western Xinjiang from west Eurasians were a consequence of the early expansion of the middle and late Bronze Age steppe pastoralists (Steppe_MLBA), admixed with the indigenous populations from Central Asia. Our study provides genetic links for an early existence of the Indo-Iranian language in southwestern Xinjiang and suggests that the existence of Andronovo culture in western Xinjiang involved not only the dispersal of ideas but also population movement.}, }
@article {pmid34621003, year = {2021}, author = {Rio, J and Quilodrán, CS and Currat, M}, title = {Spatially explicit paleogenomic simulations support cohabitation with limited admixture between Bronze Age Central European populations.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {1163}, pmid = {34621003}, issn = {2399-3642}, mesh = {Archaeology ; DNA, Ancient/*analysis ; Europe ; Farmers ; *Genome, Human ; *Human Migration ; Humans ; }, abstract = {The Bronze Age is a complex period of social, cultural and economic changes. Recent paleogenomic studies have documented a large and rapid genetic change in early Bronze Age populations from Central Europe. However, the detailed demographic and genetic processes involved in this change are still debated. Here we have used spatially explicit simulations of genomic components to better characterize the demographic and migratory conditions that may have led to this change. We investigated various scenarios representing the expansion of pastoralists from the Pontic steppe, potentially linked to the Yamnaya cultural complex, and their interactions with local populations in Central Europe, considering various eco-evolutionary factors, such as population admixture, competition and long-distance dispersal. Our results do not support direct competition but rather the cohabitation of pastoralists and farmers in Central Europe, with limited gene flow between populations. They also suggest occasional long-distance migrations accompanying the expansion of pastoralists and a demographic decline in both populations following their initial contact. These results link recent archaeological and paleogenomic observations and move further the debate of genomic changes during the early Bronze Age.}, }
@article {pmid34618559, year = {2021}, author = {Kocher, A and Papac, L and Barquera, R and Key, FM and Spyrou, MA and Hübler, R and Rohrlach, AB and Aron, F and Stahl, R and Wissgott, A and van Bömmel, F and Pfefferkorn, M and Mittnik, A and Villalba-Mouco, V and Neumann, GU and Rivollat, M and van de Loosdrecht, MS and Majander, K and Tukhbatova, RI and Musralina, L and Ghalichi, A and Penske, S and Sabin, S and Michel, M and Gretzinger, J and Nelson, EA and Ferraz, T and Nägele, K and Parker, C and Keller, M and Guevara, EK and Feldman, M and Eisenmann, S and Skourtanioti, E and Giffin, K and Gnecchi-Ruscone, GA and Friederich, S and Schimmenti, V and Khartanovich, V and Karapetian, MK and Chaplygin, MS and Kufterin, VV and Khokhlov, AA and Chizhevsky, AA and Stashenkov, DA and Kochkina, AF and Tejedor-Rodríguez, C and de Lagrán, &#xcd;G and Arcusa-Magallón, H and Garrido-Pena, R and Royo-Guillén, JI and Nováček, J and Rottier, S and Kacki, S and Saintot, S and Kaverzneva, E and Belinskiy, AB and Velemínský, P and Limburský, P and Kostka, M and Loe, L and Popescu, E and Clarke, R and Lyons, A and Mortimer, R and Sajantila, A and de Armas, YC and Hernandez Godoy, ST and Hernández-Zaragoza, DI and Pearson, J and Binder, D and Lefranc, P and Kantorovich, AR and Maslov, VE and Lai, L and Zoledziewska, M and Beckett, JF and Langová, M and Danielisová, A and Ingman, T and Atiénzar, GG and de Miguel Ibáñez, MP and Romero, A and Sperduti, A and Beckett, S and Salter, SJ and Zilivinskaya, ED and Vasil'ev, DV and von Heyking, K and Burger, RL and Salazar, LC and Amkreutz, L and Navruzbekov, M and Rosenstock, E and Alonso-Fernández, C and Slavchev, V and Kalmykov, AA and Atabiev, BC and Batieva, E and Calmet, MA and Llamas, B and Schultz, M and Krauß, R and Jiménez-Echevarría, J and Francken, M and Shnaider, S and de Knijff, P and Altena, E and Van de Vijver, K and Fehren-Schmitz, L and Tung, TA and Lösch, S and Dobrovolskaya, M and Makarov, N and Read, C and Van Twest, M and Sagona, C and Ramsl, PC and Akar, M and Yener, KA and Ballestero, EC and Cucca, F and Mazzarello, V and Utrilla, P and Rademaker, K and Fernández-Domínguez, E and Baird, D and Semal, P and Márquez-Morfín, L and Roksandic, M and Steiner, H and Salazar-García, DC and Shishlina, N and Erdal, YS and Hallgren, F and Boyadzhiev, Y and Boyadzhiev, K and Küßner, M and Sayer, D and Onkamo, P and Skeates, R and Rojo-Guerra, M and Buzhilova, A and Khussainova, E and Djansugurova, LB and Beisenov, AZ and Samashev, Z and Massy, K and Mannino, M and Moiseyev, V and Mannermaa, K and Balanovsky, O and Deguilloux, MF and Reinhold, S and Hansen, S and Kitov, EP and Dobeš, M and Ernée, M and Meller, H and Alt, KW and Prüfer, K and Warinner, C and Schiffels, S and Stockhammer, PW and Bos, K and Posth, C and Herbig, A and Haak, W and Krause, J and Kühnert, D}, title = {Ten millennia of hepatitis B virus evolution.}, journal = {Science (New York, N.Y.)}, volume = {374}, number = {6564}, pages = {182-188}, doi = {10.1126/science.abi5658}, pmid = {34618559}, issn = {1095-9203}, mesh = {Americas ; Asia ; Asian People ; Communicable Diseases, Emerging/*history/virology ; Europe ; *Evolution, Molecular ; Genetic Variation ; Genomics ; Hepatitis B/*history/virology ; Hepatitis B virus/*classification/*genetics ; History, Ancient ; Humans ; Paleontology ; Phylogeny ; White People ; American Indian or Alaska Native ; }, abstract = {Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.}, }
@article {pmid34616690, year = {2021}, author = {Shiba, T and Komatsu, K and Sudo, T and Sawafuji, R and Saso, A and Ueda, S and Watanabe, T and Nemoto, T and Kano, C and Nagai, T and Ohsugi, Y and Katagiri, S and Takeuchi, Y and Kobayashi, H and Iwata, T}, title = {Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {723821}, pmid = {34616690}, issn = {2235-2988}, mesh = {Actinobacteria ; Actinomyces ; Bacteria/*classification ; Fusobacterium ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Japan ; *Periodontitis/diagnosis/history/microbiology ; Porphyromonas gingivalis ; Prevotella ; Treponema ; X-Ray Microtomography ; }, abstract = {Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603-1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history.}, }
@article {pmid34610848, year = {2021}, author = {Pfrengle, S and Neukamm, J and Guellil, M and Keller, M and Molak, M and Avanzi, C and Kushniarevich, A and Montes, N and Neumann, GU and Reiter, E and Tukhbatova, RI and Berezina, NY and Buzhilova, AP and Korobov, DS and Suppersberger Hamre, S and Matos, VMJ and Ferreira, MT and González-Garrido, L and Wasterlain, SN and Lopes, C and Santos, AL and Antunes-Ferreira, N and Duarte, V and Silva, AM and Melo, L and Sarkic, N and Saag, L and Tambets, K and Busso, P and Cole, ST and Avlasovich, A and Roberts, CA and Sheridan, A and Cessford, C and Robb, J and Krause, J and Scheib, CL and Inskip, SA and Schuenemann, VJ}, title = {Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {220}, pmid = {34610848}, issn = {1741-7007}, support = {/WT_/Wellcome Trust/United Kingdom ; 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Europe ; Genome, Bacterial/genetics ; Humans ; Leprosy/genetics ; *Mycobacterium leprae/genetics ; Population Dynamics ; }, abstract = {BACKGROUND: Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.<br><br>RESULTS: Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.<br><br>CONCLUSIONS: Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.}, }
@article {pmid34601464, year = {2021}, author = {Scheib, CL}, title = {Ancient Health Landscape: foundations and perspectives.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {99}, number = {}, pages = {167-170}, doi = {10.4436/JASS.99011}, pmid = {34601464}, issn = {2037-0644}, }
@article {pmid34601461, year = {2021}, author = {Hellenthal, G}, title = {Methodological challenges and opportunities for inferring human demography.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {99}, number = {}, pages = {175-177}, doi = {10.4436/JASS.99010}, pmid = {34601461}, issn = {2037-0644}, }
@article {pmid34601460, year = {2021}, author = {Bergström, A}, title = {From domestication genomics towards molecular ecology of human environments.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {99}, number = {}, pages = {163-166}, doi = {10.4436/JASS.99007}, pmid = {34601460}, issn = {2037-0644}, }
@article {pmid34593021, year = {2021}, author = {Granehäll, L and Huang, KD and Tett, A and Manghi, P and Paladin, A and O'Sullivan, N and Rota-Stabelli, O and Segata, N and Zink, A and Maixner, F}, title = {Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {197}, pmid = {34593021}, issn = {2049-2618}, mesh = {*Archaea/genetics ; Dental Calculus ; Humans ; *Metagenome ; Methanobrevibacter/genetics ; Middle Aged ; Phylogeny ; }, abstract = {BACKGROUND: Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE).<br><br>RESULTS: We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods.<br><br>CONCLUSIONS: We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract.}, }
@article {pmid34582623, year = {2022}, author = {Suchan, T and Kusliy, MA and Khan, N and Chauvey, L and Tonasso-Calvière, L and Schiavinato, S and Southon, J and Keller, M and Kitagawa, K and Krause, J and Bessudnov, AN and Bessudnov, AA and Graphodatsky, AS and Valenzuela-Lamas, S and Wilczyński, J and Pospuła, S and Tunia, K and Nowak, M and Moskal-delHoyo, M and Tishkin, AA and Pryor, AJE and Outram, AK and Orlando, L}, title = {Performance and automation of ancient DNA capture with RNA hyRAD probes.}, journal = {Molecular ecology resources}, volume = {22}, number = {3}, pages = {891-907}, pmid = {34582623}, issn = {1755-0998}, support = {//CNRS International Research Project (IRP AMADEUS)/ ; //CNRS Programme de Recherche Conjoint (PRC)/ ; 681605//H2020 European Research Council/ ; 797449//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 19-59-15001//Russian Foundation for Basic Research/ ; //University Paul Sabatier IDEX Chaire d'Excellence (OURASI)/ ; }, mesh = {Animals ; Automation ; *DNA, Ancient ; Horses/genetics ; *RNA/genetics ; RNA Probes ; Sequence Analysis, DNA/methods ; }, abstract = {DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%-30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post-mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.}, }
@article {pmid34573393, year = {2021}, author = {Vai, S and Lari, M and Caramelli, D}, title = {Ancient and Archaic Genomes.}, journal = {Genes}, volume = {12}, number = {9}, pages = {}, pmid = {34573393}, issn = {2073-4425}, mesh = {Animals ; *DNA, Ancient/analysis ; Evolution, Molecular ; Fossils/pathology ; Genome/*genetics ; Genome, Human ; History, Ancient ; Hominidae/genetics ; Humans ; }, abstract = {The first data obtained from ancient DNA samples were published more than thirty years ago [...].}, }
@article {pmid34569945, year = {2021}, author = {Rotival, M and Quintana-Murci, L}, title = {Towards a functional understanding of adaptive phenotypes in humans.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {99}, number = {}, pages = {171-174}, doi = {10.4436/JASS.99006}, pmid = {34569945}, issn = {2037-0644}, }
@article {pmid34555285, year = {2021}, author = {Card, DC and Shapiro, B and Giribet, G and Moritz, C and Edwards, SV}, title = {Museum Genomics.}, journal = {Annual review of genetics}, volume = {55}, number = {}, pages = {633-659}, doi = {10.1146/annurev-genet-071719-020506}, pmid = {34555285}, issn = {1545-2948}, mesh = {Biodiversity ; Biological Evolution ; *Genomics ; *Museums ; Reproducibility of Results ; }, abstract = {Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.}, }
@article {pmid34554811, year = {2021}, author = {Liu, Y and Mao, X and Krause, J and Fu, Q}, title = {Insights into human history from the first decade of ancient human genomics.}, journal = {Science (New York, N.Y.)}, volume = {373}, number = {6562}, pages = {1479-1484}, doi = {10.1126/science.abi8202}, pmid = {34554811}, issn = {1095-9203}, mesh = {Africa ; Americas ; Animals ; Asia ; Biological Evolution ; *DNA, Ancient ; Europe ; *Genome, Human ; *Genomics ; History, Ancient ; Human Migration ; Humans ; Neanderthals/genetics ; Oceania ; *Population Dynamics ; Siberia ; }, abstract = {Recent advancements in DNA sequencing technologies and laboratory preparation protocols have rapidly expanded the scope of ancient DNA research over the past decade, both temporally and geographically. Discoveries include interactions between archaic and modern humans as well as modern human population dynamics, including those coinciding with the Last Glacial Maximum and the settlement history of most world regions. This new type of data allows us to examine the deep past of human population dynamics and sharpen the current understanding of our present. The continued development in the ancient DNA field has transformed our understanding of human genetic history and will keep uncovering the further mysteries of our recent evolutionary past.}, }
@article {pmid34547027, year = {2021}, author = {Wu, X and Ning, C and Key, FM and Andrades Valtueña, A and Lankapalli, AK and Gao, S and Yang, X and Zhang, F and Liu, L and Nie, Z and Ma, J and Krause, J and Herbig, A and Cui, Y}, title = {A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road.}, journal = {PLoS pathogens}, volume = {17}, number = {9}, pages = {e1009886}, pmid = {34547027}, issn = {1553-7374}, support = {646612/ERC_/European Research Council/International ; }, mesh = {China ; DNA, Ancient ; Evolution, Molecular ; History, Ancient ; Humans ; Phylogeny ; Salmonella Infections/*genetics/*history/*transmission ; Salmonella enterica/*genetics ; Virulence Factors/genetics ; }, abstract = {Salmonella enterica (S. enterica) has infected humans for a long time, but its evolutionary history and geographic spread across Eurasia is still poorly understood. Here, we screened for pathogen DNA in 14 ancient individuals from the Bronze Age Quanergou cemetery (XBQ), Xinjiang, China. In 6 individuals we detected S. enterica. We reconstructed S. enterica genomes from those individuals, which form a previously undetected phylogenetic branch basal to Paratyphi C, Typhisuis and Choleraesuis-the so-called Para C lineage. Based on pseudogene frequency, our analysis suggests that the ancient S. enterica strains were not host adapted. One genome, however, harbors the Salmonella pathogenicity island 7 (SPI-7), which is thought to be involved in (para)typhoid disease in humans. This offers first evidence that SPI-7 was acquired prior to the emergence of human-adapted Paratyphi C around 1,000 years ago. Altogether, our results show that Salmonella enterica infected humans in Eastern Eurasia at least 3,000 years ago, and provide the first ancient DNA evidence for the spread of a pathogen along the Proto-Silk Road.}, }
@article {pmid34533260, year = {2022}, author = {Tamburrini, C and de Saint Pierre, M and Bravi, CM and Bailliet, G and Jurado Medina, L and Velázquez, IF and Real, LE and Holley, A and Tedeschi, CM and Basso, NG and Parolin, ML}, title = {Uniparental origins of the admixed Argentine Patagonia.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {34}, number = {4}, pages = {e23682}, doi = {10.1002/ajhb.23682}, pmid = {34533260}, issn = {1520-6300}, mesh = {*DNA, Mitochondrial/genetics ; Genetic Markers ; *Genetics, Population ; Haplotypes ; Humans ; Male ; Racial Groups ; }, abstract = {OBJECTIVES: We aimed to contribute to the understanding of the ancient geographic origins of the uniparentally inherited markers in modern admixed Argentinian populations from central Patagonia with new information provided for the city of Trelew. We attempted to highlight the importance of combining different genetic markers when studying population history.<br><br>METHODS: The mtDNA control region sequence was typified in 89 individuals and 12 Y-STR and 15 Y-SNP loci were analyzed in 66 males. With these data, analysis of molecular variance and Network analyses were carried out. We exhaustively compared the modern data with ancient mtDNA information. Finally, we tested the differences in continental origins estimated by uniparental and previously published biparental markers.<br><br>RESULTS: Native American mtDNAs (53.9%) increased when maternal ancestors were born in the northern (81.8%) and southern (58.5%) regions of Argentina or in Chile (77.8%). Population substructure was only observed for Y-chromosome haplotypes. Some mtDNA haplogroups have been present in the area for at least ca. 2762-2430 and ca. 500 (D1g and D1g4 haplogroups) and ca. 6736 and ca. 6620 (C1b and C1c haplogroups) years, respectively. In contrast, haplogroups B2i2 and C1b13, frequent in modern Patagonia populations, had not been found in previous ancient DNA studies of the region.<br><br>CONCLUSIONS: The results suggest that Native American ancestry is well preserved in the region. Trelew samples had characteristic native mtDNA haplogroups previously described in Chilean and Argentine Patagonian populations, but not observed in ancient samples until now. These findings support the idea that these lineages have a recent regional origin. Finally, the estimated proportions of continental ancestry depend on the genetic marker analyzed.}, }
@article {pmid34527890, year = {2021}, author = {de-Dios, T and Carrión, P and Olalde, I and Llovera Nadal, L and Lizano, E and Pàmies, D and Marques-Bonet, T and Balloux, F and van Dorp, L and Lalueza-Fox, C}, title = {Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts.}, journal = {iScience}, volume = {24}, number = {9}, pages = {103021}, pmid = {34527890}, issn = {2589-0042}, abstract = {Ancient pathogen genomics is an emerging field allowing reconstruction of past epidemics. The demise of post-contact American populations may, at least in part, have been caused by paratyphoid fever brought by Europeans. We retrieved genome-wide data from two Spanish soldiers who were besieging the city of Barcelona in 1652, during the Reapers' War. Their ancestry derived from the Basque region and Sardinia, respectively, (at that time, this island belonged to the Spanish kingdom). Despite the proposed plague epidemic, we could not find solid evidence for the presence of the causative plague agent in these individuals. However, we retrieved from one individual a substantial fraction of the Salmonella enterica serovar Paratyphi C lineage linked to paratyphoid fever in colonial period Mexico. Our results support a growing body of evidence that Paratyphi C enteric fever was more prevalent in Europe and the Americas in the past than it is today.}, }
@article {pmid34521843, year = {2021}, author = {Ringbauer, H and Novembre, J and Steinrücken, M}, title = {Parental relatedness through time revealed by runs of homozygosity in ancient DNA.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5425}, pmid = {34521843}, issn = {2041-1723}, support = {R01 GM132383/GM/NIGMS NIH HHS/United States ; R01 HG007089/HG/NHGRI NIH HHS/United States ; }, mesh = {Agriculture/history ; DNA, Ancient/*analysis ; Female ; *Genome, Human ; *Haplotypes ; History, Ancient ; *Homozygote ; Humans ; *Inheritance Patterns ; Male ; Population Dynamics/*history ; }, abstract = {Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.}, }
@article {pmid34518562, year = {2021}, author = {Silva, M and Oteo-García, G and Martiniano, R and Guimarães, J and von Tersch, M and Madour, A and Shoeib, T and Fichera, A and Justeau, P and Foody, MGB and McGrath, K and Barrachina, A and Palomar, V and Dulias, K and Yau, B and Gandini, F and Clarke, DJ and Rosa, A and Brehm, A and Flaquer, A and Rito, T and Olivieri, A and Achilli, A and Torroni, A and Gómez-Carballa, A and Salas, A and Bryk, J and Ditchfield, PW and Alexander, M and Pala, M and Soares, PA and Edwards, CJ and Richards, MB}, title = {Biomolecular insights into North African-related ancestry, mobility and diet in eleventh-century Al-Andalus.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18121}, pmid = {34518562}, issn = {2045-2322}, mesh = {Africa, Northern ; Anthropology ; Archaeology ; *Diet ; Genetic Background ; *Genetics, Population ; Genome, Human ; History, Medieval ; *Human Migration ; Humans ; Phylogeny ; Phylogeography ; Spain ; }, abstract = {Historical records document medieval immigration from North Africa to Iberia to create Islamic al-Andalus. Here, we present a low-coverage genome of an eleventh century CE man buried in an Islamic necropolis in Segorbe, near Valencia, Spain. Uniparental lineages indicate North African ancestry, but at the autosomal level he displays a mosaic of North African and European-like ancestries, distinct from any present-day population. Altogether, the genome-wide evidence, stable isotope results and the age of the burial indicate that his ancestry was ultimately a result of admixture between recently arrived Amazigh people (Berbers) and the population inhabiting the Peninsula prior to the Islamic conquest. We detect differences between our sample and a previously published group of contemporary individuals from Valencia, exemplifying how detailed, small-scale aDNA studies can illuminate fine-grained regional and temporal differences. His genome demonstrates how ancient DNA studies can capture portraits of past genetic variation that have been erased by later demographic shifts-in this case, most likely the seventeenth century CE expulsion of formerly Islamic communities as tolerance dissipated following the Reconquista by the Catholic kingdoms of the north.}, }
@article {pmid34499030, year = {2021}, author = {Pimenoff, VN and Houldcroft, CJ}, title = {How infectious diseases arrived in the colonial Americas.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34499030}, issn = {2050-084X}, mesh = {Americas/epidemiology ; *Communicable Diseases/epidemiology ; Humans ; Mexico/epidemiology ; }, abstract = {Analysis of viral DNA from human remains suggests that the transatlantic slave trade may have introduced new pathogens that contributed to the devastating disease outbreaks in colonial Mexico.}, }
@article {pmid34483440, year = {2021}, author = {Sedig, JW and Olade, I and Patterson, N and Harney, &#xc9; and Reich, D}, title = {COMBINING ANCIENT DNA AND RADIOCARBON DATING DATA TO INCREASE CHRONOLOGICAL ACCURACY.}, journal = {Journal of archaeological science}, volume = {133}, number = {}, pages = {}, pmid = {34483440}, issn = {0305-4403}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; }, abstract = {This paper examines how ancient DNA data can enhance radiocarbon dating. Because there is a limit to the number of years that can separate the dates of death of related individuals, the ability to identify relatives through ancient DNA analysis can serve as a constraint on radiocarbon date range estimates. To determine the number of years that can separate related individuals, we modeled maximums derived from biological extremes of human reproduction and death ages and compiled data from historic and genealogical death records. We used these data to jointly study the date ranges of a global dataset of individuals that have been radiocarbon dated and for which ancient DNA analysis identified at least one relative. We found that many of these individuals could have their date uncertainties reduced by building in date of death separation constraints. We examined possible reasons for date discrepancies of related individuals, such as dating of different skeletal elements or wiggles in the radiocarbon curve. We also developed a program, refinedate, which researchers can download and use to help refine the radiocarbon date distributions of related individuals. Our research demonstrates that when combined, radiocarbon dating and ancient DNA analysis can provide a refined and richer view of the past.}, }
@article {pmid34475454, year = {2021}, author = {Kehlmaier, C and López-Jurado, LF and Hernández-Acosta, N and Mateo-Miras, A and Fritz, U}, title = {"Ancient DNA" reveals that the scientific name for an extinct tortoise from Cape Verde refers to an extant South American species.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17537}, pmid = {34475454}, issn = {2045-2322}, mesh = {Animals ; Cabo Verde ; DNA, Ancient/*analysis ; *Ecosystem ; *Extinction, Biological ; Genome, Mitochondrial ; Phylogeny ; South America ; Turtles/classification/*genetics ; }, abstract = {We examined the type material of the extinct tortoise species Geochelone atlantica López-Jurado, Mateo and García-Márquez, 1998 from Sal Island, Cape Verde, using aDNA approaches and AMS radiocarbon dating. High-quality mitochondrial genomes obtained from the three type specimens support that all type material belongs to the same individual. In phylogenetic analyses using mitochondrial genomes of all species groups and genera of extant and some recently extinct tortoises, the type material clusters within the extant South American red-footed tortoise Chelonoidis carbonarius (Spix, 1824). Our radiocarbon date indicates that the tortoise from which the type series of G. atlantica originates was still alive during 1962 and 1974. These results provide firm evidence that the type material of G. atlantica does not belong to the Quaternary tortoise bones excavated on Sal Island in the 1930s, as originally thought. Thus, the extinct tortoise species remains unstudied and lacks a scientific name, and the name G. atlantica has to be relegated into the synonymy of C. carbonarius. The circumstances that led to this confusion currently cannot be disentangled.}, }
@article {pmid34465619, year = {2021}, author = {Bramanti, B and Wu, Y and Yang, R and Cui, Y and Stenseth, NC}, title = {Assessing the origins of the European Plagues following the Black Death: A synthesis of genomic, historical, and ecological information.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {36}, pages = {}, pmid = {34465619}, issn = {1091-6490}, mesh = {DNA, Bacterial/genetics ; Europe ; Genome, Bacterial/genetics ; Genomics/methods ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Humans ; Pandemics/history ; Phylogeny ; Plague/*epidemiology/*etiology/*genetics ; Virulence/genetics ; Yersinia pestis/genetics/pathogenicity ; }, abstract = {The second plague pandemic started in Europe with the Black Death in 1346 and lasted until the 19th century. Based on ancient DNA studies, there is a scientific disagreement over whether the bacterium, Yersinia pestis, came into Europe once (Hypothesis 1) or repeatedly over the following four centuries (Hypothesis 2). Here, we synthesize the most updated phylogeny together with historical, archeological, evolutionary, and ecological information. On the basis of this holistic view, we conclude that Hypothesis 2 is the most plausible. We also suggest that Y. pestis lineages might have developed attenuated virulence during transmission, which can explain the convergent evolutionary signals, including pla decay, that appeared at the end of the pandemics.}, }
@article {pmid34459345, year = {2021}, author = {Feldman, M and Gnecchi-Ruscone, GA and Lamnidis, TC and Posth, C}, title = {Where Asia meets Europe - recent insights from ancient human genomics.}, journal = {Annals of human biology}, volume = {48}, number = {3}, pages = {191-202}, doi = {10.1080/03014460.2021.1949039}, pmid = {34459345}, issn = {1464-5033}, mesh = {Animals ; Asia ; DNA, Ancient/*analysis ; Europe ; *Gene Flow ; *Genome, Human ; Genomics ; *Human Migration ; Humans ; Middle East ; }, abstract = {CONTEXT: The peopling of Europe by modern humans is a widely debated topic in the field of modern and ancient genomics. While several recent syntheses have focussed on this topic, little has been discussed about the genetic history of populations in the continent's surrounding regions.<br><br>OBJECTIVE: We explore genetic transformations in three key areas that played an essential role in the formation of the European genetic landscape through time, focussing on the periods spanning from the Epipalaeolithic/Mesolithic and up until the Iron Age.<br><br>METHODS: We review published ancient genomic studies and integrate the associated data to provide a quantification and visualisation of major trends in the population histories of the Near East, the western Eurasian Steppe and North East Europe.<br><br>RESULTS: We describe cross-regional as well as localised prehistoric demographic shifts and discuss potential research directions while highlighting geo-temporal gaps in the data.<br><br>CONCLUSION: In recent years, archaeogenetic studies have contributed to the understanding of human genetic diversity through time in regions located at the doorstep of Europe. Further studies focussing on these areas will allow for a better characterisation of genetic shifts and regionally-specific patterns of admixture across western Eurasia.}, }
@article {pmid34459344, year = {2021}, author = {Modi, A and Vai, S and Posth, C and Vergata, C and Zaro, V and Diroma, MA and Boschin, F and Capecchi, G and Ricci, S and Ronchitelli, A and Catalano, G and Lauria, G and D'Amore, G and Sineo, L and Caramelli, D and Lari, M}, title = {More data on ancient human mitogenome variability in Italy: new mitochondrial genome sequences from three Upper Palaeolithic burials.}, journal = {Annals of human biology}, volume = {48}, number = {3}, pages = {213-222}, doi = {10.1080/03014460.2021.1942549}, pmid = {34459344}, issn = {1464-5033}, mesh = {Archaeology ; DNA, Ancient/*analysis ; *Genome, Human ; *Genome, Mitochondrial ; Humans ; Italy ; }, abstract = {BACKGROUND: Recently, the study of mitochondrial variability in ancient humans has allowed the definition of population dynamics that characterised Europe in the Late Pleistocene and Early Holocene. Despite the abundance of sites and skeletal remains few data are available for Italy.<br><br>AIM: We reconstructed the mitochondrial genomes of three Upper Palaeolithic individuals for some of the most important Italian archaeological contexts: Paglicci (South-Eastern Italy), San Teodoro (South-Western Italy) and Arene Candide (North-Western Italy) caves.<br><br>SUBJECTS AND METHODS: We explored the phylogenetic relationships of the three mitogenomes in the context of Western Eurasian ancient and modern variability.<br><br>RESULTS: Paglicci 12 belongs to sub-haplogroup U8c, described in only two other Gravettian individuals; San Teodoro 2 harbours a U2'3'4'7'8'9 sequence, the only lineage found in Sicily during the Late Pleistocene and Early Holocene; Arene Candide 16 displays an ancestral U5b1 haplotype already detected in other Late Pleistocene hunter-gatherers from Central Europe.<br><br>CONCLUSION: Regional genetic continuity is highlighted in the Gravettian groups that succeeded in Paglicci. Data from one of the oldest human remains from Sicily reinforce the hypothesis that Epigravettian groups carrying U2'3'4'7'8'9 could be the first inhabitants of the island. The first pre-Neolithic mitogenome from North-Western Italy, sequenced here, shows more affinity with continental Europe than with the Italian peninsula.}, }
@article {pmid34459342, year = {2021}, author = {Serrano, JG and Ordóñez, AC and Fregel, R}, title = {Paleogenomics of the prehistory of Europe: human migrations, domestication and disease.}, journal = {Annals of human biology}, volume = {48}, number = {3}, pages = {179-190}, doi = {10.1080/03014460.2021.1942205}, pmid = {34459342}, issn = {1464-5033}, mesh = {Archaeology ; Communicable Diseases/*epidemiology/microbiology/parasitology/virology ; DNA, Ancient/*analysis ; *Domestication ; Europe ; *Genome, Human ; Genomics ; *Human Migration ; Humans ; }, abstract = {A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate.}, }
@article {pmid34459340, year = {2021}, author = {Sarno, S and Cilli, E and Serventi, P and De Fanti, S and Corona, A and Fontani, F and Traversari, M and Ferri, G and Fariselli, AC and Luiselli, D}, title = {Insights into Punic genetic signatures in the southern necropolis of Tharros (Sardinia).}, journal = {Annals of human biology}, volume = {48}, number = {3}, pages = {247-259}, doi = {10.1080/03014460.2021.1937699}, pmid = {34459340}, issn = {1464-5033}, mesh = {Child ; Child, Preschool ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Female ; *Genetic Variation ; *Human Migration ; Humans ; Infant ; Infant, Newborn ; Italy ; Male ; Population Dynamics ; Tunisia ; }, abstract = {BACKGROUND: Phoenician and Punic expansions have been protagonists of intense trade networks and settlements in the Mediterranean Sea.<br><br>AIMS: The maternal genetic variability of ancient Punic samples from the Sardinian necropolis of Tharros was analysed, with the aim to explore genetic interactions and signatures of past population events.<br><br>SUBJECTS AND METHODS: The mtDNA HVS-I and coding region SNPs were analysed in 14 Punic samples and 74 modern individuals from Cabras and Belv&#xec; (for which the HVS-II region was also analysed). The results were compared with 5,590 modern Euro-Mediterranean sequences and 127 ancient samples.<br><br>RESULTS: While contemporary groups fall within the genetic variability of other modern Sardinians, our Punic samples reveal proximity to present-day North-African and Iberian populations. Furthermore, Cabras and Belv&#xec; cluster mainly with pre-Phoenician groups, while samples from Tharros project with other Punic Sardinian individuals.<br><br>CONCLUSION: This study provides the first preliminary insights into the population dynamics of the Punic site of Tharros. While the number of currently available samples does not allow definitive investigation of the connection with indigenous Sardinian groups, our results seem to confirm internal migratory phenomena in the central-western Mediterranean and female participation in the Punic mobility.}, }
@article {pmid34459338, year = {2021}, author = {De Angelis, F and Veltre, V and Romboni, M and Di Corcia, T and Scano, G and Martínez-Labarga, C and Catalano, P and Rickards, O}, title = {Ancient genomes from a rural site in Imperial Rome (1[st]-3[rd] cent. CE): a genetic junction in the Roman Empire.}, journal = {Annals of human biology}, volume = {48}, number = {3}, pages = {234-246}, doi = {10.1080/03014460.2021.1944313}, pmid = {34459338}, issn = {1464-5033}, mesh = {Adolescent ; Archaeology ; Child ; Child, Preschool ; DNA, Ancient/*analysis ; Female ; *Genome, Human ; *Human Migration ; Humans ; Infant ; Infant, Newborn ; Italy ; Male ; Roman World ; *Rural Population ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Rome became the prosperous Capital of the Roman Empire through the political and military conquests of neighbouring areas. People were able to move Romeward modifying the Rome area's demographic structure. However, the genomic evidence for the population of one of the broadest Empires in antiquity has been sparse until recently.<br><br>AIM: The genomic analysis of people buried in Quarto Cappello del Prete (QCP) necropolis was carried out to help elucidate the genomic structure of Imperial Rome inhabitants.<br><br>SUBJECTS AND METHODS: We recruited twenty-five individuals from QCP for ancient DNA analysis through whole-genome sequencing. Multiple investigations were carried out to unveil the genetic components featuring in the studied samples and the community's putative demographic structure.<br><br>RESULTS: We generated reliable whole-genome data for 7 samples surviving quality controls. The distribution of Imperial Romans from QCP partly overlaps with present-day Southern Mediterranean and Southern-Near Eastern populations.<br><br>CONCLUSION: The genomic legacy with the south-eastern shores of the Mediterranean Sea and the Central and Western Northern-African coast funerary influence pave the way for considering people buried in QCP as resembling a Punic-derived human group.}, }
@article {pmid34456378, year = {2020}, author = {Forin, N and Vizzini, A and Nigris, S and Ercole, E and Voyron, S and Girlanda, M and Baldan, B}, title = {Illuminating type collections of nectriaceous fungi in Saccardo's fungarium.}, journal = {Persoonia}, volume = {45}, number = {}, pages = {221-249}, pmid = {34456378}, issn = {0031-5850}, abstract = {Specimens of Nectria spp. and Nectriella rufofusca were obtained from the fungarium of Pier Andrea Saccardo, and investigated via a morphological and molecular approach based on MiSeq technology. ITS1 and ITS2 sequences were successfully obtained from 24 specimens identified as 'Nectria' sensu Saccardo (including 20 types) and from the type specimen of Nectriella rufofusca. For Nectria ambigua, N. radians and N. tjibodensis only the ITS1 sequence was recovered. On the basis of morphological and molecular analyses new nomenclatural combinations for Nectria albofimbriata, N. ambigua, N. ambigua var. pallens, N. granuligera, N. peziza subsp. reyesiana, N. radians, N. squamuligera, N. tjibodensis and new synonymies for N. congesta, N. flageoletiana, N. phyllostachydis, N. sordescens and N. tjibodensis var. crebrior are proposed. Furthermore, the current classification is confirmed for Nectria coronata, N. cyanostoma, N. dolichospora, N. illudens, N. leucotricha, N. mantuana, N. raripila and Nectriella rufofusca. This is the first time that these more than 100-yr-old specimens are subjected to molecular analysis, thereby providing important new DNA sequence data authentic for these names.}, }
@article {pmid34456066, year = {2021}, author = {Raxworthy, CJ and Smith, BT}, title = {Mining museums for historical DNA: advances and challenges in museomics.}, journal = {Trends in ecology &amp; evolution}, volume = {36}, number = {11}, pages = {1049-1060}, doi = {10.1016/j.tree.2021.07.009}, pmid = {34456066}, issn = {1872-8383}, mesh = {Biological Evolution ; *DNA/genetics ; *Museums ; Sequence Analysis, DNA/methods ; Specimen Handling/methods ; }, abstract = {Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.}, }
@article {pmid34455262, year = {2021}, author = {Buck, LT and Katz, DC and Ackermann, RR and Hlusko, LJ and Kanthaswamy, S and Weaver, TD}, title = {Effects of hybridization on pelvic morphology: A macaque model.}, journal = {Journal of human evolution}, volume = {159}, number = {}, pages = {103049}, doi = {10.1016/j.jhevol.2021.103049}, pmid = {34455262}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Fossils ; *Hominidae ; Macaca ; *Neanderthals ; Pelvis ; }, abstract = {Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.}, }
@article {pmid34442857, year = {2021}, author = {Nwosu, EC and Roeser, P and Yang, S and Ganzert, L and Dellwig, O and Pinkerneil, S and Brauer, A and Dittmann, E and Wagner, D and Liebner, S}, title = {From Water into Sediment-Tracing Freshwater Cyanobacteria via DNA Analyses.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442857}, issn = {2076-2607}, support = {BR2208/11-1//Deutsche Forschungsgemeinschaft/ ; VH-NG-919//Helmholtz-Gemeinschaft/ ; SAW-2017-IOW-2 649//Leibniz-Gemeinschaft/ ; Terrestrial Environmental Observatory Infrastructure Initiative (TERENO Observatory NE Germany//Helmholtz Association/ ; }, abstract = {Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May-October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations.}, }
@article {pmid34437844, year = {2021}, author = {Brealey, JC and Leitão, HG and Hofstede, T and Kalthoff, DC and Guschanski, K}, title = {The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans.}, journal = {Current biology : CB}, volume = {31}, number = {20}, pages = {4650-4658.e6}, doi = {10.1016/j.cub.2021.08.010}, pmid = {34437844}, issn = {1879-0445}, mesh = {Animals ; Animals, Wild ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; *Microbiota/genetics ; Sweden ; *Ursidae ; }, abstract = {Following the advent of industrial-scale antibiotic production in the 1940s,[1] antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.[2][,][3] Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.[4] However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.[4][,][5] One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.}, }
@article {pmid34429408, year = {2021}, author = {Beyer, RM and Krapp, M and Eriksson, A and Manica, A}, title = {Climatic windows for human migration out of Africa in the past 300,000 years.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4889}, pmid = {34429408}, issn = {2041-1723}, mesh = {Africa ; Animals ; Biological Evolution ; *DNA, Ancient ; Emigration and Immigration ; Fossils ; Genetic Variation ; Genome, Human ; History, Ancient ; Hominidae/*genetics ; Human Migration/*history ; Humans ; Models, Genetic ; }, abstract = {Whilst an African origin of modern humans is well established, the timings and routes of their expansions into Eurasia are the subject of heated debate, due to the scarcity of fossils and the lack of suitably old ancient DNA. Here, we use high-resolution palaeoclimate reconstructions to estimate how difficult it would have been for humans in terms of rainfall availability to leave the African continent in the past 300k years. We then combine these results with an anthropologically and ecologically motivated estimate of the minimum level of rainfall required by hunter-gatherers to survive, allowing us to reconstruct when, and along which geographic paths, expansions out of Africa would have been climatically feasible. The estimated timings and routes of potential contact with Eurasia are compatible with archaeological and genetic evidence of human expansions out of Africa, highlighting the key role of palaeoclimate variability for modern human dispersals.}, }
@article {pmid34428961, year = {2021}, author = {Dussex, N and Bergfeldt, N and de Anca Prado, V and Dehasque, M and Díez-Del-Molino, D and Ersmark, E and Kanellidou, F and Larsson, P and Lemež, &#x160; and Lord, E and Mármol-Sánchez, E and Meleg, IN and Måsviken, J and Naidoo, T and Studerus, J and Vicente, M and von Seth, J and Götherström, A and Dalén, L and Heintzman, PD}, title = {Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1957}, pages = {20211252}, pmid = {34428961}, issn = {1471-2954}, mesh = {*DNA, Ancient ; *Ecosystem ; Fossils ; Geologic Sediments ; }, abstract = {Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.}, }
@article {pmid34428419, year = {2021}, author = {Linderholm, A}, title = {Palaeogenetics: Dirt, what is it good for? Everything.}, journal = {Current biology : CB}, volume = {31}, number = {16}, pages = {R993-R995}, doi = {10.1016/j.cub.2021.06.074}, pmid = {34428419}, issn = {1879-0445}, mesh = {*DNA, Ancient ; *Geologic Sediments ; }, abstract = {Researchers in the ancient DNA community have suspected for well over a decade that ancient whole genomes can be found in sediments. Three new studies now provide such evidence and, with it, endless possibilities for future studies of sedimentary ancient DNA.}, }
@article {pmid34424926, year = {2021}, author = {Zacho, CM and Bager, MA and Margaryan, A and Gravlund, P and Galatius, A and Rasmussen, AR and Allentoft, ME}, title = {Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0256353}, pmid = {34424926}, issn = {1932-6203}, mesh = {Animals ; *Ethanol ; *Metagenomics/methods ; *Genomics/methods ; Snakes/genetics ; Museums ; DNA, Ancient/analysis ; Genome ; Sequence Analysis, DNA/methods ; Liver/metabolism ; Preservation, Biological/methods ; Metagenome ; }, abstract = {Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.}, }
@article {pmid34424406, year = {2021}, author = {Kumar, L and Farias, K and Prakash, S and Mishra, A and Mustak, MS and Rai, N and Thangaraj, K}, title = {Dissecting the genetic history of the Roman Catholic populations of West Coast India.}, journal = {Human genetics}, volume = {140}, number = {10}, pages = {1487-1498}, pmid = {34424406}, issn = {1432-1203}, mesh = {*Catholicism ; Ethnicity/*genetics/statistics &amp; numerical data ; Europe ; *Evolution, Molecular ; *Genetic Variation ; Genetics, Population/*statistics &amp; numerical data ; *Geography ; Humans ; India ; Jews/genetics ; Phylogeny ; *Population Dynamics ; }, abstract = {Migration and admixture history of populations have always been curious and an interesting theme. The West Coast of India harbours a rich diversity, bestowing various ethno-linguistic groups, with many of them having well-documented history of migrations. The Roman Catholic is one such distinct group, whose origin was much debated. While some historians and anthropologists relating them to ancient group of Gaud Saraswat Brahmins, others relating them for being members of the Jews Lost Tribes in the first Century migration to India. Historical records suggests that this community was later forcibly converted to Christianity by the Portuguese in Goa during the Sixteenth Century. Till date, no genetic study was done on this group to infer their origin and genetic affinity. Hence, we analysed 110 Roman Catholics from three different locations of West Coast of India including Goa, Kumta and Mangalore using both uniparental and autosomal markers to understand their genetic history. We found that the Roman Catholics have close affinity with the Indo-European linguistic groups, particularly Brahmins. Additionally, we detected genetic signal of Jews in the linkage disequilibrium-based admixture analysis, which was absent in other Indo-European populations, who are inhabited in the same geographical regions. Haplotype-based analysis suggests that the Roman Catholics consist of South Asian-specific ancestry and showed high drift. Ancestry-specific historical population size estimation points to a possible bottleneck around the time of Goan inquisition (fifteenth century). Analysis of the Roman Catholics data along with ancient DNA data of Neolithic and bronze age revealed that the Roman Catholics fits well in a basic model of ancient ancestral composition, typical of most of the Indo-European caste groups of India. Mitochondrial DNA (mtDNA) analysis suggests that most of the Roman Catholics have aboriginal Indian maternal genetic ancestry; while the Y chromosomal DNA analysis indicates high frequency of R1a lineage, which is predominant in groups with higher ancestral North Indian (ANI) component. Therefore, we conclude that the Roman Catholics of Goa, Kumta and Mangalore regions are the remnants of very early lineages of Brahmin community of India, having Indo-Europeans genetic affinity along with cryptic Jewish admixture, which needs to be explored further.}, }
@article {pmid34422004, year = {2021}, author = {Irving-Pease, EK and Muktupavela, R and Dannemann, M and Racimo, F}, title = {Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution?.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {703541}, pmid = {34422004}, issn = {1664-8021}, abstract = {Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human archaeological remains are now easier than ever to obtain, and provide a direct window into changes in frequencies of trait-associated alleles in the past. This has generated a new wave of studies aiming to analyse the genetic component of traits in historic and prehistoric times using ancient DNA, and to determine whether any such traits were subject to natural selection. In humans, however, issues about the portability and robustness of complex trait inference across different populations are particularly concerning when predictions are extended to individuals that died thousands of years ago, and for which little, if any, phenotypic validation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodate ancient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations.}, }
@article {pmid34421956, year = {2021}, author = {Li, W and Ma, Q and Yin, P and Wen, J and Pei, Y and Niu, L and Lin, H}, title = {The GA 20-Oxidase Encoding Gene MSD1 Controls the Main Stem Elongation in Medicago truncatula.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {709625}, pmid = {34421956}, issn = {1664-462X}, abstract = {Plant height is an important agronomic trait that is closely related to biomass yield and crop production. Despite legumes comprise one of the largest monophyletic families that are second only to grasses in terms of economic and nutritional values, due to an ancient genome duplication event, most legume plants have complex genomes, thus the molecular mechanisms that determine plant height are less known in legumes. Here, we report the identification and characterization of MAIN STEM DWARF1 (MSD1), which is required for the plant height in the model legume Medicago truncatula. Loss of function of MSD1 leads to severely reduced main stem height but normal lateral branch elongation in M. truncatula. Histological analysis revealed that the msd1-1 main stem has shorter internodes with reduced cell size and number compared with the wild type, indicating that MSD1 affects cell elongation and cell proliferation. MSD1 encodes a putative GA 20-oxidase that is expressed at significantly higher levels in the main shoot apex than in the lateral shoot apices, suggesting that MSD1 expression is associated with its effect on the main stem elongation. UPLC-MS/MS analysis showed that GA9 and GA4, two identified products of the GA 20-oxidase, were severely reduced in msd1-1, and the dwarf phenotype of msd1-1 could be rescued by supplementation with gibberellic acid GA3, confirming that MSD1 functions as a biologically active GA 20-oxidase. Moreover, we found that disruption of either MtGA20ox7 or MtGA20ox8, homologs of MSD1, has little effects on the elongation of the main stem, while the msd1-1 mtga20ox7-1 mtga20ox8 triple mutants exhibits a severe short main shoot and lateral branches, as well as reduced leaf size, suggesting that MSD1 and its homologs MtGA20ox7 and MtGA20ox8, redundantly regulate M. truncatula shoot elongation and leaf development. Taken together, our findings demonstrate the molecular mechanism of MSD1-mediated regulation of main stem elongation in M. truncatula and provide insights into understanding the functional diversity of GA 20-oxidases in optimizing plant architecture in legumes.}, }
@article {pmid34419425, year = {2021}, author = {Liu, Y and Wang, T and Wu, X and Fan, X and Wang, W and Xie, G and Li, Z and Yang, Q and Cao, P and Yang, R and Liu, F and Dai, Q and Feng, X and Ping, W and Miao, B and Wu, Y and Liu, Y and Fu, Q}, title = {Maternal genetic history of southern East Asians over the past 12,000 years.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {48}, number = {10}, pages = {899-907}, doi = {10.1016/j.jgg.2021.06.002}, pmid = {34419425}, issn = {1673-8527}, support = {55008731/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Female ; Humans ; Asia, Eastern ; *Asian People/genetics ; China ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Genetics, Population ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; History, Ancient ; Maternal Inheritance/genetics ; }, abstract = {Southern East Asia, including Guangxi and Fujian provinces in China, is home to diverse ethnic groups, languages, and cultures. Previous studies suggest a high complexity regarding population dynamics and the history of southern East Asians. However, large-scale genetic studies on ancient populations in this region are hindered by limited sample preservation. Here, using highly efficient DNA capture techniques, we obtain 48 complete mitochondrial genomes of individuals from Guangxi and Fujian in China and reconstruct their maternal genetic history over the past 12,000 years. We find a strong connection between southern East Asians dating to ~12,000-6000 years ago and present-day Southeast Asians. In addition, stronger genetic affinities to northern East Asians are observed in historical southern East Asians than Neolithic southern East Asians, suggesting increased interactions between northern and southern East Asians over time. Overall, we reveal dynamic connections between ancient southern East Asians and populations located in surrounding regions, as well as a shift in maternal genetic structure within the populations over time.}, }
@article {pmid34411538, year = {2021}, author = {Kivisild, T and Saag, L and Hui, R and Biagini, SA and Pankratov, V and D'Atanasio, E and Pagani, L and Saag, L and Rootsi, S and Mägi, R and Metspalu, E and Valk, H and Malve, M and Irdt, K and Reisberg, T and Solnik, A and Scheib, CL and Seidman, DN and Williams, AL and ,  and Tambets, K and Metspalu, M}, title = {Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population.}, journal = {American journal of human genetics}, volume = {108}, number = {9}, pages = {1792-1806}, pmid = {34411538}, issn = {1537-6605}, support = {/WT_/Wellcome Trust/United Kingdom ; 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; R35 GM133805/GM/NIGMS NIH HHS/United States ; 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Alleles ; DNA, Ancient/*analysis ; Estonia ; Female ; Finland ; Gene Frequency ; Genealogy and Heraldry ; *Genome, Human ; High-Throughput Nucleotide Sequencing ; History, 21st Century ; History, Ancient ; History, Medieval ; Human Migration/*history ; Humans ; Language/history ; Male ; *Pedigree ; }, abstract = {The Finnish population is a unique example of a genetic isolate affected by a recent founder event. Previous studies have suggested that the ancestors of Finnic-speaking Finns and Estonians reached the circum-Baltic region by the 1[st] millennium BC. However, high linguistic similarity points to a more recent split of their languages. To study genetic connectedness between Finns and Estonians directly, we first assessed the efficacy of imputation of low-coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23×) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1× coverage can be reliably used in principal-component analyses without projection. By searching for long shared allele intervals (LSAIs; similar to identity-by-descent segments) in unphased data for >143,000 present-day Estonians, 99 Finns, and 14 imputed ancient genomes from Estonia, we find unexpectedly high levels of individual connectedness between Estonians and Finns for the last eight centuries in contrast to their clear differentiation by allele frequencies. High levels of sharing of these segments between Estonians and Finns predate the demographic expansion and late settlement process of Finland. One plausible source of this extensive sharing is the 8[th]-10[th] centuries AD migration event from North Estonia to Finland that has been proposed to explain uniquely shared linguistic features between the Finnish language and the northern dialect of Estonian and shared Christianity-related loanwords from Slavic. These results suggest that LSAI detection provides a computationally tractable way to detect fine-scale structure in large cohorts.}, }
@article {pmid34410642, year = {2021}, author = {Moore, NE and Weyrich, LS}, title = {A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2327}, number = {}, pages = {93-118}, pmid = {34410642}, issn = {1940-6029}, mesh = {DNA, Ancient ; *Dental Calculus ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Ancient dental calculus provides a challenging, yet unparalleled, opportunity to reconstruct ancient oral microbial communities and trace the origins of modern microbiota-associated diseases. Metagenomic analysis of ancient dental calculus using high-throughput DNA sequencing has proven itself as an effective method to accurately reconstruct microorganisms that once lived in the mouths of ancient humans. Here, we provide the strategy, methodologies, and approaches used to establish an ancient dental calculus project, from project conception, community engagement, sampling, extracting DNA, and preparing shotgun metagenomic DNA libraries for sequencing on an Illumina platform. We also discuss techniques to minimize background or contaminant DNA by monitoring and reducing contamination in calculus data sets, utilizing appropriate protective gear, and employing the use of sample decontamination strategies. In this methodology chapter, we hope to promote transparency in the ancient dental calculus research field and encourage collaboration across the ancient DNA research community.}, }
@article {pmid34410389, year = {2021}, author = {Sato, T and Adachi, N and Kimura, R and Hosomichi, K and Yoneda, M and Oota, H and Tajima, A and Toyoda, A and Kanzawa-Kiriyama, H and Matsumae, H and Koganebuchi, K and Shimizu, KK and Shinoda, KI and Hanihara, T and Weber, A and Kato, H and Ishida, H}, title = {Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan.}, journal = {Genome biology and evolution}, volume = {13}, number = {9}, pages = {}, pmid = {34410389}, issn = {1759-6653}, mesh = {Asia, Eastern ; Female ; *Genome, Human ; *Genomics ; Human Migration ; Humans ; Japan ; Paleontology ; Skeleton ; }, abstract = {Recent studies on paleogenomics have reported some Paleolithic and Neolithic genomes that have provided new insights into the human population history in East and Northeast Asia. However, there remain some cases where more recent migration events need to be examined to elucidate the detailed formation process of local populations. Although the area around northern Japan is one of the regions archaeologically suggested to have been affected by migration waves after the Neolithic period, the genetic source of these migrations are still unclear. Thus, genomic data from such past migrant populations would be highly informative to clarify the detailed formation process of local populations in this region. Here, we report the genome sequence of a 900-year-old adult female (NAT002) belonging to the prehistoric Okhotsk people, who have been considered to be the past migrants to northern Japan after the Neolithic period. We found a close relationship between NAT002 and modern Lower Amur populations and past admixture events between the Amur, Jomon, and Kamchatka ancestries. The admixture dating suggested migration of Amur-related ancestry at approximately 1,600 BP, which is compatible with the archaeological evidence regarding the settlement of the Okhotsk people. Our results also imply migration of Kamchatka-related ancestry at approximately 2,000 BP. In addition, human leukocyte antigen (HLA) typing detected the HLA-B*40 allele, which is reported to increase the risk of arthritis, suggesting the genetic vulnerability of NAT002 to hyperostosis, which was observed around her chest clavicle.}, }
@article {pmid34408163, year = {2021}, author = {Freilich, S and Ringbauer, H and Los, D and Novak, M and Pavičić, DT and Schiffels, S and Pinhasi, R}, title = {Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {16729}, pmid = {34408163}, issn = {2045-2322}, mesh = {*Archaeology ; Croatia ; *DNA, Ancient ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Male ; }, abstract = {Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies. Present-day Croatia lies at the heart of ancient migration routes through Europe, yet our knowledge about social and genetic processes here remains sparse. To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE-400 CE from two sites in present-day eastern Croatia. In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple closely related males suggesting a patrilocal social organisation. We also find in that community an unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today.}, }
@article {pmid34395085, year = {2021}, author = {Borry, M and Hübner, A and Rohrlach, AB and Warinner, C}, title = {PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11845}, pmid = {34395085}, issn = {2167-8359}, abstract = {DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets.}, }
@article {pmid34394175, year = {2021}, author = {Lysak, MA and Weiss-Schneeweiss, H}, title = {Editorial: Chromosomal Evolution in Plants.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {726330}, pmid = {34394175}, issn = {1664-462X}, }
@article {pmid34386259, year = {2021}, author = {Segawa, T and Yonezawa, T and Mori, H and Akiyoshi, A and Allentoft, ME and Kohno, A and Tokanai, F and Willerslev, E and Kohno, N and Nishihara, H}, title = {Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages.}, journal = {Royal Society open science}, volume = {8}, number = {8}, pages = {210518}, pmid = {34386259}, issn = {2054-5703}, abstract = {Little is known about how mammalian biogeography on islands was affected by sea-level fluctuations. In the Japanese Archipelago, brown bears (Ursus arctos) currently inhabit only Hokkaido, the northern island, but Pleistocene fossils indicate a past distribution throughout Honshu, Japan's largest island. However, the difficulty of recovering ancient DNA from fossils in temperate East Asia has limited our understanding of their evolutionary history. Here, we analysed mitochondrial DNA from a 32 500-year-old brown bear fossil from Honshu. Our results show that this individual belonged to a previously unknown lineage that split approximately 160 Ka from its sister lineage, the southern Hokkaido clade. This divergence time and fossil record suggest that brown bears migrated from the Eurasian continent to Honshu at least twice; the first population was an early-diverging lineage (greater than 340 Ka), and the second migrated via Hokkaido after approximately 160 Ka, during the ice age. Thus, glacial-age sea-level falls might have facilitated migrations of large mammals more frequently than previously thought, which may have had a substantial impact on ecosystem dynamics in these isolated islands.}, }
@article {pmid34374411, year = {2021}, author = {Syndercombe Court, D}, title = {Mitochondrial DNA in forensic use.}, journal = {Emerging topics in life sciences}, volume = {5}, number = {3}, pages = {415-426}, pmid = {34374411}, issn = {2397-8554}, mesh = {*DNA, Mitochondrial/genetics ; *Forensic Genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria/genetics ; Sequence Analysis, DNA ; }, abstract = {Genetic analysis of mitochondrial DNA (mtDNA) has always been a useful tool for forensic geneticists, mainly because of its ubiquitous presence in biological material, even in the absence of nuclear DNA. Sequencing, however, is not a skill that is part of the routine forensic analysis because of the relative rarity of requests, and the need for retention of necessary skill sets and associated accreditation issues. While standard Sanger sequencing may be relatively simple, many requests are made in the face of compromised biological samples. Newer technologies, provided through massively parallel sequencing (MPS), will increase the opportunity for scientists to include this tool in their routine, particularly for missing person investigations. MPS has also enabled a different approach to sequencing that can increase sensitivity in a more targeted approach. In these circumstances it is likely that only a laboratory that specialises in undertaking forensic mtDNA analysis will be able to take these difficult cases forward, more so because reviews of the literature have revealed significantly high levels of typing errors in publications reporting mtDNA sequences. The forensic community has set out important guidelines, not only in the practical aspects of analysis, but also in the interpretation of that sequence to ensure that accurate comparisons can be made. Analysis of low-level, compromised and ancient DNA is not easy, however, as contamination is extremely difficult to eliminate and circumstances leading to sequencing errors are all too easily introduced. These problems, and solutions, are discussed in the article in relation to several historic cases.}, }
@article {pmid34350829, year = {2021}, author = {Guzmán-Solís, AA and Villa-Islas, V and Bravo-López, MJ and Sandoval-Velasco, M and Wesp, JK and Gómez-Valdés, JA and Moreno-Cabrera, ML and Meraz, A and Solís-Pichardo, G and Schaaf, P and TenOever, BR and Blanco-Melo, D and Ávila Arcos, MC}, title = {Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34350829}, issn = {2050-084X}, support = {/WT_/Wellcome Trust/United Kingdom ; 208934/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Black People/history ; DNA, Ancient/*analysis ; Enslaved Persons/*history ; Genome, Viral/*genetics ; Hepatitis B virus/*genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; History, 16th Century ; History, 17th Century ; History, 18th Century ; Humans ; Metagenomics ; Parvovirus B19, Human/*genetics/isolation &amp; purification ; }, abstract = {After the European colonization of the Americas, there was a dramatic population collapse of the Indigenous inhabitants caused in part by the introduction of new pathogens. Although there is much speculation on the etiology of the Colonial epidemics, direct evidence for the presence of specific viruses during the Colonial era is lacking. To uncover the diversity of viral pathogens during this period, we designed an enrichment assay targeting ancient DNA (aDNA) from viruses of clinical importance and applied it to DNA extracts from individuals found in a Colonial hospital and a Colonial chapel (16th-18th century) where records suggest that victims of epidemics were buried during important outbreaks in Mexico City. This allowed us to reconstruct three ancient human parvovirus B19 genomes and one ancient human hepatitis B virus genome from distinct individuals. The viral genomes are similar to African strains, consistent with the inferred morphological and genetic African ancestry of the hosts as well as with the isotopic analysis of the human remains, suggesting an origin on the African continent. This study provides direct molecular evidence of ancient viruses being transported to the Americas during the transatlantic slave trade and their subsequent introduction to New Spain. Altogether, our observations enrich the discussion about the etiology of infectious diseases during the Colonial period in Mexico.}, }
@article {pmid34335597, year = {2021}, author = {Haller, M and Bonczarowska, JH and Rieger, D and Lenz, TL and Nebel, A and Krause-Kyora, B}, title = {Ancient DNA Study in Medieval Europeans Shows an Association Between HLA-DRB1*03 and Paratyphoid Fever.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {691475}, pmid = {34335597}, issn = {1664-3224}, mesh = {DNA, Ancient ; Genetic Predisposition to Disease ; Germany ; HLA-DRB1 Chains/*genetics ; Humans ; Paratyphoid Fever/*genetics ; White People/*genetics ; }, abstract = {Outbreaks of infectious diseases repeatedly affected medieval Europe, leaving behind a large number of dead often inhumed in mass graves. Human remains interred in two burial pits from 14[th] century CE Germany exhibited molecular evidence of Salmonella enterica Paratyphi C (S. Paratyphi C) infection. The pathogen is responsible for paratyphoid fever, which was likely the cause of death for the buried individuals. This finding presented the unique opportunity to conduct a paratyphoid fever association study in a European population. We focused on HLA-DRB1*03:01 that is a known risk allele for enteric fever in present-day South Asians. We generated HLA profiles for 29 medieval S. Paratyphi C cases and 24 contemporaneous controls and compared these to a modern German population. The frequency of the risk allele was higher in the medieval cases (29.6%) compared to the contemporaneous controls (13%; p = 0.189), albeit not significantly so, possibly because of small sample sizes. Indeed, in comparison with the modern controls (n = 39,689; 10.2%; p = 0.005) the frequency difference became statistically significant. This comparison also suggested a slight decrease in the allele's prevalence between the medieval and modern controls. Up to now, this is the first study on the genetic predisposition to Salmonella infection in Europeans and the only association analysis on paratyphoid fever C. Functional investigation using computational binding prediction between HLA variants and S. Paratyphi and S. Typhi peptides supported a reduced recognition capacity of bacterial proteins by DRB1*03:01 relative to other common DRB1 variants. This pattern could potentially explain the disease association. Our results suggest a slightly reduced predisposition to paratyphoid fever in modern Europeans. The causative allele, however, is still common today, which can be explained by a trade-off, as DRB1*03:01 is protective against infectious respiratory diseases such as severe respiratory syndrome (SARS). It is thus possible that the allele also provided resistance to corona-like viruses in the past.}, }
@article {pmid34332322, year = {2021}, author = {Wang, M and He, G and Zou, X and Liu, J and Ye, Z and Ming, T and Du, W and Wang, Z and Hou, Y}, title = {Genetic insights into the paternal admixture history of Chinese Mongolians via high-resolution customized Y-SNP SNaPshot panels.}, journal = {Forensic science international. Genetics}, volume = {54}, number = {}, pages = {102565}, doi = {10.1016/j.fsigen.2021.102565}, pmid = {34332322}, issn = {1878-0326}, mesh = {China ; Chromosomes, Human, Y ; Ethnicity/genetics ; Genetics, Population ; Haplotypes ; Humans ; *Language ; Microsatellite Repeats ; *Polymorphism, Single Nucleotide ; }, abstract = {The Mongolian people, one of the Mongolic-speaking populations, are native to the Mongolian Plateau in North China and southern Siberia. Many ancient DNA studies recently reported extensive population transformations during the Paleolithic to historic periods in this region, while little is known about the paternal genetic legacy of modern geographically different Mongolians. Here, we genotyped 215 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and 37 Y-chromosomal short tandem repeats (Y-STRs) among 679 Mongolian individuals from Hohhot, Hulunbuir, and Ordos in North China using the AGCU Y37 kit and our developed eight Y-SNP SNaPshot panels (including two panels first reported herein). The C-M130 Y-SNP SNaPshot panel defines 28 subhaplogroups, and the N/O/Q complementary Y-SNP SNaPshot panel defines 30 subhaplogroups of N1b-F2930, N1a1a1a1a3-B197, Q-M242, and O2a2b1a1a1a4a-CTS4658, which improved the resolution our developed Y-SNP SNaPshot panel set and could be applied for dissecting the finer-scale paternal lineages of Mongolic speakers. We found a strong association between Mongolian-prevailing haplogroups and some observed microvariants among the newly generated Y-STR haplotype data, suggesting the possibility of haplogroup prediction based on the distribution of Y-STR haplotypes. We identified three main ancestral sources of the observed Mongolian-dominant haplogroups, including the local lineage of C2*-M217 and incoming lineages from other regions of southern East Asia (O2*-M122, O1b*-P31, and N1*-CTS3750) and western Eurasia (R1*-M173). We also observed DE-M145, D1*-M174, C1*-F3393, G*-M201, I-M170, J*-M304, L-M20, O1a*-M119, and Q*-M242 at relatively low frequencies (< 5.00%), suggesting a complex admixture history between Mongolians and other incoming Eurasians from surrounding regions. Genetic clustering analyses indicated that the studied Mongolians showed close genetic affinities with other Altaic-speaking populations and Sinitic-speaking Hui people. The Y-SNP haplotype/haplogroup-based genetic legacy not only revealed that the stratification among geographically/linguistically/ethnically different Chinese populations was highly consistent with the geographical division and language classification, but also demonstrated that patrilineal genetic materials could provide fine-scale genetic structures among geographically different Mongolian people, suggesting that our developed high-resolution Y-SNP SNaPshot panels have the potential for forensic pedigree searches and biogeographical ancestry inference.}, }
@article {pmid34330702, year = {2021}, author = {Rijal, DP and Heintzman, PD and Lammers, Y and Yoccoz, NG and Lorberau, KE and Pitelkova, I and Goslar, T and Murguzur, FJA and Salonen, JS and Helmens, KF and Bakke, J and Edwards, ME and Alm, T and Bråthen, KA and Brown, AG and Alsos, IG}, title = {Sedimentary ancient DNA shows terrestrial plant richness continuously increased over the Holocene in northern Fennoscandia.}, journal = {Science advances}, volume = {7}, number = {31}, pages = {}, pmid = {34330702}, issn = {2375-2548}, mesh = {Climate Change ; *DNA, Ancient ; Ecosystem ; Humans ; Lakes ; *Plants/genetics ; Pollen ; }, abstract = {The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that richness increased steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase thereafter, although the climate was stable, with richness and the regional species pool only stabilizing during the past three millennia. Furthermore, overall increases in richness were greater in catchments with higher soil nutrient availability. We suggest that richness will increase with ongoing warming, especially at localities with high nutrient availability and assuming that human activity remains low in the region, although lags of millennia may be expected.}, }
@article {pmid34320653, year = {2021}, author = {Kumar, V and Bennett, EA and Zhao, D and Liang, Y and Tang, Y and Ren, M and Dai, Q and Feng, X and Cao, P and Yang, R and Liu, F and Ping, W and Zhang, M and Ding, M and Yang, MA and Amridin, B and Muttalib, H and Wang, J and Fu, Q}, title = {Genetic Continuity of Bronze Age Ancestry with Increased Steppe-Related Ancestry in Late Iron Age Uzbekistan.}, journal = {Molecular biology and evolution}, volume = {38}, number = {11}, pages = {4908-4917}, pmid = {34320653}, issn = {1537-1719}, support = {55008731/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Archaeology ; DNA, Ancient ; Farmers ; Genome, Human ; History, Ancient ; *Human Migration ; Humans ; Iran ; Uzbekistan ; }, abstract = {Although Uzbekistan and Central Asia are known for the well-studied Bronze Age civilization of the Bactria-Margiana Archaeological Complex (BMAC), the lesser-known Iron Age was also a dynamic period that resulted in increased interaction and admixture among different cultures from this region. To broaden our understanding of events that impacted the demography and population structure of this region, we generated 27 genome-wide single-nucleotide polymorphism capture data sets of Late Iron Age individuals around the Historical Kushan time period (∼2100-1500 BP) from three sites in South Uzbekistan. Overall, Bronze Age ancestry persists into the Iron Age in Uzbekistan, with no major replacements of populations with Steppe-related ancestry. However, these individuals suggest diverse ancestries related to Iranian farmers, Anatolian farmers, and Steppe herders, with a small amount of West European Hunter Gatherer, East Asian, and South Asian Hunter Gatherer ancestry as well. Genetic affinity toward the Late Bronze Age Steppe herders and a higher Steppe-related ancestry than that found in BMAC populations suggest an increased mobility and interaction of individuals from the Northern Steppe in a Southward direction. In addition, a decrease of Iranian and an increase of Anatolian farmer-like ancestry in Uzbekistan Iron Age individuals were observed compared with the BMAC populations from Uzbekistan. Thus, despite continuity from the Bronze Age, increased admixture played a major role in the shift from the Bronze to the Iron Age in southern Uzbekistan. This mixed ancestry is also observed in other parts of the Steppe and Central Asia, suggesting more widespread admixture among local populations.}, }
@article {pmid34312252, year = {2021}, author = {Ottoni, C and Borić, D and Cheronet, O and Sparacello, V and Dori, I and Coppa, A and Antonović, D and Vujević, D and Price, TD and Pinhasi, R and Cristiani, E}, title = {Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {32}, pages = {}, pmid = {34312252}, issn = {1091-6490}, mesh = {Agriculture/*history ; Bacteria/genetics ; Balkan Peninsula ; *DNA, Ancient ; Dental Calculus/chemistry/*genetics/*microbiology ; Drug Resistance, Microbial/genetics ; Europe ; History, Ancient ; History, Medieval ; Humans ; Microbiota/*genetics ; Phylogeny ; Plants/chemistry ; }, abstract = {Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.}, }
@article {pmid34312232, year = {2021}, author = {Lazagabaster, IA and Rovelli, V and Fabre, PH and Porat, R and Ullman, M and Davidovich, U and Lavi, T and Ganor, A and Klein, E and Weiss, K and Nuriel, P and Meiri, M and Marom, N}, title = {Rare crested rat subfossils unveil Afro-Eurasian ecological corridors synchronous with early human dispersals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {31}, pages = {}, pmid = {34312232}, issn = {1091-6490}, mesh = {Africa ; *Animal Distribution ; Animals ; Asia ; Europe ; *Human Migration ; Humans ; Rodentia/*anatomy &amp; histology/physiology ; }, abstract = {Biotic interactions between Africa and Eurasia across the Levant have invoked particular attention among scientists aiming to unravel early human dispersals. However, it remains unclear whether behavioral capacities enabled early modern humans to surpass the Saharo-Arabian deserts or if climatic changes triggered punctuated dispersals out of Africa. Here, we report an unusual subfossil assemblage discovered in a Judean Desert's cliff cave near the Dead Sea and dated to between ∼42,000 and at least 103,000 y ago. Paleogenomic and morphological comparisons indicate that the specimens belong to an extinct subspecies of the eastern African crested rat, Lophiomys imhausi maremortum subspecies nova, which diverged from the modern eastern African populations in the late Middle Pleistocene ∼226,000 to 165,000 y ago. The reported paleomitogenome is the oldest so far in the Levant, opening the door for future paleoDNA analyses in the region. Species distribution modeling points to the presence of continuous habitat corridors connecting eastern Africa with the Levant during the Last Interglacial ∼129,000 to 116,000 y ago, providing further evidence of the northern ingression of African biomes into Eurasia and reinforcing previous suggestions of the critical role of climate change in Late Pleistocene intercontinental biogeography. Furthermore, our study complements other paleoenvironmental proxies with local-instead of interregional-paleoenvironmental data, opening an unprecedented window into the Dead Sea rift paleolandscape.}, }
@article {pmid34308549, year = {2021}, author = {Juras, A and Ehler, E and Chyleński, M and Pospieszny, &#x141; and Spinek, AE and Malmström, H and Krzewińska, M and Szostek, K and Pasterkiewicz, W and Florek, M and Wilk, S and Mnich, B and Kruk, J and Szmyt, M and Kozieł, S and Götherström, A and Jakobsson, M and Dabert, M}, title = {Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.}, journal = {American journal of physical anthropology}, volume = {176}, number = {2}, pages = {223-236}, doi = {10.1002/ajpa.24372}, pmid = {34308549}, issn = {1096-8644}, mesh = {Anthropology, Physical ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Haplotypes/genetics ; History, Ancient ; Humans ; Poland ; White People/*genetics ; }, abstract = {OBJECTIVE: We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe.<br><br>MATERIALS AND METHODS: We conducted ancient DNA studies from populations associated with Z&#x142;ota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture.<br><br>RESULTS: The maternal genetic composition found in Z&#x142;ota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Z&#x142;ota group, Globular Amphora, and Funnel Beaker cultures.<br><br>DISCUSSION: The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Z&#x142;ota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Z&#x142;ota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.}, }
@article {pmid34301898, year = {2021}, author = {Davesne, D and Friedman, M and Schmitt, AD and Fernandez, V and Carnevale, G and Ahlberg, PE and Sanchez, S and Benson, RBJ}, title = {Fossilized cell structures identify an ancient origin for the teleost whole-genome duplication.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {30}, pages = {}, pmid = {34301898}, issn = {1091-6490}, mesh = {Animals ; *Evolution, Molecular ; Fishes/*genetics ; *Fossils ; *Gene Duplication ; *Genome ; Genomics/*methods ; Phylogeny ; }, abstract = {Teleost fishes comprise one-half of all vertebrate species and possess a duplicated genome. This whole-genome duplication (WGD) occurred on the teleost stem lineage in an ancient common ancestor of all living teleosts and is hypothesized as a trigger of their exceptional evolutionary radiation. Genomic and phylogenetic data indicate that WGD occurred in the Mesozoic after the divergence of teleosts from their closest living relatives but before the origin of the extant teleost groups. However, these approaches cannot pinpoint WGD among the many extinct groups that populate this 50- to 100-million-y lineage, preventing tests of the evolutionary effects of WGD. We infer patterns of genome size evolution in fossil stem-group teleosts using high-resolution synchrotron X-ray tomography to measure the bone cell volumes, which correlate with genome size in living species. Our findings indicate that WGD occurred very early on the teleost stem lineage and that all extinct stem-group teleosts known so far possessed duplicated genomes. WGD therefore predates both the origin of proposed key innovations of the teleost skeleton and the onset of substantial morphological diversification in the clade. Moreover, the early occurrence of WGD allowed considerable time for postduplication reorganization prior to the origin of the teleost crown group. This suggests at most an indirect link between WGD and evolutionary success, with broad implications for the relationship between genomic architecture and large-scale evolutionary patterns in the vertebrate Tree of Life.}, }
@article {pmid34301878, year = {2021}, author = {Mitchell, KJ}, title = {Ancient DNA from the koala lemur puts Madagascar on the paleogenomic map.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {30}, pages = {}, pmid = {34301878}, issn = {1091-6490}, mesh = {Animal Distribution ; Animals ; Biological Evolution ; DNA/*genetics ; Genomics ; Lemuridae/*genetics ; Madagascar ; }, }
@article {pmid34294811, year = {2021}, author = {Rohrlach, AB and Papac, L and Childebayeva, A and Rivollat, M and Villalba-Mouco, V and Neumann, GU and Penske, S and Skourtanioti, E and van de Loosdrecht, M and Akar, M and Boyadzhiev, K and Boyadzhiev, Y and Deguilloux, MF and Dobeš, M and Erdal, YS and Ernée, M and Frangipane, M and Furmanek, M and Friederich, S and Ghesquière, E and Hałuszko, A and Hansen, S and Küßner, M and Mannino, M and Özbal, R and Reinhold, S and Rottier, S and Salazar-García, DC and Diaz, JS and Stockhammer, PW and de Togores Muñoz, CR and Yener, KA and Posth, C and Krause, J and Herbig, A and Haak, W}, title = {Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15005}, pmid = {34294811}, issn = {2045-2322}, mesh = {*Alleles ; *Chromosomes, Human, Y ; DNA, Mitochondrial ; Genetic Markers ; Genetic Testing ; *Genetics, Population/methods ; *Haplotypes ; Humans ; Polymorphism, Single Nucleotide ; }, abstract = {Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.}, }
@article {pmid34283930, year = {2021}, author = {Grewe, F and Kronforst, MR and Pierce, NE and Moreau, CS}, title = {Museum genomics reveals the Xerces blue butterfly (Glaucopsyche xerces) was a distinct species driven to extinction.}, journal = {Biology letters}, volume = {17}, number = {7}, pages = {20210123}, pmid = {34283930}, issn = {1744-957X}, support = {R35 GM131828/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Butterflies/genetics ; *Extinction, Biological ; *Genome, Mitochondrial ; Genomics ; Museums ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The last Xerces blue butterfly was seen in the early 1940s, and its extinction is credited to human urban development. This butterfly has become a North American icon for insect conservation, but some have questioned whether it was truly a distinct species, or simply an isolated population of another living species. To address this question, we leveraged next-generation sequencing using a 93-year-old museum specimen. We applied a genome skimming strategy that aimed for the organellar genome and high-copy fractions of the nuclear genome by a shallow sequencing approach. From these data, we were able to recover over 200 million nucleotides, which assembled into several phylogenetically informative markers and the near-complete mitochondrial genome. From our phylogenetic analyses and haplotype network analysis we conclude that the Xerces blue butterfly was a distinct species driven to extinction.}, }
@article {pmid34265517, year = {2021}, author = {Hofreiter, M and Sneberger, J and Pospisek, M and Vanek, D}, title = {Progress in forensic bone DNA analysis: Lessons learned from ancient DNA.}, journal = {Forensic science international. Genetics}, volume = {54}, number = {}, pages = {102538}, doi = {10.1016/j.fsigen.2021.102538}, pmid = {34265517}, issn = {1878-0326}, mesh = {Aged ; *DNA/genetics ; DNA Degradation, Necrotic ; DNA Fingerprinting ; *DNA, Ancient ; Forensic Genetics ; Humans ; }, abstract = {Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable.}, }
@article {pmid34256582, year = {2021}, author = {Rossi, C and Ruß-Popa, G and Mattiangeli, V and McDaid, F and Hare, AJ and Davoudi, H and Laleh, H and Lorzadeh, Z and Khazaeli, R and Fathi, H and Teasdale, MD and A'ali, A and Stöllner, T and Mashkour, M and Daly, KG}, title = {Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrābād, Iran.}, journal = {Biology letters}, volume = {17}, number = {7}, pages = {20210222}, pmid = {34256582}, issn = {1744-957X}, mesh = {Animals ; DNA, Ancient ; Genome ; Iran ; *Mummies ; Phenotype ; Sheep/genetics ; }, abstract = {Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole-genome sequences (3.94 X) of an approximately 1600-year-old naturally mummified sheep recovered from Chehrābād, a salt mine in northwestern Iran. Comparative analyses of published ancient sequences revealed the remarkable DNA integrity of this mummy. Hallmarks of postmortem damage, fragmentation and hydrolytic deamination are substantially reduced, likely owing to the high salinity of this taphonomic environment. Metagenomic analyses reflect the profound influence of high-salt content on decomposition; its microbial profile is predominated by halophilic archaea and bacteria, possibly contributing to the remarkable preservation of the sample. Applying population genomic analyses, we find clustering of this sheep with Southwest Asian modern breeds, suggesting ancestry continuity. Genotyping of a locus influencing the woolly phenotype showed the presence of an ancestral 'hairy' allele, consistent with hair fibre imaging. This, along with derived alleles associated with the fat-tail phenotype, provides genetic evidence that Sasanian-period Iranians maintained specialized sheep flocks for different uses, with the 'hairy', 'fat-tailed'-genotyped sheep likely kept by the rural community of Chehrābād's miners.}, }
@article {pmid34256019, year = {2021}, author = {Gelabert, P and Sawyer, S and Bergström, A and Margaryan, A and Collin, TC and Meshveliani, T and Belfer-Cohen, A and Lordkipanidze, D and Jakeli, N and Matskevich, Z and Bar-Oz, G and Fernandes, DM and Cheronet, O and Özdoğan, KT and Oberreiter, V and Feeney, RNM and Stahlschmidt, MC and Skoglund, P and Pinhasi, R}, title = {Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment.}, journal = {Current biology : CB}, volume = {31}, number = {16}, pages = {3564-3574.e9}, pmid = {34256019}, issn = {1879-0445}, support = {852558/ERC_/European Research Council/International ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Animals ; *Bison/genetics ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Georgia (Republic) ; Humans ; Phylogeny ; *Wolves/genetics ; }, abstract = {Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.}, }
@article {pmid34242562, year = {2021}, author = {Pinhasi, R and Douka, K}, title = {Before and after farming: The genetic structure of South China and Southeast Asia.}, journal = {Cell}, volume = {184}, number = {14}, pages = {3597-3598}, doi = {10.1016/j.cell.2021.06.016}, pmid = {34242562}, issn = {1097-4172}, mesh = {*Agriculture ; Asia, Southeastern ; China ; *DNA, Ancient ; Genetic Structures ; Humans ; }, abstract = {In this issue of Cell, Wang et al. harness ancient DNA methods to produce and analyze new genomic data from 31 individuals from South China, dated between 500 and 10,000-12,000 years ago. The study reveals a complex interplay between groups of three different genetic ancestries and provides a new perspective on interactions and agricultural dispersals in South China and Southeast Asia.}, }
@article {pmid34213855, year = {2021}, author = {Rotival, M and Cossart, P and Quintana-Murci, L}, title = {Reconstructing 50,000 years of human history from our DNA: lessons from modern genomics.}, journal = {Comptes rendus biologies}, volume = {344}, number = {2}, pages = {177-187}, doi = {10.5802/crbiol.55}, pmid = {34213855}, issn = {1768-3238}, mesh = {Africa ; Animals ; Archaeology ; *DNA ; Dogs ; Genome ; Genome, Human ; *Genomics ; History, Ancient ; Horses ; Humans ; }, abstract = {The advent of high throughput sequencing approaches and ancient DNA techniques have enabled reconstructing the history of human populations at an unprecedented level of resolution. The symposium from the French Academy of Sciences "50,000 ans d'épopée humaine dans notre ADN" has reviewed some of the latest contributions from the fields of genomics, archaeology, and linguistics to our understanding of >300,000 years of human history. DNA has revealed the richness of the human journey, from the deep divergences between human populations in Africa, to the first encounters of Homo Sapiens with other hominins on their way to Eurasia and the peopling of Remote Oceania. The symposium has also emphasized how migrations, cultural practices, and environmental pathogens have contributed to shape the genetic diversity of modern humans, through admixture, genetic drift or genetic adaptation. Finally, special attention was also given to how human behaviours have shaped the genome of other species, through the spreading of microbes and pathogens, as in the case of Yersinia Pestis, or through domestication, as elegantly demonstrated for dogs, horses, and apples. Altogether, this conference illustrated how the complex history of human populations is tightly linked with their contemporary genetic diversity that, in turn, has direct effects on their identity and health.}, }
@article {pmid34210535, year = {2021}, author = {de Vareilles, A and Pelling, R and Woodbridge, J and Fyfe, R}, title = {Archaeology and agriculture: plants, people, and past land-use.}, journal = {Trends in ecology &amp; evolution}, volume = {36}, number = {10}, pages = {943-954}, doi = {10.1016/j.tree.2021.06.003}, pmid = {34210535}, issn = {1872-8383}, mesh = {Agriculture ; *Archaeology ; *Botany ; Humans ; Plants ; }, abstract = {As a specialised branch of archaeology requiring specific field and laboratory methodologies, the contributions of archaeobotany have often been overlooked by the ecological research community. Developments in the fields of botany, chemistry, and ancient DNA analyses have greatly increased the potential for archaeobotany to contribute to topical questions relating to the Anthropocene and landscape transformations. We review the role of archaeobotany in identifying and describing past arable land use. Analytical techniques are illustrated with examples at both local and regional scales, demonstrating how archaeobotany can provide unique details of the wide array of past subsistence and land-use strategies. These data and their potential should be better recognised as important information that could underpin models seeking to evaluate or predict the effects of socioenvironmental interactions.}, }
@article {pmid34208224, year = {2021}, author = {Vai, S and Diroma, MA and Cannariato, C and Budnik, A and Lari, M and Caramelli, D and Pilli, E}, title = {How a Paleogenomic Approach Can Provide Details on Bioarchaeological Reconstruction: A Case Study from the Globular Amphorae Culture.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34208224}, issn = {2073-4425}, mesh = {Archaeology/*methods ; Biological Evolution ; *DNA, Ancient ; Genome, Human ; Genomics/*methods ; Humans ; Pedigree ; Social Evolution ; }, abstract = {Ancient human remains have the potential to explain a great deal about the prehistory of humankind. Due to recent technological and bioinformatics advances, their study, at the palaeogenomic level, can provide important information about population dynamics, culture changes, and the lifestyles of our ancestors. In this study, mitochondrial and nuclear genome data obtained from human bone remains associated with the Neolithic Globular Amphorae culture, which were recovered in the Megalithic barrow of Kierzkowo (Poland), were reanalysed to gain insight into the social organisation and use of the archaeological site and to provide information at the individual level. We were able to successfully estimate the minimum number of individuals, sex, kin relationships, and phenotypic traits of the buried individuals, despite the low level of preservation of the bone samples and the intricate taphonomic conditions. In addition, the evaluation of damage patterns allowed us to highlight the presence of "intruders"-that is, of more recent skeletal remains that did not belong to the original burial. Due to its characteristics, the study of the Kierzkowo barrow represented a challenge for the reconstruction of the biological profile of the human community who exploited it and an excellent example of the contribution that ancient genomic analysis can provide to archaeological reconstruction.}, }
@article {pmid34206575, year = {2021}, author = {Klecel, W and Martyniuk, E}, title = {From the Eurasian Steppes to the Roman Circuses: A Review of Early Development of Horse Breeding and Management.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {7}, pages = {}, pmid = {34206575}, issn = {2076-2615}, abstract = {The domestication of the horse began about 5500 years ago in the Eurasian steppes. In the following millennia horses spread across the ancient world, and their role in transportation and warfare affected every ancient culture. Ownership of horses became an indicator of wealth and social status. The importance of horses led to a growing interest in their breeding and management. Many phenotypic traits, such as height, behavior, and speed potential, have been proven to be a subject of selection; however, the details of ancient breeding practices remain mostly unknown. From the fourth millennium BP, through the Iron Age, many literature sources thoroughly describe horse training systems, as well as various aspects of husbandry, many of which are still in use today. The striking resemblance of ancient and modern equine practices leaves us wondering how much was accomplished through four thousand years of horse breeding.}, }
@article {pmid34198074, year = {2021}, author = {Sahoo, S and Samal, R and Biswas, S}, title = {Efficacy of a novel bone preprocessing method for better DNA yield.}, journal = {Forensic science international}, volume = {325}, number = {}, pages = {110887}, doi = {10.1016/j.forsciint.2021.110887}, pmid = {34198074}, issn = {1872-6283}, mesh = {DNA/*analysis ; *DNA Fingerprinting ; Femur/*chemistry ; Forensic Genetics/methods ; Humans ; *Microsatellite Repeats ; Multiplex Polymerase Chain Reaction ; Specimen Handling/*methods ; }, abstract = {In cases involving identification of missing persons, mass disasters and ancient DNA investigations, bone and teeth samples are often the only, and almost always the best, biological material available for DNA profiling. Standard methods for extraction of DNA from such samples involve grinding of the bone and teeth samples. Here, we present an extremely efficient protocol for recovery of DNA from bone samples by a method of scrapping. The study was carried out on 25 samples and it was found that the quantity of DNA isolated by the scrapping method was up to 1.131 ng/µl with a success rate of 93% as compared to a much lower yield of 0.359 ng/µl DNA isolated with a success rate of 28% through the grinding method. The scrapping method of DNA extraction has been proven to be extremely useful in forensic examination of challenging samples that had multiple failures using the traditional grinding method.}, }
@article {pmid34191795, year = {2021}, author = {Ingman, T and Eisenmann, S and Skourtanioti, E and Akar, M and Ilgner, J and Gnecchi Ruscone, GA and le Roux, P and Shafiq, R and Neumann, GU and Keller, M and Freund, C and Marzo, S and Lucas, M and Krause, J and Roberts, P and Yener, KA and Stockhammer, PW}, title = {Human mobility at Tell Atchana (Alalakh), Hatay, Turkey during the 2nd millennium BC: Integration of isotopic and genomic evidence.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0241883}, pmid = {34191795}, issn = {1932-6203}, mesh = {Humans ; Turkey ; *Human Migration/history ; History, Ancient ; *DNA, Ancient/analysis ; *Strontium Isotopes/analysis ; Oxygen Isotopes/analysis ; Genomics/methods ; Dental Enamel/chemistry ; Archaeology ; Male ; Female ; }, abstract = {The Middle and Late Bronze Age, a period roughly spanning the 2nd millennium BC (ca. 2000-1200 BC) in the Near East, is frequently referred to as the first 'international age', characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh, located in Hatay, Turkey), we explored the role of mobility at the capital of a regional kingdom, named Mukish during the Late Bronze Age, which spanned the Amuq Valley and some areas beyond. We generated strontium and oxygen isotope data from dental enamel for 53 individuals and 77 individuals, respectively, and added ancient DNA data of 10 newly sequenced individuals to a dataset of 27 individuals published in 2020. Additionally, we improved the DNA coverage of one individual from this 2020 dataset. The DNA data revealed a very homogeneous gene pool. This picture of an overwhelmingly local ancestry was consistent with the evidence of local upbringing in most of the individuals indicated by the isotopic data, where only five were found to be non-local. High levels of contact, trade, and exchange of ideas and goods in the Middle and Late Bronze Ages, therefore, seem not to have translated into high levels of individual mobility detectable at Tell Atchana.}, }
@article {pmid34191029, year = {2021}, author = {Pérez-Escobar, OA and Bellot, S and Przelomska, NAS and Flowers, JM and Nesbitt, M and Ryan, P and Gutaker, RM and Gros-Balthazard, M and Wells, T and Kuhnhäuser, BG and Schley, R and Bogarín, D and Dodsworth, S and Diaz, R and Lehmann, M and Petoe, P and Eiserhardt, WL and Preick, M and Hofreiter, M and Hajdas, I and Purugganan, M and Antonelli, A and Gravendeel, B and Leitch, IJ and Jimenez, MFT and Papadopulos, AST and Chomicki, G and Renner, SS and Baker, WJ}, title = {Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication.}, journal = {Molecular biology and evolution}, volume = {38}, number = {10}, pages = {4475-4492}, pmid = {34191029}, issn = {1537-1719}, mesh = {Domestication ; Egypt ; *Phoeniceae/genetics ; Plant Breeding ; Plant Leaves/genetics ; }, abstract = {The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.}, }
@article {pmid34187204, year = {2021}, author = {Euskirchen, A and Hartmann, L and Mazanec, J and Wittmeier, P and Hummel, S}, title = {The influence of sample quantity and lysis parameters on the success of ancient DNA extraction from skeletal remains.}, journal = {BioTechniques}, volume = {71}, number = {1}, pages = {376-381}, doi = {10.2144/btn-2020-0169}, pmid = {34187204}, issn = {1940-9818}, mesh = {*Body Remains ; DNA Fingerprinting ; *DNA, Ancient/isolation &amp; purification ; Humans ; Microsatellite Repeats ; }, abstract = {DNA extraction is of utmost importance in archaeobiology, as it determines the success of further DNA analyses. This study concentrates on the success of ancient DNA extraction using silica spin columns and PCR-based analysis from archaeological skeletal material and investigates the influence of sample quantity, lysis time and lysis temperature during sample preparation. The results show that lysis times ranging from 2 to 48 h are suitable, and that lysis should be carried out at a constant temperature of 56°C. Concerning sample quantity, 10 mg for mitochondrial DNA and 50 mg for chromosomal DNA are sufficient for high quality analyses. Thus invaluable sample material can be saved, and time of sample preparation can be reduced considerably.}, }
@article {pmid34184252, year = {2021}, author = {Bisso-Machado, R and Fagundes, NJR}, title = {Uniparental genetic markers in Native Americans: A summary of all available data from ancient and contemporary populations.}, journal = {American journal of physical anthropology}, volume = {176}, number = {3}, pages = {445-458}, doi = {10.1002/ajpa.24357}, pmid = {34184252}, issn = {1096-8644}, mesh = {*Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Female ; Genetic Markers/genetics ; Genetic Variation/genetics ; Genetics, Population ; Haplotypes ; Humans ; Male ; *American Indian or Alaska Native ; }, abstract = {OBJECTIVES: The aim of this study was to create a comprehensive summary of available mtDNA and Y-chromosome data for Native Americans from North, Central, and South America, including both modern and ancient DNA. To illustrate the usefulness of this dataset we present a broad picture of the genetic variation for both markers across the Americas.<br><br>METHODS: We searched PubMed, ResearchGate, Google Scholar for studies about mtDNA or Y-chromosome variation in Native American populations, including geographic, linguistic, ecological (ecoregion), archeological and chronological information. We used AMOVA to estimate the genetic structure associated with language and ecoregion grouping and Mantel tests to evaluate the correlation between genetic and geographic distances.<br><br>RESULTS: Genetic data were obtained from 321 primary sources, including 22,569 individuals from 298 contemporary populations, and 3628 individuals from 202 archeological populations. MtDNA lineages of probable non-Amerindian origin were rare, in contrast with Y-chromosome lineages. Mantel tests showed a statistically significant correlation for the whole continent considering mtDNA but not the Y-chromosome. Genetic structure between groups was always stronger for mtDNA than for the Y-chromosome.<br><br>CONCLUSIONS: This study summarizes decades of research conducted in Native American populations for both mtDNA and the Y-chromosome. Continental or sub-continental patterns of variation reveal that most of the genetic variation occurs within populations rather than among linguistic or ecoregional groups, and that isolation by distance is barely detectable in most population sets. The genetic structure among groups was always larger for mtDNA than for the Y-chromosome, suggesting between-sex differences in gene flow.}, }
@article {pmid34172741, year = {2021}, author = {Groppi, A and Liu, S and Cornille, A and Decroocq, S and Bui, QT and Tricon, D and Cruaud, C and Arribat, S and Belser, C and Marande, W and Salse, J and Huneau, C and Rodde, N and Rhalloussi, W and Cauet, S and Istace, B and Denis, E and Carrère, S and Audergon, JM and Roch, G and Lambert, P and Zhebentyayeva, T and Liu, WS and Bouchez, O and Lopez-Roques, C and Serre, RF and Debuchy, R and Tran, J and Wincker, P and Chen, X and Pétriacq, P and Barre, A and Nikolski, M and Aury, JM and Abbott, AG and Giraud, T and Decroocq, V}, title = {Population genomics of apricots unravels domestication history and adaptive events.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3956}, pmid = {34172741}, issn = {2041-1723}, mesh = {Chromosomes, Plant/genetics ; Disease Resistance/genetics ; *Domestication ; Evolution, Molecular ; Fruit/classification/genetics/growth &amp; development ; Gene Flow ; Genetic Variation ; Genome, Plant/*genetics ; Life Cycle Stages/genetics ; Metagenomics ; Phenotype ; Phylogeny ; Prunus armeniaca/classification/*genetics/growth &amp; development ; Selection, Genetic ; }, abstract = {Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.}, }
@article {pmid34171307, year = {2021}, author = {Wang, T and Wang, W and Xie, G and Li, Z and Fan, X and Yang, Q and Wu, X and Cao, P and Liu, Y and Yang, R and Liu, F and Dai, Q and Feng, X and Wu, X and Qin, L and Li, F and Ping, W and Zhang, L and Zhang, M and Liu, Y and Chen, X and Zhang, D and Zhou, Z and Wu, Y and Shafiey, H and Gao, X and Curnoe, D and Mao, X and Bennett, EA and Ji, X and Yang, MA and Fu, Q}, title = {Human population history at the crossroads of East and Southeast Asia since 11,000 years ago.}, journal = {Cell}, volume = {184}, number = {14}, pages = {3829-3841.e21}, doi = {10.1016/j.cell.2021.05.018}, pmid = {34171307}, issn = {1097-4172}, support = {55008731/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Asia, Southeastern ; Asia, Eastern ; *Genetics, Population ; Geography ; Humans ; }, abstract = {Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest humans sequenced from southern China. We discovered a deeply diverged East Asian ancestry in the Guangxi region that persisted until at least 6,000 years ago. We found that ∼9,000- to 6,000-year-old Guangxi populations were a mixture of local ancestry, southern ancestry previously sampled in Fujian, and deep Asian ancestry related to Southeast Asian Hòabìnhian hunter-gatherers, showing broad admixture in the region predating the appearance of farming. Historical Guangxi populations dating to ∼1,500 to 500 years ago are closely related to Tai-Kadai and Hmong-Mien speakers. Our results show heavy interactions among three distinct ancestries at the crossroads of East and Southeast Asia.}, }
@article {pmid34164993, year = {2021}, author = {Essel, E and Korlević, P and Meyer, M}, title = {A method for the temperature-controlled extraction of DNA from ancient bones.}, journal = {BioTechniques}, volume = {71}, number = {1}, pages = {382-386}, doi = {10.2144/btn-2021-0025}, pmid = {34164993}, issn = {1940-9818}, mesh = {*Body Remains ; *Bone and Bones ; *DNA, Ancient/isolation &amp; purification ; Humans ; Temperature ; }, abstract = {Contamination with microbial and other exogenous DNA poses a significant challenge in the generation of genome-wide sequence data from ancient skeletal remains. Here we describe a method for separating ancient DNA into multiple fractions during DNA extraction by sequential temperature-controlled release of DNA into sodium phosphate buffer. An evaluation of the effectiveness of the method using a set of three ancient bones resulted in between 1.6- and 32-fold enrichment of endogenous DNA compared with regular DNA extraction. For two bones, the method outperformed previous methods of decontaminating ancient bones, including hypochlorite treatment, which resulted in near-complete destruction of DNA in the worst-preserved sample. This extraction method expands the spectrum of methods available for depleting contaminant DNA from ancient skeletal remains.}, }
@article {pmid34162703, year = {2021}, author = {Marciniak, S and Mughal, MR and Godfrey, LR and Bankoff, RJ and Randrianatoandro, H and Crowley, BE and Bergey, CM and Muldoon, KM and Randrianasy, J and Raharivololona, BM and Schuster, SC and Malhi, RS and Yoder, AD and Louis, EE and Kistler, L and Perry, GH}, title = {Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {26}, pages = {}, pmid = {34162703}, issn = {1091-6490}, mesh = {Amino Acids/genetics ; Animals ; Base Sequence ; Cell Nucleus/*genetics ; Evolution, Molecular ; *Extinction, Biological ; *Genome ; Genomics ; Herbivory/physiology ; Lemur/*genetics ; *Phylogeny ; }, abstract = {No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal "subfossil" remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ∼160 kg) and other extraordinary Malagasy megafauna that survived into the past millennium. Yet, much about the evolutionary biology of these now-extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and subtropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here, we present a nuclear genome sequence (∼2× coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (∼85 kg). To support the testing of key phylogenetic and evolutionary hypotheses, we also generated high-coverage nuclear genomes for two extant lemurs, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemurs and 47 nonlemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and an extant folivore (a colobine monkey) and an herbivore (horse) in genes encoding proteins that function in plant toxin biodegradation and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.}, }
@article {pmid34146486, year = {2021}, author = {Baleka, S and Herridge, VL and Catalano, G and Lister, AM and Dickinson, MR and Di Patti, C and Barlow, A and Penkman, KEH and Hofreiter, M and Paijmans, JLA}, title = {Estimating the dwarfing rate of an extinct Sicilian elephant.}, journal = {Current biology : CB}, volume = {31}, number = {16}, pages = {3606-3612.e7}, doi = {10.1016/j.cub.2021.05.037}, pmid = {34146486}, issn = {1879-0445}, support = {310763/ERC_/European Research Council/International ; }, mesh = {Animals ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Elephants/genetics ; Extinction, Biological ; *Fossils ; Phylogeny ; Sicily ; }, abstract = {Evolution on islands, together with the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of phenotypic traits of extinct animals can be challenging, in part due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily).[1] Despite the challenges associated with recovering ancient DNA from warm climates,[2] we successfully retrieved a mitogenome from a sample with an estimated age between 175,500 and 50,000 years. Our results suggest that this specific Sicilian elephant lineage evolved from one of the largest terrestrial mammals that ever lived[3] to an island species weighing less than 20% of its original mass with an estimated mass reduction between 0.74 and 200.95 kg and height reduction between 0.15 and 41.49 mm per generation. We show that combining ancient DNA with paleontological and geochronological evidence can constrain the timing of phenotypic changes with greater accuracy than could be achieved using any source of evidence in isolation.}, }
@article {pmid34142055, year = {2021}, author = {Roca-Rada, X and Politis, G and Messineo, PG and Scheifler, N and Scabuzzo, C and González, M and Harkins, KM and Reich, D and Souilmi, Y and Teixeira, JC and Llamas, B and Fehren-Schmitz, L}, title = {Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America.}, journal = {iScience}, volume = {24}, number = {6}, pages = {102553}, pmid = {34142055}, issn = {2589-0042}, abstract = {The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.}, }
@article {pmid34135378, year = {2021}, author = {Smith, AD and Kamiński, MJ and Kanda, K and Sweet, AD and Betancourt, JL and Holmgren, CA and Hempel, E and Alberti, F and Hofreiter, M}, title = {Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12635}, pmid = {34135378}, issn = {2045-2322}, mesh = {Animals ; Arthropods/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Fossils ; Gene Library ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA/*veterinary ; Sigmodontinae/genetics/*parasitology ; }, abstract = {The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.}, }
@article {pmid34129037, year = {2021}, author = {Speidel, L and Cassidy, L and Davies, RW and Hellenthal, G and Skoglund, P and Myers, SR}, title = {Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies.}, journal = {Molecular biology and evolution}, volume = {38}, number = {9}, pages = {3497-3511}, pmid = {34129037}, issn = {1537-1719}, support = {/MRC_/Medical Research Council/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; 220457/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; 212284/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; /CRUK_/Cancer Research UK/United Kingdom ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; 852558/ERC_/European Research Council/International ; 200186/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*DNA, Ancient ; Gene Flow ; Genetics, Population ; *Genome ; Geography ; History, Ancient ; Population Dynamics ; }, abstract = {Ancient genomes anchor genealogies in directly observed historical genetic variation and contextualize ancestral lineages with archaeological insights into their geography and cultural associations. However, the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies. Here, we present a fast and scalable method, Colate, the first approach for inferring ancestral relationships through time between low-coverage genomes without requiring phasing or imputation. Our approach leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. For deeply sequenced ancient genomes, we additionally introduce an extension of the Relate algorithm for joint inference of genealogies incorporating such genomes. Application to 278 present-day and 430 ancient DNA samples of >0.5x mean coverage allows us to identify dynamic population structure and directional gene flow between early farmer and European hunter-gatherer groups. We further show that the previously reported, but still unexplained, increase in the TCC/TTC mutation rate, which is strongest in West Eurasia today, was already present at similar strength and widespread in the Late Glacial Period ~10k-15k years ago, but is not observed in samples >30k years old. It is strongest in Neolithic farmers, and highly correlated with recent coalescence rates between other genomes and a 10,000-year-old Anatolian hunter-gatherer. This suggests gene-flow among ancient peoples postdating the last glacial maximum as widespread and localizes the driver of this mutational signal in both time and geography in that region. Our approach should be widely applicable in future for addressing other evolutionary questions, and in other species.}, }
@article {pmid34128784, year = {2021}, author = {Dorman, MJ and Thomson, NR and Campos, J}, title = {Genomic contextualisation of ancient DNA molecular data from an Argentinian fifth pandemic Vibrio cholerae infection.}, journal = {Microbial genomics}, volume = {7}, number = {6}, pages = {}, pmid = {34128784}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Americas/epidemiology ; Argentina/epidemiology ; Cholera/*epidemiology/microbiology ; *DNA, Ancient ; DNA, Bacterial/genetics ; *Genomics ; Humans ; *Pandemics ; Vibrio cholerae/*genetics ; }, abstract = {Specific lineages of serogroup O1 Vibrio cholerae are notorious for causing cholera pandemics, of which there have been seven since the 1800s. Much is known about the sixth pandemic (1899–1923) and the ongoing seventh pandemic (1961–present), but we know very little about the bacteriology of pandemics 1 to 5. Moreover, although we are learning about the contribution of non-O1 non-pandemic V. cholerae to cholera dynamics during the current pandemic, we know almost nothing about their role in the past. A recent ancient DNA study has presented what may be the first molecular evidence of a V. cholerae infection from the fifth cholera pandemic period (1886–1887 AD) in Argentina. Here, we place the molecular evidence from that study into the genomic context of non-pandemic V. cholerae from Latin America and elsewhere, and show that a gene fragment amplified from ancient DNA is most similar to that of V. cholerae from the Americas, and from Argentina. Our results corroborate and reinforce the findings of the original study, and collectively suggest that even in the 1880s, non-pandemic V. cholerae local to the Americas may have caused sporadic infections in Argentina, just as we know this to have happened during the seventh pandemic in Latin America.}, }
@article {pmid36654346, year = {2021}, author = {Liu, J and Zeng, W and Sun, B and Mao, X and Zhao, Y and Wang, F and Li, Z and Luan, F and Guo, J and Zhu, C and Wang, Z and Wei, C and Zhang, M and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Hou, W and Ping, W and Wu, X and Andrew Bennett, E and Liu, Y and Fu, Q}, title = {Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago.}, journal = {Science bulletin}, volume = {66}, number = {11}, pages = {1129-1135}, doi = {10.1016/j.scib.2021.01.029}, pmid = {36654346}, issn = {2095-9281}, abstract = {Archaeological and ancient DNA studies revealed that Shandong, a multi-culture center in northern coastal China, was home to ancient populations having ancestry related to both northern and southern East Asian populations. However, the limited temporal and geographical range of previous studies have been insufficient to describe the population history of this region in greater detail. Here, we report the analysis of 86 complete mitochondrial genomes from the remains of 9500 to 1800-year-old humans from 12 archaeological sites across Shandong. For samples older than 4600 years before present (BP), we found haplogroups D4, D5, B4c1, and B5b2, which are observed in present-day northern and southern East Asians. For samples younger than 4600 BP, haplogroups C (C7a1 and C7b), M9 (M9a1), and F (F1a1, F2a, and F4a1) begin to appear, indicating changes in the Shandong maternal genetic structure starting from the beginning of the Longshan cultural period. Within Shandong, the genetic exchange is possible between the coastal and inland regions after 3100 BP. We also discovered the B5b2 lineage in Shandong populations, with the oldest Bianbian individual likely related to the ancestors of some East Asians and North Asians. By reconstructing a maternal genetic structure of Shandong populations, we provide greater resolution of the population dynamics of the northern coastal East Asia over the past nine thousand years.}, }
@article {pmid36618122, year = {2021}, author = {Margaryan, A and Sinding, MS and Carøe, C and Yamshchikov, V and Burtsev, I and Gilbert, MTP}, title = {The genomic origin of Zana of Abkhazia.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {2}, number = {2}, pages = {e10051}, pmid = {36618122}, issn = {2641-6573}, abstract = {Enigmatic phenomena have sparked the imagination of people around the globe into creating folkloric creatures. One prime example is Zana of Abkhazia (South Caucasus), a well-documented 19th century female who was captured living wild in the forest. Zana's appearance was sufficiently unusual, that she was referred to by locals as an Almasty-the analog of Bigfoot in the Caucasus. Although the exact location of Zana's burial site was unknown, the grave of her son, Khwit, was identified in 1971. The genomes of Khwit and the alleged Zana skeleton were sequenced to an average depth of ca. 3× using ancient DNA techniques. The identical mtDNA and parent-offspring relationship between the two indicated that the unknown woman was indeed Zana. Population genomic analyses demonstrated that Zana's immediate genetic ancestry can likely be traced to present-day East-African populations. We speculate that Zana might have had a genetic disorder such as congenital generalized hypertrichosis which could partially explain her strange behavior, lack of speech, and long body hair. Our findings elucidate Zana's unfortunate story and provide a clear example of how prejudices of the time led to notions of cryptic hominids that are still held and transmitted by some today.}, }
@article {pmid34108947, year = {2021}, author = {Locarnini, SA and Littlejohn, M and Yuen, LKW}, title = {Origins and Evolution of the Primate Hepatitis B Virus.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {653684}, pmid = {34108947}, issn = {1664-302X}, abstract = {Recent interest in the origins and subsequent evolution of the hepatitis B virus (HBV) has strengthened with the discovery of ancient HBV sequences in fossilized remains of humans dating back to the Neolithic period around 7,000 years ago. Metagenomic analysis identified a number of African non-human primate HBV sequences in the oldest samples collected, indicating that human HBV may have at some stage, evolved in Africa following zoonotic transmissions from higher primates. Ancestral genotype A and D isolates were also discovered from the Bronze Age, not in Africa but rather Eurasia, implying a more complex evolutionary and migratory history for HBV than previously recognized. Most full-length ancient HBV sequences exhibited features of inter genotypic recombination, confirming the importance of recombination and the mutation rate of the error-prone viral replicase as drivers for successful HBV evolution. A model for the origin and evolution of HBV is proposed, which includes multiple cross-species transmissions and favors subsequent recombination events that result in a pathogen and can successfully transmit and cause persistent infection in the primate host.}, }
@article {pmid34102887, year = {2021}, author = {Irish, JD and Usai, D}, title = {The transition from hunting-gathering to agriculture in Nubia: dental evidence for and against selection, population continuity and discontinuity.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1952}, pages = {20210969}, pmid = {34102887}, issn = {1471-2954}, mesh = {Africa ; *Agriculture ; Arizona ; *Fossils ; History, Ancient ; Humans ; }, abstract = {Some researchers posit population continuity between Late Palaeolithic hunter-gatherers of the late Pleistocene and Holocene agriculturalists from Lower (northern) Nubia, in northeast Africa. Substantial craniodental differences in these time-successive groups are suggested to result from in situ evolution. Specifically, these populations are considered a model example for subsistence-related selection worldwide in the transition to agriculture. Others question continuity, with findings indicating that the largely homogeneous Holocene populations differ significantly from late Pleistocene Lower Nubians. If the latter are representative of the local populace, post-Pleistocene discontinuity is implied. So who was ancestral to the Holocene agriculturalists? Dental morphological analyses of 18 samples (1075 individuals), including one dated to the 12th millennium BCE from Al Khiday, near the Upper Nubian border, may provide an answer. It is the first Late Palaeolithic sample (n = 55) recovered within the region in approximately 50 years. Using the Arizona State University Dental Anthropology System to record traits and multivariate statistics to estimate biological affinities, Al Khiday is comparable to several Holocene samples, yet also highly divergent from contemporaneous Lower Nubians. Thus, population continuity is indicated after all, but with late Pleistocene Upper-rather than Lower Nubians as originally suggested-assuming dental traits are adequate proxies for ancient DNA.}, }
@article {pmid34099576, year = {2021}, author = {Daly, KG and Mattiangeli, V and Hare, AJ and Davoudi, H and Fathi, H and Doost, SB and Amiri, S and Khazaeli, R and Decruyenaere, D and Nokandeh, J and Richter, T and Darabi, H and Mortensen, P and Pantos, A and Yeomans, L and Bangsgaard, P and Mashkour, M and Zeder, MA and Bradley, DG}, title = {Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {25}, pages = {}, pmid = {34099576}, issn = {1091-6490}, mesh = {Animals ; Animals, Domestic/genetics ; Archaeology ; DNA, Mitochondrial/genetics ; *Domestication ; Female ; Genetic Markers ; Genetic Variation ; *Genome ; Genomics ; Geography ; Goats/*genetics ; Haplotypes/genetics ; Iran ; Male ; Mitochondria/genetics ; Selection, Genetic ; Y Chromosome/genetics ; }, abstract = {The Aceramic Neolithic (∼9600 to 7000 cal BC) period in the Zagros Mountains, western Iran, provides some of the earliest archaeological evidence of goat (Capra hircus) management and husbandry by circa 8200 cal BC, with detectable morphological change appearing ∼1,000 y later. To examine the genomic imprint of initial management and its implications for the goat domestication process, we analyzed 14 novel nuclear genomes (mean coverage 1.13X) and 32 mitochondrial (mtDNA) genomes (mean coverage 143X) from two such sites, Ganj Dareh and Tepe Abdul Hosein. These genomes show two distinct clusters: those with domestic affinity and a minority group with stronger wild affinity, indicating that managed goats were genetically distinct from wild goats at this early horizon. This genetic duality, the presence of long runs of homozygosity, shared ancestry with later Neolithic populations, a sex bias in archaeozoological remains, and demographic profiles from across all layers of Ganj Dareh support management of genetically domestic goat by circa 8200 cal BC, and represent the oldest to-this-date reported livestock genomes. In these sites a combination of high autosomal and mtDNA diversity, contrasting limited Y chromosomal lineage diversity, an absence of reported selection signatures for pigmentation, and the wild morphology of bone remains illustrates domestication as an extended process lacking a strong initial bottleneck, beginning with spatial control, demographic manipulation via biased male culling, captive breeding, and subsequently phenotypic and genomic selection.}, }
@article {pmid34083588, year = {2021}, author = {Brown, AG and Van Hardenbroek, M and Fonville, T and Davies, K and Mackay, H and Murray, E and Head, K and Barratt, P and McCormick, F and Ficetola, GF and Gielly, L and Henderson, ACG and Crone, A and Cavers, G and Langdon, PG and Whitehouse, NJ and Pirrie, D and Alsos, IG}, title = {Ancient DNA, lipid biomarkers and palaeoecological evidence reveals construction and life on early medieval lake settlements.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11807}, pmid = {34083588}, issn = {2045-2322}, mesh = {Animals ; *Archaeology/methods ; *Biomarkers ; *DNA, Ancient ; History, Medieval ; Humans ; Ireland ; *Lakes ; *Lipids ; Minerals/analysis ; Radiometric Dating ; United Kingdom ; }, abstract = {Direct evidence of ancient human occupation is typically established through archaeological excavation. Excavations are costly and destructive, and practically impossible in some lake and wetland environments. We present here an alternative approach, providing direct evidence from lake sediments using DNA metabarcoding, steroid lipid biomarkers (bile acids) and from traditional environmental analyses. Applied to an early Medieval Celtic settlement in Ireland (a crannog) this approach provides a site chronology and direct evidence of human occupation, crops, animal farming and on-site slaughtering. This is the first independently-dated, continuous molecular archive of human activity from an archeological site, demonstrating a link between animal husbandry, food resources, island use. These sites are under threat but are impossible to preserve in-situ so this approach can be used, with or without excavation, to produce a robust and full site chronology and provide direct evidence of occupation, the use of plants and animals, and activities such as butchery.}, }
@article {pmid34078291, year = {2021}, author = {Eriksson, JS and Bacon, CD and Bennett, DJ and Pfeil, BE and Oxelman, B and Antonelli, A}, title = {Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae).}, journal = {BMC ecology and evolution}, volume = {21}, number = {1}, pages = {107}, pmid = {34078291}, issn = {2730-7182}, support = {2009-5206//Vetenskapsr&#xe5;det/ ; 2019-05191//Vetenskapsr&#xe5;det/ ; FFL15-0196//Stiftelsen f&#xf6;r&#xa0;Strategisk Forskning/ ; }, mesh = {Gene Duplication ; Genome, Plant/genetics ; *Hibiscus/genetics ; *Malvaceae/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events.<br><br>RESULTS: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in&#x2009;>&#x2009;54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus.<br><br>CONCLUSIONS: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.}, }
@article {pmid34048699, year = {2021}, author = {Mao, X and Zhang, H and Qiao, S and Liu, Y and Chang, F and Xie, P and Zhang, M and Wang, T and Li, M and Cao, P and Yang, R and Liu, F and Dai, Q and Feng, X and Ping, W and Lei, C and Olsen, JW and Bennett, EA and Fu, Q}, title = {The deep population history of northern East Asia from the Late Pleistocene to the Holocene.}, journal = {Cell}, volume = {184}, number = {12}, pages = {3256-3266.e13}, doi = {10.1016/j.cell.2021.04.040}, pmid = {34048699}, issn = {1097-4172}, mesh = {DNA, Ancient/analysis ; Asia, Eastern ; Female ; Genetic Variation ; Genetics, Population ; Genome, Human ; Geography ; Humans ; Ice Cover ; Likelihood Functions ; Male ; Models, Genetic ; Phylogeny ; *Population Dynamics ; Principal Component Analysis ; Time Factors ; }, abstract = {Northern East Asia was inhabited by modern humans as early as 40 thousand years ago (ka), as demonstrated by the Tianyuan individual. Using genome-wide data obtained from 25 individuals dated to 33.6-3.4 ka from the Amur region, we show that Tianyuan-related ancestry was widespread in northern East Asia before the Last Glacial Maximum (LGM). At the close of the LGM stadial, the earliest northern East Asian appeared in the Amur region, and this population is basal to ancient northern East Asians. Human populations in the Amur region have maintained genetic continuity from 14 ka, and these early inhabitants represent the closest East Asian source known for Ancient Paleo-Siberians. We also observed that EDAR V370A was likely to have been elevated to high frequency after the LGM, suggesting the possible timing for its selection. This study provides a deep look into the population dynamics of northern East Asia.}, }
@article {pmid34044198, year = {2021}, author = {van Spelde, AM and Schroeder, H and Kjellström, A and Lidén, K}, title = {Approaches to osteoporosis in paleopathology: How did methodology shape bone loss research?.}, journal = {International journal of paleopathology}, volume = {33}, number = {}, pages = {245-257}, doi = {10.1016/j.ijpp.2021.05.001}, pmid = {34044198}, issn = {1879-9825}, mesh = {Archaeology ; Bone Density ; Bone and Bones ; Humans ; *Osteoporosis ; Paleopathology ; }, abstract = {OBJECTIVE: This paper will review how different methods employed to study bone loss in the past were used to explore different questions and aspects of bone loss, how methodology has changed over time, and how these different approaches have informed our understanding of bone loss in the past.<br><br>MATERIALS AND METHODS: A review and discussion is conducted on research protocols and results of 84 paleopathology publications on bone loss in archaeological skeletal collections published between 1969 and 2021.<br><br>CONCLUSIONS: The variety in research protocols confounds accurate meta-analysis of previously published research; however, more recent publications incorporate a combination of bone mass and bone quality based methods. Biased sample selection has resulted in a predominance of European and Medieval publications, limiting more general observations on bone loss in the past. Collection of dietary or paleopathological covariables is underemployed in the effort to interpret bone loss patterns.<br><br>SIGNIFICANCE: Paleopathology publications have demonstrated differences in bone loss between distinct archaeological populations, between sex and age groups, and have suggested factors underlying observed differences. However, a lack of a gold standard has encouraged the use of a wide range of methods. Understanding how this array of methods effects results is crucial in contextualizing our knowledge of bone loss in the past.<br><br>LIMITATIONS: The development of a research protocol is also influenced by available expertise, available equipment, restrictions imposed by the curator, and site-specific taphonomic aspects. These factors will likely continue to cause (minor) biases even if a best practice can be established.<br><br>Greater effort to develop uniform terminology and operational definitions of osteoporosis in skeletal remains, as well as the expansion of time scale and geographical areas studied. The Next-Generation Sequencing revolution has also opened up the possibility of ancient DNA analyses to study genetic predisposition to bone loss in the past.}, }
@article {pmid34043940, year = {2021}, author = {Danko, D and Bezdan, D and Afshin, EE and Ahsanuddin, S and Bhattacharya, C and Butler, DJ and Chng, KR and Donnellan, D and Hecht, J and Jackson, K and Kuchin, K and Karasikov, M and Lyons, A and Mak, L and Meleshko, D and Mustafa, H and Mutai, B and Neches, RY and Ng, A and Nikolayeva, O and Nikolayeva, T and Png, E and Ryon, KA and Sanchez, JL and Shaaban, H and Sierra, MA and Thomas, D and Young, B and Abudayyeh, OO and Alicea, J and Bhattacharyya, M and Blekhman, R and Castro-Nallar, E and Cañas, AM and Chatziefthimiou, AD and Crawford, RW and De Filippis, F and Deng, Y and Desnues, C and Dias-Neto, E and Dybwad, M and Elhaik, E and Ercolini, D and Frolova, A and Gankin, D and Gootenberg, JS and Graf, AB and Green, DC and Hajirasouliha, I and Hastings, JJA and Hernandez, M and Iraola, G and Jang, S and Kahles, A and Kelly, FJ and Knights, K and Kyrpides, NC and Łabaj, PP and Lee, PKH and Leung, MHY and Ljungdahl, PO and Mason-Buck, G and McGrath, K and Meydan, C and Mongodin, EF and Moraes, MO and Nagarajan, N and Nieto-Caballero, M and Noushmehr, H and Oliveira, M and Ossowski, S and Osuolale, OO and Özcan, O and Paez-Espino, D and Rascovan, N and Richard, H and Rätsch, G and Schriml, LM and Semmler, T and Sezerman, OU and Shi, L and Shi, T and Siam, R and Song, LH and Suzuki, H and Court, DS and Tighe, SW and Tong, X and Udekwu, KI and Ugalde, JA and Valentine, B and Vassilev, DI and Vayndorf, EM and Velavan, TP and Wu, J and Zambrano, MM and Zhu, J and Zhu, S and Mason, CE and , }, title = {A global metagenomic map of urban microbiomes and antimicrobial resistance.}, journal = {Cell}, volume = {184}, number = {13}, pages = {3376-3393.e17}, pmid = {34043940}, issn = {1097-4172}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; T32 GM083937/GM/NIGMS NIH HHS/United States ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; UL1 TR000457/TR/NCATS NIH HHS/United States ; R25 EB020393/EB/NIBIB NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R35 GM138152/GM/NIGMS NIH HHS/United States ; }, mesh = {Biodiversity ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Humans ; *Metagenomics ; Microbiota/*genetics ; *Urban Population ; }, abstract = {We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.}, }
@article {pmid34042097, year = {2021}, author = {Gaeta, R}, title = {Ancient DNA and paleogenetics: risks and potentiality.}, journal = {Pathologica}, volume = {113}, number = {2}, pages = {141-146}, pmid = {34042097}, issn = {1591-951X}, mesh = {Animals ; *DNA, Ancient ; Humans ; *Paleopathology ; Phylogeny ; }, abstract = {Paleopathology, the science that studies the diseases of the past, has always been addressed to the future in the use of new diagnostic methods. One of its relatively recent branches is paleogenetics, which is the study of genetic material from the past. Nuclear and mitochondrial DNA recovered from archaeological and paleontological specimens is called ancient DNA (aDNA), which can be extracted from a large variety of biological materials, of different origin, state of preservation and age, such as bones, teeth, coprolites, mummified tissues and hairs. There are many applications for ancient DNA research in the field of archaeology and paleopathology: population demography, genealogy, disease studies, archaeological reconstruction of plant vegetation, calibration of the molecular clock, phylogenetic relationship between different mammals and interpretation of the paleoclimate. However, the study of ancient genetic material is extremely difficult due to its poor quality and quantity, as well possible contamination with modern DNA. New advanced methods will allow extracting DNA from a greater variety of materials, and improvements in sequencing techniques will unveil data that are currently concealed. The aim of this paper is to provide initial insights into paleogenetics and ancient DNA study and to illustrate the limits, risks and potentiality of the research on the genetic material of ancient specimens, whose results have a strong impact on the present and future medicine.}, }
@article {pmid34039840, year = {2021}, author = {Yang, S and Ye, K}, title = {Recent advances in understanding the adaptive evolution of metabolic genes and traits.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {24}, number = {4}, pages = {308-314}, doi = {10.1097/MCO.0000000000000770}, pmid = {34039840}, issn = {1473-6519}, mesh = {*Diabetes Mellitus, Type 2/genetics ; Genome ; Genome-Wide Association Study ; Humans ; *MicroRNAs ; Phenotype ; }, abstract = {PURPOSE OF REVIEW: This review summarizes the recent advances in understanding the adaptive evolution of metabolic genes and traits, providing insights into gene-diet interactions in human evolution and health.<br><br>RECENT FINDINGS: The rapid accumulation of ancient DNA across time and geography illuminates unprecedented details of some well-established examples of genetic adaptation to diet, such as the LCT and FADS genes. Novel cases of thrifty genes were identified, especially a microRNA at the LCT locus that controls energy expenditure and glucose homeostasis, connecting the historical adaptation to present-day metabolic disorders. A new example of gene-diet-microbiota interactions was established among the AMY1 copy number, starchy diets, and resistant-starch-digesting Ruminococcus. The explosion of genome-wide association studies in large cohorts unravels the present-day health implications of historically adaptive genetic variants. It also enables studies into the polygenic adaptation of metabolic traits, revealing intriguing adaptive signals for increased bone mineral density, blood pressure, and risk of type 2 diabetes, but decreased body mass index and HbA1c.<br><br>SUMMARY: The rapid accumulation of ancient and modern DNA has fueled the characterization of novel and existing cases of genetic adaptation. However, transferring these evolutionary insights into genome-informed precision nutrition requires extensive mechanistic studies and genotype-aware clinical trials.}, }
@article {pmid34038549, year = {2021}, author = {Kuhlwilm, M and Fontsere, C and Han, S and Alvarez-Estape, M and Marques-Bonet, T}, title = {HuConTest: Testing Human Contamination in Great Ape Samples.}, journal = {Genome biology and evolution}, volume = {13}, number = {6}, pages = {}, pmid = {34038549}, issn = {1759-6653}, mesh = {Animals ; *DNA Contamination ; Hominidae/*genetics ; Humans ; }, abstract = {Modern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in noninvasive samples. Here, we present a simple method to detect human contamination in short-read sequencing data from different species: HuConTest. We demonstrate its feasibility using blood and tissue samples from these species. This test is particularly useful for more complex samples (such as museum and noninvasive samples) which have smaller amounts of endogenous DNA, as we show here.}, }
@article {pmid34037863, year = {2021}, author = {Yu, X and Li, H}, title = {Origin of ethnic groups, linguistic families, and civilizations in China viewed from the Y chromosome.}, journal = {Molecular genetics and genomics : MGG}, volume = {296}, number = {4}, pages = {783-797}, pmid = {34037863}, issn = {1617-4623}, support = {2020YFE0201600//the National Key R&amp;D Program of China/ ; 91731303//National Natural Science Foundation of China/ ; 31671297//National Natural Science Foundation of China/ ; 18490750300//B&amp;R Joint Laboratory of Eurasian Anthropology/ ; ERC-2019-AdG-TRAM-883700//European Research Council project/ ; }, mesh = {Anthropology, Cultural ; Asian People/classification/ethnology/genetics ; China/ethnology ; Chromosomes, Human, Y/*genetics ; Civilization/*history ; Ethnicity/classification/genetics/*history ; Asia, Eastern/ethnology ; Gene Flow ; Genetics, Population/history ; History, Ancient ; Humans ; Linguistics/classification/history ; Phylogeny ; }, abstract = {East Asia, geographically extending to the Pamir Plateau in the west, to the Himalayan Mountains in the southwest, to Lake Baikal in the north and to the South China Sea in the south, harbors a variety of people, cultures, and languages. To reconstruct the natural history of East Asians is a mission of multiple disciplines, including genetics, archaeology, linguistics, and ethnology. Geneticists confirm the recent African origin of modern East Asians. Anatomically modern humans arose in Africa and immigrated into East Asia via a southern route approximately 50,000 years ago. Following the end of the Last Glacial Maximum approximately 12,000 years ago, rice and millet were domesticated in the south and north of East Asia, respectively, which allowed human populations to expand and linguistic families and ethnic groups to develop. These Neolithic populations produced a strong relation between the present genetic structures and linguistic families. The expansion of the Hongshan people from northeastern China relocated most of the ethnic populations on a large scale approximately 5300 years ago. Most of the ethnic groups migrated to remote regions, producing genetic structure differences between the edge and center of East Asia. In central China, pronounced population admixture occurred and accelerated over time, which subsequently formed the Han Chinese population and eventually the Chinese civilization. Population migration between the north and the south throughout history has left a smooth gradient in north-south changes in genetic structure. Observation of the process of shaping the genetic structure of East Asians may help in understanding the global natural history of modern humans.}, }
@article {pmid34036732, year = {2021}, author = {Straube, N and Lyra, ML and Paijmans, JLA and Preick, M and Basler, N and Penner, J and Rödel, MO and Westbury, MV and Haddad, CFB and Barlow, A and Hofreiter, M}, title = {Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens.}, journal = {Molecular ecology resources}, volume = {21}, number = {7}, pages = {2299-2315}, doi = {10.1111/1755-0998.13433}, pmid = {34036732}, issn = {1755-0998}, support = {#2013/50741-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; #2017/2616-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; #2018/15425-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 351649567//Deutsche Forschungsgemeinschaft/ ; 431589/2016-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 306623/2018-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*DNA, Ancient ; DNA, Mitochondrial/genetics ; *Museums ; Sequence Analysis, DNA ; Specimen Handling ; }, abstract = {Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.}, }
@article {pmid34035421, year = {2021}, author = {Hekkala, E and Gatesy, J and Narechania, A and Meredith, R and Russello, M and Aardema, ML and Jensen, E and Montanari, S and Brochu, C and Norell, M and Amato, G}, title = {Author Correction: Paleogenomics illuminates the evolutionary history of the extinct Holocene "horned" crocodile of Madagascar, Voay robustus.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {648}, doi = {10.1038/s42003-021-02216-9}, pmid = {34035421}, issn = {2399-3642}, }
@article {pmid34030792, year = {2021}, author = {Brooks, SA}, title = {Genomics in the Horse Industry: Discovering New Questions at Every Turn.}, journal = {Journal of equine veterinary science}, volume = {100}, number = {}, pages = {103456}, doi = {10.1016/j.jevs.2021.103456}, pmid = {34030792}, issn = {0737-0806}, mesh = {Animals ; DNA, Ancient ; *Genome ; *Genomics ; Horses/genetics ; Pedigree ; }, abstract = {The sheer diversity of heritable physiological traits, and the ingenuity of genome derived research technologies, extends the study of genetics to impact diverse scientific fields. Equine science is no exception, experiencing a number of genome-enabled discoveries that spur further research in areas like nutrition, reproduction, and exercise physiology. Yet unexpected findings, especially those that over-turn commonly held beliefs in the horse industry, can create challenges in outreach, education and communication with stakeholders. For example, studies of ancient DNA revealed that the oldest domesticated equids in the archeological record were in fact another species, the Przewalski's horse, leaving the origins of our modern horses a mystery yet to be solved. Genomic analysis of ancestry can illuminate relationships older than our prized pedigree records, and in some cases, identify unexpected inconsistencies in those pedigrees. Even our interpretation of what constitutes a genetic disease is changing, as we re-examine common disease alleles; how these alleles impact equine physiology, and how they are perceived by breeders and professionals in the industry. Effectively translating genetic tools for utilization in horse management and preparing our community for the debate surrounding ethical questions that may arise from genomic studies, may be the next great challenges we face as scientists and educators.}, }
@article {pmid34029658, year = {2021}, author = {Nodari, R and Drancourt, M and Barbieri, R}, title = {Paleomicrobiology of the human digestive tract: A review.}, journal = {Microbial pathogenesis}, volume = {157}, number = {}, pages = {104972}, doi = {10.1016/j.micpath.2021.104972}, pmid = {34029658}, issn = {1096-1208}, mesh = {Gastrointestinal Tract ; Humans ; *Metagenomics ; *Microbiota ; }, abstract = {The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.}, }
@article {pmid34016962, year = {2021}, author = {Liu, S and Kruse, S and Scherler, D and Ree, RH and Zimmermann, HH and Stoof-Leichsenring, KR and Epp, LS and Mischke, S and Herzschuh, U}, title = {Sedimentary ancient DNA reveals a threat of warming-induced alpine habitat loss to Tibetan Plateau plant diversity.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2995}, pmid = {34016962}, issn = {2041-1723}, mesh = {Altitude ; *Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Ancient/*analysis ; DNA, Plant/*analysis ; Ecology/methods ; Forests ; *Global Warming ; Paleontology/methods ; Plants/*genetics ; Tibet ; }, abstract = {Studies along elevational gradients worldwide usually find the highest plant taxa richness in mid-elevation forest belts. Hence, an increase in upper elevation diversity is expected in the course of warming-related treeline rise. Here, we use a time-series approach to infer past taxa richness from sedimentary ancient DNA from the south-eastern Tibetan Plateau over the last ~18,000 years. We find the highest total plant taxa richness during the cool phase after glacier retreat when the area contained extensive and diverse alpine habitats (14-10 ka); followed by a decline when forests expanded during the warm early- to mid-Holocene (10-3.6 ka). Livestock grazing since 3.6 ka promoted plant taxa richness only weakly. Based on these inferred dependencies, our simulation yields a substantive decrease in plant taxa richness in response to warming-related alpine habitat loss over the next centuries. Accordingly, efforts of Tibetan biodiversity conservation should include conclusions from palaeoecological evidence.}, }
@article {pmid34002224, year = {2021}, author = {Immel, A and Key, FM and Szolek, A and Barquera, R and Robinson, MK and Harrison, GF and Palmer, WH and Spyrou, MA and Susat, J and Krause-Kyora, B and Bos, KI and Forrest, S and Hernández-Zaragoza, DI and Sauter, J and Solloch, U and Schmidt, AH and Schuenemann, VJ and Reiter, E and Kairies, MS and Weiß, R and Arnold, S and Wahl, J and Hollenbach, JA and Kohlbacher, O and Herbig, A and Norman, PJ and Krause, J}, title = {Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes.}, journal = {Molecular biology and evolution}, volume = {38}, number = {10}, pages = {4059-4076}, pmid = {34002224}, issn = {1537-1719}, support = {R01 AI158410/AI/NIAID NIH HHS/United States ; R01 AI158861/AI/NIAID NIH HHS/United States ; R56 AI151549/AI/NIAID NIH HHS/United States ; }, mesh = {DNA ; Genomics ; Humans ; Pandemics/history ; *Plague/genetics ; *Yersinia pestis/genetics ; }, abstract = {Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes, we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggest that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.}, }
@article {pmid33997698, year = {2021}, author = {Haller, M and Callan, K and Susat, J and Flux, AL and Immel, A and Franke, A and Herbig, A and Krause, J and Kupczok, A and Fouquet, G and Hummel, S and Rieger, D and Nebel, A and Krause-Kyora, B}, title = {Mass burial genomics reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city Lübeck.}, journal = {iScience}, volume = {24}, number = {5}, pages = {102419}, pmid = {33997698}, issn = {2589-0042}, abstract = {Medieval Europe was repeatedly affected by outbreaks of infectious diseases, some of which reached epidemic proportions. A Late Medieval mass burial next to the Heiligen-Geist-Hospital in Lübeck (present-day Germany) contained the skeletal remains of more than 800 individuals who had presumably died from infectious disease. From 92 individuals, we screened the ancient DNA extracts for the presence of pathogens to determine the cause of death. Metagenomic analysis revealed evidence of Salmonella enterica subsp. enterica serovar Paratyphi C, suggesting an outbreak of enteric paratyphoid fever. Three reconstructed S. Paratyphi C genomes showed close similarity to a strain from Norway (1200 CE). Radiocarbon dates placed the disease outbreak in Lübeck between 1270 and 1400 cal CE, with historical records indicating 1367 CE as the most probable year. The deceased were of northern and eastern European descent, confirming Lübeck as an important trading center of the Hanseatic League in the Baltic region.}, }
@article {pmid33992907, year = {2021}, author = {Kerner, G and Patin, E and Quintana-Murci, L}, title = {New insights into human immunity from ancient genomics.}, journal = {Current opinion in immunology}, volume = {72}, number = {}, pages = {116-125}, pmid = {33992907}, issn = {1879-0372}, mesh = {Animals ; COVID-19/epidemiology/genetics/*immunology ; Evolution, Molecular ; Genetic Predisposition to Disease ; Genetics, Population ; Genomics ; Hominidae ; Humans ; Immunity/*genetics ; SARS-CoV-2/*physiology ; }, abstract = {Population genetic studies have clearly indicated that immunity and host defense are among the functions most frequently subject to natural selection, and increased our understanding of the biological relevance of the corresponding genes and their contribution to variable immune traits and diseases. Herein, we will focus on some recently studied forms of human adaptation to infectious agents, including hybridization with now-extinct hominins, such as Neanderthals and Denisovans, and admixture between modern human populations. These studies, which are partly enabled by the technological advances in the sequencing of DNA from ancient remains, provide new insight into the sources of immune response variation in contemporary humans, such as the recently reported link between Neanderthal heritage and susceptibility to severe COVID-19 disease. Furthermore, ancient DNA analyses, in both humans and pathogens, allow to measure the action of natural selection on immune genes across time and to reconstruct the impact of past epidemics on the evolution of human immunity.}, }
@article {pmid33988685, year = {2021}, author = {Toussaint, EFA and Gauthier, J and Bilat, J and Gillett, CPDT and Gough, HM and Lundkvist, H and Blanc, M and Muñoz-Ramírez, CP and Alvarez, N}, title = {HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {33988685}, issn = {1759-6653}, mesh = {Animals ; *Coleoptera/genetics ; DNA, Mitochondrial/genetics ; Exome ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosomaburchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.}, }
@article {pmid33986442, year = {2021}, author = {Prakash, A and Banerjee, M}, title = {Genomic selection signatures in autism spectrum disorder identifies cognitive genomic tradeoff and its relevance in paradoxical phenotypes of deficits versus potentialities.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10245}, pmid = {33986442}, issn = {2045-2322}, mesh = {Autism Spectrum Disorder/*genetics/metabolism ; Bayes Theorem ; Biological Evolution ; Cognition/*physiology ; Databases, Genetic ; Gain of Function Mutation/physiology ; Genetic Predisposition to Disease/genetics ; Genome ; Genome-Wide Association Study/methods ; Genomics ; Genotype ; Humans ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Risk Factors ; }, abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder characterized by paradoxical phenotypes of deficits as well as gain in brain function. To address this a genomic tradeoff hypothesis was tested and followed up with the biological interaction and evolutionary significance of positively selected ASD risk genes. SFARI database was used to retrieve the ASD risk genes while for population datasets 1000 genome data was used. Common risk SNPs were subjected to machine learning as well as independent tests for selection, followed by Bayesian analysis to identify the cumulative effect of selection on risk SNPs. Functional implication of these positively selected risk SNPs was assessed and subjected to ontology analysis, pertaining to their interaction and enrichment of biological and cellular functions. This was followed by comparative analysis with the ancient genomes to identify their evolutionary patterns. Our results identified significant positive selection signals in 18 ASD risk SNPs. Functional and ontology analysis indicate the role of biological and cellular processes associated with various brain functions. The core of the biological interaction network constitutes genes for cognition and learning while genes in the periphery of the network had direct or indirect impact on brain function. Ancient genome analysis identified de novo and conserved evolutionary selection clusters. The de-novo evolutionary cluster represented genes involved in cognitive function. Relative enrichment of the ASD risk SNPs from the respective evolutionary cluster or biological interaction networks may help in addressing the phenotypic diversity in ASD. This cognitive genomic tradeoff signatures impacting the biological networks can explain the paradoxical phenotypes in ASD.}, }
@article {pmid33977786, year = {2021}, author = {Rey-Iglesia, A and Lister, AM and Campos, PF and Brace, S and Mattiangeli, V and Daly, KG and Teasdale, MD and Bradley, DG and Barnes, I and Hansen, AJ}, title = {Exploring the phylogeography and population dynamics of the giant deer (Megaloceros giganteus) using Late Quaternary mitogenomes.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1950}, pages = {20201864}, pmid = {33977786}, issn = {1471-2954}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Deer/genetics ; Europe ; Fossils ; Genetic Variation ; *Genome, Mitochondrial ; Phylogeny ; Phylogeography ; Population Dynamics ; }, abstract = {Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer (Megaloceros giganteus) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia. However, during the Holocene, its range contracted to eastern Europe and western Siberia, where the last populations of the species occurred. Here, we generated 35 Late Pleistocene and Holocene giant deer mitogenomes to explore the genetics of the demise of this iconic species. Bayesian phylogenetic analyses of the mitogenomes suggested five main clades for the species: three pre-Last Glacial Maximum clades that did not appear in the post-Last Glacial Maximum genetic pool, and two clades that showed continuity into the Holocene. Our study also identified a decrease in genetic diversity starting in Marine Isotope Stage 3 and accelerating during the Last Glacial Maximum. This reduction in genetic diversity during the Last Glacial Maximum, coupled with a major contraction of fossil occurrences, suggests that climate was a major driver in the dynamics of the giant deer.}, }
@article {pmid33974873, year = {2021}, author = {Roesti, M}, title = {Evolution: Predictability and the promise of ancient DNA.}, journal = {Current biology : CB}, volume = {31}, number = {9}, pages = {R446-R448}, doi = {10.1016/j.cub.2021.03.063}, pmid = {33974873}, issn = {1879-0445}, mesh = {Animals ; *DNA, Ancient ; Genome ; *Smegmamorpha/genetics ; }, abstract = {Is evolution predictable? Genomes from thousands-of-years-old stickleback suggest that, despite substantial stochasticity in the course of evolution, our understanding of the recent evolutionary past of this species was generally valid.}, }
@article {pmid33974848, year = {2021}, author = {Saupe, T and Montinaro, F and Scaggion, C and Carrara, N and Kivisild, T and D'Atanasio, E and Hui, R and Solnik, A and Lebrasseur, O and Larson, G and Alessandri, L and Arienzo, I and De Angelis, F and Rolfo, MF and Skeates, R and Silvestri, L and Beckett, J and Talamo, S and Dolfini, A and Miari, M and Metspalu, M and Benazzi, S and Capelli, C and Pagani, L and Scheib, CL}, title = {Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula.}, journal = {Current biology : CB}, volume = {31}, number = {12}, pages = {2576-2591.e12}, doi = {10.1016/j.cub.2021.04.022}, pmid = {33974848}, issn = {1879-0445}, mesh = {*DNA, Ancient ; Datasets as Topic ; Genetics, Population ; Genome, Human/*genetics ; Genomics ; History, Ancient ; Human Migration/*history ; Humans ; Italy ; Leprosy/genetics ; Phenotype ; }, abstract = {Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.}, }
@article {pmid33971396, year = {2021}, author = {Maixner, F and Gresky, J and Zink, A}, title = {Ancient DNA analysis of rare genetic bone disorders.}, journal = {International journal of paleopathology}, volume = {33}, number = {}, pages = {182-187}, doi = {10.1016/j.ijpp.2021.04.009}, pmid = {33971396}, issn = {1879-9825}, mesh = {*Bone Diseases/genetics ; Bone and Bones ; *DNA, Ancient ; Humans ; Paleopathology ; Rare Diseases ; }, abstract = {OBJECTIVE: Review of the current advancements in the field of paleogenetics that provide new opportunities in studying the evolution of rare genetic bone diseases.<br><br>MATERIAL AND METHODS: Based on cases from the literature, the genetics of rare bone diseases will be introduced and the main methodological issues will be addressed, focusing on the opportunities presented by the application of aDNA analyses in the field of paleopathology.<br><br>RESULTS: Medical literature provides large datasets on the genes responsible for rare bone disorders. These genes, subdivided in functional categories, display important future targets when analyzing rare genetic bone disorders in ancient human remains.<br><br>CONCLUSIONS: Knowledge on both phenotype and genotype is required to study rare diseases in ancient human remains.<br><br>SIGNIFICANCE: The proposed interdisciplinary research will provide new insight into the occurrence and spread of genetic risk factors in the past and will help in the diagnostics of these rare and often neglected diseases.<br><br>LIMITATIONS: The current limitations in ancient DNA research and targeting the disease-causing specific mutations (e.g., somatic or germline).<br><br>Methodological advancements and candidate gene lists provide the optimal basis for future interdisciplinary studies of rare genetic bone disorders in ancient human remains.}, }
@article {pmid33951239, year = {2021}, author = {Gopalan, S and Atkinson, EG and Buck, LT and Weaver, TD and Henn, BM}, title = {Inferring archaic introgression from hominin genetic data.}, journal = {Evolutionary anthropology}, volume = {30}, number = {3}, pages = {199-220}, pmid = {33951239}, issn = {1520-6505}, support = {R35 GM133531/GM/NIGMS NIH HHS/United States ; K12-GM102778/NH/NIH HHS/United States ; K01-MH121659/NH/NIH HHS/United States ; R35-GM133531/NH/NIH HHS/United States ; K01 MH121659/MH/NIMH NIH HHS/United States ; K12 GM102778/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Genetic Introgression/*genetics ; Hominidae/classification/genetics ; Humans ; Neanderthals/classification/*genetics ; }, abstract = {Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.}, }
@article {pmid33941705, year = {2021}, author = {Gros-Balthazard, M and Flowers, JM and Hazzouri, KM and Ferrand, S and Aberlenc, F and Sallon, S and Purugganan, MD}, title = {The genomes of ancient date palms germinated from 2,000 y old seeds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {19}, pages = {}, pmid = {33941705}, issn = {1091-6490}, mesh = {Crops, Agricultural/*history ; DNA, Plant/analysis/genetics ; Genome, Plant/*genetics ; Genotype ; Germination/*genetics ; History, Ancient ; Phoeniceae/*genetics ; Polymorphism, Single Nucleotide ; Seeds/*genetics/growth &amp; development ; Sequence Analysis, DNA/methods ; }, abstract = {Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated from the fourth century BCE to the second century CE, were recovered from archaeological sites in the Southern Levant and germinated to yield viable plants. We conducted whole-genome sequencing of these germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of these previously extinct Judean date palms. We find that the oldest seeds from the fourth to first century BCE are related to modern West Asian date varieties, but later material from the second century BCE to second century CE showed increasing genetic affinities to present-day North African date palms. Population genomic analysis reveals that by ∼2,400 to 2,000 y ago, the P. dactylifera gene pool in the Eastern Mediterranean already contained introgressed segments from the Cretan palm Phoenix theophrasti, a crucial genetic feature of the modern North African date palm populations. The P. theophrasti introgression fraction content is generally higher in the later samples, while introgression tracts are longer in these ancient germinated date palms compared to modern North African varieties. These results provide insights into crop evolution arising from an analysis of plants originating from ancient germinated seeds and demonstrate what can be accomplished with the application of a resurrection genomics approach.}, }
@article {pmid33930288, year = {2021}, author = {Clemente, F and Unterländer, M and Dolgova, O and Amorim, CEG and Coroado-Santos, F and Neuenschwander, S and Ganiatsou, E and Cruz Dávalos, DI and Anchieri, L and Michaud, F and Winkelbach, L and Blöcher, J and Arizmendi Cárdenas, YO and Sousa da Mota, B and Kalliga, E and Souleles, A and Kontopoulos, I and Karamitrou-Mentessidi, G and Philaniotou, O and Sampson, A and Theodorou, D and Tsipopoulou, M and Akamatis, I and Halstead, P and Kotsakis, K and Urem-Kotsou, D and Panagiotopoulos, D and Ziota, C and Triantaphyllou, S and Delaneau, O and Jensen, JD and Moreno-Mayar, JV and Burger, J and Sousa, VC and Lao, O and Malaspinas, AS and Papageorgopoulou, C}, title = {The genomic history of the Aegean palatial civilizations.}, journal = {Cell}, volume = {184}, number = {10}, pages = {2565-2586.e21}, pmid = {33930288}, issn = {1097-4172}, support = {R01 GM135899/GM/NIGMS NIH HHS/United States ; R35 GM139383/GM/NIGMS NIH HHS/United States ; }, mesh = {Civilization/*history ; DNA, Ancient ; *Genome, Human ; *Genome, Mitochondrial ; Greece, Ancient ; History, Ancient ; Human Migration/*history ; Humans ; }, abstract = {The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.}, }
@article {pmid33922908, year = {2021}, author = {Fontani, F and Cilli, E and Arena, F and Sarno, S and Modi, A and De Fanti, S and Andrews, AJ and Latorre, A and Abondio, P and Larocca, F and Lari, M and Caramelli, D and Gualdi-Russo, E and Luiselli, D}, title = {First Bronze Age Human Mitogenomes from Calabria (Grotta Della Monaca, Southern Italy).}, journal = {Genes}, volume = {12}, number = {5}, pages = {}, pmid = {33922908}, issn = {2073-4425}, mesh = {*DNA, Ancient ; Evolution, Molecular ; *Genome, Human ; *Genome, Mitochondrial ; Humans ; Italy ; }, abstract = {The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA studies in Southern Italy are, at present, still limited to prehistoric and Roman Apulia. Here, we present the first mitogenomes from a Middle Bronze Age cave burial in Calabria to address this knowledge gap. We adopted a hybridization capture approach, which enabled the recovery of one complete and one partial mitochondrial genome. Phylogenetic analysis assigned these two individuals to the H1e and H5 subhaplogroups, respectively. This preliminary phylogenetic analysis supports affinities with coeval Sicilian populations, along with Linearbandkeramik and Bell Beaker cultures maternal lineages from Central Europe and Iberia. Our work represents a starting point which contributes to the comprehension of migrations and population dynamics in Southern Italy, and highlights this knowledge gap yet to be filled by genomic studies.}, }
@article {pmid33911223, year = {2021}, author = {Clyde, D}, title = {Bone-free ancient DNA.}, journal = {Nature reviews. Genetics}, volume = {22}, number = {6}, pages = {342}, pmid = {33911223}, issn = {1471-0064}, mesh = {*Bone and Bones ; *DNA, Ancient ; Fossils ; Humans ; }, }
@article {pmid33907305, year = {2021}, author = {Hekkala, E and Gatesy, J and Narechania, A and Meredith, R and Russello, M and Aardema, ML and Jensen, E and Montanari, S and Brochu, C and Norell, M and Amato, G}, title = {Paleogenomics illuminates the evolutionary history of the extinct Holocene "horned" crocodile of Madagascar, Voay robustus.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {505}, pmid = {33907305}, issn = {2399-3642}, mesh = {Alligators and Crocodiles/*genetics ; Animals ; *Biological Evolution ; DNA, Ancient/*analysis ; *Extinction, Biological ; *Fossils ; Genomics/*methods ; Madagascar ; Paleontology ; Phylogeny ; }, abstract = {Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300-1400 year old specimens (n = 2) of the extinct "horned" crocodile, Voay robustus, collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.}, }
@article {pmid33906608, year = {2021}, author = {Scarsbrook, L and Sherratt, E and Hitchmough, RA and Rawlence, NJ}, title = {Skeletal variation in extant species enables systematic identification of New Zealand's large, subfossil diplodactylids.}, journal = {BMC ecology and evolution}, volume = {21}, number = {1}, pages = {67}, pmid = {33906608}, issn = {2730-7182}, mesh = {Animals ; *Fossils ; Humans ; *Lizards ; New Zealand ; Phylogeny ; }, abstract = {New Zealand's diplodactylid geckos exhibit high species-level diversity, largely independent of discernible osteological changes. Consequently, systematic affinities of isolated skeletal elements (fossils) are primarily determined by comparisons of size, particularly in the identification of Hoplodactylus duvaucelii, New Zealand's largest extant gecko species. Here, three-dimensional geometric morphometrics of maxillae (a common fossilized element) was used to determine whether consistent shape and size differences exist between genera, and if cryptic extinctions have occurred in subfossil 'Hoplodactylus cf. duvaucelii'. Sampling included 13 diplodactylid species from five genera, and 11 Holocene subfossil 'H. cf. duvaucelii' individuals. We found phylogenetic history was the most important predictor of maxilla morphology among extant diplodactylid genera. Size comparisons could only differentiate Hoplodactylus from other genera, with the remaining genera exhibiting variable degrees of overlap. Six subfossils were positively identified as H. duvaucelii, confirming their proposed Holocene distribution throughout New Zealand. Conversely, five subfossils showed no clear affinities with any modern diplodactylid genera, implying either increased morphological diversity in mainland 'H. cf. duvaucelii' or the presence of at least one extinct, large, broad-toed diplodactylid species.}, }
@article {pmid33898948, year = {2021}, author = {Caparros, M and Prat, S}, title = {A Phylogenetic Networks perspective on reticulate human evolution.}, journal = {iScience}, volume = {24}, number = {4}, pages = {102359}, pmid = {33898948}, issn = {2589-0042}, abstract = {We present a methodological phylogenetic reconstruction approach combining Maximum Parsimony and Phylogenetic Networks methods for the study of human evolution applied to phenotypic craniodental characters of 22 hominin species. The approach consists in selecting and validating a tree-like most parsimonious scenario out of several parsimony runs based on various numerical constraints. An intermediate step from tree to network methods is implemented by running an analysis with a reduced apomorphous character dataset that generates multiple parsimonious trees. These most parsimonious trees are then used as input for a Phylogenetic Networks analysis that results in consensus and reticulate networks. We show here that the phylogenetic tree-like definition of the genus Homo is a relative concept linked to craniodental characters that come in support of hypothetical Last Common Ancestors of the most parsimonious scenario and infer that the Homo reticulate network concords with recent findings in paleogenomic research regarding its mode of evolution.}, }
@article {pmid33890614, year = {2021}, author = {Neukamm, J and Peltzer, A and Nieselt, K}, title = {DamageProfiler: fast damage pattern calculation for ancient DNA.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {20}, pages = {3652-3653}, doi = {10.1093/bioinformatics/btab190}, pmid = {33890614}, issn = {1367-4811}, abstract = {MOTIVATION: In ancient DNA research, the authentication of ancient samples based on specific features remains a crucial step in data analysis. Because of this central importance, researchers lacking deeper programming knowledge should be able to run a basic damage authentication analysis. Such software should be user-friendly and easy to integrate into an analysis pipeline.<br><br>RESULTS: DamageProfiler is a Java-based, stand-alone software to determine damage patterns in ancient DNA. The results are provided in various file formats and plots for further processing. DamageProfiler has an intuitive graphical as well as command line interface that allows the tool to be easily embedded into an analysis pipeline.<br><br>All of the source code is freely available on GitHub (https://github.com/Integrative-Transcriptomics/DamageProfiler).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid33887182, year = {2021}, author = {Siano, R and Lassudrie, M and Cuzin, P and Briant, N and Loizeau, V and Schmidt, S and Ehrhold, A and Mertens, KN and Lambert, C and Quintric, L and Noël, C and Latimier, M and Quéré, J and Durand, P and Penaud, A}, title = {Sediment archives reveal irreversible shifts in plankton communities after World War II and agricultural pollution.}, journal = {Current biology : CB}, volume = {31}, number = {12}, pages = {2682-2689.e7}, doi = {10.1016/j.cub.2021.03.079}, pmid = {33887182}, issn = {1879-0445}, mesh = {Biodiversity ; *Dinoflagellida/genetics ; Ecosystem ; Geologic Sediments ; Humans ; *Plankton/genetics ; Retrospective Studies ; World War II ; }, abstract = {To evaluate the stability and resilience[1] of coastal ecosystem communities to perturbations that occurred during the Anthropocene,[2] pre-industrial biodiversity baselines inferred from paleoarchives are needed.[3][,][4] The study of ancient DNA (aDNA) from sediments (sedaDNA)[5] has provided valuable information about past dynamics of microbial species[6-8] and communities[9-18] in relation to ecosystem variations. Shifts in planktonic protist communities might significantly affect marine ecosystems through cascading effects,[19-21] and therefore the analysis of this compartment is essential for the assessment of ecosystem variations. Here, sediment cores collected from different sites of the Bay of Brest (northeast Atlantic, France) allowed ca. 1,400 years of retrospective analyses of the effects of human pollution on marine protists. Comparison of sedaDNA extractions and metabarcoding analyses with different barcode regions (V4 and V7 18S rDNA) revealed that protist assemblages in ancient sediments are mainly composed of species known to produce resting stages. Heavy-metal pollution traces in sediments were ascribed to the World War II period and coincided with community shifts within dinoflagellates and stramenopiles. After the war and especially from the 1980s to 1990s, protist genera shifts followed chronic contaminations of agricultural origin. Community composition reconstruction over time showed that there was no recovery to a Middle Ages baseline composition. This demonstrates the irreversibility of the observed shifts after the cumulative effect of war and agricultural pollutions. Developing a paleoecological approach, this study highlights how human contaminations irreversibly affect marine microbial compartments, which contributes to the debate on coastal ecosystem preservation and restoration.}, }
@article {pmid33887180, year = {2021}, author = {Bortolini, E and Pagani, L and Oxilia, G and Posth, C and Fontana, F and Badino, F and Saupe, T and Montinaro, F and Margaritora, D and Romandini, M and Lugli, F and Papini, A and Boggioni, M and Perrini, N and Oxilia, A and Cigliano, RA and Barcelona, R and Visentin, D and Fasser, N and Arrighi, S and Figus, C and Marciani, G and Silvestrini, S and Bernardini, F and Menghi Sartorio, JC and Fiorenza, L and Cecchi, JM and Tuniz, C and Kivisild, T and Gianfrancesco, F and Peresani, M and Scheib, CL and Talamo, S and D'Esposito, M and Benazzi, S}, title = {Early Alpine occupation backdates westward human migration in Late Glacial Europe.}, journal = {Current biology : CB}, volume = {31}, number = {11}, pages = {2484-2493.e7}, doi = {10.1016/j.cub.2021.03.078}, pmid = {33887180}, issn = {1879-0445}, mesh = {Climate ; Europe ; *Human Migration ; Humans ; *Ice Cover ; Occupations ; }, abstract = {Before the end of the Last Glacial Maximum (LGM, ∼16.5 ka ago)[1] set in motion major shifts in human culture and population structure,[2] a consistent change in lithic technology, material culture, settlement pattern, and adaptive strategies is recorded in Southern Europe at ∼18-17 ka ago. In this time frame, the landscape of Northeastern Italy changed considerably, and the retreat of glaciers allowed hunter-gatherers to gradually recolonize the Alps.[3-6] Change within this renewed cultural frame (i.e., during the Late Epigravettian phase) is currently associated with migrations favored by warmer climate linked to the Bølling-Allerød onset (14.7 ka ago),[7-11] which replaced earlier genetic lineages with ancestry found in an individual who lived ∼14 ka ago at Riparo Villabruna, Italy, and shared among different contexts (Villabruna Cluster).[9] Nevertheless, these dynamics and their chronology are still far from being disentangled due to fragmentary evidence for long-distance interactions across Europe.[12] Here, we generate new genomic data from a human mandible uncovered at Riparo Tagliente (Veneto, Italy), which we directly dated to 16,980-16,510 cal BP (2σ). This individual, affected by focal osseous dysplasia, is genetically affine to the Villabruna Cluster. Our results therefore backdate by at least 3 ka the diffusion in Southern Europe of a genetic component linked to Balkan/Anatolian refugia, previously believed to have spread during the later Bølling/Allerød event. In light of the new genetic evidence, this population replacement chronologically coincides with the very emergence of major cultural transitions in Southern and Western Europe.}, }
@article {pmid33872864, year = {2021}, author = {Alterauge, A and Lösch, S and Sulzer, A and Gysi, M and Haas, C}, title = {Beyond simple kinship and identification: aDNA analyses from a 17th-19th century crypt in Germany.}, journal = {Forensic science international. Genetics}, volume = {53}, number = {}, pages = {102498}, doi = {10.1016/j.fsigen.2021.102498}, pmid = {33872864}, issn = {1878-0326}, mesh = {Chromosomes, Human, Y ; DNA Fingerprinting ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Famous Persons ; Germany ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Microsatellite Repeats ; *Pedigree ; }, abstract = {Ancient DNA (aDNA) analysis is a powerful tool in multidisciplinary research on human remains, potentially leading to kinship scenarios and historical identifications. In this study, we present a genetic investigation of three noble families from the 17th to 19th centuries AD entombed in burial crypts at the cloister church of Riesa (Germany). Tests were aimed at identifying anticipated and incidental genetic relationships in our sample and the implications thereof for the assumed identity of the deceased. A total of 17 individuals were investigated via morphological, radiographic and aDNA analysis, yielding complete and partial autosomal and Y-STR profiles and reliable mtDNA sequences. Biostatistics and lineage markers revealed the presence of first to third degree relationships within the cohort. The pedigrees of the families Hanisch/von Odeleben and von Welck were thereby successfully reproduced, while four previously unknown individuals could be linked to the von Felgenhauer family. However, limitations of biostatistical kinship analysis became evident when the kinship scenario went beyond simple relationships. A combined analysis with archaeological data and historical records resulted in (almost) unambiguous identification of 14 of the 17 individuals.}, }
@article {pmid33857427, year = {2021}, author = {Yaka, R and Mapelli, I and Kaptan, D and Doğu, A and Chyleński, M and Erdal, &#xd6;D and Koptekin, D and Vural, KB and Bayliss, A and Mazzucato, C and Fer, E and Çokoğlu, SS and Lagerholm, VK and Krzewińska, M and Karamurat, C and Gemici, HC and Sevkar, A and Dağtaş, ND and Kılınç, GM and Adams, D and Munters, AR and Sağlıcan, E and Milella, M and Schotsmans, EMJ and Yurtman, E and Çetin, M and Yorulmaz, S and Altınışık, NE and Ghalichi, A and Juras, A and Bilgin, CC and Günther, T and Storå, J and Jakobsson, M and de Kleijn, M and Mustafaoğlu, G and Fairbairn, A and Pearson, J and Togan, &#x130; and Kayacan, N and Marciniak, A and Larsen, CS and Hodder, I and Atakuman, &#xc7; and Pilloud, M and Sürer, E and Gerritsen, F and Özbal, R and Baird, D and Erdal, YS and Duru, G and Özbaşaran, M and Haddow, SD and Knüsel, CJ and Götherström, A and Özer, F and Somel, M}, title = {Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.}, journal = {Current biology : CB}, volume = {31}, number = {11}, pages = {2455-2468.e18}, pmid = {33857427}, issn = {1879-0445}, mesh = {*Archaeology ; History, Ancient ; Humans ; Pedigree ; *Social Structure ; Turkey ; }, abstract = {The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,[1] mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,[2] household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,[3-5] and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.}, }
@article {pmid33857143, year = {2021}, author = {Lanman, RB and Hylkema, L and Boone, CM and Allée, B and Castillo, RO and Moreno, SA and Flores, MF and DeSilva, U and Bingham, B and Kemp, BM}, title = {Ancient DNA analysis of archaeological specimens extends Chinook salmon's known historic range to San Francisco Bay's tributaries and southernmost watershed.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0244470}, pmid = {33857143}, issn = {1932-6203}, mesh = {Animal Migration/*physiology ; Animals ; DNA, Ancient/*analysis ; Ecosystem ; Fossils/pathology ; Oncorhynchus mykiss/genetics ; Pacific Ocean ; Rivers ; Salmon/*genetics ; San Francisco ; }, abstract = {Understanding a species' historic range guides contemporary management and habitat restoration. Chinook salmon (Oncorhynchus tshawytscha) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropogenic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Through the morphology-based analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara (CA-SCL-30H), Santa Clara County, circa 1781-1834 CE, 88 salmonid vertebrae were identified. Ancient DNA sequencing identified three separate individuals as Chinook salmon and the remainder as steelhead/rainbow trout (Oncorhynchus mykiss). These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their documented historic range to include San Francisco Bay's southernmost tributary watershed.}, }
@article {pmid33855818, year = {2021}, author = {Zhang, M and Cao, P and Dai, Q and Wang, Y and Feng, X and Wang, H and Wu, H and Ko, AM and Mao, X and Liu, Y and Yu, L and Roos, C and Nadler, T and Xiao, W and Bennett, EA and Fu, Q}, title = {Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples.}, journal = {Zoological research}, volume = {42}, number = {3}, pages = {280-286}, pmid = {33855818}, issn = {2095-8137}, mesh = {Animals ; DNA, Ancient/*analysis ; *Dogs ; Museums ; *Presbytini ; Sequence Analysis, DNA/methods/*veterinary ; Specimen Handling/methods/*veterinary ; }, abstract = {DNA studies of endangered or extinct species often rely on ancient or degraded remains. The majority of ancient DNA (aDNA) extraction protocols focus on skeletal elements, with skin and hair samples rarely explored. Similar to that found in bones and teeth, DNA extracted from historical or ancient skin and fur samples is also extremely fragmented with low endogenous content due to natural degradation processes. Thus, the development of effective DNA extraction methods is required for these materials. Here, we compared the performance of two DNA extraction protocols (commercial and custom laboratory aDNA methods) on hair and skin samples from decades-old museum specimens to Iron Age archaeological material. We found that apart from the impact sample-specific taphonomic and handling history has on the quantity and quality of DNA preservation, skin yielded more endogenous DNA than hair of the samples and protocols tested. While both methods recovered DNA from ancient soft tissue, the laboratory method performed better overall in terms of DNA yield and quality, which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.}, }
@article {pmid33844838, year = {2021}, author = {Cascardo, P and Pucu, E and Leles, D}, title = {REVIEW OF PARASITES FOUND IN EXTINCT ANIMALS: WHAT CAN BE REVEALED.}, journal = {The Journal of parasitology}, volume = {107}, number = {2}, pages = {275-283}, doi = {10.1645/20-30}, pmid = {33844838}, issn = {1937-2345}, mesh = {Amber ; Animals ; Bone and Bones/microbiology/parasitology/pathology ; *Extinction, Biological ; Fossils/*parasitology ; Geologic Sediments/*parasitology ; History, Ancient ; Mummies/parasitology ; *Paleopathology ; Parasitic Diseases, Animal/*history ; }, abstract = {Parasitism is inherent to life and observed in all species. Extinct animals have been studied to understand what they looked like, where and how they lived, what they fed on, and the reasons they became extinct. Paleoparasitology helps to clarify these questions based on the study of the parasites and microorganisms that infected those animals, using as a source material coprolites, fossils in rock, tissue, bone, mummy, and amber, analyses of ancient DNA, immunodiagnosis, and microscopy.}, }
@article {pmid33834210, year = {2021}, author = {Oliva, A and Tobler, R and Cooper, A and Llamas, B and Souilmi, Y}, title = {Systematic benchmark of ancient DNA read mapping.}, journal = {Briefings in bioinformatics}, volume = {22}, number = {5}, pages = {}, doi = {10.1093/bib/bbab076}, pmid = {33834210}, issn = {1477-4054}, mesh = {Algorithms ; Benchmarking/*methods ; Computational Biology/*methods ; DNA, Ancient/*analysis/chemistry ; Genome, Human/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA 'reads') against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30-80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software-BWA-aln, BWA-mem, NovoAlign and Bowtie2-and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.}, }
@article {pmid33833423, year = {2021}, author = {Taylor, WTT and Pruvost, M and Posth, C and Rendu, W and Krajcarz, MT and Abdykanova, A and Brancaleoni, G and Spengler, R and Hermes, T and Schiavinato, S and Hodgins, G and Stahl, R and Min, J and Alisher Kyzy, S and Fedorowicz, S and Orlando, L and Douka, K and Krivoshapkin, A and Jeong, C and Warinner, C and Shnaider, S}, title = {Evidence for early dispersal of domestic sheep into Central Asia.}, journal = {Nature human behaviour}, volume = {5}, number = {9}, pages = {1169-1179}, pmid = {33833423}, issn = {2397-3374}, mesh = {Animal Husbandry/*history ; Animals ; Asia ; DNA, Mitochondrial/*history ; History, Ancient ; Humans ; Kazakhstan ; Kyrgyzstan ; Sheep ; *Sheep, Domestic ; Tajikistan ; Uzbekistan ; }, abstract = {The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca. 6,000 BCE. Zooarchaeological and collagen peptide mass fingerprinting show exploitation of Ovis and Capra, while cementum analysis of intact teeth implicates possible pastoral slaughter during the fall season. Most significantly, ancient DNA reveals these directly dated specimens as the domestic O. aries, within the genetic diversity of domesticated sheep lineages. Together, these results provide the earliest evidence for the use of livestock in the mountains of the Ferghana Valley, predating previous evidence by 3,000 years and suggesting that domestic animal economies reached the mountains of interior Central Asia far earlier than previously recognized.}, }
@article {pmid33831350, year = {2021}, author = {Psonis, N and Vassou, D and Kafetzopoulos, D}, title = {Testing a series of modifications on genomic library preparation methods for ancient or degraded DNA.}, journal = {Analytical biochemistry}, volume = {623}, number = {}, pages = {114193}, doi = {10.1016/j.ab.2021.114193}, pmid = {33831350}, issn = {1096-0309}, mesh = {DNA/*analysis/chemistry/metabolism ; DNA Primers/chemistry ; DNA, Ancient/*analysis/chemistry ; DNA, Single-Stranded/analysis/chemistry ; *Genomic Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; Uracil-DNA Glycosidase/chemistry/metabolism ; }, abstract = {Technological advancements have revolutionized ancient and degraded DNA analysis, moving the field to the Next Generation Sequencing era. One of the advancements, the ancient DNA-oriented high-throughput library preparation methods, enabled the sequencing of more endogenous molecules. Although fairly optimized, both single- and double-stranded library preparation methods hold the potential for further improvement. Here, we test a series of modifications made at different steps of both single- and double-stranded library preparation methods. Given all the modifications tested, we found that two of them provide further benefits, including the use of Endonuclease VIII as a pre-treatment step before preparing single-stranded libraries and the use of a modified second adapter of the single stranded-libraries as an alternative option to enable sequencing of single stranded-libraries with the standard Illumina sequencing primer instead of the custom designed as described in the single stranded library preparation method. Furthermore, we propose uracil-DNA-glycosylase (UDG) could also be considered for both single- and double-stranded library preparation methods, although additional parameters should be taken into account depending on the sequencing strategy and the sample characteristics. Further modifications were also tested and although they were not advantageous, they could be considered as equivalent to the published options.}, }
@article {pmid33821116, year = {2022}, author = {Bendrey, R and Martin, D}, title = {Zoonotic diseases: New directions in human-animal pathology.}, journal = {International journal of osteoarchaeology}, volume = {32}, number = {3}, pages = {548-552}, pmid = {33821116}, issn = {1047-482X}, abstract = {Zoonotic diseases-human diseases of animal origin-represent one of the world's greatest health challenges, both today and in the past. Since the Neolithic, zoonotic diseases have been one of the major factors shaping and influencing human adaptation. Archaeology is ideally situated to provide the long view on human-animal-pathogen relationships through combining cultural, environmental and biological datasets, yet long-term studies of linked human and animal records have often been overlooked and undertheorized. The seven papers in this special issue "Zoonotic diseases: New directions in human-animal pathology" cover a range of diseases caused by bacterial, viral, and parasitic pathogens, from case studies drawn from across Europe, Asia, Africa and the Americas. They speak to the diversity of human-animal-environment interactions that shaped disease emergence and transmission. They also review methodological advancements relating to disease identification and interpretation and discuss interdisciplinary approaches to effectively investigate these complex processes in the past. This introduction highlights their key themes and outcomes and identifies research priorities moving forward.}, }
@article {pmid33814550, year = {2021}, author = {Geigl, EM}, title = {[Discussion about the presentation: "PCR and paleogenetics: for best and for worst"].}, journal = {Bulletin de l'Academie nationale de medecine}, volume = {205}, number = {4}, pages = {420-421}, doi = {10.1016/j.banm.2021.02.009}, pmid = {33814550}, issn = {0001-4079}, }
@article {pmid33811235, year = {2021}, author = {Farrer, AG and Wright, SL and Skelly, E and Eisenhofer, R and Dobney, K and Weyrich, LS}, title = {Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7456}, pmid = {33811235}, issn = {2045-2322}, mesh = {Biodiversity ; DNA, Ancient/*analysis ; *Decontamination ; Dental Calculus/*genetics/*microbiology ; Environment ; Humans ; Metagenomics ; Mouth/microbiology ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.}, }
@article {pmid33809280, year = {2021}, author = {Kusliy, MA and Vorobieva, NV and Tishkin, AA and Makunin, AI and Druzhkova, AS and Trifonov, VA and Iderkhangai, TO and Graphodatsky, AS}, title = {Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33809280}, issn = {2073-4425}, mesh = {Animals ; China ; DNA, Mitochondrial/genetics ; Genetic Variation/genetics ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Horses/*genetics ; Italy ; Middle East ; Mitochondria/*genetics ; Mongolia ; }, abstract = {The Mongolian horse is one of the most ancient and relatively unmanaged horse breeds. The population history of the Mongolian horse remains poorly understood due to a lack of information on ancient and modern DNA. Here, we report nearly complete mitochondrial genome data obtained from five ancient Mongolian horse samples of the Khereksur and Deer Stone culture (late 2nd to 1st third of the 1st millennium BC) and one ancient horse specimen from the Xiongnu culture (1st century BC to 1st century AD) using target enrichment and high-throughput sequencing methods. Phylogenetic analysis involving ancient, historical, and modern mitogenomes of horses from Mongolia and other regions showed the presence of three mitochondrial haplogroups in the ancient Mongolian horse populations studied here and similar haplotype composition of ancient and modern horse populations of Mongolia. Our results revealed genetic continuity between the Mongolian horse populations of the Khereksur and Deer Stone culture and those of the Xiongnu culture owing to the presence of related mitotypes. Besides, we report close phylogenetic relationships between haplotypes of the Khereksur and Deer Stone horses and the horses of indigenous breeds of the Middle East (Caspian and Iranian), China (Naqu, Yunnan, and Jinjiang), and Italy (Giara) as well as genetic similarity between the Xiongnu Mongolian horses and those of the most ancient breeds of the Middle East (Arabian) and Central Asia (Akhal-Teke). Despite all the migrations of the Mongolian peoples over the past 3000 years, mitochondrial haplogroup composition of Mongolian horse populations remains almost unchanged.}, }
@article {pmid33807307, year = {2021}, author = {Talas, L and Stivrins, N and Veski, S and Tedersoo, L and Kisand, V}, title = {Sedimentary Ancient DNA (sedaDNA) Reveals Fungal Diversity and Environmental Drivers of Community Changes throughout the Holocene in the Present Boreal Lake Lielais Svētiņu (Eastern Latvia).}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33807307}, issn = {2076-2607}, support = {PUT1389//Eesti Teadusagentuur/ ; }, abstract = {Fungi are ecologically important in several ecosystem processes, yet their community composition, ecophysiological roles, and responses to changing environmental factors in historical sediments are rarely studied. Here we explored ancient fungal DNA from lake Lielais Svētiņu sediment throughout the Holocene (10.5 kyr) using the ITS metabarcoding approach. Our data revealed diverse fungal taxa and smooth community changes during most of the Holocene with rapid changes occurring in the last few millennia. More precisely, plankton parasitic fungi became more diverse from the Late Holocene (2-4 kyr) which could be related to a shift towards a cooler climate. The Latest Holocene (~2 kyr) showed a distinct increase in the richness of plankton parasites, mycorrhizal, and plant pathogenic fungi which can be associated with an increased transfer rate of plant material into the lake and blooms of planktonic organisms influenced by increased, yet moderate, human impact. Thus, major community shifts in plankton parasites and mycorrhizal fungi could be utilized as potential paleo-variables that accompany host-substrate dynamics. Our work demonstrates that fungal aDNA with predicted ecophysiology and host specificity can be employed to reconstruct both aquatic and surrounding terrestrial ecosystems and to estimate the influence of environmental change.}, }
@article {pmid33801556, year = {2021}, author = {Lindo, J and DeGiorgio, M}, title = {Understanding the Adaptive Evolutionary Histories of South American Ancient and Present-Day Populations via Genomics.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33801556}, issn = {2073-4425}, support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; DNA, Ancient/*analysis ; Evolution, Molecular ; Gene Flow ; Genetics, Population ; Genomics/*methods ; Humans ; Selection, Genetic ; South America/ethnology ; }, abstract = {The South American continent is remarkably diverse in its ecological zones, spanning the Amazon rainforest, the high-altitude Andes, and Tierra del Fuego. Yet the original human populations of the continent successfully inhabited all these zones, well before the buffering effects of modern technology. Therefore, it is likely that the various cultures were successful, in part, due to positive natural selection that allowed them to successfully establish populations for thousands of years. Detecting positive selection in these populations is still in its infancy, as the ongoing effects of European contact have decimated many of these populations and introduced gene flow from outside of the continent. In this review, we explore hypotheses of possible human biological adaptation, methods to identify positive selection, the utilization of ancient DNA, and the integration of modern genomes through the identification of genomic tracts that reflect the ancestry of the first populations of the Americas.}, }
@article {pmid33790303, year = {2021}, author = {Aznar-Cormano, L and Bonnald, J and Krief, S and Guma, N and Debruyne, R}, title = {Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7227}, pmid = {33790303}, issn = {2045-2322}, mesh = {Animals ; DNA/*genetics ; Elephants/*genetics ; *Genotype ; *Genotyping Techniques ; Mammoths/*genetics ; *Phylogeny ; }, abstract = {It is important to determine the sex of elephants from their samples-faeces from the field or seized ivory-for forensic reasons or to understand population demography and genetic structure. Molecular sexing methods developed in the last two decades have often shown limited efficiency, particularly in terms of sensitivity and specificity, due to the degradation of DNA in these samples. These limitations have also prevented their use with ancient DNA samples of elephants or mammoths. Here we propose a novel TaqMan-MGB qPCR assay to address these difficulties. We designed it specifically to allow the characterization of the genetic sex for highly degraded samples of all elephantine taxa (elephants and mammoths). In vitro experiments demonstrated a high level of sensitivity and low contamination risks. We applied this assay in two actual case studies where it consistently recovered the right genotype for specimens of known sex a priori. In the context of a modern conservation survey of African elephants, it allowed determining the sex for over 99% of fecal samples. In a paleogenetic analysis of woolly mammoths, it produced a robust hypothesis of the sex for over 65% of the specimens out of three PCR replicates. This simple, rapid, and cost-effective procedure makes it readily applicable to large sample sizes.}, }
@article {pmid33787889, year = {2021}, author = {Yair, S and Lee, KM and Coop, G}, title = {The timing of human adaptation from Neanderthal introgression.}, journal = {Genetics}, volume = {218}, number = {1}, pages = {}, pmid = {33787889}, issn = {1943-2631}, support = {R01 GM108779/GM/NIGMS NIH HHS/United States ; R01 GM121372/GM/NIGMS NIH HHS/United States ; R35 GM136290/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics/physiology ; Adaptation, Physiological/genetics ; Alleles ; Animals ; Biological Evolution ; Evolution, Molecular ; Gene Frequency/genetics ; Genetic Introgression/*genetics ; Genome, Human/genetics ; Haplotypes/genetics ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Selection, Genetic/genetics ; }, abstract = {Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long-term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of adaptive Neanderthal introgression. From these, we identify cases in which Neanderthal-introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.}, }
@article {pmid33782109, year = {2021}, author = {Capriles, JM and Santoro, CM and George, RJ and Flores Bedregal, E and Kennett, DJ and Kistler, L and Rothhammer, F}, title = {Pre-Columbian transregional captive rearing of Amazonian parrots in the Atacama Desert.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {15}, pages = {}, pmid = {33782109}, issn = {1091-6490}, mesh = {Amazona/classification/*physiology ; Animals ; Chile ; Diet ; Feathers/anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Pets/classification/*physiology ; Phylogeography ; }, abstract = {The feathers of tropical birds were one of the most significant symbols of economic, social, and sacred status in the pre-Columbian Americas. In the Andes, finely produced clothing and textiles containing multicolored feathers of tropical parrots materialized power, prestige, and distinction and were particularly prized by political and religious elites. Here we report 27 complete or partial remains of macaws and amazon parrots from five archaeological sites in the Atacama Desert of northern Chile to improve our understanding of their taxonomic identity, chronology, cultural context, and mechanisms of acquisition. We conducted a multiproxy archaeometric study that included zooarchaeological analysis, isotopic dietary reconstruction, accelerated mass spectrometry radiocarbon dating, and paleogenomic analysis. The results reveal that during the Late Intermediate Period (1100 to 1450 CE), Atacama oasis communities acquired scarlet macaws (Ara macao) and at least five additional translocated parrot species through vast exchange networks that extended more than 500 km toward the eastern Amazonian tropics. Carbon and nitrogen stable isotopes indicate that Atacama aviculturalists sustained these birds on diets rich in marine bird guano-fertilized maize-based foods. The captive rearing of these colorful, exotic, and charismatic birds served to unambiguously signal relational wealth in a context of emergent intercommunity competition.}, }
@article {pmid33781248, year = {2021}, author = {Tagore, D and Aghakhanian, F and Naidu, R and Phipps, ME and Basu, A}, title = {Insights into the demographic history of Asia from common ancestry and admixture in the genomic landscape of present-day Austroasiatic speakers.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {61}, pmid = {33781248}, issn = {1741-7007}, mesh = {*Demography ; *Genome, Human ; Humans ; India ; Indigenous Peoples/*genetics ; *Language ; Malaysia ; }, abstract = {BACKGROUND: The demographic history of South and Southeast Asia (S&amp;SEA) is complex and contentious, with multiple waves of human migration. Some of the earliest footfalls were of the ancestors of modern Austroasiatic (AA) language speakers. Understanding the history of the AA language family, comprising of over 150 languages and their speakers distributed across broad geographical region in isolated small populations of various sizes, can help shed light on the peopling of S&amp;SEA. Here we investigated the genetic relatedness of two AA groups, their relationship with other ethno-linguistically distinct populations, and the relationship of these groups with ancient genomes of individuals living in S&amp;SEA at different time periods, to infer about the demographic history of this region.<br><br>RESULTS: We analyzed 1451 extant genomes, 189 AAs from India and Malaysia, and 43 ancient genomes from S&amp;SEA. Population structure analysis reveals neither language nor geography appropriately correlates with genetic diversity. The inconsistency between "language and genetics" or "geography and genetics" can largely be attributed to ancient admixture with East Asian populations. We estimated a pre-Neolithic origin of AA language speakers, with shared ancestry between Indian and Malaysian populations until about 470 generations ago, contesting the existing model of Neolithic expansion of the AA culture. We observed a spatio-temporal transition in the genetic ancestry of SEA with genetic contribution from East Asia significantly increasing in the post-Neolithic period.<br><br>CONCLUSION: Our study shows that contrary to assumptions in many previous studies and despite having linguistic commonality, Indian AAs have a distinct genomic structure compared to Malaysian AAs. This linguistic-genetic discordance is reflective of the complex history of population migration and admixture shaping the genomic landscape of S&amp;SEA. We postulate that pre-Neolithic ancestors of today's AAs were widespread in S&amp;SEA, and the fragmentation and dissipation of the population have largely been a resultant of multiple migrations of East Asian farmers during the Neolithic period. It also highlights the resilience of AAs in continuing to speak their language in spite of checkered population distribution and possible dominance from other linguistic groups.}, }
@article {pmid33777521, year = {2021}, author = {Fellows Yates, JA and Lamnidis, TC and Borry, M and Andrades Valtueña, A and Fagernäs, Z and Clayton, S and Garcia, MU and Neukamm, J and Peltzer, A}, title = {Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10947}, pmid = {33777521}, issn = {2167-8359}, abstract = {The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.}, }
@article {pmid33772284, year = {2021}, author = {Harney, &#xc9; and Patterson, N and Reich, D and Wakeley, J}, title = {Assessing the performance of qpAdm: a statistical tool for studying population admixture.}, journal = {Genetics}, volume = {217}, number = {4}, pages = {}, pmid = {33772284}, issn = {1943-2631}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; DNA, Ancient ; Evolution, Molecular ; Genetics, Population/*methods ; Humans ; Pedigree ; Population/*genetics ; Practice Guidelines as Topic ; Software/*standards ; }, abstract = {qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and nonhuman) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.}, }
@article {pmid33768239, year = {2021}, author = {Kapp, JD and Green, RE and Shapiro, B}, title = {A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA.}, journal = {The Journal of heredity}, volume = {112}, number = {3}, pages = {241-249}, pmid = {33768239}, issn = {1465-7333}, mesh = {*DNA, Ancient ; Gene Library ; Genomic Library ; *High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; }, abstract = {We present a protocol to prepare extracted DNA for sequencing on the Illumina sequencing platform that has been optimized for ancient and degraded DNA. Our approach, the Santa Cruz Reaction or SCR, uses directional splinted ligation of Illumina's P5 and P7 adapters to convert natively single-stranded DNA and heat denatured double-stranded DNA into sequencing libraries in a single enzymatic reaction. To demonstrate its efficacy in converting degraded DNA molecules, we prepare 5 ancient DNA extracts into sequencing libraries using the SCR and 2 of the most commonly used approaches for preparing degraded DNA for sequencing: BEST, which targets and converts double-stranded DNA, and ssDNA2.0, which targets and converts single-stranded DNA. We then compare the efficiency with which each approach recovers unique molecules, or library complexity, given a standard amount of DNA input. We find that the SCR consistently outperforms the BEST protocol in recovering unique molecules and, despite its relative simplicity to perform and low cost per library, has similar performance to ssDNA2.0 across a wide range of DNA inputs. The SCR is a cost- and time-efficient approach that minimizes the loss of unique molecules and makes accessible a taxonomically, geographically, and a temporally broader sample of preserved remains for genomic analysis.}, }
@article {pmid33767840, year = {2021}, author = {Neov, B and Spassov, N and Hristova, L and Hristov, P and Radoslavov, G}, title = {New data on the evolutionary history of the European bison (Bison bonasus) based on subfossil remains from Southeastern Europe.}, journal = {Ecology and evolution}, volume = {11}, number = {6}, pages = {2842-2848}, pmid = {33767840}, issn = {2045-7758}, abstract = {The origin and evolutionary history of the European bison Bison bonasus (wisent) have become clearer after several morphological, genomic, and paleogenomic studies in the last few years, but these paleogenomic studies have raised new questions about the evolution of the species. Here, we present additional information about the population diversity of the species based on the analysis of new subfossil Holocene remains from the Balkan Peninsula. Seven ancient samples excavated from caves in Western Stara Planina in Bulgaria were investigated by mitochondrial D-loop (HVR1) sequence analysis. The samples were dated to 3,800 years BP by radiocarbon analysis. Additionally, a phylogenetic analysis was performed to investigate the genetic relationship among the investigated samples and all mitochondrial DNA sequences from the genus Bison available in GenBank. The results clustered with the sequences from the extinct Holocene South-Eastern (Balkan) wisent to the fossil Alpine population from France, Austria, and Switzerland, but not with those from the recent Central European (North Sea) one and the now extinct Caucasian population. In conclusion, these data indicate that the Balkan wisent that existed in historical time represented a relict and probably an isolated population of the Late Pleistocene-Holocene South-Western mountainous population of the wisent.}, }
@article {pmid33767248, year = {2021}, author = {Modi, A and Vergata, C and Zilli, C and Vischioni, C and Vai, S and Tagliazucchi, GM and Lari, M and Caramelli, D and Taccioli, C}, title = {Successful extraction of insect DNA from recent copal inclusions: limits and perspectives.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {6851}, pmid = {33767248}, issn = {2045-2322}, mesh = {Amber/*chemistry ; Animals ; DNA, Ancient/*analysis/*isolation &amp; purification ; *Fossils ; Insecta/*genetics ; Resins, Plant/*chemistry ; Sequence Analysis, DNA/*methods ; }, abstract = {Insects entombed in copal, the sub-fossilized resin precursor of amber, represent a potential source of genetic data for extinct and extant, but endangered or elusive, species. Despite several studies demonstrated that it is not possible to recover endogenous DNA from insect inclusions, the preservation of biomolecules in fossilized resins samples is still under debate. In this study, we tested the possibility of obtaining endogenous ancient DNA (aDNA) molecules from insects preserved in copal, applying experimental protocols specifically designed for aDNA recovery. We were able to extract endogenous DNA molecules from one of the two samples analyzed, and to identify the taxonomic status of the specimen. Even if the sample was found well protected from external contaminants, the recovered DNA was low concentrated and extremely degraded, compared to the sample age. We conclude that it is possible to obtain genomic data from resin-entombed organisms, although we discourage aDNA analysis because of the destructive method of extraction protocols and the non-reproducibility of the results.}, }
@article {pmid33734062, year = {2021}, author = {Waglechner, N and Culp, EJ and Wright, GD}, title = {Ancient Antibiotics, Ancient Resistance.}, journal = {EcoSal Plus}, volume = {9}, number = {2}, pages = {}, pmid = {33734062}, issn = {2324-6200}, support = {FRN-148463//CIHR/Canada ; }, mesh = {*Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial/genetics ; Humans ; *Multigene Family ; Phylogeny ; }, abstract = {As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a preantibiotic era requires the discovery of new drugs. While therapeutic use of antibiotics followed by the inevitable selection of resistance is a modern phenomenon, these molecules and the genetic determinants of resistance were in use by environmental microbes long before humans discovered them. In this review, we discuss evidence that antibiotics and resistance were present in the environment before anthropogenic use, describing techniques including direct sampling of ancient DNA and phylogenetic analyses that are used to reconstruct the past. We also pay special attention to the ecological and evolutionary forces that have shaped the natural history of antibiotic biosynthesis, including a discussion of competitive versus signaling roles for antibiotics, proto-resistance, and substrate promiscuity of biosynthetic and resistance enzymes. Finally, by applying an evolutionary lens, we describe concepts governing the origins and evolution of biosynthetic gene clusters and cluster-associated resistance determinants. These insights into microbes' use of antibiotics in nature, a game they have been playing for millennia, can provide inspiration for discovery technologies and management strategies to combat the growing resistance crisis.}, }
@article {pmid33726563, year = {2021}, author = {Oswald, JA and Terrill, RS and Stucky, BJ and LeFebvre, MJ and Steadman, DW and Guralnick, RP and Allen, JM}, title = {Ancient DNA from the extinct Haitian cave-rail (Nesotrochis steganinos) suggests a biogeographic connection between the Caribbean and Old World.}, journal = {Biology letters}, volume = {17}, number = {3}, pages = {20200760}, pmid = {33726563}, issn = {1744-957X}, mesh = {Africa ; Animals ; Caribbean Region ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Fossils ; Haiti ; Humans ; Islands ; New Zealand ; Phylogeny ; }, abstract = {Worldwide decline in biodiversity during the Holocene has impeded a comprehensive understanding of pre-human biodiversity and biogeography. This is especially true on islands, because many recently extinct island taxa were morphologically unique, complicating assessment of their evolutionary relationships using morphology alone. The Caribbean remains an avian hotspot but was more diverse before human arrival in the Holocene. Among the recently extinct lineages is the enigmatic genus Nesotrochis, comprising three flightless species. Based on morphology, Nesotrochis has been considered an aberrant rail (Rallidae) or related to flufftails (Sarothruridae). We recovered a nearly complete mitochondrial genome of Nesotrochis steganinos from fossils, discovering that it is not a rallid but instead is sister to Sarothruridae, volant birds now restricted to Africa and New Guinea, and the recently extinct, flightless Aptornithidae of New Zealand. This result suggests a widespread or highly dispersive most recent common ancestor of the group. Prior to human settlement, the Caribbean avifauna had a far more cosmopolitan origin than is evident from extant species.}, }
@article {pmid33724183, year = {2021}, author = {Diaz-Maroto, P and Rey-Iglesia, A and Cartajena, I and Núñez, L and Westbury, MV and Varas, V and Moraga, M and Campos, PF and Orozco-terWengel, P and Marin, JC and Hansen, AJ}, title = {Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33724183}, issn = {2050-084X}, support = {1070040//Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica/ ; 1020316//Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica/ ; 1130917//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 1140785//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, mesh = {Animals ; Animals, Domestic/genetics ; Animals, Wild/genetics ; Archaeology/methods ; Camelids, New World/*genetics ; Chile ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; *Domestication ; Genetic Variation ; Genome, Mitochondrial ; Hybridization, Genetic ; }, abstract = {The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en masse. In this study, we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 and 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period, as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.}, }
@article {pmid33723011, year = {2021}, author = {Crump, SE and Fréchette, B and Power, M and Cutler, S and de Wet, G and Raynolds, MK and Raberg, JH and Briner, JP and Thomas, EK and Sepúlveda, J and Shapiro, B and Bunce, M and Miller, GH}, title = {Ancient plant DNA reveals High Arctic greening during the Last Interglacial.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {13}, pages = {}, pmid = {33723011}, issn = {1091-6490}, mesh = {Arctic Regions ; *Climate Change ; DNA, Ancient/*analysis ; DNA, Plant/*analysis ; Fossils ; Geologic Sediments/analysis ; Lakes ; Paleontology ; *Plant Dispersal ; Pollen/*genetics ; }, abstract = {Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., Nat. Clim. Chang. (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., Philos. Trans. A Math. Phys. Eng. Sci. (371), 20130097 (2013) and Post et al., SciAdv (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.}, }
@article {pmid33721688, year = {2021}, author = {Mothé, D and de Oliveira, K and Rotti, A and Román-Carrión, JL and Bertolino, LC and Krepsky, N and Avilla, L}, title = {The micro from mega: Dental calculus description and the first record of fossilized oral bacteria from an extinct proboscidean.}, journal = {International journal of paleopathology}, volume = {33}, number = {}, pages = {55-60}, doi = {10.1016/j.ijpp.2021.02.004}, pmid = {33721688}, issn = {1879-9825}, mesh = {Bacteria ; Biofilms ; Dental Calculus ; Humans ; *Microbiota ; *Tooth ; }, abstract = {OBJECTIVE: This study explores the chemical composition and surface aspects of fossilized dental calculus from the South American Quaternary proboscidean Notiomastodon platensis and the first record of fossilized oral bacteria from extinct megafauna.<br><br>MATERIALS: Blocks of dental calculus removed from the third molar of five specimens of Notiomastodon platensis collected from Brazil, Argentina, and Ecuador.<br><br>METHODS: We analyzed five samples of dental calculus by SEM and SEM-EDS, following a rigid protocol to avoid bacterial contamination.<br><br>RESULTS: The dental calculus surface is homogeneous, porous, with various crystals, and composed mainly by oxygen and calcium. One sample revealed a well-preserved mineralized biofilm, with several rods and cocci bacteria.<br><br>CONCLUSIONS: This is the first fossilized record of oral bacterial communities associated with extinct proboscideans.<br><br>SIGNIFICANCE: This record confirms the parasitism between oral bacteria and Notiomastodon platensis and will enable the study of paleogenomic aspects of oral microbiota of proboscideans.<br><br>LIMITATIONS: Fossilization conditions of proboscidean teeth with dental calculus are variable among specimens. Although rare, the preservation of oral bacteria is expected because of the oral biofilm composition.}, }
@article {pmid33721099, year = {2021}, author = {Oliver-Guimerá, A and Hejtmánková, A and Jackson, K and Pesavento, PA}, title = {A polyomavirus detected in American black bear (Ursus americanus).}, journal = {Archives of virology}, volume = {166}, number = {5}, pages = {1521-1524}, pmid = {33721099}, issn = {1432-8798}, mesh = {Animals ; Base Sequence ; DNA, Viral/genetics ; Genome, Viral/genetics ; Phylogeny ; Polyomavirus/*classification/genetics ; Polyomavirus Infections/pathology/*veterinary/virology ; Tumor Virus Infections/pathology/*veterinary/virology ; United States ; Ursidae/*virology ; Viral Proteins/genetics ; }, abstract = {Polyomaviruses are ancient DNA viruses that infect several species of animals. While recognition of the family Polyomaviridae has grown rapidly, there are few studies that consider their potential association with disease. Carnivora are a diverse and widespread order affected by polyomaviruses (PyVs) that have co-evolved with their hosts for millions of years. PyVs have been identified in sea lions, raccoons, badgers, Weddell seals, and dogs. We have discovered a polyomavirus, tentatively named "Ursus americanus polyomavirus 1" (UaPyV1) in black bears (Ursus americanus). UaPyV1 was detectable in various tissues of six out of seven bears submitted for necropsy. Based on viral phylogenetic clustering and detection of the virus in multiple individuals, we suggest that black bears are the natural hosts for UaPyV1. In this albeit small group, there is no clear relationship between UaPyV1 infection and any specific disease.}, }
@article {pmid33717447, year = {2021}, author = {Meucci, S and Schulte, L and Zimmermann, HH and Stoof-Leichsenring, KR and Epp, L and Bronken Eidesen, P and Herzschuh, U}, title = {Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses.}, journal = {Ecology and evolution}, volume = {11}, number = {5}, pages = {2173-2193}, pmid = {33717447}, issn = {2045-7758}, abstract = {Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.}, }
@article {pmid33717442, year = {2021}, author = {Seersholm, FV and Hansen, KL and Heydenrych, M and Hansen, AJ and Bunce, M and Allentoft, ME}, title = {Ancient DNA preserved in small bone fragments from the P.W. Lund collection.}, journal = {Ecology and evolution}, volume = {11}, number = {5}, pages = {2064-2071}, pmid = {33717442}, issn = {2045-7758}, abstract = {The Lund collection is one of the oldest subfossil collections in the world. The vast assemblage of subfossils was collected in the 1830s and 1840s by Peter Wilhelm Lund in Lagoa Santa, Brazil, and was shipped to Copenhagen in 1848, where it was stored in various locations around the city with little attention for the future preservation of the collection. So far, successful genetic research on the material collected by Lund has been limited to two samples of human petrous bone. However, less is known about the preservation conditions of the vast amounts of small and fragmentary bones stored in the collection. To address this, we studied ancient DNA from bulk bone samples of approximately 100 bone fragments from the P.W. Lund collection from boxes with varying degrees of physical preservation conditions. Using bulk bone metabarcoding, we found a high species diversity in all samples. In total, we identified 17 species, representing 11 mammals, two birds, one fish, and three frogs. Of these, two species are new to the collection. Collectively, these results exhibit the potential of future genetic studies on the famous P.W. Lund collection and suggest that the effects of poor storage conditions are probably negligible compared with the long-term in situ degradation that specimens undergo before excavation.}, }
@article {pmid33705715, year = {2021}, author = {Kirch, M and Romundset, A and Gilbert, MTP and Jones, FC and Foote, AD}, title = {Ancient and modern stickleback genomes reveal the demographic constraints on adaptation.}, journal = {Current biology : CB}, volume = {31}, number = {9}, pages = {2027-2036.e8}, doi = {10.1016/j.cub.2021.02.027}, pmid = {33705715}, issn = {1879-0445}, mesh = {Alleles ; Animals ; Demography ; Genomics ; Humans ; Infant, Newborn ; Lakes ; Paleontology ; *Smegmamorpha/genetics ; }, abstract = {Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it has been questioned whether these individuals are good proxies for the actual ancestors.[1] To address this, we applied a paleogenomics approach[2] to directly access the ancestral genepool: partially sequencing the genomes of two 11- to 13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes[3] and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord, in addition to a global dataset of 20 genomes.[4] The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects, and subsequent drift and selection. Freshwater-adaptive alleles found in one ancient stickleback genome have not risen to high frequency in the present-day population from the same lake. Comparison to the global dataset suggested incomplete adaptation to freshwater in our modern lake populations. Our findings reveal the impact of population bottlenecks in constraining adaptation due to reduced efficacy of selection on standing variation present in founder populations.}, }
@article {pmid33690651, year = {2021}, author = {Novak, M and Olalde, I and Ringbauer, H and Rohland, N and Ahern, J and Balen, J and Janković, I and Potrebica, H and Pinhasi, R and Reich, D}, title = {Genome-wide analysis of nearly all the victims of a 6200 year old massacre.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0247332}, pmid = {33690651}, issn = {1932-6203}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Croatia ; Disaster Victims/*history ; Female ; Forensic Anthropology/*methods ; History, Ancient ; Humans ; Male ; Pedigree ; Whole Genome Sequencing/*methods ; }, abstract = {Paleogenomic and bioanthropological studies of ancient massacres have highlighted sites where the victims were male and plausibly died all in battle, or were executed members of the same family as might be expected from a killing intentionally directed at subsets of a community, or where the massacred individuals were plausibly members of a migrant community in conflict with previously established groups, or where there was evidence that the killing was part of a religious ritual. Here we provide evidence of killing on a massive scale in prehistory that was not directed to a specific family, based on genome-wide ancient DNA for 38 of the 41 documented victims of a 6,200 year old massacre in Potočani, Croatia and combining our results with bioanthropological data. We highlight three results: (i) the majority of individuals were unrelated and instead were a sample of what was clearly a large farming population, (ii) the ancestry of the individuals was homogenous which makes it unlikely that the massacre was linked to the arrival of new genetic ancestry, and (iii) there were approximately equal numbers of males and females. Combined with the bioanthropological evidence that the victims were of a wide range of ages, these results show that large-scale indiscriminate killing is a horror that is not just a feature of the modern and historic periods, but was also a significant process in pre-state societies.}, }
@article {pmid33679884, year = {2021}, author = {Diroma, MA and Modi, A and Lari, M and Sineo, L and Caramelli, D and Vai, S}, title = {New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {619950}, pmid = {33679884}, issn = {1664-8021}, abstract = {Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Polizzello (Sicily, Italy). The pipeline includes several modules from well-established tools for aDNA analysis and a recently released variant caller, which was specifically conceived for mtDNA, applied for the first time to aDNA data. Through a fine-tuned filtering on variant allele sequencing features, we were able to accurately reconstruct nearly complete (>88%) mtDNA genome for almost all the analyzed samples (27 out of 30), depending on the degree of preservation and the sequencing throughput, and to get a reliable set of variants allowing haplogroup prediction. Additionally, we provide guidelines to deal with possible artifact sources, including nuclear mitochondrial sequence (NumtS) contamination, an often-neglected issue in ancient mtDNA surveys. Potential heteroplasmy levels were also estimated, although most variants were likely homoplasmic, and validated by data simulations, proving that new sequencing technologies and software are sensitive enough to detect partially mutated sites in ancient genomes and discriminate true variants from artifacts. A thorough functional annotation of detected and filtered mtDNA variants was also performed for a comprehensive evaluation of these ancient samples.}, }
@article {pmid33671794, year = {2021}, author = {Kazarina, A and Petersone-Gordina, E and Kimsis, J and Kuzmicka, J and Zayakin, P and Griškjans, &#x17d; and Gerhards, G and Ranka, R}, title = {The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles.}, journal = {Genes}, volume = {12}, number = {2}, pages = {}, pmid = {33671794}, issn = {2073-4425}, mesh = {Adolescent ; Adult ; Archaeology ; Body Remains ; Burial ; Child ; DNA, Ancient/analysis ; DNA, Bacterial/*genetics ; Dental Calculus/genetics/*microbiology ; Dental Plaque/genetics/*microbiology ; Female ; Humans ; Latvia/epidemiology ; Male ; Metagenome/genetics ; Microbiota/*genetics ; Middle Aged ; Soil Microbiology ; Young Adult ; }, abstract = {Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16-17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.}, }
@article {pmid33667394, year = {2021}, author = {Kerner, G and Laval, G and Patin, E and Boisson-Dupuis, S and Abel, L and Casanova, JL and Quintana-Murci, L}, title = {Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years.}, journal = {American journal of human genetics}, volume = {108}, number = {3}, pages = {517-524}, pmid = {33667394}, issn = {1537-6605}, support = {R01 AI088364/AI/NIAID NIH HHS/United States ; }, mesh = {Body Remains ; DNA, Ancient/*analysis ; Europe ; Female ; Genome, Human/genetics ; History, Ancient ; Humans ; Male ; Polymorphism, Genetic/*genetics ; TYK2 Kinase/*genetics ; Tuberculosis/*genetics/history/microbiology ; }, abstract = {Tuberculosis (TB), usually caused by Mycobacterium tuberculosis bacteria, is the first cause of death from an infectious disease at the worldwide scale, yet the mode and tempo of TB pressure on humans remain unknown. The recent discovery that homozygotes for the P1104A polymorphism of TYK2 are at higher risk to develop clinical forms of TB provided the first evidence of a common, monogenic predisposition to TB, offering a unique opportunity to inform on human co-evolution with a deadly pathogen. Here, we investigate the history of human exposure to TB by determining the evolutionary trajectory of the TYK2 P1104A variant in Europe, where TB is considered to be the deadliest documented infectious disease. Leveraging a large dataset of 1,013 ancient human genomes and using an approximate Bayesian computation approach, we find that the P1104A variant originated in the common ancestors of West Eurasians ∼30,000 years ago. Furthermore, we show that, following large-scale population movements of Anatolian Neolithic farmers and Eurasian steppe herders into Europe, P1104A has markedly fluctuated in frequency over the last 10,000 years of European history, with a dramatic decrease in frequency after the Bronze Age. Our analyses indicate that such a frequency drop is attributable to strong negative selection starting ∼2,000 years ago, with a relative fitness reduction on homozygotes of 20%, among the highest in the human genome. Together, our results provide genetic evidence that TB has imposed a heavy burden on European health over the last two millennia.}, }
@article {pmid33659839, year = {2020}, author = {Malyarchuk, BA}, title = {[Genetic markers on the distribution of ancient marine hunters in Priokhotye].}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {24}, number = {5}, pages = {539-544}, doi = {10.18699/VJ20.646}, pmid = {33659839}, issn = {2500-0462}, abstract = {This is a review of studies on the genetic polymorphism of modern and ancient populations of the north of Asia and America, with the aim of reconstructing the history of migrations of ancient marine hunters in the Okhotsk Sea region. The data on mitochondrial DNA polymorphism and the "Arctic" mutation distribution - the rs80356779-A variant of the CPT1A gene - were analyzed. It is known that the "Arctic" variant of the CPT1A gene is widely distributed in modern populations of the Eskimos, Chukchis, Koryaks, and other peoples of the Okhotsk Sea region, whose economic structure is associated with marine hunting. According to paleogenomic data, the earliest cases of the "Arctic" variant of the CPT1A gene were found in the Greenland and Canadian Paleoeskimos (4 thousand years ago), among representatives of the Tokarev culture of the Northern Priokhotye (3 thousand years ago), and among the bearers of the culture of the late Jomon of Hokkaido (3.5-3.8 thousand years ago). The results of the analysis revealed several migration events associated with the spread of marine hunters in the Okhotsk Sea region. The latest migration, which left traces on bearers of the Epi-Jomon culture (2.0-2.5 thousand years ago), introduced the mitochondrial haplogroup G1b and the "Arctic" variant of the CPT1A gene from the north of Priokhotye to Hokkaido and neighboring territories of the Amur Region. Traces of earlier migration, which also brought the "Arctic" mutation, were recorded in the Hokkaido population of the late Jomon period (3.5-3.8 thousand years ago). A phylogenetic analysis of mitochondrial genomes belonging to the rare haplogroup C1a, found in populations of the Far East and Japan, but phylogenetically related to the C1-haplogroups of the Amerindians, was carried out. The results of the analysis showed that the divergence of mitochondrial lineages within the C1a haplogroup occurred in the range from 7.9 to 6.6 thousand years ago, and the age of the Japanese branch of the C1a haplogroup is approximately 5.2 thousand years. It is not yet known whether this migration is associated with the spread of the "Arctic" variant of the CPT1A gene or the presence of C1a haplotypes in the population of the Japanese islands marks another, earlier, episode of the migration history linking the populations of Northwest Pacific and North America.}, }
@article {pmid33650010, year = {2021}, author = {Yao, H and Wang, M and Zou, X and Li, Y and Yang, X and Li, A and Yeh, HY and Wang, P and Wang, Z and Bai, J and Guo, J and Chen, J and Ding, X and Zhang, Y and Lin, B and Wang, CC and He, G}, title = {New insights into the fine-scale history of western-eastern admixture of the northwestern Chinese population in the Hexi Corridor via genome-wide genetic legacy.}, journal = {Molecular genetics and genomics : MGG}, volume = {296}, number = {3}, pages = {631-651}, pmid = {33650010}, issn = {1617-4623}, support = {X2123302//Nanqiang Outstanding Young Talents Program of Xiamen University/ ; 31801040//National Natural Science Foundation of China/ ; }, mesh = {Asian People/*genetics ; China ; Chromosomes, Human, Y/genetics ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Ethnicity/genetics ; Genetics, Population/methods ; Genome/*genetics ; Genome-Wide Association Study/methods ; Human Migration ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Trans-Eurasian cultural and genetic exchanges have significantly influenced the demographic dynamics of Eurasian populations. The Hexi Corridor, located along the southeastern edge of the Eurasian steppe, served as an important passage of the ancient Silk Road in Northwest China and intensified the transcontinental exchange and interaction between populations on the Central Plain and in Western Eurasia. Historical and archeological records indicate that the Western Eurasian cultural elements were largely brought into North China via this geographical corridor, but there is debate on the extent to which the spread of barley/wheat agriculture into North China and subsequent Bronze Age cultural and technological mixture/shifts were achieved by the movement of people or dissemination of ideas. Here, we presented higher-resolution genome-wide autosomal and uniparental Y/mtDNA SNP or STR data for 599 northwestern Han Chinese individuals and conducted 2 different comprehensive genetic studies among Neolithic-to-present-day Eurasians. Genetic studies based on lower-resolution STR markers via PCA, STRUCTURE, and phylogenetic trees showed that northwestern Han Chinese individuals had increased genetic homogeneity relative to northern Mongolic/Turkic/Tungusic speakers and Tibeto-Burman groups. The genomic signature constructed based on modern/ancient DNA further illustrated that the primary ancestry of the northwestern Han was derived from northern millet farmer ancestors, which was consistent with the hypothesis of Han origin in North China and more recent northwestward population expansion. This was subsequently confirmed via excess shared derived alleles in f3/f4 statistical analyses and by more northern East Asian-related ancestry in the qpAdm/qpGraph models. Interestingly, we identified one western Eurasian admixture signature that was present in northwestern Han but absent from southern Han, with an admixture time dated to approximately 1000 CE (Tang and Song dynasties). Generally, we provided supporting evidence that historic Trans-Eurasian communication was primarily maintained through population movement, not simply cultural diffusion. The observed population dynamics in northwestern Han Chinese not only support the North China origin hypothesis but also reflect the multiple sources of the genetic diversity observed in this population.}, }
@article {pmid33643377, year = {2021}, author = {Liu, Y and Wang, M and Chen, P and Wang, Z and Liu, J and Yao, L and Wang, F and Tang, R and Zou, X and He, G}, title = {Combined Low-/High-Density Modern and Ancient Genome-Wide Data Document Genomic Admixture History of High-Altitude East Asians.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {582357}, pmid = {33643377}, issn = {1664-8021}, abstract = {The Tibetan Plateau (TP) is considered to be one of the last terrestrial environments conquered by the anatomically modern human. Understanding of the genetic background of highland Tibetans plays a pivotal role in archeology, anthropology, genetics, and forensic investigations. Here, we genotyped 22 forensic genetic markers in 1,089 Tibetans residing in Nagqu Prefecture and collected 1,233,013 single nucleotide polymorphisms (SNPs) in the highland East Asians (Sherpa and Tibetan) from the Simons Genome Diversity Project and ancient Tibetans from Nepal and Neolithic farmers from northeastern Qinghai-Tibetan Plateau from public databases. We subsequently merged our two datasets with other worldwide reference populations or eastern ancient Eurasians to gain new insights into the genetic diversity, population movements, and admixtures of high-altitude East Asians via comprehensive population genetic statistical tools [principal component analysis (PCA), multidimensional scaling plot (MDS), STRUCTURE/ADMIXTURE, f3 , f4 , qpWave/qpAdm, and qpGraph]. Besides, we also explored their forensic characteristics and extended the Chinese National Database based on STR data. We identified 231 alleles with the corresponding allele frequencies spanning from 0.0005 to 0.5624 in the forensic low-density dataset, in which the combined powers of discrimination and the probability of exclusion were 1-1.22E-24 and 0.999999998, respectively. Additionally, comprehensive population comparisons in our low-density data among 57 worldwide populations via the Nei's genetic distance, PCA, MDS, NJ tree, and STRUCTURE analysis indicated that the highland Tibeto-Burman speakers kept the close genetic relationship with ethnically close populations. Findings from the 1240K high-density dataset not only confirmed the close genetic connection between modern Highlanders, Nepal ancients (Samdzong, Mebrak, and Chokhopani), and the upper Yellow River Qijia people, suggesting the northeastern edge of the TP served as a geographical corridor for ancient population migrations and interactions between highland and lowland regions, but also evidenced that late Neolithic farmers permanently colonized into the TP by adopting cold-tolerant barley agriculture that was mediated via the acculturation of idea via the millet farmer and not via the movement of barley agriculturalist as no obvious western Eurasian admixture signals were identified in our analyzed modern and ancient populations. Besides, results from the qpAdm-based admixture proportion estimation and qpGraph-based phylogenetic relationship reconstruction consistently demonstrated that all ancient and modern highland East Asians harbored and shared the deeply diverged Onge/Hoabinhian-related eastern Eurasian lineage, suggesting a common Paleolithic genetic legacy existed in high-altitude East Asians as the first layer of their gene pool.}, }
@article {pmid33639719, year = {2021}, author = {Matsumura, S and Terai, Y and Hongo, H and Ishiguro, N}, title = {Analysis of the Mitochondrial Genomes of Japanese Wolf Specimens in the Siebold Collection, Leiden.}, journal = {Zoological science}, volume = {38}, number = {1}, pages = {60-66}, doi = {10.2108/zs200019}, pmid = {33639719}, issn = {0289-0003}, mesh = {Animals ; Dogs/genetics ; *Genome, Mitochondrial ; Japan ; Phylogeny ; Sequence Analysis, DNA ; Wolves/*classification/*genetics ; }, abstract = {The taxonomic status of extinct Japanese or Honshu wolves (Canis lupus hodophilax) has been disputed since the name hodophilax was first proposed by Temminck in 1839 on the basis of specimens stored in Leiden, the Netherlands. Points of controversy include whether the type specimen of hodophilax (Jentink c: RMNH.MAM.39181) and the other two specimens from Leiden (Jentink a: RMNH.MAM.39182 and Jentink b: RMNH.MAM.39183) represent different varieties or subspecies of Japanese wolves or not. Two Japanese names, ookami and jamainu, used to describe wild Canis species, further complicate the issue. In this study, the taxonomic status of Japanese wolves was clarified using mitochondrial DNA of the three specimens stored at the Naturalis Biodiversity Center in Leiden, in addition to three Japanese wolf specimens stored at the Museum für Naturkunde in Berlin and five new samples from Japan. The mitochondrial genomes of the type specimen of hodophilax (Jentink c) and another sample from Leiden (Jentink b) as well as Berlin specimens were included in the cluster of Japanese wolves distinct from other grey wolves. However, the other sample from Leiden (Jentink a) was identified as a domestic dog. A mitochondrial genome analysis suggested that Japanese wolves could be categorized into two distinct clusters. Studies of nuclear genomes are needed to further clarify the taxonomic status, divergence time, and population genetic structure of Japanese wolves.}, }
@article {pmid33638983, year = {2021}, author = {Yelmen, B and Marnetto, D and Molinaro, L and Flores, R and Mondal, M and Pagani, L}, title = {Improving Selection Detection with Population Branch Statistic on Admixed Populations.}, journal = {Genome biology and evolution}, volume = {13}, number = {4}, pages = {}, pmid = {33638983}, issn = {1759-6653}, mesh = {Asian People/genetics ; Computer Simulation ; Haplotypes ; Humans ; Polymorphism, Single Nucleotide ; *Selection, Genetic ; }, abstract = {Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. (2019) for cross-population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared with the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations.}, }
@article {pmid37588356, year = {2020}, author = {Cui, Y and Zhang, F and Ma, P and Fan, L and Ning, C and Zhang, Q and Zhang, W and Wang, L and Robbeets, M}, title = {Bioarchaeological perspective on the expansion of Transeurasian languages in Neolithic Amur River basin.}, journal = {Evolutionary human sciences}, volume = {2}, number = {}, pages = {e15}, pmid = {37588356}, issn = {2513-843X}, abstract = {Owing to the development of sequencing technology, paleogenomics has become an important source of information on human migration and admixture, complementing findings from archaeology and linguistics. In this study, we retrieved the whole genome and Y chromosome lineage from late Neolithic Honghe individuals in the Middle Amur region in order to provide a bioarchaeological perspective on the origin and expansion of Transeurasian languages in the Amur River basin. Our genetic analysis reveals that the population of the Amur River basin has a stable and continuous genetic structure from the Mesolithic Age up to date. Integrating linguistic and archaeological evidence, we support the hypothesis that the expansion of the Transeurasian language system in the Amur River basin is related to the agricultural development and expansion of the southern Hongshan culture. The spread of agricultural technology resulted in the addition of millet cultivation to the original subsistence mode of fishing and hunting. It played a vital role in the expansion of the population of the region, which in its turn has contributed to the spread of language.}, }
@article {pmid37588383, year = {2020}, author = {Wang, CC and Robbeets, M}, title = {The homeland of Proto-Tungusic inferred from contemporary words and ancient genomes.}, journal = {Evolutionary human sciences}, volume = {2}, number = {}, pages = {e8}, pmid = {37588383}, issn = {2513-843X}, abstract = {The Tungusic languages form a language family spoken in Xinjiang, Siberia, Manchuria and the Russian Far East. There is a general consensus that these languages are genealogically related and descend from a common ancestral language, conventionally called 'Proto-Tungusic'. However, the exact geographical location where the ancestral speakers of Proto-Tungusic originated from is subject to debate. Here we take an unprecedented approach to this problem, by integrating linguistic, archaeological and genetic evidence in a single study. Our analysis of ancient DNA suggests genetic continuity between an ancient Amur genetic lineage and the contemporary speakers of the Tungusic languages. Adding an archaeolinguistic perspective, we infer that the most plausible homeland for the speakers of Proto-Tungusic is the region around Lake Khanka in the Russian Far East. Our study pushes the field forward in answering the tantalizing question about the location of the Tungusic homeland and in illustrating how these three disciplines can converge into a holistic approach to the human past.}, }
@article {pmid37588379, year = {2020}, author = {Hudson, MJ and Nakagome, S and Whitman, JB}, title = {The evolving Japanese: the dual structure hypothesis at 30.}, journal = {Evolutionary human sciences}, volume = {2}, number = {}, pages = {e6}, pmid = {37588379}, issn = {2513-843X}, abstract = {The population history of Japan has been one of the most intensively studied anthropological questions anywhere in the world, with a huge literature dating back to the nineteenth century and before. A growing consensus over the 1980s that the modern Japanese comprise an admixture of a Neolithic population with Bronze Age migrants from the Korean peninsula was crystallised in Kazurō Hanihara's influential 'dual structure hypothesis' published in 1991. Here, we use recent research in biological anthropology, historical linguistics and archaeology to evaluate this hypothesis after three decades. Although the major assumptions of Hanihara's model have been supported by recent work, we discuss areas where new findings have led to a re-evaluation of aspects of the hypothesis and emphasise the need for further research in key areas including ancient DNA and archaeology.}, }
@article {pmid39574513, year = {2020}, author = {Catalano, G and Vetro, DL and Fabbri, PF and Mallick, S and Reich, D and Rohland, N and Sineo, L and Mathieson, I and Martini, F}, title = {Late Upper Palaeolithic hunter-gatherers in the Central Mediterranean: new archaeological and genetic data from the Late Epigravettian burial Oriente C (Favignana, Sicily).}, journal = {Quaternary international : the journal of the International Union for Quaternary Research}, volume = {537}, number = {}, pages = {24-32}, pmid = {39574513}, issn = {1040-6182}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {Grotta d'Oriente, a small coastal cave located on the island of Favignana (Sicily, Italy) is a key site for the study of the early human colonization of Sicily. The individual known as Oriente C was found in the lower portion of an anthropogenic deposit containing typical local Late Upper Palaeolithic (Late Epigravettian) stone assemblages. Two radiocarbon dates on charcoal from the deposit containing the burial are consistent with the archaeological context and refer Oriente C to a period spanning about 14,200-13,800 cal. BP. Anatomical features are similar to those of Late Upper Palaeolithic populations of the Mediterranean and show some affinity with Palaeolithic individuals of San Teodoro (Messina, Sicily). Here we present new ancient DNA data from Oriente C. Our results, confirming previous genetic analysis, suggest a substantial genetic homogeneity among Late Epigravettian hunter-gatherer populations of Central Mediterranean, presumably as a consequence of continuous gene flow among different groups, or a range expansion following the Last Glacial Maximum (LGM).}, }
@article {pmid33654708, year = {2020}, author = {Aouizerat, T and Maeir, AM and Paz, Y and Gadot, Y and Szitenberg, A and Alkalay-Oren, S and Coppenhagen-Glazer, S and Klutstein, M and Hazan, R}, title = {Isolation and Characterization of Live Yeast Cells from Ancient Clay Vessels.}, journal = {Bio-protocol}, volume = {10}, number = {1}, pages = {e3473}, pmid = {33654708}, issn = {2331-8325}, abstract = {Ancient fermented food has been studied mainly based on residue analysis and recipes and reconstruction attempts were performed using modern domesticated yeast. Furthermore, microorganisms which participated in fermentation were studied using ancient-DNA techniques. In a recent paper, we presented a novel approach based on the hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. Here we present a pipeline for isolation of yeast from clay vessels uncovered in archeological sites and transferred to the microbiology lab where they can be isolated and characterized. This method opens new avenues for experimental archeology and enables attempts to recreate ancient food and beverages using the original microorganisms.}, }
@article {pmid33951887, year = {2019}, author = {Caldararo, N}, title = {Probability, Populations, Phylogenetics, and Hominin Speciation.}, journal = {Human biology}, volume = {90}, number = {2}, pages = {129-155}, doi = {10.13110/humanbiology.90.2.04}, pmid = {33951887}, issn = {1534-6617}, abstract = {A number of recent articles have appeared on the hominin Denisova fossil remains. Many of them focus on attempts to produce DNA sequences from the extracted samples. Often these project mitochondrial DNA (mtDNA) sequences from the fossils of a number of Neandertals and the Denisovans in an attempt to understand the evolution of Middle Pleistocene human ancestors. These articles introduce a number of problems in the interpretation of speciation in hominins. One concerns the degradation of the ancient DNA and its interpretation as authentic genetic information. Another problem concerns the ideas of "species" versus "population" and the use of these ideas in building evolutionary diagrams to indicate ancestry and extinction. A third issue concerns the theory of haplotypes in the mtDNA. Given the severe constraints on mutations in the mtDNA genome to maintain functionality and the purifying processes to reduce such mutations in the ovaries, putative geographic and historical variations seem contradictory. Local diversity and variations in supposed "macrohaplotypes" are explained as back migrations or back mutations, which dilutes the robust nature of the theory. A central issue involves what human variation means, how much population variation there has been in the past, and whether this variation distinguishes hominid speciation or is simply a process of anagenesis. This brings up the question of how much can be interpreted from the analysis of DNA. Some businesses today claim to be able to use DNA analysis to discover past ethnic identities, and a new niche in restaurants is producing "DNA" menus. Perhaps some caution is in order.}, }
@article {pmid39529860, year = {2019}, author = {Spriggs, M and Valentin, F and Bedford, S and Pinhasi, R and Skoglund, P and Reich, D and Lipson, M}, title = {Revisiting ancient DNA insights into the human history of the Pacific Islands.}, journal = {Oceania; a journal devoted to the study of the native peoples of Australia, New Guinea, and the Islands of the Pacific}, volume = {54}, number = {1}, pages = {53-56}, pmid = {39529860}, issn = {0029-8077}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {We respond to issues raised in the recent Forum on "Ancient DNA and its contribution to understanding the human history of the Pacific Islands" in AO (Bedford et al. 2018). We first present an emerging model for the early peopling of Vanuatu combining the genetic and archaeological evidence. Secondly, we respond specifically to the criticisms of two contributors: Matisoo-Smith and Sand. We discuss various misconceptions about the Teouma Lapita cemetery and about sampling issues in DNA research.}, }
@article {pmid39564545, year = {2019}, author = {Spriggs, M and Reich, D}, title = {AN ANCIENT DNA PACIFIC JOURNEY: A CASE STUDY OF COLLABORATION BETWEEN ARCHAEOLOGISTS AND GENETICISTS.}, journal = {World archaeology}, volume = {51}, number = {4}, pages = {620-639}, pmid = {39564545}, issn = {0043-8243}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {We present a case-study of a collaboration between archaeologists and geneticists that has helped settle a long-standing controversy and opened up new research questions for the Pacific region. The work provided insights into the history of human settlement and cultural changes in Vanuatu in the western Pacific, which in turn shed light on the origins of the cultural and linguistic diversity that characterizes the archipelago. Close interdisciplinary collaborations like this maximize the potential of ancient DNA to contribute to our understanding of the past and advance the scholarship of practitioners in both disciplines.}, }
@article {pmid33873507, year = {2004}, author = {Parducci, L and Petit, RJ}, title = {Ancient DNA - unlocking plants' fossil secrets.}, journal = {The New phytologist}, volume = {161}, number = {2}, pages = {335-339}, pmid = {33873507}, issn = {1469-8137}, }
@article {pmid33618348, year = {2021}, author = {Wang, CC and Yeh, HY and Popov, AN and Zhang, HQ and Matsumura, H and Sirak, K and Cheronet, O and Kovalev, A and Rohland, N and Kim, AM and Mallick, S and Bernardos, R and Tumen, D and Zhao, J and Liu, YC and Liu, JY and Mah, M and Wang, K and Zhang, Z and Adamski, N and Broomandkhoshbacht, N and Callan, K and Candilio, F and Carlson, KSD and Culleton, BJ and Eccles, L and Freilich, S and Keating, D and Lawson, AM and Mandl, K and Michel, M and Oppenheimer, J and Özdoğan, KT and Stewardson, K and Wen, S and Yan, S and Zalzala, F and Chuang, R and Huang, CJ and Looh, H and Shiung, CC and Nikitin, YG and Tabarev, AV and Tishkin, AA and Lin, S and Sun, ZY and Wu, XM and Yang, TL and Hu, X and Chen, L and Du, H and Bayarsaikhan, J and Mijiddorj, E and Erdenebaatar, D and Iderkhangai, TO and Myagmar, E and Kanzawa-Kiriyama, H and Nishino, M and Shinoda, KI and Shubina, OA and Guo, J and Cai, W and Deng, Q and Kang, L and Li, D and Li, D and Lin, R and Nini,  and Shrestha, R and Wang, LX and Wei, L and Xie, G and Yao, H and Zhang, M and He, G and Yang, X and Hu, R and Robbeets, M and Schiffels, S and Kennett, DJ and Jin, L and Li, H and Krause, J and Pinhasi, R and Reich, D}, title = {Genomic insights into the formation of human populations in East Asia.}, journal = {Nature}, volume = {591}, number = {7850}, pages = {413-419}, pmid = {33618348}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /ERC_/European Research Council/International ; }, mesh = {China ; Crop Production/history ; Female ; Genome, Human/*genetics ; *Genomics ; Haplotypes/genetics ; History, Ancient ; Human Migration/*history ; Humans ; Japan ; Language/history ; Male ; Mongolia ; Nepal ; Oryza ; Polymorphism, Single Nucleotide/genetics ; Siberia ; Taiwan ; }, abstract = {The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people[1,2]. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.}, }
@article {pmid33597786, year = {2021}, author = {Callaway, E}, title = {Million-year-old mammoth genomes shatter record for oldest ancient DNA.}, journal = {Nature}, volume = {590}, number = {7847}, pages = {537-538}, pmid = {33597786}, issn = {1476-4687}, mesh = {Animals ; DNA, Ancient/*isolation &amp; purification ; Evolution, Molecular ; Fossils ; History, Ancient ; Hominidae/genetics ; Humans ; Mammoths/classification/*genetics ; Permafrost ; Phylogeny ; Siberia ; Time Factors ; Tooth ; }, }
@article {pmid33595921, year = {2021}, author = {Sullivan, AP and Marciniak, S and O'Dea, A and Wake, TA and Perry, GH}, title = {Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama.}, journal = {Molecular ecology resources}, volume = {21}, number = {5}, pages = {1517-1528}, doi = {10.1111/1755-0998.13361}, pmid = {33595921}, issn = {1755-0998}, support = {//Smithsonian Tropical Research Institute/ ; //Secretar&#xed;a Nacional de Ciencia y Tecnolog&#xed;a e Innovaci&#xf3;n/ ; BCS-1554834//National Science Foundation/ ; DGE-1255832//National Science Foundation/ ; }, mesh = {Animals ; Caribbean Region ; Cell Nucleus/genetics ; Chromosome Mapping ; DNA ; *DNA, Ancient ; *Evolution, Molecular ; *Gastropoda/genetics ; *Genome, Mitochondrial ; Humans ; Panama ; Sequence Analysis, DNA ; }, abstract = {Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n = 3), Late Holocene (984-1258 before present [BP]) archaeological midden (n = 5), and mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n = 5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n = 5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7× higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behaviour on mollusc evolutionary biology.}, }
@article {pmid33594237, year = {2021}, author = {Lammers, Y and Heintzman, PD and Alsos, IG}, title = {Environmental palaeogenomic reconstruction of an Ice Age algal population.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {220}, pmid = {33594237}, issn = {2399-3642}, mesh = {Chloroplasts/*genetics ; DNA, Algal/*genetics ; DNA, Ancient/*analysis ; *Fossils ; *Genome, Mitochondrial ; Geologic Sediments ; Haplotypes ; *Metagenomics ; Microalgae/*genetics ; *Paleontology ; Phylogeny ; *Polymorphism, Single Nucleotide ; }, abstract = {Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA.}, }
@article {pmid33592193, year = {2021}, author = {Barlow, A and Paijmans, JLA and Alberti, F and Gasparyan, B and Bar-Oz, G and Pinhasi, R and Foronova, I and Puzachenko, AY and Pacher, M and Dalén, L and Baryshnikov, G and Hofreiter, M}, title = {Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.}, journal = {Current biology : CB}, volume = {31}, number = {8}, pages = {1771-1779.e7}, doi = {10.1016/j.cub.2021.01.073}, pmid = {33592193}, issn = {1879-0445}, mesh = {Animals ; DNA, Mitochondrial ; Fossils ; Genome ; Genomics ; Phylogeny ; *Ursidae/genetics ; }, abstract = {Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.[1] As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.}, }
@article {pmid33579752, year = {2021}, author = {Harney, &#xc9; and Cheronet, O and Fernandes, DM and Sirak, K and Mah, M and Bernardos, R and Adamski, N and Broomandkhoshbacht, N and Callan, K and Lawson, AM and Oppenheimer, J and Stewardson, K and Zalzala, F and Anders, A and Candilio, F and Constantinescu, M and Coppa, A and Ciobanu, I and Dani, J and Gallina, Z and Genchi, F and Nagy, EG and Hajdu, T and Hellebrandt, M and Horváth, A and Király, &#xc1; and Kiss, K and Kolozsi, B and Kovács, P and Köhler, K and Lucci, M and Pap, I and Popovici, S and Raczky, P and Simalcsik, A and Szeniczey, T and Vasilyev, S and Virag, C and Rohland, N and Reich, D and Pinhasi, R}, title = {A minimally destructive protocol for DNA extraction from ancient teeth.}, journal = {Genome research}, volume = {31}, number = {3}, pages = {472-483}, pmid = {33579752}, issn = {1549-5469}, mesh = {DNA, Ancient/*isolation &amp; purification ; Dental Cementum/*chemistry ; Humans ; Male ; Tooth/anatomy &amp; histology/*chemistry ; }, abstract = {Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.}, }
@article {pmid33575627, year = {2020}, author = {Freeman, L and Brimacombe, CS and Elhaik, E}, title = {aYChr-DB: a database of ancient human Y haplogroups.}, journal = {NAR genomics and bioinformatics}, volume = {2}, number = {4}, pages = {lqaa081}, pmid = {33575627}, issn = {2631-9268}, support = {MR/R025126/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Ancient Y-Chromosomal DNA is an invaluable tool for dating and discerning the origins of migration routes and demographic processes that occurred thousands of years ago. Driven by the adoption of high-throughput sequencing and capture enrichment methods in paleogenomics, the number of published ancient genomes has nearly quadrupled within the last three years (2018-2020). Whereas ancient mtDNA haplogroup repositories are available, no similar resource exists for ancient Y-Chromosomal haplogroups. Here, we present aYChr-DB-a comprehensive collection of 1797 ancient Eurasian human Y-Chromosome haplogroups ranging from 44 930 BC to 1945 AD. We include descriptors of age, location, genomic coverage and associated archaeological cultures. We also produced a visualization of ancient Y haplogroup distribution over time. The aYChr-DB database is a valuable resource for population genomic and paleogenomic studies.}, }
@article {pmid33565584, year = {2021}, author = {Ontano, AZ and Gainett, G and Aharon, S and Ballesteros, JA and Benavides, LR and Corbett, KF and Gavish-Regev, E and Harvey, MS and Monsma, S and Santibáñez-López, CE and Setton, EVW and Zehms, JT and Zeh, JA and Zeh, DW and Sharma, PP}, title = {Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions.}, journal = {Molecular biology and evolution}, volume = {38}, number = {6}, pages = {2446-2467}, pmid = {33565584}, issn = {1537-1719}, mesh = {Animals ; Female ; Gene Duplication ; Genes, Homeobox ; Male ; *Phylogeny ; Scorpions/*classification/genetics ; }, abstract = {Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with long-branch attraction artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale data sets. Pseudoscorpion placement is particularly variable across data sets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount long-branch attraction, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.}, }
@article {pmid33559126, year = {2021}, author = {Yüncü, E and Açan, SC and Onar, V and Karakulak, FS and Gökoğlu, M and Alıçlı, TZ and Chiriboga, F and Togan, &#x130; and Özer, F}, title = {Demography of swordfish (Xiphias gladius Linneus) populations from the coasts of Turkey, based on mitochondrial DNA and microsatellites.}, journal = {Journal of fish biology}, volume = {99}, number = {1}, pages = {37-48}, doi = {10.1111/jfb.14696}, pmid = {33559126}, issn = {1095-8649}, support = {BAP-07-02-2012-101-9//Orta Do&#x11f;u Teknik &#xdc;niversitesi/ ; 113Z405//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;tirma Kurumu/ ; }, mesh = {Animals ; *DNA, Mitochondrial/genetics ; Demography ; Female ; Mediterranean Sea ; Microsatellite Repeats ; *Perciformes ; Turkey ; }, abstract = {The genetic diversity of the Mediterranean swordfish (Xiphias gladius Linneus) has not been explored extensively at its easternmost range so far. In this study, modern X. gladius samples from the eastern part of the Mediterranean basin, north of the Aegean Sea (Aegean-2013, n = 26) and the Mediterranean coast of Turkey (N.Levantine-2013, n = 42) were studied genetically, along with ancient samples from Yenikapı excavation (n = 6). Partial mitochondrial DNA control region sequences (entire sequences, clade I and clade II) were evaluated spatially and temporally together with previously published sequences (Alvarado Bremer et al., Molecular Phylogenetics and Evolution, 2005, 36, 169-187; Viñas et al., ICES Journal of Marine Science, 2010, 67, 1222-1229; Righi et al., Diversity, 2020, 12, 170) from the rest of the Mediterranean Sea. Pair-wise FST and pair-wise AMOVA tests showed that, in general, groups of eastern populations and western Mediterranean populations have not genetically differed from each other significantly nearly in the past 20 years. Therefore, the results direct reconsideration of previous descriptions of population sub-structure within the Mediterranean and support high gene flow throughout the region. On the contrary, the results of this study confirmed the existence of genetic diversity differences between western and eastern Mediterranean, with eastern being low. One-tailed permutation tests revealed that θ, which is directly proportional to long-term female effective population size (Ne), decreased significantly (P < 0.05) in both regions over the past two decades. On the Turkish coasts, θ is not significantly different from that of the nearly contemporary eastern Mediterranean population. Nonetheless, θ of the ancient sample was consistently and significantly (P < 0.001) higher than those of the eastern and western Mediterranean populations in clade I and clade II. Furthermore, it contains two mitochondrial haplotypes that are not observed in modern samples, suggesting that the Ne of X. gladius in the eastern was high in Byzantium times. Eight microsatellite loci were also genotyped in modern samples. The microsatellite-based present Ne estimate of the pooled Aegean-2013 and N.Levantine-2013 populations was lower than 1000 according to the upper limit of 95% c.i. and possibly even lower than 100 according to the mean of posterior distribution of the present Ne estimate calculated by the software package MSVAR. These alarming genetic signals for the sustainability of X. gladius on the coasts of Turkey are in agreement with the nearly collapsing X. gladius fisheries as depicted also in the fisheries statistics. Overall, congruent with the previous studies, the data presented here show that sustainability of the X. gladius population in Mediterranean is under major threat. Therefore, X. gladius around the Turkish coasts need an immediate stringent action and management plan.}, }
@article {pmid33558418, year = {2021}, author = {Sun, XF and Wen, SQ and Lu, CQ and Zhou, BY and Curnoe, D and Lu, HY and Li, HC and Wang, W and Cheng, H and Yi, SW and Jia, X and Du, PX and Xu, XH and Lu, YM and Lu, Y and Zheng, HX and Zhang, H and Sun, C and Wei, LH and Han, F and Huang, J and Edwards, RL and Jin, L and Li, H}, title = {Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {8}, pages = {}, pmid = {33558418}, issn = {1091-6490}, mesh = {*Archaeology ; Caves/*chemistry ; China ; DNA, Ancient/*analysis ; *Fossils ; Geologic Sediments/*analysis ; History, Ancient ; Human Migration/*history ; Humans ; Radiometric Dating/*methods ; }, abstract = {The expansion of anatomically modern humans (AMHs) from Africa around 65,000 to 45,000 y ago (ca. 65 to 45 ka) led to the establishment of present-day non-African populations. Some paleoanthropologists have argued that fossil discoveries from Huanglong, Zhiren, Luna, and Fuyan caves in southern China indicate one or more prior dispersals, perhaps as early as ca. 120 ka. We investigated the age of the human remains from three of these localities and two additional early AMH sites (Yangjiapo and Sanyou caves, Hubei) by combining ancient DNA (aDNA) analysis with a multimethod geological dating strategy. Although U-Th dating of capping flowstones suggested they lie within the range ca. 168 to 70 ka, analyses of aDNA and direct AMS [14]C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS [14]C analysis of mammal teeth and charcoal also demonstrated major discrepancies from the flowstone ages; the difference between them being an order of magnitude or more at most of these localities. Our work highlights the surprisingly complex depositional history recorded at these subtropical caves which involved one or more episodes of erosion and redeposition or intrusion as recently as the late Holocene. In light of our findings, the first appearance datum for AMHs in southern China should probably lie within the timeframe set by molecular data of ca. 50 to 45 ka.}, }
@article {pmid33556115, year = {2021}, author = {Plomp, KA and Gestsdóttir, H and Dobney, K and Price, N and Collard, M}, title = {The composition of the founding population of Iceland: A new perspective from 3D analyses of basicranial shape.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0246059}, pmid = {33556115}, issn = {1932-6203}, mesh = {*Archaeology ; Female ; Humans ; Iceland ; *Imaging, Three-Dimensional ; Male ; Population Dynamics ; Skull Base/*anatomy &amp; histology/*diagnostic imaging ; }, abstract = {The settlement of Iceland in the Viking Age has been the focus of much research, but the composition of the founding population remains the subject of debate. Some lines of evidence suggest that almost all the founding population were Scandinavian, while others indicate a mix of Scandinavians and people of Scottish and Irish ancestry. To explore this issue further, we used three-dimensional techniques to compare the basicrania of skeletons from archaeological sites in Iceland, Scandinavia, and the British Isles. Our analyses yielded two main results. One was that the founding population likely consisted of roughly equal numbers of Scandinavians and people from the British Isles. The other was that the immigrants who originated from the British Isles included individuals of southern British ancestry as well as individuals of Scottish and Irish ancestry. The first of these findings is consistent with the results of recent analyses of modern and ancient DNA, while the second is novel. Our study, therefore, strengthens the idea that the founding population was a mix of Scandinavians and people from the British Isles, but also raises a new possibility regarding the regions from which the settlers originated.}, }
@article {pmid33547403, year = {2021}, author = {Rampelli, S and Turroni, S and Mallol, C and Hernandez, C and Galván, B and Sistiaga, A and Biagi, E and Astolfi, A and Brigidi, P and Benazzi, S and Lewis, CM and Warinner, C and Hofman, CA and Schnorr, SL and Candela, M}, title = {Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {169}, pmid = {33547403}, issn = {2399-3642}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaeology ; DNA, Ancient/isolation &amp; purification ; Ecosystem ; Feces/*microbiology ; Fossils/microbiology ; *Gastrointestinal Microbiome ; Geologic Sediments/analysis/microbiology ; History, Ancient ; Humans ; Metagenomics ; Neanderthals/*microbiology ; Sequence Analysis, DNA ; Spain ; }, abstract = {A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.}, }
@article {pmid33547359, year = {2021}, author = {Armbrecht, L and Hallegraeff, G and Bolch, CJS and Woodward, C and Cooper, A}, title = {Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3220}, pmid = {33547359}, issn = {2045-2322}, mesh = {Animals ; Aquatic Organisms/genetics ; *DNA Damage ; DNA, Ancient/*analysis ; Eukaryota/genetics ; Geologic Sediments/analysis ; Metagenome ; Nucleic Acid Hybridization ; Phytoplankton/*genetics ; Zooplankton/*genetics ; }, abstract = {Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture 'baits' technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, 'Planktonbaits1'; and harmful algal bloom taxa, 'HABbaits1'), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool 'HOPS' to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, "% eukaryote sedaDNA damage", that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.}, }
@article {pmid33540755, year = {2021}, author = {Davidson, R and Fehren-Schmitz, L and Llamas, B}, title = {A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations.}, journal = {Genes}, volume = {12}, number = {2}, pages = {}, pmid = {33540755}, issn = {2073-4425}, mesh = {Archaeology/*history ; Hispanic or Latino/*history ; History, 15th Century ; Human Migration/*history ; Humans ; Policy ; South America ; }, abstract = {The rulers of the Inka empire conquered approximately 2 million km[2] of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.}, }
@article {pmid33518701, year = {2021}, author = {Ma, X and Zhang, L and Pei, Z and Zhang, L and Liu, Z and Liu, D and Hao, X and Jin, Z and Pei, Y}, title = {Hydrogen sulfide promotes flowering in heading Chinese cabbage by S-sulfhydration of BraFLCs.}, journal = {Horticulture research}, volume = {8}, number = {1}, pages = {19}, pmid = {33518701}, issn = {2662-6810}, abstract = {Heading Chinese cabbage (Brassica rapa L. syn. B. campestris L. ssp. chinensis Makino var. pekinensis (Rupr.) J. Cao et Sh. Cao) is a cruciferous Brassica vegetable that has a triplicate genome, owing to an ancient genome duplication event. It is unclear whether the duplicated homologs have conserved or diversified functions. Hydrogen sulfide (H2S) is a plant gasotransmitter that plays important physiological roles in growth, development, and responses to environmental stresses. The modification of cysteines through S-sulfhydration is an important mechanism of H2S, which regulates protein functions. H2S promotes flowering in Arabidopsis and heading Chinese cabbage. Here we investigated the molecular mechanisms of H2S used to promote flowering in the latter. Four, five, and four BraFLC, BraSOC I, and BraFT homologs were identified in heading Chinese cabbage. Different BraFLC proteins were bound to different CArG boxes in the promoter regions of the BraSOC I and BraFT homologs, producing different binding patterns. Thus, there may be functionally diverse BraFLC homologs in heading Chinese cabbage. Exogenous H2S at 100 μmol L[-1] significantly promoted flowering by compensating for insufficient vernalization. BraFLC 1 and BraFLC 3 underwent S-sulfhydration by H2S, after which their abilities to bind most BraSOC I or BraFT promoter probes weakened or even disappeared. These changes in binding ability were consistent with the expression pattern of the BraFT and BraSOC I homologs in seedlings treated with H2S. These results indicated that H2S signaling regulates flowering time. In summary, H2S signaling promoted plant flowering by weakening or eliminating the binding abilities of BraFLCs to downstream promoters through S-sulfhydration.}, }
@article {pmid33514313, year = {2021}, author = {García-Rodríguez, O and Hardouin, EA and Hambleton, E and Monteith, J and Randall, C and Richards, MB and Edwards, CJ and Stewart, JR}, title = {Ancient mitochondrial DNA connects house mice in the British Isles to trade across Europe over three millennia.}, journal = {BMC ecology and evolution}, volume = {21}, number = {1}, pages = {9}, pmid = {33514313}, issn = {2730-7182}, mesh = {Animals ; *DNA, Ancient ; *DNA, Mitochondrial/genetics ; Europe ; Humans ; Mice ; Mitochondria ; United Kingdom ; }, abstract = {BACKGROUND: The earliest records in Britain for the western European house mouse (Mus musculus domesticus) date from the Late Bronze Age. The arrival of this commensal species in Britain is thought to be related to human transport and trade with continental Europe. In order to study this arrival, we collected a total of 16 ancient mouse mandibulae from four early British archaeological sites, ranging from the Late Bronze Age to the Roman period.<br><br>RESULTS: From these, we obtained ancient mitochondrial DNA (mtDNA) house mouse sequences from eight house mice from two of the sites dating from the Late Bronze to Middle Iron Age. We also obtained five ancient mtDNA wood mouse (Apodemus spp.) sequences from all four sites. The ancient house mouse sequences found in this study were from haplogroups E (N&#x2009;=&#x2009;6) and D (N&#x2009;=&#x2009;2). Modern British house mouse mtDNA sequences are primarily characterised by haplogroups E and F and, much less commonly, haplogroup D.<br><br>CONCLUSIONS: The presence of haplogroups D and E in our samples and the dating of the archaeological sites provide evidence of an early house mouse colonisation that may relate to Late Bronze Age/Iron Age trade and/or human expansion. Our results confirm the hypothesis, based on zooarchaeological evidence and modern mtDNA predictions, that house mice, with haplogroups D and E, were established in Britain by the Iron Age and, in the case of haplogroup E, possibly as early as the Late Bronze Age.}, }
@article {pmid33504886, year = {2021}, author = {Hayer, S and Brandis, D and Immel, A and Susat, J and Torres-Oliva, M and Ewers-Saucedo, C and Krause-Kyora, B}, title = {Phylogeography in an "oyster" shell provides first insights into the genetic structure of an extinct Ostrea edulis population.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2307}, pmid = {33504886}, issn = {2045-2322}, support = {01UQ1711//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 01UQ1711//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {Animals ; Ostrea/classification/*genetics ; Phylogeny ; Refugium ; }, abstract = {The historical phylogeography of Ostrea edulis was successfully depicted in its native range for the first time using ancient DNA methods on dry shells from museum collections. This research reconstructed the historical population structure of the European flat oyster across Europe in the 1870s-including the now extinct population in the Wadden Sea. In total, four haplogroups were identified with one haplogroup having a patchy distribution from the North Sea to the Atlantic coast of France. This irregular distribution could be the result of translocations. The other three haplogroups are restricted to narrow geographic ranges, which may indicate adaptation to local environmental conditions or geographical barriers to gene flow. The phylogenetic reconstruction of the four haplogroups suggests the signatures of glacial refugia and postglacial expansion. The comparison with present-day O. edulis populations revealed a temporally stable population genetic pattern over the past 150 years despite large-scale translocations. This historical phylogeographic reconstruction was able to discover an autochthonous population in the German and Danish Wadden Sea in the late nineteenth century, where O. edulis is extinct today. The genetic distinctiveness of a now-extinct population hints at a connection between the genetic background of O. edulis in the Wadden Sea and for its absence until today.}, }
@article {pmid33502509, year = {2021}, author = {Cong, Q and Shen, J and Zhang, J and Li, W and Kinch, LN and Calhoun, JV and Warren, AD and Grishin, NV}, title = {Genomics Reveals the Origins of Historical Specimens.}, journal = {Molecular biology and evolution}, volume = {38}, number = {5}, pages = {2166-2176}, pmid = {33502509}, issn = {1537-1719}, support = {R35 GM127390/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Altitude ; Animals ; Butterflies/*genetics ; DNA, Ancient/*analysis ; Genomics/*methods ; Pigmentation/genetics ; }, abstract = {Centuries of zoological studies have amassed billions of specimens in collections worldwide. Genomics of these specimens promises to reinvigorate biodiversity research. However, because DNA degrades with age in historical specimens, it is a challenge to obtain genomic data for them and analyze degraded genomes. We developed experimental and computational protocols to overcome these challenges and applied our methods to resolve a series of long-standing controversies involving a group of butterflies. We deduced the geographical origins of several historical specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old specimens that serve as irreplaceable embodiments of species concepts cannot be confidently assigned to extant species or population due to the lack of diagnostic morphological features and clear documentation of the collection locality. The ability to determine where they were collected will resolve many on-going disputes. More broadly, we show the utility of applying genomics to historical museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.}, }
@article {pmid33500403, year = {2021}, author = {Fellows Yates, JA and Andrades Valtueña, A and Vågene, &#xc5;J and Cribdon, B and Velsko, IM and Borry, M and Bravo-Lopez, MJ and Fernandez-Guerra, A and Green, EJ and Ramachandran, SL and Heintzman, PD and Spyrou, MA and Hübner, A and Gancz, AS and Hider, J and Allshouse, AF and Zaro, V and Warinner, C}, title = {Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {31}, pmid = {33500403}, issn = {2052-4463}, support = {208934/Z/17/Z//Wellcome Trust (Wellcome)/International ; EXC 2051-Project-ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; T32 GM007197/GM/NIGMS NIH HHS/United States ; DGE1255832//National Science Foundation (NSF)/International ; ERC-2014-ADG 670518//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/International ; IA201219 PAPIIT-DGAPA- UNAM//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico (National Autonomous University of Mexico)/International ; AH/N005015/1//RCUK | Arts and Humanities Research Council (AHRC)/International ; }, mesh = {*Databases, Genetic ; Humans ; Metadata ; *Metagenome ; *Metagenomics ; Publications ; }, abstract = {Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.}, }
@article {pmid33499784, year = {2021}, author = {Hu, J and Westbury, MV and Yuan, J and Zhang, Z and Chen, S and Xiao, B and Hou, X and Ji, H and Lai, X and Hofreiter, M and Sheng, G}, title = {Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1943}, pages = {20202934}, pmid = {33499784}, issn = {1471-2954}, mesh = {Animals ; Asia ; Bayes Theorem ; China ; Female ; *Genome, Mitochondrial ; *Hyaenidae/genetics ; Phylogeny ; }, abstract = {Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62-2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.}, }
@article {pmid33499220, year = {2021}, author = {Xavier, C and Eduardoff, M and Bertoglio, B and Amory, C and Berger, C and Casas-Vargas, A and Pallua, J and Parson, W}, title = {Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age.}, journal = {Genes}, volume = {12}, number = {2}, pages = {}, pmid = {33499220}, issn = {2073-4425}, mesh = {Age Determination by Skeleton/*methods ; Age Factors ; *Bone and Bones/metabolism ; *DNA, Ancient ; DNA, Mitochondrial ; Forensic Genetics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Microsatellite Repeats ; Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille's overall increased gain of DNA when enough tissue is available and Dabney's improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.}, }
@article {pmid33499169, year = {2021}, author = {Taron, UH and Paijmans, JLA and Barlow, A and Preick, M and Iyengar, A and Drăgușin, V and Vasile, &#x218; and Marciszak, A and Roblíčková, M and Hofreiter, M}, title = {Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe.}, journal = {Genes}, volume = {12}, number = {2}, pages = {}, pmid = {33499169}, issn = {2073-4425}, support = {310763/ERC_/European Research Council/International ; }, mesh = {Animal Migration ; Animals ; Canidae/anatomy &amp; histology/*classification/*genetics ; *DNA, Ancient ; DNA, Mitochondrial ; Europe ; Fossils ; Genome, Mitochondrial ; Hybridization, Genetic ; *Phylogeny ; }, abstract = {The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.}, }
@article {pmid33495362, year = {2021}, author = {Perri, AR and Feuerborn, TR and Frantz, LAF and Larson, G and Malhi, RS and Meltzer, DJ and Witt, KE}, title = {Dog domestication and the dual dispersal of people and dogs into the Americas.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {6}, pages = {}, pmid = {33495362}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM128946/GM/NIGMS NIH HHS/United States ; }, mesh = {Americas ; Animal Migration/*physiology ; Animals ; Dogs/*physiology ; *Domestication ; Geography ; Haplotypes/genetics ; *Human Migration ; Humans ; Phylogeny ; Siberia ; Time Factors ; }, abstract = {Advances in the isolation and sequencing of ancient DNA have begun to reveal the population histories of both people and dogs. Over the last 10,000 y, the genetic signatures of ancient dog remains have been linked with known human dispersals in regions such as the Arctic and the remote Pacific. It is suspected, however, that this relationship has a much deeper antiquity, and that the tandem movement of people and dogs may have begun soon after the domestication of the dog from a gray wolf ancestor in the late Pleistocene. Here, by comparing population genetic results of humans and dogs from Siberia, Beringia, and North America, we show that there is a close correlation in the movement and divergences of their respective lineages. This evidence places constraints on when and where dog domestication took place. Most significantly, it suggests that dogs were domesticated in Siberia by ∼23,000 y ago, possibly while both people and wolves were isolated during the harsh climate of the Last Glacial Maximum. Dogs then accompanied the first people into the Americas and traveled with them as humans rapidly dispersed into the continent beginning ∼15,000 y ago.}, }
@article {pmid33486547, year = {2021}, author = {Selberg, AGA and Gaucher, EA and Liberles, DA}, title = {Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond.}, journal = {Journal of molecular evolution}, volume = {89}, number = {3}, pages = {157-164}, pmid = {33486547}, issn = {1432-1432}, support = {R01 AR069137/AR/NIAMS NIH HHS/United States ; }, mesh = {*Algorithms ; *Evolution, Molecular ; Likelihood Functions ; Phylogeny ; Proteins/genetics ; }, abstract = {As both a computational and an experimental endeavor, ancestral sequence reconstruction remains a timely and important technique. Modern approaches to conduct ancestral sequence reconstruction for proteins are built upon a conceptual framework from journal founder Emile Zuckerkandl. On top of this, work on maximum likelihood phylogenetics published in Journal of Molecular Evolution in 1996 was one of the first approaches for generating maximum likelihood ancestral sequences of proteins. From its computational history, future model development needs as well as potential applications in areas as diverse as computational systems biology, molecular community ecology, infectious disease therapeutics and other biomedical applications, and biotechnology are discussed. From its past in this journal, there is a bright future for ancestral sequence reconstruction in the field of evolutionary biology.}, }
@article {pmid33482498, year = {2021}, author = {Melo, L and Matos, VMJ and Santos, AL and Ferreira, C and Silva, AM}, title = {The first probable evidence of leprosy in a male individual (17th-19th century AD) unearthed in Northern Portugal (Travanca, Santa Maria da Feira).}, journal = {International journal of paleopathology}, volume = {32}, number = {}, pages = {80-86}, doi = {10.1016/j.ijpp.2020.12.001}, pmid = {33482498}, issn = {1879-9825}, mesh = {*Bone and Bones ; Cemeteries ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Leprosy/*history ; Male ; Paleopathology ; Portugal ; }, abstract = {OBJECTIVE: This study describes the first evidence of a probable paleopathological case of leprosy from northern Portugal.<br><br>MATERIALS: An adult male, skeleton 403, exhumed from the Christian cemetery associated with the church dedicated to Saint Mamede (Travanca, Santa Maria da Feira), dated from the 17th-19th century AD.<br><br>METHODS: Standard bioarchaeological methods were used for sex and age-at-death determinations, and leprosy-related bone lesions were identified through macroscopic analysis guided by paleopathological diagnostic criteria.<br><br>RESULTS: The macroscopic observation revealed probable leprosy-related skeletal lesions, namely tenuous rhinomaxillary changes, bilateral proliferative periosteal reactions on the tibiae and fibulae, as well as concentric atrophy, acro-osteolysis and ankyloses of foot bones.<br><br>CONCLUSIONS: Skeleton 403 represents a probable case of leprosy according to the nature and distribution pattern of bony lesions observed.<br><br>SIGNIFICANCE: This finding fills an important gap in the history of leprosy in Portugal. Although historical sources show that the majority of leprosaria were located in the northern part of the country, suggesting that leprosy was more prevalent in this area of Portugal in the past, no paleopathological evidence of this disease was reported for this region to date. Furthermore, the inhumation of a leprosy sufferer in a 17th-19th century AD Christian parish cemetery is deeply imbued with social meaning.<br><br>The future detailed study of the remaining skeletons unearthed from the cemetery of the Church of S&#xe3;o Mamede will hopefully reveal further osteological evidence of leprosy in addition to the application of ancient DNA analysis to confirm the presence of the pathogen of this disease. Also, further documentary research is needed in order to expand appreciation of the epidemiological and social impact of leprosy in the 17th-19th century AD Portugal.}, }
@article {pmid33482383, year = {2021}, author = {Phillips, MJ and Shazwani Zakaria, S}, title = {Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals.}, journal = {Molecular phylogenetics and evolution}, volume = {158}, number = {}, pages = {107082}, doi = {10.1016/j.ympev.2021.107082}, pmid = {33482383}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/classification/genetics ; Eutheria/genetics ; Female ; Genetic Heterogeneity ; Likelihood Functions ; Mammals/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Pregnancy ; }, abstract = {Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.}, }
@article {pmid33475153, year = {2021}, author = {Gowland, R and Stewart, NA and Crowder, KD and Hodson, C and Shaw, H and Gron, KJ and Montgomery, J}, title = {Sex estimation of teeth at different developmental stages using dimorphic enamel peptide analysis.}, journal = {American journal of physical anthropology}, volume = {174}, number = {4}, pages = {859-869}, doi = {10.1002/ajpa.24231}, pmid = {33475153}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Amelogenin/*analysis/chemistry ; Archaeology ; Burial/history ; Child ; Child, Preschool ; Dental Enamel/chemistry/growth &amp; development ; England ; Female ; History, 18th Century ; History, 19th Century ; Humans ; Infant ; Infant, Newborn ; Male ; Mass Spectrometry ; Sex Determination Analysis/*methods ; Tooth/*chemistry/*growth &amp; development ; Young Adult ; }, abstract = {OBJECTIVES: This study tests, for the first time, the applicability of a new method of sex estimation utilizing enamel peptides on a sample of deciduous and permanent teeth at different stages of mineralization, from nonadults of unknown sex, including perinates.<br><br>MATERIALS AND METHODS: A total of 43 teeth from 29 nonadult individuals aged from 40 gestational weeks to 19&#x2009;years old were analyzed. The sample included pairs of fully mineralized and just developing teeth from the same individual. The individuals were from four archaeological sites in England: Piddington (1st-2nd centuries AD), Coach Lane, Victoria Gate, and Fewston (all 18th-19th centuries). A method that identifies sex chromosome-linked isoforms of the peptide amelogenin from human tooth enamel was applied. The method utilizes a minimally destructive acid etching procedure and subsequent nano liquid chromatography tandem mass spectrometry.<br><br>RESULTS: It was possible to determine the sex of 28 of the nonadult individuals sampled (males = 20, females = 8, undetermined = 1). Only one sample failed (CL9), due to insufficient mineralization of the sampled tooth enamel. Data are available via ProteomeXchange with identifier PXD021683.<br><br>DISCUSSION: Sufficient peptide material to determine sex can be recovered even from the crowns of developing perinatal teeth that are not fully mineralized. The minimally destructive and inexpensive (compared to ancient DNA) nature of this procedure has significant implications for bioarchaeological studies of infancy and childhood.}, }
@article {pmid33463014, year = {2021}, author = {Keighley, X and Bro-Jørgensen, MH and Ahlgren, H and Szpak, P and Ciucani, MM and Sánchez Barreiro, F and Howse, L and Gotfredsen, AB and Glykou, A and Jordan, P and Lidén, K and Olsen, MT}, title = {Predicting sample success for large-scale ancient DNA studies on marine mammals.}, journal = {Molecular ecology resources}, volume = {21}, number = {4}, pages = {1149-1166}, pmid = {33463014}, issn = {1755-0998}, support = {//Joint Proxies Research Group, financed by Research Council of Norway (RCN) Grant Number 246899 and Faculty for Humanities, Social Sciences and Education, UiT The Arctic University of Norway/ ; 2015-02151//Swedish Research Council, Sweden/ ; #676154//European Union's Framework Programme for Research and Innovation Horizon 2020/ ; }, mesh = {Animals ; Aquatic Organisms/*genetics ; Archaeology ; Arctic Regions ; Caniformia/*genetics ; *DNA, Ancient ; }, abstract = {In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.}, }
@article {pmid33455740, year = {2021}, author = {Mitchell, KJ and Rawlence, NJ}, title = {Examining Natural History through the Lens of Palaeogenomics.}, journal = {Trends in ecology &amp; evolution}, volume = {36}, number = {3}, pages = {258-267}, doi = {10.1016/j.tree.2020.10.005}, pmid = {33455740}, issn = {1872-8383}, mesh = {*Fossils ; *Genomics ; Humans ; Paleontology ; }, abstract = {The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.}, }
@article {pmid33453495, year = {2021}, author = {Ramirez, DA and Saka, HA and Nores, R}, title = {Detection of Vibrio cholerae aDNA in human burials from the fifth cholera pandemic in Argentina (1886-1887 AD).}, journal = {International journal of paleopathology}, volume = {32}, number = {}, pages = {74-79}, doi = {10.1016/j.ijpp.2020.12.004}, pmid = {33453495}, issn = {1879-9825}, mesh = {Argentina/epidemiology ; Burial ; *Cholera/epidemiology ; Humans ; Pandemics ; *Vibrio cholerae/genetics ; }, abstract = {OBJECTIVE: Detecting traces of ancient DNA of Vibrio cholerae to provide genetic information associated with the fifth cholera pandemic.<br><br>MATERIALS: Sediment samples from the sacral foramina of four individuals were analyzed, recovered from a mass grave near an institution dedicated exclusively to the isolation and treatment of citizens infected with cholera in the late 19th century in the city of Cordoba, Argentina.<br><br>METHODS: Paleogenetic techniques (ancient DNA extraction, PCR amplification, and Sanger sequencing) were applied. Specific primers for Vibrio cholerae (VCR, ctxA, ctxB, and tcpA) were designed.<br><br>RESULTS: By amplifying and sequencing the Vibrio cholerae repeats fragment, the infection in at least one individual was confirmed.<br><br>CONCLUSIONS: The synthesis of the paleogenetic results with the archaeological and historical evidence strongly supports that at least one individual from the mass grave in Cordoba, Argentina, was a victim of the fifth cholera pandemic.<br><br>SIGNIFICANCE: Confirming the presence of the disease through multiple lines of evidence, including genetic, archaeological, and historical analyses, strengthens and affirms our understanding of the presence, effects, and potential evolutionary paths of the disease in the past.<br><br>LIMITATIONS: Vibrio cholerae repeats were sequenced in one individual, while the remaining genes could not be amplified, which is likely related to gene copy number.<br><br>Paleogenetic examination of ancient samples from different locations will broaden our understanding of the origin, evolution, and past dissemination of Vibrio cholerae epidemic strains.}, }
@article {pmid33443182, year = {2021}, author = {Ju, D and Mathieson, I}, title = {The evolution of skin pigmentation-associated variation in West Eurasia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {1}, pages = {}, pmid = {33443182}, issn = {1091-6490}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; T32 GM008216/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Asia ; Asian People/genetics ; Biological Evolution ; DNA, Ancient/*analysis ; Databases, Genetic ; Europe ; Gene Frequency/genetics ; Genome-Wide Association Study/methods ; Genotype ; Haplotypes/genetics ; Humans ; Multifactorial Inheritance/genetics ; Polymorphism, Single Nucleotide/genetics ; Selection, Genetic/*genetics ; Skin Pigmentation/*genetics/physiology ; White People/genetics ; }, abstract = {Skin pigmentation is a classic example of a polygenic trait that has experienced directional selection in humans. Genome-wide association studies have identified well over a hundred pigmentation-associated loci, and genomic scans in present-day and ancient populations have identified selective sweeps for a small number of light pigmentation-associated alleles in Europeans. It is unclear whether selection has operated on all of the genetic variation associated with skin pigmentation as opposed to just a small number of large-effect variants. Here, we address this question using ancient DNA from 1,158 individuals from West Eurasia covering a period of 40,000 y combined with genome-wide association summary statistics from the UK Biobank. We find a robust signal of directional selection in ancient West Eurasians on 170 skin pigmentation-associated variants ascertained in the UK Biobank. However, we also show that this signal is driven by a limited number of large-effect variants. Consistent with this observation, we find that a polygenic selection test in present-day populations fails to detect selection with the full set of variants. Our data allow us to disentangle the effects of admixture and selection. Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation.}, }
@article {pmid33443177, year = {2021}, author = {Pugach, I and Hübner, A and Hung, HC and Meyer, M and Carson, MT and Stoneking, M}, title = {Ancient DNA from Guam and the peopling of the Pacific.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {1}, pages = {}, pmid = {33443177}, issn = {1091-6490}, mesh = {Archaeology ; Chromosomes, Human, Y/*genetics ; Computer Simulation ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Genome ; Guam ; Haplotypes ; History, Ancient ; Human Migration/*history ; Humans ; Indonesia ; Micronesia ; Native Hawaiian or Pacific Islander/*genetics ; New Guinea ; Philippines ; Phylogeny ; Polymorphism, Single Nucleotide ; Polynesia ; Vanuatu ; }, abstract = {Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.}, }
@article {pmid33437437, year = {2021}, author = {Xu, W and Lin, Y and Zhao, K and Li, H and Tian, Y and Ngatia, JN and Ma, Y and Sahu, SK and Guo, H and Guo, X and Xu, YC and Liu, H and Kristiansen, K and Lan, T and Zhou, X}, title = {An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data.}, journal = {Ecology and evolution}, volume = {11}, number = {1}, pages = {390-401}, pmid = {33437437}, issn = {2045-7758}, abstract = {Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole-genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA.}, }
@article {pmid33434506, year = {2021}, author = {Seguin-Orlando, A and Donat, R and Der Sarkissian, C and Southon, J and Thèves, C and Manen, C and Tchérémissinoff, Y and Crubézy, E and Shapiro, B and Deleuze, JF and Dalén, L and Guilaine, J and Orlando, L}, title = {Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.}, journal = {Current biology : CB}, volume = {31}, number = {5}, pages = {1072-1083.e10}, doi = {10.1016/j.cub.2020.12.015}, pmid = {33434506}, issn = {1879-0445}, mesh = {*DNA, Ancient ; Europe ; France ; Genome, Human ; Genomics ; History, Ancient ; *Human Migration ; Humans ; }, abstract = {The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.[1] These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes[2][,][3] into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.[4-8] This transition is documented through extensive ancient genomic data from present-day Britain,[9][,][10] Ireland,[11][,][12] Iberia,[13] Mediterranean islands,[14][,][15] and Germany.[8] It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),[8][,][9][,][16] with the exception of one Late Neolithic genome sequenced at 0.05× coverage.[16] This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.}, }
@article {pmid33429070, year = {2021}, author = {Kévin, R and Nicolas, C and Elsa, P and Paolo, L and Pasquino, P and Raffaella, B and Matthieu, LB}, title = {Gastrointestinal parasite burden in 4th-5th c. CE Florence highlighted by microscopy and paleogenetics.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {90}, number = {}, pages = {104713}, doi = {10.1016/j.meegid.2021.104713}, pmid = {33429070}, issn = {1567-7257}, mesh = {Animals ; Ascariasis/*history/parasitology ; Ascaris/*isolation &amp; purification ; Cities ; Dicrocoeliasis/*history/parasitology ; Dicrocoelium/*isolation &amp; purification ; History, Ancient ; Humans ; Intestinal Diseases, Parasitic/*history/parasitology ; Italy ; Trichuriasis/*history/parasitology ; Trichuris/*isolation &amp; purification ; }, abstract = {The study of ancient parasites, named paleoparasitology, traditionally focused on microscopic eggs disseminated in past environments and archaeological structures by humans and other animals infested by gastrointestinal parasites. Since the development of paleogenetics in the early 1980s, few paleoparasitological studies have been based on the ancient DNA (aDNA) of parasites, although such studies have clearly proven their utility and reliability. In this paper, we describe our integrative approach for the paleoparasitological study of an ancient population from Florence in Italy, dated to the 4th-5th c. CE. The first stage consisted in the study of sediment samples from the pelvic area of 18 individuals under light microscopy. This allowed us to detect Ascarid-type eggs belonging very probably to the human-infesting roundworm Ascaris lumbricoides. Ten subsamples were selected corresponding to five individuals, and we extracted their whole DNA following sediment aDNA protocols. A targeted approach allowed us to detect two nematodes and one trematode aDNA fragments, namely Ascaris sp., Trichuris trichiura, and Dicrocoelium dendriticum. Among the five individuals tested for microscopic eggs and aDNA, three of them showed the remains of eggs (only Ascarid-type), but all of them tested positive to the presence of at least one parasite aDNA. Microscopic diagnosis first guided our research for the selection of promising samples while the targeted aDNA approach significantly improved our knowledge in terms of parasitic diversity and frequency in this population subgroup. These results enabled us to discuss the possible impact of latent parasitism in this past population at the time of an epidemic, as suggested in Florence. In particular, the singular case of D. dendriticum detection is discussed in light of the present-day scarcity of genuine human infections. Nevertheless, actual infections are known in the paleoparasitological record, and food habits may have led to false parasitism in this historical context. aDNA leaching from overlying strata may also explain this detection. This study strongly pleads for a systematic integrative approach combining microscopy and aDNA in paleoparasitology.}, }
@article {pmid33418451, year = {2021}, author = {Nowaczewska, W and Binkowski, M and Benazzi, S and Vazzana, A and Nadachowski, A and Stefaniak, K and Żarski, M and Talamo, S and Compton, T and Stringer, CB and Hajdinjak, M and Hublin, JJ}, title = {New hominin teeth from Stajnia Cave, Poland.}, journal = {Journal of human evolution}, volume = {151}, number = {}, pages = {102929}, doi = {10.1016/j.jhevol.2020.102929}, pmid = {33418451}, issn = {1095-8606}, mesh = {Animals ; Caves ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Paleodontology ; Poland ; Tooth/*anatomy &amp; histology ; }, }
@article {pmid33417716, year = {2021}, author = {Greer, C and Bhakta, H and Ghanem, L and Refai, F and Linn, E and Avella, M}, title = {Deleterious variants in genes regulating mammalian reproduction in Neanderthals, Denisovans and extant humans.}, journal = {Human reproduction (Oxford, England)}, volume = {36}, number = {3}, pages = {734-755}, doi = {10.1093/humrep/deaa347}, pmid = {33417716}, issn = {1460-2350}, mesh = {Animals ; Europe ; Genome, Human ; *Hominidae/genetics ; Humans ; Male ; *Neanderthals/genetics ; Nuclear Proteins ; Reproduction/genetics ; Trans-Activators ; }, abstract = {STUDY QUESTION: Were Neanderthals and Denisovans (referred here also as extinct hominidae) carrying deleterious variants in genes regulating reproduction?<br><br>SUMMARY ANSWER: The majority of extinct hominidae analyzed here, presented a considerable number of deleterious variants per individual in proteins regulating different aspects of reproduction, including gonad and uterine function, and gametogenesis.<br><br>WHAT IS KNOWN ALREADY: Neanderthals, Denisovans and extant humans were interfertile and hybridized while occupying geographically overlapping areas in Europe and Asia. This is evidenced by the small archaic genome component (average &#x223c;2%) present in non-African extant humans.<br><br>STUDY DESIGN, SIZE, DURATION: The genome of eight extinct hominidae, together with five human genome databases, plus 44 mothers and 48 fathers (fertile controls), were screened to look for deleterious variants in 1734 protein-coding genes regulating reproduction.<br><br>Ancient DNA from six Neanderthals and two Denisovans dated between &#x223c;82&#xa0;000 and 43&#xa0;000 calibrated years was retrieved from the public European Nucleotide Archive. The hominins analyzed include Altai, Vindija 33.15, 33.19, 33.25 and 33.26, El Sidron 1253, Denisova 3 and 11. Their DNA was analyzed using the CLC Genomics Workbench 12, by mapping overlapping paired-end reads (Illumina, FASTQ files) to the human genome assembly GRCh37 (hg19) (Vindija 33.19, 33.25, 33.26, Denisova 3 and Denisova 11) or by analyzing BAM files (Altai, El Sidron 1253 and Vindija 33.15) (human genome reference, GRCh37 (hg19)). Non-synonymous reproductive variants were classified as deleterious or tolerated (PolyPhen-2 and SIFT analyses) and were compared to deleterious variants obtained from extant human genome databases (Genome Aggregation Database (GnomAD), 1000 Genomes, the Haplotype Map (HapMap), Single Nucleotide Polymorphism Database (dbSNPs)) across different populations. A genetic intersection between extant or extinct DNA variants and other genetic disorders was evaluated by annotating the obtained variants with the Clinical Variant (ClinVar) database.<br><br>Among the eight extinct hominidae analyzed, a total of 9650 non-synonymous variants (only coverage &#x2265;20 reads included; frameshift mutations were excluded) in 1734 reproductive protein-coding genes were found, 24% of which were classified as deleterious. The majority (73%) of the deleterious alleles present in extant humans that are shared between extant humans and extinct hominidae were found to be rare (<1%) in extant human populations. A set of 8044 variants were found uniquely in extinct hominidae. At the single-gene level, no extinct individual was found to be homozygous for deleterious variants in genes necessary for gamete recognition and fusion, and no higher chance of embryo-lethality (calculated by Mendelian Genetics) was found upon simulated mating between extant human and extinct hominidae compared to extant human-extant human. However, three of the eight extinct hominidae were found to be homozygous for 48-69 deleterious variants in 55 genes controlling ovarian and uterine functions, or oogenesis (AKAP1, BUB1B, CCDC141, CDC73, DUSP6, ESR1, ESR2, PATL2, PSMC3IP, SEMA3A, WT1 and WNT4). Moreover, we report the distribution of nine Neanderthal variants in genes associated with a human fertility phenotype found in extant human populations, one of which has been associated with polycystic ovarian syndrome and primary congenital glaucoma.<br><br>While analyzing archaic DNA, stringent filtering criteria were adopted to screen for deleterious variants in Neanderthals and Denisovans, which could result in missing a number of variants. Such restraints preserve the potential for detection of additional deleterious variants in reproductive proteins in extinct hominidae.<br><br>This study provides a comprehensive overview of putatively deleterious variants in extant human populations and extinct individuals occurring in 1734 protein-coding genes controlling reproduction and provides the fundaments for future functional studies of extinct variants in human reproduction.<br><br>This study was supported by the Department of Biological Science and by the Office of Research and Sponsored Programs at the University of Tulsa (Faculty Research Grant and Faculty Research Summer Fellowship) to M.A. and the University of Tulsa, Tulsa Undergraduate Research Challenge (TURC) program to E.L.; no conflict of interest to declare.<br><br>TRIAL REGISTRATION NUMBER: N/A.}, }
@article {pmid33373911, year = {2021}, author = {Mckinnon, M and Higgins, D}, title = {Comparison of bone demineralisation procedures for DNA recovery from burned remains.}, journal = {Forensic science international. Genetics}, volume = {51}, number = {}, pages = {102448}, doi = {10.1016/j.fsigen.2020.102448}, pmid = {33373911}, issn = {1878-0326}, mesh = {Animals ; Body Remains ; Bone Demineralization Technique/*methods ; Cell Nucleus ; DNA/*analysis ; Femur/*chemistry ; *Fires ; Forensic Genetics/methods ; Models, Animal ; Real-Time Polymerase Chain Reaction ; Swine ; }, abstract = {Recovering DNA from modern incinerated bones can be challenging and may require alteration of routine DNA extraction protocols. It has been postulated that incinerated bones share some similarities with ancient bones, including fragmented DNA, surface contamination and highly mineralised structure, all of which can inhibit the successful recovery of genetic material. For this reason, ancient DNA extraction protocols are often used for incinerated modern samples; however, their effectiveness is still somewhat unclear. Much of this uncertainty exists around the demineralisation step of extraction, specifically the length of incubation and retention or removal of supernatant. As obtaining human samples for forensic research can be challenging, porcine models (Sus scrofa domesticus) are often used as substitutes. This study developed real time PCR assays for porcine nuclear DNA in order to investigate the effects of modified demineralisation protocols on DNA yield from femurs exposed to either short (60 min) or prolonged (120 min) burning. Gradient PCR results indicated 56 °C was the ideal amplification temperature for targeted amplicons, with melt curve analysis showing short and long amplicons corresponded to 80.3 °C and 83 °C peaks respectively. Results of altered extraction protocol showed a trend towards higher DNA yields from longer demineralisation periods however this was not significant. By comparison, retaining supernatant post-demineralisation resulted in significantly greater DNA yields compared to discarding it (P < 0.009). Although DNA content yield decreased with burn duration, the demineralisation treatment variations appeared to have the same effect for all burn lengths. These results suggest that for incinerated modern bone retaining the supernatant following demineralisation can dramatically increase DNA yield.}, }
@article {pmid33366505, year = {2019}, author = {Nedoluzhko, AV and Sharko, FS and Boulygina, ES and Tsygankova, SV and Slobodova, NV and Gruzdeva, NM and Rastorguev, SM and Spasskaya, NN and Maschenko, EN}, title = {The complete mitochondrial genome of the extinct Pleistocene horse (Equus cf. lenensis) from Kotelny Island (New Siberian Islands, Russia) and its phylogenetic assessment.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {5}, number = {1}, pages = {243-245}, pmid = {33366505}, issn = {2380-2359}, abstract = {The complete mitochondrial genome from the Pleistocene stallion horse (Equus cf. lenensis) which complete skull was found in 1901 on Kotelny Island (New Siberian Archipelago, Sakha Republic, Russia) is published in this paper. The mitochondrial DNA (mtDNA) is 16,584 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. The overall base composition of the genome in descending order was 32.3% - A, 28.5% - C, 13.4% - G, 25.8% - T without a significant AT bias of 58.2%.}, }
@article {pmid33366359, year = {2019}, author = {Grond, J and Płecha, M and Hahn, C and Wiig, &#xd8; and Bachmann, L}, title = {Mitochondrial genomes of ancient bowhead whales (Balaena mysticetus) from Svalbard.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {4}, number = {2}, pages = {4152-4154}, pmid = {33366359}, issn = {2380-2359}, abstract = {The endangered Spitsbergen stock of bowhead whales (Balaena mysticetus) has once been large with up to estimated 100,000 individuals. Genetic diversity of the extant Spitsbergen stock is unknown. We present 10 complete mitochondrial genomes of heterochronous ancient bowhead whale samples from Svalbard ([14]C age estimate range: 215-8885 years) obtained via NGS of total genomic DNA extracts. The ten mitogenomes differed by nucleotide substitutions and/or indels, and there was a total of 160 variable positions. The average nucleotide diversity was π = 0.0029. There was no statistically significant correlation between genetic divergence and time.}, }
@article {pmid33352129, year = {2020}, author = {Friedlaender, JS and Tucci, S}, title = {Human Migrations: Tales of the Pacific.}, journal = {Current biology : CB}, volume = {30}, number = {24}, pages = {R1478-R1481}, doi = {10.1016/j.cub.2020.11.008}, pmid = {33352129}, issn = {1879-0445}, mesh = {*DNA, Ancient ; *Human Migration ; Humans ; Native Hawaiian or Pacific Islander ; Pacific Islands ; Vanuatu ; }, abstract = {The mode and tempo of human dispersal to the far-flung Pacific Islands has been a source of fascination for centuries. New ancient DNA data from the archipelago of Vanuatu shed light on the ancient migrations that shaped the history of human settlement in the Pacific.}, }
@article {pmid33351947, year = {2020}, author = {Hong, JH and Seo, M and Oh, CS and Chai, JY and Shin, DH}, title = {Metagonimus yokogawai Ancient DNA Recovered from 16th- to 17th-Century Korean Mummy Feces of the Joseon Dynasty.}, journal = {The Journal of parasitology}, volume = {106}, number = {6}, pages = {802-808}, doi = {10.1645/20-42}, pmid = {33351947}, issn = {1937-2345}, mesh = {Animals ; DNA, Helminth/history/*isolation &amp; purification ; Feces/parasitology ; Female ; Heterophyidae/*genetics/isolation &amp; purification ; History, 16th Century ; History, 17th Century ; Humans ; Korea ; Male ; Mummies/*history/*parasitology ; Trematode Infections/*history/parasitology ; }, abstract = {Metagonimiasis is foodborne intestinal parasitism occurring by the definitive hosts' ingestion of raw or undercooked fish, mostly commonly sweetfish. Most Metagonimus infection is caused by Metagonimus yokogawai but also rarely by Metagonimus takahashii as well as Metagonimus miyatai. Despite recent molecular work on Metagonimus spp., there are still insufficient data to reveal the genetic characteristics of ancient M. yokogawai in a wide geo-historical scope. In this study, we were successful in the analysis of M. yokogawai ancient DNA (aDNA) using coprolite samples retrieved from 16th- to 17th-century Korean mummies. In BLAST and phylogenetic analyses, M. yokogawai 28S rDNA of Korean mummies were clustered along with the 28S rDNA taxa of M. takahashii and M. miyatai in GenBank. Conversely, the cytochrome c oxidase subunit I (COI) of M. yokogawai aDNA from Korean mummies was distinctly clustered apart from M. takahashii and M. miyatai sequences. This study is the first report of its kind to identify M. yokogawai aDNA retrieved from the archaeological specimens and confirms the usefulness of COI in molecular diagnosis of M. yokogawai. Considering the rarity of reports on the genetics of genus Metagonimus spp., our study will be fundamental for the future study of M. yokogawai paleogenetics.}, }
@article {pmid33340848, year = {2021}, author = {Senovska, A and Drozdova, E and Vaculik, O and Pardy, F and Brzobohata, K and Fialova, D and Smerda, J and Kos, P}, title = {Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA.}, journal = {Forensic science international}, volume = {319}, number = {}, pages = {110638}, doi = {10.1016/j.forsciint.2020.110638}, pmid = {33340848}, issn = {1872-6283}, mesh = {Cost-Benefit Analysis ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Forensic Genetics/methods ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Polymerase Chain Reaction ; }, abstract = {Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.}, }
@article {pmid33340012, year = {2019}, author = {Lewis, D}, title = {Head of ancient-DNA lab sacked for 'serious misconduct'.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-019-03932-3}, pmid = {33340012}, issn = {1476-4687}, }
@article {pmid33338432, year = {2021}, author = {de Flamingh, A and Coutu, A and Sealy, J and Chirikure, S and Bastos, ADS and Libanda-Mubusisi, NM and Malhi, RS and Roca, AL}, title = {Sourcing Elephant Ivory from a Sixteenth-Century Portuguese Shipwreck.}, journal = {Current biology : CB}, volume = {31}, number = {3}, pages = {621-628.e4}, doi = {10.1016/j.cub.2020.10.086}, pmid = {33338432}, issn = {1879-0445}, mesh = {Africa, Southern ; Animals ; Conservation of Natural Resources ; *Elephants/genetics ; Hunting ; Isotopes ; Portugal ; }, abstract = {The oldest known shipwreck in southern Africa was found in Namibia in 2008.[1-4] Forty tons of cargo, including gold and silver coins, helped identify the ship as the Bom Jesus, a Portuguese nau (trading vessel) lost in 1533 while headed to India.[4-6] The cargo included >100 elephant tusks,[7] which we examined using paleogenomic and stable isotope analyses. Nuclear DNA identified the ivory source as African forest (Loxodonta cyclotis) rather than savanna (Loxodonta africana) elephants. Mitochondrial sequences traced them to West and not Central Africa and from ≥17 herds with distinct haplotypes. Four of the haplotypes are known from modern populations; others were potentially lost to subsequent hunting of elephants for ivory. Stable isotope analyses (δ[13]C and δ[15]N) indicated that the elephants were not from deep rainforests but from savanna and mixed habitats. Such habitats surround the Guinean forest block of West Africa[8] and accord with the locations of major historic Portuguese trading ports.[9,10] West African forest elephants currently range into savanna habitats;[11-13] our findings suggest that this was not consequent to regional decimation of savanna elephants for their ivory in the 19[th] and 20[th] centuries. During the time of the Bom Jesus, ivory was a central driver in the formation of maritime trading systems connecting Europe, Africa, and Asia. Our integration of paleogenomic, archeological, and historical methods to analyze the Bom Jesus ivory provides a framework for examining vast collections of archaeological ivories around the world, in shipwrecks and other contexts.}, }
@article {pmid33331897, year = {2021}, author = {Fortes-Lima, C and Verdu, P}, title = {Anthropological genetics perspectives on the transatlantic slave trade.}, journal = {Human molecular genetics}, volume = {30}, number = {R1}, pages = {R79-R87}, doi = {10.1093/hmg/ddaa271}, pmid = {33331897}, issn = {1460-2083}, mesh = {Americas/ethnology ; Anthropology ; Atlantic Ocean ; Black People/*genetics ; Enslaved Persons/*history ; Enslavement/ethnology/history ; Genetics, Population/*methods ; Genomics/*methods ; History, 15th Century ; Humans ; Paleography ; }, abstract = {During the Trans-Atlantic Slave Trade (TAST), around twelve million Africans were enslaved and forcibly moved from Africa to the Americas and Europe, durably influencing the genetic and cultural landscape of a large part of humanity since the 15th century. Following historians, archaeologists, and anthropologists, population geneticists have, since the 1950's mainly, extensively investigated the genetic diversity of populations on both sides of the Atlantic. These studies shed new lights into the largely unknown genetic origins of numerous enslaved-African descendant communities in the Americas, by inferring their genetic relationships with extant African, European, and Native American populations. Furthermore, exploring genome-wide data with novel statistical and bioinformatics methods, population geneticists have been increasingly able to infer the last 500 years of admixture histories of these populations. These inferences have highlighted the diversity of histories experienced by enslaved-African descendants, and the complex influences of socioeconomic, political, and historical contexts on human genetic diversity patterns during and after the slave trade. Finally, the recent advances of paleogenomics unveiled crucial aspects of the life and health of the first generation of enslaved-Africans in the Americas. Altogether, human population genetics approaches in the genomic and paleogenomic era need to be coupled with history, archaeology, anthropology, and demography in interdisciplinary research, to reconstruct the multifaceted and largely unknown history of the TAST and its influence on human biological and cultural diversities today. Here, we review anthropological genomics studies published over the past 15 years and focusing on the history of enslaved-African descendant populations in the Americas.}, }
@article {pmid33323528, year = {2020}, author = {Fromm, B and Tarbier, M and Smith, O and Marmol-Sanchez, E and Dalen, L and Gilbert, TP and Friedlander, MR}, title = {Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene.}, journal = {RNA (New York, N.Y.)}, volume = {27}, number = {3}, pages = {324-334}, pmid = {33323528}, issn = {1469-9001}, abstract = {DNA sequencing is the current key technology for historic or ancient biological samples and has led to many exciting discoveries in the field of paleogenomics. However, functional insights into tissue identity, cellular composition or gene regulation cannot be gained from DNA. Recent analyses have shown that, under favorable conditions, RNA can also be sequenced from ancient samples, enabling studies at the transcriptomic and regulatory level. Analyzing ancient RNA data from a Pleistocene canid, we find hundreds of intact microRNAs that are taxonomically informative, show tissue-specificity and have functionally predictive characteristics. With an extraordinary age of 14,300 years, these microRNA sequences are by far the oldest ever reported. The authenticity of the sequences is further supported by a) the presence of canid / Caniformia-specific sequences that never evolved outside of this clade, b) tissue-specific expression patterns (cartilage, liver and muscle) that resemble those of modern dogs and c) RNA damage patterns that are clearly distinct from those of fresh samples. By performing computational microRNA-target enrichment analyses on the ancient sequences, we predict microRNA functions consistent with their tissue pattern of expression. For instance, we find a liver-specific microRNA that regulates carbohydrate metabolism and starvation responses in canids. In summary, we show that straightforward paleotranscriptomic microRNA analyses can give functional glimpses into tissue identity, cellular composition and gene regulatory activity of ancient samples and biological processes that took place in the Pleistocene, thus holding great promise for deeper insights into gene regulation in extinct animals based on ancient RNA sequencing. .}, }
@article {pmid33319428, year = {2021}, author = {Schulte, L and Bernhardt, N and Stoof-Leichsenring, K and Zimmermann, HH and Pestryakova, LA and Epp, LS and Herzschuh, U}, title = {Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest.}, journal = {Molecular ecology resources}, volume = {21}, number = {3}, pages = {801-815}, doi = {10.1111/1755-0998.13311}, pmid = {33319428}, issn = {1755-0998}, support = {EP98/2-1//German Research Foundation/ ; 772852//European Research Council/International ; }, mesh = {*DNA, Ancient ; DNA, Plant/genetics ; Forests ; *Genome, Chloroplast ; Geologic Sediments ; Lakes ; *Larix/genetics ; *Nucleic Acid Hybridization/methods ; Siberia ; }, abstract = {Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.}, }
@article {pmid33318213, year = {2020}, author = {Kistler, L and Thakar, HB and VanDerwarker, AM and Domic, A and Bergström, A and George, RJ and Harper, TK and Allaby, RG and Hirth, K and Kennett, DJ}, title = {Archaeological Central American maize genomes suggest ancient gene flow from South America.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {52}, pages = {33124-33129}, pmid = {33318213}, issn = {1091-6490}, support = {FC001595/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; }, mesh = {Central America ; *Evolution, Molecular ; *Gene Flow ; Genome, Plant ; Hybridization, Genetic ; *Plant Breeding ; South America ; Zea mays/*genetics ; }, abstract = {Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300-1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica.}, }
@article {pmid33304512, year = {2020}, author = {Padró, J and Lambertucci, SA and Perrig, PL and Pauli, JN}, title = {Andean and California condors possess dissimilar genetic composition but exhibit similar demographic histories.}, journal = {Ecology and evolution}, volume = {10}, number = {23}, pages = {13011-13021}, pmid = {33304512}, issn = {2045-7758}, abstract = {While genetic diversity of threatened species is a major concern of conservation biologists, historic patterns of genetic variation are often unknown. A powerful approach to assess patterns and processes of genetic erosion is via ancient DNA techniques. Herein, we analyzed mtDNA from historical samples (1800s to present) of Andean Condors (Vultur gryphus) to investigate whether contemporary low genetic variability is the result of recent human expansion and persecution, and compared this genetic history to that of California condors (Gymnogyps californianus).We then explored historic demographies for both species via coalescent simulations. We found that Andean condors have lost at least 17% of their genetic variation in the early 20th century. Unlike California condors, however, low mtDNA diversity in the Andean condor was mostly ancient, before European arrival. However, we found that both condor species shared similar demographies in that population bottlenecks were recent and co-occurred with the introduction of livestock to the Americas and the global collapse of marine mammals. Given the combined information on genetic and demographic processes, we suggest that the protection of key habitats should be targeted for conserving extant genetic diversity and facilitate the natural recolonization of lost territories, while nuclear genomic data should be used to inform translocation plans.}, }
@article {pmid33304488, year = {2020}, author = {Garrett Vieira, F and Samaniego Castruita, JA and Gilbert, MTP}, title = {Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction.}, journal = {Ecology and evolution}, volume = {10}, number = {23}, pages = {12700-12709}, pmid = {33304488}, issn = {2045-7758}, abstract = {Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.}, }
@article {pmid33299013, year = {2020}, author = {Balzeau, A and Turq, A and Talamo, S and Daujeard, C and Guérin, G and Welker, F and Crevecoeur, I and Fewlass, H and Hublin, JJ and Lahaye, C and Maureille, B and Meyer, M and Schwab, C and Gómez-Olivencia, A}, title = {Pluridisciplinary evidence for burial for the La Ferrassie 8 Neandertal child.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21230}, pmid = {33299013}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Bone and Bones/metabolism ; Burial/*history/*methods ; Child, Preschool ; DNA, Mitochondrial/genetics ; Fossils ; France ; Geology ; History, Ancient ; Hominidae ; Humans ; Mass Spectrometry/methods ; Neanderthals/*psychology ; Paleontology ; }, abstract = {The origin of funerary practices has important implications for the emergence of so-called modern cognitive capacities and behaviour. We provide new multidisciplinary information on the archaeological context of the La Ferrassie 8 Neandertal skeleton (grand abri of La Ferrassie, Dordogne, France), including geochronological data -[14]C and OSL-, ZooMS and ancient DNA data, geological and stratigraphic information from the surrounding context, complete taphonomic study of the skeleton and associated remains, spatial information from the 1968-1973 excavations, and new (2014) fieldwork data. Our results show that a pit was dug in a sterile sediment layer and the corpse of a two-year-old child was laid there. A hominin bone from this context, identified through Zooarchaeology by Mass Spectrometry (ZooMS) and associated with Neandertal based on its mitochondrial DNA, yielded a direct [14]C age of 41.7-40.8 ka cal BP (95%), younger than the [14]C dates of the overlying archaeopaleontological layers and the OSL age of the surrounding sediment. This age makes the bone one of the most recent directly dated Neandertals. It is consistent with the age range for the Châtelperronian in the site and in this region and represents the third association of Neandertal taxa to Initial Upper Palaeolithic lithic technocomplex in Western Europe. A detailed multidisciplinary approach, as presented here, is essential to advance understanding of Neandertal behavior, including funerary practices.}, }
@article {pmid33272282, year = {2020}, author = {Duggan, AT and Holmes, EC and Poinar, HN}, title = {Response to Brinkmann et al. "Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States".}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {287}, pmid = {33272282}, issn = {1474-760X}, mesh = {American Civil War ; Genomics ; Humans ; *Orthopoxvirus/genetics ; *Smallpox/prevention &amp; control ; *Smallpox Vaccine ; United States ; }, abstract = {We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with ancient DNA.}, }
@article {pmid33267779, year = {2020}, author = {Dussex, N and Alberti, F and Heino, MT and Olsen, RA and van der Valk, T and Ryman, N and Laikre, L and Ahlgren, H and Askeyev, IV and Askeyev, OV and Shaymuratova, DN and Askeyev, AO and Döppes, D and Friedrich, R and Lindauer, S and Rosendahl, W and Aspi, J and Hofreiter, M and Lidén, K and Dalén, L and Díez-Del-Molino, D}, title = {Moose genomes reveal past glacial demography and the origin of modern lineages.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {854}, pmid = {33267779}, issn = {1471-2164}, support = {grant 2018-01640//FORMAS/ ; grant 2017-04647//Vetenskapsr&#xe5;det/ ; CTS 17:109//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; CTS 19:257//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Deer/genetics ; Demography ; Europe ; *Genetic Variation ; North America ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.<br><br>RESULTS: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.<br><br>CONCLUSIONS: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.}, }
@article {pmid33259759, year = {2020}, author = {Wellman, HP and Austin, RM and Dagtas, ND and Moss, ML and Rick, TC and Hofman, CA}, title = {Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1940}, pages = {20202343}, pmid = {33259759}, issn = {1471-2954}, mesh = {Alaska ; Animals ; *Archaeology ; British Columbia ; *Genome, Mitochondrial ; *Otters ; Washington ; }, abstract = {Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter (Enhydra lutris) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters (n = 20) represent 10 haplotypes, which cluster with haplotypes from Alaska, Washington and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.}, }
@article {pmid33256612, year = {2020}, author = {Feuerborn, TR and Palkopoulou, E and van der Valk, T and von Seth, J and Munters, AR and Pečnerová, P and Dehasque, M and Ureña, I and Ersmark, E and Lagerholm, VK and Krzewińska, M and Rodríguez-Varela, R and Götherström, A and Dalén, L and Díez-Del-Molino, D}, title = {Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {844}, pmid = {33256612}, issn = {1471-2164}, support = {VR 2012-3869//Swedish Research Council/ ; 2015-676//Svenska Forskningsr&#xe5;det Formas/ ; 676154//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 210119/Z/18/Z//Velux Fonden/ ; CTS17:109//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; }, mesh = {*DNA Contamination ; DNA, Ancient ; *Genome ; Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.<br><br>RESULTS: Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.<br><br>CONCLUSIONS: We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.}, }
@article {pmid33256122, year = {2020}, author = {Koupadi, K and Fontani, F and Ciucani, MM and Maini, E and De Fanti, S and Cattani, M and Curci, A and Nenzioni, G and Reggiani, P and Andrews, AJ and Sarno, S and Bini, C and Pelotti, S and Caniglia, R and Luiselli, D and Cilli, E}, title = {Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age.}, journal = {Genes}, volume = {11}, number = {12}, pages = {}, pmid = {33256122}, issn = {2073-4425}, mesh = {Animals ; Canidae/*genetics ; DNA Fragmentation ; DNA, Mitochondrial/genetics ; Dogs ; Domestication ; Evolution, Molecular ; Fossils ; Genetic Variation/genetics ; Italy ; Phylogeny ; Population Dynamics ; Wolves/genetics ; }, abstract = {Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a ~24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions.}, }
@article {pmid33254911, year = {2021}, author = {García-Rodríguez, F and Piccini, C and Carrizo, D and Sánchez-García, L and Pérez, L and Crisci, C and Oaquim, ABJ and Evangelista, H and Soutullo, A and Azcune, G and Lüning, S}, title = {Centennial glacier retreat increases sedimentation and eutrophication in Subantarctic periglacial lakes: A study case of Lake Uruguay.}, journal = {The Science of the total environment}, volume = {754}, number = {}, pages = {142066}, doi = {10.1016/j.scitotenv.2020.142066}, pmid = {33254911}, issn = {1879-1026}, mesh = {Antarctic Regions ; Eutrophication ; *Ice Cover ; *Lakes ; Uruguay ; }, abstract = {High resolution XRF scanning documented inter-annual paleolimnological changes of a Subantarctic periglacial lake, during a process of centennial glacier retreat in King George Island, Antarctica. Two major paleoenvironmental stages were inferred from the combined analysis of elemental, molecular and isotopic biomarkers, with a boundary or transition set at about 3200 yr BP. The first stage was characterized by a relatively low allochthonous organic content, reduced productivity and nitrogen levels. Such paleoenvironmental conditions are interpreted as a terrestrial system under periglacial influence, where material influx was related to erosion process from the melt water discharge, because of the proximity to the Collins Glacier ice cap. After the major Holocene glacier advance dated at about 3500 yr BP, the ice cap retreat led to the formation of Lake Uruguay, which involved in filling processes leading to moraine deposits, proglacial meltwater channels, and lakes next to the land glacier. During the second stage, with the onset of the Current Warm Period, prior to 1900 CE the stabilization of the Zr/Rb ratio within the laminated sediments documented the origin of the lacustrine sedimentation system, with subsequent increases in the sedimentation rate and biomass content (total nitrogen and organic carbon). Time series analyses revealed that the lake displayed variability cycles related to El Niño Southern Oscillation (ENSO), as reflected by high resolution sedimentological proxies for grain size, weathering, allochthonous inputs from the watershed, increase of biomass and productivity, and changes in redox conditions, all of which displayed similar oscillation cycles from 2 to 6 yr. During this periglacial recession and associated eutrophication process, we detected a striking loss in both bacterial specific richness and diversity as inferred from preliminary selected ancient DNA analyses. Thus, the Antarctic warming scenario leading to glacier depletion appears to exert deterioration consequences on the Subantarctic microbial web.}, }
@article {pmid33250022, year = {2021}, author = {Loog, L}, title = {Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {376}, number = {1816}, pages = {20190719}, pmid = {33250022}, issn = {1471-2970}, mesh = {*Archaeology ; DNA, Ancient/*analysis ; *Demography ; *Genetic Variation ; *Genetics, Population ; Humans ; *Models, Genetic ; *Population Density ; }, abstract = {Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.}, }
@article {pmid33242324, year = {2020}, author = {Wester, JVWC and Vilchez, VJS and Torre, CEW and Rodriguez-Delfin, LA}, title = {Molecular characterization of mitochondrial Amerindian haplogroups and the amelogenin gene in human ancient DNA from three archaeological sites in Lambayeque - Peru.}, journal = {Genetics and molecular biology}, volume = {43}, number = {4}, pages = {e20190265}, pmid = {33242324}, issn = {1415-4757}, abstract = {Important pre-Inca civilizations, known by their great political and religious structures, inhabited the northern coast of Peru. Archeological and anthropological studies have shown that people from these villages have hierarchical strata, but the genetic structure has been poorly studied. Here, we aimed to perform a molecular characterization of the Amerindian maternal lineages and the amelogenin gene in skeletons collected from three archeological sites in Lambayeque. Ancient DNA (aDNA) samples were analyzed with conventional PCR to assess the nine-base pair (9 bp) deletion corresponding to mitochondrial haplogroup B and the identification of haplogroups A, C, and D were obtained with PCR-RFLP experiments. The sex was characterized via amplification of the AMEL(X/Y) locus. Haplogroup frequencies were compared with available data from other ancient and modern civilizations from the Peruvian coast and highlands using statistical methods. Our results showed that haplogroup C had the highest frequency, while haplogroup B showed variable diversity in the analyzed populations. The meta-analysis revealed a positive correlation among some coastal villages. We concluded that ancient populations analyzed in our study showed the presence of four Amerindian mitochondrial haplogroups, which is consistent with previous studies.}, }
@article {pmid33241578, year = {2021}, author = {Sun, J and Ma, PC and Cheng, HZ and Wang, CZ and Li, YL and Cui, YQ and Yao, HB and Wen, SQ and Wei, LH}, title = {Post-last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans.}, journal = {American journal of physical anthropology}, volume = {174}, number = {2}, pages = {363-374}, doi = {10.1002/ajpa.24173}, pmid = {33241578}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Asia, Northern ; *Asian People/classification/genetics/history ; Chromosomes, Human, Y/*genetics ; History, Ancient ; Human Migration/*history ; Humans ; Male ; North America ; Phylogeny ; *American Indian or Alaska Native/classification/genetics/history ; }, abstract = {OBJECTIVES: Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins.<br><br>MATERIALS AND METHODS: Sequences of rare subbranches (n =&#x2009;43) and ancient individuals (n =&#x2009;37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software.<br><br>RESULTS: C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000&#x2009;years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves.<br><br>DISCUSSION: We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.}, }
@article {pmid33226710, year = {2021}, author = {Weyrich, LS}, title = {The evolutionary history of the human oral microbiota and its implications for modern health.}, journal = {Periodontology 2000}, volume = {85}, number = {1}, pages = {90-100}, doi = {10.1111/prd.12353}, pmid = {33226710}, issn = {1600-0757}, mesh = {Diet ; Humans ; *Microbiota/genetics ; *Mouth Diseases ; Oral Health ; }, abstract = {Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future.}, }
@article {pmid33218283, year = {2021}, author = {Gregory, MD and Kippenhan, JS and Kohn, P and Eisenberg, DP and Callicott, JH and Kolachana, B and Berman, KF}, title = {Neanderthal-Derived Genetic Variation is Associated with Functional Connectivity in the Brains of Living Humans.}, journal = {Brain connectivity}, volume = {11}, number = {1}, pages = {38-44}, pmid = {33218283}, issn = {2158-0022}, support = {ZIA MH002942/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; Brain ; Genetic Variation/genetics ; Humans ; Magnetic Resonance Imaging ; *Neanderthals/genetics ; }, abstract = {Aim: To determine whether Neanderthal-derived genetic variation relates to functional connectivity patterns in the brains of living modern humans. Introduction: Nearly 50,000 years ago, Neanderthals interbred with ancestors of modern humans, imparting a genetic legacy that lives on today. The vestiges of this Neanderthal-derived genetic variation have been previously shown to be enriched in genes coding for neurogenesis and myelination and to alter skull shape and brain structure in living people. Materials and Methods: Using two independent cohorts totaling 553 healthy individuals, we employed multivariate distance matrix regression (MDMR) to determine whether any brain areas exhibited whole-brain functional connectivity patterns that significantly related to the degree of Neanderthal introgression. Identified clusters were then used as regions of interest in follow-up seed-based functional connectivity analyses to determine the connectivity patterns driving the relationships. Results: The MDMR analysis revealed that the percentage of Neanderthal-originating polymorphisms was significantly associated with the functional connectivity patterns of an area of the intraparietal sulcus (IPS) that was nearly identical in both cohorts. Using these IPS clusters as regions of interest in seed-based connectivity analyses, we found, again in both cohorts, that individuals with a higher proportion of Neanderthal-derived genetic variation showed increased IPS functional connectivity with visual processing regions, but decreased IPS connectivity with regions underlying social cognition. Conclusions: These findings demonstrate that the remnants of Neanderthal admixture continue to influence human brain function today, in ways that are consistent with anthropological conceptualizations of Neanderthal phenotypes, including the possibility that Neanderthals may have depended upon visual processing capabilities at the expense of social cognition, and this may have contributed to the extinction of this species through reduced cultural maintenance and inability to cope with fluctuating resources. This and other studies capitalizing on the emerging science surrounding ancient DNA provide a window through which to view an ancient lineage long past.}, }
@article {pmid33211414, year = {2020}, author = {Latorre, SM and Lang, PLM and Burbano, HA and Gutaker, RM}, title = {Isolation, Library Preparation, and Bioinformatic Analysis of Historical and Ancient Plant DNA.}, journal = {Current protocols in plant biology}, volume = {5}, number = {4}, pages = {e20121}, doi = {10.1002/cppb.20121}, pmid = {33211414}, issn = {2379-8068}, mesh = {Animals ; Computational Biology ; *DNA, Ancient ; DNA, Plant/genetics ; Gene Library ; Humans ; Sequence Analysis, DNA ; }, abstract = {The ability to sequence DNA retrieved from ancient and historical material plays a crucial role in reinforcing evolutionary and anthropological inference. While the focus of the field is largely on analyzing DNA from ancient hominids and other animals, we have also learned from plant ancient DNA (aDNA), in particular, about human farming practices, crop domestication, environment management, species invasion, and adaptation to various environmental conditions. In the following protocols, we outline best practices for plant aDNA isolation, preparation for sequencing, bioinformatic processing, and authentication. We describe the process all the way from processing of archaeological or historical plant material to characterizing and authenticating sequencing reads. In alternative protocols, we include modifications to this process that are tailored to strongly degraded DNA. Throughout, we stress the importance of precautionary measures to successfully analyze aDNA. Finally, we discuss the evolution of the archaeogenomics field and the development of new methods, which both shaped this protocol. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Isolation of aDNA Alternate Protocol 1: Isolation of ultra-short DNA (Dabney modification) Support Protocol 1: Preparation of PTB-based mix Support Protocol 2: Preparation of binding buffer Basic Protocol 2: Preparation of genomic libraries Alternate Protocol 2: Preparation of genomic libraries with uracil removal Basic Protocol 3: Bioinformatic processing and authentication of aDNA.}, }
@article {pmid33202852, year = {2020}, author = {Roca-Rada, X and Souilmi, Y and Teixeira, JC and Llamas, B}, title = {Ancient DNA Studies in Pre-Columbian Mesoamerica.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33202852}, issn = {2073-4425}, mesh = {Archaeology ; Central America ; *DNA, Ancient ; Genetics, Population/*history ; History, Ancient ; Humans ; Population Dynamics ; }, abstract = {Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE-150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900-1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses.}, }
@article {pmid33202099, year = {2021}, author = {Wang, T and Dong, Q and Wang, W and Chen, S and Cheng, Y and Tian, H and Li, X and Hussain, S and Wang, L and Gong, L and Wang, S}, title = {Evolution of AITR family genes in cotton and their functions in abiotic stress tolerance.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {23 Suppl 1}, number = {}, pages = {58-68}, doi = {10.1111/plb.13218}, pmid = {33202099}, issn = {1438-8677}, support = {LYDX2019BS039//Startup funding from Linyi University/ ; 2016YFD0101900//National Key R&amp;D Program of China/ ; 32071938//National Natural Science Foundation of China/ ; }, mesh = {Droughts ; *Gene Expression Regulation, Plant ; *Gossypium/genetics/metabolism ; Phylogeny ; Plant Proteins/genetics/metabolism ; Stress, Physiological/genetics ; }, abstract = {Abiotic stresses are major environmental factors inhibiting plant growth and development. AITRs (ABA-induced transcription repressors) are a novel family of transcription factors regulating ABA (abscisic acid) signalling and plant responses to abiotic stresses in Arabidopsis. However, the composition and evolution history of AITRs and their roles in the cotton genus are largely unknown. A total of 12 putative AITRs genes were identified in cultivated tetraploid cotton, Gossypium hirsutum. Phylogenetic analysis of GhAITRs in these tetraploid cottons and their closely related species implicate ancient genome-wide duplication occurring after speciation of Gossypium, and Theobroma could generate duplicates of GhAITRs. Duplicated GhAITRs were stably inherited following diploid speciation and further allotetraploidy in Gossypium. Homologous GhAITRs shared common expression patterns in response to ABA, drought and salinity treatments, and drought tolerance induced in transgenic Arabidopsis plants expressing GhAITR-A1. Together, our findings reveal that duplicates in the GhAITRs gene family were achieved by whole genome duplication rather than three individual duplication events, and that GhAITRs function as transcription repressors and are involved in the regulation of plant responses to ABA and drought stress. These results provide insights towards the improvement of abiotic stress tolerance in cotton using GhAITRs.}, }
@article {pmid33197207, year = {2021}, author = {Librado, P and Orlando, L}, title = {Genomics and the Evolutionary History of Equids.}, journal = {Annual review of animal biosciences}, volume = {9}, number = {}, pages = {81-101}, doi = {10.1146/annurev-animal-061220-023118}, pmid = {33197207}, issn = {2165-8110}, mesh = {Animals ; *Biological Evolution ; Domestication ; Equidae/classification/*genetics ; Extinction, Biological ; Genetic Speciation ; *Genomics ; }, abstract = {The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.}, }
@article {pmid33189847, year = {2021}, author = {Froment, C and Zanolli, C and Hourset, M and Mouton-Barbosa, E and Moreira, A and Burlet-Schiltz, O and Mollereau, C}, title = {Protein sequence comparison of human and non-human primate tooth proteomes.}, journal = {Journal of proteomics}, volume = {231}, number = {}, pages = {104045}, doi = {10.1016/j.jprot.2020.104045}, pmid = {33189847}, issn = {1876-7737}, mesh = {Animals ; *Hominidae ; Humans ; Phylogeny ; Primates ; Proteome ; *Tooth ; }, abstract = {In the context of human evolution, the study of proteins may overcome the limitation of the high degradation of ancient DNA over time to provide biomolecular information useful for the phylogenetic reconstruction of hominid taxa. In this study, we used a shotgun proteomics approach to compare the tooth proteomes of extant human and non-human primates (gorilla, chimpanzee, orangutan and baboon) in order to search for a panel of peptides able to discriminate between taxa and further help reconstructing the evolutionary relationships of fossil primates. Among the 25 proteins shared by the five genera datasets, we found a combination of peptides with sequence variations allowing to differentiate the hominid taxa in the proteins AHSG, AMBN, APOA1, BGN, C9, COL11A2, COL22A1, COL3A1, DSPP, F2, LUM, OMD, PCOLCE and SERPINA1. The phylogenetic tree confirms the placement of the samples in the appropriate genus branches. Altogether, the results provide experimental evidence that a shotgun proteomics approach on dental tissue has the potential to detect taxonomic variation, which is promising for future investigations of uncharacterized and/or fossil hominid/hominin specimens. SIGNIFICANCE: A shotgun proteomics approach on human and non-human primate teeth allowed to identify peptides with taxonomic interest, highlighting the potential for future studies on hominid fossils.}, }
@article {pmid33180850, year = {2020}, author = {Vorobieva, NV and Makunin, AI and Druzhkova, AS and Kusliy, MA and Trifonov, VA and Popova, KO and Polosmak, NV and Molodin, VI and Vasiliev, SK and Shunkov, MV and Graphodatsky, AS}, title = {High genetic diversity of ancient horses from the Ukok Plateau.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241997}, pmid = {33180850}, issn = {1932-6203}, mesh = {Animals ; Animals, Domestic/*genetics ; Animals, Wild/*genetics ; DNA, Ancient/analysis ; Evolution, Molecular ; Extinction, Biological ; Fossils/history ; Genome, Mitochondrial ; Haplotypes ; High-Throughput Nucleotide Sequencing/veterinary ; History, Ancient ; Horses ; Mitochondria/*genetics ; Phylogeny ; Russia ; Whole Genome Sequencing/*veterinary ; }, abstract = {A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area.}, }
@article {pmid33179040, year = {2020}, author = {Silva, M and Pratas, D and Pinho, AJ}, title = {Efficient DNA sequence compression with neural networks.}, journal = {GigaScience}, volume = {9}, number = {11}, pages = {}, pmid = {33179040}, issn = {2047-217X}, mesh = {Algorithms ; Base Sequence ; *High-Throughput Nucleotide Sequencing ; Neural Networks, Computer ; Sequence Analysis, DNA ; *Software ; }, abstract = {BACKGROUND: The increasing production of genomic data has led to an intensified need for models that can cope efficiently with the lossless compression of DNA sequences. Important applications include long-term storage and compression-based data analysis. In the literature, only a few recent articles propose the use of neural networks for DNA sequence compression. However, they fall short when compared with specific DNA compression tools, such as GeCo2. This limitation is due to the absence of models specifically designed for DNA sequences. In this work, we combine the power of neural networks with specific DNA models. For this purpose, we created GeCo3, a new genomic sequence compressor that uses neural networks for mixing multiple context and substitution-tolerant context models.<br><br>FINDINGS: We benchmark GeCo3 as a reference-free DNA compressor in 5 datasets, including a balanced and comprehensive dataset of DNA sequences, the Y-chromosome and human mitogenome, 2 compilations of archaeal and virus genomes, 4 whole genomes, and 2 collections of FASTQ data of a human virome and ancient DNA. GeCo3 achieves a solid improvement in compression over the previous version (GeCo2) of $2.4\%$, $7.1\%$, $6.1\%$, $5.8\%$, and $6.0\%$, respectively. To test its performance as a reference-based DNA compressor, we benchmark GeCo3 in 4 datasets constituted by the pairwise compression of the chromosomes of the genomes of several primates. GeCo3 improves the compression in $12.4\%$, $11.7\%$, $10.8\%$, and $10.1\%$ over the state of the art. The cost of this compression improvement is some additional computational time (1.7-3 times slower than GeCo2). The RAM use is constant, and the tool scales efficiently, independently of the sequence size. Overall, these values outperform the state of the art.<br><br>CONCLUSIONS: GeCo3 is a genomic sequence compressor with a neural network mixing approach that provides additional gains over top specific genomic compressors. The proposed mixing method is portable, requiring only the probabilities of the models as inputs, providing easy adaptation to other data compressors or compression-based data analysis tools. GeCo3 is released under GPLv3 and is available for free download at https://github.com/cobilab/geco3.}, }
@article {pmid33167482, year = {2020}, author = {Thomas, C and Francke, A and Vogel, H and Wagner, B and Ariztegui, D}, title = {Weak Influence of Paleoenvironmental Conditions on the Subsurface Biosphere of Lake Ohrid over the Last 515 ka.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33167482}, issn = {2076-2607}, support = {200021_166308 / 1//Schweizerischer Nationalfonds zur F&#x00F6;rderung der Wissenschaftlichen Forschung/ ; }, abstract = {Lacustrine sediments are widely used to investigate the impact of climatic change on biogeochemical cycling. In these sediments, subsurface microbial communities are major actors of this cycling but can also affect the sedimentary record and overprint the original paleoenvironmental signal. We therefore investigated the subsurface microbial communities of the oldest lake in Europe, Lake Ohrid (North Macedonia, Albania), to assess the potential connection between microbial diversity and past environmental change using 16S rRNA gene sequences. Along the upper ca. 200 m of the DEEP site sediment record spanning ca. 515 thousand years (ka), our results show that Atribacteria, Bathyarchaeia and Gammaproteobacteria structured the community independently from each other. Except for the latter, these taxa are common in deep lacustrine and marine sediments due to their metabolic versatility adapted to low energy environments. Gammaproteobacteria were often co-occurring with cyanobacterial sequences or soil-related OTUs suggesting preservation of ancient DNA from the water column or catchment back to at least 340 ka, particularly in dry glacial intervals. We found significant environmental parameters influencing the overall microbial community distribution, but no strong relationship with given phylotypes and paleoclimatic signals or sediment age. Our results support a weak recording of early diagenetic processes and their actors by bulk prokaryotic sedimentary DNA in Lake Ohrid, replaced by specialized low-energy clades of the deep biosphere and a marked imprint of erosional processes on the subsurface DNA pool of Lake Ohrid.}, }
@article {pmid33159124, year = {2020}, author = {Psonis, N and de Carvalho, CN and Figueiredo, S and Tabakaki, E and Vassou, D and Poulakakis, N and Kafetzopoulos, D}, title = {Molecular identification and geographic origin of a post-Medieval elephant finding from southwestern Portugal using high-throughput sequencing.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19252}, pmid = {33159124}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/*analysis ; Elephants/*genetics ; *High-Throughput Nucleotide Sequencing ; *Phylogeny ; Portugal ; }, abstract = {Molecular species identification plays a crucial role in archaeology and palaeontology, especially when diagnostic morphological characters are unavailable. Molecular markers have been used in forensic science to trace the geographic origin of wildlife products, such as ivory. So far, only a few studies have applied genetic methods to both identify the species and circumscribe the provenance of historic wildlife trade material. Here, by combining ancient DNA methods and genome skimming on a historical elephantid tooth found in southwestern Portugal, we aimed to identify its species, infer its placement in the elephantid phylogenetic tree, and triangulate its geographic origin. According to our results the specimen dates back to the eighteenth century CE and belongs to a female African forest elephant (non-hybrid Loxodonta cyclotis individual) geographically originated from west-west-central Africa, from areas where one of the four major mitochondrial clades of L. cyclotis is distributed. Historical evidence supports our inference, pointing out that the tooth should be considered as post-Medieval raw ivory trade material between West Africa and Portugal. Our study provides a comprehensive approach to study historical products and artefacts using archaeogenetics and contributes towards enlightening cultural and biological historical aspects of ivory trade in western Europe.}, }
@article {pmid33159107, year = {2020}, author = {Teschler-Nicola, M and Fernandes, D and Händel, M and Einwögerer, T and Simon, U and Neugebauer-Maresch, C and Tangl, S and Heimel, P and Dobsak, T and Retzmann, A and Prohaska, T and Irrgeher, J and Kennett, DJ and Olalde, I and Reich, D and Pinhasi, R}, title = {Ancient DNA reveals monozygotic newborn twins from the Upper Palaeolithic.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {650}, pmid = {33159107}, issn = {2399-3642}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Burial ; DNA/*genetics ; History, Ancient ; Humans ; Infant, Newborn ; Paleontology ; Twins, Monozygotic/*genetics ; }, abstract = {The Upper Palaeolithic double burial of newborns and the single burial of a ca. 3-month-old infant uncovered at the Gravettian site of Krems-Wachtberg, Austria, are of paramount importance given the rarity of immature human remains from this time. Genome-wide ancient DNA shows that the male infants of the double grave are the earliest reported case of monozygotic twins, while the single grave´s individual was their 3rd-degree male relative. We assessed the individuals´ age at death by applying histological and µCT inspection of the maxillary second incisors (i2) in conjunction with C- and N-isotope ratios and Barium (Ba) intake as biomarker for breastfeeding. The results show that the twins were full-term newborns, and that while individual 2 died at birth, individual 1 survived for about 50 days. The findings show that Gravettian mortuary behaviour also included re-opening of a grave and manipulation of its layout and content.}, }
@article {pmid33157037, year = {2020}, author = {Jeong, C and Wang, K and Wilkin, S and Taylor, WTT and Miller, BK and Bemmann, JH and Stahl, R and Chiovelli, C and Knolle, F and Ulziibayar, S and Khatanbaatar, D and Erdenebaatar, D and Erdenebat, U and Ochir, A and Ankhsanaa, G and Vanchigdash, C and Ochir, B and Munkhbayar, C and Tumen, D and Kovalev, A and Kradin, N and Bazarov, BA and Miyagashev, DA and Konovalov, PB and Zhambaltarova, E and Miller, AV and Haak, W and Schiffels, S and Krause, J and Boivin, N and Erdene, M and Hendy, J and Warinner, C}, title = {A Dynamic 6,000-Year Genetic History of Eurasia's Eastern Steppe.}, journal = {Cell}, volume = {183}, number = {4}, pages = {890-904.e29}, pmid = {33157037}, issn = {1097-4172}, mesh = {Archaeology ; Europe ; Female ; Gene Frequency/genetics ; Gene Pool ; Genetic Heterogeneity ; *Genetics, Population ; Genome, Human ; Geography ; *Grassland ; Haplotypes/genetics ; History, Ancient ; Humans ; Male ; Mongolia ; Principal Component Analysis ; Time Factors ; }, abstract = {The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region's population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.}, }
@article {pmid33151956, year = {2020}, author = {Abbona, CC and Adolfo, GN and Johnson, J and Kim, T and Gil, AF and Wolverton, S}, title = {Were domestic camelids present on the prehispanic South American agricultural frontier? An ancient DNA study.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0240474}, pmid = {33151956}, issn = {1932-6203}, mesh = {Agriculture/*history ; Animals ; Animals, Domestic/*genetics ; Animals, Wild/*genetics ; Archaeology/methods ; Argentina ; Camelids, New World/*genetics ; DNA, Ancient/*analysis ; Domestication ; Genome, Mitochondrial ; History, 15th Century ; History, 16th Century ; Whole Genome Sequencing ; }, abstract = {The southern boundary of prehispanic farming in South America occurs in central Mendoza Province, Argentina at approximately 34 degrees south latitude. Archaeological evidence of farming includes the recovery of macrobotanical remains of cultigens and isotopic chemistry of human bone. Since the 1990s, archaeologists have also hypothesized that the llama (Lama glama), a domesticated South American camelid, was also herded near the southern boundary of prehispanic farming. The remains of a wild congeneric camelid, the guanaco (Lama guanicoe), however, are common in archaeological sites throughout Mendoza Province. It is difficult to distinguish bones of the domestic llama from wild guanaco in terms of osteological morphology, and therefore, claims that llama were in geographic areas where guanaco were also present based on osteometric analysis alone remain equivocal. A recent study, for example, claimed that twenty-five percent of the camelid remains from the high elevation Andes site of Laguna del Diamante S4 were identified based on osteometric evidence as domestic llama, but guanaco are also a likely candidate since the two species overlap in size. We test the hypothesis that domesticated camelids occurred in prehispanic, southern Mendoza through analysis of ancient DNA. We generated whole mitochondrial genome datasets from 41 samples from southern Mendoza late Holocene archaeological sites, located between 450 and 3400 meters above sea level (masl). All camelid samples from those sites were identified as guanaco; thus, we have no evidence to support the hypothesis that the domestic llama occurred in prehispanic southern Mendoza.}, }
@article {pmid33148818, year = {2020}, author = {Garner, RE and Gregory-Eaves, I and Walsh, DA}, title = {Sediment Metagenomes as Time Capsules of Lake Microbiomes.}, journal = {mSphere}, volume = {5}, number = {6}, pages = {}, pmid = {33148818}, issn = {2379-5042}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification/virology ; Bacteriophages/genetics ; Canada ; Genetic Variation ; Geologic Sediments/*microbiology ; Lakes/*microbiology ; *Metagenome ; Microbiota/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudovirales) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria ("Candidatus Nanopelagicales") and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators.IMPORTANCE Lakes are critical freshwater resources under mounting pressure from climate change and other anthropogenic stressors. The reconstruction of ecological time series from sediment archives with paleolimnological techniques has been shown to be an effective means of understanding how humans are modifying lake ecosystems over extended timescales. In this study, we combined shotgun DNA sequencing with a novel comparative analysis of surface water and sediment metagenomes to expose the diversity of microorganisms preserved in lake sediments. The detection of DNA from a broad diversity of preserved microbes serves to more fully reconstruct historical microbiomes and describe preimpact lake conditions.}, }
@article {pmid33142099, year = {2020}, author = {Saag, L}, title = {Human Genetics: Lactase Persistence in a Battlefield.}, journal = {Current biology : CB}, volume = {30}, number = {21}, pages = {R1311-R1313}, doi = {10.1016/j.cub.2020.08.087}, pmid = {33142099}, issn = {1879-0445}, mesh = {Child, Preschool ; Europe ; Gene Frequency ; Humans ; *Lactase/genetics ; Prevalence ; *White People ; }, abstract = {Lactase persistence is a common genetic trait in Europeans and other pastoralists. New ancient DNA evidence from a Bronze Age battlefield indicates that selection for lactase persistence was strong and on-going in the last 3,000 years.}, }
@article {pmid33139852, year = {2021}, author = {Lall, GM and Larmuseau, MHD and Wetton, JH and Batini, C and Hallast, P and Huszar, TI and Zadik, D and Aase, S and Baker, T and Balaresque, P and Bodmer, W and Børglum, AD and de Knijff, P and Dunn, H and Harding, SE and Løvvik, H and Dupuy, BM and Pamjav, H and Tillmar, AO and Tomaszewski, M and Tyler-Smith, C and Verdugo, MP and Winney, B and Vohra, P and Story, J and King, TE and Jobling, MA}, title = {Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain.}, journal = {European journal of human genetics : EJHG}, volume = {29}, number = {3}, pages = {512-523}, pmid = {33139852}, issn = {1476-5438}, support = {084060//Wellcome Trust/United Kingdom ; 072974//Wellcome Trust/United Kingdom ; BB/M016706/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 087576//Wellcome Trust/United Kingdom ; 057559//Wellcome Trust/United Kingdom ; 088262//Wellcome Trust/United Kingdom ; //Wellcome Trust/United Kingdom ; PG/16/49/32176/BHF_/British Heart Foundation/United Kingdom ; 098051//Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Human, Y/*genetics ; Evolution, Molecular ; *Haplotypes ; *Human Migration ; Humans ; Male ; Minisatellite Repeats ; Pedigree ; Polymorphism, Single Nucleotide ; Scandinavian and Nordic Countries ; United Kingdom ; }, abstract = {The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia.}, }
@article {pmid33135465, year = {2020}, author = {Furtwängler, A and Neukamm, J and Böhme, L and Reiter, E and Vollstedt, M and Arora, N and Singh, P and Cole, ST and Knauf, S and Calvignac-Spencer, S and Krause-Kyora, B and Krause, J and Schuenemann, VJ and Herbig, A}, title = {Comparison of target enrichment strategies for ancient pathogen DNA.}, journal = {BioTechniques}, volume = {69}, number = {6}, pages = {455-459}, doi = {10.2144/btn-2020-0100}, pmid = {33135465}, issn = {1940-9818}, support = {//Senckenberg Centre for Human Evolution and Palaeoenvironment/ ; //Max-Planck Society/ ; //R2STOP Canada/ ; //ICMR, DBT India/ ; //the Leprosy Research Initiative Netherlands/ ; //University of Zurich's University Research Priority Program "Evolution in Action: From Genomes to Ecosystems"/ ; }, mesh = {DNA, Ancient/*analysis ; Humans ; Mycobacterium leprae/*genetics ; Nucleic Acid Hybridization/*methods ; Reproducibility of Results ; Treponema pallidum/*genetics ; }, abstract = {In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods - array-based hybridization capture and in-solution capture using either RNA or DNA baits - have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits.}, }
@article {pmid33134892, year = {2020}, author = {Hao, S and Han, K and Meng, L and Huang, X and Cao, W and Shi, C and Zhang, M and Wang, Y and Liu, Q and Zhang, Y and Sun, H and Seim, I and Xu, X and Liu, X and Fan, G}, title = {African Arowana Genome Provides Insights on Ancient Teleost Evolution.}, journal = {iScience}, volume = {23}, number = {11}, pages = {101662}, pmid = {33134892}, issn = {2589-0042}, abstract = {Osteoglossiformes is a basal clade of teleost, evolving since the Jurassic period. The genomes of Osteoglossiformes species would shed light on the evolution and adaptation of teleost. Here, we established a chromosome-level genome of African arowana. Together with the genomes of pirarucu and Asian arowana, we found that they diverged at ∼106.1 million years ago (MYA) and ∼59.2 MYA, respectively, which are coincident with continental separation. Interestingly, we identified a dynamic genome evolution characterized by a fast evolutionary rate and a high pseudogenization rate in African arowana and pirarucu. Additionally, more transposable elements were found in Asian arowana which confer more gene duplications. Moreover, we found the contraction of olfactory receptor and the expansion of UGT in African arowana might be related to its transformation from carnivore to be omnivore. Taken together, we provided valuable genomic resource of Osteoglossidae and revealed the correlation of biogeography and teleost evolution.}, }
@article {pmid33125870, year = {2021}, author = {Ramos-Madrigal, J and Sinding, MS and Carøe, C and Mak, SST and Niemann, J and Samaniego Castruita, JA and Fedorov, S and Kandyba, A and Germonpré, M and Bocherens, H and Feuerborn, TR and Pitulko, VV and Pavlova, EY and Nikolskiy, PA and Kasparov, AK and Ivanova, VV and Larson, G and Frantz, LAF and Willerslev, E and Meldgaard, M and Petersen, B and Sicheritz-Ponten, T and Bachmann, L and Wiig, &#xd8; and Hansen, AJ and Gilbert, MTP and Gopalakrishnan, S}, title = {Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages.}, journal = {Current biology : CB}, volume = {31}, number = {1}, pages = {198-206.e8}, pmid = {33125870}, issn = {1879-0445}, support = {/WT_/Wellcome Trust/United Kingdom ; UNS53502/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biodiversity ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Dogs/anatomy &amp; histology/*genetics ; Extinction, Biological ; Asia, Eastern ; Fossils ; *Genome ; Geography ; Phylogeny ; Siberia ; Skull/anatomy &amp; histology ; Wolves/anatomy &amp; histology/*genetics ; }, abstract = {Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.[1] Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)[1-3] and replaced local wolf populations.[4] Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.[35] Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.[67] However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.}, }
@article {pmid33122697, year = {2020}, author = {Hui, R and D'Atanasio, E and Cassidy, LM and Scheib, CL and Kivisild, T}, title = {Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18542}, pmid = {33122697}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {DNA, Ancient/*analysis ; Genome, Human/*genetics ; Genotype ; Humans ; Polymorphism, Single Nucleotide/genetics ; Software ; }, abstract = {Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate genotype imputation from > 1 × coverage data have recently become a routine, a large proportion of ancient samples remain unusable for downstream analyses due to their low coverage. Here, we evaluate a two-step pipeline for the imputation of common variants in ancient genomes at 0.05-1 × coverage. We use the genotype likelihood input mode in Beagle and filter for confident genotypes as the input to impute missing genotypes. This procedure, when tested on ancient genomes, outperforms a single-step imputation from genotype likelihoods, suggesting that current genotype callers do not fully account for errors in ancient sequences and additional quality controls can be beneficial. We compared the effect of various genotype likelihood calling methods, post-calling, pre-imputation and post-imputation filters, different reference panels, as well as different imputation tools. In a Neolithic Hungarian genome, we obtain ~ 90% imputation accuracy for heterozygous common variants at coverage 0.05 × and > 97% accuracy at coverage 0.5 ×. We show that imputation can mitigate, though not eliminate reference bias in ultra-low coverage ancient genomes.}, }
@article {pmid33106554, year = {2020}, author = {Parker, C and Rohrlach, AB and Friederich, S and Nagel, S and Meyer, M and Krause, J and Bos, KI and Haak, W}, title = {A systematic investigation of human DNA preservation in medieval skeletons.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18225}, pmid = {33106554}, issn = {2045-2322}, mesh = {Archaeology ; Bone and Bones/*metabolism ; DNA, Ancient/analysis/*chemistry/*isolation &amp; purification ; Ear, Inner/*metabolism ; Germany ; History, Medieval ; Humans ; Petrous Bone/*metabolism ; Preservation, Biological/*methods ; Tooth/*metabolism ; }, abstract = {Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.}, }
@article {pmid33106412, year = {2020}, author = {Guellil, M and Kersten, O and Namouchi, A and Luciani, S and Marota, I and Arcini, CA and Iregren, E and Lindemann, RA and Warfvinge, G and Bakanidze, L and Bitadze, L and Rubini, M and Zaio, P and Zaio, M and Neri, D and Stenseth, NC and Bramanti, B}, title = {A genomic and historical synthesis of plague in 18th century Eurasia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {45}, pages = {28328-28335}, pmid = {33106412}, issn = {1091-6490}, mesh = {DNA, Bacterial ; Europe ; *Genome, Bacterial ; History, 18th Century ; History, Medieval ; Humans ; Pandemics/history ; Phylogeny ; Plague/genetics/*history/*microbiology ; Russia ; Yersinia pestis/classification/*genetics ; }, abstract = {Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe.}, }
@article {pmid33077602, year = {2020}, author = {Chen, N and Ren, L and Du, L and Hou, J and Mullin, VE and Wu, D and Zhao, X and Li, C and Huang, J and Qi, X and Capodiferro, MR and Achilli, A and Lei, C and Chen, F and Su, B and Dong, G and Zhang, X}, title = {Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {45}, pages = {28150-28159}, pmid = {33077602}, issn = {1091-6490}, mesh = {Animal Migration ; Animals ; *Biodiversity ; *Cattle/classification/genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial ; Genome/*genetics ; History, Ancient ; Homing Behavior ; Humans ; Perissodactyla/classification/genetics ; Population Dynamics/history ; Ruminants/classification/genetics ; Tibet ; }, abstract = {Local wild bovids have been determined to be important prey on the northeastern Tibetan Plateau (NETP), where hunting game was a major subsistence strategy until the late Neolithic, when farming lifestyles dominated in the neighboring Loess Plateau. However, the species affiliation and population ecology of these prehistoric wild bovids in the prehistoric NETP remain unknown. Ancient DNA (aDNA) analysis is highly informative in decoding this puzzle. Here, we applied aDNA analysis to fragmented bovid and rhinoceros specimens dating ∼5,200 y B.P. from the Neolithic site of Shannashuzha located in the marginal area of the NETP. Utilizing both whole genomes and mitochondrial DNA, our results demonstrate that the range of the present-day tropical gaur (Bos gaurus) extended as far north as the margins of the NETP during the late Neolithic from ∼29°N to ∼34°N. Furthermore, comparative analysis with zooarchaeological and paleoclimatic evidence indicated that a high summer temperature in the late Neolithic might have facilitated the northward expansion of tropical animals (at least gaur and Sumatran-like rhinoceros) to the NETP. This enriched the diversity of wildlife, thus providing abundant hunting resources for humans and facilitating the exploration of the Tibetan Plateau as one of the last habitats for hunting game in East Asia.}, }
@article {pmid33065008, year = {2020}, author = {Barnett, R and Westbury, MV and Sandoval-Velasco, M and Vieira, FG and Jeon, S and Zazula, G and Martin, MD and Ho, SYW and Mather, N and Gopalakrishnan, S and Ramos-Madrigal, J and de Manuel, M and Zepeda-Mendoza, ML and Antunes, A and Baez, AC and De Cahsan, B and Larson, G and O'Brien, SJ and Eizirik, E and Johnson, WE and Koepfli, KP and Wilting, A and Fickel, J and Dalén, L and Lorenzen, ED and Marques-Bonet, T and Hansen, AJ and Zhang, G and Bhak, J and Yamaguchi, N and Gilbert, MTP}, title = {Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.}, journal = {Current biology : CB}, volume = {30}, number = {24}, pages = {5018-5025.e5}, pmid = {33065008}, issn = {1879-0445}, support = {681396/ERC_/European Research Council/International ; }, mesh = {Animal Distribution ; Animals ; Cuspid ; DNA, Ancient ; Extinction, Biological ; Felidae/anatomy &amp; histology/*genetics ; Fossils/anatomy &amp; histology ; *Genetic Drift ; *Genetic Speciation ; Genomics ; Hybridization, Genetic ; Phylogeny ; Recombination, Genetic ; }, abstract = {Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.}, }
@article {pmid33065004, year = {2020}, author = {Lipson, M and Spriggs, M and Valentin, F and Bedford, S and Shing, R and Zinger, W and Buckley, H and Petchey, F and Matanik, R and Cheronet, O and Rohland, N and Pinhasi, R and Reich, D}, title = {Three Phases of Ancient Migration Shaped the Ancestry of Human Populations in Vanuatu.}, journal = {Current biology : CB}, volume = {30}, number = {24}, pages = {4846-4856.e6}, pmid = {33065004}, issn = {1879-0445}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Anthropology/methods ; Body Remains ; DNA, Ancient ; Female ; Haplotypes ; History, Ancient ; Human Migration/*history ; Humans ; Male ; *Phylogeny ; Vanuatu ; }, abstract = {The archipelago of Vanuatu has been at the crossroads of human population movements in the Pacific for the past three millennia. To help address several open questions regarding the history of these movements, we generated genome-wide data for 11 ancient individuals from the island of Efate dating from its earliest settlement to the recent past, including five associated with the Chief Roi Mata's Domain World Heritage Area, and analyzed them in conjunction with 34 published ancient individuals from Vanuatu and elsewhere in Oceania, as well as present-day populations. Our results outline three distinct periods of population transformations. First, the four earliest individuals, from the Lapita-period site of Teouma, are concordant with eight previously described Lapita-associated individuals from Vanuatu and Tonga in having almost all of their ancestry from a "First Remote Oceanian" source related to East and Southeast Asians. Second, both the Papuan ancestry predominating in Vanuatu for the past 2,500 years and the smaller component of Papuan ancestry found in Polynesians can be modeled as deriving from a single source most likely originating in New Britain, suggesting that the movement of people carrying this ancestry to Remote Oceania closely followed that of the First Remote Oceanians in time and space. Third, the Chief Roi Mata's Domain individuals descend from a mixture of Vanuatu- and Polynesian-derived ancestry and are related to Polynesian-influenced communities today in central, but not southern, Vanuatu, demonstrating Polynesian genetic input in multiple groups with independent histories.}, }
@article {pmid33059357, year = {2021}, author = {Gad, YZ and Hassan, NA and Mousa, DM and Fouad, FA and El-Sayed, SG and Abdelazeem, MA and Mahdy, SM and Othman, HY and Ibrahim, DW and Khairat, R and Ismail, S}, title = {Insights from ancient DNA analysis of Egyptian human mummies: clues to disease and kinship.}, journal = {Human molecular genetics}, volume = {30}, number = {R1}, pages = {R24-R28}, doi = {10.1093/hmg/ddaa223}, pmid = {33059357}, issn = {1460-2083}, mesh = {Communicable Diseases/*epidemiology/history ; DNA, Ancient/*analysis ; Egypt/epidemiology ; Family/history ; Genetics, Population ; Genomics ; History, Ancient ; Humans ; Mummies/*history ; Paleography ; }, abstract = {The molecular Egyptology field started in the mid-eighties with the first publication on the ancient DNA (aDNA) analysis of an Egyptian mummy. Egypt has been a major interest for historians, archeologists, laymen as well as scientists. The aDNA research on Egyptian biological remains has been fueled by their abundance and relatively well-preserved states through artificial mummification and by the advanced analytical techniques. Early doubts of aDNA integrity within the Egyptian mummies and data authenticity were later abated with studies proving successfully authenticated aDNA retrieval. The current review tries to recapitulate the published studies presenting paleogenomic evidence of disease diagnosis and kinship establishment for the Egyptian human remains. Regarding disease diagnosis, the prevailing literature was on paleogenomic evidence of infectious diseases in the human remains. A series of reports presented evidence for the presence of tuberculosis and/or malaria. In addition, there were solitary reports of the presence of leprosy, diphtheria, bacteremia, toxoplasmosis, schistosomiasis and leishmaniasis. On the contrary, paleogenomic evidence of the presence of rare diseases was quite scarce and mentioned only in two articles. On the other hand, kinship analysis of Egyptian human remains, including that of Tutankhamen, was done using both mitochondrial DNA sequences and nuclear DNA markers, to establish family relationships in four studies. It is clear that the field of molecular Egyptology is still a largely unexplored territory. Nevertheless, the paleogenomic investigation of Egyptian remains could make significant contributions to biomedical sciences (e.g. elucidation of coevolution of human host-microbe interrelationship) as well as to evidence-based archeology.}, }
@article {pmid33057138, year = {2020}, author = {Lasa-Fernandez, H and Mosqueira-Martín, L and Alzualde, A and Lasa-Elgarresta, J and Vallejo-Illarramendi, A}, title = {A genotyping method combining primer competition PCR with HRM analysis to identify point mutations in Duchenne animal models.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17224}, pmid = {33057138}, issn = {2045-2322}, mesh = {Animals ; Birefringence ; *Disease Models, Animal ; Drug Evaluation, Preclinical ; Genotyping Techniques/*methods ; Mice, Inbred C57BL ; Mice, Inbred mdx ; Molecular Diagnostic Techniques/*methods ; Muscular Dystrophy, Duchenne/*genetics ; *Point Mutation ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Zebrafish ; }, abstract = {Dystrophin-null sapje zebrafish is an excellent model for better understanding the pathological mechanisms underlying Duchenne muscular dystrophy, and it has recently arisen as a powerful tool for high-throughput screening of therapeutic candidates for this disease. While dystrophic phenotype in sapje larvae can be easily detected by birefringence, zebrafish genotyping is necessary for drug screening experiments, where the potential rescue of larvae phenotype is the primary outcome. Genotyping is also desirable during colony husbandry since heterozygous progenitors need to be selected. Currently, sapje zebrafish are genotyped through techniques involving sequencing or multi-step PCR, which are often costly, tedious, or require special equipment. Here we report a simple, precise, cost-effective, and versatile PCR genotyping method based on primer competition. Genotypes can be resolved by standard agarose gel electrophoresis and high-resolution melt assay, the latter being especially useful for genotyping a large number of samples. Our approach has shown high sensitivity, specificity, and reproducibility in detecting the A/T point mutation in sapje zebrafish and the C/T mutation in the mdx mouse model of Duchenne. Hence, this method can be applied to other single nucleotide substitutions and may be further optimized to detect small insertions and deletions. Given its robust performance with crude DNA extracts, our strategy may be particularly well-suited for detecting single nucleotide variants in poor-quality samples such as ancient DNA or DNA from formalin-fixed, paraffin-embedded material.}, }
@article {pmid33046824, year = {2020}, author = {Drosou, K and Collin, TC and Freeman, PJ and Loynes, R and Freemont, T}, title = {The first reported case of the rare mitochondrial haplotype H4a1 in ancient Egypt.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17037}, pmid = {33046824}, issn = {2045-2322}, support = {MR/N00583X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {DNA, Mitochondrial/*genetics ; Egypt, Ancient ; Female ; Haplotypes/*genetics ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Humans ; Mitochondria/*genetics ; }, abstract = {Takabuti, was a female who lived in ancient Egypt during the 25th Dynasty, c.660 BCE. Her mummified remains were brought to Belfast, Northern Ireland, in 1834 and are currently displayed in the Ulster Museum. To gain insight into Takabuti's ancestry, we used deep sampling of vertebral bone, under X-ray control, to obtain non-contaminated bone tissue from which we extracted ancient DNA (aDNA) using established protocols. We targeted the maternally inherited mitochondrial DNA (mtDNA), known to be highly informative for human ancestry, and identified 38 single nucleotide variants using next generation sequencing. The specific combination of these SNVs suggests that Takabuti belonged to mitochondrial haplogroup H4a1. Neither H4 nor H4a1 have been reported in ancient Egyptian samples, prior to this study. The modern distribution of H4a1 is rare and sporadic and has been identified in areas including the Canary Islands, southern Iberia and the Lebanon. H4a1 has also been reported in ancient samples from Bell Beaker and Unetice contexts in Germany, as well as Bronze Age Bulgaria. We believe that this is an important finding because first, it adds to the depth of knowledge about the distribution of the H4a1 haplogroup in existing mtDNA, thus creating a baseline for future occurrences of this haplogroup in ancient Egyptian remains. Second, it is of great importance for archaeological sciences, since a predominantly European haplogroup has been identified in an Egyptian individual in Southern Egypt, prior to the Roman and Greek influx (332BCE).}, }
@article {pmid33035304, year = {2021}, author = {Woods, R and Barnes, I and Brace, S and Turvey, ST}, title = {Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents.}, journal = {Molecular biology and evolution}, volume = {38}, number = {1}, pages = {84-95}, pmid = {33035304}, issn = {1537-1719}, mesh = {Animals ; DNA, Ancient/*analysis ; Phylogeography ; Rodentia/*genetics ; West Indies ; }, abstract = {Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining "ancestral-type" characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage.}, }
@article {pmid33028848, year = {2020}, author = {Rao, H and Yang, Y and Liu, J and Westbury, MV and Zhang, C and Shao, Q}, title = {Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16674}, pmid = {33028848}, issn = {2045-2322}, mesh = {Animals ; *Biological Evolution ; Asia, Eastern ; *Fossils ; Hyaenidae/genetics/*metabolism ; Proteomics ; }, abstract = {The spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, also known as cave hyena, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for molecular phylogenetic reconstructions of ancient fauna previously thought to be unreachable using ancient DNA.}, }
@article {pmid33022266, year = {2020}, author = {Duchêne, S and Ho, SYW and Carmichael, AG and Holmes, EC and Poinar, H}, title = {The Recovery, Interpretation and Use of Ancient Pathogen Genomes.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {R1215-R1231}, pmid = {33022266}, issn = {1879-0445}, mesh = {Animals ; Bacteria/genetics/*pathogenicity ; Biological Evolution ; DNA, Ancient/*analysis ; DNA, Bacterial/*genetics ; Evolution, Molecular ; Genome/genetics ; Genome, Bacterial/genetics ; Genomics/methods ; Humans ; Microbiota/genetics ; Mycobacterium leprae/genetics ; Mycobacterium tuberculosis/genetics ; Phylogeny ; Treponema/genetics ; Variola virus/genetics ; Vibrio cholerae/genetics ; Yersinia pestis/genetics ; }, abstract = {The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest - pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) - and for three equally important endemic human disease agents - Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20[th] century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.}, }
@article {pmid33022107, year = {2021}, author = {Fleskes, RE and Ofunniyin, AA and Gilmore, JK and Poplin, E and Abel, SM and Bueschgen, WD and Juarez, C and Butler, N and Mishoe, G and Oubré, L and Cabana, GS and Schurr, TG}, title = {Ancestry, health, and lived experiences of enslaved Africans in 18th century Charleston: An osteobiographical analysis.}, journal = {American journal of physical anthropology}, volume = {175}, number = {1}, pages = {3-24}, doi = {10.1002/ajpa.24149}, pmid = {33022107}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Anthropology, Physical ; Bone and Bones/chemistry ; Burial/history ; Child ; Child, Preschool ; Enslaved Persons/*history/statistics &amp; numerical data ; Enslavement/*ethnology/*history ; Family/ethnology/history ; Female ; Genome, Mitochondrial/genetics ; Health Status ; History, 18th Century ; Humans ; Infant ; Infant, Newborn ; Male ; South Carolina/ethnology ; Strontium Isotopes/analysis ; Tooth/chemistry/pathology ; Young Adult ; }, abstract = {OBJECTIVES: In 2013, the burials of 36 individuals of putative African ancestry were discovered during renovation of the Gaillard Center in downtown Charleston, South Carolina. The Charleston community facilitated a bioarchaeological and mitogenomic study to gain insights into the lives of these unknown persons, referred to as the Anson Street Ancestors, including their ancestry, health, and lived experiences in the 18th century.<br><br>METHODS: Metric and morphological assessments of skeletal and dental characteristics were recorded, and enamel and cortical bone strontium stable isotope values generated. Whole mitochondrial genomes were sequenced and analyzed.<br><br>RESULTS: Osteological analysis identified adults, both females and males, and subadults at the site, and estimated African ancestry for most individuals. Skeletal trauma and pathology were infrequent, but many individuals exhibited dental decay and abscesses. Strontium isotope data suggested these individuals mostly originated in Charleston or sub-Saharan Africa, with many being long-term residents of Charleston. Nearly all had mitochondrial lineages belonging to African haplogroups (L0-L3, H1cb1a), with two individuals sharing the same L3e2a haplotype, while one had a Native American A2 mtDNA.<br><br>DISCUSSION: This study generated detailed osteobiographies of the Anson Street Ancestors, who were likely of enslaved status. Our results indicate that the Ancestors have diverse maternal African ancestries and are largely unrelated, with most being born locally. These details reveal the demographic impact of the trans-Atlantic slave trade. Our analysis further illuminates the lived experiences of individuals buried at Anson Street, and expands our understanding of 18th century African history in Charleston.}, }
@article {pmid33012235, year = {2020}, author = {Ferrari, G and Neukamm, J and Baalsrud, HT and Breidenstein, AM and Ravinet, M and Phillips, C and Rühli, F and Bouwman, A and Schuenemann, VJ}, title = {Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190572}, pmid = {33012235}, issn = {1471-2970}, mesh = {Animals ; England ; *Evolution, Molecular ; *Genome, Viral ; History, 18th Century ; Humans ; Infant ; Museums ; Phylogeny ; Smallpox/*history ; Variola virus/*genetics ; }, abstract = {Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, }
@article {pmid33012233, year = {2020}, author = {Bravo-Lopez, M and Villa-Islas, V and Rocha Arriaga, C and Villaseñor-Altamirano, AB and Guzmán-Solís, A and Sandoval-Velasco, M and Wesp, JK and Alcantara, K and López-Corral, A and Gómez-Valdés, J and Mejía, E and Herrera, A and Meraz-Moreno, A and Moreno-Cabrera, ML and Moreno-Estrada, A and Nieves-Colón, MA and Olvera, J and Pérez-Pérez, J and Iversen, KH and Rasmussen, S and Sandoval, K and Zepeda, G and Ávila-Arcos, MC}, title = {Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190580}, pmid = {33012233}, issn = {1471-2970}, support = {208934/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; *Genome, Bacterial ; Genomics ; Gram-Negative Bacterial Infections/*history/microbiology ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, Ancient ; History, Medieval ; Humans ; Mexico ; Periodontitis/*history/microbiology ; Tannerella forsythia/*genetics ; }, abstract = {The 'red complex' is an aggregate of three oral bacteria (Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient T.forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from the Pre-Hispanic to the Colonial period in Mexico. We recovered twelve partial ancient T. forsythia genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the T. forsythia ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa. This study highlights the potential for studying ancient T. forsythia genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, }
@article {pmid33012232, year = {2020}, author = {Flammer, PG and Smith, AL}, title = {Intestinal helminths as a biomolecular complex in archaeological research.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190570}, pmid = {33012232}, issn = {1471-2970}, support = {BB/K004468/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K001388/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Archaeology/*methods ; DNA, Ancient/*analysis ; Helminths/*genetics ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Ancient ; History, Medieval ; Humans ; Intestinal Diseases, Parasitic/diagnosis/*history/parasitology ; }, abstract = {Enteric helminths are common parasites in many parts of the world and in the past were much more widespread both geographically and socially. Many enteric helminths are relatively long-lived in the human host, often benign or of low pathogenicity while producing large numbers of environmentally resistant eggs voided in the faeces or found associated with individual remains (skeletons and mummies). The combination of helminth characters offers opportunities to the field of historical pathogen research that are quite different to that of some of the more intensively studied high impact pathogens. Historically, a wealth of studies has employed microscopic techniques to diagnose infection using the morphology of the helminth eggs. More recently, various ancient DNA (aDNA) approaches have been applied in the archaeoparasitological context and these are revolutionizing the field, allowing much more specific diagnosis as well as interrogating the epidemiology of helminths. These advances have enhanced the potential for the field to provide unique information on past populations including using diseases to consider many aspects of life (e.g. sanitation, hygiene, diet, culinary practices and other aspects of society). Here, we consider the impact of helminth archaeoparasitology and more specifically the impact and potential for application of aDNA technologies as a part of the archaeologists' toolkit. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, }
@article {pmid33012228, year = {2020}, author = {Achtman, M and Zhou, Z}, title = {Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190573}, pmid = {33012228}, issn = {1471-2970}, support = {/WT_/Wellcome Trust/United Kingdom ; 202792/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; BB/L020319/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Dental Caries/*history/*microbiology ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Ancient ; History, Medieval ; Humans ; *Metagenome ; *Microbiota ; Mouth/*microbiology ; Phylogeny ; Saliva/microbiology ; Streptococcus mutans/classification/*genetics ; Streptococcus sobrinus/classification/*genetics ; }, abstract = {We have recently developed bioinformatic tools to accurately assign metagenomic sequence reads to microbial taxa: SPARSE for probabilistic, taxonomic classification of sequence reads; EToKi for assembling and polishing genomes from short-read sequences; and GrapeTree, a graphic visualizer of genetic distances between large numbers of genomes. Together, these methods support comparative analyses of genomes from ancient skeletons and modern humans. Here, we illustrate these capabilities with 784 samples from historical dental calculus, modern saliva and modern dental plaque. The analyses revealed 1591 microbial species within the oral microbiome. We anticipated that the oral complexes of Socransky et al., which were defined in 1998, would predominate among taxa whose frequencies differed by source. However, although some species discriminated between sources, we could not confirm the existence of the complexes. The results also illustrate further functionality of our pipelines with two species that are associated with dental caries, Streptococcus mutans and Streptococcus sobrinus. They were rare in historical dental calculus but common in modern plaque, and even more common in saliva. Reconstructed draft genomes of these two species from metagenomic samples in which they were abundant were combined with modern public genomes to provide a detailed overview of their core genomic diversity. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, }
@article {pmid33012227, year = {2020}, author = {Fotakis, AK and Denham, SD and Mackie, M and Orbegozo, MI and Mylopotamitaki, D and Gopalakrishnan, S and Sicheritz-Pontén, T and Olsen, JV and Cappellini, E and Zhang, G and Christophersen, A and Gilbert, MTP and Vågene, &#xc5;J}, title = {Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190584}, pmid = {33012227}, issn = {1471-2970}, mesh = {Adult ; Archaeology ; DNA, Ancient/*analysis ; Dental Calculus/*history/microbiology ; Female ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; History, 16th Century ; Humans ; Leprosy/*history/microbiology ; Middle Aged ; Mycobacterium leprae/*genetics ; Norway ; Sequence Analysis, DNA ; }, abstract = {Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. Mycobacterium leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, }
@article {pmid33012225, year = {2020}, author = {Morozova, I and Kasianov, A and Bruskin, S and Neukamm, J and Molak, M and Batieva, E and Pudło, A and Rühli, FJ and Schuenemann, VJ}, title = {New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190569}, pmid = {33012225}, issn = {1471-2970}, mesh = {Animals ; Disease Reservoirs/*veterinary ; *Genome, Bacterial ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; Phylogeny ; Plague/*history/transmission ; Poland ; Rats ; Rodent Diseases/microbiology ; Russia ; Yersinia pestis/classification/*genetics ; }, abstract = {Yersinia pestis, the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of Y. pestis have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period. To address this, we present four newly assembled Y. pestis genomes from Eastern Europe (Poland and Southern Russia), dating from the fifteenth to eighteenth century AD. The analysis of polymorphisms in these genomes and their phylogenetic relationships with other ancient and modern Y. pestis strains may suggest several independent introductions of plague into Eastern Europe or its persistence in different reservoirs. Furthermore, with the reconstruction of a partial Y. pestis genome from rat skeletal remains found in a Polish ossuary, we were able to identify a potential animal reservoir in late medieval Europe. Overall, our results add new information concerning Y. pestis transmission and its evolutionary history in Eastern Europe. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, }
@article {pmid33012223, year = {2020}, author = {Eisenhofer, R and Kanzawa-Kiriyama, H and Shinoda, KI and Weyrich, LS}, title = {Investigating the demographic history of Japan using ancient oral microbiota.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190578}, pmid = {33012223}, issn = {1471-2970}, mesh = {Chloroflexi/classification/*genetics ; Demography ; Dental Caries/*history/microbiology ; *Genome, Bacterial ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, Ancient ; Humans ; Japan ; *Microbiota ; Mouth/*microbiology ; Periodontal Diseases/*history/microbiology ; Phylogeny ; Population Dynamics ; }, abstract = {While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter-gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400-150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species-Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, }
@article {pmid33007831, year = {2020}, author = {Horsburgh, KA and Gosling, AL}, title = {Systematic Ancient DNA Species Identification Fails to Find Late Holocene Domesticated Cattle in Southern Africa.}, journal = {Biology}, volume = {9}, number = {10}, pages = {}, pmid = {33007831}, issn = {2079-7737}, support = {BCS-0634669//National Science Foundation/ ; None//Southern Methodist University/ ; }, abstract = {Establishing robust temporal control of the arrival of domesticated stock and the associated husbandry skills and lifeways in Southern Africa remains frustrated by the osteological similarities between domestic stock and wild endemic fauna. We report the results of a systematic ancient DNA survey of appropriately sized bovid remains from Later Stone Age deposits in four South African archaeological sites. We show that none of the tested remains originated in domesticated cattle. The precise date of arrival of domestic cattle in the region awaits further study, although we also report new radiocarbon determinations which further refine the local chronology.}, }
@article {pmid33004016, year = {2020}, author = {Robène, I and Maillot-Lebon, V and Chabirand, A and Moreau, A and Becker, N and Moumène, A and Rieux, A and Campos, P and Gagnevin, L and Gaudeul, M and Baider, C and Chiroleu, F and Pruvost, O}, title = {Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {296}, pmid = {33004016}, issn = {1471-2180}, support = {2014FR06RDRP004//European Union Agricultural Fund for Rural Development/ ; GURDT I2016-1731-0006632//European Regional Development Fund/ ; 1504-004//Agropolis Fondation/ ; ANR-17-CE35-0009-01//Agence Nationale de la Recherche (FR)/ ; }, mesh = {Bacterial Proteins/*genetics ; *Bacterial Typing Techniques ; Benchmarking ; Citrus/*microbiology ; DNA, Bacterial/genetics ; Gene Expression ; Humans ; Membrane Proteins/*genetics ; Plant Diseases/microbiology ; ROC Curve ; Real-Time Polymerase Chain Reaction/*methods/standards ; Reproducibility of Results ; Xanthomonas/*genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols.<br><br>RESULTS: Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD95%&#xa0;=&#x2009;754&#x2009;CFU&#x2009;ml[-&#x2009;1] (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD95%&#xa0;=&#x2009;5234&#x2009;CFU&#x2009;ml[-&#x2009;1] (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays.<br><br>CONCLUSIONS: We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.}, }
@article {pmid33002384, year = {2021}, author = {Boukhdoud, L and Saliba, C and Parker, LD and Rotzel McInerney, N and Ishak Mouawad, G and Kharrat, M and Kahale, R and Chahine, T and Maldonado, JE and Bou Dagher-Kharrat, M}, title = {First DNA sequence reference library for mammals and plants of the Eastern Mediterranean Region.}, journal = {Genome}, volume = {64}, number = {1}, pages = {39-49}, doi = {10.1139/gen-2019-0194}, pmid = {33002384}, issn = {1480-3321}, mesh = {Animals ; Base Sequence ; Biodiversity ; DNA Barcoding, Taxonomic ; Ecosystem ; *Gene Library ; Genetic Markers ; Mammals/*genetics ; Mediterranean Region ; Plant Leaves/genetics ; Plants/*genetics ; }, abstract = {The Mediterranean region is identified as one of the world's 36 biodiversity hotspots, with the Earth's most biologically rich yet threatened areas. Lebanon is a hub for Eastern Mediterranean Region (EMR) biodiversity with 9116 characterized plant and animal species (4486 fauna and 4630 flora). Using DNA barcoding as a tool has become crucial in the accurate identification of species in multiple contexts. It can also complement species morphological descriptions, which will add to our understanding of the biodiversity and richness of ecosystems and benefit conservation projects for endangered and endemic species. In this study, we create the first reference library of standard DNA markers for mammals and plants in the EMR, with a focus on endemic and endangered species. Plant leaves were collected from different nature reserves in Mount Lebanon, and mammal samples were obtained from taxidermized museum specimens or road kills. We generated the 12S rRNA sequences of 18 mammal species from 6 orders and 13 different families. We also obtained the trnL and rbcL barcode sequences of 52 plant species from 24 different families. Twenty-five plant species and two mammal species included in this study were sequenced for the first time using these markers.}, }
@article {pmid32994538, year = {2021}, author = {Nishimura, L and Sugimoto, R and Inoue, J and Nakaoka, H and Kanzawa-Kiriyama, H and Shinoda, KI and Inoue, I}, title = {Identification of ancient viruses from metagenomic data of the Jomon people.}, journal = {Journal of human genetics}, volume = {66}, number = {3}, pages = {287-296}, pmid = {32994538}, issn = {1435-232X}, mesh = {Actinomycetaceae/virology ; *Asian People/history ; Clustered Regularly Interspaced Short Palindromic Repeats ; Contig Mapping ; DNA, Viral/*isolation &amp; purification ; Dental Pulp/chemistry/*virology ; *Ethnicity/history ; Female ; Fossils/history/microbiology/*virology ; *Genome, Viral ; History, Ancient ; Humans ; Japan ; Likelihood Functions ; Male ; *Metagenome ; Molecular Sequence Annotation ; Mouth/microbiology/virology ; Open Reading Frames/genetics ; Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Siphoviridae/genetics/*isolation &amp; purification ; Whole Genome Sequencing ; }, abstract = {Ancient DNA studies provide genomic information about the origins, population structures, and physical characteristics of ancient humans that cannot be solely examined by archeological studies. The DNAs extracted from ancient human bones, teeth, or tissues are often contaminated with coexisting bacterial and viral genomes that contain DNA from ancient microbes infecting those of ancient humans. Information on ancient viral genomes is useful in making inferences about the viral evolution. Here, we have utilized metagenomic sequencing data from the dental pulp of five Jomon individuals, who lived on the Japanese archipelago more than 3000 years ago; this is to detect ancient viral genomes. We conducted de novo assembly of the non-human reads where we have obtained 277,387 contigs that were longer than 1000 bp. These contigs were subjected to homology searches against a collection of modern viral genome sequences. We were able to detect eleven putative ancient viral genomes. Among them, we reconstructed the complete sequence of the Siphovirus contig89 (CT89) viral genome. The Jomon CT89-like sequence was determined to contain 59 open reading frames, among which five genes known to encode phage proteins were under strong purifying selection. The host of CT89 was predicted to be Schaalia meyeri, a bacterium residing in the human oral cavity. Finally, the CT89 phylogenetic tree showed two clusters, from both of which the Jomon sequence was separated. Our results suggest that metagenomic information from the dental pulp of the Jomon people is essential in retrieving ancient viral genomes used to examine their evolution.}, }
@article {pmid32986737, year = {2020}, author = {Peris, D and Janssen, K and Barthel, HJ and Bierbaum, G and Delclòs, X and Peñalver, E and Solórzano-Kraemer, MM and Jordal, BH and Rust, J}, title = {DNA from resin-embedded organisms: Past, present and future.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0239521}, pmid = {32986737}, issn = {1932-6203}, mesh = {Amber/chemistry ; Animals ; Coleoptera/genetics ; DNA, Ancient/*chemistry ; Fossils ; Hymenaea/chemistry ; Insecta/genetics ; Madagascar ; Reproducibility of Results ; Resins, Plant/*chemistry ; }, abstract = {Past claims have been made for fossil DNA recovery from various organisms (bacteria, plants, insects and mammals, including humans) dating back in time from thousands to several million years BP. However, many of these recoveries, especially those described from million-year-old amber (fossil resin), have faced criticism as being the result of modern environmental contamination and for lack of reproducibility. Using modern genomic techniques, DNA can be obtained with confidence from a variety of substrates (e.g. bones, teeth, gum, museum specimens and fossil insects) of different ages, albeit always less than one million years BP, and results can also be obtained from much older materials using palaeoproteomics. Nevertheless, new attempts to determine if ancient DNA (aDNA) is present in insects preserved in 40 000-year old sub-fossilised resin, the precursor of amber, have been unsuccessful or not well documented. Resin-embedded specimens are therefore regarded as unsuitable for genetic studies. However, we demonstrate here, for the first time, that although a labile molecule, DNA is still present in platypodine beetles (Coleoptera: Curculionidae) embedded in six-year-old and two-year-old resin pieces from Hymenaea verrucosa (Angiospermae: Fabaceae) collected in Madagascar. We describe an optimised method which meets all the requirements and precautions for aDNA experiments for our purpose: to explore the DNA preservation limits in resin. Our objective is far from starting an uncontrolled search for aDNA in amber as it was in the past, but to start resolving basic aspects from the DNA preservation in resin and search from the most modern samples to the ancient ones, step by step. We conclude that it is therefore possible to study genomics from resin-embedded organisms, although the time limits remain to be determined.}, }
@article {pmid32973032, year = {2020}, author = {Petr, M and Hajdinjak, M and Fu, Q and Essel, E and Rougier, H and Crevecoeur, I and Semal, P and Golovanova, LV and Doronichev, VB and Lalueza-Fox, C and de la Rasilla, M and Rosas, A and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Vernot, B and Meyer, M and Kelso, J}, title = {The evolutionary history of Neanderthal and Denisovan Y chromosomes.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6511}, pages = {1653-1656}, doi = {10.1126/science.abb6460}, pmid = {32973032}, issn = {1095-9203}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Chromosomes, Human, Y/genetics ; DNA, Ancient ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Humans ; *Life History Traits ; Male ; Neanderthals/classification/*genetics ; Phylogeny ; Y Chromosome/*genetics ; }, abstract = {Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.}, }
@article {pmid32963029, year = {2020}, author = {Bokelmann, L and Glocke, I and Meyer, M}, title = {Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples.}, journal = {Genome research}, volume = {30}, number = {10}, pages = {1449-1457}, pmid = {32963029}, issn = {1549-5469}, mesh = {Animals ; Cell-Free Nucleic Acids/blood ; Cytosine/metabolism ; DNA/blood ; DNA, Ancient/*chemistry ; Deamination ; High-Throughput Nucleotide Sequencing ; Humans ; Neanderthals/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Extensive manipulations involved in the preparation of DNA samples for sequencing have hitherto made it impossible to determine the precise structure of double-stranded DNA fragments being sequenced, such as the presence of blunt ends, single-stranded overhangs, or single-strand breaks. We here describe MatchSeq, a method that combines single-stranded DNA library preparation from diluted DNA samples with computational sequence matching, allowing the reconstruction of double-stranded DNA fragments on a single-molecule level. The application of MatchSeq to Neanderthal DNA, a particularly complex source of degraded DNA, reveals that 1- or 2-nt overhangs and blunt ends dominate the ends of ancient DNA molecules and that short gaps exist, which are predominantly caused by the loss of individual purines. We further show that deamination of cytosine to uracil occurs in both single- and double-stranded contexts close to the ends of molecules, and that single-stranded parts of DNA fragments are enriched in pyrimidines. MatchSeq provides unprecedented resolution for interrogating the structures of fragmented double-stranded DNA and can be applied to fragmented double-stranded DNA isolated from any biological source. The method relies on well-established laboratory techniques and can easily be integrated into routine data generation. This possibility is shown by the successful reconstruction of double-stranded DNA fragments from previously published single-stranded sequence data, allowing a more comprehensive characterization of the biochemical properties not only of ancient DNA but also of cell-free DNA from human blood plasma, a clinically relevant marker for the diagnosis and monitoring of disease.}, }
@article {pmid32960653, year = {2020}, author = {Orlando, L}, title = {The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics.}, journal = {Annual review of genetics}, volume = {54}, number = {}, pages = {563-581}, doi = {10.1146/annurev-genet-021920-011805}, pmid = {32960653}, issn = {1545-2948}, mesh = {Animals ; Biological Evolution ; DNA, Ancient ; Domestication ; Genome/*genetics ; Genomics/methods ; Horses/*genetics ; Humans ; }, abstract = {The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.}, }
@article {pmid32958830, year = {2020}, author = {Ermakova, GV and Kucheryavyy, AV and Zaraisky, AG and Bayramov, AV}, title = {Publisher Correction: Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {532}, doi = {10.1038/s42003-020-01272-x}, pmid = {32958830}, issn = {2399-3642}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32957467, year = {2020}, author = {Recht, J and Schuenemann, VJ and Sánchez-Villagra, MR}, title = {Host Diversity and Origin of Zoonoses: The Ancient and the New.}, journal = {Animals : an open access journal from MDPI}, volume = {10}, number = {9}, pages = {}, pmid = {32957467}, issn = {2076-2615}, support = {31003A_149605/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {Bacterial, viral, and parasitic zoonotic diseases are transmitted to humans from a wide variety of animal species that act as reservoir hosts for the causative organisms. Zoonoses contribute an estimated 75% of new or reemerging infectious diseases in humans. All groups of mammals have been shown to act as hosts for transmission of different organisms that cause zoonoses, followed in importance by birds; with both wild and domestic species identified as hosts in specific cases. There has been considerable research progress leading to a better understanding of the host range, animal origin, evolution, and transmission of important zoonoses, including those caused by the ingestion of food and products derived from animals. Paleopathology studies of ancient human bone lesions, in combination with ancient DNA analysis of the causative pathogen, have contributed to our understanding of the origin of zoonotic diseases, including brucellosis and mycobacterial zoonoses. However, there are still knowledge gaps and new confirmed and potential hosts are reported locally with some frequency. Both the economic cost and burden of disease of zoonoses are substantial at local and global levels, as reflected by recent coronavirus pandemics that spread rapidly around the world. Evidence-based prevention strategies are currently a global priority increasingly recognized, especially in zoonoses-affected regions.}, }
@article {pmid32953046, year = {2020}, author = {Røed, KH and Kvie, KS and Losey, RJ and Kosintsev, PA and Hufthammer, AK and Dwyer, MJ and Goncharov, V and Klokov, KB and Arzyutov, DV and Plekhanov, A and Anderson, DG}, title = {Temporal and structural genetic variation in reindeer (Rangifer tarandus) associated with the pastoral transition in Northwestern Siberia.}, journal = {Ecology and evolution}, volume = {10}, number = {17}, pages = {9060-9072}, pmid = {32953046}, issn = {2045-7758}, abstract = {Just as the domestication of livestock is often cited as a key element in the Neolithic transition to settled, the emergence of large-scaled reindeer husbandry was a fundamental social transformation for the indigenous peoples of Arctic Eurasia. To better understand the history of reindeer domestication, and the genetic processes associated with the pastoral transition in the Eurasian Arctic, we analyzed archaeological and contemporary reindeer samples from Northwestern Siberia. The material represents Rangifer genealogies spanning from 15,000 years ago to the 18th century, as well as modern samples from the wild Taĭmyr population and from domestic herds managed by Nenetses. The wild and the domestic population are the largest populations of their kind in Northern Eurasia, and some Nenetses hold their domestic reindeer beside their wild cousins. Our analyses of 197 modern and 223 ancient mitochondrial DNA sequences revealed two genetic clusters, which are interpreted as representing the gene pools of contemporary domestic and past wild reindeer. Among a total of 137 different mitochondrial haplotypes identified in both the modern and archaeological samples, only 21 were detected in the modern domestic gene pool, while 11 of these were absent from the wild gene pool. The significant temporal genetic shift that we associate with the pastoral transition suggests that the emergence and spread of reindeer pastoralism in Northwestern Siberia originated with the translocation and subsequent selective breeding of a special type of animal from outside the region. The distinct and persistent domestic characteristics of the haplotype structure since the 18th century suggests little genetic exchange since then. The absence of the typical domestic clade in modern nearby wild populations suggests that the contemporary Nenets domestic breed feature an ancestry from outside its present main distribution, possibly from further South.}, }
@article {pmid32943505, year = {2020}, author = {Curry, A}, title = {Ancient DNA tracks Vikings across Europe.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6510}, pages = {1416-1417}, doi = {10.1126/science.369.6510.1416}, pmid = {32943505}, issn = {1095-9203}, mesh = {*DNA, Ancient ; History, Ancient ; Human Migration/*history ; Humans ; Scandinavian and Nordic Countries/ethnology ; Skeleton ; }, }
@article {pmid32943086, year = {2020}, author = {Martiniano, R and Garrison, E and Jones, ER and Manica, A and Durbin, R}, title = {Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {250}, pmid = {32943086}, issn = {1474-760X}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; WT207492/WT_/Wellcome Trust/United Kingdom ; WT206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {DNA, Ancient/*analysis ; *Genome, Human ; Humans ; *INDEL Mutation ; Reference Standards ; Sequence Analysis, DNA/*methods/standards ; }, abstract = {BACKGROUND: During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for aDNA and compare with existing methods.<br><br>RESULTS: We use vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants and compare with the same data aligned with bwa to the human linear reference genome. Using vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias but can have lower sensitivity than vg, particularly for indels.<br><br>CONCLUSIONS: Our findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analyzing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.}, }
@article {pmid32939074, year = {2020}, author = {Gibbon, VE}, title = {African ancient DNA research requires robust ethics and permission protocols.}, journal = {Nature reviews. Genetics}, volume = {21}, number = {11}, pages = {645-647}, pmid = {32939074}, issn = {1471-0064}, mesh = {Africa ; Archaeology/*ethics ; Body Remains ; *DNA, Ancient ; Genetic Research/*ethics ; Genomics/*ethics ; Humans ; Informed Consent ; }, }
@article {pmid32939067, year = {2020}, author = {Margaryan, A and Lawson, DJ and Sikora, M and Racimo, F and Rasmussen, S and Moltke, I and Cassidy, LM and Jørsboe, E and Ingason, A and Pedersen, MW and Korneliussen, T and Wilhelmson, H and Buś, MM and de Barros Damgaard, P and Martiniano, R and Renaud, G and Bhérer, C and Moreno-Mayar, JV and Fotakis, AK and Allen, M and Allmäe, R and Molak, M and Cappellini, E and Scorrano, G and McColl, H and Buzhilova, A and Fox, A and Albrechtsen, A and Schütz, B and Skar, B and Arcini, C and Falys, C and Jonson, CH and Błaszczyk, D and Pezhemsky, D and Turner-Walker, G and Gestsdóttir, H and Lundstrøm, I and Gustin, I and Mainland, I and Potekhina, I and Muntoni, IM and Cheng, J and Stenderup, J and Ma, J and Gibson, J and Peets, J and Gustafsson, J and Iversen, KH and Simpson, L and Strand, L and Loe, L and Sikora, M and Florek, M and Vretemark, M and Redknap, M and Bajka, M and Pushkina, T and Søvsø, M and Grigoreva, N and Christensen, T and Kastholm, O and Uldum, O and Favia, P and Holck, P and Sten, S and Arge, SV and Ellingvåg, S and Moiseyev, V and Bogdanowicz, W and Magnusson, Y and Orlando, L and Pentz, P and Jessen, MD and Pedersen, A and Collard, M and Bradley, DG and Jørkov, ML and Arneborg, J and Lynnerup, N and Price, N and Gilbert, MTP and Allentoft, ME and Bill, J and Sindbæk, SM and Hedeager, L and Kristiansen, K and Nielsen, R and Werge, T and Willerslev, E}, title = {Population genomics of the Viking world.}, journal = {Nature}, volume = {585}, number = {7825}, pages = {390-396}, pmid = {32939067}, issn = {1476-4687}, mesh = {Alleles ; Datasets as Topic ; England ; Evolution, Molecular ; Gene Flow/*genetics ; *Genetics, Population ; Genome, Human/*genetics ; *Genomics ; Greenland ; History, Medieval ; Human Migration/*history ; Humans ; Immunity/genetics ; Ireland ; Lactase/genetics/metabolism ; Male ; Scandinavian and Nordic Countries ; Selection, Genetic ; Spatio-Temporal Analysis ; Young Adult ; }, abstract = {The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history[1,2]. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.}, }
@article {pmid32938925, year = {2020}, author = {François, O and Jay, F}, title = {Factor analysis of ancient population genomic samples.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4661}, pmid = {32938925}, issn = {2041-1723}, mesh = {Algorithms ; DNA, Ancient/*analysis ; England ; Europe ; *Factor Analysis, Statistical ; Gene Frequency ; Genetic Drift ; Genetics, Population/statistics &amp; numerical data ; *Genome, Human ; Humans ; Metagenomics/*statistics &amp; numerical data ; Models, Genetic ; Principal Component Analysis ; }, abstract = {The recent years have seen a growing number of studies investigating evolutionary questions using ancient DNA. To address these questions, one of the most frequently-used method is principal component analysis (PCA). When PCA is applied to temporal samples, the sample dates are, however, ignored during analysis, leading to imperfect representations of samples in PC plots. Here, we present a factor analysis (FA) method in which individual scores are corrected for the effect of allele frequency drift over time. We obtained exact solutions for the estimates of corrected factors, and we provided a fast algorithm for their computation. Using computer simulations and ancient European samples, we compared geometric representations obtained from FA with PCA and with ancestry estimation programs. In admixture analyses, FA estimates agreed with tree-based statistics, and they were more accurate than those obtained from PCA projections and from ancestry estimation programs. A great advantage of FA over existing approaches is to improve descriptive analyses of ancient DNA samples without requiring inclusion of outgroup or present-day samples.}, }
@article {pmid32938680, year = {2020}, author = {Guimaraes, S and Arbuckle, BS and Peters, J and Adcock, SE and Buitenhuis, H and Chazin, H and Manaseryan, N and Uerpmann, HP and Grange, T and Geigl, EM}, title = {Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age.}, journal = {Science advances}, volume = {6}, number = {38}, pages = {}, pmid = {32938680}, issn = {2375-2548}, abstract = {Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic studies. Anatolia is a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. Our paleogenetic study of pre- and protohistoric horses in Anatolia and the Caucasus, based on a diachronic sample from the early Neolithic to the Iron Age (~8000 to ~1000 BCE) that encompasses the presumed transition from wild to domestic horses (4000 to 3000 BCE), shows the rapid and large-scale introduction of domestic horses at the end of the third millennium BCE. Thus, our results argue strongly against autochthonous independent domestication of horses in Anatolia.}, }
@article {pmid32934321, year = {2020}, author = {Pawłowska, J and Wollenburg, JE and Zajączkowski, M and Pawlowski, J}, title = {Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15102}, pmid = {32934321}, issn = {2045-2322}, support = {31003A_179125/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Arctic Regions ; *Biodiversity ; DNA, Ancient/*analysis ; Evolution, Molecular ; Foraminifera/classification/*genetics/*growth &amp; development ; Fossils ; *Genetic Variation ; Genomics/*methods ; Geologic Sediments/*analysis ; Paleography ; Phylogeny ; }, abstract = {Deciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the high-throughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies.}, }
@article {pmid32933569, year = {2020}, author = {Peyrégne, S and Peter, BM}, title = {AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {246}, pmid = {32933569}, issn = {1474-760X}, support = {694707/ERC_/European Research Council/International ; }, mesh = {*DNA Contamination ; *DNA Damage ; DNA, Ancient/*analysis ; Humans ; Models, Genetic ; *Software ; }, abstract = {Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.}, }
@article {pmid32915387, year = {2020}, author = {Nores, R and Rena, V and Angeletti, SC and Demarchi, DA and Modesti, N and Fabra, M}, title = {Biological kinship in 750 year old human remains from Central Argentina with signs of interpersonal violence.}, journal = {Forensic science, medicine, and pathology}, volume = {16}, number = {4}, pages = {649-658}, doi = {10.1007/s12024-020-00296-3}, pmid = {32915387}, issn = {1556-2891}, support = {FONCyT, PICT 2015-3155//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/International ; PID 2018-79//Ministerio de Ciencia y Tecnolog&#xed;a de la Provincia de C&#xf3;rdoba/International ; }, mesh = {Argentina ; Burial ; Child ; Child, Preschool ; *Chromosomes, Human, Y ; *DNA Fingerprinting ; DNA, Mitochondrial/genetics ; Electrophoresis, Capillary ; Forensic Anthropology ; Forensic Genetics ; Haplotypes ; History, Ancient ; Humans ; Male ; *Microsatellite Repeats ; *Pedigree ; *Physical Abuse ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Rib Fractures ; Skull Fracture, Depressed ; Young Adult ; }, abstract = {Human skeletal remains of an adult male (20-24 years old) and a juvenile (4-8 years old), dated to 750 ± 85 [14]C years BP, were found on the southern margin of Mar Chiquita Lagoon (Córdoba, Argentina). Both individuals show signs of being victims of interpersonal violence, with arrowheads associated with the remains and perimortem lesions on the juvenile, as well as an unusual form of burial, with the juvenile partially overlapped with the adult. The aim of this work is to study a possible kin relationship between these two individuals through ancient DNA analysis. Biological kinship was evaluated by autosomal and Y-chromosome STR (short tandem repeat) typing, PCR-APLP for SNP determination and hypervariable region I sequencing of the mitochondrial DNA. Genetic analyses indicated that these individuals shared the same Y-chromosomal haplotype but different mitochondrial lineages. The likelihood ratio based on autosomal loci indicates that the genetic profiles of the human remains would be more likely to be that indicating a father-son bond. The paleogenetic approach combined with forensic genetic methods applied to this study allowed us to confirm a hypothesis that originated in bioarchaeological evidence. This study constitutes a unique case in Argentina of kinship determination based on DNA profiles of human remains in an archaeological context of interpersonal violence. It is important to highlight the contribution made by these studies to address topics usually hidden in bioarchaeological studies, such as community organization, cultural customs and mortuary practices.}, }
@article {pmid32913324, year = {2020}, author = {Ermakova, GV and Kucheryavyy, AV and Zaraisky, AG and Bayramov, AV}, title = {Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {501}, pmid = {32913324}, issn = {2399-3642}, mesh = {Animals ; Carrier Proteins/*genetics ; *Evolution, Molecular ; Gene Duplication/genetics ; Gene Expression Regulation, Developmental/genetics ; Genome/*genetics ; Lampreys/*genetics ; Phylogeny ; }, abstract = {The secreted protein Noggin1 was the first discovered natural embryonic inducer produced by cells of the Spemann organizer. Thereafter, it was shown that vertebrates have a whole family of Noggin genes with different expression patterns and functional properties. For example, Noggin1 and Noggin2 inhibit the activity of BMP, Nodal/Activin and Wnt-beta-catenin signalling, while Noggin4 cannot suppress BMP but specifically modulates Wnt signalling. In this work, we described and investigated phylogeny and expression patterns of four Noggin genes in lampreys, which represent the most basally divergent group of extant vertebrates, the cyclostomes, belonging to the superclass Agnatha. Assuming that lampreys have Noggin homologues in all representatives of another superclass of vertebrates, the Gnathostomata, we propose a model for Noggin family evolution in vertebrates. This model is in agreement with the hypotheses suggesting two rounds of genome duplication in the ancestor of vertebrates before the divergence of Agnatha and Gnathostomata.}, }
@article {pmid32901061, year = {2020}, author = {Picin, A and Hajdinjak, M and Nowaczewska, W and Benazzi, S and Urbanowski, M and Marciszak, A and Fewlass, H and Bosch, MD and Socha, P and Stefaniak, K and Żarski, M and Wiśniewski, A and Hublin, JJ and Nadachowski, A and Talamo, S}, title = {New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14778}, pmid = {32901061}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; *Caves ; DNA, Mitochondrial/*analysis/genetics ; *Fossils ; Humans ; Neanderthals/classification/*genetics ; Phylogeny ; Poland ; Radiometric Dating ; Sequence Analysis, DNA ; Tooth/*anatomy &amp; histology/physiology ; }, abstract = {The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.}, }
@article {pmid32898493, year = {2020}, author = {Ringbauer, H and Steinrücken, M and Fehren-Schmitz, L and Reich, D}, title = {Increased rate of close-kin unions in the central Andes in the half millennium before European contact.}, journal = {Current biology : CB}, volume = {30}, number = {17}, pages = {R980-R981}, pmid = {32898493}, issn = {1879-0445}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {DNA, Ancient/*analysis ; History, Ancient ; History, Medieval ; Humans ; Inbreeding/*history/*methods ; *Reproduction ; South America ; }, abstract = {Analyzing ancient DNA of the central Andes, Ringbauer and colleagues identify a markedly elevated rate of unions of closely related parents after ca. 1000 CE. This change of mating preferences sheds new light on a unique system of social organization based on ancestry ("ayllu") whereby within-group unions were preferred to facilitate sharing of resources.}, }
@article {pmid32895707, year = {2020}, author = {Duchene, S and Lemey, P and Stadler, T and Ho, SYW and Duchene, DA and Dhanasekaran, V and Baele, G}, title = {Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations.}, journal = {Molecular biology and evolution}, volume = {37}, number = {11}, pages = {3363-3379}, doi = {10.1093/molbev/msaa163}, pmid = {32895707}, issn = {1537-1719}, support = {HHSN272201400006C/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Bayes Theorem ; Bordetella pertussis/genetics ; Computer Simulation ; Coronavirus/genetics ; Dogs ; *Evolution, Molecular ; Hepatitis B virus/genetics ; Influenza A Virus, H1N1 Subtype/genetics ; *Models, Genetic ; }, abstract = {Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here, we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) sampling times, and a model in which the samples are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behavior of this classification in analyses of five empirical data sets: modern samples of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus, and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.}, }
@article {pmid32888333, year = {2020}, author = {Eerkens, JW and Ryder, A and Evoy, A and Hull, B}, title = {Hydrogen isotopes in serial hair samples record season of death in a mummified child from 19th century San Francisco, CA.}, journal = {American journal of physical anthropology}, volume = {173}, number = {3}, pages = {606-614}, doi = {10.1002/ajpa.24137}, pmid = {32888333}, issn = {1096-8644}, mesh = {Child, Preschool ; Deuterium/*analysis ; Female ; Forensic Anthropology/*methods ; Hair/*chemistry ; Humans ; Keratins/chemistry ; Mummies ; San Francisco ; *Seasons ; }, abstract = {BACKGROUND: The mummified body of a small child was found in a sealed Barstow cast iron casket during construction activity in San Francisco in 2016. Using historical records and ancient DNA the child was determined to be Edith H. Cook. She was born 28 November, 1873 in the city of San Francisco, and died of "marasmus" on 13 October, 1876 also in San Francisco.<br><br>AIMS: Currently, there are few techniques for estimating human season of death in archaeological cases. Hydrogen isotope ratios (&#x3b4;2H) in hair keratin is known to strongly correlate with drinking water. We explore &#x3b4;2H in serial hair samples as a potential technique to estimate season of death by comparing the &#x3b4;2H record from hair to the known date of death.<br><br>MATERIALS &amp; METHODS: Approximately 50 hairs were removed from the scalp, aligned from the root, and cut into 5cm serial sections, each representing approximately 2 weeks of growth, and the total sequence a total of 1 year of growth. &#x3b4;2H was measured on each 5cm segment and compared to previously-reported &#x3b4;13C, &#x3b4;15N, and &#x3b4;34S values.<br><br>RESULTS: &#x3b4;2H in the serial hair samples ranged between -56&#x2030; and -48&#x2030;, consistent with her water values recorded in surface waters from San Francisco, and follow a sinusoidal pattern. Decreasing &#x3b4;2H in terminal samples before death suggest Fall as the season of death, consistent with the known date of death.<br><br>DISCUSSION: This test case shows that archaeological hair preserves a seasonal signature in the form of changing keratin &#x3b4;2H values that correlate to changing &#x3b4;2H in surface drinking water. Terminal values in root record water ingested during the final week(s) before death.<br><br>CONCLUSIONS: We argue that this technique can be used to estimate season of death in future archaeological or forensic cases where hair has been preserved but date of death is unknown.}, }
@article {pmid32879432, year = {2020}, author = {Lord, E and Collins, C and deFrance, S and LeFebvre, MJ and Pigière, F and Eeckhout, P and Erauw, C and Fitzpatrick, SM and Healy, PF and Martínez-Polanco, MF and Garcia, JL and Ramos Roca, E and Delgado, M and Sánchez Urriago, A and Peña Léon, GA and Toyne, JM and Dahlstedt, A and Moore, KM and Laguer Diaz, C and Zori, C and Matisoo-Smith, E}, title = {Author Correction: Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14783}, doi = {10.1038/s41598-020-71841-x}, pmid = {32879432}, issn = {2045-2322}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32863518, year = {2020}, author = {Pfeiffer, S}, title = {Disease as a Factor in the African Archaeological Record.}, journal = {The African archaeological review}, volume = {37}, number = {3}, pages = {487-490}, pmid = {32863518}, issn = {0263-0338}, abstract = {It is clear from their natural histories that various kinds of diseases would have affected African communities in the distant past. Climatic factors may have reduced the impact of plague-like epidemics across much of the continent. Because of the link between environment and disease vectors, the presence of a disease may have been a stimulus for some group movements in the African past. Evidence of the direct effects of diseases on human populations is generally elusive. Paleopathologists can identify some endemic diseases, but evidence from Africa is sparse. Paleogenomics research can also identify some (not all) endemic and epidemic disease vectors. Recent African aDNA discoveries of inherited resistance to endemic diseases suggest that future paleogenomic research may help us learn much more about the impact of diseases on the African past.}, }
@article {pmid32859198, year = {2020}, author = {Neukamm, J and Pfrengle, S and Molak, M and Seitz, A and Francken, M and Eppenberger, P and Avanzi, C and Reiter, E and Urban, C and Welte, B and Stockhammer, PW and Teßmann, B and Herbig, A and Harvati, K and Nieselt, K and Krause, J and Schuenemann, VJ}, title = {2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {108}, pmid = {32859198}, issn = {1741-7007}, support = {845479//the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie/International ; ALTF 1086-2018//European Molecular Biology Organization (EMBO) long-term fellowship/International ; }, mesh = {DNA, Ancient/analysis ; Egypt ; *Genome, Bacterial ; *Genome, Viral ; Hepatitis B virus/*genetics ; Humans ; Metagenomics ; Microbiota ; Mummies/*microbiology/virology ; Mycobacterium leprae/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging.<br><br>RESULTS: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed.<br><br>CONCLUSIONS: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.}, }
@article {pmid32828254, year = {2020}, author = {Hofreiter, M and Hartmann, S}, title = {Reconstructing protein-coding sequences from ancient DNA.}, journal = {Methods in enzymology}, volume = {642}, number = {}, pages = {21-33}, doi = {10.1016/bs.mie.2020.05.008}, pmid = {32828254}, issn = {1557-7988}, mesh = {Base Sequence ; *DNA, Ancient ; *Fossils ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including miscoding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.}, }
@article {pmid32826299, year = {2020}, author = {He, Z and Dai, X and Beaumont, M and Yu, F}, title = {Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations.}, journal = {Genetics}, volume = {216}, number = {2}, pages = {521-541}, pmid = {32826299}, issn = {1943-2631}, mesh = {Animals ; Bayes Theorem ; DNA, Ancient ; Diploidy ; *Gene Frequency ; *Genetic Linkage ; Genetic Loci ; Horses/genetics ; Likelihood Functions ; Markov Chains ; *Models, Genetic ; *Selection, Genetic ; Skin Pigmentation/genetics ; }, abstract = {Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modeling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses.}, }
@article {pmid32815536, year = {2020}, author = {Pratas, D and Toppinen, M and Pyöriä, L and Hedman, K and Sajantila, A and Perdomo, MF}, title = {A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level.}, journal = {GigaScience}, volume = {9}, number = {8}, pages = {}, pmid = {32815536}, issn = {2047-217X}, mesh = {Base Sequence ; *Genome, Viral ; Genomics ; Humans ; Sequence Alignment ; *Software ; }, abstract = {BACKGROUND: Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data.<br><br>FINDINGS: TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs.<br><br>CONCLUSIONS: TRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.}, }
@article {pmid32811443, year = {2020}, author = {Woods, R and Turvey, ST and Brace, S and McCabe, CV and Dalén, L and Rayfield, EJ and Brown, MJF and Barnes, I}, title = {Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean "island-shrews".}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {106}, pmid = {32811443}, issn = {1471-2148}, support = {NE/L501803/1//Natural Environment Research Council/International ; BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Body Size ; DNA, Ancient/analysis ; *Fossils ; Phylogeny ; Shrews/*classification ; West Indies ; }, abstract = {BACKGROUND: The Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region's Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae ("island-shrews") became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history of Nesophontes species from Hispaniola, the second-largest Caribbean island.<br><br>RESULTS: Principal component analysis of 65 Nesophontes mandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated Hispaniolan Nesophontes species. We were also able to extract and sequence ancient DNA from a&#x2009;~&#x2009;750-year-old specimen of Nesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes. Nesophontes paramicrus (39-47&#x2009;g) and N. zamicrus (~&#x2009;10&#x2009;g) diverged recently during the Middle Pleistocene (mean estimated divergence&#x2009;=&#x2009;0.699&#x2009;Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values for N. paramicrus and N. zamicrus based on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs.<br><br>CONCLUSIONS: Our combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in Hispaniolan Nesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola's extant non-volant land mammals. Different components of Hispaniola's mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution in Nesophontes is also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.}, }
@article {pmid32795443, year = {2020}, author = {Majander, K and Pfrengle, S and Kocher, A and Neukamm, J and du Plessis, L and Pla-Díaz, M and Arora, N and Akgül, G and Salo, K and Schats, R and Inskip, S and Oinonen, M and Valk, H and Malve, M and Kriiska, A and Onkamo, P and González-Candelas, F and Kühnert, D and Krause, J and Schuenemann, VJ}, title = {Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {3788-3803.e10}, doi = {10.1016/j.cub.2020.07.058}, pmid = {32795443}, issn = {1879-0445}, mesh = {Archaeology ; DNA, Ancient/*analysis ; Europe ; Genetic Variation/genetics ; Genome, Bacterial/*genetics ; History, 15th Century ; History, Medieval ; Humans ; Syphilis/genetics/history/microbiology ; Treponema pallidum/*genetics/metabolism ; Yaws/genetics/history/microbiology ; }, abstract = {Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15[th] century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.}, }
@article {pmid32795436, year = {2020}, author = {Lord, E and Dussex, N and Kierczak, M and Díez-Del-Molino, D and Ryder, OA and Stanton, DWG and Gilbert, MTP and Sánchez-Barreiro, F and Zhang, G and Sinding, MS and Lorenzen, ED and Willerslev, E and Protopopov, A and Shidlovskiy, F and Fedorov, S and Bocherens, H and Nathan, SKSS and Goossens, B and van der Plicht, J and Chan, YL and Prost, S and Potapova, O and Kirillova, I and Lister, AM and Heintzman, PD and Kapp, JD and Shapiro, B and Vartanyan, S and Götherström, A and Dalén, L}, title = {Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {3871-3879.e7}, doi = {10.1016/j.cub.2020.07.046}, pmid = {32795436}, issn = {1879-0445}, mesh = {Animals ; Archaeology/*methods ; Climate Change ; DNA, Ancient/*analysis ; Extinction, Biological ; Fossils ; Genome/genetics ; Genomics/methods ; Perissodactyla/*genetics ; Population Density ; Population Dynamics ; }, abstract = {Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.}, }
@article {pmid32788984, year = {2020}, author = {Ford, BM and Cornellas, A and Leonard, JA and Weir, RD and Russello, MA}, title = {Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation.}, journal = {Ecology and evolution}, volume = {10}, number = {15}, pages = {8345-8357}, pmid = {32788984}, issn = {2045-7758}, abstract = {Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The "southerly refugia model" has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star-like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice-free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range-wide patterns and identifies unique genetic units that can likely be used to inform conservation of at-risk populations at the northern periphery.}, }
@article {pmid32778142, year = {2020}, author = {Nakatsuka, N and Harney, &#xc9; and Mallick, S and Mah, M and Patterson, N and Reich, D}, title = {ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {199}, pmid = {32778142}, issn = {1474-760X}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; HG006399/NH/NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; GM007753/GM/NIGMS NIH HHS/United States ; GM100233/NH/NIH HHS/United States ; }, mesh = {*DNA Contamination ; DNA, Ancient/*analysis ; Haplotypes ; *Linkage Disequilibrium ; *Software ; }, abstract = {We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000 sequences covering SNPs. This method is optimized for application to aDNA, taking advantage of characteristic aDNA damage patterns to provide calibrated contamination estimates, and is available at https://github.com/nathan-nakatsuka/ContamLD .}, }
@article {pmid32778135, year = {2020}, author = {Sabin, S and Herbig, A and Vågene, &#xc5;J and Ahlström, T and Bozovic, G and Arcini, C and Kühnert, D and Bos, KI}, title = {A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {201}, pmid = {32778135}, issn = {1474-760X}, mesh = {Africa ; Bayes Theorem ; *Genome, Bacterial ; History, 17th Century ; Humans ; Lung ; Metagenomics ; Mycobacterium tuberculosis/classification/*genetics ; Phylogeny ; Phylogeography ; Tuberculosis/history/microbiology ; }, abstract = {BACKGROUND: Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679).<br><br>RESULTS: A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent.<br><br>CONCLUSIONS: The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.}, }
@article {pmid32769100, year = {2020}, author = {He, Z and Dai, X and Beaumont, M and Yu, F}, title = {Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach.}, journal = {Genetics}, volume = {216}, number = {2}, pages = {463-480}, pmid = {32769100}, issn = {1943-2631}, mesh = {Animals ; DNA, Ancient ; Diploidy ; *Gene Frequency ; Humans ; Likelihood Functions ; Markov Chains ; *Models, Genetic ; *Selection, Genetic ; }, abstract = {Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process is a Wright-Fisher diffusion conditioned to survive until the time of the most recent sample. This formulation circumvents the assumption required in existing methods that the allele is created by mutation at a certain low frequency. We calculate the likelihood by numerically solving the resulting Kolmogorov backward equation backward in time while reweighting the solution with the emission probabilities of the observation at each sampling time point. This procedure reduces the two-dimensional numerical search for the maximum of the likelihood surface, for both the selection coefficient and the allele age, to a one-dimensional search over the selection coefficient only. We illustrate through extensive simulations that our method can produce accurate estimates of the selection coefficient and the allele age under both constant and nonconstant demographic histories. We apply our approach to reanalyze ancient DNA data associated with horse base coat colors. We find that ignoring demographic histories or grouping raw samples can significantly bias the inference results.}, }
@article {pmid32767894, year = {2020}, author = {Parolin, ML and Cortés, LI and Basso, N and Scattolin, MC}, title = {New Evidence of Ancient Mitochondrial DNA of the Southern Andes (Calchaquí Valleys, Northwest Argentina, 3,600-1,900 Years before Present).}, journal = {Human biology}, volume = {91}, number = {4}, pages = {225-247}, doi = {10.13110/humanbiology.91.4.02}, pmid = {32767894}, issn = {1534-6617}, mesh = {Adult ; Archaeology ; Argentina/epidemiology ; Child ; Child, Preschool ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics/history ; Female ; Genetic Variation ; Haplotypes/*genetics ; History, Ancient ; Humans ; Indians, South American/genetics ; Male ; Middle Aged ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Genetic studies on pre-Hispanic populations of the Southern Andes have been increasing steadily in the last decade. Nevertheless, ancient DNA characterization of Formative Period archaeological human remains is particularly scant, especially for Northwest Argentina. To expand current information on genetic characterization of the first agricultural communities of the southern Calchaquí Valleys, we present and discuss the first mitochondrial ancient DNA information obtained on samples dated to ca. 3,600-1,900 years before present from the Cajón Valley, Catamarca Province. Reproducible mtDNA hypervariable region 1 (HVR-1) sequences were obtained in seven individuals. Mitochondrial HVR-1 haplotypes were assigned to three of the four founding haplogroups, D1 (57.1%), C1 (28.5%), and B2 (14.2%), with absence of A2. Our results show that the Cajón Valley sample, with predominance of D1 and C1, differs from that commonly observed in ancient and modern Andean populations, which usually show a high prevalence of haplogroup B2. The fact that the Cajón Valley and Pampa Grande (Salta Province, Argentina) share a prevalence of haplogroup D1 could provide additional evidence to support possible genetic affinities between the valleys and the eastern sub-Andean region during the Formative Period in Northwest Argentina, expanding the archaeological evidence of contact between both populations. Future complete mitogenomic analysis will provide substantial information to formulate new hypotheses about the origins and phylogenetic relationships between the individuals of the Cajón Valley and other groups from the Andes, Gran Chaco, and the Amazon.}, }
@article {pmid32763189, year = {2020}, author = {Wagner, JK and Colwell, C and Claw, KG and Stone, AC and Bolnick, DA and Hawks, J and Brothers, KB and Garrison, NA}, title = {Fostering Responsible Research on Ancient DNA.}, journal = {American journal of human genetics}, volume = {107}, number = {2}, pages = {183-195}, pmid = {32763189}, issn = {1537-6605}, support = {K01 HG008818/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient/*analysis ; Foster Home Care ; Humans ; }, abstract = {Anticipating and addressing the social implications of scientific work is a fundamental responsibility of all scientists. However, expectations for ethically sound practices can evolve over time as the implications of science come to be better understood. Contemporary researchers who work with ancient human remains, including those who conduct ancient DNA research, face precisely this challenge as it becomes clear that practices such as community engagement are needed to address the important social implications of this work. To foster and promote ethical engagement between researchers and communities, we offer five practical recommendations for ancient DNA researchers: (1) formally consult with communities; (2) address cultural and ethical considerations; (3) engage communities and support capacity building; (4) develop plans to report results and manage data; and (5) develop plans for long-term responsibility and stewardship. Ultimately, every member of a research team has an important role in fostering ethical research on ancient DNA.}, }
@article {pmid32760427, year = {2020}, author = {Barrera-Redondo, J and Piñero, D and Eguiarte, LE}, title = {Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {742}, pmid = {32760427}, issn = {1664-8021}, abstract = {In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.}, }
@article {pmid32747648, year = {2020}, author = {Nakatsuka, N and Luisi, P and Motti, JMB and Salemme, M and Santiago, F and D'Angelo Del Campo, MD and Vecchi, RJ and Espinosa-Parrilla, Y and Prieto, A and Adamski, N and Lawson, AM and Harper, TK and Culleton, BJ and Kennett, DJ and Lalueza-Fox, C and Mallick, S and Rohland, N and Guichón, RA and Cabana, GS and Nores, R and Reich, D}, title = {Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3868}, pmid = {32747648}, issn = {2041-1723}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Archaeology/methods ; Argentina ; Bone and Bones/metabolism ; Chile ; DNA, Ancient/*analysis ; DNA, Mitochondrial/classification/genetics ; *Fossils ; *Gene Flow ; Genetic Variation ; Genome, Human/*genetics ; Geography ; *Human Migration ; Humans ; Phylogeny ; Radiometric Dating/methods ; Sequence Analysis, DNA/methods ; Tooth/metabolism ; }, abstract = {Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.}, }
@article {pmid32745952, year = {2020}, author = {Mathieson, I}, title = {Human adaptation over the past 40,000 years.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {97-104}, pmid = {32745952}, issn = {1879-0380}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; DNA, Ancient/*analysis ; *Evolution, Molecular ; Genomics/*history ; History, Ancient ; Humans ; *Multifactorial Inheritance ; Phenotype ; *Selection, Genetic ; }, abstract = {Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits.}, }
@article {pmid32743069, year = {2020}, author = {Shillito, LM and Whelton, HL and Blong, JC and Jenkins, DL and Connolly, TJ and Bull, ID}, title = {Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon.}, journal = {Science advances}, volume = {6}, number = {29}, pages = {eaba6404}, pmid = {32743069}, issn = {2375-2548}, abstract = {When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.}, }
@article {pmid32721847, year = {2020}, author = {Tsosie, KS and Begay, RL and Fox, K and Garrison, NA}, title = {Generations of genomes: advances in paleogenomics technology and engagement for Indigenous people of the Americas.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {91-96}, pmid = {32721847}, issn = {1879-0380}, support = {K01 HG008818/HG/NHGRI NIH HHS/United States ; P20 GM103442/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genome, Human ; Genomics/*methods ; *Human Migration ; Humans ; Indigenous Peoples/*genetics ; *Paleontology ; Population Groups/*genetics ; United States ; }, abstract = {For decades, scientists have collected genomic information from Indigenous peoples and their ancestors with the goal of elucidating human migration events, understanding ancestral origins, and identifying ancestral variants contributing to disease. However, such studies may not have offered much benefit to the Indigenous groups who contributed DNA, and many have instead perpetuated stereotypes and other harms. With recent advances in genomic technology facilitating the study of both ancient and present-day DNA, researchers and Indigenous communities have new opportunities to begin collaboratively addressing important questions about human health and history. Yet, while there are increased efforts to ethically engage Indigenous communities, more work is still needed as the discipline struggles to absolve itself of the racialized science and extractive biocolonialism that defined its past.}, }
@article {pmid32696095, year = {2020}, author = {Peeters, S and Zwart, H}, title = {Neanderthals as familiar strangers and the human spark: How the 'golden years' of Neanderthal research reopen the question of human uniqueness.}, journal = {History and philosophy of the life sciences}, volume = {42}, number = {3}, pages = {33}, pmid = {32696095}, issn = {1742-6316}, mesh = {Animals ; *Biological Evolution ; Humans ; Neanderthals/*psychology ; }, abstract = {During the past decades, our image of Homo neanderthalensis has changed dramatically. Initially, Neanderthals were seen as primitive brutes. Increasingly, however, Neanderthals are regarded as basically human. New discoveries and technologies have led to an avalanche of data, and as a result of that it becomes increasingly difficult to pinpoint what the difference between modern humans and Neanderthals really is. And yet, the persistent quest for a minimal difference which separates them from us is still noticeable in Neanderthal research. Neanderthal discourse is a vantage point from which the logic of 'us' versus 'other' is critically reconsidered. Studying contemporary academic literature and science autobiographies from an oblique perspective, focusing not on Neanderthals as objects, but on the dynamics of interaction between Neanderthal researchers and their finds, basic convictions at work in this type of research are retrieved. What is at issue is not the actual distinction between modern humans and Neanderthals (which is continuously being redefined), but rather the dualistic construction of human and nonhuman. Neanderthal understanding is affected by the desire to safeguard human uniqueness. The overall trend is to identify the human mark or spark, which defines us as favoured 'winners'. The paradoxes emerging in contemporary Neanderthal discourse are symptomatic of the fact that a dualistic style of thinking is no longer tenable.}, }
@article {pmid32693300, year = {2020}, author = {Cao, X and Xu, X and Bian, R and Wang, Y and Yu, H and Xu, Y and Duan, G and Bi, L and Chen, P and Gao, S and Wang, J and Peng, J and Qu, J}, title = {Sedimentary ancient DNA metabarcoding delineates the contrastingly temporal change of lake cyanobacterial communities.}, journal = {Water research}, volume = {183}, number = {}, pages = {116077}, doi = {10.1016/j.watres.2020.116077}, pmid = {32693300}, issn = {1879-2448}, mesh = {Cyanobacteria/*genetics ; DNA Barcoding, Taxonomic ; DNA, Ancient ; Ecosystem ; *Lakes ; }, abstract = {Harmful cyanobacterial blooms consisting of toxic taxa can produce a wide variety of toxins to threaten water quality, ecosystem functions and services. Of greater concern was the changing patterns of cyanobacterial assemblage were not well understood due to the lack of long-term monitoring data over the temporal scale. Biodiversity change in cyanobacterial community and paleoenvironmental variables over the past 170 years in Lake Chenghai were investigated based on sedimentary ancient DNA metabarcoding and traditional paleolimnological analysis. The results showed species richness and homogenization of cyanobacterial assemblage increased in the most recent decades, which were synchronized with the growth of artificial fertilization and decline in precipitation. Cyanobacterial co-occurrence network analysis revealed more complex interactions and weak community stability after the change point of ∼1987, while the rare cyanobacterial genera such as Anabaena, Planktothrix, Oscillatoria and Microcystis were identified to be keystone taxa affecting cyanobacterial assemblage. Furthermore, an increase of toxin-producing cyanobacterial taxa was significantly and positively associated with TN and TP, as well as TN/IP and TN/TP, which was verified by quantitative real-time PCR of mcyA and rpoC1 genes. Threshold in total nitrogen (TN) concentration should be targeted no more than 0.60 mg/L to alleviate nuisance cyanobacterial blooms in Lake Chenghai. These findings reinforce the comprehensive understanding for the long-term dynamics of cyanobacterial assemblage responding to environmental change, which could contribute to proactively regulate environmental conditions for avoiding undesirable ecological consequences.}, }
@article {pmid32688244, year = {2020}, author = {Zhang, M and Fu, Q}, title = {Human evolutionary history in Eastern Eurasia using insights from ancient DNA.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {78-84}, doi = {10.1016/j.gde.2020.06.009}, pmid = {32688244}, issn = {1879-0380}, support = {55008731/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Archaeology ; Asian People/*genetics ; *Biological Evolution ; DNA, Ancient/*analysis ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; }, abstract = {Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia-some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia.}, }
@article {pmid32684155, year = {2020}, author = {Duggan, AT and Klunk, J and Porter, AF and Dhody, AN and Hicks, R and Smith, GL and Humphreys, M and McCollum, AM and Davidson, WB and Wilkins, K and Li, Y and Burke, A and Polasky, H and Flanders, L and Poinar, D and Raphenya, AR and Lau, TTY and Alcock, B and McArthur, AG and Golding, GB and Holmes, EC and Poinar, HN}, title = {The origins and genomic diversity of American Civil War Era smallpox vaccine strains.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {175}, pmid = {32684155}, issn = {1474-760X}, support = {/WT_/Wellcome Trust/United Kingdom ; PJT-156214//CIHR/Canada ; }, mesh = {American Civil War ; Genetic Variation ; *Genome, Viral ; History, 19th Century ; Humans ; Metagenome ; Smallpox Vaccine/*history ; Vaccination/instrumentation ; Vaccinia virus/*genetics ; }, abstract = {Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.}, }
@article {pmid32682389, year = {2020}, author = {Sheng, G and Hu, J and Tong, H and Llamas, B and Yuan, J and Hou, X and Chen, S and Xiao, B and Lai, X}, title = {Ancient DNA of northern China Hystricidae sub-fossils reveals the evolutionary history of old world porcupines in the Late Pleistocene.}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {88}, pmid = {32682389}, issn = {1471-2148}, support = {41672017//National Natural Science Foundation of China/International ; }, mesh = {Animals ; *Biological Evolution ; China ; *DNA, Ancient ; *Fossils ; Geography ; Likelihood Functions ; Phylogeny ; Porcupines/*anatomy &amp; histology/*genetics ; RNA, Ribosomal/genetics ; Species Specificity ; Time Factors ; }, abstract = {BACKGROUND: Old World porcupines (Family: Hystricidae) are the third-largest rodents and inhabit southern Europe, Asia, and most regions of Africa. They are a typical indicator of warm climate and their distribution is restricted to tropical and subtropical zones. In China, porcupines are widely distributed in southern areas of the Yangtze River. However, fossil remains have been identified in a few sites in northern China, among which Tianyuan Cave-near Zhoukoudian site-represents the latest known porcupine fossil record. So far, studies have focused mainly on porcupines' husbandry and domestication but little is known about their intrafamilial phylogenetic relationships and evolutionary history.<br><br>RESULTS: In this study, we sequence partial mitochondrial 12S rRNA and cyt b genes for seven Late Pleistocene porcupine individuals from Northern, Southern and Central China. Phylogenetic analyses show that the Tianyuan Cave porcupines, which had been morphologically identified as Hystrix subcristata, have a closer relationship to Hystrix brachyura.<br><br>CONCLUSION: Together with morphological adaptation characteristics, associated fauna, and climate change evidence, the molecular results reveal that a Late Quaternary extirpation has occurred during the evolutionary history of porcupines.}, }
@article {pmid32678112, year = {2020}, author = {Li, J and Zarzar, TG and White, JD and Indencleef, K and Hoskens, H and Matthews, H and Nauwelaers, N and Zaidi, A and Eller, RJ and Herrick, N and Günther, T and Svensson, EM and Jakobsson, M and Walsh, S and Van Steen, K and Shriver, MD and Claes, P}, title = {Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11850}, pmid = {32678112}, issn = {2045-2322}, support = {R01 DE027023/DE/NIDCR NIH HHS/United States ; }, mesh = {Biometric Identification/*methods ; Datasets as Topic ; Face/*anatomy &amp; histology ; Facial Recognition/physiology ; Female ; Genetics, Population/methods ; *Genome, Human ; Genome-Wide Association Study ; History, 21st Century ; History, Ancient ; Human Genetics/*methods ; Humans ; Image Processing, Computer-Assisted ; *Inheritance Patterns ; Male ; *Models, Statistical ; Racial Groups/history ; }, abstract = {Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case-control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively.}, }
@article {pmid32674620, year = {2020}, author = {Mizuno, F and Taniguchi, Y and Kondo, O and Hayashi, M and Kurosaki, K and Ueda, S}, title = {A study of 8,300-year-old Jomon human remains in Japan using complete mitogenome sequences obtained by next-generation sequencing.}, journal = {Annals of human biology}, volume = {47}, number = {6}, pages = {555-559}, doi = {10.1080/03014460.2020.1797164}, pmid = {32674620}, issn = {1464-5033}, mesh = {Archaeology ; Body Remains ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Humans ; Japan ; }, abstract = {Ancient human remains have been assigned to their mitochondrial DNA (mtDNA) haplogroups. To obtain efficiently deep and reliable nucleotide sequences of ancient DNA of interest, we achieved target enrichment followed by next-generation sequencing (NGS). Complete mitochondrial genome (mitogenome) sequences were obtained for three human remains from the Iyai rock-shelter site of the Initial Jomon Period in Japan. All the Jomon mitogenomes belong to haplogroup N9b, but no sequences among them were identical. High genetic diversity was clarified even among the Jomon human remains belonging to haplogroup N9b, which has been described as a haplogroup representing the Jomon people.}, }
@article {pmid32666166, year = {2021}, author = {Hallast, P and Agdzhoyan, A and Balanovsky, O and Xue, Y and Tyler-Smith, C}, title = {A Southeast Asian origin for present-day non-African human Y chromosomes.}, journal = {Human genetics}, volume = {140}, number = {2}, pages = {299-307}, pmid = {32666166}, issn = {1432-1203}, support = {/WT_/Wellcome Trust/United Kingdom ; PUT1036//Eesti Teadusagentuur/ ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa ; Asian People/*genetics ; Chromosomes, Human, Y/*genetics ; DNA/genetics ; Emigration and Immigration ; Genetics, Population/methods ; Genome, Human/genetics ; Haplotypes/genetics ; Humans ; Male ; Phylogeny ; Phylogeography/methods ; }, abstract = {The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000-70,000 years ago, followed by mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. Here, we show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 50,000-55,000 years ago of all known surviving non-African male lineages (apart from recent migrants). This observation contrasts with the expectation of a West Eurasian origin predicted by a simple model of expansion from a source near Africa, and can be interpreted as resulting from extensive genetic drift in the initial population or replacement of early western Y lineages from the east, thus informing and constraining models of the initial expansion.}, }
@article {pmid32664326, year = {2020}, author = {Iwasaki, RL and Ishiya, K and Kanzawa-Kiriyama, H and Kawai, Y and Gojobori, J and Satta, Y}, title = {Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population.}, journal = {Genes}, volume = {11}, number = {7}, pages = {}, pmid = {32664326}, issn = {2073-4425}, mesh = {Antigens, Neoplasm/*genetics ; *Evolution, Molecular ; GPI-Linked Proteins/genetics ; Gene Frequency ; Humans ; Japan ; Neoplasm Proteins/*genetics ; *Polymorphism, Single Nucleotide ; Population/*genetics ; Selection, Genetic ; Stomach Neoplasms/*genetics ; }, abstract = {A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese.}, }
@article {pmid32661160, year = {2020}, author = {Bongers, JL and Nakatsuka, N and O'Shea, C and Harper, TK and Tantaleán, H and Stanish, C and Fehren-Schmitz, L}, title = {Integration of ancient DNA with transdisciplinary dataset finds strong support for Inca resettlement in the south Peruvian coast.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {31}, pages = {18359-18368}, pmid = {32661160}, issn = {1091-6490}, support = {T32 GM007753/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaeology ; DNA, Ancient/*chemistry ; Hispanic or Latino ; History, Ancient ; *Human Migration ; Humans ; Indians, South American/*genetics/*history ; Peru ; }, abstract = {Ancient DNA (aDNA) analysis provides a powerful means of investigating human migration, social organization, and a plethora of other crucial questions about humanity's past. Recently, specialists have suggested that the ideal research design involving aDNA would include multiple independent lines of evidence. In this paper, we adopt a transdisciplinary approach integrating aDNA with archaeological, biogeochemical, and historical data to investigate six individuals found in two cemeteries that date to the Late Horizon (1400 to 1532 CE) and Colonial (1532 to 1825 CE) periods in the Chincha Valley of southern Peru. Genomic analyses indicate that these individuals are genetically most similar to ancient and present-day populations from the north Peruvian coast located several hundred kilometers away. These genomic data are consistent with 16th century written records as well as ceramic, textile, and isotopic data. These results provide some of the strongest evidence yet of state-sponsored resettlement in the pre-Colonial Andes. This study highlights the power of transdisciplinary research designs when using aDNA data and sets a methodological standard for investigating ancient mobility in complex societies.}, }
@article {pmid32659643, year = {2020}, author = {Mendes, M and Alvim, I and Borda, V and Tarazona-Santos, E}, title = {The history behind the mosaic of the Americas.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {72-77}, doi = {10.1016/j.gde.2020.06.007}, pmid = {32659643}, issn = {1879-0380}, mesh = {Americas ; Colombia ; DNA, Ancient/*analysis ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Haplotypes ; History, Ancient ; Human Migration/*history ; Humans ; *Mosaicism ; *Selection, Genetic ; }, abstract = {Focusing on literature published in 2018-2020, we review inferences about: (i) how ancient DNA is contributing to clarify the peopling of the Americas and the dispersal of its first inhabitants, (ii) how the interplay between environmental diversity and culture has influenced the genetic structure and adaptation of Andean and Amazon populations, (iii) how genetics has contributed to our understanding of the Pre-Columbian Tupi expansion in Eastern South America, (iv) the subcontinental origins and dynamics of Post-Columbian admixture in the Americas, and finally, (v) episodes of adaptive natural selection in the American continent, particularly in the high altitudes of the Andes.}, }
@article {pmid32653893, year = {2020}, author = {Bai, F and Zhang, X and Ji, X and Cao, P and Feng, X and Yang, R and Peng, M and Pei, S and Fu, Q}, title = {Paleolithic genetic link between Southern China and Mainland Southeast Asia revealed by ancient mitochondrial genomes.}, journal = {Journal of human genetics}, volume = {65}, number = {12}, pages = {1125-1128}, pmid = {32653893}, issn = {1435-232X}, support = {91731303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41925009//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41630102//National Natural Science Foundation of China (National Science Foundation of China)/ ; XDB26000000//Chinese Academy of Sciences (CAS)/ ; }, mesh = {Asia, Southeastern ; Asian People/*genetics ; China/epidemiology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/classification/*genetics ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; History, Ancient ; Humans ; }, abstract = {The genetic history of Southern East Asians is not well-known, especially prior to the Neolithic period. To address this, we successfully sequenced two complete mitochondrial genomes of 11,000-year-old human individuals from Southern China, thus generating the oldest ancient DNA sequences from this area. Integrating published mitochondrial genomes, we characterized M71d, a new subhaplogroup of haplogroup M71. Our results suggest a possible early migration between Southern China and mainland Southeast Asia by at least 22,000 BP.}, }
@article {pmid32650941, year = {2020}, author = {Morrison, J and McColl, S and Louhelainen, J and Sheppard, K and May, A and Girdland-Flink, L and Watts, G and Dawnay, N}, title = {Assessing the performance of quantity and quality metrics using the QIAGEN Investigator® Quantiplex® pro RGQ kit.}, journal = {Science &amp; justice : journal of the Forensic Science Society}, volume = {60}, number = {4}, pages = {388-397}, doi = {10.1016/j.scijus.2020.03.002}, pmid = {32650941}, issn = {1876-4452}, mesh = {*Benchmarking ; DNA/analysis ; *DNA Fingerprinting/methods ; Female ; Humans ; Male ; Microsatellite Repeats ; }, abstract = {The Quantiplex® Pro RGQ kit quantifies DNA in a sample, supports the detection of mixtures and assesses the extent of DNA degradation based on relative ratios of amplified autosomal and male markers. Data show no significant difference in the accuracy and sensitivity of quantification between this and the Promega PowerQuant® System, both detecting the lowest amount of DNA tested, 4 pg. Laboratory controlled mixed male:female DNA samples together with mock sexual assault samples were quantified across a range of mixture ratios. Analysis software detected mixed DNA samples across all ratios for both quantification kits. Subsequent STR analysis using the Investigator® 24Plex QS Kit was able to corroborate mixture detection down to 1:25 male:female DNA ratios, past which point mixtures appeared identical to single-source female samples. Analysis software also detected laboratory degraded DNA samples, with data showing a positive trend between the Degradation Index (DI) and length of time of sonication. When used on ancient remains the assay was able to triage samples for further analysis, and STR profiles were concordant with DNA quantification results in all instances. STR analyses of laboratory-controlled sensitivity, mixture, and degradation studies supports the quality metric obtained from quantification. These data support the use of the Quantiplex® Pro RGQ kit for sample screening and quantification in forensic casework and ancient DNA studies.}, }
@article {pmid32648350, year = {2020}, author = {Peyrégne, S and Prüfer, K}, title = {Present-Day DNA Contamination in Ancient DNA Datasets.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {9}, pages = {e2000081}, doi = {10.1002/bies.202000081}, pmid = {32648350}, issn = {1521-1878}, support = {694707/ERC_/European Research Council/International ; //Max-Planck-Gesellschaft/International ; }, mesh = {*DNA Contamination ; *DNA, Ancient ; Humans ; }, abstract = {Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.}, }
@article {pmid32642779, year = {2020}, author = {Santiago, E and Novo, I and Pardiñas, AF and Saura, M and Wang, J and Caballero, A}, title = {Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium.}, journal = {Molecular biology and evolution}, volume = {37}, number = {12}, pages = {3642-3653}, doi = {10.1093/molbev/msaa169}, pmid = {32642779}, issn = {1537-1719}, support = {MC_PC_17212/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Algorithms ; Animals ; Computer Simulation ; *Genetic Techniques ; Humans ; *Linkage Disequilibrium ; *Models, Genetic ; *Population Density ; *Recombination, Genetic ; }, abstract = {Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.}, }
@article {pmid32632332, year = {2020}, author = {Betti, L and Beyer, RM and Jones, ER and Eriksson, A and Tassi, F and Siska, V and Leonardi, M and Maisano Delser, P and Bentley, LK and Nigst, PR and Stock, JT and Pinhasi, R and Manica, A}, title = {Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE.}, journal = {Nature human behaviour}, volume = {4}, number = {10}, pages = {1004-1010}, pmid = {32632332}, issn = {2397-3374}, mesh = {Agriculture/*history ; *Climate ; *DNA, Ancient ; Europe ; History, Ancient ; Humans ; Middle East ; *Paleontology ; Population Dynamics/*history ; }, abstract = {The Neolithic transition in Europe was driven by the rapid dispersal of Near Eastern farmers who, over a period of 3,500 years, brought food production to the furthest corners of the continent. However, this wave of expansion was far from homogeneous, and climatic factors may have driven a marked slowdown observed at higher latitudes. Here, we test this hypothesis by assembling a large database of archaeological dates of first arrival of farming to quantify the expansion dynamics. We identify four axes of expansion and observe a slowdown along three axes when crossing the same climatic threshold. This threshold reflects the quality of the growing season, suggesting that Near Eastern crops might have struggled under more challenging climatic conditions. This same threshold also predicts the mixing of farmers and hunter-gatherers as estimated from ancient DNA, suggesting that unreliable yields in these regions might have favoured the contact between the two groups.}, }
@article {pmid32621020, year = {2020}, author = {Navarro-Romero, MT and Muñoz, ML and Alcala-Castañeda, E and Terreros-Espinosa, E and Domínguez-de-la-Cruz, E and García-Hernández, N and Moreno-Galeana, M&#xc1;}, title = {A novel method of male sex identification of human ancient skeletal remains.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {28}, number = {3-4}, pages = {277-291}, pmid = {32621020}, issn = {1573-6849}, mesh = {Alleles ; Amelogenin/genetics ; *Body Remains ; Chromosomes, Human, X ; Chromosomes, Human, Y/genetics ; Female ; Forensic Anthropology/*methods ; Forensic Medicine/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; }, abstract = {Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in subadult, or fragmented, incomplete skeletons or when the DNA is highly degraded. Most of the methods include the identification of the male and female sexes, but the absence of a specific marker for the males does not mean that the sample obtained was from a female. This study aims (1) to identify new male-specific regions that allow male identification; (2) to contrast the effectiveness of these markers against AMELX/AMELY and anthropometric measurement procedures; and (3) to test the efficacy of these markers in archaeological samples. For the first two aims, we used known sex samples, and for the third aim, we used samples from different archaeological sites. A novel molecular technique to identify male-specific regions by amplification of TTTY7, TSPY3, TTTY2, and TTTY22 genes of the human Y chromosome was developed. The results showed amplification of the specific DNA regions of Y chromosome in male individuals, with no amplification being observed in any of the female samples, confirming their specificity for male individuals. This approach complements the current procedures, such as the AMELX/AMELY test and anthropometric principle.}, }
@article {pmid32610222, year = {2020}, author = {Olalde, I and Posth, C}, title = {Latest trends in archaeogenetic research of west Eurasians.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {36-43}, doi = {10.1016/j.gde.2020.05.021}, pmid = {32610222}, issn = {1879-0380}, mesh = {Archaeology/*methods ; DNA, Ancient/*analysis ; *Gene Flow ; *Genetic Variation ; *Genome, Human ; Human Migration/*trends ; Humans ; White People/*genetics ; }, abstract = {During the past ten years, archaeogenetic research has exponentially grown to study the genetic history of human populations, using genome-wide data from large numbers of ancient individuals. Of the entire globe, Europe and the Near East are the regions where ancient DNA data is by far most abundant with over 2500 genomes published at present. In this review, we focus on archaeological contexts that have received less attention in the literature, specifically those associated with west Eurasian hunter-gatherers as well as populations from the Iron Age and later historical periods. In addition, we emphasize a recent shift from continent-wide to regional and even site-specific studies, which is starting to provide novel insights into sociocultural aspects of past societies.}, }
@article {pmid32603999, year = {2020}, author = {Barquera, R and Krause, J}, title = {An ancient view on host pathogen interaction across time and space.}, journal = {Current opinion in immunology}, volume = {65}, number = {}, pages = {65-69}, doi = {10.1016/j.coi.2020.05.004}, pmid = {32603999}, issn = {1879-0372}, mesh = {HLA Antigens/genetics/*immunology ; Host-Pathogen Interactions/genetics/*immunology ; Humans ; }, abstract = {The ancient DNA revolution provided diverse fields with an unprecedented opportunity to look back into the past and shed light on research aspects that were until now subject to speculation and inference from modern data. In particular enrichment methods that allow the targeted retrieval of millions of SNP positions from ancient human genomes, or even complete bacterial and viral genomes have the potential to revolutionize our understanding of host pathogen interactions. Ancient DNA combined with new bioinformatic tools now even allows actual allele calling for immunogenetic systems such as Human Leukocyte Antigen (HLA) across time and space. The coming years will provide us with frequency data of human immunity genes, such as HLA, as well as genome wide data of ancient pathogens from many time periods of human history, and will therefore provide us with a dynamic view on historical human adaptation to pathogen exposure on a population wide scale.}, }
@article {pmid32598277, year = {2020}, author = {Arning, N and Wilson, DJ}, title = {The past, present and future of ancient bacterial DNA.}, journal = {Microbial genomics}, volume = {6}, number = {7}, pages = {}, pmid = {32598277}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101237/Z/13/B/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/*classification/genetics ; Bone and Bones/microbiology ; DNA, Ancient/*analysis ; Dental Pulp/microbiology ; Feces/microbiology ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Humans ; Mummies/microbiology ; Sequence Analysis, DNA/*methods ; }, abstract = {Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.}, }
@article {pmid32595682, year = {2020}, author = {Xue, JY and Wang, Y and Chen, M and Dong, S and Shao, ZQ and Liu, Y}, title = {Maternal Inheritance of U's Triangle and Evolutionary Process of Brassica Mitochondrial Genomes.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {805}, pmid = {32595682}, issn = {1664-462X}, abstract = {The sequences and genomic structures of plant mitochondrial (mt) genomes provide unique material for phylogenetic studies. The nature of uniparental inheritance renders an advantage when utilizing mt genomes for determining the parental sources of hybridized taxa. In this study, a concatenated matrix of mt genes was used to infer the phylogenetic relationships of six cultivated Brassica taxa and explore the maternal origins of three allotetraploids. The well-resolved sister relationships between two pairs of diploid and allotetraploid taxa suggest that Brassica carinata (car) possessed a maternal origin from Brassica nigra, while Brassica juncea (jun) was maternally derived from Brassica rapa (cam). Another allotetraploid taxon, Brassica napus (cv. Wester) may have been maternally derived from the common ancestor of B. rapa and Brassica oleracea (ole), and/or have undergone (an) extra hybridization event(s) along its evolutionary history. The characteristics of Brassica mt genomic structures also supported the phylogenetic results. Sinapis arvensis was nested inside the Brassica species, sister to the B. nigra-B. carinata lineage, and possessed an mt genome structure that mostly resembled B. nigra. Collectively, the evidence supported a systematic revision that placed S. arvensis within Brassica. Finally, ancestral mt genomes at each evolutionary node of Brassica were reconstructed, and the detailed and dynamic evolution of Brassica mt genomes was successfully reproduced. The mt genome of B. nigra structurally resembled that of the Brassica ancestor the most, with only one reversion of a block, and the Brassica oleracea underwent the most drastic changes. These findings suggested that repeat-mediated recombinations were largely responsible for the observed structural variations in the evolutionary history of Brassica mt genomes.}, }
@article {pmid32586278, year = {2020}, author = {Weiß, CL and Gansauge, MT and Aximu-Petri, A and Meyer, M and Burbano, HA}, title = {Mining ancient microbiomes using selective enrichment of damaged DNA molecules.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {432}, pmid = {32586278}, issn = {1471-2164}, support = {Presidential Innovation Fund//Max-Planck-Gesellschaft/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; DNA, Ancient/*analysis/chemistry ; DNA, Bacterial/genetics ; Data Mining ; Fossils/*microbiology ; Gene Library ; Metagenomics ; Microbiota ; Neanderthals/microbiology ; Plants/microbiology ; Sequence Analysis, DNA/*methods ; Uracil/*chemistry ; }, abstract = {BACKGROUND: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains.<br><br>RESULTS: We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach.<br><br>CONCLUSIONS: Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.}, }
@article {pmid32584871, year = {2020}, author = {Kontopoulos, I and Penkman, K and Mullin, VE and Winkelbach, L and Unterländer, M and Scheu, A and Kreutzer, S and Hansen, HB and Margaryan, A and Teasdale, MD and Gehlen, B and Street, M and Lynnerup, N and Liritzis, I and Sampson, A and Papageorgopoulou, C and Allentoft, ME and Burger, J and Bradley, DG and Collins, MJ}, title = {Screening archaeological bone for palaeogenetic and palaeoproteomic studies.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0235146}, pmid = {32584871}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; Bone and Bones/*chemistry/metabolism ; DNA, Ancient/*analysis/chemistry ; *Fossils ; Humans ; *Proteomics ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals' size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.}, }
@article {pmid32582847, year = {2020}, author = {Wang, K and Goldstein, S and Bleasdale, M and Clist, B and Bostoen, K and Bakwa-Lufu, P and Buck, LT and Crowther, A and Dème, A and McIntosh, RJ and Mercader, J and Ogola, C and Power, RC and Sawchuk, E and Robertshaw, P and Wilmsen, EN and Petraglia, M and Ndiema, E and Manthi, FK and Krause, J and Roberts, P and Boivin, N and Schiffels, S}, title = {Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa.}, journal = {Science advances}, volume = {6}, number = {24}, pages = {eaaz0183}, pmid = {32582847}, issn = {2375-2548}, abstract = {Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.}, }
@article {pmid32574964, year = {2020}, author = {Mathov, Y and Batyrev, D and Meshorer, E and Carmel, L}, title = {Harnessing epigenetics to study human evolution.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {23-29}, doi = {10.1016/j.gde.2020.05.023}, pmid = {32574964}, issn = {1879-0380}, mesh = {*DNA Methylation ; *Epigenesis, Genetic ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Human ; Humans ; }, abstract = {Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates.}, }
@article {pmid32572090, year = {2020}, author = {Debortoli, G and Abbatangelo, C and Ceballos, F and Fortes-Lima, C and Norton, HL and Ozarkar, S and Parra, EJ and Jonnalagadda, M}, title = {Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10075}, pmid = {32572090}, issn = {2045-2322}, mesh = {Ethnicity/*genetics ; Genetic Drift ; Genotyping Techniques ; Humans ; India/ethnology ; Population Density ; Social Class ; Whole Genome Sequencing/*methods ; }, abstract = {The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.}, }
@article {pmid32563853, year = {2020}, author = {Vicente, M and Schlebusch, CM}, title = {African population history: an ancient DNA perspective.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {8-15}, doi = {10.1016/j.gde.2020.05.008}, pmid = {32563853}, issn = {1879-0380}, mesh = {Black People/*genetics ; DNA, Ancient/*analysis ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Humans ; *Population Dynamics ; }, abstract = {The history of human populations in Africa is complex and includes various demographic events that influenced patterns of genetic variation across the continent. Through genetic studies of modern-day, and most recently, ancient African genetic variation, it became evident that deep African history is captured by the relationships among hunter-gatherers. Furthermore, it was shown that agriculture had a large influence on the distribution of current-day Africans. These later population movements changed the demographic face of the continent and descendants of farming groups today form the majority populations across Africa. Ancient DNA methods are continually evolving, and we see evidence of this in how research has advanced in the last decade. With the increased availability of full genomic data from diverse sets of modern-day and prehistoric Africans we now have more power to infer human demography. Future ancient DNA research promises to reveal more detailed stories of human prehistory in Africa.}, }
@article {pmid32557548, year = {2020}, author = {Goude, G and Salazar-García, DC and Power, RC and Rivollat, M and Gourichon, L and Deguilloux, MF and Pemonge, MH and Bouby, L and Binder, D}, title = {New insights on Neolithic food and mobility patterns in Mediterranean coastal populations.}, journal = {American journal of physical anthropology}, volume = {173}, number = {2}, pages = {218-235}, doi = {10.1002/ajpa.24089}, pmid = {32557548}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Bone and Bones/chemistry ; DNA, Ancient/analysis ; DNA, Mitochondrial ; Dental Calculus/history ; Diet/*history ; Edible Grain/genetics ; Food/history ; France ; History, Ancient ; Human Migration/*history ; Humans ; Isotopes/analysis ; Mediterranean Region ; }, abstract = {OBJECTIVES: The aims of this research are to explore the diet, mobility, social organization, and environmental exploitation patterns of early Mediterranean farmers, particularly the role of marine and plant resources in these foodways. In addition, this work strives to document possible gendered patterns of behavior linked to the neolithization of this ecologically rich area. To achieve this, a set of multiproxy analyses (isotopic analyses, dental calculus, microremains analysis, ancient DNA) were performed on an exceptional deposit (n = 61) of human remains from the Les Bréguières site (France), dating to the transition of the sixth to the fifth millennium BCE.<br><br>MATERIALS AND METHODS: The samples used in this study were excavated from the Les Br&#xe9;gui&#xe8;res site (Mougins, Alpes-Maritimes, France), located along the southeastern Mediterranean coastline of France. Stable isotope analyses (C, N) on bone collagen (17 coxal bones, 35 craniofacial elements) were performed as a means to infer protein intake during tissue development. Sulfur isotope ratios were used as indicators of geographical and environmental points of origin. The study of ancient dental calculus helped document the consumption of plants. Strontium isotope analysis on tooth enamel (n = 56) was conducted to infer human provenance and territorial mobility. Finally, ancient DNA analysis was performed to study maternal versus paternal diversity within this Neolithic group (n = 30).<br><br>RESULTS: Stable isotope ratios for human bones range from -20.3 to -18.1&#x2030; for C, from 8.9 to 11.1&#x2030; for N and from 6.4 to 15&#x2030; for S. Domestic animal data range from -22.0 to -20.2&#x2030; for C, from 4.1 to 6.9&#x2030; for N, and from 10.2 to 12.5&#x2030; for S. Human enamel [87] Sr/[86] Sr range from 0.7081 to 0.7102, slightly wider than the animal range (between 0.7087 and 0.7096). Starch and phytolith microremains were recovered as well as other types of remains (e.g., hairs, diatoms, fungal spores). Starch grains include Triticeae type and phytolith includes dicotyledons and monocot types as panicoid grasses. Mitochondrial DNA characterized eight different maternal lineages: H1, H3, HV (5.26%), J (10.53%), J1, K, T (5.2%), and U5 (10.53%) but no sample yielded reproducible Y chromosome SNPs, preventing paternal lineage characterization.<br><br>DISCUSSION: Carbon and nitrogen stable isotope ratios indicate a consumption of protein by humans mainly focused on terrestrial animals and possible exploitation of marine resources for one male and one undetermined adult. Sulfur stable isotope ratios allowed distinguishing groups with different geographical origins, including two females possibly more exposed to the sea spray effect. While strontium isotope data do not indicate different origins for the individuals, mitochondrial lineage diversity from petrous bone DNA suggests the burial includes genetically differentiated groups or a group practicing patrilocality. Moreover, the diversity of plant microremains recorded in dental calculus provide the first evidence that the groups of Les Br&#xe9;gui&#xe8;res consumed a wide breadth of plant foods (as cereals and wild taxa) that required access to diverse environments. This transdisciplinary research paves the way for new perspectives and highlights the relevance for novel research of contexts (whether recently discovered or in museum collections) excavated near shorelines, due to the richness of the biodiversity and the wide range of edible resources available.}, }
@article {pmid32539695, year = {2020}, author = {Philips, A and Stolarek, I and Handschuh, L and Nowis, K and Juras, A and Trzciński, D and Nowaczewska, W and Wrzesińska, A and Potempa, J and Figlerowicz, M}, title = {Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {402}, pmid = {32539695}, issn = {1471-2164}, support = {R21 DE026280/DE/NIDCR NIH HHS/United States ; R21DE026280/DE/NIDCR NIH HHS/United States ; }, mesh = {Body Remains/*microbiology ; Fossils/*microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics ; Humans ; Metagenome ; Mouth/*microbiology ; Periodontitis/microbiology ; Periodontium/microbiology ; Tannerella forsythia/*genetics/*pathogenicity ; Tooth/microbiology ; Virulence Factors/*genetics ; }, abstract = {BACKGROUND: Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death.<br><br>RESULTS: In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. forsythia-containing samples were obtained revealed the pathogenic alveolar bone loss in tooth areas characteristic for advanced periodontitis. Finally, we analyzed the genetic material of ancient T. forsythia strains. As a result, we assembled four ancient T. forsythia genomes - one 2000- and three 1000- year-old. Their comparison with contemporary T. forsythia genomes revealed a lower genetic diversity within the four ancient strains than within contemporary strains. We also investigated the genes of T. forsythia virulence factors and found that several of them (KLIKK protease and bspA genes) differ significantly between ancient and modern bacteria.<br><br>CONCLUSIONS: In summary, we showed that NGS screening of the ancient human microbiome is a valid approach for the identification of disease-associated microbes. Following this protocol, we provided a new set of information on the emergence, evolution and virulence factors of T. forsythia, the member of the oral dysbiotic microbiome.}, }
@article {pmid32523989, year = {2020}, author = {Rivollat, M and Jeong, C and Schiffels, S and Küçükkalıpçı, &#x130; and Pemonge, MH and Rohrlach, AB and Alt, KW and Binder, D and Friederich, S and Ghesquière, E and Gronenborn, D and Laporte, L and Lefranc, P and Meller, H and Réveillas, H and Rosenstock, E and Rottier, S and Scarre, C and Soler, L and Wahl, J and Krause, J and Deguilloux, MF and Haak, W}, title = {Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers.}, journal = {Science advances}, volume = {6}, number = {22}, pages = {eaaz5344}, pmid = {32523989}, issn = {2375-2548}, abstract = {Starting from 12,000 years ago in the Middle East, the Neolithic lifestyle spread across Europe via separate continental and Mediterranean routes. Genomes from early European farmers have shown a clear Near Eastern/Anatolian genetic affinity with limited contribution from hunter-gatherers. However, no genomic data are available from modern-day France, where both routes converged, as evidenced by a mosaic cultural pattern. Here, we present genome-wide data from 101 individuals from 12 sites covering today's France and Germany from the Mesolithic (N = 3) to the Neolithic (N = 98) (7000-3000 BCE). Using the genetic substructure observed in European hunter-gatherers, we characterize diverse patterns of admixture in different regions, consistent with both routes of expansion. Early western European farmers show a higher proportion of distinctly western hunter-gatherer ancestry compared to central/southeastern farmers. Our data highlight the complexity of the biological interactions during the Neolithic expansion by revealing major regional variations.}, }
@article {pmid32511234, year = {2020}, author = {Segurel, L and Guarino-Vignon, P and Marchi, N and Lafosse, S and Laurent, R and Bon, C and Fabre, A and Hegay, T and Heyer, E}, title = {Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA.}, journal = {PLoS biology}, volume = {18}, number = {6}, pages = {e3000742}, pmid = {32511234}, issn = {1545-7885}, mesh = {Animals ; Asia ; *DNA, Ancient ; Ethnicity/genetics ; Europe ; Fermentation ; Gene Frequency/genetics ; Genotype ; Humans ; Lactase/*genetics ; Milk ; *Selection, Genetic ; Time Factors ; }, abstract = {The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?}, }
@article {pmid32497501, year = {2020}, author = {Díez-Del-Molino, D and Dalén, L}, title = {Unroll Please: Deciphering the Genetic Code in Scrolls and Other Ancient Materials.}, journal = {Cell}, volume = {181}, number = {6}, pages = {1200-1201}, doi = {10.1016/j.cell.2020.05.031}, pmid = {32497501}, issn = {1097-4172}, mesh = {*DNA, Ancient ; Genetic Code ; }, abstract = {The unrelenting development of ancient DNA methods now allows researchers to obtain archaeogenetic data from increasingly diverse sources. In a new study in this issue of Cell, researchers apply the latest DNA technologies to unravel the mysteries of the Dead Sea Scrolls, one of the world's most famous and influential sets of ancient parchments.}, }
@article {pmid32497286, year = {2020}, author = {Coutinho, A and Günther, T and Munters, AR and Svensson, EM and Götherström, A and Storå, J and Malmström, H and Jakobsson, M}, title = {The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.}, journal = {American journal of physical anthropology}, volume = {172}, number = {4}, pages = {638-649}, doi = {10.1002/ajpa.24079}, pmid = {32497286}, issn = {1096-8644}, mesh = {Burial/history ; Chromosomes, Human, Y/genetics ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; Genome, Human/genetics ; History, Ancient ; Human Migration/*history ; Humans ; Male ; Scandinavian and Nordic Countries/ethnology ; Tooth/chemistry ; *White People/ethnology/genetics ; }, abstract = {OBJECTIVES: In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences.<br><br>METHODS: We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools.<br><br>RESULTS: The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style.<br><br>CONCLUSION: We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.}, }
@article {pmid32497204, year = {2020}, author = {Buckley, M and Harvey, VL and Orihuela, J and Mychajliw, AM and Keating, JN and Milan, JNA and Lawless, C and Chamberlain, AT and Egerton, VM and Manning, PL}, title = {Collagen Sequence Analysis Reveals Evolutionary History of Extinct West Indies Nesophontes (Island-Shrews).}, journal = {Molecular biology and evolution}, volume = {37}, number = {10}, pages = {2931-2943}, pmid = {32497204}, issn = {1537-1719}, mesh = {Animals ; *Biological Evolution ; Collagen/*chemistry ; Female ; Male ; Mandible/anatomy &amp; histology ; Phylogeography ; Sequence Analysis, Protein ; Sex Characteristics ; Shrews/anatomy &amp; histology/*genetics ; West Indies ; }, abstract = {Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to assist species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba toward Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to N. major rather than N. micrus as previously speculated. This proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to the approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.}, }
@article {pmid32492404, year = {2020}, author = {Anava, S and Neuhof, M and Gingold, H and Sagy, O and Munters, A and Svensson, EM and Afshinnekoo, E and Danko, D and Foox, J and Shor, P and Riestra, B and Huchon, D and Mason, CE and Mizrahi, N and Jakobsson, M and Rechavi, O}, title = {Illuminating Genetic Mysteries of the Dead Sea Scrolls.}, journal = {Cell}, volume = {181}, number = {6}, pages = {1218-1231.e27}, doi = {10.1016/j.cell.2020.04.046}, pmid = {32492404}, issn = {1097-4172}, mesh = {Animals ; Base Sequence/*genetics ; Christianity/history ; Genetics/*history ; History, Ancient ; Humans ; Israel ; Judaism/history ; Skin/*metabolism ; }, abstract = {The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. "Piecing together" scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to "fingerprint" pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.}, }
@article {pmid32488006, year = {2020}, author = {Seersholm, FV and Werndly, DJ and Grealy, A and Johnson, T and Keenan Early, EM and Lundelius, EL and Winsborough, B and Farr, GE and Toomey, R and Hansen, AJ and Shapiro, B and Waters, MR and McDonald, G and Linderholm, A and Stafford, TW and Bunce, M}, title = {Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2770}, pmid = {32488006}, issn = {2041-1723}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Biodiversity ; *Climate Change ; *Ecosystem ; *Extinction, Biological ; Fossils ; High-Throughput Nucleotide Sequencing ; Paleontology ; Plants/genetics ; Sequence Analysis ; Texas ; }, abstract = {Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall's Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.}, }
@article {pmid32483316, year = {2020}, author = {Lord, E and Collins, C and deFrance, S and LeFebvre, MJ and Pigière, F and Eeckhout, P and Erauw, C and Fitzpatrick, SM and Healy, PF and Martínez-Polanco, MF and Garcia, JL and Ramos Roca, E and Delgado, M and Sánchez Urriago, A and Peña Léon, GA and Toyne, JM and Dahlstedt, A and Moore, KM and Laguer Diaz, C and Zori, C and Matisoo-Smith, E}, title = {Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8901}, pmid = {32483316}, issn = {2045-2322}, mesh = {Animals ; Belgium ; Bolivia ; Colombia ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Domestication ; Evolution, Molecular ; Guinea Pigs/*classification/genetics ; Mitochondria/*genetics ; Peru ; Phylogeny ; Phylogeography ; Population Dynamics ; Puerto Rico ; Sequence Analysis, DNA/*veterinary ; United States ; }, abstract = {Guinea pigs (Cavia spp.) have a long association with humans. From as early as 10,000 years ago they were a wild food source. Later, domesticated Cavia porcellus were dispersed well beyond their native range through pre-Columbian exchange networks and, more recently, widely across the globe. Here we present 46 complete mitogenomes of archaeological guinea pigs from sites in Peru, Bolivia, Colombia, the Caribbean, Belgium and the United States to elucidate their evolutionary history, origins and paths of dispersal. Our results indicate an independent centre of domestication of Cavia in the eastern Colombian Highlands. We identify a Peruvian origin for the initial introduction of domesticated guinea pigs (Cavia porcellus) beyond South America into the Caribbean. We also demonstrate that Peru was the probable source of the earliest known guinea pigs transported, as part of the exotic pet trade, to both Europe and the southeastern United States. Finally, we identify a modern reintroduction of guinea pigs to Puerto Rico, where local inhabitants use them for food. This research demonstrates that the natural and cultural history of guinea pigs is more complex than previously known and has implications for other studies regarding regional to global-scale studies of mammal domestication, translocation, and distribution.}, }
@article {pmid32470401, year = {2020}, author = {Skourtanioti, E and Erdal, YS and Frangipane, M and Balossi Restelli, F and Yener, KA and Pinnock, F and Matthiae, P and Özbal, R and Schoop, UD and Guliyev, F and Akhundov, T and Lyonnet, B and Hammer, EL and Nugent, SE and Burri, M and Neumann, GU and Penske, S and Ingman, T and Akar, M and Shafiq, R and Palumbi, G and Eisenmann, S and D'Andrea, M and Rohrlach, AB and Warinner, C and Jeong, C and Stockhammer, PW and Haak, W and Krause, J}, title = {Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus.}, journal = {Cell}, volume = {181}, number = {5}, pages = {1158-1175.e28}, doi = {10.1016/j.cell.2020.04.044}, pmid = {32470401}, issn = {1097-4172}, mesh = {Archaeology/methods ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Ethnicity/*genetics/history ; Gene Flow/*genetics/physiology ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Human/genetics ; Genomics/methods ; Haplotypes ; History, Ancient ; Human Migration/history ; Humans ; Mediterranean Region ; Middle East ; Sequence Analysis, DNA ; }, abstract = {Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6[th] millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today's Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age. VIDEO ABSTRACT.}, }
@article {pmid32470400, year = {2020}, author = {Agranat-Tamir, L and Waldman, S and Martin, MAS and Gokhman, D and Mishol, N and Eshel, T and Cheronet, O and Rohland, N and Mallick, S and Adamski, N and Lawson, AM and Mah, M and Michel, M and Oppenheimer, J and Stewardson, K and Candilio, F and Keating, D and Gamarra, B and Tzur, S and Novak, M and Kalisher, R and Bechar, S and Eshed, V and Kennett, DJ and Faerman, M and Yahalom-Mack, N and Monge, JM and Govrin, Y and Erel, Y and Yakir, B and Pinhasi, R and Carmi, S and Finkelstein, I and Carmel, L and Reich, D}, title = {The Genomic History of the Bronze Age Southern Levant.}, journal = {Cell}, volume = {181}, number = {5}, pages = {1146-1157.e11}, pmid = {32470400}, issn = {1097-4172}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Archaeology/methods ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Ethnicity/*genetics/history ; Gene Flow/*genetics/physiology ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Human/genetics ; Genomics/methods ; Haplotypes ; History, Ancient ; Human Migration/history ; Humans ; Mediterranean Region ; Middle East ; Sequence Analysis, DNA ; }, abstract = {We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the "Canaanite" material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different "Canaanite" groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze-Age migrations into the region over the past 3,000 years.}, }
@article {pmid32467975, year = {2020}, author = {Brealey, JC and Leitão, HG and van der Valk, T and Xu, W and Bougiouri, K and Dalén, L and Guschanski, K}, title = {Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome.}, journal = {Molecular biology and evolution}, volume = {37}, number = {10}, pages = {3003-3022}, pmid = {32467975}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Dental Calculus/*microbiology ; Diet ; Drug Resistance, Microbial/genetics ; Gorilla gorilla ; Mammals/*microbiology ; Metagenome ; *Microbiota ; Mouth/*microbiology ; Reindeer ; Ursidae ; }, abstract = {Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.}, }
@article {pmid32457149, year = {2020}, author = {Brunel, S and Bennett, EA and Cardin, L and Garraud, D and Barrand Emam, H and Beylier, A and Boulestin, B and Chenal, F and Ciesielski, E and Convertini, F and Dedet, B and Desbrosse-Degobertiere, S and Desenne, S and Dubouloz, J and Duday, H and Escalon, G and Fabre, V and Gailledrat, E and Gandelin, M and Gleize, Y and Goepfert, S and Guilaine, J and Hachem, L and Ilett, M and Lambach, F and Maziere, F and Perrin, B and Plouin, S and Pinard, E and Praud, I and Richard, I and Riquier, V and Roure, R and Sendra, B and Thevenet, C and Thiol, S and Vauquelin, E and Vergnaud, L and Grange, T and Geigl, EM and Pruvost, M}, title = {Ancient genomes from present-day France unveil 7,000 years of its demographic history.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {23}, pages = {12791-12798}, pmid = {32457149}, issn = {1091-6490}, mesh = {Chromosomes, Human, Y/genetics ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Female ; France ; Gene Flow ; *Genome, Human ; *Human Migration ; Humans ; Male ; Polymorphism, Genetic ; Population/*genetics ; }, abstract = {Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotypes of a number of nuclear loci of interest of 243 individuals sampled across present-day France over a period spanning 7,000 y, complemented with a partially overlapping dataset of 58 low-coverage genomes. This panel provides a high-resolution transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Parental lineages and genomic data both revealed demographic patterns in France for the Neolithic and Bronze Age transitions consistent with neighboring regions, first with a migration wave of Anatolian farmers followed by varying degrees of admixture with autochthonous hunter-gatherers, and then substantial gene flow from individuals deriving part of their ancestry from the Pontic steppe at the onset of the Bronze Age. Our data have also highlighted the persistence of Magdalenian-associated ancestry in hunter-gatherer populations outside of Spain and thus provide arguments for an expansion of these populations at the end of the Paleolithic Period more northerly than what has been described so far. Finally, no major demographic changes were detected during the transition between the Bronze and Iron Ages.}, }
@article {pmid32446165, year = {2020}, author = {Gonzalez, A and Cannet, C and Zvénigorosky, V and Geraut, A and Koch, G and Delabarde, T and Ludes, B and Raul, JS and Keyser, C}, title = {The petrous bone: Ideal substrate in legal medicine?.}, journal = {Forensic science international. Genetics}, volume = {47}, number = {}, pages = {102305}, doi = {10.1016/j.fsigen.2020.102305}, pmid = {32446165}, issn = {1878-0326}, mesh = {DNA Degradation, Necrotic ; *DNA Fingerprinting ; Forensic Genetics ; Genotype ; Humans ; Microsatellite Repeats ; Molar/chemistry/pathology ; Petrous Bone/*chemistry/pathology ; Polymerase Chain Reaction ; }, abstract = {Over the last few years, palaeogenomic studies of the petrous bone (the densest part of the temporal bone) have shown that it is a source of DNA in both larger quantities and of better quality than other bones. This dense bone around the otic capsule has therefore been called the choice substrate in palaeogenomics. Because the practice of forensic genetics responds to different imperatives, we implemented a study aimed at (i) understanding how and why the petrous bone is an advantageous substrate in ancient DNA studies and (ii) establishing whether it is advantageous in forensic STR typing. We selected 50 individual skeletal remains and extracted DNA from one tooth and one petrous bone from each. We then amplified 24 STR markers commonly used in forensic identification and compared the quality of that amplification using the RFU intensities of the signal as read on the STR profiles. We also performed histological analyses to compare (i) the microscopic structure of a petrous bone and of a tooth and (ii) the microscopic structure of fresh petrous bone and of an archaeological or forensic sample. We show that the RFU intensities read on STR profiles are systematically higher in experiments using DNA extracted from petrous bones rather than teeth. For this reason, we were more likely to obtain a complete STR profile from petrous bone material, increasing the chance of identification in a forensic setting. Histological analyses revealed peculiar microstructural characteristics (tissue organization), unique to the petrous bone, that might explain the good preservation of DNA in that substrate. Therefore, it appears that despite the necessity of analysing longer fragments in forensic STR typing compared to NGS palaeogenomics, the use of petrous bones in forensic genetics could prove valuable, especially in cases involving infants, toothless individuals or very degraded skeletal remains.}, }
@article {pmid32430331, year = {2020}, author = {Gryseels, S and Watts, TD and Kabongo Mpolesha, JM and Larsen, BB and Lemey, P and Muyembe-Tamfum, JJ and Teuwen, DE and Worobey, M}, title = {A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {22}, pages = {12222-12229}, pmid = {32430331}, issn = {1091-6490}, support = {R01 AI084691/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Cell Lineage/*genetics ; Democratic Republic of the Congo ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Viral ; HIV Infections/*genetics/virology ; HIV-1/*genetics ; Humans ; Male ; Paraffin Embedding/*methods ; Phylogeny ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long prediscovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,645 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Central Africa between 1958 and 1966. We report the near-complete viral genome in one HIV-1 positive specimen from Kinshasa, Democratic Republic of Congo (DRC), from 1966 ("DRC66")-a nonrecombinant sister lineage to subtype C that constitutes the oldest HIV-1 near full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of the DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978 to 2014, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to a time period around the turn of the 20th century (1881 to 1918). In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.}, }
@article {pmid32428013, year = {2020}, author = {Aoki, K}, title = {A three-population wave-of-advance model for the European early Neolithic.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0233184}, pmid = {32428013}, issn = {1932-6203}, mesh = {Agriculture/*history ; *DNA, Ancient ; History, Ancient ; Human Migration/*history ; Humans ; *Models, Biological ; }, abstract = {Ancient DNA studies have shown that early farming spread through most of Europe by the range expansion of farmers of Anatolian origin rather than by the conversion to farming of the local hunter-gatherers, and have confirmed that these hunter-gatherers continued to coexist with the incoming farmers. In this short report, I extend a previous three-population wave-of-advance model to accommodate these new findings, and derive the conditions supportive of such a scenario in terms of the relative magnitudes of the parameters. The revised model predicts that the conversion rate must, not surprisingly, be low, but also that the hunter-gatherers must compete more strongly with the converted farmers than with the alien farmers. Moreover, competition with the hunter-gatherers diminishes the speed of the wave-of advance of the farmers. In addition, I briefly consider how the wave-of-advance approach may contribute to interpreting the results of archaeological studies using the summed probability distribution of radiocarbon dates.}, }
@article {pmid32421727, year = {2020}, author = {Peña-Ahumada, B and Saldarriaga-Córdoba, M and Kardailsky, O and Moncada, X and Moraga, M and Matisoo-Smith, E and Seelenfreund, D and Seelenfreund, A}, title = {A tale of textiles: Genetic characterization of historical paper mulberry barkcloth from Oceania.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0233113}, pmid = {32421727}, issn = {1932-6203}, mesh = {Broussonetia/*genetics ; Genotyping Techniques ; Humans ; Microsatellite Repeats/genetics ; Pacific Islands ; Taiwan ; *Textiles ; }, abstract = {Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.}, }
@article {pmid32409524, year = {2020}, author = {Yang, MA and Fan, X and Sun, B and Chen, C and Lang, J and Ko, YC and Tsang, CH and Chiu, H and Wang, T and Bao, Q and Wu, X and Hajdinjak, M and Ko, AM and Ding, M and Cao, P and Yang, R and Liu, F and Nickel, B and Dai, Q and Feng, X and Zhang, L and Sun, C and Ning, C and Zeng, W and Zhao, Y and Zhang, M and Gao, X and Cui, Y and Reich, D and Stoneking, M and Fu, Q}, title = {Ancient DNA indicates human population shifts and admixture in northern and southern China.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6501}, pages = {282-288}, doi = {10.1126/science.aba0909}, pmid = {32409524}, issn = {1095-9203}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Asia, Southeastern ; Asian People/genetics ; China ; *DNA, Ancient ; Gene Flow ; *Genetics, Population ; Genome, Human ; *Human Migration ; Humans ; Siberia ; Vietnam ; }, abstract = {Human genetic history in East Asia is poorly understood. To clarify population relationships, we obtained genome-wide data from 26 ancient individuals from northern and southern East Asia spanning 9500 to 300 years ago. Genetic differentiation in this region was higher in the past than the present, which reflects a major episode of admixture involving northern East Asian ancestry spreading across southern East Asia after the Neolithic, thereby transforming the genetic ancestry of southern China. Mainland southern East Asian and Taiwan Strait island samples from the Neolithic show clear connections with modern and ancient individuals with Austronesian-related ancestry, which supports an origin in southern China for proto-Austronesians. Connections among Neolithic coastal groups from Siberia and Japan to Vietnam indicate that migration and gene flow played an important role in the prehistory of coastal Asia.}, }
@article {pmid32406954, year = {2020}, author = {Li, J and Cai, D and Zhang, Y and Zhu, H and Zhou, H}, title = {Ancient DNA reveals two paternal lineages C2a1a1b1a/F3830 and C2b1b/F845 in past nomadic peoples distributed on the Mongolian Plateau.}, journal = {American journal of physical anthropology}, volume = {172}, number = {3}, pages = {402-411}, doi = {10.1002/ajpa.24076}, pmid = {32406954}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Chromosomes, Human, Y/*genetics ; DNA, Ancient/*analysis ; Ethnicity/*genetics/history ; Genome, Human/genetics ; Genomics/methods ; History, Ancient ; Humans ; Male ; Mongolia ; Sequence Analysis, DNA/methods ; Transients and Migrants/*history ; }, abstract = {OBJECTIVES: Since the third century CE, a series of nomadic tribes have been active on the eastern part of the Mongolian Plateau. Characterizing the genetic compositions of past nomadic people is significant for research on the nomadic cultures of the Eurasian Steppe region. Ancient DNA analysis facilitates a deeper understanding of the relationship between historical and modern nomadic populations.<br><br>MATERIALS AND METHODS: Whole-genome shotgun sequencing and capture sequencing of the nonrecombining region of the Y chromosome were performed for six ancient Hg C2/M217 individuals. The individuals were interred at six separate sites on the Mongolian Plateau and represent dates spanning the late Neolithic to Yuan Dynasty (~3,500-700 BP).<br><br>RESULTS: After NRY capture sequencing, three of the six ancient samples were attributed to C2b1b/F845 and the other three ancient samples belonged to C2a1a1b1a/F3830. Analysis of whole-genome shotgun sequencing data shows that the ancient C2b1b/F845 individuals are closely related to She, Han and other East Asian populations, while the ancient C2a1a1b1a/F3830 individuals are more similar to modern Northeast Asian peoples, such as the Ulchi and Yakut.<br><br>DISCUSSION: Hg C2/M217, widely distributed in the eastern part of the Eurasian continent, was discovered in the ancient Central Steppe and Baikal region. This study shows that there were two important subclades of Hg C2/M217 among the ancient nomadic peoples: C2a1a1b1a/F3830, which has made important genetic contributions to modern Mongolic- and Manchu-speaking populations, and C2b1b/F845, which probably originated in the farming populations of southern East Asia and made certain genetic contributions to past nomadic peoples on the Mongolian Plateau.}, }
@article {pmid32405770, year = {2020}, author = {Samida, S}, title = {[About Media Presence and Prominence of DNA-Supported Research of the Past].}, journal = {NTM}, volume = {28}, number = {2}, pages = {181-192}, doi = {10.1007/s00048-020-00249-5}, pmid = {32405770}, issn = {1420-9144}, mesh = {Archaeology/*methods ; *Communications Media ; *DNA ; Genetic Techniques ; Humans ; Molecular Biology/*methods ; Publishing ; *Research ; Science ; Writing ; }, abstract = {In recent years molecular genetics has provided a completely new approach/access to the human past. The still new and quite dynamic research field of archaeogenetics (also known as palaeogenetics or genetic history) claims to be able to write history using ancient DNA. Through numerous remarkable publications it has generated and received much interest not only in scientific discourse but also in the media. So far, however, scientists have not paid much attention to this coverage-a research desideratum this paper cannot resolve. But by looking at selected press clippings it seeks to capture first trends according to the following three theses: telling success stories, drawing boundaries, and writing in a conformist manner.}, }
@article {pmid32405262, year = {2019}, author = {Charlton, S and Booth, T and Barnes, I}, title = {The problem with petrous? A consideration of the potential biases in the utilization of pars petrosa for ancient DNA analysis.}, journal = {World archaeology}, volume = {51}, number = {4}, pages = {574-585}, pmid = {32405262}, issn = {0043-8243}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Advances in NGS sequencing technologies, improved laboratory protocols and new bioinformatic workflows have seen huge increases in ancient DNA (aDNA) research on archaeological materials. A large proportion of aDNA work now utilizes the petrous portion of the temporal bone (pars petrosa), which is recognized as an excellent skeletal element for long-term ancient endogenous (host) DNA survival. This has been significant due to the often low endogenous content of other skeletal elements, meaning that large amounts of sequencing are frequently required to obtain sufficient genetic coverage. However, exclusive sampling of the petrous for aDNA analysis introduces a new set of potential biases into our scientific studies - and these issues are yet to be considered by ancient DNA researchers. This paper aims to outline the possible biases of utilizing petrous bones to undertake aDNA analyses and highlight how these complications may potentially be overcome in future research.}, }
@article {pmid32396835, year = {2020}, author = {Rees, JS and Castellano, S and Andrés, AM}, title = {The Genomics of Human Local Adaptation.}, journal = {Trends in genetics : TIG}, volume = {36}, number = {6}, pages = {415-428}, doi = {10.1016/j.tig.2020.03.006}, pmid = {32396835}, issn = {0168-9525}, mesh = {*Adaptation, Physiological ; Animals ; *Biological Evolution ; *Genetic Variation ; Genomics/*methods ; Humans ; *Selection, Genetic ; }, abstract = {Modern humans inhabit a variety of environments and are exposed to a plethora of selective pressures, leading to multiple genetic adaptations to local environmental conditions. These include adaptations to climate, UV exposure, disease, diet, altitude, or cultural practice and have generated important genetic and phenotypic differences amongst populations. In recent years, new methods to identify the genomic signatures of natural selection underlying these adaptations, combined with novel types of genetic data (e.g., ancient DNA), have provided unprecedented insights into the origin of adaptive alleles and the modes of adaptation. As a result, numerous instances of local adaptation have been identified in humans. Here, we review the most exciting recent developments and discuss, in our view, the future of this field.}, }
@article {pmid32393839, year = {2020}, author = {Fewlass, H and Mitchell, PJ and Casanova, E and Cramp, LJE}, title = {Chemical evidence of dairying by hunter-gatherers in highland Lesotho in the late first millennium AD.}, journal = {Nature human behaviour}, volume = {4}, number = {8}, pages = {791-799}, pmid = {32393839}, issn = {2397-3374}, mesh = {Animals ; CD36 Antigens/analysis ; Cattle ; Ceramics/history ; Dairying/*history ; History, Ancient ; Humans ; Lesotho ; Lipids/analysis ; Radiometric Dating ; Sheep ; }, abstract = {The recovery of Early Iron Age artefacts and domestic animal remains from hunter-gatherer contexts at Likoaeng, Lesotho, has been argued to indicate contact between highland hunter-gatherers and Early Iron Age agropastoralist communities settled in lowland areas of southeastern Africa during the second half of the first millennium AD. However, disagreement between archaeozoological studies and ancient DNA means that the possibility that those hunter-gatherers kept livestock themselves remains controversial. Here we report analyses of pottery-absorbed organic residues from two hunter-gatherer sites and one agriculturalist site in highland Lesotho to reconstruct prehistoric subsistence practices. Our results demonstrate the exploitation of secondary products from domestic livestock by hunter-gatherers in Lesotho, directly dated to the seventh century AD at Likoaeng and the tenth century AD at the nearby site of Sehonghong. The data provide compelling evidence for the keeping of livestock by hunter-gatherer groups and their probable incorporation as ancillary resources into their subsistence strategies.}, }
@article {pmid32386546, year = {2020}, author = {Nakatsuka, N and Lazaridis, I and Barbieri, C and Skoglund, P and Rohland, N and Mallick, S and Posth, C and Harkins-Kinkaid, K and Ferry, M and Harney, &#xc9; and Michel, M and Stewardson, K and Novak-Forst, J and Capriles, JM and Durruty, MA and Álvarez, KA and Beresford-Jones, D and Burger, R and Cadwallader, L and Fujita, R and Isla, J and Lau, G and Aguirre, CL and LeBlanc, S and Maldonado, SC and Meddens, F and Messineo, PG and Culleton, BJ and Harper, TK and Quilter, J and Politis, G and Rademaker, K and Reindel, M and Rivera, M and Salazar, L and Sandoval, JR and Santoro, CM and Scheifler, N and Standen, V and Barreto, MI and Espinoza, IF and Tomasto-Cagigao, E and Valverde, G and Kennett, DJ and Cooper, A and Krause, J and Haak, W and Llamas, B and Reich, D and Fehren-Schmitz, L}, title = {A Paleogenomic Reconstruction of the Deep Population History of the Andes.}, journal = {Cell}, volume = {181}, number = {5}, pages = {1131-1145.e21}, pmid = {32386546}, issn = {1097-4172}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; /MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; /CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Anthropology/*methods ; Central America ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Gene Flow/*genetics/physiology ; Genetics, Population/methods ; Haplotypes ; Humans ; Sequence Analysis, DNA ; South America ; }, abstract = {There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.}, }
@article {pmid32375874, year = {2020}, author = {Rifkin, RF and Vikram, S and Ramond, JB and Rey-Iglesia, A and Brand, TB and Porraz, G and Val, A and Hall, G and Woodborne, S and Le Bailly, M and Potgieter, M and Underdown, SJ and Koopman, JE and Cowan, DA and Van de Peer, Y and Willerslev, E and Hansen, AJ}, title = {Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {62}, pmid = {32375874}, issn = {2049-2618}, mesh = {Africa South of the Sahara ; *Archaeology ; Feces/*microbiology ; *Gastrointestinal Microbiome ; History, 15th Century ; Humans ; Metagenomics ; }, abstract = {BACKGROUND: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.<br><br>METHODS: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM.<br><br>RESULTS: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (&#xd6;tzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.<br><br>CONCLUSIONS: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000&#x2009;years ago. Video Abtract.}, }
@article {pmid32369585, year = {2020}, author = {Liu, X}, title = {Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions.}, journal = {Molecular biology and evolution}, volume = {37}, number = {9}, pages = {2691-2698}, pmid = {32369585}, issn = {1537-1719}, support = {R01 HG009524/HG/NHGRI NIH HHS/United States ; }, mesh = {Agriculture ; *CpG Islands ; *Demography ; *Genome, Human ; Humans ; Population Growth ; }, abstract = {The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.}, }
@article {pmid32359431, year = {2020}, author = {Barquera, R and Lamnidis, TC and Lankapalli, AK and Kocher, A and Hernández-Zaragoza, DI and Nelson, EA and Zamora-Herrera, AC and Ramallo, P and Bernal-Felipe, N and Immel, A and Bos, K and Acuña-Alonzo, V and Barbieri, C and Roberts, P and Herbig, A and Kühnert, D and Márquez-Morfín, L and Krause, J}, title = {Origin and Health Status of First-Generation Africans from Early Colonial Mexico.}, journal = {Current biology : CB}, volume = {30}, number = {11}, pages = {2078-2091.e11}, doi = {10.1016/j.cub.2020.04.002}, pmid = {32359431}, issn = {1879-0445}, mesh = {Adult ; Archaeology ; Black People/history ; DNA, Ancient/*analysis ; Enslaved Persons/*history ; *Health Status ; Hepatitis B/*history ; Hepatitis B virus/isolation &amp; purification ; History, 16th Century ; Humans ; Male ; Mexico ; Treponema/isolation &amp; purification ; Yaws/*history ; Young Adult ; }, abstract = {The forced relocation of several thousand Africans during Mexico's historic period has so far been documented mostly through archival sources, which provide only sparse detail on their origins and lived experience. Here, we employ a bioarchaeological approach to explore the life history of three 16[th] century Africans from a mass burial at the San José de los Naturales Royal Hospital in Mexico City. Our approach draws together ancient genomic data, osteological analysis, strontium isotope data from tooth enamel, δ[13]C and δ[15]N isotope data from dentine, and ethnohistorical information to reveal unprecedented detail on their origins and health. Analyses of skeletal features, radiogenic isotopes, and genetic data from uniparental, genome-wide, and human leukocyte antigen (HLA) markers are consistent with a Sub-Saharan African origin for all three individuals. Complete genomes of Treponema pallidum sub. pertenue (causative agent of yaws) and hepatitis B virus (HBV) recovered from these individuals provide insight into their health as related to infectious disease. Phylogenetic analysis of both pathogens reveals their close relationship to strains circulating in current West African populations, lending support to their origins in this region. The further relationship between the treponemal genome retrieved and a treponemal genome previously typed in an individual from Colonial Mexico highlights the role of the transatlantic slave trade in the introduction and dissemination of pathogens into the New World. Putting together all lines of evidence, we were able to create a biological portrait of three individuals whose life stories have long been silenced by disreputable historical events.}, }
@article {pmid32355290, year = {2020}, author = {Pierini, F and Nutsua, M and Böhme, L and Özer, O and Bonczarowska, J and Susat, J and Franke, A and Nebel, A and Krause-Kyora, B and Lenz, TL}, title = {Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7339}, pmid = {32355290}, issn = {2045-2322}, mesh = {Alleles ; DNA, Ancient/*analysis ; Denmark ; Genetic Markers ; Genetics, Population ; Genome, Human ; *Genotype ; HLA Antigens/*genetics ; Haplotypes ; *High-Throughput Nucleotide Sequencing ; Histocompatibility Antigens Class II/*genetics ; Humans ; Pattern Recognition, Automated ; *Polymorphism, Single Nucleotide ; }, abstract = {The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.}, }
@article {pmid32324877, year = {2020}, author = {Cai, Y and Fu, W and Cai, D and Heller, R and Zheng, Z and Wen, J and Li, H and Wang, X and Alshawi, A and Sun, Z and Zhu, S and Wang, J and Yang, M and Hu, S and Li, Y and Yang, Z and Gong, M and Hou, Y and Lan, T and Wu, K and Chen, Y and Jiang, Y and Wang, X}, title = {Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China.}, journal = {Molecular biology and evolution}, volume = {37}, number = {7}, pages = {2099-2109}, pmid = {32324877}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; China ; DNA, Ancient/*chemistry ; *Genome ; Goats/*genetics ; Selection, Genetic ; }, abstract = {Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.}, }
@article {pmid32321996, year = {2020}, author = {Ferrando-Bernal, M and Morcillo-Suarez, C and de-Dios, T and Gelabert, P and Civit, S and Díaz-Carvajal, A and Ollich-Castanyer, I and Allentoft, ME and Valverde, S and Lalueza-Fox, C}, title = {Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {6843}, pmid = {32321996}, issn = {2045-2322}, mesh = {*DNA, Ancient ; Ethnicity/*genetics ; Europe ; Female ; *Genetic Variation ; History, Medieval ; Humans ; Male ; *Polymorphism, Single Nucleotide ; White People/*genetics/history ; }, abstract = {Historical genetic links among similar populations can be difficult to establish. Identity by descent (IBD) analyses find genomic blocks that represent direct genealogical relationships among individuals. However, this method has rarely been applied to ancient genomes because IBD stretches are progressively fragmented by recombination and thus not recognizable after few tens of generations. To explore such genealogical relationships, we estimated long IBD blocks among modern Europeans, generating networks to uncover the genetic structures. We found that Basques, Sardinians, Icelanders and Orcadians form, each of them, highly intraconnected sub-clusters in a European network, indicating dense genealogical links within small, isolated populations. We also exposed individual genealogical links -such as the connection between one Basque and one Icelandic individual- that cannot be uncovered with other, widely used population genetics methods such as PCA or ADMIXTURE. Moreover, using ancient DNA technology we sequenced a Late Medieval individual (Barcelona, Spain) to high genomic coverage and identified IBD blocks shared between her and modern Europeans. The Medieval IBD blocks are statistically overrepresented only in modern Spaniards, which is the geographically closest population. This approach can be used to produce a fine-scale reflection of shared ancestry across different populations of the world, offering a direct genetic link from the past to the present.}, }
@article {pmid32318826, year = {2020}, author = {Zvénigorosky, V and Sabbagh, A and Gonzalez, A and Fausser, JL and Palstra, F and Romanov, G and Solovyev, A and Barashkov, N and Fedorova, S and Crubézy, &#xc9; and Ludes, B and Keyser, C}, title = {The limitations of kinship determinations using STR data in ill-defined populations.}, journal = {International journal of legal medicine}, volume = {134}, number = {6}, pages = {1981-1990}, doi = {10.1007/s00414-020-02298-w}, pmid = {32318826}, issn = {1437-1596}, support = {Travel Grant//Universit&#xe9; Toulouse III - Paul Sabatier/ ; }, mesh = {Africa, Western/ethnology ; Benin/ethnology ; *Family ; Female ; Forensic Genetics/*methods ; Gene Frequency ; Humans ; *Likelihood Functions ; Male ; Microsatellite Repeats ; *Pedigree ; Phylogeny ; Reproducibility of Results ; Siberia/ethnology ; }, abstract = {The likelihood ratio (LR) method is commonly used to determine kinship in civil, criminal, or forensic cases. For the past 15 years, our research group has also applied LR to ancient STR data and obtained kinship results for collections of graves or necropolises. Although we were able to reconstruct large genealogies, some pairs of individuals showed ambiguous results. Second-degree relationships, half-sibling pairs for example, were often inconsistent with detected first-degree relationships, such as parent/child or brother/sister pairs. We therefore set about providing empirical estimations of the error rates for the LR method in living populations with STR allelic diversities comparable to that of the ancient populations we had previously studied. We collected biological samples in the field in North-Eastern Siberia and West Africa and studied more than 800 pairs of STR profiles from individuals with known relationships. Because commercial STR panels were constructed for specific regions (namely Europe and North America), their allelic makeup showed a significant deficit in diversity when compared to European populations, replicating a situation often faced in ancient DNA studies. We assessed the capacity of the LR method to confirm known relationships (effectiveness) and its capacity to detect those relationships (reliability). Concerns over the effectiveness of LR determinations are mostly an issue in forensic studies, while the reliability of the detection of kinship is an issue for the study of necropolises or other large gatherings of unidentified individuals, such as disaster victims or mass graves. We show that the application of LR to both test populations highlights specific issues (both false positives and false negatives) that prevent the confirmation of second-degree kinship or even full siblingship in small populations. Up to 29% of detected full sibling relationships were either overestimated half-sibling relationships or underestimated parent-offspring relationships. The error rate for detected half-sibling relationships was even higher, reaching 41%. Only parent-offspring pairs were reliably detected or confirmed. This implies that, in populations that are small, ill-defined, or for which the STR loci analyzed are inappropriate, an examiner might not be able to distinguish a pair of full siblings from a pair of half-siblings. Furthermore, half-sibling pairs might be overlooked altogether, an issue that is exacerbated by the common confusion, in many languages and cultures, between half-siblings and full siblings. Consequently, in the study of ancient populations, human remains of unknown origins, or poorly surveyed modern populations, we recommend a conservative approach to kinship determined by LR. Next-generation sequencing data should be used when possible, but the costs and technology involved might be prohibitive. Therefore, in potentially contentious situations or cases lacking sufficient external information, uniparental markers should be analyzed: ideally, complete mitochondrial genomes and Y-chromosome haplotypes (STR, SNP, and/or sequencing).}, }
@article {pmid32313686, year = {2020}, author = {Dehasque, M and Ávila-Arcos, MC and Díez-Del-Molino, D and Fumagalli, M and Guschanski, K and Lorenzen, ED and Malaspinas, AS and Marques-Bonet, T and Martin, MD and Murray, GGR and Papadopulos, AST and Therkildsen, NO and Wegmann, D and Dalén, L and Foote, AD}, title = {Inference of natural selection from ancient DNA.}, journal = {Evolution letters}, volume = {4}, number = {2}, pages = {94-108}, pmid = {32313686}, issn = {2056-3744}, abstract = {Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.}, }
@article {pmid32306514, year = {2020}, author = {Lang, PLM and Weiß, CL and Kersten, S and Latorre, SM and Nagel, S and Nickel, B and Meyer, M and Burbano, HA}, title = {Hybridization ddRAD-sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA.}, journal = {Molecular ecology resources}, volume = {20}, number = {5}, pages = {1228-1247}, doi = {10.1111/1755-0998.13168}, pmid = {32306514}, issn = {1755-0998}, support = {Project 324876998 of SPP1374//Deutsche Forschungsgemeinschaft/ ; Presidential Innovation Fund//Max-Planck-Gesellschaft/ ; 324876998//German Research Foundation/ ; SPP1374//German Research Foundation/ ; //Max Planck Society/ ; }, mesh = {Arabidopsis ; Cardamine ; DNA, Plant/*genetics ; *Genetics, Population ; *Genomics ; Nucleic Acid Hybridization ; Plants/*genetics ; Sequence Analysis, DNA ; }, abstract = {Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species-with small or large genomes-diversity is traditionally assessed using restriction-enzyme-based sequencing. However, age-related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced-representation sequencing and hybridization-capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced-representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference-free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost-efficient, large-scale integration of contemporary and historical specimens for assessment of genome-wide genetic trends over time, independent of genome size and presence of a reference genome.}, }
@article {pmid32304863, year = {2020}, author = {Zhang, X and Li, C and Zhou, Y and Huang, J and Yu, T and Liu, X and Shi, H and Liu, H and Chia, S and Huang, S and Guo, Y and Shoocongdej, R and Ji, X and Su, B}, title = {A Matrilineal Genetic Perspective of Hanging Coffin Custom in Southern China and Northern Thailand.}, journal = {iScience}, volume = {23}, number = {4}, pages = {101032}, pmid = {32304863}, issn = {2589-0042}, abstract = {Hanging Coffin is a unique and ancient burial custom that has been practiced in southern China, Southeast Asia, and near Oceania regions for more than 3,000 years. Here, we conducted mitochondrial whole-genome analyses of 41 human remains sampled from 13 Hanging Coffin sites in southern China and northern Thailand, which were dated between ∼2,500 and 660 years before present. We found that there were genetic connections between the Hanging Coffin people living in different geographic regions. Notably, the matrilineal genetic diversity of the Hanging Coffin people from southern China is much higher than those from northern Thailand, consistent with the hypothesized single origin of the Hanging Coffin custom in southern China about 3,600 years ago, followed by its dispersal in southern China through demic diffusion, whereas the major dispersal pattern in Southeast Asia is cultural assimilation in the past 2,000 years.}, }
@article {pmid32299352, year = {2020}, author = {Moriano, J and Boeckx, C}, title = {Modern human changes in regulatory regions implicated in cortical development.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {304}, pmid = {32299352}, issn = {1471-2164}, support = {FFI2016-78034-C2-1-P//SpanishMinistry of Economy and Competitiveness/FEDER/ ; PIRG-GA-2009-256413//Marie Curie International Reintegration Grant/ ; Evolinguistics: JP17H06379//MEXT/JSPS/ ; -//Fundaci&#xf3; Bosch i Gimpera (ES)/ ; 2017-SGR-341//Generalitat de Catalunya (ES)/ ; }, mesh = {Animals ; Cerebral Cortex/*growth &amp; development ; Chromatin/genetics/metabolism ; *Enhancer Elements, Genetic ; Gene Expression Regulation, Developmental ; Histone-Lysine N-Methyltransferase/genetics/metabolism ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; Neurogenesis/*genetics ; Polymorphism, Single Nucleotide ; *Promoter Regions, Genetic ; Species Specificity ; Wnt Signaling Pathway/genetics ; }, abstract = {BACKGROUND: Recent paleogenomic studies have highlighted a very small set of proteins carrying modern human-specific missense changes in comparison to our closest extinct relatives. Despite being frequently alluded to as highly relevant, species-specific differences in regulatory regions remain understudied. Here, we integrate data from paleogenomics, chromatin modification and physical interaction, and single-cell gene expression of neural progenitor cells to identify derived regulatory changes in the modern human lineage in comparison to Neanderthals/Denisovans. We report a set of genes whose enhancers and/or promoters harbor modern human single nucleotide changes and are active at early stages of cortical development.<br><br>RESULTS: We identified 212 genes controlled by regulatory regions harboring modern human changes where Neanderthals/Denisovans carry the ancestral allele. These regulatory regions significantly overlap with putative modern human positively-selected regions and schizophrenia-related genetic loci. Among the 212 genes, we identified a substantial proportion of genes related to transcriptional regulation and, specifically, an enrichment for the SETD1A histone methyltransferase complex, known to regulate WNT signaling for the generation and proliferation of intermediate progenitor cells.<br><br>CONCLUSIONS: This study complements previous research focused on protein-coding changes distinguishing our species from Neanderthals/Denisovans and highlights chromatin regulation as a functional category so far overlooked in modern human evolution studies. We present a set of candidates that will help to illuminate the investigation of modern human-specific ontogenetic trajectories.}, }
@article {pmid32297957, year = {2020}, author = {Sanchez-Mazas, A}, title = {A review of HLA allele and SNP associations with highly prevalent infectious diseases in human populations.}, journal = {Swiss medical weekly}, volume = {150}, number = {}, pages = {w20214}, doi = {10.4414/smw.2020.20214}, pmid = {32297957}, issn = {1424-3997}, mesh = {Alleles ; Case-Control Studies ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; *Hepatitis B ; Humans ; *Polymorphism, Single Nucleotide/genetics ; }, abstract = {Human leucocyte antigen (HLA) alleles and single nucleotide polymorphisms (SNPs) lying in the HLA region are known to be associated with several infectious diseases among which acquired immunodeficiency syndrome, hepatitis B, hepatitis C, tuberculosis, leprosy and malaria are highly prevalent in many human populations worldwide. Distinct approaches such as case-control comparisons, immunogenetic analyses, bioinformatic peptide-binding predictions, ancient DNA and genome-wide association studies (GWAS) have contributed to improving this knowledge during the last decade, although many results still need stronger statistical and/or functional support. The present review updates the information regarding the main HLA allele and SNP associations observed to date for six of the most widespread and some other infectious diseases, and provides a synthetic illustration of these findings on a schematic HLA genomic map. It then discusses these results by stressing the importance of integrating information on HLA population diversity in disease-association studies.}, }
@article {pmid32297323, year = {2020}, author = {Juras, A and Makarowicz, P and Chyleński, M and Ehler, E and Malmström, H and Krzewińska, M and Pospieszny, &#x141; and Górski, J and Taras, H and Szczepanek, A and Polańska, M and Włodarczak, P and Szyca, A and Lasota-Kuś, A and Wójcik, I and Jakobsson, M and Dabert, M}, title = {Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations.}, journal = {American journal of physical anthropology}, volume = {172}, number = {2}, pages = {176-188}, doi = {10.1002/ajpa.24057}, pmid = {32297323}, issn = {1096-8644}, mesh = {Adult ; Anthropology, Physical ; Cemeteries ; Child ; DNA, Ancient/*analysis ; Female ; *Genetics, Population ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; History, Ancient ; Human Migration ; Humans ; Male ; Poland ; White People/*genetics ; }, abstract = {OBJECTIVE: In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes.<br><br>MATERIALS AND METHODS: We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzy&#x17c;ow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS [14] C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples.<br><br>RESULTS: Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzy&#x17c;&#xf3;w people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study.<br><br>DISCUSSION: Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzy&#x17c;&#xf3;w-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.}, }
@article {pmid32286714, year = {2020}, author = {Schweizer, RM and Wayne, RK}, title = {Illuminating the mysteries of wolf history.}, journal = {Molecular ecology}, volume = {29}, number = {9}, pages = {1589-1591}, doi = {10.1111/mec.15438}, pmid = {32286714}, issn = {1365-294X}, mesh = {Animals ; Climate Change ; DNA, Ancient ; DNA, Mitochondrial ; Fossils ; Humans ; Wolves/*genetics ; }, abstract = {One of the most enduring surprises about the genetic history of Late Pleistocene populations is that continuity is often disturbed by upheaval. In fact, studies that support population continuity are increasingly rare in humans, a variety of vertebrate taxa, and vascular plants (Hofreiter &amp; Stewart 2009; Burbrink et al. 2016). Perhaps such continuity should not be expected as the Pleistocene is marked by episodes of climate change, glaciation and the invasions of humans into previously isolated areas. Although fossils are one of the primary sources for inferring population continuity, a problem with fossil material is that, even if similar morphological forms might exist in a place over time, they may not be from the same genetic lineage. There are now readily available methods to assess genetic continuity solely from DNA found in fossil material, provided the record is fairly continuous. In a From the Cover article in this issue of Molecular Ecology, Loog et al. (2020) apply some of these readily available methods to analyse mitochondrial genomes and model the demography of wolves over the last 50,000 years.}, }
@article {pmid32283039, year = {2020}, author = {Carr, SM}, title = {Evidence for the persistence of ancient Beothuk and Maritime Archaic mitochondrial DNA genome lineages among modern Native American peoples.}, journal = {Genome}, volume = {63}, number = {7}, pages = {349-355}, doi = {10.1139/gen-2019-0149}, pmid = {32283039}, issn = {1480-3321}, mesh = {DNA, Ancient ; *DNA, Mitochondrial ; *Evolution, Molecular ; Genome, Human ; Humans ; Indigenous Canadians/*genetics ; }, abstract = {The Beothuk were a Native American people who formerly occupied the island of Newfoundland, and who are generally accepted to have become culturally extinct in 1829. The Beothuk succeeded the Maritime Archaic people on the island after a hiatus of ca. 1.4 ka, and were themselves succeeded by the extant Mi'kmaq within historic times. Genetic continuity between ancient and modern Native Americans remains of interest. Complete aDNA mitogenomes from ancient Beothuk and Maritime Archaic were compared with the most closely related modern mitogenomes as obtained by BLAST search of GenBank. Beothuk mitogenomes in five clades are in one case identical to and otherwise differ by minima of three to eight SNPs from the most closely related modern mitogenomes. Maritime Archaic mitogenomes in 12 clades are in one case identical to and otherwise differ by minima of one to nine SNPs from the most similar modern mitogenomes. The single available modern Mi'kmaq mitogenome differs from the most similar Beothuk and Maritime Archaic mitogenomes by 12 and 22 SNPs, respectively. Phylogenetic analysis and sequence similarities imply lineage extinction of most ancient clades, as well as continuity of two Beothuk and at least one Maritime Archaic lineages in modern Native Americans and their descendants.}, }
@article {pmid32277584, year = {2020}, author = {Armbrecht, L and Herrando-Pérez, S and Eisenhofer, R and Hallegraeff, GM and Bolch, CJS and Cooper, A}, title = {An optimized method for the extraction of ancient eukaryote DNA from marine sediments.}, journal = {Molecular ecology resources}, volume = {20}, number = {4}, pages = {906-919}, doi = {10.1111/1755-0998.13162}, pmid = {32277584}, issn = {1755-0998}, support = {CE170100015//Australian Research Council/ ; DP170102261//Australian Research Council/ ; DP170104665//Australian Research Council/ ; FL140100260//Australian Research Council/ ; }, mesh = {DNA/*genetics ; DNA, Ancient/*chemistry ; Eukaryota/*genetics ; Fossils ; Gene Library ; Geologic Sediments/*chemistry ; Tasmania ; }, abstract = {Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.}, }
@article {pmid32269345, year = {2020}, author = {Welker, F and Ramos-Madrigal, J and Gutenbrunner, P and Mackie, M and Tiwary, S and Rakownikow Jersie-Christensen, R and Chiva, C and Dickinson, MR and Kuhlwilm, M and de Manuel, M and Gelabert, P and Martinón-Torres, M and Margvelashvili, A and Arsuaga, JL and Carbonell, E and Marques-Bonet, T and Penkman, K and Sabidó, E and Cox, J and Olsen, JV and Lordkipanidze, D and Racimo, F and Lalueza-Fox, C and Bermúdez de Castro, JM and Willerslev, E and Cappellini, E}, title = {The dental proteome of Homo antecessor.}, journal = {Nature}, volume = {580}, number = {7802}, pages = {235-238}, pmid = {32269345}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Dental Enamel/*chemistry/*metabolism ; *Fossils ; Georgia (Republic) ; *Hominidae ; Humans ; Male ; Molar/chemistry/metabolism ; Neanderthals ; Phosphoproteins/analysis/chemistry/metabolism ; Phosphorylation ; Phylogeny ; Proteome/*analysis/chemistry/*metabolism ; Spain ; }, abstract = {The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated[1-5]. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge[6-8]. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)[9,10] and Homo erectus from Dmanisi (Georgia)[1], two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor-that is, similar to that of modern humans-may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.}, }
@article {pmid32265525, year = {2020}, author = {Frantz, LAF and Bradley, DG and Larson, G and Orlando, L}, title = {Animal domestication in the era of ancient genomics.}, journal = {Nature reviews. Genetics}, volume = {21}, number = {8}, pages = {449-460}, pmid = {32265525}, issn = {1471-0064}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animal Husbandry ; Animals ; *Animals, Wild ; DNA, Ancient ; DNA, Mitochondrial ; *Domestication ; Founder Effect ; *Genomics/history/methods ; History, Ancient ; Models, Theoretical ; Selection, Genetic ; Spatio-Temporal Analysis ; }, abstract = {The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.}, }
@article {pmid32238559, year = {2020}, author = {Racimo, F and Woodbridge, J and Fyfe, RM and Sikora, M and Sjögren, KG and Kristiansen, K and Vander Linden, M}, title = {The spatiotemporal spread of human migrations during the European Holocene.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {16}, pages = {8989-9000}, pmid = {32238559}, issn = {1091-6490}, mesh = {Agriculture/history ; Animal Distribution ; Archaeology/*methods ; DNA, Ancient/analysis ; Datasets as Topic ; Europe ; Farmers ; Feasibility Studies ; Forests ; *Genome, Human ; Geography ; Grassland ; History, Ancient ; Human Migration/*history ; Humans ; *Models, Genetic ; Plant Dispersal ; Radiometric Dating ; *Spatio-Temporal Analysis ; }, abstract = {The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. We aim to test to what extent vegetation change through time is associated with changes in population composition as a consequence of these migrations, or with changes in climate. Using ancient DNA in combination with geostatistical techniques, we produce detailed maps of ancient population movements, which allow us to visualize how these migrations unfolded through time and space. We find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings on the cultural spread of farming from radiocarbon-dated archaeological sites. This movement, however, did not have a strong association with changes in the vegetational landscape. In contrast, the Yamnaya migration speed was at least twice as fast and coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture and natural grasslands in the continent. We demonstrate the utility of integrating ancient genomes with archaeometric datasets in a spatiotemporal statistical framework, which we foresee will enable future studies of ancient populations' movements, and their putative effects on local fauna and flora.}, }
@article {pmid32233019, year = {2020}, author = {Mai, BHA and Drancourt, M and Aboudharam, G}, title = {Ancient dental pulp: Masterpiece tissue for paleomicrobiology.}, journal = {Molecular genetics &amp; genomic medicine}, volume = {8}, number = {6}, pages = {e1202}, pmid = {32233019}, issn = {2324-9269}, mesh = {Bacterial Infections/epidemiology/*microbiology ; *DNA, Ancient ; Dental Pulp/*microbiology ; Fossils/*microbiology ; Humans ; Metagenome ; Microbiota ; }, abstract = {INTRODUCTION: Dental pulp with special structure has become a good reference sample in paleomicrobiology-related blood-borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins.<br><br>OBJECTIVES: This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20&#xa0;years following the first detection of an ancient microbe.<br><br>METHODS: The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: "ancient," "dental pulp," "teeth," "anatomy," "structure," "collection," "preservation," "selection," "photography," "radiography," "contamination," "decontamination," "DNA," "protein," "extraction," "bone," "paleomicrobiology," "bacteria," "virus," "pathogen," "molecular biology," "proteomics," "PCR," "MALDI-TOF," "LC/MS," "ELISA," "immunology," "immunochromatography," "genome," "microbiome," "metagenomics."<br><br>RESULTS: The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty-seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species.<br><br>CONCLUSIONS: Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics.}, }
@article {pmid32228443, year = {2020}, author = {Cortázar-Chinarro, M and Meyer-Lucht, Y and Van der Valk, T and Richter-Boix, A and Laurila, A and Höglund, J}, title = {Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans.}, journal = {BMC genetics}, volume = {21}, number = {1}, pages = {38}, pmid = {32228443}, issn = {1471-2156}, mesh = {Alleles ; Animals ; Anura/*genetics ; Codon/genetics ; Gene Frequency/genetics ; *Phylogeny ; Polymorphism, Genetic ; Pore Forming Cytotoxic Proteins/chemistry/*genetics ; Skin/*chemistry ; }, abstract = {BACKGROUND: While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns.<br><br>RESULTS: We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values.<br><br>CONCLUSION: Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.}, }
@article {pmid32224189, year = {2019}, author = {Zhang, L and Liu, M and Long, H and Dong, W and Pasha, A and Esteban, E and Li, W and Yang, X and Li, Z and Song, A and Ran, D and Zhao, G and Zeng, Y and Chen, H and Zou, M and Li, J and Liang, F and Xie, M and Hu, J and Wang, D and Cao, H and Provart, NJ and Zhang, L and Tan, X}, title = {Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {17}, number = {6}, pages = {558-575}, pmid = {32224189}, issn = {2210-3244}, mesh = {Aleurites/*genetics/*metabolism ; Base Sequence ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Genome, Plant/genetics ; *Genomics ; Plant Oils/*metabolism ; }, abstract = {Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further whole-genome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites; 17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.}, }
@article {pmid32219389, year = {2020}, author = {Kim, J and Jeon, S and Choi, JP and Blazyte, A and Jeon, Y and Kim, JI and Ohashi, J and Tokunaga, K and Sugano, S and Fucharoen, S and Al-Mulla, F and Bhak, J}, title = {The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences.}, journal = {Genome biology and evolution}, volume = {12}, number = {5}, pages = {553-565}, pmid = {32219389}, issn = {1759-6653}, mesh = {Chromosomes, Human, Y/genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Ethnicity/*genetics ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Genomics ; Haplotypes ; *Human Migration ; Humans ; Male ; Republic of Korea ; Whole Genome Sequencing ; }, abstract = {Koreans are thought to be an ethnic group of admixed northern and southern subgroups. However, the exact genetic origins of these two remain unclear. In addition, the past admixture is presumed to have taken place on the Korean peninsula, but there is no genomic scale analysis exploring the origin, composition, admixture, or the past migration of Koreans. Here, 88 Korean genomes compared with 91 other present-day populations showed two major genetic components of East Siberia and Southeast Asia. Additional paleogenomic analysis with 115 ancient genomes from Pleistocene hunter-gatherers to Iron Age farmers showed a gradual admixture of Tianyuan (40 ka) and Devil's gate (8 ka) ancestries throughout East Asia and East Siberia up until the Neolithic era. Afterward, the current genetic foundation of Koreans may have been established through a rapid admixture with ancient Southern Chinese populations associated with Iron Age Cambodians. We speculate that this admixing trend initially occurred mostly outside the Korean peninsula followed by continuous spread and localization in Korea, corresponding to the general admixture trend of East Asia. Over 70% of extant Korean genetic diversity is explained to be derived from such a recent population expansion and admixture from the South.}, }
@article {pmid32187203, year = {2020}, author = {Utge, J and Sévêque, N and Lartigot-Campin, AS and Testu, A and Moigne, AM and Vézian, R and Maksud, F and Begouën, R and Verna, C and Soriano, S and Elalouf, JM}, title = {A mobile laboratory for ancient DNA analysis.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0230496}, pmid = {32187203}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Bison ; DNA, Ancient/*analysis ; DNA, Mitochondrial/analysis ; Fossils ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {Mobile devices for on-field DNA analysis have been used for medical diagnostics at the point-of-care, forensic investigations and environmental surveys, but still have to be validated for ancient DNA studies. We report here on a mobile laboratory that we setup using commercially available devices, including a compact real-time PCR machine, and describe procedures to perform DNA extraction and analysis from a variety of archeological samples within 4 hours. The process is carried out on 50 mg samples that are identified at the species level using custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated the potential of this approach in museums lacking facilities for DNA studies by analyzing samples from the Enlène (MIS 2 layer) and the Portel-Ouest cave (MIS 3 deposits), and also performed experiments during an excavation campaign at the Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples only yielded DNA for the extinct steppe bison (Bison priscus), whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta crocuta spelaea) DNA together, for some of them, with DNA for the European bison sister species/subspecies (Bison schoetensacki/Bb1-X), thus highlighting the cave hyena diet. Roc-en-Pail Bovinae bone and tooth samples also contained DNA for the Bison schoetensacki/Bb1-X clade, and Cervidae bone samples only yielded reindeer (Rangifer tarandus) DNA. Subsequent DNA sequencing analyses confirmed that correct species identification had been achieved using our TaqMan assays, hence validating these assays for future studies. We conclude that our approach enables the rapid genetic characterization of tens of millennia-old archeological samples and is expected to be useful for the on-site screening of museums and freshly excavated samples for DNA content. Because our mobile laboratory is made up of commercially available instruments, this approach is easily accessible to other investigators.}, }
@article {pmid32184999, year = {2020}, author = {Moore, G and Tessler, M and Cunningham, SW and Betancourt, J and Harbert, R}, title = {Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.}, journal = {Ecology and evolution}, volume = {10}, number = {5}, pages = {2530-2544}, pmid = {32184999}, issn = {2045-7758}, abstract = {Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C[14] years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI "nt" database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.}, }
@article {pmid32183622, year = {2020}, author = {Ding, M and Wang, T and Ko, AM and Chen, H and Wang, H and Dong, G and Lu, H and He, W and Wangdue, S and Yuan, H and He, Y and Cai, L and Chen, Z and Hou, G and Zhang, D and Zhang, Z and Cao, P and Dai, Q and Feng, X and Zhang, M and Wang, H and Yang, MA and Fu, Q}, title = {Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1923}, pages = {20192968}, pmid = {32183622}, issn = {1471-2954}, support = {55008731/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Altitude ; Asian People/*genetics ; Genetic Variation ; *Genome, Mitochondrial ; Humans ; Tibet ; }, abstract = {The clarification of the genetic origins of present-day Tibetans requires an understanding of their past relationships with the ancient populations of the Tibetan Plateau. Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogroups D4j1b and M9a1a1c1b1a) that suggest some ancestors of Tibetans came from low-altitude areas 4750 to 2775 years ago and that some were involved in an expansion of people moving between high-altitude areas 2125 to 1100 years ago, we found limited evidence of recent matrilineal continuity on the plateau. Furthermore, deep learning of the ancient data incorporated into simulation models with an accuracy of 97% supports that present-day Tibetan matrilineal ancestry received partial contribution rather than complete continuity from the plateau populations of the last 5200 years.}, }
@article {pmid32172220, year = {2020}, author = {Emery, MV and Bolhofner, K and Winingear, S and Oldt, R and Montes, M and Kanthaswamy, S and Buikstra, JE and Fulginiti, LC and Stone, AC}, title = {Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques.}, journal = {Forensic science international. Genetics}, volume = {46}, number = {}, pages = {102272}, doi = {10.1016/j.fsigen.2020.102272}, pmid = {32172220}, issn = {1878-0326}, mesh = {*Body Remains ; Bone and Bones/chemistry ; *Cremation ; DNA/isolation &amp; purification ; DNA Degradation, Necrotic ; DNA Fingerprinting/*methods ; *Fires ; Humans ; *Microsatellite Repeats ; Polymerase Chain Reaction ; Tooth/chemistry ; }, abstract = {Thermal degeneration of the DNA molecule presents a special challenge to medico-legal investigations since low DNA yields, fragmented DNA molecules, and damaged nucleotide bases hinder accurate STR genotyping. As a consequence, fragments of severely burned human remains are often not amenable to standard DNA recovery. However, current ancient DNA (aDNA) extraction methods have proven highly effective at obtaining ultrashort DNA fragments (∼50 bp) from degraded palaeontological and archaeological specimens. In this study, we compare DNA yields and STR results obtained from two established aDNA and forensic DNA extraction protocols by sampling multiple skeletal elements recovered from victims (n = 23) involved in fire-related incidents. DNA yields and STR results suggest an inverse correlation between DNA yield and STR quality and increasing temperature. Despite the rapid thermal destruction of DNA at high temperatures, we generated higher quality full and partial STR profiles using the aDNA extraction protocol across all burn categories than the forensic total bone demineralization extraction method. Our analysis suggests adopting aDNA extraction methods as an alternative to current forensic practices to improve DNA yields from challenging human remains.}, }
@article {pmid32163678, year = {2020}, author = {Li, L and Zou, X and Zhang, G and Wang, H and Su, Y and Wang, M and He, G}, title = {Population genetic analysis of Shaanxi male Han Chinese population reveals genetic differentiation and homogenization of East Asians.}, journal = {Molecular genetics &amp; genomic medicine}, volume = {8}, number = {5}, pages = {e1209}, pmid = {32163678}, issn = {2324-9269}, mesh = {China ; Ethnicity/genetics ; *Evolution, Molecular ; Forensic Genetics/methods ; Genotyping Techniques/methods ; Humans ; Male ; Microsatellite Repeats ; Pedigree ; *Polymorphism, Genetic ; Population/*genetics ; }, abstract = {BACKGROUND: Shaanxi province, located in the upper Yellow River, has been evidenced as the geographic origin of Chinese civilization, Sino-Tibetan-speaking language, and foxtail or broomcorn millet farmers via the linguistic phylogenetic spectrum, archeological documents, and genetic evidence. Nowadays, Han Chinese is the dominant population in this area. The formation process of modern Shaanxi Han population reconstructed via the ancient DNA is on the way, however, the patterns of genetic relationships of modern Shaanxi Han, allele frequency distributions of high mutated short tandem repeats (STRs) and corresponding forensic parameters are remained to be explored.<br><br>METHODS: Here, we successfully genotyped 23 autosomal STRs in 630 unrelated Shaanxi male Han individuals using the recently updated Huaxia Platinum PCR amplification system. Forensic allele frequency and parameters of all autosomal STRs were assessed. And comprehensive population genetic structure was explored via various typical statistical technologies.<br><br>RESULTS: Population genetic analysis based on the raw-genotype dataset among 15,803 Eurasian individuals and frequency datasets among 56 populations generally illustrated that linguistic stratification is significantly associated with the genetic substructure of the East Asian population. Principal component analysis, multidimensional scaling plots and phylogenetic tree further demonstrated that Shaanxi Han has a close genetic relationship with geographically close Shanxi Han, and showed that Han Chinese is a homogeneous population during the historic and recent admixture from the STR variations. Except for Sinitic-speaking populations, Shaanxi Han harbored more alleles sharing with Tibeto-Burman-speaking populations than with other reference populations. Focused on the allele frequency correlation and forensic parameters, all loci are in accordance with the minimum requirements of HWE and LD. The observed combined probability of discrimination of 8.2201E-28 and the cumulative power of exclusion of 0.9999999995 in Shaanxi Han demonstrated that the studied STR loci are informative and polymorphic, and this system can be used as a powerful routine forensic tool in personal identification and parentage testing.<br><br>CONCLUSION: Both the geographical and linguistic divisions have shaped the genetic structure of modern East Asian. And more forensic reference data should be obtained for ethnically, culturally, geographically and linguistically different populations for better routine forensic practice and population genetic studies.}, }
@article {pmid32145389, year = {2020}, author = {Thang, TN and Vázquez-Prieto, S and Vilas, R and Paniagua, E and Ubeira, FM and Ichikawa-Seki, M}, title = {Genetic diversity of Fasciola hepatica in Spain and Peru.}, journal = {Parasitology international}, volume = {76}, number = {}, pages = {102100}, doi = {10.1016/j.parint.2020.102100}, pmid = {32145389}, issn = {1873-0329}, mesh = {Animals ; Carboxy-Lyases/analysis ; Cattle ; Cattle Diseases/*parasitology ; DNA Polymerase III/analysis ; Fasciola hepatica/*genetics ; Fascioliasis/parasitology/*veterinary ; Fungal Proteins/analysis ; *Genetic Variation ; Peru ; Phylogeny ; Sequence Analysis, DNA ; Sheep ; Sheep Diseases/*parasitology ; Spain ; }, abstract = {In the present study, molecular characterization of Fasciola flukes from Spain was performed to reveal the relation with the previously reported Peruvian F. hepatica population. The nuclear DNA markers, phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold), were used for species identification of Fasciola flukes. A total of 196 Fasciola flukes were identified as F. hepatica by pepck and pold, and 26 haplotypes were detected in mitochondrial NADH dehydrogenase subunit 1 (nad1). Only one of them was previously found in Spanish samples; which indicates the existence of high genetic diversity and population structure in F. hepatica from Spain. Three haplotypes were identical to those from Peruvian F. hepatica. The pairwise fixation index value confirmed a relatively close relationship between the Spanish and Peruvian F. hepatica samples. The Spanish samples showed clearly higher genetic variability than the Peruvian population. These results are discussed in relation with the hypothesis of the introduction of the parasite in America from Europe and recent evidence of pre-Hispanic F. hepatica from Argentina revealed by ancient DNA.}, }
@article {pmid32145021, year = {2020}, author = {Mathieson, I}, title = {Limited Evidence for Selection at the FADS Locus in Native American Populations.}, journal = {Molecular biology and evolution}, volume = {37}, number = {7}, pages = {2029-2033}, pmid = {32145021}, issn = {1537-1719}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Delta-5 Fatty Acid Desaturase ; *Evolution, Molecular ; Fatty Acid Desaturases/*genetics ; Haplotypes ; Humans ; Phylogeography ; *Selection, Genetic ; American Indian or Alaska Native/*genetics ; }, abstract = {The FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids. This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of long-chain polyunsaturated fatty acids varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals are confounded by independent selection-postdating the split from Native Americans-in the European and, possibly, the East Asian populations used in the population branch statistic test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. An explanation for the present-day distribution of the haplotype that is more consistent with the data is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown.}, }
@article {pmid32142382, year = {2020}, author = {Zhang, J and Lees, DC and Shen, J and Cong, Q and Huertas, B and Martin, G and Grishin, NV}, title = {The mitogenome of a Malagasy butterfly Malaza fastuosus (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (Lepidoptera).}, journal = {Genome}, volume = {63}, number = {4}, pages = {195-202}, pmid = {32142382}, issn = {1480-3321}, support = {R01 GM094575/GM/NIGMS NIH HHS/United States ; R35 GM127390/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Butterflies/*genetics ; Female ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; Lepidoptera/*genetics ; Male ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Malaza fastuosus is a lavishly patterned skipper butterfly from a genus that has three described species, all endemic to the mainland of Madagascar. To our knowledge, M. fastuosus has not been collected for nearly 50 years. To evaluate the power of our techniques to recover DNA, we used a single foreleg of an at least 140-year-old holotype specimen from the collection of the Natural History Museum London with no destruction of external morphology to extract DNA and assemble a complete mitogenome from next generation sequencing reads. The resulting 15 540 bp mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A+T rich region, similarly to other Lepidoptera mitogenomes. Here we provide the first mitogenome also for Trapezitinae (Rachelia extrusus). Phylogenetic analysis of available skipper mitogenomes places Malaza outside of Trapezitinae and Barcinae + Hesperiinae, with a possible sister relationship to Heteropterinae. Of these, at least Heteropterinae, Trapezitinae, and almost all Hesperiinae have monocot-feeding caterpillars. Malaza appears to be an evolutionarily highly distinct ancient lineage, morphologically with several unusual hesperiid features. The monotypic subfamily Malazinae Lees &amp; Grishin subfam. nov. (type genus Malaza) is proposed to reflect this morphological and molecular evidence.}, }
@article {pmid32130218, year = {2020}, author = {Sawafuji, R and Saso, A and Suda, W and Hattori, M and Ueda, S}, title = {Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0226654}, pmid = {32130218}, issn = {1932-6203}, mesh = {Archaeology/*methods ; Body Remains ; DNA Barcoding, Taxonomic ; DNA, Ancient/*isolation &amp; purification ; DNA, Fungal/isolation &amp; purification ; DNA, Plant/isolation &amp; purification ; Dental Calculus/*chemistry ; *Feeding Behavior ; Female ; Fungi/genetics ; History, 18th Century ; History, 19th Century ; Humans ; Japan ; Male ; Oryza/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th-19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.}, }
@article {pmid32127690, year = {2020}, author = {Racimo, F and Sikora, M and Vander Linden, M and Schroeder, H and Lalueza-Fox, C}, title = {Beyond broad strokes: sociocultural insights from the study of ancient genomes.}, journal = {Nature reviews. Genetics}, volume = {21}, number = {6}, pages = {355-366}, pmid = {32127690}, issn = {1471-0064}, mesh = {Archaeology/methods ; DNA, Ancient/*analysis ; Emigration and Immigration/statistics &amp; numerical data ; Genetics, Population/*methods ; History, Ancient ; Humans ; Metagenomics/*methods ; Socioeconomic Factors ; }, abstract = {In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from mostly large-scale supraregional studies to a more local perspective, shedding light on socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies showcasing these types of insights, focusing on methods used to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines - such as anthropology, archaeology, linguistics and genetics - that have until recently evolved in separation. Multidisciplinary dialogue is important for an integrated reconstruction of human history, which can yield extraordinary insights about past societies, reproductive behaviours and even lifestyle habits that would not be possible to obtain otherwise.}, }
@article {pmid32119793, year = {2020}, author = {Kistler, L and Bieker, VC and Martin, MD and Pedersen, MW and Ramos Madrigal, J and Wales, N}, title = {Ancient Plant Genomics in Archaeology, Herbaria, and the Environment.}, journal = {Annual review of plant biology}, volume = {71}, number = {}, pages = {605-629}, doi = {10.1146/annurev-arplant-081519-035837}, pmid = {32119793}, issn = {1545-2123}, mesh = {*Archaeology ; *DNA, Ancient ; Environment ; Genomics ; Plants/genetics ; }, abstract = {The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.}, }
@article {pmid32098773, year = {2020}, author = {Sirak, K and Fernandes, D and Cheronet, O and Harney, E and Mah, M and Mallick, S and Rohland, N and Adamski, N and Broomandkhoshbacht, N and Callan, K and Candilio, F and Lawson, AM and Mandl, K and Oppenheimer, J and Stewardson, K and Zalzala, F and Anders, A and Bartík, J and Coppa, A and Dashtseveg, T and Évinger, S and Farkaš, Z and Hajdu, T and Bayarsaikhan, J and McIntyre, L and Moiseyev, V and Okumura, M and Pap, I and Pietrusewsky, M and Raczky, P and Šefčáková, A and Soficaru, A and Szeniczey, T and Szőke, BM and Van Gerven, D and Vasilyev, S and Bell, L and Reich, D and Pinhasi, R}, title = {Human auditory ossicles as an alternative optimal source of ancient DNA.}, journal = {Genome research}, volume = {30}, number = {3}, pages = {427-436}, pmid = {32098773}, issn = {1549-5469}, support = {263441/ERC_/European Research Council/International ; }, mesh = {Cochlea/chemistry ; DNA, Ancient/*analysis ; Ear Ossicles/anatomy &amp; histology/*chemistry/embryology ; Humans ; Sequence Analysis, DNA ; }, abstract = {DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.}, }
@article {pmid32094539, year = {2020}, author = {Fernandes, DM and Mittnik, A and Olalde, I and Lazaridis, I and Cheronet, O and Rohland, N and Mallick, S and Bernardos, R and Broomandkhoshbacht, N and Carlsson, J and Culleton, BJ and Ferry, M and Gamarra, B and Lari, M and Mah, M and Michel, M and Modi, A and Novak, M and Oppenheimer, J and Sirak, KA and Stewardson, K and Mandl, K and Schattke, C and Özdoğan, KT and Lucci, M and Gasperetti, G and Candilio, F and Salis, G and Vai, S and Camarós, E and Calò, C and Catalano, G and Cueto, M and Forgia, V and Lozano, M and Marini, E and Micheletti, M and Miccichè, RM and Palombo, MR and Ramis, D and Schimmenti, V and Sureda, P and Teira, L and Teschler-Nicola, M and Kennett, DJ and Lalueza-Fox, C and Patterson, N and Sineo, L and Coppa, A and Caramelli, D and Pinhasi, R and Reich, D}, title = {The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {3}, pages = {334-345}, pmid = {32094539}, issn = {2397-334X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa ; *Agriculture ; Anthropology ; *DNA, Ancient ; Emigration and Immigration ; Europe ; *Genome-Wide Association Study ; Humans ; Iran ; Islands ; Sicily ; Spain ; }, abstract = {Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.}, }
@article {pmid32094358, year = {2020}, author = {Marcus, JH and Posth, C and Ringbauer, H and Lai, L and Skeates, R and Sidore, C and Beckett, J and Furtwängler, A and Olivieri, A and Chiang, CWK and Al-Asadi, H and Dey, K and Joseph, TA and Liu, CC and Der Sarkissian, C and Radzevičiūtė, R and Michel, M and Gradoli, MG and Marongiu, P and Rubino, S and Mazzarello, V and Rovina, D and La Fragola, A and Serra, RM and Bandiera, P and Bianucci, R and Pompianu, E and Murgia, C and Guirguis, M and Orquin, RP and Tuross, N and van Dommelen, P and Haak, W and Reich, D and Schlessinger, D and Cucca, F and Krause, J and Novembre, J}, title = {Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {939}, pmid = {32094358}, issn = {2041-1723}, support = {HHSN271201100005C/DA/NIDA NIH HHS/United States ; R01 GM132383/GM/NIGMS NIH HHS/United States ; R01 HG007089/HG/NHGRI NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeology/methods ; Body Remains ; Chromosomes, Human, X/genetics ; Chromosomes, Human, Y/genetics ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Datasets as Topic ; Female ; Genetics, Population/*history ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; *Human Migration ; Humans ; Italy ; Male ; *Models, Genetic ; Sequence Analysis, DNA ; }, abstract = {The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.}, }
@article {pmid32081659, year = {2020}, author = {Guedes, L and Borba, VH and Camacho, M and Neto, J and Dias, O and Iñiguez, AM}, title = {African helminth infection out of Africa: Paleoparasitological and paleogenetic investigations in Pretos Novos cemetery, Rio de Janeiro, Brazil (1769-1830).}, journal = {Acta tropica}, volume = {205}, number = {}, pages = {105399}, doi = {10.1016/j.actatropica.2020.105399}, pmid = {32081659}, issn = {1873-6254}, mesh = {Africa/epidemiology ; Animals ; Brazil/epidemiology ; *Cemeteries ; Enslavement ; Environment ; Helminthiasis/*epidemiology/*parasitology ; Helminths/*isolation &amp; purification ; Humans ; }, abstract = {Pretos Novos cemetery (PNC), Rio de Janeiro, Brazil (1769-1830) was created exclusively to bury enslaved Africans who died upon arrival at the city or before being sold in the slave market. The PNC site may be unique in the Americas in allowing the study of African parasite infections acquired in Africa. We aimed to identify parasites infecting PNC individuals through paleoparasitological and paleogenetic analyses. The bodies had been dismembered, placed in mass graves, and burned, and most human remains collected from the site are highly fragmented and show extensive degradation. Sacrum and pelvic sediments were collected from five individuals along with seven samples of sediment from other areas of the body, as controls. Samples were submitted to three parasitological techniques and, in paleogenetic analysis, to four molecular targets. Larvae, mites, pollen grains, and structure suggestive of plants and fungus were observed, but we found no evidence of helminth infection. Ascaris sp. cytb sequence was recovered in one individual. We emphasize that, even with the extensive degradation of PNC human remains and the process of curation of samples, it was possible to recover helminth aDNA. The origin of PNC individuals confirms that these infections were brought to Brazil from western and central Africa during the colonial era.}, }
@article {pmid32073242, year = {2019}, author = {Wu, X and Ning, C and Bao, Q and Gao, S and Zhang, F and Wu, S and Li, T and Fan, L and Li, T and Yang, X and Cai, D and Cui, Y}, title = {Mitochondrial Genome of an 8,400-Year-Old Individual from Northern China Reveals a Novel Subclade Under C5d.}, journal = {Human biology}, volume = {91}, number = {1}, pages = {21-30}, doi = {10.13110/humanbiology.91.1.04}, pmid = {32073242}, issn = {1534-6617}, mesh = {DNA, Ancient ; DNA, Mitochondrial ; Genome, Mitochondrial/*genetics ; Genotyping Techniques ; Haplotypes/*genetics ; History, Ancient ; Humans ; Mongolia/epidemiology ; Phylogeny ; }, abstract = {Ancient DNA studies have always refreshed our understanding of the human past that cannot be tracked by modern DNA alone. Until recently, ancient mitochondrial genomic studies in East Asia were still very limited. Here, we retrieved the whole mitochondrial genome of an 8,400-year-old individual from Inner Mongolia, China. Phylogenetic analyses show that the individual belongs to a previously undescribed clade under haplogroup C5d that most probably originated in northern Asia and may have a very low frequency in extant populations that have not yet been sampled. We further characterized the demographic history of mitochondrial haplogroups C5 and C5d and found that C5 experienced a sharp increase in population size starting around 4,000 years before present, the time when intensive millet farming was developed by populations who are associated with the Lower Xiajiadian culture and was widely adopted in northern China. We caution that people related to haplogroup C5 may have added this farming technology to their original way of life and that the various forms of subsistence may have provided abundant food sources and further contributed to the increase in population size.}, }
@article {pmid32064591, year = {2020}, author = {Harding, T and Milot, E and Moreau, C and Lefebvre, JF and Bournival, JS and Vézina, H and Laprise, C and Lalueza-Fox, C and Anglada, R and Loewen, B and Casals, F and Ribot, I and Labuda, D}, title = {Historical human remains identification through maternal and paternal genetic signatures in a founder population with extensive genealogical record.}, journal = {American journal of physical anthropology}, volume = {171}, number = {4}, pages = {645-658}, doi = {10.1002/ajpa.24024}, pmid = {32064591}, issn = {1096-8644}, mesh = {Adult ; Anthropology, Physical/*methods ; Body Remains ; *Genetic Markers ; Humans ; Male ; *Maternal Inheritance ; Middle Aged ; *Paternal Inheritance ; Quebec ; Young Adult ; }, abstract = {OBJECTIVES: We describe a method to identify human remains excavated from unmarked graves in historical Québec cemeteries by combining parental-lineage genetic markers with the whole-population genealogy of Québec contained in the BALSAC database.<br><br>MATERIALS AND METHODS: The remains of six men were exhumed from four historical cemeteries in the province of Qu&#xe9;bec, Canada. DNA was extracted from the remains and genotyped to reveal their mitochondrial and Y-chromosome haplotypes, which were compared to a collection of haplotypes of genealogically-anchored modern volunteers. Maternal and paternal genealogies were searched in the BALSAC genealogical record for parental couples matching the mitochondrial and the Y-chromosome haplotypic signatures, to identify candidate sons from whom the remains could have originated.<br><br>RESULTS: Analysis of the matching genealogies identified the parents of one man inhumed in the cemetery of the investigated parish during its operating time. The candidate individual died in 1833 at the age of 58, a plausible age at death in light of osteological analysis of the remains.<br><br>DISCUSSION: This study demonstrates the promising potential of coupling genetic information from living individuals to genealogical data in BALSAC to identify historical human remains. If genetic coverage is increased, the genealogical information in BALSAC could enable the identification of 87% of the men (n =&#x2009;178,435) married in Qu&#xe9;bec before 1850, with high discriminatory power in most cases since >75% of the parental couples have unique biparental signatures in most regions. Genotyping and identifying Qu&#xe9;bec's historical human remains are a key to reconstructing the genomes of the founders of Qu&#xe9;bec and reinhuming archeological remains with a marked grave.}, }
@article {pmid32022848, year = {2020}, author = {Mathieson, I and Abascal, F and Vinner, L and Skoglund, P and Pomilla, C and Mitchell, P and Arthur, C and Gurdasani, D and Willerslev, E and Sandhu, MS and Dewar, G}, title = {An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa.}, journal = {Genome biology and evolution}, volume = {12}, number = {4}, pages = {407-412}, pmid = {32022848}, issn = {1759-6653}, support = {MR/S003711/2/MRC_/Medical Research Council/United Kingdom ; 852558/ERC_/European Research Council/International ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; R35 GM133708/GM/NIGMS NIH HHS/United States ; MR/S003711/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; WT098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa, Southern ; Animals ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; *Genetics, Population ; Papio/*genetics ; Phylogeny ; }, abstract = {Baboons are one of the most abundant large nonhuman primates and are widely studied in biomedical, behavioral, and anthropological research. Despite this, our knowledge of their evolutionary and demographic history remains incomplete. Here, we report a 0.9-fold coverage genome sequence from a 5800-year-old baboon from the site of Ha Makotoko in Lesotho. The ancient baboon is closely related to present-day Papio ursinus individuals from southern Africa-indicating a high degree of continuity in the southern African baboon population. This level of population continuity is rare in recent human populations but may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.}, }
@article {pmid32019465, year = {2020}, author = {Macleod, R and Sinding, MS and Olsen, MT and Collins, MJ and Rowland, SJ}, title = {DNA preserved in jetsam whale ambergris.}, journal = {Biology letters}, volume = {16}, number = {2}, pages = {20190819}, pmid = {32019465}, issn = {1744-957X}, mesh = {*Ambergris ; Animals ; DNA ; Netherlands ; New Zealand ; Whales/genetics ; }, abstract = {Jetsam ambergris, found on beaches worldwide, has always been assumed to originate as a natural product of sperm whales (Physeteroidea). However, only indirect evidence has ever been produced for this, such as the presence of whale prey remains in ambergris. Here, we extracted and analysed DNA sequences from jetsam ambergris from beaches in New Zealand and Sri Lanka, and sequences from ambergris of a sperm whale beached in The Netherlands. The lipid-rich composition of ambergris facilitated high preservation-quality of endogenous DNA, upon which we performed shotgun Illumina sequencing. Alignment of mitochondrial and nuclear genome sequences with open-access reference data for multiple whale species confirms that all three jetsam samples derived originally from sperm whales (Physeter macrocephalus). Shotgun sequencing here also provides implications for metagenomic insights into ambergris-preserved DNA. These results demonstrate significant implications for elucidating the origins of jetsam ambergris as a prized natural product, and also for the understanding of sperm whale metabolism and diet, and the ecological mechanisms underlying these coproliths.}, }
@article {pmid32017876, year = {2020}, author = {Xenikoudakis, G and Ahmed, M and Harris, JC and Wadleigh, R and Paijmans, JLA and Hartmann, S and Barlow, A and Lerner, H and Hofreiter, M}, title = {Ancient DNA reveals twenty million years of aquatic life in beavers.}, journal = {Current biology : CB}, volume = {30}, number = {3}, pages = {R110-R111}, doi = {10.1016/j.cub.2019.12.041}, pmid = {32017876}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Genome, Mitochondrial ; Life History Traits ; Rodentia/genetics/*physiology ; }, abstract = {Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.}, }
@article {pmid32015858, year = {2020}, author = {Tabares, X and Zimmermann, H and Dietze, E and Ratzmann, G and Belz, L and Vieth-Hillebrand, A and Dupont, L and Wilkes, H and Mapani, B and Herzschuh, U}, title = {Vegetation state changes in the course of shrub encroachment in an African savanna since about 1850 CE and their potential drivers.}, journal = {Ecology and evolution}, volume = {10}, number = {2}, pages = {962-979}, pmid = {32015858}, issn = {2045-7758}, abstract = {Shrub encroachment has far-reaching ecological and economic consequences in many ecosystems worldwide. Yet, compositional changes associated with shrub encroachment are often overlooked despite having important effects on ecosystem functioning.We document the compositional change and potential drivers for a northern Namibian Combretum woodland transitioning into a Terminalia shrubland. We use a multiproxy record (pollen, sedimentary ancient DNA, biomarkers, compound-specific carbon (δ[13]C) and deuterium (δD) isotopes, bulk carbon isotopes (δ[13]Corg), grain size, geochemical properties) from Lake Otjikoto at high taxonomical and temporal resolution.We provide evidence that state changes in semiarid environments may occur on a scale of one century and that transitions between stable states can span around 80 years and are characterized by a unique vegetation composition. We demonstrate that the current grass/woody ratio is exceptional for the last 170 years, as supported by n-alkane distributions and the δ[13]C and δ[13]Corg records. Comparing vegetation records to environmental proxy data and census data, we infer a complex network of global and local drivers of vegetation change. While our δD record suggests physiological adaptations of woody species to higher atmospheric pCO2 concentration and drought, our vegetation records reflect the impact of broad-scale logging for the mining industry, and the macrocharcoal record suggests a decrease in fire activity associated with the intensification of farming. Impact of selective grazing is reflected by changes in abundance and taxonomical composition of grasses and by an increase of nonpalatable and trampling-resistant taxa. In addition, grain-size and spore records suggest changes in the erodibility of soils because of reduced grass cover. Synthesis. We conclude that transitions to an encroached savanna state are supported by gradual environmental changes induced by management strategies, which affected the resilience of savanna ecosystems. In addition, feedback mechanisms that reflect the interplay between management legacies and climate change maintain the encroached state.}, }
@article {pmid32004756, year = {2020}, author = {de-Dios, T and van Dorp, L and Charlier, P and Morfopoulou, S and Lizano, E and Bon, C and Le Bitouzé, C and Alvarez-Estape, M and Marquès-Bonet, T and Balloux, F and Lalueza-Fox, C}, title = {Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793).}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {80}, number = {}, pages = {104209}, pmid = {32004756}, issn = {1567-7257}, support = {206478/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 206478/WT_/Wellcome Trust/United Kingdom ; BB/R01356X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; U01 MH106874/MH/NIMH NIH HHS/United States ; MR/P007597/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Blood Stains ; DNA, Mitochondrial ; Forensic Genetics/*methods ; Genetics, Population ; Humans ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {The French revolutionary Jean-Paul Marat (1743-1793) was assassinated in 1793 in his bathtub, where he was trying to find relief from the debilitating skin disease he was suffering from. At the time of his death, Marat was annotating newspapers, which got stained with his blood and were subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain and also from another section of the newspaper, which we used for comparison. Results from the human DNA sequence analyses were compatible with a heterogeneous ancestry of Marat, with his mother being of French origin and his father born in Sardinia. Metagenomic analyses of the non-human reads uncovered the presence of fungal, bacterial and low levels of viral DNA. Relying on the presence/absence of microbial species in the samples, we could cast doubt on several putative infectious agents that have been previously hypothesised as the cause of his condition but for which we detect not a single sequencing read. Conversely, some of the species we detect are uncommon as environmental contaminants and may represent plausible infective agents. Based on all the available evidence, we hypothesize that Marat may have suffered from a fungal infection (seborrheic dermatitis), possibly superinfected with bacterial opportunistic pathogens.}, }
@article {pmid31992804, year = {2020}, author = {Oswald, JA and Allen, JM and LeFebvre, MJ and Stucky, BJ and Folk, RA and Albury, NA and Morgan, GS and Guralnick, RP and Steadman, DW}, title = {Ancient DNA and high-resolution chronometry reveal a long-term human role in the historical diversity and biogeography of the Bahamian hutia.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1373}, pmid = {31992804}, issn = {2045-2322}, mesh = {Animals ; Bahamas ; *DNA, Ancient ; *Fossils ; Humans ; *Phylogeny ; Phylogeography ; *Rodentia/classification/genetics ; }, abstract = {Quaternary paleontological and archaeological evidence often is crucial for uncovering the historical mechanisms shaping modern diversity and distributions. We take an interdisciplinary approach using multiple lines of evidence to understand how past human activity has shaped long-term animal diversity in an island system. Islands afford unique opportunities for such studies given their robust fossil and archaeological records. Herein, we examine the only non-volant terrestrial mammal endemic to the Bahamian Archipelago, the hutia Geocapromys ingrahami. This capromyine rodent once inhabited many islands but is now restricted to several small cays. Radiocarbon dated fossils indicate that hutias were present on the Great Bahama Bank islands before humans arrived at AD ~800-1000; all dates from other islands post-date human arrival. Using ancient DNA from a subset of these fossils, along with modern representatives of Bahamian hutia and related taxa, we develop a fossil-calibrated phylogeny. We found little genetic divergence among individuals from within either the northern or southern Bahamas but discovered a relatively deep North-South divergence (~750 ka). This result, combined with radiocarbon dating and archaeological evidence, reveals a pre-human biogeographic divergence, and an unexpected human role in shaping Bahamian hutia diversity and biogeography across islands.}, }
@article {pmid31990948, year = {2020}, author = {Gismondi, A and Baldoni, M and Gnes, M and Scorrano, G and D'Agostino, A and Di Marco, G and Calabria, G and Petrucci, M and Müldner, G and Von Tersch, M and Nardi, A and Enei, F and Canini, A and Rickards, O and Alexander, M and Martínez-Labarga, C}, title = {A multidisciplinary approach for investigating dietary and medicinal habits of the Medieval population of Santa Severa (7th-15th centuries, Rome, Italy).}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227433}, pmid = {31990948}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; Bone and Bones/*chemistry/metabolism ; *Cemeteries ; DNA, Ancient/*analysis ; Diet/*history ; History, Medieval ; Humans ; Rome ; }, abstract = {A multidisciplinary approach, combining stable isotope analysis from bone proteins and investigations on dental calculus using DNA analysis, light microscopy, and gas chromatography coupled with mass spectrometry, was applied to reconstruct dietary and medicinal habits of the individuals recovered in the cemetery of the Castle of Santa Severa (7th-15th centuries CE; Rome, Italy). Stable isotope analysis was performed on 120 humans, 41 faunal specimens and 8 charred seeds. Dental calculus analyses were carried out on 94 samples. Overall, isotope data indicated an omnivorous diet based on C3-terrestrial protein, although some individuals possessed carbon values indicative of C4 plant consumption. In terms of animal protein, the diet was probably based on cattle, sheep, pig and chicken products, as witnessed by the archaeozoological findings. Evidence from calculus suggested the consumption of C3 cereals, Fabaceae, Fagaceae, milk and dairy products. Secondary metabolites of herbs and wine were also detected. The detection of marine fish ancient DNA, as well as of ω3 fatty acids in calculus, hypothesized the consumption of marine foodstuffs for this coastal population, despite the lack of a clear marine isotopic signal and the presence of polyunsaturated fatty acids in plant tissues. Moreover, the knowledge of ethnopharmacological tradition and the application of medicinal plants (e.g. Punica granatum L., Ephedra sp. L.) were also identified. The detection of artemisinin, known to have antimalarial properties, led to hypothesize the presence of malaria in the area. Altogether, the combined application of microscopy and biomolecular techniques provided an innovative reconstruction of Medieval lifeways in Central Italy.}, }
@article {pmid31984637, year = {2020}, author = {Segawa, T and Yonezawa, T}, title = {Evaluation of reported sediment samples from 20 Ma using a molecular phylogenetic approach: comment on Liu et al. (2017).}, journal = {Environmental microbiology}, volume = {22}, number = {3}, pages = {813-818}, doi = {10.1111/1462-2920.14923}, pmid = {31984637}, issn = {1462-2920}, support = {JP17H01854//KAKENHI/International ; JP18H04139//KAKENHI/International ; }, mesh = {*Ascomycota/genetics ; Coal ; Fungi/genetics ; *Mycobiome ; Oceans and Seas ; Phylogeny ; }, abstract = {Liu et al. reported the cultivation and DNA sequencing of 69 fungal isolates (Ascomycota and Basidiomycota) from ancient subseafloor sediments, suggesting that they represent living fungal populations that have persisted for over 20 million years. Because these findings could bring about a paradigm shift in our understanding of the spatial breadth of the deep subsurface biosphere as well as the longevity of ancient DNA, it is extremely important to verify that their samples represent pure ancient fungi from 20 million years ago without contamination by modern species. For this purpose, we estimated the divergence times of Dikarya (Ascomycota + Basidiomycota) and Mucoromycota fungi assuming that the fungal isolates were actually sampled from 20 Ma (mega-annum) sediments and evaluated the validity of the sample ages. Using this approach, we estimate that the age of the last common ancestor of Dikarya and Mucoromycota fungi greatly exceeds the age of the Earth. Our finding emphasizes the importance of using reliable approaches to confirm the dating of ancient samples.}, }
@article {pmid31969593, year = {2020}, author = {Taylor, WTT and Clark, J and Bayarsaikhan, J and Tuvshinjargal, T and Jobe, JT and Fitzhugh, W and Kortum, R and Spengler, RN and Shnaider, S and Seersholm, FV and Hart, I and Case, N and Wilkin, S and Hendy, J and Thuering, U and Miller, B and Miller, ARV and Picin, A and Vanwezer, N and Irmer, F and Brown, S and Abdykanova, A and Shultz, DR and Pham, V and Bunce, M and Douka, K and Jones, EL and Boivin, N}, title = {Early Pastoral Economies and Herding Transitions in Eastern Eurasia.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1001}, pmid = {31969593}, issn = {2045-2322}, abstract = {While classic models for the emergence of pastoral groups in Inner Asia describe mounted, horse-borne herders sweeping across the Eurasian Steppes during the Early or Middle Bronze Age (ca. 3000-1500 BCE), the actual economic basis of many early pastoral societies in the region is poorly characterized. In this paper, we use collagen mass fingerprinting and ancient DNA analysis of some of the first stratified and directly dated archaeofaunal assemblages from Mongolia's early pastoral cultures to undertake species identifications of this rare and highly fragmented material. Our results provide evidence for livestock-based, herding subsistence in Mongolia during the late 3rd and early 2nd millennia BCE. We observe no evidence for dietary exploitation of horses prior to the late Bronze Age, ca. 1200 BCE - at which point horses come to dominate ritual assemblages, play a key role in pastoral diets, and greatly influence pastoral mobility. In combination with the broader archaeofaunal record of Inner Asia, our analysis supports models for widespread changes in herding ecology linked to the innovation of horseback riding in Central Asia in the final 2nd millennium BCE. Such a framework can explain key broad-scale patterns in the movement of people, ideas, and material culture in Eurasian prehistory.}, }
@article {pmid31964606, year = {2020}, author = {Nelson, EA and Buikstra, JE and Herbig, A and Tung, TA and Bos, KI}, title = {Advances in the molecular detection of tuberculosis in pre-contact Andean South America.}, journal = {International journal of paleopathology}, volume = {29}, number = {}, pages = {128-140}, doi = {10.1016/j.ijpp.2019.12.006}, pmid = {31964606}, issn = {1879-9825}, mesh = {DNA, Bacterial/genetics/*history ; Diffusion of Innovation ; Forecasting ; High-Throughput Nucleotide Sequencing/trends ; History, Ancient ; Humans ; Metagenomics/trends ; *Mycobacterium tuberculosis/genetics ; *Paleopathology/trends ; *Research Design/trends ; Sequence Analysis, DNA/*trends ; South America ; Tuberculosis/genetics/*history/microbiology ; }, abstract = {Andean paleopathological research has significantly enhanced knowledge about the geographical distribution and evolution of tuberculosis (TB) in pre-Columbian South America. In this paper, we review the history and progress of research on ancient tuberculosis (TB) in the Andean region, focusing on the strengths and limitations of current approaches for the molecular detection of ancient pathogens, with special attention to TB. As a case study, we describe a molecular screening approach for the detection of ancient Mycobacterium tuberculosis in individuals from Late Intermediate Period (1000-1400 CE) contexts at the site of Huari, Peru. We evaluate 34 commingled human vertebrae and combine morphological assessments of pathology with high throughput sequencing and a non-selective approach to ancient pathogen DNA screening. Our method enabled the simultaneous detection of ancient M. tuberculosis DNA and an evaluation of the environmental microbial composition of each sample. Our results show that despite the dominance of environmental DNA, molecular signatures of M. tuberculosis were identified in eight vertebrae, six of which had no observable skeletal pathology classically associated tuberculosis infection. This screening approach will assist in the identification of candidate samples for downstream genomic analyses. The method permits higher resolution disease identification in cases where pathology may be absent, or where the archaeological context may necessitate a broad differential diagnosis based on morphology alone.}, }
@article {pmid31959418, year = {2020}, author = {Napier, JD and de Lafontaine, G and Chipman, ML}, title = {The Evolution of Paleoecology.}, journal = {Trends in ecology &amp; evolution}, volume = {35}, number = {4}, pages = {293-295}, doi = {10.1016/j.tree.2019.12.006}, pmid = {31959418}, issn = {1872-8383}, mesh = {Acclimatization ; *Adaptation, Physiological/genetics ; *Climate Change ; DNA, Ancient ; }, abstract = {While the interplay between migration and adaptation dictates species response to climate change, technological limitations have obfuscated explicit tests on past adaptive responses. However, a surge in technology-driven advances in paleoecological methods coincides with breakthroughs in processing ancient DNA, providing the first opportunity to assess adaptation to past climate shifts.}, }
@article {pmid31957867, year = {2020}, author = {Schmidt, N and Schücker, K and Krause, I and Dörk, T and Klintschar, M and Hummel, S}, title = {Genome-wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains.}, journal = {American journal of physical anthropology}, volume = {172}, number = {1}, pages = {99-109}, doi = {10.1002/ajpa.23996}, pmid = {31957867}, issn = {1096-8644}, mesh = {Archaeology ; Body Remains ; DNA, Ancient/*analysis ; Eye Color/*genetics ; *Genotype ; Germany ; Hair Color/*genetics ; History, Ancient ; Humans ; *Polymorphism, Single Nucleotide ; }, abstract = {OBJECTIVE: A genome-wide high-throughput single nucleotide polymorphism (SNP) typing method was tested with respect of the applicability to ancient and degraded DNA. The results were compared to mini-sequencing data achieved through single base extension (SBE) typing. The SNPs chosen for the study allow to determine the hair colors and eye colors of humans.<br><br>MATERIAL AND METHODS: The DNA samples were extracted from the skeletal remains of 59 human individuals dating back to the Late Bronze Age. The 3,000&#x2009;years old bones had been discovered in the Lichtenstein Cave in Lower Saxony, Germany. The simultaneous typing of 24 SNPs for each of the ancient DNA samples was carried out using the 192.24 Dynamic Array&#x2122; by Fluidigm&#xae;.<br><br>RESULTS: Thirty-eight of the ancient samples (=64%) revealed full and reproducible SNP genotypes allowing hair and eye color phenotyping. In 10 samples (=17%) at least half of the SNPs were unambiguously determined, in 11 samples (=19%) the SNP typing failed. For 23 of the 59 individuals, a comparison of the SNP typing results with genotypes from an earlier performed SBE typing approach was possible. The comparison confirmed the full concordance of the results for 90% of the SNP typings. In the remaining 10% allelic dropouts were identified.<br><br>DISCUSSION: The high genotyping success rate could be achieved by introducing modifications to the preamplification protocol mainly by increasing the DNA input and the amplification cycle number. The occurrence of allelic dropouts indicates that a further increase of DNA input to the preamplification step is desirable.}, }
@article {pmid31943391, year = {2020}, author = {Öhrström, L and Tekin, A and Biedermann, P and Morozova, I and Habicht, M and Gascho, D and Bode-Lesniewska, B and Imhof, A and Rühli, F and Eppenberger, P}, title = {Experimental mummification-In the tracks of the ancient Egyptians.}, journal = {Clinical anatomy (New York, N.Y.)}, volume = {33}, number = {6}, pages = {860-871}, doi = {10.1002/ca.23568}, pmid = {31943391}, issn = {1098-2353}, support = {//M&#xe4;xi Stiftung, Z&#xfc;rich/ ; The Canopic Jar Project 162803//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {Animals ; Embalming/*methods ; Feasibility Studies ; Gastrointestinal Tract/anatomy &amp; histology ; Liver/anatomy &amp; histology ; Lung/anatomy &amp; histology ; Swine ; Tissue Preservation/*methods ; }, abstract = {Understanding natural and artificial postmortem alterations in different tissues of the human body is essential for bioarchaeology, paleogenetics, physical anthropology, forensic medicine, and many related disciplines. With this study, we tried to gain a better understanding of tissue alterations associated with the artificial mummification techniques of ancient Egypt, in particular for mummified visceral organs. We used several entire porcine organs and organ sections (liver, lung, stomach, ileum, and colon), which provided a close approximation to human organs. First, we dehydrated the specimens in artificial natron, before applying natural ointments, according to the ancient literary sources and recent publications. We periodically monitored the temperature, pH value, and weight of the specimens, in addition to radiodensity and volumetric measurements by clinical computed tomography and sampling for histological, bacteriological, and molecular analyses. After seven weeks, mummification was seen completed in all specimens. We observed a considerable loss of weight and volume, as well as similar courses in the decay of tissue architecture but varying levels of DNA degradation. Bacteriologically we did not detect any of the initially identified taxa in the samples by the end of the mummification process, nor any fungi. This feasibility study established an experimental protocol for future experiments modeling ancient Egyptian mummification of visceral organs using human specimens. Understanding desiccation and mummification processes in non-pathological tissues of specific visceral organs may help to identify and interpret disease-specific alterations in mummified tissues in ancient Egyptian canopic jars and organ packages contained in whole mummies.}, }
@article {pmid31940807, year = {2020}, author = {Gabbianelli, F and Alhaique, F and Romagnoli, G and Brancazi, L and Piermartini, L and Ottoni, C and Valentini, A and Chillemi, G}, title = {Was the Cinta Senese Pig Already a Luxury Food in the Late Middle Ages? Ancient DNA and Archaeozoological Evidence from Central Italy.}, journal = {Genes}, volume = {11}, number = {1}, pages = {}, pmid = {31940807}, issn = {2073-4425}, mesh = {Animals ; *DNA, Ancient ; History, Medieval ; Italy ; *Polymorphism, Single Nucleotide ; Proto-Oncogene Proteins c-kit/*genetics ; Swine/*genetics ; }, abstract = {The Cinta senese is a pig breed, highly esteemed for its meat and derived products, characterized by a black coat with a typical white "belt" and documented by scant iconography, since the 13[th]-14[th] century in Italy. A piece of pottery showing a Cinta pig was found in the Graffignano castle (Northern Latium, Italy) dated 15th-16th centuries, spurring us to investigate the diet of the inhabitants. Ancient DNA analysis was carried out on 21 pig specimens on three nuclear SNPs: (1) g.43597545C>T, on the KIT gene, informative for the identification of the Cinta senese breed; (2) rs81460129, on an intergenic region in chr. 16, which discriminates between domestic pigs and wild boars, and; (3) a SNP on the ZFY/ZFX homologous genes, to determine the sex of the individuals. Our results indicate that the Cinta senese was present in Northern Latium in Late Medieval time, although it was not the only breed, and that pigs, including Cinta, interbred with wild boars, suggesting free-range breeding for all types of pigs. Moreover, the unexpected high proportion of young females may be considered as evidence for the wealth of the family inhabiting the castle.}, }
@article {pmid31939994, year = {2020}, author = {Płoszaj, T and Jędrychowska-Dańska, K and Zamerska, A and Lewandowska, M and Bojarski, J and Chudziak, W and Drozd-Lipińska, A and Robaszkiewicz, A and Witas, HW}, title = {Analysis of maternal lineage structure of individuals from chamber graves placed in medieval cemetery in Kałdus, Central Poland.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {71}, number = {1}, pages = {43-50}, doi = {10.1127/homo/2020/1008}, pmid = {31939994}, issn = {1618-1301}, mesh = {Adult ; Anthropology, Physical ; Cemeteries/*history ; Child ; DNA, Mitochondrial/*genetics ; Female ; Haplotypes/*genetics ; History, Medieval ; Humans ; Male ; Poland ; White People/*genetics ; }, abstract = {The beginning of the early Middle Ages period in Poland (10[th]-14[th] century) has been widely debated in the context of an active demographic inflow from other countries and its contribution to the creation of the new country. Finding chamber graves which are considered typical for the Scandinavian ethnic group in a few cemeteries in Poland has become the basis for the anthropological inference on the potential participation of North European people in forming the social elite of medieval Poland. However, the question of whether this fact was the result of presence of people from other countries lacks an unambiguous answer. We attempted to isolate ancient DNA from the medieval necropolis in Kałdus where several chamber graves have been found and analysed the genetic diversity of maternal lineage of this population. We analysed the HVR I fragment and coding regions to assess the mitochondrial DNA haplogroup. We have identified a few relatively rare haplogroups (A2, T2b4a, HV, K1a11, J2b1a, and X2) which were previously found in early medieval sites in Norway and Denmark. Obtained results might suggest genetic relation between the people of Kałdus and past northern Europe populations. Present and further research can undoubtedly shed new light on the aspect of the formation of the early medieval Polish population.}, }
@article {pmid31913480, year = {2020}, author = {Zhang, M and Sun, G and Ren, L and Yuan, H and Dong, G and Zhang, L and Liu, F and Cao, P and Ko, AM and Yang, MA and Hu, S and Wang, GD and Fu, Q}, title = {Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs.}, journal = {Molecular biology and evolution}, volume = {37}, number = {5}, pages = {1462-1469}, pmid = {31913480}, issn = {1537-1719}, support = {55008731/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Archaeology ; China ; DNA, Mitochondrial/analysis ; Dogs/*genetics ; *Genome, Mitochondrial ; Phylogeography ; Wolves/*genetics ; }, abstract = {The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wolf and 26 domestic dogs) from the Yellow River and Yangtze River basins (YYRB). These are the first complete ancient mtDNA of Chinese dogs from the cradle of early Chinese civilization. We found that most ancient dogs (18/26) belong to the haplogroup A1b lineage that is found in high frequency in present-day Australian dingoes and precolonial Pacific Island dogs but low frequency in present-day China. Particularly, a 7,000-year-old dog from the Tianluoshan site in Zhejiang province possesses a haplotype basal to the entire haplogroup A1b lineage. We propose that A1b lineage dogs were once widely distributed in the YYRB area. Following their dispersal to South China, and then into Southeast Asia, New Guinea and remote Oceania, they were largely replaced by dogs belonging to other lineages in the last 2,000 years in present-day China, especially North China.}, }
@article {pmid31906474, year = {2020}, author = {Barlow, A and Hartmann, S and Gonzalez, J and Hofreiter, M and Paijmans, JLA}, title = {Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates.}, journal = {Genes}, volume = {11}, number = {1}, pages = {}, pmid = {31906474}, issn = {2073-4425}, support = {310763/ERC_/European Research Council/International ; }, mesh = {Algorithms ; Base Sequence/genetics ; Chromosome Mapping/methods ; Cluster Analysis ; DNA, Ancient/*analysis ; Genome/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.}, }
@article {pmid31888476, year = {2019}, author = {Silva-Pereira, TT and Ikuta, CY and Zimpel, CK and Camargo, NCS and de Souza Filho, AF and Ferreira Neto, JS and Heinemann, MB and Guimarães, AMS}, title = {Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens).}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {1030}, pmid = {31888476}, issn = {1471-2164}, support = {134266/2017-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 140003/2019-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2017/04617-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/20147-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 1539669//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 1841/2016//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; D17ZO-307//Morris Animal Foundation/ ; }, mesh = {Animals ; Computational Biology/methods ; Genetic Markers ; *Genome, Bacterial ; *Genomics/methods ; Mycobacterium/classification/*genetics/metabolism ; Phylogeny ; Proteome ; Proteomics/methods ; Sea Lions/*microbiology ; Sequence Deletion ; *Superinfection ; Tuberculosis/*veterinary ; }, abstract = {BACKGROUND: Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization.<br><br>RESULTS: We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC.<br><br>CONCLUSION: The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.}, }
@article {pmid31881841, year = {2019}, author = {Troll, CJ and Kapp, J and Rao, V and Harkins, KM and Cole, C and Naughton, C and Morgan, JM and Shapiro, B and Green, RE}, title = {A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {1023}, pmid = {31881841}, issn = {1471-2164}, support = {R43 CA239933/CA/NCI NIH HHS/United States ; }, mesh = {*Cell-Free Nucleic Acids ; *DNA, Single-Stranded ; *Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Oligonucleotides/chemical synthesis/*chemistry ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming.<br><br>RESULTS: Here we present an efficient ligation-based single-stranded library preparation method that is engineered to produce complex libraries in under 2.5&#x2009;h from as little as 1 nanogram of input DNA without alteration to the native ends of template molecules. Our method, called Single Reaction Single-stranded LibrarY or SRSLY, ligates uniquely designed Next-Generation Sequencing (NGS) adapters in a one-step combined phosphorylation/ligation reaction that foregoes end-polishing. Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation patterns to deduce nucleosome positioning and transcription factor binding.<br><br>CONCLUSIONS: SRSLY is a versatile tool for converting short and fragmented DNA molecules, like cfDNA fragments, into sequencing libraries while retaining native lengths and ends.}, }
@article {pmid31878147, year = {2019}, author = {Batyrev, D and Lapid, E and Carmel, L and Meshorer, E}, title = {Predicted Archaic 3D Genome Organization Reveals Genes Related to Head and Spinal Cord Separating Modern from Archaic Humans.}, journal = {Cells}, volume = {9}, number = {1}, pages = {}, pmid = {31878147}, issn = {2073-4409}, support = {1140/17//Israel Science Foundation/International ; }, mesh = {Animals ; DNA Methylation/genetics ; DNA, Ancient/analysis ; Databases, Genetic ; Epigenesis, Genetic/genetics ; Genome/genetics ; Genomics/methods ; Head/*anatomy &amp; histology ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; Promoter Regions, Genetic/genetics ; Spinal Cord/*anatomy &amp; histology ; }, abstract = {High coverage sequences of archaic humans enabled the reconstruction of their DNA methylation patterns. This allowed comparing gene regulation between human groups, and linking such regulatory changes to phenotypic differences. In a previous work, a detailed comparison of DNA methylation in modern humans, archaic humans, and chimpanzees revealed 873 modern human-derived differentially methylated regions (DMRs). To understand the regulatory implications of these DMRs, we defined differentially methylated genes (DMGs) as genes that harbor DMRs in their promoter or gene body. While most of the modern human-derived DMRs could be linked to DMGs, many others remained unassigned. Here, we used information on 3D genome organization to link ~70 out of the remaining 288 unassigned DMRs to genes. Combined with the previously identified DMGs, we reinforce the enrichment of these genes with vocal and facial anatomy, and additionally find significant enrichment with the spinal column, chin, hair, and scalp. These results reveal the importance of 3D genomic organization in understanding gene regulation by DNA methylation.}, }
@article {pmid31873100, year = {2019}, author = {Clarke, CL and Edwards, ME and Gielly, L and Ehrich, D and Hughes, PDM and Morozova, LM and Haflidason, H and Mangerud, J and Svendsen, JI and Alsos, IG}, title = {Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19613}, pmid = {31873100}, issn = {2045-2322}, mesh = {Arctic Regions ; *Climate Change ; *Ecosystem ; *Plant Development ; Plants/*classification ; }, abstract = {Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could "run out of space" as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical evidence is fragmentary. Here we present a 24,000-year record of species persistence based on sedimentary ancient DNA (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust evidence of long-term persistence of arctic-alpine plants through large-magnitude climate changes but document a decline in their diversity during a past expansion of woody vegetation. Nevertheless, most of the plants that were present during the last glacial interval, including all of the arctic-alpines, are still found in the region today. This underlines the conservation significance of mountain landscapes via their provision of a range of habitats that confer resilience to climate change, particularly for arctic-alpine taxa.}, }
@article {pmid31872482, year = {2020}, author = {Lavretsky, P and McInerney, NR and Mohl, JE and Brown, JI and James, HF and McCracken, KG and Fleischer, RC}, title = {Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks.}, journal = {Molecular ecology}, volume = {29}, number = {3}, pages = {578-595}, doi = {10.1111/mec.15343}, pmid = {31872482}, issn = {1365-294X}, support = {G12 MD007592/MD/NIMHD NIH HHS/United States ; }, mesh = {Animals ; Animals, Wild/*genetics ; Ducks/*genetics ; Gene Flow/genetics ; Genome/*genetics ; Genomics/methods ; Humans ; Hybridization, Genetic/genetics ; North America ; }, abstract = {Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.}, }
@article {pmid31869520, year = {2020}, author = {Vershinina, AO and Kapp, JD and Baryshnikov, GF and Shapiro, B}, title = {The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections.}, journal = {Molecular ecology resources}, volume = {20}, number = {5}, pages = {1182-1190}, doi = {10.1111/1755-0998.13130}, pmid = {31869520}, issn = {1755-0998}, support = {"Evolution of the organic world"//Russian Academy of Sciences Presidium and the Russian Ministry of Education and Science/ ; 1417036//National Science Foundation/ ; MG-30-17-0045-17//Institute of Museum and Library Services/ ; }, mesh = {Animals ; *DNA, Ancient ; *DNA, Mitochondrial ; Equidae/*genetics ; *Museums ; Phylogeny ; }, abstract = {Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccurate identification can lead to false biogeographic reconstructions with cascading impacts on paleontological and paleoecological research. Here, we analyzed an unusual Equid mandible found in the Far North of the Taymyr peninsula that was identified morphologically as Equus hemionus, an ancestor of present-day Asiatic wild asses. If correct, this identification represents the only finding of a putative Late Pleistocene hemione in the Arctic region, and is therefore critical to understanding wild ass evolution and paleoecology. To confirm the accuracy of this specimen's taxonomic assignment, we used ancient DNA and mitochondrial hybridization capture to identify and place this specimen in the larger equid phylogeny. We find that the specimen is actually a member of E. caballus, the ancestor of domestic horses. Our study demonstrates the utility of ancient DNA to validate morphological identification, in particular of incomplete, otherwise problematic, or taxonomically unusual museum specimens.}, }
@article {pmid31869003, year = {2020}, author = {De Simone, G and Pasquadibisceglie, A and Proietto, R and Polticelli, F and Aime, S and J M Op den Camp, H and Ascenzi, P}, title = {Contaminations in (meta)genome data: An open issue for the scientific community.}, journal = {IUBMB life}, volume = {72}, number = {4}, pages = {698-705}, doi = {10.1002/iub.2216}, pmid = {31869003}, issn = {1521-6551}, mesh = {Bacteria/genetics ; DNA, Ancient ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome/*genetics ; Mitochondria/genetics ; *Software ; }, abstract = {In recent years, the high throughput and the low cost of next-generation sequencing (NGS) technologies have led to an increase of the amount of (meta)genomic data, revolutionizing genomic research studies. However, the quality of sequencing data could be affected by experimental errors derived from defective methods and protocols. This represents a serious problem for the scientific community with a negative impact on the correctness of studies that involve genomic sequence analysis. As a countermeasure, several alignment and taxonomic classification tools have been developed to uncover and correct errors. In this critical review some of these integrated software tools and pipelines used to detect contaminations in reference genome databases and sequenced samples are reported. In particular, case studies of bacterial contaminations, contaminations of human origin, mitochondrial contaminations of ancient DNA, and cross contaminations are examined.}, }
@article {pmid31861931, year = {2019}, author = {Henao, E and Rzymski, P and Waters, MN}, title = {A Review on the Study of Cyanotoxins in Paleolimnological Research: Current Knowledge and Future Needs.}, journal = {Toxins}, volume = {12}, number = {1}, pages = {}, pmid = {31861931}, issn = {2072-6651}, mesh = {Bacterial Toxins/*toxicity ; Cyanobacteria/*metabolism ; Cyanobacteria Toxins ; Geologic Sediments ; Lakes/microbiology ; Limnology/*methods ; Marine Toxins/*toxicity ; Microcystins/*toxicity ; Paleontology/*methods ; }, abstract = {Cyanobacterial metabolites are increasingly studied, in regards to their biosynthesis, ecological role, toxicity, and potential biomedical applications. However, the history of cyanotoxins prior to the last few decades is virtually unknown. Only a few paleolimnological studies have been undertaken to date, and these have focused exclusively on microcystins and cylindrospermopsins, both successfully identified in lake sediments up to 200 and 4700 years old, respectively. In this paper, we review direct extraction, quantification, and application of cyanotoxins in sediment cores, and put forward future research prospects in this field. Cyanobacterial toxin research is also compared to other paleo-cyanobacteria tools, such as sedimentary pigments, akinetes, and ancient DNA isolation, to identify the role of each tool in reproducing the history of cyanobacteria. Such investigations may also be beneficial for further elucidation of the biological role of cyanotoxins, particularly if coupled with analyses of other abiotic and biotic sedimentary features. In addition, we identify current limitations as well as future directions for applications in the field of paleolimnological studies on cyanotoxins.}, }
@article {pmid31848342, year = {2019}, author = {Jensen, TZT and Niemann, J and Iversen, KH and Fotakis, AK and Gopalakrishnan, S and Vågene, &#xc5;J and Pedersen, MW and Sinding, MS and Ellegaard, MR and Allentoft, ME and Lanigan, LT and Taurozzi, AJ and Nielsen, SH and Dee, MW and Mortensen, MN and Christensen, MC and Sørensen, SA and Collins, MJ and Gilbert, MTP and Sikora, M and Rasmussen, S and Schroeder, H}, title = {A 5700 year-old human genome and oral microbiome from chewed birch pitch.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5520}, pmid = {31848342}, issn = {2041-1723}, mesh = {Animals ; Betula/*physiology ; DNA, Ancient/*analysis ; DNA, Bacterial/analysis ; Denmark ; *Genome, Human ; Geography ; Humans ; Microbiota/*genetics ; Mouth/*microbiology ; Phenotype ; Radiometric Dating ; Sex Determination Analysis ; Time Factors ; }, abstract = {The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.}, }
@article {pmid31842945, year = {2019}, author = {Hübler, R and Key, FM and Warinner, C and Bos, KI and Krause, J and Herbig, A}, title = {HOPS: automated detection and authentication of pathogen DNA in archaeological remains.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {280}, pmid = {31842945}, issn = {1474-760X}, mesh = {Archaeology/*methods ; DNA, Bacterial/*analysis ; *Genetic Techniques ; Metagenomics/*methods ; Software ; }, abstract = {High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.}, }
@article {pmid31840921, year = {2020}, author = {Loog, L and Thalmann, O and Sinding, MS and Schuenemann, VJ and Perri, A and Germonpré, M and Bocherens, H and Witt, KE and Samaniego Castruita, JA and Velasco, MS and Lundstrøm, IKC and Wales, N and Sonet, G and Frantz, L and Schroeder, H and Budd, J and Jimenez, EL and Fedorov, S and Gasparyan, B and Kandel, AW and Lázničková-Galetová, M and Napierala, H and Uerpmann, HP and Nikolskiy, PA and Pavlova, EY and Pitulko, VV and Herzig, KH and Malhi, RS and Willerslev, E and Hansen, AJ and Dobney, K and Gilbert, MTP and Krause, J and Larson, G and Eriksson, A and Manica, A}, title = {Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia.}, journal = {Molecular ecology}, volume = {29}, number = {9}, pages = {1596-1610}, pmid = {31840921}, issn = {1365-294X}, mesh = {Animals ; *Biological Evolution ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Dogs ; Gene Flow ; *Genome, Mitochondrial ; Phylogeny ; *Wolves/genetics ; }, abstract = {Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.}, }
@article {pmid31840056, year = {2019}, author = {Zanella, M and Vitriolo, A and Andirko, A and Martins, PT and Sturm, S and O'Rourke, T and Laugsch, M and Malerba, N and Skaros, A and Trattaro, S and Germain, PL and Mihailovic, M and Merla, G and Rada-Iglesias, A and Boeckx, C and Testa, G}, title = {Dosage analysis of the 7q11.23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication.}, journal = {Science advances}, volume = {5}, number = {12}, pages = {eaaw7908}, pmid = {31840056}, issn = {2375-2548}, support = {/ERC_/European Research Council/International ; }, mesh = {Cell Line ; Cell Movement ; Chromosomes, Human, Pair 7/*genetics ; Databases, Genetic ; *Domestication ; Epigenome ; Evolution, Molecular ; Face ; *Gene Dosage ; Gene Regulatory Networks ; Histone Code ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Neural Stem Cells/metabolism ; Transcription Factors/*genetics ; Williams Syndrome/*genetics ; }, abstract = {We undertook a functional dissection of chromatin remodeler BAZ1B in neural crest (NC) stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients harboring 7q11.23 copy number variants. Our results reveal a key contribution of BAZ1B to NCSC in vitro induction and migration, coupled with a crucial involvement in NC-specific transcriptional circuits and distal regulation. By intersecting our experimental data with new paleogenetic analyses comparing modern and archaic humans, we found a modern-specific enrichment for regulatory changes both in BAZ1B and its experimentally defined downstream targets, thereby providing the first empirical validation of the human self-domestication hypothesis and positioning BAZ1B as a master regulator of the modern human face. In so doing, we provide experimental evidence that the craniofacial and cognitive/behavioral phenotypes caused by alterations of the Williams-Beuren syndrome critical region can serve as a powerful entry point into the evolution of the modern human face and prosociality.}, }
@article {pmid31824712, year = {2019}, author = {Pálsdóttir, AH and Bläuer, A and Rannamäe, E and Boessenkool, S and Hallsson, JH}, title = {Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains.}, journal = {Royal Society open science}, volume = {6}, number = {10}, pages = {191059}, pmid = {31824712}, issn = {2054-5703}, abstract = {With the advent of ancient DNA, as well as other methods such as isotope analysis, destructive sampling of archaeofaunal remains has increased much faster than the effort to collect and curate them. While there has been considerable discussion regarding the ethics of destructive sampling and analysis of human remains, this dialogue has not extended to archaeofaunal material. Here we address this gap and discuss the ethical challenges surrounding destructive sampling of materials from archaeofaunal collections. We suggest ways of mitigating the negative aspects of destructive sampling and present step-by-step guidelines aimed at relevant stakeholders, including scientists, holding institutions and scientific journals. Our suggestions are in most cases easily implemented without significant increases in project costs, but with clear long-term benefits in the preservation and use of zooarchaeological material.}, }
@article {pmid31816048, year = {2020}, author = {Hernández, CL and Pita, G and Cavadas, B and López, S and Sánchez-Martínez, LJ and Dugoujon, JM and Novelletto, A and Cuesta, P and Pereira, L and Calderón, R}, title = {Human Genomic Diversity Where the Mediterranean Joins the Atlantic.}, journal = {Molecular biology and evolution}, volume = {37}, number = {4}, pages = {1041-1055}, pmid = {31816048}, issn = {1537-1719}, mesh = {Africa, Northern ; *Genetic Variation ; *Genome, Human ; *Human Migration ; Humans ; Mediterranean Region ; Phylogeography ; Polymorphism, Single Nucleotide ; }, abstract = {Throughout the past few years, a lively debate emerged about the timing and magnitude of the human migrations between the Iberian Peninsula and the Maghreb. Several pieces of evidence, including archaeological, anthropological, historical, and genetic data, have pointed to a complex and intermingled evolutionary history in the western Mediterranean area. To study to what extent connections across the Strait of Gibraltar and surrounding areas have shaped the present-day genomic diversity of its populations, we have performed a screening of 2.5 million single-nucleotide polymorphisms in 142 samples from southern Spain, southern Portugal, and Morocco. We built comprehensive data sets of the studied area and we implemented multistep bioinformatic approaches to assess population structure, demographic histories, and admixture dynamics. Both local and global ancestry inference showed an internal substructure in the Iberian Peninsula, mainly linked to a differential African ancestry. Western Iberia, from southern Portugal to Galicia, constituted an independent cluster within Iberia characterized by an enriched African genomic input. Migration time modeling showed recent historic dates for the admixture events occurring both in Iberia and in the North of Africa. However, an integrative vision of both paleogenomic and modern DNA data allowed us to detect chronological transitions and population turnovers that could be the result of transcontinental migrations dating back from Neolithic times. The present contribution aimed to fill the gaps in the modern human genomic record of a key geographic area, where the Mediterranean and the Atlantic come together.}, }
@article {pmid31808562, year = {2020}, author = {Orlando, L}, title = {Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {1}, pages = {e1900164}, doi = {10.1002/bies.201900164}, pmid = {31808562}, issn = {1521-1878}, mesh = {Animals ; Asia, Central ; Breeding ; *Domestication ; Europe ; Fossils ; *Genetic Variation ; Genome ; Horses/*genetics ; Male ; Mongolia ; Phenotype ; }, abstract = {The horse was essential to past human societies but became a recreational animal during the twentieth century as the world became increasingly mechanized. As the author reviews here, recent studies of ancient genomes have revisited the understanding of horse domestication, from the very early stages to the most modern developments. They have uncovered several extinct lineages roaming the far ends of Eurasia some 4000 years ago. They have shown that the domestic horse has been significantly reshaped during the last millennium and experienced a sharp decline in genetic diversity within the last two centuries. At a time when no truly wild horses exist any longer, this calls for enhanced conservation in all endangered populations. These include the Przewalski's horse native to Mongolia, and the many local breeds side-lined by the modern agenda, but yet representing the living heritage of over five millennia of horse breeding.}, }
@article {pmid31805075, year = {2019}, author = {Nazari, V and Tarmann, GM and Efetov, KA}, title = {Phylogenetic position of the 'extinct' Fijian coconut moth, Levuana iridescens (Lepidoptera: Zygaenidae).}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225590}, pmid = {31805075}, issn = {1932-6203}, mesh = {Animals ; Australia ; *Extinction, Biological ; Female ; Male ; Moths/*anatomy &amp; histology/*classification ; Phylogeny ; }, abstract = {Levuana iridescens Bethune-Baker, 1906, a day-flying moth purported to be endemic to the Fijian Island of Viti Levu and a former pest of its coconut palm trees, was last observed in 1956 and has been officially declared extinct by IUCN since 1996. The controversial classical biological control method that resulted in the (presumed) demise of this moth has given this species an iconic status in biological control studies. We investigated the sister-group relationships and phylogenetic placement of this moth using NGS-obtained ancient DNA sequences from museum specimens of L. iridescens collected in the 1920s, combined with 31 morphological characters used in earlier studies and 2 new characters. Our findings show that Levuana is most closely related to the Australian genus Myrtartona. The significance of these findings is discussed.}, }
@article {pmid31792176, year = {2019}, author = {Mordechai, L and Eisenberg, M and Newfield, TP and Izdebski, A and Kay, JE and Poinar, H}, title = {The Justinianic Plague: An inconsequential pandemic?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {51}, pages = {25546-25554}, pmid = {31792176}, issn = {1091-6490}, mesh = {Byzantium ; History, Medieval ; Humans ; Pandemics/*history ; Plague/*history ; Population Dynamics/*history ; Yersinia pestis ; }, abstract = {Existing mortality estimates assert that the Justinianic Plague (circa 541 to 750 CE) caused tens of millions of deaths throughout the Mediterranean world and Europe, helping to end antiquity and start the Middle Ages. In this article, we argue that this paradigm does not fit the evidence. We examine a series of independent quantitative and qualitative datasets that are directly or indirectly linked to demographic and economic trends during this two-century period: Written sources, legislation, coinage, papyri, inscriptions, pollen, ancient DNA, and mortuary archaeology. Individually or together, they fail to support the maximalist paradigm: None has a clear independent link to plague outbreaks and none supports maximalist reconstructions of late antique plague. Instead of large-scale, disruptive mortality, when contextualized and examined together, the datasets suggest continuity across the plague period. Although demographic, economic, and political changes continued between the 6th and 8th centuries, the evidence does not support the now commonplace claim that the Justinianic Plague was a primary causal factor of them.}, }
@article {pmid31791340, year = {2019}, author = {McHugo, GP and Dover, MJ and MacHugh, DE}, title = {Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {98}, pmid = {31791340}, issn = {1741-7007}, mesh = {Animals ; Animals, Domestic/*genetics ; *Biological Evolution ; *Breeding ; DNA, Ancient/*analysis ; *Domestication ; Genomics ; }, abstract = {Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.}, }
@article {pmid31789141, year = {2020}, author = {Beltrame, MO and Pruzzo, C and Sanabria, R and Pérez, A and Mora, MS}, title = {First report of pre-Hispanic Fasciola hepatica from South America revealed by ancient DNA.}, journal = {Parasitology}, volume = {147}, number = {3}, pages = {371-375}, pmid = {31789141}, issn = {1469-8161}, mesh = {*Animal Distribution ; Animals ; Argentina ; DNA, Ancient/analysis ; DNA, Helminth/analysis ; Deer/*parasitology ; Fasciola hepatica/genetics/growth &amp; development/*isolation &amp; purification ; Feces/*parasitology ; Ovum/physiology ; Phylogeny ; }, abstract = {It is generally assumed that the digenean human liver fluke, Fasciola hepatica, gained entry to South America during the 15th century upon arrival of Europeans and their livestock. Nonetheless in Patagonia, Argentina, digenean eggs similar to F. hepatica have been observed in deer coprolites dating back to 2300 years B.P. The main objective of our present study was to identify and characterize these eggs using an ancient DNA (aDNA) study. Eggs were isolated and used for aDNA extraction, amplification and sequencing of partial regions from the cytochrome c oxidase subunit 1 and the nicotinamide adenine dinucleotide dehydrogenase subunit 1 mitochondrial genes. Also, phylogenetic trees were constructed using Bayesian and maximum likelihood. Our results confirm the presence of F. hepatica in South America from at least 2300 years B.P. This is the first report and the first aDNA study of this trematode in South America prior to the arrival of the European cattle in the 15th century. The present work contributes to the study of phylogenetic and palaeobiogeographical aspects of F. hepatica and its settlement across America.}, }
@article {pmid31785113, year = {2020}, author = {Hagan, RW and Hofman, CA and Hübner, A and Reinhard, K and Schnorr, S and Lewis, CM and Sankaranarayanan, K and Warinner, CG}, title = {Comparison of extraction methods for recovering ancient microbial DNA from paleofeces.}, journal = {American journal of physical anthropology}, volume = {171}, number = {2}, pages = {275-284}, doi = {10.1002/ajpa.23978}, pmid = {31785113}, issn = {1096-8644}, support = {EXC 2051 #390713860//Deutsche Forschungsgemeinschaft/International ; //Max-Planck-Gesellschaft/International ; R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical/*methods ; Archaeology/methods ; DNA, Ancient/*analysis/*isolation &amp; purification ; Dogs ; Feces/*chemistry ; Gastrointestinal Microbiome ; Metagenomics ; Sequence Analysis, DNA/*methods/veterinary ; }, abstract = {OBJECTIVES: Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases.<br><br>METHODS: In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP).<br><br>RESULTS: Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA.<br><br>CONCLUSIONS: These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies.}, }
@article {pmid31771471, year = {2019}, author = {Ameen, C and Feuerborn, TR and Brown, SK and Linderholm, A and Hulme-Beaman, A and Lebrasseur, O and Sinding, MS and Lounsberry, ZT and Lin, AT and Appelt, M and Bachmann, L and Betts, M and Britton, K and Darwent, J and Dietz, R and Fredholm, M and Gopalakrishnan, S and Goriunova, OI and Grønnow, B and Haile, J and Hallsson, JH and Harrison, R and Heide-Jørgensen, MP and Knecht, R and Losey, RJ and Masson-MacLean, E and McGovern, TH and McManus-Fry, E and Meldgaard, M and Midtdal, &#xc5; and Moss, ML and Nikitin, IG and Nomokonova, T and Pálsdóttir, AH and Perri, A and Popov, AN and Rankin, L and Reuther, JD and Sablin, M and Schmidt, AL and Shirar, S and Smiarowski, K and Sonne, C and Stiner, MC and Vasyukov, M and West, CF and Ween, GB and Wennerberg, SE and Wiig, &#xd8; and Woollett, J and Dalén, L and Hansen, AJ and P Gilbert, MT and Sacks, BN and Frantz, L and Larson, G and Dobney, K and Darwent, CM and Evin, A}, title = {Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1916}, pages = {20191929}, pmid = {31771471}, issn = {1471-2954}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Alaska ; *Animal Distribution ; Animals ; Archaeology ; Arctic Regions ; Canada ; DNA, Ancient/analysis ; DNA, Mitochondrial/analysis ; Dogs/*anatomy &amp; histology/*genetics ; *Genome, Mitochondrial ; Greenland ; Human Migration ; *Phenotype ; }, abstract = {Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.}, }
@article {pmid31767056, year = {2019}, author = {Thomas, JE and Carvalho, GR and Haile, J and Rawlence, NJ and Martin, MD and Ho, SY and Sigfússon, A&#xde; and Jósefsson, VA and Frederiksen, M and Linnebjerg, JF and Samaniego Castruita, JA and Niemann, J and Sinding, MS and Sandoval-Velasco, M and Soares, AE and Lacy, R and Barilaro, C and Best, J and Brandis, D and Cavallo, C and Elorza, M and Garrett, KL and Groot, M and Johansson, F and Lifjeld, JT and Nilson, G and Serjeanston, D and Sweet, P and Fuller, E and Hufthammer, AK and Meldgaard, M and Fjeldså, J and Shapiro, B and Hofreiter, M and Stewart, JR and Gilbert, MTP and Knapp, M}, title = {Demographic reconstruction from ancient DNA supports rapid extinction of the great auk.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31767056}, issn = {2050-084X}, support = {NE/L501694/1//NERC Environmental Bioinformatics Centre/International ; 681396-Extinction Genomics/ERC_/European Research Council/International ; Heredity Fieldwork Grant//Genetics Society/International ; Godfrey Hewitt Mobility Award//European Society for Evolutionary Biology/International ; Rutherford Discovery Fellowship//Royal Society of New Zealand/International ; }, mesh = {Animals ; Charadriiformes/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial ; *Extinction, Biological ; Genetic Variation ; Genome, Mitochondrial/genetics ; Humans ; Phylogeny ; *Population Dynamics ; }, abstract = {The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16[th] century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.}, }
@article {pmid31758601, year = {2020}, author = {Fenderson, LE and Kovach, AI and Llamas, B}, title = {Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time.}, journal = {Molecular ecology}, volume = {29}, number = {2}, pages = {218-246}, doi = {10.1111/mec.15315}, pmid = {31758601}, issn = {1365-294X}, mesh = {*Climate Change ; Ecology ; Genetics, Population ; Phylogeography ; Population Dynamics ; }, abstract = {Genetic time-series data from historical samples greatly facilitate inference of past population dynamics and species evolution. Yet, although climate and landscape change are often touted as post-hoc explanations of biological change, our understanding of past climate and landscape change influences on evolutionary processes is severely hindered by the limited application of methods that directly relate environmental change to species dynamics through time. Increased integration of spatiotemporal environmental and genetic data will revolutionize the interpretation of environmental influences on past population processes and the quantification of recent anthropogenic impacts on species, and vastly improve prediction of species responses under future climate change scenarios, yielding widespread revelations across evolutionary biology, landscape ecology and conservation genetics. This review encourages greater use of spatiotemporal landscape genetic analyses that explicitly link landscape, climate and genetic data through time by providing an overview of analytical approaches for integrating historical genetic and environmental data in five key research areas: population genetic structure, demography, phylogeography, metapopulation connectivity and adaptation. We also include a tabular summary of key methodological information, suggest approaches for mitigating the particular difficulties in applying these techniques to ancient DNA and palaeoclimate data, and highlight areas for future methodological development.}, }
@article {pmid31758037, year = {2019}, author = {Ozga, AT and Gilby, I and Nockerts, RS and Wilson, ML and Pusey, A and Stone, AC}, title = {Oral microbiome diversity in chimpanzees from Gombe National Park.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17354}, pmid = {31758037}, issn = {2045-2322}, mesh = {Animals ; Cluster Analysis ; DNA, Ancient/analysis ; DNA, Bacterial/analysis/genetics ; Dental Plaque/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota/genetics ; Mouth/*microbiology ; Pan troglodytes/*microbiology ; Parks, Recreational ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; Tanzania ; }, abstract = {Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.}, }
@article {pmid31754290, year = {2019}, author = {Maixner, F and Thorell, K and Granehäll, L and Linz, B and Moodley, Y and Rattei, T and Engstrand, L and Zink, A}, title = {Helicobacter pylori in ancient human remains.}, journal = {World journal of gastroenterology}, volume = {25}, number = {42}, pages = {6289-6298}, pmid = {31754290}, issn = {2219-2840}, mesh = {Body Remains/*microbiology ; DNA, Ancient/*analysis ; DNA, Bacterial/analysis ; Genome, Bacterial ; Helicobacter Infections/*microbiology ; Helicobacter pylori/isolation &amp; purification ; Humans ; *Mummies ; Stomach/microbiology ; Virulence ; }, abstract = {The bacterium Helicobacter pylori (H. pylori) infects the stomachs of approximately 50% of all humans. With its universal occurrence, high infectivity and virulence properties it is considered as one of the most severe global burdens of modern humankind. It has accompanied humans for many thousands of years, and due to its high genetic variability and vertical transmission, its population genetics reflects the history of human migrations. However, especially complex demographic events such as the colonisation of Europe cannot be resolved with population genetic analysis of modern H. pylori strains alone. This is best exemplified with the reconstruction of the 5300-year-old H. pylori genome of the Iceman, a European Copper Age mummy. Our analysis provided precious insights into the ancestry and evolution of the pathogen and underlined the high complexity of ancient European population history. In this review we will provide an overview on the molecular analysis of H. pylori in mummified human remains that were done so far and we will outline methodological advancements in the field of ancient DNA research that support the reconstruction and authentication of ancient H. pylori genome sequences.}, }
@article {pmid31745634, year = {2020}, author = {Müller, P and Sell, C and Hadrys, T and Hedman, J and Bredemeyer, S and Laurent, FX and Roewer, L and Achtruth, S and Sidstedt, M and Sijen, T and Trimborn, M and Weiler, N and Willuweit, S and Bastisch, I and Parson, W and , }, title = {Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA.}, journal = {International journal of legal medicine}, volume = {134}, number = {1}, pages = {185-198}, pmid = {31745634}, issn = {1437-1596}, support = {IZ25-5793-2015-30 2017-2020//Horizon 2020 Framework Programme/ ; HOME/2014/ISFP/AG/LAWX/4000007135//Horizon 2020/ ; }, mesh = {Alleles ; Austria ; DNA Fingerprinting/*methods ; Electrophoresis, Capillary ; Female ; France ; *Gene Library ; Germany ; *High-Throughput Nucleotide Sequencing ; Humans ; Laboratories ; Male ; *Microsatellite Repeats ; Netherlands ; Polymerase Chain Reaction ; *Polymorphism, Single Nucleotide ; Sensitivity and Specificity ; *Sequence Analysis, DNA ; Sweden ; }, abstract = {We present results from an inter-laboratory massively parallel sequencing (MPS) study in the framework of the SeqForSTRs project to evaluate forensically relevant parameters, such as performance, concordance, and sensitivity, using a standardized sequencing library including reference material, mixtures, and ancient DNA samples. The standardized library was prepared using the ForenSeq DNA Signature Prep Kit (primer mix A). The library was shared between eight European laboratories located in Austria, France, Germany, The Netherlands, and Sweden to perform MPS on their particular MiSeq FGx sequencers. Despite variation in performance between sequencing runs, all laboratories obtained quality metrics that fell within the manufacturer's recommended ranges. Furthermore, differences in locus coverage did not inevitably adversely affect heterozygous balance. Inter-laboratory concordance showed 100% concordant genotypes for the included autosomal and Y-STRs, and still, X-STR concordance exceeded 83%. The exclusive reasons for X-STR discordances were drop-outs at DXS10103. Sensitivity experiments demonstrated that correct allele calling varied between sequencing instruments in particular for lower DNA amounts (≤ 125 pg). The analysis of compromised DNA samples showed the drop-out of one sample (FA10013B01A) while for the remaining three degraded DNA samples MPS was able to successfully type ≥ 87% of all aSTRs, ≥ 78% of all Y-STRs, ≥ 68% of all X-STRs, and ≥ 92% of all iSNPs demonstrating that MPS is a promising tool for human identity testing, which in return, has to undergo rigorous in-house validation before it can be implemented into forensic routine casework.}, }
@article {pmid31744094, year = {2019}, author = {Grugni, V and Raveane, A and Colombo, G and Nici, C and Crobu, F and Ongaro, L and Battaglia, V and Sanna, D and Al-Zahery, N and Fiorani, O and Lisa, A and Ferretti, L and Achilli, A and Olivieri, A and Francalacci, P and Piazza, A and Torroni, A and Semino, O}, title = {Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case.}, journal = {International journal of molecular sciences}, volume = {20}, number = {22}, pages = {}, pmid = {31744094}, issn = {1422-0067}, support = {2006.194//Compagnia di San Paolo/ ; }, mesh = {Chromosomes, Human, Y/classification/*genetics ; DNA, Ancient/analysis ; Gene Frequency ; Genetic Linkage ; *Genetics, Population ; Haplotypes ; Humans ; Islands ; Italy ; Male ; Phylogeny ; Principal Component Analysis ; White People/genetics ; }, abstract = {Many anthropological, linguistic, genetic and genomic analyses have been carried out to evaluate the potential impact that evolutionary forces had in shaping the present-day Sardinian gene pool, the main outlier in the genetic landscape of Europe. However, due to the homogenizing effect of internal movements, which have intensified over the past fifty years, only partial information has been obtained about the main demographic events. To overcome this limitation, we analyzed the male-specific region of the Y chromosome in three population samples obtained by reallocating a large number of Sardinian subjects to the place of origin of their monophyletic surnames, which are paternally transmitted through generations in most of the populations, much like the Y chromosome. Three Y-chromosome founding lineages, G2-L91, I2-M26 and R1b-V88, were identified as strongly contributing to the definition of the outlying position of Sardinians in the European genetic context and marking a significant differentiation within the island. The present distribution of these lineages does not always mirror that detected in ancient DNAs. Our results show that the analysis of the Y-chromosome gene pool coupled with a sampling method based on the origin of the family name, is an efficient approach to unravelling past heterogeneity, often hidden by recent movements, in the gene pool of modern populations. Furthermore, the reconstruction and comparison of past genetic isolates represent a starting point to better assess the genetic information deriving from the increasing number of available ancient DNA samples.}, }
@article {pmid31737039, year = {2019}, author = {Chen, P and Wu, J and Luo, L and Gao, H and Wang, M and Zou, X and Li, Y and Chen, G and Luo, H and Yu, L and Han, Y and Jia, F and He, G}, title = {Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {1045}, pmid = {31737039}, issn = {1664-8021}, abstract = {Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.}, }
@article {pmid31729399, year = {2019}, author = {Översti, S and Majander, K and Salmela, E and Salo, K and Arppe, L and Belskiy, S and Etu-Sihvola, H and Laakso, V and Mikkola, E and Pfrengle, S and Putkonen, M and Taavitsainen, JP and Vuoristo, K and Wessman, A and Sajantila, A and Oinonen, M and Haak, W and Schuenemann, VJ and Krause, J and Palo, JU and Onkamo, P}, title = {Human mitochondrial DNA lineages in Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16883}, pmid = {31729399}, issn = {2045-2322}, mesh = {Agriculture ; *Crosses, Genetic ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis/genetics ; Europe ; Farmers/statistics &amp; numerical data ; Farms ; Finland ; Genome, Mitochondrial/genetics ; History, Ancient ; *Human Migration/history ; Humans ; Iron ; Maternal Inheritance/*genetics ; Oceans and Seas ; White People/*genetics ; }, abstract = {Human ancient DNA studies have revealed high mobility in Europe's past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300-1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns.}, }
@article {pmid31719710, year = {2019}, author = {Swift, JA and Bunce, M and Dortch, J and Douglass, K and Faith, JT and Fellows Yates, JA and Field, J and Haberle, SG and Jacob, E and Johnson, CN and Lindsey, E and Lorenzen, ED and Louys, J and Miller, G and Mychajliw, AM and Slon, V and Villavicencio, NA and Waters, MR and Welker, F and Wood, R and Petraglia, M and Boivin, N and Roberts, P}, title = {Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene.}, journal = {Bioscience}, volume = {69}, number = {11}, pages = {877-887}, pmid = {31719710}, issn = {0006-3568}, abstract = {Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today.}, }
@article {pmid31714695, year = {2018}, author = {González-Oliver, A and Pineda-Vázquez, D and Garfias-Morales, E and La Cruz-Laina, I and Medrano-González, L and Márquez-Morfín, L and Ortega-Muñoz, A}, title = {Genetic Overview of the Maya Populations: Mitochondrial DNA Haplogroups.}, journal = {Human biology}, volume = {90}, number = {4}, pages = {281-300}, doi = {10.13110/humanbiology.90.4.03}, pmid = {31714695}, issn = {1534-6617}, mesh = {Adolescent ; Adult ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; *Gene Flow ; Genetic Variation/genetics ; Genetics, Population/*statistics &amp; numerical data ; Haplotypes/*genetics ; Humans ; Indians, North American/*genetics ; Male ; Mexico/ethnology ; Phylogeny ; Young Adult ; }, abstract = {We identified mitochondrial DNA haplogroups A, B, C, and D in 75 present-day Maya individuals, 24 Maya individuals of the colonial period, and 1 pre-Columbian Maya individual from Quintana Roo, Mexico. We examined these data together with those of 21 Maya populations reported in the literature, comprising 647 present-day Maya individuals and 71 ancient Maya individuals. A demographic study based on analysis of fertility and endogamy was carried out in two modern Maya populations to identify cultural factors that influence the mitochondrial haplogroup genetic diversity. Most present-day and ancient Maya populations show a distribution pattern of mitochondrial haplogroup frequencies A, C, B, and D in decreasing order, with haplogroup D absent in several populations. Considering only modern Maya populations with at least 50 individuals analyzed, the present-day Tzotzil and Lacandon populations from Chiapas show the highest and lowest genetic diversity, 0.706 and 0.025, respectively. Our results show small genetic differences between the Maya populations, with the exception of the present-day Tojolabal and Lacandon populations from Chiapas. The present-day Lacandon population from Chiapas differs from other Maya populations in showing almost only haplogroup A. This result suggests a long history of isolation and endogamy as well as a possible founder effect inside the Lacandonian rain forest. The contemporary Tojolabal population is the only one with an unusual mitochondrial haplogroup pattern, exhibiting a frequency of haplogroup B higher than A and the absence of haplogroup C. With a small sample size, the pre-Columbian Copán Maya show a high content of haplogroup C and a low frequency of haplogroup D. The genetic homogeneity of the Maya populations is indicative of a common origin and nearly continuous gene flow in the long term within a general isolation of the whole group, in contrast to the Nahua populations that had different origins. Our demographic study showed high fertility rates and high levels of endogamy in the present-day Maya populations from Quintana Roo that are consistent with their general low genetic diversity. We propose that the genetic similarity among ancient and present-day Maya populations persists due to a strong sense of social cohesion and identity that impacts their marriage practices, keeping this cultural group isolated. These factors have constrained gene flow inside the Maya region and have impeded the differentiation among the Maya. Discernment of genetic differentiation within the peninsula is constrained by the lack of sampling documentation in the literature.}, }
@article {pmid31710665, year = {2020}, author = {Nieves-Colón, MA and Pestle, WJ and Reynolds, AW and Llamas, B and de la Fuente, C and Fowler, K and Skerry, KM and Crespo-Torres, E and Bustamante, CD and Stone, AC}, title = {Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {611-626}, doi = {10.1093/molbev/msz267}, pmid = {31710665}, issn = {1537-1719}, mesh = {Bone and Bones ; Chromosomes, Human/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Dental Calculus/*genetics ; Fossils ; Genetics, Population ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Human Migration ; Humans ; Indigenous Peoples/*genetics ; Puerto Rico/ethnology ; Tooth ; }, abstract = {Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.}, }
@article {pmid31697387, year = {2020}, author = {van Dorp, L and Gelabert, P and Rieux, A and de Manuel, M and de-Dios, T and Gopalakrishnan, S and Carøe, C and Sandoval-Velasco, M and Fregel, R and Olalde, I and Escosa, R and Aranda, C and Huijben, S and Mueller, I and Marquès-Bonet, T and Balloux, F and Gilbert, MTP and Lalueza-Fox, C}, title = {Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {773-785}, pmid = {31697387}, issn = {1537-1719}, support = {MR/P007597/1/MRC_/Medical Research Council/United Kingdom ; BB/R01356X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Americas ; Asia ; Evolution, Molecular ; Genetics, Population ; Genome, Protozoan ; High-Throughput Nucleotide Sequencing ; Humans ; Malaria, Vivax/*parasitology ; Oceania ; Phylogeny ; Phylogeography ; Plasmodium vivax/*classification/*genetics ; Spain ; Whole Genome Sequencing/*methods ; }, abstract = {The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.}, }
@article {pmid31697016, year = {2019}, author = {Wolinsky, H}, title = {Ancient DNA and contemporary politics: The analysis of ancient DNA challenges long-held beliefs about identity and history with potential for political abuse.}, journal = {EMBO reports}, volume = {20}, number = {12}, pages = {e49507}, pmid = {31697016}, issn = {1469-3178}, mesh = {Americas ; *DNA, Ancient ; Emigration and Immigration/history ; Europe ; Genetics, Population/history ; History, Ancient ; Human Genetics ; Human Migration/*history ; Humans ; *Politics ; Racism ; }, abstract = {The sequencing and analysis of ancient human DNA has helped to rewrite human history. But it is also tempting politicians, nationalists and supremacists to abuse this research for their agendas.}, }
@article {pmid31679935, year = {2019}, author = {Serra-Vidal, G and Lucas-Sanchez, M and Fadhlaoui-Zid, K and Bekada, A and Zalloua, P and Comas, D}, title = {Heterogeneity in Palaeolithic Population Continuity and Neolithic Expansion in North Africa.}, journal = {Current biology : CB}, volume = {29}, number = {22}, pages = {3953-3959.e4}, doi = {10.1016/j.cub.2019.09.050}, pmid = {31679935}, issn = {1879-0445}, mesh = {Africa South of the Sahara ; Africa, Northern ; Black People/*genetics ; Fossils ; Gene Flow/*genetics ; Gene Pool ; Genetic Variation ; Genetics, Population/methods ; Genome/genetics ; Haplotypes ; History, Ancient ; Human Migration/history ; Humans ; Polymorphism, Single Nucleotide ; White People/genetics ; }, abstract = {North Africa is located at the crossroads of the Mediterranean Sea, the Middle East, and the Sahara Desert. Extensive migrations and gene flow in the region have shaped many different cultures and ancestral genetic components through time [1-6]. DNA data from ancient Moroccan sites [7, 8] has recently shed some light to the population continuity-versus-replacement debate, i.e., the question of whether current North African populations descend from Palaeolithic groups or, on the contrary, subsequent migrations swept away all pre-existing genetic signal in the region. In the present study, we analyze 21 complete North African genomes and compare them with extant and ancient genome data in order to address the demographic continuity-versus-replacement debate, to assess whether these demographic events were homogeneous (including Berber and Arabic-speaking groups), and to explore the effect of Neolithization and posterior migration waves. The North African genetic pool is defined as a melting pot of genetic components, including an endemic North African Epipalaeolithic component at low frequency that forms a declining gradient from Western to Eastern North Africa. This scenario is consistent with Neolithization having shaped most of the current genetic variation in the region when compared to posterior back-to-North-Africa migration waves such as the Arabization. A common and distinct genetic history of the region is shown, with internal different proportions of genetic components owing to differential admixture with surrounding groups as well as to genetic drift due to isolation and endogamy in certain populations.}, }
@article {pmid31679495, year = {2019}, author = {Larsson, P and von Seth, J and Hagen, IJ and Götherström, A and Androsov, S and Germonpré, M and Bergfeldt, N and Fedorov, S and Eide, NE and Sokolova, N and Berteaux, D and Angerbjörn, A and Flagstad, &#xd8; and Plotnikov, V and Norén, K and Díez-Del-Molino, D and Dussex, N and Stanton, DWG and Dalén, L}, title = {Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1788}, pages = {20190212}, pmid = {31679495}, issn = {1471-2970}, mesh = {*Animal Distribution ; Animals ; *Climate Change ; DNA, Ancient/analysis ; Fossils ; Foxes/genetics/*physiology ; *Genetic Variation ; Genome, Mitochondrial ; *Human Activities ; Population Dynamics ; Scandinavian and Nordic Countries ; }, abstract = {Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'}, }
@article {pmid31646208, year = {2019}, author = {Poma, A and Cesare, P and Bonfigli, A and Vecchiotti, G and Colafarina, S and Savini, F and Redi, F and Zarivi, O}, title = {Analysis of ancient mtDNA from the medieval archeological site of Amiternum (L'Aquila), central Italy.}, journal = {Heliyon}, volume = {5}, number = {10}, pages = {e02586}, pmid = {31646208}, issn = {2405-8440}, abstract = {Study of ancient DNA makes it possible to analyze genetic relationships between individuals and populations of past and present. In this paper we have analyzed remains of human bones, dating back to the 8th-10th century AD, from the burials found in the Cathedral of Santa Maria in Civitate, archaeological site of Amiternum, L'Aquila, Italy. As a genetic marker, the hypervariable region 1 of mitochondrial DNA (HVR1) was selected. To obtain reliable sequences from the hypervariable region 1 of mtDNA (HVR1) were performed: multiple extractions, template quantification and cloning of PCR products. The sequences obtained were compared with Anderson's sequence for the identification of polymorphisms (SNP) and haplogroups. The data obtained were analyzed with various software and phylogenetic methods. For the comparison between populations, ancient and modern sequences found in databases and literature have been used. This work provides preliminary information on the correlation between the population of Amiternum, the migrant populations transited and/or established in the territory of Amiternum such as Byzantines, Longobards (Lombards), which dominated the Italian peninsula between 568 and 774 AD, and the current populations of Italy. The study of haplogroups, the analysis of genetic variability and phylogenesis studies on the sequences considered show a genetic closeness between the individuals of Amiternum, the current population of central-northern Italy and the Germanic tribe of Longobards, however, also highlights genetic traits of Byzantines in some samples of Amiternum. Using the analysis of amelogenin gene fragments, we successfully determined the sex of the bone remains on all samples.}, }
@article {pmid31638147, year = {2020}, author = {Liu, Y and Weyrich, LS and Llamas, B}, title = {More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment.}, journal = {Molecular biology and evolution}, volume = {37}, number = {2}, pages = {307-319}, doi = {10.1093/molbev/msz231}, pmid = {31638147}, issn = {1537-1719}, mesh = {*Adaptation, Physiological ; Animals ; Confounding Factors, Epidemiologic ; DNA Methylation ; DNA, Ancient/*analysis ; Epigenesis, Genetic ; Epigenomics/*methods ; Evolution, Molecular ; Mammals/*genetics/*microbiology/physiology ; Microbiota ; Paleontology ; }, abstract = {Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.}, }
@article {pmid31626767, year = {2019}, author = {Raghavan, M and Schroeder, H and Malaspinas, AS}, title = {An Ancient Genome from the Indus Valley Civilization.}, journal = {Cell}, volume = {179}, number = {3}, pages = {586-588}, doi = {10.1016/j.cell.2019.09.027}, pmid = {31626767}, issn = {1097-4172}, mesh = {Archaeology ; Asia ; *Cemeteries ; *Civilization ; Humans ; India ; }, abstract = {Shinde et al. report the first genome-wide data from an ancient individual from the Indus Valley Civilization in South Asia. Their findings have implications for the origins and spread of farming and Indo-European languages in the region and the makings of the South Asian gene pool.}, }
@article {pmid31611588, year = {2019}, author = {Shamoon-Pour, M and Li, M and Merriwether, DA}, title = {Rare human mitochondrial HV lineages spread from the Near East and Caucasus during post-LGM and Neolithic expansions.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14751}, pmid = {31611588}, issn = {2045-2322}, mesh = {Armenia ; Asia ; Asian People/genetics ; DNA, Mitochondrial/*genetics ; Europe ; Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Middle East ; Mitochondria/genetics ; Phylogeography ; White People/genetics ; }, abstract = {Of particular significance to human population history in Eurasia are the migratory events that connected the Near East to Europe after the Last Glacial Maximum (LGM). Utilizing 315 HV*(xH,V) mitogenomes, including 27 contemporary lineages first reported here, we found the genetic signatures for distinctive movements out of the Near East and South Caucasus both westward into Europe and eastward into South Asia. The parallel phylogeographies of rare, yet widely distributed HV*(xH,V) subclades reveal a connection between the Italian Peninsula and South Caucasus, resulting from at least two (post-LGM, Neolithic) waves of migration. Many of these subclades originated in a population ancestral to contemporary Armenians and Assyrians. One such subclade, HV1b-152, supports a postexilic, northern Mesopotamian origin for the Ashkenazi HV1b2 lineages. In agreement with ancient DNA findings, our phylogenetic analysis of HV12 and HV14, the two exclusively Asian subclades of HV*(xH,V), point to the migration of lineages originating in Iran to South Asia before and during the Neolithic period. With HV12 being one of the oldest HV subclades, our results support an origin of HV haplogroup in the region defined by Western Iran, Mesopotamia, and the South Caucasus, where the highest prevalence of HV has been found.}, }
@article {pmid31607556, year = {2019}, author = {Tett, A and Huang, KD and Asnicar, F and Fehlner-Peach, H and Pasolli, E and Karcher, N and Armanini, F and Manghi, P and Bonham, K and Zolfo, M and De Filippis, F and Magnabosco, C and Bonneau, R and Lusingu, J and Amuasi, J and Reinhard, K and Rattei, T and Boulund, F and Engstrand, L and Zink, A and Collado, MC and Littman, DR and Eibach, D and Ercolini, D and Rota-Stabelli, O and Huttenhower, C and Maixner, F and Segata, N}, title = {The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {5}, pages = {666-679.e7}, pmid = {31607556}, issn = {1934-6069}, support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; 716575/ERC_/European Research Council/International ; R24 DK110499/DK/NIDDK NIH HHS/United States ; R01 DK103358/DK/NIDDK NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; }, mesh = {Diet ; Ethiopia ; Feces/microbiology ; Fossils/*microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Ghana ; Humans ; Prevotella/*classification/*genetics/isolation &amp; purification ; Tanzania ; }, abstract = {Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.}, }
@article {pmid31603617, year = {2019}, author = {Crump, SE and Miller, GH and Power, M and Sepúlveda, J and Dildar, N and Coghlan, M and Bunce, M}, title = {Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada.}, journal = {Global change biology}, volume = {25}, number = {12}, pages = {4244-4256}, doi = {10.1111/gcb.14836}, pmid = {31603617}, issn = {1365-2486}, support = {DGE1144083//NSF/ ; BCS1657743//NSF/ ; ARC1737712//NSF/ ; //National Geographic Society/ ; //Geological Society of America/ ; //CU Department of Geological Sciences/ ; //CU Center for the Study of Origins/ ; //INSTAAR/ ; }, mesh = {Arctic Regions ; Canada ; Climate Change ; *Lakes ; *Tundra ; }, abstract = {Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global-scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be biased by the influx of exotic pollen to tundra settings. Here, we reconstruct past plant communities using sedimentary ancient DNA (sedaDNA), which has a more local source area than pollen. We additionally reconstruct past temperature variability using bacterial cell membrane lipids (branched glycerol dialkyl glycerol tetraethers) and an aquatic productivity indicator (biogenic silica) to evaluate the relative timing of postglacial ecological and climate changes at a lake on southern Baffin Island, Arctic Canada. The sedaDNA record tightly constrains the colonization of dwarf birch (Betula, a thermophilous shrub) to 5.9 ± 0.1 ka, ~3 ka after local deglaciation as determined by cosmogenic [10] Be moraine dating and >2 ka later than Betula pollen is recorded in nearby lake sediment. We then assess the paleovegetation history within the context of summer temperature and find that paleotemperatures were highest prior to 6.3 ka, followed by cooling in the centuries preceding Betula establishment. Together, these molecular proxies reveal that Betula colonization lagged peak summer temperatures, suggesting that inefficient dispersal, rather than climate, may have limited Arctic shrub migration in this region. In addition, these data suggest that pollen-based climate reconstructions from high latitudes, which rely heavily on the presence and abundance of pollen from thermophilous taxa like Betula, can be compromised by both exotic pollen fluxes and vegetation migration lags.}, }
@article {pmid31594846, year = {2019}, author = {Cox, SL and Ruff, CB and Maier, RM and Mathieson, I}, title = {Genetic contributions to variation in human stature in prehistoric Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {43}, pages = {21484-21492}, pmid = {31594846}, issn = {1091-6490}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; }, mesh = {*Body Height ; DNA, Ancient/*chemistry ; Europe ; *Genetic Variation ; Genetics, Population/history ; History, Ancient ; Human Genetics/*history ; Humans ; Paleontology ; Phenotype ; Polymorphism, Single Nucleotide ; White People/*genetics/*history ; }, abstract = {The relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 y in European height predicted using DNA from 1,071 ancient individuals are consistent with changes observed in 1,159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height-consistent with genetic predictions-although genetics predicts a small post-Neolithic increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change.}, }
@article {pmid31594508, year = {2019}, author = {Malmström, H and Günther, T and Svensson, EM and Juras, A and Fraser, M and Munters, AR and Pospieszny, &#x141; and Tõrv, M and Lindström, J and Götherström, A and Storå, J and Jakobsson, M}, title = {The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1912}, pages = {20191528}, pmid = {31594508}, issn = {1471-2954}, mesh = {Baltic States ; Base Sequence ; *Culture ; DNA, Ancient ; Europe ; Farmers ; Genomics ; *History, Ancient ; *Human Migration ; Humans ; Poland ; Population Dynamics ; Scandinavian and Nordic Countries ; Sweden ; White People ; }, abstract = {The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24× coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.}, }
@article {pmid31565086, year = {2019}, author = {Robson, HK and Skipitytė, R and Piličiauskienė, G and Lucquin, A and Heron, C and Craig, OE and Piličiauskas, G}, title = {Diet, cuisine and consumption practices of the first farmers in the southeastern Baltic.}, journal = {Archaeological and anthropological sciences}, volume = {11}, number = {8}, pages = {4011-4024}, pmid = {31565086}, issn = {1866-9557}, abstract = {With the arrival of the Early Neolithic Globular Amphora and Corded Ware cultures into the southeastern Baltic, ca. 2900/2800-2400 cal BC, a new type of economy was introduced, animal husbandry. However, the degree to which this transformed the subsistence economy is unknown. Here, we conducted organic residue analyses of 64 ceramic vessels to identify their contents. The vessels were sampled from 10 Lithuanian archaeological sites dating across the Subneolithic-Neolithic transition to the Early Bronze Age (ca. 2900/2800-1300 cal BC). Our results demonstrate that regardless of location or vessel type, many ceramics were used to process aquatic resources. Against our expectations, this association continued even after marked economic change concurrent with the migration of pastoralists from central and southeastern Europe, as evidenced by recent ancient DNA analysis of human remains. Moreover, we observed dairy fats in pottery from all cultures of the Early Neolithic (i.e. Rzucewo, Globular Amphora and Corded Ware) but unlike other regions of Europe, it seems that these were incorporated into indigenous culinary practices. Furthermore, some vessels were used to process plant foods, and others may have been used for the production and/or storage of birch bark tar. However, evidence for domesticated plant processing, for example millet, was absent. We show that organic residue analysis of pottery provides a different picture of past consumption patterns compared to the stable isotope analysis of human remains from isolated burials where a clear dietary shift is evident.}, }
@article {pmid31563810, year = {2019}, author = {Jones, R and Velasco, MS and Harris, LG and Morgan, S and Temple, M and Ruddy, MC and Williams, R and Perry, MD and Hitchings, M and Wilkinson, TS and Humphrey, T and Gilbert, MTP and Davies, AP}, title = {Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {119}, number = {}, pages = {101865}, doi = {10.1016/j.tube.2019.101865}, pmid = {31563810}, issn = {1873-281X}, mesh = {Child ; DNA, Bacterial/*genetics ; Disease Outbreaks ; Genome, Bacterial/*genetics ; Global Health ; Humans ; Multilocus Sequence Typing ; Mycobacterium tuberculosis/*genetics ; *Polymorphism, Single Nucleotide ; Tuberculosis/epidemiology/*microbiology ; Whole Genome Sequencing ; }, abstract = {This study describes the analysis of DNA from heat-killed (boilate) isolates of Mycobacterium tuberculosis from two UK outbreaks where DNA was of sub-optimal quality for the standard methodologies routinely used in microbial genomics. An Illumina library construction method developed for sequencing ancient DNA was successfully used to obtain whole genome sequences, allowing analysis of the outbreak by gene-by-gene MLST, SNP mapping and phylogenetic analysis. All cases were spoligotyped to the same Haarlem H1 sub-lineage. This is the first described application of ancient DNA library construction protocols to allow whole genome sequencing of a clinical tuberculosis outbreak. Using this method it is possible to obtain epidemiologically meaningful data even when DNA is of insufficient quality for standard methods.}, }
@article {pmid31561553, year = {2019}, author = {Yankova, I and Marinov, M and Neov, B and Petrova, M and Spassov, N and Hristov, P and Radoslavov, G}, title = {Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages.}, journal = {Genes}, volume = {10}, number = {10}, pages = {}, pmid = {31561553}, issn = {2073-4425}, mesh = {Animal Distribution ; Animals ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; Evolution, Molecular ; *Fossils ; Haplotypes ; *Phylogeny ; }, abstract = {The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs' populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire.}, }
@article {pmid31558742, year = {2019}, author = {Morley, MW and Goldberg, P and Uliyanov, VA and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Jacobs, Z and Roberts, RG}, title = {Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13785}, pmid = {31558742}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; *Caves ; Cold Climate ; DNA, Ancient/isolation &amp; purification ; *Fossils ; History, Ancient ; *Hominidae/genetics ; Humans ; Neanderthals/genetics ; Paleontology ; Siberia ; }, abstract = {Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal-Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.}, }
@article {pmid31552062, year = {2019}, author = {Wang, C and Lu, H and Zhang, J and Mao, L and Ge, Y}, title = {Bulliform Phytolith Size of Rice and Its Correlation With Hydrothermal Environment: A Preliminary Morphological Study on Species in Southern China.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1037}, pmid = {31552062}, issn = {1664-462X}, abstract = {In the last decade, our understanding of rice domestication has improved by new archaeological findings using advanced analytical techniques such as morphological and morphometric analyses on rice grains, spikelet bases and phytoliths, and ancient DNA analysis on rice remains. Previous studies have considered the size of rice bulliform phytoliths as a proxy for tracking the domestication process. These phytoliths are often abundant and well preserved in sediments, and their shape is under the control of numerous genes, which may shift toward larger sizes by genetic mutation in domestication. Therefore, it has been assumed that the bulliforms of domesticated rice are usually larger than those of wild ones; however, morphometric data supporting this assumption are lacking in the literature, thereby requiring additional evidence to test its veracity. In this study, the vertical and horizonal lengths of bulliform phytoliths were measured in four rice species (domesticated Oryza sativa and wild Oryza rufipogon, Oryza officinalis, and Oryza meyeriana) from different regions of southern China. We found that the bulliform morphometric data of wild and domesticated rice overlapped and that there was no statistically significant difference between them. Therefore, bulliform size could not be used as a diagnostic indicator to distinguish domesticated rice from wild species and is a supporting rather than conclusive proxy for determining the domesticated status of rice in archaeological research. We further found that larger rice bulliform sizes likely occurred at the locations with higher temperature, precipitation, and water levels, indicating hydrothermal environment is an alternative factor influencing the size of rice bulliform phytoliths. For further archaeological use of an increasing size trend of bulliform phytoliths to reveal the process of rice domestication, we present some suggestions for controlling the influence of hydrothermal factors. Even so, the combination of bulliform phytolith size with other established criteria is strongly suggested to provide precise identification of wild and domesticated rice in future research.}, }
@article {pmid33365931, year = {2019}, author = {Stelbrink, B and Kehlmaier, C and Wilke, T and Albrecht, C}, title = {The near-complete mitogenome of the critically endangered Pseudocleopatra dartevellei (Caenogastropoda: Paludomidae) from the Congo River assembled from historical museum material.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {4}, number = {2}, pages = {3229-3231}, pmid = {33365931}, issn = {2380-2359}, abstract = {Here, we present the first near-complete mitogenome of a member of the freshwater gastropod family Paludomidae, Pseudocleopatra dartevellei. This Congo River species is of particular importance because the sister to the Lake Tanganyika radiation is supposed to be a paludomid riverine species. We used ancient DNA (aDNA) techniques including single-stranded DNA library preparation in order to assemble the mitogenome from historical museum material collected in 1937. The mitogenome was 15,368 bp long and showed typical characteristics as identified in other freshwater gastropods. The present phylogeny shows a closer relationship between Pseudocleoptra dartevellei and another non-Tanganyikan species, Cleopatra johnstoni.}, }
@article {pmid31542986, year = {2019}, author = {Chen, SG and Li, J and Zhang, F and Xiao, B and Hu, JM and Cui, YQ and Hofreiter, M and Hou, XD and Sheng, GL and Lai, XL and Yuan, JX}, title = {Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {30}, number = {7}, pages = {786-793}, doi = {10.1080/24701394.2019.1659250}, pmid = {31542986}, issn = {2470-1408}, mesh = {Animals ; Camelus/*genetics ; China ; Computational Biology ; Female ; Genome, Mitochondrial/*genetics ; Phylogeny ; *Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. years before present (yBP). Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis suggest a slow increase in female effective population size of C. bactrianus from 5000 years ago, which corresponds to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.}, }
@article {pmid31539495, year = {2019}, author = {Gokhman, D and Mishol, N and de Manuel, M and de Juan, D and Shuqrun, J and Meshorer, E and Marques-Bonet, T and Rak, Y and Carmel, L}, title = {Reconstructing Denisovan Anatomy Using DNA Methylation Maps.}, journal = {Cell}, volume = {179}, number = {1}, pages = {180-192.e10}, doi = {10.1016/j.cell.2019.08.035}, pmid = {31539495}, issn = {1097-4172}, mesh = {Animals ; Base Sequence ; DNA Methylation/*genetics ; Databases, Genetic ; Extinction, Biological ; Fossils ; Genome, Human/genetics ; Humans ; Neanderthals/*anatomy &amp; histology/*genetics ; Pan troglodytes/*anatomy &amp; histology/*genetics ; *Phenotype ; Polymorphism, Single Nucleotide/genetics ; Skeleton ; Skull ; }, abstract = {Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.}, }
@article {pmid31537848, year = {2019}, author = {Tamm, E and Di Cristofaro, J and Mazières, S and Pennarun, E and Kushniarevich, A and Raveane, A and Semino, O and Chiaroni, J and Pereira, L and Metspalu, M and Montinaro, F}, title = {Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13581}, pmid = {31537848}, issn = {2045-2322}, mesh = {Africa, Northern ; France/ethnology ; Gene Frequency ; Genetics, Population ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Italy/ethnology ; Phylogeny ; Population Dynamics ; Selection, Genetic ; White People/ethnology/*genetics ; Whole Genome Sequencing/*methods ; }, abstract = {Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians.}, }
@article {pmid31523131, year = {2019}, author = {Ishiya, K and Mizuno, F and Wang, L and Ueda, S}, title = {MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome.}, journal = {Bioinformatics and biology insights}, volume = {13}, number = {}, pages = {1177932219873884}, pmid = {31523131}, issn = {1177-9322}, abstract = {The incompleteness of partial human mitochondrial genome sequences makes it difficult to perform relevant comparisons among multiple resources. To deal with this issue, we propose a computational framework for deducing missing nucleotides in the human mitochondrial genome. We applied it to worldwide mitochondrial haplogroup lineages and assessed its performance. Our approach can deduce the missing nucleotides with a precision of 0.99 or higher in most human mitochondrial DNA lineages. Furthermore, although low-coverage mitochondrial genome sequences often lead to a blurred relationship in the multidimensional scaling analysis, our approach can correct this positional arrangement according to the corresponding mitochondrial DNA lineages. Therefore, our framework will provide a practical solution to compensate for the lack of genome coverage in partial and fragmented human mitochondrial genome sequences. In this study, we developed an open-source computer program, MitoIMP, implementing our imputation procedure. MitoIMP is freely available from https://github.com/omics-tools/mitoimp.}, }
@article {pmid31517046, year = {2019}, author = {Bennett, EA and Crevecoeur, I and Viola, B and Derevianko, AP and Shunkov, MV and Grange, T and Maureille, B and Geigl, EM}, title = {Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals.}, journal = {Science advances}, volume = {5}, number = {9}, pages = {eaaw3950}, pmid = {31517046}, issn = {2375-2548}, mesh = {Animals ; Finger Phalanges/*anatomy &amp; histology ; *Genome, Human ; Humans ; Molar/*anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology/genetics ; Species Specificity ; }, abstract = {A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.}, }
@article {pmid31513651, year = {2019}, author = {Menardo, F and Duchêne, S and Brites, D and Gagneux, S}, title = {The molecular clock of Mycobacterium tuberculosis.}, journal = {PLoS pathogens}, volume = {15}, number = {9}, pages = {e1008067}, pmid = {31513651}, issn = {1553-7374}, mesh = {Bayes Theorem ; Biological Clocks/*genetics/physiology ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genome, Bacterial ; Humans ; Models, Biological ; Molecular Epidemiology ; Mycobacterium bovis/genetics/physiology ; Mycobacterium tuberculosis/*genetics/pathogenicity/physiology ; Phylogeny ; Polymorphism, Single Nucleotide ; Time Factors ; Tuberculosis/epidemiology/microbiology ; }, abstract = {The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.}, }
@article {pmid31511700, year = {2019}, author = {Cappellini, E and Welker, F and Pandolfi, L and Ramos-Madrigal, J and Samodova, D and Rüther, PL and Fotakis, AK and Lyon, D and Moreno-Mayar, JV and Bukhsianidze, M and Rakownikow Jersie-Christensen, R and Mackie, M and Ginolhac, A and Ferring, R and Tappen, M and Palkopoulou, E and Dickinson, MR and Stafford, TW and Chan, YL and Götherström, A and Nathan, SKSS and Heintzman, PD and Kapp, JD and Kirillova, I and Moodley, Y and Agusti, J and Kahlke, RD and Kiladze, G and Martínez-Navarro, B and Liu, S and Sandoval Velasco, M and Sinding, MS and Kelstrup, CD and Allentoft, ME and Orlando, L and Penkman, K and Shapiro, B and Rook, L and Dalén, L and Gilbert, MTP and Olsen, JV and Lordkipanidze, D and Willerslev, E}, title = {Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.}, journal = {Nature}, volume = {574}, number = {7776}, pages = {103-107}, pmid = {31511700}, issn = {1476-4687}, support = {//Wellcome Trust/United Kingdom ; 681396/ERC_/European Research Council/International ; 681605/ERC_/European Research Council/International ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bayes Theorem ; DNA, Ancient/*analysis ; Dental Enamel/*metabolism ; *Fossils ; History, Ancient ; Humans ; Male ; Perissodactyla/*classification/*genetics/metabolism ; Phosphorylation/genetics ; *Phylogeny ; Proteome/analysis/*genetics ; *Proteomics ; }, abstract = {The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa[1]. However, the irreversible post-mortem degradation[2] of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)[3]. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I[4], and suggested the presence of protein residues in fossils of the Cretaceous period[5]-although with limited phylogenetic use[6]. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch[7-9], using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)[10]. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates[11], and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.}, }
@article {pmid31504166, year = {2020}, author = {Moreno-Mayar, JV and Korneliussen, TS and Dalal, J and Renaud, G and Albrechtsen, A and Nielsen, R and Malaspinas, AS}, title = {A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {3}, pages = {828-841}, pmid = {31504166}, issn = {1367-4811}, support = {R01 GM116044/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosomes ; *DNA, Ancient ; *High-Throughput Nucleotide Sequencing ; Humans ; Likelihood Functions ; Male ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: The presence of present-day human contaminating DNA fragments is one of the challenges defining ancient DNA (aDNA) research. This is especially relevant to the ancient human DNA field where it is difficult to distinguish endogenous molecules from human contaminants due to their genetic similarity. Recently, with the advent of high-throughput sequencing and new aDNA protocols, hundreds of ancient human genomes have become available. Contamination in those genomes has been measured with computational methods often developed specifically for these empirical studies. Consequently, some of these methods have not been implemented and tested for general use while few are aimed at low-depth nuclear data, a common feature in aDNA datasets.<br><br>RESULTS: We develop a new X-chromosome-based maximum likelihood method for estimating present-day human contamination in low-depth sequencing data from male individuals. We implement our method for general use, assess its performance under conditions typical of ancient human DNA research, and compare it to previous nuclear data-based methods through extensive simulations. For low-depth data, we show that existing methods can produce unusable estimates or substantially underestimate contamination. In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5&#xd7; on the X-chromosome when contamination is below 25%. Moreover, our method still yields meaningful estimates in very challenging situations, i.e. when the contaminant and the target come from closely related populations or with increased error rates. With a running time below 5&#xa0;min, our method is applicable to large scale aDNA genomic studies.<br><br>The method is implemented in C++ and R and is available in github.com/sapfo/contaminationX and popgen.dk/angsd.}, }
@article {pmid31495572, year = {2019}, author = {Shinde, V and Narasimhan, VM and Rohland, N and Mallick, S and Mah, M and Lipson, M and Nakatsuka, N and Adamski, N and Broomandkhoshbacht, N and Ferry, M and Lawson, AM and Michel, M and Oppenheimer, J and Stewardson, K and Jadhav, N and Kim, YJ and Chatterjee, M and Munshi, A and Panyam, A and Waghmare, P and Yadav, Y and Patel, H and Kaushik, A and Thangaraj, K and Meyer, M and Patterson, N and Rai, N and Reich, D}, title = {An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers.}, journal = {Cell}, volume = {179}, number = {3}, pages = {729-735.e10}, pmid = {31495572}, issn = {1097-4172}, support = {/HHMI_/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; }, mesh = {Asian People/genetics ; DNA, Ancient/*chemistry ; Evolution, Molecular ; *Genome, Human ; *Human Migration ; Humans ; Iran ; Pakistan ; *Pedigree ; Population/*genetics ; }, abstract = {We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.}, }
@article {pmid31486822, year = {2019}, author = {Balázs, J and Rózsa, Z and Bereczki, Z and Marcsik, A and Tihanyi, B and Karlinger, K and Pölöskei, G and Molnár, E and Donoghue, HD and Pálfi, G}, title = {Osteoarcheological and biomolecular evidence of leprosy from an 11-13[th] century CE Muslim cemetery in Europe (Orosháza, Southeast Hungary).}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {70}, number = {2}, pages = {105-118}, doi = {10.1127/homo/2019/1071}, pmid = {31486822}, issn = {1618-1301}, mesh = {Adult ; Bone and Bones/microbiology/pathology ; Cemeteries/*history ; DNA, Ancient/analysis ; DNA, Bacterial/analysis/genetics ; Female ; History, Medieval ; Humans ; Hungary ; Islam/*history ; Leprosy/*history/microbiology ; Male ; Mycobacterium leprae/genetics ; Paleopathology ; Young Adult ; }, abstract = {Orosháza site no. 10 (Southeast Hungary) contains the partially excavated archaeological remains of an 11-13[th] century CE Muslim merchant village and its cemetery located in close proximity to Christian villages of the same era. The skeleton of a young woman (grave no. 16) from the last phase of the cemetery use was identified with rhinomaxillary lesions associated with lepromatous leprosy. The right parietal bone also exhibited signs of cranial trauma, possibly caused by symbolic trepanation, a well-known ritual practice in the 9-11[th] century CE Carpathian Basin. The retrospective diagnosis of the disease was supported by ancient DNA analysis, as the samples were positive for Mycobacterium leprae aDNA, shown to be of genotype 3. Contrary to the general practice of the era, the body of the young female with severe signs of leprosy was interred among the regular graves of the Muslim cemetery in Orosháza, which may reflect the unique cultural background of the community.}, }
@article {pmid31481615, year = {2019}, author = {Gilbert, E and O'Reilly, S and Merrigan, M and McGettigan, D and Vitart, V and Joshi, PK and Clark, DW and Campbell, H and Hayward, C and Ring, SM and Golding, J and Goodfellow, S and Navarro, P and Kerr, SM and Amador, C and Campbell, A and Haley, CS and Porteous, DJ and Cavalleri, GL and Wilson, JF}, title = {The genetic landscape of Scotland and the Isles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {38}, pages = {19064-19070}, pmid = {31481615}, issn = {1091-6490}, support = {G0700704/MRC_/Medical Research Council/United Kingdom ; /ARC_/Arthritis Research UK/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; /CSO_/Chief Scientist Office/United Kingdom ; MR/K026992/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_U127592696/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; }, mesh = {DNA, Ancient/*analysis ; Ethnicity/*genetics ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Humans ; Ireland ; Islands ; Scotland ; }, abstract = {Britain and Ireland are known to show population genetic structure; however, large swathes of Scotland, in particular, have yet to be described. Delineating the structure and ancestry of these populations will allow variant discovery efforts to focus efficiently on areas not represented in existing cohorts. Thus, we assembled genotype data for 2,554 individuals from across the entire archipelago with geographically restricted ancestry, and performed population structure analyses and comparisons to ancient DNA. Extensive geographic structuring is revealed, from broad scales such as a NE to SW divide in mainland Scotland, through to the finest scale observed to date: across 3 km in the Northern Isles. Many genetic boundaries are consistent with Dark Age kingdoms of Gaels, Picts, Britons, and Norse. Populations in the Hebrides, the Highlands, Argyll, Donegal, and the Isle of Man show characteristics of isolation. We document a pole of Norwegian ancestry in the north of the archipelago (reaching 23 to 28% in Shetland) which complements previously described poles of Germanic ancestry in the east, and "Celtic" to the west. This modern genetic structure suggests a northwestern British or Irish source population for the ancient Gaels that contributed to the founding of Iceland. As rarer variants, often with larger effect sizes, become the focus of complex trait genetics, more diverse rural cohorts may be required to optimize discoveries in British and Irish populations and their considerable global diaspora.}, }
@article {pmid31481609, year = {2019}, author = {Gower, G and Fenderson, LE and Salis, AT and Helgen, KM and van Loenen, AL and Heiniger, H and Hofman-Kamińska, E and Kowalczyk, R and Mitchell, KJ and Llamas, B and Cooper, A}, title = {Widespread male sex bias in mammal fossil and museum collections.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {38}, pages = {19019-19024}, pmid = {31481609}, issn = {1091-6490}, mesh = {Animals ; Bison/genetics ; DNA, Ancient/*analysis ; Female ; *Fossils ; High-Throughput Nucleotide Sequencing ; Male ; Mammals/*genetics ; Mammoths/genetics ; *Models, Genetic ; *Museums ; Phylogeny ; Sexism/*statistics &amp; numerical data ; Ursidae/genetics ; }, abstract = {A recent study of mammoth subfossil remains has demonstrated the potential of using relatively low-coverage high-throughput DNA sequencing to genetically sex specimens, revealing a strong male-biased sex ratio [P. Pečnerová et al., Curr. Biol. 27, 3505-3510.e3 (2017)]. Similar patterns were predicted for steppe bison, based on their analogous female herd-based structure. We genetically sexed subfossil remains of 186 Holarctic bison (Bison spp.), and also 91 brown bears (Ursus arctos), which are not female herd-based, and found that ∼75% of both groups were male, very close to the ratio observed in mammoths (72%). This large deviation from a 1:1 ratio was unexpected, but we found no evidence for sex differences with respect to DNA preservation, sample age, material type, or overall spatial distribution. We further examined ratios of male and female specimens from 4 large museum mammal collections and found a strong male bias, observable in almost all mammalian orders. We suggest that, in mammals at least, 1) wider male geographic ranges can lead to considerably increased chances of detection in fossil studies, and 2) sexual dimorphic behavior or appearance can facilitate a considerable sex bias in fossil and modern collections, on a previously unacknowledged scale. This finding has major implications for a wide range of studies of fossil and museum material.}, }
@article {pmid31480978, year = {2019}, author = {Hermes, TR and Frachetti, MD and Doumani Dupuy, PN and Mar'yashev, A and Nebel, A and Makarewicz, CA}, title = {Early integration of pastoralism and millet cultivation in Bronze Age Eurasia.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1910}, pages = {20191273}, pmid = {31480978}, issn = {1471-2954}, mesh = {Agriculture/*history ; Animals ; Archaeology ; Cattle ; China ; Crops, Agricultural/*history ; Domestication ; Goats ; History, Ancient ; Humans ; Kazakhstan ; Livestock ; *Millets ; Radiometric Dating ; Sheep ; }, abstract = {Mobile pastoralists are thought to have facilitated the first trans-Eurasian dispersals of domesticated plants during the Early Bronze Age (ca 2500-2300 BC). Problematically, the earliest seeds of wheat, barley and millet in Inner Asia were recovered from human mortuary contexts and do not inform on local cultivation or subsistence use, while contemporaneous evidence for the use and management of domesticated livestock in the region remains ambiguous. We analysed mitochondrial DNA and multi-stable isotopic ratios (δ[13]C, δ[15]N and δ[18]O) of faunal remains from key pastoralist sites in the Dzhungar Mountains of southeastern Kazakhstan. At ca 2700 BC, Near Eastern domesticated sheep and goat were present at the settlement of Dali, which were also winter foddered with the region's earliest cultivated millet spreading from its centre of domestication in northern China. In the following centuries, millet cultivation and caprine management became increasingly intertwined at the nearby site of Begash. Cattle, on the other hand, received low levels of millet fodder at the sites for millennia. By primarily examining livestock dietary intake, this study reveals that the initial transmission of millet across the mountains of Inner Asia coincided with a substantial connection between pastoralism and plant cultivation, suggesting that pastoralist livestock herding was integral for the westward dispersal of millet from farming societies in China.}, }
@article {pmid31477930, year = {2019}, author = {Kreplak, J and Madoui, MA and Cápal, P and Novák, P and Labadie, K and Aubert, G and Bayer, PE and Gali, KK and Syme, RA and Main, D and Klein, A and Bérard, A and Vrbová, I and Fournier, C and d'Agata, L and Belser, C and Berrabah, W and Toegelová, H and Milec, Z and Vrána, J and Lee, H and Kougbeadjo, A and Térézol, M and Huneau, C and Turo, CJ and Mohellibi, N and Neumann, P and Falque, M and Gallardo, K and McGee, R and Tar'an, B and Bendahmane, A and Aury, JM and Batley, J and Le Paslier, MC and Ellis, N and Warkentin, TD and Coyne, CJ and Salse, J and Edwards, D and Lichtenzveig, J and Macas, J and Doležel, J and Wincker, P and Burstin, J}, title = {A reference genome for pea provides insight into legume genome evolution.}, journal = {Nature genetics}, volume = {51}, number = {9}, pages = {1411-1422}, pmid = {31477930}, issn = {1546-1718}, mesh = {Chromosome Mapping ; Chromosomes, Plant/*genetics ; *Evolution, Molecular ; Fabaceae/classification/*genetics ; Gene Expression Regulation, Plant ; Genetic Variation ; *Genome, Plant ; Genomics ; Pisum sativum/*genetics ; Phenotype ; Phylogeny ; Plant Proteins/*genetics ; *Quantitative Trait Loci ; Reference Standards ; Repetitive Sequences, Nucleic Acid ; Seed Storage Proteins/genetics ; Whole Genome Sequencing ; }, abstract = {We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.}, }
@article {pmid31462911, year = {2019}, author = {Oosting, T and Star, B and Barrett, JH and Wellenreuther, M and Ritchie, PA and Rawlence, NJ}, title = {Unlocking the potential of ancient fish DNA in the genomic era.}, journal = {Evolutionary applications}, volume = {12}, number = {8}, pages = {1513-1522}, pmid = {31462911}, issn = {1752-4571}, abstract = {Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.}, }
@article {pmid31455916, year = {2019}, author = {Lewis, D}, title = {'Paralysed by anxiety': researchers speak about life in troubled ancient-DNA lab.}, journal = {Nature}, volume = {572}, number = {7771}, pages = {571-572}, pmid = {31455916}, issn = {1476-4687}, mesh = {DNA, Ancient ; *Dental Plaque ; *Diet ; Humans ; *Microbiota ; Mouth/microbiology ; }, }
@article {pmid31437436, year = {2019}, author = {Leles, D and Frías, L and Araújo, A and Brener, B and Sudré, A and Chame, M and Laurentino, V}, title = {Are immunoenzymatic tests for intestinal protozoans reliable when used on archaeological material?.}, journal = {Experimental parasitology}, volume = {205}, number = {}, pages = {107739}, doi = {10.1016/j.exppara.2019.107739}, pmid = {31437436}, issn = {1090-2449}, mesh = {Animals ; Antigens, Protozoan/analysis/genetics ; Archaeology/*methods ; Cryptosporidium/genetics/immunology/*isolation &amp; purification ; Entamoeba/genetics/immunology/*isolation &amp; purification ; Entamoeba histolytica/genetics/immunology/isolation &amp; purification ; Feces/*parasitology ; Giardia lamblia/genetics/immunology/*isolation &amp; purification ; Humans ; Immunoenzyme Techniques/*standards ; Intestinal Diseases, Parasitic/parasitology ; Rodentia ; Sensitivity and Specificity ; South America ; }, abstract = {Intestinal protozoans found in ancient human samples have been studied primarily by microscopy and immunodiagnostic assays. However, such methods are not suitable for the detection of zoonotic genotypes. The objectives of the present study were to utilize immunoenzimatic assays for coproantigen detection of Cryptosporidium sp., Giardia duodenalis, and Entamoeba histolytica/Entamoeba dispar in sixty ancient human and animal samples collected from 14 archaeological sites in South America, and to carry out a critical analysis of G. duodenalis according to results obtained from three diagnostic methodologies: microscopy, immunodiagnostic tests (immunoenzymatic and immunofluorescence), and molecular biology (PCR and sequencing). More than half (31/60) of the samples analyzed using immunoenzymatic tests were positive for at least one of the intestinal protozoans, with 46.6% (28/60) corresponding to G. duodenalis, 26.6% (16/60) to Cryptosporidium sp., and 5% (3/60) to E. histolytica/E. dispar. Cryptosporidium sp. and G. duodenalis coinfection was observed in 15% (9/60) of the samples, whereas all three protozoans were found in 5% (3/60) of samples. In the Northeast Region of Brazil, by immunoenzymatic tests there is evidence that G. duodenlais and Cryptosporidium sp. have infected humans and rodents for at least 7150 years. However, for G. duodenalis, the results from the three diagnostic tests were discordant. Specifically, despite the efficiency of the molecular biology assay in the experimental models, G. duodenalis DNA could not be amplified from the ancient samples. These results raise the following question: Are all ancient samples positive for coproantigen of G. duodenalis by immunoenzymatic tests truly positive? This scenario highlights the importance of further studies to evaluate the sensitivity and specificity of the immunoenzymatic method in the archaeological context.}, }
@article {pmid31433816, year = {2019}, author = {Fernandes, D and Sirak, K and Cheronet, O and Howcroft, R and Čavka, M and Los, D and Burmaz, J and Pinhasi, R and Novak, M}, title = {Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0216366}, pmid = {31433816}, issn = {1932-6203}, mesh = {Adolescent ; *Archaeology ; Croatia ; *Genetic Variation ; *Human Migration ; Humans ; Male ; Skull/*abnormalities/diagnostic imaging ; Tomography, X-Ray Computed ; }, abstract = {Three individuals dating to the Great Migration Period (5th century CE) were discovered in a pit at the Hermanov vinograd site in Osijek, Croatia. We were inspired to study these individuals based on their unusual burial context as well as the identification of two different types of artificial cranial deformation in two of the individuals. We combine bioarchaeological analysis with radiographic imaging, stable isotopes analysis, and ancient DNA to analyze their dietary patterns, molecular sex, and genetic affinities in the context of the archaeological data and their bioarchaeological attributes. While all three individuals were adolescent males with skeletal evidence of severe malnutrition and similar diets, the most striking observation is that they had major differences in their genetic ancestry. Results of the genetic analyses of the nuclear ancient DNA data for these individuals indicate that the individual without artificial cranial deformation shows broadly West Eurasian associated-ancestry, the individual with tabular oblique-type has East Asian ancestry and the third individual with circular erect-type has Near Eastern associated-ancestry. Based on these results, we speculate that artificial cranial deformation type may have been a visual indicator membership in a specific cultural group, and that these groups were interacting intimately on the Pannonian Plain during the Migration Period.}, }
@article {pmid31431750, year = {2019}, author = {Lewis, D}, title = {Head of prestigious ancient-DNA lab suspended amid bullying allegations.}, journal = {Nature}, volume = {572}, number = {7770}, pages = {424-425}, doi = {10.1038/d41586-019-02490-y}, pmid = {31431750}, issn = {1476-4687}, mesh = {Bullying/ethics/*prevention &amp; control ; *DNA, Ancient ; Research Personnel/*ethics/*legislation &amp; jurisprudence ; South Australia ; Universities ; }, }
@article {pmid31431628, year = {2019}, author = {Harney, &#xc9; and Nayak, A and Patterson, N and Joglekar, P and Mushrif-Tripathy, V and Mallick, S and Rohland, N and Sedig, J and Adamski, N and Bernardos, R and Broomandkhoshbacht, N and Culleton, BJ and Ferry, M and Harper, TK and Michel, M and Oppenheimer, J and Stewardson, K and Zhang, Z and Harashawaradhana,  and Bartwal, MS and Kumar, S and Diyundi, SC and Roberts, P and Boivin, N and Kennett, DJ and Thangaraj, K and Reich, D and Rai, N}, title = {Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3670}, pmid = {31431628}, issn = {2041-1723}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Body Remains/*cytology ; DNA/*genetics ; Diet ; *Fossils ; Human Migration ; Humans ; India ; Mediterranean Region ; Polymorphism, Single Nucleotide/genetics ; Racial Groups/*genetics ; Radiometric Dating ; }, abstract = {Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.}, }
@article {pmid31424543, year = {2019}, author = {Aris-Brosou, S}, title = {Direct Evidence of an Increasing Mutational Load in Humans.}, journal = {Molecular biology and evolution}, volume = {36}, number = {12}, pages = {2823-2829}, doi = {10.1093/molbev/msz192}, pmid = {31424543}, issn = {1537-1719}, mesh = {Alleles ; Disease/*genetics ; Gene Frequency ; *Genetic Load ; *Genome, Human ; Homozygote ; Humans ; Mutation ; }, abstract = {The extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. Although the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes, and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations.}, }
@article {pmid31412470, year = {2019}, author = {Legrand, B and Miras, Y and Beauger, A and Dussauze, M and Latour, D}, title = {Akinetes and ancient DNA reveal toxic cyanobacterial recurrences and their potential for resurrection in a 6700-year-old core from a eutrophic lake.}, journal = {The Science of the total environment}, volume = {687}, number = {}, pages = {1369-1380}, doi = {10.1016/j.scitotenv.2019.07.100}, pmid = {31412470}, issn = {1879-1026}, mesh = {Cyanobacteria/*genetics ; Cyanobacteria Toxins ; *Environmental Monitoring ; Eutrophication ; Geologic Sediments/microbiology ; Lakes/microbiology ; Microcystins ; Recurrence ; Seasons ; Tropanes ; Water Pollution/*statistics &amp; numerical data ; }, abstract = {In order to evaluate the recurrence of toxic cyanobacterial blooms and to determine the survival capabilities of the resistance cells through time, a sedimentary core spanning 6700 years was drilled in the eutrophic Lake Aydat. A multiproxy approach (density, magnetic susceptibility, XRF, pollen and non-pollen palynomorph analyses), was used initially to determine the sedimentation model and the land uses around the lake. Comparison with the akinete count revealed that Nostocales cyanobacteria have been present in Lake Aydat over a six thousand year period. This long-term cyanobacterial recurrence also highlights the past presence of both the anaC and mcyB genes, involved in anatoxin-a and microcystin biosynthesis, respectively, throughout the core. The first appearance of cyanobacteria seems to be linked to the natural damming of the river, while the large increase in akinete density around 1800 cal.yr BP can be correlated with the intensification of human activities (woodland clearance, crop planting, grazing, etc.) in the catchment area of the lake, and marks the beginning of a long period of eutrophication. This first investigation into the viability and germination potential of cyanobacteria over thousands of years reveals the ability of intact akinetes to undergo cell divisions even after 1800 years of sedimentation, which is 10 times longer than previously observed. This exceptional cellular resistance, coupled with the long-term eutrophic conditions of this lake, could partly explain the past and current recurrences of cyanobacterial proliferations.}, }
@article {pmid31397436, year = {2019}, author = {Kornienko, IV and Faleeva, TG and Oreshkova, NV and Grigoriev, SE and Grigorieva, LV and Putintseva, YA and Krutovsky, KV}, title = {[Structural and Functional Organization of the Mitochondrial DNA Control Region in the Woolly Mammoth (Mammuthus primigenius)].}, journal = {Molekuliarnaia biologiia}, volume = {53}, number = {4}, pages = {627-637}, doi = {10.1134/S0026898419040062}, pmid = {31397436}, issn = {0026-8984}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Fossils ; Genome, Mitochondrial/*genetics ; Locus Control Region/*genetics ; Mammoths/*genetics ; }, abstract = {The woolly mammoth mitochondrial genome (including the Malolyakhovsky mammoth) has been previously sequenced, followed by the annotation of all its genes (MF770243). In this study, based on the Malolyakhovsky mammoth, we describe for the first time the sites of functional significance in the control region of the woolly mammoth mitogenome.}, }
@article {pmid31389360, year = {2019}, author = {Das, R}, title = {OnPeopling of India: Ancient DNA perspectives By K Thangaraj and Niraj Rai.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389360}, issn = {0973-7138}, mesh = {*DNA, Ancient ; India ; }, }
@article {pmid31389359, year = {2019}, author = {Thangaraj, K and Rai, N}, title = {Peopling of India: Ancient DNA perspectives.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389359}, issn = {0973-7138}, mesh = {Anthropology/methods ; Archaeology/methods ; Asian People/*history ; Biological Evolution ; DNA, Ancient/*analysis ; Ethnicity ; Female ; Genetic Variation ; *Genetics, Population ; History, Ancient ; Human Migration/*trends ; Humans ; India/ethnology ; Language/*history ; Male ; Selection, Genetic ; White People/*history ; }, abstract = {To reconstruct and explain patterns of genetic diversity of modern humans, understanding their past and present genetic profile is crucial. While genomes of contemporary people can provide information about present day population structure, analysis of ancient genomes may provide unprecedented insights about the past demographic events that have shaped the contemporary gene pool. Population genetics has recently witnessed an explosion in studies on ancient human population histories, primarily from Europe and America. South Asia has no representation in the ancient genomics literature, despite the wealth of archaeological richness in the form of human skeletal remains that exist in collections all over the country. Representing one-fifth of present day humanity calls for understanding the demographic history of south Asia not merely as a prerequisite but as an urgent need to understand its genetic variations on a global scale. Although the overall picture is taking form, new archaeological and genetic information from the region has started to reveal a more complex scenario of ancient human migrations and admixtures than was ever known before. In this article, we discuss a meaningful insight on the current status of ancient DNA (aDNA) research in India. We have also summarized a few but important aDNA studies, which have been successfully carried out in India. Furthermore, we have highlighted the potential opportunity of aDNA research in the Indian subcontinent.}, }
@article {pmid31386837, year = {2019}, author = {Valente, L and Etienne, RS and Garcia-R, JC}, title = {Deep Macroevolutionary Impact of Humans on New Zealand's Unique Avifauna.}, journal = {Current biology : CB}, volume = {29}, number = {15}, pages = {2563-2569.e4}, doi = {10.1016/j.cub.2019.06.058}, pmid = {31386837}, issn = {1879-0445}, mesh = {Animals ; *Biodiversity ; *Biological Evolution ; *Birds ; *Conservation of Natural Resources ; DNA, Ancient ; *Extinction, Biological ; Fossils ; New Zealand ; }, abstract = {Islands are at the frontline of the anthropogenic extinction crisis [1]. A vast number of island birds have gone extinct since human colonization [2], and an important proportion is currently threatened with extinction [3]. While the number of lost or threatened avian species has often been quantified [4], the macroevolutionary consequences of human impact on island biodiversity have rarely been measured [5]. Here, we estimate the amount of evolutionary time that has been lost or is under threat due to anthropogenic activity in a classic example, New Zealand. Half of its bird taxa have gone extinct since humans arrived [6, 7] and many are threatened [8], including lineages forming highly distinct branches in the avian tree of life [9-11]. Using paleontological and ancient DNA information, we compiled a dated phylogenetic dataset for New Zealand's terrestrial avifauna. We extend the method DAISIE developed for island biogeography [12] to allow for the fact that many of New Zealand's birds are evolutionarily isolated and use it to estimate natural rates of speciation, extinction, and colonization. Simulating under a range of human-induced extinction scenarios, we find that it would take approximately 50 million years (Ma) to recover the number of species lost since human colonization of New Zealand and up to 10 Ma to return to today's species numbers if currently threatened species go extinct. This study puts into macroevolutionary perspective the impact of humans in an isolated fauna and reveals how conservation decisions we take today will have repercussions for millions of years.}, }
@article {pmid31381968, year = {2019}, author = {Oswald, JA and Allen, JM and Witt, KE and Folk, RA and Albury, NA and Steadman, DW and Guralnick, RP}, title = {Ancient DNA from a 2,500-year-old Caribbean fossil places an extinct bird (Caracara creightoni) in a phylogenetic context.}, journal = {Molecular phylogenetics and evolution}, volume = {140}, number = {}, pages = {106576}, doi = {10.1016/j.ympev.2019.106576}, pmid = {31381968}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Birds/genetics ; Caribbean Region ; DNA, Ancient/*analysis ; *Extinction, Biological ; Falconiformes/*classification/*genetics ; *Fossils ; Genome, Mitochondrial ; Geography ; *Phylogeny ; }, abstract = {Since the late Pleistocene humans have caused the extinction of species across our planet. Placing these extinct species in the tree of life with genetic data is essential to understanding the ecological and evolutionary implications of these losses. While ancient DNA (aDNA) techniques have advanced rapidly in recent decades, aDNA from tropical species, especially birds, has been historically difficult to obtain, leaving a gap in our knowledge of the extinction processes that have influenced current distributions and biodiversity. Here we report the recovery of a nearly complete mitochondrial genome from a 2,500 year old (late Holocene) bone of an extinct species of bird, Caracara creightoni, recovered from the anoxic saltwater environment of a blue hole in the Bahamas. Our results suggest that this extinct species is sister (1.6% sequence divergence) to a clade containing the extant C. cheriway and C. plancus. Caracara creightoni shared a common ancestor with these extant species during the Pleistocene (1.2-0.4 MYA) and presumably survived on Cuba when the Bahamas was mostly underwater during Quaternary interglacial intervals (periods of high sea levels). Tropical blue holes have been collecting animals for thousands of years and will continue to improve our understanding of faunal extinctions and distributions. In particular, new aDNA techniques combined with radiocarbon dating from Holocene Bahamian fossils will allow us to place other extinct (species-level loss) and extirpated (population-level loss) vertebrate taxa in improved phylogenetic, evolutionary, biogeographic, and temporal contexts.}, }
@article {pmid31361744, year = {2019}, author = {Smith, O and Dunshea, G and Sinding, MS and Fedorov, S and Germonpre, M and Bocherens, H and Gilbert, MTP}, title = {Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival.}, journal = {PLoS biology}, volume = {17}, number = {7}, pages = {e3000166}, pmid = {31361744}, issn = {1545-7885}, mesh = {Animals ; Canidae/classification/*genetics ; Cartilage/metabolism ; *Fossils ; High-Throughput Nucleotide Sequencing/methods ; Liver/*metabolism ; Organ Specificity/*genetics ; Permafrost/chemistry ; RNA/*genetics/metabolism ; Sequence Analysis, RNA/methods ; Skin/metabolism ; Species Specificity ; Transcriptome/*genetics ; Wolves/genetics ; }, abstract = {While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology.}, }
@article {pmid31353181, year = {2019}, author = {Ning, C and Wang, CC and Gao, S and Yang, Y and Zhang, X and Wu, X and Zhang, F and Nie, Z and Tang, Y and Robbeets, M and Ma, J and Krause, J and Cui, Y}, title = {Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan.}, journal = {Current biology : CB}, volume = {29}, number = {15}, pages = {2526-2532.e4}, doi = {10.1016/j.cub.2019.06.044}, pmid = {31353181}, issn = {1879-0445}, mesh = {Archaeology ; Asian People/genetics ; China ; DNA, Ancient/*analysis ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Language ; White People/genetics ; }, abstract = {Recent studies of early Bronze Age human genomes revealed a massive population expansion by individuals-related to the Yamnaya culture, from the Pontic Caspian steppe into Western and Eastern Eurasia, likely accompanied by the spread of Indo-European languages [1-5]. The south eastern extent of this migration is currently not known. Modern-day human populations from the Xinjiang region in northwestern China show a complex population history, with genetic links to both Eastern and Western Eurasia [6-10]. However, due to the lack of ancient genomic data, it remains unclear which source populations contributed to the Xinjiang population and what was the timing and the number of admixture events. Here, we report the first genome-wide data of 10 ancient individuals from northeastern Xinjiang. They are dated to around 2,200 years ago and were found at the Iron Age Shirenzigou site. We find them to be already genetically admixed between Eastern and Western Eurasians. We also find that the majority of the East Eurasian ancestry in the Shirenzigou individuals is-related to northeastern Asian populations, while the West Eurasian ancestry is best presented by ∼20% to 80% Yamnaya-like ancestry. Our data thus suggest a Western Eurasian steppe origin for at least part of the ancient Xinjiang population. Our findings furthermore support a Yamnaya-related origin for the now extinct Tocharian languages in the Tarim Basin, in southern Xinjiang.}, }
@article {pmid31351222, year = {2019}, author = {Molto, JE and Kirkpatrick, CL and Keron, J}, title = {The paleoepidemiology of Sacral Spina Bifida Occulta in population samples from the Dakhleh Oasis, Egypt.}, journal = {International journal of paleopathology}, volume = {26}, number = {}, pages = {93-103}, doi = {10.1016/j.ijpp.2019.06.006}, pmid = {31351222}, issn = {1879-9825}, mesh = {Adult ; Egypt ; Female ; History, Ancient ; Humans ; Male ; *Paleopathology ; Prevalence ; Sacrococcygeal Region ; Spina Bifida Occulta/*epidemiology/*history ; Young Adult ; }, abstract = {OBJECTIVE: To document sacral spina bifida occulta (SSB0) prevalence in a population sample from the Dakhleh Oasis, Egypt, and address methodological issues in recording and quantifying SSBO variations.<br><br>MATERIALS: 442 adult sacra from two temporally disjunct samples from the same deme traversing the 3rd intermediate (TIP) and the Roman Periods.<br><br>METHODS: Sacra were scored for SSBO, excluding the sacral hiatus. Risk of SSBO was calculated with the common odds ratio and statistical significance by X[2]. Data were compared to other archaeological SSBO data.<br><br>RESULTS: SSBO was present in 15.6% of the sample with a slight, but not significant, temporal increase (TIP to Roman Period) in males, and a significant age-correlated increase in both sexes. Most open sacra occurred in young adults.<br><br>CONCLUSIONS: Data support that SSBO can be considered as a morphogenetic variant. Dakhleh data fall within the prevalence range for most populations, however inter-population comparisons are complicated by methodological inconsistencies.<br><br>SIGNIFICANCE: SSBO can be used in paleogenetic research.<br><br>LIMITATIONS: Methodological differences in scoring SSBO prevent effective comparative study.<br><br>SUGGESTED FUTURE RESEARCH: Future studies require more rigorous and standardized scoring methods. aDNA may be used to corroborate the morphogenetic value of SSBO and determine its clinical significance.}, }
@article {pmid31350885, year = {2019}, author = {Barbieri, C and Barquera, R and Arias, L and Sandoval, JR and Acosta, O and Zurita, C and Aguilar-Campos, A and Tito-Álvarez, AM and Serrano-Osuna, R and Gray, RD and Mafessoni, F and Heggarty, P and Shimizu, KK and Fujita, R and Stoneking, M and Pugach, I and Fehren-Schmitz, L}, title = {The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast.}, journal = {Molecular biology and evolution}, volume = {36}, number = {12}, pages = {2698-2713}, pmid = {31350885}, issn = {1537-1719}, mesh = {*Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Language ; Peru ; Phylogeography ; }, abstract = {Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.}, }
@article {pmid31348818, year = {2019}, author = {Günther, T and Nettelblad, C}, title = {The presence and impact of reference bias on population genomic studies of prehistoric human populations.}, journal = {PLoS genetics}, volume = {15}, number = {7}, pages = {e1008302}, pmid = {31348818}, issn = {1553-7404}, mesh = {Animals ; Bias ; DNA, Ancient/*analysis ; Genome, Human ; High-Throughput Nucleotide Sequencing/methods ; Hominidae/*genetics ; Humans ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.}, }
@article {pmid31328768, year = {2019}, author = {Mas-Sandoval, A and Arauna, LR and Gouveia, MH and Barreto, ML and Horta, BL and Lima-Costa, MF and Pereira, AC and Salzano, FM and Hünemeier, T and Tarazona-Santos, E and Bortolini, MC and Comas, D}, title = {Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry.}, journal = {Genome biology and evolution}, volume = {11}, number = {9}, pages = {2593-2604}, pmid = {31328768}, issn = {1759-6653}, mesh = {Brazil ; Genetic Variation ; Genome, Human ; Geography ; Haplotypes ; Humans ; Indians, South American/*genetics ; Population Density ; }, abstract = {After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.}, }
@article {pmid31318917, year = {2019}, author = {Prufer, KM and Alsgaard, AV and Robinson, M and Meredith, CR and Culleton, BJ and Dennehy, T and Magee, S and Huckell, BB and Stemp, WJ and Awe, JJ and Capriles, JM and Kennett, DJ}, title = {Linking late Paleoindian stone tool technologies and populations in North, Central and South America.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219812}, pmid = {31318917}, issn = {1932-6203}, mesh = {Americas ; *Archaeology/methods ; Geography ; Humans ; *Technology ; }, abstract = {From the perspective of Central and South America, the peopling of the New World was a complex process lasting thousands of years and involving multiple waves of Pleistocene and early Holocene period immigrants entering into the neotropics. These Paleoindian colonists initially brought with them technologies developed for adaptation to environments and resources found in North America. As the ice age ended across the New World people adapted more generalized stone tools to exploit changing environments and resources. In the neotropics these changes would have been pronounced as patchy forests and grasslands gave way to broadleaf tropical forests. We document a late Pleistocene/early Holocene stone tool tradition from Belize, located in southern Mesoamerica. This represents the first endogenous Paleoindian stone tool technocomplex recovered from well dated stratigraphic contexts for Mesoamerica. Previously designated Lowe, these artifacts share multiple features with contemporary North and South American Paleoindian tool types. Once hafted, these bifaces appear to have served multiple functions for cutting, hooking, thrusting, or throwing. The tools were developed at a time of technological regionalization reflecting the diverse demands of a period of pronounced environmental change and population movement. Combined stratigraphic, technological, and population paleogenetic data suggests that there were strong ties between lowland neotropic regions at the onset of the Holocene.}, }
@article {pmid31310584, year = {2019}, author = {Hong, JH and Seo, M and Oh, CS and Shin, DH}, title = {Genetic Analysis of Small-Subunit Ribosomal RNA, Internal Transcribed Spacer 2, and ATP Synthase Subunit 8 of Trichuris trichiura Ancient DNA Retrieved from the 15th to 18th Century Joseon Dynasty Mummies' Coprolites from Korea.}, journal = {The Journal of parasitology}, volume = {105}, number = {4}, pages = {539-545}, pmid = {31310584}, issn = {1937-2345}, mesh = {Animals ; DNA, Helminth/analysis/genetics/history ; Feces/parasitology ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; Humans ; Korea ; Mitochondrial Proton-Translocating ATPases/analysis/genetics/history ; Mummies/*history ; Phylogeny ; RNA, Ribosomal/genetics/history ; Trichuriasis/*history ; Trichuris/classification/genetics/*isolation &amp; purification ; }, abstract = {Although parasitic infection by Trichuris trichiura is a very common intestinal helminthic disease worldwide, there is still insufficient information on the genetic characteristics of ancient T. trichiura in different spatiotemporal perspectives. Utilizing coprolite specimens obtained from 15th-18th century mummies dating to the Joseon Dynasty, we analyzed small-subunit ribosomal RNA, internal transcribed spacer 2, and ATP synthase subunit 8 of T. trichiura ancient DNA (aDNA). In BLAST and phylogenetic analyses, the T. trichiura aDNA sequences of this study belong to a separate cluster that is evidently distinct from the other genus Trichuris spp. reported in GenBank. This report characterizes T. trichiura aDNA of pre-20th century East Asia, and in so doing, it also proves the potential of aDNA analysis for differential diagnosis of T. trichiura in cases where ancient parasite eggs are morphologically indeterminate for species identification.}, }
@article {pmid31308224, year = {2019}, author = {Bokelmann, L and Hajdinjak, M and Peyrégne, S and Brace, S and Essel, E and de Filippo, C and Glocke, I and Grote, S and Mafessoni, F and Nagel, S and Kelso, J and Prüfer, K and Vernot, B and Barnes, I and Pääbo, S and Meyer, M and Stringer, C}, title = {A genetic analysis of the Gibraltar Neanderthals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {31}, pages = {15610-15615}, pmid = {31308224}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; 100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *DNA, Ancient ; Gibraltar ; History, Ancient ; Humans ; Neanderthals/*genetics ; *Oligonucleotide Array Sequence Analysis ; }, abstract = {The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.}, }
@article {pmid31303491, year = {2019}, author = {Järve, M and Saag, L and Scheib, CL and Pathak, AK and Montinaro, F and Pagani, L and Flores, R and Guellil, M and Saag, L and Tambets, K and Kushniarevich, A and Solnik, A and Varul, L and Zadnikov, S and Petrauskas, O and Avramenko, M and Magomedov, B and Didenko, S and Toshev, G and Bruyako, I and Grechko, D and Okatenko, V and Gorbenko, K and Smyrnov, O and Heiko, A and Reida, R and Sapiehin, S and Sirotin, S and Tairov, A and Beisenov, A and Starodubtsev, M and Vasilev, V and Nechvaloda, A and Atabiev, B and Litvinov, S and Ekomasova, N and Dzhaubermezov, M and Voroniatov, S and Utevska, O and Shramko, I and Khusnutdinova, E and Metspalu, M and Savelev, N and Kriiska, A and Kivisild, T and Villems, R}, title = {Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance.}, journal = {Current biology : CB}, volume = {29}, number = {14}, pages = {2430-2441.e10}, doi = {10.1016/j.cub.2019.06.019}, pmid = {31303491}, issn = {1879-0445}, mesh = {Archaeology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Ethnicity/genetics ; *Genetic Drift ; Genome, Human ; History, Ancient ; *Human Migration ; Humans ; Male ; Ukraine ; }, abstract = {The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.}, }
@article {pmid31303107, year = {2019}, author = {Houldcroft, CJ and Rifkin, RF and Underdown, SJ}, title = {Human biology and ancient DNA: exploring disease, domestication and movement.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {95-98}, doi = {10.1080/03014460.2019.1629536}, pmid = {31303107}, issn = {1464-5033}, mesh = {Archaeology ; *Biological Evolution ; DNA, Ancient/*analysis ; Domestication ; Genetic Predisposition to Disease/*etiology/history ; History, Ancient ; Human Migration/*history ; Humans ; }, }
@article {pmid31297530, year = {2019}, author = {Koch, EM and Schweizer, RM and Schweizer, TM and Stahler, DR and Smith, DW and Wayne, RK and Novembre, J}, title = {De Novo Mutation Rate Estimation in Wolves of Known Pedigree.}, journal = {Molecular biology and evolution}, volume = {36}, number = {11}, pages = {2536-2547}, pmid = {31297530}, issn = {1537-1719}, support = {R01 GM108805/GM/NIGMS NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; }, abstract = {Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obtain an estimate of ∼4.5 × 10-9 per base pair per generation and provide conservative bounds between 2.6 × 10-9 and 7.1 × 10-9. Although our estimate is consistent with recent mutation rate estimates from ancient DNA (4.0 × 10-9 and 3.0-4.5 × 10-9), it suggests a wider possible range. We also examined the consequences of our rate and the accompanying interval for dating several critical events in canid demographic history. For example, applying our full range of rates to coalescent models of dog and wolf demographic history implies a wide set of possible divergence times between the ancestral populations of dogs and extant Eurasian wolves (16,000-64,000 years ago) although our point estimate indicates a date between 25,000 and 33,000 years ago. Aside from one study in mice, ours provides the only direct mammalian mutation rate outside of primates and is likely to be vital to future investigations of mutation rate evolution.}, }
@article {pmid31296442, year = {2019}, author = {Cornille, A and Antolín, F and Garcia, E and Vernesi, C and Fietta, A and Brinkkemper, O and Kirleis, W and Schlumbaum, A and Roldán-Ruiz, I}, title = {A Multifaceted Overview of Apple Tree Domestication.}, journal = {Trends in plant science}, volume = {24}, number = {8}, pages = {770-782}, doi = {10.1016/j.tplants.2019.05.007}, pmid = {31296442}, issn = {1878-4372}, mesh = {Breeding ; Crops, Agricultural ; Domestication ; Fruit ; *Malus ; }, abstract = {The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.}, }
@article {pmid31291259, year = {2019}, author = {Zimmermann, HH and Harms, L and Epp, LS and Mewes, N and Bernhardt, N and Kruse, S and Stoof-Leichsenring, KR and Pestryakova, LA and Wieczorek, M and Trense, D and Herzschuh, U}, title = {Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0216966}, pmid = {31291259}, issn = {1932-6203}, mesh = {Chromosome Mapping ; DNA, Ancient ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Genetic Variation ; Genetics, Population ; Genome, Chloroplast ; Genome, Mitochondrial ; Genome, Plant ; Haplotypes ; History, Ancient ; Larix/classification/*genetics ; Polymorphism, Single Nucleotide ; Siberia ; Taiga ; Tundra ; }, abstract = {Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.}, }
@article {pmid31284503, year = {2019}, author = {Lan, TM and Lin, Y and Njaramba-Ngatia, J and Guo, XS and Li, RG and Li, HM and Kumar-Sahu, S and Wang, X and Yang, XJ and Guo, HB and Xu, WH and Kristiansen, K and Liu, H and Xu, YC}, title = {Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data.}, journal = {Genes}, volume = {10}, number = {7}, pages = {}, pmid = {31284503}, issn = {2073-4425}, mesh = {Algorithms ; Animals ; DNA, Mitochondrial ; Genome ; Goats/*genetics ; High-Throughput Nucleotide Sequencing ; Horses/*genetics ; Humans ; Mammoths/*genetics ; Paleontology ; Ruminants/*genetics ; }, abstract = {The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.}, }
@article {pmid31283430, year = {2019}, author = {Bos, KI and Kühnert, D and Herbig, A and Esquivel-Gomez, LR and Andrades Valtueña, A and Barquera, R and Giffin, K and Kumar Lankapalli, A and Nelson, EA and Sabin, S and Spyrou, MA and Krause, J}, title = {Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens.}, journal = {Annual review of microbiology}, volume = {73}, number = {}, pages = {639-666}, doi = {10.1146/annurev-micro-090817-062436}, pmid = {31283430}, issn = {1545-3251}, mesh = {Biological Evolution ; Communicable Diseases/*history ; DNA, Ancient/*analysis ; DNA, Bacterial ; Fossils/*microbiology/parasitology ; Genome, Bacterial ; Genomics/methods ; Helicobacter pylori/genetics ; High-Throughput Nucleotide Sequencing/methods ; History, Ancient ; Humans ; Mycobacterium leprae/genetics ; Mycobacterium tuberculosis/genetics ; Paleontology/methods ; Paleopathology/*methods ; Phylogeny ; Yersinia pestis/genetics ; }, abstract = {The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.}, }
@article {pmid31281897, year = {2019}, author = {Feldman, M and Master, DM and Bianco, RA and Burri, M and Stockhammer, PW and Mittnik, A and Aja, AJ and Jeong, C and Krause, J}, title = {Ancient DNA sheds light on the genetic origins of early Iron Age Philistines.}, journal = {Science advances}, volume = {5}, number = {7}, pages = {eaax0061}, pmid = {31281897}, issn = {2375-2548}, mesh = {*DNA, Ancient ; *Genetics, Population ; Genome-Wide Association Study ; History, Ancient ; *Human Migration ; Humans ; White People/history/*legislation &amp; jurisprudence ; }, abstract = {The ancient Mediterranean port city of Ashkelon, identified as "Philistine" during the Iron Age, underwent a marked cultural change between the Late Bronze and the early Iron Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called "Sea Peoples." Here, we report genome-wide data of 10 Bronze and Iron Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European-related admixture. This genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze to Iron Age transition in Ashkelon but did not leave a long-lasting genetic signature.}, }
@article {pmid31270812, year = {2019}, author = {Fleskes, RE and Bruwelheide, KS and West, FL and Owsley, DW and Griffith, DR and Barca, KG and Cabana, GS and Schurr, TG}, title = {Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier.}, journal = {American journal of physical anthropology}, volume = {170}, number = {2}, pages = {232-245}, doi = {10.1002/ajpa.23887}, pmid = {31270812}, issn = {1096-8644}, support = {//The University of Pennsylvania/International ; }, mesh = {Adult ; Archaeology ; *Black People/ethnology/genetics/history ; Cemeteries/history ; Child, Preschool ; Colonialism/*history ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Delaware ; Enslavement/*history ; Female ; History, 17th Century ; History, 18th Century ; Humans ; Infant ; Male ; Middle Aged ; *White People/ethnology/genetics/history ; Black or African American ; }, abstract = {OBJECTIVES: Ancient DNA (aDNA) and standard osteological analyses applied to 11 skeletons at a late 17th to early 18th century farmstead site in Delaware to investigate the biological and social factors of settlement and slavery in colonial America.<br><br>MATERIALS AND METHODS: Osteological analysis and mitochondrial DNA (mtDNA) sequencing were conducted for all individuals and the resulting data contextualized with archaeological and documentary evidence.<br><br>RESULTS: Individuals of European and African descent were spatially separated in this colonial cemetery. The skeletal remains exhibited differences in osteological features and maternal genetic ancestry. A specific mtDNA haplotype appeared in a subset of the European-descended individuals suggesting they were maternally related. Individuals of African descent were not maternally related, and instead showed a diversity of haplotypes affiliated with present-day Western, Central, and Eastern regions of Africa.<br><br>DISCUSSION: Along with the bioarchaeological and documentary evidence, the aDNA findings contribute to our understanding of life on the colonial Delaware frontier. Evidence of maternal relatedness among European-descended individuals at the site demonstrates kin-based settlements in 17th century Delaware and provides preliminary identifications of individuals. The maternal genetic diversity of the individuals with African descent aligns with the routes of the trans-Atlantic slave trade but broadens our understanding of the ancestries of persons involved in it. Burial positioning, osteological pathology, and lack of maternal kinship among individuals of African descent provide tangible evidence for the emergence of racialized labor and society in Delaware during the late 17th century.}, }
@article {pmid31256878, year = {2019}, author = {Joseph, TA and Pe'er, I}, title = {Inference of Population Structure from Time-Series Genotype Data.}, journal = {American journal of human genetics}, volume = {105}, number = {2}, pages = {317-333}, pmid = {31256878}, issn = {1537-6605}, support = {U01 CA217858/CA/NCI NIH HHS/United States ; U54 CA209997/CA/NCI NIH HHS/United States ; }, mesh = {*Algorithms ; Europe ; Gene Frequency ; Genetic Predisposition to Disease ; *Genetic Variation ; *Genetics, Population ; Genome-Wide Association Study ; Genotype ; Humans ; Middle East ; *Models, Genetic ; *Models, Statistical ; Population Groups/*genetics ; Time Factors ; }, abstract = {Sequencing ancient DNA can offer direct probing of population history. Yet, such data are commonly analyzed with standard tools that assume DNA samples are all contemporary. We present DyStruct, a model and inference algorithm for inferring shared ancestry from temporally sampled genotype data. DyStruct explicitly incorporates temporal dynamics by modeling individuals as mixtures of unobserved populations whose allele frequencies drift over time. We develop an efficient inference algorithm for our model using stochastic variational inference. On simulated data, we show that DyStruct outperforms the current state of the art when individuals are sampled over time. Using a dataset of 296 modern and 80 ancient samples, we demonstrate DyStruct is able to capture a well-supported admixture event of steppe ancestry into modern Europe. We further apply DyStruct to a genome-wide dataset of 2,067 modern and 262 ancient samples used to study the origin of farming in the Near East. We show that DyStruct provides new insight into population history when compared with alternate approaches, within feasible run time.}, }
@article {pmid31251487, year = {2019}, author = {Angelici, FM and Ciucani, MM and Angelini, S and Annesi, F and Caniglia, R and Castiglia, R and Fabbri, E and Galaverni, M and Palumbo, D and Ravegnini, G and Rossi, L and Siracusa, AM and Cilli, E}, title = {The Sicilian Wolf: Genetic Identity of a Recently Extinct Insular Population.}, journal = {Zoological science}, volume = {36}, number = {3}, pages = {189-197}, doi = {10.2108/zs180180}, pmid = {31251487}, issn = {0289-0003}, mesh = {Animal Distribution ; Animals ; DNA, Mitochondrial/genetics ; Extinction, Biological ; Genotype ; Haplotypes ; Phylogeny ; Sicily ; Wolves/*genetics ; }, abstract = {Historically, many local grey wolf (Canis lupus) populations have undergone substantial reductions in size or become extinct. Among these, the wolf population once living in Sicily, the largest island in the Mediterranean Sea, was completely eradicated by human activity in the early decades of the 20th century. To gain a better understanding of the genetic identity of the Sicilian wolf, we used techniques for the study of ancient DNA to analyze the mitochondrial (mt) variability of six specimens stored in Italian museums. We were able to amplify a diagnostic mtDNA fragment of the control region (CR) in four of the samples. Two of the samples shared the same haplotype, differing by two substitutions from the currently most diffused Italian wolf haplotype (W14) and one substitution from the only other Italian haplotype (W16). The third sample showed a previously unreported wolf-like haplotype, and the fourth a haplotype commonly found in dogs. All of the wolf haplotypes analyzed in this study belonged to the mitochondrial haplogroup that includes haplotypes detected in all the known European Pleistocene wolves and in several modern southern European populations. Unfortunately, this endemic island population, which exhibited unique mtDNA variability, was definitively lost before it was possible to understand its taxonomic uniqueness and conservational value.}, }
@article {pmid31249793, year = {2019}, author = {Silva, PC and Malabarba, MC and Vari In Memoriam, R and Malabarba, LR}, title = {Comparison and optimization for DNA extraction of archived fish specimens.}, journal = {MethodsX}, volume = {6}, number = {}, pages = {1433-1442}, pmid = {31249793}, issn = {2215-0161}, abstract = {The DNA extracted from museum alcohol-fixed specimens can be a valuable source of information for solving taxonomic, phylogenetic, ecological and conservational questions. However, this type of DNA, also called ancient DNA, is routinely obtained in small portions and highly fragmented. We have tested two different extraction kits in museum type-specimens of the fish family Characidae. Aiming to increase the DNA yield, we made modifications on a Qiagen manufacturer protocol, in the elution step. Also, to overcome the issue of DNA fragmentation, we applied our efforts in Sanger sequencing, to find a highly variable and, in result, informative COI fragment. Based on our results, there is no correlation between amount of the DNA extracted and the age of the sample. The Sanger sequencing generated sequences which are useful in solving taxonomic puzzles. Here are presented the customization and guidelines that allowed us to recover DNA from the archived fish specimens. •DNA extraction from archived fish specimens is more effective when using silica columns.•Change of the elution times from minutes in room temperature to 24 h in freezer greatly improved the DNA yielded.•Short but highly variable sequences replace the need to sequence the entire gene to identify a species.}, }
@article {pmid31235841, year = {2019}, author = {De Schepper, S and Ray, JL and Skaar, KS and Sadatzki, H and Ijaz, UZ and Stein, R and Larsen, A}, title = {The potential of sedimentary ancient DNA for reconstructing past sea ice evolution.}, journal = {The ISME journal}, volume = {13}, number = {10}, pages = {2566-2577}, pmid = {31235841}, issn = {1751-7370}, mesh = {Arctic Regions ; Biodiversity ; Climate ; DNA, Ancient/*analysis ; Eukaryota/*genetics/isolation &amp; purification ; Fossils ; Geologic Sediments/*chemistry ; Greenland ; Ice Cover/*chemistry ; }, abstract = {Sea ice is a crucial component of the Arctic climate system, yet the tools to document the evolution of sea ice conditions on historical and geological time scales are few and have limitations. Such records are essential for documenting and understanding the natural variations in Arctic sea ice extent. Here we explore sedimentary ancient DNA (aDNA), as a novel tool that unlocks and exploits the genetic (eukaryote) biodiversity preserved in marine sediments specifically for past sea ice reconstructions. Although use of sedimentary aDNA in paleoceanographic and paleoclimatic studies is still in its infancy, we use here metabarcoding and single-species quantitative DNA detection methods to document the sea ice conditions in a Greenland Sea marine sediment core. Metabarcoding has allowed identifying biodiversity changes in the geological record back to almost ~100,000 years ago that were related to changing sea ice conditions. Detailed bioinformatic analyses on the metabarcoding data revealed several sea-ice-associated taxa, most of which previously unknown from the fossil record. Finally, we quantitatively traced one known sea ice dinoflagellate in the sediment core. We show that aDNA can be recovered from deep-ocean sediments with generally oxic bottom waters and that past sea ice conditions can be documented beyond instrumental time scales. Our results corroborate sea ice reconstructions made by traditional tools, and thus demonstrate the potential of sedimentary aDNA, focusing primarily on microbial eukaryotes, as a new tool to better understand sea ice evolution in the climate system.}, }
@article {pmid31220249, year = {2019}, author = {Borówka, P and Pułaski, &#x141; and Marciniak, B and Borowska-Strugińska, B and Dziadek, J and Żądzińska, E and Lorkiewicz, W and Strapagiel, D}, title = {Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples.}, journal = {GigaScience}, volume = {8}, number = {6}, pages = {}, pmid = {31220249}, issn = {2047-217X}, mesh = {Body Remains/*microbiology ; Bone and Bones/microbiology ; DNA Barcoding, Taxonomic/*methods ; *DNA, Ancient ; DNA, Bacterial ; Female ; High-Throughput Nucleotide Sequencing/*methods ; History, Ancient ; Humans ; Male ; Mycobacterium tuberculosis/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Recent advances in ancient DNA studies, especially in increasing isolated DNA yields and quality, have opened the possibility of analysis of ancient host microbiome. However, such pitfalls as spurious identification of pathogens based on fragmentary data or environmental contamination could lead to incorrect epidaemiological conclusions. Within the Mycobacterium genus, Mycobacterium tuberculosis complex members responsible for tuberculosis share up to ∼99% genomic sequence identity, while other more distantly related Mycobacteria other than M. tuberculosis can be causative agents for pulmonary diseases or soil dwellers. Therefore, reliable determination of species complex is crucial for interpretation of sequencing results.<br><br>RESULTS: Here we present a novel bioinformatical approach, used for screening of ancient tuberculosis in sequencing data, derived from 28 individuals (dated 4400-4000 and 3100-2900 BC) from central Poland. We demonstrate that cost-effective next-generation screening sequencing data (&#x223c;20M reads per sample) could yield enough information to provide statistically supported identification of probable ancient disease cases.<br><br>CONCLUSIONS: Application of appropriate bioinformatic tools, including an unbiased selection of genomic alignment targets for species specificity, makes it possible to extract valid data from full-sample sequencing results (without subjective targeted enrichment procedures). This approach broadens the potential scope of palaeoepidaemiology both to older, suboptimally preserved samples and to pathogens with difficult intrageneric taxonomy.}, }
@article {pmid31216503, year = {2019}, author = {Xavier, C and Eduardoff, M and Strobl, C and Parson, W}, title = {SD quants-Sensitive detection tetraplex-system for nuclear and mitochondrial DNA quantification and degradation inference.}, journal = {Forensic science international. Genetics}, volume = {42}, number = {}, pages = {39-44}, doi = {10.1016/j.fsigen.2019.06.004}, pmid = {31216503}, issn = {1878-0326}, mesh = {Bone and Bones/chemistry ; Cell Nucleus/*genetics ; DNA/*analysis ; *DNA Degradation, Necrotic ; *DNA Fingerprinting ; DNA, Mitochondrial/*analysis ; Hair/chemistry ; Humans ; Real-Time Polymerase Chain Reaction/*methods ; Tooth/chemistry ; }, abstract = {Measuring the quantity of DNA present in a forensic sample is relevant in a number of ways. First, it informs the analyst about the general DNA content to adjust the volume of DNA extract used for the genotyping assay to the optimal conditions (when possible). Second, quantification values can serve as plausibility checks for the performance of the DNA extraction method used as extraction positive and negative controls demand expected values. Third and relevant to highly compromised specimens, DNA quantification can inform about the degradation state of the DNA extracted from the unknown biological sample and aid the choice of downstream genotyping assays. While there are different, commercial products for the quantification of nuclear DNA available, commercial mitochondrial DNA (mtDNA) quantification systems are rare. Even more so, the simultaneous quantification of nuclear and mtDNA that is of relevance in highly degraded forensic specimens has rarely been described. We present here a novel real-time qPCR based tetraplex system termed SD quants that targets two different-sized mtDNA and a nuclear DNA region and includes an internal positive control to monitor potential inhibition. SD quants was compared to other existing quantification systems and subjected to analysis of severely degraded DNA present in ancient DNA and aged forensic specimens. This study complies with the MIQE (Bustin et al., 2009) guidelines (when applicable).}, }
@article {pmid31216315, year = {2019}, author = {Wren, CD and Burke, A}, title = {Habitat suitability and the genetic structure of human populations during the Last Glacial Maximum (LGM) in Western Europe.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0217996}, pmid = {31216315}, issn = {1932-6203}, mesh = {Archaeology ; *Biological Evolution ; Climate ; DNA, Mitochondrial/*genetics ; Ecosystem ; Europe ; France ; *Genetics, Population ; Haplotypes ; Humans ; Italy ; Paleontology ; Phylogeny ; *Phylogeography ; Population Density ; Refugium ; Sequence Analysis, DNA ; Spain ; }, abstract = {Human populations in Western Europe during the Last Glacial Maximum were geographically constrained to glacial refugia by the severity of the climate and ecological risk factors. In this research we use an agent-based model of human mobility and interaction, based on ethnographic and archaeological data, to explore the impact of ecological risk on human population structure via a reconstructed landscape of habitat suitability. The agent-based model allows us to evaluate the size and location of glacial refugia, the size of the populations occupying them and the degree of genetic relatedness between people occupying these areas. To do this, we model the probability of an agent foraging groups' survival as a function of habitat suitability. The model's simulated "genomes" (composed of regionally specific genetic markers) allow us to track long-term trends of inter-regional interaction and mobility. The results agree with previous archaeological studies situating a large glacial refugium spanning southern France and northeastern Spain, but we expand on those studies by demonstrating that higher rates of population growth in this central refugium led to continuous out-migration and therefore genetic homogeneity across Western Europe, with the possible exception of the Italian peninsula. These results concur with material culture data from known archaeological sites dating to the Last Glacial Maximum and make predictions for future ancient DNA studies.}, }
@article {pmid31216119, year = {2019}, author = {Epp, LS}, title = {A global perspective for biodiversity history with ancient environmental DNA.}, journal = {Molecular ecology}, volume = {28}, number = {10}, pages = {2456-2458}, doi = {10.1111/mec.15118}, pmid = {31216119}, issn = {1365-294X}, mesh = {Animals ; Australia ; Biodiversity ; Climate Change ; Coral Reefs ; DNA, Ancient/*analysis ; DNA, Environmental/*genetics ; *Ecosystem ; Geologic Sediments/analysis ; Humans ; }, abstract = {The past centuries have seen tremendous turnovers in species distributions and biodiversity due to anthropogenic impacts on a global scale. The processes are ongoing and mostly not well documented. Long-term records of biotic change can be recovered from sedimentary deposits, but traditional analyses were restricted to organisms that leave behind visible traces and molecular genetic tools were mostly employed on samples that promised good DNA preservation. In this issue of Molecular Ecology, Shaw, Weyrich, Hallegraeff and Cooper (2019) and Gomez Cabrera et al. (2019) present two studies on marine sedimentary records from warm environments, in which they successfully analyze ancient environmental DNA (aeDNA) on a decadal and centennial scale. Notably, the studies were conducted on novel samples with nonoptimal preservation conditions for ancient DNA - historical collections of ship ballast tank sediments from Australia and two coral reef cores spanning up to 750 years (Figure 1) - but yielded a high diversity of taxa. This highlights that aeDNA is a promising tool to globally study biodiversity history on scales of decades to centuries - the timeframe most relevant to human society in the context of both current climate change and direct anthropogenic modifications of the environment.}, }
@article {pmid31196226, year = {2019}, author = {Petrigh, RS and Martínez, JG and Mondini, M and Fugassa, MH}, title = {Ancient parasitic DNA reveals Toxascaris leonina presence in Final Pleistocene of South America.}, journal = {Parasitology}, volume = {146}, number = {10}, pages = {1284-1288}, doi = {10.1017/S0031182019000787}, pmid = {31196226}, issn = {1469-8161}, mesh = {Animals ; Argentina ; DNA, Ancient/*isolation &amp; purification ; DNA, Mitochondrial/genetics/isolation &amp; purification ; Feces/parasitology ; Ovum/cytology ; Puma/*parasitology ; Toxascariasis/*parasitology/*veterinary ; Toxascaris/*genetics/*isolation &amp; purification ; }, abstract = {Parasitological analysis of coprolites has allowed exploring ecological relationships in ancient times. Ancient DNA analysis contributes to the identification of coprolites and their parasites. Pleistocene mammalian carnivore coprolites were recovered from paleontological and archaeological site Peñas de las Trampas 1.1 in the southern Puna of Argentina. With the aim of exploring ancient ecological relationships, parasitological analysis was performed to one of them, dated to 16 573-17 002 calibrated years BP, with 95.4% probability. Parasite eggs attributed to Toxascaris sp. by morphological characters were isolated. DNA of coprolite and eggs was extracted to molecular identification. Ancient mitochondrial DNA analysis confirmed the zoological origin of the coprolite as Puma concolor and that of parasite eggs as Toxascaris leonina. This is the oldest molecular parasite record worldwide, and it supports the presence of this parasite since the Pleistocene in America. These findings have implications for the biogeographic history of parasites and for the natural history of the region.}, }
@article {pmid31184205, year = {2019}, author = {Scheib, CL and Hui, R and D'Atanasio, E and Wohns, AW and Inskip, SA and Rose, A and Cessford, C and O'Connell, TC and Robb, JE and Evans, C and Patten, R and Kivisild, T}, title = {East Anglian early Neolithic monument burial linked to contemporary Megaliths.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {145-149}, pmid = {31184205}, issn = {1464-5033}, support = {/WT_/Wellcome Trust/United Kingdom ; 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; Burial/*history ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; England ; History, Ancient ; Humans ; Male ; Whole Genome Sequencing ; }, abstract = {In the fourth millennium BCE a cultural phenomenon of monumental burial structures spread along the Atlantic façade. Megalithic burials have been targeted for aDNA analyses, but a gap remains in East Anglia, where Neolithic structures were generally earthen or timber. An early Neolithic (3762-3648 cal. BCE) burial monument at the site of Trumpington Meadows, Cambridgeshire, UK, contained the partially articulated remains of at least three individuals. To determine whether this monument fits a pattern present in megalithic burials regarding sex bias, kinship, diet and relationship to modern populations, teeth and ribs were analysed for DNA and carbon and nitrogen isotopic values, respectively. Whole ancient genomes were sequenced from two individuals to a mean genomic coverage of 1.6 and 1.2X and genotypes imputed. Results show that they were brothers from a small population genetically and isotopically similar to previously published British Neolithic individuals, with a level of genome-wide homozygosity consistent with a small island population sourced from continental Europe, but bearing no signs of recent inbreeding. The first Neolithic whole genomes from a monumental burial in East Anglia confirm that this region was connected with the larger pattern of Neolithic megaliths in the British Isles and the Atlantic façade.}, }
@article {pmid31178321, year = {2019}, author = {Delsuc, F and Kuch, M and Gibb, GC and Karpinski, E and Hackenberger, D and Szpak, P and Martínez, JG and Mead, JI and McDonald, HG and MacPhee, RDE and Billet, G and Hautier, L and Poinar, HN}, title = {Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths.}, journal = {Current biology : CB}, volume = {29}, number = {12}, pages = {2031-2042.e6}, doi = {10.1016/j.cub.2019.05.043}, pmid = {31178321}, issn = {1879-0445}, mesh = {Animal Distribution ; Animals ; *Biological Evolution ; DNA, Ancient/*analysis ; *Genome, Mitochondrial ; *Phylogeny ; Sloths/*classification/genetics/physiology ; }, abstract = {Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history.}, }
@article {pmid31171860, year = {2019}, author = {Presslee, S and Slater, GJ and Pujos, F and Forasiepi, AM and Fischer, R and Molloy, K and Mackie, M and Olsen, JV and Kramarz, A and Taglioretti, M and Scaglia, F and Lezcano, M and Lanata, JL and Southon, J and Feranec, R and Bloch, J and Hajduk, A and Martin, FM and Salas Gismondi, R and Reguero, M and de Muizon, C and Greenwood, A and Chait, BT and Penkman, K and Collins, M and MacPhee, RDE}, title = {Palaeoproteomics resolves sloth relationships.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {7}, pages = {1121-1130}, doi = {10.1038/s41559-019-0909-z}, pmid = {31171860}, issn = {2397-334X}, mesh = {Animals ; DNA, Mitochondrial ; Fossils ; Phylogeny ; *Sloths ; }, abstract = {The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.}, }
@article {pmid31164419, year = {2019}, author = {Keller, M and Spyrou, MA and Scheib, CL and Neumann, GU and Kröpelin, A and Haas-Gebhard, B and Päffgen, B and Haberstroh, J and Ribera I Lacomba, A and Raynaud, C and Cessford, C and Durand, R and Stadler, P and Nägele, K and Bates, JS and Trautmann, B and Inskip, SA and Peters, J and Robb, JE and Kivisild, T and Castex, D and McCormick, M and Bos, KI and Harbeck, M and Herbig, A and Krause, J}, title = {Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {25}, pages = {12363-12372}, pmid = {31164419}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; 200368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Disease Outbreaks/*history ; Europe/epidemiology ; *Genome, Bacterial ; History, Medieval ; Humans ; Plague/epidemiology/history/*microbiology ; Yersinia pestis/*genetics/pathogenicity ; }, abstract = {The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.}, }
@article {pmid31163991, year = {2019}, author = {Santander, C and Montinaro, F and Capelli, C}, title = {Searching for archaic contribution in Africa.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {129-139}, doi = {10.1080/03014460.2019.1624823}, pmid = {31163991}, issn = {1464-5033}, mesh = {Africa ; Animals ; Black People/*genetics ; DNA, Ancient/*analysis ; Genome, Human ; Hominidae/*genetics ; Humans ; *Hybridization, Genetic ; }, abstract = {Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence of Homo sapiens. However, once humans dispersed beyond Africa, the history of those who stayed remains vastly under-studied, lacking the proper attention the birthplace of both modern and archaic humans deserves. The sequencing of Neanderthal and Denisovan genomes has elucidated evidence of admixture between archaic and modern humans outside of Africa, but has not aided efforts in answering whether archaic admixture happened within Africa. Objectives: This article reviews the state of research for archaic introgression in African populations and discusses recent insights into this topic. Methods: Gathering published sources and recently released preprints, this review reports on the different methods developed for detecting archaic introgression. Particularly it discusses how relevant these are when implemented on African populations and what findings these studies have shown so far. Results: Methods for detecting archaic introgression have been predominantly developed and implemented on non-African populations. Recent preprints present new methods considering African populations. While a number of studies using these methods suggest archaic introgression in Africa, without an African archaic genome to validate these results, such findings remain as putative archaic introgression. Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent.}, }
@article {pmid31161006, year = {2019}, author = {Ersmark, E and Baryshnikov, G and Higham, T and Argant, A and Castaños, P and Döppes, D and Gasparik, M and Germonpré, M and Lidén, K and Lipecki, G and Marciszak, A and Miller, R and Moreno-García, M and Pacher, M and Robu, M and Rodriguez-Varela, R and Rojo Guerra, M and Sabol, M and Spassov, N and Storå, J and Valdiosera, C and Villaluenga, A and Stewart, JR and Dalén, L}, title = {Genetic turnovers and northern survival during the last glacial maximum in European brown bears.}, journal = {Ecology and evolution}, volume = {9}, number = {10}, pages = {5891-5905}, pmid = {31161006}, issn = {2045-7758}, abstract = {The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.}, }
@article {pmid31147405, year = {2019}, author = {Prendergast, ME and Lipson, M and Sawchuk, EA and Olalde, I and Ogola, CA and Rohland, N and Sirak, KA and Adamski, N and Bernardos, R and Broomandkhoshbacht, N and Callan, K and Culleton, BJ and Eccles, L and Harper, TK and Lawson, AM and Mah, M and Oppenheimer, J and Stewardson, K and Zalzala, F and Ambrose, SH and Ayodo, G and Gates, HL and Gidna, AO and Katongo, M and Kwekason, A and Mabulla, AZP and Mudenda, GS and Ndiema, EK and Nelson, C and Robertshaw, P and Kennett, DJ and Manthi, FK and Reich, D}, title = {Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.}, journal = {Science (New York, N.Y.)}, volume = {365}, number = {6448}, pages = {}, pmid = {31147405}, issn = {1095-9203}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Agriculture/*history ; DNA, Ancient ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Kenya ; Occupations/*history ; Tanzania ; }, abstract = {How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.}, }
@article {pmid31137975, year = {2019}, author = {Donoghue, HD}, title = {Tuberculosis and leprosy associated with historical human population movements in Europe and beyond - an overview based on mycobacterial ancient DNA.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {120-128}, doi = {10.1080/03014460.2019.1624822}, pmid = {31137975}, issn = {1464-5033}, mesh = {DNA, Ancient/*analysis ; Europe ; Genotype ; History, 17th Century ; History, 18th Century ; History, Medieval ; Human Migration/*history ; Humans ; Leprosy/*history/microbiology ; Mycobacterium leprae/*genetics ; Mycobacterium tuberculosis/*genetics ; Paleopathology ; Polymerase Chain Reaction ; Tuberculosis/*history/microbiology ; Whole Genome Sequencing ; }, abstract = {Context: Tuberculosis and leprosy are readily recognised in human remains due to their typical palaeopathology. Both Mycobacterium tuberculosis (MTB) and Mycobacterium leprae (ML) are obligate pathogens and have been detected in ancient human populations. Objective: To demonstrate historical tuberculosis and leprosy cases in Europe and beyond using molecular methods, as human populations are associated with different mycobacterial genotypes. Methods: MTB and ML ancient DNA (aDNA) has been detected by DNA amplification using PCR, or by whole genome sequencing. Mycobacterial cell wall lipids also provide specific markers for identification. Results: In 18th century Hungary, the European indigenous MTB genotype 4 strains have been found. However, many individuals were co-infected with up to three MTB sub-genotypes. In 8th-14th century Europe significant differences in ML genotypes were found between northwest Europe compared with central, southern, or eastern Europe. In addition, several co-infections of MTB and ML were detected in historical samples. Conclusion: Both MTB and ML strain types differ between geographically separate populations. This is associated with ancient human migration after an evolutionary bottleneck and clonal expansion. The absence of indigenous leprosy in Europe today may be due to the greater mortality of tuberculosis in individuals who are co-infected with both organisms.}, }
@article {pmid31134682, year = {2019}, author = {Wu, X and Ding, B and Zhang, B and Feng, J and Wang, Y and Ning, C and Wu, H and Zhang, F and Zhang, Q and Li, N and Zhang, Z and Sun, X and Zhang, Q and Li, W and Liu, B and Cui, Y and Gong, L}, title = {Phylogenetic and population structural inference from genomic ancestry maintained in present-day common wheat Chinese landraces.}, journal = {The Plant journal : for cell and molecular biology}, volume = {99}, number = {2}, pages = {201-215}, doi = {10.1111/tpj.14421}, pmid = {31134682}, issn = {1365-313X}, mesh = {China ; DNA, Plant/chemistry ; Gene Frequency ; *Genome, Plant ; Phylogeny ; Seed Dispersal ; Seeds/anatomy &amp; histology/genetics ; Sequence Analysis, RNA ; Triticum/anatomy &amp; histology/*genetics ; }, abstract = {Hexaploid common wheat is one of the most important food crops worldwide. Common wheat domestication began in the Fertile Crescent of the Near East approximately 10 000 years ago and then spread west into Europe and eastward into East Asia and China. However, the possible spreading route into and within China is still unclear. In this study, we successfully extracted DNA from single ancient wheat seeds and sequenced the whole genome of seven ancient samples from Xiaohe and Gumugou cemeteries in Xinjiang, China. Genomic inference and morphological observation confirmed their identity as hexaploid common wheat grown in prehistoric China at least 3200 years before present (BP). Phylogenetic and admixture analyses with RNA-seq data of modern hexaploid wheat cultivars from both China and Western countries demonstrated a close kinship of the ancient wheat to extant common wheat landraces in southwestern China. The highly similar allelic frequencies in modern landraces of the Qinghai-Tibetan plateau with the ancient wheat support the previously suggested southwestern spreading route into highland China. A subsequent dispersal route from the Qinghai-Tibetan plateau margins to the Yangtze valley was proposed in this study. Furthermore, the common wheat populations grown in the Middle and Lower Yangtze valley wheat zones were also proposed to be established by population admixture with the wheat grown in the Upper Yangtze valley. Our study reports ancient common wheat sequences at a genome-wide scale, providing important information on the origin, dispersal, and genetic improvement under cultivation of present-day wheat landraces grown in China.}, }
@article {pmid31124326, year = {2019}, author = {Hong, JH and Oh, CS and Chai, JY and Seo, M and Shin, DH}, title = {Cytochrome C Oxidase Subunit 1, Internal Transcribed Spacer 1, Nicotinamide Adenine Dinucleotide Hydrogen Dehydrogenase Subunits 2 and 5 of Clonorchis sinensis Ancient DNA Retrieved from Joseon Dynasty Mummy Specimens.}, journal = {Journal of Korean medical science}, volume = {34}, number = {20}, pages = {e149}, pmid = {31124326}, issn = {1598-6357}, support = {NRF-2016R1A2B4015669/NRF/National Research Foundation of Korea/Korea ; }, mesh = {Animals ; Clonorchiasis/diagnosis/epidemiology ; Clonorchis sinensis/classification/*genetics ; DNA, Ancient/*chemistry/isolation &amp; purification ; Electron Transport Complex IV/chemistry/classification/*genetics ; Humans ; Mummies/parasitology ; Oxidoreductases/chemistry/classification/*genetics ; Phylogeny ; Protein Subunits/chemistry/classification/genetics ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {We analyzed Clonorchis sinensis ancient DNA (aDNA) acquired from the specimens of the Joseon mummies. The target regions were cytochrome C oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits 2 (NAD2) and 5 (NAD5). The sequences of C. sinensis aDNA was completely or almost identical to modern C. sinensis sequences in GenBank. We also found that ITS1, NAD2 and NAD5 could be good markers for molecular diagnosis between C. sinensis and the other trematode parasite species. The current result could improve our knowledge about genetic history of C. sinensis.}, }
@article {pmid31123709, year = {2019}, author = {Kashuba, N and Kırdök, E and Damlien, H and Manninen, MA and Nordqvist, B and Persson, P and Götherström, A}, title = {Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {185}, pmid = {31123709}, issn = {2399-3642}, mesh = {Anthropology, Cultural/history ; Betula/chemistry ; Chewing Gum/history ; DNA, Ancient/*isolation &amp; purification ; DNA, Mitochondrial/genetics/history ; Genetics, Population/history ; History, Ancient ; Human Migration/history ; Humans ; Mastic Resin/history ; Resins, Plant/history ; Scandinavian and Nordic Countries ; }, abstract = {Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations.}, }
@article {pmid31116227, year = {2019}, author = {Hong, JH and Oh, CS and Seo, M and Shin, DH}, title = {Analysis of COI and ITS2 regions of DNA obtained from Paragonimus westermani eggs in ancient coprolites on Joseon dynasty mummies.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {114}, number = {}, pages = {e180595}, pmid = {31116227}, issn = {1678-8060}, mesh = {Animals ; Asia ; DNA, Helminth/*genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Feces/*parasitology ; Humans ; Mummies/*parasitology ; Paleodontology ; Paragonimus westermani/genetics/*isolation &amp; purification ; Parasite Egg Count ; Phylogeny ; }, abstract = {The genetic information of ancient Paragonimus westermani, the oriental lung fluke infecting over 20 million people worldwide, has not been thoroughly investigated thus far. We analysed genetic markers (COI and ITS2) of P. westermani from coprolite specimens (n = 6) obtained from 15th to 18th century Korean mummies. Our results indicated that all P. westermani sequences were generally distinct from the other species of the genus Paragonimus. The sequences were clustered into three groups: Group I for East Asia; Group II for South and Southeast Asia; and Group III for India and Sri Lanka. In this study, we found that ancient P. westermani sequences in Korea belong to Group I, adding invaluable information to the existing knowledge of Paragonimus paleogenetics.}, }
@article {pmid31113254, year = {2019}, author = {Ham, E and Underdown, SJ and Houldcroft, CJ}, title = {The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {99-108}, doi = {10.1080/03014460.2019.1622038}, pmid = {31113254}, issn = {1464-5033}, mesh = {Alleles ; Animals ; Europe ; Gene Frequency ; Humans ; Longevity/*genetics ; Mothers/*statistics &amp; numerical data ; Neanderthals/genetics ; P-Selectin/*genetics/metabolism ; Physical Abuse/*statistics &amp; numerical data ; Polymorphism, Single Nucleotide/*genetics ; *Selection, Genetic ; Tanzania ; Thrombophilia/genetics ; White People ; }, abstract = {Background: Simonti et al. reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious, but can also help prevent blood loss. Aim: To investigate two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth. Subjects and methods: Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture. Results: National census data indicates a positive correlation between the presence of rs3917862 and decreased maternal mortality ratios. When the maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862. Conclusion: These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.}, }
@article {pmid31109769, year = {2019}, author = {Perry, GH and Makarewicz, CA}, title = {Horse Paleogenomes and Human-Animal Interactions in Prehistory.}, journal = {Trends in genetics : TIG}, volume = {35}, number = {7}, pages = {473-475}, doi = {10.1016/j.tig.2019.04.006}, pmid = {31109769}, issn = {0168-9525}, mesh = {Animals ; *Genome ; Horses ; Humans ; }, abstract = {A new analysis of paleogenomic data from 278 ancient horses (Fages et al. Cellhttp://doi.org/10.1016/j.cell.2019.03.049) finds that this animal - crucially important to many ancient and contemporary human societies for subsistence, transportation, conflict, and more - was domesticated in at least two different regions, but with the geographic and cultural origins of the modern domestic horse lineage remaining unknown. By tracing ancient horse population movements and inferring the spatiotemporal trajectories of phenotypic adaptations, this study provides fresh perspectives on past human group interactions and activities.}, }
@article {pmid31092597, year = {2019}, author = {Bennett, RJ and Baker, KS}, title = {Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes.}, journal = {Journal of clinical microbiology}, volume = {57}, number = {8}, pages = {}, pmid = {31092597}, issn = {1098-660X}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 106690/A/14/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/pathogenicity ; DNA, Ancient/*analysis ; Drug Resistance, Multiple, Bacterial/genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Bacterial ; Humans ; Mycobacterium leprae/genetics/pathogenicity ; Mycobacterium tuberculosis/genetics/pathogenicity ; Phylogeny ; *Sequence Analysis, DNA ; Yersinia pestis/genetics/pathogenicity ; }, abstract = {Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens.}, }
@article {pmid31088861, year = {2019}, author = {Renaud, G and Hanghøj, K and Korneliussen, TS and Willerslev, E and Orlando, L}, title = {Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.}, journal = {Genetics}, volume = {212}, number = {3}, pages = {587-614}, pmid = {31088861}, issn = {1943-2631}, mesh = {Animals ; Bayes Theorem ; *DNA, Ancient ; Genotyping Techniques/*methods/standards ; *Heterozygote ; *Homozygote ; Humans ; Markov Chains ; }, abstract = {Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6× and down to 7-8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.}, }
@article {pmid31080083, year = {2019}, author = {Saag, L and Laneman, M and Varul, L and Malve, M and Valk, H and Razzak, MA and Shirobokov, IG and Khartanovich, VI and Mikhaylova, ER and Kushniarevich, A and Scheib, CL and Solnik, A and Reisberg, T and Parik, J and Saag, L and Metspalu, E and Rootsi, S and Montinaro, F and Remm, M and Mägi, R and D'Atanasio, E and Crema, ER and Díez-Del-Molino, D and Thomas, MG and Kriiska, A and Kivisild, T and Villems, R and Lang, V and Metspalu, M and Tambets, K}, title = {The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East.}, journal = {Current biology : CB}, volume = {29}, number = {10}, pages = {1701-1711.e16}, pmid = {31080083}, issn = {1879-0445}, support = {/WT_/Wellcome Trust/United Kingdom ; 261213/ERC_/European Research Council/International ; 100719/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; DNA, Ancient/*analysis ; Estonia ; Female ; *Gene Flow ; History, Ancient ; History, Medieval ; *Human Migration ; Humans ; Male ; *Phenotype ; }, abstract = {In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200-400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC-50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC-450 AD) (IngIA) and 7 Middle Age Estonian (1200-1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1-5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic. VIDEO ABSTRACT.}, }
@article {pmid31075917, year = {2019}, author = {Merheb, M and Matar, R and Hodeify, R and Siddiqui, SS and Vazhappilly, CG and Marton, J and Azharuddin, S and Al Zouabi, H}, title = {Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases.}, journal = {Cells}, volume = {8}, number = {5}, pages = {}, pmid = {31075917}, issn = {2073-4409}, mesh = {*Civilization ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; *Domestication ; History, 18th Century ; Homicide/*history ; Humans ; *Music ; }, abstract = {Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases-and profiling, in certain conditions-especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven's grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.}, }
@article {pmid31074010, year = {2019}, author = {Maurer-Alcalá, XX and Nowacki, M}, title = {Evolutionary origins and impacts of genome architecture in ciliates.}, journal = {Annals of the New York Academy of Sciences}, volume = {1447}, number = {1}, pages = {110-118}, pmid = {31074010}, issn = {1749-6632}, support = {//NCCR RNA &amp; Disease/International ; G-EDIT//H2020 European Research Council/International ; }, mesh = {Animals ; Ciliophora/*genetics ; Epigenesis, Genetic/*genetics ; *Evolution, Molecular ; Humans ; }, abstract = {Genome architecture is well diversified among eukaryotes in terms of size and content, with many being radically shaped by ancient and ongoing genome conflicts with transposable elements (e.g., the large transposon-rich genomes common among plants). In ciliates, a group of microbial eukaryotes with distinct somatic and germ-line genomes present in a single cell, the consequences of these genome conflicts are most apparent in their developmentally programmed genome rearrangements. This complicated developmental phenomenon has largely overshadowed and outpaced our understanding of how germ-line and somatic genome architectures have influenced the evolutionary dynamism and potential in these taxa. In our review, we highlight three central concepts: how the evolution of atypical ciliate germ-line genome architectures is linked to ancient genome conflicts; how the complex, epigenetically guided transformation of germline to soma during development can generate widespread genetic variation; and how these features, coupled with their unusual life cycle, have increased the rate of molecular evolution linked to genome architecture in these taxa.}, }
@article {pmid31061125, year = {2019}, author = {Schroeder, H and Margaryan, A and Szmyt, M and Theulot, B and Włodarczak, P and Rasmussen, S and Gopalakrishnan, S and Szczepanek, A and Konopka, T and Jensen, TZT and Witkowska, B and Wilk, S and Przybyła, MM and Pospieszny, &#x141; and Sjögren, KG and Belka, Z and Olsen, J and Kristiansen, K and Willerslev, E and Frei, KM and Sikora, M and Johannsen, NN and Allentoft, ME}, title = {Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {22}, pages = {10705-10710}, pmid = {31061125}, issn = {1091-6490}, mesh = {Adolescent ; Adult ; Archaeology ; Burial/*history ; Child ; Child, Preschool ; DNA, Ancient/*analysis ; Female ; History, Ancient ; Human Migration ; Humans ; Infant ; Male ; Middle Aged ; Pedigree ; Poland ; Violence/*history ; Young Adult ; }, abstract = {The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300-2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community.}, }
@article {pmid31056281, year = {2019}, author = {Fages, A and Hanghøj, K and Khan, N and Gaunitz, C and Seguin-Orlando, A and Leonardi, M and McCrory Constantz, C and Gamba, C and Al-Rasheid, KAS and Albizuri, S and Alfarhan, AH and Allentoft, M and Alquraishi, S and Anthony, D and Baimukhanov, N and Barrett, JH and Bayarsaikhan, J and Benecke, N and Bernáldez-Sánchez, E and Berrocal-Rangel, L and Biglari, F and Boessenkool, S and Boldgiv, B and Brem, G and Brown, D and Burger, J and Crubézy, E and Daugnora, L and Davoudi, H and de Barros Damgaard, P and de Los Ángeles de Chorro Y de Villa-Ceballos, M and Deschler-Erb, S and Detry, C and Dill, N and do Mar Oom, M and Dohr, A and Ellingvåg, S and Erdenebaatar, D and Fathi, H and Felkel, S and Fernández-Rodríguez, C and García-Viñas, E and Germonpré, M and Granado, JD and Hallsson, JH and Hemmer, H and Hofreiter, M and Kasparov, A and Khasanov, M and Khazaeli, R and Kosintsev, P and Kristiansen, K and Kubatbek, T and Kuderna, L and Kuznetsov, P and Laleh, H and Leonard, JA and Lhuillier, J and Liesau von Lettow-Vorbeck, C and Logvin, A and Lõugas, L and Ludwig, A and Luis, C and Arruda, AM and Marques-Bonet, T and Matoso Silva, R and Merz, V and Mijiddorj, E and Miller, BK and Monchalov, O and Mohaseb, FA and Morales, A and Nieto-Espinet, A and Nistelberger, H and Onar, V and Pálsdóttir, AH and Pitulko, V and Pitskhelauri, K and Pruvost, M and Rajic Sikanjic, P and Rapan Papeša, A and Roslyakova, N and Sardari, A and Sauer, E and Schafberg, R and Scheu, A and Schibler, J and Schlumbaum, A and Serrand, N and Serres-Armero, A and Shapiro, B and Sheikhi Seno, S and Shevnina, I and Shidrang, S and Southon, J and Star, B and Sykes, N and Taheri, K and Taylor, W and Teegen, WR and Trbojević Vukičević, T and Trixl, S and Tumen, D and Undrakhbold, S and Usmanova, E and Vahdati, A and Valenzuela-Lamas, S and Viegas, C and Wallner, B and Weinstock, J and Zaibert, V and Clavel, B and Lepetz, S and Mashkour, M and Helgason, A and Stefánsson, K and Barrey, E and Willerslev, E and Outram, AK and Librado, P and Orlando, L}, title = {Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.}, journal = {Cell}, volume = {177}, number = {6}, pages = {1419-1435.e31}, pmid = {31056281}, issn = {1097-4172}, support = {681605/ERC_/European Research Council/International ; U01 MH106874/MH/NIMH NIH HHS/United States ; W 1225/FWF_/Austrian Science Fund FWF/Austria ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Asia ; Biological Evolution ; Breeding/history ; DNA, Ancient/analysis ; Domestication ; Equidae/genetics ; Europe ; Female ; Genetic Variation/genetics ; Genome/genetics ; History, Ancient ; Horses/*genetics ; Male ; Phylogeny ; }, abstract = {Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.}, }
@article {pmid31040238, year = {2019}, author = {Aouizerat, T and Gutman, I and Paz, Y and Maeir, AM and Gadot, Y and Gelman, D and Szitenberg, A and Drori, E and Pinkus, A and Schoemann, M and Kaplan, R and Ben-Gedalya, T and Coppenhagen-Glazer, S and Reich, E and Saragovi, A and Lipschits, O and Klutstein, M and Hazan, R}, title = {Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, pmid = {31040238}, issn = {2150-7511}, mesh = {Archaeology/*methods ; Fossils/*microbiology ; Genotype ; Geologic Sediments/*microbiology ; Microbiological Techniques/*methods ; Yeasts/*isolation &amp; purification ; }, abstract = {Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.IMPORTANCE So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products.}, }
@article {pmid31036834, year = {2019}, author = {Stahlschmidt, MC and Collin, TC and Fernandes, DM and Bar-Oz, G and Belfer-Cohen, A and Gao, Z and Jakeli, N and Matskevich, Z and Meshveliani, T and Pritchard, JK and McDermott, F and Pinhasi, R}, title = {Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6628}, pmid = {31036834}, issn = {2045-2322}, mesh = {Animals ; *DNA, Ancient ; DNA, Plant/*genetics ; Georgia ; Mammals/*genetics ; Paleontology ; }, abstract = {Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.}, }
@article {pmid31036632, year = {2019}, author = {Shaw, B and Burrell, CL and Green, D and Navarro-Martinez, A and Scott, D and Daroszewska, A and van 't Hof, R and Smith, L and Hargrave, F and Mistry, S and Bottrill, A and Kessler, BM and Fischer, R and Singh, A and Dalmay, T and Fraser, WD and Henneberger, K and King, T and Gonzalez, S and Layfield, R}, title = {Molecular insights into an ancient form of Paget's disease of bone.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {21}, pages = {10463-10472}, pmid = {31036632}, issn = {1091-6490}, support = {//Wellcome Trust/United Kingdom ; MR/P020941/1/MRC_/Medical Research Council/United Kingdom ; 107720/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bone and Bones/*metabolism/pathology ; History, Medieval ; Humans ; MicroRNAs/metabolism ; Osteitis Deformans/complications/*metabolism/pathology ; Osteosarcoma/etiology/metabolism ; Paleopathology ; *Proteome ; Sequence Analysis, DNA ; Sequestosome-1 Protein/chemistry/*metabolism ; }, abstract = {Paget's disease of bone (PDB) is a chronic skeletal disorder that can affect one or several bones in individuals older than 55 y of age. PDB-like changes have been reported in archaeological remains as old as Roman, although accurate diagnosis and natural history of the disease is lacking. Six skeletons from a collection of 130 excavated at Norton Priory in the North West of England, which dates to medieval times, show atypical and extensive pathological changes resembling contemporary PDB affecting as many as 75% of individual skeletons. Disease prevalence in the remaining collection is high, at least 16% of adults, with age at death estimations as low as 35 y. Despite these atypical features, paleoproteomic analysis identified sequestosome 1 (SQSTM1) or p62, a protein central to the pathological milieu of PDB, as one of the few noncollagenous human sequences preserved in skeletal samples. Targeted proteomic analysis detected >60% of the ancient p62 primary sequence, with Western blotting indicating p62 abnormalities, including in dentition. Direct sequencing of ancient DNA excluded contemporary PDB-associated SQSTM1 mutations. Our observations indicate that the ancient p62 protein is likely modified within its C-terminal ubiquitin-associated domain. Ancient miRNAs were remarkably preserved in an osteosarcoma from a skeleton with extensive disease, with miR-16 expression consistent with that reported in contemporary PDB-associated bone tumors. Our work displays the use of proteomics to inform diagnosis of ancient diseases such as atypical PDB, which has unusual features presumably potentiated by yet-unidentified environmental or genetic factors.}, }
@article {pmid31006515, year = {2019}, author = {Haber, M and Doumet-Serhal, C and Scheib, CL and Xue, Y and Mikulski, R and Martiniano, R and Fischer-Genz, B and Schutkowski, H and Kivisild, T and Tyler-Smith, C}, title = {A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences.}, journal = {American journal of human genetics}, volume = {104}, number = {5}, pages = {977-984}, pmid = {31006515}, issn = {1537-6605}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/analysis/genetics ; Ethnicity/*genetics/*history ; Female ; *Gene Flow ; *Genetics, Population ; *Genome, Human ; History, Ancient ; Humans ; Lebanon/ethnology ; Male ; White People/*genetics ; }, abstract = {During the medieval period, hundreds of thousands of Europeans migrated to the Near East to take part in the Crusades, and many of them settled in the newly established Christian states along the Eastern Mediterranean coast. Here, we present a genetic snapshot of these events and their aftermath by sequencing the whole genomes of 13 individuals who lived in what is today known as Lebanon between the 3[rd] and 13[th] centuries CE. These include nine individuals from the "Crusaders' pit" in Sidon, a mass burial in South Lebanon identified from the archaeology as the grave of Crusaders killed during a battle in the 13[th] century CE. We show that all of the Crusaders' pit individuals were males; some were Western Europeans from diverse origins, some were locals (genetically indistinguishable from present-day Lebanese), and two individuals were a mixture of European and Near Eastern ancestries, providing direct evidence that the Crusaders admixed with the local population. However, these mixtures appear to have had limited genetic consequences since signals of admixture with Europeans are not significant in any Lebanese group today-in particular, Lebanese Christians are today genetically similar to local people who lived during the Roman period which preceded the Crusades by more than four centuries.}, }
@article {pmid31004175, year = {2019}, author = {Membrebe, JV and Suchard, MA and Rambaut, A and Baele, G and Lemey, P}, title = {Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates.}, journal = {Molecular biology and evolution}, volume = {36}, number = {8}, pages = {1793-1803}, pmid = {31004175}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI107034/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; *Evolution, Molecular ; *Genetic Techniques ; Mammoths/*genetics ; Time Factors ; Viruses/*genetics ; }, abstract = {Many factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.}, }
@article {pmid31004132, year = {2019}, author = {Hanghøj, K and Renaud, G and Albrechtsen, A and Orlando, L}, title = {DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, pmid = {31004132}, issn = {2047-217X}, mesh = {Algorithms ; Autopsy ; *Computational Biology/methods ; CpG Islands ; DNA Damage ; *DNA Methylation ; Epigenomics/*methods ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing ; Humans ; *Software ; }, abstract = {BACKGROUND: Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons.<br><br>FINDINGS: Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data. It builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post-mortem cytosine deamination rates at both methylated and unmethylated sites. To validate DamMet, we extended gargammel, a sequence simulator for ancient DNA data, by introducing methylation-dependent features of post-mortem DNA decay. This new simulator provides direct validation of DamMet predictions. Additionally, the methylation levels inferred by DamMet were found to be correlated to those inferred by epiPALEOMIX and both on par and directly comparable to those measured from whole-genome bisulphite sequencing experiments of fresh tissues.<br><br>CONCLUSIONS: DamMet provides genuine estimates for local DNA methylation levels in ancient individual genomes. The returned estimates are directly cross-sample comparable, and the software is available as an open-source C++ program hosted at https://gitlab.com/KHanghoj/DamMet along with a manual and tutorial.}, }
@article {pmid30994442, year = {2019}, author = {Meffray, A and Perrin, M and Richier, A and Schmitt, A and Ardagna, Y and Biagini, P}, title = {Molecular detection of Treponema pallidum subspecies pallidum in 150-year-old foetal remains, southeastern France.}, journal = {Journal of medical microbiology}, volume = {68}, number = {5}, pages = {761-769}, doi = {10.1099/jmm.0.000978}, pmid = {30994442}, issn = {1473-5644}, mesh = {Archaeology ; Cemeteries ; DNA, Ancient/*isolation &amp; purification ; Fetus/microbiology ; France ; History, 19th Century ; Humans ; Infant ; Mycobacterium tuberculosis/genetics ; Plasmodium falciparum/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Syphilis, Congenital/history/*microbiology ; Treponema pallidum/classification/*isolation &amp; purification ; }, abstract = {PURPOSE: Syphilis, caused by Treponema pallidum subspecies pallidum , is considered as an old disease affecting humans; traces of such infections, including congenital syphilis, are potentially identifiable in archaeological samples. The aim of this research was to perform macroscopic and molecular investigations of T. pallidum on six infant remains, buried between 1837 and 1867, from the cemetery of 'Les Crottes' in Marseille city (southeastern France).<br><br>METHODOLOGY: Pathological analysis of bones from individuals, aged from the twenty-ninth week of amenorrhea to 4-9&#x2009;months, was performed. Samples served also as a source of ancient DNA (aDNA) for PCR-based molecular investigations targeting T. pallidum DNA; all samples were also tested for Mycobacterium tuberculosis and Plasmodium falciparum DNA. Sequences characterized were cloned and sequenced, and compared to those available in databases.Results/Key findings. All samples tested displayed widespread osteoporotic lesions across the skeleton possibly related to some metabolic or infectious disorders. Subsequent molecular analysis revealed that one individual, SP332 (unborn, 29 amenorrhea weeks, inhumation date 1864-1866), exhibited positive signals for the five T. pallidum amplification systems tested; sequence analysis provided strong evidence for the effective detection of T. pallidum subspecies pallidum DNA.<br><br>CONCLUSIONS: Individual SP332 is the first PCR-confirmed palaeopathological case of syphilis identified in France, and the youngest specimen ever to be diagnosed with certainty for congenital syphilis. Future research aimed at better characterizing this 150-year-old treponeme genome and exploring new archaelogical cases of syphilis in the very young should contribute to a better comprehension of the disease's history.}, }
@article {pmid30992585, year = {2019}, author = {Phillips, N}, title = {Indigenous groups look to ancient DNA to bring their ancestors home.}, journal = {Nature}, volume = {568}, number = {7752}, pages = {294-297}, pmid = {30992585}, issn = {1476-4687}, mesh = {Archaeology ; *Body Remains ; *DNA, Ancient ; DNA, Mitochondrial ; Humans ; }, }
@article {pmid30988490, year = {2019}, author = {Brace, S and Diekmann, Y and Booth, TJ and van Dorp, L and Faltyskova, Z and Rohland, N and Mallick, S and Olalde, I and Ferry, M and Michel, M and Oppenheimer, J and Broomandkhoshbacht, N and Stewardson, K and Martiniano, R and Walsh, S and Kayser, M and Charlton, S and Hellenthal, G and Armit, I and Schulting, R and Craig, OE and Sheridan, A and Parker Pearson, M and Stringer, C and Reich, D and Thomas, MG and Barnes, I}, title = {Ancient genomes indicate population replacement in Early Neolithic Britain.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {5}, pages = {765-771}, pmid = {30988490}, issn = {2397-334X}, support = {/WT_/Wellcome Trust/United Kingdom ; 100713/WT_/Wellcome Trust/United Kingdom ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA, Ancient ; Europe ; *Genome ; Humans ; Population Dynamics ; United Kingdom ; }, abstract = {The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.}, }
@article {pmid30988179, year = {2019}, author = {Sánchez-Quinto, F and Malmström, H and Fraser, M and Girdland-Flink, L and Svensson, EM and Simões, LG and George, R and Hollfelder, N and Burenhult, G and Noble, G and Britton, K and Talamo, S and Curtis, N and Brzobohata, H and Sumberova, R and Götherström, A and Storå, J and Jakobsson, M}, title = {Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {19}, pages = {9469-9474}, pmid = {30988179}, issn = {1091-6490}, mesh = {Agriculture/history ; *Archaeology ; Burial ; Chromosomes, Human, Y/*genetics ; Female ; *Genome, Human ; *Haplotypes ; History, Ancient ; Humans ; Male ; United Kingdom ; }, abstract = {Paleogenomic and archaeological studies show that Neolithic lifeways spread from the Fertile Crescent into Europe around 9000 BCE, reaching northwestern Europe by 4000 BCE. Starting around 4500 BCE, a new phenomenon of constructing megalithic monuments, particularly for funerary practices, emerged along the Atlantic façade. While it has been suggested that the emergence of megaliths was associated with the territories of farming communities, the origin and social structure of the groups that erected them has remained largely unknown. We generated genome sequence data from human remains, corresponding to 24 individuals from five megalithic burial sites, encompassing the widespread tradition of megalithic construction in northern and western Europe, and analyzed our results in relation to the existing European paleogenomic data. The various individuals buried in megaliths show genetic affinities with local farming groups within their different chronological contexts. Individuals buried in megaliths display (past) admixture with local hunter-gatherers, similar to that seen in other Neolithic individuals in Europe. In relation to the tomb populations, we find significantly more males than females buried in the megaliths of the British Isles. The genetic data show close kin relationships among the individuals buried within the megaliths, and for the Irish megaliths, we found a kin relation between individuals buried in different megaliths. We also see paternal continuity through time, including the same Y-chromosome haplotypes reoccurring. These observations suggest that the investigated funerary monuments were associated with patrilineal kindred groups. Our genomic investigation provides insight into the people associated with this long-standing megalith funerary tradition, including their social dynamics.}, }
@article {pmid30980085, year = {2019}, author = {Kutanan, W and Kampuansai, J and Srikummool, M and Brunelli, A and Ghirotto, S and Arias, L and Macholdt, E and Hübner, A and Schröder, R and Stoneking, M}, title = {Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations.}, journal = {Molecular biology and evolution}, volume = {36}, number = {7}, pages = {1490-1506}, pmid = {30980085}, issn = {1537-1719}, mesh = {Chromosomes, Human, Y/*genetics ; Demography ; *Family Characteristics ; Female ; Genetic Variation ; *Genome, Mitochondrial ; Human Migration ; Humans ; Language ; Laos ; Male ; Thailand ; }, abstract = {The human demographic history of Mainland Southeast Asia (MSEA) has not been well studied; in particular, there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major Mainland Southeast Asia families: Austroasiatic, Tai-Kadai, and Sino-Tibetan. Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* [O-M95*] and O2a* [O-M324*]) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyze complete mitochondrial DNA genome sequences published previously from the same groups and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of postmarital residence pattern on genetic diversity in patrilocal versus matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 ka), with two later major male-specific expansions during the Neolithic period (∼4-5 ka) and the Bronze/Iron Age (∼2.0-2.5 ka). These two later expansions are characteristic of the modern Austroasiatic and Tai-Kadai groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion, and cultural diffusion) of major Thai groups and find different results from mitochondrial DNA simulations, supporting contrasting male and female genetic histories.}, }
@article {pmid30964548, year = {2019}, author = {Klunk, J and Duggan, AT and Redfern, R and Gamble, J and Boldsen, JL and Golding, GB and Walter, BS and Eaton, K and Stangroom, J and Rouillard, JM and Devault, A and DeWitte, SN and Poinar, HN}, title = {Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark.}, journal = {American journal of physical anthropology}, volume = {169}, number = {2}, pages = {240-252}, doi = {10.1002/ajpa.23820}, pmid = {30964548}, issn = {1096-8644}, support = {APP1065106//National Health and Medical Research Council (NHMRC)/International ; RGPIN-2015-04477//Natural Sciences and Engineering Research Council of Canada (NSERC)/International ; 430-2017-01193//Social Sciences and Humanities Research Council of Canada (SSHRC)/International ; 435-2018-0465//Social Sciences and Humanities Research Council of Canada (SSHRC)/International ; //Arbor Biosciences/International ; //McMaster University/International ; //Canada Research Chair Program/International ; //University of Toronto/International ; }, mesh = {Bone and Bones/chemistry ; DNA, Ancient/analysis ; DNA, Mitochondrial/analysis ; Denmark ; Female ; Genetic Variation/*genetics ; Genome, Mitochondrial/*genetics ; History, Medieval ; Human Migration/history ; Humans ; London ; Male ; Plague/*history ; Tooth/chemistry ; }, abstract = {OBJECTIVES: In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isotope data. This study uses ancient DNA (aDNA) isolated from skeletal remains to examine whether evidence for large-scale population movement can be gleaned from the complete mitochondrial genomes of 264 medieval individuals from England (London) and Denmark.<br><br>MATERIALS AND METHODS: Using a novel library-conserving approach to targeted capture, we recovered 264 full mitochondrial genomes from the petrous portion of the temporal bones and teeth and compared genetic diversity across the medieval period within and between English (London) and Danish populations and with contemporary populations through population pairwise &#x3a6;ST analysis.<br><br>RESULTS: We find no evidence of significant differences in genetic diversity spatially or temporally in our dataset, yet there is a high degree of haplotype diversity in our medieval samples with little exact sequence sharing.<br><br>DISCUSSION: The mitochondrial genomes of both medieval Londoners and medieval Danes suggest high mitochondrial diversity before, during and after the Black Death. While our mitochondrial genomic data lack geographically correlated signals, these data could be the result of high, continual female migration before and after the Black Death or may simply indicate a large female effective population size unaffected by the upheaval of the medieval period. Either scenario suggests a genetic resiliency in areas of northwestern medieval Europe.}, }
@article {pmid30963935, year = {2019}, author = {Nakagome, S and Hudson, RR and Di Rienzo, A}, title = {Inferring the model and onset of natural selection under varying population size from the site frequency spectrum and haplotype structure.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1896}, pages = {20182541}, pmid = {30963935}, issn = {1471-2954}, support = {R01 GM101682/GM/NIGMS NIH HHS/United States ; }, mesh = {Bayes Theorem ; DNA, Ancient/*analysis ; Europe ; *Gene Frequency ; Haplotypes/*genetics ; *Human Migration ; Humans ; Models, Genetic ; Population Density ; *Selection, Genetic ; Skin Pigmentation/*genetics ; Time Factors ; }, abstract = {A fundamental question about adaptation in a population is the time of onset of the selective pressure acting on beneficial alleles. Inferring this time, in turn, depends on the selection model. We develop a framework of approximate Bayesian computation (ABC) that enables the use of the full site frequency spectrum and haplotype structure to test the goodness-of-fit of selection models and estimate the timing of selection under varying population size scenarios. We show that our method has sufficient power to distinguish natural selection from neutrality even if relatively old selection increased the frequency of a pre-existing allele from 20% to 50% or from 40% to 80%. Our ABC can accurately estimate the time of onset of selection on a new mutation. However, estimates are prone to bias under the standing variation model, possibly due to the uncertainty in the allele frequency at the onset of selection. We further extend our approach to take advantage of ancient DNA data that provides information on the allele frequency path of the beneficial allele. Applying our ABC, including both modern and ancient human DNA data, to four pigmentation alleles in Europeans, we detected selection on standing variants that occurred after the dispersal from Africa even though models of selection on a new mutation were initially supported for two of these alleles without the ancient data.}, }
@article {pmid30957607, year = {2019}, author = {Siripan, S and Wonnapinij, P and Auetrakulvit, P and Wangthongchaicharoen, N and Surat, W}, title = {Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {30}, number = {4}, pages = {609-617}, doi = {10.1080/24701394.2019.1597072}, pmid = {30957607}, issn = {2470-1408}, mesh = {Animals ; Cattle/*genetics ; DNA, Mitochondrial/genetics ; Haplotypes ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Thailand ; }, abstract = {Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B.taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.}, }
@article {pmid30954285, year = {2019}, author = {Brunson, K and Reich, D}, title = {The Promise of Paleogenomics Beyond Our Own Species.}, journal = {Trends in genetics : TIG}, volume = {35}, number = {5}, pages = {319-329}, doi = {10.1016/j.tig.2019.02.006}, pmid = {30954285}, issn = {0168-9525}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Biological Evolution ; DNA, Ancient ; Genome-Wide Association Study ; *Genomics/methods ; Geography ; Horses ; Humans ; *Paleontology/methods ; Species Specificity ; Zea mays/genetics ; }, abstract = {Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.}, }
@article {pmid30953039, year = {2019}, author = {Spyrou, MA and Bos, KI and Herbig, A and Krause, J}, title = {Ancient pathogen genomics as an emerging tool for infectious disease research.}, journal = {Nature reviews. Genetics}, volume = {20}, number = {6}, pages = {323-340}, pmid = {30953039}, issn = {1471-0064}, mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; Biological Evolution ; Communicable Diseases/*history/microbiology/parasitology/virology ; DNA, Ancient/*analysis/isolation &amp; purification ; Fossils ; *Genome ; Genomics/*methods ; Global Health/history ; High-Throughput Nucleotide Sequencing/*methods ; History, 19th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Public Health Surveillance/methods ; Viruses/genetics/isolation &amp; purification ; }, abstract = {Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.}, }
@article {pmid30952160, year = {2019}, author = {Yelmen, B and Mondal, M and Marnetto, D and Pathak, AK and Montinaro, F and Gallego Romero, I and Kivisild, T and Metspalu, M and Pagani, L}, title = {Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations.}, journal = {Molecular biology and evolution}, volume = {36}, number = {8}, pages = {1628-1642}, pmid = {30952160}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Demography ; *Genome, Human ; Genomics/*methods ; Haplotypes ; Humans ; India ; Pakistan ; Phylogeography ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Selection, Genetic ; }, abstract = {Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high-quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations and showed our approach to be robust via coalescent simulations. Our f3 and f4 statistics-based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex interpopulation relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively.}, }
@article {pmid30946645, year = {2019}, author = {Sélem-Mojica, N and Aguilar, C and Gutiérrez-García, K and Martínez-Guerrero, CE and Barona-Gómez, F}, title = {EvoMining reveals the origin and fate of natural product biosynthetic enzymes.}, journal = {Microbial genomics}, volume = {5}, number = {12}, pages = {}, pmid = {30946645}, issn = {2057-5858}, mesh = {Acetolactate Synthase/genetics/*metabolism ; Actinobacteria/enzymology/genetics ; Bacterial Proteins/*genetics/metabolism ; Cyanobacteria/enzymology/genetics ; *Evolution, Molecular ; Glutamate Dehydrogenase/*genetics/metabolism ; Indoles/*metabolism ; Phenols/*metabolism ; Pseudomonas/enzymology/genetics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {Natural products (NPs), or specialized metabolites, are important for medicine and agriculture alike, and for the fitness of the organisms that produce them. NP genome-mining aims at extracting biosynthetic information from the genomes of microbes presumed to produce these compounds. Typically, canonical enzyme sequences from known biosynthetic systems are identified after sequence similarity searches. Despite this being an efficient process, the likelihood of identifying truly novel systems by this approach is low. To overcome this limitation, we previously introduced EvoMining, a genome-mining approach that incorporates evolutionary principles. Here, we release and use our latest EvoMining version, which includes novel visualization features and customizable databases, to analyse 42 central metabolic enzyme families (EFs) conserved throughout Actinobacteria, Cyanobacteria, Pseudomonas and Archaea. We found that expansion-and-recruitment profiles of these 42 families are lineage specific, opening the metabolic space related to 'shell' enzymes. These enzymes, which have been overlooked, are EFs with orthologues present in most of the genomes of a taxonomic group, but not in all. As a case study of canonical shell enzymes, we characterized the expansion and recruitment of glutamate dehydrogenase and acetolactate synthase into scytonemin biosynthesis, and into other central metabolic pathways driving Archaea and Bacteria adaptive evolution. By defining the origin and fate of enzymes, EvoMining complements traditional genome-mining approaches as an unbiased strategy and opens the door to gaining insights into the evolution of NP biosynthesis. We anticipate that EvoMining will be broadly used for evolutionary studies, and for generating predictions of unprecedented chemical scaffolds and new antibiotics. This article contains data hosted by Microreact.}, }
@article {pmid30944772, year = {2019}, author = {Ciucani, MM and Palumbo, D and Galaverni, M and Serventi, P and Fabbri, E and Ravegnini, G and Angelini, S and Maini, E and Persico, D and Caniglia, R and Cilli, E}, title = {Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6424}, pmid = {30944772}, issn = {2167-8359}, abstract = {BACKGROUND: The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated.<br><br>METHODS: In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses.<br><br>RESULTS: Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1.<br><br>DISCUSSION: In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence in this area. Moreover, the unexpected discovery of a 24,700-year-old sample carrying a haplotype that, from the fragment here obtained, falls within the canine clade A, could represent the oldest evidence in Europe of such dog-rich clade. All these findings suggest complex population dynamics that deserve to be further investigated based on mitochondrial or whole genome sequencing.}, }
@article {pmid30942856, year = {2019}, author = {Harris, DN and Ruczinski, I and Yanek, LR and Becker, LC and Becker, DM and Guio, H and Cui, T and Chilton, FH and Mathias, RA and O'Connor, TD}, title = {Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World.}, journal = {Genome biology and evolution}, volume = {11}, number = {5}, pages = {1417-1430}, pmid = {30942856}, issn = {1759-6653}, support = {R01 AT008621/AT/NCCIH NIH HHS/United States ; R01 HL087698/HL/NHLBI NIH HHS/United States ; R01 HL112064/HL/NHLBI NIH HHS/United States ; U01 HL072518/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Fatty Acid Desaturases/*genetics/metabolism ; Fatty Acids, Unsaturated/*metabolism ; Hominidae/*genetics/metabolism ; Humans ; Indians, North American/genetics ; Selection, Genetic ; Siberia ; }, abstract = {The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (>20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.}, }
@article {pmid30913508, year = {2019}, author = {Traversari, M and Serrangeli, MC and Catalano, G and Petrella, E and Piciucchi, S and Feletti, F and Oxilia, G and Cristiani, E and Vazzana, A and Sorrentino, R and De Fanti, S and Luiselli, D and Calcagnile, L and Saragoni, L and Feeney, RNM and Gruppioni, G and Cilli, E and Benazzi, S}, title = {Multi-analytic study of a probable case of fibrous dysplasia (FD) from certosa monumental cemetery (Bologna, Italy).}, journal = {International journal of paleopathology}, volume = {25}, number = {}, pages = {1-8}, doi = {10.1016/j.ijpp.2019.03.003}, pmid = {30913508}, issn = {1879-9825}, mesh = {Adult ; Amino Acid Substitution ; Cemeteries/history ; Craniofacial Fibrous Dysplasia/*diagnostic imaging/genetics/history/pathology ; Fibrous Dysplasia, Polyostotic/diagnostic imaging/history/pathology ; History, 19th Century ; History, 20th Century ; Humans ; Italy ; Male ; Mutation ; Osteitis Deformans/diagnostic imaging/pathology ; Osteosarcoma/diagnostic imaging/history/pathology ; Tomography, X-Ray Computed/history ; }, abstract = {OBJECTIVE: To evaluate, via a multidisciplinary approach, a distinctive paleopathological condition believed to be fibrous dysplasia, found on a 19th/20th century skeleton from Certosa Monumental Cemetery, Bologna, Italy.<br><br>MATERIALS: A skeletonized cranium and mandible recovered from an ossuary in 2014.<br><br>METHODS: Pathological alterations were analysed by radiological examination, dental macrowear, histopathological and genetic analyses.<br><br>RESULT: The skeleton is believed to be an adult male. Differential diagnoses include Paget's disease, McCune-Albright syndrome, osteochondroma and osteosarcoma. The radiographic findings, along with the solitary nature of the lesions, are strong evidence for the diagnosis of fibrous dysplasia (FD). Genetic analysis further revealed a frequency of &#x2dc;1% of mutant alleles with the R201C substitution, one of the post-zygotic activating mutation frequently associated with FD.<br><br>CONCLUSIONS: The multi-analytical method employed suggests a diagnosis of monostotic form of FD. The diagnostic design incorporates multiple lines of evidence, including macroscopic, histopathological, and genetic analyses.<br><br>SIGNIFICANCE: Through the use of a multi-analytic approach, robust diagnoses can be offered. This case serves as one of the oldest examples of FD from an historical context. The genetic mutation detected, associated with FD, has not been previously reported in historical/ancient samples.}, }
@article {pmid30893326, year = {2019}, author = {Di Maida, G and Mannino, MA and Krause-Kyora, B and Jensen, TZT and Talamo, S}, title = {Radiocarbon dating and isotope analysis on the purported Aurignacian skeletal remains from Fontana Nuova (Ragusa, Italy).}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213173}, pmid = {30893326}, issn = {1932-6203}, mesh = {Body Remains/chemistry ; Carbon Radioisotopes/*analysis ; Fossils/*history ; History, Ancient ; Humans ; Italy ; Radiometric Dating/*methods ; Tooth/chemistry ; }, abstract = {Proving voyaging at sea by Palaeolithic humans is a difficult archaeological task, even for short distances. In the Mediterranean, a commonly accepted sea crossing is that from the Italian Peninsula to Sicily by anatomically modern humans, purportedly of the Aurignacian culture. This claim, however, was only supported by the typological attribution to the Aurignacian of the lithic industries from the insular site of Fontana Nuova. AMS radiocarbon dating undertaken as part of our research shows that the faunal remains, previously considered Aurignacian, actually date to the Holocene. Absolute dating on dentinal collagen also attributes the human teeth from the site to the early Holocene, although we were unable to obtain ancient DNA to evaluate their ancestry. Ten radiocarbon dates on human and other taxa are comprised between 9910-9700 cal. BP and 8600-8480 cal. BP, indicating that Fontana Nuova was occupied by Mesolithic and not Aurignacian hunter-gatherers. Only a new study of the lithic assemblage could establish if the material from Fontana Nuova is a mixed collection that includes both late Upper Palaeolithic (Epigravettian) and Mesolithic artefacts, as can be suggested by taking into account both the results of our study and of the most recent reinterpretation of the lithics. Nevertheless, this research suggests that the notion that Aurignacian groups were present in Sicily should now be revised. Another outcome of our study is that we found that three specimens, attributed on grounds both of morphological and ZooMS identifications to Cervus elaphus, had δ13C values significantly higher than any available for such species in Europe.}, }
@article {pmid30887686, year = {2019}, author = {Weyrich, LS and Farrer, AG and Eisenhofer, R and Arriola, LA and Young, J and Selway, CA and Handsley-Davis, M and Adler, CJ and Breen, J and Cooper, A}, title = {Laboratory contamination over time during low-biomass sample analysis.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {982-996}, pmid = {30887686}, issn = {1755-0998}, support = {DECRA 150101574//Australian Research Council/ ; }, mesh = {*DNA Contamination ; *Diagnostic Errors ; Metagenomics/*methods ; Molecular Biology/*methods ; }, abstract = {Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.}, }
@article {pmid30886779, year = {2019}, author = {Eisenhofer, R and Weyrich, LS}, title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6594}, pmid = {30886779}, issn = {2167-8359}, abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.}, }
@article {pmid30884759, year = {2019}, author = {Abondio, P and Sazzini, M and Garagnani, P and Boattini, A and Monti, D and Franceschi, C and Luiselli, D and Giuliani, C}, title = {The Genetic Variability of APOE in Different Human Populations and Its Implications for Longevity.}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, pmid = {30884759}, issn = {2073-4425}, mesh = {Apolipoproteins E/*genetics ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; *Longevity ; Multifactorial Inheritance ; }, abstract = {Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer's disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved.}, }
@article {pmid30880015, year = {2019}, author = {Villalba-Mouco, V and van de Loosdrecht, MS and Posth, C and Mora, R and Martínez-Moreno, J and Rojo-Guerra, M and Salazar-García, DC and Royo-Guillén, JI and Kunst, M and Rougier, H and Crevecoeur, I and Arcusa-Magallón, H and Tejedor-Rodríguez, C and García-Martínez de Lagrán, I and Garrido-Pena, R and Alt, KW and Jeong, C and Schiffels, S and Utrilla, P and Krause, J and Haak, W}, title = {Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula.}, journal = {Current biology : CB}, volume = {29}, number = {7}, pages = {1169-1177.e7}, doi = {10.1016/j.cub.2019.02.006}, pmid = {30880015}, issn = {1879-0445}, mesh = {DNA, Ancient/*analysis ; *Genome, Human ; *Human Migration ; Humans ; Spain ; }, abstract = {The Iberian Peninsula in southwestern Europe represents an important test case for the study of human population movements during prehistoric periods. During the Last Glacial Maximum (LGM), the peninsula formed a periglacial refugium [1] for hunter-gatherers (HGs) and thus served as a potential source for the re-peopling of northern latitudes [2]. The post-LGM genetic signature was previously described as a cline from Western HG (WHG) to Eastern HG (EHG), further shaped by later Holocene expansions from the Near East and the North Pontic steppes [3-9]. Western and central Europe were dominated by ancestry associated with the ∼14,000-year-old individual from Villabruna, Italy, which had largely replaced earlier genetic ancestry, represented by 19,000-15,000-year-old individuals associated with the Magdalenian culture [2]. However, little is known about the genetic diversity in southern European refugia, the presence of distinct genetic clusters, and correspondence with geography. Here, we report new genome-wide data from 11 HGs and Neolithic individuals that highlight the late survival of Paleolithic ancestry in Iberia, reported previously in Magdalenian-associated individuals. We show that all Iberian HGs, including the oldest, a ∼19,000-year-old individual from El Mirón in Spain, carry dual ancestry from both Villabruna and the Magdalenian-related individuals. Thus, our results suggest an early connection between two potential refugia, resulting in a genetic ancestry that survived in later Iberian HGs. Our new genomic data from Iberian Early and Middle Neolithic individuals show that the dual Iberian HG genomic legacy pertains in the peninsula, suggesting that expanding farmers mixed with local HGs. VIDEO ABSTRACT.}, }
@article {pmid30875055, year = {2019}, author = {Hahn, C}, title = {Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {195-213}, doi = {10.1007/978-1-4939-9176-1_18}, pmid = {30875055}, issn = {1940-6029}, mesh = {DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Reference Standards ; Sequence Analysis, DNA/methods/*standards ; Software ; }, abstract = {Recent methodological advances have transformed the field of ancient DNA (aDNA). Basic bioinformatics skills are becoming essential requirements to process and analyze the sheer amounts of data generated by current aDNA studies and in biomedical research in general. This chapter is intended as a practical guide to the assembly of ancient mitochondrial genomes, directly from genomic DNA-derived next-generation sequencing (NGS) data, specifically in the absence of closely related reference genomes. In a hands-on tutorial suitable for readers with little to no prior bioinformatics experience, we reconstruct the mitochondrial genome of a woolly mammoth deposited ~45,000 years ago. We introduce key software tools and outline general strategies for mitogenome assembly, including the critical quality assessment of assembly results without a reference genome.}, }
@article {pmid30875054, year = {2019}, author = {Renaud, G and Schubert, M and Sawyer, S and Orlando, L}, title = {Authentication and Assessment of Contamination in Ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {163-194}, doi = {10.1007/978-1-4939-9176-1_17}, pmid = {30875054}, issn = {1940-6029}, mesh = {Cell Nucleus/*genetics ; *DNA Contamination ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial ; Humans ; Sequence Analysis, DNA/*methods ; }, abstract = {Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.}, }
@article {pmid30875053, year = {2019}, author = {Nichols, RV and Curd, E and Heintzman, PD and Shapiro, B}, title = {Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {149-161}, doi = {10.1007/978-1-4939-9176-1_16}, pmid = {30875053}, issn = {1940-6029}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Ancient/*analysis ; Environmental Monitoring/*methods ; Geologic Sediments/*analysis ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleic Acid Amplification Techniques/*methods ; Polymerase Chain Reaction/*methods ; }, abstract = {All organisms release their DNA into the environment through processes such as excretion and the senescence of tissues and limbs. This DNA, often referred to as environmental DNA (eDNA) or sedimentary ancient DNA (sedaDNA), can be recovered from both present-day and ancient soils, fecal samples, bodies of water and lake cores, and even air. While eDNA is a potentially useful record of past and present biodiversity, several challenges complicate data generation and interpretation of results. Most importantly, eDNA samples tend to be highly taxonomically mixed, and the target organism or group of organisms may be present at very low abundance within this mixture. To overcome this challenge, enrichment approaches are often used to target specific taxa of interest. Here, we describe a protocol to amplify metabarcodes or short, variable loci that identify lineages within broad taxonomic groups (e.g., plants, mammals), using the polymerase chain reaction (PCR) with established generic "barcode" primers. We also provide a catalog of animal and plant barcode primers that, because they target relatively short fragments of DNA, are potentially suitable for use with degraded DNA.}, }
@article {pmid30875052, year = {2019}, author = {Wutke, S and Ludwig, A}, title = {Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {141-147}, doi = {10.1007/978-1-4939-9176-1_15}, pmid = {30875052}, issn = {1940-6029}, mesh = {DNA Fingerprinting/*methods ; DNA, Ancient/*analysis ; Forensic Genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Multiplex Polymerase Chain Reaction/*methods ; *Polymorphism, Single Nucleotide ; }, abstract = {The analysis of single-nucleotide polymorphisms (SNPs) has proven to be advantageous for addressing variation within samples of highly degraded or low-quality DNA samples. This is because only short fragments need to be amplified to analyze SNPs, and this can be achieved by multiplex PCR. Here, we present a sensitive method for the targeted sequencing of SNP loci that requires only small amounts of template DNA. The approach combines multiplex amplification of very short fragments covering SNP positions followed by sample barcoding and next-generation sequencing. This method allows generation of data from large sample sets of poorly preserved specimens, such as fossil remains, forensic samples, and museum specimens. The approach is cost-effective, rapid, and applicable to forensics, population genetics, and phylogenetic research questions.}, }
@article {pmid30875051, year = {2019}, author = {Paijmans, JLA and González Fortes, G and Förster, DW}, title = {Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {129-139}, doi = {10.1007/978-1-4939-9176-1_14}, pmid = {30875051}, issn = {1940-6029}, mesh = {DNA, Ancient/chemistry/*isolation &amp; purification ; *Gene Library ; *Genome, Mitochondrial ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleic Acid Hybridization/*methods ; RNA/*chemistry/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted "contaminant" DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment.}, }
@article {pmid30875050, year = {2019}, author = {Soares, AER}, title = {Hybridization Capture of Ancient DNA Using RNA Baits.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {121-128}, doi = {10.1007/978-1-4939-9176-1_13}, pmid = {30875050}, issn = {1940-6029}, mesh = {*DNA Contamination ; DNA, Ancient/chemistry/*isolation &amp; purification ; Gene Library ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleic Acid Hybridization/*methods ; RNA/chemistry/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The majority of DNA recovered from ancient remains is derived from organisms that colonize the remains post-mortem, such as soil microbes, or from contaminants, such as DNA from living humans. Additionally, some ancient DNA research projects aim to target specific genomic regions, such as mitochondrial genomes or variable single nucleotide polymorphisms (SNPs). To overcome the challenge of targeting specific fragments of DNA from within a complex DNA extract, methods have been developed to enrich ancient DNA extracts for target DNA relative to nontarget DNA. This chapter describes a method for target DNA enrichment that uses hybridization to biotinylated RNA baits to capture and amplify specific ancient DNA fragments from within the pool of extracted fragments.}, }
@article {pmid30875049, year = {2019}, author = {Snyder-Mackler, N and Voyles, T and Tung, J}, title = {Generating RNA Baits for Capture-Based Enrichment.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {107-120}, doi = {10.1007/978-1-4939-9176-1_12}, pmid = {30875049}, issn = {1940-6029}, mesh = {Biotin/*chemistry ; DNA, Ancient/chemistry/*isolation &amp; purification ; *Gene Library ; *Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; RNA/*chemistry/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Capture-based enrichment techniques have revolutionized genomic analysis of species and populations for which only low-quality or contaminated DNA samples (e.g., ancient DNA, noninvasively collected DNA, environmental DNA) are available. This chapter outlines an optimized laboratory protocol for generating RNA "baits" for genome-wide capture of target DNA from a larger pool of DNA. This method relies on the in vitro transcription of biotinylated RNA baits, which has the dual benefit of eliminating the high cost of synthesizing custom baits and producing a bait set that targets the majority of regions genome-wide. We provide a detailed protocol for the three main steps involved in bait library construction: (1) making a DNA library from a high-quality DNA sample for the organism of interest or a closely related species; (2) using duplex-specific nuclease digestion to reduce the representation of repetitive regions in the DNA library; and (3) performing in vitro transcription of the repetitive region-depleted DNA library to generate biotinylated RNA baits. Where applicable, we include notes and recommendations based on our own experiences.}, }
@article {pmid30875048, year = {2019}, author = {González Fortes, G and Paijmans, JLA}, title = {Whole-Genome Capture of Ancient DNA Using Homemade Baits.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {93-105}, doi = {10.1007/978-1-4939-9176-1_11}, pmid = {30875048}, issn = {1940-6029}, mesh = {Biotin/*chemistry ; DNA, Ancient/chemistry/*isolation &amp; purification ; *Gene Library ; *Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; }, abstract = {For many archaeological and paleontological samples, the relative content of endogenous compared to contaminant DNA is low. In such cases, enriching sequencing libraries for endogenous DNA, prior to sequencing can make the final research project more cost-effective. Here, we present an in-solution enrichment protocol based on homemade baits that can be applied to recover complete nuclear genomes from ancient remains. The approach is based on the preparation of DNA baits by biotinylated adapter ligation. The procedure has been developed for use with human remains but can be adapted to other species or target regions by choosing the appropriate template DNA from which to build the capture baits. By using homemade rather than commercially acquired baits, this protocol may offer increased flexibility and cost efficiency.}, }
@article {pmid30875046, year = {2019}, author = {Gansauge, MT and Meyer, M}, title = {A Method for Single-Stranded Ancient DNA Library Preparation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {75-83}, doi = {10.1007/978-1-4939-9176-1_9}, pmid = {30875046}, issn = {1940-6029}, mesh = {DNA, Ancient/*analysis/chemistry/isolation &amp; purification ; DNA, Single-Stranded/*genetics ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Genomic library preparation from highly degraded DNA is more efficient when library molecules are prepared separately from the complementary strands of DNA fragments. We describe a protocol in which libraries are constructed from single DNA strands in a three-step procedure: single-stranded ligation of the first adapter with T4 DNA ligase in the presence of a splinter oligonucleotide, copying of the DNA strand with a proofreading polymerase, and blunt-end ligation of the second double-stranded adapter with T4 DNA ligase.}, }
@article {pmid30875045, year = {2019}, author = {Henneberger, K and Barlow, A and Paijmans, JLA}, title = {Double-Stranded Library Preparation for Ancient and Other Degraded Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {65-73}, doi = {10.1007/978-1-4939-9176-1_8}, pmid = {30875045}, issn = {1940-6029}, mesh = {DNA/*genetics ; *DNA Damage ; DNA, Ancient/*analysis/chemistry/isolation &amp; purification ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {High-throughput sequencing (HTS) allows fast and cost-efficient sequencing of ancient DNA (aDNA) without prior information about what sequences should be targeted. One necessary step for HTS is the preparation of a sequencing library. Commercial kits are available for this purpose, but many of these are not suitable for aDNA or other types of damaged DNA. Here, we outline a protocol for HTS library preparation that is optimized for ancient DNA. We report the library conversion rate for a range of input template and adapter concentrations. Our results show that the protocol performs at a high efficiency.}, }
@article {pmid30875044, year = {2019}, author = {Campos, PF and Gilbert, MTP}, title = {DNA Extraction from Keratin and Chitin.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {57-63}, doi = {10.1007/978-1-4939-9176-1_7}, pmid = {30875044}, issn = {1940-6029}, mesh = {Animals ; Chitin/*chemistry ; DNA/*analysis/*isolation &amp; purification ; Endopeptidase K/metabolism ; Humans ; Keratins/*chemistry ; Silicon Dioxide/chemistry ; }, abstract = {DNA extracted from keratinous and chitinous materials can be a useful source of genetic information. To effectively liberate the DNA from these materials, buffers containing relatively high levels of DTT, proteinase K, and detergent are recommended, followed by purification using either silica column or organic methods.}, }
@article {pmid30875043, year = {2019}, author = {Wales, N and Kistler, L}, title = {Extraction of Ancient DNA from Plant Remains.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {45-55}, doi = {10.1007/978-1-4939-9176-1_6}, pmid = {30875043}, issn = {1940-6029}, mesh = {DNA, Ancient/*analysis/*isolation &amp; purification ; DNA, Plant/*analysis/*isolation &amp; purification ; Plants/classification/*genetics ; Specimen Handling/*methods ; }, abstract = {Ancient plant remains from archaeological sites, paleoenvironmental contexts, and herbaria provide excellent opportunities for interrogating plant genetics over Quaternary timescales using ancient DNA (aDNA)-based analyses. A variety of plant tissues, preserved primarily by desiccation and anaerobic waterlogging, have proven to be viable sources of aDNA. Plant tissues are anatomically and chemically diverse and therefore require optimized DNA extraction approaches. Here, we describe a plant DNA isolation protocol that performs well in most contexts. We include recommendations for optimization to retain the very short DNA fragments that are expected to be preserved in degraded tissues.}, }
@article {pmid30875042, year = {2019}, author = {Epp, LS and Zimmermann, HH and Stoof-Leichsenring, KR}, title = {Sampling and Extraction of Ancient DNA from Sediments.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {31-44}, doi = {10.1007/978-1-4939-9176-1_5}, pmid = {30875042}, issn = {1940-6029}, mesh = {DNA, Ancient/*analysis/*isolation &amp; purification ; DNA, Plant/*analysis/*isolation &amp; purification ; Ecosystem ; Geologic Sediments/*analysis ; Plants/classification/*genetics ; Specimen Handling/*methods ; }, abstract = {Environmental DNA preserved in sediments is rapidly gaining importance as a tool in paleoecology. Sampling procedures for sedimentary ancient DNA (sedaDNA) have to be well planned to ensure clean subsampling of the inside of sediment cores and avoid introducing contamination. Additionally, ancient DNA extraction protocols may need to be optimized for the recovery of DNA from sediments, which may contain inhibitors. Here we describe procedures for subsampling both nonfrozen and frozen sediment cores, and we describe an efficient method for ancient DNA extraction from such samples.}, }
@article {pmid30875041, year = {2019}, author = {Dabney, J and Meyer, M}, title = {Extraction of Highly Degraded DNA from Ancient Bones and Teeth.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {25-29}, doi = {10.1007/978-1-4939-9176-1_4}, pmid = {30875041}, issn = {1940-6029}, mesh = {Bone and Bones/*metabolism ; *DNA Degradation, Necrotic ; DNA, Ancient/*isolation &amp; purification ; Edetic Acid/*metabolism ; Endopeptidase K/*metabolism ; Humans ; Silicon Dioxide/chemistry ; Tooth/*metabolism ; }, abstract = {We provide a DNA extraction protocol optimized for the recovery of highly fragmented molecules preserved within bones and teeth. In this method, the hard tissue matrix is degraded using an EDTA/Proteinase K lysis buffer, and the DNA is purified using spin columns with silica membranes. This method efficiently recovers molecules as short as 35 base-pairs long.}, }
@article {pmid30875040, year = {2019}, author = {Schroeder, H and de Barros Damgaard, P and Allentoft, ME}, title = {Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {21-24}, doi = {10.1007/978-1-4939-9176-1_3}, pmid = {30875040}, issn = {1940-6029}, mesh = {Bone and Bones/*metabolism ; *DNA Contamination ; DNA, Ancient/*analysis/*isolation &amp; purification ; Edetic Acid/*metabolism ; Endopeptidase K/*metabolism ; Humans ; Tooth/*metabolism ; }, abstract = {Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.}, }
@article {pmid30875039, year = {2019}, author = {Korlević, P and Meyer, M}, title = {Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {15-19}, doi = {10.1007/978-1-4939-9176-1_2}, pmid = {30875039}, issn = {1940-6029}, mesh = {Animals ; Bone and Bones/*metabolism ; DNA/*analysis/chemistry/*isolation &amp; purification ; *DNA Contamination ; Decontamination ; Neanderthals ; Phosphates/*chemistry ; Polymerase Chain Reaction ; Sodium Hypochlorite/*chemistry ; Specimen Handling/methods ; Tooth/*metabolism ; }, abstract = {DNA isolated from ancient bones and teeth comprises a mixture of microbial contamination and DNA from the organism under study. In addition, analyses of ancient human remains are often complicated by contamination with present-day human DNA, which can be introduced during excavation and subsequent handling of the specimens. In most cases, the relative abundance of contaminant DNA is much greater than that of the target organism. Here we present two techniques for reducing the proportion of contaminant DNA in bones and teeth. The first and most efficient technique uses a sodium hypochlorite (bleach) pretreatment to destroy contaminant DNA that may be bound or otherwise attached to the surface of bone/tooth powder. The second, less destructive pretreatment uses a phosphate buffer to release surface-bound DNA.}, }
@article {pmid30875038, year = {2019}, author = {Fulton, TL and Shapiro, B}, title = {Setting Up an Ancient DNA Laboratory.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {1-13}, doi = {10.1007/978-1-4939-9176-1_1}, pmid = {30875038}, issn = {1940-6029}, mesh = {Animals ; *DNA Contamination ; DNA Damage ; DNA, Ancient/*analysis/chemistry/isolation &amp; purification ; Fossils ; Humans ; Laboratories/standards ; Sequence Analysis, DNA/*methods/standards ; }, abstract = {Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential is high for contamination of ancient samples, ancient DNA extracts, and genomic sequencing libraries prepared from these extracts with non-degraded DNA from the present-day environment. To minimize the risk of contamination in ancient DNA environments, experimental protocols specific to handling ancient specimens, including those that outline the design and layout of laboratory space, have been introduced. Here, we outline challenges associated with working with ancient samples, including providing guidelines for setting up a new ancient DNA laboratory. We also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination of ancient DNA experiments with exogenous sources of DNA.}, }
@article {pmid30872771, year = {2019}, author = {Rey-Iglesia, A and García-Vázquez, A and Treadaway, EC and van der Plicht, J and Baryshnikov, GF and Szpak, P and Bocherens, H and Boeskorov, GG and Lorenzen, ED}, title = {Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4462}, pmid = {30872771}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; Body Remains ; Carbon Isotopes/analysis ; Carnivora ; *DNA, Ancient ; *DNA, Mitochondrial ; History, Ancient ; Nitrogen Isotopes/analysis ; Siberia ; Ursidae/*genetics ; }, abstract = {Over 60% of the modern distribution range of brown bears falls within Russia, yet palaeoecological data from the region remain scarce. Complete modern Russian brown bear mitogenomes are abundant in the published literature, yet examples of their ancient counterparts are absent. Similarly, there is only limited stable isotopic data of prehistoric brown bears from the region. We used ancient DNA and stable carbon (δ[13]C) and nitrogen (δ[15]N) isotopes retrieved from five Pleistocene Yakutian brown bears (one Middle Pleistocene and four Late Pleistocene), to elucidate the evolutionary history and palaeoecology of the species in the region. We were able to reconstruct the complete mitogenome of one of the Late Pleistocene specimens, but we were unable to assign it to any of the previously published brown bear mitogenome clades. A subsequent analysis of published mtDNA control region sequences, which included sequences of extinct clades from other geographic regions, assigned the ancient Yakutian bear to the extinct clade 3c; a clade previously identified from Late Quaternary specimens from Eastern Beringia and Northern Spain. Our analyses of stable isotopes showed relatively high δ[15]N values in the Pleistocene Yakutian brown bears, suggesting a more carnivorous diet than contemporary brown bears from Eastern Beringia.}, }
@article {pmid30862131, year = {2019}, author = {Chyleński, M and Ehler, E and Somel, M and Yaka, R and Krzewińska, M and Dabert, M and Juras, A and Marciniak, A}, title = {Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities.}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, pmid = {30862131}, issn = {2073-4425}, mesh = {*DNA, Ancient ; Evolution, Molecular ; *Genome, Mitochondrial ; Humans ; *Maternal Inheritance ; *Pedigree ; Turkey ; }, abstract = {Çatalhöyük is one of the most widely recognized and extensively researched Neolithic settlements. The site has been used to discuss a wide range of aspects associated with the spread of the Neolithic lifestyle and the social organization of Neolithic societies. Here, we address both topics using newly generated mitochondrial genomes, obtained by direct sequencing and capture-based enrichment of genomic libraries, for a group of individuals buried under a cluster of neighboring houses from the classical layer of the site's occupation. Our data suggests a lack of maternal kinship between individuals interred under the floors of Çatalhöyük buildings. The findings could potentially be explained either by a high variability of maternal lineages within a larger kin group, or alternatively, an intentional selection of individuals for burial based on factors other than biological kinship. Our population analyses shows that Neolithic Central Anatolian groups, including Çatalhöyük, share the closest affinity with the population from the Marmara Region and are, in contrast, set further apart from the Levantine populations. Our findings support the hypothesis about the emergence and the direction of spread of the Neolithic within Anatolian Peninsula and beyond, emphasizing a significant role of Central Anatolia in this process.}, }
@article {pmid30848092, year = {2020}, author = {van der Valk, T and Vezzi, F and Ormestad, M and Dalén, L and Guschanski, K}, title = {Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.}, journal = {Molecular ecology resources}, volume = {20}, number = {5}, pages = {1171-1181}, doi = {10.1111/1755-0998.13009}, pmid = {30848092}, issn = {1755-0998}, support = {//Jan L&#xf6;fqvist Endowments of the Royal Physiographic Society of Lund/ ; 2015-676//Svenska Forskningsr&#xe5;det Formas/ ; 2016-00835//Svenska Forskningsr&#xe5;det Formas/ ; //Science for Life Laboratory/ ; //Knut and Alice Wallenberg Foundation/ ; //National Genomics Infrastructure funded by the Swedish Research Council/ ; //Uppsala Multidisciplinary Center for Advanced Computational Science/ ; }, mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic ; *DNA, Ancient ; Gorilla gorilla/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Sequence Analysis, DNA/methods ; }, abstract = {The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low-quantity and low-quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100-year old museum-preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample-specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.}, }
@article {pmid30842617, year = {2019}, author = {Pinhasi, R and Fernandes, DM and Sirak, K and Cheronet, O}, title = {Isolating the human cochlea to generate bone powder for ancient DNA analysis.}, journal = {Nature protocols}, volume = {14}, number = {4}, pages = {1194-1205}, pmid = {30842617}, issn = {1750-2799}, mesh = {Cochlea/anatomy &amp; histology/*chemistry ; DNA, Ancient/*analysis/isolation &amp; purification ; Gene Library ; History, Ancient ; Humans ; Liquid-Liquid Extraction/*methods ; Petrous Bone/anatomy &amp; histology/*chemistry ; Powders ; Sequence Analysis, DNA/methods ; }, abstract = {The cortical bone that forms the structure of the cochlea, part of the osseous labyrinth of the inner ear, is now one of the most frequently used skeletal elements in analyses of human ancient DNA. However, there is currently no published, standardized method for its sampling. This protocol describes the preparation of bone powder from the cochlea of fragmented skulls in which the petrous pyramid of the temporal bone is accessible. Using a systematic process of bone removal based on distinct anatomical landmarks and the identification of relevant morphological features, a petrous pyramid is cleaned with a sandblaster, and the cochlea is located, isolated, and reduced to a homogeneous bone powder. All steps are carried out in dedicated ancient DNA facilities, thus reducing the introduction of contamination. This protocol requires an understanding of ancient DNA clean-room procedures and basic knowledge of petrous pyramid anatomy. In 50-65 min, it results in bone powder with endogenous DNA yields that can exceed those from teeth and other bones by up to two orders of magnitude. Compared with drilling methods, this method facilitates a more precise targeting of the cochlea, allows the user to visually inspect the cochlea and remove any residual sediment before the generation of bone powder, and confines the damage to the inner ear region and surface of the petrous portion of fragmentary crania.}, }
@article {pmid30840642, year = {2019}, author = {Prieto, G and Verano, JW and Goepfert, N and Kennett, D and Quilter, J and LeBlanc, S and Fehren-Schmitz, L and Forst, J and Lund, M and Dement, B and Dufour, E and Tombret, O and Calmon, M and Gadison, D and Tschinkel, K}, title = {A mass sacrifice of children and camelids at the Huanchaquito-Las Llamas site, Moche Valley, Peru.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0211691}, pmid = {30840642}, issn = {1932-6203}, mesh = {Animals ; Archaeology/methods ; Artifacts ; Camelids, New World/*physiology ; Carbon/chemistry ; Ceremonial Behavior ; Child ; Environment ; Female ; Humans ; Male ; Nitrogen/chemistry ; Peru ; Radiometric Dating/methods ; }, abstract = {Here we report the results of excavation and interdisciplinary study of the largest child and camelid sacrifice known from the New World. Stratigraphy, associated artifacts, and radiocarbon dating indicate that it was a single mass killing of more than 140 children and over 200 camelids directed by the Chimú state, c. AD 1450. Preliminary DNA analysis indicates that both boys and girls were chosen for sacrifice. Variability in forms of cranial modification (head shaping) and stable isotope analysis of carbon and nitrogen suggest that the children were a heterogeneous sample drawn from multiple regions and ethnic groups throughout the Chimú state. The Huanchaquito-Las Llamas mass sacrifice opens a new window on a previously unknown sacrificial ritual from fifteenth century northern coastal Peru. While the motivation for such a massive sacrifice is a subject for further research, there is archaeological evidence that it was associated with a climatic event (heavy rainfall and flooding) that could have impacted the economic, political and ideological stability of one of the most powerful states in the New World during the fifteenth century A.D.}, }
@article {pmid30828717, year = {2019}, author = {Signore, AV and Paijmans, JLA and Hofreiter, M and Fago, A and Weber, RE and Springer, MS and Campbell, KL}, title = {Emergence of a Chimeric Globin Pseudogene and Increased Hemoglobin Oxygen Affinity Underlie the Evolution of Aquatic Specializations in Sirenia.}, journal = {Molecular biology and evolution}, volume = {36}, number = {6}, pages = {1134-1147}, pmid = {30828717}, issn = {1537-1719}, mesh = {*Adaptation, Biological ; Animals ; *Evolution, Molecular ; Gene Conversion ; Globins/*genetics/metabolism ; Male ; Multigene Family ; Mutant Chimeric Proteins ; Oxygen/metabolism ; *Pseudogenes ; Selection, Genetic ; Sirenia/*genetics/metabolism ; }, abstract = {As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller's sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb-O2 affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb-O2 affinity in (sub)Arctic Steller's sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.}, }
@article {pmid30805020, year = {2019}, author = {Ballard, JWO and Wilson, LAB}, title = {The Australian dingo: untamed or feral?.}, journal = {Frontiers in zoology}, volume = {16}, number = {}, pages = {2}, pmid = {30805020}, issn = {1742-9994}, abstract = {BACKGROUND: The Australian dingo continues to cause debate amongst Aboriginal people, pastoralists, scientists and the government in Australia. A lingering controversy is whether the dingo has been tamed and has now reverted to its ancestral wild state or whether its ancestors were domesticated and it now resides on the continent as a feral dog. The goal of this article is to place the discussion onto a theoretical framework, highlight what is currently known about dingo origins and taxonomy and then make a series of experimentally testable organismal, cellular and biochemical predictions that we propose can focus future research.<br><br>DISCUSSION: We consider a canid that has been unconsciously selected as a tamed animal and the endpoint of methodical or what we now call artificial selection as a domesticated animal. We consider wild animals that were formerly tamed as untamed and those wild animals that were formerly domesticated as feralized. Untamed canids are predicted to be marked by a signature of unconscious selection whereas feral animals are hypothesized to be marked by signatures of both unconscious and artificial selection. First, we review the movement of dingo ancestors into Australia. We then discuss how differences between taming and domestication may influence the organismal traits of skull morphometrics, brain and size, seasonal breeding, and sociability. Finally, we consider cellular and molecular level traits including hypotheses concerning the phylogenetic position of dingoes, metabolic genes that appear to be under positive selection and the potential for micronutrient compensation by the gut microbiome.<br><br>CONCLUSIONS: Western Australian Government policy is currently being revised to allow the widespread killing of the Australian dingo. These policies are based on an incomplete understanding of the evolutionary history of the canid and assume the dingo is feralized. However, accumulated evidence does not definitively show that the dingo was ever domesticated and additional focused research is required. We suggest that incorporating ancient DNA data into the debate concerning dingo origins will be pivotal to understanding the evolutionary history of the canid. Further, we advocate that future morphological, behavioural and genetic studies should focus on including genetically pure Alpine and Desert dingoes and not dingo-dog hybrids. Finally, we propose that future studies critically examine genes under selection in the dingo and employ the genome from a wild canid for comparison.}, }
@article {pmid30804909, year = {2019}, author = {Dick, JM and Yu, M and Tan, J and Lu, A}, title = {Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {120}, pmid = {30804909}, issn = {1664-302X}, abstract = {There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator.}, }
@article {pmid30798090, year = {2019}, author = {Mao, Y and Satoh, N}, title = {A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora.}, journal = {iScience}, volume = {13}, number = {}, pages = {20-32}, pmid = {30798090}, issn = {2589-0042}, abstract = {Whole-genome duplication (WGD) has been recognized as a significant evolutionary force in the origin and diversification of multiple organisms. Acropora, a speciose reef-building coral genus, is suspected to have originated by polyploidy. Yet, there is no genetic evidence to support this hypothesis. Using comprehensive phylogenomic and comparative genomic approaches, we analyzed six Acroporid genomes and found that a WGD event likely occurred ∼31 million years ago in the most recent common ancestor of Acropora, concurrent with a worldwide coral extinction. We found that duplicated genes were highly enriched in gene regulation functions, including those of stress responses. The functional clusters of duplicated genes are related to the divergence of gene expression patterns during development. Some proteinaceous toxins were generated by WGD in Acropora compared with other cnidarian species. Collectively, this study provides evidence for an ancient WGD event in corals, which helps explain the origin and diversification of Acropora.}, }
@article {pmid30793442, year = {2019}, author = {Shaw, JLA and Weyrich, LS and Hallegraeff, G and Cooper, A}, title = {Retrospective eDNA assessment of potentially harmful algae in historical ship ballast tank and marine port sediments.}, journal = {Molecular ecology}, volume = {28}, number = {10}, pages = {2476-2485}, doi = {10.1111/mec.15055}, pmid = {30793442}, issn = {1365-294X}, mesh = {Aquaculture ; Australia ; *Climate Change ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Geologic Sediments/microbiology ; *Harmful Algal Bloom ; Microalgae/*growth &amp; development/pathogenicity ; Retrospective Studies ; Ships ; }, abstract = {Microalgal bloom events can cause major ecosystem disturbances, devastate local marine economies, and endanger public health. Therefore, detecting and monitoring harmful microalgal taxa is essential to ensure effective risk management in waterways used for fisheries, aquaculture, recreational activity, and shipping. To fully understand the current status and future direction of algal bloom distributions, we need to know how populations and ecosystems have changed over time. This baseline knowledge is critical for predicting ecosystem responses to future anthropogenic change and will assist in the future management of coastal ecosystems. We explore a NGS metabarcoding approach to rapidly identify potentially harmful microalgal taxa in 63 historic and modern Australian marine port and ballast tank sediment samples. The results provide a record of past microalgal distribution and important baseline data that can be used to assess the efficacy of shipping guidelines, nutrient pollution mitigation, and predict the impact of climate change. Critically, eDNA surveys of archived sediments were able to detect harmful algal taxa that do not produce microscopic fossils, such as Chattonella, Heterosigma, Karlodinium, and Noctiluca. Our data suggest a potential increase in Australian harmful microalgal taxa over the past 30 years, and confirm ship ballast tanks as key dispersal vectors. These molecular mapping tools will assist in the creation of policies aimed at reducing the global increase and spread of harmful algal taxa and help prevent economic and public-health problems caused by harmful algal blooms.}, }
@article {pmid30773819, year = {2019}, author = {Grealy, A and Bunce, M and Holleley, CE}, title = {Avian mitochondrial genomes retrieved from museum eggshell.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {1052-1062}, doi = {10.1111/1755-0998.13007}, pmid = {30773819}, issn = {1755-0998}, support = {DP160104473//Australian Research Council/ ; DP180100021//Australian Research Council/ ; //CSIRO Strategic Investment Funds (NCRA)/ ; }, mesh = {Animals ; Australia ; *Birds ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; Egg Shell/*chemistry ; *Genome, Mitochondrial ; Museums ; Sequence Analysis, DNA ; }, abstract = {Avian eggshell is a bio-ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historical populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more-diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40-60-year-old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterize the yield and quality of such DNA. In doing so, we describe the first protocol for successful extraction of intracrystalline DNA from neognath eggshells, with the view to unlocking the potential of vast museum egg collections for genetic research. We were able to retrieve DNA fragments over 200 bp in length from 10 mg of eggshell powder from all three specimens, and demonstrate that expanding the existing blow-hole can allow sufficient material to be collected for DNA extraction while minimizing damage to the appearance and structural integrity of the egg. Furthermore, we were able to reconstruct near-complete mitochondrial genomes at a coverage of 40-83X through shotgun sequencing of these extracts on three NextSeq lanes. Given the current extinction and extirpation rates of many avian species world-wide, genetic data from eggshell could provide a rapid and cost-effective approach to examining temporal changes in avian diversity, which is not only becoming crucial for conservation management, but also serve to deepen our understanding of genome-wide evolutionary processes.}, }
@article {pmid30753886, year = {2019}, author = {Knapp, M and Thomas, JE and Haile, J and Prost, S and Ho, SYW and Dussex, N and Cameron-Christie, S and Kardailsky, O and Barnett, R and Bunce, M and Gilbert, MTP and Scofield, RP}, title = {Mitogenomic evidence of close relationships between New Zealand's extinct giant raptors and small-sized Australian sister-taxa.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {122-128}, doi = {10.1016/j.ympev.2019.01.026}, pmid = {30753886}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Body Size/*genetics ; *Extinction, Biological ; *Genome, Mitochondrial ; New Zealand ; Phylogeny ; Raptors/*anatomy &amp; histology/*genetics ; }, abstract = {Prior to human arrival in the 13th century, two large birds of prey were the top predators in New Zealand. In the absence of non-volant mammals, the extinct Haast's eagle (Hieraaetus moorei), the largest eagle in the world, and the extinct Eyles' harrier (Circus teauteensis) the largest harrier in the world, had filled ecological niches that are on other landmasses occupied by animals such as large cats or canines. The evolutionary and biogeographic history of these island giants has long been a mystery. Here we reconstruct the origin and evolution of New Zealand's giant raptors using complete mitochondrial genome data. We show that both Eyles' harrier and Haast's eagle diverged from much smaller, open land adapted Australasian relatives in the late Pliocene to early Pleistocene. These events coincided with the development of open habitat in the previously densely forested islands of New Zealand. Our study provides evidence of rapid evolution of island gigantism in New Zealand's extinct birds of prey. Early Pleistocene climate and environmental changes were likely to have triggered the establishment of Australian raptors into New Zealand. Our results shed light on the evolution of two of the most impressive cases of island gigantism in the world.}, }
@article {pmid30744646, year = {2019}, author = {Pont, C and Wagner, S and Kremer, A and Orlando, L and Plomion, C and Salse, J}, title = {Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {29}, pmid = {30744646}, issn = {1474-760X}, mesh = {DNA, Ancient/*analysis ; DNA, Plant/analysis ; *Evolution, Molecular ; *Genome, Plant ; Genomics/*methods ; Paleontology ; }, abstract = {How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.}, }
@article {pmid30742038, year = {2019}, author = {Tennant, RK and Lux, TM and Sambles, CM and Kuhn, NJ and Petticrew, EL and Oldfield, R and Parker, DA and Hatton, J and Moore, KA and Lee, R and Turney, CSM and Jones, RT and Love, J}, title = {Palaeogenomics of the Hydrocarbon Producing Microalga Botryococcus braunii.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1776}, pmid = {30742038}, issn = {2045-2322}, support = {WT097835MF/WT_/Wellcome Trust/United Kingdom ; BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/M008924/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {DNA, Plant/genetics ; *Fossils ; *Genome, Plant ; Hydrocarbons/*metabolism ; Microalgae/*genetics/*metabolism ; }, abstract = {Botryococcus braunii is a colonial microalga that appears early in the fossil record and is a sensitive proxy of environmental and hydroclimatic conditions. Palaeozoic Botryococcus fossils which contribute up to 90% of oil shales and approximately 1% of crude oil, co-localise with diagnostic geolipids from the degradation of source-signature hydrocarbons. However more recent Holocene sediments demonstrate no such association. Consequently, Botryococcus are identified in younger sediments by morphology alone, where potential misclassifications could lead to inaccurate paleoenvironmental reconstructions. Here we show that a combination of flow cytometry and ancient DNA (aDNA) sequencing can unambiguously identify Botryococcus microfossils in Holocene sediments with hitherto unparalleled accuracy and rapidity. The application of aDNA sequencing to microfossils offers a far-reaching opportunity for understanding environmental change in the recent geological record. When allied with other high-resolution palaeoenvironmental information such as aDNA sequencing of humans and megafauna, aDNA from microfossils may allow a deeper and more precise understanding of past environments, ecologies and migrations.}, }
@article {pmid30723959, year = {2019}, author = {Del Carmen Gomez Cabrera, M and Young, JM and Roff, G and Staples, T and Ortiz, JC and Pandolfi, JM and Cooper, A}, title = {Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA.}, journal = {Molecular ecology}, volume = {28}, number = {10}, pages = {2636-2652}, doi = {10.1111/mec.15038}, pmid = {30723959}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*genetics ; *Biodiversity ; *Coral Reefs ; DNA Barcoding, Taxonomic ; DNA, Ancient/*analysis ; Ecology ; Ecosystem ; Humans ; Paleontology ; RNA, Ribosomal, 18S/genetics ; Seaweed/classification/genetics ; }, abstract = {Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high-throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft-bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft-bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales.}, }
@article {pmid30722030, year = {2019}, author = {Cole, TL and Ksepka, DT and Mitchell, KJ and Tennyson, AJD and Thomas, DB and Pan, H and Zhang, G and Rawlence, NJ and Wood, JR and Bover, P and Bouzat, JL and Cooper, A and Fiddaman, SR and Hart, T and Miller, G and Ryan, PG and Shepherd, LD and Wilmshurst, JM and Waters, JM}, title = {Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation.}, journal = {Molecular biology and evolution}, volume = {36}, number = {4}, pages = {784-797}, doi = {10.1093/molbev/msz017}, pmid = {30722030}, issn = {1537-1719}, mesh = {Animals ; Fossils ; *Genetic Speciation ; *Genome, Mitochondrial ; *Islands ; New Zealand ; Phylogeography ; Spheniscidae/*genetics ; }, abstract = {The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand's Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami diverged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the diversification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere's isolated archipelagos.}, }
@article {pmid30712776, year = {2019}, author = {Costedoat, C and Adalian, P and Bouzaid, E and Martinet, A and Vanrell, L and von Gartzen, L and Castellano, P and Signoli, M and Tzortzis, S and Stevanovitch, A}, title = {When a lost "Petit Prince" meets Antoine de Saint Exupéry: An anthropological case report.}, journal = {Forensic science international}, volume = {296}, number = {}, pages = {145-152}, doi = {10.1016/j.forsciint.2019.01.015}, pmid = {30712776}, issn = {1872-6283}, mesh = {Age Determination by Skeleton/methods ; Age Determination by Teeth/methods ; Bone and Bones/*chemistry/*pathology ; DNA/isolation &amp; purification ; *DNA Fingerprinting ; DNA, Mitochondrial/genetics ; *Forensic Anthropology ; France ; History, 20th Century ; Humans ; Male ; Microsatellite Repeats ; Military Personnel ; *Pilots ; Polymerase Chain Reaction ; Radiometric Dating ; Sex Determination by Skeleton/methods ; World War II ; }, abstract = {This case study reports the anthropological analysis of bones remains discovered on Riou Island (Marseille, France) and the story of two World War II fighter pilots. The discovery of bones on "The Fountain of the Greeks" square on Riou Island occurred in the 1960's and a first anthropological study described a 35-year-old man, about 1.77 m tall, buried since an estimated period between the 13th and 16th centuries. The case was "closed" and the bones were considered as isolated archaeological remains. Few years later, near the coasts of Riou Island, parts of two planes were discovered. One was from of a German Messerschmitt Bf 109 F-4 of the Luftwaffe piloted by Prince Alexis fürst zu Bentheim und Steinfurt, and the other from a French P-38 Lightning F-5 B piloted by Antoine de Saint-Exupery. Therefore, the identification of the skeletal remains mentioned above was then thought to be perhaps one of the two World War II pilots. In this particular context we performed forensic and molecular biology analyses to resolve this identification.}, }
@article {pmid30706600, year = {2019}, author = {Díaz, FP and Latorre, C and Carrasco-Puga, G and Wood, JR and Wilmshurst, JM and Soto, DC and Cole, TL and Gutiérrez, RA}, title = {Multiscale climate change impacts on plant diversity in the Atacama Desert.}, journal = {Global change biology}, volume = {25}, number = {5}, pages = {1733-1745}, doi = {10.1111/gcb.14583}, pmid = {30706600}, issn = {1365-2486}, mesh = {*Biodiversity ; Chile ; *Climate Change ; DNA, Ancient/analysis ; *Desert Climate ; Ecosystem ; Fossils ; Plant Dispersal ; *Plants/classification/genetics ; Population Dynamics ; }, abstract = {Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo-informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future.}, }
@article {pmid30700787, year = {2019}, author = {Rusu, I and Modi, A and Radu, C and Mircea, C and Vulpoi, A and Dobrinescu, C and Bodolică, V and Potârniche, T and Popescu, O and Caramelli, D and Kelemen, B}, title = {Mitochondrial ancestry of medieval individuals carelessly interred in a multiple burial from southeastern Romania.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {961}, pmid = {30700787}, issn = {2045-2322}, mesh = {Archaeology ; Bone and Bones/metabolism ; Burial/*history ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; Genome, Human ; Genome, Mitochondrial ; Geography ; Haplotypes/genetics ; History, Medieval ; Humans ; Male ; Mitochondria/*genetics ; *Phylogeny ; Romania ; }, abstract = {The historical province of Dobruja, located in southeastern Romania, has experienced intense human population movement, invasions, and conflictual episodes during the Middle Ages, being an important intersection point between Asia and Europe. The most informative source of maternal population histories is the complete mitochondrial genome of archaeological specimens, but currently, there is insufficient ancient DNA data available for the medieval period in this geographical region to complement the archaeological findings. In this study, we reconstructed, by using Next Generation Sequencing, the entire mitochondrial genomes (mitogenomes) of six medieval individuals neglectfully buried in a multiple burial from Capidava necropolis (Dobruja), some presenting signs of a violent death. Six distinct maternal lineages (H11a1, U4d2, J1c15, U6a1a1, T2b, and N1a3a) with different phylogenetic background were identified, pointing out the heterogeneous genetic aspect of the analyzed medieval group. Using population genetic analysis based on high-resolution mitochondrial data, we inferred the genetic affinities of the available medieval dataset from Capidava to other ancient Eurasian populations. The genetic data were integrated with the archaeological and anthropological information in order to sketch a small, local piece of the mosaic that is the image of medieval European population history.}, }
@article {pmid30682121, year = {2019}, author = {Slepchenko, SM and Gusev, AV and Svyatova, EO and Hong, JH and Oh, CS and Lim, DS and Shin, DH}, title = {Medieval mummies of Zeleny Yar burial ground in the Arctic Zone of Western Siberia.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210718}, pmid = {30682121}, issn = {1932-6203}, mesh = {Arctic Regions ; Burial ; Cemeteries ; DNA, Mitochondrial/genetics ; Haplotypes ; Humans ; *Mummies ; Siberia ; }, abstract = {Notwithstanding the pioneering achievements of studies on arctic mummies in Siberia, there are insufficient data for any comprehensive understanding of the bio-cultural details of medieval people living in the region. In the Western Siberian arctic, permafrost mummies have been found in 12th to 13th century graves located in the Zeleny Yar (Z-Y) burial ground (66°19'4.54"С; 67°21'13.54"В). In 2013-2016, we were fortunate to be able to excavate that cemetery, locating a total of 47 burials, including cases of mummification. Some of these mummies had been wrapped in a multi-layered birch-bark cocoon. After removal of the cocoon, we conducted interdisciplinary studies using various scientific techniques. Gross anatomical examination and CT radiography showed that the internal organs were still well preserved inside the body cavities. Under light and electron microscopy, the histological findings were very similar to those for naturally mummified specimens discovered in other countries. Ancient DNA analysis showed that the Z-Y mummies' mtDNA haplotypes belong to five different haplogroups, namely U5a (#34), H3ao (#53), D (#67-1), U4b1b1 (#67-2), and D4j8 (#68), which distinguish them for their unique combination of Western- and Eastern Siberia-specific mtDNA haplogroups. Our interdisciplinary study obtained fundamental information that will form the foundation of successful future investigations on medieval mummies found in the Western Siberian arctic.}, }
@article {pmid30633908, year = {2019}, author = {O'Connor, TD}, title = {Native American Genomic Diversity through Ancient DNA.}, journal = {Cell}, volume = {176}, number = {1-2}, pages = {405-406}, doi = {10.1016/j.cell.2018.12.033}, pmid = {30633908}, issn = {1097-4172}, }
@article {pmid30628076, year = {2019}, author = {Tackney, J and Jensen, AM and Kisielinski, C and O'Rourke, DH}, title = {Molecular analysis of an ancient Thule population at Nuvuk, Point Barrow, Alaska.}, journal = {American journal of physical anthropology}, volume = {168}, number = {2}, pages = {303-317}, doi = {10.1002/ajpa.23746}, pmid = {30628076}, issn = {1096-8644}, support = {OPP-0732846//Office of Polar Programs/International ; OPP-0732857//Office of Polar Programs/International ; OPP-0637246//Office of Polar Programs/International ; OPP-0535356//Office of Polar Programs/International ; OPP-1460387//Office of Polar Programs/International ; OPP-0820790//Office of Polar Programs/International ; OPP-0726253//Office of Polar Programs/International ; OPP-0820790//National Science Foundation (NSF)/International ; ARC-0726253//National Science Foundation (NSF)/International ; OPP-1460387//National Science Foundation (NSF)/International ; OPP-0535356//National Science Foundation (NSF)/International ; OPP-0637246//National Science Foundation (NSF)/International ; OPP-0732857//International Polar Year grant/International ; OPP-0732846//International Polar Year grant/International ; }, mesh = {Alaska ; Anthropology, Physical ; Arctic Regions ; DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; Haplotypes/genetics ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, Medieval ; Humans ; Inuit/*genetics/*history ; Phylogeography ; }, abstract = {OBJECTIVES: The North American archaeological record supports a Holocene origin of Arctic Indigenous peoples. Although the Paleo-Inuit were present for millennia, archaeological and genetic studies suggest that modern peoples descend from a second, more recent tradition known as the Neo-Inuit. Origins of the Neo-Inuit and their relations to the earlier and later Indigenous peoples are an area of active study. Here, we genetically analyze the maternal lineages present at Nuvuk, once the northernmost community in Alaska and located in a region identified as a possible origin point of the Neo-Inuit Thule. The cemetery at Nuvuk contains human remains representing a nearly one thousand year uninterrupted occupation from early Thule to post-contact Iñupiat.<br><br>MATERIALS AND METHODS: We selected 44 individuals from Nuvuk with calibrated dates between 981 AD and 1885 AD for molecular analysis. We amplified and sequenced the hypervariable segment I of the mitogenome. We compared the Nuvuk data with previously published sequences from 68 modern and ancient communities from across Asia and North America. Phylogeographic analyses suggest possible scenarios of Holocene Arctic and sub-Arctic population movements.<br><br>RESULTS: We successfully retrieved sequence data from 39 individuals. Haplogroup frequencies in Nuvuk were typed as 66.7% A2b1, 25.6% A2a, and 7.7% D4b1a2a1a. These results suggest that the population at Nuvuk was closest to the ancient Thule and modern Inuit of Canada, and to the Siberian Naukan people. We confirm that haplogroups A2a, A2b1, D2a, and D4b1a2a1a appear at high frequency in Arctic and sub-Arctic populations of North America and Chukotka. Sister clades D2b and D4b1a2a1b are present in Asian and Eastern European populations.<br><br>DISCUSSION: The ancient mitochondrial sequences from Nuvuk confirm the link between the North Slope and the Thule who later spread east, and the maternal discontinuity between the Neo-Inuit and Paleo-Inuit. We suggest haplogroups A2a, A2b, and D4b1a2a1a are linked to the ancestors of the Thule in eastern Beringia, whereas the D2 and D4b1a2a1 clades appear to have Asian Holocene origins. Further Siberian and Alaskan genomes are necessary to clarify these population migrations beyond a simple two-wave scenario of Neo-Inuit and Paleo-Inuit.}, }
@article {pmid30622634, year = {2019}, author = {Wales, N and Akman, M and Watson, RHB and Sánchez Barreiro, F and Smith, BD and Gremillion, KJ and Gilbert, MTP and Blackman, BK}, title = {Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement.}, journal = {Evolutionary applications}, volume = {12}, number = {1}, pages = {38-53}, pmid = {30622634}, issn = {1752-4571}, abstract = {Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in-depth gene-based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species.}, }
@article {pmid30586168, year = {2019}, author = {Ziesemer, KA and Ramos-Madrigal, J and Mann, AE and Brandt, BW and Sankaranarayanan, K and Ozga, AT and Hoogland, M and Hofman, CA and Salazar-García, DC and Frohlich, B and Milner, GR and Stone, AC and Aldenderfer, M and Lewis, CM and Hofman, CL and Warinner, C and Schroeder, H}, title = {The efficacy of whole human genome capture on ancient dental calculus and dentin.}, journal = {American journal of physical anthropology}, volume = {168}, number = {3}, pages = {496-509}, pmid = {30586168}, issn = {1096-8644}, support = {319209//H2020 European Research Council/International ; 649307DK-TAF 5662//Horizon 2020 Framework Programme/International ; BCS 1516633//National Science Foundation/International ; BCS&#x2010;1528698//National Science Foundation/International ; }, mesh = {Archaeology ; *DNA, Ancient/analysis/isolation &amp; purification ; Dental Calculus/*chemistry/microbiology ; Dentin/*chemistry ; Female ; Genome, Human/*genetics ; Genomics/*methods ; Humans ; Male ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.<br><br>MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing.<br><br>RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction.<br><br>DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.}, }
@article {pmid30554877, year = {2019}, author = {Mohni, KN and Wessel, SR and Zhao, R and Wojciechowski, AC and Luzwick, JW and Layden, H and Eichman, BF and Thompson, PS and Mehta, KPM and Cortez, D}, title = {HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA.}, journal = {Cell}, volume = {176}, number = {1-2}, pages = {144-153.e13}, pmid = {30554877}, issn = {1097-4172}, support = {T32 CA009582/CA/NCI NIH HHS/United States ; P01 CA092584/CA/NCI NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; F32 GM126646/GM/NIGMS NIH HHS/United States ; F30 CA228242/CA/NCI NIH HHS/United States ; R01 GM116616/GM/NIGMS NIH HHS/United States ; }, mesh = {5-Methylcytosine/*analogs &amp; derivatives/metabolism ; Apurinic Acid/metabolism ; DNA/metabolism ; DNA Damage/physiology ; DNA Repair/*physiology ; DNA Replication/physiology ; DNA, Single-Stranded/metabolism/*physiology ; DNA-Binding Proteins/genetics/metabolism ; Endonucleases ; Escherichia coli/metabolism ; Polynucleotides/metabolism ; Proliferating Cell Nuclear Antigen/metabolism ; }, abstract = {Abasic sites are one of the most common DNA lesions. All known abasic site repair mechanisms operate only when the damage is in double-stranded DNA. Here, we report the discovery of 5-hydroxymethylcytosine (5hmC) binding, ESC-specific (HMCES) as a sensor of abasic sites in single-stranded DNA. HMCES acts at replication forks, binds PCNA and single-stranded DNA, and generates a DNA-protein crosslink to shield abasic sites from error-prone processing. This unusual HMCES DNA-protein crosslink intermediate is resolved by proteasome-mediated degradation. Acting as a suicide enzyme, HMCES prevents translesion DNA synthesis and the action of endonucleases that would otherwise generate mutations and double-strand breaks. HMCES is evolutionarily conserved in all domains of life, and its biochemical properties are shared with its E. coli ortholog. Thus, HMCES is an ancient DNA lesion recognition protein that preserves genome integrity by promoting error-free repair of abasic sites in single-stranded DNA.}, }
@article {pmid30550639, year = {2019}, author = {Winters, M and Monroe, C and Barta, JL and Kemp, BM}, title = {Evaluating the Efficiency of Primer Extension Capture as a Method to Enrich DNA Extractions.}, journal = {Journal of forensic sciences}, volume = {64}, number = {4}, pages = {1145-1151}, doi = {10.1111/1556-4029.13973}, pmid = {30550639}, issn = {1556-4029}, support = {2011-DN-BX- K549//National Institute of Justice/ ; //Office of Justice Programs/ ; //U.S. Department of Justice/ ; }, mesh = {DNA/*isolation &amp; purification ; *DNA Primers ; Forensic Genetics/methods ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; Streptavidin/chemistry ; }, abstract = {In this study, we sought to document the efficiency of primer extension capture (PEC) as a method to enrich DNA eluates of targeted DNA molecules and remove nontarget molecules from pools containing both. Efficiency of the method was estimated by comparing number of "copies in" to "copies out" by quantitative polymerase chain reaction. PEC retention of DNA targets ranging 109-288 base pairs (bps) in length was 15.88-2.14% (i.e., loss of 84.12-97.86% of target molecules). Experimental modifications of the PEC method resulted in no significant improvements. However, the benefit of PEC was revealed in its ability to remove most nontarget DNA molecules (99.99%). We also discovered that many (56.69%) of the target molecules are "lost" prior to their immobilization on the streptavidin-coated beads. These estimates of methodological efficiency are directly comparable to previous ones observed following "fishing" for DNA, an alternative method for DNA enrichment.}, }
@article {pmid30545160, year = {2018}, author = {Esposito, U and Das, R and Syed, S and Pirooznia, M and Elhaik, E}, title = {Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians.}, journal = {Genes}, volume = {9}, number = {12}, pages = {}, pmid = {30545160}, issn = {2073-4425}, support = {MC_PC_14115/MRC_/Medical Research Council/United Kingdom ; MR/R025126/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, thereby, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA, provided that the high missingness rates in ancient-and oftentimes haploid-DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories.}, }
@article {pmid30528431, year = {2019}, author = {Rascovan, N and Sjögren, KG and Kristiansen, K and Nielsen, R and Willerslev, E and Desnues, C and Rasmussen, S}, title = {Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline.}, journal = {Cell}, volume = {176}, number = {1-2}, pages = {295-305.e10}, doi = {10.1016/j.cell.2018.11.005}, pmid = {30528431}, issn = {1097-4172}, mesh = {Biological Evolution ; DNA, Bacterial/genetics ; Europe ; Genome, Bacterial ; History, Ancient ; Humans ; Pandemics ; Phylogeny ; Plague/*history ; Yersinia pestis/*classification/*pathogenicity ; }, abstract = {Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.}, }
@article {pmid30521562, year = {2018}, author = {Fischer, CE and Lefort, A and Pemonge, MH and Couture-Veschambre, C and Rottier, S and Deguilloux, MF}, title = {The multiple maternal legacy of the Late Iron Age group of Urville-Nacqueville (France, Normandy) documents a long-standing genetic contact zone in northwestern France.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207459}, pmid = {30521562}, issn = {1932-6203}, mesh = {Archaeology/methods ; DNA, Ancient/analysis ; DNA, Mitochondrial/analysis/*genetics ; Europe/ethnology ; France/ethnology ; Gene Pool ; Genetic Variation/genetics ; Genetics, Population/methods ; Genotype ; Haplotypes ; History, Ancient ; Humans ; United Kingdom ; White People/*genetics ; }, abstract = {The compilation of archaeological and genetic data for ancient European human groups has provided persuasive evidence for a complex series of migrations, population replacements and admixture until the Bronze Age. If the Bronze-to-Iron Age transition has been well documented archaeologically, ancient DNA (aDNA) remains rare for the latter period and does not precisely reflect the genetic diversity of European Celtic groups. In order to document the evolution of European communities, we analysed 45 individuals from the Late Iron Age (La Tène) Urville-Nacqueville necropolis in northwestern France, a region recognized as a major cultural contact zone between groups from both sides of the Channel. The characterization of 37 HVS-I mitochondrial sequences and 40 haplogroups provided the largest maternal gene pool yet recovered for the European Iron Age. First, descriptive analyses allowed us to demonstrate the presence of substantial amounts of steppe-related mitochondrial ancestry in the community, which is consistent with the expansion of Bell Beaker groups bearing an important steppe legacy in northwestern Europe at approximately 2500 BC. Second, maternal genetic affinities highlighted with Bronze Age groups from Great Britain and the Iberian Peninsula regions tends to support the idea that the continuous cultural exchanges documented archaeologically across the Channel and along the Atlantic coast (during and after the Bronze Age period) were accompanied by significant gene flow. Lastly, our results suggest a maternal genetic continuity between Bronze Age and Iron Age groups that would argue in favour of a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. The palaeogenetic data gathered for the Urville-Nacqueville group constitute an important step in the biological characterization of European Iron age groups. Clearly, more numerous and diachronic aDNA data are needed to fully understand the complex relationship between the cultural and biological evolution of groups from the period.}, }
@article {pmid30517116, year = {2018}, author = {Winkel, T and Aguirre, MG and Arizio, CM and Aschero, CA and Babot, MDP and Benoit, L and Burgarella, C and Costa-Tártara, S and Dubois, MP and Gay, L and Hocsman, S and Jullien, M and López-Campeny, SML and Manifesto, MM and Navascués, M and Oliszewski, N and Pintar, E and Zenboudji, S and Bertero, HD and Joffre, R}, title = {Discontinuities in quinoa biodiversity in the dry Andes: An 18-century perspective based on allelic genotyping.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207519}, pmid = {30517116}, issn = {1932-6203}, mesh = {Alleles ; Argentina ; Biodiversity ; Chenopodium quinoa/*genetics ; DNA, Ancient/analysis ; Gene Pool ; Genetic Variation/genetics ; Genotype ; Genotyping Techniques/history/*methods ; History, 18th Century ; Seeds ; }, abstract = {History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries-a time of agricultural intensification well before the Inka and Spanish conquests-and then between the 13th century and today-a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories.}, }
@article {pmid30514893, year = {2018}, author = {Zalloua, P and Collins, CJ and Gosling, A and Biagini, SA and Costa, B and Kardailsky, O and Nigro, L and Khalil, W and Calafell, F and Matisoo-Smith, E}, title = {Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17567}, pmid = {30514893}, issn = {2045-2322}, mesh = {Archaeology ; Black People/genetics/*history ; Body Remains ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Emigration and Immigration/*history ; Genetic Variation ; Genome, Mitochondrial/genetics ; History, Ancient ; Humans ; Male ; Phylogeography ; Spain ; White People/genetics/*history ; }, abstract = {Ibiza was permanently settled around the 7[th] century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4[th] century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island's modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated.}, }
@article {pmid30514813, year = {2019}, author = {Thompson, TQ and Bellinger, MR and O'Rourke, SM and Prince, DJ and Stevenson, AE and Rodrigues, AT and Sloat, MR and Speller, CF and Yang, DY and Butler, VL and Banks, MA and Miller, MR}, title = {Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {1}, pages = {177-186}, pmid = {30514813}, issn = {1091-6490}, mesh = {*Adaptation, Physiological/genetics ; Alleles ; Animal Migration ; Animals ; *Ecosystem ; Genetic Loci/genetics ; Genetic Variation/genetics ; Oregon ; *Salmon/genetics ; }, abstract = {Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.}, }
@article {pmid30498238, year = {2018}, author = {Epp, LS and Kruse, S and Kath, NJ and Stoof-Leichsenring, KR and Tiedemann, R and Pestryakova, LA and Herzschuh, U}, title = {Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17436}, pmid = {30498238}, issn = {2045-2322}, mesh = {Biodiversity ; *DNA, Mitochondrial ; Forests ; Geography ; *Haplotypes ; Larix/*genetics ; Mitochondria/*genetics ; Siberia ; Spatio-Temporal Analysis ; }, abstract = {Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.}, }
@article {pmid30481358, year = {2019}, author = {Cascini, M and Mitchell, KJ and Cooper, A and Phillips, MJ}, title = {Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence.}, journal = {Systematic biology}, volume = {68}, number = {3}, pages = {520-537}, doi = {10.1093/sysbio/syy080}, pmid = {30481358}, issn = {1076-836X}, mesh = {Animals ; Classification ; DNA/*genetics ; DNA, Ancient ; Fossils/*anatomy &amp; histology ; Macropodidae/anatomy &amp; histology/*classification/genetics ; *Phylogeny ; }, abstract = {Combined "total evidence" analysis of molecular and morphological data offers the opportunity to objectively merge fossils into the tree of life, and challenges the primacy of solely DNA based phylogenetic and dating inference, even among modern taxa. To investigate the relative utility of DNA, morphology, and total evidence for evolutionary inference, we sequenced the first near-complete mitochondrial genomes from extinct Australian megafauna: a 40-50 thousand year old giant short-faced kangaroo (Simosthenurus occidentalis) and giant wallaby (Protemnodon anak). We analyzed the ancient DNA and fossil data alongside comparable data from extant species to infer phylogeny, divergence times, and ancestral body mass among macropods (kangaroos and wallabies). Our results confirm a close relationship between Protemnodon and the iconic kangaroo genus complex "Macropus", and unite the giant Simothenurus with the hare-sized Lagostrophus fasciatus (banded hare-wallaby), suggesting that the latter is the closest living link to the once diverse sthenurine kangaroo radiation. We find that large body size evolved multiple times among kangaroos, coincident with expansion of open woodland habitats beginning in the Late Miocene. In addition, our results suggest that morphological data mislead macropod phylogeny reconstruction and in turn can distort total evidence estimation of divergence dates. However, a novel result with potentially broad application is that the accuracy and precision of reconstructing ancestral body mass was improved by tracing body mass on morphological branch lengths. This is likely due to positive allometric correlation between morphological and body size variation-a relationship that may be masked or even misleadingly inverted with the temporal or molecular branch lengths that typically underpin ancestral body size reconstruction. Our study supports complementary roles for DNA and morphology in evolutionary inference, and opens a new window into the evolution of Australia's unique marsupial fauna.}, }
@article {pmid30479341, year = {2018}, author = {Lamnidis, TC and Majander, K and Jeong, C and Salmela, E and Wessman, A and Moiseyev, V and Khartanovich, V and Balanovsky, O and Ongyerth, M and Weihmann, A and Sajantila, A and Kelso, J and Pääbo, S and Onkamo, P and Haak, W and Krause, J and Schiffels, S}, title = {Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5018}, pmid = {30479341}, issn = {2041-1723}, mesh = {Archaeology ; Female ; Finland ; *Genealogy and Heraldry ; Genetics, Population ; *Genome, Human ; Geography ; Humans ; Male ; Principal Component Analysis ; Siberia ; }, abstract = {European population history has been shaped by migrations of people, and their subsequent admixture. Recently, ancient DNA has brought new insights into European migration events linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland.}, }
@article {pmid30478041, year = {2018}, author = {Namouchi, A and Guellil, M and Kersten, O and Hänsch, S and Ottoni, C and Schmid, BV and Pacciani, E and Quaglia, L and Vermunt, M and Bauer, EL and Derrick, M and Jensen, A&#xd8; and Kacki, S and Cohn, SK and Stenseth, NC and Bramanti, B}, title = {Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {50}, pages = {E11790-E11797}, pmid = {30478041}, issn = {1091-6490}, mesh = {DNA, Bacterial/genetics/isolation &amp; purification ; Europe/epidemiology ; Evolution, Molecular ; Fossils/microbiology ; Genome, Bacterial ; History, Medieval ; Humans ; Pandemics/*history ; Phylogeny ; Plague/epidemiology/*history/microbiology ; Polymorphism, Single Nucleotide ; Time Factors ; Yersinia pestis/classification/*genetics ; }, abstract = {Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.}, }
@article {pmid30471018, year = {2019}, author = {Santi, R and Rizzolo, P and Pietragalla, M and Valentini, V and Zelli, V and Galassi, FM and Ottini, L and Nesi, G}, title = {The antiquity of hydrocephalus: the first full palaeo-neuropathological description.}, journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology}, volume = {40}, number = {6}, pages = {1315-1322}, pmid = {30471018}, issn = {1590-3478}, support = {no grant number//M&#xe4;xi Foundation/ ; }, mesh = {DNA, Ancient ; History, 19th Century ; Humans ; Hydrocephalus/diagnostic imaging/*genetics/history/*pathology ; Infant ; Italy ; Male ; *Models, Anatomic ; Museums ; Sculpture ; Waxes ; }, abstract = {The Pathology Museum of the University of Florence houses a rich collection of anatomical specimens and over a hundred waxworks portraying pathological conditions occurring in the nineteenth century, when the museum was established. Clinical and autopsy findings of these cases can still be retrieved from the original museum catalogue, offering a rare opportunity for retrospective palaeo-pathological diagnostics. We present a historical case of severe hydrocephalus backed by modern-day anthropological, radiological and molecular analyses conducted on the skeleton of an 18-month-old male infant deceased in 1831. Luigi Calamai (1796-1851), a wax craftsman of La Specola workshop in Florence, was commissioned to create a life-sized wax model of the child's head, neck and upper thorax. This artwork allows us to appreciate the cranial and facial alterations determined by 30 lb of cerebrospinal fluid (CSF) accumulated within the cerebral ventricular system. Based on the autopsy report, gross malformations of the neural tube, tumours and haemorrhage could be excluded. A molecular approach proved helpful in confirming sex. We present this case as the so-far most compelling case of hydrocephalus in palaeo-pathological research.}, }
@article {pmid30468917, year = {2019}, author = {Buckley, M and Lawless, C and Rybczynski, N}, title = {Collagen sequence analysis of fossil camels, Camelops and c.f. Paracamelus, from the Arctic and sub-Arctic of Plio-Pleistocene North America.}, journal = {Journal of proteomics}, volume = {194}, number = {}, pages = {218-225}, doi = {10.1016/j.jprot.2018.11.014}, pmid = {30468917}, issn = {1876-7737}, support = {BB/L002817/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Arctic Regions ; Camelids, New World/*genetics ; Collagen/*genetics ; *DNA, Ancient ; *Fossils ; North America ; *Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Proteomic analyses of ancient remains are increasing in number and offer great potential to recover phylogenetic information on extinct animals beyond the reach of ancient DNA, but limitations in proteomic techniques remain unclear. Here we carry out LC-MS/MS sequence analysis of a ~3.5 million year old giant camel specimen from Nunavut along with the younger Pleistocene remains of the Yukon giant camel (c.f. Paracamelus) and the western camel (Camelops hesternus) for comparison with complete sequences to both extant camels (Bactrian and Dromedary) and the alpaca. Although not complete (~75-80% sequence coverage), no amino acid sequence differences were confidently observed between the giant camels and the extant Dromedary, indicative of a closer relationship than that of the extant Bactrian lineage. However, multiple amino acid changes were observed for the western camel (Camelops) collagen sequence, placing it as a sister group to these members of the Camelini tribe consistent recent ancient DNA analyses. Although this supports a role for the sequencing of ancient collagen in the understanding of vertebrate evolution, these analyses highlight the limitations in phylogenetic reconstructions based on partial sequence data retrieved from proteomic analyses, particularly, the impact of omitting even only a single peptide on the resulting tree topology. The presence of other non-collagenous proteins, such as biglycan and PEDF, indicates a further resource for phylogenetic information, but none more promising than the degraded camel albumin seemingly observed in the Pliocene specimen. SIGNIFICANCE: As proteomics is becoming more frequently used in the study of ancient proteins, an emerging field known as 'palaeoproteomics' (or 'paleoproteomics'), understanding the limitations of the technique is essential. Here, through the study of the oldest undisputed collagen sequences obtained from proteomics, we confirm that some peptides following diagenetic modifications of tryptic sites are no longer matched with standard searches, but can be matched with Error Tolerant searches. We also demonstrate the ability to retrieve phylogenetic information consistent with that of ancient DNA methods, but that with the omission of only one or more key peptides, the inferred evolutionary relationships change. This is a significant finding for the field of palaeoproteomics implying a need for better understanding the particular composition of the partial sequences retrieved from proteomic analyses.}, }
@article {pmid30464240, year = {2018}, author = {Wood, JR and Díaz, FP and Latorre, C and Wilmshurst, JM and Burge, OR and Gutiérrez, RA}, title = {Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17208}, pmid = {30464240}, issn = {2045-2322}, support = {Core funding for Crown Research Institutes//Ministry of Business, Innovation and Employment (MBIE)/International ; Core funding to Crown Research Institutes//Ministry for Business Innovation and Employment (MBIE)/International ; }, mesh = {Animals ; Chile ; *Climate Change ; DNA, Ancient/*isolation &amp; purification ; DNA, Fungal/*isolation &amp; purification ; Desert Climate ; Feces/chemistry ; *Fossils ; Fungi/*classification/*genetics ; Metagenomics/methods ; Plant Diseases/*microbiology ; RNA, Ribosomal, 18S/genetics ; Rodentia ; }, abstract = {Future climate change has the potential to alter the distribution and prevalence of plant pathogens, which may have significant implications for both agricultural crops and natural plant communities. However, there are few long-term datasets against which modelled predictions of pathogen responses to climate change can be tested. Here, we use 18S metabarcoding of 28 rodent middens (solidified deposits of rodent coprolites and nesting material) from the Central Atacama, spanning the last ca. 49 ka, to provide the first long-term late Quaternary record of change in plant pathogen communities in response to changing climate. Plant pathogen richness was significantly greater in middens deposited during the Central Andean Pluvial Event (CAPE); a period of increased precipitation between 17.5-8.5 ka. Moreover, the occurrence frequency of Pucciniaceae (rust fungi) was significantly greater during the CAPE, and the highest relative abundances for five additional potentially pathogenic taxa also occurred during this period. The results demonstrate the promising potential for ancient DNA analysis of late Quaternary samples to reveal insights into how plant pathogens responded to past climatic and environmental change, which could help predict how pathogens may responded to future change.}, }
@article {pmid30455210, year = {2018}, author = {Andrew, C and Diez, J and James, TY and Kauserud, H}, title = {Fungarium specimens: a largely untapped source in global change biology and beyond.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1763}, pages = {}, pmid = {30455210}, issn = {1471-2970}, mesh = {*Climate Change ; *Fungi ; *Museums ; Specimen Handling ; }, abstract = {For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.}, }
@article {pmid30445034, year = {2018}, author = {O'Connor, TD}, title = {Native American Genomic Diversity through Ancient DNA.}, journal = {Cell}, volume = {175}, number = {5}, pages = {1173-1174}, doi = {10.1016/j.cell.2018.10.058}, pmid = {30445034}, issn = {1097-4172}, mesh = {*DNA, Ancient ; Genetics, Population ; Genomics ; Humans ; *Indians, North American ; South America ; }, abstract = {Ancient DNA is a powerful tool to understand the evolutionary dynamics of both current and ancestral populations. Posth et al. use ancient DNA to elucidate important questions surrounding the peopling of Central and South America, giving us greater insights into the ancestry of genetically understudied populations.}, }
@article {pmid30420497, year = {2018}, author = {Woods, R and Turvey, ST and Brace, S and MacPhee, RDE and Barnes, I}, title = {Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {50}, pages = {12769-12774}, pmid = {30420497}, issn = {1091-6490}, mesh = {Adaptation, Physiological/genetics ; Animals ; Biodiversity ; Caribbean Region ; Cell Nucleus/genetics ; DNA, Ancient/*analysis ; Fossils ; Genome, Mitochondrial/genetics ; Haplorhini/*genetics ; Phylogeny ; Water ; }, abstract = {The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5-18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations.}, }
@article {pmid30415837, year = {2018}, author = {Posth, C and Nakatsuka, N and Lazaridis, I and Skoglund, P and Mallick, S and Lamnidis, TC and Rohland, N and Nägele, K and Adamski, N and Bertolini, E and Broomandkhoshbacht, N and Cooper, A and Culleton, BJ and Ferraz, T and Ferry, M and Furtwängler, A and Haak, W and Harkins, K and Harper, TK and Hünemeier, T and Lawson, AM and Llamas, B and Michel, M and Nelson, E and Oppenheimer, J and Patterson, N and Schiffels, S and Sedig, J and Stewardson, K and Talamo, S and Wang, CC and Hublin, JJ and Hubbe, M and Harvati, K and Nuevo Delaunay, A and Beier, J and Francken, M and Kaulicke, P and Reyes-Centeno, H and Rademaker, K and Trask, WR and Robinson, M and Gutierrez, SM and Prufer, KM and Salazar-García, DC and Chim, EN and Müller Plumm Gomes, L and Alves, ML and Liryo, A and Inglez, M and Oliveira, RE and Bernardo, DV and Barioni, A and Wesolowski, V and Scheifler, NA and Rivera, MA and Plens, CR and Messineo, PG and Figuti, L and Corach, D and Scabuzzo, C and Eggers, S and DeBlasis, P and Reindel, M and Méndez, C and Politis, G and Tomasto-Cagigao, E and Kennett, DJ and Strauss, A and Fehren-Schmitz, L and Krause, J and Reich, D}, title = {Reconstructing the Deep Population History of Central and South America.}, journal = {Cell}, volume = {175}, number = {5}, pages = {1185-1197.e22}, pmid = {30415837}, issn = {1097-4172}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; FC001595/MRC_/Medical Research Council/United Kingdom ; T32 GM007753/GM/NIGMS NIH HHS/United States ; FC001595/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Central America ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetics, Population/*history ; *Genome, Human ; History, Ancient ; Humans ; Models, Theoretical ; South America ; }, abstract = {We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.}, }
@article {pmid30409866, year = {2018}, author = {Wade, L}, title = {Ancient DNA tracks migrations around Americas.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6415}, pages = {627-628}, doi = {10.1126/science.362.6415.627}, pmid = {30409866}, issn = {1095-9203}, mesh = {Americas ; DNA, Ancient/*analysis ; History, Ancient ; Human Migration/*history ; Humans ; }, }
@article {pmid30408154, year = {2019}, author = {Quillen, EE and Norton, HL and Parra, EJ and Lona-Durazo, F and Ang, KC and Illiescu, FM and Pearson, LN and Shriver, MD and Lasisi, T and Gokcumen, O and Starr, I and Lin, YL and Martin, AR and Jablonski, NG}, title = {Shades of complexity: New perspectives on the evolution and genetic architecture of human skin.}, journal = {American journal of physical anthropology}, volume = {168 Suppl 67}, number = {}, pages = {4-26}, doi = {10.1002/ajpa.23737}, pmid = {30408154}, issn = {1096-8644}, support = {1714867//National Science Foundation/International ; }, mesh = {Anthropology, Physical ; Antiporters/genetics ; *Biological Evolution ; Genetics, Population ; Guanine Nucleotide Exchange Factors/genetics ; Humans ; Membrane Proteins/genetics ; Membrane Transport Proteins/genetics ; Receptor, Melanocortin, Type 1/genetics ; Skin/metabolism ; *Skin Physiological Phenomena ; *Skin Pigmentation/genetics/physiology ; Ubiquitin-Protein Ligases ; }, abstract = {Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.}, }
@article {pmid30406142, year = {2018}, author = {Guedes, L and Dias, O and Neto, J and Ribeiro da Silva, LDP and Mendonça de Souza, SMF and Iñiguez, AM}, title = {First Paleogenetic Evidence of Probable Syphilis and Treponematoses Cases in the Brazilian Colonial Period.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {8304129}, pmid = {30406142}, issn = {2314-6141}, mesh = {Adolescent ; Adult ; Base Sequence ; Brazil ; Female ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Male ; *Paleopathology ; Syphilis/*genetics/*history/pathology ; Treponema/genetics ; Treponemal Infections/*genetics/*history/pathology ; Young Adult ; }, abstract = {Despite interest in the origins of syphilis, paleopathological analysis has not provided answers, and paleogenetic diagnosis remains a challenge. Even venereal syphilis has low infectivity which means there are few circulating bacteria for most of the individual's life. Human remains recovered from the Nossa Senhora do Carmo Church (17th to 19th centuries) and the Praça XV Cemetery (18th to 19th centuries), Rio de Janeiro, Brazil, were subjected to Treponema paleogenetic analysis. Historical data point to endemic treponemal infections in the city, including venereal syphilis. Based on the physiopathology of Treponema pallidum infection, 25 samples, mostly from skull remains of young adults, with no visible paleopathological evidence of treponematoses, were analyzed. PCR with three molecular targets, tpp47, polA, and tpp15, were applied. Ancient DNA tpp15 sequences were recovered from two young adults from each archaeological site and revealed the polymorphism that characterizes T. p. subsp. pallidum in a female up to 18 years old, suggesting a probable case of syphilis infection. The results indicated that the epidemiological context and the physiopathology of the disease should be considered in syphilis paleogenetic detection. The findings of Treponema sp. aDNA are consistent with historical documents that describe venereal syphilis and yaws as endemic diseases in Rio de Janeiro. Data on the epidemiological characteristics of the disease and its pathophysiology offer new perspectives in paleopathology.}, }
@article {pmid30399480, year = {2019}, author = {Pfeiffer, S and Harrington, L and Lombard, M}, title = {The people behind the samples: Biographical features of Past Hunter-Gatherers from KwaZulu-Natal who yielded aDNA.}, journal = {International journal of paleopathology}, volume = {24}, number = {}, pages = {158-164}, doi = {10.1016/j.ijpp.2018.10.008}, pmid = {30399480}, issn = {1879-9825}, mesh = {Adult ; Base Sequence/genetics ; Bone and Bones/*pathology ; Child ; DNA, Ancient/*analysis ; Humans ; Malaria ; Male ; Schistosomiasis/diagnosis/*pathology ; Skull/*pathology ; South Africa ; }, abstract = {PURPOSE: Skeletons sampled for ancient human DNA analysis are sometimes complete enough to provide information about the lives of the people they represent. We focus on three Later Stone Age skeletons, ca. 2000 B.P., from coastal KwaZulu-Natal, South Africa, whose ancient genomes have been sequenced (Schlebusch et al., 2017).<br><br>METHODS: Bioarchaeological approaches are integrated with aDNA information.<br><br>RESULTS: All skeletons are male. Dental development shows that the boy, with prominent cribra orbitalia, died at age 6-7 years. Two men show cranial and spinal trauma, extensive tooth wear, plus mild cribra orbitalia in one.<br><br>CONCLUSIONS: Dental wear and trauma of the adults are consistent with hunter-gatherer lives. Even partial aDNA evidence contributes to sex determination. Parasitic infection such as schistosomiasis is the best-fit cause for the child's anemia in this case.<br><br>CONTRIBUTION TO KNOWLEDGE: The convergence of genomic and bioarchaeological approaches expands our knowledge of the past lives of a boy and two men whose lives as hunter-gatherers included episodes of trauma and disease.<br><br>LIMITATIONS: The skeletons are incomplete, in variable condition, and from poorly characterized local cultural contexts.<br><br>Thorough osteobiographic analysis should accompany paleogenomic investigations. Such disciplinary collaboration enriches our understanding of the human past.}, }
@article {pmid30397125, year = {2018}, author = {Jeong, C and Wilkin, S and Amgalantugs, T and Bouwman, AS and Taylor, WTT and Hagan, RW and Bromage, S and Tsolmon, S and Trachsel, C and Grossmann, J and Littleton, J and Makarewicz, CA and Krigbaum, J and Burri, M and Scott, A and Davaasambuu, G and Wright, J and Irmer, F and Myagmar, E and Boivin, N and Robbeets, M and Rühli, FJ and Krause, J and Frohlich, B and Hendy, J and Warinner, C}, title = {Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {48}, pages = {E11248-E11255}, pmid = {30397125}, issn = {1091-6490}, support = {T32 ES007069/ES/NIEHS NIH HHS/United States ; T42 OH008416/OH/NIOSH CDC HHS/United States ; }, mesh = {Animal Husbandry/*history ; Animals ; Archaeology ; DNA, Mitochondrial/genetics ; Europe ; Female ; *Genome, Human ; History, Ancient ; Human Migration/history ; Humans ; Male ; Mongolia ; Population Dynamics/*history ; }, abstract = {Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300-2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380-975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.}, }
@article {pmid30379865, year = {2018}, author = {Taylor, W and Shnaider, S and Abdykanova, A and Fages, A and Welker, F and Irmer, F and Seguin-Orlando, A and Khan, N and Douka, K and Kolobova, K and Orlando, L and Krivoshapkin, A and Boivin, N}, title = {Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205646}, pmid = {30379865}, issn = {1932-6203}, mesh = {*Animal Husbandry/economics/history ; Animals ; Camelus/*genetics ; Cattle ; *DNA Fingerprinting ; History, Ancient ; Horses/*genetics ; Humans ; Kyrgyzstan ; Selective Breeding/*history ; Sheep/*genetics ; }, abstract = {The Silk Road was an important trade route that channeled trade goods, people, plants, animals, and ideas across the continental interior of Eurasia, fueling biotic exchange and key social developments across the Old World. Nestled between the Pamir and Alay ranges at a baseline elevation of nearly 3000m, Kyrgyzstan's high Alay Valley forms a wide geographic corridor that comprised one of the primary channels of the ancient Silk Road. Recent archaeological survey reveals a millennia-long history of pastoral occupation of Alay from the early Bronze Age through the Medieval period, and a stratified Holocene sequence at the site of Chegirtke Cave. Faunal remains were recovered from test excavations as well as surface collection of material from recent marmot activity. Although recovered specimens were highly fragmented and mostly unidentifiable using traditional zooarchaeological methods, species identification via collagen mass fingerprinting (ZooMS) coupled with sex and first-generation hybrid identification through ancient DNA enabled preliminary characterization of the animal economy of Alay herders. Our new results indicate primary reliance on sheep at Chegirtke Cave (ca. 2200 BCE), with cattle and goat also present. The discovery of a large grinding stone at a spatially associated Bronze or Iron Age habitation structure suggests a mixed agropastoral economic strategy, rather than a unique reliance on domestic animals. Radiocarbon-dated faunal assemblages from habitation structures at nearby localities in the Alay Valley demonstrate the presence of domestic horse, as well as Bactrian camel during later periods. The current study reveals that agropastoral occupation of the high-mountain Alay corridor started millennia before the formal establishment of the Silk Road, and posits that ZooMS, when paired with radiocarbon dates and ancient DNA, is a powerful and cost-effective tool for investigating shifts in the use of animal domesticates in early pastoral economies.}, }
@article {pmid30375193, year = {2018}, author = {Geigl, EM and Grange, T}, title = {Ancient DNA: The quest for the best.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1185-1187}, doi = {10.1111/1755-0998.12931}, pmid = {30375193}, issn = {1755-0998}, mesh = {Animals ; Bone and Bones ; *DNA ; *DNA, Ancient ; Petrous Bone ; Tomography, X-Ray Computed ; }, abstract = {It is the dream of all researchers working with ancient DNA to identify prior to DNA extraction from bone the specimens or specific zones within them that contain the highest proportion of endogenous DNA. As it impacts the sacrifice of precious ancient specimens and the financial support needed for the analyses, the question is of high importance to the scientific field of palaeogenomics. The "Holy Grail" of palaeogenomics was reached when Cristina Gamba et al. () discovered that it was in the petrosal part of the temporal bone, the densest part of the mammalian skeleton, where DNA is exceptionally well preserved. As a consequence, osteological collections experienced a rush from palaeogenomicists to "harvest" these precious bone parts. In this issue of Molecular Ecology Resources, Alberti et al. () describe the discovery of another promising source of relatively well-preserved endogenous DNA, that they had identified through computed tomography (CT scans), the outermost layer of cortical bone. These bones being larger and more abundant than petrous bones, this discovery increases markedly the source material for high-quality palaeogenomic studies and releases the pressure on osteological collections.}, }
@article {pmid30374172, year = {2018}, author = {Zarrillo, S and Gaikwad, N and Lanaud, C and Powis, T and Viot, C and Lesur, I and Fouet, O and Argout, X and Guichoux, E and Salin, F and Solorzano, RL and Bouchez, O and Vignes, H and Severts, P and Hurtado, J and Yepez, A and Grivetti, L and Blake, M and Valdez, F}, title = {The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {12}, pages = {1879-1888}, doi = {10.1038/s41559-018-0697-x}, pmid = {30374172}, issn = {2397-334X}, mesh = {Archaeology ; Cacao/*chemistry/*genetics ; DNA, Ancient/analysis ; *Domestication ; Ecuador ; }, abstract = {Cacao (Theobroma cacao L.) is an important economic crop, yet studies of its domestication history and early uses are limited. Traditionally, cacao is thought to have been first domesticated in Mesoamerica. However, genomic research shows that T. cacao's greatest diversity is in the upper Amazon region of northwest South America, pointing to this region as its centre of origin. Here, we report cacao use identified by three independent lines of archaeological evidence-cacao starch grains, absorbed theobromine residues and ancient DNA-dating from approximately 5,300 years ago recovered from the Santa Ana-La Florida (SALF) site in southeast Ecuador. To our knowledge, these findings constitute the earliest evidence of T. cacao use in the Americas and the first unequivocal archaeological example of its pre-Columbian use in South America. They also reveal the upper Amazon region as the oldest centre of cacao domestication yet identified.}, }
@article {pmid30369466, year = {2018}, author = {Tian, JY and Li, YC and Kong, QP and Zhang, YP}, title = {[The origin and evolution history of East Asian populations from genetic perspectives].}, journal = {Yi chuan = Hereditas}, volume = {40}, number = {10}, pages = {814-824}, doi = {10.16288/j.yczz.18-202}, pmid = {30369466}, issn = {0253-9772}, mesh = {Asia ; Asian People/*genetics ; Evolution, Molecular ; *Genetics, Population ; Human Genetics ; Humans ; Phylogeny ; }, abstract = {East Asia is widely concerned as one of the important places for the dispersal and evolution of the Anatomically Modern Human (AMH). How the diverse ethnic groups in East Asia originated and diversified is also widely focused by different disciplines of Anthropology. The adoption of genetic data had provided new clues for reconstructing the genetic history of East Asian populations. Genetic studies supported the hypothesis that the AMHs originated from Africa's Homo sapiens at about 200 kilo years ago (kya) and then migrated out of Africa at ~100 kya, followed by expansions into the whole East Asia since their arrival in Southern East Asia at 5~6 kya along the coastal route. Early Homo Sapiens might have genetic contribution to the non-African AMHs. Early settlement, cultural assimilation, population migration and genetic exchanges are crucial in the origination and evolution of East Asia populations. Previous studies made detailed analysis for the genetic history of East Asian populations, which largely resolved the longstanding divergence between archaeology and history. However, this needs further verification by whole-genome sequencing and ancient DNA studies. Here we briefly reviewed the progresses of genetic studies in exploring the population origin, dispersal and diversification in East Asia, which improved understanding of the evolution of East Asian populations. We also prospected the future of genetic studies in revealing the prehistory of East Asians.}, }
@article {pmid30367976, year = {2019}, author = {Cole, TL and Rawlence, NJ and Dussex, N and Ellenberg, U and Houston, DM and Mattern, T and Miskelly, CM and Morrison, KW and Scofield, RP and Tennyson, AJD and Thompson, DR and Wood, JR and Waters, JM}, title = {Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world's most diverse penguin clade.}, journal = {Molecular phylogenetics and evolution}, volume = {131}, number = {}, pages = {72-79}, doi = {10.1016/j.ympev.2018.10.025}, pmid = {30367976}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; DNA, Ancient/*analysis ; Electron Transport Complex IV/genetics ; Fossils ; *Genetic Variation ; Haplotypes/genetics ; Humans ; New Zealand ; Pacific Ocean ; *Phylogeny ; Population Dynamics ; Spheniscidae/classification/*genetics ; Time Factors ; }, abstract = {Human impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the diverse crested penguin genus Eudyptes. While this species-rich genus has been little studied genetically, recent population estimates indicate that several Eudyptes taxa are experiencing demographic declines. Although crested penguins are currently limited to southern regions of the New Zealand archipelago, prehistoric fossil and archaeological deposits suggest a wider distribution during prehistoric times, with breeding ranges perhaps extending to the North Island. Here, we analyse ancient, historic and modern DNA sequences to explore two hypotheses regarding the recent history of Eudyptes in New Zealand, testing for (1) human-driven extinction of Eudyptes lineages; and (2) reduced genetic diversity in surviving lineages. From 83 prehistoric bone samples, each tentatively identified as 'Eudyptes spp.', we genetically identified six prehistoric penguin taxa from mainland New Zealand, including one previously undescribed genetic lineage. Moreover, our Bayesian coalescent analyses indicated that, while the range of Fiordland crested penguin (E. pachyrhynchus) may have contracted markedly over the last millennium, genetic DNA diversity within this lineage has remained relatively constant. This result contrasts with human-driven biodiversity reductions previously detected in several New Zealand coastal vertebrate taxa.}, }
@article {pmid30359256, year = {2018}, author = {de Filippo, C and Meyer, M and Prüfer, K}, title = {Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences.}, journal = {BMC biology}, volume = {16}, number = {1}, pages = {121}, pmid = {30359256}, issn = {1741-7007}, mesh = {Animals ; *Base Sequence ; DNA, Ancient/*analysis ; Fossils ; Neanderthals/*genetics ; Sequence Alignment/*methods ; Spain ; }, abstract = {BACKGROUND: The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short.<br><br>RESULTS: Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~&#x2009;430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17-150%. This allows us to place a third specimen from the site on the Neandertal lineage.<br><br>CONCLUSIONS: Our method maximizes the sequence data amenable to genetic analysis from highly degraded ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.}, }
@article {pmid30348080, year = {2018}, author = {Paijmans, JLA and Barlow, A and Förster, DW and Henneberger, K and Meyer, M and Nickel, B and Nagel, D and Worsøe Havmøller, R and Baryshnikov, GF and Joger, U and Rosendahl, W and Hofreiter, M}, title = {Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {156}, pmid = {30348080}, issn = {1471-2148}, support = {310763/ERC_/European Research Council/International ; }, mesh = {Animals ; Asia ; Calibration ; DNA, Mitochondrial/genetics ; Europe ; *Extinction, Biological ; Genome, Mitochondrial ; Panthera/*classification/genetics ; Phylogeny ; *Phylogeography ; }, abstract = {BACKGROUND: Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?<br><br>RESULTS: In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~&#x2009;710 Ka), with the European ancient samples as sister to all Asian lineages (~&#x2009;483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~&#x2009;122 Ka), and we find one Javan sample nested within these.<br><br>CONCLUSIONS: The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.}, }
@article {pmid30344633, year = {2018}, author = {Silva, NM and Rio, J and Kreutzer, S and Papageorgopoulou, C and Currat, M}, title = {Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations.}, journal = {Evolutionary applications}, volume = {11}, number = {9}, pages = {1642-1655}, pmid = {30344633}, issn = {1752-4571}, abstract = {The retrieval of ancient DNA from osteological material provides direct evidence of human genetic diversity in the past. Ancient DNA samples are often used to investigate whether there was population continuity in the settlement history of an area. Methods based on the serial coalescent algorithm have been developed to test whether the population continuity hypothesis can be statistically rejected by analysing DNA samples from the same region but of different ages. Rejection of this hypothesis is indicative of a large genetic shift, possibly due to immigration occurring between two sampling times. However, this approach is only able to reject a model of full continuity model (a total absence of genetic input from outside), but admixture between local and immigrant populations may lead to partial continuity. We have recently developed a method to test for population continuity that explicitly considers the spatial and temporal dynamics of populations. Here, we extended this approach to estimate the proportion of genetic continuity between two populations, using ancient genetic samples. We applied our original approach to the question of the Neolithic transition in Central Europe. Our results confirmed the rejection of full continuity, but our approach represents an important step forward by estimating the relative contribution of immigrant farmers and of local hunter-gatherers to the final Central European Neolithic genetic pool. Furthermore, we show that a substantial proportion of genes brought by the farmers in this region were assimilated from other hunter-gatherer populations along the way from Anatolia, which was not detectable by previous continuity tests. Our approach is also able to jointly estimate demographic parameters, as we show here by finding both low density and low migration rate for pre-Neolithic hunter-gatherers. It provides a useful tool for the analysis of the numerous ancient DNA data sets that are currently being produced for many different species.}, }
@article {pmid30333260, year = {2018}, author = {Ollivier, M and Tresset, A and Frantz, LAF and Bréhard, S and Bălăşescu, A and Mashkour, M and Boroneanţ, A and Pionnier-Capitan, M and Lebrasseur, O and Arbogast, RM and Bartosiewicz, L and Debue, K and Rabinovich, R and Sablin, MV and Larson, G and Hänni, C and Hitte, C and Vigne, JD}, title = {Dogs accompanied humans during the Neolithic expansion into Europe.}, journal = {Biology letters}, volume = {14}, number = {10}, pages = {}, pmid = {30333260}, issn = {1744-957X}, mesh = {Agriculture ; Animals ; *Archaeology ; *DNA, Mitochondrial ; Dogs/classification/*genetics ; Europe ; Fossils ; Haplotypes ; Humans ; Sequence Analysis, DNA ; }, abstract = {Near Eastern Neolithic farmers introduced several species of domestic plants and animals as they dispersed into Europe. Dogs were the only domestic species present in both Europe and the Near East prior to the Neolithic. Here, we assessed whether early Near Eastern dogs possessed a unique mitochondrial lineage that differentiated them from Mesolithic European populations. We then analysed mitochondrial DNA sequences from 99 ancient European and Near Eastern dogs spanning the Upper Palaeolithic to the Bronze Age to assess if incoming farmers brought Near Eastern dogs with them, or instead primarily adopted indigenous European dogs after they arrived. Our results show that European pre-Neolithic dogs all possessed the mitochondrial haplogroup C, and that the Neolithic and Post-Neolithic dogs associated with farmers from Southeastern Europe mainly possessed haplogroup D. Thus, the appearance of haplogroup D most probably resulted from the dissemination of dogs from the Near East into Europe. In Western and Northern Europe, the turnover is incomplete and haplogroup C persists well into the Chalcolithic at least. These results suggest that dogs were an integral component of the Neolithic farming package and a mitochondrial lineage associated with the Near East was introduced into Europe alongside pigs, cows, sheep and goats. It got diluted into the native dog population when reaching the Western and Northern margins of Europe.}, }
@article {pmid30313742, year = {2018}, author = {Vences, M and Hildenbrand, A and Warmuth, KM and Andreone, F and Glaw, F}, title = {A new riparian Mantidactylus (Brygoomantis) frog from the Tsaratanana and Manongarivo Massifs in northern Madagascar.}, journal = {Zootaxa}, volume = {4486}, number = {4}, pages = {575-588}, doi = {10.11646/zootaxa.4486.4.10}, pmid = {30313742}, issn = {1175-5334}, mesh = {Animals ; *Anura ; DNA ; Madagascar ; *Phylogeny ; }, abstract = {The subgenus Brygoomantis in the Madagascar-endemic genus Mantidactylus contains 12 nominal species but is in urgent need of taxonomic revision as many additional, genetically divergent but undescribed candidate species have been identified. We here take a first step towards a better resolution of this group by describing a new species, Mantidactylus schulzi sp. nov., occurring at the Tsaratanana and Manongarivo Massifs, differentiated in genetic, bioacoustic and sometimes morphological characters from its closest relatives. We show that upon detailed study, most species in Brygoomantis can be delimited by concordant differentiation of mitochondrial and nuclear DNA, and by bioacoustic and morphological differences. We flag this group of morphologically similar frogs as a test case where molecular data on historical type specimens by ancient DNA methods might be needed to reach a satisfying clarification of taxonomy and nomenclature. However, the status of the new species M. schulzi is not in doubt as it is morphologically distinct from most historical type specimens, and microendemic to a region in northern Madagascar from where no earlier names exist.}, }
@article {pmid30291256, year = {2018}, author = {Fernandes, DM and Strapagiel, D and Borówka, P and Marciniak, B and Żądzińska, E and Sirak, K and Siska, V and Grygiel, R and Carlsson, J and Manica, A and Lorkiewicz, W and Pinhasi, R}, title = {A genomic Neolithic time transect of hunter-farmer admixture in central Poland.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14879}, pmid = {30291256}, issn = {2045-2322}, support = {GOIPG/2013/36//Irish Research Council/International ; }, mesh = {Agriculture/history ; Archaeology ; Chromosomes, Human, Y/genetics ; DNA, Ancient/analysis ; DNA, Mitochondrial/analysis/genetics ; Europe ; Farmers ; Genetic Drift ; Genetics, Population ; Genome, Human ; Genome-Wide Association Study ; Genomics ; History, Ancient ; *Human Migration ; Humans ; Middle East ; Poland ; }, abstract = {Ancient DNA genome-wide analyses of Neolithic individuals from central and southern Europe indicate an overall population turnover pattern in which migrating farmers from Anatolia and the Near East largely replaced autochthonous Mesolithic hunter-gatherers. However, the genetic history of the Neolithic transition in areas lying north of the European Neolithic core region involved different levels of admixture with hunter-gatherers. Here we analyse genome-wide data of 17 individuals spanning from the Middle Neolithic to the Early Bronze Age (4300-1900 BCE) in order to assess the Neolithic transition in north-central Poland, and the local impacts of hunter-farmer contacts and Late Neolithic steppe migrations. We evaluate the influence of these on local populations and assess if and how they change through time, reporting evidence of recurrent hunter-farmer admixture over three millennia, and the co-existence of unadmixed hunter-gatherers as late as 4300 BCE. During the Late Neolithic we report the appearance of steppe ancestry, but on a lesser scale than previously described for other central European regions, with evidence of stronger affinities to hunter-gatherers than to steppe pastoralists. These results help understand the Neolithic palaeogenomics of another central European area, Kuyavia, and highlight the complexity of population interactions during those times.}, }
@article {pmid30286387, year = {2018}, author = {Metspalu, M and Mondal, M and Chaubey, G}, title = {The genetic makings of South Asia.}, journal = {Current opinion in genetics &amp; development}, volume = {53}, number = {}, pages = {128-133}, doi = {10.1016/j.gde.2018.09.003}, pmid = {30286387}, issn = {1879-0380}, mesh = {Asia ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Genetics, Population ; Genome, Human/*genetics ; Human Migration ; Humans ; Iran ; Selection, Genetic/*genetics ; }, abstract = {South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for disentangling the genetic makings of South Asia. In this review we shall give brief account on the recent developments in the field. Advances are made in two fronts simultaneously. Whole genome characterisation of many extant South Asians paint the picture of the genetic diversity and its implications to health-care. On the other hand ancient DNA studies, which are finally reaching South Asia, provide new incites to the demographic history of the subcontinent. Before the spread of agriculture, South Asia was likely inhabited by hunter-gatherer groups deriving much of their ancestry from a population that split from the rest of humanity soon after expanding from Africa. Early Iranian agriculturalists mixing with these local hunter-gatherers probably formed the population that flourished during the blossoming of the Indus Valley Civilisation. Further admixture with the still persisting HG groups and population(s) from the Eurasian Steppe, formed the two ancestral populations (ANI and ASI), the north-south mixing pattern of whom is known today as the 'Indian Cline'. Studies on natural selection in South Asia have so far revealed strong signals of sweeps that are shared with West Eurasians. Future studies will have to fully unlock the aDNA promise for South Asia.}, }
@article {pmid30282648, year = {2018}, author = {Flammer, PG and Dellicour, S and Preston, SG and Rieger, D and Warren, S and Tan, CKW and Nicholson, R and Přichystalová, R and Bleicher, N and Wahl, J and Faria, NR and Pybus, OG and Pollard, M and Smith, AL}, title = {Molecular archaeoparasitology identifies cultural changes in the Medieval Hanseatic trading centre of Lübeck.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1888}, pages = {}, pmid = {30282648}, issn = {1471-2954}, support = {204311/Z/16/Z//Wellcome Trust/United Kingdom ; BB/K004468/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K001388/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Archaeology ; Cities/epidemiology ; *Cultural Evolution ; DNA, Ancient/analysis ; Feces/*parasitology ; Genetic Variation ; Germany/epidemiology ; Helminths/classification/*physiology ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, Ancient ; History, Medieval ; Humans ; Parasite Egg Count ; Parasitology ; Trichuriasis/epidemiology/*history/parasitology ; Trichuris/genetics/physiology ; }, abstract = {Throughout history, humans have been afflicted by parasitic worms, and eggs are readily detected in archaeological deposits. This study integrated parasitological and ancient DNA methods with a large sample set dating between Neolithic and Early Modern periods to explore the utility of molecular archaeoparasitology as a new approach to study the past. Molecular analyses provided unequivocal species-level parasite identification and revealed location-specific epidemiological signatures. Faecal-oral transmitted nematodes (Ascaris lumbricoides and Trichuris trichiura) were ubiquitous across time and space. By contrast, high numbers of food-associated cestodes (Diphyllobothrium latum and Taenia saginata) were restricted to medieval Lübeck. The presence of these cestodes and changes in their prevalence at approximately 1300 CE indicate substantial alterations in diet or parasite availability. Trichuris trichiura ITS-1 sequences grouped into two clades; one ubiquitous and one restricted to medieval Lübeck and Bristol. The high sequence diversity of T.tITS-1 detected in Lübeck is consistent with its importance as a Hanseatic trading centre. Collectively, these results introduce molecular archaeoparasitology as an artefact-independent source of historical evidence.}, }
@article {pmid30272210, year = {2018}, author = {Mathieson, S and Mathieson, I}, title = {FADS1 and the Timing of Human Adaptation to Agriculture.}, journal = {Molecular biology and evolution}, volume = {35}, number = {12}, pages = {2957-2970}, pmid = {30272210}, issn = {1537-1719}, mesh = {*Adaptation, Biological ; *Agriculture ; Biological Evolution ; Delta-5 Fatty Acid Desaturase ; Diet ; Fatty Acid Desaturases/*genetics ; Genome, Human ; Haplotypes ; Humans ; Lipid Metabolism/genetics ; *Selection, Genetic ; White People/*genetics ; }, abstract = {Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced ∼8,500 years ago by Early Neolithic farming populations. However, we also show that it was not under strong selection in these populations. We find that this allele, and other proposed agricultural adaptations at LCT/MCM6 and SLC22A4, were not strongly selected until much later, perhaps as late as the Bronze Age. Similarly, increased copy number variation at the salivary amylase gene AMY1 is not linked to the development of agriculture although, in this case, the putative adaptation precedes the agricultural transition. Our analysis shows that selection at the FADS locus was not tightly linked to the initial introduction of agriculture and the Neolithic transition. Further, it suggests that the strongest signals of recent human adaptation in Europe did not coincide with the Neolithic transition but with more recent changes in environment, diet, or efficiency of selection due to increases in effective population size.}, }
@article {pmid30268682, year = {2018}, author = {Pośpiech, E and Chen, Y and Kukla-Bartoszek, M and Breslin, K and Aliferi, A and Andersen, JD and Ballard, D and Chaitanya, L and Freire-Aradas, A and van der Gaag, KJ and Girón-Santamaría, L and Gross, TE and Gysi, M and Huber, G and Mosquera-Miguel, A and Muralidharan, C and Skowron, M and Carracedo, &#xc1; and Haas, C and Morling, N and Parson, W and Phillips, C and Schneider, PM and Sijen, T and Syndercombe-Court, D and Vennemann, M and Wu, S and Xu, S and Jin, L and Wang, S and Zhu, G and Martin, NG and Medland, SE and Branicki, W and Walsh, S and Liu, F and Kayser, M and , }, title = {Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA.}, journal = {Forensic science international. Genetics}, volume = {37}, number = {}, pages = {241-251}, doi = {10.1016/j.fsigen.2018.08.017}, pmid = {30268682}, issn = {1878-0326}, mesh = {Adult ; DNA/*genetics ; Genome-Wide Association Study ; Genotyping Techniques/instrumentation ; *Hair ; High-Throughput Nucleotide Sequencing ; Humans ; Logistic Models ; Models, Genetic ; *Phenotype ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Human head hair shape, commonly classified as straight, wavy, curly or frizzy, is an attractive target for Forensic DNA Phenotyping and other applications of human appearance prediction from DNA such as in paleogenetics. The genetic knowledge underlying head hair shape variation was recently improved by the outcome of a series of genome-wide association and replication studies in a total of 26,964 subjects, highlighting 12 loci of which 8 were novel and introducing a prediction model for Europeans based on 14 SNPs. In the present study, we evaluated the capacity of DNA-based head hair shape prediction by investigating an extended set of candidate SNP predictors and by using an independent set of samples for model validation. Prediction model building was carried out in 9674 subjects (6068 from Europe, 2899 from Asia and 707 of admixed European and Asian ancestries), used previously, by considering a novel list of 90 candidate SNPs. For model validation, genotype and phenotype data were newly collected in 2415 independent subjects (2138 Europeans and 277 non-Europeans) by applying two targeted massively parallel sequencing platforms, Ion Torrent PGM and MiSeq, or the MassARRAY platform. A binomial model was developed to predict straight vs. non-straight hair based on 32 SNPs from 26 genetic loci we identified as significantly contributing to the model. This model achieved prediction accuracies, expressed as AUC, of 0.664 in Europeans and 0.789 in non-Europeans; the statistically significant difference was explained mostly by the effect of one EDAR SNP in non-Europeans. Considering sex and age, in addition to the SNPs, slightly and insignificantly increased the prediction accuracies (AUC of 0.680 and 0.800, respectively). Based on the sample size and candidate DNA markers investigated, this study provides the most robust, validated, and accurate statistical prediction models and SNP predictor marker sets currently available for predicting head hair shape from DNA, providing the next step towards broadening Forensic DNA Phenotyping beyond pigmentation traits.}, }
@article {pmid30262928, year = {2018}, author = {Kessler, SE and Bonnell, TR and Setchell, JM and Chapman, CA}, title = {Social Structure Facilitated the Evolution of Care-giving as a Strategy for Disease Control in the Human Lineage.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13997}, pmid = {30262928}, issn = {2045-2322}, mesh = {Animals ; *Biological Evolution ; *Fossils ; Hominidae/*physiology ; Humans ; *Social Behavior ; }, abstract = {Humans are the only species to have evolved cooperative care-giving as a strategy for disease control. A synthesis of evidence from the fossil record, paleogenomics, human ecology, and disease transmission models, suggests that care-giving for the diseased evolved as part of the unique suite of cognitive and socio-cultural specializations that are attributed to the genus Homo. Here we demonstrate that the evolution of hominin social structure enabled the evolution of care-giving for the diseased. Using agent-based modeling, we simulate the evolution of care-giving in hominin networks derived from a basal primate social system and the three leading hypotheses of ancestral human social organization, each of which would have had to deal with the elevated disease spread associated with care-giving. We show that (1) care-giving is an evolutionarily stable strategy in kin-based cooperatively breeding groups, (2) care-giving can become established in small, low density groups, similar to communities that existed before the increases in community size and density that are associated with the advent of agriculture in the Neolithic, and (3) once established, care-giving became a successful method of disease control across social systems, even as community sizes and densities increased. We conclude that care-giving enabled hominins to suppress disease spread as social complexity, and thus socially-transmitted disease risk, increased.}, }
@article {pmid30262781, year = {2018}, author = {Santiago-Rodriguez, TM and Toranzos, GA}, title = {On Controls in Ancient Microbiome Studies, and Microbial Resilience in Ancient Samples.}, journal = {Genes}, volume = {9}, number = {10}, pages = {}, pmid = {30262781}, issn = {2073-4425}, abstract = {In the following comment, we reply to Eisenhofer and Weyrich's letter "Proper authentication of ancient DNA is still essential" responding to the article "Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies" by Santiago-Rodriguez et al. One of the concerns raised was the possibility that the patterns noted in the gut microbiome of pre-Inca/Inca and Italian nobility mummies were due to contamination of the blank control. When examining the blank controls and filtering the operational taxonomic units (OTUs) present in the blank controls, and further performing in-silico contamination analyses, we noticed very similar patterns as those previously reported. We also discuss controls in ancient microbiome studies, and aspects of microbial resilience in ancient samples.}, }
@article {pmid30261278, year = {2019}, author = {Kavlick, MF}, title = {Development of a triplex mtDNA qPCR assay to assess quantification, degradation, inhibition, and amplification target copy numbers.}, journal = {Mitochondrion}, volume = {46}, number = {}, pages = {41-50}, doi = {10.1016/j.mito.2018.09.007}, pmid = {30261278}, issn = {1872-8278}, mesh = {Animals ; DNA, Mitochondrial/*analysis/genetics ; Female ; Humans ; Male ; Multiplex Polymerase Chain Reaction/*methods/standards ; Real-Time Polymerase Chain Reaction/*methods/standards ; Reference Standards ; }, abstract = {A hybrid absolute/relative qPCR assay which provides information regarding the condition of mitochondrial DNA (mtDNA) in a DNA sample is described. MtDNA concentration (copy number/μL) is determined via absolute quantification using a standard curve of a synthetic duplex DNA previously described (Kavlick et al., 2011). The state of mtDNA degradation is determined via the relative quantification of a mtDNA target found within the 16 s rRNA gene which is 3× longer than that of the short target in the former duplex assay, using the delta, delta Ct (ΔΔCt) method. The presence or absence of PCR inhibitors in the sample is qualitatively determined using a custom internal positive control (IPC) system which targets a unique and non-naturally occurring duplex DNA sequence. This IPC effectively detected inhibition by humic acid, tannic acid, melanin, and EDTA. All three assay components utilize sensitive and specific hydrolysis probes. The utility of ΔΔCt method was demonstrated in a series of experiments involving laboratory-fragmented DNA. Also described is a method for estimating copy number of any mtDNA target longer than the two targets amplified. The described triplex assay works well for intact and for fragmented or degraded mtDNA and therefore may be useful in forensic and ancient DNA disciplines as well as in biomedical research or practice.}, }
@article {pmid30253810, year = {2018}, author = {Beeravolu, CR and Hickerson, MJ and Frantz, LAF and Lohse, K}, title = {ABLE: blockwise site frequency spectra for inferring complex population histories and recombination.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {145}, pmid = {30253810}, issn = {1474-760X}, support = {ERC-2013-StG-337574-UNDEAD//European Research Council/International ; ACI-1126113//National Science Foundation/International ; BIOTA, 2013/50297-0//FAPESP/International ; CNS-0958379//National Science Foundation/International ; 337574/ERC_/European Research Council/International ; NE/L011522/1//Natural Environment Research Council (GB)/International ; DOB 1343578//National Science Foundation (US)/International ; DEB-1253710//National Science Foundation/International ; CNS-0855217//National Science Foundation (US)/International ; }, mesh = {Animals ; Demography ; Genomics/*methods ; Pongo/genetics ; *Recombination, Genetic ; Sample Size ; }, abstract = {We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide multi-locus data (for example, RADSeq) and can also accommodate arbitrarily large samples. We use simulations to demonstrate the accuracy of this method to infer complex histories of divergence and gene flow and reanalyze whole genome data from two species of orangutan. ABLE is available for download at https://github.com/champost/ABLE .}, }
@article {pmid30249639, year = {2018}, author = {Guellil, M and Kersten, O and Namouchi, A and Bauer, EL and Derrick, M and Jensen, A&#xd8; and Stenseth, NC and Bramanti, B}, title = {Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {41}, pages = {10422-10427}, pmid = {30249639}, issn = {1091-6490}, mesh = {Adult ; Animals ; Bacterial Proteins/*genetics ; Borrelia/classification/*genetics/pathogenicity ; Child ; Female ; *Genome, Bacterial ; History, 15th Century ; Humans ; *Metagenomics ; Phylogeny ; Relapsing Fever/*genetics/history/microbiology ; Scandinavian and Nordic Countries ; }, abstract = {Louse-borne relapsing fever (LBRF) is known to have killed millions of people over the course of European history and remains a major cause of mortality in parts of the world. Its pathogen, Borrelia recurrentis, shares a common vector with global killers such as typhus and plague and is known for its involvement in devastating historical epidemics such as the Irish potato famine. Here, we describe a European and historical genome of Brecurrentis, recovered from a 15th century skeleton from Oslo. Our distinct European lineage has a discrete genomic makeup, displaying an ancestral oppA-1 gene and gene loss in antigenic variation sites. Our results illustrate the potential of ancient DNA research to elucidate dynamics of reductive evolution in a specialized human pathogen and to uncover aspects of human health usually invisible to the archaeological record.}, }
@article {pmid30237547, year = {2018}, author = {Harney, &#xc9; and May, H and Shalem, D and Rohland, N and Mallick, S and Lazaridis, I and Sarig, R and Stewardson, K and Nordenfelt, S and Patterson, N and Hershkovitz, I and Reich, D}, title = {Publisher Correction: Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3913}, doi = {10.1038/s41467-018-06484-8}, pmid = {30237547}, issn = {2041-1723}, abstract = {In the original version of this Article, references in the format 'First author et al.' were inappropriately deleted. These errors have been corrected in the PDF and HTML versions of the Article.}, }
@article {pmid30232557, year = {2018}, author = {Kivisild, T}, title = {Correction to: The study of human Y chromosome variation through ancient DNA.}, journal = {Human genetics}, volume = {137}, number = {10}, pages = {863}, doi = {10.1007/s00439-018-1937-5}, pmid = {30232557}, issn = {1432-1203}, abstract = {The following sentence on the 11th page of the article.}, }
@article {pmid30232341, year = {2018}, author = {Furtwängler, A and Reiter, E and Neumann, GU and Siebke, I and Steuri, N and Hafner, A and Lösch, S and Anthes, N and Schuenemann, VJ and Krause, J}, title = {Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14075}, pmid = {30232341}, issn = {2045-2322}, mesh = {Bone and Bones/chemistry ; Cell Nucleus/*genetics ; DNA Contamination ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Female ; Haploidy ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Sequence Analysis, DNA/methods ; Sex Factors ; }, abstract = {In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.}, }
@article {pmid30230470, year = {2018}, author = {Charlier, P and Coppens, Y and Héry-Arnaud, G and Hassin, J}, title = {[A biological anthropology of the disappearance of the Neandertal Man: recent data].}, journal = {Medecine sciences : M/S}, volume = {34}, number = {8-9}, pages = {745-748}, doi = {10.1051/medsci/20183408024}, pmid = {30230470}, issn = {1958-5381}, mesh = {Animals ; Anthropology/*methods ; Anthropology, Physical ; Biological Evolution ; *Extinction, Biological ; Female ; Fossils ; Humans ; Male ; *Neanderthals ; }, abstract = {What could have been the causes of the disappearance of Neanderthals? We will try here to make a synthesis between one of the fundamental questions of biological anthropology relating to human evolution (hypotheses on the causes of the extinction of Neanderthals) and evolutionary bio-medical concepts, some of which have recently been reformulated thanks to the progress of paleogenomics (ancestral inheritance of the current human immune system, paleo-microbiology, host-pathogen relationship…).}, }
@article {pmid30225046, year = {2018}, author = {Miller, EF and Manica, A and Amos, W}, title = {Global demographic history of human populations inferred from whole mitochondrial genomes.}, journal = {Royal Society open science}, volume = {5}, number = {8}, pages = {180543}, pmid = {30225046}, issn = {2054-5703}, support = {BB/M011194/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from the 1000 Genomes Project Phase 3, to explore changes in populations sizes in five populations for each of four major geographical regions, using a sophisticated coalescent-based Bayesian method (extended Bayesian skyline plots) and mutation rates calibrated with ancient DNA. Despite the power and sophistication of our analysis, we fail to find size changes that correspond to the Neolithic transitions of the study populations. However, we do detect a number of size changes, which tend to be replicated in most populations within each region. These changes are mostly much older than the Neolithic transition and could reflect either population expansion or changes in population structure. Given the amount of migration and population mixing that occurred after these ancient signals were generated, we caution that modern populations will often carry ghost signals of demographic events that occurred far away from their current location.}, }
@article {pmid30224645, year = {2018}, author = {Chiang, CWK and Marcus, JH and Sidore, C and Biddanda, A and Al-Asadi, H and Zoledziewska, M and Pitzalis, M and Busonero, F and Maschio, A and Pistis, G and Steri, M and Angius, A and Lohmueller, KE and Abecasis, GR and Schlessinger, D and Cucca, F and Novembre, J}, title = {Genomic history of the Sardinian population.}, journal = {Nature genetics}, volume = {50}, number = {10}, pages = {1426-1434}, pmid = {30224645}, issn = {1546-1718}, support = {R01 GM108805/GM/NIGMS NIH HHS/United States ; RC2 HG005552/HG/NHGRI NIH HHS/United States ; U01 HG006513/HG/NHGRI NIH HHS/United States ; T32 NS048004/NS/NINDS NIH HHS/United States ; F32 GM106656/GM/NIGMS NIH HHS/United States ; R01 HG007089/HG/NHGRI NIH HHS/United States ; HHSN271201100005C/DA/NIDA NIH HHS/United States ; N01 AG012109/AG/NIA NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; R01 HG007022/HG/NHGRI NIH HHS/United States ; U01 HL117626/HL/NHLBI NIH HHS/United States ; R01 HL117626/HL/NHLBI NIH HHS/United States ; RC2 HG005581/HG/NHGRI NIH HHS/United States ; }, mesh = {Case-Control Studies ; Demography ; Female ; Gene Frequency ; *Genetic Variation ; *Genetics, Population ; Genome-Wide Association Study ; History, Ancient ; Human Migration/statistics &amp; numerical data ; Humans ; Italy/epidemiology ; Longitudinal Studies ; Male ; Mediterranean Region/epidemiology ; *Phylogeny ; }, abstract = {The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of complex disease traits and, based on ancient DNA studies of mainland Europe, Sardinia is hypothesized to be a unique refuge for early Neolithic ancestry. To provide new insights on the genetic history of this flagship population, we analyzed 3,514 whole-genome sequenced individuals from Sardinia. Sardinian samples show elevated levels of shared ancestry with Basque individuals, especially samples from the more historically isolated regions of Sardinia. Our analysis also uniquely illuminates how levels of genetic similarity with mainland ancient DNA samples varies subtly across the island. Together, our results indicate that within-island substructure and sex-biased processes have substantially impacted the genetic history of Sardinia. These results give new insight into the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.}, }
@article {pmid30215675, year = {2018}, author = {Kawash, JK and Smith, SD and Karaiskos, S and Grigoriev, A}, title = {ARIADNA: machine learning method for ancient DNA variant discovery.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {25}, number = {6}, pages = {619-627}, pmid = {30215675}, issn = {1756-1663}, support = {R15 CA220059/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient/*chemistry ; *Genetic Variation ; Genome ; *Machine Learning ; Mammoths/genetics ; Mutation ; Neanderthals/genetics ; }, abstract = {Ancient DNA (aDNA) studies often rely on standard methods of mutation calling, optimized for high-quality contemporary DNA but not for excessive contamination, time- or environment-related damage of aDNA. In the absence of validated datasets and despite showing extreme sensitivity to aDNA quality, these methods have been used in many published studies, sometimes with additions of arbitrary filters or modifications, designed to overcome aDNA degradation and contamination problems. The general lack of best practices for aDNA mutation calling may lead to inaccurate results. To address these problems, we present ARIADNA (ARtificial Intelligence for Ancient DNA), a novel approach based on machine learning techniques, using specific aDNA characteristics as features to yield improved mutation calls. In our comparisons of variant callers across several ancient genomes, ARIADNA consistently detected higher-quality genome variants with fast runtimes, while reducing the false positive rate compared with other approaches.}, }
@article {pmid30206220, year = {2018}, author = {Amorim, CEG and Vai, S and Posth, C and Modi, A and Koncz, I and Hakenbeck, S and La Rocca, MC and Mende, B and Bobo, D and Pohl, W and Baricco, LP and Bedini, E and Francalacci, P and Giostra, C and Vida, T and Winger, D and von Freeden, U and Ghirotto, S and Lari, M and Barbujani, G and Krause, J and Caramelli, D and Geary, PJ and Veeramah, KR}, title = {Understanding 6th-century barbarian social organization and migration through paleogenomics.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3547}, pmid = {30206220}, issn = {2041-1723}, support = {1450606//National Science Foundation (NSF)/International ; }, mesh = {Archaeology ; Cemeteries ; *Genomics ; Geography ; History, Medieval ; Human Migration/*history ; Humans ; Paleontology/*history ; Phylogeny ; Principal Component Analysis ; *Social Behavior ; Strontium Isotopes ; }, abstract = {Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data are consistent with the proposed long-distance migration from Pannonia to Northern Italy.}, }
@article {pmid30200636, year = {2018}, author = {Pratas, D and Hosseini, M and Grilo, G and Pinho, AJ and Silva, RM and Caetano, T and Carneiro, J and Pereira, F}, title = {Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard.}, journal = {Genes}, volume = {9}, number = {9}, pages = {}, pmid = {30200636}, issn = {2073-4425}, support = {PD/BD/113969/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BPD/111148/2015//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BPD/77900/2011//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BPD/100912/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/01356/2012//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/BIM/04501/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/CEC/00127/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/AMB/50017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTCD/EEI-SII/6608/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination.}, }
@article {pmid30200350, year = {2018}, author = {Ferrari, G and Lischer, HEL and Neukamm, J and Rayo, E and Borel, N and Pospischil, A and Rühli, F and Bouwman, AS and Campana, MG}, title = {Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf.}, journal = {Genes}, volume = {9}, number = {9}, pages = {}, pmid = {30200350}, issn = {2073-4425}, support = {URPP Evolution in Action: from Genomes to Ecosystems//Universit&#xe4;t Z&#xfc;rich/ ; n/a//M&#xe4;xi Foundation Zurich/ ; n/a//Smithsonian Institution/ ; }, abstract = {The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. Here we attempted to reconstruct the tissue-specific metagenomes of a 42,000-year-old, permafrost-preserved woolly mammoth calf through shotgun high-throughput sequencing. We analyzed the taxonomic composition of all tissue samples together with environmental and non-template experimental controls and compared them to metagenomes obtained from permafrost and elephant fecal samples. Preliminary results suggested the presence of tissue-specific metagenomic signals. We identified bacterial species that were present in only one experimental sample, absent from controls, and consistent with the nature of the samples. However, we failed to further authenticate any of these signals and conclude that, even when experimental samples are distinct from environmental and laboratory controls, this does not necessarily indicate endogenous presence of ancient host-associated microbiomic signals.}, }
@article {pmid30192911, year = {2019}, author = {Al-Asadi, H and Dey, KK and Novembre, J and Stephens, M}, title = {Inference and visualization of DNA damage patterns using a grade of membership model.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {8}, pages = {1292-1298}, pmid = {30192911}, issn = {1367-4811}, support = {R01 HG002585/HG/NHGRI NIH HHS/United States ; U01 CA198933/CA/NCI NIH HHS/United States ; }, mesh = {Cytosine ; *DNA Damage ; DNA, Ancient ; *Genome ; Humans ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: Quality control plays a major role in the analysis of ancient DNA (aDNA). One key step in this quality control is assessment of DNA damage: aDNA contains unique signatures of DNA damage that distinguish it from modern DNA, and so analyses of damage patterns can help confirm that DNA sequences obtained are from endogenous aDNA rather than from modern contamination. Predominant signatures of DNA damage include a high frequency of cytosine to thymine substitutions (C-to-T) at the ends of fragments, and elevated rates of purines (A &amp; G) before the 5' strand-breaks. Existing QC procedures help assess damage by simply plotting for each sample, the C-to-T mismatch rate along the read and the composition of bases before the 5' strand-breaks. Here we present a more flexible and comprehensive model-based approach to infer and visualize damage patterns in aDNA, implemented in an R package aRchaic. This approach is based on a 'grade of membership' model (also known as 'admixture' or 'topic' model) in which each sample has an estimated grade of membership in each of K damage profiles that are estimated from the data.<br><br>RESULTS: We illustrate aRchaic on data from several aDNA studies and modern individuals from 1000 Genomes Project Consortium (2012). Here, aRchaic clearly distinguishes modern from ancient samples irrespective of DNA extraction, lab and sequencing protocols. Additionally, through an in-silico contamination experiment, we show that the aRchaic grades of membership reflect relative levels of exogenous modern contamination. Together, the outputs of aRchaic provide a concise visual summary of DNA damage patterns, as well as other processes generating mismatches in the data.<br><br>aRchaic is available for download from https://www.github.com/kkdey/aRchaic.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30191172, year = {2018}, author = {O'Sullivan, N and Posth, C and Coia, V and Schuenemann, VJ and Price, TD and Wahl, J and Pinhasi, R and Zink, A and Krause, J and Maixner, F}, title = {Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard.}, journal = {Science advances}, volume = {4}, number = {9}, pages = {eaao1262}, pmid = {30191172}, issn = {2375-2548}, mesh = {Archaeology ; *Cemeteries ; *DNA, Mitochondrial ; Female ; Genome-Wide Association Study/*methods ; Germany ; Haplotypes ; History, Medieval ; Humans ; Male ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Sex Determination Analysis ; }, abstract = {From historical and archeological records, it is posited that the European medieval household was a combination of close relatives and recruits. However, this kinship structure has not yet been directly tested at a genomic level on medieval burials. The early 7th century CE burial at Niederstotzingen, discovered in 1962, is the most complete and richest example of Alemannic funerary practice in Germany. Excavations found 13 individuals who were buried with an array of inscribed bridle gear, jewelry, armor, and swords. These artifacts support the view that the individuals had contact with France, northern Italy, and Byzantium. This study analyzed genome-wide sequences recovered from the remains, in tandem with analysis of the archeological context, to reconstruct kinship and the extent of outside contact. Eleven individuals had sufficient DNA preservation to genetically sex them as male and identify nine unique mitochondrial haplotypes and two distinct Y chromosome lineages. Genome-wide analyses were performed on eight individuals to estimate genetic affiliation to modern west Eurasians and genetic kinship at the burial. Five individuals were direct relatives. Three other individuals were not detectably related; two of these showed genomic affinity to southern Europeans. The genetic makeup of the individuals shares no observable pattern with their orientation in the burial or the cultural association of their grave goods, with the five related individuals buried with grave goods associated with three diverse cultural origins. These findings support the idea that not only were kinship and fellowship held in equal regard: Diverse cultural appropriation was practiced among closely related individuals as well.}, }
@article {pmid30187463, year = {2018}, author = {Leonardi, M and Sandionigi, A and Conzato, A and Vai, S and Lari, M and Tassi, F and Ghirotto, S and Caramelli, D and Barbujani, G}, title = {The female ancestor's tale: Long-term matrilineal continuity in a nonisolated region of Tuscany.}, journal = {American journal of physical anthropology}, volume = {167}, number = {3}, pages = {497-506}, doi = {10.1002/ajpa.23679}, pmid = {30187463}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Bayes Theorem ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Female ; Genetic Variation ; *Genotype ; Genotyping Techniques ; Humans ; Italy ; }, abstract = {OBJECTIVES: With the advent of ancient DNA analyses, it has been possible to disentangle the contribution of ancient populations to the genetic pool of the modern inhabitants of many regions. Reconstructing the maternal ancestry has often highlighted genetic continuity over several millennia, but almost always in isolated areas. Here we analyze North-western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast.<br><br>MATERIALS AND METHODS: We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000&#x2009;years: Prehistory, Etruscan age, Roman age, Renaissance, and Present-day. We used serial coalescent simulations in an approximate Bayesian computation framework to test for continuity between the mentioned groups.<br><br>RESULTS: Our analyses always favor continuity over discontinuity for all groups considered, with the Etruscans being part of the genealogy. Moreover, the posterior distributions of the parameters support very small female effective population sizes.<br><br>CONCLUSIONS: The observed signals of long-term genetic continuity and isolation are in contrast with the history of the region, conquered several times (Etruscans, Romans, Lombards, and French). While the Etruscans appear as a local population, intermediate between the prehistoric and the other samples, we suggest that the other conquerors-arriving from far-had a consistent social or sex bias, hence only marginally affecting the maternal lineages. At the same time, our results show that long-term genealogical continuity is not necessarily linked to geographical isolation.}, }
@article {pmid30183732, year = {2018}, author = {Guedes, L and Jaeger, LH and Liryo, A and Rodrigues-Carvalho, C and Mendonça de Souza, S and Iñiguez, AM}, title = {Tuberculosis in post-contact Native Americans of Brazil: Paleopathological and paleogenetic evidence from the Tenetehara-Guajajara.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0202394}, pmid = {30183732}, issn = {1932-6203}, mesh = {Bacterial Proteins/genetics ; Base Sequence ; Bone and Bones/*microbiology ; Brazil ; Catalase/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Mitochondrial/genetics ; Fossils/*microbiology ; Haplotypes ; Humans ; Indians, South American/*genetics ; Mycobacterium tuberculosis/genetics/*physiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Tuberculosis/diagnosis/*microbiology ; Type C Phospholipases/genetics ; }, abstract = {Tuberculosis (TB) has been described in Native American populations prior to the arrival of European explorers, and in Brazilian populations dating from the Colonial Period. There are no studies demonstrating TB infection in native Brazilians, and the history and epidemiological scenario of TB in Brazil is still unknown. The aim of this study was to verify the presence of TB infection among the native Tenetehara-Guajajara population from Maranhão State, Brazil, 210 ± 40 years ago. A Tenetehara-Guajajara skeleton collection was submitted to paleopathological analysis, and rib bone samples (n = 17) were used for paleogenetic analysis based on Mycobacterium tuberculosis complex (MTC) targets. Porotic hyperostosis and cribra orbitalia were found in 10 and 13 individuals, respectively. Maternal ancestry analysis revealed Native American mtDNA haplogroups A and C1 in three individuals. Three samples showed osteological evidence suggestive of TB. katG and mtp40 sequences were detected in three individuals, indicating probable TB infection by two MTC lineages. Tuberculosis infection in the Tenetehara-Guajajara population since the 18th century points to a panorama of the disease resulting, most probably, from European contact. However, the important contribution of African slaves in the population of Maranhão State, could be also considered as a source of the disease. This study provides new data on TB during the Brazilian Colonial Period. This is the first report integrating paleopathological and paleogenetic data for the study of TB in Brazil.}, }
@article {pmid30160314, year = {2019}, author = {Lang, PLM and Willems, FM and Scheepens, JF and Burbano, HA and Bossdorf, O}, title = {Using herbaria to study global environmental change.}, journal = {The New phytologist}, volume = {221}, number = {1}, pages = {110-122}, pmid = {30160314}, issn = {1469-8137}, support = {BO 3241/7-1//German Research Foundation/International ; BU 3422/1-1//German Research Foundation/International ; //Presidential Innovation Fund of the Max Planck Society/International ; }, mesh = {Academies and Institutes ; Carbon Dioxide ; Climate Change ; *Ecosystem ; Environmental Monitoring/*methods ; *Environmental Pollution ; Gardens ; Industry ; *Introduced Species ; Metals, Heavy/analysis ; Museums ; Nitrogen ; *Plants ; }, abstract = {During the last centuries, humans have transformed global ecosystems. With their temporal dimension, herbaria provide the otherwise scarce long-term data crucial for tracking ecological and evolutionary changes over this period of intense global change. The sheer size of herbaria, together with their increasing digitization and the possibility of sequencing DNA from the preserved plant material, makes them invaluable resources for understanding ecological and evolutionary species' responses to global environmental change. Following the chronology of global change, we highlight how herbaria can inform about long-term effects on plants of at least four of the main drivers of global change: pollution, habitat change, climate change and invasive species. We summarize how herbarium specimens so far have been used in global change research, discuss future opportunities and challenges posed by the nature of these data, and advocate for an intensified use of these 'windows into the past' for global change research and beyond.}, }
@article {pmid30158639, year = {2018}, author = {Eisenmann, S and Bánffy, E and van Dommelen, P and Hofmann, KP and Maran, J and Lazaridis, I and Mittnik, A and McCormick, M and Krause, J and Reich, D and Stockhammer, PW}, title = {Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13003}, pmid = {30158639}, issn = {2045-2322}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Archaeology/*methods ; DNA, Ancient ; *Fossils ; Genomics/*methods ; Humans ; Skeleton ; *Terminology as Topic ; }, abstract = {Genome-wide ancient DNA analysis of skeletons retrieved from archaeological excavations has provided a powerful new tool for the investigation of past populations and migrations. An important objective for the coming years is to properly integrate ancient genomics into archaeological research. This article aims to contribute to developing a better understanding and cooperation between the two disciplines and beyond. It focuses on the question of how best to name clusters encountered when analysing the genetic makeup of past human populations. Recent studies have frequently borrowed archaeological cultural designations to name these genetic groups, while neglecting the historically problematic nature of the concept of cultures in archaeology. After reviewing current practices in naming genetic clusters, we introduce three possible nomenclature systems ('numeric system', 'mixed system (a)', 'geographic-temporal system') along with their advantages and challenges.}, }
@article {pmid30146150, year = {2018}, author = {Krzewińska, M and Kjellström, A and Günther, T and Hedenstierna-Jonson, C and Zachrisson, T and Omrak, A and Yaka, R and Kılınç, GM and Somel, M and Sobrado, V and Evans, J and Knipper, C and Jakobsson, M and Storå, J and Götherström, A}, title = {Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.}, journal = {Current biology : CB}, volume = {28}, number = {17}, pages = {2730-2738.e10}, doi = {10.1016/j.cub.2018.06.053}, pmid = {30146150}, issn = {1879-0445}, mesh = {Bone and Bones/chemistry ; Cities ; DNA/*genetics ; *Emigration and Immigration/history ; Female ; *Genome-Wide Association Study ; Genomics ; History, Ancient ; Humans ; Male ; Strontium/*chemistry ; Strontium Isotopes ; Sweden ; }, abstract = {The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10[th] to 12[th] century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.}, }
@article {pmid30139851, year = {2018}, author = {Vogel, G}, title = {Ancient DNA reveals tryst between extinct human species.}, journal = {Science (New York, N.Y.)}, volume = {361}, number = {6404}, pages = {737}, doi = {10.1126/science.361.6404.737}, pmid = {30139851}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Bone and Bones ; *DNA, Ancient ; *Extinction, Biological ; Fathers/history ; Female ; History, Ancient ; Humans ; Mothers/history ; Neanderthals/*genetics ; Women/*history ; }, }
@article {pmid30130765, year = {2018}, author = {Senti, S and Habicht, ME and Rayo, E and Eppenberger, PE and Rühli, FJ and Galassi, FM}, title = {Egyptian Canopic Jars at the Crossroad of Medicine and Archaeology: Overview of 100 Years of Research and Future Scientific Expectations.}, journal = {Pathobiology : journal of immunopathology, molecular and cellular biology}, volume = {85}, number = {5-6}, pages = {267-275}, doi = {10.1159/000490797}, pmid = {30130765}, issn = {1423-0291}, mesh = {Archaeology/*history ; Egypt ; History, 20th Century ; History, 21st Century ; History, Ancient ; Humans ; Motivation ; Mummies/history/*pathology ; Research/*history ; Retrospective Studies ; }, abstract = {Ancient Egyptian human remains have been of interest in the fields of both medical and Egyptological research for decades. However, canopic jar holders for internal organs (liver, lungs, stomach, intestines) of Egyptian mummies appear to be but a very occasional source of data for such investigations. The few medical approaches focusing on the content of these jars are summarized and listed according to pathogens and diseases to give a structured overview of this field of study. An extensive search of the literature has been conducted from different bibliographic databases with a total of n = 26 studies found. The majority of diseases found consisted of infectious diseases and internal medicine conditions such as schistosomiasis or emphysema. These are just 2 examples of many that, instead of primarily affecting bone, muscle or skin, specifically target internal organs. Hence, a better understanding of the evolution of diseases that still affect mankind could be gained. In conclusion, this reassessment shows that canopic jars represent a highly underestimated source for histological, radiological and ancient DNA examination of Ancient Egyptian remains and should, thus, be more and more brought back into the focus of retrospective medical research.}, }
@article {pmid30127404, year = {2018}, author = {Harney, &#xc9; and May, H and Shalem, D and Rohland, N and Mallick, S and Lazaridis, I and Sarig, R and Stewardson, K and Nordenfelt, S and Patterson, N and Hershkovitz, I and Reich, D}, title = {Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3336}, pmid = {30127404}, issn = {2041-1723}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Caves ; *Culture ; DNA, Ancient/*analysis ; Genetic Heterogeneity ; Genetic Variation ; *Genetics, Population ; *Geologic Sediments ; Humans ; Israel ; Mutation/genetics ; }, abstract = {The material culture of the Late Chalcolithic period in the southern Levant (4500-3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. Here, to test the hypothesis that the advent and decline of this culture was influenced by movements of people, we generated genome-wide ancient DNA from 22 individuals from Peqi'in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi'in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi'in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.}, }
@article {pmid30127280, year = {2018}, author = {Sereno, D and Dorkeld, F and Akhoundi, M and Perrin, P}, title = {Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools.}, journal = {Genes}, volume = {9}, number = {8}, pages = {}, pmid = {30127280}, issn = {2073-4425}, abstract = {Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. Nevertheless, assigning ancient DNA at the species level is a challenging process. Recently, the gut microbiome analysis of three pre-Columbian Andean mummies (Santiago-Rodriguez et al., 2016) has called into question the identification of Leishmania in South America. The accurate assignment would be important because it will provide some key elements that are linked to the evolutionary scenario for visceral leishmaniasis agents in South America. Here, we recovered the metagenomic data filed in the metagenomics RAST server (MG-RAST) to identify the different members of the Trypanosomatidae family that have infected these ancient remains. For this purpose, we used the ultrafast metagenomic sequence classifier, based on an exact alignment of k-mers (Kraken) and Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The analyses, which have been conducted on the most exhaustive genomic database possible on Trypanosomatidae, show that species assignments could be biased by a lack of some genomic sequences of Trypanosomatidae species (strains). Nevertheless, our work raises the issue of possible co-infections by multiple members of the Trypanosomatidae family in these three pre-Columbian mummies. In the three mummies, we show the presence of DNA that is reminiscent of a probable co-infection with Leptomonas seymouri, a parasite of insect's gut, and Lotmaria.}, }
@article {pmid30125802, year = {2018}, author = {Hoef-Emden, K}, title = {Revision of the Genus Chroomonas HANSGIRG: The Benefits of DNA-containing Specimens.}, journal = {Protist}, volume = {169}, number = {5}, pages = {662-681}, doi = {10.1016/j.protis.2018.04.005}, pmid = {30125802}, issn = {1618-0941}, mesh = {Cryptophyta/*classification/*genetics/growth &amp; development/ultrastructure ; DNA, Ribosomal/genetics ; Microscopy, Electron, Scanning ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {For years the genus Chroomonas was defined as being a cryptophyte with rectangular periplast plates, with a gullet and with biliprotein types PC 630 or 645. In phylogenetic trees the genus proved to be paraphyletic. Moreover, cells with hexagonal periplast plates were found in an SEM preparation from material of the type species C. nordstedtii. In this study, material of Hansgirg's C. nordstedtii was subjected to PCR and to sequencing of two short DNA tags. These tags allowed for an unambiguous identification of the real C. nordstedtii in the phylogeny of the blue-green cryptophytes. The genus Chroomonas corresponds to subclade 1, whereas subclades 3 and 4 do not belong to Chroomonas, if Hemiselmis is maintained. Additional examination by light and scanning electron microscopy and by spectrophotometry demonstrate that subclade 1 comprises only cells with hexagonal periplast plates and PC 630, whereas rectangular periplast plates are found only in subclades 3 and 4. Consequently the genus Chroomonas and its type species, C. nordstedtii, are revised and two novel species, C. debatzensis and C. gentoftensis sp. nov., are described.}, }
@article {pmid30121342, year = {2018}, author = {Bover, P and Llamas, B and Thomson, VA and Pons, J and Cooper, A and Mitchell, KJ}, title = {Molecular resolution to a morphological controversy: The case of North American fossil muskoxen Bootherium and Symbos.}, journal = {Molecular phylogenetics and evolution}, volume = {129}, number = {}, pages = {70-76}, doi = {10.1016/j.ympev.2018.08.008}, pmid = {30121342}, issn = {1095-9513}, mesh = {Alaska ; Animals ; Bayes Theorem ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Female ; *Fossils ; Genome, Mitochondrial ; Male ; Phylogeny ; Ruminants/*anatomy &amp; histology/*genetics ; Texas ; }, abstract = {The musk ox (Ovibos moschatus) is the only surviving member of a group of Pleistocene North American musk ox genera (Praeovibos, Ovibos, Bootherium, Euceratherium, and Soergelia) whose taxonomy is uncertain. The helmeted musk ox (Bootherium bombifrons) and the woodland musk ox (Symbos cavifrons) have been synonymised as male and female forms of a single Nearctic species found from Alaska, in the north, to Texas, in the south. However, this reclassification has not been tested using molecular data, despite the potential to use ancient DNA to examine these late Pleistocene taxa. In the present study, we sequenced mitochondrial genomes from seven subfossil musk ox specimens (originally identified as Bootherium and/or Symbos), allowing us to evaluate the identity of these muskoxen, explore their phylogeography, and estimate the timeline for their evolution. We also used nuclear genomic data to determine the sex of six of our seven samples. Ultimately, our molecular data support the synonymisation of the North American muskoxen Bootherium and Symbos.}, }
@article {pmid30108597, year = {2018}, author = {Zhu, B and Li, H and Wen, J and Mysore, KS and Wang, X and Pei, Y and Niu, L and Lin, H}, title = {Functional Specialization of Duplicated AGAMOUS Homologs in Regulating Floral Organ Development of Medicago truncatula.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {854}, pmid = {30108597}, issn = {1664-462X}, abstract = {The C function gene AGAMOUS (AG) encodes for a MADS-box transcription factor required for floral organ identity and floral meristem (FM) determinacy in angiosperms. Unlike Arabidopsis, most legume plants possess two AG homologs arose by an ancient genome duplication event. Recently, two euAGAMOUS genes, MtAGa and MtAGb, were characterized and shown to fulfill the C function activity in the model legume Medicago truncatula. Here, we reported the isolation and characterization of a new mtaga allele by screening the Medicago Tnt1 insertion mutant collection. We found that MtAGa was not only required for controlling the stamen and carpel identity but also affected pod and seed development. Genetic analysis indicated that MtAGa and MtAGb redundantly control Medicago floral organ identity, but have minimal distinct functions in regulating stamen and carpel development in a dose-dependent manner. Interestingly, the stamens and carpels are mostly converted to numerous vexillum-like petals in the double mutant of mtaga mtagb, which is distinguished from Arabidopsis ag. Further qRT-PCR analysis in different mtag mutants revealed that MtAGa and MtAGb can repress the expression of putative A and B function genes as well as MtWUS, but promote putative D function genes expression in M. truncatula. In addition, we found that the abnormal dorsal petal phenotype observed in the mtaga mtagb double mutant is associated with the upregulation of CYCLOIDEA (CYC)-like TCP genes. Taken together, our data suggest that the redundant MtAGa and MtAGb genes of M. truncatula employ a conserved mechanism of action similar to Arabidopsis in determining floral organ identity and FM determinacy but may have evolved distinct function in regulating floral symmetry by coordinating with specific floral dorsoventral identity factors.}, }
@article {pmid30107783, year = {2018}, author = {Cruz-Dávalos, DI and Nieves-Colón, MA and Sockell, A and Poznik, GD and Schroeder, H and Stone, AC and Bustamante, CD and Malaspinas, AS and Ávila-Arcos, MC}, title = {In-solution Y-chromosome capture-enrichment on ancient DNA libraries.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {608}, pmid = {30107783}, issn = {1471-2164}, support = {IA206817//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; FP7/2007-2013, grant no. 290344, EUROTAST//European Research Council/International ; }, mesh = {*Chromosomes, Human, Y ; DNA, Ancient/*analysis/*isolation &amp; purification ; *Gene Library ; Genomics ; History, Ancient ; Humans ; Sequence Analysis, DNA/*methods ; Whole Genome Sequencing/*methods ; }, abstract = {BACKGROUND: As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach-in-solution capture-enrichment-retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries.<br><br>RESULTS: The six samples show different levels of initial endogenous content, with very low (<&#x2009;0.05%, 4 samples) or low (0.1-1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12-9549 times more targeted unique Y-chromosome sequences after capture, where 0.0-6.2% (WGC&#x2009;+&#x2009;YCC) and 0.0-23.5% (YCC) of the sequence reads were on-target, compared to 0.0-0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC&#x2009;+&#x2009;YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries' initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins.<br><br>CONCLUSIONS: We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC&#x2009;+&#x2009;YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round.}, }
@article {pmid30104352, year = {2018}, author = {George, RJ and Plog, S and Watson, AS and Schmidt, KL and Culleton, BJ and Harper, TK and Gilman, PA and LeBlanc, SA and Amato, G and Whiteley, P and Kistler, L and Kennett, DJ}, title = {Archaeogenomic evidence from the southwestern US points to a pre-Hispanic scarlet macaw breeding colony.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {35}, pages = {8740-8745}, pmid = {30104352}, issn = {1091-6490}, mesh = {Animals ; *Breeding ; *Fossils ; *Models, Biological ; Parrots/*physiology ; Phylogeography ; Southwestern United States ; }, abstract = {Hundreds of scarlet macaw (Ara macao cyanoptera) skeletons have been recovered from archaeological contexts in the southwestern United States and northwestern Mexico (SW/NW). The location of these skeletons, >1,000 km outside their Neotropical endemic range, has suggested a far-reaching pre-Hispanic acquisition network. Clear evidence for scarlet macaw breeding within this network is only known from the settlement of Paquimé in NW dating between 1250 and 1450 CE. Although some scholars have speculated on the probable existence of earlier breeding centers in the SW/NW region, there has been no supporting evidence. In this study, we performed an ancient DNA analysis of scarlet macaws recovered from archaeological sites in Chaco Canyon and the contemporaneous Mimbres area of New Mexico. All samples were directly radiocarbon dated between 900 and 1200 CE. We reconstructed complete or near-complete mitochondrial genome sequences of 14 scarlet macaws from five different sites. We observed remarkably low genetic diversity in this sample, consistent with breeding of a small founder population translocated outside their natural range. Phylogeographic comparisons of our ancient DNA mitogenomes with mitochondrial sequences from macaws collected during the last 200 years from their endemic Neotropical range identified genetic affinity between the ancient macaws and a single rare haplogroup (Haplo6) observed only among wild macaws in Mexico and northern Guatemala. Our results suggest that people at an undiscovered pre-Hispanic settlement dating between 900 and 1200 CE managed a macaw breeding colony outside their endemic range and distributed these symbolically important birds through the SW.}, }
@article {pmid30101195, year = {2018}, author = {Potter, BA and Baichtal, JF and Beaudoin, AB and Fehren-Schmitz, L and Haynes, CV and Holliday, VT and Holmes, CE and Ives, JW and Kelly, RL and Llamas, B and Malhi, RS and Miller, DS and Reich, D and Reuther, JD and Schiffels, S and Surovell, TA}, title = {Current evidence allows multiple models for the peopling of the Americas.}, journal = {Science advances}, volume = {4}, number = {8}, pages = {eaat5473}, pmid = {30101195}, issn = {2375-2548}, mesh = {Americas ; *Biological Evolution ; Emigration and Immigration/*history ; History, Ancient ; Humans ; *Models, Theoretical ; Population Dynamics ; }, abstract = {Some recent academic and popular literature implies that the problem of the colonization of the Americas has been largely resolved in favor of one specific model: a Pacific coastal migration, dependent on high marine productivity, from the Bering Strait to South America, thousands of years before Clovis, the earliest widespread cultural manifestation south of the glacial ice. Speculations on maritime adaptations and typological links (stemmed points) across thousands of kilometers have also been advanced. A review of the current genetic, archeological, and paleoecological evidence indicates that ancestral Native American population expansion occurred after 16,000 years ago, consistent with the archeological record, particularly with the earliest securely dated sites after ~15,000 years ago. These data are largely consistent with either an inland (ice-free corridor) or Pacific coastal routes (or both), but neither can be rejected at present. Systematic archeological and paleoecological investigations, informed by geomorphology, are required to test each hypothesis.}, }
@article {pmid30099804, year = {2018}, author = {Iliescu, FM and Chaplin, G and Rai, N and Jacobs, GS and Basu Mallick, C and Mishra, A and Thangaraj, K and Jablonski, NG}, title = {The influences of genes, the environment, and social factors on the evolution of skin color diversity in India.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {30}, number = {5}, pages = {e23170}, doi = {10.1002/ajhb.23170}, pmid = {30099804}, issn = {1520-6300}, support = {//Darwin Trust of Edinburgh/International ; //Department of Biotechnology, Ministry of Science and Technology/International ; //Marie Sklodowska-Curie Actions Individual Fellowship/International ; RG47772//UK-India Education Research Initiative/International ; }, mesh = {*Biological Evolution ; Female ; Humans ; India ; Male ; *Phenotype ; *Selection, Genetic ; Sex Factors ; Skin Pigmentation/genetics/*physiology/radiation effects ; Ultraviolet Rays ; }, abstract = {OBJECTIVES: Skin color is a highly visible and variable trait across human populations. It is not yet clear how evolutionary forces interact to generate phenotypic diversity. Here, we sought to unravel through an integrative framework the role played by three factors-demography and migration, sexual selection, and natural selection-in driving skin color diversity in India.<br><br>METHODS: Skin reflectance data were collected from 10 diverse socio-cultural populations along the latitudinal expanse of India, including both sexes. We first looked at how skin color varies within and between these populations. Second, we compared patterns of sexual dimorphism in skin color. Third, we studied the influence of ultraviolet radiation on skin color throughout India. Finally, we attempted to disentangle the interactions between these factors in the context of available genetic data.<br><br>RESULTS: We found that the relative importance of these forces varied between populations. Social factors and population structure have played a stronger role than natural selection in shaping skin color diversity across India. Phenotypic overprinting resulted from additional genetic mutations overriding the skin lightening effect of variants such as the SLC24A5 rs1426654-A allele in some populations, in the context of the variable influence of sexual selection. Furthermore, specific genotypes are not associated reliably with specific skin color phenotypes. This result has relevance for DNA forensics and ancient DNA research.<br><br>CONCLUSIONS: India is a crucible of macro- and micro-evolutionary forces, and the complex interactions of physical and social forces are visible in the patterns of skin color seen today in the country.}, }
@article {pmid30089624, year = {2018}, author = {Star, B and Barrett, JH and Gondek, AT and Boessenkool, S}, title = {Ancient DNA reveals the chronology of walrus ivory trade from Norse Greenland.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1884}, pages = {}, pmid = {30089624}, issn = {1471-2954}, mesh = {Animals ; Commerce/*history ; Cuspid/*chemistry ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Greenland ; History, Medieval ; Walruses/*genetics ; }, abstract = {The importance of the Atlantic walrus ivory trade for the colonization, peak, and collapse of the medieval Norse colonies on Greenland has been extensively debated. Nevertheless, no studies have directly traced medieval European ivory back to distinct Arctic populations of walrus. Analysing the entire mitogenomes of 37 archaeological specimens from Europe, Svalbard, and Greenland, we here discover that Atlantic walrus comprises two monophyletic mitochondrial (MT) clades, which diverged between 23 400 and 251 120 years ago. Our improved genomic resolution allows us to reinterpret the geographical distribution of partial MT data from 306 modern and nineteenth-century specimens, finding that one of these clades was exclusively accessible to Greenlanders. With this discovery, we ascertain the biological origin of 23 archaeological specimens from Europe (most dated between 900 and 1400 CE). These results reveal a significant shift in trade from an early, predominantly eastern source towards a near exclusive representation of Greenland ivory. Our study provides empirical evidence for how this remote Arctic resource was progressively integrated into a medieval pan-European trade network, contributing to both the resilience and vulnerability of Norse Greenland society.}, }
@article {pmid30081254, year = {2018}, author = {Veeramah, KR}, title = {The importance of fine-scale studies for integrating paleogenomics and archaeology.}, journal = {Current opinion in genetics &amp; development}, volume = {53}, number = {}, pages = {83-89}, doi = {10.1016/j.gde.2018.07.007}, pmid = {30081254}, issn = {1879-0380}, mesh = {Archaeology/*trends ; Cultural Evolution ; DNA, Ancient ; Genetics, Population/*trends ; *Genomics ; *Human Migration ; Humans ; Paleontology/trends ; }, abstract = {There has been an undercurrent of intellectual tension between geneticists studying human population history and archaeologists for almost 40 years. The rapid development of paleogenomics, with geneticists working on the very material discovered by archaeologists, appears to have recently heightened this tension. The relationship between these two fields thus far has largely been of a multidisciplinary nature, with archaeologists providing the raw materials for sequencing, as well as a scaffold of hypotheses based on interpretation of archaeological cultures from which the geneticists can ground their inferences from the genomic data. Much of this work has taken place in the context of western Eurasia, which is acting as testing ground for the interaction between the disciplines. Perhaps the major finding has not been any particular historical episode, but rather the apparent pervasiveness of migration events, some apparently of substantial scale, over the past ∼5000 years, challenging the prevailing view of archaeology that largely dismissed migration as a driving force of cultural change in the 1960s. However, while the genetic evidence for `migration' is generally statistically sound, the description of these events as structured behaviours is lacking, which, coupled with often over simplistic archaeological definitions, prevents the use of this information by archaeologists for studying the social processes they are interested in. In order to integrate paleogenomics and archaeology in a truly interdisciplinary manner, it will be necessary to focus less on grand narratives over space and time, and instead integrate genomic data with other form of archaeological information at the level of individual communities to understand the internal social dynamics, which can then be connected amongst communities to model migration at a regional level. A smattering of recent studies have begun to follow this approach, resulting in inferences that are not only helping ask questions that are currently relevant to archaeologists, but also potentially opening up new avenues of research.}, }
@article {pmid30079081, year = {2018}, author = {Shriner, D}, title = {Re-analysis of Whole Genome Sequence Data From 279 Ancient Eurasians Reveals Substantial Ancestral Heterogeneity.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {268}, pmid = {30079081}, issn = {1664-8021}, support = {ZIA HG200362//Intramural NIH HHS/United States ; }, abstract = {Supervised clustering or projection analysis is a staple technique in population genetic analysis. The utility of this technique depends critically on the reference panel. The most commonly used reference panel in the analysis of ancient DNA to date is based on the Human Origins array. We previously described a larger reference panel that captures more ancestries on the global level. Here, I reanalyzed DNA data from 279 ancient Eurasians using our reference panel. I found substantially more ancestral heterogeneity than has been reported. Reanalysis provides evidence against a resurgence of Western hunter-gatherer ancestry in the Middle to Late Neolithic and evidence for a common ancestor of farmers characterized by Western Asian ancestry, a transition of the spread of agriculture from demic to cultural diffusion, at least two migrations between the Pontic-Caspian steppes and Bronze Age Europe, and a sub-Saharan African component in Natufians that localizes to present-day southern Ethiopia.}, }
@article {pmid30065103, year = {2018}, author = {Larmuseau, MHD and Bodner, M}, title = {The biological relevance of a medieval king's DNA.}, journal = {Biochemical Society transactions}, volume = {46}, number = {4}, pages = {1013-1020}, doi = {10.1042/BST20170173}, pmid = {30065103}, issn = {1470-8752}, mesh = {Archaeology ; DNA, Mitochondrial/*genetics ; Forensic Anthropology ; Forensic Genetics ; Humans ; Pedigree ; Privacy ; United Kingdom ; }, abstract = {The discovery of the presumably lost grave of the controversial English king Richard III in Leicester (U.K.) was one of the most important archaeological achievements of the last decennium. The skeleton was identified beyond reasonable doubt, mainly by the match of mitochondrial DNA to that of living maternal relatives, along with the specific archaeological context. Since the genetic genealogical analysis only involved the DNA sequences of a single 15th century individual and a few reference persons, biologists might consider this investigation a mere curiosity. This mini-review shows that the unique context of a historical king's DNA also has relevance for biological research per se - in addition to the more obvious historical, societal and educational value. In the first place, the historical identification appeared to be a renewed forensic case realising a conservative statement with statistical power based on genetic and non-genetic data, including discordant elements. Secondly, the observation of historical non-paternity events within Richard III's patrilineage has given rise to new research questions about potential factors influencing the extra-pair paternity rate in humans and the importance of biological relatedness for the legal recognition of a child in the past. Thirdly, the identification of a named and dated skeleton with the known historical context serves as a reference for bioarchaeological investigations and studies on the spatio-temporal distribution of particular genetic variance. Finally, the Richard III case revealed privacy issues for living relatives which appear to be inherent to any publication of genetic genealogical data.}, }
@article {pmid30053542, year = {2018}, author = {Leles, D and Cascardo, P and Pucu, E and Brener, B and Sudré, A and Alves, E and Uchoa, F and Fajardo, P and Millar, P and Mattos, D and Chame, M and Cartelle, C}, title = {Methodological innovations for the study of irreplaceable samples reveal giardiasis in extinct animals (Nothrotherium maquinense and Palaeolama maior).}, journal = {Parasitology international}, volume = {67}, number = {6}, pages = {776-780}, doi = {10.1016/j.parint.2018.07.011}, pmid = {30053542}, issn = {1873-0329}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Brazil ; *Camelids, New World ; Cytoskeletal Proteins/analysis ; DNA, Ancient/*analysis ; Giardia lamblia/isolation &amp; purification ; Giardiasis/parasitology/*veterinary ; Immunologic Tests/methods/veterinary ; Paleontology/*methods ; Parasitology/*methods ; Protozoan Proteins/analysis ; *Xenarthra ; }, abstract = {The use of diagnostic methods that prevent irreplaceable samples (from museum collections, archaeological and paleontological samples) of being consumed or that increase their yield is relevant. For museum collections, archaeological and paleontological samples it is essential to conserve samples, subsamples or portions for future research. We are addressing methods for conservation of irreplaceable samples that could be fully consumed. Innovations in methodologies that are used in studies of Paleoparasitology and Paleomicrobiology will contribute to the preservation of collections. Therefore, to the development of archaeology and paleontology in the future, we evaluated whether the discarded material of the immunochromatography test could be used for molecular diagnosis and vice versa. We used a genotyped experimental coprolite positive for Giardia duodenalis. The diagnosis was positive for giardiasis in both cases. This methodology can be corroborated with the coprolite of a Paleolama maior (extinct llama) previously diagnosed for G. duodenalis with an immunoenzymatic test. The residue of the pre-digestion step of the DNA extraction before adding Proteinase K was confirmed positive with the immunochromatographic test. Also, the DNA extraction residue from a coprolite of Nothrotherium maquinense (ground sloth) was tested positive with immunochromatographic test for G. duodenalis. These are the oldest findings for G. duodenalis confirming that this intestinal parasite occurred among Northeastern Brazilian Megafauna animals from the late Pleistocene period, correlated to human occupation. The relevance of these results will allow the study by different methodological approaches from a small amount of material, reusing discarded materials.}, }
@article {pmid30051821, year = {2018}, author = {Rodrigues, ASL and Charpentier, A and Bernal-Casasola, D and Gardeisen, A and Nores, C and Pis Millán, JA and McGrath, K and Speller, CF}, title = {Forgotten Mediterranean calving grounds of grey and North Atlantic right whales: evidence from Roman archaeological records.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1882}, pages = {}, pmid = {30051821}, issn = {1471-2954}, mesh = {Animals ; Archaeology ; DNA Barcoding, Taxonomic ; Homing Behavior ; Mediterranean Sea ; *Sexual Behavior, Animal ; Whales/genetics/*physiology ; }, abstract = {Right whales (Eubalaena glacialis) were extirpated from the eastern North Atlantic by commercial whaling. Grey whales (Eschrichtius robustus) disappeared from the entire North Atlantic in still-mysterious circumstances. Here, we test the hypotheses that both species previously occurred in the Mediterranean Sea, an area not currently considered part of their historical range. We used ancient DNA barcoding and collagen fingerprinting methods to taxonomically identify a rare set of 10 presumed whale bones from Roman and pre-Roman archaeological sites in the Strait of Gibraltar region, plus an additional bone from the Asturian coast. We identified three right whales, and three grey whales, demonstrating that the ranges of both of these species historically encompassed the Gibraltar region, probably including the Mediterranean Sea as calving grounds. Our results significantly extend the known range of the Atlantic grey whale, and suggest that 2000 years ago, right and grey whales were common when compared with other whale species. The disappearance of right and grey whales from the Mediterranean region is likely to have been accompanied by broader ecosystem impacts, including the disappearance of their predators (killer whales) and a reduction in marine primary productivity. The evidence that these two coastal and highly accessible species were present along the shores of the Roman Empire raises the hypothesis that they may have formed the basis of a forgotten whaling industry.}, }
@article {pmid30047322, year = {2017}, author = {Long, J}, title = {Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, by David Reich.}, journal = {Human biology}, volume = {89}, number = {4}, pages = {303-304}, pmid = {30047322}, issn = {1534-6617}, }
@article {pmid30037043, year = {2018}, author = {Honka, J and Heino, MT and Kvist, L and Askeyev, IV and Shaymuratova, DN and Askeyev, OV and Askeyev, AO and Heikkinen, ME and Searle, JB and Aspi, J}, title = {Over a Thousand Years of Evolutionary History of Domestic Geese from Russian Archaeological Sites, Analysed Using Ancient DNA.}, journal = {Genes}, volume = {9}, number = {7}, pages = {}, pmid = {30037043}, issn = {2073-4425}, abstract = {The European domestic goose is a widely farmed species known to have descended from the wild greylag goose (Anser anser). However, the evolutionary history of this domesticate is still poorly known. Ancient DNA studies have been useful for many species, but there has been little such work on geese. We have studied temporal genetic variation among domestic goose specimens excavated from Russian archaeological sites (4th[-]18th centuries) using a 204 base pair fragment of the mitochondrial control region. Specimens fell into three different genetic clades: the domestic D-haplogroup, the F-haplogroup that includes both wild and domestic geese, and a clade comprising another species, the taiga bean goose. Most of the subfossil geese carried typical domestic D-haplotypes. The domestication status of the geese carrying F-haplotypes is less certain, as the haplotypes identified were not present among modern domestic geese and could represent wild geese (misclassified as domestics), introgression from wild geese, or local domestication events. The bones of taiga bean goose were most probably misidentified as domestic goose but the domestication of bean goose or hybridization with domestic goose is also possible. Samples from the 4th to 10th century were clearly differentiated from the later time periods due to a haplotype that was found only in this early period, but otherwise no temporal or geographical variation in haplotype frequencies was apparent.}, }
@article {pmid30035382, year = {2018}, author = {Kisand, V and Talas, L and Kisand, A and Stivrins, N and Reitalu, T and Alliksaar, T and Vassiljev, J and Liiv, M and Heinsalu, A and Seppä, H and Veski, S}, title = {From microbial eukaryotes to metazoan vertebrates: Wide spectrum paleo-diversity in sedimentary ancient DNA over the last ~14,500 years.}, journal = {Geobiology}, volume = {16}, number = {6}, pages = {628-639}, doi = {10.1111/gbi.12307}, pmid = {30035382}, issn = {1472-4669}, support = {//European Regional Development Fund through the Centre of Excellence in Chemical Biology/International ; //Biotieteiden ja Ymp&#xe4;rist&#xf6;n Tutkimuksen Toimikunta/International ; IUT1-8//Eesti Teadusagentuur/International ; IUT21-2//Eesti Teadusagentuur/International ; PUT134//Eesti Teadusagentuur/International ; PUT1389//Eesti Teadusagentuur/International ; //EBOR project, Academy of Finland/International ; }, mesh = {Animals ; DNA, Ancient/*analysis ; Geologic Sediments/*microbiology ; RNA, Ribosomal, 18S/analysis ; Sequence Analysis, DNA ; Vertebrates ; }, abstract = {Most studies that utilize ancient DNA have focused on specific groups of organisms or even single species. Instead, the whole biodiversity of eukaryotes can be described using universal phylogenetic marker genes found within well-preserved sediment cores that cover the post-glacial period. Sedimentary ancient DNA samples from Lake Lielais Svētiņu, eastern Latvia, at a core depth of 1,050 cm in ~150 year intervals were used to determine phylotaxonomy in domain Eukaryota. Phylotaxonomic affiliation of >1,200 eukaryotic phylotypes revealed high richness in all major eukaryotic groups-Alveolata, Stramenopiles, Cercozoa, Chlorophyta, Charophyta, Nucletmycea, and Holozoa. The share of organisms that originate from terrestrial ecosystems was about one third, of which the most abundant molecular operational taxonomic units were Fungi and tracheal/vascular plants, which demonstrates the usefulness of using lake sediments to reconstruct the terrestrial paleoecosystems that surround them. Phylotypes that originate from the lake ecosystem belonged to various planktonic organisms; phyto-, proto,- and macrozooplankton, and vascular aquatic plants. We observed greater richness of several planktonic organisms that can be associated with higher trophic status during the warm climate period between 4,000 and 8,000 years ago and an increase in eukaryotic richness possibly associated with moderate human impact over the last 2,000 years.}, }
@article {pmid30035235, year = {2018}, author = {Velsko, IM and Frantz, LAF and Herbig, A and Larson, G and Warinner, C}, title = {Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research.}, journal = {mSystems}, volume = {3}, number = {4}, pages = {}, pmid = {30035235}, issn = {2379-5077}, support = {/WT_/Wellcome Trust/United Kingdom ; 337574/ERC_/European Research Council/International ; R01 GM089886/GM/NIGMS NIH HHS/United States ; }, abstract = {Metagenomics enables the study of complex microbial communities from myriad sources, including the remains of oral and gut microbiota preserved in archaeological dental calculus and paleofeces, respectively. While accurate taxonomic assignment is essential to this process, DNA damage characteristic of ancient samples (e.g., reduction in fragment size and cytosine deamination) may reduce the accuracy of read taxonomic assignment. Using a set of in silico-generated metagenomic data sets, we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely used profilers: QIIME/UCLUST, MetaPhlAn2, MIDAS, CLARK-S, and MALT. In silico-generated data sets were designed to mimic dental plaque, consisting of 40, 100, and 200 microbial species/strains, both with and without simulated aDNA damage patterns. Following taxonomic assignment, the profiles were evaluated for species presence/absence, relative abundance, alpha diversity, beta diversity, and specific taxonomic assignment biases. Unifrac metrics indicated that both MIDAS and MetaPhlAn2 reconstructed the most accurate community structure. QIIME/UCLUST, CLARK-S, and MALT had the highest number of inaccurate taxonomic assignments; false-positive rates were highest by CLARK-S and QIIME/UCLUST. Filtering out species present at <0.1% abundance greatly increased the accuracy of CLARK-S and MALT. All programs except CLARK-S failed to detect some species from the input file that were in their databases. The addition of ancient DNA damage resulted in minimal differences in species detection and relative abundance between simulated ancient and modern data sets for most programs. Overall, taxonomic profiling biases are program specific rather than damage dependent, and the choice of taxonomic classification program should be tailored to specific research questions. IMPORTANCE Ancient biomolecules from oral and gut microbiome samples have been shown to be preserved in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offers a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to accurately reconstruct community assemblages. It is therefore necessary to assess whether ancient DNA (aDNA) damage patterns affect metagenomic taxonomic profiling. Here, we assessed biases in community structure, diversity, species detection, and relative abundance estimates by five popular metagenomic taxonomic classification programs using in silico-generated data sets with and without aDNA damage. Damage patterns had minimal impact on the taxonomic profiles produced by each program, while false-positive rates and biases were intrinsic to each program. Therefore, the most appropriate classification program is one that minimizes the biases related to the questions being addressed.}, }
@article {pmid30033331, year = {2018}, author = {Zhou, Z and Lundstrøm, I and Tran-Dien, A and Duchêne, S and Alikhan, NF and Sergeant, MJ and Langridge, G and Fotakis, AK and Nair, S and Stenøien, HK and Hamre, SS and Casjens, S and Christophersen, A and Quince, C and Thomson, NR and Weill, FX and Ho, SYW and Gilbert, MTP and Achtman, M}, title = {Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.}, journal = {Current biology : CB}, volume = {28}, number = {15}, pages = {2420-2428.e10}, pmid = {30033331}, issn = {1879-0445}, support = {BB/L027801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; R01 GM114817/GM/NIGMS NIH HHS/United States ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; 202792/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BB/L020319/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {DNA, Ancient/*analysis ; DNA, Bacterial/*analysis ; Female ; *Genomic Instability ; Genomic Islands ; Humans ; Norway ; Salmonella enterica/*genetics ; Typhoid Fever/*microbiology ; }, abstract = {Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia [1]. Paratyphi C is very rare in Europe and North America except for occasional travelers from South and East Asia or Africa, where the disease is more common [2, 3]. However, early 20[th]-century observations in Eastern Europe [3, 4] suggest that Paratyphi C enteric fever may once have had a wide-ranging impact on human societies. Here, we describe a draft Paratyphi C genome (Ragna) recovered from the 800-year-old skeleton (SK152) of a young woman in Trondheim, Norway. Paratyphi C sequences were recovered from her teeth and bones, suggesting that she died of enteric fever and demonstrating that these bacteria have long caused invasive salmonellosis in Europeans. Comparative analyses against modern Salmonella genome sequences revealed that Paratyphi C is a clade within the Para C lineage, which also includes serovars Choleraesuis, Typhisuis, and Lomita. Although Paratyphi C only infects humans, Choleraesuis causes septicemia in pigs and boar [5] (and occasionally humans), and Typhisuis causes epidemic swine salmonellosis (chronic paratyphoid) in domestic pigs [2, 3]. These different host specificities likely evolved in Europe over the last ∼4,000 years since the time of their most recent common ancestor (tMRCA) and are possibly associated with the differential acquisitions of two genomic islands, SPI-6 and SPI-7. The tMRCAs of these bacterial clades coincide with the timing of pig domestication in Europe [6].}, }
@article {pmid30027753, year = {2018}, author = {Palomo-Díez, S and Esparza Arroyo, &#xc1; and Tirado-Vizcaíno, M and Velasco Vázquez, J and López-Parra, AM and Gomes, C and Baeza-Richer, C and Arroyo-Pardo, E}, title = {Kinship analysis and allelic dropout: a forensic approach on an archaeological case.}, journal = {Annals of human biology}, volume = {45}, number = {4}, pages = {365-368}, doi = {10.1080/03014460.2018.1484159}, pmid = {30027753}, issn = {1464-5033}, mesh = {Adolescent ; Adult ; Archaeology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Family ; *Family Relations ; Female ; Fetus ; Genetic Markers ; Humans ; Infant, Newborn ; Male ; Microsatellite Repeats/*genetics ; Spain ; Young Adult ; }, abstract = {BACKGROUND: This study relies on the discovery of two pit burials (LTA and LTB) of the Bronze Age Cogotas I archaeological culture (circa 3600-2950 BP) in Spain. LTA was a single burial and LTB contained three skeletal remains of two adults and a newborn or foetus at term.<br><br>AIM: The central question posed by this find was whether the LTB tomb constituted a traditional nuclear family (father, mother and son or daughter).<br><br>METHODS: Ancient and forensic DNA protocols were employed to obtain reliable results. Autosomal, X-STR markers and mitochondrial DNA were amplified. Subsequently, different kinship probabilities were estimated by means of LR values calculated using the Familias 3 software. Furthermore, an allelic dropout sensitivity test was developed in order to evaluate the influence of allelic dropout phenomena on the results.<br><br>RESULTS: It was possible to determine the molecular sex of all individuals and to establish a maternal relationship between the perinatal individual and one of the adults.<br><br>CONCLUSION: The remains in the LTB tomb were not a traditional nuclear family (father, mother and son/daughter) and it was probably a tomb where two women, one of them pregnant, were buried.}, }
@article {pmid30017480, year = {2018}, author = {Maixner, F and Turaev, D and Cazenave-Gassiot, A and Janko, M and Krause-Kyora, B and Hoopmann, MR and Kusebauch, U and Sartain, M and Guerriero, G and O'Sullivan, N and Teasdale, M and Cipollini, G and Paladin, A and Mattiangeli, V and Samadelli, M and Tecchiati, U and Putzer, A and Palazoglu, M and Meissen, J and Lösch, S and Rausch, P and Baines, JF and Kim, BJ and An, HJ and Gostner, P and Egarter-Vigl, E and Malfertheiner, P and Keller, A and Stark, RW and Wenk, M and Bishop, D and Bradley, DG and Fiehn, O and Engstrand, L and Moritz, RL and Doble, P and Franke, A and Nebel, A and Oeggl, K and Rattei, T and Grimm, R and Zink, A}, title = {The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals.}, journal = {Current biology : CB}, volume = {28}, number = {14}, pages = {2348-2355.e9}, pmid = {30017480}, issn = {1879-0445}, support = {P50 GM076547/GM/NIGMS NIH HHS/United States ; R01 GM087221/GM/NIGMS NIH HHS/United States ; S10 RR027584/RR/NCRR NIH HHS/United States ; }, mesh = {Archaeology ; Austria ; Diet/*history ; Dietary Fats ; Edible Grain ; History, Ancient ; Humans ; Italy ; Male ; Meat ; *Mummies ; }, abstract = {The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.}, }
@article {pmid29993816, year = {2018}, author = {Luhmann, N and Chauve, C and Stoye, J and Wittler, R}, title = {Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {15}, number = {6}, pages = {2094-2100}, doi = {10.1007/978-3-319-12418-6_17}, pmid = {29993816}, issn = {1557-9964}, mesh = {Algorithms ; Animals ; *DNA/analysis/classification/genetics ; DNA, Ancient/*analysis ; Evolution, Molecular ; Genomics/*methods ; History, Ancient ; History, Medieval ; Humans ; Models, Genetic ; Paleontology ; Phylogeny ; Plague/history/microbiology ; Rats ; Sequence Alignment/methods ; Sequence Analysis, DNA/*methods ; Yersinia pestis/classification/genetics ; }, abstract = {Ancestral genome reconstruction is an important task to analyze the evolution of genomes. Recent progress in sequencing ancient DNA led to the publication of so-called paleogenomes and allows the integration of this sequencing data in genome evolution analysis. However, the de novo assembly of ancient genomes is usually fragmented due to DNA degradation over time among others. Integrated phylogenetic assembly addresses the issue of genome fragmentation in the ancient DNA assembly while aiming to improve the reconstruction of all ancient genomes in the phylogeny simultaneously. The fragmented assembly of the ancient genome can be represented as an assembly graph, indicating contradicting ordering information of contigs. In this setting, our approach is to compare the ancient data with extant finished genomes. We generalize a reconstruction approach minimizing the Single-Cut-or-Join rearrangement distance towards multifurcating trees and include edge lengths to improve the reconstruction in practice. This results in a polynomial time algorithm that includes additional ancient DNA data at one node in the tree, resulting in consistent reconstructions of ancestral genomes.}, }
@article {pmid29987016, year = {2018}, author = {Seersholm, FV and Cole, TL and Grealy, A and Rawlence, NJ and Greig, K and Knapp, M and Stat, M and Hansen, AJ and Easton, LJ and Shepherd, L and Tennyson, AJD and Scofield, RP and Walter, R and Bunce, M}, title = {Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {30}, pages = {7771-7776}, pmid = {29987016}, issn = {1091-6490}, mesh = {Animals ; *Biodiversity ; *Bone and Bones ; DNA/chemistry/*genetics/isolation &amp; purification ; *Fossils ; *Gene Pool ; New Zealand ; }, abstract = {New Zealand's geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans 750 y ago, its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and timing of past extinctions. The exact temporal and spatial dynamics of New Zealand's extinct fauna, however, can be difficult to interpret, as only a small proportion of animals are preserved as morphologically identifiable fossils. Here, we conduct a large-scale genetic survey of subfossil bone assemblages to elucidate the impact of humans on the environment in New Zealand. By genetically identifying more than 5,000 nondiagnostic bone fragments from archaeological and paleontological sites, we reconstruct a rich faunal record of 110 species of birds, fish, reptiles, amphibians, and marine mammals. We report evidence of five whale species rarely reported from New Zealand archaeological middens and characterize extinct lineages of leiopelmatid frog (Leiopelma sp.) and kākāpō (Strigops habroptilus) haplotypes lost from the gene pool. Taken together, this molecular audit of New Zealand's subfossil record not only contributes to our understanding of past biodiversity and precontact Māori subsistence practices but also provides a more nuanced snapshot of anthropogenic impacts on native fauna after first human arrival.}, }
@article {pmid29977605, year = {2018}, author = {Larsen, BB and Cole, KL and Worobey, M}, title = {Ancient DNA provides evidence of 27,000-year-old papillomavirus infection and long-term codivergence with rodents.}, journal = {Virus evolution}, volume = {4}, number = {1}, pages = {vey014}, pmid = {29977605}, issn = {2057-1577}, abstract = {The long-term evolutionary history of many viral lineages is poorly understood. Novel sources of ancient DNA combined with phylogenetic analyses can provide insight into the time scale of virus evolution. Here we report viral sequences from ancient North American packrat middens. We screened samples up to 27,000-years old and found evidence of papillomavirus (PV) infection in Neotoma cinerea (Bushy-tailed packrat). Phylogenetic analysis placed the PV sequences in a clade with other previously published PV sequences isolated from rodents. Concordance between the host and virus tree topologies along with a correlation in branch lengths suggests a shared evolutionary history between rodents and PVs. Based on host divergence times, PVs have likely been circulating in rodents for at least 17 million years. These results have implications for our understanding of PV evolution and for further research with ancient DNA from Neotoma middens.}, }
@article {pmid29976814, year = {2018}, author = {Bellwood, P}, title = {The search for ancient DNA heads east.}, journal = {Science (New York, N.Y.)}, volume = {361}, number = {6397}, pages = {31-32}, doi = {10.1126/science.aat8662}, pmid = {29976814}, issn = {1095-9203}, mesh = {*DNA, Ancient ; *DNA, Mitochondrial ; History, Ancient ; Phylogeny ; }, }
@article {pmid29967156, year = {2018}, author = {Mühlemann, B and Margaryan, A and Damgaard, PB and Allentoft, ME and Vinner, L and Hansen, AJ and Weber, A and Bazaliiskii, VI and Molak, M and Arneborg, J and Bogdanowicz, W and Falys, C and Sablin, M and Smrčka, V and Sten, S and Tashbaeva, K and Lynnerup, N and Sikora, M and Smith, DJ and Fouchier, RAM and Drosten, C and Sjögren, KG and Kristiansen, K and Willerslev, E and Jones, TC}, title = {Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {29}, pages = {7557-7562}, pmid = {29967156}, issn = {1091-6490}, mesh = {Erythema Infectiosum/*genetics/history ; *Evolution, Molecular ; *Genome, Viral ; *Genotype ; History, 19th Century ; History, 20th Century ; Humans ; Parvovirus B19, Human/*genetics ; *Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to ∼70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9-99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from ∼0.5 to ∼6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed ∼12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to ∼5.0-6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.}, }
@article {pmid29960127, year = {2018}, author = {Lazaridis, I}, title = {The evolutionary history of human populations in Europe.}, journal = {Current opinion in genetics &amp; development}, volume = {53}, number = {}, pages = {21-27}, doi = {10.1016/j.gde.2018.06.007}, pmid = {29960127}, issn = {1879-0380}, mesh = {Animals ; DNA, Ancient ; Europe ; *Genetics, Population ; Genome, Human/*genetics ; *Genomics ; Human Migration ; Humans ; Neanderthals/genetics ; White People/*genetics ; }, abstract = {I review the evolutionary history of human populations in Europe with an emphasis on what has been learned in recent years through the study of ancient DNA. Human populations in Europe ∼430-39kya (archaic Europeans) included Neandertals and their ancestors, who were genetically differentiated from other archaic Eurasians (such as the Denisovans of Siberia), as well as modern humans. Modern humans arrived to Europe by ∼45kya, and are first genetically attested by ∼39kya when they were still mixing with Neandertals. The first Europeans who were recognizably genetically related to modern ones appeared in the genetic record shortly thereafter at ∼37kya. At ∼15kya a largely homogeneous set of hunter-gatherers became dominant in most of Europe, but with some admixture from Siberian hunter-gatherers in the eastern part of the continent. These hunter-gatherers were joined by migrants from the Near East beginning at ∼8-9kya: Anatolian farmers settled most of mainland Europe, and migrants from the Caucasus reached eastern Europe, forming steppe populations. After ∼5kya there was migration from the steppe into mainland Europe and vice versa. Present-day Europeans (ignoring the long-distance migrations of the modern era) are largely the product of this Bronze Age collision of steppe pastoralists with Neolithic farmers.}, }
@article {pmid29939091, year = {2018}, author = {Gondek, AT and Boessenkool, S and Star, B}, title = {A stainless-steel mortar, pestle and sleeve design for the efficient fragmentation of ancient bone.}, journal = {BioTechniques}, volume = {64}, number = {6}, pages = {266-269}, doi = {10.2144/btn-2018-0008}, pmid = {29939091}, issn = {1940-9818}, mesh = {Animals ; Bone and Bones/*chemistry ; DNA, Ancient/analysis/*isolation &amp; purification ; Equipment Design ; Genetic Techniques/*instrumentation ; Humans ; Specimen Handling/*instrumentation ; }, abstract = {Different types of milling equipment - such as oscillating ball mills, freezer mills, mortar and pestle - can be used to fragment ancient bone prior to DNA extraction. However, each of these tools is associated with practical drawbacks. Here, we present the design for a stainless-steel mortar and pestle, with a removable sleeve to contain bone material. The tool is easy to clean, practical and its simplicity allows university workshops equipped with a lathe, boring tools and a milling machine to make these components at local expense. This design allows for the efficient fragmentation of ancient bone and improves sample throughput. This design is recommended as a useful, economical addition to existing laboratory equipment for the handling of ancient bone.}, }
@article {pmid29931305, year = {2018}, author = {Prüfer, K}, title = {snpAD: an ancient DNA genotype caller.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {24}, pages = {4165-4171}, pmid = {29931305}, issn = {1367-4811}, mesh = {Computational Biology ; *DNA, Ancient ; *Genome ; Genotype ; *Genotyping Techniques ; Humans ; Sequence Analysis, DNA ; *Software ; }, abstract = {MOTIVATION: The study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling.<br><br>RESULTS: I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals.<br><br>The C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid29924800, year = {2018}, author = {Tams, KW and Jensen Søe, M and Merkyte, I and Valeur Seersholm, F and Henriksen, PS and Klingenberg, S and Willerslev, E and Kjær, KH and Hansen, AJ and Kapel, CMO}, title = {Parasitic infections and resource economy of Danish Iron Age settlement through ancient DNA sequencing.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0197399}, pmid = {29924800}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Cattle ; DNA, Ancient/*analysis ; Denmark ; Feces/parasitology ; Horses/parasitology ; Humans ; Parasites/*genetics/isolation &amp; purification ; Plants/genetics ; *Sequence Analysis, DNA ; Sheep/parasitology ; Swine/parasitology ; Trichuris/*genetics/isolation &amp; purification/pathogenicity ; }, abstract = {In this study, we screen archaeological soil samples by microscopy and analyse the samples by next generation sequencing to obtain results with parasites at species level and untargeted findings of plant and animal DNA. Three separate sediment layers of an ancient man-made pond in Hoby, Denmark, ranging from 100 BC to 200 AD, were analysed by microscopy for presence of intestinal worm eggs and DNA analysis were performed to identify intestinal worms and dietary components. Ancient DNA of parasites, domestic animals and edible plants revealed a change in use of the pond over time reflecting the household practice in the adjacent Iron Age settlement. The most abundant parasite found belonged to the Ascaris genus, which was not possible to type at species level. For all sediment layers the presence of eggs of the human whipworm Trichuris trichiura and the beef tapeworm Taenia saginata suggests continuous disposal of human faeces in the pond. Moreover, the continuous findings of T. saginata further imply beef consumption and may suggest that cattle were living in the immediate surrounding of the site throughout the period. Findings of additional host-specific parasites suggest fluctuating presence of other domestic animals over time: Trichuris suis (pig), Parascaris univalens (horse), Taenia hydatigena (dog and sheep). Likewise, alternating occurrence of aDNA of edible plants may suggest changes in agricultural practices. Moreover, the composition of aDNA of parasites, plants and vertebrates suggests a significant change in the use of the ancient pond over a period of three centuries.}, }
@article {pmid29921229, year = {2018}, author = {Cabrera, VM and Marrero, P and Abu-Amero, KK and Larruga, JM}, title = {Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {98}, pmid = {29921229}, issn = {1471-2148}, support = {CGL2010-16195//Spanish Ministerio de Ciencia e Innovaci&#xf3;n/International ; }, mesh = {Africa ; Asia ; Base Sequence ; Chromosomes, Human, Y/genetics ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; Female ; Genetics, Population ; Haplotypes/*genetics ; Heterozygote ; Humans ; Male ; *Phylogeny ; Phylogeography ; Time Factors ; }, abstract = {BACKGROUND: The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya.<br><br>RESULTS: The coalescence ages of all Eurasian (M,N) and African (L3) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.<br><br>CONCLUSIONS: These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis.}, }
@article {pmid29920259, year = {2018}, author = {Min-Shan Ko, A and Zhang, Y and Yang, MA and Hu, Y and Cao, P and Feng, X and Zhang, L and Wei, F and Fu, Q}, title = {Mitochondrial genome of a 22,000-year-old giant panda from southern China reveals a new panda lineage.}, journal = {Current biology : CB}, volume = {28}, number = {12}, pages = {R693-R694}, doi = {10.1016/j.cub.2018.05.008}, pmid = {29920259}, issn = {1879-0445}, mesh = {Animals ; DNA, Ancient/*analysis ; Ecosystem ; Fossils ; *Genome, Mitochondrial ; Phylogeny ; Ursidae/*genetics ; }, abstract = {Present-day giant pandas (Ailuropoda melanoleuca) are estimated to have diverged from their closest relatives, all other bears, ∼20 million years ago, based on molecular data [1]. With fewer than 2,500 individuals living today [2], it is unclear how well genetic data from extant and historical giant pandas [3] reflect the past [3]. To date, there has been no complete mitochondrial DNA (mtDNA) sequenced from an ancient giant panda. Here, we use ancient DNA capture techniques [4] to sequence the complete mitochondrial genome of a ∼22,000-year-old giant panda specimen (radiocarbon date of 21,910-21,495 cal BP with ± 2σ at 95.4% probability; Lab.no Beta-473743) from the Cizhutuo Cave, in Leye County, Guangxi Province, China (Figure 1A). Its date and location in Guangxi, where no wild giant pandas live today, as well as the difficulty of DNA preservation in a hot and humid region, place it as a unique specimen to learn about ancient giant pandas from the last glacial maximum. We find that the mtDNA lineage of the Cizhutuo panda coalesced with present-day pandas ∼183 thousand years ago (kya, 95% HPD, 227-144 kya), earlier than the time to the most recent common ancestor (TMRCA) of mtDNA lineages shared by present-day pandas (∼72 kya, 95% HPD, 94-55 kya, Supplemental Information). Furthermore, the Cizhutuo panda possessed 18 non-synonymous mutations across six mitochondrial genes. Our results show that the Cizhutuo mtDNA lineage underwent a distinct history from that of present-day populations.}, }
@article {pmid29902423, year = {2018}, author = {Fugassa, MH and Petrigh, RS and Fernández, PM and Carballido Catalayud, M and Belleli, C}, title = {Fox parasites in pre-Columbian times: Evidence from the past to understand the current helminth assemblages.}, journal = {Acta tropica}, volume = {185}, number = {}, pages = {380-384}, doi = {10.1016/j.actatropica.2018.06.007}, pmid = {29902423}, issn = {1873-6254}, mesh = {Animals ; Foxes/*parasitology ; Helminths/genetics/*physiology ; Intestines/*parasitology ; *Paleopathology ; }, abstract = {This work aims to increase the information on the entero-parasitism in Holocene carnivores, by examining coprolites found in Patagonia. Molecular analysis was conducted following the Authenticity Criteria to Determine Ancient DNA sequences. The nucleotide sequences showed 99% of identity with the Control Region sequences of Lycalopex culpaeus (culpeo fox). Coprolites were positive for gastrointestinal parasites. The presence of Alaria sp. and Clonorchis sp. represents the first record for pre-Columbian America. The parasitological findings suggest the importance of these carnivores for the dissemination of their own parasites and those to their prey in rockshelters, areas with high re-use of space.}, }
@article {pmid29900529, year = {2018}, author = {Hollard, C and Zvénigorosky, V and Kovalev, A and Kiryushin, Y and Tishkin, A and Lazaretov, I and Crubézy, E and Ludes, B and Keyser, C}, title = {New genetic evidence of affinities and discontinuities between bronze age Siberian populations.}, journal = {American journal of physical anthropology}, volume = {167}, number = {1}, pages = {97-107}, doi = {10.1002/ajpa.23607}, pmid = {29900529}, issn = {1096-8644}, support = {//French Ministry for Research and Education (MESR)/International ; 14.Z50.31.0010//Altai State University/International ; }, mesh = {Anthropology, Physical ; Asian People/*genetics ; Chromosomes, Human, Y/*genetics ; DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; Genetics, Population ; History, Ancient ; Human Migration ; Humans ; Male ; Siberia ; }, abstract = {OBJECTIVES: This work focuses on the populations of South Siberia during the Eneolithic and Bronze Age and specifically on the contribution of uniparental lineage and phenotypical data to the question of the genetic affinities and discontinuities between western and eastern populations.<br><br>MATERIALS AND METHODS: We performed molecular analyses on the remains of 28 ancient humans (10 Afanasievo (3600-2500 BC) and 18 Okunevo (2500-1800 BC) individuals). For each sample, two uniparentally inherited systems (mitochondrial DNA and Y-chromosome DNA) were studied, in order to trace back maternal and paternal lineages. Phenotype-informative SNPs (Single Nucleotide Polymorphisms) were also analyzed, along with autosomal STRs (Short Tandem Repeats).<br><br>RESULTS: Most of the Afanasievo men submitted to analysis belonged to a single sub-haplogroup, R1b1a1a, which reveals the predominance of this haplogroup in these early Bronze Age populations. Conversely, Okunevo individuals carried more diverse paternal lineages that mostly belonged to Asian/Siberian haplogroups. These differences are also apparent, although less strongly, in mitochondrial lineage composition and phenotype marker variant frequencies.<br><br>DISCUSSION: This study provides new elements that contribute to our understanding of the genetic interactions between populations in Eneolithic and Bronze Age southern Siberia. Our results support the hypothesis of a genetic link between Afanasievo and Yamnaya (in western Eurasia), as suggested by previous studies of other markers. However, we found no Y-chromosome lineage evidence of a possible Afanasievo migration to the Tarim Basin. Moreover, the presence of Y-haplogroup Q in Okunevo individuals links them to Native American populations, as was suggested by whole-genome sequencing.}, }
@article {pmid29895688, year = {2018}, author = {Fregel, R and Méndez, FL and Bokbot, Y and Martín-Socas, D and Camalich-Massieu, MD and Santana, J and Morales, J and Ávila-Arcos, MC and Underhill, PA and Shapiro, B and Wojcik, G and Rasmussen, M and Soares, AER and Kapp, J and Sockell, A and Rodríguez-Santos, FJ and Mikdad, A and Trujillo-Mederos, A and Bustamante, CD}, title = {Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {26}, pages = {6774-6779}, pmid = {29895688}, issn = {1091-6490}, mesh = {Africa, Northern ; Agriculture/history ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Ethnicity/*genetics/history ; Europe ; Gene Flow ; Gene Library ; Genetics, Population ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Middle East ; Morocco ; Sequence Analysis, DNA ; Spain/ethnology ; }, abstract = {The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals' genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.}, }
@article {pmid29894925, year = {2018}, author = {Dannemann, M and Racimo, F}, title = {Something old, something borrowed: admixture and adaptation in human evolution.}, journal = {Current opinion in genetics &amp; development}, volume = {53}, number = {}, pages = {1-8}, doi = {10.1016/j.gde.2018.05.009}, pmid = {29894925}, issn = {1879-0380}, mesh = {Adaptation, Physiological/*genetics ; Animals ; *Biological Evolution ; DNA, Ancient ; *Evolution, Molecular ; Genetics, Population ; Genome, Human/genetics ; Haplotypes ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; }, abstract = {The sequencing of ancient DNA from archaic humans-Neanderthals and Denisovans-has revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Was the introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full. Here, we review the recent literature characterizing introgressed DNA and the likely biological consequences for their modern human carriers. We focus particularly on archaic human haplotypes that were beneficial to modern humans as they expanded across the globe, and on ways to understand how populations harboring these haplotypes evolved over time.}, }
@article {pmid29877032, year = {2018}, author = {Alberti, F and Gonzalez, J and Paijmans, JLA and Basler, N and Preick, M and Henneberger, K and Trinks, A and Rabeder, G and Conard, NJ and Münzel, SC and Joger, U and Fritsch, G and Hildebrandt, T and Hofreiter, M and Barlow, A}, title = {Optimized DNA sampling of ancient bones using Computed Tomography scans.}, journal = {Molecular ecology resources}, volume = {18}, number = {6}, pages = {1196-1208}, doi = {10.1111/1755-0998.12911}, pmid = {29877032}, issn = {1755-0998}, support = {310763//ERC consolidator grant GeneFlow/ ; 00.298.2016//Klaus Tschira foundation/ ; }, mesh = {Bone and Bones/*chemistry ; DNA, Ancient/*analysis/*isolation &amp; purification ; *Fossils ; Humans ; Tomography, X-Ray Computed/*methods ; }, abstract = {The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.}, }
@article {pmid29866821, year = {2018}, author = {Ayuso-Fernández, I and Ruiz-Dueñas, FJ and Martínez, AT}, title = {Evolutionary convergence in lignin-degrading enzymes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {25}, pages = {6428-6433}, pmid = {29866821}, issn = {1091-6490}, mesh = {Biological Evolution ; Carbon Cycle/physiology ; Fungal Proteins/metabolism ; Fungi/metabolism ; Lignin/*metabolism ; Oxidation-Reduction ; Peroxidases/*metabolism ; Phylogeny ; Polymers/metabolism ; Polyporales/metabolism ; }, abstract = {The resurrection of ancestral enzymes of now-extinct organisms (paleogenetics) is a developing field that allows the study of evolutionary hypotheses otherwise impossible to be tested. In the present study, we target fungal peroxidases that play a key role in lignin degradation, an essential process in the carbon cycle and often a limiting step in biobased industries. Ligninolytic peroxidases are secreted by wood-rotting fungi, the origin of which was recently established in the Carboniferous period associated with the appearance of these enzymes. These first peroxidases were not able to degrade lignin directly and used diffusible metal cations to attack its phenolic moiety. The phylogenetic analysis of the peroxidases of Polyporales, the order in which most extant wood-rotting fungi are included, suggests that later in evolution these enzymes would have acquired the ability to degrade nonphenolic lignin using a tryptophanyl radical interacting with the bulky polymer at the surface of the enzyme. Here, we track this powerful strategy for lignin degradation as a phenotypic trait in fungi and show that it is not an isolated event in the evolution of Polyporales. Using ancestral enzyme resurrection, we study the molecular changes that led to the appearance of the same surface oxidation site in two distant peroxidase lineages. By characterization of the resurrected enzymes, we demonstrate convergent evolution at the amino acid level during the evolution of these fungi and track the different changes leading to phylogenetically distant ligninolytic peroxidases from ancestors lacking the ability to degrade nonphenolic lignin.}, }
@article {pmid29854947, year = {2018}, author = {Lesnek, AJ and Briner, JP and Lindqvist, C and Baichtal, JF and Heaton, TH}, title = {Deglaciation of the Pacific coastal corridor directly preceded the human colonization of the Americas.}, journal = {Science advances}, volume = {4}, number = {5}, pages = {eaar5040}, pmid = {29854947}, issn = {2375-2548}, mesh = {Alaska ; Americas ; *Environment ; Geography ; *Human Migration ; Humans ; }, abstract = {The route and timing of early human migration to the Americas have been a contentious topic for decades. Recent paleogenetic analyses suggest that the initial colonization from Beringia took place as early as 16 thousand years (ka) ago via a deglaciated corridor along the North Pacific coast. However, the feasibility of such a migration depends on the extent of the western Cordilleran Ice Sheet (CIS) and the available resources along the hypothesized coastal route during this timeframe. We date the culmination of maximum CIS conditions in southeastern Alaska, a potential bottleneck region for human migration, to ~20 to 17 ka ago with cosmogenic [10]Be exposure dating and [14]C dating of bones from an ice-overrun cave. We also show that productive marine and terrestrial ecosystems were established almost immediately following deglaciation. We conclude that CIS retreat ensured that an open and ecologically viable pathway through southeastern Alaska was available after 17 ka ago, which may have been traversed by early humans as they colonized the Americas.}, }
@article {pmid29852022, year = {2018}, author = {Wolf, AB and Akey, JM}, title = {Outstanding questions in the study of archaic hominin admixture.}, journal = {PLoS genetics}, volume = {14}, number = {5}, pages = {e1007349}, pmid = {29852022}, issn = {1553-7404}, support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; R01GM110068/NH/NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Animals ; *Evolution, Molecular ; Gene Flow ; Genetics, Population ; Genome, Human/*genetics ; Hominidae/*genetics ; Humans ; Models, Genetic ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete sequencing of archaic and modern human genomes has revolutionized the study of human history and evolution. The application of paleogenomics has answered questions that were beyond the scope of archaeology alone-definitively proving admixture between archaic and modern humans. Despite the remarkable progress made in the study of archaic-modern human admixture, many outstanding questions remain. Here, we review some of these questions, which include how frequent archaic-modern human admixture was in history, to what degree drift and selection are responsible for the loss and retention of introgressed sequences in modern human genomes, and how surviving archaic sequences affect human phenotypes.}, }
@article {pmid29782156, year = {2018}, author = {Tse, TJ and Doig, LE and Tang, S and Zhang, X and Sun, W and Wiseman, SB and Feng, CX and Liu, H and Giesy, JP and Hecker, M and Jones, PD}, title = {Combining High-Throughput Sequencing of sedaDNA and Traditional Paleolimnological Techniques To Infer Historical Trends in Cyanobacterial Communities.}, journal = {Environmental science &amp; technology}, volume = {52}, number = {12}, pages = {6842-6853}, doi = {10.1021/acs.est.7b06386}, pmid = {29782156}, issn = {1520-5851}, mesh = {Canada ; *Cyanobacteria ; *DNA, Ancient ; Lakes ; RNA, Ribosomal, 16S ; }, abstract = {Freshwaters worldwide are under increasing pressure from anthropogenic activities and changing climate. Unfortunately, many inland waters lack sufficient long-term monitoring to assess environmental trends. Analysis of sedimentary ancient DNA (sedaDNA) is emerging as a means to reconstruct the past occurrence of microbial communities of inland waters. The purpose of this study was to assess a combination of high-throughput sequencing (16S rRNA) of sedaDNA and traditional paleolimnological analyses to explore multidecadal relationships among cyanobacterial community composition, the potential for cyanotoxin production, and paleoenvironmental proxies. DNA was extracted from two sediment cores collected from a northern Canadian Great Plains reservoir. Diversity indices illustrated significant community-level changes since reservoir formation. Furthermore, higher relative abundances in more recent years were observed for potentially toxic cyanobacterial genera including Dolichospermum. Correlation-based network analysis revealed this trend significantly and positively correlated to abundances of the microcystin synthetase gene (mcyA) and other paleoproxies (nutrients, pigments, stanols, sterols, and certain diatom species), demonstrating synchrony between molecular and more standard proxies. These findings demonstrate a novel approach to infer long-term dynamics of cyanobacterial diversity in inland waters and highlight the power of high-throughput sequencing to reconstruct trends in environmental quality and inform lake and reservoir management and monitoring program design.}, }
@article {pmid29773666, year = {2018}, author = {Lipson, M and Cheronet, O and Mallick, S and Rohland, N and Oxenham, M and Pietrusewsky, M and Pryce, TO and Willis, A and Matsumura, H and Buckley, H and Domett, K and Nguyen, GH and Trinh, HH and Kyaw, AA and Win, TT and Pradier, B and Broomandkhoshbacht, N and Candilio, F and Changmai, P and Fernandes, D and Ferry, M and Gamarra, B and Harney, E and Kampuansai, J and Kutanan, W and Michel, M and Novak, M and Oppenheimer, J and Sirak, K and Stewardson, K and Zhang, Z and Flegontov, P and Pinhasi, R and Reich, D}, title = {Ancient genomes document multiple waves of migration in Southeast Asian prehistory.}, journal = {Science (New York, N.Y.)}, volume = {361}, number = {6397}, pages = {92-95}, pmid = {29773666}, issn = {1095-9203}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Agriculture/history ; Asia, Southeastern ; Asian People/genetics ; DNA, Ancient ; Genetic Variation ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Language/*history ; Radiometric Dating ; }, abstract = {Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.}, }
@article {pmid33474257, year = {2018}, author = {Kornienko, IV and Faleeva, TG and Oreshkova, NV and Grigoriev, SE and Grigoreva, LV and Simonov, EP and Kolesnikova, AI and Putintseva, YA and Krutovsky, KV}, title = {Complete mitochondrial genome of a woolly mammoth (Mammuthus primigenius) from Maly Lyakhovsky Island (New Siberian Islands, Russia) and its phylogenetic assessment.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {3}, number = {2}, pages = {596-598}, pmid = {33474257}, issn = {2380-2359}, abstract = {We present a complete sequence and an annotation of the mitochondrial genome of the woolly mammoth (Mammuthus primigenius) found in 2012 on Maly Lyakhovsky Island (North-Eastern Siberia, Russia). The genome was 16,851 bp long and contained 13 protein-coding, 22 tRNA, and 2 rRNA genes. It was AT reach (61.3%) with A = 32.9%, T = 28.4%, C = 25.3%, and G = 13.4%.}, }
@article {pmid29769358, year = {2018}, author = {Delsuc, F and Kuch, M and Gibb, GC and Hughes, J and Szpak, P and Southon, J and Enk, J and Duggan, AT and Poinar, HN}, title = {Resolving the phylogenetic position of Darwin's extinct ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1878}, pages = {}, pmid = {29769358}, issn = {1471-2954}, mesh = {Animals ; Chile ; DNA, Ancient/*analysis ; DNA, Mitochondrial/analysis ; Exons/genetics ; Fossils ; *Genome, Mitochondrial ; Phylogeny ; Sloths/classification/genetics ; Xenarthra/*classification/genetics ; }, abstract = {Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12 880-year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient subfossil, probably the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra. Additionally, we enriched over 15 kb of sequence data from seven nuclear exons, using target sequence capture designed against a wide xenarthran dataset. Phylogenetic and dating analyses of the mitogenomic dataset including all extant species of xenarthrans and the assembled nuclear supermatrix unambiguously place Mylodon darwinii as the sister-group of modern two-fingered sloths, from which it diverged around 22 million years ago. These congruent results from both the mitochondrial and nuclear data support the diphyly of the two modern sloth lineages, implying the convergent evolution of their unique suspensory behaviour as an adaption to arboreality. Our results offer promising perspectives for whole-genome sequencing of this emblematic extinct taxon.}, }
@article {pmid29769015, year = {2018}, author = {Tong, KJ and Duchêne, DA and Duchêne, S and Geoghegan, JL and Ho, SYW}, title = {A comparison of methods for estimating substitution rates from ancient DNA sequence data.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {70}, pmid = {29769015}, issn = {1471-2148}, support = {FT160100167//Australian Research Council/International ; }, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Computer Simulation ; *DNA, Ancient ; Evolution, Molecular ; Genome, Mitochondrial ; Genomics/*methods ; Horses ; Mutation/*genetics ; Phylogeny ; Time Factors ; Uncertainty ; Vertebrates/*genetics ; }, abstract = {BACKGROUND: Phylogenetic analysis of DNA from modern and ancient samples allows the reconstruction of important demographic and evolutionary processes. A critical component of these analyses is the estimation of evolutionary rates, which can be calibrated using information about the ages of the samples. However, the reliability of these rate estimates can be negatively affected by among-lineage rate variation and non-random sampling. Using a simulation study, we compared the performance of three phylogenetic methods for inferring evolutionary rates from time-structured data sets: regression of root-to-tip distances, least-squares dating, and Bayesian inference. We also applied these three methods to time-structured mitogenomic data sets from six vertebrate species.<br><br>RESULTS: Our results from 12 simulation scenarios show that the three methods produce reliable estimates when the substitution rate is high, rate variation is low, and samples of similar ages are not all grouped together in the tree (i.e., low phylo-temporal clustering). The interaction of these factors is particularly important for least-squares dating and Bayesian estimation of evolutionary rates. The three estimation methods produced consistent estimates of rates across most of the six mitogenomic data sets, with sequence data from horses being an exception.<br><br>CONCLUSIONS: We recommend that phylogenetic studies of ancient DNA sequences should use multiple methods of inference and test for the presence of temporal signal, among-lineage rate variation, and phylo-temporal clustering in the data.}, }
@article {pmid29768437, year = {2018}, author = {Willmann, C and Mata, X and Hanghoej, K and Tonasso, L and Tisseyre, L and Jeziorski, C and Cabot, E and Chevet, P and Crubézy, E and Orlando, L and Esclassan, R and Thèves, C}, title = {Oral health status in historic population: Macroscopic and metagenomic evidence.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196482}, pmid = {29768437}, issn = {1932-6203}, mesh = {DNA, Ancient/isolation &amp; purification ; DNA, Bacterial/genetics/history/isolation &amp; purification ; Dental Caries/history/microbiology/pathology ; Female ; France ; Health Status ; History, 18th Century ; Humans ; Male ; Metagenomics ; Microbiota/genetics ; Oral Health/*history ; Paleodontology ; Periodontitis/history/microbiology/pathology ; Rural Population/history ; }, abstract = {Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked. In this study, we used shotgun sequencing to characterize the bacterial composition from historical subjects showing macroscopic evidence of oral pathologies. We first carried out a macroscopic analysis aimed at identifying carious or periodontal diseases in subjects belonging to a French rural population of the 18th century AD. We next examined radiographically six subjects showing specific, characteristic dental pathologies and applied HTS shotgun sequencing to characterize the microbial communities present in and on the dental material. The presence of Streptococcus mutans and also Rothia dentocariosa, Actinomyces viscosus, Porphyromonas gingivalis, Tannerella forsythia, Pseudoramibacter alactolyticus, Olsenella uli and Parvimonas micra was confirmed through the presence of typical signatures of post-mortem DNA damage at an average depth-of-coverage ranging from 0.5 to 7X, with a minimum of 35% (from 35 to 93%) of the positions in the genome covered at least once. Each sampled tooth showed a specific bacterial signature associated with carious or periodontal pathologies. This work demonstrates that from a healthy independent tooth, without visible macroscopic pathology, we can identify a signature of specific pathogens and deduce the oral health status of an individual.}, }
@article {pmid29764946, year = {2018}, author = {Wang, Y and Stata, M and Wang, W and Stajich, JE and White, MM and Moncalvo, JM}, title = {Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis.}, journal = {mBio}, volume = {9}, number = {3}, pages = {}, pmid = {29764946}, issn = {2150-7511}, mesh = {Animals ; Fungal Proteins/genetics/metabolism ; Fungi/classification/*genetics/isolation &amp; purification/physiology ; *Genome, Fungal ; Genomics ; Host-Pathogen Interactions ; Insecta/genetics/*microbiology/physiology ; Phylogeny ; *Symbiosis ; }, abstract = {Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects.IMPORTANCE Insect guts harbor various microbes that are important for host digestion, immune response, and disease dispersal in certain cases. Bacteria, which are among the primary endosymbionts, have been studied extensively. However, fungi, which are also frequently encountered, are poorly known with respect to their biology within the insect guts. To understand the genomic features and related biology, we produced the whole-genome sequences of nine gut commensal fungi from disease-bearing insects (black flies, midges, and mosquitoes). The results show that insect gut fungi tend to have low GC content across their genomes. By comparing these commensals with entomopathogenic and free-living fungi that have available genome sequences, we found a universal core gene toolbox that is unique and thus potentially important for the insect-fungus symbiosis. This comparative work also uncovered different host invasion strategies employed by insect pathogens and commensals, as well as a model system to study ancient fungal genome duplication within the gut of insects.}, }
@article {pmid29763671, year = {2018}, author = {Lewandowska, M and Jędrychowska-Dańska, K and Płoszaj, T and Witas, P and Zamerska, A and Mańkowska-Pliszka, H and Witas, HW}, title = {Searching for signals of recent natural selection in genes of the innate immune response - ancient DNA study.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {63}, number = {}, pages = {62-72}, doi = {10.1016/j.meegid.2018.05.008}, pmid = {29763671}, issn = {1567-7257}, mesh = {Archaeology ; DNA/*genetics ; DNA, Ancient/*isolation &amp; purification ; Evolution, Molecular ; Genotype ; Humans ; Immunity, Innate/*genetics ; Poland ; Selection, Genetic/*genetics ; }, abstract = {The last decade has seen sharp progress in the field of human evolutionary genetics and a great amount of genetic evidence of natural selection has been provided so far. Since host-pathogen co-evolution is difficult to trace due to the polygenic nature of human susceptibility to microbial diseases, of particular interest is any signal of natural selection in response to the strong selective pressure exerted by pathogens. Analysis of ancient DNA allows for the direct insight into changes of a gene pool content over time and enables monitoring allele frequency fluctuations. Among pathogenic agents, mycobacteria are proved to have remained in an intimate, long-lasting relation with humans, reflected by the current high level of host resistance. Therefore, we aimed to investigate the prevalence of several polymorphisms within innate immune response genes related to susceptibility to mycobacterial diseases (in SLC11A1, MBL2, TLR2, P2RX7, IL10, TNFA) in time series data from North and East Poland (1st-18th century AD, n = 207). The comparison of allele frequencies over time revealed a predominant role of genetic drift in shaping past gene pool of small, probably isolated groups, which was explained by the high level of population differentiation and limited gene flow. However, the trajectory of frequency fluctuations of two SNPs suggested the possibility of their non-neutral evolution and the results of applied forward simulations further strengthened the hypothesis of natural selection acting on those loci. However, we observed an unusual excess of homozygosity in the profile of several SNPs, which pinpoints to the necessity of further research on temporally and spatially diverse samples to support our inference on non-stochastic evolution, ideally employing pathway-based approaches. Nevertheless, our study confirms that time series data could help to decipher very recent human adaptation to life-threatening pathogens and assisting demographic events.}, }
@article {pmid29746569, year = {2018}, author = {Gamarra, B and Howcroft, R and McCall, A and Dani, J and Hajdú, Z and Nagy, EG and Szabó, LD and Domboróczki, L and Pap, I and Raczky, P and Marcsik, A and Zoffmann, ZK and Hajdu, T and Feeney, RNM and Pinhasi, R}, title = {5000 years of dietary variations of prehistoric farmers in the Great Hungarian Plain.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0197214}, pmid = {29746569}, issn = {1932-6203}, mesh = {Agriculture/*history ; *Anthropology, Cultural ; *Diet ; Female ; History, Ancient ; Humans ; Hungary ; Male ; }, abstract = {The development of farming was a catalyst for the evolution of the human diet from the varied subsistence practices of hunter-gatherers to the more globalised food economy we depend upon today. Although there has been considerable research into the dietary changes associated with the initial spread of farming, less attention has been given to how dietary choices continued to develop during subsequent millennia. A paleogenomic time transect for 5 millennia of human occupation in the Great Hungarian Plain spanning from the advent of the Neolithic to the Iron Age, showed major genomic turnovers. Here we assess where these genetic turnovers are associated with corresponding dietary shifts, by examining the carbon and nitrogen stable isotope ratios of 52 individuals. Results provide evidence that early Neolithic individuals, which were genetically characterised as Mesolithic hunter-gatherers, relied on wild resources to a greater extent than those whose genomic attributes were of typical Neolithic European farmers. Other Neolithic individuals and those from the Copper Age to Bronze Age periods relied mostly on terrestrial C3 plant resources. We also report a carbon isotopic ratio typical of C4 plants, which may indicate millet consumption in the Late Bronze Age, despite suggestions of the crop's earlier arrival in Europe during the Neolithic.}, }
@article {pmid29746563, year = {2018}, author = {Schuenemann, VJ and Avanzi, C and Krause-Kyora, B and Seitz, A and Herbig, A and Inskip, S and Bonazzi, M and Reiter, E and Urban, C and Dangvard Pedersen, D and Taylor, GM and Singh, P and Stewart, GR and Velemínský, P and Likovsky, J and Marcsik, A and Molnár, E and Pálfi, G and Mariotti, V and Riga, A and Belcastro, MG and Boldsen, JL and Nebel, A and Mays, S and Donoghue, HD and Zakrzewski, S and Benjak, A and Nieselt, K and Cole, ST and Krause, J}, title = {Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.}, journal = {PLoS pathogens}, volume = {14}, number = {5}, pages = {e1006997}, pmid = {29746563}, issn = {1553-7374}, mesh = {DNA, Bacterial/genetics/history ; Europe/epidemiology ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; History, Medieval ; Host-Pathogen Interactions/genetics ; Humans ; Leprosy/epidemiology/*history/microbiology ; Mycobacterium leprae/classification/*genetics/pathogenicity ; Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide ; }, abstract = {Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.}, }
@article {pmid29745896, year = {2018}, author = {Krause-Kyora, B and Susat, J and Key, FM and Kühnert, D and Bosse, E and Immel, A and Rinne, C and Kornell, SC and Yepes, D and Franzenburg, S and Heyne, HO and Meier, T and Lösch, S and Meller, H and Friederich, S and Nicklisch, N and Alt, KW and Schreiber, S and Tholey, A and Herbig, A and Nebel, A and Krause, J}, title = {Neolithic and medieval virus genomes reveal complex evolution of hepatitis B.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29745896}, issn = {2050-084X}, support = {PMPDP3_171320/1//Swiss National Science Foundation/Switzerland ; APGREID//European Research Council/International ; }, mesh = {*Evolution, Molecular ; Fossils/*virology ; *Genome, Viral ; Germany ; Hepatitis B virus/classification/*genetics/isolation &amp; purification ; Humans ; Phylogeny ; Proteome/analysis ; Sequence Analysis, DNA ; Skeleton/chemistry/virology ; Viral Proteins/analysis ; }, abstract = {The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genome by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results demonstrated that HBV has circulated in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. The ancient viruses appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses.}, }
@article {pmid29745246, year = {2017}, author = {Claw, KG and Lippert, D and Bardill, J and Cordova, A and Fox, K and Yracheta, JM and Bader, AC and Bolnick, DA and Malhi, RS and TallBear, K and Garrison, NA}, title = {Chaco Canyon Dig Unearths Ethical Concerns.}, journal = {Human biology}, volume = {89}, number = {3}, pages = {177-180}, pmid = {29745246}, issn = {1534-6617}, support = {F32 GM119237/GM/NIGMS NIH HHS/United States ; R25 HG007158/HG/NHGRI NIH HHS/United States ; }, mesh = {Communication ; DNA, Ancient ; Genomics/*ethics ; Humans ; Indians, North American/ethnology/*genetics ; New Mexico/ethnology ; Paleontology/*ethics ; Researcher-Subject Relations/ethics ; }, abstract = {The field of paleogenomics (the study of ancient genomes) is rapidly advancing, with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to as ancestors, are used in research. We highlight a 2017 article by Kennett et al., "Archaeogenomic evidence reveals prehistoric matrilineal dynasty," that brings to light several ethical issues that should be addressed in paleogenomics research. The study helps elucidate the matrilineal relationships in ancient Chacoan society through ancient DNA analysis. However, we, as Indigenous researchers and allies, raise ethical concerns with the study's scientific conclusions that can be problematic for Native American communities: (1) the lack of tribal consultation, (2) the use of culturally insensitive descriptions, and (3) the potential impact on marginalized groups. Further, we explore the limitations of the Native American Graves Protection and Repatriation Act, which addresses repatriation but not research, because clear ethical guidelines have not been established for research involving Native American ancestors, especially those deemed "culturally unaffiliated." Multiple studies of "culturally unaffiliated" remains have been initiated recently, so it is imperative that researchers consider the ethical ramifications of paleogenomics research. Past research indiscretions have created a history of mistrust and exploitation in many Native American communities. To promote ethical engagement of Native American communities in research, we therefore suggest careful attention to ethical considerations, strong tribal consultation requirements, and greater collaborations among museums, federal agencies, researchers, scientific journals, and granting agencies.}, }
@article {pmid29744957, year = {2018}, author = {Russo, MG and Dejean, CB and Avena, SA and Seldes, V and Ramundo, P}, title = {Mitochondrial lineage A2ah found in a pre-Hispanic individual from the Andean region.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {30}, number = {4}, pages = {e23134}, doi = {10.1002/ajhb.23134}, pmid = {29744957}, issn = {1520-6300}, mesh = {Adolescent ; Adult ; Archaeology ; Argentina ; Child ; Child, Preschool ; DNA, Mitochondrial/analysis ; Female ; *Gene Flow ; *Genetic Variation ; *Haplotypes ; Humans ; Indians, South American/*genetics ; Infant ; Male ; Middle Aged ; Young Adult ; }, abstract = {OBJECTIVES: The aim of this study was to contribute to the knowledge of pre-Hispanic Andean mitochondrial diversity by analyzing an individual from the archaeological site Pukara de La Cueva (North-western Argentina). The date of the discovery context (540 ± 60 BP) corresponds to the Regional Developments II period.<br><br>METHODS: Two separate DNA extractions were performed from dentin powder of one tooth. HVR I was amplified by PCR from each extract in three overlapping fragments and the haplotype was determined by consensus among all obtained sequences. The procedures were carried out under strict protocols developed for working with ancient DNA.<br><br>RESULTS: The individual belonged to the A2ah lineage due to the presence of the 16097C and 16098G transitions, which constitute its distinctive motif. This lineage is very rare in Native American populations and was described in four individuals from current groups inhabiting the Bolivian Llanos, two from South-eastern Brazil, and one from the Gran Chaco region. In addition, two other mutations (16260T and 16286T) were shared with one of the individuals from the Bolivian Llanos region.<br><br>CONCLUSIONS: Considering that the origin of this lineage was postulated for the South American lowlands, the present pre-Hispanic discovery in the Andean area could be taken as a new evidence of gene flow between these regions. Also, it allows the questioning of the geographical origin of this mitochondrial lineage.}, }
@article {pmid29732264, year = {2018}, author = {Harbert, RS}, title = {Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities.}, journal = {Applications in plant sciences}, volume = {6}, number = {3}, pages = {e1034}, pmid = {29732264}, issn = {2168-0450}, abstract = {PREMISE OF THE STUDY: DNA may be preserved for thousands of years in very cold or dry environments, and plant tissue fragments and pollen trapped in soils and shallow aquatic sediments are well suited for the molecular characterization of past floras. However, one obstacle in this area of study is the limiting bias in the bioinformatic classification of short fragments of degraded DNA from the large, complex genomes of plants.<br><br>METHODS: To establish one possible baseline protocol for the rapid classification of short-read shotgun metagenomic data for reconstructing plant communities, the read classification programs Kraken, Centrifuge, and MegaBLAST were tested on simulated and ancient data with classification against a reference database targeting plants.<br><br>RESULTS: Performance tests on simulated data suggest that Kraken and Centrifuge outperform MegaBLAST. Kraken tends to be the most conservative approach with high precision, whereas Centrifuge has higher sensitivity. Reanalysis of 13,000 years of ancient sedimentary DNA from North America characterizes potential post-glacial vegetation succession.<br><br>DISCUSSION: Classification method choice has an impact on performance and any downstream interpretation of results. The reanalysis of ancient DNA from glacial lake sediments yielded vegetation histories that varied depending on method, potentially changing paleoecological conclusions drawn from molecular evidence.}, }
@article {pmid29723195, year = {2018}, author = {Key, FM and Abdul-Aziz, MA and Mundry, R and Peter, BM and Sekar, A and D'Amato, M and Dennis, MY and Schmidt, JM and Andrés, AM}, title = {Human local adaptation of the TRPM8 cold receptor along a latitudinal cline.}, journal = {PLoS genetics}, volume = {14}, number = {5}, pages = {e1007298}, pmid = {29723195}, issn = {1553-7404}, support = {R01 HG007089/NH/NIH HHS/United States ; R00 NS083627/NS/NINDS NIH HHS/United States ; R01 HG007089/HG/NHGRI NIH HHS/United States ; T32 GM007377/GM/NIGMS NIH HHS/United States ; R00NS083627/NH/NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Africa ; Asia ; Bayes Theorem ; *Cold Temperature ; Europe ; Gene Expression Profiling ; Gene Frequency ; Genetics, Population/statistics &amp; numerical data ; Genotype ; Humans ; Linkage Disequilibrium ; *Polymorphism, Single Nucleotide ; Selection, Genetic ; TRPM Cation Channels/*genetics ; }, abstract = {Ambient temperature is a critical environmental factor for all living organisms. It was likely an important selective force as modern humans recently colonized temperate and cold Eurasian environments. Nevertheless, as of yet we have limited evidence of local adaptation to ambient temperature in populations from those environments. To shed light on this question, we exploit the fact that humans are a cosmopolitan species that inhabit territories under a wide range of temperatures. Focusing on cold perception-which is central to thermoregulation and survival in cold environments-we show evidence of recent local adaptation on TRPM8. This gene encodes for a cation channel that is, to date, the only temperature receptor known to mediate an endogenous response to moderate cold. The upstream variant rs10166942 shows extreme population differentiation, with frequencies that range from 5% in Nigeria to 88% in Finland (placing this SNP in the 0.02% tail of the FST empirical distribution). When all populations are jointly analyzed, allele frequencies correlate with latitude and temperature beyond what can be explained by shared ancestry and population substructure. Using a Bayesian approach, we infer that the allele originated and evolved neutrally in Africa, while positive selection raised its frequency to different degrees in Eurasian populations, resulting in allele frequencies that follow a latitudinal cline. We infer strong positive selection, in agreement with ancient DNA showing high frequency of the allele in Europe 3,000 to 8,000 years ago. rs10166942 is important phenotypically because its ancestral allele is protective of migraine. This debilitating disorder varies in prevalence across human populations, with highest prevalence in individuals of European descent-precisely the population with the highest frequency of rs10166942 derived allele. We thus hypothesize that local adaptation on previously neutral standing variation may have contributed to the genetic differences that exist in the prevalence of migraine among human populations today.}, }
@article {pmid29722813, year = {2018}, author = {Jobin, M and Schurz, H and Henn, BM}, title = {IMPUTOR: Phylogenetically Aware Software for Imputation of Errors in Next-Generation Sequencing.}, journal = {Genome biology and evolution}, volume = {10}, number = {5}, pages = {1248-1254}, pmid = {29722813}, issn = {1759-6653}, mesh = {*Algorithms ; Chromosomes, Human, Y/classification/genetics ; Gene Frequency ; Genome-Wide Association Study ; Genomics/methods ; Haplotypes ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; *Phylogeny ; Polymorphism, Single Nucleotide ; *Software ; }, abstract = {We introduce IMPUTOR, software for phylogenetically aware imputation of missing haploid nonrecombining genomic data. Targeted for next-generation sequencing data, IMPUTOR uses the principle of parsimony to impute data marked as missing due to low coverage. Along with efficiently imputing missing variant genotypes, IMPUTOR is capable of reliably and accurately correcting many nonmissing sites that represent spurious sequencing errors. Tests on simulated data show that IMPUTOR is capable of detecting many induced mutations without making erroneous imputations/corrections, with as many as 95% of missing sites imputed and 81% of errors corrected under optimal conditions. We tested IMPUTOR with human Y-chromosomes from pairs of close relatives and demonstrate IMPUTOR's efficacy in imputing missing and correcting erroneous calls.}, }
@article {pmid29719544, year = {2018}, author = {Di Donato, A and Filippone, E and Ercolano, MR and Frusciante, L}, title = {Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {441}, pmid = {29719544}, issn = {1664-462X}, abstract = {The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture.}, }
@article {pmid29717136, year = {2018}, author = {Krause-Kyora, B and Nutsua, M and Boehme, L and Pierini, F and Pedersen, DD and Kornell, SC and Drichel, D and Bonazzi, M and Möbus, L and Tarp, P and Susat, J and Bosse, E and Willburger, B and Schmidt, AH and Sauter, J and Franke, A and Wittig, M and Caliebe, A and Nothnagel, M and Schreiber, S and Boldsen, JL and Lenz, TL and Nebel, A}, title = {Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1569}, pmid = {29717136}, issn = {2041-1723}, mesh = {*DNA, Ancient ; DNA, Bacterial/genetics ; Denmark ; Fossils ; *Genetic Predisposition to Disease ; Genome, Bacterial ; HLA-DQ beta-Chains/genetics ; HLA-DRB1 Chains/genetics ; High-Throughput Screening Assays ; Humans ; Leprosy/*genetics ; Mycobacterium leprae/genetics ; White People/*genetics ; }, abstract = {Leprosy, a chronic infectious disease caused by Mycobacterium leprae (M. leprae), was very common in Europe till the 16th century. Here, we perform an ancient DNA study on medieval skeletons from Denmark that show lesions specific for lepromatous leprosy (LL). First, we test the remains for M. leprae DNA to confirm the infection status of the individuals and to assess the bacterial diversity. We assemble 10 complete M. leprae genomes that all differ from each other. Second, we evaluate whether the human leukocyte antigen allele DRB1*15:01, a strong LL susceptibility factor in modern populations, also predisposed medieval Europeans to the disease. The comparison of genotype data from 69 M. leprae DNA-positive LL cases with those from contemporary and medieval controls reveals a statistically significant association in both instances. In addition, we observe that DRB1*15:01 co-occurs with DQB1*06:02 on a haplotype that is a strong risk factor for inflammatory diseases today.}, }
@article {pmid29709204, year = {2018}, author = {Skoglund, P and Mathieson, I}, title = {Ancient Genomics of Modern Humans: The First Decade.}, journal = {Annual review of genomics and human genetics}, volume = {19}, number = {}, pages = {381-404}, doi = {10.1146/annurev-genom-083117-021749}, pmid = {29709204}, issn = {1545-293X}, mesh = {Animals ; Biological Evolution ; *Genome, Human ; Hominidae/*genetics ; Human Migration ; Humans ; }, abstract = {The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent-in particular the effect of agricultural expansions in Africa, Europe, and Oceania-and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.}, }
@article {pmid29709200, year = {2018}, author = {Cappellini, E and Prohaska, A and Racimo, F and Welker, F and Pedersen, MW and Allentoft, ME and de Barros Damgaard, P and Gutenbrunner, P and Dunne, J and Hammann, S and Roffet-Salque, M and Ilardo, M and Moreno-Mayar, JV and Wang, Y and Sikora, M and Vinner, L and Cox, J and Evershed, RP and Willerslev, E}, title = {Ancient Biomolecules and Evolutionary Inference.}, journal = {Annual review of biochemistry}, volume = {87}, number = {}, pages = {1029-1060}, doi = {10.1146/annurev-biochem-062917-012002}, pmid = {29709200}, issn = {1545-4509}, mesh = {Animals ; Biological Evolution ; *DNA, Ancient ; *Evolution, Molecular ; Extinction, Biological ; Fossils ; Genomics ; Humans ; Lipids/genetics ; Paleontology ; Phylogeny ; Proteins/genetics ; Proteomics ; }, abstract = {Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.}, }
@article {pmid29706345, year = {2018}, author = {Lindo, J and Rogers, M and Mallott, EK and Petzelt, B and Mitchell, J and Archer, D and Cybulski, JS and Malhi, RS and DeGiorgio, M}, title = {Patterns of Genetic Coding Variation in a Native American Population before and after European Contact.}, journal = {American journal of human genetics}, volume = {102}, number = {5}, pages = {806-815}, pmid = {29706345}, issn = {1537-6605}, mesh = {Base Pairing/genetics ; Gene Frequency/genetics ; Gene Pool ; *Genetic Variation ; Heterozygote ; Humans ; Indians, North American/*genetics ; Polymorphism, Single Nucleotide/genetics ; Time Factors ; White People/*genetics ; }, abstract = {The effects of European colonization on the genomes of Native Americans may have produced excesses of potentially deleterious features, mainly due to the severe reductions in population size and corresponding losses of genetic diversity. This assumption, however, neither considers actual genomic patterns that existed before colonization nor does it adequately capture the effects of admixture. In this study, we analyze the whole-exome sequences of modern and ancient individuals from a Northwest Coast First Nation, with a demographic history similar to other indigenous populations from the Americas. We show that in approximately ten generations from initial European contact, the modern individuals exhibit reduced levels of novel and low-frequency variants, a lower proportion of potentially deleterious alleles, and decreased heterozygosity when compared to their ancestors. This pattern can be explained by a dramatic population decline, resulting in the loss of potentially damaging low-frequency variants, and subsequent admixture. We also find evidence that the indigenous population was on a steady decline in effective population size for several thousand years before contact, which emphasizes regional demography over the common conception of a uniform expansion after entry into the Americas. This study examines the genomic consequences of colonialism on an indigenous group and describes the continuing role of gene flow among modern populations.}, }
@article {pmid29700256, year = {2018}, author = {Bardill, J and Bader, AC and Garrison, NA and Bolnick, DA and Raff, JA and Walker, A and Malhi, RS and , }, title = {Advancing the ethics of paleogenomics.}, journal = {Science (New York, N.Y.)}, volume = {360}, number = {6387}, pages = {384-385}, pmid = {29700256}, issn = {1095-9203}, support = {K01 HG008818/HG/NHGRI NIH HHS/United States ; R25 HG007158/HG/NHGRI NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bioethical Issues ; *Body Remains ; Europe ; Genomics/*ethics ; Humans ; Paleontology/*ethics ; Population Groups/genetics ; United States ; }, }
@article {pmid29694397, year = {2018}, author = {Søe, MJ and Nejsum, P and Seersholm, FV and Fredensborg, BL and Habraken, R and Haase, K and Hald, MM and Simonsen, R and Højlund, F and Blanke, L and Merkyte, I and Willerslev, E and Kapel, CMO}, title = {Ancient DNA from latrines in Northern Europe and the Middle East (500 BC-1700 AD) reveals past parasites and diet.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195481}, pmid = {29694397}, issn = {1932-6203}, mesh = {Agriculture ; Animals ; Archaeology/methods ; Biodiversity ; *DNA, Ancient ; DNA, Mitochondrial ; DNA, Plant ; *Diet ; Eggs ; Europe ; Feces/*chemistry/*parasitology ; History, Ancient ; Humans ; Metagenome ; Middle East ; Parasites/genetics ; Parasitic Diseases/epidemiology/history ; Phylogeny ; Sequence Analysis, DNA ; *Toilet Facilities ; }, abstract = {High-resolution insight into parasitic infections and diet of past populations in Northern Europe and the Middle East (500 BC- 1700 AD) was obtained by pre-concentration of parasite eggs from ancient latrines and deposits followed by shotgun sequencing of DNA. Complementary profiling of parasite, vertebrate and plant DNA proved highly informative in the study of ancient health, human-animal interactions as well as animal and plant dietary components. Most prominent were finding of soil-borne parasites transmitted directly between humans, but also meat-borne parasites that require consumption of raw or undercooked fish and pork. The detection of parasites for which sheep, horse, dog, pig, and rodents serves as definitive hosts are clear markers of domestic and synanthropic animals living in closer proximity of the respective sites. Finally, the reconstruction of full mitochondrial parasite genomes from whipworm (Ascaris lumbricoides) and roundworm species (Trichuris trichiura and Trichuris muris) and estimates of haplotype frequencies elucidates the genetic diversity and provides insights into epidemiology and parasite biology.}, }
@article {pmid29684051, year = {2018}, author = {Monroy Kuhn, JM and Jakobsson, M and Günther, T}, title = {Estimating genetic kin relationships in prehistoric populations.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195491}, pmid = {29684051}, issn = {1932-6203}, mesh = {Chromosomes, Human, Y ; Computer Simulation ; DNA Fragmentation ; DNA, Ancient/*analysis ; DNA, Mitochondrial ; *Family ; Germany ; Haplotypes ; Humans ; Male ; Models, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Archaeogenomic research has proven to be a valuable tool to trace migrations of historic and prehistoric individuals and groups, whereas relationships within a group or burial site have not been investigated to a large extent. Knowing the genetic kinship of historic and prehistoric individuals would give important insights into social structures of ancient and historic cultures. Most archaeogenetic research concerning kinship has been restricted to uniparental markers, while studies using genome-wide information were mainly focused on comparisons between populations. Applications which infer the degree of relationship based on modern-day DNA information typically require diploid genotype data. Low concentration of endogenous DNA, fragmentation and other post-mortem damage to ancient DNA (aDNA) makes the application of such tools unfeasible for most archaeological samples. To infer family relationships for degraded samples, we developed the software READ (Relationship Estimation from Ancient DNA). We show that our heuristic approach can successfully infer up to second degree relationships with as little as 0.1x shotgun coverage per genome for pairs of individuals. We uncover previously unknown relationships among prehistoric individuals by applying READ to published aDNA data from several human remains excavated from different cultural contexts. In particular, we find a group of five closely related males from the same Corded Ware culture site in modern-day Germany, suggesting patrilocality, which highlights the possibility to uncover social structures of ancient populations by applying READ to genome-wide aDNA data. READ is publicly available from https://bitbucket.org/tguenther/read.}, }
@article {pmid29681138, year = {2018}, author = {Li, J and Zhang, Y and Zhao, Y and Chen, Y and Ochir, A and Sarenbilige,  and Zhu, H and Zhou, H}, title = {The genome of an ancient Rouran individual reveals an important paternal lineage in the Donghu population.}, journal = {American journal of physical anthropology}, volume = {166}, number = {4}, pages = {895-905}, doi = {10.1002/ajpa.23491}, pmid = {29681138}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Asian People/*genetics ; Chromosomes, Human, Y/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Genetics, Population ; Genome/*genetics ; Haplotypes/genetics ; Humans ; Male ; Mongolia ; Phylogeny ; Transients and Migrants ; }, abstract = {OBJECTIVES: Following the Xiongnu and Xianbei, the Rouran Khaganate (Rouran) was the third great nomadic tribe on the Mongolian Steppe. However, few human remains from this tribe are available for archaeologists and geneticists to study, as traces of the tombs of these nomadic people have rarely been found. In 2014, the IA-M1 remains (TL1) at the Khermen Tal site from the Rouran period were found by a Sino-Mongolian joint archaeological team in Mongolia, providing precious material for research into the genetic imprint of the Rouran.<br><br>MATERIALS AND METHODS: The mtDNA hypervariable sequence I (HVS-I) and Y-chromosome SNPs were analyzed, and capture of the paternal non-recombining region of the Y chromosome (NRY) and whole-genome shotgun sequencing of TL1 were performed. The materials from three sites representing the three ancient nationalities (Donghu, Xianbei, and Shiwei) were selected for comparison with the TL1 individual.<br><br>RESULTS: The mitochondrial haplotype of the TL1 individual was D4b1a2a1. The Y-chromosome haplotype was C2b1a1b/F3830 (ISOGG 2015), which was the same as that of the other two ancient male nomadic samples (ZHS5 and GG3) related to the Xianbei and Shiwei, which were also detected as F3889; this haplotype was reported to be downstream of F3830 by Wei et al. ().<br><br>DISCUSSION: We conclude that F3889 downstream of F3830 is an important paternal lineage of the ancient Donghu nomads. The Donghu-Xianbei branch is expected to have made an important paternal genetic contribution to Rouran. This component of gene flow ultimately entered the gene pool of modern Mongolic- and Manchu-speaking populations.}, }
@article {pmid29674573, year = {2018}, author = {Wade, L}, title = {Ancient DNA untangles South Asian roots.}, journal = {Science (New York, N.Y.)}, volume = {360}, number = {6386}, pages = {252}, doi = {10.1126/science.360.6386.252}, pmid = {29674573}, issn = {1095-9203}, mesh = {Asia, Southeastern/ethnology ; Asian People/*ethnology/*genetics ; *Biological Evolution ; *DNA, Ancient ; Humans ; }, }
@article {pmid29653594, year = {2018}, author = {Hammer, SE and Tautscher, B and Pucher, E and Kowarik, K and Reschreiter, H and Kern, A and Haring, E}, title = {Bronze Age meat industry: ancient mitochondrial DNA analyses of pig bones from the prehistoric salt mines of Hallstatt (Austria).}, journal = {BMC research notes}, volume = {11}, number = {1}, pages = {243}, pmid = {29653594}, issn = {1756-0500}, mesh = {Animals ; Austria ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Mining ; Pilot Projects ; Sequence Analysis, DNA/*methods ; *Sodium Chloride ; Sus scrofa/*genetics ; }, abstract = {OBJECTIVE: In the Bronze Age Hallstatt metropolis ('Salzkammergut' region, Upper Austria), salt richness enabled the preservation of pork meat to sustain people's livelihood suggesting an organized meat production industry on a yearly basis of hundreds of pigs. To pattern the geographic and temporal framework of the early management of pig populations in the surrounding areas of Hallstatt, we want to gain insights into the phylogeographic network based on DNA sequence variation among modern pigs, wild boars and prehistoric (likely) domestic pigs.<br><br>RESULTS: In this pilot study, we successfully adapted ancient DNA extraction and sequencing approaches for the analysis of mitochondrial DNA sequence variation in ten prehistoric porcine teeth specimens. Minimum-spanning network analyses revealed unique mitochondrial control region DNA haplotypes ranging within the variation of modern domestic pig and wild boar lineages and even shared haplotypes between prehistoric and modern domestic pigs and wild boars were observed.}, }
@article {pmid29642393, year = {2018}, author = {Sheng, GL and Barlow, A and Cooper, A and Hou, XD and Ji, XP and Jablonski, NG and Zhong, BJ and Liu, H and Flynn, LJ and Yuan, JX and Wang, LR and Basler, N and Westbury, MV and Hofreiter, M and Lai, XL}, title = {Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene.}, journal = {Genes}, volume = {9}, number = {4}, pages = {}, pmid = {29642393}, issn = {2073-4425}, abstract = {The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.}, }
@article {pmid29632188, year = {2018}, author = {de la Fuente, C and Ávila-Arcos, MC and Galimany, J and Carpenter, ML and Homburger, JR and Blanco, A and Contreras, P and Cruz Dávalos, D and Reyes, O and San Roman, M and Moreno-Estrada, A and Campos, PF and Eng, C and Huntsman, S and Burchard, EG and Malaspinas, AS and Bustamante, CD and Willerslev, E and Llop, E and Verdugo, RA and Moraga, M}, title = {Genomic insights into the origin and diversification of late maritime hunter-gatherers from the Chilean Patagonia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {17}, pages = {E4006-E4012}, pmid = {29632188}, issn = {1091-6490}, support = {T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Chile ; Female ; *Genetic Variation ; *Genome, Human ; History, Ancient ; Humans ; Indians, South American/*genetics/history ; Male ; }, abstract = {Patagonia was the last region of the Americas reached by humans who entered the continent from Siberia ∼15,000-20,000 y ago. Despite recent genomic approaches to reconstruct the continental evolutionary history, regional characterization of ancient and modern genomes remains understudied. Exploring the genomic diversity within Patagonia is not just a valuable strategy to gain a better understanding of the history and diversification of human populations in the southernmost tip of the Americas, but it would also improve the representation of Native American diversity in global databases of human variation. Here, we present genome data from four modern populations from Central Southern Chile and Patagonia (n = 61) and four ancient maritime individuals from Patagonia (∼1,000 y old). Both the modern and ancient individuals studied in this work have a greater genetic affinity with other modern Native Americans than to any non-American population, showing within South America a clear structure between major geographical regions. Native Patagonian Kawéskar and Yámana showed the highest genetic affinity with the ancient individuals, indicating genetic continuity in the region during the past 1,000 y before present, together with an important agreement between the ethnic affiliation and historical distribution of both groups. Lastly, the ancient maritime individuals were genetically equidistant to a ∼200-y-old terrestrial hunter-gatherer from Tierra del Fuego, which supports a model with an initial separation of a common ancestral group to both maritime populations from a terrestrial population, with a later diversification of the maritime groups.}, }
@article {pmid29618519, year = {2018}, author = {Thomson, VA and Mitchell, KJ and Eberhard, R and Dortch, J and Austin, JJ and Cooper, A}, title = {Genetic diversity and drivers of dwarfism in extinct island emu populations.}, journal = {Biology letters}, volume = {14}, number = {4}, pages = {}, pmid = {29618519}, issn = {1744-957X}, mesh = {Animals ; Australia ; Dromaiidae/*anatomy &amp; histology/*genetics ; Dwarfism/*genetics ; *Fossils ; *Genetic Variation ; Islands ; }, abstract = {Australia's iconic emu (Dromaius novaehollandiae novaehollandiae) is the only living representative of its genus, but fossil evidence and reports from early European explorers suggest that three island forms (at least two of which were dwarfs) became extinct during the nineteenth century. While one of these-the King Island emu-has been found to be conspecific with Australian mainland emus, little is known about how the other two forms-Kangaroo Island and Tasmanian emus-relate to the others, or even the size of Tasmanian emus. We present a comprehensive genetic and morphological analysis of Dromaius diversity, including data from one of the few definitively genuine Tasmanian emu specimens known. Our genetic analyses suggest that all the island populations represent sub-populations of mainland Dnovaehollandiae Further, the size of island emus and those on the mainland appears to scale linearly with island size but not time since isolation, suggesting that island size-and presumably concomitant limitations on resource availability-may be a more important driver of dwarfism in island emus, though its precise contribution to emu dwarfism remains to be confirmed.}, }
@article {pmid29610337, year = {2018}, author = {Ponce de León, MS and Koesbardiati, T and Weissmann, JD and Milella, M and Reyna-Blanco, CS and Suwa, G and Kondo, O and Malaspinas, AS and White, TD and Zollikofer, CPE}, title = {Human bony labyrinth is an indicator of population history and dispersal from Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {16}, pages = {4128-4133}, pmid = {29610337}, issn = {1091-6490}, mesh = {Africa ; Anatomy, Comparative ; Animals ; *Biological Evolution ; Cephalometry/methods ; Ear, Inner/*anatomy &amp; histology/diagnostic imaging ; History, Ancient ; Human Genome Project ; Human Migration/*history ; Humans ; Imaging, Three-Dimensional ; Phenotype ; Primates/anatomy &amp; histology ; Tomography, X-Ray Computed ; }, abstract = {The dispersal of modern humans from Africa is now well documented with genetic data that track population history, as well as gene flow between populations. Phenetic skeletal data, such as cranial and pelvic morphologies, also exhibit a dispersal-from-Africa signal, which, however, tends to be blurred by the effects of local adaptation and in vivo phenotypic plasticity, and that is often deteriorated by postmortem damage to skeletal remains. These complexities raise the question of which skeletal structures most effectively track neutral population history. The cavity system of the inner ear (the so-called bony labyrinth) is a good candidate structure for such analyses. It is already fully formed by birth, which minimizes postnatal phenotypic plasticity, and it is generally well preserved in archaeological samples. Here we use morphometric data of the bony labyrinth to show that it is a surprisingly good marker of the global dispersal of modern humans from Africa. Labyrinthine morphology tracks genetic distances and geography in accordance with an isolation-by-distance model with dispersal from Africa. Our data further indicate that the neutral-like pattern of variation is compatible with stabilizing selection on labyrinth morphology. Given the increasingly important role of the petrous bone for ancient DNA recovery from archaeological specimens, we encourage researchers to acquire 3D morphological data of the inner ear structures before any invasive sampling. Such data will constitute an important archive of phenotypic variation in present and past populations, and will permit individual-based genotype-phenotype comparisons.}, }
@article {pmid29609050, year = {2018}, author = {Gallello, G and Cilli, E and Bartoli, F and Andretta, M and Calcagnile, L and Pastor, A and de la Guardia, M and Serventi, P and Marino, A and Benazzi, S and Gruppioni, G}, title = {Poisoning histories in the Italian renaissance: The case of Pico Della Mirandola and Angelo Poliziano.}, journal = {Journal of forensic and legal medicine}, volume = {56}, number = {}, pages = {83-89}, doi = {10.1016/j.jflm.2018.03.016}, pmid = {29609050}, issn = {1878-7487}, mesh = {Arsenic/*analysis ; Arsenic Poisoning/*history ; Bone and Bones/*chemistry ; Carbon Radioisotopes ; DNA, Ancient ; Environmental Exposure/adverse effects ; Forensic Toxicology ; History, 15th Century ; Humans ; Italy ; Male ; Microscopy ; Microscopy, Electron, Scanning ; Mummies ; Spectrum Analysis/methods ; }, abstract = {Giovanni Pico della Mirandola and Angelo Poliziano were two of the most important humanists of the Italian Renaissance. They died suddenly in 1494 and their deaths have been for centuries a subject of debate. The exhumation of their remains offered the opportunity to study the cause of their death through a multidisciplinary research project. Anthropological analyses, together with documentary evidences, radiocarbon dating and ancient DNA analysis supported the identification of the remains attributed to Pico. Macroscopic examination did not reveal paleopathological lesions or signs related to syphilis. Heavy metals analysis, carried out on bones and mummified tissues, showed that in Pico's remains there were potentially lethal levels of arsenic, supporting the philosopher's poisoning theory reported by documentary sources. The arsenic concentrations obtained from analysis of Poliziano's remains, are probably more related to an As chronic exposure or diagenetic processes rather than poisoning.}, }
@article {pmid29608962, year = {2018}, author = {Bover, P and Mitchell, KJ and Llamas, B and Rofes, J and Thomson, VA and Cuenca-Bescós, G and Alcover, JA and Cooper, A and Pons, J}, title = {Molecular phylogenetics supports the origin of an endemic Balearic shrew lineage (Nesiotites) coincident with the Messinian Salinity Crisis.}, journal = {Molecular phylogenetics and evolution}, volume = {125}, number = {}, pages = {188-195}, doi = {10.1016/j.ympev.2018.03.028}, pmid = {29608962}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Calibration ; Caves ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Fossils ; Genome, Mitochondrial ; *Phylogeny ; *Salinity ; Shrews/*classification/genetics ; }, abstract = {The red-toothed shrews (Soricinae) are the most widespread subfamily of shrews, distributed from northern South America to North America and Eurasia. Within this subfamily, the tribe Nectogalini includes the fossil species Nesiotites hidalgo recorded from the Late Pleistocene to Holocene of the Balearic Islands (Western Mediterranean). Although there is a consensus about the close relationship between the extinct red-toothed shrew genera Nesiotites and Asoriculus based on morphology, molecular data are necessary to further evaluate the phylogenetic relationships of the Balearic fossils. We obtained a near complete mitochondrial genome of N. hidalgo, allowing the first molecular phylogenetic analysis of this species. Analyses based on 15,167 bp of the mitochondrial genome placed N. hidalgo as close relative to the extant Himalayan shrew (Soriculus nigrescens), and a combined analysis using molecular and morphological data confirm that N. hidalgo and Asoriculus gibberodon are sister-taxa with S. nigrescens as the immediate outgroup. Molecular clock and divergence estimates suggest that the split between N. hidalgo and its closest living relative occurred around 6.44 Ma, which is in agreement with the previously proposed colonisation of the Balearic Islands from mainland Europe by nectogaline shrews during the Messinian Salinity Crisis (5.97-5.33 My ago). Our results highlight that it is possible to retrieve genetic data from extinct small mammals from marginal environments for DNA preservation. Additional finds from the fossil record of Soricinae from the Eurasian Late Miocene/Early Pliocene are needed to shed further light on the still confusing taxonomy and paleobiogeography of this clade.}, }
@article {pmid29607481, year = {2018}, author = {Russo, MG and Mendisco, F and Avena, SA and Crespo, CM and Arencibia, V and Dejean, CB and Seldes, V}, title = {Ancient DNA reveals temporal population structure within the South-Central Andes area.}, journal = {American journal of physical anthropology}, volume = {166}, number = {4}, pages = {851-860}, doi = {10.1002/ajpa.23475}, pmid = {29607481}, issn = {1096-8644}, mesh = {Archaeology ; DNA, Ancient/*analysis ; Female ; Genetic Markers/genetics ; Genetics, Population ; Humans ; Indians, South American/*genetics ; Male ; Microsatellite Repeats/genetics ; Peru ; Sequence Analysis, DNA ; Tooth/chemistry ; }, abstract = {OBJECTIVES: The main aim of this work was to contribute to the knowledge of pre-Hispanic genetic variation and population structure among the South-central Andes Area by studying individuals from Quebrada de Humahuaca, North-western (NW) Argentina.<br><br>MATERIALS AND METHODS: We analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900-1430 AD). Compiling autosomal, mitochondrial, and Y-chromosome data, we evaluated population structure and differentiation among eight South-central Andean groups from the current territories of NW Argentina and Peru.<br><br>RESULTS: Autosomal data revealed a structuring of the analyzed populations into two clusters which seemed to represent different temporalities in the Andean pre-Hispanic history: pre-Inca and Inca. All pre-Inca samples fell into the same cluster despite being from the two different territories of NW Argentina and Peru. Also, they were systematically differentiated from the Peruvian Inca group. These results were mostly confirmed by mitochondrial and Y-chromosome analyses. We mainly found a clearly different haplotype composition between clusters.<br><br>DISCUSSION: Population structure in South America has been mostly studied on current native groups, mainly showing a west-to-east differentiation between the Andean and lowland regions. Here we demonstrated that genetic population differentiation preceded the European contact and might have been more complex than thought, being found within the South-central Andes Area. Moreover, divergence among temporally different populations might be reflecting socio-political changes occurred in the evermore complex pre-Hispanic Andean societies.}, }
@article {pmid29607044, year = {2018}, author = {Margaryan, A and Hansen, HB and Rasmussen, S and Sikora, M and Moiseyev, V and Khoklov, A and Epimakhov, A and Yepiskoposyan, L and Kriiska, A and Varul, L and Saag, L and Lynnerup, N and Willerslev, E and Allentoft, ME}, title = {Ancient pathogen DNA in human teeth and petrous bones.}, journal = {Ecology and evolution}, volume = {8}, number = {6}, pages = {3534-3542}, pmid = {29607044}, issn = {2045-7758}, abstract = {Recent ancient DNA (aDNA) studies of human pathogens have provided invaluable insights into their evolutionary history and prevalence in space and time. Most of these studies were based on DNA extracted from teeth or postcranial bones. In contrast, no pathogen DNA has been reported from the petrous bone which has become the most desired skeletal element in ancient DNA research due to its high endogenous DNA content. To compare the potential for pathogenic aDNA retrieval from teeth and petrous bones, we sampled these elements from five ancient skeletons, previously shown to be carrying Yersinia pestis. Based on shotgun sequencing data, four of these five plague victims showed clearly detectable levels of Y. pestis DNA in the teeth, whereas all the petrous bones failed to produce Y. pestis DNA above baseline levels. A broader comparative metagenomic analysis of teeth and petrous bones from 10 historical skeletons corroborated these results, showing a much higher microbial diversity in teeth than petrous bones, including pathogenic and oral microbial taxa. Our results imply that although petrous bones are highly valuable for ancient genomic analyses as an excellent source of endogenous DNA, the metagenomic potential of these dense skeletal elements is highly limited. This trade-off must be considered when designing the sampling strategy for an aDNA project.}, }
@article {pmid33474186, year = {2018}, author = {de Flamingh, A and Mallott, EK and Roca, AL and Boraas, AS and Malhi, RS}, title = {Species identification and mitochondrial genomes of ancient fish bones from the Riverine Kachemak tradition of the Kenai Peninsula, Alaska.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {3}, number = {1}, pages = {409-411}, pmid = {33474186}, issn = {2380-2359}, abstract = {Seven fish vertebrae were chosen for analysis from the 49-KEN-147 archaeological site in the Kenai Peninsula, Alaska. Mitochondrial DNA analysis of the ancient fish bones revealed that they were from sockeye and coho salmon. Here, we report the ancient mitochondrial genomes for three sockeye salmon and one coho salmon fish bone.}, }
@article {pmid29603124, year = {2018}, author = {Nieves-Colón, MA and Ozga, AT and Pestle, WJ and Cucina, A and Tiesler, V and Stanton, TW and Stone, AC}, title = {Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments.}, journal = {American journal of physical anthropology}, volume = {166}, number = {4}, pages = {824-836}, doi = {10.1002/ajpa.23472}, pmid = {29603124}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Base Composition/genetics ; DNA Damage/genetics ; DNA, Ancient/*analysis ; High-Throughput Nucleotide Sequencing ; Humans ; Mexico ; Puerto Rico ; Sequence Analysis, DNA/*methods ; Tanzania ; Tooth/chemistry ; *Tropical Climate ; }, abstract = {OBJECTIVES: The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi-tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12).<br><br>MATERIALS AND METHODS: All samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step.<br><br>RESULTS: No significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments.<br><br>DISCUSSION: Both methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.}, }
@article {pmid29595789, year = {2018}, author = {}, title = {On the use and abuse of ancient DNA.}, journal = {Nature}, volume = {555}, number = {7698}, pages = {559}, doi = {10.1038/d41586-018-03857-3}, pmid = {29595789}, issn = {1476-4687}, mesh = {*DNA, Ancient ; DNA, Mitochondrial ; *Fossils ; Sequence Analysis, DNA ; }, }
@article {pmid29595343, year = {2019}, author = {Collier, A and Carr, SM}, title = {On the persistence and detectability of ancient Beothuk mitochondrial DNA genomes in living First Nations peoples.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {30}, number = {1}, pages = {68-74}, doi = {10.1080/24701394.2018.1455190}, pmid = {29595343}, issn = {2470-1408}, mesh = {*Genome, Mitochondrial ; Genotyping Techniques/methods/standards ; Haplotypes ; Humans ; Indians, North American/*genetics ; Limit of Detection ; Polymorphism, Genetic ; }, abstract = {Claims have long been made as to the survival to the present day of descendants of the Newfoundland Beothuk, a group generally accepted to have become extinct with the death of the last known member, Shanawdithit, in 1829. Interest has recently been revived by the availability of commercial genetic testing, which some claim can assign living individuals to specific Native American groups. We compare complete mitogenome sequences (16569 bp) from aDNA of eight distinct Beothuk lineages, including Shanawdithit's uncle Nonosabasut and his wife Demasduit, with three Newfoundland Mi'kmaq lineages and 21 other living Native Americans drawn from GenBank. A Newfoundland Mi'kmaq lineage in Haplogroup A is more similar to three Native Americans (1-3 SNPs) than to the most closely related Beothuk (24 SNPs). Nonosabasut in Haplogroup X is identical to a non-Beothuk Native American. Demasduit in Haplogroup C differs from three other Native Americans by 1-4 substitutions. Within a 2168 bp region of the HVS sequences available from living Mi'kmaq of the Miawpukek First Nation in Newfoundland, lineages in Haplogroups C, X, and A differ by 1, 4, and 8 substitutions, from the most similar Beothuk, and are more similar to other Native Americans. MtDNA genome sequences in living persons identical or similar to those of Beothuk do not necessarily indicate Beothuk ancestry. Mi'kmaq lineages cannot at this time be associated with any Beothuk lineages more closely than those of other Native Americans.}, }
@article {pmid29588507, year = {2018}, author = {Baca, M and Popović, D and Panagiotopoulou, H and Marciszak, A and Krajcarz, M and Krajcarz, MT and Makowiecki, D and Węgleński, P and Nadachowski, A}, title = {Human-mediated dispersal of cats in the Neolithic Central Europe.}, journal = {Heredity}, volume = {121}, number = {6}, pages = {557-563}, pmid = {29588507}, issn = {1365-2540}, mesh = {Animals ; *Animals, Domestic ; *Archaeology ; Cats/classification/*genetics ; DNA, Mitochondrial/*genetics ; Europe ; Gene Pool ; Humans ; Phylogeny ; }, abstract = {Archeological and genetic evidence suggest that all domestic cats derived from the Near Eastern wildcat (Felis silvestris lybica) and were first domesticated in the Near East around 10,000 years ago. The spread of the domesticated form in Europe occurred much later, primarily mediated by Greek and Phoenician traders and afterward by Romans who introduced cats to Western and Central Europe around 2000 years ago. We investigated mtDNA of Holocene Felis remains and provide evidence of an unexpectedly early presence of cats bearing the Near Eastern wildcat mtDNA haplotypes in Central Europe, being ahead of Roman period by over 2000 years. The appearance of the Near Eastern wildcats in Central Europe coincides with the peak of Neolithic settlement density, moreover most of those cats belonged to the same mtDNA lineages as those domesticated in the Near East. Thus, although we cannot fully exclude that the Near Eastern wildcats appeared in Central Europe as a result of introgression with European wildcat, our findings support the hypothesis that the Near Eastern wildcats spread across Europe together with the first farmers, perhaps as commensal animals. We also found that cats dated to the Neolithic period belonged to different mtDNA lineages than those brought to Central Europe in Roman times, this supports the hypothesis that the gene pool of contemporary European domestic cats might have been established from two different source populations that contributed in different periods.}, }
@article {pmid29581591, year = {2018}, author = {Hendy, J and Welker, F and Demarchi, B and Speller, C and Warinner, C and Collins, MJ}, title = {A guide to ancient protein studies.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {5}, pages = {791-799}, doi = {10.1038/s41559-018-0510-x}, pmid = {29581591}, issn = {2397-334X}, support = {R01GM089886/NH/NIH HHS/United States ; }, mesh = {*Archaeology ; *Paleontology ; Proteomics/*methods/standards ; }, abstract = {Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.}, }
@article {pmid29576952, year = {2018}, author = {McGuire, JA and Cotoras, DD and O'Connell, B and Lawalata, SZS and Wang-Claypool, CY and Stubbs, A and Huang, X and Wogan, GOU and Hykin, SM and Reilly, SB and Bi, K and Riyanto, A and Arida, E and Smith, LL and Milne, H and Streicher, JW and Iskandar, DT}, title = {Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4470}, pmid = {29576952}, issn = {2167-8359}, abstract = {We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (721 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.}, }
@article {pmid29575237, year = {2018}, author = {Gui, S and Peng, J and Wang, X and Wu, Z and Cao, R and Salse, J and Zhang, H and Zhu, Z and Xia, Q and Quan, Z and Shu, L and Ke, W and Ding, Y}, title = {Improving Nelumbo nucifera genome assemblies using high-resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements.}, journal = {The Plant journal : for cell and molecular biology}, volume = {94}, number = {4}, pages = {721-734}, doi = {10.1111/tpj.13894}, pmid = {29575237}, issn = {1365-313X}, mesh = {China ; *Chromosome Mapping ; Chromosomes, Plant/*genetics ; Genetic Linkage ; Genetic Markers/genetics ; Genome, Plant/*genetics ; Genomics ; Genotype ; High-Throughput Nucleotide Sequencing ; Karyotype ; Microsatellite Repeats/genetics ; Nelumbo/*genetics ; Plant Breeding ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA ; }, abstract = {Genetic and physical maps are powerful tools to anchor fragmented draft genome assemblies generated from next-generation sequencing. Currently, two draft assemblies of Nelumbo nucifera, the genomes of 'China Antique' and 'Chinese Tai-zi', have been released. However, there is presently no information on how the sequences are assembled into chromosomes in N. nucifera. The lack of physical maps and inadequate resolution of available genetic maps hindered the assembly of N. nucifera chromosomes. Here, a linkage map of N. nucifera containing 2371 bin markers [217 577 single nucleotide polymorphisms (SNPs)] was constructed using restriction-site associated DNA sequencing data of 181 F2 individuals and validated by adding 197 simple sequence repeat (SSR) markers. Additionally, a BioNano optical map covering 86.20% of the 'Chinese Tai-zi' genome was constructed. The draft assembly of 'Chinese Tai-zi' was improved based on the BioNano optical map, showing an increase of the scaffold N50 from 0.989 to 1.48 Mb. Using a combination of multiple maps, 97.9% of the scaffolds in the 'Chinese Tai-zi' draft assembly and 97.6% of the scaffolds in the 'China Antique' draft assembly were anchored into pseudo-chromosomes, and the centromere regions along the pseudo-chromosomes were identified. An evolutionary scenario was proposed to reach the modern N. nucifera karyotype from the seven ancestral eudicot chromosomes. The present study provides the highest-resolution linkage map, the optical map and chromosome level genome assemblies for N. nucifera, which are valuable for the breeding and cultivation of N. nucifera and future studies of comparative and evolutionary genomics in angiosperms.}, }
@article {pmid29557324, year = {2018}, author = {Wood, JR}, title = {DNA barcoding of ancient parasites.}, journal = {Parasitology}, volume = {145}, number = {5}, pages = {646-655}, doi = {10.1017/S0031182018000380}, pmid = {29557324}, issn = {1469-8161}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Ancient/analysis/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Parasites/*genetics ; Parasitic Diseases/parasitology ; }, abstract = {Ancient samples present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient samples can provide a number of unique scientific insights, for example: (1) into the parasite communities and health of prehistoric human populations; (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction; and (3) the ability to view in 'real-time' processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts. The application of DNA metabarcoding and high-throughput sequencing to ancient specimens has so far been limited, but in future promises great potential for gaining empirical data on poorly understood processes such as parasite co-extinction.}, }
@article {pmid29533977, year = {2018}, author = {Taron, UH and Lell, M and Barlow, A and Paijmans, JLA}, title = {Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool.}, journal = {Genes}, volume = {9}, number = {3}, pages = {}, pmid = {29533977}, issn = {2073-4425}, support = {310763/ERC_/European Research Council/International ; }, abstract = {High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present 'TAPAS', (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.}, }
@article {pmid29531040, year = {2018}, author = {Veeramah, KR and Rott, A and Groß, M and van Dorp, L and López, S and Kirsanow, K and Sell, C and Blöcher, J and Wegmann, D and Link, V and Hofmanová, Z and Peters, J and Trautmann, B and Gairhos, A and Haberstroh, J and Päffgen, B and Hellenthal, G and Haas-Gebhard, B and Harbeck, M and Burger, J}, title = {Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {13}, pages = {3494-3499}, pmid = {29531040}, issn = {1091-6490}, mesh = {Archaeology ; DNA, Ancient ; Female ; Genetic Variation ; *Genetics, Population ; *Genome, Human ; Genomics/*methods ; Germany ; Haplotypes ; History, Medieval ; *Human Migration ; Humans ; Phenotype ; Skull/anatomy &amp; histology/*metabolism ; White People/*genetics ; Whole Genome Sequencing ; }, abstract = {Modern European genetic structure demonstrates strong correlations with geography, while genetic analysis of prehistoric humans has indicated at least two major waves of immigration from outside the continent during periods of cultural change. However, population-level genome data that could shed light on the demographic processes occurring during the intervening periods have been absent. Therefore, we generated genomic data from 41 individuals dating mostly to the late 5th/early 6th century AD from present-day Bavaria in southern Germany, including 11 whole genomes (mean depth 5.56×). In addition we developed a capture array to sequence neutral regions spanning a total of 5 Mb and 486 functional polymorphic sites to high depth (mean 72×) in all individuals. Our data indicate that while men generally had ancestry that closely resembles modern northern and central Europeans, women exhibit a very high genetic heterogeneity; this includes signals of genetic ancestry ranging from western Europe to East Asia. Particularly striking are women with artificial skull deformations; the analysis of their collective genetic ancestry suggests an origin in southeastern Europe. In addition, functional variants indicate that they also differed in visible characteristics. This example of female-biased migration indicates that complex demographic processes during the Early Medieval period may have contributed in an unexpected way to shape the modern European genetic landscape. Examination of the panel of functional loci also revealed that many alleles associated with recent positive selection were already at modern-like frequencies in European populations ∼1,500 years ago.}, }
@article {pmid29526494, year = {2018}, author = {Jones, ED}, title = {Ancient DNA: a history of the science before Jurassic Park.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {68-69}, number = {}, pages = {1-14}, doi = {10.1016/j.shpsc.2018.02.001}, pmid = {29526494}, issn = {1879-2499}, mesh = {Animals ; *DNA, Ancient ; Extinction, Biological ; *Fossils ; Genetics/*history ; History, 20th Century ; Invertebrates/genetics ; Plants/genetics ; Vertebrates/genetics ; }, }
@article {pmid29515143, year = {2018}, author = {Korlević, P and Talamo, S and Meyer, M}, title = {A combined method for DNA analysis and radiocarbon dating from a single sample.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4127}, pmid = {29515143}, issn = {2045-2322}, mesh = {Animals ; Archaeology/*methods ; DNA, Ancient/*analysis ; *Fossils ; Humans ; Radiometric Dating/*methods ; }, abstract = {Current protocols for ancient DNA and radiocarbon analysis of ancient bones and teeth call for multiple destructive samplings of a given specimen, thereby increasing the extent of undesirable damage to precious archaeological material. Here we present a method that makes it possible to obtain both ancient DNA sequences and radiocarbon dates from the same sample material. This is achieved by releasing DNA from the bone matrix through incubation with either EDTA or phosphate buffer prior to complete demineralization and collagen extraction utilizing the acid-base-acid-gelatinization and ultrafiltration procedure established in most radiocarbon dating laboratories. Using a set of 12 bones of different ages and preservation conditions we demonstrate that on average 89% of the DNA can be released from sample powder with minimal, or 38% without any, detectable collagen loss. We also detect no skews in radiocarbon dates compared to untreated samples. Given the different material demands for radiocarbon dating (500 mg of bone/dentine) and DNA analysis (10-100 mg), combined DNA and collagen extraction not only streamlines the sampling process but also drastically increases the amount of DNA that can be recovered from limited sample material.}, }
@article {pmid29511572, year = {2018}, author = {Duchêne, S and Holmes, EC}, title = {Estimating evolutionary rates in giant viruses using ancient genomes.}, journal = {Virus evolution}, volume = {4}, number = {1}, pages = {vey006}, pmid = {29511572}, issn = {2057-1577}, abstract = {Pithovirus sibericum is a giant (610 Kpb) double-stranded DNA virus discovered in a purportedly 30,000-year-old permafrost sample. A closely related virus, Pithovirus massiliensis, was recently isolated from a sewer in southern France. An initial comparison of these two virus genomes assumed that P. sibericum was directly ancestral to P. massiliensis and gave a maximum evolutionary rate of 2.60 × 10[-5] nucleotide substitutions per site per year (subs/site/year). If correct, this would make pithoviruses among the fastest-evolving DNA viruses, with rates close to those seen in some RNA viruses. To help determine whether this unusually high rate is accurate we utilized the well-known negative association between evolutionary rate and genome size in DNA microbes. This revealed that a more plausible rate estimate for Pithovirus evolution is ∼2.23 × 10[-6] subs/site/year, with even lower estimates obtained if evolutionary rates are assumed to be time-dependent. Hence, we estimate that Pithovirus has evolved at least an order of magnitude more slowly than previously suggested. We then used our new rate estimates to infer a time-scale for Pithovirus evolution. Strikingly, this suggests that these viruses could have diverged at least hundreds of thousands of years ago, and hence have evolved over longer time-scales than previously suggested. We propose that the evolutionary rate and time-scale of pithovirus evolution should be reconsidered in the light of these observations and that future estimates of the rate of giant virus evolution should be carefully examined in the context of their biological plausibility.}, }
@article {pmid29501328, year = {2018}, author = {Lipson, M and Skoglund, P and Spriggs, M and Valentin, F and Bedford, S and Shing, R and Buckley, H and Phillip, I and Ward, GK and Mallick, S and Rohland, N and Broomandkhoshbacht, N and Cheronet, O and Ferry, M and Harper, TK and Michel, M and Oppenheimer, J and Sirak, K and Stewardson, K and Auckland, K and Hill, AVS and Maitland, K and Oppenheimer, SJ and Parks, T and Robson, K and Williams, TN and Kennett, DJ and Mentzer, AJ and Pinhasi, R and Reich, D}, title = {Population Turnover in Remote Oceania Shortly after Initial Settlement.}, journal = {Current biology : CB}, volume = {28}, number = {7}, pages = {1157-1165.e7}, pmid = {29501328}, issn = {1879-0445}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; 106289/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; PG/14/26/30509/BHF_/British Heart Foundation/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; /HHMI_/Howard Hughes Medical Institute/United States ; }, mesh = {DNA, Ancient/*analysis ; Female ; *Genetics, Population ; *Genome, Human ; Genome-Wide Association Study ; Human Migration/*statistics &amp; numerical data ; Humans ; Male ; Native Hawaiian or Pacific Islander/*genetics ; Oceania ; Phylogeny ; *Population Dynamics ; }, abstract = {Ancient DNA from Vanuatu and Tonga dating to about 2,900-2,600 years ago (before present, BP) has revealed that the "First Remote Oceanians" associated with the Lapita archaeological culture were directly descended from the population that, beginning around 5000 BP, spread Austronesian languages from Taiwan to the Philippines, western Melanesia, and eventually Remote Oceania. Thus, ancestors of the First Remote Oceanians must have passed by the Papuan-ancestry populations they encountered in New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture [1]. However, all present-day populations in Near and Remote Oceania harbor >25% Papuan ancestry, implying that additional eastward migration must have occurred. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu from 2900-150 BP, as well as 185 present-day individuals from 18 islands. We find that people of almost entirely Papuan ancestry arrived in Vanuatu by around 2300 BP, most likely reflecting migrations a few hundred years earlier at the end of the Lapita period, when there is also evidence of changes in skeletal morphology and cessation of long-distance trade between Near and Remote Oceania [2, 3]. Papuan ancestry was subsequently diluted through admixture but remains at least 80%-90% in most islands. Through a fine-grained analysis of ancestry profiles, we show that the Papuan ancestry in Vanuatu derives from the Bismarck Archipelago rather than the geographically closer Solomon Islands. However, the Papuan ancestry in Polynesia-the most remote Pacific islands-derives from different sources, documenting a third stream of migration from Near to Remote Oceania.}, }
@article {pmid29495401, year = {2018}, author = {Eisenhofer, R and Weyrich, LS}, title = {Proper Authentication of Ancient DNA Is Still Essential.}, journal = {Genes}, volume = {9}, number = {3}, pages = {}, pmid = {29495401}, issn = {2073-4425}, abstract = {Santiago-Rodriguez et al. [1] report on the putative gut microbiome and resistome of Inca and Italian mummies, and find that Italian mummies exhibit higher bacterial diversity compared to the Inca mummies.[...].}, }
@article {pmid29494531, year = {2018}, author = {Loreille, O and Ratnayake, S and Bazinet, AL and Stockwell, TB and Sommer, DD and Rohland, N and Mallick, S and Johnson, PLF and Skoglund, P and Onorato, AJ and Bergman, NH and Reich, D and Irwin, JA}, title = {Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens.}, journal = {Genes}, volume = {9}, number = {3}, pages = {}, pmid = {29494531}, issn = {2073-4425}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; }, abstract = {High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.}, }
@article {pmid29493596, year = {2018}, author = {}, title = {UK university strike, quark pioneer and the ancient-genome boom.}, journal = {Nature}, volume = {555}, number = {7694}, pages = {10-11}, doi = {10.1038/d41586-018-02389-0}, pmid = {29493596}, issn = {1476-4687}, }
@article {pmid32099188, year = {2018}, author = {}, title = {On the use and abuse of ancient DNA.}, journal = {Nature}, volume = {555}, number = {7698}, pages = {559}, doi = {10.1038/d41586-018-03857-3}, pmid = {32099188}, issn = {1476-4687}, }
@article {pmid32094882, year = {2018}, author = {}, title = {UK university strike, quark pioneer and the ancient-genome boom.}, journal = {Nature}, volume = {555}, number = {7694}, pages = {10-11}, doi = {10.1038/d41586-018-02389-0}, pmid = {32094882}, issn = {1476-4687}, }
@article {pmid29483247, year = {2018}, author = {Palkopoulou, E and Lipson, M and Mallick, S and Nielsen, S and Rohland, N and Baleka, S and Karpinski, E and Ivancevic, AM and To, TH and Kortschak, RD and Raison, JM and Qu, Z and Chin, TJ and Alt, KW and Claesson, S and Dalén, L and MacPhee, RDE and Meller, H and Roca, AL and Ryder, OA and Heiman, D and Young, S and Breen, M and Williams, C and Aken, BL and Ruffier, M and Karlsson, E and Johnson, J and Di Palma, F and Alfoldi, J and Adelson, DL and Mailund, T and Munch, K and Lindblad-Toh, K and Hofreiter, M and Poinar, H and Reich, D}, title = {A comprehensive genomic history of extinct and living elephants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {11}, pages = {E2566-E2574}, pmid = {29483247}, issn = {1091-6490}, support = {//Wellcome Trust/United Kingdom ; R01 GM100233/GM/NIGMS NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; WT098051//Wellcome Trust/United Kingdom ; WT108749/Z/15/Z//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Elephants/classification/*genetics ; Evolution, Molecular ; Extinction, Biological ; Fossils ; Gene Flow ; Genome ; Genomics/history ; History, Ancient ; Mammoths/classification/*genetics ; Mastodons/classification/*genetics ; Phylogeny ; }, abstract = {Elephantids are the world's most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ∼120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant's ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for ∼500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.}, }
@article {pmid29471451, year = {2018}, author = {Cahill, JA and Heintzman, PD and Harris, K and Teasdale, MD and Kapp, J and Soares, AER and Stirling, I and Bradley, D and Edwards, CJ and Graim, K and Kisleika, AA and Malev, AV and Monaghan, N and Green, RE and Shapiro, B}, title = {Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age.}, journal = {Molecular biology and evolution}, volume = {35}, number = {5}, pages = {1120-1129}, doi = {10.1093/molbev/msy018}, pmid = {29471451}, issn = {1537-1719}, mesh = {Animals ; *Climate Change ; *Fossils ; *Gene Flow ; *Hybridization, Genetic ; Ice Cover ; Ursidae/*genetics ; }, abstract = {Recent genomic analyses have provided substantial evidence for past periods of gene flow from polar bears (Ursus maritimus) into Alaskan brown bears (Ursus arctos), with some analyses suggesting a link between climate change and genomic introgression. However, because it has mainly been possible to sample bears from the present day, the timing, frequency, and evolutionary significance of this admixture remains unknown. Here, we analyze genomic DNA from three additional and geographically distinct brown bear populations, including two that lived temporally close to the peak of the last ice age. We find evidence of admixture in all three populations, suggesting that admixture between these species has been common in their recent evolutionary history. In addition, analyses of ten fossil bears from the now-extinct Irish population indicate that admixture peaked during the last ice age, whereas brown bear and polar bear ranges overlapped. Following this peak, the proportion of polar bear ancestry in Irish brown bears declined rapidly until their extinction. Our results support a model in which ice age climate change created geographically widespread conditions conducive to admixture between polar bears and brown bears, as is again occurring today. We postulate that this model will be informative for many admixing species pairs impacted by climate change. Our results highlight the power of paleogenomics to reveal patterns of evolutionary change that are otherwise masked in contemporary data.}, }
@article {pmid29466330, year = {2018}, author = {Mathieson, I and Alpaslan-Roodenberg, S and Posth, C and Szécsényi-Nagy, A and Rohland, N and Mallick, S and Olalde, I and Broomandkhoshbacht, N and Candilio, F and Cheronet, O and Fernandes, D and Ferry, M and Gamarra, B and Fortes, GG and Haak, W and Harney, E and Jones, E and Keating, D and Krause-Kyora, B and Kucukkalipci, I and Michel, M and Mittnik, A and Nägele, K and Novak, M and Oppenheimer, J and Patterson, N and Pfrengle, S and Sirak, K and Stewardson, K and Vai, S and Alexandrov, S and Alt, KW and Andreescu, R and Antonović, D and Ash, A and Atanassova, N and Bacvarov, K and Gusztáv, MB and Bocherens, H and Bolus, M and Boroneanţ, A and Boyadzhiev, Y and Budnik, A and Burmaz, J and Chohadzhiev, S and Conard, NJ and Cottiaux, R and Čuka, M and Cupillard, C and Drucker, DG and Elenski, N and Francken, M and Galabova, B and Ganetsovski, G and Gély, B and Hajdu, T and Handzhyiska, V and Harvati, K and Higham, T and Iliev, S and Janković, I and Karavanić, I and Kennett, DJ and Komšo, D and Kozak, A and Labuda, D and Lari, M and Lazar, C and Leppek, M and Leshtakov, K and Vetro, DL and Los, D and Lozanov, I and Malina, M and Martini, F and McSweeney, K and Meller, H and Menđušić, M and Mirea, P and Moiseyev, V and Petrova, V and Price, TD and Simalcsik, A and Sineo, L and Šlaus, M and Slavchev, V and Stanev, P and Starović, A and Szeniczey, T and Talamo, S and Teschler-Nicola, M and Thevenet, C and Valchev, I and Valentin, F and Vasilyev, S and Veljanovska, F and Venelinova, S and Veselovskaya, E and Viola, B and Virag, C and Zaninović, J and Zäuner, S and Stockhammer, PW and Catalano, G and Krauß, R and Caramelli, D and Zariņa, G and Gaydarska, B and Lillie, M and Nikitin, AG and Potekhina, I and Papathanasiou, A and Borić, D and Bonsall, C and Krause, J and Pinhasi, R and Reich, D}, title = {The genomic history of southeastern Europe.}, journal = {Nature}, volume = {555}, number = {7695}, pages = {197-203}, pmid = {29466330}, issn = {1476-4687}, support = {/HHMI_/Howard Hughes Medical Institute/United States ; 263441/ERC_/European Research Council/International ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; }, mesh = {Agriculture/history ; Asia/ethnology ; DNA, Ancient ; Europe ; Farmers/*history ; Female ; Genetics, Population ; Genome, Human/*genetics ; *Genomics ; Grassland ; History, Ancient ; Human Migration/*history ; Humans ; Male ; Sex Distribution ; }, abstract = {Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west-east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.}, }
@article {pmid29463742, year = {2018}, author = {Schroeder, H and Sikora, M and Gopalakrishnan, S and Cassidy, LM and Maisano Delser, P and Sandoval Velasco, M and Schraiber, JG and Rasmussen, S and Homburger, JR and Ávila-Arcos, MC and Allentoft, ME and Moreno-Mayar, JV and Renaud, G and Gómez-Carballa, A and Laffoon, JE and Hopkins, RJA and Higham, TFG and Carr, RS and Schaffer, WC and Day, JS and Hoogland, M and Salas, A and Bustamante, CD and Nielsen, R and Bradley, DG and Hofman, CL and Willerslev, E}, title = {Origins and genetic legacies of the Caribbean Taino.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {10}, pages = {2341-2346}, pmid = {29463742}, issn = {1091-6490}, support = {R35 GM124745/GM/NIGMS NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; American Indian or Alaska Native/*genetics ; Archaeology ; Bahamas ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; Genome, Human/*genetics ; Genomics ; Hispanic or Latino/genetics ; History, Ancient ; Human Migration/history/*statistics &amp; numerical data ; Humans ; Male ; Paleontology ; Phylogeny ; Young Adult ; }, abstract = {The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher's Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.}, }
@article {pmid29440415, year = {2018}, author = {Boast, AP and Weyrich, LS and Wood, JR and Metcalf, JL and Knight, R and Cooper, A}, title = {Coprolites reveal ecological interactions lost with the extinction of New Zealand birds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {7}, pages = {1546-1551}, pmid = {29440415}, issn = {1091-6490}, mesh = {Animals ; Behavior, Animal/*physiology ; Birds/*physiology ; DNA/*analysis/genetics ; *Ecology ; *Extinction, Biological ; *Fossils ; Fungi/genetics ; Palaeognathae/*physiology ; Parasites/genetics ; Plants/genetics ; }, abstract = {Over the past 50,000 y, biotic extinctions and declines have left a legacy of vacant niches and broken ecological interactions across global terrestrial ecosystems. Reconstructing the natural, unmodified ecosystems that preceded these events relies on high-resolution analyses of paleoecological deposits. Coprolites are a source of uniquely detailed information about trophic interactions and the behaviors, gut parasite communities, and microbiotas of prehistoric animal species. Such insights are critical for understanding the legacy effects of extinctions on ecosystems, and can help guide contemporary conservation and ecosystem restoration efforts. Here we use high-throughput sequencing (HTS) of ancient eukaryotic DNA from coprolites to reconstruct aspects of the biology and ecology of four species of extinct moa and the critically endangered kakapo parrot from New Zealand (NZ). Importantly, we provide evidence that moa and prehistoric kakapo consumed ectomycorrhizal fungi, suggesting these birds played a role in dispersing fungi that are key to NZ's natural forest ecosystems. We also provide the first DNA-based evidence that moa frequently supplemented their broad diets with ferns and mosses. Finally, we also find parasite taxa that provide insight into moa behavior, and present data supporting the hypothesis of coextinction between moa and several parasite species. Our study demonstrates that HTS sequencing of coprolites provides a powerful tool for resolving key aspects of ancient ecosystems and may rapidly provide information not obtainable by conventional paleoecological techniques, such as fossil analyses.}, }
@article {pmid29438388, year = {2018}, author = {Rodrigues, AT and McKechnie, I and Yang, DY}, title = {Ancient DNA analysis of Indigenous rockfish use on the Pacific Coast: Implications for marine conservation areas and fisheries management.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0192716}, pmid = {29438388}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; British Columbia ; Conservation of Natural Resources/*methods ; DNA, Ancient/*analysis/isolation &amp; purification ; DNA, Mitochondrial/analysis/genetics/history ; Fisheries/organization &amp; administration ; History, Ancient ; Humans ; Perciformes/*genetics ; Species Specificity ; }, abstract = {Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory.}, }
@article {pmid29436536, year = {2018}, author = {Sang, F and Zhang, Z and Yuan, L and Liu, D}, title = {Quantum dots for a high-throughput Pfu polymerase based multi-round polymerase chain reaction (PCR).}, journal = {The Analyst}, volume = {143}, number = {5}, pages = {1259-1267}, doi = {10.1039/c7an01764b}, pmid = {29436536}, issn = {1364-5528}, mesh = {DNA-Directed DNA Polymerase/*chemistry ; *Polymerase Chain Reaction ; *Quantum Dots ; Taq Polymerase ; }, abstract = {Multi-round PCR is an important technique for obtaining enough target DNA from rare DNA resources, and is commonly used in many fields including forensic science, ancient DNA analysis and cancer research. However, multi-round PCR is often aborted, largely due to the accumulation of non-specific amplification during repeated amplifications. Here, we developed a Pfu polymerase based multi-round PCR technique assisted by quantum dots (QDs). Different PCR assays, DNA polymerases (Pfu and Taq), DNA sizes and GC amounts were compared in this study. In the presence of QDs, PCR specificity could be retained even in the ninth-round amplification. Moreover, the longer and more complex the targets were, the earlier the abortion happened in multi-round PCR. However, no obvious enhancement of specificity was found in multi-round PCR using Taq DNA polymerase. Significantly, the fidelity of Pfu polymerase based multi-round PCR was not sacrificed in the presence of QDs. Besides, pre-incubation at 50 °C for an hour had no impact on multi-round PCR performance, which further authenticated the hot start effect of QDs modulated in multi-round PCR. The findings of this study demonstrated that a cost-effective and promising multi-round PCR technique for large-scale and high-throughput sample analysis could be established with high specificity, sensibility and accuracy.}, }
@article {pmid29426903, year = {2018}, author = {Marr, MM and Brace, S and Schreve, DC and Barnes, I}, title = {Identifying source populations for the reintroduction of the Eurasian beaver, Castor fiber L. 1758, into Britain: evidence from ancient DNA.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2708}, pmid = {29426903}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient ; *Environmental Restoration and Remediation ; Genetic Variation ; Phylogeny ; RNA, Transfer, Pro/*genetics ; Rodentia/*classification/*genetics ; Sequence Analysis, DNA ; United Kingdom ; }, abstract = {Establishing true phylogenetic relationships between populations is a critical consideration when sourcing individuals for translocation. This presents huge difficulties with threatened and endangered species that have become extirpated from large areas of their former range. We utilise ancient DNA (aDNA) to reconstruct the phylogenetic relationships of a keystone species which has become extinct in Britain, the Eurasian beaver Castor fiber. We sequenced seventeen 492 bp partial tRNAPro and control region sequences from Late Pleistocene and Holocene age beavers and included these in network, demographic and genealogy analyses. The mode of postglacial population expansion from refugia was investigated by employing tests of neutrality and a pairwise mismatch distribution analysis. We found evidence of a pre-Late Glacial Maximum ancestor for the Western C. fiber clade which experienced a rapid demographic expansion during the terminal Pleistocene to early Holocene period. Ancient British beavers were found to originate from the Western phylogroup but showed no phylogenetic affinity to any one modern relict population over another. Instead, we find that they formed part of a large, continuous, pan-Western European clade that harbored little internal substructure. Our study highlights the utility of aDNA in reconstructing population histories of extirpated species which has real-world implications for conservation planning.}, }
@article {pmid29412519, year = {2018}, author = {Wagner, S and Lagane, F and Seguin-Orlando, A and Schubert, M and Leroy, T and Guichoux, E and Chancerel, E and Bech-Hebelstrup, I and Bernard, V and Billard, C and Billaud, Y and Bolliger, M and Croutsch, C and Čufar, K and Eynaud, F and Heussner, KU and Köninger, J and Langenegger, F and Leroy, F and Lima, C and Martinelli, N and Momber, G and Billamboz, A and Nelle, O and Palomo, A and Piqué, R and Ramstein, M and Schweichel, R and Stäuble, H and Tegel, W and Terradas, X and Verdin, F and Plomion, C and Kremer, A and Orlando, L}, title = {High-Throughput DNA sequencing of ancient wood.}, journal = {Molecular ecology}, volume = {27}, number = {5}, pages = {1138-1154}, pmid = {29412519}, issn = {1365-294X}, support = {339728/ERC_/European Research Council/International ; 681605/ERC_/European Research Council/International ; }, mesh = {Biodiversity ; Biological Evolution ; Climate Change ; DNA, Ancient/*chemistry ; Forests ; Quercus/genetics ; Sequence Analysis, DNA/*methods ; *Wood ; }, abstract = {Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management.}, }
@article {pmid29410864, year = {2018}, author = {Manin, A and Corona-M, E and Alexander, M and Craig, A and Thornton, EK and Yang, DY and Richards, M and Speller, CF}, title = {Diversity of management strategies in Mesoamerican turkeys: archaeological, isotopic and genetic evidence.}, journal = {Royal Society open science}, volume = {5}, number = {1}, pages = {171613}, pmid = {29410864}, issn = {2054-5703}, abstract = {The turkey (Meleagris gallopavo) represents one of the few domestic animals of the New World. While current research points to distinct domestication centres in the Southwest USA and Mesoamerica, several questions regarding the number of progenitor populations, and the timing and intensity of turkey husbandry remain unanswered. This study applied ancient mitochondrial DNA and stable isotope (δ[13]C, δ[15]N) analysis to 55 archaeological turkey remains from Mexico to investigate pre-contact turkey exploitation in Mesoamerica. Three different (sub)species of turkeys were identified in the archaeological record (M. g. mexicana, M. g. gallopavo and M. ocellata), indicating the exploitation of diverse local populations, as well as the trade of captively reared birds into the Maya area. No evidence of shared maternal haplotypes was observed between Mesoamerica and the Southwest USA, in contrast with archaeological evidence for trade of other domestic products. Isotopic analysis indicates a range of feeding behaviours in ancient Mesoamerican turkeys, including wild foraging, human provisioning and mixed feeding ecologies. This variability in turkey diet decreases through time, with archaeological, genetic and isotopic evidence all pointing to the intensification of domestic turkey management and husbandry, culminating in the Postclassic period.}, }
@article {pmid29410823, year = {2018}, author = {Tiee, MS and Harrigan, RJ and Thomassen, HA and Smith, TB}, title = {Ghosts of infections past: using archival samples to understand a century of monkeypox virus prevalence among host communities across space and time.}, journal = {Royal Society open science}, volume = {5}, number = {1}, pages = {171089}, pmid = {29410823}, issn = {2054-5703}, abstract = {Infectious diseases that originate from multiple wildlife hosts can be complex and problematic to manage. A full understanding is further limited by large temporal and spatial gaps in sampling. However, these limitations can be overcome, in part, by using historical samples, such as those derived from museum collections. Here, we screened over 1000 museum specimens collected over the past 120 years to examine the historical distribution and prevalence of monkeypox virus (MPXV) in five species of African rope squirrel (Funisciurus sp.) collected across Central Africa. We found evidence of MPXV infections in host species as early as 1899, half a century earlier than the first recognized case of MPXV in 1958, supporting the suggestion that historic pox-like outbreaks in humans and non-human primates may have been caused by MPXV rather than smallpox as originally thought. MPX viral DNA was found in 93 of 1038 (9.0%) specimens from five Funisciurus species (F. anerythrus, F. carruthersi, F. congicus, F. lemniscatus and F. pyrropus), of which F. carruthersi and pyrropus had not previously been identified as potential MPXV hosts. We additionally documented relative prevalence rates of infection in museum specimens of Funisciurus and examined the spatial and temporal distribution of MPXV in these potential host species across nearly a hundred years (1899-1993).}, }
@article {pmid29399779, year = {2018}, author = {Yaka, R and Birand, A and Yılmaz, Y and Caner, C and Açan, SC and Gündüzalp, S and Parvizi, P and Erim Özdoğan, A and Togan, &#x130; and Somel, M}, title = {Archaeogenetics of Late Iron Age Çemialo Sırtı, Batman: Investigating maternal genetic continuity in north Mesopotamia since the Neolithic.}, journal = {American journal of physical anthropology}, volume = {166}, number = {1}, pages = {196-207}, doi = {10.1002/ajpa.23423}, pmid = {29399779}, issn = {1096-8644}, mesh = {Adult ; Archaeology ; Asian People/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Female ; Genetics, Population ; History, Ancient ; Humans ; Male ; Mesopotamia/ethnology ; White People/genetics ; }, abstract = {OBJECTIVES: North Mesopotamia has witnessed dramatic social change during the Holocene, but the impact of these events on its demographic history is poorly understood. Here, we study this question by analysing genetic data from the recently excavated Late Iron Age settlement of Çemialo Sırtı in Batman, southeast Turkey. Archaeological and radiocarbon evidence indicate that the site was inhabited during the second and first millennia BCE. Çemialo Sırtı reveals nomadic items of the Early Iron Age, as well as items associated with the Late Achaemenid and subsequent Hellenistic Periods. We compare Çemialo Sırtı mitochondrial DNA profiles with earlier and later populations from west Eurasia to describe genetic continuity patterns in the region.<br><br>MATERIALS AND METHODS: A total of 16 &#xc7;emialo S&#x131;rt&#x131; individuals' remains were studied. PCR and Sanger sequencing were used to obtain mitochondrial DNA HVRI-HVRII sequences. We studied haplotype diversity and pairwise genetic distances using FST , comparing the &#xc7;emialo S&#x131;rt&#x131; population with ancient and modern-day populations from west Eurasia. Coalescent simulations were carried out to test continuity for specific population comparisons.<br><br>RESULTS: Mitochondrial DNA (mtDNA) haplotypes from 12 &#xc7;emialo S&#x131;rt&#x131; individuals reveal high haplotype diversity in this population, conspicuously higher than early Holocene west Eurasian populations, which supports the notion of increasing population admixture in west Eurasia through the Holocene. In its mtDNA composition, &#xc7;emialo S&#x131;rt&#x131; shows highest affinity to Neolithic north Syria and Neolithic Anatolia among ancient populations studied, and to modern-day southwest Asian populations. Based on population genetic simulations we cannot reject continuity between Neolithic and Iron Age, or between Iron Age and present-day populations of the region.<br><br>DISCUSSION: Despite the region's complex sociopolitical history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian maternal genetic composition within the last 10,000 years.}, }
@article {pmid29395378, year = {2018}, author = {Yang, MA and Fu, Q}, title = {Insights into Modern Human Prehistory Using Ancient Genomes.}, journal = {Trends in genetics : TIG}, volume = {34}, number = {3}, pages = {184-196}, doi = {10.1016/j.tig.2017.11.008}, pmid = {29395378}, issn = {0168-9525}, support = {55008731/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; DNA, Ancient/*analysis ; Evolution, Molecular ; Fossils ; Gene Flow ; *Genetic Variation ; Genome, Human/*genetics ; Hominidae/*genetics ; Humans ; Sequence Analysis, DNA ; }, abstract = {The genetic relationship of past modern humans to today's populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa.}, }
@article {pmid29391530, year = {2018}, author = {Peltzer, A and Mittnik, A and Wang, CC and Begg, T and Posth, C and Nieselt, K and Krause, J}, title = {Inferring genetic origins and phenotypic traits of George Bähr, the architect of the Dresden Frauenkirche.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2115}, pmid = {29391530}, issn = {2045-2322}, mesh = {Archaeology ; DNA Damage ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; *Eye Color ; *Genetics, Population ; *Genome, Mitochondrial ; Humans ; Male ; Phenotype ; *Polymorphism, Single Nucleotide ; Skin Pigmentation/*genetics ; }, abstract = {For historic individuals, the outward appearance and other phenotypic characteristics remain often non-resolved. Unfortunately, images or detailed written sources are only scarcely available in many cases. Attempts to study historic individuals with genetic data so far focused on hypervariable regions of mitochondrial DNA and to some extent on complete mitochondrial genomes. To elucidate the potential of in-solution based genome-wide SNP capture methods - as now widely applied in population genetics - we extracted DNA from the 17th century remains of George Bähr, the architect of the Dresdner Frauenkirche. We were able to identify the remains to be of male origin, showing sufficient DNA damage, deriving from a single person and being thus likely authentic. Furthermore, we were able to show that George Bähr had light skin pigmentation and most likely brown eyes. His genomic DNA furthermore points to a Central European origin. We see this analysis as an example to demonstrate the prospects that new in-solution SNP capture methods can provide for historic cases of forensic interest, using methods well established in ancient DNA (aDNA) research and population genetics.}, }
@article {pmid29382278, year = {2018}, author = {Larmuseau, MHD and Ottoni, C}, title = {Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era.}, journal = {Annals of human biology}, volume = {45}, number = {1}, pages = {20-33}, doi = {10.1080/03014460.2017.1402956}, pmid = {29382278}, issn = {1464-5033}, mesh = {Africa, Northern ; Chromosomes, Human, Y/*genetics ; *Demography ; *Human Migration ; Humans ; Male ; Mediterranean Region ; Middle East ; }, abstract = {CONTEXT: Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour.<br><br>OBJECTIVE: For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available.<br><br>METHODS: A systematic literature search on Y-chromosomal studies in the Mediterranean was performed.<br><br>RESULTS: Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations.<br><br>CONCLUSIONS: There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.}, }
@article {pmid29367192, year = {2018}, author = {Zhang, TK and Yuan, ZH}, title = {Progress in plant paleogenomics.}, journal = {Yi chuan = Hereditas}, volume = {40}, number = {1}, pages = {44-56}, doi = {10.16288/j.yczz.17-191}, pmid = {29367192}, issn = {0253-9772}, mesh = {Evolution, Molecular ; Gene Duplication ; *Genome, Plant ; High-Throughput Nucleotide Sequencing ; }, abstract = {As a new branch of genomics, plant paleogenomics reconstructs ancestral genomes from actual modern species and infers palaeohistory, evolutionary and/or speciation events that have shaped the modern species. Advances in high-throughput sequencing technologies yield accurate long reads, promote the progress of plant genome sequence assembly, and thereby offer paleogenomics a large collection of valuable reference genomes from modern species. Whole-genome duplication (WGD) and polyploidization cause rapid genomic reorganization, massive gene losses and structural variations. WGD events are therefore central to plant evolution. In this review, we summarize recent progress in sequencing and assembly of plant genomes, principles of plant paleogenomics, WGD events in plant genomes, and the most likely evolutionary scenario in plants. Furthermore, we highlight some of the challenges as well as future directions.}, }
@article {pmid29355893, year = {2018}, author = {Relethford, JH and Smith, FH}, title = {Cranial measures and ancient DNA both show greater similarity of Neandertals to recent modern Eurasians than to recent modern sub-Saharan Africans.}, journal = {American journal of physical anthropology}, volume = {166}, number = {1}, pages = {170-178}, doi = {10.1002/ajpa.23413}, pmid = {29355893}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; *Black People/genetics/statistics &amp; numerical data ; Cephalometry ; DNA, Ancient/*analysis ; Female ; Humans ; Male ; *Neanderthals/anatomy &amp; histology/genetics ; Skull/*anatomy &amp; histology ; *White People/genetics/statistics &amp; numerical data ; }, abstract = {OBJECTIVES: Ancient DNA analysis has shown that present-day humans of Eurasian ancestry are more similar to Neandertals than are present-day humans of sub-Saharan African ancestry, reflecting interbreeding after modern humans first left Africa. We use craniometric data to test the hypothesis that the crania of recent modern humans show the same pattern.<br><br>MATERIALS AND METHODS: We computed Mahalanobis squared distances between a published Neandertal centroid based on 37 craniometric traits and each of 2,413 recent modern humans from the Howells global data set (N&#x2009;=&#x2009;373 sub-Saharan Africans, N&#x2009;=&#x2009;2,040 individuals of Eurasian descent).<br><br>RESULTS: The average distance to the Neandertal centroid is significantly lower for Eurasian crania than for sub-Saharan African crania as expected from the findings of ancient DNA (p&#x2009;<&#x2009;0.001). This result holds when examining distances for separate geographic regions of humans of Eurasian descent (Europeans, Asians, Australasians, Native Americans, and Pacific Islanders). Most of these results are also seen when examining distances partitioning size and shape variation.<br><br>DISCUSSION: Our results show that the genetic difference in Neandertal ancestry seen in the DNA of present-day sub-Saharan Africans and Eurasians is also found in patterns of recent modern human craniometric variation.}, }
@article {pmid29345305, year = {2018}, author = {Šebest, L and Baldovič, M and Frtús, A and Bognár, C and Kyselicová, K and Kádasi, &#x13d; and Beňuš, R}, title = {Detection of mitochondrial haplogroups in a small avar-slavic population from the eigth-ninth century AD.}, journal = {American journal of physical anthropology}, volume = {165}, number = {3}, pages = {536-553}, doi = {10.1002/ajpa.23380}, pmid = {29345305}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Anthropology, Physical ; *Asian People/genetics/history/statistics &amp; numerical data ; Child ; DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; Female ; Genetics, Population ; Haplotypes/*genetics ; History, Medieval ; Humans ; Male ; Polymorphism, Single Nucleotide/genetics ; Slovakia ; *White People/genetics/history/statistics &amp; numerical data ; Young Adult ; }, abstract = {OBJECTIVES: In the sixth century AD, Avars came to Central Europe from middle Eurasian steppes and founded a strong Empire called the Avar Khagante (568-799/803 AD) in the Pannonian basin. During the existence of this empire, they undertook many military and pugnacious campaigns. In the seventh century, they conquered the northern territory inhabited by Slavs, who were further recruited in Avar military and were commissioned with obtaining food supplies. During almost 200 years of Avar domination, a significant influence by the Avar culture (especially on the burial rite) and assimilation with indigenous population (occurrence of "East Asian"cranial features) could be noticed in this mixed area, which is supported by achaeological and anthropologcal research. Therefore we expected higher incidence of east Eurasian haplogroups (introduced by Avars) than the frequencies detected in present-day central European populations.<br><br>MATERIALS AND METHODS: Mitochondrial DNA from 62 human skeletal remains excavated from the Avar-Slavic burial site C&#xed;fer-P&#xe1;c (Slovakia) dated to the eighth and ninth century was analyzed by the sequencing of hypervariable region I and selected parts of coding region. Obtained haplotypes were compared with other present-day and historical populations and genetic distances were calculated using standard statistical method.<br><br>RESULTS AND DISCUSSION: In total, the detection of mitochondrial haplogroups was possible in 46 individuals. Our results prooved a higher frequency of east Eurasian haplogroups in our analyzed population (6.52%) than in present-day central European populations. However, it is almost three times lower than the frequency of east Eurasian haplogroups detected in other medieval Avar populations. The statistical analysis showed a greater similarity and the lowest genetic distances between the Avar-Slavic burial site Cifer-Pac and medieval European populations than the South Siberian, East and Central Asian populations.<br><br>CONCLUSION: Our results indicate that the transfer of Avar genetic variation through their mtDNA was rather weak in the analyzed mixed population.}, }
@article {pmid29340007, year = {2018}, author = {Steffani-Vallejo, JL and Brunck, ME and Acosta-Cruz, EY and Montiel, R and Barona-Gómez, F}, title = {Genomic insights into Mycobacterium simiae human colonization.}, journal = {Standards in genomic sciences}, volume = {13}, number = {}, pages = {1}, pmid = {29340007}, issn = {1944-3277}, abstract = {Mycobacterium simiae (Karassova V, Weissfeiler J, Kraszanay E, Acta Microbiol Acad Sci Hung 12:275-82, 1965) is a slow-growing nontuberculous Mycobacterium species found in environmental niches, and recently evidenced as an opportunistic Human pathogen. We report here the genome of a clinical isolate of M. simiae (MsiGto) obtained from a patient in Guanajuato, Mexico. With a size of 6,684,413 bp, the genomic sequence of strain MsiGto is the largest of the three M. simiae genomes reported to date. Gene prediction revealed 6409 CDSs in total, including 6354 protein-coding genes and 52 RNA genes. Comparative genomic analysis identified shared features between strain MsiGto and the other two reported M. simiae genomes, as well as unique genes. Our data reveals that M. simiae MsiGto harbors virulence-related genes, such as arcD, ESAT-6, and those belonging to the antigen 85 complex and mce clusters, which may explain its successful transition to the human host. We expect the genome information of strain MsiGto will provide a better understanding of infective mechanisms and virulence of this emergent pathogen.}, }
@article {pmid29328350, year = {2018}, author = {Shin, DH and Oh, CS and Hong, JH and Lee, H and Lee, SD and Lee, E}, title = {Helicobacter pylori DNA obtained from the stomach specimens of two 17[th] century Korean mummies.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {75}, number = {1}, pages = {75-87}, doi = {10.1127/anthranz/2018/0780}, pmid = {29328350}, issn = {0003-5548}, mesh = {DNA, Bacterial/analysis/*isolation &amp; purification ; *Helicobacter Infections/ethnology/history/microbiology ; *Helicobacter pylori/genetics/isolation &amp; purification ; History, 17th Century ; Humans ; *Mummies/history/microbiology ; Republic of Korea/ethnology ; Stomach/*microbiology ; }, abstract = {Helicobacter pylori is a bacterium that grows in the stomach mucosal epithelium, and can induce gastric diseases. Although many studies on modern H. pylori genomes have been reported from all over the world, a comprehensive picture of H. pylori is still lacking. Therefore, there is a pressing need to obtain archaeological specimens and to subject the ancient DNA (aDNA) extracted therefrom to analysis. Considering the typically excellent state of preservation of Joseon mummies discovered in Korea, we thus tried to isolate ancient H. pylori DNA from their mummified stomach specimens. After screening Korean mummy stomachs containing remnant H. pylori DNA, vacA (s- and m-region) alleles were successfully identified in the stomach isolates of two samples. The H. pylori strains identified had vacA s1/m2 (Cheongdo mummy) and s1 (Dangjin mummy) alleles. This paper is significant in that it is the first report of presumptive ancient H. pylori DNA obtained from East Asian archaeological specimens. However, full characterization and exploitation of ancient H. pylori DNA remnant in Joseon mummy specimens will require subsequent investigations utilizing the most cutting-edge techniques established for the analysis of ancient intestinal-content samples, such as next-generation sequencing (NGS).}, }
@article {pmid29310587, year = {2018}, author = {MacConaill, LE and Burns, RT and Nag, A and Coleman, HA and Slevin, MK and Giorda, K and Light, M and Lai, K and Jarosz, M and McNeill, MS and Ducar, MD and Meyerson, M and Thorner, AR}, title = {Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {30}, pmid = {29310587}, issn = {1471-2164}, mesh = {Computational Biology/*methods ; *High-Throughput Nucleotide Sequencing/methods/standards ; Humans ; Sensitivity and Specificity ; *Sequence Analysis, DNA/methods/standards ; }, abstract = {BACKGROUND: Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. Therefore, the limit-of-detection of an MPS assay is directly related to the degree of index cross-talk.<br><br>RESULTS: Cross-talk rates up to 0.29% were observed when using standard, combinatorial adapters, resulting in 110,180 (0.1% cross-talk rate) or 1,121,074 (0.29% cross-talk rate) misassigned reads per lane in non-patterned and patterned Illumina flow cells, respectively. Here, we demonstrate that using unique, dual-matched indexed adapters dramatically reduces index cross-talk to &#x2264;1 misassigned reads per flow cell lane. While the current study was performed using dual-matched indices, using unique, dual-unrelated indices would also be an effective alternative.<br><br>CONCLUSIONS: For sensitive downstream analyses, the use of combinatorial indices for multiplexed hybrid capture and sequencing is inappropriate, as it results in an unacceptable number of misassigned reads. Cross-talk can be virtually eliminated using dual-matched indexed adapters. These results suggest that use of such adapters is critical&#xa0;to reduce false positive rates in assays that aim to identify low allele frequency events, and strongly indicate that dual-matched adapters be implemented for all sensitive MPS applications.}, }
@article {pmid29302050, year = {2018}, author = {Segawa, T and Takeuchi, N and Fujita, K and Aizen, VB and Willerslev, E and Yonezawa, T}, title = {Demographic analysis of cyanobacteria based on the mutation rates estimated from an ancient ice core.}, journal = {Heredity}, volume = {120}, number = {6}, pages = {562-573}, pmid = {29302050}, issn = {1365-2540}, mesh = {Cyanobacteria/classification/*genetics ; DNA, Ribosomal Spacer ; *Environmental Microbiology ; *Evolution, Molecular ; Ice Cover/microbiology ; Kyrgyzstan ; Metagenome ; Metagenomics/methods ; *Mutation ; *Mutation Rate ; Phylogeny ; RNA, Ribosomal, 16S ; Selection, Genetic ; }, abstract = {Despite the crucial role of cyanobacteria in various ecosystems, little is known about their evolutionary histories, especially microevolutionary dynamics, because of the lack of knowledge regarding their mutation rates. Here we directly estimated cyanobacterial mutation rates based on ancient DNA analyses of ice core samples collected from Kyrgyz Republic that dates back to ~12,500 cal years before present. We successfully sequenced the 16S rRNA and 16S-23S internal transcribed spacer (ITS) region. Two cyanobacterial operational taxonomic units (OTUs) were detected from the ancient ice core samples, and these OTUs are shared with those from the modern glacier surface. The mutation rate of ITS region was estimated by comparing ancient and modern populations, and were at the magnitude of 10[-7]substitutions/sites/year. By using a model selection framework, we also demonstrated that the ancient sequences from the ice sample were not contaminated from modern samples. Bayesian demographic analysis based on coalescent theory revealed that cyanobacterial population sizes increased over Asia regions during the Holocene. Thus, our results enhance our understanding of the enigmatic timescale of cyanobacterial microevolution, which has the potential to elucidate the environmental responses of cyanobacteria to the drastic climatic change events of the Quaternary.}, }
@article {pmid29301990, year = {2018}, author = {Price, M}, title = {Americas peopled in a single wave, ancient genome reveals.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6371}, pages = {14}, doi = {10.1126/science.359.6371.14}, pmid = {29301990}, issn = {1095-9203}, mesh = {Alaska ; Asia ; *DNA, Ancient ; *Genome, Human ; *Human Migration ; Humans ; Infant ; }, }
@article {pmid29299966, year = {2017}, author = {Bouwman, A and Shved, N and Akgül, G and Rühli, F and Warinner, C}, title = {Ancient DNA Investigation of a Medieval German Cemetery Confirms Long-Term Stability of CCR5-Δ32 Allele Frequencies in Central Europe.}, journal = {Human biology}, volume = {89}, number = {2}, pages = {119-124}, doi = {10.13110/humanbiology.89.2.02}, pmid = {29299966}, issn = {1534-6617}, mesh = {Cemeteries ; DNA, Ancient/*analysis ; Disease Outbreaks ; Ethnicity/genetics ; Gene Frequency/*genetics ; Genotype ; Germany/ethnology ; History, Medieval ; Homozygote ; Humans ; Plague/epidemiology ; Receptors, CCR5/*genetics ; Sequence Deletion/genetics ; White People/*genetics ; }, abstract = {The CCR5-Δ32 mutation present in European populations is among the most prominently debated cases of recent positive selection in humans. This allele, a 32-bp deletion that renders the T-cell CCR5 receptor nonfunctional, has important epidemiological and public health significance, as homozygous carriers are resistant to several HIV strains. However, although the function of this allele in preventing HIV infection is now well described, its human evolutionary origin is poorly understood. Initial attempts to determine the emergence of the CCR5-Δ32 allele pointed to selection during the 14th-century Black Death pandemic; however, subsequent analyses suggest that the allele rose in frequency more than 5,000 years ago, possibly through drift. Recently, three studies have identified populations predating the 14th century CE that are positive for the CCR5-Δ32 allele, supporting the claim for a more ancient origin. However, these studies also suggest poorly understood regional differences in the recent evolutionary history of the CCR5-Δ32 allele. Here a new hydrolysis-probe-based real-time PCR assay was designed to ascertain CCR5 allele frequency in 53 individuals from a 10th- to 12th-century CE church and convent complex in central Germany that predates outbreaks of the Black Death pandemic. High-confidence genotypes were obtained for 32 individuals, and results show that CCR5-Δ32 allele frequency has remained unchanged in this region of Central Europe over the last millennium, suggesting that there has been no strong positive selective pressure over this time period and confirming a more ancient origin for the allele.}, }
@article {pmid29299965, year = {2017}, author = {Taskent, RO and Gokcumen, O}, title = {The Multiple Histories of Western Asia: Perspectives from Ancient and Modern Genomes.}, journal = {Human biology}, volume = {89}, number = {2}, pages = {107-117}, doi = {10.13110/humanbiology.89.2.01}, pmid = {29299965}, issn = {1534-6617}, mesh = {Africa/ethnology ; Anthropology/history ; Archaeology/history ; Asia/ethnology ; Asia, Western/ethnology ; Europe/ethnology ; Genetic Variation/*genetics ; Genomics/*history/trends ; History, 20th Century ; History, 21st Century ; History, Ancient ; Human Migration/history ; Humans ; Racial Groups/*genetics ; Sedentary Behavior/ethnology ; }, abstract = {Western Asia lies at the heart of the Old World, in the midst of Africa, Asia, and Europe. As such, this region has been populated and repopulated by myriad peoples, starting with the first migrants from Africa. All evidence points to Western Asia for the beginnings of sedentary life, and indeed, first the villages and later the cities of this land remain as archaeological wonders, revealing complex histories of multiple peoples and their interactions. With the wondrous breakthroughs in genomic studies, we now have the power to look at these histories with a truly quantitative lens. Here, we review the recent anthropological genomics literature pertaining to this region, with an outlook for the future challenges and exciting possibilities for the field.}, }
@article {pmid29299249, year = {2017}, author = {Rey-Iglesia, A and Grandal-d'Anglade, A and Campos, PF and Hansen, AJ}, title = {Mitochondrial DNA of pre-last glacial maximum red deer from NW Spain suggests a more complex phylogeographical history for the species.}, journal = {Ecology and evolution}, volume = {7}, number = {24}, pages = {10690-10700}, pmid = {29299249}, issn = {2045-7758}, abstract = {The major climatic oscillations that characterized the Quaternary had a great influence on the evolution and distribution of several species. During cold periods, the distribution of temperate-adapted species became fragmented with many surviving in southern refugia (Iberian, Italian, and Balkan Peninsulas). Red deer was one of the species that contracted its original range to southern refugia. Currently, two main lineages have been described for the species: western and eastern. We have analyzed fossils pre-dating the last glacial maximum (LGM) from Liñares cave (NW Spain) that belongs to the peripheral range of the western clade, and fossils from the Danish Holocene belonging to the central part of the same clade. Phylogenetic analyses place our samples in the western clade. However, some specimens from Liñares represent an early split in the tree along with other pre-LGM western samples from previous studies. Despite low bootstrap values in the Bayesian phylogenies, haplotype networks connect these foreign haplotypes to the eastern clade. We suggest a mixed phylogeographical model to explain this pattern with range expansions from the east during the expansion phase after the cold periods in marine isotope stage 3. We find slight isolation by distance in post-LGM populations that could be a consequence of the recolonization from southern refugia after the LGM.}, }
@article {pmid29297348, year = {2017}, author = {Logacheva, MD and Krinitsina, AA and Belenikin, MS and Khafizov, K and Konorov, EA and Kuptsov, SV and Speranskaya, AS}, title = {Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions.}, journal = {BMC plant biology}, volume = {17}, number = {Suppl 2}, pages = {255}, pmid = {29297348}, issn = {1471-2229}, mesh = {DNA, Plant/genetics ; Genes, Plant/genetics ; Genome, Plant/genetics ; Inverted Repeat Sequences/*genetics ; Phylogeny ; Plastids/*genetics ; Tracheophyta/*genetics ; }, abstract = {BACKGROUND: Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes.<br><br>RESULTS: We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns. We also sequenced the plastome of Adianthum hispidulum (Pteridaceae). Unexpectedly, we found high variability in the IR region, including duplication of rrn16 in D. blanfordii, complete loss of trnI-GAU in D. filix-mas, its pseudogenization due to the loss of an exon in D. blanfordii. Analysis of previously reported plastomes of Polypodiales demonstrated that Woodwardia unigemmata and Lepisorus clathratus have unusual insertions in the IR region. The sequence of these inserted regions has high similarity to several LSC fragments of ferns outside of Polypodiales and to spacer between tRNA-CGA and tRNA-TTT genes of mitochondrial genome of Asplenium nidus. We suggest that this reflects the ancient DNA transfer from mitochondrial to plastid genome occurred in a common ancestor of ferns. We determined the marked conservation of gene content and relative evolution rate of genes and intergenic spacers in the IRs of Polypodiales. Faster evolution of the four intergenic regions had been demonstrated (trnA- orf42, rrn16-rps12, rps7-psbA and ycf2-trnN).<br><br>CONCLUSIONS: IRs of Polypodiales plastomes are dynamic, driven by such events as gene loss, duplication and putative lateral transfer from mitochondria.}, }
@article {pmid31007636, year = {2018}, author = {Barnett, R and Sinding, MS and Vieira, FG and Mendoza, MLZ and Bonnet, M and Araldi, A and Kienast, I and Zambarda, A and Yamaguchi, N and Henschel, P and Gilbert, MTP}, title = {No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon.}, journal = {Conservation genetics (Print)}, volume = {19}, number = {3}, pages = {611-618}, pmid = {31007636}, issn = {1566-0621}, support = {681396/ERC_/European Research Council/International ; }, abstract = {Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread population declines in what has hitherto been seen as a common species, robust to anthropogenic disturbance. Here we use non-invasive methods to recover complete mitochondrial genomes from single hair samples collected in the field in order to explore the identity of the Gabonese Plateaux Batéké lion. Comparison of the mitogenomes against a comprehensive dataset of African lion sequences that includes relevant geographically proximate lion populations from both contemporary and ancient sources, enabled us to identify the Plateaux Batéké lion as a close maternal relative to now extirpated populations found in Gabon and nearby Congo during the twentieth century, and to extant populations of Southern Africa. Our study demonstrates the relevance of ancient DNA methods to field conservation work, and the ability of trace field samples to provide copious genetic information about free-ranging animals.}, }
@article {pmid29289355, year = {2018}, author = {Díez-Del-Molino, D and Sánchez-Barreiro, F and Barnes, I and Gilbert, MTP and Dalén, L}, title = {Quantifying Temporal Genomic Erosion in Endangered Species.}, journal = {Trends in ecology &amp; evolution}, volume = {33}, number = {3}, pages = {176-185}, doi = {10.1016/j.tree.2017.12.002}, pmid = {29289355}, issn = {1872-8383}, mesh = {*Endangered Species ; Extinction, Biological ; *Genetic Variation ; *Genome ; Genomics/*methods ; Inbreeding ; }, abstract = {Many species have undergone dramatic population size declines over the past centuries. Although stochastic genetic processes during and after such declines are thought to elevate the risk of extinction, comparative analyses of genomic data from several endangered species suggest little concordance between genome-wide diversity and current population sizes. This is likely because species-specific life-history traits and ancient bottlenecks overshadow the genetic effect of recent demographic declines. Therefore, we advocate that temporal sampling of genomic data provides a more accurate approach to quantify genetic threats in endangered species. Specifically, genomic data from predecline museum specimens will provide valuable baseline data that enable accurate estimation of recent decreases in genome-wide diversity, increases in inbreeding levels, and accumulation of deleterious genetic variation.}, }
@article {pmid29285971, year = {2017}, author = {Antelope, CX and Marnetto, D and Casey, F and Huerta-Sanchez, E}, title = {Leveraging Multiple Populations across Time Helps Define Accurate Models of Human Evolution: A Reanalysis of the Lactase Persistence Adaptation.}, journal = {Human biology}, volume = {89}, number = {1}, pages = {81-97}, doi = {10.13110/humanbiology.89.1.05}, pmid = {29285971}, issn = {1534-6617}, mesh = {Adaptation, Physiological/*genetics ; Animals ; DNA Primers ; Diet ; *Evolution, Molecular ; Gene Frequency/*genetics ; Genetic Drift ; Genetics, Population ; Haplotypes/genetics ; History, Ancient ; *Hominidae ; Humans ; Lactase/*genetics/metabolism ; Lactose Tolerance Test ; Microsatellite Repeats/*genetics ; Milk ; Selection, Genetic ; }, abstract = {Access to a geographically diverse set of modern human samples from the present time and from ancient remains, combined with archaic hominin samples, provides an unprecedented level of resolution to study both human history and adaptation. The amount and quality of ancient human data continue to improve and enable tracking the trajectory of genetic variation over time. These data have the potential to help us redefine or generate new hypotheses of how human evolution occurred and to revise previous conjectures. In this article, we argue that leveraging all these data will help us better detail adaptive histories in humans. As a case in point, we focus on one of the most celebrated examples of human adaptation: the evolution of lactase persistence. We briefly review this dietary adaptation and argue that, effectively, the evolutionary history of lactase persistence is still not fully resolved. We propose that, by leveraging data from multiple populations across time and space, we will find evidence of a more nuanced history than just a simple selective sweep. We support our hypotheses with simulation results and make some cautionary notes regarding the use of haplotype-based summary statistics to estimate evolutionary parameters.}, }
@article {pmid29285967, year = {2017}, author = {Berens, AJ and Cooper, TL and Lachance, J}, title = {The Genomic Health of Ancient Hominins.}, journal = {Human biology}, volume = {89}, number = {1}, pages = {7-19}, doi = {10.13110/humanbiology.89.1.01}, pmid = {29285967}, issn = {1534-6617}, mesh = {Animals ; DNA Primers ; DNA, Mitochondrial/classification/genetics ; Evolution, Molecular ; Gene Library ; Genetic Association Studies ; Genetic Predisposition to Disease/classification/*genetics/history ; Genetic Variation/*genetics ; Genomics ; Geography/classification/history ; History, Ancient ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; Phylogeny ; }, abstract = {The genomes of ancient humans, Neandertals, and Denisovans contain many alleles that influence disease risks. Using genotypes at 3,180 disease-associated loci, we estimated the disease burden of 147 ancient genomes. After correcting for missing data, genetic risk scores (GRS) were generated for nine disease categories and the set of all combined diseases. We used these genetic risk scores to examine the effects of different types of subsistence, geography, and sample age on the number of risk alleles in each ancient genome. On a broad scale, hereditary disease risks are similar for ancient hominins and modern-day humans, and the GRS percentiles of ancient individuals span the full range of what is observed in present-day individuals. In addition, there is evidence that ancient pastoralists may have had healthier genomes than hunter-gatherers and agriculturalists. We also observed a temporal trend whereby genomes from the recent past are more likely to be healthier than genomes from the deep past. This calls into question the idea that modern lifestyles have caused genetic load to increase over time. Focusing on individual genomes, we found that the overall genomic health of the Altai Neandertal is worse than 97% of present-day humans and that Ötzi, the Tyrolean Iceman, had a genetic predisposition for gastrointestinal and cardiovascular diseases. As demonstrated by this work, ancient genomes afford us new opportunities to diagnose past human health, which has previously been limited by the quality and completeness of remains.}, }
@article {pmid29285965, year = {2017}, author = {Harris, AM and DeGiorgio, M}, title = {Admixture and Ancestry Inference from Ancient and Modern Samples through Measures of Population Genetic Drift.}, journal = {Human biology}, volume = {89}, number = {1}, pages = {21-46}, doi = {10.13110/humanbiology.89.1.02}, pmid = {29285965}, issn = {1534-6617}, mesh = {*Evolution, Molecular ; *Genetic Drift ; Genetic Predisposition to Disease ; Genetic Variation/*genetics ; *Genetics, Population ; Genome-Wide Association Study ; History, Ancient ; Humans ; Models, Genetic ; Racial Groups/*genetics ; }, abstract = {Methods that leverage the information about population history contained within the increasingly abundant genetic sequences of extant and extinct hominid populations are diverse in form and versatile in application. Here, we review key methods recently developed to detect and quantify admixture and ancestry in modern human populations. We begin with an overview of the f- and D-statistics, covering their conceptual principles and important applications, as well as any extensions developed for them. We then cover a combination of more recent and more complex methods for admixture and ancestry inference, discussing tests for direct ancestry between two populations, quantification of admixture in large data sets, and determination of admixture dates. These methods have revolutionized our understanding of human population history and highlight its complexity. Therefore, we emphasize that current methods may not capture this population history in its entirety but nonetheless provide a reasonable picture that is supported by data from multiple methods and from the historical record.}, }
@article {pmid29277873, year = {2018}, author = {Anselmetti, Y and Luhmann, N and Bérard, S and Tannier, E and Chauve, C}, title = {Comparative Methods for Reconstructing Ancient Genome Organization.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1704}, number = {}, pages = {343-362}, doi = {10.1007/978-1-4939-7463-4_13}, pmid = {29277873}, issn = {1940-6029}, mesh = {*Biological Evolution ; Chromosomes ; Computational Biology/*methods ; DNA, Ancient/*analysis ; Gene Order ; *Genome ; Genomics/methods ; *Models, Genetic ; Software ; }, abstract = {Comparative genomics considers the detection of similarities and differences between extant genomes, and, based on more or less formalized hypotheses regarding the involved evolutionary processes, inferring ancestral states explaining the similarities and an evolutionary history explaining the differences. In this chapter, we focus on the reconstruction of the organization of ancient genomes into chromosomes. We review different methodological approaches and software, applied to a wide range of datasets from different kingdoms of life and at different evolutionary depths. We discuss relations with genome assembly, and potential approaches to validate computational predictions on ancient genomes that are almost always only accessible through these predictions.}, }
@article {pmid29273718, year = {2017}, author = {Morales-Arce, AY and Hofman, CA and Duggan, AT and Benfer, AK and Katzenberg, MA and McCafferty, G and Warinner, C}, title = {Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {18100}, pmid = {29273718}, issn = {2045-2322}, mesh = {Central America ; *DNA, Ancient ; Genetics, Population ; *Genome, Mitochondrial ; *Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Mexico ; }, abstract = {The northern and southern peripheries of ancient Mesoamerica are poorly understood. There has been speculation over whether borderland cultures such as Greater Nicoya and Casas Grandes represent Mesoamerican outposts in the Isthmo-Colombian area and the Greater Southwest, respectively. Poor ancient DNA preservation in these regions challenged previous attempts to resolve these questions using conventional genetic techniques. We apply advanced in-solution mitogenome capture and high-throughput sequencing to fourteen dental samples obtained from the Greater Nicoya sites of Jícaro and La Cascabel in northwest Costa Rica (n = 9; A.D. 800-1250) and the Casas Grandes sites of Paquimé and Convento in northwest Mexico (n = 5; A.D. 1200-1450). Full mitogenome reconstruction was successful for three individuals from Jícaro and five individuals from Paquimé and Convento. The three Jícaro individuals belong to haplogroup B2d, a haplogroup found today only among Central American Chibchan-speakers. The five Paquimé and Convento individuals belong to haplogroups C1c1a, C1c5, B2f and B2a which, are found in contemporary populations in North America and Mesoamerica. We report the first successfully reconstructed ancient mitogenomes from Central America, and the first genetic evidence of ancestry affinity of the ancient inhabitants of Greater Nicoya and Casas Grandes with contemporary Isthmo-Columbian and Greater Southwest populations, respectively.}, }
@article {pmid29262846, year = {2017}, author = {Basler, N and Xenikoudakis, G and Westbury, MV and Song, L and Sheng, G and Barlow, A}, title = {Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone.}, journal = {BMC research notes}, volume = {10}, number = {1}, pages = {754}, pmid = {29262846}, issn = {1756-0500}, support = {41672017//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Base Composition ; Bone and Bones/*metabolism ; DNA Damage ; DNA, Ancient/*analysis/*isolation &amp; purification ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Ursidae/*genetics ; }, abstract = {OBJECTIVE: A key challenge in ancient DNA research is massive microbial DNA contamination from the deposition site which accumulates post mortem in the study organism's remains. Two simple and cost-effective methods to enrich the relative endogenous fraction of DNA in ancient samples involve treatment of sample powder with either bleach or Proteinase K pre-digestion prior to DNA extraction. Both approaches have yielded promising but varying results in other studies. Here, we contribute data on the performance of these methods using a comprehensive and systematic series of experiments applied to a single ancient bone fragment from a giant panda (Ailuropoda melanoleuca).<br><br>RESULTS: Bleach and pre-digestion treatments increased the endogenous DNA content up to ninefold. However, the absolute amount of DNA retrieved was dramatically reduced by all treatments. We also observed reduced DNA damage patterns in pre-treated libraries compared to untreated ones, resulting in longer mean fragment lengths and reduced thymine over-representation at fragment ends. Guanine-cytosine (GC) contents of both mapped and total reads are consistent between treatments and conform to general expectations, indicating no obvious biasing effect of the applied methods. Our results therefore confirm the value of bleach and pre-digestion as tools in palaeogenomic studies, providing sufficient material is available.}, }
@article {pmid29261166, year = {2017}, author = {Cotoras, DD and Murray, GGR and Kapp, J and Gillespie, RG and Griswold, C and Simison, WB and Green, RE and Shapiro, B}, title = {Ancient DNA Resolves the History of Tetragnatha (Araneae, Tetragnathidae) Spiders on Rapa Nui.}, journal = {Genes}, volume = {8}, number = {12}, pages = {}, pmid = {29261166}, issn = {2073-4425}, abstract = {Rapa Nui is one of the most remote islands in the world. As a young island, its biota is a consequence of both natural dispersals over the last ~1 million years and recent human introductions. It therefore provides an opportunity to study a unique community assemblage. Here, we extract DNA from museum-preserved and newly field-collected spiders from the genus Tetragnatha to explore their history on Rapa Nui. Using an optimized protocol to recover ancient DNA from museum-preserved spiders, we sequence and assemble partial mitochondrial genomes from nine Tetragnatha species, two of which were found on Rapa Nui, and estimate the evolutionary relationships between these and other Tetragnatha species. Our phylogeny shows that the two Rapa Nui species are not closely related. One, the possibly extinct, T. paschae, is nested within a circumtropical species complex (T. nitens), and the other (Tetragnatha sp. Rapa Nui) appears to be a recent human introduction. Our results highlight the power of ancient DNA approaches in identifying cryptic and rare species, which can contribute to our understanding of the global distribution of biodiversity in all taxonomic lineages.}, }
@article {pmid29247849, year = {2018}, author = {Buckner, JC and Ellingson, R and Gold, DA and Jones, TL and Jacobs, DK}, title = {Mitogenomics supports an unexpected taxonomic relationship for the extinct diving duck Chendytes lawi and definitively places the extinct Labrador Duck.}, journal = {Molecular phylogenetics and evolution}, volume = {122}, number = {}, pages = {102-109}, doi = {10.1016/j.ympev.2017.12.008}, pmid = {29247849}, issn = {1095-9513}, support = {T32 HG002536/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Ducks/*classification/*genetics ; Extinction, Biological ; Feeding Behavior ; Genome, Mitochondrial/*genetics ; *Genomics ; Phylogeny ; }, abstract = {Chendytes lawi, an extinct flightless diving anseriform from coastal California, was traditionally classified as a sea duck, tribe Mergini, based on similarities in osteological characters. We recover and analyze mitochondrial genomes of C. lawi and five additional Mergini species, including the extinct Labrador Duck, Camptorhynchus labradorius. Despite its diving morphology, C. lawi is reconstructed as an ancient relictual lineage basal to the dabbling ducks (tribe Anatini), revealing an additional example of convergent evolution of characters related to feeding behavior among ducks. The Labrador Duck is sister to Steller's Eider which may provide insights into the evolution and ecology of this poorly known extinct species. Our results demonstrate that inclusion of full length mitogenomes, from taxonomically distributed ancient and modern sources can improve phylogeny reconstruction of groups previously assessed with shorter single-gene mitochondrial sequences.}, }
@article {pmid29246100, year = {2017}, author = {Silva, NM and Rio, J and Currat, M}, title = {Investigating population continuity with ancient DNA under a spatially explicit simulation framework.}, journal = {BMC genetics}, volume = {18}, number = {1}, pages = {114}, pmid = {29246100}, issn = {1471-2156}, support = {grant 31003A_156853//Swiss NSF/ ; Marie Curie initial training BEAN (GA 289966)//European Research Council/International ; }, mesh = {*Biological Evolution ; *Computer Simulation ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Emigration and Immigration ; Europe ; Genetic Variation ; Genetics, Population ; Humans ; White People/*genetics ; }, abstract = {BACKGROUND: Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory. Comparing samples taken in the same region but at different times, hereafter called "serial samples", may indicate whether there is continuity in the peopling history of that area or whether an immigration of a genetically different population has occurred between the two sampling times. However, the exploration of genetic relationships between serial samples generally ignores their geographical locations and the spatiotemporal dynamics of populations. Here, we present a new coalescent-based, spatially explicit modelling approach to investigate population continuity using aDNA, which includes two fundamental elements neglected in previous methods: population structure and migration. The approach also considers the extensive temporal and geographical variance that is commonly found in aDNA population samples.<br><br>RESULTS: We first showed that our spatially explicit approach is more conservative than the previous (panmictic) approach and should be preferred to test for population continuity, especially when small and isolated populations are considered. We then applied our method to two mitochondrial datasets from Germany and France, both including modern and ancient lineages dating from the early Neolithic. The results clearly reject population continuity for the maternal line over the last 7500&#xa0;years for the German dataset but not for the French dataset, suggesting regional heterogeneity in post-Neolithic migratory processes.<br><br>CONCLUSIONS: Here, we demonstrate the benefits of using a spatially explicit method when investigating population continuity with aDNA. It constitutes an improvement over panmictic methods by considering the spatiotemporal dynamics of genetic lineages and the precise location of ancient samples. The method can be used to investigate population continuity between any pair of serial samples (ancient-ancient or ancient-modern) and to investigate more complex evolutionary scenarios. Although we based our study on mitochondrial DNA sequences, diploid molecular markers of different types (DNA, SNP, STR) can also be simulated with our approach. It thus constitutes a promising tool for the analysis of the numerous aDNA datasets being produced, including genome wide data, in humans but also in many other species.}, }
@article {pmid29243821, year = {2018}, author = {Lendvay, B and Hartmann, M and Brodbeck, S and Nievergelt, D and Reinig, F and Zoller, S and Parducci, L and Gugerli, F and Büntgen, U and Sperisen, C}, title = {Improved recovery of ancient DNA from subfossil wood - application to the world's oldest Late Glacial pine forest.}, journal = {The New phytologist}, volume = {217}, number = {4}, pages = {1737-1748}, doi = {10.1111/nph.14935}, pmid = {29243821}, issn = {1469-8137}, mesh = {DNA, Plant/genetics/*isolation &amp; purification ; Decontamination ; *Forests ; *Fossils ; Picea/genetics ; Pinus/classification/*genetics ; Species Specificity ; Wood/*genetics ; }, abstract = {Ancient DNA from historical and subfossil wood has a great potential to provide new insights into the history of tree populations. However, its extraction and analysis have not become routine, mainly because contamination of the wood with modern plant material can complicate the verification of genetic information. Here, we used sapwood tissue from 22 subfossil pines that were growing c. 13 000 yr bp in Zurich, Switzerland. We developed and evaluated protocols to eliminate surface contamination, and we tested ancient DNA authenticity based on plastid DNA metabarcoding and the assessment of post-mortem DNA damage. A novel approach using laser irradiation coupled with bleaching and surface removal was most efficient in eliminating contaminating DNA. DNA metabarcoding confirmed which ancient DNA samples repeatedly amplified pine DNA and were free of exogenous plant taxa. Pine DNA sequences of these samples showed a high degree of cytosine to thymine mismatches, typical of post-mortem damage. Stringent decontamination of wood surfaces combined with DNA metabarcoding and assessment of post-mortem DNA damage allowed us to authenticate ancient DNA retrieved from the oldest Late Glacial pine forest. These techniques can be applied to any subfossil wood and are likely to improve the accessibility of relict wood for genome-scale ancient DNA studies.}, }
@article {pmid29229569, year = {2018}, author = {Wuyun, TN and Wang, L and Liu, H and Wang, X and Zhang, L and Bennetzen, JL and Li, T and Yang, L and Liu, P and Du, L and Wang, L and Huang, M and Qing, J and Zhu, L and Bao, W and Li, H and Du, Q and Zhu, J and Yang, H and Yang, S and Liu, H and Yue, H and Hu, J and Yu, G and Tian, Y and Liang, F and Hu, J and Wang, D and Gao, R and Li, D and Du, H}, title = {The Hardy Rubber Tree Genome Provides Insights into the Evolution of Polyisoprene Biosynthesis.}, journal = {Molecular plant}, volume = {11}, number = {3}, pages = {429-442}, doi = {10.1016/j.molp.2017.11.014}, pmid = {29229569}, issn = {1752-9867}, mesh = {Genome, Plant/*genetics ; Hemiterpenes/*metabolism ; Hevea/*genetics/*metabolism ; Phylogeny ; Plant Proteins/genetics ; }, abstract = {Eucommia ulmoides, also called hardy rubber tree, is an economically important tree; however, the lack of its genome sequence restricts the fundamental biological research and applied studies of this plant species. Here, we present a high-quality assembly of its ∼1.2-Gb genome (scaffold N50 = 1.88 Mb) with at least 26 723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which was obtained using an integrated strategy combining Illumina sequencing, PacBio sequencing, and BioNano mapping. As a sister taxon to lamiids and campanulids, E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication in the last ∼125 million years. E. ulmoides exhibits high expression levels and/or gene number expansion for multiple genes involved in stress responses and the biosynthesis of secondary metabolites, which may account for its considerable environmental adaptability. In contrast to the rubber tree (Hevea brasiliensis), which produces cis-polyisoprene, E. ulmoides has evolved to synthesize long-chain trans-polyisoprene via farnesyl diphosphate synthases (FPSs). Moreover, FPS and rubber elongation factor/small rubber particle protein gene families were expanded independently from the H. brasiliensis lineage. These results provide new insights into the biology of E. ulmoides and the origin of polyisoprene biosynthesis.}, }
@article {pmid29219264, year = {2017}, author = {Wang, CZ and Wen, SQ and Shi, MS and Yu, XE and Wang, XJ and Pan, YL and Zhang, YF and Li, H and Tan, JZ}, title = {[Identification of Y-chromosomal Genetic Types for the Soldier's Remains from Huaihai Campaign].}, journal = {Fa yi xue za zhi}, volume = {33}, number = {4}, pages = {357-362}, doi = {10.3969/j.issn.1004-5619.2017.04.005}, pmid = {29219264}, issn = {1004-5619}, mesh = {China ; Chromosomes, Human, Y/*genetics ; DNA ; *DNA Fingerprinting ; Genetics, Population ; Genotype ; Haplotypes ; Humans ; Male ; Microsatellite Repeats/*genetics ; *Military Personnel ; Multiplex Polymerase Chain Reaction ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {OBJECTIVES: To identify the Y-chromosomal genetic types for the soldier's remains from Huaihai Campaign, and to offer a clue for search of their paternal relatives.<br><br>METHODS: DNA of the remains were extracted by the ancient DNA extraction method. Yfiler kit was used for the multiplex amplification of 17 Y-STR loci. The haplogroups of the samples were speculated. Detailed genotyping of the selected Y-SNP was performed based on the latest Y-chromosome phylogenetic tree. Haplotype-sharing analysis was done based on the data of Y-SNP and Y-STR, the closest modern individual information to the genetic relationship of remains was gained.<br><br>RESULTS: A total of 8 Y-STR haplotypes were observed on 17 Y-STR loci of 8 male individuals. Furthermore, 6 Y-SNP haplogroups were identified, which were O2a1-M95+, O1a1-P203+, O3*-M122+/M234-, D1-M15+, C3*-ST and R1a1-M17+.<br><br>CONCLUSIONS: Identification of Y-chromosomal genetic types for the soldier's remains from Huaihai Campaign shows a reference value on inferring the geographical origins of old materials.}, }
@article {pmid29216758, year = {2018}, author = {Serventi, P and Panicucci, C and Bodega, R and De Fanti, S and Sarno, S and Fondevila Alvarez, M and Brisighelli, F and Trombetta, B and Anagnostou, P and Ferri, G and Vazzana, A and Delpino, C and Gruppioni, G and Luiselli, D and Cilli, E}, title = {Iron Age Italic population genetics: the Piceni from Novilara (8th-7th century BC).}, journal = {Annals of human biology}, volume = {45}, number = {1}, pages = {34-43}, doi = {10.1080/03014460.2017.1414876}, pmid = {29216758}, issn = {1464-5033}, mesh = {Archaeology ; DNA, Ancient/analysis ; DNA, Mitochondrial/*analysis ; Female ; *Genetic Variation ; *Haplotypes ; Humans ; Italy ; Male ; *Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed.<br><br>AIMS: To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis.<br><br>SUBJECTS AND METHODS: In a first set of 10 individuals from Novilara, we performed deep sequencing of the HVS-I region of the mtDNA, combined with the genotyping of 22 SNPs in the coding region and the analysis of several autosomal markers.<br><br>RESULTS: The results show a low nucleotide diversity for the inhabitants of Novilara and highlight a genetic affinity of this ancient population with the current inhabitants of central Italy. No family relationship was observed between the individuals analysed here.<br><br>CONCLUSIONS: This study provides a preliminary characterisation of the mtDNA variability of the Piceni of Novilara, as well as a kinship assessment of two peculiar burials.}, }
@article {pmid29202706, year = {2017}, author = {Li, J and Zeng, W and Zhang, Y and Ko, AM and Li, C and Zhu, H and Fu, Q and Zhou, H}, title = {Ancient DNA reveals genetic connections between early Di-Qiang and Han Chinese.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {239}, pmid = {29202706}, issn = {1471-2148}, support = {31371266//National Natural Science Foundation of China/International ; 31200935//National Natural Science Foundation of China/International ; 11&amp;ZD182//National Social Science Foundation of China/International ; }, mesh = {Asian People/*genetics ; Bayes Theorem ; China ; Chromosomes, Human, Y/genetics ; Computer Simulation ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Ethnicity/*genetics ; Genetics, Population ; Geography ; Haplotypes/genetics ; Humans ; Male ; Models, Genetic ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Probability ; Time Factors ; }, abstract = {BACKGROUND: Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~4000 years old) and compared them to other ancient DNA across China, including an early Han-related site (Hengbei site dated ~3000 years old) to establish the underlying genetic relationship between the Di-Qiang and ancestors of Han Chinese.<br><br>RESULTS: We found Mogou mtDNA haplogroups were highly diverse, comprising 14 haplogroups: A, B, C, D (D*, D4, D5), F, G, M7, M8, M10, M13, M25, N*, N9a, and Z. In contrast, Mogou males were all Y-DNA haplogroup O3a2/P201; specifically one male was further assigned to O3a2c1a/M117 using targeted unique regions on the non-recombining region of the Y-chromosome. We compared Mogou to 7 other ancient and 38 modern Chinese groups, in a total of 1793 individuals, and found that Mogou shared close genetic distances with Taojiazhai (a more recent Di-Qiang population), Hengbei, and Northern Han. We modeled their interactions using Approximate Bayesian Computation, and support was given to a potential admixture of ~13-18% between the Mogou and Northern Han around 3300-3800&#xa0;years ago.<br><br>CONCLUSIONS: Mogou harbors the earliest genetically identifiable Di-Qiang, ancestral to the Taojiazhai, and up to ~33% paternal and ~70% of its maternal haplogroups could be found in present-day Northern Han Chinese.}, }
@article {pmid29193490, year = {2018}, author = {Manco, L and Albuquerque, J and Sousa, MF and Martiniano, R and de Oliveira, RC and Marques, S and Gomes, V and Amorim, A and Alvarez, L and Prata, MJ}, title = {The Eastern side of the Westernmost Europeans: Insights from subclades within Y-chromosome haplogroup J-M304.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {30}, number = {2}, pages = {}, doi = {10.1002/ajhb.23082}, pmid = {29193490}, issn = {1520-6300}, mesh = {Alleles ; Chromosomes, Human, Y/*genetics ; Genetic Markers/genetics ; Haplotypes/*genetics ; Humans ; Male ; *Microsatellite Repeats ; Phylogeography ; *Polymorphism, Single Nucleotide ; Portugal ; }, abstract = {OBJECTIVES: We examined internal lineages and haplotype diversity in Portuguese samples belonging to J-M304 to improve the spatial and temporal understanding of the introduction of this haplogroup in Iberia, using the available knowledge about the phylogeography of its main branches, J1-M267 and J2-M172.<br><br>METHODS: A total of 110 males of Portuguese descent were analyzed for 17 Y-chromosome bi-allelic markers and seven Y-chromosome short tandem repeats (Y-STR) loci.<br><br>RESULTS: Among J1-M267 individuals (n&#x2009;=&#x2009;36), five different sub-haplogroups were identified, with the most common being J1a2b2-L147.1 (&#x223c;72%), which encompassed the majority of representatives of the J1a2b-P58 subclade. One sample belonged to the rare J1a1-M365.1 lineage and presented a core Y-STR haplotype consistent with the Iberian settlement during the fifth century by the Alans, a people of Iranian heritage. The analysis of J2-M172 Portuguese males (n&#x2009;=&#x2009;74) enabled the detection of the two main subclades at very dissimilar frequencies, J2a-M410 (&#x223c;80%) and J2b-M12 (&#x223c;20%), among which the most common branches were J2a1(xJ2a1b,h)-L26 (22.9%), J2a1b(xJ2a1b1)-M67 (20.3%), J2a1h-L24 (27%), and J2b2-M241 (20.3%).<br><br>CONCLUSIONS: While previous inferences based on modern haplogroup J Y-chromosomes implicated a main Neolithic dissemination, here we propose a later arrival of J lineages into Iberia using a combination of novel Portuguese Y-chromosomal data and recent evidence from ancient DNA. Our analysis suggests that a substantial tranche of J1-M267 lineages was likely carried into the Iberian Peninsula as a consequence of the trans-Mediterranean contacts during the first millennium BC, while most of the J2-M172 lineages may be associated with post-Neolithic population movements within Europe.}, }
@article {pmid33120599, year = {2017}, author = {Keyser, C}, title = {Virus and ancient DNA: back to the future.}, journal = {Virologie (Montrouge, France)}, volume = {21}, number = {6}, pages = {247-254}, doi = {10.1684/vir.2017.0714}, pmid = {33120599}, issn = {1267-8694}, abstract = {Paleovirology, the study of ancient viruses, is a recent scientific development. It belongs to the domain of ancient DNA studies, paleogenetics. The analytical power of this discipline, that has many applications, is nevertheless limited by the poor conservation of DNA (and RNA) found in fossils and the subsequent methodological problems (amplification issues, post-mortem lesions, contaminations). These issues must be addressed in order to exploit the full potential of preserved nucleic acids within ancient remains. Once these difficulties have been overcome, it becomes possible to characterize ancient viruses and particular steps of their evolution or even adaptation to their hosts. Shedding light on key aspects of past epidemics allows for a better comprehension of present situations and for the anticipation of future situations where viral pathogens emerge or re-emerge. The examples described in this article illustrate these facts.}, }
@article {pmid29182148, year = {2017}, author = {Heintzman, PD and Zazula, GD and MacPhee, R and Scott, E and Cahill, JA and McHorse, BK and Kapp, JD and Stiller, M and Wooller, MJ and Orlando, L and Southon, J and Froese, DG and Shapiro, B}, title = {A new genus of horse from Pleistocene North America.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {29182148}, issn = {2050-084X}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Biometry ; DNA/chemistry/genetics ; *Fossils ; Genotype ; Horses/anatomy &amp; histology/*classification/genetics ; North America ; Phenotype ; Sequence Analysis, DNA ; }, abstract = {The extinct 'New World stilt-legged', or NWSL, equids constitute a perplexing group of Pleistocene horses endemic to North America. Their slender distal limb bones resemble those of Asiatic asses, such as the Persian onager. Previous palaeogenetic studies, however, have suggested a closer relationship to caballine horses than to Asiatic asses. Here, we report complete mitochondrial and partial nuclear genomes from NWSL equids from across their geographic range. Although multiple NWSL equid species have been named, our palaeogenomic and morphometric analyses support the idea that there was only a single species of middle to late Pleistocene NWSL equid, and demonstrate that it falls outside of crown group Equus. We therefore propose a new genus, Haringtonhippus, for the sole species H. francisci. Our combined genomic and phenomic approach to resolving the systematics of extinct megafauna will allow for an improved understanding of the full extent of the terminal Pleistocene extinction event.}, }
@article {pmid29174893, year = {2017}, author = {Andrades Valtueña, A and Mittnik, A and Key, FM and Haak, W and Allmäe, R and Belinskij, A and Daubaras, M and Feldman, M and Jankauskas, R and Janković, I and Massy, K and Novak, M and Pfrengle, S and Reinhold, S and Šlaus, M and Spyrou, MA and Szécsényi-Nagy, A and Tõrv, M and Hansen, S and Bos, KI and Stockhammer, PW and Herbig, A and Krause, J}, title = {The Stone Age Plague and Its Persistence in Eurasia.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {3683-3691.e8}, doi = {10.1016/j.cub.2017.10.025}, pmid = {29174893}, issn = {1879-0445}, mesh = {Archaeology ; DNA, Ancient/*analysis ; Europe ; Genome, Bacterial/*genetics ; Humans ; Phylogeny ; Plague/microbiology ; Yersinia pestis/classification/*genetics ; }, abstract = {Yersinia pestis, the etiologic agent of plague, is a bacterium associated with wild rodents and their fleas. Historically it was responsible for three pandemics: the Plague of Justinian in the 6[th] century AD, which persisted until the 8[th] century [1]; the renowned Black Death of the 14[th] century [2, 3], with recurrent outbreaks until the 18[th] century [4]; and the most recent 19[th] century pandemic, in which Y. pestis spread worldwide [5] and became endemic in several regions [6]. The discovery of molecular signatures of Y. pestis in prehistoric Eurasian individuals and two genomes from Southern Siberia suggest that Y. pestis caused some form of disease in humans prior to the first historically documented pandemic [7]. Here, we present six new European Y. pestis genomes spanning the Late Neolithic to the Bronze Age (LNBA; 4,800 to 3,700 calibrated years before present). This time period is characterized by major transformative cultural and social changes that led to cross-European networks of contact and exchange [8, 9]. We show that all known LNBA strains form a single putatively extinct clade in the Y. pestis phylogeny. Interpreting our data within the context of recent ancient human genomic evidence that suggests an increase in human mobility during the LNBA, we propose a possible scenario for the early spread of Y. pestis: the pathogen may have entered Europe from Central Eurasia following an expansion of people from the steppe, persisted within Europe until the mid-Bronze Age, and moved back toward Central Eurasia in parallel with human populations.}, }
@article {pmid29167366, year = {2017}, author = {Kılınç, GM and Koptekin, D and Atakuman, &#xc7; and Sümer, AP and Dönertaş, HM and Yaka, R and Bilgin, CC and Büyükkarakaya, AM and Baird, D and Altınışık, E and Flegontov, P and Götherström, A and Togan, &#x130; and Somel, M}, title = {Archaeogenomic analysis of the first steps of Neolithization in Anatolia and the Aegean.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1867}, pages = {}, pmid = {29167366}, issn = {1471-2954}, mesh = {Agriculture/*history ; Archaeology ; Farmers/history ; *Gene Flow ; *Genome, Human ; Genomics ; Greece ; History, Ancient ; Human Migration/*history ; Humans ; Turkey ; }, abstract = {The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter-gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.}, }
@article {pmid29167359, year = {2017}, author = {Tassi, F and Vai, S and Ghirotto, S and Lari, M and Modi, A and Pilli, E and Brunelli, A and Susca, RR and Budnik, A and Labuda, D and Alberti, F and Lalueza-Fox, C and Reich, D and Caramelli, D and Barbujani, G}, title = {Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1867}, pages = {}, pmid = {29167359}, issn = {1471-2954}, support = {295733/ERC_/European Research Council/International ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeology ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Europe ; *Genetic Variation ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Language/*history ; }, abstract = {It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people.}, }
@article {pmid29167200, year = {2018}, author = {Schraiber, JG}, title = {Assessing the Relationship of Ancient and Modern Populations.}, journal = {Genetics}, volume = {208}, number = {1}, pages = {383-398}, pmid = {29167200}, issn = {1943-2631}, support = {R35 GM124745/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Alleles ; *DNA, Ancient ; *Genetics, Population ; Humans ; *Models, Genetic ; Polymorphism, Single Nucleotide ; }, abstract = {Genetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach, such as selecting a read at random for each site, to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship of an ancient sample with a modern population, while accounting for sequencing error and postmortem damage by analyzing raw reads from multiple ancient individuals simultaneously. We show that, when analyzing SNP data, it is better to sequence more ancient samples to low coverage: two samples sequenced to 0.5× coverage provide better resolution than a single sample sequenced to 2× coverage. We also examined the power to detect whether an ancient sample is directly ancestral to a modern population, finding that, with even a few high coverage individuals, even ancient samples that are very slightly diverged from the modern population can be detected with ease. When we applied our approach to European samples, we found that no ancient samples represent direct ancestors of modern Europeans. We also found that, as shown previously, the most ancient Europeans appear to have had the smallest effective population sizes, indicating a role for agriculture in modern population growth.}, }
@article {pmid29165562, year = {2017}, author = {Elhaik, E and Yusuf, L and Anderson, AIJ and Pirooznia, M and Arnellos, D and Vilshansky, G and Ercal, G and Lu, Y and Webster, T and Baird, ML and Esposito, U}, title = {The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3225-3237}, pmid = {29165562}, issn = {1759-6653}, mesh = {Anthropology/*methods ; DNA Copy Number Variations ; DNA, Ancient ; Evolution, Molecular ; Genetic Markers ; Genetics, Population/*methods ; *Genome, Human ; Genotype ; Humans ; Microarray Analysis ; Pedigree ; Polymorphism, Single Nucleotide ; Precision Medicine/*methods ; }, abstract = {The human population displays wide variety in demographic history, ancestry, content of DNA derived from hominins or ancient populations, adaptation, traits, copy number variation, drug response, and more. These polymorphisms are of broad interest to population geneticists, forensics investigators, and medical professionals. Historically, much of that knowledge was gained from population survey projects. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism genotyping, their design specifications are limited and they do not allow a full exploration of biodiversity. We thereby aimed to design the Diversity of REcent and Ancient huMan (DREAM)-an all-inclusive microarray that would allow both identification of known associations and exploration of standing questions in genetic anthropology, forensics, and personalized medicine. DREAM includes probes to interrogate ancestry informative markers obtained from over 450 human populations, over 200 ancient genomes, and 10 archaic hominins. DREAM can identify 94% and 61% of all known Y and mitochondrial haplogroups, respectively, and was vetted to avoid interrogation of clinically relevant markers. To demonstrate its capabilities, we compared its FST distributions with those of the 1000 Genomes Project and commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, DREAM's autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. DREAM performances are further illustrated in biogeographical, identical by descent, and copy number variation analyses. In summary, with approximately 800,000 markers spanning nearly 2,000 genes, DREAM is a useful tool for genetic anthropology, forensic, and personalized medicine studies.}, }
@article {pmid29162904, year = {2017}, author = {Solé-Morata, N and García-Fernández, C and Urasin, V and Bekada, A and Fadhlaoui-Zid, K and Zalloua, P and Comas, D and Calafell, F}, title = {Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81).}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15941}, pmid = {29162904}, issn = {2045-2322}, mesh = {Africa, Northern ; Base Sequence ; Bayes Theorem ; Black People/*genetics ; Chromosomes, Human, Y/*genetics ; Haplotypes/genetics ; Humans ; Male ; Microsatellite Repeats/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Time Factors ; }, abstract = {E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup. Moreover, for the first time, by using both SNP and STR data, we have provided updated estimates of the times-to-the-most-recent-common-ancestor (TMRCA) for E-M183, which evidenced an extremely recent origin of this haplogroup (2,000-3,000 ya). Our results also showed a lack of population structure within the E-M183 branch, which could be explained by the recent and rapid expansion of this haplogroup. In spite of a reduction in STR heterozygosity towards the West, which would point to an origin in the Near East, ancient DNA evidence together with our TMRCA estimates point to a local origin of E-M183 in NW Africa.}, }
@article {pmid29151852, year = {2017}, author = {Rifkin, RF and Potgieter, M and Ramond, JB and Cowan, DA}, title = {Ancient oncogenesis, infection and human evolution.}, journal = {Evolutionary applications}, volume = {10}, number = {10}, pages = {949-964}, pmid = {29151852}, issn = {1752-4571}, abstract = {The recent discovery that malignant neoplastic lesions date back nearly 2 million years ago not only highlights the antiquity of cancer in the human lineage, but also provides remarkable insight into ancestral hominin disease pathology. Using these Early Pleistocene examples as a point of departure, we emphasize the prominent role of viral and bacterial pathogens in oncogenesis and evaluate the impact of pathogens on human evolutionary processes in Africa. In the Shakespearean vernacular "what's past is prologue," we highlight the significance of novel information derived from ancient pathogenic DNA. In particular, and given the temporal depth of human occupation in sub-Saharan Africa, it is emphasized that the region is ideally positioned to play a strategic role in the discovery of ancient pathogenic drivers of not only human mortality, but also human evolution. Ancient African pathogen genome data can provide novel revelations concerning human-pathogen coevolutionary processes, and such knowledge is essential for forecasting the ways in which emerging zoonotic and increasingly transmissible diseases might influence human demography and longevity in the future.}, }
@article {pmid29144465, year = {2017}, author = {Lipson, M and Szécsényi-Nagy, A and Mallick, S and Pósa, A and Stégmár, B and Keerl, V and Rohland, N and Stewardson, K and Ferry, M and Michel, M and Oppenheimer, J and Broomandkhoshbacht, N and Harney, E and Nordenfelt, S and Llamas, B and Gusztáv Mende, B and Köhler, K and Oross, K and Bondár, M and Marton, T and Osztás, A and Jakucs, J and Paluch, T and Horváth, F and Csengeri, P and Koós, J and Sebők, K and Anders, A and Raczky, P and Regenye, J and Barna, JP and Fábián, S and Serlegi, G and Toldi, Z and Gyöngyvér Nagy, E and Dani, J and Molnár, E and Pálfi, G and Márk, L and Melegh, B and Bánfai, Z and Domboróczki, L and Fernández-Eraso, J and Antonio Mujika-Alustiza, J and Alonso Fernández, C and Jiménez Echevarría, J and Bollongino, R and Orschiedt, J and Schierhold, K and Meller, H and Cooper, A and Burger, J and Bánffy, E and Alt, KW and Lalueza-Fox, C and Haak, W and Reich, D}, title = {Parallel palaeogenomic transects reveal complex genetic history of early European farmers.}, journal = {Nature}, volume = {551}, number = {7680}, pages = {368-372}, pmid = {29144465}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Ancient/analysis ; Datasets as Topic ; Farmers/*history ; Female ; Gene Flow/*genetics ; *Genetic Variation ; Germany ; History, Ancient ; Human Migration/*history ; Humans ; Hungary ; Male ; Population Dynamics ; Spain ; Spatio-Temporal Analysis ; }, abstract = {Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000-2900 bc, n = 100), Germany (5500-3000 bc, n = 42) and Spain (5500-2200 bc, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.}, }
@article {pmid29142317, year = {2017}, author = {Szécsényi-Nagy, A and Roth, C and Brandt, G and Rihuete-Herrada, C and Tejedor-Rodríguez, C and Held, P and García-Martínez-de-Lagrán, &#xcd; and Arcusa Magallón, H and Zesch, S and Knipper, C and Bánffy, E and Friederich, S and Meller, H and Bueno Ramírez, P and Barroso Bermejo, R and de Balbín Behrmann, R and Herrero-Corral, AM and Flores Fernández, R and Alonso Fernández, C and Jiménez Echevarria, J and Rindlisbacher, L and Oliart, C and Fregeiro, MI and Soriano, I and Vicente, O and Micó, R and Lull, V and Soler Díaz, J and López Padilla, JA and Roca de Togores Muñoz, C and Hernández Pérez, MS and Jover Maestre, FJ and Lomba Maurandi, J and Avilés Fernández, A and Lillios, KT and Silva, AM and Magalhães Ramalho, M and Oosterbeek, LM and Cunha, C and Waterman, AJ and Roig Buxó, J and Martínez, A and Ponce Martínez, J and Hunt Ortiz, M and Mejías-García, JC and Pecero Espín, JC and Cruz-Auñón Briones, R and Tomé, T and Carmona Ballestero, E and Cardoso, JL and Araújo, AC and Liesau von Lettow-Vorbeck, C and Blasco Bosqued, C and Ríos Mendoza, P and Pujante, A and Royo-Guillén, JI and Esquembre Beviá, MA and Dos Santos Goncalves, VM and Parreira, R and Morán Hernández, E and Méndez Izquierdo, E and Vega Y Miguel, J and Menduiña García, R and Martínez Calvo, V and López Jiménez, O and Krause, J and Pichler, SL and Garrido-Pena, R and Kunst, M and Risch, R and Rojo-Guerra, MA and Haak, W and Alt, KW}, title = {The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15644}, pmid = {29142317}, issn = {2045-2322}, mesh = {Agriculture/history ; *DNA, Ancient ; DNA, Mitochondrial/*genetics/history ; Europe ; Genetic Variation/*genetics ; *Genetics, Population ; Haplotypes ; History, Ancient ; Humans ; }, abstract = {Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focus on the maternal genetic makeup of the Neolithic (~ 5500-3000 BCE), Chalcolithic (~ 3000-2200 BCE) and Early Bronze Age (~ 2200-1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character.}, }
@article {pmid29134102, year = {2017}, author = {Turvey, ST and Barnes, I and Marr, M and Brace, S}, title = {Imperial trophy or island relict? A new extinction paradigm for Père David's deer: a Chinese conservation icon.}, journal = {Royal Society open science}, volume = {4}, number = {10}, pages = {171096}, pmid = {29134102}, issn = {2054-5703}, abstract = {Determining the 'dynamic biogeography' of range collapse in threatened species is essential for effective conservation, but reconstruction of spatio-temporal patterns of population vulnerability and resilience can require use of non-standard ecological data such as historical archives. Père David's deer or milu, one of the few living mammal species that has become extinct in the wild, is historically known only from a small captive herd of unknown provenance that survived until 1900 in the Imperial Hunting Park near Beijing, from which all living individuals are descended. Using ancient DNA analysis, we demonstrate that two fawns collected in 1868 from Hainan Island, off the southern Chinese mainland, represent the only known wild milu specimens and were sampled from probably the last wild population. The Hainan milu population shows extremely low genetic differentiation from descendants of the Beijing herd, suggesting that this now-extinct population may have been the source of the captive herd. This revised extinction model refutes the supposed long-term survival of a captive milu herd for centuries or millennia after final extinction of wild populations, highlighting the vulnerability of remnant mammal populations in the absence of proactive management and the importance of historical museum collections for providing unique new insights on evolution, biogeography and conservation. Milu experienced a pattern of final population persistence on an island at the periphery of their former range, consistent with the 'range eclipse' or 'contagion' model of range collapse, and matching the spatial extinction dynamics of other extinct mammals such as the thylacine and woolly mammoth.}, }
@article {pmid29134095, year = {2017}, author = {Teasdale, MD and Fiddyment, S and Vnouček, J and Mattiangeli, V and Speller, C and Binois, A and Carver, M and Dand, C and Newfield, TP and Webb, CC and Bradley, DG and Collins, MJ}, title = {The York Gospels: a 1000-year biological palimpsest.}, journal = {Royal Society open science}, volume = {4}, number = {10}, pages = {170988}, pmid = {29134095}, issn = {2054-5703}, abstract = {Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.}, }
@article {pmid29117125, year = {2017}, author = {Woods, R and Marr, MM and Brace, S and Barnes, I}, title = {The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species.}, journal = {Genes}, volume = {8}, number = {11}, pages = {}, pmid = {29117125}, issn = {2073-4425}, abstract = {The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.}, }
@article {pmid29114402, year = {2017}, author = {Luhmann, N and Doerr, D and Chauve, C}, title = {Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes.}, journal = {Microbial genomics}, volume = {3}, number = {9}, pages = {e000123}, pmid = {29114402}, issn = {2057-5858}, mesh = {Contig Mapping/*methods ; *DNA, Ancient ; DNA, Bacterial ; Evolution, Molecular ; France/epidemiology ; *Genome, Bacterial ; History, 18th Century ; History, Medieval ; Humans ; London/epidemiology ; Pandemics/history ; Phylogeny ; Plague/epidemiology/history/*microbiology ; Yersinia pestis/*genetics ; }, abstract = {Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Y. pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements. It has recently been shown that comparative scaffolding approaches can improve the assembly of ancient Y. pestis genomes at a chromosome level. In the present work, we address the last step of genome assembly, the gap-filling stage. We describe an optimization-based method AGapEs (ancestral gap estimation) to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads. We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and comparative signal. We applied our method to two Y. pestis data sets from the London and Marseilles outbreaks, for which we obtained highly improved genome assemblies for both genomes, comprised of, respectively, five and six scaffolds with 95 % of the assemblies supported by ancient reads. We analysed the genome evolution between both ancient genomes in terms of genome rearrangements, and observed a high level of synteny conservation between these strains.}, }
@article {pmid29112870, year = {2017}, author = {Meachen, JA}, title = {Ancient DNA: Saber-Toothed Cats Are the Same Beasts After All.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {R1165-R1167}, doi = {10.1016/j.cub.2017.09.024}, pmid = {29112870}, issn = {1879-0445}, mesh = {*DNA, Ancient ; Europe ; Fossils ; North America ; *Tooth ; }, abstract = {Ancient DNA from the saber-toothed cat Homotherium reveals that the late Pleistocene species from Europe and North America were the same. Homotherium turns out to be only distantly related to the well-known saber-toothed Smilodon.}, }
@article {pmid29107554, year = {2017}, author = {Rodríguez-Varela, R and Günther, T and Krzewińska, M and Storå, J and Gillingwater, TH and MacCallum, M and Arsuaga, JL and Dobney, K and Valdiosera, C and Jakobsson, M and Götherström, A and Girdland-Flink, L}, title = {Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {3396-3402.e5}, doi = {10.1016/j.cub.2017.09.059}, pmid = {29107554}, issn = {1879-0445}, mesh = {Africa, Northern ; Archaeology/methods ; Body Remains ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Emigration and Immigration/*statistics &amp; numerical data ; Genetic Markers ; Genetics, Population ; Genome, Human/*genetics ; Genome, Mitochondrial/*genetics ; Humans ; Polymorphism, Single Nucleotide/genetics ; Racial Groups/*genetics ; Spain ; Tooth/anatomy &amp; histology ; }, abstract = {The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5[th] century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7[th]-11[th] centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.}, }
@article {pmid29103934, year = {2017}, author = {Pečnerová, P and Díez-Del-Molino, D and Dussex, N and Feuerborn, T and von Seth, J and van der Plicht, J and Nikolskiy, P and Tikhonov, A and Vartanyan, S and Dalén, L}, title = {Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.}, journal = {Current biology : CB}, volume = {27}, number = {22}, pages = {3505-3510.e3}, doi = {10.1016/j.cub.2017.09.064}, pmid = {29103934}, issn = {1879-0445}, mesh = {Animals ; Behavior, Animal ; Elephants/genetics ; Extinction, Biological ; Female ; Fossils ; Genome ; Genomics ; Male ; Mammoths/anatomy &amp; histology/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sex Determination Analysis/*methods ; Sex Determination by Skeleton/*methods ; Sex Ratio ; Sexual Behavior/physiology ; Social Behavior ; }, abstract = {While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 woolly mammoth (Mammuthus primigenius) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. We hypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely.}, }
@article {pmid29101892, year = {2017}, author = {Marshall, C and Sturk-Andreaggi, K and Daniels-Higginbotham, J and Oliver, RS and Barritt-Ross, S and McMahon, TP}, title = {Performance evaluation of a mitogenome capture and Illumina sequencing protocol using non-probative, case-type skeletal samples: Implications for the use of a positive control in a next-generation sequencing procedure.}, journal = {Forensic science international. Genetics}, volume = {31}, number = {}, pages = {198-206}, doi = {10.1016/j.fsigen.2017.09.001}, pmid = {29101892}, issn = {1878-0326}, mesh = {DNA Degradation, Necrotic ; DNA, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Haplotypes ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Humans ; Polymerase Chain Reaction ; *Sequence Analysis, DNA ; }, abstract = {Next-generation ancient DNA technologies have the potential to assist in the analysis of degraded DNA extracted from forensic specimens. Mitochondrial genome (mitogenome) sequencing, specifically, may be of benefit to samples that fail to yield forensically relevant genetic information using conventional PCR-based techniques. This report summarizes the Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory's (AFMES-AFDIL) performance evaluation of a Next-Generation Sequencing protocol for degraded and chemically treated past accounting samples. The procedure involves hybridization capture for targeted enrichment of mitochondrial DNA, massively parallel sequencing using Illumina chemistry, and an automated bioinformatic pipeline for forensic mtDNA profile generation. A total of 22 non-probative samples and associated controls were processed in the present study, spanning a range of DNA quantity and quality. Data were generated from over 100 DNA libraries by ten DNA analysts over the course of five months. The results show that the mitogenome sequencing procedure is reliable and robust, sensitive to low template (one ng control DNA) as well as degraded DNA, and specific to the analysis of the human mitogenome. Haplotypes were overall concordant between NGS replicates and with previously generated Sanger control region data. Due to the inherent risk for contamination when working with low-template, degraded DNA, a contamination assessment was performed. The consumables were shown to be void of human DNA contaminants and suitable for forensic use. Reagent blanks and negative controls were analyzed to determine the background signal of the procedure. This background signal was then used to set analytical and reporting thresholds, which were designated at 4.0X (limit of detection) and 10.0X (limit of quantiation) average coverage across the mitogenome, respectively. Nearly all human samples exceeded the reporting threshold, although coverage was reduced in chemically treated samples resulting in a ∼58% passing rate for these poor-quality samples. A concordance assessment demonstrated the reliability of the NGS data when compared to known Sanger profiles. One case sample was shown to be mixed with a co-processed sample and two reagent blanks indicated the presence of DNA above the analytical threshold. This contamination was attributed to sequencing crosstalk from simultaneously sequenced high-quality samples to include the positive control. Overall this study demonstrated that hybridization capture and Illumina sequencing provide a viable method for mitogenome sequencing of degraded and chemically treated skeletal DNA samples, yet may require alternative measures of quality control.}, }
@article {pmid29087301, year = {2017}, author = {Loog, L and Mirazón Lahr, M and Kovacevic, M and Manica, A and Eriksson, A and Thomas, MG}, title = {Estimating mobility using sparse data: Application to human genetic variation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {46}, pages = {12213-12218}, pmid = {29087301}, issn = {1091-6490}, support = {//Wellcome Trust/United Kingdom ; 100719/Z/12/Z//Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Europe ; *Genetics, Population ; History, Ancient ; *Human Migration ; Humans ; *Models, Statistical ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; }, abstract = {Mobility is one of the most important processes shaping spatiotemporal patterns of variation in genetic, morphological, and cultural traits. However, current approaches for inferring past migration episodes in the fields of archaeology and population genetics lack either temporal resolution or formal quantification of the underlying mobility, are poorly suited to spatially and temporally sparsely sampled data, and permit only limited systematic comparison between different time periods or geographic regions. Here we present an estimator of past mobility that addresses these issues by explicitly linking trait differentiation in space and time. We demonstrate the efficacy of this estimator using spatiotemporally explicit simulations and apply it to a large set of ancient genomic data from Western Eurasia. We identify a sequence of changes in human mobility from the Late Pleistocene to the Iron Age. We find that mobility among European Holocene farmers was significantly higher than among European hunter-gatherers both pre- and postdating the Last Glacial Maximum. We also infer that this Holocene rise in mobility occurred in at least three distinct stages: the first centering on the well-known population expansion at the beginning of the Neolithic, and the second and third centering on the beginning of the Bronze Age and the late Iron Age, respectively. These findings suggest a strong link between technological change and human mobility in Holocene Western Eurasia and demonstrate the utility of this framework for exploring changes in mobility through space and time.}, }
@article {pmid29085065, year = {2017}, author = {Sandoval-Castellanos, E and Wutke, S and Gonzalez-Salazar, C and Ludwig, A}, title = {Coat colour adaptation of post-glacial horses to increasing forest vegetation.}, journal = {Nature ecology &amp; evolution}, volume = {1}, number = {12}, pages = {1816-1819}, doi = {10.1038/s41559-017-0358-5}, pmid = {29085065}, issn = {2397-334X}, mesh = {Adaptation, Biological ; Animal Fur/chemistry ; Animals ; *Color ; *Ecosystem ; Horses/*physiology ; Paleontology ; *Pigmentation ; }, abstract = {Wild horses unexpectedly survived terminal Pleistocene megafaunal extinctions until eventual European extirpation in the twentieth century. This survival is tied to either their occurrence in cryptic open habitats or their adaptation to forests. Our niche modelling inferred an increasing presence of horses in post-glacial forests, and our analysis of ancient DNA suggested significant selection for black phenotypes as indicating adaptation to forests.}, }
@article {pmid29065293, year = {2017}, author = {Raff, J}, title = {Genetics: Ancient DNA Clarifies Population Histories of the Northeastern Margin of North America.}, journal = {Current biology : CB}, volume = {27}, number = {20}, pages = {R1116-R1118}, doi = {10.1016/j.cub.2017.09.036}, pmid = {29065293}, issn = {1879-0445}, mesh = {Canada ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Humans ; Indians, North American/*genetics ; Newfoundland and Labrador ; North America ; }, abstract = {A new study of ancient mitochondrial DNA from Newfoundland and Labrador indicates that this region at the northeastern margin of North America was populated three times in succession by different indigenous groups. This research helps shed light on the movement of populations across the continent, following the initial peopling of the Americas.}, }
@article {pmid29056454, year = {2017}, author = {Paijmans, JLA and Barnett, R and Gilbert, MTP and Zepeda-Mendoza, ML and Reumer, JWF and de Vos, J and Zazula, G and Nagel, D and Baryshnikov, GF and Leonard, JA and Rohland, N and Westbury, MV and Barlow, A and Hofreiter, M}, title = {Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {3330-3336.e5}, doi = {10.1016/j.cub.2017.09.033}, pmid = {29056454}, issn = {1879-0445}, support = {310763/ERC_/European Research Council/International ; }, mesh = {Animals ; *Biological Evolution ; Cats ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Felidae/*genetics ; Fossils ; Phylogeny ; Tooth ; }, abstract = {Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1-3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (∼18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6].}, }
@article {pmid29046620, year = {2017}, author = {Velsko, IM and Overmyer, KA and Speller, C and Klaus, L and Collins, MJ and Loe, L and Frantz, LAF and Sankaranarayanan, K and Lewis, CM and Martinez, JBR and Chaves, E and Coon, JJ and Larson, G and Warinner, C}, title = {The dental calculus metabolome in modern and historic samples.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {13}, number = {11}, pages = {134}, pmid = {29046620}, issn = {1573-3882}, support = {337574/ERC_/European Research Council/International ; R01 GM089886/GM/NIGMS NIH HHS/United States ; R35 GM118110/GM/NIGMS NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; }, abstract = {INTRODUCTION: Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens.<br><br>OBJECTIVE: We present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach.<br><br>METHODS: Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) quantified 285 metabolites in modern and historic (200&#xa0;years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography-MS (GC-MS) and UPLC-MS/MS for further characterization of metabolites and lipids. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss.<br><br>RESULTS: Dipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples.<br><br>CONCLUSIONS: The results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies.}, }
@article {pmid29045412, year = {2017}, author = {Theofanopoulou, C and Gastaldon, S and O'Rourke, T and Samuels, BD and Martins, PT and Delogu, F and Alamri, S and Boeckx, C}, title = {Self-domestication in Homo sapiens: Insights from comparative genomics.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0185306}, pmid = {29045412}, issn = {1932-6203}, mesh = {Alleles ; Animals ; *Domestication ; Gene Expression Profiling ; *Genomics ; Hominidae/genetics ; Humans ; Selection, Genetic ; Species Specificity ; Synteny/genetics ; }, abstract = {This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the "domestication syndrome" in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.}, }
@article {pmid29033334, year = {2017}, author = {Fehren-Schmitz, L and Jarman, CL and Harkins, KM and Kayser, M and Popp, BN and Skoglund, P}, title = {Genetic Ancestry of Rapanui before and after European Contact.}, journal = {Current biology : CB}, volume = {27}, number = {20}, pages = {3209-3215.e6}, doi = {10.1016/j.cub.2017.09.029}, pmid = {29033334}, issn = {1879-0445}, mesh = {Archaeology ; Female ; *Genetic Variation ; *Genome, Human ; Genome, Mitochondrial ; *Human Migration ; Humans ; Indians, South American/*genetics ; Male ; Polynesia ; }, abstract = {The origins and lifeways of the inhabitants of Rapa Nui (Easter Island), a remote island in the southeast Pacific Ocean, have been debated for generations. Archaeological evidence substantiates the widely accepted view that the island was first settled by people of Polynesian origin, as late as 1200 CE [1-4]. What remains controversial, however, is the nature of events in the island's population history prior to the first historic contact with Europeans in 1722 CE. Purported contact between Rapa Nui and South America is particularly contentious, and recent studies have reported genetic evidence for Native American admixture in present-day indigenous inhabitants of Rapa Nui [5-8]. Statistical modeling has suggested that this genetic contribution might have occurred prior to European contact [6]. Here we directly test the hypothesis that the Native American admixture of the current Rapa Nui population predates the arrival of Europeans with a paleogenomic analysis of five individual samples excavated from Ahu Nau Nau, Anakena, dating to pre- and post-European contact, respectively. Complete mitochondrial genomes and low-coverage autosomal genomes show that the analyzed individuals fall within the genetic diversity of present-day and ancient Polynesians, and we can reject the hypothesis that any of these individuals had substantial Native American ancestry. Our data thus suggest that the Native American ancestry in contemporary Easter Islanders was not present on the island prior to European contact and may thus be due to events in more recent history.}, }
@article {pmid29033327, year = {2017}, author = {Yang, MA and Gao, X and Theunert, C and Tong, H and Aximu-Petri, A and Nickel, B and Slatkin, M and Meyer, M and Pääbo, S and Kelso, J and Fu, Q}, title = {40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia.}, journal = {Current biology : CB}, volume = {27}, number = {20}, pages = {3202-3208.e9}, pmid = {29033327}, issn = {1879-0445}, support = {694707/ERC_/European Research Council/International ; R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeology ; Biological Variation, Population ; China ; DNA, Ancient/*analysis ; *Genome, Human ; *Human Migration ; Humans ; Male ; Phylogeny ; }, abstract = {By at least 45,000 years before present, anatomically modern humans had spread across Eurasia [1-3], but it is not well known how diverse these early populations were and whether they contributed substantially to later people or represent early modern human expansions into Eurasia that left no surviving descendants today. Analyses of genome-wide data from several ancient individuals from Western Eurasia and Siberia have shown that some of these individuals have relationships to present-day Europeans [4, 5] while others did not contribute to present-day Eurasian populations [3, 6]. As contributions from Upper Paleolithic populations in Eastern Eurasia to present-day humans and their relationship to other early Eurasians is not clear, we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China, [1, 7] to study his relationship to ancient and present-day humans. We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia [8] and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia.}, }
@article {pmid29033326, year = {2017}, author = {Duggan, AT and Harris, AJT and Marciniak, S and Marshall, I and Kuch, M and Kitchen, A and Renaud, G and Southon, J and Fuller, B and Young, J and Fiedel, S and Golding, GB and Grimes, V and Poinar, H}, title = {Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada.}, journal = {Current biology : CB}, volume = {27}, number = {20}, pages = {3149-3156.e11}, doi = {10.1016/j.cub.2017.08.053}, pmid = {29033326}, issn = {1879-0445}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Archaeology ; Child ; Child, Preschool ; DNA, Ancient/*analysis ; Female ; *Genetic Variation ; *Genome, Human ; *Genome, Mitochondrial ; *Human Migration ; Humans ; Indians, North American ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Newfoundland and Labrador ; Young Adult ; }, abstract = {Situated at the furthest northeastern edge of Canada, the island of Newfoundland (approximately 110,000 km[2]) and Labrador (approximately 295,000 km[2]) today constitute a province characterized by abundant natural resources but low population density. Both landmasses were covered by the Laurentide ice sheet during the Last Glacial Maximum (18,000 years before present [YBP]); after the glacier retreated, ice patches remained on the island until ca. 9,000 calibrated (cal) YBP [1]. Nevertheless, indigenous peoples, whose ancestors had trekked some 5,000 km from the west coast, arrived approximately 10,000 cal YBP in Labrador and ca. 6,000 cal YBP in Newfoundland [2, 3]. Differential features in material culture indicate at least three settlement episodes by distinct cultural groups, including the Maritime Archaic, Palaeoeskimo, and Beothuk. Newfoundland has remained home to indigenous peoples until present day with only one apparent hiatus (3,400-2,800 YBP). This record suggests abandonment, severe constriction, or local extinction followed by subsequent immigrations from single or multiple source populations, but the specific dynamics and the cultural and biological relationships, if any, among these successive peoples remain enigmatic [4]. By examining the mitochondrial genome diversity and isotopic ratios of 74 ancient remains in conjunction with the archaeological record, we have provided definitive evidence for the genetic discontinuity between the maternal lineages of these populations. This northeastern margin of North America appears to have been populated multiple times by distinct groups that did not share a recent common ancestry, but rather one much deeper in time at the entry point into the continent.}, }
@article {pmid29030957, year = {2017}, author = {Coutellec, MA}, title = {Mollusc shells as metagenomic archives: The true treasure is the chest itself.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {854-857}, doi = {10.1111/1755-0998.12716}, pmid = {29030957}, issn = {1755-0998}, mesh = {Animals ; *DNA, Ancient ; Genomics ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mollusca ; }, abstract = {Mollusc shells, beyond the treasure of information inherently conveyed through their morphology and chemical composition also have the capacity to preserve DNA sequences over the long term in their inner structure. This has been clearly demonstrated for the first time in the study published in this issue of Molecular Ecology Resources by Der Sarkissian et al. (). With a methodology specifically dedicated to ancient DNA and solid matrices, the authors were able to successfully extract and amplify DNA from marine shells spanning the last 7,000 years. Furthermore, using metagenomic analyses, they could identify important factors affecting DNA recovery. Using reference genomes and sequences in a targeted approach to assign high-throughput sequencing reads, the authors revealed both the presence of endogenous mollusc DNA and a potent pathogen of Manilla clam. Collectively, the results presented in this study open extremely promising research avenues, from palaeogenomics and evolutionary biology to ecological genomics at population and community levels, as well as the opportunity to fine-tune diagnostic tools for conservation and aquaculture purposes. Last but not least, this study also offers exciting perspectives in epigenomics and the evolution of regulatory processes in the context of adaptation to global change. It can be easily expected that the approach developed by Der Sarkissian et al. () will be pursued and extensively investigated in the near future by the scientific community interested in these issues.}, }
@article {pmid29027988, year = {2017}, author = {Zimmermann, HH and Raschke, E and Epp, LS and Stoof-Leichsenring, KR and Schirrmeister, L and Schwamborn, G and Herzschuh, U}, title = {The History of Tree and Shrub Taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data.}, journal = {Genes}, volume = {8}, number = {10}, pages = {}, pmid = {29027988}, issn = {2073-4425}, abstract = {Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.}, }
@article {pmid29027332, year = {2017}, author = {Harris, EE}, title = {Demic and cultural diffusion in prehistoric Europe in the age of ancient genomes.}, journal = {Evolutionary anthropology}, volume = {26}, number = {5}, pages = {228-241}, doi = {10.1002/evan.21545}, pmid = {29027332}, issn = {1520-6505}, mesh = {Anthropology, Physical ; Biological Evolution ; *Cultural Evolution ; DNA, Ancient ; Europe ; Genome, Human/*genetics ; *Human Migration ; Humans ; Metagenomics ; *Population Dynamics ; }, abstract = {Ancient genomes can help us detect prehistoric migrations, population contractions, and admixture among populations. Knowing the dynamics of demography is invaluable for understanding culture change in prehistory, particularly the roles played by demic and cultural diffusion in transformations of material cultures. Prehistoric Europe is a region where ancient genome analyses can help illuminate the interplay between demography and culture change. In Europe, there is more archeological evidence, in terms of detailed studies, radiometric dates, and explanatory hypotheses that can be evaluated, than in any other region of the world. Here I show some important ways that ancient genomes have given us insights into population movements in European prehistory. I also propose that studies might be increasingly focused on specific questions of culture change, for example in evaluating the makers of "transitional" industries as well as the origins of the Gravettian and spread of the Magdalenian. I also discuss genomic evidence supporting the large role that demic expansion has played in the Neolithization of Europe and the formation of the European population during the Bronze Age.}, }
@article {pmid29023628, year = {2018}, author = {Adachi, N and Kakuda, T and Takahashi, R and Kanzawa-Kiriyama, H and Shinoda, KI}, title = {Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data.}, journal = {American journal of physical anthropology}, volume = {165}, number = {1}, pages = {139-148}, pmid = {29023628}, issn = {1096-8644}, mesh = {Asian People/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/classification/*genetics ; Ethnicity/*genetics ; Genetics, Population ; Haplotypes/genetics ; Humans ; Japan ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Siberia ; }, abstract = {OBJECTIVES: The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern-day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large-scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido.<br><br>MATERIALS AND METHODS: Mitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup-defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations.<br><br>RESULTS: Our findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan.<br><br>DISCUSSION: Our results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual-structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.}, }
@article {pmid29023552, year = {2017}, author = {Bourgeois, Q and Kroon, E}, title = {The impact of male burials on the construction of Corded Ware identity: Reconstructing networks of information in the 3rd millennium BC.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0185971}, pmid = {29023552}, issn = {1932-6203}, mesh = {Burial/*history ; Culture ; Europe ; History, Ancient ; Humans ; Information Dissemination/*history ; Male ; }, abstract = {The emergence of Corded Ware Groups throughout Europe in the 3rd millennium BC is one of the most defining events in European history. From the Wolga to the Rhine communities start to speak Indo-European languages and bury their dead in an extremely similar fashion. Recent ancient DNA-analyses identify a massive migration from the Eurasian steppe as the prime cause for this event. However, there is a fundamental difference between expressing a Corded Ware identity-the sharing of world views and ideas-and having a specific DNA-profile. Therefore, we argue that investigating the exchange of cultural information on burial rites between these communities serves as a crucial complement to the exchange of biological information. By adopting a practice perspective to 1161 Corded Ware burials throughout north-western Europe, combined with similarity indexes and network representations, we demonstrate a high degree of information sharing on the burial ritual between different regions. Moreover, we show that male burials are much more international in character than female burials and as such can be considered as the vector along which cultural information and Corded Ware identity was transmitted. This finding highlights an underlying complex societal organization of Corded Ware burial rites in which gender roles had a significant impact on the composition and transmission of cultural information. Our findings corroborate recent studies that suggest the Corded Ware was a male focused society.}, }
@article {pmid28993800, year = {2017}, author = {Mans, BJ and Featherston, J and de Castro, MH and Pienaar, R}, title = {Gene Duplication and Protein Evolution in Tick-Host Interactions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {7}, number = {}, pages = {413}, pmid = {28993800}, issn = {2235-2988}, mesh = {Adaptation, Physiological ; Animals ; Biological Evolution ; Chromosome Duplication/genetics ; *Evolution, Molecular ; Face/physiopathology ; Feeding Behavior/physiology ; *Gene Duplication ; Genetic Drift ; Genetic Speciation ; Host-Parasite Interactions/*genetics/*physiology ; Multigene Family/genetics ; Phylogeny ; Salivary Glands/metabolism ; Ticks/classification/*genetics/pathogenicity/*physiology ; Transcriptome ; }, abstract = {Ticks modulate their hosts' defense responses by secreting a biopharmacopiea of hundreds to thousands of proteins and bioactive chemicals into the feeding site (tick-host interface). These molecules and their functions evolved over millions of years as ticks adapted to blood-feeding, tick lineages diverged, and host-shifts occurred. The evolution of new proteins with new functions is mainly dependent on gene duplication events. Central questions around this are the rates of gene duplication, when they occurred and how new functions evolve after gene duplication. The current review investigates these questions in the light of tick biology and considers the possibilities of ancient genome duplication, lineage specific expansion events, and the role that positive selection played in the evolution of tick protein function. It contrasts current views in tick biology regarding adaptive evolution with the more general view that neutral evolution may account for the majority of biological innovations observed in ticks.}, }
@article {pmid28984839, year = {2017}, author = {Molto, JE and Loreille, O and Mallott, EK and Malhi, RS and Fast, S and Daniels-Higginbotham, J and Marshall, C and Parr, R}, title = {Complete Mitochondrial Genome Sequencing of a Burial from a Romano-Christian Cemetery in the Dakhleh Oasis, Egypt: Preliminary Indications.}, journal = {Genes}, volume = {8}, number = {10}, pages = {}, pmid = {28984839}, issn = {2073-4425}, abstract = {The curse of ancient Egyptian DNA was lifted by a recent study which sequenced the mitochondrial genomes (mtGenome) of 90 ancient Egyptians from the archaeological site of Abusir el-Meleq. Surprisingly, these ancient inhabitants were more closely related to those from the Near East than to contemporary Egyptians. It has been accepted that the timeless highway of the Nile River seeded Egypt with African genetic influence, well before pre-Dynastic times. Here we report on the successful recovery and analysis of the complete mtGenome from a burial recovered from a remote Romano-Christian cemetery, Kellis 2 (K2). K2 serviced the ancient municipality of Kellis, a village located in the Dakhleh Oasis in the southwest desert in Egypt. The data were obtained by high throughput sequencing (HTS) performed independently at two ancient DNA facilities (Armed Forces DNA Identification Laboratory, Dover, DE, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA). These efforts produced concordant haplotypes representing a U1a1a haplogroup lineage. This result indicates that Near Eastern maternal influence previously identified at Abusir el-Meleq was also present further south, in ancient Kellis during the Romano-Christian period.}, }
@article {pmid28984227, year = {2017}, author = {Inskip, S and Taylor, GM and Anderson, S and Stewart, G}, title = {Leprosy in pre-Norman Suffolk, UK: biomolecular and geochemical analysis of the woman from Hoxne.}, journal = {Journal of medical microbiology}, volume = {66}, number = {11}, pages = {1640-1649}, doi = {10.1099/jmm.0.000606}, pmid = {28984227}, issn = {1473-5644}, mesh = {Adult ; Female ; Genotype ; History, Medieval ; Humans ; Leprosy, Lepromatous/diagnosis/*epidemiology/history/microbiology ; Mycobacterium leprae/classification/*genetics/*isolation &amp; purification ; Osteology ; Skull/microbiology ; United Kingdom ; }, abstract = {PURPOSE: A woman's skull, exhibiting features of lepromatous leprosy (LL), was recovered from a garden in Hoxne, Suffolk. The absence of post crania and lack of formal excavation meant that diagnosis and dating was uncertain. The aim of this research was to confirm the diagnosis using biomolecular means and second, to place it in context with other British leprosy cases using SNP genotyping and radiocarbon dating.<br><br>METHODOLOGY: Bone from the skull was analysed by ancient DNA (aDNA) methods and subjected to radiocarbon dating. As a result, stable carbon and nitrogen isotope values were produced, both useful for assessing aspects of the woman's diet.Results/Key findings. aDNA confirmed the presence of mycobacterium leprae and genotyping demonstrated an ancestral variant of subtype 3I, the same lineage recently identified in living squirrels in the south of England. Radiocarbon dating revealed the woman lived approximately between 885-1015 AD, providing evidence for endurance of this subtype in East Anglia, having been previously identified as early as the fifth-sixth century (Great Chesterford) and as late as the thirteenth century (Ipswich).<br><br>CONCLUSIONS: The confirmation of a new pre-Norman leprosy case in East Anglia is of interest as this is where a high proportion of cases are located. Possible factors for this may include preservation and excavation biases, population density, but also connection and trade, possibly of fur, with the continent. Future research on other British LL cases should focus on exploring these aspects to advance understanding of the disease's history, here and on the continent.}, }
@article {pmid28977014, year = {2017}, author = {Osipowicz, G and Witas, H and Lisowska-Gaczorek, A and Reitsema, L and Szostek, K and Płoszaj, T and Kuriga, J and Makowiecki, D and Jędrychowska-Dańska, K and Cienkosz-Stepańczak, B}, title = {Origin of the ornamented bâton percé from the Gołębiewo site 47 as a trigger of discussion on long-distance exchange among Early Mesolithic communities of Central Poland and Northern Europe.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0184560}, pmid = {28977014}, issn = {1932-6203}, mesh = {*Animal Migration ; Animals ; *Antlers ; Artifacts ; DNA/genetics ; Europe ; *Fossils ; Humans ; Paleontology ; Poland ; Polymorphism, Single Nucleotide ; *Reindeer ; Sequence Analysis, DNA ; }, abstract = {This article describes evidence for contact and exchange among Mesolithic communities in Poland and Scandinavia, based on the interdisciplinary analysis of an ornamented bâton percé from Gołębiewo site 47 (Central Poland). Typological and chronological-cultural analyses show the artefact to be most likely produced in the North European Plain, during the Boreal period. Carbon-14 dating confirms the antiquity of the artefact. Ancient DNA analysis shows the artefact to be of Rangifer tarandus antler. Following this species designation, a dispersion analysis of Early-Holocene reindeer remains in Europe was conducted, showing this species to exist only in northern Scandinavia and north-western Russia in this period. Therefore, the bâton from Gołębiewo constitutes the youngest reindeer remains in the European Plain and south-western Scandinavia known to date. An attempt was made to determine the biogeographic region from which the antler used to produce the artefact originates from. To this end, comprehensive δ18O, δ13C and δ15N isotope analyses were performed. North Karelia and South Lapland were determined as the most probable regions in terms of isotopic data, results which correspond to the known distribution range of Rangifer tarandus at this time. In light of these finds, the likelihood of contact between Scandinavia and Central Europe in Early Holocene is evaluated. The bâton percé from Gołębiewo is likely key evidence for long-distance exchange during the Boreal period.}, }
@article {pmid28962023, year = {2017}, author = {Casas-Marce, M and Marmesat, E and Soriano, L and Martínez-Cruz, B and Lucena-Perez, M and Nocete, F and Rodríguez-Hidalgo, A and Canals, A and Nadal, J and Detry, C and Bernáldez-Sánchez, E and Fernández-Rodríguez, C and Pérez-Ripoll, M and Stiller, M and Hofreiter, M and Rodríguez, A and Revilla, E and Delibes, M and Godoy, JA}, title = {Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA.}, journal = {Molecular biology and evolution}, volume = {34}, number = {11}, pages = {2893-2907}, pmid = {28962023}, issn = {1537-1719}, mesh = {Animals ; Conservation of Natural Resources ; DNA, Ancient/analysis ; Endangered Species ; Extinction, Biological ; Genetic Drift ; Genetic Variation/genetics ; Genome ; Genome, Mitochondrial/genetics ; Lynx/*genetics ; Microsatellite Repeats/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions.}, }
@article {pmid28957511, year = {2017}, author = {Gokhman, D and Malul, A and Carmel, L}, title = {Inferring Past Environments from Ancient Epigenomes.}, journal = {Molecular biology and evolution}, volume = {34}, number = {10}, pages = {2429-2438}, pmid = {28957511}, issn = {1537-1719}, mesh = {Animals ; DNA/genetics ; DNA Methylation/genetics/physiology ; DNA, Ancient/*analysis ; Environment ; Epigenesis, Genetic/genetics ; Epigenomics/*methods ; Hominidae/genetics ; Humans ; }, abstract = {Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more. We demonstrate this approach by showing that hunger-related DNA methylation changes are found in ancient hunter-gatherers. The strategy we present here opens a window to reconstruct previously inaccessible aspects of the lives of past individuals.}, }
@article {pmid28956829, year = {2017}, author = {Porter, AF and Duggan, AT and Poinar, HN and Holmes, EC}, title = {Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum.}, journal = {Viruses}, volume = {9}, number = {10}, pages = {}, pmid = {28956829}, issn = {1999-4915}, mesh = {Czech Republic ; Evolution, Molecular ; Genome, Viral ; Humans ; Museums ; Phylogeny ; *Smallpox ; Variola virus/*genetics ; }, abstract = {The complete genome sequences of two strains of variola virus (VARV) sampled from human smallpox specimens present in the Czech National Museum, Prague, were recently determined, with one of the sequences estimated to date to the mid-19th century. Using molecular clock methods, the authors of this study go on to infer that the currently available strains of VARV share an older common ancestor, at around 1350 AD, than some recent estimates based on other archival human samples. Herein, we show that the two Czech strains exhibit anomalous branch lengths given their proposed age, and by assuming a constant rate of evolutionary change across the rest of the VARV phylogeny estimate that their true age in fact lies between 1918 and 1937. We therefore suggest that the age of the common ancestor of currently available VARV genomes most likely dates to late 16th and early 17th centuries and not ~1350 AD.}, }
@article {pmid28955047, year = {2017}, author = {Doan, K and Zachos, FE and Wilkens, B and Vigne, JD and Piotrowska, N and Stanković, A and Jędrzejewska, B and Stefaniak, K and Niedziałkowska, M}, title = {Erratum: Phylogeography of the Tyrrhenian red deer (Cervus elaphus corsicanus) resolved using ancient DNA of radiocarbon-dated subfossils.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12360}, doi = {10.1038/s41598-017-12272-z}, pmid = {28955047}, issn = {2045-2322}, abstract = {A corarection to this Article has been published and is linked from the HTML version of this paper. The error has not been fixed in the paper.}, }
@article {pmid28945399, year = {2017}, author = {Benner, S}, title = {Uniting Natural History with the Molecular Sciences. The Ultimate Multidisciplinarity.}, journal = {Accounts of chemical research}, volume = {50}, number = {3}, pages = {498-502}, doi = {10.1021/acs.accounts.6b00496}, pmid = {28945399}, issn = {1520-4898}, abstract = {Life and the Earth have coevolved over the past four billion years to deliver a rich diversity of biological structure, from biomolecules to macrophysiology. One grand challenge seeks to interconnect these structures, in ways acceptable to both natural historians and physical scientists, to give an interconnecting web of models and experiments to create a planetary understanding of the phenomenon that we call "life". The molecular scientist wants experiments; the natural historian wants reference to Darwinian fitness. Paleogenetics offers both.}, }
@article {pmid28940759, year = {2017}, author = {Wu, S and Shamimuzzaman, M and Sun, H and Salse, J and Sui, X and Wilder, A and Wu, Z and Levi, A and Xu, Y and Ling, KS and Fei, Z}, title = {The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ring-spot virus resistance locus.}, journal = {The Plant journal : for cell and molecular biology}, volume = {92}, number = {5}, pages = {963-975}, doi = {10.1111/tpj.13722}, pmid = {28940759}, issn = {1365-313X}, mesh = {Biological Evolution ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Cucurbita/*genetics/virology ; Cucurbitaceae/*genetics ; Disease Resistance/*genetics ; Genetic Loci/*genetics ; Genome, Plant/*genetics ; Plant Diseases/virology ; Potyvirus/*metabolism ; }, abstract = {Bottle gourd (Lagenaria siceraria) is an important vegetable crop as well as a rootstock for other cucurbit crops. In this study, we report a high-quality 313.4-Mb genome sequence of a bottle gourd inbred line, USVL1VR-Ls, with a scaffold N50 of 8.7 Mb and the longest of 19.0 Mb. About 98.3% of the assembled scaffolds are anchored to the 11 pseudomolecules. Our comparative genomic analysis identifies chromosome-level syntenic relationships between bottle gourd and other cucurbits, as well as lineage-specific gene family expansions in bottle gourd. We reconstructed the genome of the most recent common ancestor of Cucurbitaceae, which revealed that the ancestral Cucurbitaceae karyotypes consisted of 12 protochromosomes with 18 534 protogenes. The 12 protochromosomes are largely retained in the modern melon genome, while have undergone different degrees of shuffling events in other investigated cucurbit genomes. The 11 bottle gourd chromosomes derive from the ancestral Cucurbitaceae karyotypes followed by 19 chromosomal fissions and 20 fusions. The bottle gourd genome sequence has facilitated the mapping of a dominant monogenic locus, Prs, conferring Papaya ring-spot virus (PRSV) resistance in bottle gourd, to a 317.8-kb region on chromosome 1. We have developed a cleaved amplified polymorphic sequence (CAPS) marker tightly linked to the Prs locus and demonstrated its potential application in marker-assisted selection of PRSV resistance in bottle gourd. This study provides insights into the paleohistory of Cucurbitaceae genome evolution, and the high-quality genome sequence of bottle gourd provides a useful resource for plant comparative genomics studies and cucurbit improvement.}, }
@article {pmid28938123, year = {2017}, author = {Skoglund, P and Thompson, JC and Prendergast, ME and Mittnik, A and Sirak, K and Hajdinjak, M and Salie, T and Rohland, N and Mallick, S and Peltzer, A and Heinze, A and Olalde, I and Ferry, M and Harney, E and Michel, M and Stewardson, K and Cerezo-Román, JI and Chiumia, C and Crowther, A and Gomani-Chindebvu, E and Gidna, AO and Grillo, KM and Helenius, IT and Hellenthal, G and Helm, R and Horton, M and López, S and Mabulla, AZP and Parkington, J and Shipton, C and Thomas, MG and Tibesasa, R and Welling, M and Hayes, VM and Kennett, DJ and Ramesar, R and Meyer, M and Pääbo, S and Patterson, N and Morris, AG and Boivin, N and Pinhasi, R and Krause, J and Reich, D}, title = {Reconstructing Prehistoric African Population Structure.}, journal = {Cell}, volume = {171}, number = {1}, pages = {59-71.e21}, pmid = {28938123}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; 263441/ERC_/European Research Council/International ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; }, mesh = {Africa ; Black People/*genetics ; Bone and Bones/chemistry ; DNA, Ancient/analysis ; Female ; Fossils ; Genetics, Medical ; Genetics, Population ; *Genome, Human ; Genome-Wide Association Study ; Humans ; Life Style ; Male ; }, abstract = {We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.}, }
@article {pmid28935946, year = {2017}, author = {Batini, C and Hallast, P and Vågene, &#xc5;J and Zadik, D and Eriksen, HA and Pamjav, H and Sajantila, A and Wetton, JH and Jobling, MA}, title = {Population resequencing of European mitochondrial genomes highlights sex-bias in Bronze Age demographic expansions.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12086}, pmid = {28935946}, issn = {2045-2322}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Human, Y/genetics ; DNA, Ancient/*analysis/chemistry ; DNA, Mitochondrial/chemistry/*genetics ; Europe ; Female ; Genetics, Population ; Genome, Mitochondrial/*genetics ; Haplotypes ; Humans ; Male ; Middle East ; Mitochondria/genetics ; Phylogeography ; Sequence Analysis, DNA/*methods ; }, abstract = {Interpretations of genetic data concerning the prehistory of Europe have long been a subject of great debate, but increasing amounts of ancient and modern DNA data are now providing new and more informative evidence. Y-chromosome resequencing studies in Europe have highlighted the prevalence of recent expansions of male lineages, and focused interest on the Bronze Age as a period of cultural and demographic change. These findings contrast with phylogeographic studies based on mitochondrial DNA (mtDNA), which have been interpreted as supporting expansions from glacial refugia. Here we have undertaken a population-based resequencing of complete mitochondrial genomes in Europe and the Middle East, in 340 samples from 17 populations for which Y-chromosome sequence data are also available. Demographic reconstructions show no signal of Bronze Age expansion, but evidence of Paleolithic expansions in all populations except the Saami, and with an absence of detectable geographical pattern. In agreement with previous inference from modern and ancient DNA data, the unbiased comparison between the mtDNA and Y-chromosome population datasets emphasizes the sex-biased nature of recent demographic transitions in Europe.}, }
@article {pmid28934125, year = {2017}, author = {Eduardoff, M and Xavier, C and Strobl, C and Casas-Vargas, A and Parson, W}, title = {Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin.}, journal = {Genes}, volume = {8}, number = {10}, pages = {}, pmid = {28934125}, issn = {2073-4425}, abstract = {The analysis of mitochondrial DNA (mtDNA) has proven useful in forensic genetics and ancient DNA (aDNA) studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR) is commonly sequenced using established Sanger-type Sequencing (STS) protocols involving fragment sizes down to approximately 150 base pairs (bp). Recent developments include Massively Parallel Sequencing (MPS) of (multiplex) PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC) methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less), and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples), and tested challenging forensic samples (n = 2) as well as compromised solid tissue samples (n = 15) up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS method for final implementation in forensic genetic laboratories.}, }
@article {pmid28926213, year = {2018}, author = {Lack, JB and Weider, LJ and Jeyasingh, PD}, title = {Whole genome amplification and sequencing of a Daphnia resting egg.}, journal = {Molecular ecology resources}, volume = {18}, number = {1}, pages = {118-127}, doi = {10.1111/1755-0998.12720}, pmid = {28926213}, issn = {1755-0998}, mesh = {Animals ; Daphnia/*genetics ; Genetics, Population/methods ; Nucleic Acid Amplification Techniques/*methods ; Whole Genome Sequencing/*methods ; *Zygote ; }, abstract = {Resting eggs banks are unique windows that allow us to directly observe shifts in population genetics, and phenotypes over time as natural populations evolve. Though a variety of planktonic organisms also produce resting stages, the keystone freshwater consumer, Daphnia, is a well-known model for paleogenetics and resurrection ecology. Nevertheless, paleogenomic investigations are limited largely because resting eggs do not contain enough DNA for genomic sequencing. In fact, genomic studies even on extant populations include a laborious preparatory phase of batch culturing dozens of individuals to generate sufficient genomic DNA. Here, we furnish a protocol to generate whole genomes of single ephippial (resting) eggs and single daphniids. Whole genomes of single ephippial eggs and single adults were amplified using Qiagen REPLI-g Single Cell kit reaction, followed by NEBNext Ultra DNA Library Prep Kit for library construction and Illumina sequencing. We compared the quality of the single-egg and single-individual amplified genomes to the standard batch genomic DNA extraction in the absence of genome amplification. At mean 20× depth, coverage was essentially identical for the amplified single individual relative to the unamplified batch extracted genome (>90% of the genome was covered and callable). Finally, while amplification resulted in the slight loss of heterozygosity for the amplified genomes, estimates were largely comparable and illustrate the utility and limitations of this approach in estimating population genetic parameters over long periods of time in natural populations of Daphnia and also other small species known to produce resting stages.}, }
@article {pmid28890534, year = {2017}, author = {Marciniak, S and Perry, GH}, title = {Harnessing ancient genomes to study the history of human adaptation.}, journal = {Nature reviews. Genetics}, volume = {18}, number = {11}, pages = {659-674}, pmid = {28890534}, issn = {1471-0064}, mesh = {Animals ; *Adaptation, Physiological ; *Biological Evolution ; *Genome, Human ; *Neanderthals/genetics ; Humans ; }, abstract = {The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.}, }
@article {pmid28874531, year = {2017}, author = {Knipper, C and Mittnik, A and Massy, K and Kociumaka, C and Kucukkalipci, I and Maus, M and Wittenborn, F and Metz, SE and Staskiewicz, A and Krause, J and Stockhammer, PW}, title = {Female exogamy and gene pool diversification at the transition from the Final Neolithic to the Early Bronze Age in central Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {38}, pages = {10083-10088}, pmid = {28874531}, issn = {1091-6490}, mesh = {*Anthropology, Cultural ; Europe ; Female ; *Gene Pool ; *Genome, Mitochondrial ; History, Ancient ; Humans ; Male ; }, abstract = {Human mobility has been vigorously debated as a key factor for the spread of bronze technology and profound changes in burial practices as well as material culture in central Europe at the transition from the Neolithic to the Bronze Age. However, the relevance of individual residential changes and their importance among specific age and sex groups are still poorly understood. Here, we present ancient DNA analysis, stable isotope data of oxygen, and radiogenic isotope ratios of strontium for 84 radiocarbon-dated skeletons from seven archaeological sites of the Late Neolithic Bell Beaker Complex and the Early Bronze Age from the Lech River valley in southern Bavaria, Germany. Complete mitochondrial genomes documented a diversification of maternal lineages over time. The isotope ratios disclosed the majority of the females to be nonlocal, while this is the case for only a few males and subadults. Most nonlocal females arrived in the study area as adults, but we do not detect their offspring among the sampled individuals. The striking patterns of patrilocality and female exogamy prevailed over at least 800 y between about 2500 and 1700 BC. The persisting residential rules and even a direct kinship relation across the transition from the Neolithic to the Bronze Age add to the archaeological evidence of continuing traditions from the Bell Beaker Complex to the Early Bronze Age. The results also attest to female mobility as a driving force for regional and supraregional communication and exchange at the dawn of the European metal ages.}, }
@article {pmid28859116, year = {2017}, author = {Alterauge, A and Kellinghaus, M and Jackowski, C and Shved, N and Rühli, F and Maixner, F and Zink, A and Rosendahl, W and Lösch, S}, title = {The Sommersdorf mummies-An interdisciplinary investigation on human remains from a 17th-19th century aristocratic crypt in southern Germany.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0183588}, pmid = {28859116}, issn = {1932-6203}, mesh = {Anthropology ; Archaeology ; DNA, Ancient/*analysis/isolation &amp; purification ; DNA, Mitochondrial/*analysis/genetics ; *Fossils ; Germany ; Humans ; *Mummies ; }, abstract = {Sommersdorf Castle (Bavaria, Germany) is a medieval castle complex which has been inhabited by the aristocratic family von Crailsheim. The deceased were entombed in a crypt located in the parapets underneath the castle's church, resulting in mummification of the bodies. Based on the family chronicle and oral history, identities have been ascribed to the mummies. The aim of the study is therefore to test the accuracy of the historical records in comparison to archaeological, anthropological and genetic data. Today, the crypt houses eleven wooden coffins from the 17th to 19th century AD. In ten of these, mummified and scattered human remains were found. Archive records were studied in order to identify names, ancestry, titles, occupation, date of birth and death, and place of interment of the individuals. The coffins were visually inspected and dated by typo-chronology, and the mummified and scattered skeletal remains were subjected to a physical anthropological examination. In total, the crypt contains the remains of a minimum number of nine individuals, among them three adult males, five adult females and one infant. A detailed scientific examination, including prior conservation, ancient DNA analyses, and computed tomography (CT), was performed on five mummies. By means of the CT data age at death, sex, body height, pathologies, and anatomical variants were investigated. CT analysis further showed that the bodies were naturally mummified. Mitochondrial DNA analyses revealed that the tested individuals are not maternally related. In addition, health, living conditions and circumstances of death of the entombed individuals could be highlighted. Being confronted with the strengths, weaknesses and limitations of each methodological approach, probable identification was achieved in two cases.}, }
@article {pmid28854615, year = {2017}, author = {Mak, SST and Gopalakrishnan, S and Carøe, C and Geng, C and Liu, S and Sinding, MS and Kuderna, LFK and Zhang, W and Fu, S and Vieira, FG and Germonpré, M and Bocherens, H and Fedorov, S and Petersen, B and Sicheritz-Pontén, T and Marques-Bonet, T and Zhang, G and Jiang, H and Gilbert, MTP}, title = {Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.}, journal = {GigaScience}, volume = {6}, number = {8}, pages = {1-13}, pmid = {28854615}, issn = {2047-217X}, support = {681396/ERC_/European Research Council/International ; U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Base Composition ; DNA/chemistry ; DNA, Mitochondrial/chemistry ; Genomics/*methods/*standards ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction-amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.}, }
@article {pmid28836000, year = {2017}, author = {Zhou, B and Wen, S and Wang, L and Jin, L and Li, H and Zhang, H}, title = {AntCaller: an accurate variant caller incorporating ancient DNA damage.}, journal = {Molecular genetics and genomics : MGG}, volume = {292}, number = {6}, pages = {1419-1430}, pmid = {28836000}, issn = {1617-4623}, mesh = {Animals ; *DNA Damage ; *DNA, Ancient ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Neanderthals ; Ploidies ; Postmortem Changes ; }, abstract = {Ancient DNA obtained from ancient samples, such as sediments, bones, and teeth, is an important genetic resource that can be used to reconstruct an evolutional history of humans, animals, and plants. The application of high-throughput sequencing enables the research of ancient DNA to be conducted in a whole genome scale. However, post-mortem DNA damage mainly caused by deamination of cytosine to uracil (or methylated cytosine to thymine) may confound the variant calling and downstream analysis. In this article, we develop a Python program to implement a new variant caller, "AntCaller", which extracts the information on nucleotide substitutions from sequencing data and calculates the probability of each genotype based on a Bayesian rule. Through both simulation studies and real data analyses, it was shown that our method reduced the false discovery rate caused by nucleotide misincorporations and outperformed two mainstream variant callers (i.e., GATK and SAMtools) in terms of calling accuracy. In a real application with serious DNA damage, AntCaller still outperformed GATK and SAMtools combined with quality score recalling.}, }
@article {pmid28817590, year = {2017}, author = {Prendergast, ME and Buckley, M and Crowther, A and Frantz, L and Eager, H and Lebrasseur, O and Hutterer, R and Hulme-Beaman, A and Van Neer, W and Douka, K and Veall, MA and Quintana Morales, EM and Schuenemann, VJ and Reiter, E and Allen, R and Dimopoulos, EA and Helm, RM and Shipton, C and Mwebi, O and Denys, C and Horton, M and Wynne-Jones, S and Fleisher, J and Radimilahy, C and Wright, H and Searle, JB and Krause, J and Larson, G and Boivin, NL}, title = {Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182565}, pmid = {28817590}, issn = {1932-6203}, support = {337574/ERC_/European Research Council/International ; }, mesh = {Africa ; Animals ; Animals, Domestic/genetics ; Archaeology ; Asia ; Chickens ; Collagen/analysis/genetics ; DNA Fingerprinting ; History, Ancient ; Introduced Species/*history ; Radiometric Dating ; Rats ; }, abstract = {Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.}, }
@article {pmid28815959, year = {2017}, author = {Bermúdez de Castro, JM and Martinón-Torres, M and Arsuaga, JL and Carbonell, E}, title = {Twentieth anniversary of Homo antecessor (1997-2017): a review.}, journal = {Evolutionary anthropology}, volume = {26}, number = {4}, pages = {157-171}, doi = {10.1002/evan.21540}, pmid = {28815959}, issn = {1520-6505}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; *Fossils ; Hominidae/*anatomy &amp; histology ; Humans ; Neanderthals ; Spain ; }, abstract = {It has been twenty years since diagnosis and publication of the species Homo antecessor.[1] Since then, new human fossils recovered from the TD6 level of the Gran Dolina site (Sierra de Atapuerca, northern Spain) have helped to refine its taxonomic and phylogenetic position. In this paper, we present a synthesis of the most characteristic features of this species, as well as our interpretation derived from the latest investigations. We focus on the phylogenetic interpretation of Homo antecessor, taking into account the most recent paleogenetic analyses and a reassessment of the European Middle Pleistocene hominin record. We try to show that, twenty years after its publication, H. antecessor provides a good opportunity to address the morphology of the last common ancestor of Neandertals and modern humans.}, }
@article {pmid28813480, year = {2017}, author = {Shin, DH and Oh, CS and Hong, JH and Kim, Y and Lee, SD and Lee, E}, title = {Paleogenetic study on the 17th century Korean mummy with atherosclerotic cardiovascular disease.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0183098}, pmid = {28813480}, issn = {1932-6203}, mesh = {Atherosclerosis/*genetics ; Cardiovascular Diseases/*genetics ; Female ; *Genetic Predisposition to Disease ; Genotype ; History, 17th Century ; Humans ; *Mummies ; Polymorphism, Single Nucleotide ; Republic of Korea ; }, abstract = {While atherosclerotic cardiovascular disease (ASCVD) is known to be common among modern people exposed to various risk factors, recent paleopathological studies have shown that it affected ancient populations much more frequently than expected. In 2010, we investigated a 17th century Korean female mummy with presumptive ASCVD signs. Although the resulting report was a rare and invaluable conjecture on the disease status of an ancient East Asian population, the diagnosis had been based only on anatomical and radiological techniques, and so could not confirm the existence of ASCVD in the mummy. In the present study, we thus performed a paleogenetic analysis to supplement the previous conventional diagnosis of ASCVD. In aDNA extracted from the same Korean mummy, we identified the risk alleles of seven different SNPs (rs5351, rs10757274, rs2383206, rs2383207, rs10757278, rs4380028 and rs1333049) that had already been revealed to be the major risk loci of ASCVD in East Asian populations. The reliability of this study could be enhanced by cross-validation using two different analyses: Sanger and SNaPshot techniques. We were able to establish that the 17th century Korean female had a strong genetic predisposition to increased risk of ASCVD. The current paleogenetic diagnosis, the first of its kind outside Europe, re-confirms its utility as an adjunct modality for confirmatory diagnosis of ancient ASCVD.}, }
@article {pmid28803756, year = {2017}, author = {Rawlence, NJ and Till, CE and Easton, LJ and Spencer, HG and Schuckard, R and Melville, DS and Scofield, RP and Tennyson, AJD and Rayner, MJ and Waters, JM and Kennedy, M}, title = {Speciation, range contraction and extinction in the endemic New Zealand King Shag complex.}, journal = {Molecular phylogenetics and evolution}, volume = {115}, number = {}, pages = {197-209}, doi = {10.1016/j.ympev.2017.07.011}, pmid = {28803756}, issn = {1095-9513}, mesh = {Animals ; Birds/*classification/genetics ; Bone and Bones/anatomy &amp; histology ; Cytochromes b/classification/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Discriminant Analysis ; Extinction, Biological ; Fossils/anatomy &amp; histology ; New Zealand ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA ; }, abstract = {New Zealand's endemic King Shag (Leucocarbo carunculatus) has occupied only a narrow portion of the northeastern South Island for at least the past 240years. However, pre-human Holocene fossil and archaeological remains have suggested a far more widespread distribution of the three Leucocarbo species (King, Otago, Foveaux) on mainland New Zealand at the time of Polynesian settlement in the late 13th Century CE. We use modern and ancient DNA, and morphometric and osteological analyses, of modern King Shags and Holocene fossil Leucocarbo remains to assess the pre-human distribution and taxonomic status of the King Shag on mainland New Zealand, and the resultant conservation implications. Our analyses show that the King Shag was formerly widespread around southern coasts of the North Island and the northern parts of the South Island but experienced population and lineage extinctions, and range contraction, probably after Polynesian arrival. This history parallels range contractions of other New Zealand seabirds. Conservation management of the King Shag should take into account this species narrow distribution and probable reduced genetic diversity. Moreover, combined genetic, morphometric and osteological analyses of prehistoric material from mainland New Zealand suggest that the now extinct northern New Zealand Leucocarbo populations comprised a unique lineage. Although these distinctive populations were previously assigned to the King Shag (based on morphological similarities and geographic proximity to modern Leucocarbo populations), we herein describe them as a new species, the Kohatu Shag (Leucocarbo septentrionalis). The extinction of this species further highlights the dramatic impacts Polynesians and introduced predators had on New Zealand's coastal and marine biodiversity. The prehistoric presence of at least four species of Leucocarbo shag on mainland NZ further highlights its status as a biodiversity hotspot for Phalacrocoracidae.}, }
@article {pmid28799621, year = {2017}, author = {Płoszaj, T and Jędrychowska-Dańska, K and Zamerska, A and Drozd-Lipińska, A and Poliński, D and Janowski, A and Witas, H}, title = {Ancient DNA analysis might suggest external origin of individuals from chamber graves placed in medieval cemetery in Pień, Central Poland.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {74}, number = {4}, pages = {319-337}, doi = {10.1127/anthranz/2017/0727}, pmid = {28799621}, issn = {0003-5548}, mesh = {Adult ; Archaeology ; Cemeteries/*history ; Child ; DNA, Ancient/*analysis ; Genetics, Population ; Haplotypes/genetics ; History, Medieval ; Human Migration/*history ; Humans ; Poland ; Scandinavian and Nordic Countries ; White People/*genetics ; }, abstract = {The participation of immigrants during early days in Poland of Piast's dynasty is a debated issue among archaeologists and anthropologists alike. Such hypotheses were formulated on the basis of, amongst others, the discovery of early medieval chamber graves characterized by construction features typical of the Scandinavian culture area. Archaeological and anthropological studies to date have not provided an unequivocal answer as to whether the individuals interred in those graves were autochthons who adopted a different burial rite, or perhaps immigrants from foreign lands. To characterize the gene pool of this population we analyzed the C/T allele of the nuclear gene LCT-13910 as well as fragments of the mitochondrial genome from individuals buried in very richly furnished chamber graves at the medieval cemetery in Pień. The obtained results for the nuclear allele and mtDNA do not corroborate the Scandinavian origin of the analyzed population. Moreover, we did not find haplogroup I, which is the one typical of populations that historically inhabited the north of Europe; and the frequency of the LCT-13910 T allele was similar to that of past and present Polish populations. On the other hand, we identified the atypical haplogroup C5c1, which suggests Asian origin of the studied individuals and confirms our previous reports concerning ancient human migrations from Asia to the territory of present-day Poland. While our findings do not conclusively disprove a Scandinavian lineage of the studied population, they certainly shed some new light on the origin of the individuals buried in chamber graves, which may be very different from the one initially proposed by archaeologists.}, }
@article {pmid28798742, year = {2017}, author = {Vuillemin, A and Horn, F and Alawi, M and Henny, C and Wagner, D and Crowe, SA and Kallmeyer, J}, title = {Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1440}, pmid = {28798742}, issn = {1664-302X}, abstract = {Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia. We applied 16S rRNA gene Illumina sequencing on both fractions to discriminate exogenous from endogenous sources of extracellular DNA in the sediment. Environmental sequences exclusively found as extracellular DNA in the sediment originated from multiple sources. For instance, Actinobacteria, Verrucomicrobia, and Acidobacteria derived from soils in the catchment. Limited primary productivity in the water column resulted in few sequences of Cyanobacteria in the oxic photic zone, whereas stratification of the water body mainly led to secondary production by aerobic and anaerobic heterotrophs. Chloroflexi and Planctomycetes, the main degraders of sinking organic matter and planktonic sequences at the water-sediment interface, were preferentially preserved during the initial phase of burial. To trace endogenous sources of extracellular DNA, we used relative abundances of taxa in the intracellular DNA to define which microbial populations grow, decline or persist at low density with sediment depth. Cell lysis became an important additional source of extracellular DNA, gradually covering previous genetic assemblages as other microbial genera became more abundant with depth. The use of extracellular DNA as nutrient by active microorganisms led to selective removal of sequences with lowest GC contents. We conclude that extracellular DNA preserved in shallow lacustrine sediments reflects the initial environmental context, but is gradually modified and thereby shifts from its stratigraphic context. Discrimination of exogenous and endogenous sources of extracellular DNA allows simultaneously addressing in-lake and post-depositional processes. In deeper sediments, the accumulation of resting stages and sequences from cell lysis would require stringent extraction and specific primers if ancient DNA is targeted.}, }
@article {pmid28796208, year = {2017}, author = {Makarewicz, C and Marom, N and Bar-Oz, G}, title = {Palaeobiology: Ensure equal access to ancient DNA.}, journal = {Nature}, volume = {548}, number = {7666}, pages = {158}, pmid = {28796208}, issn = {1476-4687}, mesh = {*DNA ; *DNA, Ancient ; Fossils ; Humans ; Sequence Analysis, DNA ; }, }
@article {pmid28784790, year = {2017}, author = {Star, B and Boessenkool, S and Gondek, AT and Nikulina, EA and Hufthammer, AK and Pampoulie, C and Knutsen, H and André, C and Nistelberger, HM and Dierking, J and Petereit, C and Heinrich, D and Jakobsen, KS and Stenseth, NC and Jentoft, S and Barrett, JH}, title = {Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {34}, pages = {9152-9157}, pmid = {28784790}, issn = {1091-6490}, mesh = {Animals ; Arctic Regions ; Atlantic Ocean ; Bone and Bones/metabolism ; DNA, Ancient/*analysis/isolation &amp; purification ; *Ecosystem ; Fisheries/*history ; Fossils ; Gadus morhua/*genetics ; Geography ; Germany ; History, Medieval ; Norway ; United Kingdom ; }, abstract = {Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.}, }
@article {pmid28778150, year = {2017}, author = {Chintalapati, M and Dannemann, M and Prüfer, K}, title = {Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {179}, pmid = {28778150}, issn = {1471-2148}, mesh = {Animals ; *Evolution, Molecular ; Gene Frequency/genetics ; Gene Ontology ; *Genome ; Genome-Wide Association Study ; Humans ; INDEL Mutation/*genetics ; Neanderthals/*genetics ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Primates/genetics ; }, abstract = {BACKGROUND: Small insertions and deletions occur in humans at a lower rate compared to nucleotide changes, but evolve under more constraint than nucleotide changes. While the evolution of insertions and deletions have been investigated using ape outgroups, the now available genome of a Neandertal can shed light on the evolution of indels in more recent times.<br><br>RESULTS: We used the Neandertal genome together with several primate outgroup genomes to differentiate between human insertion/deletion changes that likely occurred before the split from Neandertals and those that likely arose later. Changes that pre-date the split from Neandertals show a smaller proportion of deletions than those that occurred later. The presence of a Neandertal-shared allele in Europeans or Asians but the absence in Africans was used to detect putatively introgressed indels in Europeans and Asians. A larger proportion of these variants reside in intergenic regions compared to other modern human variants, and some variants are linked to SNPs that have been associated with traits in modern humans.<br><br>CONCLUSIONS: Our results are in agreement with earlier results that suggested that deletions evolve under more constraint than insertions. When considering Neandertal introgressed variants, we find some evidence that negative selection affected these variants more than other variants segregating in modern humans. Among introgressed variants we also identify indels that may influence the phenotype of their carriers. In particular an introgressed deletion associated with a decrease in the time to menarche may constitute an example of a former Neandertal-specific trait contributing to modern human phenotypic diversity.}, }
@article {pmid28753598, year = {2017}, author = {Marx, V}, title = {Genetics: new tales from ancient DNA.}, journal = {Nature methods}, volume = {14}, number = {8}, pages = {771-774}, pmid = {28753598}, issn = {1548-7105}, mesh = {DNA, Ancient/*isolation &amp; purification ; Fossils ; *Genetics, Population/history/methods ; *Genome, Human ; History, Ancient ; Humans ; }, }
@article {pmid28747476, year = {2017}, author = {Rawlence, NJ and Kardamaki, A and Easton, LJ and Tennyson, AJD and Scofield, RP and Waters, JM}, title = {Ancient DNA and morphometric analysis reveal extinction and replacement of New Zealand's unique black swans.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1859}, pages = {}, pmid = {28747476}, issn = {1471-2954}, mesh = {Animals ; Anseriformes/*classification ; Australia ; *DNA, Ancient ; *Extinction, Biological ; Humans ; Islands ; New Zealand ; }, abstract = {Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans (Cygnus atratus) including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage (C. sumnerensis, Poūwa), divergent from modern (Australian) C. atratus Morphological analyses indicate C. sumnerensis exhibited classic signs of the 'island rule' effect, being larger, and likely flight-reduced compared to C. atratus Our research reveals sudden extinction and replacement events within this anatid species complex, coinciding with recent human colonization of New Zealand. This research highlights the role of anthropogenic processes in rapidly reshaping island ecosystems and raises new questions for avian conservation, ecosystem re-wilding, and de-extinction.}, }
@article {pmid28737475, year = {2017}, author = {Hong, JH and Oh, CS and Seo, M and Chai, JY and Shin, DH}, title = {Ancient Ascaris DNA Sequences of Cytochrome B, Cytochrome C Oxidase Subunit 1, NADH Dehydrogenase Subunit 1, and Internal Transcribed Spacer 1 Genes from Korean Joseon Mummy Feces.}, journal = {The Journal of parasitology}, volume = {103}, number = {6}, pages = {795-800}, doi = {10.1645/16-102}, pmid = {28737475}, issn = {1937-2345}, mesh = {Animals ; Ascaris/classification/enzymology/*genetics ; Base Sequence ; Consensus Sequence ; Cytochromes b/genetics/history ; DNA, Intergenic/genetics/history ; Electron Transport Complex IV/genetics/history ; Feces/*parasitology ; Female ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; Humans ; Korea ; Likelihood Functions ; Male ; Mummies/history/*parasitology ; NADH Dehydrogenase/genetics/history ; Pelvic Bones/parasitology ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; }, abstract = {We analyzed Ascaris ancient DNA of cytochrome b, cytochrome c oxidase subunit 1, NADH dehydrogenase subunit 1, and internal transcribed spacer 1 genes extracted from the feces or precipitates of 15- to 18th-century Korean mummies. After multiple Ascaris genes in ancient samples were successfully amplified by polymerase chain reaction (PCR), consensus sequences could be determined by the alignment of the sequences of cloned PCR products. The obtained sequences of each gene were highly similar to those of Ascaris spp. reported thus far but were genetically distinct from Baylisascaris, Parascaris, and Toxascaris spp. The current report establishes that the genetic characteristics of the Ascaris spp. infecting pre-modern Korean societies were not uniform but were diverse to some degree.}, }
@article {pmid28725674, year = {2017}, author = {Pucu, E and Cascardo, P and Chame, M and Felice, G and Guidon, N and Cleonice Vergne, M and Campos, G and Roberto Machado-Silva, J and Leles, D}, title = {Study of infectious diseases in archaeological bone material - A dataset.}, journal = {Data in brief}, volume = {13}, number = {}, pages = {692-695}, pmid = {28725674}, issn = {2352-3409}, abstract = {Bones of human and ground sloth remains were analyzed for presence of Trypanosoma cruzi by conventional PCR using primers TC, TC1 and TC2. Sequence results amplified a fragment with the same product size as the primers (300 and 350pb). Amplified PCR product was sequenced and analyzed on GenBank, using Blast. Although these sequences did not match with these parasites they showed high amplification with species of bacteria. This article presents the methodology used and the alignment of the sequences. The display of this dataset will allow further analysis of our results and discussion presented in the manuscript "Finding the unexpected: a critical view on molecular diagnosis of infectious diseases in archaeological samples" (Pucu et al. 2017) [1].}, }
@article {pmid28718817, year = {2017}, author = {Grealy, A and Rawlence, NJ and Bunce, M}, title = {Time to Spread Your Wings: A Review of the Avian Ancient DNA Field.}, journal = {Genes}, volume = {8}, number = {7}, pages = {}, pmid = {28718817}, issn = {2073-4425}, abstract = {Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of "avian ancient DNA" by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100-1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.}, }
@article {pmid28715914, year = {2017}, author = {Rubini, M and Zaio, P and Spigelman, M and Donoghue, HD}, title = {Leprosy in a Lombard-Avar cemetery in central Italy (Campochiaro, Molise, 6th-8th century AD): ancient DNA evidence and demography.}, journal = {Annals of human biology}, volume = {44}, number = {6}, pages = {510-521}, doi = {10.1080/03014460.2017.1346709}, pmid = {28715914}, issn = {1464-5033}, mesh = {Cemeteries ; DNA, Ancient/*analysis/isolation &amp; purification ; Demography ; History, Medieval ; Humans ; Italy ; Leprosy/*history/microbiology ; Mycobacterium leprae/genetics/*isolation &amp; purification ; Paleopathology ; }, abstract = {BACKGROUND: The study of past infectious diseases increases knowledge of the presence, impact and spread of pathogens within ancient populations.<br><br>AIM: Polymerase chain reaction (PCR) was used to examine bones for the presence of Mycobacterium leprae ancient DNA (aDNA) as, even when leprosy is present, bony changes are not always pathognomonic of the disease. This study also examined the demographic profile of this population and compared it with two other populations to investigate any changes in mortality trends between different infectious diseases and between the pre-antibiotic and antibiotic eras.<br><br>SUBJECTS AND METHODS: The individuals were from a site in Central Italy (6th-8th CE) and were examined for the presence of Mycobacterium leprae aDNA. In addition, an abridged life mortality table was constructed.<br><br>RESULTS: Two individuals had typical leprosy palaeopathology, and one was positive for Mycobacterium leprae aDNA. However, the demographic profile shows a mortality curve similar to that of the standard, in contrast to a population that had been subjected to bubonic plague.<br><br>CONCLUSIONS: This study shows that, in the historical population with leprosy, the risk factors for health seem to be constant and distributed across all age classes, similar to what is found today in the antibiotic era. There were no peaks of mortality equivalent to those found in fatal diseases such as the plague, probably due to the long clinical course of leprosy.}, }
@article {pmid28712569, year = {2017}, author = {Saag, L and Varul, L and Scheib, CL and Stenderup, J and Allentoft, ME and Saag, L and Pagani, L and Reidla, M and Tambets, K and Metspalu, E and Kriiska, A and Willerslev, E and Kivisild, T and Metspalu, M}, title = {Extensive Farming in Estonia Started through a Sex-Biased Migration from the Steppe.}, journal = {Current biology : CB}, volume = {27}, number = {14}, pages = {2185-2193.e6}, doi = {10.1016/j.cub.2017.06.022}, pmid = {28712569}, issn = {1879-0445}, mesh = {Agriculture/*history ; Chromosomes, Human, X/genetics ; Chromosomes, Human, Y/genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/chemistry ; Estonia ; Genome, Human/*genetics ; History, Ancient ; *Human Migration ; Humans ; }, abstract = {The transition from hunting and gathering to farming in Europe was brought upon by arrival of new people carrying novel material culture and genetic ancestry. The exact nature and scale of the transition-both material and genetic-varied in different parts of Europe [1-7]. Farming-based economies appear relatively late in Northeast Europe, and the extent to which they involve change in genetic ancestry is not fully understood due to the lack of relevant ancient DNA data. Here we present the results from new low-coverage whole-genome shotgun sequence data from five hunter-gatherers and five first farmers of Estonia whose remains date to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X chromosome, and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic culture are closest to Eastern hunter-gatherers, which is in contrast to earlier hunter-gatherers from the Baltics, who are close to Western hunter-gatherers [8, 9]. The Estonian first farmers of Corded Ware culture show high similarity in their autosomes with European hunter-gatherers, Steppe Eneolithic and Bronze Age populations, and European Late Neolithic/Bronze Age populations, while their X chromosomes are in addition equally closely related to European and Anatolian and Levantine early farmers. These findings suggest that the shift to intensive cultivation and animal husbandry in Estonia was triggered by the arrival of new people with predominantly Steppe ancestry but whose ancestors had undergone sex-specific admixture with early farmers with Anatolian ancestry.}, }
@article {pmid28710361, year = {2017}, author = {Kupczik, K and Cagan, A and Brauer, S and Fischer, MS}, title = {The dental phenotype of hairless dogs with FOXI3 haploinsufficiency.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5459}, pmid = {28710361}, issn = {2045-2322}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bicuspid/*anatomy &amp; histology/diagnostic imaging ; Cuspid/*anatomy &amp; histology/diagnostic imaging ; Dentition, Permanent ; Dogs ; *Exons ; Female ; Forkhead Transcription Factors/*genetics ; Fossils ; Gene Expression ; Hair/abnormalities ; Incisor/*anatomy &amp; histology/diagnostic imaging ; Male ; Mandible/anatomy &amp; histology/diagnostic imaging ; Maxilla/anatomy &amp; histology/diagnostic imaging ; Molar/*anatomy &amp; histology/diagnostic imaging ; Mutagenesis, Insertional ; Phenotype ; Tomography, X-Ray Computed ; Tooth, Deciduous/anatomy &amp; histology/diagnostic imaging ; }, abstract = {Hairless dog breeds show a form of ectodermal dysplasia characterised by a lack of hair and abnormal tooth morphology. This has been attributed to a semi-dominant 7-base-pair duplication in the first exon of the forkhead box I3 gene (FOXI3) shared by all three breeds. Here, we identified this FOXI3 variant in a historical museum sample of pedigreed hairless dog skulls by using ancient DNA extraction and present the associated dental phenotype. Unlike in the coated wild type dogs, the hairless dogs were characterised in both the mandibular and maxillary dentition by a loss of the permanent canines, premolars and to some extent incisors. In addition, the deciduous fourth premolars and permanent first and second molars consistently lacked the distal and lingual cusps; this resulted in only a single enlarged cusp in the basin-like heel (talonid in lower molars, talon in upper molars). This molar phenotype is also found among several living and fossil carnivorans and the extinct order Creodonta in which it is associated with hypercarnivory. We therefore suggest that FOXI3 may generally be involved in dental (cusp) development within and across mammalian lineages including the hominids which are known to exhibit marked variability in the presence of lingual cusps.}, }
@article {pmid28703741, year = {2017}, author = {Green, EJ and Speller, CF}, title = {Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles.}, journal = {Genes}, volume = {8}, number = {7}, pages = {}, pmid = {28703741}, issn = {2073-4425}, abstract = {Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.}, }
@article {pmid28703210, year = {2017}, author = {Callaway, E}, title = {Ancient-genome studies grapple with Africa's past.}, journal = {Nature}, volume = {547}, number = {7662}, pages = {149}, doi = {10.1038/nature.2017.22272}, pmid = {28703210}, issn = {1476-4687}, mesh = {Africa/ethnology ; DNA, Ancient/*analysis ; Genome, Human/*genetics ; History, Ancient ; Human Migration/*history ; Humans ; Male ; }, }
@article {pmid28690805, year = {2017}, author = {Linck, EB and Hanna, ZR and Sellas, A and Dumbacher, JP}, title = {Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens.}, journal = {Ecology and evolution}, volume = {7}, number = {13}, pages = {4755-4767}, pmid = {28690805}, issn = {2045-7758}, support = {S10 OD018174/OD/NIH HHS/United States ; }, abstract = {Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site-associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens. The hyRAD method employs fragments produced in a restriction site-associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here, we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affect sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.}, }
@article {pmid28688671, year = {2017}, author = {Key, FM and Posth, C and Krause, J and Herbig, A and Bos, KI}, title = {Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication.}, journal = {Trends in genetics : TIG}, volume = {33}, number = {8}, pages = {508-520}, doi = {10.1016/j.tig.2017.05.005}, pmid = {28688671}, issn = {0168-9525}, mesh = {*DNA, Ancient ; *Data Mining ; *Datasets as Topic ; High-Throughput Nucleotide Sequencing/methods ; *Metagenome ; }, abstract = {While a comparatively young area of research, investigations relying on ancient DNA data have been highly valuable in revealing snapshots of genetic variation in both the recent and the not-so-recent past. Born out of a tradition of single-locus PCR-based approaches that often target individual species, stringent criteria for both data acquisition and analysis were introduced early to establish high standards of data quality. Today, the immense volume of data made available through next-generation sequencing has significantly increased the analytical resolution offered by processing ancient tissues and permits parallel analyses of host and microbial communities. The adoption of this new approach to data acquisition, however, requires an accompanying update on methods of DNA authentication, especially given that ancient molecules are expected to exist in low proportions in archaeological material, where an environmental signal is likely to dominate. In this review, we provide a summary of recent data authentication approaches that have been successfully used to distinguish between endogenous and nonendogenous DNA sequences in metagenomic data sets. While our discussion mostly centers on the detection of ancient human and ancient bacterial pathogen DNA, their applicability is far wider.}, }
@article {pmid28681914, year = {2017}, author = {Viganó, C and Haas, C and Rühli, FJ and Bouwman, A}, title = {2,000 Year old β-thalassemia case in Sardinia suggests malaria was endemic by the Roman period.}, journal = {American journal of physical anthropology}, volume = {164}, number = {2}, pages = {362-370}, doi = {10.1002/ajpa.23278}, pmid = {28681914}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/analysis/genetics ; Endemic Diseases/history ; Female ; Haplotypes/genetics ; History, Ancient ; Humans ; Italy ; Malaria/history ; Male ; Mutation/genetics ; beta-Globins/*genetics ; beta-Thalassemia/*genetics/*history ; }, abstract = {OBJECTIVES: The island of Sardinia has one of the highest incidence rates of β-thalassemia in Europe due to its long history of endemic malaria, which, according to historical records, was introduced around 2,600 years ago by the Punics and only became endemic around the Middle Ages. In particular, the cod39 mutation is responsible for more than 95% of all β-thalassemia cases observed on the island. Debates surround the origin of the mutation. Some argue that its presence in the Western Mediterranean reflects the migration of people away from Sardinia, others that it reflects the colonization of the island by the Punics who might have carried the disease allele. The aim of this study was to investigate β-globin mutations, including cod39, using ancient DNA (aDNA) analysis, to better understand the history and origin of β-thalassemia and malaria in Sardinia.<br><br>MATERIALS AND METHODS: PCR analysis followed by sequencing were used to investigate the presence of &#x3b2;-thalassemia mutations in 19 individuals from three different Roman and Punic necropolises in Sardinia.<br><br>RESULTS: The cod39 mutation was identified in one male individual buried in a necropolis from the Punic/Roman period. Further analyses have shown that his mitochondrial DNA (mtDNA) and Y-chromosome haplogroups were U5a and I2a1a1, respectively, indicating the individual was probably of Sardinian origin.<br><br>CONCLUSIONS: This is the earliest documented case of &#x3b2;-thalassemia in Sardinia to date. The presence of such a pathogenic mutation and its persistence until present day indicates that malaria was likely endemic on the island by the Roman period, earlier than the historical sources suggest.}, }
@article {pmid28680441, year = {2017}, author = {Das, R and Wexler, P and Pirooznia, M and Elhaik, E}, title = {The Origins of Ashkenaz, Ashkenazic Jews, and Yiddish.}, journal = {Frontiers in genetics}, volume = {8}, number = {}, pages = {87}, pmid = {28680441}, issn = {1664-8021}, support = {MC_PC_14115/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Recently, the geographical origins of Ashkenazic Jews (AJs) and their native language Yiddish were investigated by applying the Geographic Population Structure (GPS) to a cohort of exclusively Yiddish-speaking and multilingual AJs. GPS localized most AJs along major ancient trade routes in northeastern Turkey adjacent to primeval villages with names that resemble the word "Ashkenaz." These findings were compatible with the hypothesis of an Irano-Turko-Slavic origin for AJs and a Slavic origin for Yiddish and at odds with the Rhineland hypothesis advocating a Levantine origin for AJs and German origins for Yiddish. We discuss how these findings advance three ongoing debates concerning (1) the historical meaning of the term "Ashkenaz;" (2) the genetic structure of AJs and their geographical origins as inferred from multiple studies employing both modern and ancient DNA and original ancient DNA analyses; and (3) the development of Yiddish. We provide additional validation to the non-Levantine origin of AJs using ancient DNA from the Near East and the Levant. Due to the rising popularity of geo-localization tools to address questions of origin, we briefly discuss the advantages and limitations of popular tools with focus on the GPS approach. Our results reinforce the non-Levantine origins of AJs.}, }
@article {pmid28678860, year = {2017}, author = {Beau, A and Rivollat, M and Réveillas, H and Pemonge, MH and Mendisco, F and Thomas, Y and Lefranc, P and Deguilloux, MF}, title = {Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0179742}, pmid = {28678860}, issn = {1932-6203}, mesh = {Burial ; *Ceremonial Behavior ; Chromosomes, Human, Y/genetics ; DNA, Ancient/*isolation &amp; purification ; DNA, Mitochondrial/genetics/isolation &amp; purification ; Farmers ; Female ; France ; Human Migration ; Humans ; Male ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in "non-conventional" positions (deposited in the pits without any particular treatment). If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace). At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses) permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i) the occidental origin of the Michelsberg groups and (ii) the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution.}, }
@article {pmid28675384, year = {2017}, author = {Posth, C and Wißing, C and Kitagawa, K and Pagani, L and van Holstein, L and Racimo, F and Wehrberger, K and Conard, NJ and Kind, CJ and Bocherens, H and Krause, J}, title = {Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {16046}, pmid = {28675384}, issn = {2041-1723}, mesh = {Animals ; Black People/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Femur ; *Gene Flow ; Genome, Human/genetics ; *Genome, Mitochondrial ; Germany ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; Time Factors ; }, abstract = {Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein-Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.}, }
@article {pmid28669760, year = {2017}, author = {Margaryan, A and Derenko, M and Hovhannisyan, H and Malyarchuk, B and Heller, R and Khachatryan, Z and Avetisyan, P and Badalyan, R and Bobokhyan, A and Melikyan, V and Sargsyan, G and Piliposyan, A and Simonyan, H and Mkrtchyan, R and Denisova, G and Yepiskoposyan, L and Willerslev, E and Allentoft, ME}, title = {Eight Millennia of Matrilineal Genetic Continuity in the South Caucasus.}, journal = {Current biology : CB}, volume = {27}, number = {13}, pages = {2023-2028.e7}, doi = {10.1016/j.cub.2017.05.087}, pmid = {28669760}, issn = {1879-0445}, mesh = {Archaeology ; Armenia ; Azerbaijan ; Bayes Theorem ; DNA, Ancient/analysis ; *Gene Pool ; *Genetic Variation ; *Genome, Human ; *Genome, Mitochondrial ; Human Migration ; Humans ; }, abstract = {The South Caucasus, situated between the Black and Caspian Seas, geographically links Europe with the Near East and has served as a crossroad for human migrations for many millennia [1-7]. Despite a vast archaeological record showing distinct cultural turnovers, the demographic events that shaped the human populations of this region is not known [8, 9]. To shed light on the maternal genetic history of the region, we analyzed the complete mitochondrial genomes of 52 ancient skeletons from present-day Armenia and Artsakh spanning 7,800 years and combined this dataset with 206 mitochondrial genomes of modern Armenians. We also included previously published data of seven neighboring populations (n = 482). Coalescence-based analyses suggest that the population size in this region rapidly increased after the Last Glacial Maximum ca. 18 kya. We find that the lowest genetic distance in this dataset is between modern Armenians and the ancient individuals, as also reflected in both network analyses and discriminant analysis of principal components. We used approximate Bayesian computation to test five different demographic scenarios explaining the formation of the modern Armenian gene pool. Despite well documented cultural shifts in the South Caucasus across this time period, our results strongly favor a genetic continuity model in the maternal gene pool. This has implications for interpreting prehistoric migration dynamics and cultural shifts in this part of the world.}, }
@article {pmid28662199, year = {2017}, author = {Chen, S and Zheng, H and Kishima, Y}, title = {Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences.}, journal = {PLoS pathogens}, volume = {13}, number = {6}, pages = {e1006413}, pmid = {28662199}, issn = {1553-7374}, mesh = {Adaptation, Biological ; Endogenous Retroviruses/classification/genetics/isolation &amp; purification/physiology ; Evolution, Molecular ; Fossils/*virology ; Genome, Viral ; Genomics ; Phylogeny ; Plant Diseases/*virology ; Poaceae/*virology ; RNA, Untranslated/genetics ; RNA, Viral/genetics ; Retroviridae/classification/*genetics/isolation &amp; purification/physiology ; Untranslated Regions ; }, abstract = {The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs), have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs) in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.}, }
@article {pmid28635635, year = {2017}, author = {Dalén, L and Lagerholm, VK and Nylander, JAA and Barton, N and Bochenski, ZM and Tomek, T and Rudling, D and Ericson, PGP and Irestedt, M and Stewart, JR}, title = {Identifying Bird Remains Using Ancient DNA Barcoding.}, journal = {Genes}, volume = {8}, number = {6}, pages = {}, pmid = {28635635}, issn = {2073-4425}, abstract = {Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.}, }
@article {pmid28633358, year = {2017}, author = {Payacan, C and Moncada, X and Rojas, G and Clarke, A and Chung, KF and Allaby, R and Seelenfreund, D and Seelenfreund, A}, title = {Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific.}, journal = {Annals of botany}, volume = {120}, number = {3}, pages = {387-404}, pmid = {28633358}, issn = {1095-8290}, mesh = {Broussonetia/*genetics ; DNA, Chloroplast/genetics ; DNA, Ribosomal Spacer/genetics ; *Genetic Variation ; *Genetics, Population ; Genotype ; Haplotypes ; Islands ; Microsatellite Repeats ; Oceania ; Phylogeography ; Polynesia ; Reproduction, Asexual ; }, abstract = {BACKGROUND AND AIMS: Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred.<br><br>METHODS: DNA from 47 herbarium specimens of B. papyrifera collected from 1882 to 2006 from different islands of the Pacific was obtained under ancient DNA protocols. Genetic characterization was based on the ribosomal internal transcribed spacer ITS-1 sequence, a sex marker, the chloroplast ndhF-rpl32 intergenic spacer and a set of ten microsatellites developed for B. papyrifera.<br><br>KEY RESULTS: Microsatellites allowed detection of 15 genotypes in Near and Remote Oceanian samples, in spite of the vegetative propagation of B. papyrifera in the Pacific. These genotypes are structured in two groups separating West and East Polynesia, and place Pitcairn in a pivotal position. We also detected the presence of male plants that carry the Polynesian chloroplast DNA (cpDNA) haplotype, in contrast to findings in contemporary B. papyrifera populations where only female plants bear the Polynesian cpDNA haplotype.<br><br>CONCLUSIONS: For the first time, genetic diversity was detected among paper mulberry accessions from Remote Oceania. A clear separation between West and East Polynesia was found that may be indicative of pulses during its dispersal history. The pattern linking the genotypes within Remote Oceania reflects the importance of central Polynesia as a dispersal hub, in agreement with archaeological evidence.}, }
@article {pmid28632161, year = {2017}, author = {Schroeder, O and Benecke, N and Frölich, K and Peng, Z and Kaniuth, K and Sverchkov, L and Reinhold, S and Belinskiy, A and Ludwig, A}, title = {Endogenous Retroviral Insertions Indicate a Secondary Introduction of Domestic Sheep Lineages to the Caucasus and Central Asia between the Bronze and Iron Age.}, journal = {Genes}, volume = {8}, number = {6}, pages = {}, pmid = {28632161}, issn = {2073-4425}, abstract = {Sheep were one of the first livestock species domesticated by humans. After initial domestication in the Middle East they were spread across Eurasia. The modern distribution of endogenous Jaagsiekte sheep retrovirus insertions in domestic sheep breeds suggests that over the course of millennia, successive introductions of improved lineages and selection for wool quality occurred in the Mediterranean region and most of Asia. Here we present a novel ancient DNA approach using data of endogenous retroviral insertions in Bronze and Iron Age domestic sheep from the Caucasus and Pamir mountain areas. Our findings support a secondary introduction of wool sheep from the Middle East between the Late Bronze Age and Iron Age into most areas of Eurasia.}, }
@article {pmid28625158, year = {2017}, author = {Sirak, KA and Fernandes, DM and Cheronet, O and Novak, M and Gamarra, B and Balassa, T and Bernert, Z and Cséki, A and Dani, J and Gallina, JZ and Kocsis-Buruzs, G and Kővári, I and László, O and Pap, I and Patay, R and Petkes, Z and Szenthe, G and Szeniczey, T and Hajdu, T and Pinhasi, R}, title = {A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis.}, journal = {BioTechniques}, volume = {62}, number = {6}, pages = {283-289}, doi = {10.2144/000114558}, pmid = {28625158}, issn = {1940-9818}, mesh = {Anthropology/methods ; DNA, Ancient/*analysis ; Gene Library ; Humans ; Minimally Invasive Surgical Procedures/methods ; Orthopedic Procedures/methods ; Petrous Bone/anatomy &amp; histology/*chemistry/surgery ; Sequence Analysis, DNA/methods ; Skull/anatomy &amp; histology/surgery ; Specimen Handling/methods ; }, abstract = {Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base. Here, we describe a novel cranial base drilling method (CBDM) for accessing the osseous labyrinth from the cranial base that prevents damaging the surrounding cranial features, making it highly complementary to morphological analyses. We assessed this method by comparing the aDNA results from one petrous bone processed using our novel method to its pair, which was processed using established protocols for sampling disarticulated petrous bones. We show a decrease in endogenous DNA and molecular copy numbers when the drilling method is used; however, we also show that this method produces more endogenous DNA and higher copy numbers than any postcranial bone. Our results demonstrate that this minimally-invasive method reduces the loss of genetic data associated with the use of other skeletal elements and enables the combined craniometric and genetic study of individuals with archeological, cultural, and evolutionary value.}, }
@article {pmid28625153, year = {2017}, author = {Blow, N}, title = {STORIES IN ANCIENT DNA.}, journal = {BioTechniques}, volume = {62}, number = {6}, pages = {245-250}, doi = {10.2144/000114553}, pmid = {28625153}, issn = {1940-9818}, mesh = {Animals ; Caves ; DNA, Ancient/*analysis ; Fossils ; Genome ; Humans ; Mammoths/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Technology developments are leading to rapid advances in ancient DNA analysis. Nathan Blow talks to researchers peering into the past through ancient DNA.}, }
@article {pmid28617333, year = {2017}, author = {Thomas, JE and Carvalho, GR and Haile, J and Martin, MD and Castruita, JAS and Niemann, J and Sinding, MS and Sandoval-Velasco, M and Rawlence, NJ and Fuller, E and Fjeldså, J and Hofreiter, M and Stewart, JR and Gilbert, MTP and Knapp, M}, title = {An ‛Aukward' Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks.}, journal = {Genes}, volume = {8}, number = {6}, pages = {}, pmid = {28617333}, issn = {2073-4425}, abstract = {One hundred and seventy-three years ago, the last two Great Auks, Pinguinusimpennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which-if any-of Fuller's candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars' minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.}, }
@article {pmid28615043, year = {2017}, author = {Chaubey, G and Ayub, Q and Rai, N and Prakash, S and Mushrif-Tripathy, V and Mezzavilla, M and Pathak, AK and Tamang, R and Firasat, S and Reidla, M and Karmin, M and Rani, DS and Reddy, AG and Parik, J and Metspalu, E and Rootsi, S and Dalal, K and Khaliq, S and Mehdi, SQ and Singh, L and Metspalu, M and Kivisild, T and Tyler-Smith, C and Villems, R and Thangaraj, K}, title = {"Like sugar in milk": reconstructing the genetic history of the Parsi population.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {110}, pmid = {28615043}, issn = {1474-760X}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Ethnicity/*genetics/history ; Female ; *Genetics, Population ; Geography ; Haplotypes ; History, Ancient ; Humans ; India ; Iran ; Pakistan ; Phylogeny ; }, abstract = {BACKGROUND: The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India.<br><br>RESULTS: Among present-day populations, the Parsis are genetically closest to Iranian and the Caucasus populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ~1,200&#xa0;years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement. Finally, we show that Parsis are genetically closer to Neolithic Iranians than to modern Iranians, who have witnessed a more recent wave of admixture from the Near East.<br><br>CONCLUSIONS: Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7th century and in agreement with their assimilation into the Indian sub-continent's population and cultural milieu "like sugar in milk". Moreover, in a wider context our results support a major demographic transition in West Asia due to the Islamic conquest.}, }
@article {pmid28613039, year = {2017}, author = {Bašić, &#x17d; and Kružić, I and Jerković, I and Anđelinović, D and Anđelinović, &#x160;}, title = {Sex estimation standards for medieval and contemporary Croats.}, journal = {Croatian medical journal}, volume = {58}, number = {3}, pages = {222-230}, pmid = {28613039}, issn = {1332-8166}, mesh = {Croatia ; DNA/*analysis ; DNA, Ancient/analysis ; Discriminant Analysis ; Female ; Forensic Anthropology ; Humans ; Male ; Sex Characteristics ; Sex Determination by Skeleton/methods/*standards ; }, abstract = {AIM: To develop discriminant functions for sex estimation on medieval Croatian population and test their application on contemporary Croatian population.<br><br>METHODS: From a total of 519 skeletons, we chose 84 adult excellently preserved skeletons free of antemortem or postmortem changes and took all standard measurements. Sex was estimated/determined using standard anthropological procedures and ancient DNA (amelogenin analysis) where pelvis was insufficiently preserved or where sex morphological indicators were not consistent. We explored which measurements showed sexual dimorphism and used them for developing univariate and multivariate discriminant functions for sex estimation. We included only those functions that reached accuracy rate &#x2265;80%. We tested the applicability of developed functions on modern Croatian sample (n=37).<br><br>RESULTS: From 69 standard skeletal measurements used in this study, 56 of them showed statistically significant sexual dimorphism (74.7%). We developed five univariate discriminant functions with classification rate 80.6%-85.2% and seven multivariate discriminant functions with an accuracy rate of 81.8%-93.0%. When tested on the modern population functions showed classification rates 74.1%-100%, and ten of them reached aimed accuracy rate. Females showed higher classified in the mediaeval populations, whereas males were better classification rates in the modern populations.<br><br>CONCLUSION: Developed discriminant functions are sufficiently accurate for reliable sex estimation in both medieval Croatian population and modern Croatian samples and may be used in forensic settings. The methodological issues that emerged regarding the importance of considering external factors in development and application of discriminant functions for sex estimation should be further explored.}, }
@article {pmid28609785, year = {2017}, author = {Philips, A and Stolarek, I and Kuczkowska, B and Juras, A and Handschuh, L and Piontek, J and Kozlowski, P and Figlerowicz, M}, title = {Comprehensive analysis of microorganisms accompanying human archaeological remains.}, journal = {GigaScience}, volume = {6}, number = {7}, pages = {1-13}, pmid = {28609785}, issn = {2047-217X}, mesh = {Archaeology/*methods ; Bone and Bones/microbiology ; *DNA, Ancient ; Fossils/microbiology ; Humans ; Metagenome ; *Microbiota ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.}, }
@article {pmid28604700, year = {2017}, author = {Luo, H and Huang, Y and Stepanauskas, R and Tang, J}, title = {Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {17091}, pmid = {28604700}, issn = {2058-5276}, mesh = {Alphaproteobacteria/*genetics/physiology ; Amino Acid Substitution/genetics ; Amino Acids/*genetics ; Biota ; Evolution, Molecular ; Gammaproteobacteria/*genetics/physiology ; *Gene Deletion ; Genetic Drift ; *Genome, Bacterial ; Phylogeny ; Plankton/genetics ; Prochlorococcus/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Surface ocean waters are dominated by planktonic bacterial lineages with highly reduced genomes. The best examples are the cyanobacterial genus Prochlorococcus, the alphaproteobacterial clade SAR11 and the gammaproteobacterial clade SAR86, which together represent over 50% of the cells in surface oceans. Several studies have identified signatures of selection on these lineages in today's ocean and have postulated selection as the primary force throughout their evolutionary history. However, massive loss of genomic DNA in these lineages often occurred in the distant past, and the selective pressures underlying these ancient events have not been assessed. Here, we probe ancient selective pressures by computing %GC-corrected rates of conservative and radical nonsynonymous nucleotide substitutions. Surprisingly, we found an excess of radical changes in several of these lineages in comparison to their relatives with larger genomes. Furthermore, analyses of allelic genome sequences of several populations within these lineages consistently supported that radical replacements are more likely to be deleterious than conservative changes. Our results suggest coincidence of massive genomic DNA losses and increased power of genetic drift, but we also suggest that additional evidence independent of the nucleotide substitution analyses is needed to support a primary role of genetic drift driving ancient genome reduction of marine bacterioplankton lineages.}, }
@article {pmid28593700, year = {2017}, author = {Calvignac-Spencer, S and Lenz, TL}, title = {The One Past Health workshop: connecting ancient DNA and zoonosis research.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {7}, pages = {}, doi = {10.1002/bies.201700075}, pmid = {28593700}, issn = {1521-1878}, mesh = {Animals ; *DNA, Ancient ; *Evolution, Molecular ; Humans ; Research ; Zoonoses/*genetics/pathology ; }, }
@article {pmid28588137, year = {2017}, author = {Parducci, L and Bennett, KD}, title = {The real significance of ancient DNA.}, journal = {American journal of botany}, volume = {104}, number = {6}, pages = {800-802}, doi = {10.3732/ajb.1700073}, pmid = {28588137}, issn = {1537-2197}, mesh = {*Biodiversity ; DNA, Ancient/*analysis ; DNA, Plant/analysis ; Plants/*genetics ; }, }
@article {pmid28585920, year = {2017}, author = {Meyer, M and Palkopoulou, E and Baleka, S and Stiller, M and Penkman, KEH and Alt, KW and Ishida, Y and Mania, D and Mallick, S and Meijer, T and Meller, H and Nagel, S and Nickel, B and Ostritz, S and Rohland, N and Schauer, K and Schüler, T and Roca, AL and Reich, D and Shapiro, B and Hofreiter, M}, title = {Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28585920}, issn = {2050-084X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Elephants/*genetics ; *Evolution, Molecular ; *Fossils ; Genome, Mitochondrial ; *Genomics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods ~120 and ~244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.}, }
@article {pmid28584090, year = {2017}, author = {Thompson, JR and Erkenbrack, EM and Hinman, VF and McCauley, BS and Petsios, E and Bottjer, DJ}, title = {Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {23}, pages = {5870-5877}, pmid = {28584090}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; *Gene Regulatory Networks ; Genomics ; Phylogeny ; Strongylocentrotus purpuratus/*genetics ; }, abstract = {Establishing a timeline for the evolution of novelties is a common, unifying goal at the intersection of evolutionary and developmental biology. Analyses of gene regulatory networks (GRNs) provide the ability to understand the underlying genetic and developmental mechanisms responsible for the origin of morphological structures both in the development of an individual and across entire evolutionary lineages. Accurately dating GRN novelties, thereby establishing a timeline for GRN evolution, is necessary to answer questions about the rate at which GRNs and their subcircuits evolve, and to tie their evolution to paleoenvironmental and paleoecological changes. Paleogenomics unites the fossil record and all aspects of deep time, with modern genomics and developmental biology to understand the evolution of genomes in evolutionary time. Recent work on the regulatory genomic basis of development in cidaroid echinoids, sand dollars, heart urchins, and other nonmodel echinoderms provides an ideal dataset with which to explore GRN evolution in a comparative framework. Using divergence time estimation and ancestral state reconstructions, we have determined the age of the double-negative gate (DNG), the subcircuit which specifies micromeres and skeletogenic cells in Strongylocentrotus purpuratus We have determined that the DNG has likely been used for euechinoid echinoid micromere specification since at least the Late Triassic. The innovation of the DNG thus predates the burst of post-Paleozoic echinoid morphological diversification that began in the Early Jurassic. Paleogenomics has wide applicability for the integration of deep time and molecular developmental data, and has wide utility in rigorously establishing timelines for GRN evolution.}, }
@article {pmid28568904, year = {2017}, author = {Dymova, MA and Zadorozhny, AV and Mishukova, OV and Khrapov, EA and Druzhkova, AS and Trifonov, VA and Kichigin, IG and Tishkin, AA and Grushin, SP and Filipenko, ML}, title = {Mitochondrial DNA analysis of ancient sheep from Altai.}, journal = {Animal genetics}, volume = {48}, number = {5}, pages = {615-618}, doi = {10.1111/age.12569}, pmid = {28568904}, issn = {1365-2052}, mesh = {Animals ; Archaeology ; Breeding ; DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genetic Variation ; Haplotypes ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Sheep/*genetics ; Siberia ; }, abstract = {A comparative analysis of the genetic diversity of ancient and modern sheep can shed light on the origin of these animals and their distribution as well as help to evaluate the role of humans at each formation stage of different sheep breeds. Here we isolated ancient DNA and performed sequencing of the mitochondrial DNA D-loop from 17 sheep bone remains (~4000-1000 years old) found in the archaeological complexes in the south of Altai (Western Siberia). The length of the sequences obtained ranged between 318 and 586 bp. The haplotype diversity and nucleotide diversity were 0.801 ± 0.081 and 0.0096 ± 0.0014 respectively. The average number of nucleotide differences was ~3.1. Nucleotide sequence analysis revealed that 15 specimens were nested within previously described A,B,C,D and E lineages and that two specimens had a basal position relative to the rest of the analyzed samples. A relatively high diversity of sheep haplotypes, including the presence of two basal haplotypes, indicates that the Altai region may have been a transport route of human migration. Further ancient DNA analysis of other specimens and deeper genome sequencing of samples with novel haplotypes is needed to better understand the demographic history of sheep in Southern Siberia.}, }
@article {pmid28552360, year = {2017}, author = {González-Fortes, G and Jones, ER and Lightfoot, E and Bonsall, C and Lazar, C and Grandal-d'Anglade, A and Garralda, MD and Drak, L and Siska, V and Simalcsik, A and Boroneanţ, A and Vidal Romaní, JR and Vaqueiro Rodríguez, M and Arias, P and Pinhasi, R and Manica, A and Hofreiter, M}, title = {Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin.}, journal = {Current biology : CB}, volume = {27}, number = {12}, pages = {1801-1810.e10}, pmid = {28552360}, issn = {1879-0445}, support = {263441/ERC_/European Research Council/International ; }, mesh = {*Archaeology ; Cultural Evolution ; DNA, Ancient/*analysis ; *Diet ; Farmers ; *Genome, Human ; *Human Migration ; Humans ; Life Style ; Romania ; }, abstract = {The transition from hunting and gathering to farming involved profound cultural and technological changes. In Western and Central Europe, these changes occurred rapidly and synchronously after the arrival of early farmers of Anatolian origin [1-3], who largely replaced the local Mesolithic hunter-gatherers [1, 4-6]. Further east, in the Baltic region, the transition was gradual, with little or no genetic input from incoming farmers [7]. Here we use ancient DNA to investigate the relationship between hunter-gatherers and farmers in the Lower Danube basin, a geographically intermediate area that is characterized by a rapid Neolithic transition but also by the presence of archaeological evidence that points to cultural exchange, and thus possible admixture, between hunter-gatherers and farmers. We recovered four human paleogenomes (1.1× to 4.1× coverage) from Romania spanning a time transect between 8.8 thousand years ago (kya) and 5.4 kya and supplemented them with two Mesolithic genomes (1.7× and 5.3×) from Spain to provide further context on the genetic background of Mesolithic Europe. Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. Dietary stable-isotope analysis of this sample suggests a mixed terrestrial/aquatic diet. Our results provide support for complex interactions among hunter-gatherers and farmers in the Danube basin, demonstrating that in some regions, demic and cultural diffusion were not mutually exclusive, but merely the ends of a continuum for the process of Neolithization.}, }
@article {pmid28543951, year = {2017}, author = {Martin, MD and Jay, F and Castellano, S and Slatkin, M}, title = {Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations.}, journal = {Molecular ecology}, volume = {26}, number = {16}, pages = {4145-4157}, pmid = {28543951}, issn = {1365-294X}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {*Computer Simulation ; *Genome, Human ; Genotype ; Humans ; *Models, Genetic ; *Pedigree ; Polymorphism, Single Nucleotide ; Software ; }, abstract = {We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present-day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available.}, }
@article {pmid28539631, year = {2017}, author = {Doan, K and Zachos, FE and Wilkens, B and Vigne, JD and Piotrowska, N and Stanković, A and Jędrzejewska, B and Stefaniak, K and Niedziałkowska, M}, title = {Phylogeography of the Tyrrhenian red deer (Cervus elaphus corsicanus) resolved using ancient DNA of radiocarbon-dated subfossils.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2331}, pmid = {28539631}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; Deer/*genetics ; France ; *Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Humans ; Italy ; *Phylogeography ; }, abstract = {We present ancient mitochondrial DNA analyses of 31 complete cytochrome b gene sequences from subfossil red deer remains from the Tyrrhenian islands (Corsica and Sardinia) and mainland Italy in a European-wide phylogeographic framework. Tyrrhenian and North African red deer, both going back to human introductions, were previously the only red deer to harbour the mitochondrial B lineage whose origin, however, remained unknown. Our ancient Italian samples from the central part of the peninsula that were radiocarbon-dated to an age of ca. 6300 to 15 600 cal BP all showed B haplotypes, closely related or even identical to those found on Sardinia. Genetic diversity in the mainland population was considerably higher than on the islands. Together with palaeontological evidence our genetic results identify the Italian Peninsula as the ultimate origin of the B lineage and thus the Tyrrhenian and North African red deer. This is in line with previous biogeographic findings that uncovered distinct intraspecific phylogeographic lineages in Italian mammals, underlining Italy's status as a hotspot of European mammalian diversity.}, }
@article {pmid28526291, year = {2017}, author = {Douka, K and Slon, V and Stringer, C and Potts, R and Hübner, A and Meyer, M and Spoor, F and Pääbo, S and Higham, T}, title = {Direct radiocarbon dating and DNA analysis of the Darra-i-Kur (Afghanistan) human temporal bone.}, journal = {Journal of human evolution}, volume = {107}, number = {}, pages = {86-93}, doi = {10.1016/j.jhevol.2017.03.003}, pmid = {28526291}, issn = {1095-8606}, support = {324139/ERC_/European Research Council/International ; }, mesh = {Afghanistan ; *Fossils ; Humans ; Male ; Radiometric Dating/*methods ; *Temporal Bone ; }, abstract = {The temporal bone discovered in the 1960s from the Darra-i-Kur cave in Afghanistan is often cited as one of the very few Pleistocene human fossils from Central Asia. Here we report the first direct radiocarbon date for the specimen and the genetic analyses of DNA extracted and sequenced from two areas of the bone. The new radiocarbon determination places the find to ∼4500 cal BP (∼2500 BCE) contradicting an assumed Palaeolithic age of ∼30,000 years, as originally suggested. The DNA retrieved from the specimen originates from a male individual who carried mitochondrial DNA of the modern human type. The petrous part yielded more endogenous ancient DNA molecules than the squamous part of the same bone. Molecular dating of the Darra-i-Kur mitochondrial DNA sequence corroborates the radiocarbon date and suggests that the specimen is younger than previously thought. Taken together, the results consolidate the fact that the human bone is not associated with the Pleistocene-age deposits of Darra-i-Kur; instead it is intrusive, possibly re-deposited from upper levels dating to much later periods (Neolithic). Despite its Holocene age, the Darra-i-Kur specimen is, so far, the first and only ancient human from Afghanistan whose DNA has been sequenced.}, }
@article {pmid28516942, year = {2017}, author = {Callaway, E}, title = {Ancient-genome study finds Bronze Age 'Beaker culture' invaded Britain.}, journal = {Nature}, volume = {545}, number = {7654}, pages = {276-277}, pmid = {28516942}, issn = {1476-4687}, mesh = {Agriculture/history ; *DNA, Ancient ; Europe/ethnology ; *Genome, Human ; Genomics ; History, Ancient ; Human Migration/*history ; Humans ; United Kingdom/ethnology ; Workforce ; }, }
@article {pmid28511559, year = {2017}, author = {Houldcroft, CJ and Ramond, JB and Rifkin, RF and Underdown, SJ}, title = {Migrating microbes: what pathogens can tell us about population movements and human evolution.}, journal = {Annals of human biology}, volume = {44}, number = {5}, pages = {397-407}, doi = {10.1080/03014460.2017.1325515}, pmid = {28511559}, issn = {1464-5033}, mesh = {Africa South of the Sahara ; Animal Distribution ; Animals ; *Archaeology ; *Biological Evolution ; Communicable Diseases/epidemiology ; *Human Migration ; Humans ; }, abstract = {BACKGROUND: The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases.<br><br>METHODS: This study explores which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts.<br><br>RESULTS: Three stories are then presented of germs on a journey. The first is the story of HIV's spread on the back of colonialism and the railway networks over the last 150&#x2009;years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2.<br><br>CONCLUSIONS: Evidence from modern African pathogen genomes can provide data on human behaviour and migration in deep time and contribute to the improvement of human quality-of-life and longevity.}, }
@article {pmid28486705, year = {2017}, author = {Kistler, L and Ware, R and Smith, O and Collins, M and Allaby, RG}, title = {A new model for ancient DNA decay based on paleogenomic meta-analysis.}, journal = {Nucleic acids research}, volume = {45}, number = {11}, pages = {6310-6320}, pmid = {28486705}, issn = {1362-4962}, support = {R21 DC020560/DC/NIDCD NIH HHS/United States ; }, mesh = {Base Composition ; Base Sequence ; DNA Fragmentation ; DNA, Ancient/analysis/*chemistry ; DNA, Mitochondrial/analysis/chemistry/genetics ; DNA, Plant/genetics ; Deamination ; Genome, Human ; Genome, Mitochondrial ; Humans ; Meta-Analysis as Topic ; Models, Chemical ; Paleontology/methods ; Sequence Analysis, DNA ; Thermodynamics ; }, abstract = {The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics.}, }
@article {pmid28460196, year = {2017}, author = {Warinner, C and Herbig, A and Mann, A and Fellows Yates, JA and Weiß, CL and Burbano, HA and Orlando, L and Krause, J}, title = {A Robust Framework for Microbial Archaeology.}, journal = {Annual review of genomics and human genetics}, volume = {18}, number = {}, pages = {321-356}, pmid = {28460196}, issn = {1545-293X}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaea/genetics/*isolation &amp; purification ; Archaeology/methods ; Bacteria/genetics/*isolation &amp; purification ; DNA, Ancient/*analysis ; Genome, Archaeal ; Genome, Bacterial ; Humans ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field.}, }
@article {pmid28455625, year = {2017}, author = {Balanovsky, O}, title = {Toward a consensus on SNP and STR mutation rates on the human Y-chromosome.}, journal = {Human genetics}, volume = {136}, number = {5}, pages = {575-590}, pmid = {28455625}, issn = {1432-1203}, mesh = {Chromosomes, Human, Y/*genetics ; Genetics, Population ; Haplotypes ; Humans ; Male ; *Microsatellite Repeats ; *Mutation ; *Mutation Rate ; Pedigree ; Phylogeny ; *Polymorphism, Single Nucleotide ; }, abstract = {The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate. The current estimate of the "envelope rate" is 0.75-0.89 substitutions per billion base pairs per year. The available Y-SNP mutation rates can be applied to high-coverage data from the entire X-degenerate region, but other datasets may demand recalibrated rates. While a consensus on Y-SNP rates is approaching, the debate on Y-STR rates has continued for two decades, because multiple genealogical rates were consistent with each other but three times faster than the single evolutionary estimate. Applying Y-SNP and Y-STR rates to the same haplogroups recently helped to clarify the issue. Genealogical and evolutionary STR rates typically provide lower and upper bounds of the "true" (SNP-based) age. The genealogical rate often-but not always-works well for haplogroups less than 7000 years old. The evolutionary rate, although calibrated using recent events, inflates ages of young haplogroups and deflates the age of the entire Y-chromosomal tree, but often provides reasonable estimates for intermediate ages (old haplogroups). Future rate estimates and accumulating case studies should further clarify the Y-SNP rates.}, }
@article {pmid28444234, year = {2017}, author = {Loog, L and Thomas, MG and Barnett, R and Allen, R and Sykes, N and Paxinos, PD and Lebrasseur, O and Dobney, K and Peters, J and Manica, A and Larson, G and Eriksson, A}, title = {Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices.}, journal = {Molecular biology and evolution}, volume = {34}, number = {8}, pages = {1981-1990}, pmid = {28444234}, issn = {1537-1719}, support = {//Wellcome Trust/United Kingdom ; 337574/ERC_/European Research Council/International ; 647787/ERC_/European Research Council/International ; 100719/Z/12/Z//Wellcome Trust/United Kingdom ; }, mesh = {Alleles ; Animal Husbandry ; Animals ; Animals, Domestic/genetics ; Bayes Theorem ; Breeding ; Chickens/*genetics ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Dioxygenases/genetics ; Gene Frequency/genetics ; Poultry/genetics ; Receptors, Thyrotropin/genetics ; Selection, Genetic/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here, we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both hypothesised to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of preindustrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition, our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection.}, }
@article {pmid28422985, year = {2017}, author = {Neparáczki, E and Kocsy, K and Tóth, GE and Maróti, Z and Kalmár, T and Bihari, P and Nagy, I and Pálfi, G and Molnár, E and Raskó, I and Török, T}, title = {Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0174886}, pmid = {28422985}, issn = {1932-6203}, mesh = {Bone and Bones/chemistry ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics/history ; Fossils ; *Haplotypes ; High-Throughput Nucleotide Sequencing/*methods ; History, Medieval ; Humans ; Hungary ; Molecular Typing/*methods ; *Paleontology ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination.}, }
@article {pmid28409264, year = {2017}, author = {Pamjav, H and Fóthi, &#xc1; and Fehér, T and Fóthi, E}, title = {A study of the Bodrogköz population in north-eastern Hungary by Y chromosomal haplotypes and haplogroups.}, journal = {Molecular genetics and genomics : MGG}, volume = {292}, number = {4}, pages = {883-894}, pmid = {28409264}, issn = {1617-4623}, mesh = {Chromosomes, Human, Y/*genetics ; Ethnicity/*genetics ; Genetics, Population ; Haplotypes/*genetics ; Humans ; Hungary ; Male ; Microsatellite Repeats/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Rural Population ; }, abstract = {We have determined the distribution of Y chromosomal haplotypes and haplogroups in population samples from one of the most important areas in north-eastern Hungary from many villages in the Bodrogköz. The Bodrogköz region was chosen due to its isolated nature, because this area was a moorland encircled by the Tisza, Bodrog, and Latorca Rivers and inhabitants of this part of Hungary escaped from both Tatar and Ottoman invasions, which decimated the post-Hungarian Conquest populations in many parts of the country. Furthermore, in the first half of the tenth century, this region served as the Palatial Centre and burial grounds of the Hungarian tribes. It has thus been assumed that the present population in this area is likely to be more similar to the population that lived in the Conquest period. We analysed male-specific markers, 23 Y-STRs and more than 30 Y-SNPs, that reflect the past and recent genetic history. We found that the general haplogroup distribution of the samples showed high genetic similarity to non-Bodrogköz Hungarians and neighbouring populations, despite its sheltered location and historical record. We were able to classify the Y-chromosomal haplogroups into four large groups based on STR mutation events: pre-Roman/Roman ancient lineage, Finno-Ugric speakers arriving into the Carpathian Basin, Migration period admixture, and post-Hungarian Conquest admixture. It is clear that a significantly larger database with deep haplogroup resolution, including ancient DNA data, is required to strengthen this research.}, }
@article {pmid28402470, year = {2017}, author = {Toranzos, GA and Santiago-Rodriguez, TM and Cano, RJ and Fornaciari, G}, title = {Proper authentication of ancient DNA is essential, yes; but so are undogmatic approaches.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, doi = {10.1093/femsec/fix043}, pmid = {28402470}, issn = {1574-6941}, mesh = {DNA/*genetics ; *DNA, Ancient ; Humans ; }, }
@article {pmid28396504, year = {2017}, author = {Theunert, C and Racimo, F and Slatkin, M}, title = {Joint Estimation of Relatedness Coefficients and Allele Frequencies from Ancient Samples.}, journal = {Genetics}, volume = {206}, number = {2}, pages = {1025-1035}, pmid = {28396504}, issn = {1943-2631}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Bone and Bones ; *Fossils ; Gene Frequency/*genetics ; Genome, Human/*genetics ; Humans ; Likelihood Functions ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; }, abstract = {Here, we develop and test a method to address whether DNA samples sequenced from a group of fossil hominin bone or tooth fragments originate from the same individual or from closely related individuals. Our method assumes low amounts of retrievable DNA, significant levels of sequencing error, and contamination from one or more present-day humans. We develop and implement a maximum likelihood method that estimates levels of contamination, sequencing error rates, and pairwise relatedness coefficients in a set of individuals. We assume that there is no reference panel for the ancient population to provide allele and haplotype frequencies. Our approach makes use of single nucleotide polymorphisms (SNPs) and does not make assumptions about the underlying demographic model. By artificially mating genomes from the 1000 Genomes Project, we determine the numbers of individuals at a given genomic coverage that are required to detect different levels of genetic relatedness with confidence.}, }
@article {pmid28394451, year = {2017}, author = {Der Sarkissian, C and Pichereau, V and Dupont, C and Ilsøe, PC and Perrigault, M and Butler, P and Chauvaud, L and Eiríksson, J and Scourse, J and Paillard, C and Orlando, L}, title = {Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {835-853}, doi = {10.1111/1755-0998.12679}, pmid = {28394451}, issn = {1755-0998}, mesh = {*Animal Shells ; Animals ; Aquatic Organisms/genetics ; *Body Remains ; DNA/chemistry/genetics/isolation &amp; purification ; DNA, Ancient/*analysis/chemistry ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; Metagenomics/*methods ; Mollusca/*genetics ; *Sequence Analysis, DNA ; Vibrio/genetics ; }, abstract = {Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.}, }
@article {pmid28392981, year = {2017}, author = {Seitz, A and Nieselt, K}, title = {Improving ancient DNA genome assembly.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3126}, pmid = {28392981}, issn = {2167-8359}, abstract = {Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated. In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer. We used this two-layer assembly to generate assemblies for two different ancient samples and compared the results to current de novo assembly approaches. We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions.}, }
@article {pmid28389681, year = {2017}, author = {Bösl, E}, title = {[aDNA Research From a Historical Perspective].}, journal = {NTM}, volume = {25}, number = {1}, pages = {99-142}, pmid = {28389681}, issn = {1420-9144}, mesh = {*Archaeology ; DNA, Ancient/*analysis ; Fossils ; *Genetics ; Historiography ; *History ; Humans ; Interdisciplinary Communication ; Polymerase Chain Reaction ; *Research ; Sequence Analysis, DNA ; }, abstract = {aDNA studies are a cooperative field of research with a broad range of applications including evolutionary biology, genetics, anthropology and archaeology. Scientists are using ancient molecules as source material for historical questions. Colleagues from the humanities are observing this with both interest and concern because aDNA research is affecting academic identities and both concepts of history and historiography. aDNA research developed in a way that can be described as a Hype Cycle (Chackie Fenn). Technological triggers such as Sanger Sequencing and the Polymerase Chain Reaction kicked off a multitude of experiments with ancient DNA during the 1980s and 1990s. Geneticists, microbiologists, anthropologists and many more euphorically joined a "molecule hunt". aDNA was promoted as a time machine. Media attention was enormous. As experiments and implementations began to fail and contamination was discovered to be a tremendous problem, media interest waned and many labs lost their interest. Some turned their disillusionment into systematic research into methodology and painstakingly established lab routines. The authenticity problem was first addressed by control oriented measures but later approached from a more cognitive theoretical perspective as the pitfalls and limits of aDNA became clearer. By the end of the 2000s the field reached its current plateau of productivity. Cross-disciplinary debates, conflicts and collaborations are increasing critical reflection among all participants. Historians should consider joining the field in a kind of critical friendship to both make the most of its possibilities and give an input from a constructivist perspective.}, }
@article {pmid28386123, year = {2017}, author = {Meiri, M and Stockhammer, PW and Marom, N and Bar-Oz, G and Sapir-Hen, L and Morgenstern, P and Macheridis, S and Rosen, B and Huchon, D and Maran, J and Finkelstein, I}, title = {Eastern Mediterranean Mobility in the Bronze and Early Iron Ages: Inferences from Ancient DNA of Pigs and Cattle.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {701}, pmid = {28386123}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Cattle ; *DNA, Ancient ; DNA, Mitochondrial ; Gene Frequency ; Geography ; Haplotypes ; History, 15th Century ; History, 16th Century ; History, Medieval ; *Human Migration/history ; Phylogeny ; }, abstract = {The Late Bronze of the Eastern Mediterranean (1550-1150 BCE) was a period of strong commercial relations and great prosperity, which ended in collapse and migration of groups to the Levant. Here we aim at studying the translocation of cattle and pigs during this period. We sequenced the first ancient mitochondrial and Y chromosome DNA of cattle from Greece and Israel and compared the results with morphometric analysis of the metacarpal in cattle. We also increased previous ancient pig DNA datasets from Israel and extracted the first mitochondrial DNA for samples from Greece. We found that pigs underwent a complex translocation history, with links between Anatolia with southeastern Europe in the Bronze Age, and movement from southeastern Europe to the Levant in the Iron I (ca. 1150-950 BCE). Our genetic data did not indicate movement of cattle between the Aegean region and the southern Levant. We detected the earliest evidence for crossbreeding between taurine and zebu cattle in the Iron IIA (ca. 900 BCE). In light of archaeological and historical evidence on Egyptian imperial domination in the region in the Late Bronze Age, we suggest that Egypt attempted to expand dry farming in the region in a period of severe droughts.}, }
@article {pmid28384042, year = {2017}, author = {Brzobohatá, K and Drozdová, E and Smutný, J and Zeman, T and Beňuš, R}, title = {Comparison of Suitability of the Most Common Ancient DNA Quantification Methods.}, journal = {Genetic testing and molecular biomarkers}, volume = {21}, number = {4}, pages = {265-271}, doi = {10.1089/gtmb.2016.0197}, pmid = {28384042}, issn = {1945-0257}, mesh = {DNA/genetics ; DNA, Ancient/*analysis/*isolation &amp; purification ; Humans ; Polymerase Chain Reaction/methods ; Real-Time Polymerase Chain Reaction/*methods ; }, abstract = {AIMS: Ancient DNA (aDNA) extracted from historical bones is damaged and fragmented into short segments, present in low quantity, and usually copurified with microbial DNA. A wide range of DNA quantification methods are available. The aim of this study was to compare the five most common DNA quantification methods for aDNA.<br><br>MATERIALS AND METHODS: Quantification methods were tested on DNA extracted from skeletal material originating from an early medieval burial site. The tested methods included ultraviolet (UV) absorbance, real-time quantitative polymerase chain reaction (qPCR) based on SYBR[&#xae;] green detection, real-time qPCR based on a forensic kit, quantification via fluorescent dyes bonded to DNA, and fragmentary analysis. Differences between groups were tested using a paired t-test.<br><br>RESULTS: Methods that measure total DNA present in the sample (NanoDrop[&#x2122;] UV spectrophotometer and Qubit[&#xae;] fluorometer) showed the highest concentrations. Methods based on real-time qPCR underestimated the quantity of aDNA. The most accurate method of aDNA quantification was fragmentary analysis, which also allows DNA quantification of the desired length and is not affected by PCR inhibitors.<br><br>CONCLUSIONS: Methods based on the quantification of the total amount of DNA in samples are unsuitable for ancient samples as they overestimate the amount of DNA presumably due to the presence of microbial DNA. Real-time qPCR methods give undervalued results due to DNA damage and the presence of PCR inhibitors. DNA quantification methods based on fragment analysis show not only the quantity of DNA but also fragment length.}, }
@article {pmid28382719, year = {2017}, author = {Morales-Arce, AY and Snow, MH and Kelley, JH and Anne Katzenberg, M}, title = {Ancient mitochondrial DNA and ancestry of Paquimé inhabitants, Casas Grandes (A.D. 1200-1450).}, journal = {American journal of physical anthropology}, volume = {163}, number = {3}, pages = {616-626}, doi = {10.1002/ajpa.23223}, pmid = {28382719}, issn = {1096-8644}, mesh = {Anthropology, Physical ; *DNA, Ancient/analysis/isolation &amp; purification ; *DNA, Mitochondrial/analysis/genetics/isolation &amp; purification ; Human Migration ; Humans ; Indians, Central American/*genetics ; Mexico ; Tooth/chemistry ; }, abstract = {OBJECTIVES: The Casas Grandes (Paquimé) culture, located in the Northwest of Chihuahua, Mexico reached its apogee during the Medio Period (A.D. 1200-1450). Paquimé was abandoned by the end of the Medio Period (A.D. 1450), and the ancestry of its inhabitants remains unsolved. Some authors suggest that waves of Mesoamerican immigrants, possibly merchants, stimulated Paquimé's development during the Medio Period. Archaeological evidence suggests possible ties to groups that inhabited the Southwestern US cultures. This study uses ancient DNA analysis from fourteen samples to estimate genetic affinities of ancient Paquimé inhabitants.<br><br>MATERIALS AND METHODS: DNA was extracted from 14 dental ancient samples from Paquim&#xe9;. PCR and Sanger sequencing were used to obtain mitochondrial control region sequences. Networks, PCoA, and Nei genetic distances were estimated to compare Paquim&#xe9; haplotypes against available past haplotypes data from Southwestern and Mesoamerican groups.<br><br>RESULTS: Haplogroups were characterized for 11 of the samples, and the results revealed the presence of four distinct Amerindian mitochondrial lineages: B (n&#x2009;=&#x2009;5; 45%), A (n&#x2009;=&#x2009;3; 27%), C (n&#x2009;=&#x2009;2; 18%) and D (n&#x2009;=&#x2009;1; 10%). Statistical analysis of the haplotypes, haplogroup frequencies, and Nei genetic distances showed close affinity of Paquim&#xe9; with Mimbres.<br><br>DISCUSSION: Although our results provide strong evidence of genetic affinities between Paquim&#xe9; and Mimbres, with the majority of haplotypes shared or derived from ancient Southwest populations, the causes of cultural development at Paquim&#xe9; still remain a question. These preliminary results provide evidence in support of other bioarchaeological studies, which have shown close biological affinities between Paquim&#xe9; and Mimbres, a Puebloan culture, in the Southwestern US.}, }
@article {pmid28377518, year = {2017}, author = {Lindo, J and Achilli, A and Perego, UA and Archer, D and Valdiosera, C and Petzelt, B and Mitchell, J and Worl, R and Dixon, EJ and Fifield, TE and Rasmussen, M and Willerslev, E and Cybulski, JS and Kemp, BM and DeGiorgio, M and Malhi, RS}, title = {Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {16}, pages = {4093-4098}, pmid = {28377518}, issn = {1091-6490}, mesh = {Archaeology ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; *Evolution, Molecular ; Female ; *Genetic Variation ; *Genetics, Population ; *Genome, Mitochondrial ; Genomics/*methods ; Humans ; Indians, North American/*genetics ; Male ; Phylogeny ; }, abstract = {Recent genomic studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific Northwest Coast proves an intriguing focus for these studies because of its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here, we report the low-coverage genome sequence of an ancient individual known as "Shuká Káa" ("Man Ahead of Us") recovered from the On Your Knees Cave (OYKC) in southeastern Alaska (archaeological site 49-PET-408). The human remains date to ∼10,300 calendar (cal) y B.P. We also analyze low-coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from ∼6,075 to 1,750 cal y B.P. From the resulting time series of genetic data, we show that the Pacific Northwest Coast exhibits genetic continuity for at least the past 10,300 cal y B.P. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared with other North American individuals from the late Pleistocene or early Holocene (i.e., Anzick-1 and Kennewick Man). Despite regional shifts in mtDNA haplogroups, we conclude from individuals sampled through time that people of the northern Northwest Coast belong to an early genetic lineage that may stem from a late Pleistocene coastal migration into the Americas.}, }
@article {pmid28376731, year = {2017}, author = {Schaefer, NK and Shapiro, B and Green, RE}, title = {AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {203}, pmid = {28376731}, issn = {1471-2105}, support = {T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Genetic Speciation ; *Genome ; Humans ; *Hybridization, Genetic ; Markov Chains ; Polymorphism, Single Nucleotide ; *Software ; Ursidae/*genetics ; }, abstract = {BACKGROUND: Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA.<br><br>RESULTS: We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87-91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Finally, we demonstrate that AD-LIBS is more effective than HAPMIX at inferring ancestry when preexisting phased reference data are unavailable and genomes are sequenced to low coverage.<br><br>CONCLUSIONS: AD-LIBS is an effective tool for ancestry inference that can be used even when few individuals are available for comparison or when genomes are sequenced to low coverage. AD-LIBS is therefore likely to be useful in studies of non-model or ancient organisms that lack large amounts of genomic DNA. AD-LIBS can therefore expand the range of studies in which admixture mapping is a viable tool.}, }
@article {pmid28369385, year = {2017}, author = {Eisenhofer, R and Cooper, A and Weyrich, LS}, title = {Reply to Santiago-Rodriguez et al.: proper authentication of ancient DNA is essential.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, doi = {10.1093/femsec/fix042}, pmid = {28369385}, issn = {1574-6941}, mesh = {*DNA, Ancient ; Humans ; }, }
@article {pmid28363818, year = {2017}, author = {Perry, T and van Loenen, AL and Heiniger, H and Lee, C and Gongora, J and Cooper, A and Mitchell, KJ}, title = {Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus).}, journal = {Molecular phylogenetics and evolution}, volume = {112}, number = {}, pages = {258-267}, doi = {10.1016/j.ympev.2017.03.024}, pmid = {28363818}, issn = {1095-9513}, mesh = {Animals ; Artiodactyla/*genetics ; Bayes Theorem ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Extinction, Biological ; Fossils ; Genetic Variation ; Genome, Mitochondrial ; Geography ; Haplotypes/genetics ; North America ; Phylogeny ; }, abstract = {The geographical range of extant peccaries extends from the southwestern United States through Central America and into northern Argentina. However, from the Miocene until the Pleistocene now-extinct peccary species inhabited the entirety of North America. Relationships among the living and extinct species have long been contentious. Similarly, how and when peccaries moved from North to South America is unclear. The North American flat-headed peccary (Platygonus compressus) became extinct at the end of the Pleistocene and is one of the most abundant subfossil taxa found in North America, yet despite this extensive fossil record its phylogenetic position has not been resolved. This study is the first to present DNA data from the flat-headed peccary and full mitochondrial genome sequences of all the extant peccary species. We performed a molecular phylogenetic analysis to determine the relationships among ancient and extant peccary species. Our results suggested that the flat-headed peccary is sister-taxon to a clade comprising the extant peccary species. Divergence date estimates from our molecular dating analyses suggest that if extant peccary diversification occurred in South America then their common ancestor must have dispersed from North America to South America well before the establishment of the Isthmus of Panama. We also investigated the genetic diversity of the flat-headed peccary by performing a preliminary population study on specimens from Sheriden Cave, Ohio. Flat-headed peccaries from Sheriden Cave appear to be genetically diverse and show no signature of population decline prior to extinction. Including additional extinct Pleistocene peccary species in future phylogenetic analyses will further clarify peccary evolution.}, }
@article {pmid28348834, year = {2016}, author = {Duchêne, S and Holt, KE and Weill, FX and Le Hello, S and Hawkey, J and Edwards, DJ and Fourment, M and Holmes, EC}, title = {Genome-scale rates of evolutionary change in bacteria.}, journal = {Microbial genomics}, volume = {2}, number = {11}, pages = {e000094}, pmid = {28348834}, issn = {2057-5858}, mesh = {Bacteria/classification/*genetics ; Biological Evolution ; *Evolution, Molecular ; Genetic Variation ; Genome, Bacterial/*genetics ; *Models, Genetic ; Mutation ; }, abstract = {Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with 'ancient DNA' data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from approximately 10[-5] to 10[-8] nucleotide substitutions per site year[-1]. This variation was negatively associated with sampling time, with this relationship best described by an exponential decay curve. To avoid potential estimation biases, such time-dependency should be considered when inferring evolutionary time-scales in bacteria.}, }
@article {pmid28330913, year = {2017}, author = {Pereira, JB and Costa, MD and Vieira, D and Pala, M and Bamford, L and Harich, N and Cherni, L and Alshamali, F and Hatina, J and Rychkov, S and Stefanescu, G and King, T and Torroni, A and Soares, P and Pereira, L and Richards, MB}, title = {Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1851}, pages = {}, pmid = {28330913}, issn = {1471-2954}, mesh = {DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Ethnicity ; Europe ; Founder Effect ; *Genetic Variation ; *Genome, Human ; Haplotypes ; Humans ; Mediterranean Region ; Middle East ; White People ; }, abstract = {Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.}, }
@article {pmid29776878, year = {2018}, author = {Fornaciari, G}, title = {Histology of ancient soft tissue tumors: A review.}, journal = {International journal of paleopathology}, volume = {21}, number = {}, pages = {64-76}, doi = {10.1016/j.ijpp.2017.02.007}, pmid = {29776878}, issn = {1879-9825}, mesh = {Adult ; Humans ; Infant ; Male ; Middle Aged ; History, 15th Century ; History, Ancient ; History, Medieval ; *Mummies/pathology ; *Soft Tissue Neoplasms/history/pathology ; }, abstract = {Ancient neoplasms diagnosed in the soft tissues of mummies are limited to 18 cases so far, with only 5 malignant tumors. The apparent paucity of neoplasms in ancient populations is sometimes attributed to shorter life spans and fewer oncogenic substances in the environment. However, this paucity may also be a result of the scarcity of autopsies of mummies, together with technical difficulties in detecting neoplastic lesions in mummified tissues. An exception, and example of the benefits of thorough systematic analysis, is the small sample of 10 Renaissance mummies from Naples (15th-16th centuries), in which 3 cases of cancer were found. In order to increase detection of soft tissue tumors, it is imperative that mummies undergo systematic autopsies and histological examinations performed by skilled paleopathologists. This review of the known ancient soft tissue neoplasms demonstrates the state of histology of malignant and benign soft tissue neoplasms in mummies, and the potential for further study. The limitations of paleopathological diagnosis will be discussed and an argument will be made for the use of autopsies and histological analysis on mummified human remains.}, }
@article {pmid28316114, year = {2017}, author = {Kasulin, L and Rowan, BA and León, RJC and Schuenemann, VJ and Weigel, D and Botto, JF}, title = {A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina.}, journal = {Molecular ecology}, volume = {26}, number = {13}, pages = {3389-3404}, doi = {10.1111/mec.14107}, pmid = {28316114}, issn = {1365-294X}, mesh = {Adaptation, Physiological ; Arabidopsis/*genetics/radiation effects ; Argentina ; Gene Expression Regulation, Plant ; *Genetics, Population ; *Haplotypes ; *Light ; Phenotype ; Phytochrome/genetics ; }, abstract = {The growing collection of sequenced or genotyped Arabidopsis thaliana accessions includes mostly individuals from the native Eurasian and N. African range and introduced North American populations. Here, we describe the genetic and phenotypic diversity, along with habitats and life history, of A. thaliana plants collected at the southernmost end of its worldwide distribution. Seed samples were harvested from plants growing in four sites within a ~3500-km[2] -area in Patagonia, Argentina, and represent the first germplasm to be collected in South America for this species. Whole-genome resequencing revealed that plants from the four sites and a Patagonia herbarium specimen collected in 1967 formed a single haplogroup (Pat), indicating that the phenotypic variation observed in the field reflected plastic responses to the environment. admixture and principal components analyses suggest that the ancestor of the Pat haplogroup either came from Italy or the Balkan/Caucasus regions of Eurasia. In the laboratory, plants from the Pat haplogroup were hyposensitive to continuous red (Rc) and shade light, with corresponding changes in the expression of phytochrome signalling genes. Pat had higher PIF3 and PIF5 and lower HY5 expression under Rc light; and lower expression of PIL1, ATHB2 and HFR1 under shade compared to Col-0. In addition, Pat plants had a strong vernalization requirement associated with high levels of FLC expression. We conclude that including Pat in studies of natural variation and in comparison with other introduced populations will provide additional information for association studies and allow for a more detailed assessment of the demographic events following colonization.}, }
@article {pmid28302068, year = {2017}, author = {Chyleński, M and Juras, A and Ehler, E and Malmström, H and Piontek, J and Jakobsson, M and Marciniak, A and Dabert, M}, title = {Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5[th] millennium BC.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {80}, pmid = {28302068}, issn = {1471-2148}, mesh = {DNA, Mitochondrial/*genetics ; Europe ; Genetics, Medical ; Genome, Mitochondrial ; Haplotypes ; *Human Migration ; Humans ; Poland ; White People/genetics ; }, abstract = {BACKGROUND: Recent aDNA studies are progressively focusing on various Neolithic and Hunter - Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities.<br><br>RESULTS: Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK.<br><br>CONCLUSIONS: We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities.}, }
@article {pmid28300151, year = {2017}, author = {Caliebe, A and Nebel, A and Makarewicz, C and Krawczak, M and Krause-Kyora, B}, title = {Insights into early pig domestication provided by ancient DNA analysis.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {44550}, pmid = {28300151}, issn = {2045-2322}, mesh = {Animals ; Animals, Domestic/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; *Domestication ; Europe ; Haplotypes/genetics ; Phylogeny ; Sus scrofa/*genetics ; Swine ; }, abstract = {Pigs (Sus scrofa) were first domesticated between 8,500 and 8,000 cal BC in the Near East, from where they were subsequently brought into Europe by agriculturalists. Soon after the arrival of the first domestic pigs in northern Europe (~4500 BC), farmers are thought to have started to incorporate local wild boars into their swine herds. This husbandry strategy ultimately resulted in the domestication of European wild boars. Here, we set out to provide a more precise geographic and temporal framework of the early management of suid populations in northern Europe, drawing upon mitochondrial DNA haplotype data from 116 Neolithic Sus specimens. We developed a quantitative mathematical model tracing the haplotypes of the domestic pigs back to their most likely geographic origin. Our modelling results suggest that, between 5000 and 4000 BC, almost all matrilines in the north originated from domesticated animals from the south of central Europe. In the following period (4000-3000 BC), an estimated 78-100% of domesticates in the north were of northern matrilineal origin, largely from local wild boars. These findings point towards a dramatic change in suid management strategies taking place throughout south-central and northern Europe after 4000 BC.}, }
@article {pmid28289222, year = {2017}, author = {Froese, D and Stiller, M and Heintzman, PD and Reyes, AV and Zazula, GD and Soares, AE and Meyer, M and Hall, E and Jensen, BJ and Arnold, LJ and MacPhee, RD and Shapiro, B}, title = {Fossil and genomic evidence constrains the timing of bison arrival in North America.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {13}, pages = {3457-3462}, pmid = {28289222}, issn = {1091-6490}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bison/classification/*genetics/physiology ; DNA, Mitochondrial/genetics ; Fossils/history ; Genome, Mitochondrial ; Genomics ; History, Ancient ; North America ; Phylogeny ; }, abstract = {The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada's Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf. priscus We extracted and sequenced mitochondrial genomes from both this bison and from the remains of a recently discovered, ∼120,000-y-old giant long-horned bison, Bison latifrons, from Snowmass, Colorado. We analyzed these and 44 other bison mitogenomes with ages that span the Late Pleistocene, and identified two waves of bison dispersal into North America from Asia, the earliest of which occurred ∼195-135 thousand y ago and preceded the morphological diversification of North American bison, and the second of which occurred during the Late Pleistocene, ∼45-21 thousand y ago. This chronological arc establishes that bison first entered North America during the sea level lowstand accompanying marine isotope stage 6, rejecting earlier records of bison in North America. After their invasion, bison rapidly colonized North America during the last interglaciation, spreading from Alaska through continental North America; they have been continuously resident since then.}, }
@article {pmid28288112, year = {2017}, author = {Murat, F and Armero, A and Pont, C and Klopp, C and Salse, J}, title = {Reconstructing the genome of the most recent common ancestor of flowering plants.}, journal = {Nature genetics}, volume = {49}, number = {4}, pages = {490-496}, pmid = {28288112}, issn = {1546-1718}, mesh = {Evolution, Molecular ; Flowers/*genetics ; Genome, Plant/*genetics ; Genomics ; Magnoliopsida/genetics ; Mutation/genetics ; Phylogeny ; }, abstract = {We describe here the reconstruction of the genome of the most recent common ancestor (MRCA) of modern monocots and eudicots, accounting for 95% of extant angiosperms, with its potential repertoire of 22,899 ancestral genes conserved in present-day crops. The MRCA provides a starting point for deciphering the reticulated evolutionary plasticity between species (rapidly versus slowly evolving lineages), subgenomes (pre- versus post-duplication blocks), genomic compartments (stable versus labile loci), genes (ancestral versus species-specific genes) and functions (gained versus lost ontologies), the key mutational forces driving the success of polyploidy in crops. The estimation of the timing of angiosperm evolution, based on MRCA genes, suggested that this group emerged 214 million years ago during the late Triassic era, before the oldest recorded fossil. Finally, the MRCA constitutes a unique resource for scientists to dissect major agronomic traits in translational genomics studies extending from model species to crops.}, }
@article {pmid28279935, year = {2017}, author = {Xavier, C and Parson, W}, title = {Evaluation of the Illumina ForenSeq™ DNA Signature Prep Kit - MPS forensic application for the MiSeq FGx™ benchtop sequencer.}, journal = {Forensic science international. Genetics}, volume = {28}, number = {}, pages = {188-194}, doi = {10.1016/j.fsigen.2017.02.018}, pmid = {28279935}, issn = {1878-0326}, mesh = {Chromosomes, Human, X ; Chromosomes, Human, Y ; *DNA Fingerprinting ; Female ; Forensic Genetics ; High-Throughput Nucleotide Sequencing/*instrumentation ; Humans ; Male ; *Microsatellite Repeats ; *Polymorphism, Single Nucleotide ; Reproducibility of Results ; }, abstract = {Massively Parallel (Next Generation) Sequencing (MPS) technologies have recently been proven useful and successful in typing various markers relevant in forensic genetics, such as STRs, SNPs and mitochondrial genomes. Early studies investigated self-developed DNA libraries, commercially supplied kits are currently being made available to allow a smoother and gradual implementation of such technologies in forensic laboratories. The ForenSeq™ DNA Signature Prep Kit (Illumina, CA) is the first commercially available STR kit that can be used on the MiSeq FGx™ (Illumina, CA) benchtop high-throughput sequencer. This kit allows the simultaneous typing of 59 STRs and up to 172 SNPs in a single reaction and presents a short library preparation protocol adapted to contemporary forensic requirements. In this study, we evaluated the beta version of the ForenSeq DNA Signature Prep Kit MiSeq FGx system by investigating reproducibility, sensitivity, mixtures, concordance, casework-type and aDNA samples and found it to perform successfully, proving to be a robust method for future forensic applications. MPS brings the possibility of complex multiplexing, high sensitivity and sequencing resolution to forensics; however, the need for consensual directions on databasing, data storage and nomenclature must be taken into consideration.}, }
@article {pmid28273082, year = {2017}, author = {Jain, S and Rai, N and Kumar, G and Pruthi, PA and Thangaraj, K and Bajpai, S and Pruthi, V}, title = {Ancient DNA Reveals Late Pleistocene Existence of Ostriches in Indian Sub-Continent.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0164823}, pmid = {28273082}, issn = {1932-6203}, mesh = {Animals ; DNA, Ancient/*analysis ; Egg Shell/metabolism/pathology ; Fossils ; India ; Microscopy, Confocal ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Struthioniformes/classification/*genetics ; }, abstract = {Ancient DNA (aDNA) analysis of extinct ratite species is of considerable interest as it provides important insights into their origin, evolution, paleogeographical distribution and vicariant speciation in congruence with continental drift theory. In this study, DNA hotspots were detected in fossilized eggshell fragments of ratites (dated ≥25000 years B.P. by radiocarbon dating) using confocal laser scanning microscopy (CLSM). DNA was isolated from five eggshell fragments and a 43 base pair (bp) sequence of a 16S rRNA mitochondrial-conserved region was successfully amplified and sequenced from one of the samples. Phylogenetic analysis of the DNA sequence revealed a 92% identity of the fossil eggshells to Struthio camelus and their position basal to other palaeognaths, consistent with the vicariant speciation model. Our study provides the first molecular evidence for the presence of ostriches in India, complementing the continental drift theory of biogeographical movement of ostriches in India, and opening up a new window into the evolutionary history of ratites.}, }
@article {pmid28273061, year = {2017}, author = {Weyrich, LS and Duchene, S and Soubrier, J and Arriola, L and Llamas, B and Breen, J and Morris, AG and Alt, KW and Caramelli, D and Dresely, V and Farrell, M and Farrer, AG and Francken, M and Gully, N and Haak, W and Hardy, K and Harvati, K and Held, P and Holmes, EC and Kaidonis, J and Lalueza-Fox, C and de la Rasilla, M and Rosas, A and Semal, P and Soltysiak, A and Townsend, G and Usai, D and Wahl, J and Huson, DH and Dobney, K and Cooper, A}, title = {Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.}, journal = {Nature}, volume = {544}, number = {7650}, pages = {357-361}, doi = {10.1038/nature21674}, pmid = {28273061}, issn = {1476-4687}, mesh = {Animals ; Belgium ; Carnivory ; Caves ; DNA, Ancient/*analysis ; Dental Calculus/*chemistry ; Diet/*history ; Enterocytozoon/genetics/isolation &amp; purification ; *Food Preferences ; Genome, Bacterial/genetics ; Health/*history ; History, Ancient ; Humans ; Intestines/microbiology ; Meat/history ; Methanobrevibacter/genetics/isolation &amp; purification ; Mouth/microbiology ; Neanderthals/*microbiology/*psychology ; Pan troglodytes/microbiology ; Penicillium/chemistry ; Perissodactyla ; Sheep ; Spain ; Stomach/microbiology ; Symbiosis ; Time Factors ; Vegetarians/history ; }, abstract = {Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.}, }
@article {pmid28260210, year = {2017}, author = {Kivisild, T}, title = {The study of human Y chromosome variation through ancient DNA.}, journal = {Human genetics}, volume = {136}, number = {5}, pages = {529-546}, pmid = {28260210}, issn = {1432-1203}, mesh = {Chromosomes, Human, Y/*genetics ; *DNA, Ancient ; Humans ; Male ; Phylogeography ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.}, }
@article {pmid28253255, year = {2017}, author = {Rogers, RL and Slatkin, M}, title = {Excess of genomic defects in a woolly mammoth on Wrangel island.}, journal = {PLoS genetics}, volume = {13}, number = {3}, pages = {e1006601}, pmid = {28253255}, issn = {1553-7404}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient/analysis ; Evolution, Molecular ; *Fossils ; *Genome ; Genomics/*methods ; Islands ; Mammoths/*genetics ; Mutation ; Russia ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Woolly mammoths (Mammuthus primigenius) populated Siberia, Beringia, and North America during the Pleistocene and early Holocene. Recent breakthroughs in ancient DNA sequencing have allowed for complete genome sequencing for two specimens of woolly mammoths (Palkopoulou et al. 2015). One mammoth specimen is from a mainland population 45,000 years ago when mammoths were plentiful. The second, a 4300 yr old specimen, is derived from an isolated population on Wrangel island where mammoths subsisted with small effective population size more than 43-fold lower than previous populations. These extreme differences in effective population size offer a rare opportunity to test nearly neutral models of genome architecture evolution within a single species. Using these previously published mammoth sequences, we identify deletions, retrogenes, and non-functionalizing point mutations. In the Wrangel island mammoth, we identify a greater number of deletions, a larger proportion of deletions affecting gene sequences, a greater number of candidate retrogenes, and an increased number of premature stop codons. This accumulation of detrimental mutations is consistent with genomic meltdown in response to low effective population sizes in the dwindling mammoth population on Wrangel island. In addition, we observe high rates of loss of olfactory receptors and urinary proteins, either because these loci are non-essential or because they were favored by divergent selective pressures in island environments. Finally, at the locus of FOXQ1 we observe two independent loss-of-function mutations, which would confer a satin coat phenotype in this island woolly mammoth.}, }
@article {pmid28241055, year = {2017}, author = {Christensen, KA and Davidson, WS}, title = {Autopolyploidy genome duplication preserves other ancient genome duplications in Atlantic salmon (Salmo salar).}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0173053}, pmid = {28241055}, issn = {1932-6203}, mesh = {Animals ; Chromosome Mapping ; Chromosomes ; Computational Biology ; Databases, Genetic ; Evolution, Molecular ; *Gene Duplication ; Genes, Duplicate ; *Genome ; Genomics ; Mutation ; Phylogeny ; *Polyploidy ; Salmo salar/*genetics ; }, abstract = {Salmonids (e.g. Atlantic salmon, Pacific salmon, and trouts) have a long legacy of genome duplication. In addition to three ancient genome duplications that all teleosts are thought to share, salmonids have had one additional genome duplication. We explored a methodology for untangling these duplications from each other to better understand them in Atlantic salmon. In this methodology, homeologous regions (paralogous/duplicated genomic regions originating from a whole genome duplication) from the most recent genome duplication were assumed to have duplicated genes at greater density and have greater sequence similarity. This assumption was used to differentiate duplicated gene pairs in Atlantic salmon that are either from the most recent genome duplication or from earlier duplications. From a comparison with multiple vertebrate species, it is clear that Atlantic salmon have retained more duplicated genes from ancient genome duplications than other vertebrates--often at higher density in the genome and containing fewer synonymous mutations. It may be that polysomic inheritance is the mechanism responsible for maintaining ancient gene duplicates in salmonids. Polysomic inheritance (when multiple chromosomes pair during meiosis) is thought to be relatively common in salmonids compared to other vertebrate species. These findings illuminate how genome duplications may not only increase the number of duplicated genes, but may also be involved in the maintenance of them from previous genome duplications as well.}, }
@article {pmid28229564, year = {2017}, author = {Martin, KJ and Holland, PWH}, title = {Diversification of Hox Gene Clusters in Osteoglossomorph Fish in Comparison to Other Teleosts and the Spotted Gar Outgroup.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {328}, number = {7}, pages = {638-644}, doi = {10.1002/jez.b.22726}, pmid = {28229564}, issn = {1552-5015}, support = {268513/ERC_/European Research Council/International ; }, mesh = {Animals ; Fishes/classification/*genetics ; Gene Duplication ; Gene Expression Regulation ; Genes, Homeobox/*genetics ; Genetic Speciation ; *Genetic Variation ; Genome ; *Multigene Family ; Species Specificity ; }, abstract = {An ancient genome duplication (TGD or 3R) occurred in teleost fish after divergence from the lineage leading to gar. This genome duplication is shared by the three extant teleost lineages: Osteoglossomorpha (bony-tongues), Elopomorpha (eels and tarpons), and Clupeocephala (a large clade including salmon, carp, medaka, zebrafish, cichlids, pufferfish, stickleback, and ∼26,000 other species). After TGD, different clupeocephalan species retained different gene duplicates; this is seen clearly in Hox gene clusters but extends to all genes. Since divergent resolution of TGD paralogs is a potential driving force for speciation, it is possible this contributed to diversification of this clade. The extent to which divergent resolution of TGD paralogs occurred within Osteoglossomorpha has not been investigated in detail, and Hox cluster organization has been reported for just two species: Pantodon buchholzi (Pantodontidae) and Scleropages formosus (Osteoglossidae). We applied survey-scale genome sequencing and de novo assembly to three further osteoglossomorph taxa: Osteoglossum bicirrhosum (Osteoglossidae), Chitala ornata (Notopteridae), and Gnathonemus petersii (Mormyridae). We find that each retained more Hox genes than clupeocephalan taxa (excluding those that underwent additional genome duplication), but fewer than eels. Several Hox genes are missing in all teleosts, including duplicates of two Hox genes present in the slow evolving pre-TGD genome of the spotted gar. We find divergent resolution through individual gene losses, and whole cluster losses have been rampant across osteoglossomorphs, despite their extant species paucity. We suggest that reciprocal gene loss following TGD was probably insufficient to drive the exceptional diversification of teleosts.}, }
@article {pmid28205612, year = {2017}, author = {Faerman, M and Bar-Gal, GK and Boaretto, E and Boeskorov, GG and Dokuchaev, NE and Ermakov, OA and Golenishchev, FN and Gubin, SV and Mintz, E and Simonov, E and Surin, VL and Titov, SV and Zanina, OG and Formozov, NA}, title = {DNA analysis of a 30,000-year-old Urocitellus glacialis from northeastern Siberia reveals phylogenetic relationships between ancient and present-day arctic ground squirrels.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42639}, pmid = {28205612}, issn = {2045-2322}, mesh = {Animals ; Arctic Regions ; Cytochromes b/genetics ; *DNA, Ancient ; DNA, Mitochondrial ; Evolution, Molecular ; *Fossils ; Geography ; *Phylogeny ; Phylogeography ; Sciuridae/*classification/*genetics ; Siberia ; }, abstract = {In contrast to the abundant fossil record of arctic ground squirrels, Urocitellus parryii, from eastern Beringia, only a limited number of fossils is known from its western part. In 1946, unnamed GULAG prisoners discovered a nest with three mummified carcasses of arctic ground squirrels in the permafrost sediments of the El'ga river, Yakutia, Russia, that were later attributed to a new species, Citellus (Urocitellus) glacialis Vinogr. To verify this assignment and to explore phylogenetic relationships between ancient and present-day arctic ground squirrels, we performed [14]C dating and ancient DNA analyses of one of the El'ga mummies and four contemporaneous fossils from Duvanny Yar, northeastern Yakutia. Phylogenetic reconstructions, based on complete cytochrome b gene sequences of five Late Pleistocene arctic ground squirrels and those of modern U. parryii from 21 locations across western Beringia, provided no support for earlier proposals that ancient arctic ground squirrels from Siberia constitute a distinct species. In fact, we observed genetic continuity of the glacialis mitochondrial DNA lineage in modern U. parryii of the Kamchatka peninsula. When viewed in a broader geographic perspective, our findings provide new insights into the genetic history of U. parryii in Late Pleistocene Beringia.}, }
@article {pmid28197171, year = {2017}, author = {Braud, M and Magee, DA and Park, SD and Sonstegard, TS and Waters, SM and MacHugh, DE and Spillane, C}, title = {Genome-Wide microRNA Binding Site Variation between Extinct Wild Aurochs and Modern Cattle Identifies Candidate microRNA-Regulated Domestication Genes.}, journal = {Frontiers in genetics}, volume = {8}, number = {}, pages = {3}, pmid = {28197171}, issn = {1664-8021}, abstract = {The domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non-coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs. To investigate this, we analyzed the open reading frame DNA sequence of 19,994 orthologous protein-coding gene pairs from extant Bos taurus genomes and a single extinct B. primigenius genome. We identified miRNA binding site polymorphisms in the 3' UTRs of 1,620 of these orthologous genes. These 1,620 genes with altered miRNA binding sites between the B. taurus and B. primigenius lineages represent candidate domestication genes. Using a novel Score Site ratio metric we have ranked these miRNA-regulated genes according to the extent of divergence between miRNA binding site presence, frequency and copy number between the orthologous genes from B. taurus and B. primigenius. This provides an unbiased approach to identify cattle genes that have undergone the most changes in miRNA binding (i.e., regulation) between the wild aurochs and modern-day cattle breeds. In addition, we demonstrate that these 1,620 candidate domestication genes are enriched for roles in pigmentation, fertility, neurobiology, metabolism, immunity and production traits (including milk quality and feed efficiency). Our findings suggest that directional selection of miRNA regulatory variants was important in the domestication and subsequent artificial selection that gave rise to modern taurine cattle.}, }
@article {pmid28193151, year = {2017}, author = {Gutaker, RM and Reiter, E and Furtwängler, A and Schuenemann, VJ and Burbano, HA}, title = {Extraction of ultrashort DNA molecules from herbarium specimens.}, journal = {BioTechniques}, volume = {62}, number = {2}, pages = {76-79}, doi = {10.2144/000114517}, pmid = {28193151}, issn = {1940-9818}, mesh = {Cetrimonium ; Cetrimonium Compounds ; DNA, Ancient/chemistry/isolation &amp; purification ; DNA, Plant/*chemistry/genetics/*isolation &amp; purification ; Gene Library ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; Thiazoles ; }, abstract = {DNA extracted from herbarium specimens is highly fragmented; therefore, it is crucial to use extraction protocols that retrieve short DNA molecules. Improvements in extraction and DNA library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. Here, we applied these improvements to DNA extraction protocols for herbarium specimens and evaluated extraction performance by shotgun sequencing, which allows an accurate estimation of the distribution of DNA fragment lengths. Extraction with N-phenacylthiazolium bromide (PTB) buffer decreased median fragment length by 35% when compared with cetyl-trimethyl ammonium bromide (CTAB); modifying the binding conditions of DNA to silica allowed for an additional decrease of 10%. We did not observe a further decrease in length for single-stranded DNA (ssDNA) versus double-stranded DNA (dsDNA) library preparation methods. Our protocol enables the retrieval of ultrashort molecules from herbarium specimens, which will help to unlock the genetic information stored in herbaria.}, }
@article {pmid28188902, year = {2017}, author = {Drancourt, M and Aboudharam, G and Croce, O and Armougom, F and Robert, C and Raoult, D}, title = {Dental pulp as a source of low-contaminated DNA.}, journal = {Microbial pathogenesis}, volume = {105}, number = {}, pages = {63-67}, doi = {10.1016/j.micpath.2017.02.007}, pmid = {28188902}, issn = {1096-1208}, mesh = {Animals ; Computational Biology ; DNA/chemistry/genetics/*isolation &amp; purification ; Dental Pulp/*chemistry ; Dogs ; *Fossils ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Biology/*methods ; Paleontology/*methods ; Sequence Analysis, DNA ; }, abstract = {The in-laboratory contamination of the ancient samples hinders the result interpretation of the investigations in the field of paleomicrobiology. We had promoted the dental pulp as a sample that limits the risks of in-laboratory contamination of the ancient material. In this work, we measured the contamination of the dental pulp manipulated according to paleomicrobiology protocol, used as a source of a total DNA for metagenomics. First, total DNA extracted from two dog canines was sequenced using next generation sequencing. This yielded a total of 487,828 trimmed reads with a length of 227 ± 35 bp. Sequence analysis of the final dataset using Blast algorithm search and stringent thresholds for sequence identity and coverage against a database including both Canis lupus familiaris and Homo sapiens complete genomes showed that 95% of reads were assigned to C. familiaris whereas 0.03% was assigned to H. sapiens. In a second step, two teeth collected from two 12th century mammals were manipulated following the same protocol. A total of 13,890 trimmed reads with a 157 ± 67 bp length yielded 0-0.35% reads assigned to H. sapiens. This study indicates that the dental pulp is a useful for detecting the significant nucleic sequences in both modern and ancient samples.}, }
@article {pmid28187706, year = {2017}, author = {Palacio, P and Berthonaud, V and Guérin, C and Lambourdière, J and Maksud, F and Philippe, M and Plaire, D and Stafford, T and Marsolier-Kergoat, MC and Elalouf, JM}, title = {Genome data on the extinct Bison schoetensacki establish it as a sister species of the extant European bison (Bison bonasus).}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {48}, pmid = {28187706}, issn = {1471-2148}, mesh = {Animals ; Bison/*genetics ; Caves ; DNA, Mitochondrial/genetics ; Europe ; *Fossils ; France ; Genome, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The European bison (Bison bonasus), now found in Europe and the Caucasus, has been proposed to originate either from the extinct steppe/extant American bison lineage or from the extinct Bison schoetensacki lineage. Bison schoetensacki remains are documented in Eurasian Middle Pleistocene sites, but their presence in Upper Pleistocene sites has been questioned. Despite extensive genetic studies carried out on the steppe and European bison, no remains from the fossil record morphologically identified as Bison schoetensacki has been analyzed up to now.<br><br>RESULTS: In this paper, we analyzed a 36,000-year-old Bison schoetensaki bone sample from the Sir&#xe9;jol cave (France) and a cave hyena coprolite (fossilized feces) found in a nearby cave and containing large amounts of Bovinae DNA. We show that the Bovinae mitochondrial DNA sequences from both samples, including a complete mitochondrial genome sequence, belong to a clade recently reported in the literature. This clade only includes ancient bison specimens without taxonomic identification and displays a sister relationship with the extant European bison. The genetic proximity of Bison schoetensacki with specimens from this clade is corroborated by the analysis of nuclear DNA single nucleotide polymorphisms.<br><br>CONCLUSIONS: This work provides genetic evidence supporting the continuing presence of Bison schoetensacki up to the Upper Pleistocene. Bison schoetensacki turns out to be a sister species of Bison bonasus, excluding the steppe bison Bison priscus as a direct ancestor of the European bison.}, }
@article {pmid28182971, year = {2017}, author = {Pont, C and Salse, J}, title = {Wheat paleohistory created asymmetrical genomic evolution.}, journal = {Current opinion in plant biology}, volume = {36}, number = {}, pages = {29-37}, doi = {10.1016/j.pbi.2017.01.001}, pmid = {28182971}, issn = {1879-0356}, mesh = {Adaptation, Biological ; Diploidy ; *Evolution, Molecular ; *Genome, Plant ; *Polyploidy ; Triticum/*genetics ; }, abstract = {Following the triplication reported in Brassiceae ∼10million years ago, and at the basis of rosids ∼100million years ago, bias in organization and regulation, known as subgenome dominance, has been reported between the three post-polyploidy compartments referenced to as less fractionated (LF), medium fractionated (MF1) and more fractionated (MF2), that have been proposed to derive from an hexaploidization event involving ancestors of 7-14-21 chromosomes. Modern bread wheat experienced similar paleohistory during the last half million year of evolution opening a new hypothesis where the wheat genome is at the earliest stages on the road of diploidization through subgenome dominance driving asymmetry in gene content, gene expression abundance, transposable element content as dynamics and epigenetic control between the A, B and D subgenomes.}, }
@article {pmid28177087, year = {2017}, author = {Olivieri, A and Sidore, C and Achilli, A and Angius, A and Posth, C and Furtwängler, A and Brandini, S and Capodiferro, MR and Gandini, F and Zoledziewska, M and Pitzalis, M and Maschio, A and Busonero, F and Lai, L and Skeates, R and Gradoli, MG and Beckett, J and Marongiu, M and Mazzarello, V and Marongiu, P and Rubino, S and Rito, T and Macaulay, V and Semino, O and Pala, M and Abecasis, GR and Schlessinger, D and Conde-Sousa, E and Soares, P and Richards, MB and Cucca, F and Torroni, A}, title = {Mitogenome Diversity in Sardinians: A Genetic Window onto an Island's Past.}, journal = {Molecular biology and evolution}, volume = {34}, number = {5}, pages = {1230-1239}, pmid = {28177087}, issn = {1537-1719}, support = {HHSN271201100005C/DA/NIDA NIH HHS/United States ; }, mesh = {DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; Demography ; Ethnicity/genetics ; Evolution, Molecular ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Humans ; Islands ; Italy/ethnology ; Phylogeny ; Sequence Analysis, DNA/methods ; White People/genetics ; }, abstract = {Sardinians are "outliers" in the European genetic landscape and, according to paleogenomic nuclear data, the closest to early European Neolithic farmers. To learn more about their genetic ancestry, we analyzed 3,491 modern and 21 ancient mitogenomes from Sardinia. We observed that 78.4% of modern mitogenomes cluster into 89 haplogroups that most likely arose in situ. For each Sardinian-specific haplogroup (SSH), we also identified the upstream node in the phylogeny, from which non-Sardinian mitogenomes radiate. This provided minimum and maximum time estimates for the presence of each SSH on the island. In agreement with demographic evidence, almost all SSHs coalesce in the post-Nuragic, Nuragic and Neolithic-Copper Age periods. For some rare SSHs, however, we could not dismiss the possibility that they might have been on the island prior to the Neolithic, a scenario that would be in agreement with archeological evidence of a Mesolithic occupation of Sardinia.}, }
@article {pmid28173586, year = {2017}, author = {Leonardi, M and Librado, P and Der Sarkissian, C and Schubert, M and Alfarhan, AH and Alquraishi, SA and Al-Rasheid, KA and Gamba, C and Willerslev, E and Orlando, L}, title = {Evolutionary Patterns and Processes: Lessons from Ancient DNA.}, journal = {Systematic biology}, volume = {66}, number = {1}, pages = {e1-e29}, pmid = {28173586}, issn = {1076-836X}, mesh = {*Biological Evolution ; *DNA, Ancient ; Evolution, Molecular ; Fossils ; Genomics/trends ; Research/*trends ; }, abstract = {Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.}, }
@article {pmid28170092, year = {2017}, author = {Duval, M and Martín-Francés, L}, title = {Quantifying the impact of µCT-scanning of human fossil teeth on ESR age results.}, journal = {American journal of physical anthropology}, volume = {163}, number = {1}, pages = {205-212}, doi = {10.1002/ajpa.23180}, pmid = {28170092}, issn = {1096-8644}, mesh = {Animals ; Dental Enamel/diagnostic imaging/*radiation effects ; Electron Spin Resonance Spectroscopy ; Fossils/*diagnostic imaging ; Hominidae ; Humans ; Neanderthals ; *Paleontology/methods/standards ; Tooth/diagnostic imaging/*radiation effects ; X-Ray Microtomography ; }, abstract = {Fossil human teeth are nowadays systematically CT-scanned by palaeoanthropologists prior to any further analysis. It has been recently demonstrated that this noninvasive technique has, in most cases, virtually no influence on ancient DNA preservation. However, it may have nevertheless an impact on other techniques, like Electron Spin Resonance (ESR) dating, by artificially ageing the apparent age of the sample. To evaluate this impact, we µCT-scanned several modern enamel fragments following the standard analytical procedures employed by the Dental Anthropology Group at CENIEH, Spain, and then performed ESR dose reconstruction for each of them. The results of our experiment demonstrate that the systematic high-resolution µCT-scanning of fossil hominin remains introduces a nonnegligible X-ray dose into the tooth enamel, equivalent to 15-30 Gy depending on the parameters used. This dose may be multiplied by a factor of ∼8 if no metallic filter is used. However, this dose estimate cannot be universally extrapolated to any µCT-scan experiment but has instead to be specifically assessed for each device and set of parameters employed. The impact on the ESR age results is directly dependent on the magnitude of the geological dose measured in fossil enamel but could potentially lead to an age overestimation up to 40% in case of Late Pleistocene samples, if not taken into consideration.}, }
@article {pmid28166504, year = {2019}, author = {Luhmann, N and Lafond, M and Thevenin, A and Ouangraoua, A and Wittler, R and Chauve, C}, title = {The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {16}, number = {4}, pages = {1364-1373}, doi = {10.1109/TCBB.2017.2661761}, pmid = {28166504}, issn = {1557-9964}, mesh = {*Algorithms ; Animals ; Biological Evolution ; Computational Biology/*methods ; Computer Simulation ; Databases, Genetic ; Evolution, Molecular ; Gene Order ; Genetic Markers/genetics ; *Genome, Bacterial ; Genomics/*methods ; Models, Genetic ; Opossums/genetics ; Phylogeny ; Plasmids/metabolism ; Probability ; Reproducibility of Results ; Swine/genetics ; Yersinia/genetics ; }, abstract = {Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies, and either try to reconstruct all ancestral genomes under a global evolutionary parsimony criterion, or, focusing on a single ancestral genome, use a scaffolding approach to select a subset of ancestral gene adjacencies, generally aiming at reducing the fragmentation of the reconstructed ancestral genome. In this paper, we describe an exact algorithm for the Small Parsimony Problem that combines both approaches. We consider that gene adjacencies at internal nodes of the species phylogeny are weighted, and we introduce an objective function defined as a convex combination of these weights and the evolutionary cost under the Single-Cut-or-Join (SCJ) model. The weights of ancestral gene adjacencies can, e.g., be obtained through the recent availability of ancient DNA sequencing data, which provide a direct hint at the genome structure of the considered ancestor, or through probabilistic analysis of gene adjacencies evolution. We show the NP-hardness of our problem variant and propose a Fixed-Parameter Tractable algorithm based on the Sankoff-Rousseau dynamic programming algorithm that also allows to sample co-optimal solutions. We apply our approach to mammalian and bacterial data providing different degrees of complexity. We show that including adjacency weights in the objective has a significant impact in reducing the fragmentation of the reconstructed ancestral gene orders. An implementation is available at http://github.com/nluhmann/PhySca.}, }
@article {pmid28162894, year = {2017}, author = {Jones, ER and Zarina, G and Moiseyev, V and Lightfoot, E and Nigst, PR and Manica, A and Pinhasi, R and Bradley, DG}, title = {The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers.}, journal = {Current biology : CB}, volume = {27}, number = {4}, pages = {576-582}, pmid = {28162894}, issn = {1879-0445}, support = {263441/ERC_/European Research Council/International ; }, mesh = {Agriculture/*history ; Archaeology ; *Cultural Evolution ; DNA, Ancient/analysis ; *Farmers ; Genome, Human/*genetics ; History, Ancient ; Human Migration ; Humans ; Latvia ; Ukraine ; White People/genetics ; }, abstract = {The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the Neolithic transition across Europe, we analyzed eight ancient genomes: six samples (four to ∼1- to 4-fold coverage) from a 3,500 year temporal transect (∼8,300-4,800 calibrated years before present) through the Baltic region dating from the Mesolithic to the Late Neolithic and two samples spanning the Mesolithic-Neolithic boundary from the Dnieper Rapids region of Ukraine. We find evidence that some hunter-gatherer ancestry persisted across the Neolithic transition in both regions. However, we also find signals consistent with influxes of non-local people, most likely from northern Eurasia and the Pontic Steppe. During the Late Neolithic, this Steppe-related impact coincides with the proposed emergence of Indo-European languages in the Baltic region [3, 4]. These influences are distinct from the early farmer admixture that transformed the genetic landscape of central Europe, suggesting that changes associated with the Neolithic package in the Baltic were not driven by the same Anatolian-sourced genetic exchange.}, }
@article {pmid28162001, year = {2016}, author = {Ochoa-Lugo, MI and Muñoz, ML and Pérez-Ramírez, G and Beaty, KG and López-Armenta, M and Cervini-Silva, J and Moreno-Galeana, M and Meza, AM and Ramos, E and Crawford, MH and Romano-Pacheco, A}, title = {Genetic Affiliation of Pre-Hispanic and Contemporary Mayas Through Maternal Linage.}, journal = {Human biology}, volume = {88}, number = {2}, pages = {136-167}, doi = {10.13110/humanbiology.88.2.0136}, pmid = {28162001}, issn = {1534-6617}, mesh = {Archaeology ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Flow ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Indians, Central American/*genetics ; Phylogeography ; }, abstract = {Maya civilization developed in Mesoamerica and encompassed the Yucatan Peninsula, Guatemala, Belize, part of the Mexican states of Tabasco and Chiapas, and the western parts of Honduras and El Salvador. This civilization persisted approximately 3,000 years and was one of the most advanced of its time, possessing the only known full writing system at the time, as well as art, sophisticated architecture, and mathematical and astronomical systems. This civilization reached the apex of its power and influence during the Preclassic period, from 2000 BCE to 250 CE. Genetic variation in the pre-Hispanic Mayas from archaeological sites in the Mexican states of Yucatan, Chiapas, Quintana Roo, and Tabasco and their relationship with the contemporary communities in these regions have not been previously studied. Consequently, the principal aim of this study was to determine mitochondrial DNA (mtDNA) variation in the pre-Hispanic Maya population and to assess the relationship of these individuals with contemporary Mesoamerican Maya and populations from Asia, Beringia, and North, Central, and South America. Our results revealed interactions and gene flow between populations in the different archaeological sites assessed in this study. The mtDNA haplogroup frequency in the pre-Hispanic Maya population (60.53%, 34.21%, and 5.26% for haplogroups A, C, and D, respectively) was similar to that of most Mexican and Guatemalan Maya populations, with haplogroup A exhibiting the highest frequency. Haplogroup B most likely arrived independently and mixed with populations carrying haplogroups A and C based on its absence in the pre-Hispanic Mexican Maya populations and low frequencies in most Mexican and Guatemalan Maya populations, although this also may be due to drift. Maya and Ciboneys sharing haplotype H10 belonged to haplogroup C1 and haplotype H4 of haplogroup D, suggesting shared regional haplotypes. This may indicate a shared genetic ancestry, suggesting more regional interaction between populations in the circum-Caribbean region than previously demonstrated. Haplotype sharing between the pre-Hispanic Maya and the indigenous populations from Asia, the Aleutian Islands, and North, Central, and South America provides evidence for gene flow from the ancestral Amerindian population of the pre-Hispanic Maya to Central and South America.}, }
@article {pmid28160617, year = {2017}, author = {Gutaker, RM and Burbano, HA}, title = {Reinforcing plant evolutionary genomics using ancient DNA.}, journal = {Current opinion in plant biology}, volume = {36}, number = {}, pages = {38-45}, doi = {10.1016/j.pbi.2017.01.002}, pmid = {28160617}, issn = {1879-0356}, mesh = {*DNA, Ancient ; *Evolution, Molecular ; *Genome, Plant ; Genomics ; Sequence Analysis, DNA ; }, abstract = {Improved understanding of ancient DNA (aDNA) biochemical properties coupled with application of next generation sequencing (NGS) methods enabled sequencing and authenticating genomes of historical samples. This advancement ignited a revolution in plant evolutionary genomics by allowing direct observations of past molecular diversity. Analyses of genomes sequenced from temporally distributed samples of Gossypium sp., Phytophthora infestans and Arabidopsis thaliana improved our understanding of the evolutionary rates and time scales at which genome remodeling takes place. Comparison of historical samples of barley (Hordeum vulgare) and maize (Zea mays ssp. mays) with their present-day counterparts enabled assessment of selection during different stages of domestication. These examples show how aDNA already improved our evolutionary inferences. Increasing quality and amount of sequencing data retrieved from historical plants will further advance our understanding of plant evolution.}, }
@article {pmid28134350, year = {2017}, author = {Fernandes, D and Sirak, K and Novak, M and Finarelli, JA and Byrne, J and Connolly, E and Carlsson, JE and Ferretti, E and Pinhasi, R and Carlsson, J}, title = {The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41529}, pmid = {28134350}, issn = {2045-2322}, support = {263441/ERC_/European Research Council/International ; }, mesh = {DNA Damage ; DNA, Mitochondrial ; Family ; Genetics, Population ; *Genome, Human ; *Genomics/methods ; Haplotypes ; History, 20th Century ; *Homozygote ; Humans ; Ireland ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; White People/*genetics/history ; }, abstract = {Thomas Kent was an Irish rebel who was executed by British forces in the aftermath of the Easter Rising armed insurrection of 1916 and buried in a shallow grave on Cork prison's grounds. In 2015, ninety-nine years after his death, a state funeral was offered to his living family to honor his role in the struggle for Irish independence. However, inaccuracies in record keeping did not allow the bodily remains that supposedly belonged to Kent to be identified with absolute certainty. Using a novel approach based on homozygous single nucleotide polymorphisms, we identified these remains to be those of Kent by comparing his genetic data to that of two known living relatives. As the DNA degradation found on Kent's DNA, characteristic of ancient DNA, rendered traditional methods of relatedness estimation unusable, we forced all loci homozygous, in a process we refer to as "forced homozygote approach". The results were confirmed using simulated data for different relatedness classes. We argue that this method provides a necessary alternative for relatedness estimations, not only in forensic analysis, but also in ancient DNA studies, where reduced amounts of genetic information can limit the application of traditional methods.}, }
@article {pmid28129388, year = {2017}, author = {Hansen, HB and Damgaard, PB and Margaryan, A and Stenderup, J and Lynnerup, N and Willerslev, E and Allentoft, ME}, title = {Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0170940}, pmid = {28129388}, issn = {1932-6203}, mesh = {DNA, Ancient/*chemistry/isolation &amp; purification ; DNA, Mitochondrial/*chemistry/genetics ; Dental Cementum/*chemistry ; Humans ; Petrous Bone/*chemistry ; Tooth/chemistry ; }, abstract = {Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively) than parietal skull bone (average of 2.2%). Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001). This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (<10% endogenous DNA). In the remaining skeletons there is no systematic difference between the two substrates. A crude preservation (good/bad) applied to each sample prior to DNA-extraction predicted the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, we observe signficantly higher levels of cytosine to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons of sampling the different elements.}, }
@article {pmid28119419, year = {2017}, author = {Gansauge, MT and Gerber, T and Glocke, I and Korlevic, P and Lippik, L and Nagel, S and Riehl, LM and Schmidt, A and Meyer, M}, title = {Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase.}, journal = {Nucleic acids research}, volume = {45}, number = {10}, pages = {e79}, pmid = {28119419}, issn = {1362-4962}, mesh = {Animals ; Bone and Bones/chemistry ; DNA/genetics/metabolism ; DNA Ligases/*genetics/metabolism ; DNA Primers/chemistry/metabolism ; DNA, Single-Stranded/*genetics/metabolism ; Fossils ; *Gene Library ; High-Throughput Nucleotide Sequencing ; Horses ; Humans ; Liver/chemistry ; Nucleic Acid Hybridization ; Oligonucleotides/genetics/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Swine ; }, abstract = {DNA library preparation for high-throughput sequencing of genomic DNA usually involves ligation of adapters to double-stranded DNA fragments. However, for highly degraded DNA, especially ancient DNA, library preparation has been found to be more efficient if each of the two DNA strands are converted into library molecules separately. We present a new method for single-stranded library preparation, ssDNA2.0, which is based on single-stranded DNA ligation with T4 DNA ligase utilizing a splinter oligonucleotide with a stretch of random bases hybridized to a 3΄ biotinylated donor oligonucleotide. A thorough evaluation of this ligation scheme shows that single-stranded DNA can be ligated to adapter oligonucleotides in higher concentration than with CircLigase (an RNA ligase that was previously chosen for end-to-end ligation in single-stranded library preparation) and that biases in ligation can be minimized when choosing splinters with 7 or 8 random nucleotides. We show that ssDNA2.0 tolerates higher quantities of input DNA than CircLigase-based library preparation, is less costly and better compatible with automation. We also provide an in-depth comparison of library preparation methods on degraded DNA from various sources. Most strikingly, we find that single-stranded library preparation increases library yields from tissues stored in formalin for many years by several orders of magnitude.}, }
@article {pmid28100615, year = {2017}, author = {Palmenberg, AC}, title = {Rhinovirus C, Asthma, and Cell Surface Expression of Virus Receptor CDHR3.}, journal = {Journal of virology}, volume = {91}, number = {7}, pages = {}, pmid = {28100615}, issn = {1098-5514}, support = {U19 AI104317/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cadherin Related Proteins ; Cadherins/genetics/*metabolism ; Common Cold/*virology ; Evolution, Molecular ; Gene Expression ; Host-Pathogen Interactions ; Humans ; Membrane Proteins/genetics/*metabolism ; Rhinovirus/*genetics/metabolism ; Virus Attachment ; }, abstract = {Human rhinoviruses (RVs) of the A, B, and C species are defined agents of the common cold. But more than that, RV-A and RV-C are the dominant causes of hospitalization category infections in young children, especially those with asthma. The use of cadherin-related family member 3 (CDHR3) by RV-C as its cellular receptor creates a direct phenotypic link between human genetics (G versus A alleles cause Cys529 versus Tyr529 protein variants) and the efficiency with which RV-C can infect cells. With a lower cell surface display density, the human-specific Cys529 variant apparently confers partial protection from the severest virus-induced asthma episodes. Selective pressure favoring the Cys529 codon may have coemerged with the evolution of RV-C and helped shape modern human genomes against the virus-susceptible, albeit ancestral Tyr529.}, }
@article {pmid28095329, year = {2017}, author = {Wadsworth, C and Procopio, N and Anderung, C and Carretero, JM and Iriarte, E and Valdiosera, C and Elburg, R and Penkman, K and Buckley, M}, title = {Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites.}, journal = {Journal of proteomics}, volume = {158}, number = {}, pages = {1-8}, doi = {10.1016/j.jprot.2017.01.004}, pmid = {28095329}, issn = {1876-7737}, mesh = {Animals ; Cattle/*genetics ; DNA/*genetics ; Europe ; *Fossils ; *Tooth ; }, abstract = {UNLABELLED: Ancient DNA (aDNA) is the most informative biomolecule extracted from skeletal remains at archaeological sites, but its survival is unpredictable and its extraction and analysis is time consuming, expensive and often fails. Several proposed methods for better understanding aDNA survival are based upon the characterisation of some aspect of protein survival, but these are typically non-specific; proteomic analyses may offer an attractive method for understanding preservation processes. In this study, in-depth proteomic (LC-Orbitrap-MS/MS) analyses were carried out on 69 archaeological bovine bone and dentine samples from multiple European archaeological sites and compared with mitochondrial aDNA and amino acid racemisation (AAR) data. Comparisons of these data, including estimations of the relative abundances for seven selected non-collagenous proteins, indicate that the survival of aDNA in bone or dentine may correlate with the survival of some proteins, and that proteome complexity is a more useful predictor of aDNA survival than protein abundance or AAR. The lack of a strong correlation between the recovery of aDNA and the proteome abundance may indicate that the survival of aDNA is more closely linked to its ability to associate with bone hydroxyapatite crystals rather than to associate with proteins.<br><br>SIGNIFICANCE: Ancient biomolecule survival remains poorly understood, even with great advancements in 'omics' technologies, both in genomics and proteomics. This study investigates the survival of ancient DNA in relation to that of proteins, taking into account proteome complexity and the relative protein abundances to improve our understanding of survival mechanisms. The results show that although protein abundance is not necessarily directly related to aDNA survival, proteome complexity appears to be.}, }
@article {pmid28089793, year = {2017}, author = {Grealy, A and Phillips, M and Miller, G and Gilbert, MTP and Rouillard, JM and Lambert, D and Bunce, M and Haile, J}, title = {Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell.}, journal = {Molecular phylogenetics and evolution}, volume = {109}, number = {}, pages = {151-163}, doi = {10.1016/j.ympev.2017.01.005}, pmid = {28089793}, issn = {1095-9513}, mesh = {Animals ; *Biological Evolution ; Birds/*anatomy &amp; histology/*genetics ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Egg Shell/*anatomy &amp; histology ; *Fossils ; Genetic Variation ; Genome ; Genome, Mitochondrial ; *Genomics ; Geography ; Madagascar ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Palaeognaths, the sister group of all other living birds (neognaths), were once considered to be vicariant relics from the breakup of the Gondwanan supercontinent. However, recent molecular studies instead argue for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing their evolutionary relationships and dating their divergences, which often relies on phylogenetic information from extinct relatives and nuclear genomes. Mitogenomes from the extinct elephant birds of Madagascar have helped inform the palaeognath phylogeny; however, nuclear information has remained unavailable. Here, we use ancient DNA (aDNA) extracted from fossil eggshell, together with target enrichment and next-generation sequencing techniques, to reconstruct an additional new mitogenome from Aepyornis sp. with 33.5X coverage. We also recover the first elephant bird nuclear aDNA, represented by 12,500bp of exonic information. While we confirm that elephant birds are sister taxa to the kiwi, our data suggests that, like neognaths, palaeognaths underwent an explosive radiation between 69 and 52Ma-well after the break-up of Gondwana, and more rapidly than previously estimated from mitochondrial data alone. These results further support the idea that ratites primarily diversified immediately following the Cretaceous-Palaeogene mass extinction and convergently evolved flightlessness. Our study reinforces the importance of including information from the nuclear genome of extinct taxa for recovering deep evolutionary relationships. Furthermore, with approximately 3% endogenous aDNA retrieved, avian eggshell can be a valuable substrate for recovering high quality aDNA. We suggest that elephant bird whole genome recovery is ultimately achievable, and will provide future insights into the evolution these birds.}, }
@article {pmid28077774, year = {2017}, author = {Kehlmaier, C and Barlow, A and Hastings, AK and Vamberger, M and Paijmans, JL and Steadman, DW and Albury, NA and Franz, R and Hofreiter, M and Fritz, U}, title = {Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1846}, pages = {}, pmid = {28077774}, issn = {1471-2954}, mesh = {Africa ; Animals ; Atlantic Ocean ; Caribbean Region ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Ecuador ; *Extinction, Biological ; Genome, Mitochondrial ; Humans ; Islands ; *Phylogeny ; South America ; Tropical Climate ; Turtles/*genetics ; }, abstract = {Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1 000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galápagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galápagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.}, }
@article {pmid28072390, year = {2017}, author = {Devault, AM and Mortimer, TD and Kitchen, A and Kiesewetter, H and Enk, JM and Golding, GB and Southon, J and Kuch, M and Duggan, AT and Aylward, W and Gardner, SN and Allen, JE and King, AM and Wright, G and Kuroda, M and Kato, K and Briggs, DE and Fornaciari, G and Holmes, EC and Poinar, HN and Pepperell, CS}, title = {A molecular portrait of maternal sepsis from Byzantine Troy.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28072390}, issn = {2050-084X}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; T32 GM007215/GM/NIGMS NIH HHS/United States ; }, mesh = {Abscess/microbiology/*pathology ; DNA, Bacterial/genetics/isolation &amp; purification ; Female ; *Fossils ; Gardnerella vaginalis/classification/genetics ; Gram-Positive Bacterial Infections/microbiology/*pathology ; Humans ; Microscopy, Electron, Scanning ; Pregnancy ; Pregnancy Complications, Infectious/*pathology ; Staphylococcus saprophyticus/classification/genetics ; }, abstract = {Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman's remains. Scanning electron microscopy of the tissue revealed 'ghost cells', resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed that G. vaginalis Troy fell within contemporary genetic diversity, whereas S. saprophyticus Troy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology of S. saprophyticus infection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. These results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections.}, }
@article {pmid28059070, year = {2017}, author = {Lyu, J}, title = {Maize domestication: An ancient genome speaks.}, journal = {Nature plants}, volume = {3}, number = {}, pages = {16215}, doi = {10.1038/nplants.2016.215}, pmid = {28059070}, issn = {2055-0278}, }
@article {pmid28049632, year = {2017}, author = {Beckers, A and Fernandes, D and Fina, F and Novak, M and Abati, A and Rostomyan, L and Thiry, A and Ouafik, L and Pasture, B and Pinhasi, R and Daly, AF}, title = {Paleogenetic study of ancient DNA suggestive of X-linked acrogigantism.}, journal = {Endocrine-related cancer}, volume = {24}, number = {2}, pages = {L17-L20}, doi = {10.1530/ERC-16-0558}, pmid = {28049632}, issn = {1479-6821}, mesh = {DNA, Ancient/*analysis ; Genetic Diseases, X-Linked/*genetics ; Gigantism/*genetics ; Humans ; }, }
@article {pmid28034339, year = {2018}, author = {Kefi, R and Hechmi, M and Naouali, C and Jmel, H and Hsouna, S and Bouzaid, E and Abdelhak, S and Beraud-Colomb, E and Stevanovitch, A}, title = {On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {1}, pages = {147-157}, doi = {10.1080/24701394.2016.1258406}, pmid = {28034339}, issn = {2470-1408}, mesh = {Africa, Northern ; *DNA, Ancient ; *DNA, Mitochondrial ; Gene Flow ; Genetic Variation ; Genetics, Population ; Genome, Mitochondrial ; History, Ancient ; Humans ; Mediterranean Region ; *Phylogeny ; Sequence Analysis, DNA ; White People/*genetics ; }, abstract = {The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000-11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000-10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations. The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.}, }
@article {pmid28029148, year = {2017}, author = {Rivollat, M and Rottier, S and Couture, C and Pemonge, MH and Mendisco, F and Thomas, MG and Deguilloux, MF and Gerbault, P}, title = {Investigating mitochondrial DNA relationships in Neolithic Western Europe through serial coalescent simulations.}, journal = {European journal of human genetics : EJHG}, volume = {25}, number = {3}, pages = {388-392}, pmid = {28029148}, issn = {1476-5438}, mesh = {DNA, Mitochondrial/*genetics ; Europe ; *Evolution, Molecular ; Female ; Genetic Drift ; Human Migration ; Humans ; Male ; *Models, Genetic ; Pedigree ; White People/genetics ; }, abstract = {Recent ancient DNA studies on European Neolithic human populations have provided persuasive evidence of a major migration of farmers originating from the Aegean, accompanied by sporadic hunter-gatherer admixture into early Neolithic populations, but increasing toward the Late Neolithic. In this context, ancient mitochondrial DNA data collected from the Neolithic necropolis of Gurgy (Paris Basin, France), the largest mitochondrial DNA sample obtained from a single archeological site for the Early/Middle Neolithic period, indicate little differentiation from farmers associated to both the Danubian and Mediterranean Neolithic migration routes, as well as from Western European hunter-gatherers. To test whether this pattern of differentiation could arise in a single unstructured population by genetic drift alone, we used serial coalescent simulations. We explore female effective population size parameter combinations at the time of the colonization of Europe 45000 years ago and the most recent of the Neolithic samples analyzed in this study 5900 years ago, and identify conditions under which population panmixia between hunter-gatherers/Early-Middle Neolithic farmers and Gurgy cannot be rejected. In relation to other studies on the current debate of the origins of Europeans, these results suggest increasing hunter-gatherer admixture into farmers' group migrating farther west in Europe.}, }
@article {pmid28018628, year = {2016}, author = {Ollivier, M and Tresset, A and Bastian, F and Lagoutte, L and Axelsson, E and Arendt, ML and Bălăşescu, A and Marshour, M and Sablin, MV and Salanova, L and Vigne, JD and Hitte, C and Hänni, C}, title = {Amy2B copy number variation reveals starch diet adaptations in ancient European dogs.}, journal = {Royal Society open science}, volume = {3}, number = {11}, pages = {160449}, pmid = {28018628}, issn = {2054-5703}, abstract = {Extant dog and wolf DNA indicates that dog domestication was accompanied by the selection of a series of duplications on the Amy2B gene coding for pancreatic amylase. In this study, we used a palaeogenetic approach to investigate the timing and expansion of the Amy2B gene in the ancient dog populations of Western and Eastern Europe and Southwest Asia. Quantitative polymerase chain reaction was used to estimate the copy numbers of this gene for 13 ancient dog samples, dated to between 15 000 and 4000 years before present (cal. BP). This evidenced an increase of Amy2B copies in ancient dogs from as early as the 7th millennium cal. BP in Southeastern Europe. We found that the gene expansion was not fixed across all dogs within this early farming context, with ancient dogs bearing between 2 and 20 diploid copies of the gene. The results also suggested that selection for the increased Amy2B copy number started 7000 years cal. BP, at the latest. This expansion reflects a local adaptation that allowed dogs to thrive on a starch rich diet, especially within early farming societies, and suggests a biocultural coevolution of dog genes and human culture.}, }
@article {pmid28007976, year = {2017}, author = {Wecek, K and Hartmann, S and Paijmans, JL and Taron, U and Xenikoudakis, G and Cahill, JA and Heintzman, PD and Shapiro, B and Baryshnikov, G and Bunevich, AN and Crees, JJ and Dobosz, R and Manaserian, N and Okarma, H and Tokarska, M and Turvey, ST and Wójcik, JM and Zyla, W and Szymura, JM and Hofreiter, M and Barlow, A}, title = {Complex Admixture Preceded and Followed the Extinction of Wisent in the Wild.}, journal = {Molecular biology and evolution}, volume = {34}, number = {3}, pages = {598-612}, pmid = {28007976}, issn = {1537-1719}, mesh = {Animals ; Animals, Domestic/genetics ; Biological Evolution ; Bison/*genetics ; Breeding ; Cattle ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Gene Flow/genetics ; Genetic Variation ; Genomics/methods ; Hybridization, Genetic/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe's largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognized subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridization with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies.}, }
@article {pmid27994125, year = {2017}, author = {Llamas, B and Willerslev, E and Orlando, L}, title = {Human evolution: a tale from ancient genomes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1713}, pages = {}, pmid = {27994125}, issn = {1471-2970}, mesh = {Animals ; DNA, Ancient/*analysis ; *Evolution, Molecular ; *Genome, Human ; Hominidae/*genetics ; Humans ; }, abstract = {The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.}, }
@article {pmid27989673, year = {2017}, author = {Yonezawa, T and Segawa, T and Mori, H and Campos, PF and Hongoh, Y and Endo, H and Akiyoshi, A and Kohno, N and Nishida, S and Wu, J and Jin, H and Adachi, J and Kishino, H and Kurokawa, K and Nogi, Y and Tanabe, H and Mukoyama, H and Yoshida, K and Rasoamiaramanana, A and Yamagishi, S and Hayashi, Y and Yoshida, A and Koike, H and Akishinonomiya, F and Willerslev, E and Hasegawa, M}, title = {Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites.}, journal = {Current biology : CB}, volume = {27}, number = {1}, pages = {68-77}, doi = {10.1016/j.cub.2016.10.029}, pmid = {27989673}, issn = {1879-0445}, mesh = {Animals ; Cell Nucleus/genetics ; *Evolution, Molecular ; *Extinction, Biological ; *Fossils ; Genome ; Genomics ; Models, Genetic ; Palaeognathae/*genetics ; *Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1-3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence. Here, we recovered nuclear genome fragments from extinct elephant birds, which enabled us to reconstruct a reliable phylogenomic time tree for the Palaeognathae. Based on the tree, we identified homoplasies in morphological traits of paleognaths and reconstructed their morphology-based phylogeny including fossil species without molecular data. In contrast to the prevailing theories, the fossil paleognaths from the Northern Hemisphere were placed as the basal lineages. Combined with our stable divergence time estimates that enabled a valid argument regarding the correlation with geological events, we propose a new evolutionary scenario that contradicts the traditional view. The ancestral Palaeognathae were volant, as estimated from their molecular evolutionary rates, and originated during the Late Cretaceous in the Northern Hemisphere. They migrated to the Southern Hemisphere and speciated explosively around the Cretaceous-Paleogene boundary. They then extended their distribution to the Gondwana-derived landmasses, such as New Zealand and Madagascar, by overseas dispersal. Gigantism subsequently occurred independently on each landmass.}, }
@article {pmid27988972, year = {2017}, author = {Dyomin, AG and Danilova, MI and Mwacharo, JM and Masharsky, AE and Panteleev, AV and Druzhkova, AS and Trifonov, VA and Galkina, SA}, title = {Mitochondrial DNA D-loop haplogroup contributions to the genetic diversity of East European domestic chickens from Russia.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {134}, number = {2}, pages = {98-108}, doi = {10.1111/jbg.12248}, pmid = {27988972}, issn = {1439-0388}, mesh = {Animals ; Chickens/*genetics ; China ; DNA, Mitochondrial/*genetics ; Europe, Eastern ; Fossils ; *Genetic Variation ; Haplotypes ; Phylogeny ; }, abstract = {To elucidate geographical and historical aspects of chicken dispersal across Eastern Europe, we analysed the complete mitochondrial DNA D-loop sequence of 86 representatives from chicken breeds traditionally raised in the territory of the East European Plain (Orloff, Pavlov, Russian White, Yurlov Crower, Uzbek Game and Naked Neck). From the 1231-1232 bp D-loop sequence, 35 variable sites that defined 22 haplotypes were identified in modern chicken. All populations, except Uzbek Game, exhibited high values of haplotype and nucleotide diversity suggesting a wide variation in maternal diversity. Inclusion of mtDNA sequences from other European and Asian countries revealed representatives from this study belonging to haplogroups A, E1 and C1. We also assessed fossil chicken material dated to the 9th-18th century from archaeological sites in Northern and Eastern Europe. Three haplotypes found in the fossil specimens belonged to haplogroup E1, while one sample dated to the 18th century was assigned to the C1 haplogroup. This is the first report of the occurrence of the C1 haplogroup in European chicken populations prior to the 20th century based on the fossil material. These results provide evidence for a relatively recent introduction of all haplotypes other than E1 into the East European chicken gene pool with the significant impact of the C1 haplogroup mainly distributed in Southern China.}, }
@article {pmid27939314, year = {2016}, author = {Duggan, AT and Perdomo, MF and Piombino-Mascali, D and Marciniak, S and Poinar, D and Emery, MV and Buchmann, JP and Duchêne, S and Jankauskas, R and Humphreys, M and Golding, GB and Southon, J and Devault, A and Rouillard, JM and Sahl, JW and Dutour, O and Hedman, K and Sajantila, A and Smith, GL and Holmes, EC and Poinar, HN}, title = {17[th] Century Variola Virus Reveals the Recent History of Smallpox.}, journal = {Current biology : CB}, volume = {26}, number = {24}, pages = {3407-3412}, pmid = {27939314}, issn = {1879-0445}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Child, Preschool ; DNA, Viral/*genetics/isolation &amp; purification ; *Evolution, Molecular ; Genome, Viral ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Humans ; Mummies/history/virology ; Phylogeny ; Smallpox/*history/virology ; Smallpox Vaccine/history ; Vaccination/history ; Variola virus/*genetics ; }, abstract = {Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1-4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4-9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4-6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20[th] century VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18[th] and 19[th] centuries, concomitant with the development of modern vaccination.}, }
@article {pmid27929050, year = {2016}, author = {Westbury, M and Prost, S and Seelenfreund, A and Ramírez, JM and Matisoo-Smith, EA and Knapp, M}, title = {First complete mitochondrial genome data from ancient South American camelids - The mystery of the chilihueques from Isla Mocha (Chile).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {38708}, pmid = {27929050}, issn = {2045-2322}, mesh = {Animals ; Camelids, New World/*genetics ; Chile ; *Genome, Mitochondrial ; Islands ; *Phylogeny ; }, abstract = {In South American societies, domesticated camelids were of great cultural importance and subject to trade and translocation. South American camelids were even found on remote and hard to reach islands, emphasizing their importance to historic and pre-historic South American populations. Isla Mocha, a volcanic island 35 km offshore of Central-South Chile, is an example of such an island. When Dutch and Spanish explorers reached the island in the early 17th century, they found that domesticated camelids called "chilihueque" played a major role in the island's society. The origin and taxonomy of these enigmatic camelids is unclear and controversial. This study aims to resolve this controversy through genetic analyses of Isla Mocha camelid remains dating from pre-Columbian to early historic times. A recent archaeological excavation of site P21-3 on Isla Mocha yielded a number of camelid remains. Three complete mitochondrial genomes were successfully recovered and analysed. Phylogenetic analyses suggest that "chilihueque" was a local term for a domesticated guanaco. Results from phylogeographic analyses are consistent with Isla Mocha camelids being sourced from Southern Chilean guanaco populations. Our data highlights the capability of ancient DNA to answer questions about extinct populations which includes species identity, potential translocation events and origins of founding individuals.}, }
@article {pmid27923126, year = {2016}, author = {Marciniak, S and Prowse, TL and Herring, DA and Klunk, J and Kuch, M and Duggan, AT and Bondioli, L and Holmes, EC and Poinar, HN}, title = {Plasmodium falciparum malaria in 1[st]-2[nd] century CE southern Italy.}, journal = {Current biology : CB}, volume = {26}, number = {23}, pages = {R1220-R1222}, doi = {10.1016/j.cub.2016.10.016}, pmid = {27923126}, issn = {1879-0445}, mesh = {Cadaver ; DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; History, Ancient ; Humans ; Italy/epidemiology ; Malaria, Falciparum/epidemiology/*history ; Molar/chemistry ; Plasmodium falciparum/genetics/*isolation &amp; purification ; Roman World/history ; }, abstract = {The historical record attests to the devastation malaria exacted on ancient civilizations, particularly the Roman Empire [1]. However, evidence for the presence of malaria during the Imperial period in Italy (1st-5th century CE) is based on indirect sources, such as historical, epigraphic, or skeletal evidence. Although these sources are crucial for revealing the context of this disease, they cannot establish the causative species of Plasmodium. Importantly, definitive evidence for the presence of malaria is now possible through the implementation of ancient DNA technology. As malaria is presumed to have been at its zenith during the Imperial period [1], we selected first or second molars from 58 adults from three cemeteries from this time: Isola Sacra (associated with Portus Romae, 1st-3rd century CE), Velia (1st-2nd century CE), and Vagnari (1st-4th century CE). We performed hybridization capture using baits designed from the mitochondrial (mtDNA) genomes of Plasmodium spp. on a prioritized subset of 11 adults (informed by metagenomic sequencing). The mtDNA sequences generated provided compelling phylogenetic evidence for the presence of P. falciparum in two individuals. This is the first genomic data directly implicating P. falciparum in Imperial period southern Italy in adults.}, }
@article {pmid27915106, year = {2017}, author = {Donoghue, HD}, title = {Insights gained from ancient biomolecules into past and present tuberculosis-a personal perspective.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {56}, number = {}, pages = {176-180}, doi = {10.1016/j.ijid.2016.11.413}, pmid = {27915106}, issn = {1878-3511}, mesh = {Coinfection/genetics/immunology ; DNA, Bacterial/genetics ; Evolution, Molecular ; History, Ancient ; Humans ; Morbidity ; Mycobacterium tuberculosis/*genetics ; *Paleopathology ; Tuberculosis/*history/immunology/*microbiology ; }, abstract = {Ancient and historical tuberculosis (TB) can be recognized by its typical paleopathology in human remains. Using paleomicrobiology, it is possible to detect many more individuals infected with TB but with no visible lesions. Due to advances in molecular analysis over the past two decades, it is clear that TB was widespread in humans from the Neolithic period and has remained so until the present day. Past human populations were associated with different lineages of the Mycobacterium tuberculosis complex, thereby elucidating early human migrations. Using paleomicrobiology, it is possible to detect individuals infected with TB who are also co-infected with other bacteria or parasites. TB is also found in hosts with co-morbidities such as neoplasms, or metabolic disorders such as rickets and scurvy. In well-preserved human skeletal or mummified tissue, whole genome sequencing has detected individuals with multiple infections of different M. tuberculosis strains. Such studies put modern findings into context and emphasize the importance of human population density in such circumstances.}, }
@article {pmid27907810, year = {2017}, author = {Zupanič Pajnič, I and Zupanc, T and Balažic, J and Geršak, &#x17d;M and Stojković, O and Skadrić, I and Črešnar, M}, title = {Prediction of autosomal STR typing success in ancient and Second World War bone samples.}, journal = {Forensic science international. Genetics}, volume = {27}, number = {}, pages = {17-26}, doi = {10.1016/j.fsigen.2016.11.004}, pmid = {27907810}, issn = {1878-0326}, mesh = {Bone and Bones/*chemistry ; DNA/*genetics ; DNA Degradation, Necrotic ; DNA Fingerprinting/*methods ; *DNA, Ancient ; Humans ; Male ; *Microsatellite Repeats ; Multiplex Polymerase Chain Reaction ; Slovenia ; World War II ; }, abstract = {Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded. Therefore the new commercial qPCR kits able to assess the degree of degradation are potentially able to predict the success of downstream short tandem repeat (STR) typing. The goal of this study was to verify the quantification step using the PowerQuant kit with regard to its suitability as a screening method for autosomal STR typing success on ancient and Second World War (WWII) skeletal remains. We analysed 60 skeletons excavated from five archaeological sites and four WWII mass graves from Slovenia. The bones were cleaned, surface contamination was removed and the bones ground to a powder. Genomic DNA was obtained from 0.5g of bone powder after total demineralization. The DNA was purified using a Biorobot EZ1 device. Following PowerQuant quantification, DNA samples were subjected to autosomal STR amplification using the NGM kit. Up to 2.51ng DNA/g of powder were extracted. No inhibition was detected in any of bones analysed. 82% of the WWII bones gave full profiles while 73% of the ancient bones gave profiles not suitable for interpretation. Four bone extracts yielded no detectable amplification or zero quantification results and no profiles were obtained from any of them. Full or useful partial profiles were produced only from bone extracts where short autosomal (Auto) and long degradation (Deg) PowerQuant targets were detected. It is concluded that STR typing of old bones after quantification with the PowerQuant should be performed only when both Auto and Deg targets are detected simultaneously with no respect to [Auto]/[Deg] ratio. Prediction of STR typing success could be made according to successful amplification of Deg fragment. The PowerQuant kit is capable of identifying bone DNA samples that will not yield useful STR profiles using the NGM kit, and it can be used as a predictor of autosomal STR typing success of bone extracts obtained from ancient and WWII skeletal remains.}, }
@article {pmid27881876, year = {2016}, author = {Nistelberger, HM and Smith, O and Wales, N and Star, B and Boessenkool, S}, title = {The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37347}, pmid = {27881876}, issn = {2045-2322}, mesh = {Animals ; Archaeology/*methods ; Crops, Agricultural/genetics ; DNA, Plant/chemistry/genetics ; *Fossils ; High-Throughput Nucleotide Sequencing/*methods ; Plants/*genetics ; }, abstract = {The majority of archaeological plant material is preserved in a charred state. Obtaining reliable ancient DNA data from these remains has presented challenges due to high rates of nucleotide damage, short DNA fragment lengths, low endogenous DNA content and the potential for modern contamination. It has been suggested that high-throughput sequencing (HTS) technologies coupled with DNA enrichment techniques may overcome some of these limitations. Here we report the findings of HTS and target enrichment on four important archaeological crops (barley, grape, maize and rice) performed in three different laboratories, presenting the largest HTS assessment of charred archaeobotanical specimens to date. Rigorous analysis of our data - excluding false-positives due to background contamination or incorrect index assignments - indicated a lack of endogenous DNA in nearly all samples, except for one lightly-charred maize cob. Even with target enrichment, this sample failed to yield adequate data required to address fundamental questions in archaeology and biology. We further reanalysed part of an existing dataset on charred plant material, and found all purported endogenous DNA sequences were likely to be spurious. We suggest these technologies are not suitable for use with charred archaeobotanicals and urge great caution when interpreting data obtained by HTS of these remains.}, }
@article {pmid27872313, year = {2016}, author = {Vallebueno-Estrada, M and Rodríguez-Arévalo, I and Rougon-Cardoso, A and Martínez González, J and García Cook, A and Montiel, R and Vielle-Calzada, JP}, title = {The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {49}, pages = {14151-14156}, pmid = {27872313}, issn = {1091-6490}, mesh = {Archaeology ; *Domestication ; Genetic Variation ; *Genome, Plant ; Inbreeding ; Mexico ; Zea mays/*genetics ; }, abstract = {Pioneering archaeological expeditions lead by Richard MacNeish in the 1960s identified the valley of Tehuacán as an important center of early Mesoamerican agriculture, providing by far the widest collection of ancient crop remains, including maize. In 2012, a new exploration of San Marcos cave (Tehuacán, Mexico) yielded nonmanipulated maize specimens dating at a similar age of 5,300-4,970 calibrated y B.P. On the basis of shotgun sequencing and genomic comparisons to Balsas teosinte and modern maize, we show herein that the earliest maize from San Marcos cave was a partial domesticate diverging from the landraces and containing ancestral allelic variants that are absent from extant maize populations. Whereas some domestication loci, such as teosinte branched1 (tb1) and brittle endosperm2 (bt2), had already lost most of the nucleotide variability present in Balsas teosinte, others, such as teosinte glume architecture1 (tga1) and sugary1 (su1), conserved partial levels of nucleotide variability that are absent from extant maize. Genetic comparisons among three temporally convergent samples revealed that they were homozygous and identical by descent across their genome. Our results indicate that the earliest maize from San Marcos was already inbred, opening the possibility for Tehuacán maize cultivation evolving from reduced founder populations of isolated and perhaps self-pollinated individuals.}, }
@article {pmid27869396, year = {2016}, author = {Pérez, LA and Rodríguez, F and Langebaek, CH and Groot, H}, title = {[Real-time quantification to analyze historical Colombian samples detecting a short fragment of hypervariable region II of mitochondrial DNA].}, journal = {Biomedica : revista del Instituto Nacional de Salud}, volume = {36}, number = {3}, pages = {475-482}, doi = {10.7705/biomedica.v36i3.3098}, pmid = {27869396}, issn = {2590-7379}, mesh = {Colombia ; *DNA, Mitochondrial ; Humans ; *Real-Time Polymerase Chain Reaction ; }, abstract = {Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples. Materials and methods: The proposed method is based on the use of mini-primers for the specific amplification of short fragments of mitochondrial DNA. The subsequent purification of these amplified fragments allows a standard curve to be constructed with concentrations in accordance to the state of degradation of the samples. Results: The proposed method successfully detected DNA from ancient samples including bone remains and mummified tissue. DNA inhibitory substances were also detected. Conclusion: The proposed method represents a simpler and cost-effective way to detect low amounts of aDNA, and a tool to differentiate DNA-free samples from samples with inhibitory substances.}, }
@article {pmid27866890, year = {2016}, author = {Ramos-Madrigal, J and Smith, BD and Moreno-Mayar, JV and Gopalakrishnan, S and Ross-Ibarra, J and Gilbert, MTP and Wales, N}, title = {Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication.}, journal = {Current biology : CB}, volume = {26}, number = {23}, pages = {3195-3201}, doi = {10.1016/j.cub.2016.09.036}, pmid = {27866890}, issn = {1879-0445}, mesh = {Crops, Agricultural/*genetics ; DNA, Plant/genetics ; *Genome, Plant ; Selection, Genetic ; Zea mays/*genetics ; }, abstract = {The complex evolutionary history of maize (Zea mays L. ssp. mays) has been clarified with genomic-level data from modern landraces and wild teosinte grasses [1, 2], augmenting archaeological findings that suggest domestication occurred between 10,000 and 6,250 years ago in southern Mexico [3, 4]. Maize rapidly evolved under human selection, leading to conspicuous phenotypic transformations, as well as adaptations to varied environments [5]. Still, many questions about the domestication process remain unanswered because modern specimens do not represent the full range of past diversity due to abandonment of unproductive lineages, genetic drift, on-going natural selection, and recent breeding activity. To more fully understand the history and spread of maize, we characterized the draft genome of a 5,310-year-old archaeological cob excavated in the Tehuacan Valley of Mexico. We compare this ancient sample against a reference panel of modern landraces and teosinte grasses using D statistics, model-based clustering algorithms, and multidimensional scaling analyses, demonstrating the specimen derives from the same source population that gave rise to modern maize. We find that 5,310 years ago, maize in the Tehuacan Valley was on the whole genetically closer to modern maize than to its wild counterpart. However, many genes associated with key domestication traits existed in the ancestral state, sharply contrasting with the ubiquity of derived alleles in living landraces. These findings suggest much of the evolution during domestication may have been gradual and encourage further paleogenomic research to address provocative questions about the world's most produced cereal.}, }
@article {pmid27863491, year = {2016}, author = {Lenstra, JA and Liu, J}, title = {The Year of the Wisent.}, journal = {BMC biology}, volume = {14}, number = {1}, pages = {100}, pmid = {27863491}, issn = {1741-7007}, mesh = {Animals ; Bison/*genetics ; Caves ; *Climate Change ; }, abstract = {Delving into European prehistory, two recent studies analyze ancient DNA from bison species depicted by our ancestors on the walls of their caves. The DNA tells a story of migrations driven by climate change but leaves some mystery clouding the genetic descent and climate preference of the still-extant wisent, otherwise known as the European bison.See research articles: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0317-7 http://www.nature.com/articles/ncomms13158.}, }
@article {pmid27859602, year = {2017}, author = {West, C and Hofman, CA and Ebbert, S and Martin, J and Shirazi, S and Dunning, S and Maldonado, JE}, title = {Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {31}, number = {5}, pages = {1163-1172}, doi = {10.1111/cobi.12865}, pmid = {27859602}, issn = {1523-1739}, mesh = {Alaska ; Animals ; Archaeology ; *Conservation of Natural Resources ; *DNA, Ancient ; Humans ; *Introduced Species ; Islands ; *Sciuridae ; }, abstract = {The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human-mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation.}, }
@article {pmid27853601, year = {2016}, author = {Wood, JR and Herrera, MJ and Scofield, RP and Wilmshurst, JM}, title = {Origin and timing of New Zealand's earliest domestic chickens: Polynesian commensals or European introductions?.}, journal = {Royal Society open science}, volume = {3}, number = {8}, pages = {160258}, pmid = {27853601}, issn = {2054-5703}, abstract = {Human settlers transported chickens (Gallus gallus domesticus) to most East Polynesian archipelagos between AD 1000 and 1300; however, it has long been assumed that New Zealand was an exception. Despite the fact that chicken bones have been recovered from localities of early archaeological middens in New Zealand, their age and genetic relationships have never been critically assessed. Here, we test the assumption that chickens were not introduced to New Zealand during prehistory through ancient DNA and radiocarbon analyses of chicken bones from sites of Māori middens containing prehistoric material. The chickens belong to the widespread mitochondrial control region haplogroup E. Radiocarbon dating reveals that the bones are not prehistoric, but are still the earliest chicken remains known from New Zealand. Two of the bones pre-date permanent European settlement (ca 1803s onwards) but overlap with the arrival of James Cook's second voyage (1773-1774), and, therefore, they are likely to be chickens, or progeny thereof, liberated during that voyage. Our results support the idea that chickens were first introduced to New Zealand by Europeans, and provide new insights into Māori uptake and integration of resources introduced during the early post-European period.}, }
@article {pmid27848937, year = {2016}, author = {Marshall, S and Das, R and Pirooznia, M and Elhaik, E}, title = {Reconstructing Druze population history.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35837}, pmid = {27848937}, issn = {2045-2322}, support = {MC_PC_14115/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anthropology, Cultural ; Emigration and Immigration/*history ; Ethnicity/*genetics/*history ; Female ; History, Ancient ; Humans ; Israel ; Lebanon ; Male ; Phylogeography ; Syria ; }, abstract = {The Druze are an aggregate of communities in the Levant and Near East living almost exclusively in the mountains of Syria, Lebanon and Israel whose ~1000 year old religion formally opposes mixed marriages and conversions. Despite increasing interest in genetics of the population structure of the Druze, their population history remains unknown. We investigated the genetic relationships between Israeli Druze and both modern and ancient populations. We evaluated our findings in light of three hypotheses purporting to explain Druze history that posit Arabian, Persian or mixed Near Eastern-Levantine roots. The biogeographical analysis localised proto-Druze to the mountainous regions of southeastern Turkey, northern Iraq and southeast Syria and their descendants clustered along a trajectory between these two regions. The mixed Near Eastern-Middle Eastern localisation of the Druze, shown using both modern and ancient DNA data, is distinct from that of neighbouring Syrians, Palestinians and most of the Lebanese, who exhibit a high affinity to the Levant. Druze biogeographic affinity, migration patterns, time of emergence and genetic similarity to Near Eastern populations are highly suggestive of Armenian-Turkish ancestries for the proto-Druze.}, }
@article {pmid27847329, year = {2017}, author = {Lewandowska, M and Jędrychowska-Dańska, K and Zamerska, A and Płoszaj, T and Witas, HW}, title = {The genetic profile of susceptibility to infectious diseases in Roman-Period populations from Central Poland.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {47}, number = {}, pages = {1-8}, doi = {10.1016/j.meegid.2016.11.011}, pmid = {27847329}, issn = {1567-7257}, mesh = {Cation Transport Proteins/genetics ; Communicable Diseases/*genetics ; DNA, Ancient/*analysis ; Genetic Drift ; Genetic Predisposition to Disease/*genetics ; History, Ancient ; Humans ; Immunity, Innate/genetics ; Poland ; Polymorphism, Single Nucleotide/genetics ; Roman World ; }, abstract = {For thousands of years human beings have resisted life-threatening pathogens. This ongoing battle is considered to be the major force shaping our gene pool as every micro-evolutionary process provokes specific shifts in the genome, both that of the host and the pathogen. Past populations were more susceptible to changes in allele frequencies not only due to selection pressure, but also as a result of genetic drift, migration and inbreeding. In the present study we have investigated the frequency of five polymorphisms within innate immune-response genes (SLC11A1 D543N, MBL2 G161A, P2RX7 A1513C, IL10 A-1082G, TLR2 -196 to -174 ins/del) related to susceptibility to infections in humans. The DNA of individuals from two early Roman-Period populations of Linowo and Rogowo was analysed. The distribution of three mutations varied significantly when compared to the modern Polish population. The TAFT analysis suggests that the decreased frequency of SLC11A1 D543N in modern Poles as compared to 2nd century Linowo samples is the result of non-stochastic mechanisms, such as purifying or balancing selection. The disparity in frequency of other mutations is most likely the result of genetic drift, an evolutionary force which is remarkably amplified in low-size groups. Together with the FST analysis, mtDNA haplotypes' distribution and deviation from the Hardy-Weinberg equilibrium, we suggest that the two populations were not interbreeding (despite the close proximity between them), but rather inbreeding, the results of which are particularly pronounced among Rogowo habitants.}, }
@article {pmid27846491, year = {2016}, author = {Fan, S and Hansen, ME and Lo, Y and Tishkoff, SA}, title = {Going global by adapting local: A review of recent human adaptation.}, journal = {Science (New York, N.Y.)}, volume = {354}, number = {6308}, pages = {54-59}, pmid = {27846491}, issn = {1095-9203}, support = {R01 DK104339/DK/NIDDK NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; R01 LM010098/LM/NLM NIH HHS/United States ; R01 LM009012/LM/NLM NIH HHS/United States ; T32 ES019851/ES/NIEHS NIH HHS/United States ; R01 GM113657/GM/NIGMS NIH HHS/United States ; DP1 ES022577/ES/NIEHS NIH HHS/United States ; }, mesh = {Acclimatization/genetics ; Adaptation, Physiological/*genetics ; Altitude ; Dairy Products ; Environment ; *Gene-Environment Interaction ; Humans ; Radiation Exposure ; Rainforest ; Selection, Genetic ; Tropical Climate ; }, abstract = {The spread of modern humans across the globe has led to genetic adaptations to diverse local environments. Recent developments in genomic technologies, statistical analyses, and expanded sampled populations have led to improved identification and fine-mapping of genetic variants associated with adaptations to regional living conditions and dietary practices. Ongoing efforts in sequencing genomes of indigenous populations, accompanied by the growing availability of "-omics" and ancient DNA data, promises a new era in our understanding of recent human evolution and the origins of variable traits and disease risks.}, }
@article {pmid27824339, year = {2016}, author = {Seersholm, FV and Pedersen, MW and Søe, MJ and Shokry, H and Mak, SS and Ruter, A and Raghavan, M and Fitzhugh, W and Kjær, KH and Willerslev, E and Meldgaard, M and Kapel, CM and Hansen, AJ}, title = {DNA evidence of bowhead whale exploitation by Greenlandic Paleo-Inuit 4,000 years ago.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13389}, pmid = {27824339}, issn = {2041-1723}, mesh = {Animals ; Archaeology ; Biodiversity ; Bowhead Whale/*genetics ; DNA/*genetics ; DNA Damage ; DNA, Plant/genetics ; Fossils ; Geography ; Geologic Sediments ; Greenland ; Helminths/classification ; Humans ; *Inuit ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The demographic history of Greenland is characterized by recurrent migrations and extinctions since the first humans arrived 4,500 years ago. Our current understanding of these extinct cultures relies primarily on preserved fossils found in their archaeological deposits, which hold valuable information on past subsistence practices. However, some exploited taxa, though economically important, comprise only a small fraction of these sub-fossil assemblages. Here we reconstruct a comprehensive record of past subsistence economies in Greenland by sequencing ancient DNA from four well-described midden deposits. Our results confirm that the species found in the fossil record, like harp seal and ringed seal, were a vital part of Inuit subsistence, but also add a new dimension with evidence that caribou, walrus and whale species played a more prominent role for the survival of Paleo-Inuit cultures than previously reported. Most notably, we report evidence of bowhead whale exploitation by the Saqqaq culture 4,000 years ago.}, }
@article {pmid27821740, year = {2016}, author = {Bayless, AM and Smith, JM and Song, J and McMinn, PH and Teillet, A and August, BK and Bent, AF}, title = {Disease resistance through impairment of α-SNAP-NSF interaction and vesicular trafficking by soybean Rhg1.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {47}, pages = {E7375-E7382}, pmid = {27821740}, issn = {1091-6490}, mesh = {Animals ; *Disease Resistance ; Mutation ; N-Ethylmaleimide-Sensitive Proteins/*metabolism ; Nematoda/physiology ; Plant Diseases/parasitology ; Plant Proteins/genetics/metabolism ; Protein Binding ; Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins/genetics/*metabolism ; Glycine max/genetics/*metabolism/parasitology ; Transport Vesicles/*metabolism ; }, abstract = {α-SNAP [soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein] and NSF proteins are conserved across eukaryotes and sustain cellular vesicle trafficking by mediating disassembly and reuse of SNARE protein complexes, which facilitate fusion of vesicles to target membranes. However, certain haplotypes of the Rhg1 (resistance to Heterodera glycines 1) locus of soybean possess multiple repeat copies of an α-SNAP gene (Glyma.18G022500) that encodes atypical amino acids at a highly conserved functional site. These Rhg1 loci mediate resistance to soybean cyst nematode (SCN; H. glycines), the most economically damaging pathogen of soybeans worldwide. Rhg1 is widely used in agriculture, but the mechanisms of Rhg1 disease resistance have remained unclear. In the present study, we found that the resistance-type Rhg1 α-SNAP is defective in interaction with NSF. Elevated in planta expression of resistance-type Rhg1 α-SNAPs depleted the abundance of SNARE-recycling 20S complexes, disrupted vesicle trafficking, induced elevated abundance of NSF, and caused cytotoxicity. Soybean, due to ancient genome duplication events, carries other loci that encode canonical (wild-type) α-SNAPs. Expression of these α-SNAPs counteracted the cytotoxicity of resistance-type Rhg1 α-SNAPs. For successful growth and reproduction, SCN dramatically reprograms a set of plant root cells and must sustain this sedentary feeding site for 2-4 weeks. Immunoblots and electron microscopy immunolocalization revealed that resistance-type α-SNAPs specifically hyperaccumulate relative to wild-type α-SNAPs at the nematode feeding site, promoting the demise of this biotrophic interface. The paradigm of disease resistance through a dysfunctional variant of an essential gene may be applicable to other plant-pathogen interactions.}, }
@article {pmid27821432, year = {2017}, author = {Kousathanas, A and Leuenberger, C and Link, V and Sell, C and Burger, J and Wegmann, D}, title = {Inferring Heterozygosity from Ancient and Low Coverage Genomes.}, journal = {Genetics}, volume = {205}, number = {1}, pages = {317-332}, pmid = {27821432}, issn = {1943-2631}, mesh = {Base Sequence ; Chromosome Mapping/methods ; DNA, Ancient/*analysis ; Genetic Carrier Screening/*methods ; Genetic Variation ; Genetics, Population/methods ; Genome, Human ; Heterozygote ; Humans ; Male ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {While genetic diversity can be quantified accurately from high coverage sequencing data, it is often desirable to obtain such estimates from data with low coverage, either to save costs or because of low DNA quality, as is observed for ancient samples. Here, we introduce a method to accurately infer heterozygosity probabilistically from sequences with average coverage [Formula: see text] of a single individual. The method relaxes the infinite sites assumption of previous methods, does not require a reference sequence, except for the initial alignment of the sequencing data, and takes into account both variable sequencing errors and potential postmortem damage. It is thus also applicable to nonmodel organisms and ancient genomes. Since error rates as reported by sequencing machines are generally distorted and require recalibration, we also introduce a method to accurately infer recalibration parameters in the presence of postmortem damage. This method does not require knowledge about the underlying genome sequence, but instead works with haploid data (e.g., from the X-chromosome from mammalian males) and integrates over the unknown genotypes. Using extensive simulations we show that a few megabasepairs of haploid data are sufficient for accurate recalibration, even at average coverages as low as [Formula: see text] At similar coverages, our method also produces very accurate estimates of heterozygosity down to [Formula: see text] within windows of about 1 Mbp. We further illustrate the usefulness of our approach by inferring genome-wide patterns of diversity for several ancient human samples, and we found that 3000-5000-year-old samples showed diversity patterns comparable to those of modern humans. In contrast, two European hunter-gatherer samples exhibited not only considerably lower levels of diversity than modern samples, but also highly distinct distributions of diversity along their genomes. Interestingly, these distributions were also very different between the two samples, supporting earlier conclusions of a highly diverse and structured population in Europe prior to the arrival of farming.}, }
@article {pmid27821149, year = {2016}, author = {Quintana-Murci, L}, title = {Understanding rare and common diseases in the context of human evolution.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {225}, pmid = {27821149}, issn = {1474-760X}, mesh = {Demography ; Disease/*genetics ; *Evolution, Molecular ; *Genetics, Population ; Humans ; Models, Genetic ; Mutation ; Polymorphism, Genetic ; *Selection, Genetic ; }, abstract = {The wealth of available genetic information is allowing the reconstruction of human demographic and adaptive history. Demography and purifying selection affect the purge of rare, deleterious mutations from the human population, whereas positive and balancing selection can increase the frequency of advantageous variants, improving survival and reproduction in specific environmental conditions. In this review, I discuss how theoretical and empirical population genetics studies, using both modern and ancient DNA data, are a powerful tool for obtaining new insight into the genetic basis of severe disorders and complex disease phenotypes, rare and common, focusing particularly on infectious disease risk.}, }
@article {pmid27813680, year = {2017}, author = {MacHugh, DE and Larson, G and Orlando, L}, title = {Taming the Past: Ancient DNA and the Study of Animal Domestication.}, journal = {Annual review of animal biosciences}, volume = {5}, number = {}, pages = {329-351}, doi = {10.1146/annurev-animal-022516-022747}, pmid = {27813680}, issn = {2165-8110}, mesh = {Animals ; Animals, Domestic ; *DNA, Ancient ; *Domestication ; Livestock ; *Selection, Genetic ; }, abstract = {During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.}, }
@article {pmid27803981, year = {2017}, author = {Neparáczki, E and Juhász, Z and Pamjav, H and Fehér, T and Csányi, B and Zink, A and Maixner, F and Pálfi, G and Molnár, E and Pap, I and Kustár, &#xc1; and Révész, L and Raskó, I and Török, T}, title = {Genetic structure of the early Hungarian conquerors inferred from mtDNA haplotypes and Y-chromosome haplogroups in a small cemetery.}, journal = {Molecular genetics and genomics : MGG}, volume = {292}, number = {1}, pages = {201-214}, pmid = {27803981}, issn = {1617-4623}, mesh = {Algorithms ; Archaeology ; Cemeteries ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; Female ; Genetics, Medical/methods ; Genetics, Population ; Genome, Human ; *Haplotypes ; Human Migration ; Humans ; Hungary ; Male ; Phylogeny ; White People/*genetics ; }, abstract = {We applied ancient DNA methods to shed light on the origin of ancient Hungarians and their relation to modern populations. Hungarians moved into the Carpathian Basin from the Eurasian Pontic steppes in the year 895 AD as a confederation of seven tribes, but their further origin remains obscure. Here, we present 17 mtDNA haplotypes and four Y-chromosome haplogroups, which portray the genetic composition of an entire small cemetery of the first generation Hungarians. Using novel algorithms to compare these mitochondrial DNA haplogroups with other ancient and modern Eurasian data, we revealed that a significant portion of the Hungarians probably originated from a long ago consolidated gene pool in Central Asia-South Siberia, which still persists in modern Hungarians. Another genetic layer of the early Hungarians was obtained during their westward migrations by admixing with various populations of European origin, and an important component of these was derived from the Caucasus region. Most of the modern populations, which are genetically closest relatives of ancient Hungarians, today speak non-Indo-European languages. Our results contribute to our understanding of the peopling of Europe by providing ancient DNA data from a still genetically poorly studied period of medieval human migrations.}, }
@article {pmid27795845, year = {2016}, author = {Zhenilo, SV and Sokolov, AS and Prokhortchouk, EB}, title = {Epigenetics of Ancient DNA.}, journal = {Acta naturae}, volume = {8}, number = {3}, pages = {72-76}, pmid = {27795845}, issn = {2075-8251}, abstract = {Initially, the study of DNA isolated from ancient specimens had been based on the analysis of the primary nucleotide sequence. This approach has allowed researchers to study the evolutionary changes that occur in different populations and determine the influence of the environment on genetic selection. However, the improvement of methodological approaches to genome-wide analysis has opened up new possibilities in the search for the epigenetic mechanisms involved in the regulation of gene expression. It was discovered recently that the methylation status of the regulatory elements of the HOXD cluster and MEIS1 gene changed during human evolution. Epigenetic changes in these genes played a key role in the evolution of the limbs of modern humans. Recent works have demonstrated that it is possible to determine the transcriptional activity of genes in ancient DNA samples by combining information on DNA methylation and the DNAaseI hypersensitive sequences located at the transcription start sites of genes. In the nearest future, if a preserved fossils brain is found, it will be possible to identify the evolutionary changes in the higher nervous system associated with epigenetic differences.}, }
@article {pmid27794556, year = {2017}, author = {Renaud, G and Hanghøj, K and Willerslev, E and Orlando, L}, title = {gargammel: a sequence simulator for ancient DNA.}, journal = {Bioinformatics (Oxford, England)}, volume = {33}, number = {4}, pages = {577-579}, pmid = {27794556}, issn = {1367-4811}, mesh = {Animals ; *Computer Simulation ; DNA Contamination ; *DNA Damage ; DNA, Ancient/*chemistry ; Humans ; *Postmortem Changes ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {SUMMARY: Ancient DNA has emerged as a remarkable tool to infer the history of extinct species and past populations. However, many of its characteristics, such as extensive fragmentation, damage and contamination, can influence downstream analyses. To help investigators measure how these could impact their analyses in silico , we have developed gargammel, a package that simulates ancient DNA fragments given a set of known reference genomes. Our package simulates the entire molecular process from post-mortem DNA fragmentation and DNA damage to experimental sequencing errors, and reproduces most common bias observed in ancient DNA datasets.<br><br>The package is publicly available on github: https://grenaud.github.io/gargammel/ and released under the GPL.<br><br>CONTACT: gabriel.renaud@snm.ku.dk.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid27790833, year = {2017}, author = {Boessenkool, S and Hanghøj, K and Nistelberger, HM and Der Sarkissian, C and Gondek, AT and Orlando, L and Barrett, JH and Star, B}, title = {Combining bleach and mild predigestion improves ancient DNA recovery from bones.}, journal = {Molecular ecology resources}, volume = {17}, number = {4}, pages = {742-751}, doi = {10.1111/1755-0998.12623}, pmid = {27790833}, issn = {1755-0998}, mesh = {Animals ; *Bone and Bones ; DNA, Ancient/*isolation &amp; purification ; Gadus morhua ; Gene Library ; High-Throughput Nucleotide Sequencing ; Horses ; Sequence Analysis, DNA ; Sodium Hypochlorite/*chemistry ; }, abstract = {The feasibility of genome-scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre-extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole-genome sequencing.}, }
@article {pmid27785127, year = {2016}, author = {Abdul-Aziz, MA and Cooper, A and Weyrich, LS}, title = {Exploring Relationships between Host Genome and Microbiome: New Insights from Genome-Wide Association Studies.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1611}, pmid = {27785127}, issn = {1664-302X}, abstract = {As our understanding of the human microbiome expands, impacts on health and disease continue to be revealed. Alterations in the microbiome can result in dysbiosis, which has now been linked to subsequent autoimmune and metabolic diseases, highlighting the need to identify factors that shape the microbiome. Research has identified that the composition and functions of the human microbiome can be influenced by diet, age, sex, and environment. More recently, studies have explored how human genetic variation may also influence the microbiome. Here, we review several recent analytical advances in this new research area, including those that use genome-wide association studies to examine host genome-microbiome interactions, while controlling for the influence of other factors. We find that current research is limited by small sample sizes, lack of cohort replication, and insufficient confirmatory mechanistic studies. In addition, we discuss the importance of understanding long-term interactions between the host genome and microbiome, as well as the potential impacts of disrupting this relationship, and explore new research avenues that may provide information about the co-evolutionary history of humans and their microorganisms.}, }
@article {pmid27698418, year = {2016}, author = {Skoglund, P and Posth, C and Sirak, K and Spriggs, M and Valentin, F and Bedford, S and Clark, GR and Reepmeyer, C and Petchey, F and Fernandes, D and Fu, Q and Harney, E and Lipson, M and Mallick, S and Novak, M and Rohland, N and Stewardson, K and Abdullah, S and Cox, MP and Friedlaender, FR and Friedlaender, JS and Kivisild, T and Koki, G and Kusuma, P and Merriwether, DA and Ricaut, FX and Wee, JT and Patterson, N and Krause, J and Pinhasi, R and Reich, D}, title = {Genomic insights into the peopling of the Southwest Pacific.}, journal = {Nature}, volume = {538}, number = {7626}, pages = {510-513}, pmid = {27698418}, issn = {1476-4687}, support = {/HHMI/HHMI/ ; 261213/ERC_/European Research Council/International ; GM100233//National Institute of Health/International ; R01 GM100233/GM/NIGMS NIH HHS/United States ; 263441/ERC_/European Research Council/International ; }, mesh = {Asian People/*genetics ; Female ; Genetics, Population ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/*history ; Humans ; Male ; Native Hawaiian or Pacific Islander/*genetics ; New Guinea/ethnology ; *Phylogeny ; Polynesia/ethnology ; Tonga ; Vanuatu ; }, abstract = {The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100-2,700 years before present) and one from Tonga (about 2,700-2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceania. However, our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands.}, }
@article {pmid27782796, year = {2016}, author = {Soares, AE and Novak, BJ and Haile, J and Heupink, TH and Fjeldså, J and Gilbert, MT and Poinar, H and Church, GM and Shapiro, B}, title = {Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {230}, pmid = {27782796}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; Columbidae/classification/*genetics ; Extinction, Biological ; Genetic Variation ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context.<br><br>RESULTS: We used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves.<br><br>CONCLUSIONS: Our analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.}, }
@article {pmid27586443, year = {2016}, author = {Waters, JM and Grosser, S}, title = {Managing shifting species: Ancient DNA reveals conservation conundrums in a dynamic world.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {11}, pages = {1177-1184}, doi = {10.1002/bies.201600044}, pmid = {27586443}, issn = {1521-1878}, mesh = {Animals ; *Biological Evolution ; Climate Change ; *Conservation of Natural Resources ; DNA, Ancient/*analysis ; *Ecosystem ; Introduced Species ; New Zealand ; }, abstract = {The spread of exotic species represents a major driver of biological change across the planet. While dispersal and colonization are natural biological processes, we suggest that the failure to recognize increasing rates of human-facilitated self-introductions may represent a threat to native lineages. Notably, recent biogeographic analyses have revealed numerous cases of biological range shifts in response to anthropogenic impacts and climate change. In particular, ancient DNA analyses have revealed several cases in which lineages traditionally thought to be long-established "natives" are in fact recent colonizers. Such range expansion events have apparently occurred in response to human-mediated native biodiversity declines and ecosystem change, particularly in recently colonized, isolated ecosystems such as New Zealand. While such events can potentially boost local biodiversity, the spread of exotic lineages may also hasten the decline of indigenous species, so it is essential that conservation managers recognize these rapid biotic shifts. .}, }
@article {pmid27771467, year = {2017}, author = {Juras, A and Chyleński, M and Krenz-Niedbała, M and Malmström, H and Ehler, E and Pospieszny, &#x141; and Łukasik, S and Bednarczyk, J and Piontek, J and Jakobsson, M and Dabert, M}, title = {Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.}, journal = {Forensic science international. Genetics}, volume = {26}, number = {}, pages = {30-39}, doi = {10.1016/j.fsigen.2016.10.008}, pmid = {27771467}, issn = {1878-0326}, mesh = {Bone and Bones/chemistry ; Carbon Isotopes ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Female ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Nitrogen Isotopes ; *Pedigree ; Poland ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Sex Determination Analysis ; Tooth/chemistry ; }, abstract = {We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq™ Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS [14]C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used. We found distinct mitochondrial genomes belonging to haplogroups U5b2a1a, K1c and H3d in the first grave cluster, and excluded maternal kin patterns among the three analyzed individuals. In the second grave cluster one individual belonged to K1a4. However, we could not affiliate the second individual to a certain haplogroup due to the fragmented state of the mitochondrial genome. Although the individuals from the second grave cluster differ at position 6643, we believe that more data is needed to fully resolve this issue. We retrieved between 26 and 77 autosomal SNPs from three of the individuals. Based on kinship estimations, taking into account the allelic dropout distribution, we could not exclude first degree kin relation between the two individuals from the second grave cluster. We could, however, exclude a first degree kinship between these two individuals and an individual from the first grave cluster. Presumably, not only biological kinship, but also social relations played an important role in the funerary practice during this time period. We further conclude that the HID-Ion AmpliSeq™ Identity Panel may prove useful for first degree kin relation studies for samples with good DNA preservation, and that mitochondrial genome capture enrichment is a powerful tool for excluding direct maternal relationship in ancient individuals.}, }
@article {pmid27769298, year = {2016}, author = {Massilani, D and Guimaraes, S and Brugal, JP and Bennett, EA and Tokarska, M and Arbogast, RM and Baryshnikov, G and Boeskorov, G and Castel, JC and Davydov, S and Madelaine, S and Putelat, O and Spasskaya, NN and Uerpmann, HP and Grange, T and Geigl, EM}, title = {Past climate changes, population dynamics and the origin of Bison in Europe.}, journal = {BMC biology}, volume = {14}, number = {1}, pages = {93}, pmid = {27769298}, issn = {1741-7007}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Bison/*classification/genetics ; *Climate Change ; Europe ; Extinction, Biological ; Genetic Variation/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *Population Dynamics ; }, abstract = {BACKGROUND: Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe's megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene.<br><br>RESULTS: Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene. Fifty-seven complete and partial ancient mitogenomes from throughout Europe, the Caucasus, and Siberia reveal that three populations of wisent (Bison bonasus) and steppe bison (B. priscus) alternately occupied Western Europe, correlating with climate-induced environmental changes. The Late Pleistocene European steppe bison originated from northern Eurasia, whereas the modern wisent population emerged from a refuge in the southern Caucasus after the last glacial maximum. A population overlap during a transition period is reflected in ca. 36,000-year-old paintings in the French Chauvet cave. Bayesian analyses of these complete ancient mitogenomes yielded new dates of the various branching events during the evolution of Bison and its radiation with Bos, which lead us to propose that the genetic affiliation between the wisent and cattle mitogenomes result from incomplete lineage sorting rather than post-speciation gene flow.<br><br>CONCLUSION: The paleogenetic analysis of bison remains from the last 50,000 years reveals the influence of climate changes on the dynamics of the various bison populations in Europe, only one of which survived into the Holocene, where it experienced severe reductions in its genetic diversity. The time depth and geographical scope of this study enables us to propose temperate Western Europe as a suitable biotope for the wisent compatible with its reintroduction.}, }
@article {pmid27613970, year = {2016}, author = {Madel, MB and Niederstätter, H and Parson, W}, title = {TriXY-Homogeneous genetic sexing of highly degraded forensic samples including hair shafts.}, journal = {Forensic science international. Genetics}, volume = {25}, number = {}, pages = {166-174}, doi = {10.1016/j.fsigen.2016.09.001}, pmid = {27613970}, issn = {1878-0326}, mesh = {Animals ; *Chromosomes, Human, X ; *Chromosomes, Human, Y ; DNA/*genetics ; DNA Degradation, Necrotic ; *DNA, Intergenic ; Female ; Hair/chemistry ; Humans ; Male ; *Real-Time Polymerase Chain Reaction ; Sex Determination Analysis/*methods ; Species Specificity ; }, abstract = {Sexing of biological evidence is an important aspect in forensic investigations. A routinely used molecular-genetic approach to this endeavour is the amelogenin sex test, which is integrated in most commercially available polymerase chain reaction (PCR) kits for human identification. However, this assay is not entirely effective in respect to highly degraded DNA samples. This study presents a homogeneous PCR assay for robust sex diagnosis, especially for the analysis of severely fragmented DNA. The introduced triplex for the X and Y chromosome (TriXY) is based on real-time PCR amplification of short intergenic sequences (<50bp) on both gonosomes. Subsequent PCR product examination and molecular-genetic sex-assignment rely on high-resolution melting (HRM) curve analysis. TriXY was optimized using commercially available multi-donor human DNA preparations of either male or female origin and successfully evaluated on challenging samples, including 46 ancient DNA specimens from archaeological excavations and a total of 16 DNA samples extracted from different segments of eight hair shafts of male and female donors. Additionally, sensitivity and cross-species amplification were examined to further test the assay's utility in forensic investigations. TriXY's closed-tube format avoids post-PCR sample manipulations and, therefore, distinctly reduces the risk of PCR product carry-over contamination and sample mix-up, while reducing labour and financial expenses at the same time. The method is sensitive down to the DNA content of approximately two diploid cells and has proven highly useful on severely fragmented and low quantity ancient DNA samples. Furthermore, it even allowed for sexing of proximal hair shafts with very good results. In summary, TriXY facilitates highly sensitive, rapid, and costeffective genetic sex-determination. It outperforms existing sexing methods both in terms of sensitivity and minimum required template molecule lengths. Therefore, we feel confident that TriXY will prove to be a reliable addition to the toolbox currently used for sex-typing in forensic genetics and other fields of research.}, }
@article {pmid27500649, year = {2016}, author = {Zvénigorosky, V and Crubézy, E and Gibert, M and Thèves, C and Hollard, C and Gonzalez, A and Fedorova, SA and Alexeev, AN and Bravina, RI and Ludes, B and Keyser, C}, title = {The genetics of kinship in remote human groups.}, journal = {Forensic science international. Genetics}, volume = {25}, number = {}, pages = {52-62}, doi = {10.1016/j.fsigen.2016.07.018}, pmid = {27500649}, issn = {1878-0326}, mesh = {Chromosomes, Human, Y ; *DNA Fingerprinting ; *DNA, Ancient ; Ethnicity/*genetics ; Female ; Gene Frequency ; Genetics, Population ; Genotype ; Humans ; Male ; *Microsatellite Repeats ; *Pedigree ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Russia ; }, abstract = {For fifteen years, part of the work of our research team has been focused on the study of parental links between individuals living hundreds or thousands of years ago, whose remains have been found in single graves or large funerary complexes. These studies have been undertaken using methods developed by forensic genetics to identify individuals, mainly based on the genotyping of autosomal STR (Short Tandem Repeats). Issues arose from this work, namely the limits of studying small numbers of subjects, originating from groups of finite sizes where kinships cannot be inferred a priori and for which reference allelic frequencies do not exist. Although ideal human populations are rare when undertaking such studies, the Yakuts of Eastern Siberia constitute a very advantageous model, with large numbers of small pastoral communities and well-preserved archaeological material. The study of kinship in the ancient Yakuts allowed us to highlight the difficulties in analysing genetic data from small ancient human groups and to develop a strategy to improve the accuracy of statistical computations. This work describes this strategy and possible solutions to the study of populations outside of the frame of reference of global meta-populations, due either to isolation, remoteness or antiquity.}, }
@article {pmid27447353, year = {2016}, author = {Rivollat, M and Réveillas, H and Mendisco, F and Pemonge, MH and Justeau, P and Couture, C and Lefranc, P and Féliu, C and Deguilloux, MF}, title = {Ancient mitochondrial DNA from the middle neolithic necropolis of Obernai extends the genetic influence of the LBK to west of the Rhine.}, journal = {American journal of physical anthropology}, volume = {161}, number = {3}, pages = {522-529}, doi = {10.1002/ajpa.23055}, pmid = {27447353}, issn = {1096-8644}, mesh = {Agriculture ; Anthropology, Physical ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics/*history ; France ; Haplotypes/genetics ; History, Ancient ; Humans ; }, abstract = {OBJECTIVES: The arrival of Neolithic farmers in Europe was the source of major cultural and genetic transitions. Neolithic settlers brought a new set of maternal lineages (mitochondrial DNA), recently well-characterized on the continental road, from the Balkans to West Germany (Rhine River). In the present study, the first mitochondrial DNA data from groups associated with this continental expansion wave located west of the Rhine River has been provided and their genetic affinities with contemporary groups have been discussed.<br><br>MATERIAL AND METHODS: The mitochondrial DNA analysis of 27 human remains originating from Obernai (5,000-4,400 cal. BC), a necropolis located in French Alsace Region and attributed to Grossgartach, Planig-Friedberg, and Roessen cultures was conducted.<br><br>RESULTS AND DISCUSSION: Among the 27 individuals studied, 15 HVR-I sequences and 17 mitochondrial haplogroups could be determined. The analysis of the Obernai gene pool clearly confirmed the genetic homogeneity of Linearbandkeramik (LBK) groups on both sides of the Rhine River. Notably, one N1a sequence found in Obernai is shared with LBK farmers from Central Europe, including one individual from the Flomborn site located approximately 200 km north-east of Obernai. On the whole, data gathered so far showed major genetic influence of the Danubian wave from Transdanubia to Atlantic French Coast, going by Alsace Region. However, the genetic influence of descendants from the Mediterranean Neolithic expansion and the significant hunter-gatherer admixture detected further west in the Paris Basin were not perceived in the Obernai necropolis.<br><br>CONCLUSIONS: Genetic homogeneity and continuity within LBK groups can be proposed on both sides of the Rhine River for the middle Neolithic groups. Nevertheless, mitochondrial data gathered so far for Neolithic groups from the entire extant French Territory clearly point out the complexity and the variability of Neolithic communities interactions that is worthy of further investigation.}, }
@article {pmid27762483, year = {2017}, author = {Lagerholm, VK and Sandoval-Castellanos, E and Vaniscotte, A and Potapova, OR and Tomek, T and Bochenski, ZM and Shepherd, P and Barton, N and Van Dyck, MC and Miller, R and Höglund, J and Yoccoz, NG and Dalén, L and Stewart, JR}, title = {Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds.}, journal = {Global change biology}, volume = {23}, number = {4}, pages = {1425-1435}, doi = {10.1111/gcb.13522}, pmid = {27762483}, issn = {1365-2486}, mesh = {Adaptation, Physiological ; Animals ; Birds/*genetics ; Climate ; *Climate Change ; Cold Temperature ; *DNA, Ancient ; Ecosystem ; Europe ; }, abstract = {Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum.}, }
@article {pmid27756828, year = {2017}, author = {Racimo, F and Marnetto, D and Huerta-Sánchez, E}, title = {Signatures of Archaic Adaptive Introgression in Present-Day Human Populations.}, journal = {Molecular biology and evolution}, volume = {34}, number = {2}, pages = {296-317}, pmid = {27756828}, issn = {1537-1719}, support = {R01 HG003229/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Biological/*genetics ; Alleles ; Animals ; Biological Evolution ; Computer Simulation ; DNA, Ancient/*analysis ; Databases, Nucleic Acid ; Evolution, Molecular ; Gene Frequency ; Genetics, Population ; Haplotypes ; Humans ; Neanderthals ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA/*methods ; }, abstract = {Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process-adaptive introgression-may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions.}, }
@article {pmid27754477, year = {2016}, author = {Soubrier, J and Gower, G and Chen, K and Richards, SM and Llamas, B and Mitchell, KJ and Ho, SY and Kosintsev, P and Lee, MS and Baryshnikov, G and Bollongino, R and Bover, P and Burger, J and Chivall, D and Crégut-Bonnoure, E and Decker, JE and Doronichev, VB and Douka, K and Fordham, DA and Fontana, F and Fritz, C and Glimmerveen, J and Golovanova, LV and Groves, C and Guerreschi, A and Haak, W and Higham, T and Hofman-Kamińska, E and Immel, A and Julien, MA and Krause, J and Krotova, O and Langbein, F and Larson, G and Rohrlach, A and Scheu, A and Schnabel, RD and Taylor, JF and Tokarska, M and Tosello, G and van der Plicht, J and van Loenen, A and Vigne, JD and Wooley, O and Orlando, L and Kowalczyk, R and Shapiro, B and Cooper, A}, title = {Early cave art and ancient DNA record the origin of European bison.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13158}, pmid = {27754477}, issn = {2041-1723}, mesh = {Animals ; Bison/classification/*genetics ; Cattle ; *Caves ; Cell Nucleus/genetics ; DNA, Ancient/*chemistry ; DNA, Mitochondrial/chemistry/genetics ; Europe ; Evolution, Molecular ; *Fossils ; Genome, Mitochondrial/genetics ; *Paintings ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21-18 kya).}, }
@article {pmid27744411, year = {2016}, author = {Caspermeyer, J}, title = {Ancient DNA Traces Extinct Caribbean "Island Murderer" Back to the Dawn of Mammals.}, journal = {Molecular biology and evolution}, volume = {33}, number = {12}, pages = {3317-3318}, doi = {10.1093/molbev/msw208}, pmid = {27744411}, issn = {1537-1719}, mesh = {Animals ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Fossils ; Mammals/*genetics ; Phylogeny ; West Indies ; }, }
@article {pmid27741281, year = {2016}, author = {Amanzougaghene, N and Mumcuoglu, KY and Fenollar, F and Alfi, S and Yesilyurt, G and Raoult, D and Mediannikov, O}, title = {High Ancient Genetic Diversity of Human Lice, Pediculus humanus, from Israel Reveals New Insights into the Origin of Clade B Lice.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0164659}, pmid = {27741281}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; DNA/history/isolation &amp; purification/metabolism ; *Genetic Variation ; Haplotypes ; History, Ancient ; Humans ; Israel ; Likelihood Functions ; Molecular Sequence Data ; Ovum/metabolism ; Pediculus/classification/*genetics/growth &amp; development ; Phylogeny ; RNA, Ribosomal/chemistry/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; }, abstract = {The human head louse, Pediculus humanus capitis, is subdivided into several significantly divergent mitochondrial haplogroups, each with particular geographical distributions. Historically, they are among the oldest human parasites, representing an excellent marker for tracking older events in human evolutionary history. In this study, ancient DNA analysis using real-time polymerase chain reaction (qPCR), combined with conventional PCR, was applied to the remains of twenty-four ancient head lice and their eggs from the Roman period which were recovered from Israel. The lice and eggs were found in three combs, one of which was recovered from archaeological excavations in the Hatzeva area of the Judean desert, and two of which found in Moa, in the Arava region, close to the Dead Sea. Results show that the head lice remains dating approximately to 2,000 years old have a cytb haplogroup A, which is worldwide in distribution, and haplogroup B, which has thus far only been found in contemporary lice from America, Europe, Australia and, most recently, Africa. More specifically, this haplogroup B has a B36 haplotype, the most common among B haplogroups, and has been present in America for at least 4,000 years. The present findings confirm that clade B lice existed, at least in the Middle East, prior to contacts between Native Americans and Europeans. These results support a Middle Eastern origin for clade B followed by its introduction into the New World with the early peoples. Lastly, the presence of Acinetobacter baumannii DNA was demonstrated by qPCR and sequencing in four head lice remains belonging to clade A.}, }
@article {pmid27730265, year = {2016}, author = {Baca, M and Popović, D and Stefaniak, K and Marciszak, A and Urbanowski, M and Nadachowski, A and Mackiewicz, P}, title = {Retreat and extinction of the Late Pleistocene cave bear (Ursus spelaeus sensu lato).}, journal = {Die Naturwissenschaften}, volume = {103}, number = {11-12}, pages = {92}, pmid = {27730265}, issn = {1432-1904}, mesh = {Animal Distribution ; Animals ; Climate ; Extinction, Biological ; *Fossils ; Haplotypes/genetics ; Ursidae/classification/genetics/*physiology ; }, abstract = {The cave bear (Ursus spelaeus sensu lato) is a typical representative of Pleistocene megafauna which became extinct at the end of the Last Glacial. Detailed knowledge of cave bear extinction could explain this spectacular ecological transformation. The paper provides a report on the youngest remains of the cave bear dated to 20,930 ± 140 [14]C years before present (BP). Ancient DNA analyses proved its affiliation to the Ursus ingressus haplotype. Using this record and 205 other dates, we determined, following eight approaches, the extinction time of this mammal at 26,100-24,300 cal. years BP. The time is only slightly earlier, i.e. 27,000-26,100 cal. years BP, when young dates without associated collagen data are excluded. The demise of cave bear falls within the coldest phase of the last glacial period, Greenland Stadial 3. This finding and the significant decrease in the cave bear records with cooling indicate that the drastic climatic changes were responsible for its extinction. Climate deterioration lowered vegetation productivity, on which the cave bear strongly depended as a strict herbivore. The distribution of the last cave bear records in Europe suggests that this animal was vanishing by fragmentation into subpopulations occupying small habitats. One of them was the Kraków-Częstochowa Upland in Poland, where we discovered the latest record of the cave bear and also two other, younger than 25,000 [14]C years BP. The relatively long survival of this bear in karst regions may result from suitable microclimate and continuous access to water provided by deep aquifers, indicating a refugial role of such regions in the Pleistocene for many species.}, }
@article {pmid27729493, year = {2016}, author = {Librado, P and Fages, A and Gaunitz, C and Leonardi, M and Wagner, S and Khan, N and Hanghøj, K and Alquraishi, SA and Alfarhan, AH and Al-Rasheid, KA and Der Sarkissian, C and Schubert, M and Orlando, L}, title = {The Evolutionary Origin and Genetic Makeup of Domestic Horses.}, journal = {Genetics}, volume = {204}, number = {2}, pages = {423-434}, pmid = {27729493}, issn = {1943-2631}, mesh = {Animals ; Animals, Domestic/*genetics ; *Biological Evolution ; Cattle ; Dogs ; Horses/*genetics ; Humans ; Selective Breeding/*genetics ; }, abstract = {The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.}, }
@article {pmid27726818, year = {2016}, author = {Dutour, O}, title = {Paleopathology of Human Infections: Old Bones, Antique Books, Ancient and Modern Molecules.}, journal = {Microbiology spectrum}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/microbiolspec.PoH-0014-2015}, pmid = {27726818}, issn = {2165-0497}, mesh = {Animals ; Archaeology/*methods ; Communicable Diseases/*epidemiology/*veterinary ; Fossils/*microbiology ; History ; Humans ; Paleopathology/*methods ; }, abstract = {Paleopathology studies the traces of disease on human and animal remains from ancient times. Infectious diseases have been, for over a century, one of its main fields of interest. The applications of paleogenetics methods to microbial aDNA, that started in the 90s combined to the recent development of new sequencing techniques allowing 'paleogenomics' approaches, have completely renewed the issue of the infections in the past. These advances open up new challenges in the understanding of the evolution of human-pathogen relationships, integrated in "One Health" concept.In this perspective, an integrative multidisciplinary approach combining data from ancient texts and old bones to those of old molecules is of great interest for reconstructing the past of human infections. Despite some too optimistic prediction of their eradication in the late 20th century, some of these ancient human diseases, such as plague, leprosy or tuberculosis, are still present and continue their evolution at the beginning of this 21rst century. Better know the past to predict a part of the future of human diseases remains, more than ever, the motto of the paleopathological science.}, }
@article {pmid27726782, year = {2016}, author = {Donoghue, HD}, title = {Paleomicrobiology of Human Tuberculosis.}, journal = {Microbiology spectrum}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/microbiolspec.PoH-0003-2014}, pmid = {27726782}, issn = {2165-0497}, mesh = {Americas ; Animals ; DNA, Bacterial/genetics/isolation &amp; purification ; Egypt ; Europe ; Fossils/*microbiology ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Microbiological Techniques/*methods ; Mycobacterium tuberculosis/classification/genetics/*isolation &amp; purification ; Paleopathology/*methods ; Phylogeny ; Polymerase Chain Reaction ; Tuberculosis/*epidemiology/history/*microbiology ; }, abstract = {Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections. These can be recognized in historical and archaeological material, along with nonspecific paleopathology such as new bone formation (periostitis), especially on ribs. Based on such lesions, tuberculosis has been found in ancient Egypt, pre-Columbian America, and Neolithic Europe. The detection of M. tuberculosis ancient DNA (aDNA) by using PCR led to the development of the new field of paleomicrobiology. As a result, a large number of tuberculosis cases were recognized in mummified tissue and bones with nonspecific or no lesions. In parallel with these developments, M. tuberculosis cell wall lipid biomarkers have detected tuberculosis suggested by paleopathology and confirmed aDNA findings. In well-preserved cases, molecular typing has identified M. tuberculosis lineages and genotypes. The current interest in targeted enrichment, shotgun sequencing, and metagenomic analysis reveals ancient mixed infections with different M. tuberculosis strains and other pathogens. Identification of M. tuberculosis lineages from samples of known age enables the date of the emergence of strains and lineages to be calculated directly rather than by making assumptions on the rate of evolutionary change.}, }
@article {pmid27726770, year = {2016}, author = {Rivera-Perez, JI and Santiago-Rodriguez, TM and Toranzos, GA}, title = {Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology.}, journal = {Microbiology spectrum}, volume = {4}, number = {4}, pages = {}, pmid = {27726770}, issn = {2165-0497}, support = {R25 GM061151/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA/genetics/isolation &amp; purification ; Forensic Medicine/*methods ; Fossils/*microbiology ; Humans ; Microbiological Techniques/*methods ; Paleopathology/*methods ; }, abstract = {Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.}, }
@article {pmid27706187, year = {2016}, author = {Mittnik, A and Wang, CC and Svoboda, J and Krause, J}, title = {A Molecular Approach to the Sexing of the Triple Burial at the Upper Paleolithic Site of Dolní Věstonice.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0163019}, pmid = {27706187}, issn = {1932-6203}, mesh = {Archaeology ; Bone and Bones/*metabolism ; Chromosomes, Human, X/*genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Karyotype ; Male ; Sequence Analysis, DNA ; Sex ; }, abstract = {In the past decades ancient DNA research has brought numerous insights to archaeological research where traditional approaches were limited. The determination of sex in human skeletal remains is often challenging for physical anthropologists when dealing with incomplete, juvenile or pathological specimens. Molecular approaches allow sexing on the basis of sex-specific markers or by calculating the ratio of DNA derived from different chromosomes. Here we propose a novel approach that relies on the ratio of X chromosome-derived shotgun sequencing data to the autosomal coverage, thus establishing the probability of an XX or XY karyotype. Applying this approach to the individuals of the Upper Paleolithic triple burial of Dolní Věstonice reveals that all three skeletons, including the individual DV 15, whose sex has long been debated due to a pathological condition, were male.}, }
@article {pmid27692243, year = {2016}, author = {Ruiz-Núñez, B and Dijck-Brouwer, DA and Muskiet, FA}, title = {The relation of saturated fatty acids with low-grade inflammation and cardiovascular disease.}, journal = {The Journal of nutritional biochemistry}, volume = {36}, number = {}, pages = {1-20}, doi = {10.1016/j.jnutbio.2015.12.007}, pmid = {27692243}, issn = {1873-4847}, mesh = {Animals ; Cardiovascular Diseases/epidemiology/*etiology/immunology/prevention &amp; control ; Diet, Fat-Restricted/adverse effects ; Diet, Healthy ; Dietary Fats/*adverse effects ; *Evidence-Based Medicine ; Fatty Acids/*adverse effects ; Healthy Lifestyle ; Humans ; Immunity, Innate ; Risk ; Systemic Vasculitis/epidemiology/*etiology/immunology/prevention &amp; control ; }, abstract = {The mantra that dietary (saturated) fat must be minimized to reduce cardiovascular disease (CVD) risk has dominated nutritional guidelines for decades. Parallel to decreasing intakes of fat and saturated fatty acids (SFA), there have been increases in carbohydrate and sugar intakes, overweight, obesity and type 2 diabetes mellitus. The "lipid hypothesis" coined the concept that fat, especially SFA, raises blood low-density lipoprotein-cholesterol and thereby CVD risk. In view of current controversies regarding their adequate intakes and effects, this review aims to summarize research regarding this heterogenic group of fatty acids and the mechanisms relating them to (chronic) systemic low-grade inflammation, insulin resistance, metabolic syndrome and notably CVD. The intimate relationship between inflammation and metabolism, including glucose, fat and cholesterol metabolism, revealed that the dyslipidemia in Western societies, notably increased triglycerides, "small dense" low-density lipoprotein and "dysfunctional" high-density lipoprotein, is influenced by many unfavorable lifestyle factors. Dietary SFA is only one of these, not necessarily the most important, in healthy, insulin-sensitive people. The environment provides us not only with many other proinflammatory stimuli than SFA but also with many antiinflammatory counterparts. Resolution of the conflict between our self-designed environment and ancient genome may rather rely on returning to the proinflammatory/antiinflammatory balance of the Paleolithic era in consonance with the 21st century culture. Accordingly, dietary guidelines might reconsider recommendations for SFA replacement and investigate diet in a broader context, together with nondietary lifestyle factors. This should be a clear priority, opposed to the reductionist approach of studying the effects of single nutrients, such as SFA.}, }
@article {pmid27677399, year = {2017}, author = {Scofield, RP and Mitchell, KJ and Wood, JR and De Pietri, VL and Jarvie, S and Llamas, B and Cooper, A}, title = {The origin and phylogenetic relationships of the New Zealand ravens.}, journal = {Molecular phylogenetics and evolution}, volume = {106}, number = {}, pages = {136-143}, doi = {10.1016/j.ympev.2016.09.022}, pmid = {27677399}, issn = {1095-9513}, mesh = {Animals ; Australia ; Biological Evolution ; Crows/*classification/genetics ; Cytochromes b/classification/genetics/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; Fossils ; New Zealand ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Skull/anatomy &amp; histology ; }, abstract = {The relationships of the extinct New Zealand ravens (Corvus spp.) are poorly understood. We sequenced the mitogenomes of the two currently recognised species and found they were sister-taxa to a clade comprising the Australian raven, little raven, and forest raven (C.coronoides, C. mellori and C. tasmanicus respectively). The divergence between the New Zealand ravens and Australian raven clade occurred in the latest Pliocene, which coincides with the onset of glacial deforestation. We also found that the divergence between the two putative New Zealand species C. antipodum and C. moriorum probably occurred in the late Pleistocene making their separation as species untenable. Consequently, we consider Corax antipodum (Forbes, 1893) to be a subspecies of Corvus moriorum Forbes, 1892. We re-examine the osteological evidence that led 19th century researchers to assign the New Zealand taxa to a separate genus, and re-assess these features in light of our new phylogenetic hypotheses. Like previous researchers, we conclude that the morphology of the palate of C. moriorum is unique among the genus Corvus, and suggest this may be an adaptation for a specialist diet.}, }
@article {pmid27671660, year = {2016}, author = {Gelabert, P and Sandoval-Velasco, M and Olalde, I and Fregel, R and Rieux, A and Escosa, R and Aranda, C and Paaijmans, K and Mueller, I and Gilbert, MT and Lalueza-Fox, C}, title = {Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {41}, pages = {11495-11500}, pmid = {27671660}, issn = {1091-6490}, support = {681396/ERC_/European Research Council/International ; }, mesh = {DNA, Mitochondrial/*genetics ; DNA, Protozoan/genetics ; *Disease Eradication ; Haplotypes/genetics ; Likelihood Functions ; Phylogeny ; Plasmodium falciparum/*genetics ; Plasmodium vivax/*genetics ; Sequence Analysis, DNA ; Spain ; }, abstract = {Phylogenetic analysis of Plasmodium parasites has indicated that their modern-day distribution is a result of a series of human-mediated dispersals involving transport between Africa, Europe, America, and Asia. A major outstanding question is the phylogenetic affinity of the malaria causing parasites Plasmodium vivax and falciparum in historic southern Europe-where it was endemic until the mid-20th century, after which it was eradicated across the region. Resolving the identity of these parasites will be critical for answering several hypotheses on the malaria dispersal. Recently, a set of slides with blood stains of malaria-affected people from the Ebro Delta (Spain), dated between 1942 and 1944, have been found in a local medical collection. We extracted DNA from three slides, two of them stained with Giemsa (on which Plasmodium parasites could still be seen under the microscope) and another one consisting of dried blood spots. We generated the data using Illumina sequencing after using several strategies aimed at increasing the Plasmodium DNA yield: depletion of the human genomic (g)DNA content through hybridization with human gDNA baits, and capture-enrichment using gDNA derived from P. falciparum Plasmodium mitochondrial genome sequences were subsequently reconstructed from the resulting data. Phylogenetic analysis of the eradicated European P. vivax mtDNA genome indicates that the European isolate is closely related to the most common present-day American haplotype and likely entered the American continent post-Columbian contact. Furthermore, the European P. falciparum mtDNA indicates a link with current Indian strains that is in agreement with historical accounts.}, }
@article {pmid27662060, year = {2016}, author = {Novembre, J and Peter, BM}, title = {Recent advances in the study of fine-scale population structure in humans.}, journal = {Current opinion in genetics &amp; development}, volume = {41}, number = {}, pages = {98-105}, pmid = {27662060}, issn = {1879-0380}, support = {R01 GM108805/GM/NIGMS NIH HHS/United States ; R01 HG007089/HG/NHGRI NIH HHS/United States ; U01 CA198933/CA/NCI NIH HHS/United States ; }, mesh = {DNA, Mitochondrial/genetics ; *Genetic Variation ; *Genetics, Population ; Genotype ; History, Ancient ; Human Migration/*history ; Humans ; }, abstract = {Empowered by modern genotyping and large samples, population structure can be accurately described and quantified even when it only explains a fraction of a percent of total genetic variance. This is especially relevant and interesting for humans, where fine-scale population structure can both confound disease-mapping studies and reveal the history of migration and divergence that shaped our species' diversity. Here we review notable recent advances in the detection, use, and understanding of population structure. Our work addresses multiple areas where substantial progress is being made: improved statistics and models for better capturing differentiation, admixture, and the spatial distribution of variation; computational speed-ups that allow methods to scale to modern data; and advances in haplotypic modeling that have wide ranging consequences for the analysis of population structure. We conclude by outlining four important open challenges: the limitations of discrete population models, uncertainty in individual origins, the incorporation of both fine-scale structure and ancient DNA in parametric models, and the development of efficient computational tools, particularly for haplotype-based methods.}, }
@article {pmid27654468, year = {2016}, author = {Forst, J and Brown, TA}, title = {Inability of 'Whole Genome Amplification' to Improve Success Rates for the Biomolecular Detection of Tuberculosis in Archaeological Samples.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0163031}, pmid = {27654468}, issn = {1932-6203}, abstract = {We assessed the ability of whole genome amplification (WGA) to improve the efficiency of downstream polymerase chain reactions (PCRs) directed at ancient DNA (aDNA) of members of the Mycobacterium tuberculosis complex (MTBC). Using extracts from a variety of bones and a tooth from human skeletons with or without lesions indicative of tuberculosis, from multiple time periods, we obtained inconsistent results. We conclude that WGA does not provide any advantage in studies of MTBC aDNA. The sporadic nature of our results are probably due to the fact that WGA is itself a PCR-based procedure which, although designed to deal with fragmented DNA, might be inefficient with the low concentration of templates in an aDNA extract. As such, WGA is subject to similar, if not the same, restrictions as PCR when applied to aDNA.}, }
@article {pmid27654125, year = {2017}, author = {Anmarkrud, JA and Lifjeld, JT}, title = {Complete mitochondrial genomes of eleven extinct or possibly extinct bird species.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {334-341}, doi = {10.1111/1755-0998.12600}, pmid = {27654125}, issn = {1755-0998}, mesh = {Animals ; Birds/*classification/*genetics ; DNA, Mitochondrial/*chemistry/*genetics ; Extinction, Biological ; *Genome, Mitochondrial ; Museums ; Phylogeny ; Preservation, Biological ; Sequence Analysis, DNA ; }, abstract = {Natural history museum collections represent a vast source of ancient and historical DNA samples from extinct taxa that can be utilized by high-throughput sequencing tools to reveal novel genetic and phylogenetic information about them. Here, we report on the successful sequencing of complete mitochondrial genome sequences (mitogenomes) from eleven extinct bird species, using de novo assembly of short sequences derived from toepad samples of degraded DNA from museum specimens. For two species (the Passenger Pigeon Ectopistes migratorius and the South Island Piopio Turnagra capensis), whole mitogenomes were already available from recent studies, whereas for five others (the Great Auk Pinguinis impennis, the Imperial Woodpecker Campehilus imperialis, the Huia Heteralocha acutirostris, the Kauai Oo Moho braccathus and the South Island Kokako Callaeas cinereus), there were partial mitochondrial sequences available for comparison. For all seven species, we found sequence similarities of >98%. For the remaining four species (the Kamao Myadestes myadestinus, the Paradise Parrot Psephotellus pulcherrimus, the Ou Psittirostra psittacea and the Lesser Akialoa Akialoa obscura), there was no sequence information available for comparison, so we conducted blast searches and phylogenetic analyses to determine their phylogenetic positions and identify their closest extant relatives. These mitogenomes will be valuable for future analyses of avian phylogenetics and illustrate the importance of museum collections as repositories for genomics resources.}, }
@article {pmid27649620, year = {2017}, author = {Lega, C and Fulgione, D and Genovese, A and Rook, L and Masseti, M and Meiri, M and Cinzia Marra, A and Carotenuto, F and Raia, P}, title = {Like a pig out of water: seaborne spread of domestic pigs in Southern Italy and Sardinia during the Bronze and Iron Ages.}, journal = {Heredity}, volume = {118}, number = {2}, pages = {154-159}, pmid = {27649620}, issn = {1365-2540}, mesh = {*Animal Distribution ; Animals ; Animals, Domestic/genetics ; Commerce ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Domestication ; Haplotypes ; Human Migration ; Italy ; Sequence Analysis, DNA ; Sicily ; Sus scrofa/*genetics ; Transportation ; }, abstract = {Southern Italy has a long history of human occupation and passage of different cultures since the Early Holocene. Repeated, ancient introductions of pigs in several geographic areas in Europe make it difficult to understand pig translocation and domestication in Italy. The archeozoological record may provide fundamental information on this, hence shedding light on peopling and on trading among different ancient cultures in the Mediterranean. Yet, because of the scanty nature of the fossil record, ancient remains from human-associated animals are somewhat rare. Fortunately, ancient DNA analysis as applied to domestic species proved to be a powerful tool in revealing human migrations. Herein, we analyzed 80-bp fragment of mitochondrial DNA control region from 27 Sus scrofa ancient samples retrieved from Southern Italian and Sardinian archeological sites, spanning in age from the Mesolithic to the Roman period. Our results surprisingly indicate the presence of the Near Eastern haplotype Y1 on both Italy's major islands (Sardinia and Sicily) during the Bronze Age, suggesting the seaborne transportation of domestic pigs by humans at least during 1600-1300 BC. The presence of the Italian E2 clade in domestic contexts shows that the indigenous wild boar was effectively domesticated or incorporated into domestic stocks in Southern Italy during the Bronze Age, although the E2 haplotype has never been found in modern domestic breeds. Pigs belonging to the endemic E2 clade were thus traded between the Peninsula and Sardinia by the end of the second millennium BC and this genetic signature is still detected in Sardinian feral pigs.}, }
@article {pmid27624717, year = {2016}, author = {Hanghøj, K and Seguin-Orlando, A and Schubert, M and Madsen, T and Pedersen, JS and Willerslev, E and Orlando, L}, title = {Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.}, journal = {Molecular biology and evolution}, volume = {33}, number = {12}, pages = {3284-3298}, pmid = {27624717}, issn = {1537-1719}, mesh = {Chromatin Assembly and Disassembly ; Computer Simulation ; Cytosine/metabolism ; DNA/genetics ; *DNA Methylation ; DNA, Ancient/*analysis ; Epigenesis, Genetic ; Genome ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleosomes/*genetics ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.}, }
@article {pmid27624716, year = {2016}, author = {Brace, S and Thomas, JA and Dalén, L and Burger, J and MacPhee, RD and Barnes, I and Turvey, ST}, title = {Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family.}, journal = {Molecular biology and evolution}, volume = {33}, number = {12}, pages = {3095-3103}, doi = {10.1093/molbev/msw186}, pmid = {27624716}, issn = {1537-1719}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Eulipotyphla/*classification/*genetics ; Genome, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA/*methods ; West Indies ; }, abstract = {The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a ∼750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as "museums" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history.}, }
@article {pmid27618404, year = {2016}, author = {Andam, CP and Worby, CJ and Chang, Q and Campana, MG}, title = {Microbial Genomics of Ancient Plagues and Outbreaks.}, journal = {Trends in microbiology}, volume = {24}, number = {12}, pages = {978-990}, doi = {10.1016/j.tim.2016.08.004}, pmid = {27618404}, issn = {1878-4380}, mesh = {Communicable Diseases/*epidemiology/etiology/history ; DNA, Ancient ; *Disease Outbreaks/history ; Epidemics/history ; Genome, Bacterial ; *Genomics ; High-Throughput Nucleotide Sequencing/methods ; History, 19th Century ; History, Ancient ; Humans ; Phylogeny ; Plague/*epidemiology/history/microbiology ; Virulence ; Yersinia pestis/*genetics/pathogenicity ; }, abstract = {The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illustrate how microbial genomics has provided new insights into the nature and etiology of infectious diseases of historical importance, such as plague, tuberculosis, and leprosy. Sequenced isolates collected from archaeological remains also provide evidence for the timing of historical evolutionary events as well as geographic spread of these pathogens. Elucidating the genomic basis of virulence in historical diseases can provide relevant information on how we can effectively understand the emergence and re-emergence of infectious diseases today and in the future.}, }
@article {pmid27617196, year = {2016}, author = {Broussard, JL and Devkota, S}, title = {The changing microbial landscape of Western society: Diet, dwellings and discordance.}, journal = {Molecular metabolism}, volume = {5}, number = {9}, pages = {737-742}, pmid = {27617196}, issn = {2212-8778}, abstract = {BACKGROUND: The last 50-100 years has been marked by a sharp rise in so-called "Western-diseases" in those countries that have experienced major industrial advances and shifts towards urbanized living. These diseases include obesity, type 2 diabetes, inflammatory bowel diseases, and food allergies in which chronic dysregulation of metabolic and/or immune processes appear to be involved, and are likely a byproduct of new environmental influences on our ancient genome. What we now appreciate is that this genome consists of both human and co-evolved microbial genes of the trillions of microbes residing in our body. Together, host-microbe interactions may be determined by the changing diets and behaviors of the Western lifestyle, influencing the etiopathogenesis of "new-age" diseases.<br><br>SCOPE OF REVIEW: This review takes an anthropological approach to the potential interplay of the host and its gut microbiome in the post-industrialization rise in chronic inflammatory and metabolic diseases. The discussion highlights both the changes in diet and the physical environment that have co-occurred with these diseases and the latest evidence demonstrating the role of host-microbe interactions in understanding biological responses to the changing environment.<br><br>MAJOR CONCLUSIONS: Technological advances that have led to changes in agriculture and engineering have altered our eating and living behaviors in ways never before possible in human history. These changes also have altered the bacterial communities within the human body in ways that are seemingly linked with the rise of many intestinal and systemic metabolic and inflammatory diseases. Insights into the mechanisms of this reciprocal exchange between the environment and the human gut microbiome may offer potential to attenuate the chronic health conditions that derail quality of life. This article is part of a special issue on microbiota.}, }
@article {pmid27615365, year = {2016}, author = {Immel, A and Le Cabec, A and Bonazzi, M and Herbig, A and Temming, H and Schuenemann, VJ and Bos, KI and Langbein, F and Harvati, K and Bridault, A and Pion, G and Julien, MA and Krotova, O and Conard, NJ and Münzel, SC and Drucker, DG and Viola, B and Hublin, JJ and Tafforeau, P and Krause, J}, title = {Effect of X-ray irradiation on ancient DNA in sub-fossil bones - Guidelines for safe X-ray imaging.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {32969}, pmid = {27615365}, issn = {2045-2322}, mesh = {Animals ; Bone and Bones/*diagnostic imaging ; *DNA, Ancient ; Dose-Response Relationship, Radiation ; Fossils/*diagnostic imaging ; Synchrotrons ; X-Rays ; }, abstract = {Sub-fossilised remains may still contain highly degraded ancient DNA (aDNA) useful for palaeogenetic investigations. Whether X-ray computed [micro-] tomography ([μ]CT) imaging of these fossils may further damage aDNA remains debated. Although the effect of X-ray on DNA in living organisms is well documented, its impact on aDNA molecules is unexplored. Here we investigate the effects of synchrotron X-ray irradiation on aDNA from Pleistocene bones. A clear correlation appears between decreasing aDNA quantities and accumulating X-ray dose-levels above 2000 Gray (Gy). We further find that strong X-ray irradiation reduces the amount of nucleotide misincorporations at the aDNA molecule ends. No representative effect can be detected for doses below 200 Gy. Dosimetry shows that conventional μCT usually does not reach the risky dose level, while classical synchrotron imaging can degrade aDNA significantly. Optimised synchrotron protocols and simple rules introduced here are sufficient to ensure that fossils can be scanned without impairing future aDNA studies.}, }
@article {pmid27608630, year = {2016}, author = {Rensing, SA and Ick, J and Fawcett, JA and Lang, D and Zimmer, A and Van de Peer, Y and Reski, R}, title = {Erratum to: An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {184}, pmid = {27608630}, issn = {1471-2148}, }
@article {pmid27606907, year = {2016}, author = {Slatkin, M}, title = {Statistical methods for analyzing ancient DNA from hominins.}, journal = {Current opinion in genetics &amp; development}, volume = {41}, number = {}, pages = {72-76}, pmid = {27606907}, issn = {1879-0380}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Fossils ; Genetics, Population/*statistics &amp; numerical data ; Genome/genetics ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; }, abstract = {In the past few years, the number of autosomal DNA sequences from human fossils has grown explosively and numerous partial or complete sequences are available from our closest relatives, Neanderthal and Denisovans. I review commonly used statistical methods applied to these sequences. These methods fall into three broad classes: methods for estimating levels of contamination, descriptive methods, and methods based on population genetic models. The latter two classes are largely methods developed for the analysis of present-day genomic data. When they are applied to ancient DNA (aDNA), they usually ignore the time dimension. A few methods, particularly those concerned with inferring something about selection or ancestor-descendant relationships, take explicit account of the ages of aDNA samples.}, }
@article {pmid27602278, year = {2016}, author = {Heckeberg, NS and Erpenbeck, D and Wörheide, G and Rössner, GE}, title = {Systematic relationships of five newly sequenced cervid species.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2307}, pmid = {27602278}, issn = {2167-8359}, abstract = {Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging.}, }
@article {pmid27578768, year = {2016}, author = {Feldman, M and Harbeck, M and Keller, M and Spyrou, MA and Rott, A and Trautmann, B and Scholz, HC and Päffgen, B and Peters, J and McCormick, M and Bos, K and Herbig, A and Krause, J}, title = {A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim.}, journal = {Molecular biology and evolution}, volume = {33}, number = {11}, pages = {2911-2923}, pmid = {27578768}, issn = {1537-1719}, mesh = {Base Sequence ; DNA, Ancient/*analysis ; DNA, Bacterial/genetics ; Genetic Variation ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Pandemics ; Plague/*microbiology ; Virulence/genetics ; Yersinia pestis/*genetics ; }, abstract = {The Justinianic Plague, which started in the sixth century and lasted to the mid eighth century, is thought to be the first of three historically documented plague pandemics causing massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany.}, }
@article {pmid27572991, year = {2016}, author = {Vai, S and Lari, M and Caramelli, D}, title = {DNA Sequencing in Cultural Heritage.}, journal = {Topics in current chemistry (Cham)}, volume = {374}, number = {1}, pages = {8}, doi = {10.1007/s41061-015-0009-8}, pmid = {27572991}, issn = {2365-0869}, mesh = {DNA, Ancient/*chemistry/isolation &amp; purification ; Gene Library ; Genetics, Population ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Humans ; Paleontology ; *Sequence Analysis, DNA ; }, abstract = {During the last three decades, DNA analysis on degraded samples revealed itself as an important research tool in anthropology, archaeozoology, molecular evolution, and population genetics. Application on topics such as determination of species origin of prehistoric and historic objects, individual identification of famous personalities, characterization of particular samples important for historical, archeological, or evolutionary reconstructions, confers to the paleogenetics an important role also for the enhancement of cultural heritage. A really fast improvement in methodologies in recent years led to a revolution that permitted recovering even complete genomes from highly degraded samples with the possibility to go back in time 400,000 years for samples from temperate regions and 700,000 years for permafrozen remains and to analyze even more recent material that has been subjected to hard biochemical treatments. Here we propose a review on the different methodological approaches used so far for the molecular analysis of degraded samples and their application on some case studies.}, }
@article {pmid27566552, year = {2017}, author = {Cruz-Dávalos, DI and Llamas, B and Gaunitz, C and Fages, A and Gamba, C and Soubrier, J and Librado, P and Seguin-Orlando, A and Pruvost, M and Alfarhan, AH and Alquraishi, SA and Al-Rasheid, KAS and Scheu, A and Beneke, N and Ludwig, A and Cooper, A and Willerslev, E and Orlando, L}, title = {Experimental conditions improving in-solution target enrichment for ancient DNA.}, journal = {Molecular ecology resources}, volume = {17}, number = {3}, pages = {508-522}, doi = {10.1111/1755-0998.12595}, pmid = {27566552}, issn = {1755-0998}, support = {R01 GM090087/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Composition ; CpG Islands ; DNA Probes ; DNA, Ancient/*analysis ; High-Throughput Nucleotide Sequencing ; Nucleic Acid Hybridization ; Sequence Analysis, DNA/*methods ; }, abstract = {High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.}, }
@article {pmid27534956, year = {2016}, author = {Achtman, M}, title = {How old are bacterial pathogens?.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1836}, pages = {}, pmid = {27534956}, issn = {1471-2954}, support = {BB/L020319/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; DNA, Bacterial/analysis ; *Genome, Bacterial ; Helicobacter pylori/*genetics ; Humans ; Mycobacterium tuberculosis/*genetics ; Yersinia pestis/*genetics ; }, abstract = {Only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. The global genetic diversity of Helicobacter pylori, which infects human stomachs, parallels that of its human host. The time to the most recent common ancestor (tMRCA) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence within H. pylori against major ancient human migrations. Similarly, genomic reconstructions of Mycobacterium tuberculosis, the cause of tuberculosis, from ancient skeletons in South America and mummies in Hungary support estimates of less than 6000 years for the tMRCA of M. tuberculosis Finally, modern global patterns of genetic diversity and ancient DNA studies indicate that during the last 5000 years plague caused by Yersinia pestis has spread globally on multiple occasions from China and Central Asia. Such tMRCA estimates provide only lower bounds on the ages of bacterial pathogens, and additional studies are needed for realistic upper bounds on how long humans and animals have suffered from bacterial diseases.}, }
@article {pmid27527811, year = {2016}, author = {Valleriani, A}, title = {A conditional likelihood is required to estimate the selection coefficient in ancient DNA.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31561}, pmid = {27527811}, issn = {2045-2322}, mesh = {*DNA, Ancient ; Gene Frequency ; Genetic Drift ; *Likelihood Functions ; Models, Genetic ; *Selection, Genetic ; }, abstract = {Time-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function built under the hypothesis that the available trajectory spans a sufficiently large portion of the fitness landscape. Especially for ancient DNA, however, often only one single such trajectories is available and the coverage of the fitness landscape is very limited. In fact, one single trajectory is more representative of a process conditioned both in the initial and in the final condition than of a process free to visit the available fitness landscape. Based on two models of population genetics, here we show how to build a likelihood function for the selection coefficient that takes the statistical peculiarity of single trajectories into account. We show that this conditional likelihood delivers a precise estimate of the selection coefficient also when allele frequencies are close to fixation whereas the unconditioned likelihood fails. Finally, we discuss the fact that the traditional, unconditioned likelihood always delivers an answer, which is often unfalsifiable and appears reasonable also when it is not correct.}, }
@article {pmid27517578, year = {2016}, author = {Caldararo, N}, title = {Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept.}, journal = {Journal of molecular evolution}, volume = {83}, number = {1-2}, pages = {78-87}, pmid = {27517578}, issn = {1432-1432}, mesh = {Animals ; Biological Evolution ; DNA/genetics ; DNA, Ancient/*analysis ; Fossils ; Hominidae/genetics ; Humans ; Neanderthals/*genetics ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; }, abstract = {A number of recent articles have appeared on the Denisova fossil remains and attempts to produce DNA sequences from them. One of these recently appeared in Science by Vernot et al. (Science 352:235-239, 2016). We would like to advance an alternative interpretation of the data presented. One concerns the problem of contamination/degradation of the determined DNA sequenced. Just as the publication of the first Neandertal sequence included an interpretation that argued that Neandertals had not contributed any genes to modern humans, the Denisovan interpretation has considerable influence on ideas regarding human evolution. The new papers, however, confuse established ideas concerning the nature of species, as well as the use of terms like premodern, Archaic Homo, and Homo heidelbergensis. Examination of these problems presents a solution by means of reinterpreting the results. Given the claims for gene transfer among a number of Mid Pleistocene hominids, it may be time to reexamine the idea of anagenesis in hominid evolution.}, }
@article {pmid27509860, year = {2016}, author = {McGowan, S}, title = {Ancient DNA: Muddy messages about American migration.}, journal = {Nature}, volume = {537}, number = {7618}, pages = {43-44}, pmid = {27509860}, issn = {1476-4687}, mesh = {DNA ; *DNA, Ancient ; DNA, Mitochondrial ; *Fossils ; Humans ; Sequence Analysis, DNA ; }, }
@article {pmid27507099, year = {2016}, author = {Skoglund, P and Reich, D}, title = {A genomic view of the peopling of the Americas.}, journal = {Current opinion in genetics &amp; development}, volume = {41}, number = {}, pages = {27-35}, pmid = {27507099}, issn = {1879-0380}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Americas ; Arctic Regions ; Asia ; *Genome, Human ; *Genomics ; History, Ancient ; *Human Migration ; Humans ; Indians, North American/*genetics/history ; North America ; }, abstract = {Whole-genome studies have documented that most Native American ancestry stems from a single population that diversified within the continent more than twelve thousand years ago. However, this shared ancestry hides a more complex history whereby at least four distinct streams of Eurasian migration have contributed to present-day and prehistoric Native American populations. Whole genome studies enhanced by technological breakthroughs in ancient DNA now provide evidence of a sequence of events involving initial migrations from a structured Northeast Asian source population with differential relatedness to present-day Australasian populations, followed by a divergence into northern and southern Native American lineages. During the Holocene, new migrations from Asia introduced the Saqqaq/Dorset Paleoeskimo population to the North American Arctic ∼4500 years ago, ancestry that is potentially connected with ancestry found in Athabaskan-speakers today. This was then followed by a major new population turnover in the high Arctic involving Thule-related peoples who are the ancestors of present-day Inuit. We highlight several open questions that could be addressed through future genomic research.}, }
@article {pmid27506329, year = {2016}, author = {Fortes, GG and Grandal-d'Anglade, A and Kolbe, B and Fernandes, D and Meleg, IN and García-Vázquez, A and Pinto-Llona, AC and Constantin, S and de Torres, TJ and Ortiz, JE and Frischauf, C and Rabeder, G and Hofreiter, M and Barlow, A}, title = {Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears.}, journal = {Molecular ecology}, volume = {25}, number = {19}, pages = {4907-4918}, doi = {10.1111/mec.13800}, pmid = {27506329}, issn = {1365-294X}, support = {310763/ERC_/European Research Council/International ; }, mesh = {Animals ; *Behavior, Animal ; *DNA, Ancient ; DNA, Mitochondrial ; Fossils ; Phylogeny ; *Social Behavior ; Spain ; Ursidae/*classification ; }, abstract = {Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago.}, }
@article {pmid27498567, year = {2016}, author = {Kılınç, GM and Omrak, A and Özer, F and Günther, T and Büyükkarakaya, AM and Bıçakçı, E and Baird, D and Dönertaş, HM and Ghalichi, A and Yaka, R and Koptekin, D and Açan, SC and Parvizi, P and Krzewińska, M and Daskalaki, EA and Yüncü, E and Dağtaş, ND and Fairbairn, A and Pearson, J and Mustafaoğlu, G and Erdal, YS and Çakan, YG and Togan, &#x130; and Somel, M and Storå, J and Jakobsson, M and Götherström, A}, title = {The Demographic Development of the First Farmers in Anatolia.}, journal = {Current biology : CB}, volume = {26}, number = {19}, pages = {2659-2666}, pmid = {27498567}, issn = {1879-0445}, mesh = {*Agriculture ; *Archaeology ; *Farmers ; *Genetic Variation ; Humans ; Turkey ; }, abstract = {The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [1-3]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [4]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.}, }
@article {pmid27498082, year = {2016}, author = {Gogarten, JF and Düx, A and Schuenemann, VJ and Nowak, K and Boesch, C and Wittig, RM and Krause, J and Calvignac-Spencer, S and Leendertz, FH}, title = {Tools for opening new chapters in the book of Treponema pallidum evolutionary history.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {22}, number = {11}, pages = {916-921}, doi = {10.1016/j.cmi.2016.07.027}, pmid = {27498082}, issn = {1469-0691}, mesh = {Bone and Bones/*microbiology ; Evolution, Molecular ; High-Throughput Nucleotide Sequencing/methods ; History, 15th Century ; Humans ; Phylogeny ; Sequence Analysis, DNA/methods ; Syphilis/*history/microbiology ; Treponema pallidum/classification/*genetics/isolation &amp; purification ; Yaws/*history/microbiology ; }, abstract = {Treponema pallidum infections causing yaws disease and venereal syphilis are globally widespread in human populations, infecting hundreds of thousands and millions annually respectively; endemic syphilis is much less common, and pinta has not been observed in decades. We discuss controversy surrounding the origin, evolution and history of these pathogens in light of available molecular and anthropological evidence. These bacteria (or close relatives) seem to affect many wild African nonhuman primate (NHP) species, though to date only a single NHP Treponema pallidum genome has been published, hindering detection of spillover events and our understanding of potential wildlife reservoirs. Similarly, only ten genomes of Treponema pallidum infecting humans have been published, impeding a full understanding of their diversity and evolutionary history. Research efforts have been hampered by the difficulty of culturing and propagating Treponema pallidum. Here we highlight avenues of research recently opened by the coupling of hybridization capture and next-generation sequencing. We present data generated with such an approach suggesting that asymptomatic bones from NHP occasionally contain enough treponemal DNA to recover large fractions of their genomes. We expect that these methods, which naturally can be applied to modern biopsy samples and ancient human bones, will soon considerably improve our understanding of these enigmatic pathogens and lay rest to old yet unresolved controversies.}, }
@article {pmid27482085, year = {2016}, author = {Graham, RW and Belmecheri, S and Choy, K and Culleton, BJ and Davies, LJ and Froese, D and Heintzman, PD and Hritz, C and Kapp, JD and Newsom, LA and Rawcliffe, R and Saulnier-Talbot, &#xc9; and Shapiro, B and Wang, Y and Williams, JW and Wooller, MJ}, title = {Timing and causes of mid-Holocene mammoth extinction on St. Paul Island, Alaska.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {33}, pages = {9310-9314}, pmid = {27482085}, issn = {1091-6490}, mesh = {Alaska ; Animals ; *Extinction, Biological ; Mammoths/*physiology ; Time Factors ; }, abstract = {Relict woolly mammoth (Mammuthus primigenius) populations survived on several small Beringian islands for thousands of years after mainland populations went extinct. Here we present multiproxy paleoenvironmental records to investigate the timing, causes, and consequences of mammoth disappearance from St. Paul Island, Alaska. Five independent indicators of extinction show that mammoths survived on St. Paul until 5,600 ± 100 y ago. Vegetation composition remained stable during the extinction window, and there is no evidence of human presence on the island before 1787 CE, suggesting that these factors were not extinction drivers. Instead, the extinction coincided with declining freshwater resources and drier climates between 7,850 and 5,600 y ago, as inferred from sedimentary magnetic susceptibility, oxygen isotopes, and diatom and cladoceran assemblages in a sediment core from a freshwater lake on the island, and stable nitrogen isotopes from mammoth remains. Contrary to other extinction models for the St. Paul mammoth population, this evidence indicates that this mammoth population died out because of the synergistic effects of shrinking island area and freshwater scarcity caused by rising sea levels and regional climate change. Degradation of water quality by intensified mammoth activity around the lake likely exacerbated the situation. The St. Paul mammoth demise is now one of the best-dated prehistoric extinctions, highlighting freshwater limitation as an overlooked extinction driver and underscoring the vulnerability of small island populations to environmental change, even in the absence of human influence.}, }
@article {pmid27481784, year = {2016}, author = {Speller, C and van den Hurk, Y and Charpentier, A and Rodrigues, A and Gardeisen, A and Wilkens, B and McGrath, K and Rowsell, K and Spindler, L and Collins, M and Hofreiter, M}, title = {Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1702}, pages = {}, pmid = {27481784}, issn = {1471-2970}, mesh = {Animals ; Archaeology/methods ; Biodiversity ; Cetacea/*classification ; Classification/*methods ; Collagen/analysis ; *DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing/methods ; North Sea ; }, abstract = {Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.}, }
@article {pmid27474788, year = {2017}, author = {Frisch, D and Morton, PK and Culver, BW and Edlund, MB and Jeyasingh, PD and Weider, LJ}, title = {Paleogenetic records of Daphnia pulicaria in two North American lakes reveal the impact of cultural eutrophication.}, journal = {Global change biology}, volume = {23}, number = {2}, pages = {708-718}, doi = {10.1111/gcb.13445}, pmid = {27474788}, issn = {1365-2486}, mesh = {Animals ; Daphnia/*genetics ; *Eutrophication ; Fossils ; *Genetics, Population ; Humans ; Lakes ; Phosphorus ; Pulicaria ; United States ; }, abstract = {Understanding the evolutionary consequences of the green revolution, particularly in wild populations, is an important frontier in contemporary biology. Because human impacts have occurred at varying magnitudes or time periods depending on the study ecosystem, evolutionary histories may vary considerably among populations. Paleogenetics in conjunction with paleolimnology enable us to associate microevolutionary dynamics with detailed information on environmental change. We used this approach to reconstruct changes in the temporal population genetic structure of the keystone zooplankton grazer, Daphnia pulicaria, using dormant eggs extracted from sediments in two Minnesota lakes (South Center, Hill). The extent of agriculture and human population density in the catchment of these lakes has differed markedly since European settlement in the late 19th century and is reflected in their environmental histories reconstructed here. The reconstructed environments of these two lakes differed strongly in terms of environmental stability and their associated patterns of Daphnia population structure. We detected long periods of stability in population structure and environmental conditions in South Center Lake that were followed by a dramatic temporal shift in population genetic structure after the onset of European settlement and industrialized agriculture in its watershed. In particular, we noted a 24.3-fold increase in phosphorus (P) flux between pre-European and modern sediment P accumulation rates (AR) in this lake. In contrast, no such shifts were detected in Hill Lake, where the watershed was not as impacted by European settlement and rates of change were less directional with a much smaller increase in sediment P AR (2.3-fold). We identify direct and indirect effects of eutrophication proxies on genetic structure in these lake populations and demonstrate the power of using this approach in understanding the consequences of anthropogenic environmental change on natural populations throughout historic time periods.}, }
@article {pmid27463017, year = {2016}, author = {Stiller, M and Sucker, A and Griewank, K and Aust, D and Baretton, GB and Schadendorf, D and Horn, S}, title = {Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA.}, journal = {Oncotarget}, volume = {7}, number = {37}, pages = {59115-59128}, pmid = {27463017}, issn = {1949-2553}, mesh = {Animals ; DNA, Single-Stranded/*analysis ; Formaldehyde/chemistry ; *Gene Library ; Genome ; Humans ; Neoplasms/*diagnosis/genetics ; Paraffin Embedding ; Sequence Analysis, DNA ; Tissue Fixation ; }, abstract = {DNA derived from formalin-fixed and paraffin-embedded (FFPE) tissue has been a challenge to large-scale genomic sequencing, due to its low quality and quantities. Improved techniques enabling the genome-wide analysis of FFPE material would be of great value, both from a research and clinical perspective.Comparing a single-strand DNA library preparation method originally developed for ancient DNA to conventional protocols using double-stranded DNA derived from FFPE material we obtain on average 900-fold more library molecules and improved sequence complexity from as little as 5 ng input DNA. FFPE DNA is highly fragmented, usually below 100bp, and up to 60% of reads start after or end prior to adenine residues, suggesting that crosslinks predominate at adenine residues. Similar to ancient DNA, C > T substitutions are slightly increased with maximum rates up to 3% at the ends of molecules. In whole exome sequencing of single-strand libraries from lung, breast, colorectal, prostate and skin cancers we identify known cancer mutations. In summary, we show that single-strand library preparation enables genomic sequencing, even from low amounts of degraded FFPE DNA. This method provides a clear advantage both in research and clinical settings, where FFPE material (e.g. from biopsies) often is the only source of DNA available. Improving the genetic characterization that can be performed on conventional archived FFPE tissue, the single-strand library preparation allows scarce samples to be used in personalized medicine and enables larger sample sizes in future sequencing studies.}, }
@article {pmid27461246, year = {2016}, author = {Kumagai, M and Kanehara, M and Shoda, S and Fujita, S and Onuki, S and Ueda, S and Wang, L}, title = {Rice Varieties in Archaic East Asia: Reduction of Its Diversity from Past to Present Times.}, journal = {Molecular biology and evolution}, volume = {33}, number = {10}, pages = {2496-2505}, doi = {10.1093/molbev/msw142}, pmid = {27461246}, issn = {1537-1719}, mesh = {Asia ; Crops, Agricultural/*genetics ; DNA, Ancient/*analysis ; Evolution, Molecular ; Asia, Eastern ; Genetic Variation ; Genome, Plant ; Japan ; Oryza/*genetics ; Phylogeny ; Plant Breeding ; Species Specificity ; }, abstract = {The Asian cultivated rice, Oryza sativa, is one of the most important crops feeding more than a third of global population. In spite of the studies for several decades, the origin and domestication history of rice varietal groups, japonica and indica, have not been fully unveiled. Genetic information of ancient rice remains is essential for direct and exclusive insight into the domestication history of rice. We performed ancient DNA analysis of 950- to 2,800-year-old rice remains excavated from Japan and Korea. We found the presence of both japonica- and indica-type varieties in the Yayoi period and the middle ages of Japan and the middle part of Korea Peninsula 2,000 years ago. It is popularly considered that japonica has been exclusively cultivated in northern part of East Asia including Japan and Korea. Our result disclosed unexpectedly wide diversity of rice varieties in archaic East Asia. The present results from ancient rice DNA reveal an exclusive insight for the domestication history of rice which is not provided as far as contemporary rice.}, }
@article {pmid27459054, year = {2016}, author = {Lazaridis, I and Nadel, D and Rollefson, G and Merrett, DC and Rohland, N and Mallick, S and Fernandes, D and Novak, M and Gamarra, B and Sirak, K and Connell, S and Stewardson, K and Harney, E and Fu, Q and Gonzalez-Fortes, G and Jones, ER and Roodenberg, SA and Lengyel, G and Bocquentin, F and Gasparian, B and Monge, JM and Gregg, M and Eshed, V and Mizrahi, AS and Meiklejohn, C and Gerritsen, F and Bejenaru, L and Blüher, M and Campbell, A and Cavalleri, G and Comas, D and Froguel, P and Gilbert, E and Kerr, SM and Kovacs, P and Krause, J and McGettigan, D and Merrigan, M and Merriwether, DA and O'Reilly, S and Richards, MB and Semino, O and Shamoon-Pour, M and Stefanescu, G and Stumvoll, M and Tönjes, A and Torroni, A and Wilson, JF and Yengo, L and Hovhannisyan, NA and Patterson, N and Pinhasi, R and Reich, D}, title = {Genomic insights into the origin of farming in the ancient Near East.}, journal = {Nature}, volume = {536}, number = {7617}, pages = {419-424}, pmid = {27459054}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; CZD/16/6//Chief Scientist Office/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; CZD/16/6/4/CSO_/Chief Scientist Office/United Kingdom ; 263441/ERC_/European Research Council/International ; MC_PC_U127561128/MRC_/Medical Research Council/United Kingdom ; GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa, Eastern ; Agriculture/*history ; Animals ; Armenia ; Asia ; DNA/analysis ; Europe ; *Genomics ; History, Ancient ; Human Migration/*history ; Humans ; Hybridization, Genetic/genetics ; Iran ; Israel ; Jordan ; Neanderthals/genetics ; *Phylogeny ; Phylogeography ; Racial Groups/*genetics ; Turkey ; }, abstract = {We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.}, }
@article {pmid27436340, year = {2016}, author = {Morozova, I and Flegontov, P and Mikheyev, AS and Bruskin, S and Asgharian, H and Ponomarenko, P and Klyuchnikov, V and ArunKumar, G and Prokhortchouk, E and Gankin, Y and Rogaev, E and Nikolsky, Y and Baranova, A and Elhaik, E and Tatarinova, TV}, title = {Toward high-resolution population genomics using archaeological samples.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {23}, number = {4}, pages = {295-310}, pmid = {27436340}, issn = {1756-1663}, support = {MC_PC_14115/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *DNA, Ancient ; *Evolution, Molecular ; Genetics, Population/*methods ; *Genome, Human ; Genomics/*methods ; Humans ; Sequence Analysis, DNA/*methods ; }, abstract = {The term 'ancient DNA' (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of 'molecular paleontology'. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.}, }
@article {pmid27432000, year = {2017}, author = {Fisher, SE}, title = {Evolution of language: Lessons from the genome.}, journal = {Psychonomic bulletin &amp; review}, volume = {24}, number = {1}, pages = {34-40}, pmid = {27432000}, issn = {1531-5320}, mesh = {Animals ; Biological Evolution ; *DNA, Ancient ; Evolution, Molecular ; *Genome ; Hominidae/*genetics ; Humans ; *Language ; Neural Pathways ; *Speech ; }, abstract = {The post-genomic era is an exciting time for researchers interested in the biology of speech and language. Substantive advances in molecular methodologies have opened up entire vistas of investigation that were not previously possible, or in some cases even imagined. Speculations concerning the origins of human cognitive traits are being transformed into empirically addressable questions, generating specific hypotheses that can be explicitly tested using data collected from both the natural world and experimental settings. In this article, I discuss a number of promising lines of research in this area. For example, the field has begun to identify genes implicated in speech and language skills, including not just disorders but also the normal range of abilities. Such genes provide powerful entry points for gaining insights into neural bases and evolutionary origins, using sophisticated experimental tools from molecular neuroscience and developmental neurobiology. At the same time, sequencing of ancient hominin genomes is giving us an unprecedented view of the molecular genetic changes that have occurred during the evolution of our species. Synthesis of data from these complementary sources offers an opportunity to robustly evaluate alternative accounts of language evolution. Of course, this endeavour remains challenging on many fronts, as I also highlight in the article. Nonetheless, such an integrated approach holds great potential for untangling the complexities of the capacities that make us human.}, }
@article {pmid27430899, year = {2016}, author = {Jaksch, K and Eschner, A and Rintelen, TV and Haring, E}, title = {DNA analysis of molluscs from a museum wet collection: a comparison of different extraction methods.}, journal = {BMC research notes}, volume = {9}, number = {}, pages = {348}, pmid = {27430899}, issn = {1756-0500}, mesh = {Animals ; Austria ; DNA/genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*standards ; DNA Primers/chemistry ; Electron Transport Complex IV/genetics ; Formaldehyde/chemistry ; Liquid Phase Microextraction/methods ; Mollusca/classification/*genetics ; Museums ; Polymerase Chain Reaction/*standards ; RNA, Ribosomal, 16S/genetics ; Reagent Kits, Diagnostic/*standards ; Solid Phase Microextraction/methods ; Tissue Banks ; }, abstract = {BACKGROUND: DNA isolation and PCR amplification from molluscan taxa is considered as problematic because polysaccharides in tissue and mucus presumably co-precipitate with the DNA and inhibit the activity of DNA polymerase. In the present study we tested two common extraction methods on specimens from the mollusc collection of the Natural History Museum Vienna (NHMW). We analysed a broad variety of taxa covering a large temporal span (acquisition years 1877 to 1999), which distinguishes our study from previous ones where mostly fresh material was used. We also took other factors into account: effects of sample age, effects of formaldehyde treatment and taxon-specific problems. We used several primer combinations to amplify amplicons of different lengths of two mitochondrial genes: cytochrome c oxidase subunit 1 (COI) and 16S rRNA gene (16S).<br><br>RESULTS: Overall PCR success was 43&#xa0;% in the 576 extractions (including all primer combinations). The smallest amplicon (~240&#xa0;bp) showed the best results (49&#xa0;% positive reactions), followed by the 400&#xa0;bp amplicon (40.5&#xa0;%). Both short sections yielded significantly better results than the 700&#xa0;bp long amplicon (27&#xa0;%). Comparatively, the Gen-ial-First, All-tissue DNA-Kit-extraction method performed significantly better than Promega-Tissue and Hair Extraction Kit. Generally, PCR success is age-dependent. Nonetheless, we were able to obtain the longest amplicon even from 137-year-old material. Importantly, formaldehyde traces did not totally inhibit amplification success, although very high concentrations did.<br><br>CONCLUSIONS: Museum material has gained importance for DNA analysis in recent years, especially for DNA barcoding projects. In some cases, however, the amplification of the standard barcoding region (partial sequence of the COI) is problematic with old material. Our study clearly shows that the COI barcoding region could be amplified in up to 49&#xa0;% of PCRs (varying with amplicon length), which is, for museum samples, quite a high percentage. The difference between extraction methods was minimal and we recommend using an established kit for a first attempt because experience and routine in handling might be more important than slight performance differences of the various kits. Finally, we identify fixation, storage, sample conservation and documentation of the specimens' history rather than the DNA extraction method to be the most crucial factors for PCR success.}, }
@article {pmid27429780, year = {2016}, author = {Weiß, CL and Schuenemann, VJ and Devos, J and Shirsekar, G and Reiter, E and Gould, BA and Stinchcombe, JR and Krause, J and Burbano, HA}, title = {Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens.}, journal = {Royal Society open science}, volume = {3}, number = {6}, pages = {160239}, pmid = {27429780}, issn = {2054-5703}, abstract = {Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.}, }
@article {pmid27427784, year = {2016}, author = {Lim, HC and Braun, MJ}, title = {High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements.}, journal = {Molecular ecology resources}, volume = {16}, number = {5}, pages = {1204-1223}, doi = {10.1111/1755-0998.12568}, pmid = {27427784}, issn = {1755-0998}, mesh = {Animals ; Asia, Southeastern ; Birds/*classification/*genetics ; Genotype ; Genotyping Techniques/*methods ; Museums ; *Polymorphism, Single Nucleotide ; Preservation, Biological ; }, abstract = {Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27-43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 10(6) bp (Arachnothera, modern samples) to 1.98 × 10(6) bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering.}, }
@article {pmid27425631, year = {2016}, author = {Salse, J}, title = {Deciphering the evolutionary interplay between subgenomes following polyploidy: A paleogenomics approach in grasses.}, journal = {American journal of botany}, volume = {103}, number = {7}, pages = {1167-1174}, doi = {10.3732/ajb.1500459}, pmid = {27425631}, issn = {1537-2197}, mesh = {Biological Evolution ; Genome, Plant/*genetics ; Genomics ; Karyotype ; Poaceae/*genetics ; *Polyploidy ; }, abstract = {How did plant species emerge from their most recent common ancestors (MRCAs) 250 million years ago? Modern plant genomes help to address such key questions in unveiling precise species genealogies. The field of paleogenomics is undergoing a paradigm shift for investigating species evolution from the study of ancestral genomes from extinct species to deciphering the evolutionary forces (in terms of duplication, fusion, fission, deletion, and translocation) that drove present-day plant diversity (in terms of chromosome/gene number and genome size). In this review, inferred ancestral karyotype genomes are shown to be powerful tools to (1) unravel the past history of extant species by recovering the variations of ancestral genomic compartments and (2) accelerate translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.}, }
@article {pmid27424151, year = {2017}, author = {Corlett, RT}, title = {A Bigger Toolbox: Biotechnology in Biodiversity Conservation.}, journal = {Trends in biotechnology}, volume = {35}, number = {1}, pages = {55-65}, doi = {10.1016/j.tibtech.2016.06.009}, pmid = {27424151}, issn = {1879-3096}, mesh = {*Biodiversity ; Chromosome Mapping/*methods ; Conservation of Natural Resources/*methods ; DNA Barcoding, Taxonomic/*methods ; *Databases, Genetic ; Environmental Monitoring/*methods ; Extinction, Biological ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; }, abstract = {Conservation biology needs a bigger toolbox to meet unprecedented challenges. Genomics, fueled by declining sequencing costs, offers novel tools with increased precision for genetic questions previously answered with a few molecular markers, as well as completely new possibilities. Metabarcoding promises quicker, cheaper, and more accurate assessments of biodiversity in groups that are difficult to assess by traditional methods, while sequencing low-quality DNA extends the range of useable materials to include museum specimens, archeological remains, and environmental samples. Genomic and transcriptomic data can be used to assess the potential of populations to adapt to new challenges. In the near future, gene-editing tools may help endangered species cope with change, while gene drives control unwanted species and help wanted ones. De-extinction has become a serious prospect.}, }
@article {pmid27423248, year = {2017}, author = {Miga, KH}, title = {Chromosome-Specific Centromere Sequences Provide an Estimate of the Ancestral Chromosome 2 Fusion Event in Hominin Genomes.}, journal = {The Journal of heredity}, volume = {108}, number = {1}, pages = {45-52}, doi = {10.1093/jhered/esw039}, pmid = {27423248}, issn = {1465-7333}, mesh = {Animals ; *Centromere ; Chromosomes, Human, Pair 2 ; *Chromosomes, Mammalian ; DNA, Satellite ; *Evolution, Molecular ; *Genome ; Genomics/methods ; Hominidae/*genetics ; Humans ; Pan troglodytes/genetics ; }, abstract = {Human chromosome 2 is a product of a telomere fusion of two ancestral chromosomes and loss/degeneration of one of the two original centromeres. Genomic signatures of this event are limited to inverted telomeric repeats at the precise site of chromosomal fusion and to the small amount of relic centromeric sequences that remain on 2q21.2. Unlike the site of fusion, which is enriched for sequences that are shared elsewhere in the human genome, the region of the nonfunctioning and degenerate ancestral centromere appears to share limited similarity with other sites in the human genome, thereby providing an opportunity to study this genomic arrangement in short, fragmented ancient DNA genomic datasets. Here, chromosome-assigned satellite DNAs are used to study shared centromere sequence organization in Denisovan and Neandertal genomes. By doing so, one is able to provide evidence for the presence of both active and degenerate centromeric satellite profiles on chromosome 2 in these archaic genomes, supporting the hypothesis that the chromosomal fusion event took place prior to our last common ancestor with Denisovan and Neandertal hominins and presenting a genomic reference for predicting karyotype in ancient genomic datasets.}, }
@article {pmid27419861, year = {2016}, author = {}, title = {Unlocking the Past on the "Bases" of Ancient DNA.}, journal = {Cell}, volume = {166}, number = {2}, pages = {259-261}, doi = {10.1016/j.cell.2016.06.053}, pmid = {27419861}, issn = {1097-4172}, }
@article {pmid27418483, year = {2016}, author = {Gibbons, A}, title = {ANCIENT DNA. First farmers' motley roots.}, journal = {Science (New York, N.Y.)}, volume = {353}, number = {6296}, pages = {207-208}, doi = {10.1126/science.353.6296.207}, pmid = {27418483}, issn = {1095-9203}, mesh = {Agriculture/*history ; Cell Nucleus/genetics ; DNA/analysis/genetics/*history ; Farmers/*history ; History, Ancient ; Humans ; Iran ; Tooth/chemistry ; }, }
@article {pmid27389305, year = {2016}, author = {Talamo, S and Hajdinjak, M and Mannino, MA and Fasani, L and Welker, F and Martini, F and Romagnoli, F and Zorzin, R and Meyer, M and Hublin, JJ}, title = {Direct radiocarbon dating and genetic analyses on the purported Neanderthal mandible from the Monti Lessini (Italy).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29144}, pmid = {27389305}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/*isolation &amp; purification ; *Fossils ; Genetic Testing ; Humans ; Italy ; Mandible/chemistry ; Neanderthals/*genetics ; *Radiometric Dating ; Skull/chemistry ; }, abstract = {Anatomically modern humans replaced Neanderthals in Europe around 40,000 years ago. The demise of the Neanderthals and the nature of the possible relationship with anatomically modern humans has captured our imagination and stimulated research for more than a century now. Recent chronological studies suggest a possible overlap between Neanderthals and anatomically modern humans of more than 5,000 years. Analyses of ancient genome sequences from both groups have shown that they interbred multiple times, including in Europe. A potential place of interbreeding is the notable Palaeolithic site of Riparo Mezzena in Northern Italy. In order to improve our understanding of prehistoric occupation at Mezzena, we analysed the human mandible and several cranial fragments from the site using radiocarbon dating, ancient DNA, ZooMS and isotope analyses. We also performed a more detailed investigation of the lithic assemblage of layer I. Surprisingly we found that the Riparo Mezzena mandible is not from a Neanderthal but belonged to an anatomically modern human. Furthermore, we found no evidence for the presence of Neanderthal remains among 11 of the 13 cranial and post-cranial fragments re-investigated in this study.}, }
@article {pmid27378746, year = {2016}, author = {Kimmel, M and Wojdyła, T}, title = {Genetic demographic networks: Mathematical model and applications.}, journal = {Theoretical population biology}, volume = {111}, number = {}, pages = {75-86}, doi = {10.1016/j.tpb.2016.06.004}, pmid = {27378746}, issn = {1096-0325}, mesh = {*Demography ; Genetic Variation ; *Genetics, Population ; Humans ; *Markov Chains ; *Models, Theoretical ; }, abstract = {Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans.}, }
@article {pmid27374145, year = {2017}, author = {Guimaraes, S and Pruvost, M and Daligault, J and Stoetzel, E and Bennett, EA and Côté, NM and Nicolas, V and Lalis, A and Denys, C and Geigl, EM and Grange, T}, title = {A cost-effective high-throughput metabarcoding approach powerful enough to genotype ~44 000 year-old rodent remains from Northern Africa.}, journal = {Molecular ecology resources}, volume = {17}, number = {3}, pages = {405-417}, doi = {10.1111/1755-0998.12565}, pmid = {27374145}, issn = {1755-0998}, mesh = {Animals ; Archaeology ; *DNA Barcoding, Taxonomic ; Genotype ; High-Throughput Nucleotide Sequencing ; Morocco ; Phylogeny ; Rodentia/*classification ; }, abstract = {We present a cost-effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next-generation sequencing to simultaneously analyse many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotyping of ancient rodent remains from a Moroccan cave whose stratigraphy covers the last 120 000 years. Rodents are important for epidemiology, agronomy and ecological investigations and can act as bioindicators for human- and/or climate-induced environmental changes. Efficient and reliable genotyping of ancient rodent remains has the potential to deliver valuable phylogenetic and paleoecological information. The analysis of multiple ancient skeletal remains of very small size with poor DNA preservation, however, requires a sensitive high-throughput method to generate sufficient data. We show this approach to be particularly adapted at accessing this otherwise difficult taxonomic and genetic resource. As a highly scalable, lower cost and less labour-intensive alternative to targeted sequence capture approaches, we propose the aMPlex Torrent strategy to be a useful tool for the genetic analysis of multiple degraded samples in studies involving ecology, archaeology, conservation and evolutionary biology.}, }
@article {pmid27362779, year = {2016}, author = {Bianucci, R and Loynes, RD and Sutherland, ML and Lallo, R and Kay, GL and Froesch, P and Pallen, MJ and Charlier, P and Nerlich, AG}, title = {Forensic Analysis Reveals Acute Decompensation of Chronic Heart Failure in a 3500-Year-Old Egyptian Dignitary.}, journal = {Journal of forensic sciences}, volume = {61}, number = {5}, pages = {1378-1381}, doi = {10.1111/1556-4029.13138}, pmid = {27362779}, issn = {1556-4029}, mesh = {*Atherosclerosis ; Egypt ; Forensic Anthropology ; *Heart Failure ; Humans ; Lung ; Male ; *Mummies ; }, abstract = {Naturally preserved and embalmed bodies from archeological contexts represent a powerful source of information for forensic investigators. They allow one to ascertain pathology, cause of death, to enhance diagnostic methodology, and to improve the analysis of altered remains. We investigated the complete head and lung remnants of a 3,500-year-old Egyptian dignitary by radiological, microscopic, and genetic approaches. The individual, a middle-aged male, suffered from severe periodontitis, mild atherosclerosis, and experienced cardiogenic pulmonary insufficiency with recurrent mini-bleeds and pulmonary edema. Histology and ancient DNA analyses excluded the presence of Mycobacterium tuberculosis or of any other pathogenic species. Based on our collection of evidence, we propose that acute decompensation complicating chronic cardiac insufficiency was the likely cause of death. The underlying causes for this failure remain unknown although chronic hypertension appears to be the most likely candidate. Our finding represents the earliest reported case of chronic heart failure in ancient mummies.}, }
@article {pmid27352946, year = {2016}, author = {Hou, J and Ye, N and Dong, Z and Lu, M and Li, L and Yin, T}, title = {Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral "Salicoid" Genome Duplication.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {1868-1875}, pmid = {27352946}, issn = {1759-6653}, mesh = {Chromosome Aberrations ; Chromosomes, Plant/*genetics ; Diploidy ; Genome, Plant ; *Polyploidy ; Populus/*genetics ; Salix/*genetics ; }, abstract = {Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the "salicoid" duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants.}, }
@article {pmid27346733, year = {2016}, author = {Russo, MG and Mendisco, F and Avena, SA and Dejean, CB and Seldes, V}, title = {Pre-Hispanic Mortuary Practices in Quebrada de Humahuaca (North-Western Argentina): Genetic Relatedness among Individuals Buried in the Same Grave.}, journal = {Annals of human genetics}, volume = {80}, number = {4}, pages = {210-220}, doi = {10.1111/ahg.12159}, pmid = {27346733}, issn = {1469-1809}, mesh = {Argentina ; *Cemeteries ; DNA, Mitochondrial/genetics ; Female ; Humans ; Indians, South American/*genetics ; Male ; Pedigree ; Sequence Analysis, DNA ; }, abstract = {Almost all pre-Hispanic societies from Quebrada de Humahuaca (north-western Argentina) buried their defuncts in domestic areas, demonstrating the importance of death and its daily presence among the living. Presumably, the collective graves contained related individuals, a hypothesis that can be tested through the study of ancient DNA. This study analyzes autosomal and uniparental genetic markers in individuals from two archaeological sites in Quebrada de Humahuaca occupied during the Late Formative (1450-1050 BP) and Regional Developments I (1050-700 BP) periods. Mitochondrial and Y-chromosome haplotypes were compared in order to establish possible maternal and paternal relatedness. Genotypes for 15 autosomal STRs were used to calculate pairwise relatedness coefficients and pedigree probabilities. High kinship levels among individuals buried in the same graves were found in both sites. Although only two particular cases were analyzed, these results represent an important contribution to the study of mortuary practices in the region by means of ancient DNA.}, }
@article {pmid27337483, year = {2016}, author = {Abi-Rached, L and Raoult, D}, title = {Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution.}, journal = {Microbiology spectrum}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/microbiolspec.PoH-0018-2015}, pmid = {27337483}, issn = {2165-0497}, mesh = {Communicable Diseases/*epidemiology/*immunology ; *Evolution, Molecular ; *Fossils ; Humans ; *Immune System ; Immunogenetics/*methods ; Paleopathology/*methods ; Selection, Genetic ; }, abstract = {With the advent of next-generation sequencing, paleogenetics has considerably expanded over the past few years and notably encompassed the characterization of the genomes of archaic humans who lived more than 30,000 years ago. These paleogenetics investigations have revealed that admixture between modern and archaic humans occurred, with Neanderthals having contributed to 1.5% to 2.1% of modern Eurasian genomes, and Denisovans to 3% to 6% of modern Melanesian genomes and to approximately 0.2% of modern Asian genomes. Although these contributions are modest, they played a major role in shaping immune gene families, such as the HLA class I genes, for which the archaic alleles now represent more than 50% of the alleles in Europe and Asia. Such a high frequency is consistent with these archaic HLA class I variants having been positively selected because of their protective effect against contagious and devastating epidemics, such as those due to the plague agent Yersinia pestis or to Mycobacterium tuberculosis, which is responsible for deadly tuberculosis. While the exact nature of the infectious agents that contributed to the selection of the archaic variants is unknown, we are entering an exciting period in which paleogenetics and paleomicrobiology data can be integrated to generate a clearer picture of how the immune system of modern populations was shaped and the role admixture and epidemics have played in such evolutions.}, }
@article {pmid27331397, year = {2016}, author = {Splendiani, A and Fioravanti, T and Giovannotti, M and Negri, A and Ruggeri, P and Olivieri, L and Nisi Cerioni, P and Lorenzoni, M and Caputo Barucchi, V}, title = {The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0157975}, pmid = {27331397}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Bone and Bones/anatomy &amp; histology ; Calibration ; *Climate ; DNA, Ancient/*analysis ; Fossils ; Geography ; Greenland ; Haplotypes/genetics ; Italy ; Mediterranean Region ; Mitochondria/genetics ; *Paleontology ; Time Factors ; Trout/*genetics ; }, abstract = {In this pilot study for the first time, ancient DNA has been extracted from bone remains of Salmo trutta. These samples were from a stratigraphic succession located in a coastal cave of Calabria (southern Italy) inhabited by humans from upper Palaeolithic to historical times. Seven pairs of primers were used to PCR-amplify and sequence from 128 to 410 bp of the mtDNA control region of eleven samples. Three haplotypes were observed: two (ADcs-1 and MEcs-1) already described in rivers from the Italian peninsula; one (ATcs-33) belonging to the southern Atlantic clade of the AT Salmo trutta mtDNA lineage (sensu Bernatchez). The prehistoric occurrence of this latter haplotype in the water courses of the Italian peninsula has been detected for the first time in this study. Finally, we observed a correspondence between frequency of trout remains and variation in haplotype diversity that we related with ecological and demographic changes resulting from a period of rapid cooling known as the Younger Dryas.}, }
@article {pmid27325755, year = {2016}, author = {Jeong, C and Ozga, AT and Witonsky, DB and Malmström, H and Edlund, H and Hofman, CA and Hagan, RW and Jakobsson, M and Lewis, CM and Aldenderfer, MS and Di Rienzo, A and Warinner, C}, title = {Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {27}, pages = {7485-7490}, pmid = {27325755}, issn = {1091-6490}, support = {P30 CA014599/CA/NCI NIH HHS/United States ; R01 HL119577/HL/NHLBI NIH HHS/United States ; }, mesh = {Altitude ; *Gene Flow ; *Genome, Human ; Humans ; Nepal ; Paleodontology ; Phylogeography ; Sequence Analysis, DNA ; Tibet ; }, abstract = {The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04×-7.25×, mean 2.16×) and mitochondrial genomes (20.8×-1,311.0×, mean 482.1×) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations.}, }
@article {pmid27313020, year = {2016}, author = {Gibbons, A}, title = {Ancient DNA divide.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6292}, pages = {1384-1387}, doi = {10.1126/science.352.6292.1384}, pmid = {27313020}, issn = {1095-9203}, mesh = {Anthropology/*economics ; DNA, Bacterial/*genetics/isolation &amp; purification ; Dairying/history ; Dental Plaque/microbiology ; Fossils ; Germany ; History, Ancient ; Humans ; Oklahoma ; Research Personnel/*economics ; *Research Support as Topic ; Tooth ; }, }
@article {pmid27297978, year = {2016}, author = {Niemi, M and Sajantila, A and Vilkki, J}, title = {Temporal variation in coat colour (genotypes) supports major changes in the Nordic cattle population after Iron Age.}, journal = {Animal genetics}, volume = {47}, number = {4}, pages = {495-498}, doi = {10.1111/age.12445}, pmid = {27297978}, issn = {1365-2052}, mesh = {Alleles ; Animals ; Breeding ; Cattle/*genetics ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Finland ; Gene Frequency ; *Genetics, Population ; Genotype ; Hair Color/*genetics ; Phenotype ; Receptor, Melanocortin, Type 1/*genetics ; Sequence Analysis, DNA/veterinary ; Y Chromosome/genetics ; }, abstract = {Variation in coat colour genotypes of archaeological cattle samples from Finland was studied by sequencing 69 base pairs of the extension locus (melanocortin 1-receptor, MC1R) targeting both a transition and a deletion defining the three main alleles, such as dominant black (E(D)), wild type (E(+)) and recessive red (e). The 69-bp MC1R sequence was successfully analysed from 23 ancient (1000-1800 AD) samples. All three main alleles and genotype combinations were detected with allele frequencies of 0.26, 0.17 and 0.57 for E(D) , E(+) and e respectively. Recessive red and dominant black alleles were detected in both sexes. According to the best of our knowledge, this is the first ancient DNA study defining all three main MC1R alleles. Observed MC1R alleles are in agreement with calculated phenotype frequencies from historical sources. The division of ancient Finnish cattle population into modern Finnish breeds with settled colours was dated to the 20th century. From the existing genotyped populations in Europe (43 breeds, n = 2360), the closest match to ancient MC1R genotype frequencies was with the Norwegian native multicoloured breeds. In combined published genotype data of ancient (n = 147) and genotypes and phenotypes of modern Nordic cattle (n = 738), MC1R allele frequencies showed temporal changes similar to neutral mitochondrial DNA and Y-chromosomal haplotypes analysed earlier. All three markers indicate major change in genotypes in Nordic cattle from the Late Iron Age to the Medieval period followed by slower change through the historical periods until the present.}, }
@article {pmid27297799, year = {2016}, author = {Burnham, P and Kim, MS and Agbor-Enoh, S and Luikart, H and Valantine, HA and Khush, KK and De Vlaminck, I}, title = {Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27859}, pmid = {27297799}, issn = {2045-2322}, support = {R21 AI124237/AI/NIAID NIH HHS/United States ; }, mesh = {Cell-Free Nucleic Acids/*genetics ; DNA, Single-Stranded/*genetics ; *Gene Library ; Genotype ; Humans ; Lung Transplantation ; Mitochondria/*genetics ; Nucleosomes/*genetics ; Pathology, Molecular ; Sequence Analysis, DNA ; }, abstract = {Circulating cell-free DNA (cfDNA) is emerging as a powerful monitoring tool in cancer, pregnancy and organ transplantation. Nucleosomal DNA, the predominant form of plasma cfDNA, can be adapted for sequencing via ligation of double-stranded DNA (dsDNA) adapters. dsDNA library preparations, however, are insensitive to ultrashort, degraded cfDNA. Drawing inspiration from advances in paleogenomics, we have applied a single-stranded DNA (ssDNA) library preparation method to sequencing of cfDNA in the plasma of lung transplant recipients (40 samples, six patients). We found that ssDNA library preparation yields a greater portion of sub-100 bp nuclear genomic cfDNA (p 10(-5), Mann-Whitney U Test), and an increased relative abundance of mitochondrial (10.7x, p 10(-5)) and microbial cfDNA (71.3x, p 10(-5)). The higher yield of microbial sequences from this method increases the sensitivity of cfDNA-based monitoring for infections following transplantation. We detail the fragmentation pattern of mitochondrial, nuclear genomic and microbial cfDNA over a broad fragment length range. We report the observation of donor-specific mitochondrial cfDNA in the circulation of lung transplant recipients. A ssDNA library preparation method provides a more informative window into understudied forms of cfDNA, including mitochondrial and microbial derived cfDNA and short nuclear genomic cfDNA, while retaining information provided by standard dsDNA library preparation methods.}, }
@article {pmid27292545, year = {2016}, author = {Leles, D and Lobo, A and Rhodes, T and Millar, PR and Amendoeira, MR and Araújo, A}, title = {Recovery of Toxoplasma gondii DNA in experimentally mummified skin and bones: Prospects for paleoparasitological studies to unveil the origin of toxoplasmosis.}, journal = {Experimental parasitology}, volume = {168}, number = {}, pages = {51-55}, doi = {10.1016/j.exppara.2016.06.003}, pmid = {27292545}, issn = {1090-2449}, mesh = {Animals ; Bone and Bones/parasitology ; DNA, Protozoan/*isolation &amp; purification ; History, Ancient ; Humans ; Mice ; Models, Animal ; Mummies/*parasitology ; Skin/parasitology ; Toxoplasma/*genetics/isolation &amp; purification ; Toxoplasmosis/*history ; }, abstract = {Paleoparasitology studies parasite infections by finding the parasites' remains in preserved organic remains such as natural or artificial mummy tissues, skeletons, teeth, and coprolites, among others. However, some currently important infections like toxoplasmosis have not been studied by paleoparasitology. The reasons include this parasite's complex life cycle, the resulting difficulties in locating this protozoan in the intermediate host tissues, and the limitation of coprolite studies to felines, the protozoan's definitive host. The current study thus aimed to produce an experimental model for molecular diagnosis of toxoplasmosis, prioritizing its study in bones and skin, the most abundant materials in archeological collections and sites. The study demonstrated the feasibility of recovering Toxoplasma gondii DNA from desiccated material, including bones and skin, in experimental models both with circulating tachyzoites (RH strain), characteristic of acute infection, and with cysts (ME49 cystogenic strain), characteristic of chronic infection. At present, most individuals with T. gondii infection are in the chronic phase, and the same was probably true in the past. The current study thus expands the odds of finding the parasite in archeological material, enhanced by the nature of the material in which the diagnosis was made. Finding the parasite may help answer questions that are widely debated in the literature on this protozoan's origin (Old World versus New World). In addition, when conditions do not allow ideal storage of samples for molecular tests, the methodology creates the possibility of testing oven-dried samples transported at room temperature.}, }
@article {pmid27289479, year = {2016}, author = {Bouwman, A and Rühli, F}, title = {Archaeogenetics in evolutionary medicine.}, journal = {Journal of molecular medicine (Berlin, Germany)}, volume = {94}, number = {9}, pages = {971-977}, pmid = {27289479}, issn = {1432-1440}, mesh = {Animals ; *Archaeology/methods ; DNA/genetics ; Environment ; *Evolution, Molecular ; Gene-Environment Interaction ; *Genetic Association Studies/methods ; *Genetic Predisposition to Disease ; Genetics, Population ; Genomics/methods ; Host-Pathogen Interactions/*genetics ; Humans ; }, abstract = {Archaeogenetics is the study of exploration of ancient DNA (aDNA) of more than 70 years old. It is an important part of the wider studies of many different areas of our past, including animal, plant and pathogen evolution and domestication events. Hereby, we address specifically the impact of research in archaeogenetics in the broader field of evolutionary medicine. Studies on ancient hominid genomes help to understand even modern health patterns. Human genetic microevolution, e.g. related to abilities of post-weaning milk consumption, and specifically genetic adaptation in disease susceptibility, e.g. towards malaria and other infectious diseases, are of the upmost importance in contributions of archeogenetics on the evolutionary understanding of human health and disease. With the increase in both the understanding of modern medical genetics and the ability to deep sequence ancient genetic information, the field of archaeogenetic evolutionary medicine is blossoming.}, }
@article {pmid27289078, year = {2016}, author = {Rawlence, NJ and Collins, CJ and Anderson, CN and Maxwell, JJ and Smith, IW and Robertson, BC and Knapp, M and Horsburgh, KA and Stanton, JA and Scofield, RP and Tennyson, AJ and Matisoo-Smith, EA and Waters, JM}, title = {Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations.}, journal = {Molecular ecology}, volume = {25}, number = {16}, pages = {3950-3961}, doi = {10.1111/mec.13726}, pmid = {27289078}, issn = {1365-294X}, mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Fisheries ; Human Activities ; Humans ; Islands ; New Zealand ; Sea Lions/*genetics ; }, abstract = {While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450-1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within 200 years due to overhunting, paralleling the extirpation of a similarly large endemic mainland population. Whole mitogenomic analyses confirm substantial intraspecific diversity among prehistoric lineages. Demographic models suggest that even low harvest rates would likely have driven rapid extinction of these lineages. This study indicates that surviving Phocarctos populations are remnants of a once diverse and widespread sea lion assemblage, highlighting dramatic human impacts on endemic marine biodiversity. Our findings also suggest that Phocarctos bycatch in commercial fisheries may contribute to the ongoing population decline.}, }
@article {pmid27289015, year = {2017}, author = {Mohandesan, E and Speller, CF and Peters, J and Uerpmann, HP and Uerpmann, M and De Cupere, B and Hofreiter, M and Burger, PA}, title = {Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel.}, journal = {Molecular ecology resources}, volume = {17}, number = {2}, pages = {300-313}, pmid = {27289015}, issn = {1755-0998}, support = {P 24706/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Animals, Domestic ; Animals, Wild ; Arab World ; Camelus/*classification/*genetics ; DNA, Ancient/*chemistry/*isolation &amp; purification ; DNA, Mitochondrial/chemistry/genetics/isolation &amp; purification ; Desert Climate ; Nucleic Acid Hybridization/*methods ; Sequence Analysis, DNA/*methods ; Temperature ; Time Factors ; Turkey ; }, abstract = {The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.}, }
@article {pmid27281573, year = {2016}, author = {Spyrou, MA and Tukhbatova, RI and Feldman, M and Drath, J and Kacki, S and Beltrán de Heredia, J and Arnold, S and Sitdikov, AG and Castex, D and Wahl, J and Gazimzyanov, IR and Nurgaliev, DK and Herbig, A and Bos, KI and Krause, J}, title = {Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics.}, journal = {Cell host &amp; microbe}, volume = {19}, number = {6}, pages = {874-881}, doi = {10.1016/j.chom.2016.05.012}, pmid = {27281573}, issn = {1934-6069}, mesh = {Asia/epidemiology ; Bone and Bones/microbiology ; DNA, Bacterial/genetics ; Disease Reservoirs ; Europe/epidemiology ; Genome, Bacterial ; Genotype ; High-Throughput Nucleotide Sequencing ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, Medieval ; Humans ; Molecular Epidemiology ; Pandemics/*history ; Phylogeny ; Plague/epidemiology/*history/*microbiology ; Tooth/microbiology ; Yersinia pestis/*genetics/isolation &amp; purification ; }, abstract = {Ancient DNA analysis has revealed an involvement of the bacterial pathogen Yersinia pestis in several historical pandemics, including the second plague pandemic (Europe, mid-14(th) century Black Death until the mid-18(th) century AD). Here we present reconstructed Y. pestis genomes from plague victims of the Black Death and two subsequent historical outbreaks spanning Europe and its vicinity, namely Barcelona, Spain (1300-1420 cal AD), Bolgar City, Russia (1362-1400 AD), and Ellwangen, Germany (1485-1627 cal AD). Our results provide support for (1) a single entry of Y. pestis in Europe during the Black Death, (2) a wave of plague that traveled toward Asia to later become the source population for contemporary worldwide epidemics, and (3) the presence of an historical European plague focus involved in post-Black Death outbreaks that is now likely extinct.}, }
@article {pmid27274055, year = {2016}, author = {Heupink, TH and Subramanian, S and Wright, JL and Endicott, P and Westaway, MC and Huynen, L and Parson, W and Millar, CD and Willerslev, E and Lambert, DM}, title = {Ancient mtDNA sequences from the First Australians revisited.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {25}, pages = {6892-6897}, pmid = {27274055}, issn = {1091-6490}, mesh = {Australia ; DNA, Mitochondrial/*genetics ; Humans ; Likelihood Functions ; Phylogeny ; }, abstract = {The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.}, }
@article {pmid27274049, year = {2016}, author = {Hofmanová, Z and Kreutzer, S and Hellenthal, G and Sell, C and Diekmann, Y and Díez-Del-Molino, D and van Dorp, L and López, S and Kousathanas, A and Link, V and Kirsanow, K and Cassidy, LM and Martiniano, R and Strobel, M and Scheu, A and Kotsakis, K and Halstead, P and Triantaphyllou, S and Kyparissi-Apostolika, N and Urem-Kotsou, D and Ziota, C and Adaktylou, F and Gopalan, S and Bobo, DM and Winkelbach, L and Blöcher, J and Unterländer, M and Leuenberger, C and Çilingiroğlu, &#xc7; and Horejs, B and Gerritsen, F and Shennan, SJ and Bradley, DG and Currat, M and Veeramah, KR and Wegmann, D and Thomas, MG and Papageorgopoulou, C and Burger, J}, title = {Early farmers from across Europe directly descended from Neolithic Aegeans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {25}, pages = {6886-6891}, pmid = {27274049}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; Y 528/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Agriculture ; *Anthropology ; Europe ; Genetics, Population ; Humans ; Mediterranean Region ; Principal Component Analysis ; }, abstract = {Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.}, }
@article {pmid27274046, year = {2016}, author = {Boivin, NL and Zeder, MA and Fuller, DQ and Crowther, A and Larson, G and Erlandson, JM and Denham, T and Petraglia, MD}, title = {Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {23}, pages = {6388-6396}, pmid = {27274046}, issn = {1091-6490}, mesh = {Agriculture ; Animals ; *Demography ; *Ecosystem ; Human Activities ; Humans ; Islands ; Urbanization ; }, abstract = {The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity-the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.}, }
@article {pmid27274045, year = {2016}, author = {Slatkin, M and Racimo, F}, title = {Ancient DNA and human history.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {23}, pages = {6380-6387}, pmid = {27274045}, issn = {1091-6490}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA Contamination ; *DNA, Ancient ; Fossils ; Genome ; Hominidae/*genetics ; Humans ; }, abstract = {We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history.}, }
@article {pmid27270125, year = {2016}, author = {Brietzke, A and Borchel, A and Altmann, S and Nipkow, M and Rebl, A and Brunner, RM and Goldammer, T}, title = {Transcriptome sequencing of maraena whitefish (Coregonus maraena).}, journal = {Marine genomics}, volume = {29}, number = {}, pages = {27-29}, doi = {10.1016/j.margen.2016.05.006}, pmid = {27270125}, issn = {1876-7478}, mesh = {Amino Acid Sequence ; Animals ; *Gene Duplication ; *Genome ; Genomics ; Salmonidae/*genetics ; *Transcriptome ; }, abstract = {Maraena whitefish (Coregonus maraena, Bloch, 1779) is a high-quality food fish belonging to the family Salmonidae with considerable economic relevance in the Baltic area. Aquaculture of this species is fundamental for its successful conservation and thus sustainable fisheries. Robust fishes obtained from breeding lines build the basis for effective aquaculture. Doubtless, the utilization of transcriptome sequencing and identification of genetic markers contribute to this aim. 454 FLX Titanium Sequencing provided 1.31 million sequence reads representing a first insight into the C. maraena transcriptome. The 454 Newbler Assembly arranged 29,094 contigs with an average length of 798bp. We found a whole series of transcripts highly probably resulting from ancient genome duplication and annotated 2887 different transcripts with an average length of 812bp. Functional annotation obtained a transcript composition predominantly comprising enzyme-coding genes.}, }
@article {pmid27261250, year = {2016}, author = {Mitchell, KJ and Wood, JR and Llamas, B and McLenachan, PA and Kardailsky, O and Scofield, RP and Worthy, TH and Cooper, A}, title = {Ancient mitochondrial genomes clarify the evolutionary history of New Zealand's enigmatic acanthisittid wrens.}, journal = {Molecular phylogenetics and evolution}, volume = {102}, number = {}, pages = {295-304}, doi = {10.1016/j.ympev.2016.05.038}, pmid = {27261250}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Bone and Bones/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA, Mitochondrial/chemistry/genetics/metabolism ; Extinction, Biological ; *Genome, Mitochondrial ; New Zealand ; Phylogeny ; Sequence Analysis, DNA ; Songbirds/*classification/genetics ; }, abstract = {The New Zealand acanthisittid wrens are the sister-taxon to all other "perching birds" (Passeriformes) and - including recently extinct species - represent the most diverse endemic passerine family in New Zealand. Consequently, they are important for understanding both the early evolution of Passeriformes and the New Zealand biota. However, five of the seven species have become extinct since the arrival of humans in New Zealand, complicating evolutionary analyses. The results of morphological analyses have been largely equivocal, and no comprehensive genetic analysis of Acanthisittidae has been undertaken. We present novel mitochondrial genome sequences from four acanthisittid species (three extinct, one extant), allowing us to resolve the phylogeny and revise the taxonomy of acanthisittids. Reanalysis of morphological data in light of our genetic results confirms a close relationship between the extant rifleman (Acanthisitta chloris) and an extinct Miocene wren (Kuiornis indicator), making Kuiornis a useful calibration point for molecular dating of passerines. Our molecular dating analyses reveal that the stout-legged wrens (Pachyplichas) diverged relatively recently from a more gracile (Xenicus-like) ancestor. Further, our results suggest a possible Early Oligocene origin of the basal Lyall's wren (Traversia) lineage, which would imply that Acanthisittidae survived the Oligocene marine inundation of New Zealand and therefore that the inundation was not complete.}, }
@article {pmid27257259, year = {2016}, author = {Frantz, LA and Mullin, VE and Pionnier-Capitan, M and Lebrasseur, O and Ollivier, M and Perri, A and Linderholm, A and Mattiangeli, V and Teasdale, MD and Dimopoulos, EA and Tresset, A and Duffraisse, M and McCormick, F and Bartosiewicz, L and Gál, E and Nyerges, &#xc9;A and Sablin, MV and Bréhard, S and Mashkour, M and Bălăşescu, A and Gillet, B and Hughes, S and Chassaing, O and Hitte, C and Vigne, JD and Dobney, K and Hänni, C and Bradley, DG and Larson, G}, title = {Genomic and archaeological evidence suggest a dual origin of domestic dogs.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6290}, pages = {1228-1231}, doi = {10.1126/science.aaf3161}, pmid = {27257259}, issn = {1095-9203}, mesh = {Animals ; Animals, Domestic/*genetics ; Archaeology ; DNA, Mitochondrial/genetics ; Dogs/classification/*genetics ; Europe ; Asia, Eastern ; Genomics ; Haplotypes ; Human Migration ; Phylogeny ; Wolves/*genetics ; }, abstract = {The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.}, }
@article {pmid27253909, year = {2016}, author = {Ma, Y and Fuller, BT and Sun, W and Hu, S and Chen, L and Hu, Y and Richards, MP}, title = {Tracing the locality of prisoners and workers at the Mausoleum of Qin Shi Huang: First Emperor of China (259-210 BC).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26731}, pmid = {27253909}, issn = {2045-2322}, mesh = {*Archaeology ; China ; Diet/*history ; Female ; History, Ancient ; Humans ; Male ; Prisoners/*history ; }, abstract = {The mausoleum complex of the First Emperor of China, Qin Shi Huang (259-210 BC), is one of the most famous and important archaeological sites in China, yet questions remain as to how it was constructed and by whom. Here we present isotopic results of individuals from the Liyi (n = 146) and Shanren sites (n = 14), both associated with the mausoleum complex. Those buried at Liyi represent the local workers/inhabitants of the Qin population, and the δ(13)C (-8.7 ± 1.5%) and δ(15)N (10.3 ± 0.7%) values indicate that they consumed predominately millet and/or domestic animals fed millet. In contrast, the Shanren individuals were prisoners forced to construct the mausoleum (found buried haphazardly in a mass grave and some in iron leg shackles), and their δ(13)C (-15.4 ± 2.9%) and δ(15)N (8.0 ± 0.6%) results indicate a more mixed C3/C4 diet, with possibly less domestic animals and more wild game protein consumed. This pattern of decreased millet consumption is also characteristic of archaeological sites from southern China, and possible evidence the Shanren prisoners originated from this region (possibly the ancient Chu state located in modern day Hubei Province and parts of Hunan and Anhui Provinces). Further, this finding is in agreement with historical sources and is supported by previous ancient DNA evidence that the mausoleum workers had diverse origins, with many genetically related to southern Chinese groups.}, }
@article {pmid27248693, year = {2016}, author = {Valverde, G and Barreto Romero, MI and Flores Espinoza, I and Cooper, A and Fehren-Schmitz, L and Llamas, B and Haak, W}, title = {Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru's Central Coast during the Middle Horizon.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0155508}, pmid = {27248693}, issn = {1932-6203}, mesh = {*DNA, Ancient ; DNA, Mitochondrial/genetics ; Haplotypes ; History, Ancient ; Peru ; }, abstract = {The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650-1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region's demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500-700 AD), Wari (Middle Horizon, 800-1000 AD) and Ychsma (Late Intermediate Period, 1000-1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.}, }
@article {pmid27246811, year = {2017}, author = {Zhao, J and Liu, FE and Lin, S and Liu, ZZ and Sun, ZY and Wu, XM and Zhang, HQ}, title = {Investigation on maternal lineage of a Neolithic group from northern Shaanxi based on ancient DNA.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {5}, pages = {732-739}, doi = {10.1080/24701394.2016.1177039}, pmid = {27246811}, issn = {2470-1408}, mesh = {Asian People/ethnology/*genetics ; China/ethnology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Gene Pool ; Humans ; Japan/ethnology ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA/*methods ; }, abstract = {A magnetic bead purification method was successfully used to extract ancient DNA from the skeletal remains of 10 specimens excavated from Wuzhuangguoliang (Wzhgl) site, which was located in northern Shaanxi. The multidimensional scaling (MDS) and analysis of molecular variance approach (AMOVA) revealed that ancient Wzhgl people bored a very high similarity to southern Han Chinese. By constructing the MJ-network of various modern people including Han Chinese and Japanese, the phylogenetic analysis indicated that the Wzhgl population had close maternal distance with ancient Shandong and Xinjiang people. These findings indicated that Wzhgl contributed to the gene pool of Han Chinese and modern Japanese. In addition, population migration and interflow between Wzhgl people and ancient Shandong or Xinjiang probably occurred in Neolithic period.}, }
@article {pmid27238636, year = {2016}, author = {Louvel, G and Der Sarkissian, C and Hanghøj, K and Orlando, L}, title = {metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.}, journal = {Molecular ecology resources}, volume = {16}, number = {6}, pages = {1415-1427}, doi = {10.1111/1755-0998.12546}, pmid = {27238636}, issn = {1755-0998}, mesh = {Automation ; Computational Biology/*methods ; *Environmental Microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; *Microbiota ; Sequence Analysis, DNA/*methods ; }, abstract = {Micro-organisms account for most of the Earth's biodiversity and yet remain largely unknown. The complexity and diversity of microbial communities present in clinical and environmental samples can now be robustly investigated in record times and prices thanks to recent advances in high-throughput DNA sequencing (HTS). Here, we develop metaBIT, an open-source computational pipeline automatizing routine microbial profiling of shotgun HTS data. Customizable by the user at different stringency levels, it performs robust taxonomy-based assignment and relative abundance calculation of microbial taxa, as well as cross-sample statistical analyses of microbial diversity distributions. We demonstrate the versatility of metaBIT within a range of published HTS data sets sampled from the environment (soil and seawater) and the human body (skin and gut), but also from archaeological specimens. We present the diversity of outputs provided by the pipeline for the visualization of microbial profiles (barplots, heatmaps) and for their characterization and comparison (diversity indices, hierarchical clustering and principal coordinates analyses). We show that metaBIT allows an automatic, fast and user-friendly profiling of the microbial DNA present in HTS shotgun data sets. The applications of metaBIT are vast, from monitoring of laboratory errors and contaminations, to the reconstruction of past and present microbiota, and the detection of candidate species, including pathogens.}, }
@article {pmid27224451, year = {2016}, author = {Matisoo-Smith, EA and Gosling, AL and Boocock, J and Kardailsky, O and Kurumilian, Y and Roudesli-Chebbi, S and Badre, L and Morel, JP and Sebaï, LL and Zalloua, PA}, title = {A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0155046}, pmid = {27224451}, issn = {1932-6203}, mesh = {DNA, Mitochondrial/*genetics ; *Haplotypes ; History, Ancient ; Humans ; Male ; Tunisia ; White People/*genetics ; }, abstract = {While Phoenician culture and trade networks had a significant impact on Western civilizations, we know little about the Phoenicians themselves. In 1994, a Punic burial crypt was discovered on Byrsa Hill, near the entry to the National Museum of Carthage in Tunisia. Inside this crypt were the remains of a young man along with a range of burial goods, all dating to the late 6th century BCE. Here we describe the complete mitochondrial genome recovered from the Young Man of Byrsa and identify that he carried a rare European haplogroup, likely linking his maternal ancestry to Phoenician influenced locations somewhere on the North Mediterranean coast, the islands of the Mediterranean or the Iberian Peninsula. This result not only provides the first direct ancient DNA evidence of a Phoenician individual but the earliest evidence of a European mitochondrial haplogroup, U5b2c1, in North Africa.}, }
@article {pmid27195960, year = {2016}, author = {Wang, Y and Ficklin, SP and Wang, X and Feltus, FA and Paterson, AH}, title = {Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots.}, journal = {PloS one}, volume = {11}, number = {5}, pages = {e0155637}, pmid = {27195960}, issn = {1932-6203}, mesh = {Arabidopsis/*genetics ; Biological Evolution ; Computational Biology ; Evolution, Molecular ; *Gene Duplication ; Gene Expression Profiling ; *Genes, Duplicate ; Genes, Plant ; Genetic Variation ; *Genome, Plant ; Magnoliopsida/*genetics ; Medicago truncatula/genetics ; Mutation ; Phenotype ; Phylogeny ; Protein Interaction Mapping ; }, abstract = {Different modes of gene duplication including whole-genome duplication (WGD), and tandem, proximal and dispersed duplications are widespread in angiosperm genomes. Small-scale, stochastic gene relocations and transposed gene duplications are widely accepted to be the primary mechanisms for the creation of dispersed duplicates. However, here we show that most surviving ancient dispersed duplicates in core eudicots originated from large-scale gene relocations within a narrow window of time following a genome triplication (γ) event that occurred in the stem lineage of core eudicots. We name these surviving ancient dispersed duplicates as relocated γ duplicates. In Arabidopsis thaliana, relocated γ, WGD and single-gene duplicates have distinct features with regard to gene functions, essentiality, and protein interactions. Relative to γ duplicates, relocated γ duplicates have higher non-synonymous substitution rates, but comparable levels of expression and regulation divergence. Thus, relocated γ duplicates should be distinguished from WGD and single-gene duplicates for evolutionary investigations. Our results suggest large-scale gene relocations following the γ event were associated with the diversification of core eudicots.}, }
@article {pmid27183562, year = {2016}, author = {Krause, J and Pääbo, S}, title = {Genetic Time Travel.}, journal = {Genetics}, volume = {203}, number = {1}, pages = {9-12}, pmid = {27183562}, issn = {1943-2631}, mesh = {Animals ; *Evolution, Molecular ; Extinction, Biological ; Genetic Variation ; Genetics, Population ; Genome-Wide Association Study ; Host-Pathogen Interactions/genetics ; Humans ; }, abstract = {At its core, genetics is a historical discipline. Mutations are passed on from generation to generation and accumulate as a result of chance as well as of selection within and between populations and species. However, until recently, geneticists were confined to the study of present-day genetic variation and could only indirectly make inferences about the historical processes that resulted in the variation in present-day gene pools. This "time trap" has now been overcome thanks to the ability to analyze DNA extracted from ancient remains, and this is about to revolutionize several aspects of genetics.}, }
@article {pmid27173330, year = {2016}, author = {Lech, T}, title = {Ancient DNA in historical parchments - identifying a procedure for extraction and amplification of genetic material.}, journal = {Genetics and molecular research : GMR}, volume = {15}, number = {2}, pages = {}, doi = {10.4238/gmr.15028661}, pmid = {27173330}, issn = {1676-5680}, mesh = {Animals ; DNA, Ancient/*chemistry/isolation &amp; purification ; DNA, Mitochondrial/*chemistry/isolation &amp; purification ; Humans ; Manuscripts as Topic ; }, abstract = {Historical parchments in the form of documents, manuscripts, books, or letters, make up a large portion of cultural heritage collections. Their priceless historical value is associated with not only their content, but also the information hidden in the DNA deposited on them. Analyses of ancient DNA (aDNA) retrieved from parchments can be used in various investigations, including, but not limited to, studying their authentication, tracing the development of the culture, diplomacy, and technology, as well as obtaining information on the usage and domestication of animals. This article proposes and verifies a procedure for aDNA recovery from historical parchments and its appropriate preparation for further analyses. This study involved experimental selection of an aDNA extraction method with the highest efficiency and quality of extracted genetic material, from among the multi-stage phenol-chloroform extraction methods, and the modern, column-based techniques that use selective DNA-binding membranes. Moreover, current techniques to amplify entire genetic material were questioned, and the possibility of using mitochondrial DNA for species identification was analyzed. The usefulness of the proposed procedure was successfully confirmed in identification tests of historical parchments dating back to the 13-16th century AD.}, }
@article {pmid27162355, year = {2016}, author = {Almathen, F and Charruau, P and Mohandesan, E and Mwacharo, JM and Orozco-terWengel, P and Pitt, D and Abdussamad, AM and Uerpmann, M and Uerpmann, HP and De Cupere, B and Magee, P and Alnaqeeb, MA and Salim, B and Raziq, A and Dessie, T and Abdelhadi, OM and Banabazi, MH and Al-Eknah, M and Walzer, C and Faye, B and Hofreiter, M and Peters, J and Hanotte, O and Burger, PA}, title = {Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {24}, pages = {6707-6712}, pmid = {27162355}, issn = {1091-6490}, support = {P 24706/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Animals, Domestic/genetics ; Bayes Theorem ; *Camelus ; DNA ; DNA, Mitochondrial/genetics ; *Domestication ; Genetic Variation ; Humans ; }, abstract = {Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.}, }
@article {pmid27162179, year = {2016}, author = {Klouch, KZ and Schmidt, S and Andrieux-Loyer, F and Le Gac, M and Hervio-Heath, D and Qui-Minet, ZN and Quéré, J and Bigeard, E and Guillou, L and Siano, R}, title = {Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France).}, journal = {FEMS microbiology ecology}, volume = {92}, number = {7}, pages = {}, doi = {10.1093/femsec/fiw101}, pmid = {27162179}, issn = {1574-6941}, mesh = {Bays ; DNA, Ribosomal/genetics ; Dinoflagellida/classification/genetics/*isolation &amp; purification/metabolism ; Ecosystem ; France ; Geologic Sediments/chemistry/*parasitology ; History, 20th Century ; History, 21st Century ; Paleography/history ; Real-Time Polymerase Chain Reaction ; Species Specificity ; }, abstract = {The multiannual dynamic of the cyst-forming and toxic marine dinoflagellate Alexandrium minutum was studied over a time scale of about 150 years by a paleoecological approach based on ancient DNA (aDNA) quantification and cyst revivification data obtained from two dated sediment cores of the Bay of Brest (Brittany, France). The first genetic traces of the species presence in the study area dated back to 1873 ± 6. Specific aDNA could be quantified by a newly developed real-time PCR assay in the upper core layers, in which the germination of the species (in up to 17-19-year-old sediments) was also obtained. In both cores studied, our quantitative paleogenetic data showed a statistically significant increasing trend in the abundance of A. minutum ITS1 rDNA copies over time, corroborating three decades of local plankton data that have documented an increasing trend in the species cell abundance. By comparison, paleogenetic data of the dinoflagellate Scrippsiella donghaienis did not show a coherent trend between the cores studied, supporting the hypothesis of the existence of a species-specific dynamic of A. minutum in the study area. This work contributes to the development of paleoecological research, further showing its potential for biogeographical, ecological and evolutionary studies on marine microbes.}, }
@article {pmid27159683, year = {2016}, author = {Besnard, G and Thèves, C and Mata, X and Holota, H and Rakotozafy, LM and Pedrono, M}, title = {Shotgun sequencing of the mitochondrial genome of the Aldabra giant tortoise (Aldabrachelys gigantea).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4543-4544}, doi = {10.3109/19401736.2015.1101554}, pmid = {27159683}, issn = {2470-1408}, mesh = {Animals ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA, Mitochondrial/chemistry/classification/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sequence Analysis, DNA ; Turtles/classification/*genetics ; }, abstract = {The complete mitochondrial genome of the Aldabra giant tortoise [Aldabrachelys gigantea (Schweigger, 1812): Reptilia, Testudines, Testudinidae] was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA). This genome was 16 467 bp long and presents the typical organization found in vertebrates. The mean coverage of sequencing was 116×. A phylogenetic analysis of the Testudinidae confirms the placement of Aldabrachelys in an Indian Ocean group (including Madagascar). This mitogenome constitutes a reference for ancient DNA analyses of the extinct Madagascan lineages of Aldabrachelys.}, }
@article {pmid27158910, year = {2016}, author = {Mitchell, KJ and Scanferla, A and Soibelzon, E and Bonini, R and Ochoa, J and Cooper, A}, title = {Ancient DNA from the extinct South American giant glyptodont Doedicurus sp. (Xenarthra: Glyptodontidae) reveals that glyptodonts evolved from Eocene armadillos.}, journal = {Molecular ecology}, volume = {25}, number = {14}, pages = {3499-3508}, doi = {10.1111/mec.13695}, pmid = {27158910}, issn = {1365-294X}, mesh = {Animals ; *Biological Evolution ; *DNA, Ancient ; Fossils ; *Genome, Mitochondrial ; Phylogeny ; South America ; Xenarthra/*genetics ; }, abstract = {Glyptodonts were giant (some of them up to ~2400 kg), heavily armoured relatives of living armadillos, which became extinct during the Late Pleistocene/early Holocene alongside much of the South American megafauna. Although glyptodonts were an important component of Cenozoic South American faunas, their early evolution and phylogenetic affinities within the order Cingulata (armoured New World placental mammals) remain controversial. In this study, we used hybridization enrichment and high-throughput sequencing to obtain a partial mitochondrial genome from Doedicurus sp., the largest (1.5 m tall, and 4 m long) and one of the last surviving glyptodonts. Our molecular phylogenetic analyses revealed that glyptodonts fall within the diversity of living armadillos. Reanalysis of morphological data using a molecular 'backbone constraint' revealed several morphological characters that supported a close relationship between glyptodonts and the tiny extant fairy armadillos (Chlamyphorinae). This is surprising as these taxa are among the most derived cingulates: glyptodonts were generally large-bodied and heavily armoured, while the fairy armadillos are tiny (~9-17 cm) and adapted for burrowing. Calibration of our phylogeny with the first appearance of glyptodonts in the Eocene resulted in a more precise timeline for xenarthran evolution. The osteological novelties of glyptodonts and their specialization for grazing appear to have evolved rapidly during the Late Eocene to Early Miocene, coincident with global temperature decreases and a shift from wet closed forest towards drier open woodland and grassland across much of South America. This environmental change may have driven the evolution of glyptodonts, culminating in the bizarre giant forms of the Pleistocene.}, }
@article {pmid27140627, year = {2016}, author = {Moorjani, P and Sankararaman, S and Fu, Q and Przeworski, M and Patterson, N and Reich, D}, title = {A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {20}, pages = {5652-5657}, pmid = {27140627}, issn = {1091-6490}, support = {F32 GM115006/GM/NIGMS NIH HHS/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; K99 GM111744/GM/NIGMS NIH HHS/United States ; R00 GM111744/GM/NIGMS NIH HHS/United States ; R01 GM083098/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; *Genetic Techniques ; *Genome, Human ; Humans ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide ; Radiometric Dating/*methods ; }, abstract = {The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen's age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and (14)C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the (14)C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26-30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier.}, }
@article {pmid27128618, year = {2015}, author = {Mokrousov, I}, title = {Molecular structure of Mycobacterium tuberculosis population in Russia and its interaction with neighboring countries.}, journal = {International journal of mycobacteriology}, volume = {4 Suppl 1}, number = {}, pages = {56-57}, doi = {10.1016/j.ijmyco.2014.08.002}, pmid = {27128618}, issn = {2212-554X}, mesh = {Coinfection ; Genetic Markers ; Genotype ; HIV Infections/epidemiology ; *Human Migration ; Humans ; Molecular Epidemiology ; Mycobacterium tuberculosis/*genetics/*isolation &amp; purification ; Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide ; Tuberculosis/*epidemiology/*microbiology ; USSR/epidemiology ; }, abstract = {BACKGROUND: The tuberculosis (TB) situation in Russia is aggravated by the emergence and the spread of multidrug-resistant strains, HIV co-infection and drawbacks in the health control system. The Mycobacterium tuberculosis population structure in Russia has been defined by the remarkable mass migration in the 20th century, the variable genetic background of different ethnic groups inhabiting Russia, and by the pathobiology of circulating strains. Here, I will review the phylogeography and pathobiology of: (i) the dominating Beijing family; (ii) the Latin-American Mediterranean (LAM) family, the second largest in Russia and MDR-associated in some regions; and (iii) the Ural family, endemic in Russia and thought to be less transmissible and drug resistant.<br><br>REVIEW AND ANALYSIS: M. tuberculosis variant Beijing &#x412;0/W148 is regarded as a successful clone of M. tuberculosis widespread in the former Soviet Union. However, a closer look reveals a peculiar clinal gradient of its geographic distribution; it peaks in Siberia and, to a lesser extent, in the European part of the former USSR. In contrast, its rate is sharply decreased in the Asian part of the former Soviet Union, and it is absent in the autochthonous populations elsewhere in the world. Two interdependent hypotheses will be put forward. First, B0/W148 likely originated in Siberia and its primary dispersal was driven by a massive population outflow from Siberia to European Russia in the period 1960-1980. Second, a historically recent phylogenetically demonstrated successful dissemination of the Beijing B0/W148 strain was triggered by an advent and wide use of the modern anti-TB drugs and was due to its remarkable capacity to acquire drug resistance. Robust phylogenetic markers were used to study the evolution of LAM and its major sublineages in Russia and its neighboring countries. A total of 250 M. tuberculosis isolates were assigned to LAM based on analysis of LAM-specific SNP in Rv3062 and Rv0129c. The family status was rectified for 121 isolates mis-assigned by spoligotyping to non-LAM families (T1 or T5-RUS1). The re-estimated LAM rate increased twofold in Russia and Kazakhstan and fourfold in Belarus. The majority (>90%) of LAM isolates from all three countries belonged to the LAM-RUS sublineage. In contrast, Ibero-American LAM RD-Rio sublineage was identified in only 7 Russian isolates. These findings and further analysis suggest a monophyletic origin of the LAM-RUS subfamily that is endemic in Russia. In contrast, rare LAM RD-Rio isolates were likely brought to Russia through occasional human contact. The analysis of the Ural family showed its highest prevalence in the North/East Pontic (Black Sea) area that may have been an area of its origin and primary dispersal. Ural family strains are not marked by increased pathogenic capacities, association with drug resistance (although there is a trend towards MDR Ural strains in the European part of the former USSR) or increased transmissibility. This reflects their basically low contagiosity which is why the Ural family is still moderately widespread in central Eurasia. Large-scale SNP or WGS population-based studies targeting strains from indigenous populations and, eventually, analysis of ancient DNA will better test these hypotheses. Host genetics factors likely play the most prominent role in the differential dissemination of particular M. tuberculosis genotypes.}, }
@article {pmid27126014, year = {2016}, author = {Lawler, A}, title = {ANCIENT DNA. How Europe exported the Black Death.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6285}, pages = {501-502}, doi = {10.1126/science.352.6285.501}, pmid = {27126014}, issn = {1095-9203}, mesh = {China/epidemiology ; DNA, Bacterial/*genetics ; Disease Outbreaks/*history ; Europe/epidemiology ; History, Medieval ; Humans ; Plague/epidemiology/*history/microbiology ; Yersinia pestis/*classification/genetics/pathogenicity ; }, }
@article {pmid27122559, year = {2016}, author = {Brace, S and Ruddy, M and Miller, R and Schreve, DC and Stewart, JR and Barnes, I}, title = {The colonization history of British water vole (Arvicola amphibius (Linnaeus, 1758)): origins and development of the Celtic fringe.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1829}, pages = {}, pmid = {27122559}, issn = {1471-2954}, mesh = {Animals ; Arvicolinae/classification/*genetics ; Climate ; DNA, Mitochondrial/genetics/history ; Ecosystem ; Evolution, Molecular ; Fossils ; Genetics, Population ; History, Ancient ; Phylogeny ; Phylogeography ; United Kingdom ; }, abstract = {The terminal Pleistocene and Early Holocene, a period from 15 000 to 18 000 Before Present (BP), was critical in establishing the current Holarctic fauna, with temperate-climate species largely replacing cold-adapted ones at mid-latitudes. However, the timing and nature of this process remain unclear for many taxa, a point that impacts on current and future management strategies. Here, we use an ancient DNA dataset to test more directly postglacial histories of the water vole (Arvicola amphibius, formerly A terrestris), a species that is both a conservation priority and a pest in different parts of its range. We specifically examine colonization of Britain, where a complex genetic structure can be observed today. Although we focus on population history at the limits of the species' range, the inclusion of additional European samples allows insights into European postglacial colonization events and provides a molecular perspective on water vole taxonomy.}, }
@article {pmid27110344, year = {2016}, author = {Murray, GG and Wang, F and Harrison, EM and Paterson, GK and Mather, AE and Harris, SR and Holmes, MA and Rambaut, A and Welch, JJ}, title = {The effect of genetic structure on molecular dating and tests for temporal signal.}, journal = {Methods in ecology and evolution}, volume = {7}, number = {1}, pages = {80-89}, pmid = {27110344}, issn = {2041-210X}, support = {//Wellcome Trust/United Kingdom ; 098051//Wellcome Trust/United Kingdom ; G1001787/MRC_/Medical Research Council/United Kingdom ; MR/P007201/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {'Dated-tip' methods of molecular dating use DNA sequences sampled at different times, to estimate the age of their most recent common ancestor. Several tests of 'temporal signal' are available to determine whether data sets are suitable for such analysis. However, it remains unclear whether these tests are reliable.We investigate the performance of several tests of temporal signal, including some recently suggested modifications. We use simulated data (where the true evolutionary history is known), and whole genomes of methicillin-resistant Staphylococcus aureus (to show how particular problems arise with real-world data sets).We show that all of the standard tests of temporal signal are seriously misleading for data where temporal and genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at similar times). This is not an artefact of genetic structure or tree shape per se, and can arise even when sequences have measurably evolved during the sampling period. More positively, we show that a 'clustered permutation' approach introduced by Duchêne et al. (Molecular Biology and Evolution, 32, 2015, 1895) can successfully correct for this artefact in all cases and introduce techniques for implementing this method with real data sets.The confounding of temporal and genetic structures may be difficult to avoid in practice, particularly for outbreaks of infectious disease, or when using ancient DNA. Therefore, we recommend the use of 'clustered permutation' for all analyses. The failure of the standard tests may explain why different methods of dating pathogen origins have reached such wildly different conclusions.}, }
@article {pmid27105672, year = {2016}, author = {Zhao, L and Lascoux, M and Waxman, D}, title = {An informational transition in conditioned Markov chains: Applied to genetics and evolution.}, journal = {Journal of theoretical biology}, volume = {402}, number = {}, pages = {158-170}, doi = {10.1016/j.jtbi.2016.04.021}, pmid = {27105672}, issn = {1095-8541}, mesh = {Alleles ; *Biological Evolution ; Computer Simulation ; *Markov Chains ; *Models, Genetic ; Time Factors ; }, abstract = {In this work we assume that we have some knowledge about the state of a population at two known times, when the dynamics is governed by a Markov chain such as a Wright-Fisher model. Such knowledge could be obtained, for example, from observations made on ancient and contemporary DNA, or during laboratory experiments involving long term evolution. A natural assumption is that the behaviour of the population, between observations, is related to (or constrained by) what was actually observed. The present work shows that this assumption has limited validity. When the time interval between observations is larger than a characteristic value, which is a property of the population under consideration, there is a range of intermediate times where the behaviour of the population has reduced or no dependence on what was observed and an equilibrium-like distribution applies. Thus, for example, if the frequency of an allele is observed at two different times, then for a large enough time interval between observations, the population has reduced or no dependence on the two observed frequencies for a range of intermediate times. Given observations of a population at two times, we provide a general theoretical analysis of the behaviour of the population at all intermediate times, and determine an expression for the characteristic time interval, beyond which the observations do not constrain the population's behaviour over a range of intermediate times. The findings of this work relate to what can be meaningfully inferred about a population at intermediate times, given knowledge of terminal states.}, }
@article {pmid27096009, year = {2016}, author = {Kothe, M and Seidenberg, V and Hummel, S and Piskurek, O}, title = {Alu SINE analyses of 3,000-year-old human skeletal remains: a pilot study.}, journal = {Mobile DNA}, volume = {7}, number = {}, pages = {7}, pmid = {27096009}, issn = {1759-8753}, abstract = {BACKGROUND: As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for population genetic studies. Very recent inserts are polymorphic within and between human populations. In a sample of 30 elements originating from three different Alu subfamilies, we investigated whether they are preserved in prehistorical skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. In the present study, we examined a prehistoric triad of father, mother and daughter.<br><br>RESULTS: For 26 of the 30 Alu loci investigated, definite results were obtained. We were able to demonstrate that presence/absence analyses of Alu elements can be conducted on individuals who lived 3,000&#xa0;years ago. The preservation of the ancient DNA (aDNA) is good enough in two out of three ancient individuals to routinely allow the amplification of 500&#xa0;bp fragments. The third individual revealed less well-preserved DNA, which results in allelic dropout or complete amplification failures. We here present an alternative molecular approach to deal with these degradation phenomena by using internal Alu subfamily specific primers producing short fragments of approximately 150&#xa0;bp.<br><br>CONCLUSIONS: Our data clearly show the possibility of presence/absence analyses of Alu elements in individuals from the Lichtenstein cave. Thus, we demonstrate that our method is reliably applicable for aDNA samples with good or moderate DNA preservation. This method will be very useful for further investigations with more Alu loci and larger datasets. Human population genetic studies and other large-scale investigations would provide insight into Alu SINE-based microevolutionary processes in humans during the last few thousand years and help us comprehend the evolutionary dynamics of our genome.}, }
@article {pmid27060406, year = {2016}, author = {Norhalifah, HK and Syaza, FH and Chambers, GK and Edinur, HA}, title = {The genetic history of Peninsular Malaysia.}, journal = {Gene}, volume = {586}, number = {1}, pages = {129-135}, doi = {10.1016/j.gene.2016.04.008}, pmid = {27060406}, issn = {1879-0038}, mesh = {Asian People/genetics ; Australia ; DNA, Mitochondrial ; Ethnicity/*genetics ; *Human Migration ; Humans ; Malaysia/ethnology ; Polymorphism, Single Nucleotide ; White People/genetics ; }, abstract = {This article explores the genetic history of the various sub-populations currently living in Peninsular Malaysia. This region has received multiple waves of migrants like the Orang Asli in prehistoric times and the Chinese, Indians, Europeans and Arabs during historic times. There are three highly distinct lineages that make up the Orang Asli; Semang, Senoi and Proto-Malays. The Semang, who have 'Negrito' characteristics, represent the first human settlers in Peninsular Malaysia arriving from about 50,000ya. The Senoi later migrated from Indochina and are a mix between an Asian Neolithic population and the Semang. These Asian genomes probably came in before Austroasiatic languages arrived between 5000 and 4000years ago. Semang and Senoi both now speak Austro-Asiatic languages indicative of cultural diffusion from Senoi to Semang. In contrast, the Proto-Malays who came last to the southern part of this region speak Austronesian language and are Austronesians with some Negrito admixture. It is from this group that the contemporary Malays emerged. Here we provide an overview of the best available genetic evidences (single nucleotide polymorphisms, mitochondrial DNA, Y-chromosome, blood groups, human platelet antigen, human leukocyte antigen, human neutrophil antigen and killer-cell immunoglobulin-like receptor) supporting the complex genetic history of Peninsular Malaysia. Large scale sampling and high throughput genetic screening programmes such as those using genome-wide single nucleotide polymorphism analyses have provided insights into various ancestral and admixture genetic fractions in this region. Given the now extensive admixture present in the contemporary descendants of ancient sub-populations in Peninsular Malaysia, improved reconstruction of human migration history in this region will require new evidence from ancient DNA in well-preserved skeletons. All other aspects of the highly diverse and complex genetic makeup in Peninsular Malaysia should be considered carefully for genetic mapping of disease loci and policy formation by health authorities.}, }
@article {pmid27053752, year = {2016}, author = {Stanton, DW and Mulville, JA and Bruford, MW}, title = {Colonization of the Scottish islands via long-distance Neolithic transport of red deer (Cervus elaphus).}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1828}, pages = {}, pmid = {27053752}, issn = {1471-2954}, mesh = {*Animal Distribution ; Animals ; Deer/genetics/*physiology ; Gene Flow ; *Genetic Variation ; Haplotypes ; Islands ; Scotland ; Sequence Analysis, DNA ; }, abstract = {Red deer (Cervus elaphus) have played a key role in human societies throughout history, with important cultural significance and as a source of food and materials. This relationship can be traced back to the earliest human cultures and continues to the present day. Humans are thought to be responsible for the movement of a considerable number of deer throughout history, although the majority of these movements are poorly described or understood. Studying such translocations allows us to better understand ancient human-wildlife interactions, and in the case of island colonizations, informs us about ancient human maritime practices. This study uses DNA sequences to characterise red deer genetic diversity across the Scottish islands (Inner and Outer Hebrides and Orkney) and mainland using ancient deer samples, and attempts to infer historical colonization events. We show that deer from the Outer Hebrides and Orkney are unlikely to have originated from mainland Scotland, implying that humans introduced red deer from a greater distance. Our results are also inconsistent with an origin from Ireland or Norway, suggesting long-distance maritime travel by Neolithic people to the outer Scottish Isles from an unknown source. Common haplotypes and low genetic differentiation between the Outer Hebrides and Orkney imply common ancestry and/or gene flow across these islands. Close genetic proximity between the Inner Hebrides and Ireland, however, corroborates previous studies identifying mainland Britain as a source for red deer introductions into Ireland. This study provides important information on the processes that led to the current distribution of the largest surviving indigenous land mammal in the British Isles.}, }
@article {pmid27051878, year = {2016}, author = {Llamas, B and Fehren-Schmitz, L and Valverde, G and Soubrier, J and Mallick, S and Rohland, N and Nordenfelt, S and Valdiosera, C and Richards, SM and Rohrlach, A and Romero, MI and Espinoza, IF and Cagigao, ET and Jiménez, LW and Makowski, K and Reyna, IS and Lory, JM and Torrez, JA and Rivera, MA and Burger, RL and Ceruti, MC and Reinhard, J and Wells, RS and Politis, G and Santoro, CM and Standen, VG and Smith, C and Reich, D and Ho, SY and Cooper, A and Haak, W}, title = {Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas.}, journal = {Science advances}, volume = {2}, number = {4}, pages = {e1501385}, pmid = {27051878}, issn = {2375-2548}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; GM100233/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; }, mesh = {Americas ; Archaeology ; Bayes Theorem ; Chile ; DNA, Ancient ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; *Genetic Variation ; *Genetics, Population ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Humans ; Indians, North American/genetics ; *Phylogeny ; South America ; }, abstract = {The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.}, }
@article {pmid27049965, year = {2016}, author = {Racimo, F and Renaud, G and Slatkin, M}, title = {Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans.}, journal = {PLoS genetics}, volume = {12}, number = {4}, pages = {e1005972}, pmid = {27049965}, issn = {1553-7404}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; R01-GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Base Sequence ; Computer Simulation ; DNA/*genetics ; *DNA Contamination ; DNA, Mitochondrial/genetics ; Fossils ; *Genetic Drift ; Genetics, Population ; Humans ; Markov Chains ; Monte Carlo Method ; Neanderthals/*genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters-including drift times and admixture rates-for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called 'Demographic Inference with Contamination and Error' (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%.}, }
@article {pmid27036623, year = {2016}, author = {Peltzer, A and Jäger, G and Herbig, A and Seitz, A and Kniep, C and Krause, J and Nieselt, K}, title = {EAGER: efficient ancient genome reconstruction.}, journal = {Genome biology}, volume = {17}, number = {}, pages = {60}, pmid = {27036623}, issn = {1474-760X}, mesh = {Chromosome Mapping/methods ; Fossils ; Genome ; Sequence Analysis, DNA/*methods ; Software ; Workflow ; }, abstract = {BACKGROUND: The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.<br><br>RESULTS: Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants.<br><br>CONCLUSIONS: EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.}, }
@article {pmid27016326, year = {2016}, author = {Gonçalves, D and Granja, R and Alves-Cardoso, F and Carvalho, AF}, title = {All different, all equal: Evidence of a heterogeneous Neolithic population at the Bom Santo Cave necropolis (Portugal).}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {67}, number = {3}, pages = {203-215}, doi = {10.1016/j.jchb.2015.12.004}, pmid = {27016326}, issn = {1618-1301}, mesh = {Anthropology, Physical ; Cemeteries/history ; Female ; Fossils/anatomy &amp; histology/*history ; Genetics, Population ; History, Ancient ; Humans ; Male ; Portugal ; }, abstract = {The objective of this paper was to contribute to the discussion regarding the socio-political organization of south-western Iberian Middle Neolithic populations. To that end, the preservation and distribution of human remains and the dispersion of grave goods within two rooms of the Bom Santo Cave (Rooms A and B) were investigated and combined with genetic and isotopic data previously published. Grave goods distribution and skeletal analyses highlighted an important diversity in terms of funerary practices thus corroborating data from ancient DNA and Sr/O isotopic analyses that suggested a great genetic and geographic diversity. Grave goods presented an uneven spatial distribution and were made of raw materials from different sources and using different pottery manufacturing styles albeit typologically homogeneous. The preservation and distribution of human remains suggested that Room A was mainly used for secondary depositions while Room B was used for both primary and secondary depositions. No link between the two rooms was found since remains from the same individuals were apparently exclusive of one room or another. The results suggest that this society presented substantial inner genetic, social and geographical heterogeneity. Most probably, this was due to the presence of distinct but coeval groups in the cave that shared a larger-scale social identity (as in "segmentary societies") or, less likely, to the presence of one single, but internally heterogeneous society (as in fully sedentary societies) that assimilated foreigners.}, }
@article {pmid27010022, year = {2016}, author = {Schraiber, JG and Evans, SN and Slatkin, M}, title = {Bayesian Inference of Natural Selection from Allele Frequency Time Series.}, journal = {Genetics}, volume = {203}, number = {1}, pages = {493-511}, pmid = {27010022}, issn = {1943-2631}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; R01 GM109454/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Diploidy ; *Gene Frequency ; Horses/genetics ; *Models, Genetic ; *Selection, Genetic ; Skin Pigmentation/genetics ; *Software ; }, abstract = {The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful than inferences made using patterns of linked neutral variation obtained from modern individuals. We developed a Bayesian method to make use of allele frequency time series data and infer the parameters of general diploid selection, along with allele age, in nonequilibrium populations. We introduce a novel path augmentation approach, in which we use Markov chain Monte Carlo to integrate over the space of allele frequency trajectories consistent with the observed data. Using simulations, we show that this approach has good power to estimate selection coefficients and allele age. Moreover, when applying our approach to data on horse coat color, we find that ignoring a relevant demographic history can significantly bias the results of inference. Our approach is made available in a C++ software package.}, }
@article {pmid26998604, year = {2016}, author = {Bilgic, H and Hakki, EE and Pandey, A and Khan, MK and Akkaya, MS}, title = {Ancient DNA from 8400 Year-Old Çatalhöyük Wheat: Implications for the Origin of Neolithic Agriculture.}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151974}, pmid = {26998604}, issn = {1932-6203}, mesh = {Agriculture/*history ; Archaeology ; Autoradiography ; DNA, Plant/*genetics/*history ; History, Ancient ; Molecular Weight ; Phylogeny ; Polymerase Chain Reaction ; Promoter Regions, Genetic/genetics ; Seeds ; Species Specificity ; Time Factors ; Triticum/*genetics ; Turkey ; }, abstract = {Human history was transformed with the advent of agriculture in the Fertile Crescent with wheat as one of the founding crops. Although the Fertile Crescent is renowned as the center of wheat domestication, archaeological studies have shown the crucial involvement of Çatalhöyük in this process. This site first gained attention during the 1961-65 excavations due to the recovery of primitive hexaploid wheat. However, despite the seeds being well preserved, a detailed archaeobotanical description of the samples is missing. In this article, we report on the DNA isolation, amplification and sequencing of ancient DNA of charred wheat grains from Çatalhöyük and other Turkish archaeological sites and the comparison of these wheat grains with contemporary wheat species including T. monococcum, T. dicoccum, T. dicoccoides, T. durum and T. aestivum at HMW glutenin protein loci. These ancient samples represent the oldest wheat sample sequenced to date and the first ancient wheat sample from the Middle East. Remarkably, the sequence analysis of the short DNA fragments preserved in seeds that are approximately 8400 years old showed that the Çatalhöyük wheat stock contained hexaploid wheat, which is similar to contemporary hexaploid wheat species including both naked (T. aestivum) and hulled (T. spelta) wheat. This suggests an early transitory state of hexaploid wheat agriculture from the Fertile Crescent towards Europe spanning present-day Turkey.}, }
@article {pmid26998313, year = {2016}, author = {Ottoni, C and Rasteiro, R and Willet, R and Claeys, J and Talloen, P and Van de Vijver, K and Chikhi, L and Poblome, J and Decorte, R}, title = {Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey.}, journal = {Royal Society open science}, volume = {3}, number = {2}, pages = {150250}, pmid = {26998313}, issn = {2054-5703}, abstract = {More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake.}, }
@article {pmid26996763, year = {2016}, author = {Fehren-Schmitz, L and Georges, L}, title = {Ancient DNA reveals selection acting on genes associated with hypoxia response in pre-Columbian Peruvian Highlanders in the last 8500 years.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23485}, pmid = {26996763}, issn = {2045-2322}, mesh = {*Acclimatization ; Archaeology ; DNA, Ancient/*analysis ; *Evolution, Molecular ; Genetic Drift ; Genotype ; Humans ; Hypoxia/*genetics ; Hypoxia-Inducible Factor-Proline Dioxygenases/genetics ; Nitric Oxide Synthase Type III/genetics ; Peru ; *Selection, Genetic ; }, abstract = {Archaeological evidence shows that humans began living in the high altitude Andes approximately 12,000 years ago. Andean highlanders are known to have developed the most complex societies of pre-Columbian South America despite challenges to their health and reproductive success resulting from chronic exposure to hypoxia. While the physiological adaptations to this environmental stressor are well studied in contemporary Andean highlanders, the molecular evolutionary processes associated with such adaptations remain unclear. We aim to better understand how humans managed to demographically establish in this harsh environment by addressing a central question: did exposure to hypoxia drive adaptation via natural selection within Andean populations or did an existing phenotype--characterized by reduced susceptibility to hypoxic stress--enable human settlement of the Andes? We genotyped three variable loci within the NOS3 and EGLN1 genes previously associated with adaptation to high altitude in 150 ancient human DNA samples from Peruvian high altitude and coastal low altitude sites in a time frame between ~8500-560 BP. We compare the data of 109 successful samples to forward simulations of genetic drift with natural selection and find that selection, rather than drift, explains the gradual frequency changes observed in the highland populations for two of the three SNPs.}, }
@article {pmid26994328, year = {2016}, author = {Jain, S and Bajpai, S and Kumar, G and Pruthi, V}, title = {Microstructure, crystallography and diagenetic alteration in fossil ostrich eggshells from Upper Palaeolithic sites of Indian peninsular region.}, journal = {Micron (Oxford, England : 1993)}, volume = {84}, number = {}, pages = {72-78}, doi = {10.1016/j.micron.2016.02.012}, pmid = {26994328}, issn = {1878-4291}, mesh = {Animals ; Biological Evolution ; Calcium Carbonate/analysis ; *Crystallography ; Egg Shell/chemistry/*ultrastructure ; *Fossils ; India ; Microscopy, Electron, Scanning/methods ; *Struthioniformes/embryology ; X-Ray Diffraction ; }, abstract = {Biominerals studies are of importance as they provide an understanding of natural evolutionary processes. In this study we have investigated the fossil ostrich eggshells using Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD) and Electron Backscatter Diffraction (EBSD). SEM studies demonstrated the ultrastructure of fossil eggshells and formation of calcified cuticular layer. The presence of calcified cuticle layer in eggshell is the basis for ancient DNA studies as it contains preserved biomolecules. EBSD accentuates the crystallographic structure of the ostrich eggshells with sub-micrometer resolution. It is a non-destructive tool for evaluating the extent of diagenesis in a biomineral. EBSD analysis revealed the presence of dolomite in the eggshells. This research resulted in the complete recognition of the structure of ostrich eggshells as well as the nature and extent of diagenesis in these eggshells which is vital for genetic and paleoenvironmental studies.}, }
@article {pmid26989998, year = {2016}, author = {Ozga, AT and Nieves-Colón, MA and Honap, TP and Sankaranarayanan, K and Hofman, CA and Milner, GR and Lewis, CM and Stone, AC and Warinner, C}, title = {Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus.}, journal = {American journal of physical anthropology}, volume = {160}, number = {2}, pages = {220-228}, pmid = {26989998}, issn = {1096-8644}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Anthropology, Physical ; Archaeology ; DNA, Mitochondrial/*analysis/genetics/isolation &amp; purification ; Dental Calculus/*genetics ; Genome, Mitochondrial/*genetics ; History, 15th Century ; Humans ; Sequence Analysis, DNA/*methods ; }, abstract = {OBJECTIVES: Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis.<br><br>MATERIALS AND METHODS: Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing.<br><br>RESULTS: Full mitogenomes (7-34&#xd7;) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth.<br><br>DISCUSSION: Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. &#xa9; 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.}, }
@article {pmid26986787, year = {2015}, author = {Qiu, H and Price, DC and Yang, EC and Yoon, HS and Bhattacharya, D}, title = {Evidence of ancient genome reduction in red algae (Rhodophyta).}, journal = {Journal of phycology}, volume = {51}, number = {4}, pages = {624-636}, doi = {10.1111/jpy.12294}, pmid = {26986787}, issn = {1529-8817}, abstract = {Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl-phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle.}, }
@article {pmid26985732, year = {2016}, author = {Salse, J}, title = {Ancestors of modern plant crops.}, journal = {Current opinion in plant biology}, volume = {30}, number = {}, pages = {134-142}, doi = {10.1016/j.pbi.2016.02.005}, pmid = {26985732}, issn = {1879-0356}, mesh = {Biological Evolution ; Computational Biology ; Crops, Agricultural/classification/genetics ; Genome, Plant/*genetics ; Genomics/methods ; Magnoliopsida/*classification/*genetics ; }, abstract = {Recent accumulation of plant genomic resources offers the opportunity to compare modern genomes and model their evolutionary history from their reconstructed Most Recent Common Ancestors (MRCAs) that can be used as a guide to unveil the forces driving the evolutionary success of angiosperms and ultimately to perform applied translational research from models to crops. This article reviews the current state of art of recent structural comparative genomics studies through ancestral genome reconstruction, that is, the field of in silico paleogenomics.}, }
@article {pmid26968017, year = {2016}, author = {Thèves, C and Cabot, E and Bouakaze, C and Chevet, P and Crubézy, &#xc9; and Balaresque, P}, title = {About 42% of 154 remains from the "Battle of Le Mans", France (1793) belong to women and children: Morphological and genetic evidence.}, journal = {Forensic science international}, volume = {262}, number = {}, pages = {30-36}, doi = {10.1016/j.forsciint.2016.02.029}, pmid = {26968017}, issn = {1872-6283}, mesh = {Adolescent ; Adult ; Armed Conflicts/history ; *Body Remains ; Burial ; Child ; Child, Preschool ; DNA, Ancient ; *Exhumation ; Female ; Forensic Anthropology ; France ; History, 18th Century ; Humans ; Infant ; Male ; Sex Determination Analysis ; Sex Determination by Skeleton ; Young Adult ; }, abstract = {Mass graves were discovered in Le Mans and 154 skeletons were exhumed, representing a remarkable historical series of human remains from western France. We aimed to characterise the age-class and sex of these subjects, and to determine whether their profile fits with that of the Catholic and Royal Army of Vendée, who fought against the Republican Army during the Battle of Le Mans (12th-13th December, 1793). This atypical army was composed of male soldiers, but also of civilian people who followed the troops, including the elderly, children and women. In total 154 skeletons from nine mass graves were exhumed from 2009 to 2010. Two morphological methods were used to determine the sex of the subjects: the Probabilist Sexual Diagnosis (DSP) and Secondary Sexual Diagnosis (DSS) methods. Samples were handled cautiously to avoid any pre-laboratory contamination. Molecular genetic sex-typing using a recently developed assay was used to maximise sex-diagnosis of the ancient DNA samples, and 97 successful profiles including immatures were generated. Using morphological and genetic data combined, we successfully determined the sex of 93% of the subjects; 62% were male and 31% female. About 87% of subjects could be considered adults (>18 years old), 6% adolescents (15-19 years old) and 7% infants (<15 years old). Our results of an unexpected population profile for an armed conflict (42% were women and children), in addition to traumatological and historical elements, tend to confirm that these subjects were involved in the Battle of Le Mans, either actively (Republican Army, the Catholic and Royal Army) or passively (collateral victims from the civilian population of Le Mans). They represent 5-6% of the estimated 2500-3000 victims.}, }
@article {pmid26945766, year = {2016}, author = {Lysak, MA and Mandáková, T and Schranz, ME}, title = {Comparative paleogenomics of crucifers: ancestral genomic blocks revisited.}, journal = {Current opinion in plant biology}, volume = {30}, number = {}, pages = {108-115}, doi = {10.1016/j.pbi.2016.02.001}, pmid = {26945766}, issn = {1879-0356}, mesh = {Arabidopsis/genetics/physiology ; Brassicaceae/*genetics/physiology ; Evolution, Molecular ; Genome, Plant/*genetics/physiology ; Genomics/*methods ; Polyploidy ; }, abstract = {A decade ago the concept of the Ancestral Crucifer Karyotype (ACK) and the definition of 24 conserved genomic blocks was presented. Subsequently, 35 cytogenetic reconstructions and/or draft genome sequences of crucifer species (members of the Brassicaceae family) have been analyzed in the context of this system; placing crucifers at the forefront of plant phylogenomics. In this review, we highlight how the ACK and genomic blocks have facilitated and guided genomic analysis of crucifers in the last 10 years and provide an update of this robust model.}, }
@article {pmid26940256, year = {2016}, author = {Rühli, FJ and Galassi, FM and Haeusler, M}, title = {Palaeopathology: Current challenges and medical impact.}, journal = {Clinical anatomy (New York, N.Y.)}, volume = {29}, number = {7}, pages = {816-822}, doi = {10.1002/ca.22709}, pmid = {26940256}, issn = {1098-2353}, mesh = {*Paleopathology ; }, abstract = {Palaeopathology is the science which studies ancient human diseases. Throughout its relatively young history it underwent tremendous technological and methodological improvements (from pure morphology and histology to CT scanning) that have constantly reshaped its scientific rationale. Among other achievements, the study of mummies and fossilized hominids has allowed to effectively extract ancient DNA, prove the existence of atherosclerosis in ancient times, demonstrate the presence of disease vectors, better clarify the etiology of infectious diseases otherwise only postulated on the basis of ancient accounts as well as to show the presence of spine pathology in our hominid ancestors. The research levels in this discipline are three: basic research, individual cases, population. The first and the third levels contribute most to the discipline, while the second is the one more appealing to the general public on account of its description of important cases reports. In addition, a recently introduced sub-specialty of palaeopathology, pathography is aiming to use an interdisciplinary approach to find traces of diseases in ancient literary sources and artistic representations. In spite of its discoveries, palaeopathology is not always viewed positively by clinicians because certain old-fashioned techniques are still due to technical restrictions. The authors provide a set of suggestions on how to strengthen the scientific recognition of this subject and explain at length how it could contribute to the progress of medical research. Clin. Anat. 29:816-822, 2016. © 2016 Wiley Periodicals, Inc.}, }
@article {pmid26931144, year = {2016}, author = {Plasil, M and Mohandesan, E and Fitak, RR and Musilova, P and Kubickova, S and Burger, PA and Horin, P}, title = {The major histocompatibility complex in Old World camelids and low polymorphism of its class II genes.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {167}, pmid = {26931144}, issn = {1471-2164}, support = {P 24706/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Alleles ; Animals ; Base Sequence ; Camelus/*genetics ; Exons ; *Genes, MHC Class II ; Haplotypes ; Molecular Sequence Data ; Phylogeny ; Physical Chromosome Mapping ; *Polymorphism, Genetic ; }, abstract = {BACKGROUND: The Major Histocompatibility Complex (MHC) is a genomic region containing genes with crucial roles in immune responses. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. To counteract the high variability of pathogens, the MHC evolved into a region of considerable heterogeneity in its organization, number and extent of polymorphism. Studies of MHCs in different model species contribute to our understanding of mechanisms of immunity, diseases and their evolution. Camels are economically important domestic animals and interesting biomodels. Three species of Old World camels have been recognized: the dromedary (Camelus dromedarius), Bactrian camel (Camelus bactrianus) and the wild camel (Camelus ferus). Despite their importance, little is known about the MHC genomic region, its organization and diversity in camels. The objectives of this study were to identify, map and characterize the MHC region of Old World camelids, with special attention to genetic variation at selected class MHC II loci.<br><br>RESULTS: Physical mapping located the MHC region to the chromosome 20 in Camelus dromedarius. Cytogenetic and comparative analyses of whole genome sequences showed that the order of the three major sub-regions is "Centromere - Class II - Class III - Class I". DRA, DRB, DQA and DQB exon 2 sequences encoding the antigen binding site of the corresponding class II antigen presenting molecules showed high degree of sequence similarity and extensive allele sharing across the three species. Unexpectedly low extent of polymorphism with low numbers of alleles and haplotypes was observed in all species, despite different geographic origins of the camels analyzed. The DRA locus was found to be polymorphic, with three alleles shared by all three species. DRA and DQA sequences retrieved from ancient DNA samples of Camelus dromedarius suggested that additional polymorphism might exist.<br><br>CONCLUSIONS: This study provided evidence that camels possess an MHC comparable to other mammalian species in terms of its genomic localization, organization and sequence similarity. We described ancient variation at the DRA locus, monomorphic in most species. The extent of molecular diversity of MHC class II genes seems to be substantially lower in Old World camels than in other mammalian species.}, }
@article {pmid26912899, year = {2016}, author = {}, title = {Erratum for the Report "Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa" (previously titled "Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent") by M. Gallego Llorente, E. R. Jones, A. Eriksson, V. Siska, K. W. Arthur, J. W. Arthur, M. C. Curtis, J. T. Stock, M. Coltorti, P. Pieruccini, S. Stretton, F. Brock, T. Higham, Y. Park, M. Hofreiter, D. G. Bradley, J. Bhak, R. Pinhasi, A. Manica.}, journal = {Science (New York, N.Y.)}, volume = {351}, number = {6275}, pages = {}, doi = {10.1126/science.aaf3945}, pmid = {26912899}, issn = {1095-9203}, abstract = {In the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa,” the results were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neandertals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. These changes are reflected in the corrected Fig. 2B, fig. S6, and table S5. Tables S6 and S7 have been removed from the corrected Supplementary Material, because there is no detectable Western Eurasian component in Yoruba and Mbuti. The conclusion of a migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: The Western Eurasian backflow mostly affected East Africa and only a few Sub-Saharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota. Hence, the title and abstract of the published paper did not accurately represent the geographical extent of the admixture, and both have been corrected accordingly. The authors acknowledge Pontus Skoglund and David Reich for detecting these problems.}, }
@article {pmid26898827, year = {2016}, author = {Gokhman, D and Meshorer, E and Carmel, L}, title = {Epigenetics: It's Getting Old. Past Meets Future in Paleoepigenetics.}, journal = {Trends in ecology &amp; evolution}, volume = {31}, number = {4}, pages = {290-300}, doi = {10.1016/j.tree.2016.01.010}, pmid = {26898827}, issn = {1872-8383}, mesh = {Animals ; DNA/genetics ; DNA Methylation ; *Epigenesis, Genetic ; Hominidae/*genetics ; }, abstract = {Recent years have witnessed the rise of ancient DNA (aDNA) technology, allowing comparative genomics to be carried out at unprecedented time resolution. While it is relatively straightforward to use aDNA to identify recent genomic changes, it is much less clear how to utilize it to study changes in epigenetic regulation. Here we review recent works demonstrating that highly degraded aDNA still contains sufficient information to allow reconstruction of epigenetic signals, including DNA methylation and nucleosome positioning maps. We discuss challenges arising from the tissue specificity of epigenetics, and show how some of them might in fact turn into advantages. Finally, we introduce a method to infer methylation states in tissues that do not tend to be preserved over time.}, }
@article {pmid26892244, year = {2016}, author = {Lindqvist, C and Roy, T and Lydersen, C and Kovacs, KM and Aars, J and Wiig, &#xd8; and Bachmann, L}, title = {Genetic diversity of historical Atlantic walruses (Odobenus rosmarus rosmarus) from Bjørnøya and Håøya (Tusenøyane), Svalbard, Norway.}, journal = {BMC research notes}, volume = {9}, number = {}, pages = {112}, pmid = {26892244}, issn = {1756-0500}, mesh = {Animals ; Bone and Bones/chemistry ; Electron Transport Complex IV/genetics ; Female ; *Genetic Variation ; Genetics, Population/*history ; Haplotypes ; History, 20th Century ; History, 21st Century ; *Locus Control Region ; Male ; Mitochondrial Proteins/*genetics ; NADH Dehydrogenase/genetics ; *Phylogeny ; Population Density ; Svalbard ; Walruses/classification/*genetics ; }, abstract = {BACKGROUND: The population size of Atlantic walruses (Odobenus rosmarus rosmarus) is depleted relative to historical abundance levels. In Svalbard, centuries of over-exploitation brought the walrus herds to the verge of extinction, and such bottlenecks may have caused loss of genetic variation. To address this for Svalbard walruses, mitochondrial haplotypes of historical walruses from two major haul-out sites, Bjørnøya and Håøya, within the Archipelago were explored using bone samples from animals killed during the peak period of harvesting.<br><br>RESULTS: Using ancient DNA methodologies, the mitochondrial NADH dehydrogenase 1 (ND1) gene, the cytochrome c oxidase 1 (COI) gene, and the control region (CR) were targeted for 15 specimens from Bj&#xf8;rn&#xf8;ya (of which five were entirely negative) and 9 specimens from H&#xe5;&#xf8;ya (of which one was entirely negative). While ND1 and COI sequences were obtained for only a few samples, the CR delivered the most comprehensive data set, and the average genetic distance among historic Svalbard samples was 0.0028 (SD = 0.0023).<br><br>CONCLUSIONS: The CR sequences from the historical samples appear to be nested among contemporary Atlantic walruses, and no distinct mitochondrial haplogroups were identified in the historical samples that may have been lost during the periods of extensive hunting. However, given the low sample size and poor phylogenetic resolution it cannot be excluded that such haplogroups existed.}, }
@article {pmid26888264, year = {2016}, author = {Hsieh, P and Woerner, AE and Wall, JD and Lachance, J and Tishkoff, SA and Gutenkunst, RN and Hammer, MF}, title = {Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.}, journal = {Genome research}, volume = {26}, number = {3}, pages = {291-300}, pmid = {26888264}, issn = {1549-5469}, support = {8DP1ES022577-04/DP/NCCDPHP CDC HHS/United States ; R01 HG005226/HG/NHGRI NIH HHS/United States ; 1R01GM113657-01/GM/NIGMS NIH HHS/United States ; F32HG006648/HG/NHGRI NIH HHS/United States ; R01 GM113657/GM/NIGMS NIH HHS/United States ; F32 HG006648/HG/NHGRI NIH HHS/United States ; DP1 ES022577/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Black People/*genetics ; *Evolution, Molecular ; Gene Flow ; Gene Frequency ; Genetic Loci ; *Genetics, Population ; *Genome ; *Genome, Human ; *Genomics ; Haplotypes ; Humans ; Linkage Disequilibrium ; Pan paniscus/*genetics ; Polymorphism, Single Nucleotide ; }, abstract = {Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.}, }
@article {pmid26880113, year = {2016}, author = {Rieux, A and Balloux, F}, title = {Inferences from tip-calibrated phylogenies: a review and a practical guide.}, journal = {Molecular ecology}, volume = {25}, number = {9}, pages = {1911-1924}, pmid = {26880113}, issn = {1365-294X}, support = {BB/H008802/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/P007597/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bayes Theorem ; Calibration ; DNA, Ancient ; *Evolution, Molecular ; Fossils ; Likelihood Functions ; *Models, Genetic ; Models, Statistical ; *Phylogeny ; Software ; }, abstract = {Molecular dating of phylogenetic trees is a growing discipline using sequence data to co-estimate the timing of evolutionary events and rates of molecular evolution. All molecular-dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast-evolving genomes such as viruses and some bacteria, the time span over which samples were collected may cover a significant proportion of the time since they last shared a common ancestor. This situation allows phylogenetic trees to be calibrated by associating sampling dates directly to the sequences representing the tips (terminal nodes) of the tree. The increasing availability of genomic data from ancient DNA extends the applicability of such tip-based calibration to a variety of taxa including humans, extinct megafauna and various microorganisms which typically have a scarce fossil record. The development of statistical models accounting for heterogeneity in different aspects of the evolutionary process while accommodating very large data sets (e.g. whole genomes) has allowed using tip-dating methods to reach inferences on divergence times, substitution rates, past demography or the age of specific mutations on a variety of spatiotemporal scales. In this review, we summarize the current state of the art of tip dating, discuss some recent applications, highlight common pitfalls and provide a 'how to' guide to thoroughly perform such analyses.}, }
@article {pmid26878870, year = {2016}, author = {Slater, GJ and Cui, P and Forasiepi, AM and Lenz, D and Tsangaras, K and Voirin, B and de Moraes-Barros, N and MacPhee, RD and Greenwood, AD}, title = {Evolutionary Relationships among Extinct and Extant Sloths: The Evidence of Mitogenomes and Retroviruses.}, journal = {Genome biology and evolution}, volume = {8}, number = {3}, pages = {607-621}, pmid = {26878870}, issn = {1759-6653}, support = {R01 GM092706/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics ; Mammals/genetics ; Phylogeny ; Retroviridae/*genetics ; Sloths/*genetics ; }, abstract = {Macroevolutionary trends exhibited by retroviruses are complex and not entirely understood. The sloth endogenized foamy-like retrovirus (SloEFV), which demonstrates incongruence in virus-host evolution among extant sloths (Order Folivora), has not been investigated heretofore in any extinct sloth lineages and its premodern history within folivorans is therefore unknown. Determining retroviral coevolutionary trends requires a robust phylogeny of the viral host, but the highly reduced modern sloth fauna (6 species in 2 genera) does not adequately represent what was once a highly diversified clade (∼100 genera) of placental mammals. At present, the amount of molecular data available for extinct sloth taxa is limited, and analytical results based on these data tend to conflict with phylogenetic inferences made on the basis of morphological studies. To augment the molecular data set, we applied hybridization capture and next-generation Illumina sequencing to two extinct and three extant sloth species to retrieve full mitochondrial genomes (mitogenomes) from the hosts and the polymerase gene of SloEFV. The results produced a fully resolved and well-supported phylogeny that supports dividing crown families into two major clades: 1) The three-toed sloth, Bradypus, and Nothrotheriidae and 2) Megalonychidae, including the two-toed sloth, Choloepus, and Mylodontidae. Our calibrated time tree indicates that the Miocene epoch (23.5 Ma), particularly its earlier part, was an important interval for folivoran diversification. Both extant and extinct sloths demonstrate multiple complex invasions of SloEFV into the ancestral sloth germline followed by subsequent introgressions across different sloth lineages. Thus, sloth mitogenome and SloEFV evolution occurred separately and in parallel among sloths.}, }
@article {pmid26864783, year = {2016}, author = {Chang, D and Shapiro, B}, title = {Using ancient DNA and coalescent-based methods to infer extinction.}, journal = {Biology letters}, volume = {12}, number = {2}, pages = {20150822}, pmid = {26864783}, issn = {1744-957X}, mesh = {Animals ; Conservation of Natural Resources/*methods ; DNA/*analysis ; *Extinction, Biological ; Fossils ; *Genome ; Invertebrates/genetics ; Plants/genetics ; Population Dynamics ; Vertebrates/genetics ; }, abstract = {DNA sequences extracted from preserved remains can add considerable resolution to inference of past population dynamics. For example, coalescent-based methods have been used to correlate declines in some arctic megafauna populations with habitat fragmentation during the last ice age. These methods, however, often fail to detect population declines preceding extinction, most likely owing to a combination of sparse sampling, uninformative genetic markers, and models that cannot account for the increasingly structured nature of populations as habitats decline. As ancient DNA research expands to include full-genome analyses, these data will provide greater resolution of the genomic consequences of environmental change and the genetic signatures of extinction.}, }
@article {pmid26856190, year = {2017}, author = {Płoszaj, T and Jędrychowska-Dańska, K and Masłowska, A and Kozłowski, T and Chudziak, W and Bojarski, J and Robaszkiewicz, A and Witas, HW}, title = {Analysis of medieval mtDNA from Napole cemetery provides new insights into the early history of Polish state.}, journal = {Annals of human biology}, volume = {44}, number = {1}, pages = {91-94}, doi = {10.3109/03014460.2016.1151550}, pmid = {26856190}, issn = {1464-5033}, mesh = {Adult ; Cemeteries/*history ; DNA, Mitochondrial/*genetics ; History, Medieval ; Humans ; Male ; Poland ; }, abstract = {Contemporary historical anthropology and classical archaeology are concerned not only with such fundamental issues as the origins of ancient human populations and migration routes, but also with the formation and development of inter-population relations and the mixing of gene pools as a result of inter-breeding between individuals representing different cultural units. The contribution of immigrants to the analysed autochthonous population and their effect on the gene pool of that population has proven difficult to evaluate with classical morphological methods. The burial of one individual in the studied Napole cemetery located in central Poland had the form of a chamber grave, which is typical of Scandinavian culture from that period. However, this fact cannot be interpreted as absolute proof that the individual (in the biological sense) was allochtonous. This gives rise to the question as to who was actually buried in that cemetery. The ancient DNA results indicate that one of the individuals had an mtDNA haplotype typical of Iron Age northern Europe, which suggests that he could have arrived from that area at a later period. This seems to indirectly confirm the claims of many anthropologists that the development of the early medieval Polish state was significantly and directly influenced by the Scandinavians.}, }
@article {pmid26842575, year = {2016}, author = {Grosser, S and Rawlence, NJ and Anderson, CN and Smith, IW and Scofield, RP and Waters, JM}, title = {Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1824}, pages = {}, pmid = {26842575}, issn = {1471-2954}, mesh = {*Animal Distribution ; Animals ; DNA, Mitochondrial/*genetics ; Fossils ; Molecular Sequence Data ; New Zealand ; *Phylogeny ; Radiometric Dating ; Sequence Analysis, DNA ; Spheniscidae/genetics/*physiology ; }, abstract = {The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional 'cryptic' invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts.}, }
@article {pmid26832369, year = {2016}, author = {Ambers, A and Turnbough, M and Benjamin, R and Gill-King, H and King, J and Sajantila, A and Budowle, B}, title = {Modified DOP-PCR for improved STR typing of degraded DNA from human skeletal remains and bloodstains.}, journal = {Legal medicine (Tokyo, Japan)}, volume = {18}, number = {}, pages = {7-12}, doi = {10.1016/j.legalmed.2015.10.013}, pmid = {26832369}, issn = {1873-4162}, mesh = {*Blood Stains ; *Bone and Bones ; Cell Line ; DNA Primers/*analysis/genetics ; Female ; Forensic Anthropology/*methods ; Humans ; Male ; Polymerase Chain Reaction/*methods ; }, abstract = {Forensic and ancient DNA samples often are damaged and in limited quantity as a result of exposure to harsh environments and the passage of time. Several strategies have been proposed to address the challenges posed by degraded and low copy templates, including a PCR based whole genome amplification method called degenerate oligonucleotide-primed PCR (DOP-PCR). This study assessed the efficacy of four modified versions of the original DOP-PCR primer that retain at least a portion of the 5' defined sequence and alter the number of bases on the 3' end. The use of each of the four modified primers resulted in improved STR profiles from environmentally-damaged bloodstains, contemporary human skeletal remains, American Civil War era bone samples, and skeletal remains of WWII soldiers over those obtained by previously described DOP-PCR methods and routine STR typing. Additionally, the modified DOP-PCR procedure allows for a larger volume of DNA extract to be used, reducing the need to concentrate the sample and thus mitigating the effects of concurrent concentration of inhibitors.}, }
@article {pmid26829294, year = {2015}, author = {Ozga, AT and Tito, RY and Kemp, BM and Matternes, H and Obregon-Tito, A and Neal, L and Lewis, CM}, title = {Origins of an Unmarked Georgia Cemetery Using Ancient DNA Analysis.}, journal = {Human biology}, volume = {87}, number = {2}, pages = {109-121}, doi = {10.13110/humanbiology.87.2.0109}, pmid = {26829294}, issn = {1534-6617}, mesh = {Archaeology/*methods ; *Cemeteries ; DNA, Mitochondrial/*genetics ; Genetics, Population ; Georgia ; Haplotypes ; Humans ; }, abstract = {Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and, in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the cemetery. Through examination of hypervariable region I (HVR1) in the mitochondrial genome (mtDNA), we determined haplotypes for all 20 of these individuals. Eighteen of these individuals belong to the L or U haplogroups, suggesting that Avondale Burial Place was most likely used primarily as a resting place for African Americans. After the surrounding Bibb County community expressed interest in investigating potential ancestral relationships to those within the cemetery, eight potential descendants provided saliva to obtain mtDNA HVR1 information. Three individuals from Avondale Burial Place matched three individuals with oral history ties to the cemetery. Using the online tool EMPOP, we calculated the likelihood of these exact matches occurring by chance alone (< 1%). The present findings exhibit the importance of genetic analysis of cemetery origins when archaeological and osteological data are inconclusive for estimating ancestry of anonymous historical individuals.}, }
@article {pmid26826871, year = {2016}, author = {Cooper, C and Fellner, R and Heubi, O and Maixner, F and Zink, A and Lösch, S}, title = {Tuberculosis in early medieval Switzerland--osteological and molecular evidence.}, journal = {Swiss medical weekly}, volume = {146}, number = {}, pages = {w14269}, doi = {10.4414/smw.2016.14269}, pmid = {26826871}, issn = {1424-3997}, mesh = {Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; DNA, Bacterial/*genetics ; Female ; History, Medieval ; Humans ; Male ; Middle Aged ; Mycobacterium tuberculosis/*genetics ; Osteolysis/*diagnosis/metabolism ; Paleopathology ; Polymerase Chain Reaction ; Ribs ; Switzerland ; Tuberculosis/diagnosis/metabolism ; Tuberculosis, Osteoarticular/diagnosis/metabolism ; Tuberculosis, Spinal/*diagnosis/metabolism ; Young Adult ; }, abstract = {Lesions consistent with skeletal tuberculosis were found in 13 individuals from an early medieval skeletal sample from Courroux (Switzerland). One case of Pott's disease as well as lytic lesions in vertebrae and joints, rib lesions and endocranial new bone formation were identified. Three individuals with lesions and one without were tested for the presence of Myobacterium tuberculosis complex (MTBC) ancient DNA (aDNA), and in two cases, evidence for MTBC aDNA was detected. Our results suggest the presence of tuberculosis in the analysed material, which is in accordance with other osteological and biomolecular research that reported a high prevalence of tuberculosis in medieval skeletons.}, }
@article {pmid26826668, year = {2016}, author = {Schaefer, NK and Shapiro, B and Green, RE}, title = {Detecting hybridization using ancient DNA.}, journal = {Molecular ecology}, volume = {25}, number = {11}, pages = {2398-2412}, pmid = {26826668}, issn = {1365-294X}, support = {T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *DNA, Ancient ; Fossils ; Gene Flow ; Genomics/*methods ; Hominidae/genetics ; Human Migration ; Humans ; *Hybridization, Genetic ; Models, Genetic ; Models, Statistical ; Neanderthals/genetics ; Sequence Analysis, DNA ; }, abstract = {It is well established that related species hybridize and that this can have varied but significant effects on speciation and environmental adaptation. It should therefore come as no surprise that hybridization is not limited to species that are alive today. In the last several decades, advances in technologies for recovering and sequencing DNA from fossil remains have enabled the assembly of high-coverage genome sequences for a growing diversity of organisms, including many that are extinct. Thanks to the development of new statistical approaches for detecting and quantifying admixture from genomic data, genomes from extinct populations have proven useful both in revealing previously unknown hybridization events and informing the study of hybridization between living organisms. Here, we review some of the key recent statistical innovations for detecting ancient hybridization using genomewide sequence data and discuss how these innovations have revised our understanding of human evolutionary history.}, }
@article {pmid26811782, year = {2016}, author = {Fuentes-Hurtado, M and Hof, AR and Jansson, R}, title = {Paleodistribution modeling suggests glacial refugia in Scandinavia and out-of-Tibet range expansion of the Arctic fox.}, journal = {Ecology and evolution}, volume = {6}, number = {1}, pages = {170-180}, pmid = {26811782}, issn = {2045-7758}, abstract = {Quaternary glacial cycles have shaped the geographic distributions and evolution of numerous species in the Arctic. Ancient DNA suggests that the Arctic fox went extinct in Europe at the end of the Pleistocene and that Scandinavia was subsequently recolonized from Siberia, indicating inability to track its habitat through space as climate changed. Using ecological niche modeling, we found that climatically suitable conditions for Arctic fox were found in Scandinavia both during the last glacial maximum (LGM) and the mid-Holocene. Our results are supported by fossil occurrences from the last glacial. Furthermore, the model projection for the LGM, validated with fossil records, suggested an approximate distance of 2000 km between suitable Arctic conditions and the Tibetan Plateau well within the dispersal distance of the species, supporting the recently proposed hypothesis of range expansion from an origin on the Tibetan Plateau to the rest of Eurasia. The fact that the Arctic fox disappeared from Scandinavia despite suitable conditions suggests that extant populations may be more sensitive to climate change than previously thought.}, }
@article {pmid26808107, year = {2016}, author = {Habicht, ME and Bouwman, AS and Rühli, FJ}, title = {Identifications of ancient Egyptian royal mummies from the 18th Dynasty reconsidered.}, journal = {American journal of physical anthropology}, volume = {159}, number = {Suppl 61}, pages = {S216-31}, doi = {10.1002/ajpa.22909}, pmid = {26808107}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Egypt ; Female ; Humans ; Male ; Middle Aged ; *Mummies ; Young Adult ; }, abstract = {For centuries, ancient Egyptian Royal mummies have drawn the attention both of the general public and scientists. Many royal mummies from the New Kingdom have survived. The discoveries of the bodies of these ancient rulers have always sparked much attention, yet not all identifications are clear even nowadays. This study presents a meta-analysis to demonstrate the difficulties in identifying ancient Egyptian royal mummies. Various methods and pitfalls in the identification of the Pharaohs are reassessed since new scientific methods can be used, such as ancient DNA-profiling and CT-scanning. While the ancestors of Tutankhamun have been identified, some identities are still highly controversial (e.g., the mystery of the KV-55 skeleton, recently most likely identified as the genetic father of Tutankhamun). The meta-analysis confirms the suggested identity of some mummies (e.g., Amenhotep III, Thutmosis IV, and Queen Tjye).}, }
@article {pmid26805936, year = {2016}, author = {Li, G and Dong, H and Hou, W and Wang, S and Jiang, H and Yang, J and Wu, G}, title = {Temporal Succession of Ancient Phytoplankton Community in Qinghai Lake and Implication for Paleo-environmental Change.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {19769}, pmid = {26805936}, issn = {2045-2322}, mesh = {*Biodiversity ; China ; Climate Change ; Environment ; *Environmental Monitoring ; Geography ; *Lakes ; *Phytoplankton/classification/genetics ; RNA, Ribosomal, 23S/genetics ; }, abstract = {Tibetan lake sediments in NW China are sensitive recorders of climate change. However, many important plankton members do not leave any microscopic features in sedimentary records. Here we used ancient DNA preserved in Qinghai Lake sediments to reconstruct the temporal succession of plankton communities in the past 18,500 years. Our results showed that seven classes and sixteen genera of phytoplankton in the lake underwent major temporal changes, in correlation with known climatic events. Trebouxiophyceae and Eustigmatophyceae were predominant during the cold periods, whereas Chlorophyceae, Phaeophyceae, Xanthophyceae, Bacillariophyceae, and Cyanophyceae were abundant during the warm periods. The inferred changes in temperature, nutrients, precipitation, and salinity, as driven by the Westerlies and summer Monsoon strength, likely contributed to these observed temporal changes. Based on these correlations, we propose the phytoplankton index as a proxy to reconstruct the stadial versus interstadial climate change history in Qinghai Lake. This taxon-specific index is free of terrestrial contamination, sensitive to short-term climatic oscillations, and continuous in recording all climatic events in the lake. The validity of this index and its applicability to other lakes is demonstrated by its good correlations with multiple climate records of Qinghai Lake and another lake on the Tibetan Plateau, Kusai Lake.}, }
@article {pmid26805771, year = {2016}, author = {Rannamäe, E and Lõugas, L and Niemi, M and Kantanen, J and Maldre, L and Kadõrova, N and Saarma, U}, title = {Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post-medieval period and comparison with other regions in Eurasia.}, journal = {Animal genetics}, volume = {47}, number = {2}, pages = {208-218}, doi = {10.1111/age.12407}, pmid = {26805771}, issn = {1365-2052}, mesh = {Animals ; Asia ; Breeding ; DNA, Mitochondrial/genetics ; Estonia ; Europe ; Finland ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; Male ; Phylogeography ; Sequence Analysis, DNA ; Sheep/*genetics ; Sheep, Domestic/*genetics ; Y Chromosome/genetics ; }, abstract = {Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D-loop of mitochondrial DNA (mtDNA; 213 bp) and the Y-chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G-oY1 of the Y-chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations.}, }
@article {pmid26795402, year = {2016}, author = {Bos, KI and Herbig, A and Sahl, J and Waglechner, N and Fourment, M and Forrest, SA and Klunk, J and Schuenemann, VJ and Poinar, D and Kuch, M and Golding, GB and Dutour, O and Keim, P and Wagner, DM and Holmes, EC and Krause, J and Poinar, HN}, title = {Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus.}, journal = {eLife}, volume = {5}, number = {}, pages = {e12994}, pmid = {26795402}, issn = {2050-084X}, mesh = {Europe/epidemiology ; *Genome, Bacterial ; *Genotype ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; Molecular Epidemiology ; Plague/*epidemiology/*history ; Yersinia pestis/*classification/genetics/*isolation &amp; purification ; }, abstract = {The 14th-18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague's persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.}, }
@article {pmid26794802, year = {2016}, author = {Ponti, G and Pellacani, G and Tomasi, A and Sammaria, G and Manfredini, M}, title = {Skeletal stigmata as keys to access to the composite and ancient Gorlin-Goltz syndrome history: The Egypt, Pompeii and Herculaneum lessons.}, journal = {Gene}, volume = {589}, number = {2}, pages = {104-111}, doi = {10.1016/j.gene.2016.01.012}, pmid = {26794802}, issn = {1879-0038}, mesh = {Anthropology, Medical ; Basal Cell Nevus Syndrome/epidemiology/*genetics/*history/pathology ; Bone and Bones/*pathology ; Egypt/epidemiology ; Gene Expression ; Genes, Dominant ; *Germ-Line Mutation ; Greece/epidemiology ; History, 20th Century ; History, Ancient ; Humans ; Patched-1 Receptor/*genetics ; Prevalence ; Rome/epidemiology ; }, abstract = {There are several genetic diseases with a wide spectrum of congenital bone stigmata in association to cutaneous and visceral benign and malignant neoplasms. Gorlin-Goltz syndrome, also named nevoid basal cell carcinoma syndrome, is an autosomal dominant systemic disease with almost complete penetrance and high intra-familial phenotypic variability, caused by germline mutations of the gene PTCH1. The syndrome is characterized by unusual skeletal changes and high predisposition to the development of multiple basal cell carcinomas, odontogenic keratocysts tumors and other visceral tumors. The Gorlin syndrome, clinically defined as distinct syndrome in 1963, existed during Dynastic Egyptian times, as revealed by a costellation of skeletal findings compatible with the syndrome in mummies dating back to 3000years ago and, most likely, in the ancient population of Pompeii. These paleogenetic and historical evidences, together with the clinical and biomolecular modern evidences, confirm the quite benign behavior of the syndrome and the critical value of the multiple and synchronous skeletal anomalies in the recognition of these rare and complex genetic disease.}, }
@article {pmid26791510, year = {2016}, author = {Gorgé, O and Bennett, EA and Massilani, D and Daligault, J and Pruvost, M and Geigl, EM and Grange, T}, title = {Analysis of Ancient DNA in Microbial Ecology.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1399}, number = {}, pages = {289-315}, doi = {10.1007/978-1-4939-3369-3_17}, pmid = {26791510}, issn = {1940-6029}, mesh = {Animals ; DNA, Bacterial/*genetics/isolation &amp; purification ; Fossils ; Genome, Microbial/*genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Paleontology/*methods ; Soil Microbiology ; }, abstract = {The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.}, }
@article {pmid26774058, year = {2016}, author = {Brzeski, KE and DeBiasse, MB and Rabon, DR and Chamberlain, MJ and Taylor, SS}, title = {Mitochondrial DNA Variation in Southeastern Pre-Columbian Canids.}, journal = {The Journal of heredity}, volume = {107}, number = {3}, pages = {287-293}, pmid = {26774058}, issn = {1465-7333}, mesh = {Animals ; Canidae/genetics ; Coyotes/*genetics ; DNA, Mitochondrial/*genetics ; Haplotypes ; *Hybridization, Genetic ; Paleontology ; Sequence Analysis, DNA ; Southeastern United States ; Wolves/*genetics ; }, abstract = {The taxonomic status of the red wolf (Canis rufus) is heavily debated, but could be clarified by examining historic specimens from the southeastern United States. We analyzed mitochondrial DNA (mtDNA) from 3 ancient (350-1900 year olds) putative wolf samples excavated from middens and sinkholes within the historic red wolf range. We detected 3 unique mtDNA haplotypes, which grouped with the coyote mtDNA clade, suggesting that the canids inhabiting southeastern North America prior to human colonization from Europe were either coyotes, which would vastly expand historic coyote distributions, an ancient coyote-wolf hybrid, or a North American evolved red wolf lineage related to coyotes. Should the red wolf prove to be a distinct species, our results support the idea of either an ancient hybrid origin for red wolves or a shared common ancestor between coyotes and red wolves.}, }
@article {pmid26769403, year = {2015}, author = {Emerson, BC and Alvarado-Serrano, DF and Hickerson, MJ}, title = {Model misspecification confounds the estimation of rates and exaggerates their time dependency.}, journal = {Molecular ecology}, volume = {24}, number = {24}, pages = {6013-6020}, doi = {10.1111/mec.13451}, pmid = {26769403}, issn = {1365-294X}, mesh = {Animals ; *Evolution, Molecular ; Humans ; *Models, Genetic ; *Mutation Rate ; }, abstract = {While welcoming the comment of Ho et al. (2015), we find little that undermines the strength of our criticism, and it would appear they have misunderstood our central argument. Here we respond with the purpose of reiterating that we are (i) generally critical of much of the evidence presented in support of the time-dependent molecular rate (TDMR) hypothesis and (ii) specifically critical of estimates of μ derived from tip-dated sequences that exaggerate the importance of purifying selection as an explanation for TDMR over extended timescales. In response to assertions put forward by Ho et al. (2015), we use panmictic coalescent simulations of temporal data to explore a fundamental assumption for tip-dated tree shape and associated mutation rate estimates, and the appropriateness and utility of the date randomization test. The results reveal problems for the joint estimation of tree topology, effective population size and μ with tip-dated sequences using BEAST. Given the simulations, BEAST consistently obtains incorrect topological tree structures that are consistent with the substantial overestimation of μ and underestimation of effective population size. Data generated from lower effective population sizes were less likely to fail the date randomization test yet still resulted in substantially upwardly biased estimates of rates, bringing previous estimates of μ from temporally sampled DNA sequences into question. We find that our general criticisms of both the hypothesis of time-dependent molecular evolution and Bayesian methods to estimate μ from temporally sampled DNA sequences are further reinforced.}, }
@article {pmid26769402, year = {2015}, author = {Ho, SY and Duchêne, S and Molak, M and Shapiro, B}, title = {Time-dependent estimates of molecular evolutionary rates: evidence and causes.}, journal = {Molecular ecology}, volume = {24}, number = {24}, pages = {6007-6012}, doi = {10.1111/mec.13450}, pmid = {26769402}, issn = {1365-294X}, mesh = {Animals ; *Evolution, Molecular ; Humans ; *Models, Genetic ; *Mutation Rate ; }, abstract = {We are writing in response to a recent critique by Emerson &amp; Hickerson (2015), who challenge the evidence of a time-dependent bias in molecular rate estimates. This bias takes the form of a negative relationship between inferred evolutionary rates and the ages of the calibrations on which these estimates are based. Here, we present a summary of the evidence obtained from a broad range of taxa that supports a time-dependent bias in rate estimates, with a consideration of the potential causes of these observed trends. We also describe recent progress in improving the reliability of evolutionary rate estimation and respond to the concerns raised by Emerson &amp; Hickerson (2015) about the validity of rates estimated from time-structured sequence data. In doing so, we hope to dispel some misconceptions and to highlight several research directions that will improve our understanding of time-dependent biases in rate estimates.}, }
@article {pmid26768113, year = {2016}, author = {Salis, AT and Easton, LJ and Robertson, BC and Gemmell, N and Smith, IWG and Weisler, MI and Waters, JM and Rawlence, NJ}, title = {Myth or relict: Does ancient DNA detect the enigmatic Upland seal?.}, journal = {Molecular phylogenetics and evolution}, volume = {97}, number = {}, pages = {101-106}, doi = {10.1016/j.ympev.2015.12.012}, pmid = {26768113}, issn = {1095-9513}, mesh = {Animals ; Antarctic Regions ; Australia ; DNA, Mitochondrial/*genetics ; Ecosystem ; Fur Seals/*classification/*genetics ; Genetic Drift ; Genetic Variation ; Haplotypes ; Human Activities ; Legendary Creatures ; New Zealand ; Phylogeny ; }, abstract = {The biological status of the so-called 'Upland seal' has remained contentious ever since historical records described a distinct seal from the uplands of New Zealand's (NZ) remote sub-Antarctic islands. Subsequent genetic surveys of the NZ fur seal (Arctocephalus forsteri) detected two highly-divergent mtDNA clades, hypothesized to represent a post-sealing hybrid swarm between 'mainland' (Australia-NZ; A. forsteri) and sub-Antarctic (putative 'Upland'; A. snaresensis) lineages. We present ancient-DNA analyses of prehistoric mainland NZ and sub-Antarctic fur seals, revealing that both of these genetic lineages were already widely distributed across the region at the time of human arrival. These findings indicate that anthropogenic factors did not contribute to the admixture of these lineages, and cast doubt on the validity of the Upland seal. Human-mediated impacts on Arctocephalus genetic diversity are instead highlighted by a dramatic temporal haplotype frequency-shift due to genetic drift in heavily bottlenecked populations following the cessation of industrial-scale harvesting. These extinction-recolonisation dynamics add to a growing picture of human-mediated change in NZ's coastal and marine ecosystems.}, }
@article {pmid26760973, year = {2016}, author = {Seifert, L and Wiechmann, I and Harbeck, M and Thomas, A and Grupe, G and Projahn, M and Scholz, HC and Riehm, JM}, title = {Genotyping Yersinia pestis in Historical Plague: Evidence for Long-Term Persistence of Y. pestis in Europe from the 14th to the 17th Century.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0145194}, pmid = {26760973}, issn = {1932-6203}, mesh = {Europe ; *Genotyping Techniques ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, Medieval ; Humans ; Male ; Phylogeny ; Plague/genetics/*history/microbiology ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/genetics ; Yersinia pestis/*genetics ; }, abstract = {Ancient DNA (aDNA) recovered from plague victims of the second plague pandemic (14th to 17th century), excavated from two different burial sites in Germany, and spanning a time period of more than 300 years, was characterized using single nucleotide polymorphism (SNP) analysis. Of 30 tested skeletons 8 were positive for Yersinia pestis-specific nucleic acid, as determined by qPCR targeting the pla gene. In one individual (MP-19-II), the pla copy number in DNA extracted from tooth pulp was as high as 700 gene copies/μl, indicating severe generalized infection. All positive individuals were identical in all 16 SNP positions, separating phylogenetic branches within nodes N07_N10 (14 SNPs), N07_N08 (SNP s19) and N06_N07 (s545), and were highly similar to previously investigated plague victims from other European countries. Thus, beside the assumed continuous reintroduction of Y. pestis from central Asia in multiple waves during the second pandemic, long-term persistence of Y. pestis in Europe in a yet unknown reservoir host has also to be considered.}, }
@article {pmid26753840, year = {2016}, author = {Haber, M and Mezzavilla, M and Xue, Y and Tyler-Smith, C}, title = {Ancient DNA and the rewriting of human history: be sparing with Occam's razor.}, journal = {Genome biology}, volume = {17}, number = {}, pages = {1}, pmid = {26753840}, issn = {1474-760X}, support = {098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {DNA/*genetics/history ; *History, Ancient ; Human Migration/history ; Humans ; Selection, Genetic/*genetics ; }, abstract = {Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.}, }
@article {pmid26748850, year = {2016}, author = {Omrak, A and Günther, T and Valdiosera, C and Svensson, EM and Malmström, H and Kiesewetter, H and Aylward, W and Storå, J and Jakobsson, M and Götherström, A}, title = {Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool.}, journal = {Current biology : CB}, volume = {26}, number = {2}, pages = {270-275}, doi = {10.1016/j.cub.2015.12.019}, pmid = {26748850}, issn = {1879-0445}, mesh = {DNA, Mitochondrial/*genetics ; *Gene Pool ; Genetics, Population/methods ; *Genome ; Genomics ; Humans ; Middle East ; White People/*genetics ; }, abstract = {Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [1-5]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [6-9]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [10]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia's central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic.}, }
@article {pmid26712024, year = {2016}, author = {Cassidy, LM and Martiniano, R and Murphy, EM and Teasdale, MD and Mallory, J and Hartwell, B and Bradley, DG}, title = {Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {2}, pages = {368-373}, pmid = {26712024}, issn = {1091-6490}, mesh = {Atlantic Ocean ; DNA/genetics/isolation &amp; purification ; Gene Pool ; *Genome, Human ; Haplotypes/genetics ; Homozygote ; *Human Migration ; Humans ; Ireland ; Phenotype ; Principal Component Analysis ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343-3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter-gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026-1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.}, }
@article {pmid26708057, year = {2016}, author = {Harkins, KM and Schwartz, RS and Cartwright, RA and Stone, AC}, title = {Phylogenomic reconstruction supports supercontinent origins for Leishmania.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {38}, number = {}, pages = {101-109}, doi = {10.1016/j.meegid.2015.11.030}, pmid = {26708057}, issn = {1567-7257}, mesh = {Evolution, Molecular ; Genes, Helminth ; Genetic Variation ; *Genome, Helminth ; *Genomics ; High-Throughput Nucleotide Sequencing ; Humans ; Leishmania/*classification/*genetics ; Leishmaniasis/parasitology ; *Phylogeny ; }, abstract = {Leishmania, a genus of parasites transmitted to human hosts and mammalian/reptilian reservoirs by an insect vector, is the causative agent of the human disease complex leishmaniasis. The evolutionary relationships within the genus Leishmania and its origins are the source of ongoing debate, reflected in conflicting phylogenetic and biogeographic reconstructions. This study employs a recently described bioinformatics method, SISRS, to identify over 200,000 informative sites across the genome from newly sequenced and publicly available Leishmania data. This dataset is used to reconstruct the evolutionary relationships of this genus. Additionally, we constructed a large multi-gene dataset, using it to reconstruct the phylogeny and estimate divergence dates for species. We conclude that the genus Leishmania evolved at least 90-100 million years ago, supporting a modified version of the Multiple Origins hypothesis that we call the Supercontinent hypothesis. According to this scenario, separate Leishmania clades emerged prior to, and during, the breakup of Gondwana. Additionally, we confirm that reptile-infecting Leishmania are derived from mammalian forms and that the species that infect porcupines and sloths form a clade long separated from other species. Finally, we firmly place the guinea-pig infecting species, Leishmaniaenriettii, the globally dispersed Leishmaniasiamensis, and the newly identified Australian species from a kangaroo, as sibling species whose distribution arises from the ancient connection between Australia, Antarctica, and South America.}, }
@article {pmid26702445, year = {2015}, author = {Li, Z and Baniaga, AE and Sessa, EB and Scascitelli, M and Graham, SW and Rieseberg, LH and Barker, MS}, title = {Early genome duplications in conifers and other seed plants.}, journal = {Science advances}, volume = {1}, number = {10}, pages = {e1501084}, pmid = {26702445}, issn = {2375-2548}, abstract = {Polyploidy is a common mode of speciation and evolution in angiosperms (flowering plants). In contrast, there is little evidence to date that whole genome duplication (WGD) has played a significant role in the evolution of their putative extant sister lineage, the gymnosperms. Recent analyses of the spruce genome, the first published conifer genome, failed to detect evidence of WGDs in gene age distributions and attributed many aspects of conifer biology to a lack of WGDs. We present evidence for three ancient genome duplications during the evolution of gymnosperms, based on phylogenomic analyses of transcriptomes from 24 gymnosperms and 3 outgroups. We use a new algorithm to place these WGD events in phylogenetic context: two in the ancestry of major conifer clades (Pinaceae and cupressophyte conifers) and one in Welwitschia (Gnetales). We also confirm that a WGD hypothesized to be restricted to seed plants is indeed not shared with ferns and relatives (monilophytes), a result that was unclear in earlier studies. Contrary to previous genomic research that reported an absence of polyploidy in the ancestry of contemporary gymnosperms, our analyses indicate that polyploidy has contributed to the evolution of conifers and other gymnosperms. As in the flowering plants, the evolution of the large genome sizes of gymnosperms involved both polyploidy and repetitive element activity.}, }
@article {pmid26667772, year = {2016}, author = {Giuliani, C and Cilli, E and Bacalini, MG and Pirazzini, C and Sazzini, M and Gruppioni, G and Franceschi, C and Garagnani, P and Luiselli, D}, title = {Inferring chronological age from DNA methylation patterns of human teeth.}, journal = {American journal of physical anthropology}, volume = {159}, number = {4}, pages = {585-595}, doi = {10.1002/ajpa.22921}, pmid = {26667772}, issn = {1096-8644}, mesh = {Acetyltransferases/genetics ; Adolescent ; Adult ; Age Determination by Teeth/*methods ; Aged ; Anthropology, Physical ; DNA/analysis/*chemistry/*genetics/isolation &amp; purification ; DNA Methylation/*genetics ; Fatty Acid Elongases ; Humans ; Middle Aged ; Tooth/*chemistry ; Young Adult ; }, abstract = {OBJECTIVE: Current methods to determine chronological age from modern and ancient remains rely on both morphological and molecular approaches. However, low accuracy and the lack of standardized protocols make the development of alternative methods for the estimation of individual's age even more urgent for several research fields, such as biological anthropology, biodemography, forensics, evolutionary genetics, and ancient DNA studies. Therefore, the aim of this study is to identify genomic regions whose DNA methylation level correlates with age in modern teeth.<br><br>METHODS: We used MALDI-TOF mass spectrometry to analyze DNA methylation levels of specific CpGs located in the ELOVL2, FHL2, and PENK genes. We considered methylation data from cementum, dentin and pulp of 21 modern teeth (from 17 to 77 years old) to construct a mathematical model able to exploit DNA methylation values to predict age of the individuals.<br><br>RESULTS: The median difference between the real age and that estimated using DNA methylation values is 1.20 years (SD&#x2009;=&#x2009;1.9) if DNA is recovered from both cementum and pulp of the same modern teeth, 2.25 years (SD&#x2009;=&#x2009;2.5) if DNA is recovered from dental pulp, 2.45 years (SD&#x2009;=&#x2009;3.3) if DNA is extracted from cementum and 7.07 years (SD&#x2009;=&#x2009;7.0) when DNA is recovered from dentin only.<br><br>DISCUSSION: We propose for the first time the evaluation of DNA methylation at ELOVL2, FHL2, and PENK genes as a powerful tool to predict age in modern teeth for anthropological applications. Future studies are needed to apply this method also to historical and relatively ancient human teeth.}, }
@article {pmid26660678, year = {2015}, author = {Rivera-Perez, JI and Cano, RJ and Narganes-Storde, Y and Chanlatte-Baik, L and Toranzos, GA}, title = {Retroviral DNA Sequences as a Means for Determining Ancient Diets.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0144951}, pmid = {26660678}, issn = {1932-6203}, support = {R25 GM061151/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Viral/*chemistry ; *Diet ; Feces/virology ; Fossils ; Humans ; Metagenomics ; Retroviridae/*genetics ; Sequence Analysis, DNA ; }, abstract = {For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeological specimens from various regions of the world; however the complex dynamics represented in those microbial communities still remain unclear. Theoretically, similar to eukaryote DNA the presence of genes from key microbes or enzymes, as well as the presence of DNA from viruses specific to key organisms, may suggest the ingestion of specific diet components. In this study we demonstrate that ancient virus DNA obtained from coprolites also provides information reconstructing the host's diet, as inferred from sequences obtained from pre-Columbian coprolites. This depicts a novel and reliable approach to determine new components as well as validate the previously suggested diets of extinct cultures and animals. Furthermore, to our knowledge this represents the first description of the eukaryotic viral diversity found in paleofaeces belonging to pre-Columbian cultures.}, }
@article {pmid26651516, year = {2015}, author = {Wales, N and Carøe, C and Sandoval-Velasco, M and Gamba, C and Barnett, R and Samaniego, JA and Madrigal, JR and Orlando, L and Gilbert, MT}, title = {New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA.}, journal = {BioTechniques}, volume = {59}, number = {6}, pages = {368-371}, doi = {10.2144/000114364}, pmid = {26651516}, issn = {1940-9818}, mesh = {DNA/*chemistry ; DNA, Single-Stranded/*chemistry ; *Gene Library ; Sequence Analysis, DNA/*methods/trends ; }, abstract = {An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained <3% endogenous DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.}, }
@article {pmid28802973, year = {2015}, author = {Guichón, RA and Buikstra, JE and Stone, AC and Harkins, KM and Suby, JA and Massone, M and Prieto Lglesias, A and Wilbur, A and Constantinescu, F and Rodríguez Martín, C}, title = {Pre-Columbian tuberculosis in Tierra del Fuego? Discussion of the paleopathological and molecular evidence.}, journal = {International journal of paleopathology}, volume = {11}, number = {}, pages = {92-101}, doi = {10.1016/j.ijpp.2015.09.003}, pmid = {28802973}, issn = {1879-9825}, abstract = {This work contributes to ongoing discussions about the nature of tuberculosis in the Western Hemisphere prior to the time of European contact. Our example, from the extreme south of South America was, at the time of our study, without firm temporal association or molecular characterization. In Tierra del Fuego, Constantinescu (1999) briefly described vertebral bone lesions compatible with TB in an undated skeleton from Myren 1 site (Chile). The remains of Myren are estimated to represent a man between 18 and 23 years old at the time of death. The objectives of this research are to extend this description, to present molecular results, to establish a radiocarbon date, and to report stable isotopic values for the remains. We provide further description of the remains, including tuberculosis-like skeletal pathology. Radiocarbon dating of 640±20 years BP attributes this individual to the precontact fourteenth-fifteenth centuries. Isotopic ratios for nitrogen and carbon from bone collagen suggest a mixed diet. Molecular results were positive for the rpoB quantitative PCR (qPCR) assays but negative for two independent IS6110 and IS1081 qPCR assays. Further testing using genomic methods to target any mycobacteria for specific identification are needed.}, }
@article {pmid27048093, year = {2015}, author = {Maślanka, R and Zadrąg-Tęcza, R}, title = {[Duplication of DNA--a mechanism for the development of new functionality of genes].}, journal = {Postepy biochemii}, volume = {61}, number = {4}, pages = {388-397}, pmid = {27048093}, issn = {0032-5422}, mesh = {*Chromosome Duplication ; Eukaryota/genetics ; *Evolution, Molecular ; *Gene Duplication ; Genome ; Polyploidy ; }, abstract = {The amplification of DNA is considered as a mechanism for rapid evolution of organisms. Duplication can be especially advantageous in the case of changing environmental conditions. Whole genome duplication maintains the proper balance between gene expression. This seems to be the main reason why WGD is more favorable than duplication of the fragments of DNA. The polyploidy status disappear as a result of the loss of the majority of duplicated genes. The preservation of duplicated genes is associated with the development of their new functions. Polyploidization is often noted for plants. However due to sequencing technique, the duplications episodes are more frequently reports also for the other systematic taxa, including animals. The occurrence of ancient genome duplication is also considered for yeast Saccharomyces cerevisiae. The existence of two active copies of ribosomal protein genes can be a confirmation of this process. Development of the fermentation process might be one of the probable causes of the yeast genome duplication.}, }
@article {pmid29539370, year = {2012}, author = {Bianucci, R and Giuffra, V and Bachmeier, BE and Ball, M and Pusch, CM and Fornaciari, G and Nerlich, AG}, title = {Eleonora of Toledo (1522-1562): Evidence for tuberculosis and leishmaniasis co-infection in Renaissance Italy.}, journal = {International journal of paleopathology}, volume = {2}, number = {4}, pages = {231-235}, doi = {10.1016/j.ijpp.2012.11.002}, pmid = {29539370}, issn = {1879-9825}, abstract = {Clinical reports for Eleonora of Toledo (1522-1562), the wife of Cosimo I de' Medici, imply that during her 28th year she developed pulmonary tuberculosis, which was complicated by an attack of pernicious malaria, killing her at age 40. Eleonora's autopsy indicated that she had severe lung lesions consistent with chronic pulmonary infection. To clarify her disease status, we performed paleomolecular investigations. Our results identified ancient DNA from the Mycobacterium tuberculosis complex (MTB), along with Leishmania infantum (VL). Our data are of particular interest since in Tuscany the endemic foci of L. infantum are widely distributed and overlapped with those of malaria prior to its eradication. Although we can only speculate about Eleonora's true state of health, this clear evidence of long-term co-infection with MTB and VL is of major medical and biological interest since the co-evolution of the two pathogens and host-pathogen interactions in co-infected individuals are still not fully understood.}, }
@article {pmid27264580, year = {2011}, author = {Doğan Alakoç, Y and Akar, N}, title = {The importance of studying inherited hematological disorders in ancient Anatolian populations.}, journal = {Turkish journal of haematology : official journal of Turkish Society of Haematology}, volume = {28}, number = {4}, pages = {257-263}, doi = {10.5152/tjh.2011.43}, pmid = {27264580}, issn = {1300-7777}, abstract = {Before analysis of DNA from ancient remains was possible, anthropologists studied evolution and migration patterns using data obtained from population genetic studies on modern populations combined with data obtained from morphological evaluations of ancient remains. Currently, DNA analysis of ancient populations is making a valuable contribution to these efforts. Researchers that perform ancient DNA analysis prefer to study polymorphisms on the Y chromosome or mitochondrial DNA because the results are easier to statistically evaluate. To evaluate polymorphisms on diploid genomes, which are more informative, only mutations that have been extensively examined in modern populations should be chosen. The most extensively evaluated mutations are those related to prevalent inherited disorders. As such, beta-thalassemia, sickle cell anemia, FVL mutation of globin and the factor V genes are good candidates for DNA studies in ancient populations. These mutations are common in Anatolia, host to many civilizations since the Paleolithic period. This history makes Anatolia a good place for conducting research that could enhance our understanding of human evolution and migration patterns.}, }
@article {pmid29983697, year = {2011}, author = {Benner, SA and Yang, Z and Chen, F}, title = {Synthetic Biology, Tinkering Biology, and Artificial Biology. What are We Learning?.}, journal = {Comptes rendus. Chimie (Print)}, volume = {14}, number = {4}, pages = {372-387}, pmid = {29983697}, issn = {1631-0748}, support = {R01 GM086617/GM/NIGMS NIH HHS/United States ; R01 HG004647/HG/NHGRI NIH HHS/United States ; R01 HG004831/HG/NHGRI NIH HHS/United States ; }, abstract = {While chemical theory cannot yet support an engineering vision that allows molecules, DNA sequences, and proteins to be interchangeable parts in artificial constructs without "tinkering", progress can be made in synthetic biology by pursuing challenges at the limits of existing theory. These force scientists across uncharted terrain where they must address unscripted problems where, if theory is inadequate, failure results. Thus, synthesis drives discovery and paradigm change in ways that analysis cannot. Further, if failures are analyzed, new theories emerge. Here, we illustrate this by synthesizing an artificial genetic system capable of Darwinian evolution, a feature theorized to be universal to life.}, }
@article {pmid27041193, year = {2008}, author = {Hughey, JR and Braga, JC and Aguirre, J and Woelkerling, WJ and Webster, JM}, title = {ANALYSIS OF ANCIENT DNA FROM FOSSIL CORALLINES (CORALLINALES, RHODOPHYTA)(1).}, journal = {Journal of phycology}, volume = {44}, number = {2}, pages = {374-383}, doi = {10.1111/j.1529-8817.2008.00462.x}, pmid = {27041193}, issn = {0022-3646}, abstract = {The field of molecular paleontology has recently made significant contributions to anthropology and biology. Hundreds of ancient DNA studies have been published, but none has targeted fossil coralline algae. Using regions of the SSU gene, we analyzed rDNA from fossil coralline algae of varying ages and states of preservation from Spain, Papua New Guinea (PNG), and the Great Barrier Reef (GBR). Specimens from PNG, GBR, and some localities from Spain did not contain endogenous ancient DNA. Reproducible sequence data were obtained from specimens ∼550 years old from near Cadiz, Spain, and from rocky-shore deposits in Carboneras, Almeria Province of Spain (∼78,000 years before present [YBP]). Based on BLAST searches and a phylogenetic analysis of sequences, an undescribed coralline alga belonging to the Melobesioideae was discovered in the Carboneras material as well as the following coralline genera: Jania, Lithophyllum, Lithothamnion, Mesophyllum, and Phymatolithon. DNA from fleshy brown and red macroalgae was also discovered in the specimens from Carboneras. The coralline algae identified using molecular techniques were in agreement with those based on morphological methods. The identified taxa are common in the present-day southeastern Spain littoral zone. Amino acid racemization, concentration ratios, and specific concentrations failed to show a correlation between biomolecular preservation and PCR amplification success. Results suggest that molecular investigations on fossil algae, although limited by technical difficulties, are feasible. Validity of our results was established using authentication criteria and a self-critical approach to compliance.}, }
@article {pmid28561332, year = {1996}, author = {O'Rourke, DH and Carlyle, SW and Parr, RL}, title = {Ancient DNA: Methods, progress, and perspectives.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {8}, number = {5}, pages = {557-571}, doi = {10.1002/(SICI)1520-6300(1996)8:5&lt;557::AID-AJHB2&gt;3.0.CO;2-T}, pmid = {28561332}, issn = {1520-6300}, abstract = {The advent of the polymerase chain reaction as a standard molecular genetic technique and the demonstration that nucleic acids are routinely preserved in prehistoric material have led to a dramatic increase in molecular approaches to archaeological problems. These genetic approaches to long-standing problems in prehistory hold considerable promise to clarify issues of population origins, migrations, and settlement patterns, as well as ancestor/descendant relationships. The evolving methods for manipulating and analyzing ancient DNA (aDNA) are reviewed here, as are more recent applications of these methods to anthropologically relevant samples. In addition, new preliminary material is presented on mtDNA variation in Anasazi samples from the U.S. Southwest. The initial samples analyzed indicate similarity to contemporary populations of the Greater Southwest, as evidenced by the modest frequency of a 9bp deletion in Region V of the mtDNA molecule, and the possible absence of haplogroup D. © 1996 Wiley-Liss, Inc.}, }
@article {pmid26641720, year = {2016}, author = {Jaeger, LH and Gijón-Botella, H and Del Carmen Del Arco-Aguilar, M and Martín-Oval, M and Rodríguez-Maffiotte, C and Del Arco-Aguilar, M and Araújo, A and Iñiguez, AM}, title = {Evidence of Helminth Infection in Guanche Mummies: Integrating Paleoparasitological and Paleogenetic Investigations.}, journal = {The Journal of parasitology}, volume = {102}, number = {2}, pages = {222-228}, doi = {10.1645/15-866}, pmid = {26641720}, issn = {1937-2345}, mesh = {Helminthiasis/genetics/*history ; History, Medieval ; Humans ; Mummies/history/*parasitology ; *Paleopathology ; Spain ; }, abstract = {The Guanches, ancient inhabitants of the Canary Islands, Spain, practiced mummification of their dead. A paleoparasitological and paleogenetic analysis was conducted on mummified bodies (n = 6) (AD 1200, Cal BP 750) belonging to the Guanche culture from Gran Canaria Island. Coprolite and sediment samples (n = 19) were removed from below the abdominal region or sacral foramina. The samples were rehydrated in 0.5% trisodium phosphate solution for 72 hr at 4 C, and the paleoparasitological investigation was conducted by spontaneous sedimentation method and microscopic examination. The results revealed the presence of well-preserved eggs of Ascaris sp., Trichuris trichiura , Enterobius vermicularis , and hookworms. Ancient DNA was extracted from sediment samples to elucidate the ancestry of the mummies and for molecular detection of Ascaris sp. infection. Results of paleogenetic analysis demonstrated Ascaris sp. infection using 2 molecular targets, cytb and nad1. The mtDNA haplotypes U6b, U6b1, and HV were identified, which confirmed records of Guanche ancestry. The excellent preservation of Guanche mummies facilitated the paleoparasitological and paleogenetic study, the results of which contribute to our knowledge of Guanche culture and their health status.}, }
@article {pmid26635833, year = {2015}, author = {Mikić, AM}, title = {The First Attested Extraction of Ancient DNA in Legumes (Fabaceae).}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {1006}, pmid = {26635833}, issn = {1664-462X}, abstract = {Ancient DNA (aDNA) is any DNA extracted from ancient specimens, important for diverse evolutionary researches. The major obstacles in aDNA studies are mutations, contamination and fragmentation. Its studies may be crucial for crop history if integrated with human aDNA research and historical linguistics, both general and relating to agriculture. Legumes (Fabaceae) are one of the richest end economically most important plant families, not only from Neolithic onwards, since they were used as food by Neanderthals and Paleolithic modern man. The idea of extracting and analyzing legume aDNA was considered beneficial for both basic science and applied research, with an emphasis on genetic resources and plant breeding. The first reported successful and attested extraction of the legume aDNA was done from the sample of charred seeds of pea (Pisum sativum) and bitter vetch (Vicia ervilia) from Hissar, southeast Serbia, dated to 1,350-1,000 Before Christ. A modified version of cetyltrimethylammonium bromide (CTAB) method and the commercial kit for DNA extraction QIAGEN DNAesy yielded several ng μl(-1) of aDNA of both species and, after the whole genome amplification and with a fragment of nuclear ribosomal DNA gene 26S rDNA, resulted in the detection of the aDNA among the PCR products. A comparative analysis of four informative chloroplast DNA regions (trnSG, trnK, matK, and rbcL) among the modern wild and cultivated pea taxa demonstrated not only that the extracted aDNA was genuine, on the basis of mutation rate, but also that the ancient Hissar pea was most likely an early domesticated crop, related to the modern wild pea of a neighboring region. It is anticipated that this premier extraction of legume aDNA may provide taxonomists with the answers to diverse questions, such as leaf development in legumes, as well as with novel data on the single steps in domesticating legume crops worldwide.}, }
@article {pmid26631564, year = {2015}, author = {Pilot, M and Malewski, T and Moura, AE and Grzybowski, T and Oleński, K and Ruść, A and Kamiński, S and Ruiz Fadel, F and Mills, DS and Alagaili, AN and Mohammed, OB and Kłys, G and Okhlopkov, IM and Suchecka, E and Bogdanowicz, W}, title = {On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1820}, pages = {20152189}, pmid = {26631564}, issn = {1471-2954}, mesh = {Animals ; Asia ; *Biological Evolution ; Dogs/classification/*genetics ; Europe ; Genetic Variation ; Genetics, Population ; Genome-Wide Association Study ; Phylogeography ; Polymorphism, Single Nucleotide ; }, abstract = {Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.}, }
@article {pmid26630009, year = {2015}, author = {Sawyer, S and Renaud, G and Viola, B and Hublin, JJ and Gansauge, MT and Shunkov, MV and Derevianko, AP and Prüfer, K and Kelso, J and Pääbo, S}, title = {Nuclear and mitochondrial DNA sequences from two Denisovan individuals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {51}, pages = {15696-15700}, pmid = {26630009}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*chemistry ; Evolution, Molecular ; Molecular Sequence Data ; Neanderthals/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.}, }
@article {pmid26630007, year = {2015}, author = {Kistler, L and Newsom, LA and Ryan, TM and Clarke, AC and Smith, BD and Perry, GH}, title = {Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {49}, pages = {15107-15112}, pmid = {26630007}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; Cucurbita/genetics/*physiology ; *Ecology ; *Extinction, Biological ; Genome, Plant ; Molecular Sequence Data ; Plastids/genetics ; }, abstract = {The genus Cucurbita (squashes, pumpkins, gourds) contains numerous domesticated lineages with ancient New World origins. It was broadly distributed in the past but has declined to the point that several of the crops' progenitor species are scarce or unknown in the wild. We hypothesize that Holocene ecological shifts and megafaunal extinctions severely impacted wild Cucurbita, whereas their domestic counterparts adapted to changing conditions via symbiosis with human cultivators. First, we used high-throughput sequencing to analyze complete plastid genomes of 91 total Cucurbita samples, comprising ancient (n = 19), modern wild (n = 30), and modern domestic (n = 42) taxa. This analysis demonstrates independent domestication in eastern North America, evidence of a previously unknown pathway to domestication in northeastern Mexico, and broad archaeological distributions of taxa currently unknown in the wild. Further, sequence similarity between distant wild populations suggests recent fragmentation. Collectively, these results point to wild-type declines coinciding with widespread domestication. Second, we hypothesize that the disappearance of large herbivores struck a critical ecological blow against wild Cucurbita, and we take initial steps to consider this hypothesis through cross-mammal analyses of bitter taste receptor gene repertoires. Directly, megafauna consumed Cucurbita fruits and dispersed their seeds; wild Cucurbita were likely left without mutualistic dispersal partners in the Holocene because they are unpalatable to smaller surviving mammals with more bitter taste receptor genes. Indirectly, megafauna maintained mosaic-like landscapes ideal for Cucurbita, and vegetative changes following the megafaunal extinctions likely crowded out their disturbed-ground niche. Thus, anthropogenic landscapes provided favorable growth habitats and willing dispersal partners in the wake of ecological upheaval.}, }
@article {pmid26619959, year = {2016}, author = {Hunley, KL and Cabana, GS and Long, JC}, title = {The apportionment of human diversity revisited.}, journal = {American journal of physical anthropology}, volume = {160}, number = {4}, pages = {561-569}, doi = {10.1002/ajpa.22899}, pmid = {26619959}, issn = {1096-8644}, mesh = {Anthropology, Physical/*methods ; Gene Flow/genetics ; Genetic Variation/*genetics ; *Genetics, Population ; Humans ; Microsatellite Repeats ; *Models, Statistical ; Racial Groups/genetics/statistics &amp; numerical data ; }, abstract = {OBJECTIVES: Studies of the apportionment of human genetic diversity have found that local populations harbor nearly as much diversity as the species as a whole. These studies have been a valuable cornerstone in rejecting race as a biological framework in anthropology. The current study presents new analyses that use updated statistical methods based on bifurcating trees to assess the structure of human genetic diversity and its implications for the existence of canonical biological races.<br><br>MATERIALS AND METHODS: We examine patterns of both goodness-of-fit and lack-of-fit of two bifurcating trees to patterns of diversity determined from autosomal short tandem repeat genotypes in 1,037 people representing 52 populations with worldwide distribution.<br><br>RESULTS: From goodness-of-fit, we infer a root for the tree within Africa, and we recapitulate a pattern of decreasing genetic diversity with increasing geographic distance from Africa. From lack-of-fit, we present tentative evidence for admixture events with archaic hominins. We do not find evidence that long-range migration or local gene flow have contributed appreciably to the lack of fit at a global scale.<br><br>CONCLUSION: This is the first study to find a root for a tree of human populations without comparison to a nonhuman out-group, and it is one of the first studies to identify a signature of admixture with archaic hominins without reference to ancient DNA. Our findings complement previous studies of the apportionment of human diversity and provide a more solid evolutionary foundation for the rejection of biological race. Am J Phys Anthropol 160:561-569, 2016. &#xa9; 2015 Wiley Periodicals, Inc.}, }
@article {pmid26613371, year = {2016}, author = {Malaspinas, AS}, title = {Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective.}, journal = {Molecular ecology}, volume = {25}, number = {1}, pages = {24-41}, doi = {10.1111/mec.13492}, pmid = {26613371}, issn = {1365-294X}, mesh = {Animals ; *Evolution, Molecular ; Genetic Loci ; *Genetics, Population ; Genomics/*methods ; Horses/genetics ; Humans ; Models, Genetic ; Population Density ; *Selection, Genetic ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; Zea mays/genetics ; }, abstract = {With hundreds of ancient genomes becoming available this year, ancient DNA research has now entered the genomics era. Utilizing the temporal aspect of these new data, we can now address fundamental evolutionary questions such as the characterization of selection processes shaping the genomes. The temporal dimension in the data has spurred the development in the last 10 years of new methods allowing the detection of loci evolving non-neutrally but also the inference of selection coefficients across genomes capitalizing on these time serial data. To guide empirically oriented researchers towards the statistical approach most appropriate for their data, this article reviews several of those methods, discussing their underlying assumptions and the parameter ranges for which they have been developed. While I discuss some methods developed for experimental evolution, the main focus is ancient DNA.}, }
@article {pmid26597064, year = {2015}, author = {De Baets, K and Littlewood, DT}, title = {The Importance of Fossils in Understanding the Evolution of Parasites and Their Vectors.}, journal = {Advances in parasitology}, volume = {90}, number = {}, pages = {1-51}, doi = {10.1016/bs.apar.2015.07.001}, pmid = {26597064}, issn = {2163-6079}, mesh = {Animals ; *Biological Evolution ; Disease Vectors/*classification ; *Fossils ; Parasites/*classification/*physiology ; Phylogeny ; }, abstract = {Knowledge concerning the diversity of parasitism and its reach across our current understanding of the tree of life has benefitted considerably from novel molecular phylogenetic methods. However, the timing of events and the resolution of the nature of the intimate relationships between parasites and their hosts in deep time remain problematic. Despite its vagaries, the fossil record provides the only direct evidence of parasites and parasitism in the fossil record of extant and extinct lineages. Here, we demonstrate the potential of the fossil record and other lines of geological evidence to calibrate the origin and evolution of parasitism by combining different kinds of dating evidence with novel molecular clock methodologies. Other novel methods promise to provide additional evidence for the presence or the life habit of pathogens and their vectors, including the discovery and analysis of ancient DNA and other biomolecules, as well as computed tomographic methods.}, }
@article {pmid26595274, year = {2015}, author = {Mathieson, I and Lazaridis, I and Rohland, N and Mallick, S and Patterson, N and Roodenberg, SA and Harney, E and Stewardson, K and Fernandes, D and Novak, M and Sirak, K and Gamba, C and Jones, ER and Llamas, B and Dryomov, S and Pickrell, J and Arsuaga, JL and de Castro, JM and Carbonell, E and Gerritsen, F and Khokhlov, A and Kuznetsov, P and Lozano, M and Meller, H and Mochalov, O and Moiseyev, V and Guerra, MA and Roodenberg, J and Vergès, JM and Krause, J and Cooper, A and Alt, KW and Brown, D and Anthony, D and Lalueza-Fox, C and Haak, W and Pinhasi, R and Reich, D}, title = {Genome-wide patterns of selection in 230 ancient Eurasians.}, journal = {Nature}, volume = {528}, number = {7583}, pages = {499-503}, pmid = {26595274}, issn = {1476-4687}, support = {263441/ERC_/European Research Council/International ; R01 GM100233/GM/NIGMS NIH HHS/United States ; GM100233/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; }, mesh = {Agriculture/history ; Asia/ethnology ; Body Height/genetics ; Bone and Bones ; DNA/genetics/isolation &amp; purification ; Diet/history ; Europe/ethnology ; Genetics, Population ; Genome, Human/*genetics ; Haplotypes/genetics ; History, Ancient ; Humans ; Immunity/genetics ; Male ; Multifactorial Inheritance/genetics ; Pigmentation/genetics ; Selection, Genetic/*genetics ; Sequence Analysis, DNA ; }, abstract = {Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.}, }
@article {pmid26592162, year = {2016}, author = {Duforet-Frebourg, N and Slatkin, M}, title = {Isolation-by-distance-and-time in a stepping-stone model.}, journal = {Theoretical population biology}, volume = {108}, number = {}, pages = {24-35}, pmid = {26592162}, issn = {1096-0325}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; R01-GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Gene Flow ; Gene Frequency ; *Genetics, Population ; Humans ; *Models, Genetic ; Principal Component Analysis ; }, abstract = {With the great advances in ancient DNA extraction, genetic data are now obtained from geographically separated individuals from both present and past. However, population genetics theory about the joint effect of space and time has not been thoroughly studied. Based on the classical stepping-stone model, we develop the theory of Isolation by distance and time. We derive the correlation of allele frequencies between demes in the case where ancient samples are present, and investigate the impact of edge effects with forward-in-time simulations. We also derive results about coalescent times in circular and toroidal models. As one of the most common ways to investigate population structure is principal components analysis (PCA), we evaluate the impact of our theory on PCA plots. Our results demonstrate that time between samples is an important factor. Ancient samples tend to be drawn to the center of a PCA plot.}, }
@article {pmid26563586, year = {2015}, author = {Ziesemer, KA and Mann, AE and Sankaranarayanan, K and Schroeder, H and Ozga, AT and Brandt, BW and Zaura, E and Waters-Rist, A and Hoogland, M and Salazar-García, DC and Aldenderfer, M and Speller, C and Hendy, J and Weston, DA and MacDonald, SJ and Thomas, GH and Collins, MJ and Lewis, CM and Hofman, C and Warinner, C}, title = {Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16498}, pmid = {26563586}, issn = {2045-2322}, support = {//Wellcome Trust/United Kingdom ; R01 GM089886/GM/NIGMS NIH HHS/United States ; 097829//Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; Bacteria/classification/genetics ; Dental Calculus/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; *Gene Amplification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenome/*genetics ; Metagenomics/*methods ; Methanobrevibacter/classification/genetics ; Microbiota/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/*genetics ; }, abstract = {To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.}, }
@article {pmid26561991, year = {2015}, author = {Gómez-Carballa, A and Catelli, L and Pardo-Seco, J and Martinón-Torres, F and Roewer, L and Vullo, C and Salas, A}, title = {The complete mitogenome of a 500-year-old Inca child mummy.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16462}, pmid = {26561991}, issn = {2045-2322}, mesh = {Argentina ; Child ; DNA, Mitochondrial/chemistry/classification/*genetics ; Genome, Mitochondrial/*genetics ; Haplotypes ; Humans ; *Indians, South American ; *Mummies ; Phylogeny ; Religion ; Sequence Analysis, DNA ; }, abstract = {In 1985, a frozen mummy was found in Cerro Aconcagua (Argentina). Archaeological studies identified the mummy as a seven-year-old Inca sacrifice victim who lived >500 years ago, at the time of the expansion of the Inca Empire towards the southern cone. The sequence of its entire mitogenome was obtained. After querying a large worldwide database of mitogenomes (>28,000) we found that the Inca haplotype belonged to a branch of haplogroup C1b (C1bi) that has not yet been identified in modern Native Americans. The expansion of C1b into the Americas, as estimated using 203 C1b mitogenomes, dates to the initial Paleoindian settlements (~18.3 thousand years ago [kya]); however, its internal variation differs between Mesoamerica and South America. By querying large databases of control region haplotypes (>150,000), we found only a few C1bi members in Peru and Bolivia (e.g. Aymaras), including one haplotype retrieved from ancient DNA of an individual belonging to the Wari Empire (Peruvian Andes). Overall, the results suggest that the profile of the mummy represents a very rare sub-clade that arose 14.3 (5-23.6) kya and could have been more frequent in the past. A Peruvian Inca origin for present-day C1bi haplotypes would satisfy both the genetic and paleo-anthropological findings.}, }
@article {pmid26560339, year = {2015}, author = {Scienski, K and Fay, JC and Conant, GC}, title = {Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex.}, journal = {Genome biology and evolution}, volume = {7}, number = {12}, pages = {3249-3258}, pmid = {26560339}, issn = {1759-6653}, support = {R01 GM080669/GM/NIGMS NIH HHS/United States ; }, mesh = {Evolution, Molecular ; *Gene Conversion ; *Gene Duplication ; Histones/*genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/*genetics ; *Selection, Genetic ; }, abstract = {We find evidence for interlocus gene conversion in five duplicated histone genes from six yeast species. The sequences of these duplicated genes, surviving from the ancient genome duplication, show phylogenetic patterns inconsistent with the well-resolved orthology relationships inferred from a likelihood model of gene loss after the genome duplication. Instead, these paralogous genes are more closely related to each other than any is to its nearest ortholog. In addition to simulations supporting gene conversion, we also present evidence for elevated rates of radical amino acid substitutions along the branches implicated in the conversion events. As these patterns are similar to those seen in ribosomal proteins that have undergone gene conversion, we speculate that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies.}, }
@article {pmid26545921, year = {2016}, author = {Nakagome, S and Alkorta-Aranburu, G and Amato, R and Howie, B and Peter, BM and Hudson, RR and Di Rienzo, A}, title = {Estimating the Ages of Selection Signals from Different Epochs in Human History.}, journal = {Molecular biology and evolution}, volume = {33}, number = {3}, pages = {657-669}, pmid = {26545921}, issn = {1537-1719}, support = {R01 GM101682/GM/NIGMS NIH HHS/United States ; P30 CA14599/CA/NCI NIH HHS/United States ; P30 CA014599/CA/NCI NIH HHS/United States ; R01 HL119577/HL/NHLBI NIH HHS/United States ; R01GM10168/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Evolution, Molecular ; Gene Frequency ; Genetic Variation ; *Genetics, Population ; Humans ; *Models, Genetic ; Polymorphism, Single Nucleotide ; *Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs.}, }
@article {pmid26540101, year = {2015}, author = {Buckley, M and Fariña, RA and Lawless, C and Tambusso, PS and Varela, L and Carlini, AA and Powell, JE and Martinez, JG}, title = {Collagen Sequence Analysis of the Extinct Giant Ground Sloths Lestodon and Megatherium.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0139611}, pmid = {26540101}, issn = {1932-6203}, mesh = {Animals ; Collagen/*genetics ; Extinction, Biological ; *Fossils ; Phylogeny ; Proteomics ; Sequence Analysis, DNA ; Sloths/*genetics ; }, abstract = {For over 200 years, fossils of bizarre extinct creatures have been described from the Americas that have ranged from giant ground sloths to the 'native' South American ungulates, groups of mammals that evolved in relative isolation on South America. Ground sloths belong to the South American xenarthrans, a group with modern although morphologically and ecologically very different representatives (anteaters, armadillos and sloths), which has been proposed to be one of the four main eutherian clades. Recently, proteomics analyses of bone collagen have recently been used to yield a molecular phylogeny for a range of mammals including the unusual 'Malagasy aardvark' shown to be most closely related to the afrotherian tenrecs, and the south American ungulates supporting their morphological association with condylarths. However, proteomics results generate partial sequence information that could impact upon the phylogenetic placement that has not been appropriately tested. For comparison, this paper examines the phylogenetic potential of proteomics-based sequencing through the analysis of collagen extracted from two extinct giant ground sloths, Lestodon and Megatherium. The ground sloths were placed as sister taxa to extant sloths, but with a closer relationship between Lestodon and the extant sloths than the basal Megatherium. These results highlight that proteomics methods could yield plausible phylogenies that share similarities with other methods, but have the potential to be more useful in fossils beyond the limits of ancient DNA survival.}, }
@article {pmid26525598, year = {2015}, author = {Weiß, CL and Dannemann, M and Prüfer, K and Burbano, HA}, title = {Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data.}, journal = {eLife}, volume = {4}, number = {}, pages = {}, pmid = {26525598}, issn = {2050-084X}, mesh = {DNA, Plant/*genetics/*isolation &amp; purification ; *Fossils ; Molecular Biology/methods ; Sequence Analysis, DNA ; Triticum/*genetics/*growth &amp; development ; United Kingdom ; }, abstract = {Contamination with exogenous DNA is a constant hazard to ancient DNA studies, since their validity greatly depend on the ancient origin of the retrieved sequences. Since contamination occurs sporadically, it is fundamental to show positive evidence for the authenticity of ancient DNA sequences even when preventive measures to avoid contamination are implemented. Recently the presence of wheat in the United Kingdom 8000 years before the present has been reported based on an analysis of sedimentary ancient DNA (Smith et al. 2015). Smith et al. did not present any positive evidence for the authenticity of their results due to the small number of sequencing reads that were confidently assigned to wheat. We developed a computational method that compares postmortem damage patterns of a test dataset with bona fide ancient and modern DNA. We applied this test to the putative wheat DNA and find that these reads are most likely not of ancient origin.}, }
@article {pmid26504230, year = {2015}, author = {Tackney, JC and Potter, BA and Raff, J and Powers, M and Watkins, WS and Warner, D and Reuther, JD and Irish, JD and O'Rourke, DH}, title = {Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {45}, pages = {13833-13838}, pmid = {26504230}, issn = {1091-6490}, mesh = {Alaska ; Archaeology/methods ; Base Sequence ; Bayes Theorem ; Burial/history ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetic Variation ; Geography ; Haplotypes/*genetics ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Human Migration/*history ; Humans ; Infant ; Likelihood Functions ; Models, Genetic ; *Models, Theoretical ; Molecular Sequence Data ; Oligonucleotides/genetics ; *Phylogeny ; }, abstract = {Pleistocene residential sites with multiple contemporaneous human burials are extremely rare in the Americas. We report mitochondrial genomic variation in the first multiple mitochondrial genomes from a single prehistoric population: two infant burials (USR1 and USR2) from a common interment at the Upward Sun River Site in central Alaska dating to ∼11,500 cal B.P. Using a targeted capture method and next-generation sequencing, we determined that the USR1 infant possessed variants that define mitochondrial lineage C1b, whereas the USR2 genome falls at the root of lineage B2, allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.}, }
@article {pmid26497007, year = {2015}, author = {Pacioni, C and Hunt, H and Allentoft, ME and Vaughan, TG and Wayne, AF and Baynes, A and Haouchar, D and Dortch, J and Bunce, M}, title = {Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial.}, journal = {Molecular ecology}, volume = {24}, number = {23}, pages = {5813-5828}, doi = {10.1111/mec.13430}, pmid = {26497007}, issn = {1365-294X}, mesh = {Animals ; Australia ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; *Endangered Species ; Fossils ; Gene Flow ; Genetic Markers ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Marsupialia/*genetics ; Microsatellite Repeats ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000-4000 years in association with a dramatic population decline. In addition, we obtained near-complete 11-loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of 'new' microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current-day conservation strategies.}, }
@article {pmid26496604, year = {2015}, author = {Rasmussen, S and Allentoft, ME and Nielsen, K and Orlando, L and Sikora, M and Sjögren, KG and Pedersen, AG and Schubert, M and Van Dam, A and Kapel, CM and Nielsen, HB and Brunak, S and Avetisyan, P and Epimakhov, A and Khalyapin, MV and Gnuni, A and Kriiska, A and Lasak, I and Metspalu, M and Moiseyev, V and Gromov, A and Pokutta, D and Saag, L and Varul, L and Yepiskoposyan, L and Sicheritz-Pontén, T and Foley, RA and Lahr, MM and Nielsen, R and Kristiansen, K and Willerslev, E}, title = {Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.}, journal = {Cell}, volume = {163}, number = {3}, pages = {571-582}, pmid = {26496604}, issn = {1097-4172}, mesh = {Animals ; Asia ; DNA, Bacterial/genetics ; Europe ; History, Ancient ; History, Medieval ; Humans ; Plague/history/*microbiology/transmission ; Siphonaptera/microbiology ; Tooth/microbiology ; Yersinia pestis/*classification/genetics/*isolation &amp; purification ; }, abstract = {The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.}, }
@article {pmid26478140, year = {2015}, author = {Larick, R and Ciochon, RL}, title = {Early hominin biogeography in Island Southeast Asia.}, journal = {Evolutionary anthropology}, volume = {24}, number = {5}, pages = {185-213}, doi = {10.1002/evan.21460}, pmid = {26478140}, issn = {1520-6505}, mesh = {Animal Migration ; Animals ; Anthropology, Physical ; *Biological Evolution ; Hominidae/*physiology ; Indonesia ; Islands ; Technology ; Tool Use Behavior ; }, abstract = {Island Southeast Asia covers Eurasia's tropical expanse of continental shelf and active subduction zones. Cutting between island landmasses, Wallace's Line separates Sunda and the Eastern Island Arc (the Arc) into distinct tectonic and faunal provinces. West of the line, on Sunda, Java Island yields many fossils of Homo erectus. East of the line, on the Arc, Flores Island provides one skeleton and isolated remains of Homo floresiensis. Luzon Island in the Philippines has another fossil hominin. Sulawesi preserves early hominin archeology. This insular divergence sets up a unique regional context for early hominin dispersal, isolation, and extinction. The evidence is reviewed across three Pleistocene climate periods. Patterns are discussed in relation to the pulse of global sea-level shifts, as well as regional geo-tectonics, catastrophes, stegodon dispersal, and paleogenomics. Several patterns imply evolutionary processes typical of oceanic islands. Early hominins apparently responded to changing island conditions for a million-and-a-half years, likely becoming extinct during the period in which Homo sapiens colonized the region.}, }
@article {pmid26473047, year = {2015}, author = {Hutchinson, WF and Culling, M and Orton, DC and Hänfling, B and Lawson Handley, L and Hamilton-Dyer, S and O'Connell, TC and Richards, MP and Barrett, JH}, title = {The globalization of naval provisioning: ancient DNA and stable isotope analyses of stored cod from the wreck of the Mary Rose, AD 1545.}, journal = {Royal Society open science}, volume = {2}, number = {9}, pages = {150199}, pmid = {26473047}, issn = {2054-5703}, support = {MR/L01629X/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {A comparison of ancient DNA (single-nucleotide polymorphisms) and carbon and nitrogen stable isotope evidence suggests that stored cod provisions recovered from the wreck of the Tudor warship Mary Rose, which sank in the Solent, southern England, in 1545, had been caught in northern and transatlantic waters such as the northern North Sea and the fishing grounds of Iceland and Newfoundland. This discovery, underpinned by control data from archaeological samples of cod bones from potential source regions, illuminates the role of naval provisioning in the early development of extensive sea fisheries, with their long-term economic and ecological impacts.}, }
@article {pmid26469018, year = {2015}, author = {Callaway, E}, title = {Ancient DNA from hot climes yields its secrets.}, journal = {Nature}, volume = {526}, number = {7573}, pages = {303}, pmid = {26469018}, issn = {1476-4687}, mesh = {Animals ; *Climate ; DNA/genetics/*isolation &amp; purification ; Ethiopia ; History, Ancient ; Hominidae/classification/genetics ; *Hot Temperature ; Human Migration/*history ; Humans ; Phylogeny ; Temporal Bone/anatomy &amp; histology ; Turkey ; }, }
@article {pmid26458810, year = {2015}, author = {Renaud, G and Slon, V and Duggan, AT and Kelso, J}, title = {Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.}, journal = {Genome biology}, volume = {16}, number = {}, pages = {224}, pmid = {26458810}, issn = {1474-760X}, mesh = {Animals ; Base Sequence ; *Consensus Sequence ; *DNA Contamination ; DNA, Mitochondrial/*chemistry ; *Genome, Mitochondrial ; Humans ; Neanderthals/genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {UNLABELLED: Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates.<br><br>AVAILABILITY: https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.}, }
@article {pmid26458007, year = {2016}, author = {Santana, J and Fregel, R and Lightfoot, E and Morales, J and Alamón, M and Guillén, J and Moreno, M and Rodríguez, A}, title = {The early colonial atlantic world: New insights on the African Diaspora from isotopic and ancient DNA analyses of a multiethnic 15th-17th century burial population from the Canary Islands, Spain.}, journal = {American journal of physical anthropology}, volume = {159}, number = {2}, pages = {300-312}, doi = {10.1002/ajpa.22879}, pmid = {26458007}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Africa ; Anthropology, Physical ; Carbon Isotopes/analysis ; Cemeteries/history ; Child ; DNA/*genetics ; Enslavement/*history ; Female ; History, 15th Century ; History, 16th Century ; History, 17th Century ; Humans ; Male ; Middle Aged ; Oxygen Isotopes/analysis ; Radiometric Dating ; Spain ; Tooth/chemistry ; Young Adult ; }, abstract = {OBJECTIVES: The Canary Islands are considered one of the first places where Atlantic slave plantations with labourers of African origin were established, during the 15th century AD. In Gran Canaria (Canary Islands, Spain), a unique cemetery dated to the 15th and 17th centuries was discovered adjacent to an ancient sugar plantation with funerary practices that could be related to enslaved people. In this article, we investigate the origin and possible birthplace of each individual buried in this cemetery, as well as the identity and social status of these people.<br><br>MATERIALS AND METHODS: The sample consists of 14 individuals radiocarbon dated to the 15th and 17th centuries AD. We have employed several methods, including the analysis of ancient human DNA, stable isotopes, and skeletal markers of physical activity.<br><br>RESULTS: 1) the funerary practices indicate a set of rituals not previously recorded in the Canary Islands; 2) genetic data show that some people buried in the cemetery could have North-African and sub-Saharan African lineages; 3) isotopic results suggest that some individuals were born outside Gran Canaria; and 4) markers of physical activity show a pattern of labour involving high levels of effort.<br><br>DISCUSSION: This set of evidence, along with information from historical sources, suggests that Finca Clavijo was a cemetery for a multiethnic marginalized population that had being likely enslaved. Results also indicate that this population kept practicing non-Christian rituals well into the 17th century. We propose that this was possible because the location of the Canaries, far from mainland Spain and the control of the Spanish Crown, allowed the emergence of a new society with multicultural origins that was more tolerant to foreign rituals and syncretism.}, }
@article {pmid26452301, year = {2015}, author = {Torti, A and Lever, MA and Jørgensen, BB}, title = {Origin, dynamics, and implications of extracellular DNA pools in marine sediments.}, journal = {Marine genomics}, volume = {24 Pt 3}, number = {}, pages = {185-196}, doi = {10.1016/j.margen.2015.08.007}, pmid = {26452301}, issn = {1876-7478}, mesh = {Animals ; Aquatic Organisms/*classification/*genetics ; Biodiversity ; DNA/chemistry/classification/*genetics ; Geologic Sediments/*chemistry ; }, abstract = {In marine sediments, DNA occurs both inside and outside living organisms. DNA not enclosed in living cells may account for the largest fraction of total DNA, and include molecules locked within dead cells, organic and inorganic aggregates, adsorbed onto mineral matrices, and viral DNA. This DNA comprises genetic material released in situ from sediment microbial communities, as well as DNA of pelagic and terrestrial origin deposited to the seafloor. DNA not enclosed in living cells undermines the assumption of a direct link between the overall DNA pool and the local, currently living microbial assemblages, in terms of both microbial cell abundance and diversity. At the same time, the extracellular DNA may provide an integrated view of the biodiversity and ecological processes occurring on land, in marine water columns, and sediments themselves, thereby acting as an archive of genetic information which can be used to reconstruct past changes in source environments. In this review, we identify and discuss DNA pools in marine sediments, with special focus on DNA not enclosed in living cells, its origin, dynamics, and ecological and methodological implications. Achievements in deciphering the genetic information held within each DNA pool are presented along with still-standing challenges and major gaps in current knowledge.}, }
@article {pmid26450112, year = {2015}, author = {Duchemin, W and Daubin, V and Tannier, E}, title = {Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence.}, journal = {BMC genomics}, volume = {16 Suppl 10}, number = {Suppl 10}, pages = {S9}, pmid = {26450112}, issn = {1471-2164}, mesh = {*Evolution, Molecular ; *Genome, Bacterial ; Humans ; *Phylogeny ; Plague/genetics/microbiology ; Plasmids/genetics ; Species Specificity ; Yersinia pestis/*genetics/pathogenicity ; }, abstract = {BACKGROUND: We propose the computational reconstruction of a whole bacterial ancestral genome at the nucleotide scale, and its validation by a sequence of ancient DNA. This rare possibility is offered by an ancient sequence of the late middle ages plague agent. It has been hypothesized to be ancestral to extant Yersinia pestis strains based on the pattern of nucleotide substitutions. But the dynamics of indels, duplications, insertion sequences and rearrangements has impacted all genomes much more than the substitution process, which makes the ancestral reconstruction task challenging.<br><br>RESULTS: We use a set of gene families from 13 Yersinia species, construct reconciled phylogenies for all of them, and determine gene orders in ancestral species. Gene trees integrate information from the sequence, the species tree and gene order. We reconstruct ancestral sequences for ancestral genic and intergenic regions, providing nearly a complete genome sequence for the ancestor, containing a chromosome and three plasmids.<br><br>CONCLUSION: The comparison of the ancestral and ancient sequences provides a unique opportunity to assess the quality of ancestral genome reconstruction methods. But the quality of the sequencing and assembly of the ancient sequence can also be questioned by this comparison.}, }
@article {pmid26449472, year = {2015}, author = {Gallego Llorente, M and Jones, ER and Eriksson, A and Siska, V and Arthur, KW and Arthur, JW and Curtis, MC and Stock, JT and Coltorti, M and Pieruccini, P and Stretton, S and Brock, F and Higham, T and Park, Y and Hofreiter, M and Bradley, DG and Bhak, J and Pinhasi, R and Manica, A}, title = {Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent.}, journal = {Science (New York, N.Y.)}, volume = {350}, number = {6262}, pages = {820-822}, doi = {10.1126/science.aad2879}, pmid = {26449472}, issn = {1095-9203}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Asia ; Biological Evolution ; Black People/*genetics ; Ethiopia ; Europe ; Genetic Variation ; *Genome, Human ; *Human Migration ; Humans ; Male ; }, abstract = {Characterizing genetic diversity in Africa is a crucial step for most analyses reconstructing the evolutionary history of anatomically modern humans. However, historic migrations from Eurasia into Africa have affected many contemporary populations, confounding inferences. Here, we present a 12.5× coverage ancient genome of an Ethiopian male ("Mota") who lived approximately 4500 years ago. We use this genome to demonstrate that the Eurasian backflow into Africa came from a population closely related to Early Neolithic farmers, who had colonized Europe 4000 years earlier. The extent of this backflow was much greater than previously reported, reaching all the way to Central, West, and Southern Africa, affecting even populations such as Yoruba and Mbuti, previously thought to be relatively unadmixed, who harbor 6 to 7% Eurasian ancestry.}, }
@article {pmid26444283, year = {2015}, author = {Greig, K and Boocock, J and Prost, S and Horsburgh, KA and Jacomb, C and Walter, R and Matisoo-Smith, E}, title = {Complete Mitochondrial Genomes of New Zealand's First Dogs.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0138536}, pmid = {26444283}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Geography/methods ; Haplotypes/genetics ; Indonesia ; Mitochondria/*genetics ; New Zealand ; Pacific Ocean ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Dogs accompanied people in their migrations across the Pacific Ocean and ultimately reached New Zealand, which is the southern-most point of their oceanic distribution, around the beginning of the fourteenth century AD. Previous ancient DNA analyses of mitochondrial control region sequences indicated the New Zealand dog population included two lineages. We sequenced complete mitochondrial genomes of fourteen dogs from the colonisation era archaeological site of Wairau Bar and found five closely-related haplotypes. The limited number of mitochondrial lineages present at Wairau Bar suggests that the founding population may have comprised only a few dogs; or that the arriving dogs were closely related. For populations such as that at Wairau Bar, which stemmed from relatively recent migration events, control region sequences have insufficient power to address questions about population structure and founding events. Sequencing mitogenomes provided the opportunity to observe sufficient diversity to discriminate between individuals that would otherwise be assigned the same haplotype and to clarify their relationships with each other. Our results also support the proposition that at least one dispersal of dogs into the Pacific was via a south-western route through Indonesia.}, }
@article {pmid26442080, year = {2015}, author = {Yoshida, K and Sasaki, E and Kamoun, S}, title = {Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {771}, pmid = {26442080}, issn = {1664-462X}, abstract = {The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.}, }
@article {pmid26424382, year = {2016}, author = {Chassaing, O and Desse-Berset, N and Hänni, C and Hughes, S and Berrebi, P}, title = {Phylogeography of the European sturgeon (Acipenser sturio): A critically endangered species.}, journal = {Molecular phylogenetics and evolution}, volume = {94}, number = {Pt A}, pages = {346-357}, doi = {10.1016/j.ympev.2015.09.020}, pmid = {26424382}, issn = {1095-9513}, mesh = {Animals ; Black Sea ; DNA, Mitochondrial/analysis/genetics ; *Endangered Species ; Fishes/*classification/*genetics ; France ; Genetic Variation ; Haplotypes ; Phylogeny ; Phylogeography ; }, abstract = {The European sturgeon (Acipenser sturio) was once a common species throughout Europe, but the sole remaining natural population presently inhabits the Gironde Estuary in France (Atlantic coast). The species was classified as 'Critically Endangered' in 1996, and the Gironde population is now on the verge of extinction. In this setting, and for the first time, we present the past phylogeographical features of this species throughout Europe along with an assessment of its former genetic diversity. This study was based on a molecular analysis (mtDNA CR sequencing) of 10 living specimens from the Gironde Estuary, 55 museum specimens that had been caught along 19th and 20th centuries, and 59 archaeological remains dating back to 260-5000years BP, from which mitochondrial DNA was extracted and amplified. Although discontinuous, the produced data provided a realistic image of the former structure of A. sturio in Europe. Reconstruction of the phylogenetic trees and haplotypes network led to the identification of several clades. The mitochondrial genetic diversity of this species was found to be much greater at the core (Iberian Peninsula, Mediterranean and Adriatic regions) than along the margins (Atlantic-Northern Europe, Black Sea) of its range. A series of hypotheses on the dates and causes of changes in the species' major structures are put forward on the basis of these data. Finally, competition with A. oxyrinchus, a sibling species whose presence in Northern Europe was recently reconsidered, is presented as a major factor in the evolution of this species.}, }
@article {pmid26418427, year = {2015}, author = {Ríos, L and Rosas, A and Estalrrich, A and García-Tabernero, A and Bastir, M and Huguet, R and Pastor, F and Sanchís-Gimeno, JA and de la Rasilla, M}, title = {Possible Further Evidence of Low Genetic Diversity in the El Sidrón (Asturias, Spain) Neandertal Group: Congenital Clefts of the Atlas.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0136550}, pmid = {26418427}, issn = {1932-6203}, mesh = {Animals ; Cervical Atlas/*abnormalities/pathology ; Fossils ; *Genetic Variation ; *Genetics, Population ; Neanderthals/*genetics ; Spain ; }, abstract = {We present here the first cases in Neandertals of congenital clefts of the arch of the atlas. Two atlases from El Sidrón, northern Spain, present respectively a defect of the posterior (frequency in extant modern human populations ranging from 0.73% to 3.84%), and anterior (frequency in extant modern human populations ranging from 0.087% to 0.1%) arch, a condition in most cases not associated with any clinical manifestation. The fact that two out of three observable atlases present a low frequency congenital condition, together with previously reported evidence of retained deciduous mandibular canine in two out of ten dentitions from El Sidrón, supports the previous observation based on genetic evidence that these Neandertals constituted a group with close genetic relations. Some have proposed for humans and other species that the presence of skeletal congenital conditions, although without clinical significance, could be used as a signal of endogamy or inbreeding. In the present case this interpretation would fit the general scenario of high incidence of rare conditions among Pleistocene humans and the specific scenariothat emerges from Neandertal paleogenetics, which points to long-term small and decreasing population size with reduced and isolated groups. Adverse environmental factors affecting early pregnancies would constitute an alternative, non-exclusive, explanation for a high incidence of congenital conditions. Further support or rejection of these interpretations will come from new genetic and skeletal evidence from Neandertal remains.}, }
@article {pmid26416323, year = {2015}, author = {Dong, Y and Li, C and Luan, F and Li, Z and Li, H and Cui, Y and Zhou, H and Malhi, RS}, title = {Low Mitochondrial DNA Diversity in an Ancient Population from China: Insight into Social Organization at the Fujia Site.}, journal = {Human biology}, volume = {87}, number = {1}, pages = {71-84}, doi = {10.13110/humanbiology.87.1.0071}, pmid = {26416323}, issn = {1534-6617}, mesh = {China/ethnology ; DNA, Mitochondrial/*analysis/history ; Female ; *Genetic Variation ; History, Ancient ; Humans ; Male ; Marriage/ethnology/history ; Sequence Analysis, DNA ; Social Dominance/*history ; }, abstract = {To gain insight into the social organization of a population associated with the Dawenkou period, we performed ancient DNA analysis of 18 individuals from human remains from the Fujia site in Shandong Province, China. Directly radiocarbon dated to 4800-4500 cal BP, the Fujia site is assumed to be associated with a transitional phase from matrilineal clans to patrilineal monogamous families. Our results reveal a low mitochondrial DNA diversity from the site and population. Combined with Y chromosome data, the pattern observed at the Fujia site is most consistent with a matrilineal community. The patterns also suggest that the bond of marriage was de-emphasized compared with the bonds of descent at Fujia.}, }
@article {pmid26416319, year = {2015}, author = {Nesheva, DV and Karachanak-Yankova, S and Lari, M and Yordanov, Y and Galabov, A and Caramelli, D and Toncheva, D}, title = {Mitochondrial DNA Suggests a Western Eurasian Origin for Ancient (Proto-) Bulgarians.}, journal = {Human biology}, volume = {87}, number = {1}, pages = {19-28}, doi = {10.13110/humanbiology.87.1.0019}, pmid = {26416319}, issn = {1534-6617}, mesh = {Bulgaria/ethnology ; DNA, Mitochondrial/*history ; Ethnicity/*genetics ; *Evolution, Molecular ; History, Medieval ; Humans ; White People/*genetics ; }, abstract = {Ancient (proto-) Bulgarians have long been thought of as a Turkic population. However, evidence found in the past three decades shows that this is not the case. Until now, this evidence has not included ancient mitochondrial DNA (mtDNA) analysis. To fill this void, we collected human remains from the 8th to the 10th century AD located in three necropolises in Bulgaria: Nojarevo (Silistra region) and Monastery of Mostich (Shumen region), both in northeastern Bulgaria, and Tuhovishte (Satovcha region) in southwestern Bulgaria. The phylogenetic analysis of 13 ancient DNA samples (extracted from teeth) identified 12 independent haplotypes, which we further classified into mtDNA haplogroups found in present-day European and western Eurasian populations. Our results suggest a western Eurasian matrilineal origin for proto-Bulgarians, as well as a genetic similarity between proto- and modern Bulgarians. Our future work will provide additional data that will further clarify proto-Bulgarian origins, thereby adding new clues to the current understanding of European genetic evolution.}, }
@article {pmid26402315, year = {2016}, author = {Birks, HJ and Birks, HH}, title = {How have studies of ancient DNA from sediments contributed to the reconstruction of Quaternary floras?.}, journal = {The New phytologist}, volume = {209}, number = {2}, pages = {499-506}, doi = {10.1111/nph.13657}, pmid = {26402315}, issn = {1469-8137}, mesh = {Animals ; DNA, Ancient/*analysis/*isolation &amp; purification ; DNA, Plant/genetics/*isolation &amp; purification ; Flowers/anatomy &amp; histology/*genetics ; *Fossils/anatomy &amp; histology ; Gastrointestinal Contents ; Geologic Sediments ; Lakes ; Paleontology/*methods ; Permafrost ; Pollen/genetics ; Soil ; }, abstract = {499 I. 499 II. 500 III. 500 IV. 500 V. 500 VI. 501 VII. 502 VIII. 504 504 References 505 SUMMARY: Ancient DNA (aDNA) from lake sediments, peats, permafrost soils, preserved megafaunal gut contents and coprolites has been used to reconstruct late-Quaternary floras. aDNA is either used alone for floristic reconstruction or compared with pollen and/or macrofossil results. In comparative studies, aDNA may complement pollen and macrofossil analyses by increasing the number of taxa found. We discuss the relative contributions of each fossil group to taxon richness and the number of unique taxa found, and situations in which aDNA has refined pollen identifications. Pressing problems in aDNA studies are contamination and ignorance about taphonomy (transportation, incorporation, and preservation in sediments). Progress requires that these problems are reduced to allow aDNA to reach its full potential contribution to reconstructions of Quaternary floras.}, }
@article {pmid26401836, year = {2016}, author = {Gamba, C and Hanghøj, K and Gaunitz, C and Alfarhan, AH and Alquraishi, SA and Al-Rasheid, KA and Bradley, DG and Orlando, L}, title = {Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {459-469}, doi = {10.1111/1755-0998.12470}, pmid = {26401836}, issn = {1755-0998}, mesh = {Alaska ; Bone and Bones ; DNA/*isolation &amp; purification ; *Fossils ; High-Throughput Nucleotide Sequencing/*methods ; Molecular Biology/*methods ; South America ; }, abstract = {The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms.}, }
@article {pmid26399147, year = {2015}, author = {Forshaw, R}, title = {Unlocking the past: The role of dental analysis in archaeology.}, journal = {Dental historian : Lindsay Club newsletter}, volume = {60}, number = {2}, pages = {51-62}, pmid = {26399147}, issn = {0958-6687}, mesh = {DNA/analysis ; Diet/history ; History, 15th Century ; History, Ancient ; History, Medieval ; Humans ; *Paleodontology ; Periodontal Diseases/history ; Tooth Diseases/*history ; }, abstract = {What can the study of ancient teeth tell us about the life style and dietary habits of our ancestors? Dental palaeopathology is particularly important as it can provide direct evidence of the type of diet an individual consumed during life. An analysis of the angle of tooth wear evident on the crown of the tooth can help to distinguish between early hunter-gatherers and later agriculturists, whilst microwear features on the occlusal surface can help to discern subtle dietary shifts. The distributions of stable isotopes in food webs make it possible to use them to reconstruct ancient diets as well as tracing the geographic origins and migrations of peoples. Plant microfossils have been isolated from calculus which can be identified using light microscopy. Teeth are particularly useful in ancient DNA studies due to the excellent preservation of biomaterials within the enamel shell of the tooth.}, }
@article {pmid26392548, year = {2015}, author = {Halffman, CM and Potter, BA and McKinney, HJ and Finney, BP and Rodrigues, AT and Yang, DY and Kemp, BM}, title = {Early human use of anadromous salmon in North America at 11,500 y ago.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {40}, pages = {12344-12348}, pmid = {26392548}, issn = {1091-6490}, mesh = {Alaska ; Animals ; Base Sequence ; Carbon Isotopes ; Cytochromes b/classification/genetics ; DNA/*chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; Fish Proteins/genetics ; *Fossils ; Geography ; Haplotypes ; Humans ; Molecular Sequence Data ; Nitrogen Isotopes ; Oncorhynchus keta/anatomy &amp; histology/*genetics ; Phylogeny ; Radiometric Dating/methods ; Rivers ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Spine/anatomy &amp; histology/*metabolism ; }, abstract = {Salmon represented a critical resource for prehistoric foragers along the North Pacific Rim, and continue to be economically and culturally important; however, the origins of salmon exploitation remain unresolved. Here we report 11,500-y-old salmon associated with a cooking hearth and human burials from the Upward Sun River Site, near the modern extreme edge of salmon habitat in central Alaska. This represents the earliest known human use of salmon in North America. Ancient DNA analyses establish the species as Oncorhynchus keta (chum salmon), and stable isotope analyses indicate anadromy, suggesting that salmon runs were established by at least the terminal Pleistocene. The early use of this resource has important implications for Paleoindian land use, economy, and expansions into northwest North America.}, }
@article {pmid26375610, year = {2016}, author = {Oh, CS and Lee, SD and Shin, KJ and Shin, DH}, title = {Effectiveness of Coupled Application of AmpFℓSTR Yfiler Kit and Reduced Size Y-chromosomal Short Tandem Repeat Analysis for Archeological Human Bones.}, journal = {Journal of forensic sciences}, volume = {61}, number = {2}, pages = {430-438}, doi = {10.1111/1556-4029.12950}, pmid = {26375610}, issn = {1556-4029}, mesh = {*Chromosomes, Human, Y ; *DNA Degradation, Necrotic ; DNA Fingerprinting/*methods ; DNA Primers ; Femur/*chemistry ; Humans ; Male ; *Microsatellite Repeats ; *Polymerase Chain Reaction ; }, abstract = {The AmpFℓSTR Yfiler PCR Amplification (Yfiler) kit continues to be improved for a better analytical efficiency in cases of highly degraded DNA. The authors endeavored to determine whether coupling of the Yfiler kit with supplemental multiplex amplification of some Y-STR loci is a more efficient analytical mode for poorly preserved human femurs (n = 15) discovered at Korean archeological sites. To reveal locus profiles not easily obtained by Yfiler analysis, custom-designed primers were adopted for the DYS390, DYS391, DYS392, DYS438, DYS439, and DYS635 loci. The success rate for 16 Y-STR locus profiles obtained from the 15 femurs was improved from 18.33% (in the use of Yfiler kit only) to 49.17% (the coupled use of Yfiler and custom-designed primers). In this study, the authors established that the custom-designed primers offer a markedly improved success rate for obtainment of Y-STR profiles from degraded aDNA not easily identified by sole use of the Yfiler assay.}, }
@article {pmid26374318, year = {2015}, author = {Fortes, GG and Paijmans, JL}, title = {Analysis of Whole Mitogenomes from Ancient Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1347}, number = {}, pages = {179-195}, doi = {10.1007/978-1-4939-2990-0_13}, pmid = {26374318}, issn = {1940-6029}, mesh = {*DNA, Mitochondrial ; *Genome, Mitochondrial ; Genomic Library ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Ancient mitochondrial DNA has been used in a wide variety of paleontological and archeological studies, ranging from population dynamics of extinct species to patterns of domestication. Most of these studies have traditionally been based on the analysis of short fragments from the mitochondrial control region, analyzed using PCR coupled with Sanger sequencing. With the introduction of high-throughput sequencing, as well as new enrichment technologies, the recovery of full mitochondrial genomes (mitogenomes) from ancient specimens has become significantly less complicated. Here we present a protocol to build ancient extracts into Illumina high-throughput sequencing libraries, and subsequent Agilent array-based capture to enrich for the desired mitogenome. Both are based on previously published protocols, with the introduction of several improvements aimed to increase the recovery of short DNA fragments, while keeping the cost and effort requirements low. This protocol was designed for enrichment of mitochondrial DNA in ancient or other degraded samples. However, the protocols can be easily adapted for using for building libraries for shotgun-sequencing of whole genomes, or enrichment of other genomic regions.}, }
@article {pmid26351665, year = {2015}, author = {Günther, T and Valdiosera, C and Malmström, H and Ureña, I and Rodriguez-Varela, R and Sverrisdóttir, &#xd3;O and Daskalaki, EA and Skoglund, P and Naidoo, T and Svensson, EM and Bermúdez de Castro, JM and Carbonell, E and Dunn, M and Storå, J and Iriarte, E and Arsuaga, JL and Carretero, JM and Götherström, A and Jakobsson, M}, title = {Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {38}, pages = {11917-11922}, pmid = {26351665}, issn = {1091-6490}, mesh = {DNA/*genetics ; Farmers/*history ; Gene Pool ; *Genome ; Geography ; History, Ancient ; Humans ; Population Dynamics ; Principal Component Analysis ; Sequence Analysis, DNA ; Spain ; }, abstract = {The consequences of the Neolithic transition in Europe--one of the most important cultural changes in human prehistory--is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter-gatherers. The proportion of hunter-gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.}, }
@article {pmid26345378, year = {2015}, author = {Ceruti, MC}, title = {Frozen Mummies from Andean Mountaintop Shrines: Bioarchaeology and Ethnohistory of Inca Human Sacrifice.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {439428}, pmid = {26345378}, issn = {2314-6141}, mesh = {Argentina ; Humans ; *Indians, South American ; *Mummies ; *Religion ; }, abstract = {This study will focus on frozen mummies of sacrificial victims from mounts Llullaillaco (6739 m), Quehuar (6130 m), El Toro (6160 m), and the Aconcagua massif. These finds provide bioarchaeological data from mountaintop sites that has been recovered in scientifically controlled excavations in the northwest of Argentina, which was once part of the southern province of the Inca Empire. Numerous interdisciplinary studies have been conducted on the Llullaillaco mummies, including radiological evaluations by conventional X-rays and CT scans, which provided information about condition and pathology of the bones and internal organ, as well as dental studies oriented to the estimation of the ages of the three children at the time of death. Ancient DNA studies and hair analysis were also performed in cooperation with the George Mason University, the University of Bradford, and the Laboratory of Biological Anthropology at the University of Copenhagen. Ethnohistorical sources reveal interesting aspects related to the commemorative, expiatory, propitiatory, and dedicatory aspects of human sacrifice performed under Inca rule. The selection of the victims along with the procedures followed during the performance of the capacocha ceremony will be discussed, based on the bioarchaeological evidences from frozen mummies and the accounts recorded by the Spanish chroniclers.}, }
@article {pmid26344900, year = {2015}, author = {Parson, W and Berger, C and Sänger, T and Lutz-Bonengel, S}, title = {Molecular genetic analysis on the remains of the Dark Countess: Revisiting the French Royal family.}, journal = {Forensic science international. Genetics}, volume = {19}, number = {}, pages = {252-254}, doi = {10.1016/j.fsigen.2015.08.006}, pmid = {26344900}, issn = {1878-0326}, mesh = {DNA/genetics ; DNA, Mitochondrial/*genetics ; Female ; *Forensic Anthropology ; France ; History, 19th Century ; Humans ; Male ; Pedigree ; Real-Time Polymerase Chain Reaction ; }, abstract = {The "Dark Counts" were a mysterious couple that appeared in the Thuringian village Eishausen in 1807. After living in self imposed solitude for 30 years the woman died and was buried under the name Sophia Botta. Her companion, who presented himself as Vavel de Versay, died in 1845 and was later identified as Leonardus Cornelius van der Valck, secretary of the Dutch embassy in Paris. Their lifestyle led to speculations that she was the true princess Marie Thérèse Charlotte of France, daughter of Louis XVI and Marie Antoinette. According to these speculations she was substituted by another young woman on a voyage from Paris to Vienna. Molecular genetic analyses were set out to test the remains attributed to the Dark Countess. Mitochondrial DNA testing brought concordant results determined in two forensic laboratories (Innsbruck, Austria and Freiburg, Germany) on parallel samples of the remains. The results were in exclusion to both, the mitochondrial lineage earlier reported for the French Royal family and the mitochondrial haplotype observed in a living descendant of the Royal family.}, }
@article {pmid26337550, year = {2015}, author = {Olalde, I and Schroeder, H and Sandoval-Velasco, M and Vinner, L and Lobón, I and Ramirez, O and Civit, S and García Borja, P and Salazar-García, DC and Talamo, S and María Fullola, J and Xavier Oms, F and Pedro, M and Martínez, P and Sanz, M and Daura, J and Zilhão, J and Marquès-Bonet, T and Gilbert, MT and Lalueza-Fox, C}, title = {A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures.}, journal = {Molecular biology and evolution}, volume = {32}, number = {12}, pages = {3132-3142}, pmid = {26337550}, issn = {1537-1719}, mesh = {Agriculture ; Base Sequence ; *Culture ; DNA, Mitochondrial/genetics ; *Emigration and Immigration ; Ethnicity/*genetics ; *Farmers ; Genetic Variation ; Genetics, Population ; *Genome, Human ; Haplotypes ; Humans ; Italy ; Mediterranean Region ; Sequence Analysis, DNA ; Spain ; White People ; }, abstract = {The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the Danube River into Central Europe. Although genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400-year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter-gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.}, }
@article {pmid26333404, year = {2015}, author = {Bajaj, D and Das, S and Parida, SK}, title = {CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea.}, journal = {Journal of biosciences}, volume = {40}, number = {3}, pages = {579-592}, pmid = {26333404}, issn = {0973-7138}, mesh = {Base Sequence ; Chromosome Mapping ; Cicer/*genetics ; Gene Expression Regulation, Plant/*genetics ; Genes, Plant/genetics ; Genetic Markers/genetics ; Genome, Plant/*genetics ; Microsatellite Repeats/*genetics ; Phylogeny ; Polymorphism, Genetic/genetics ; Quantitative Trait Loci/*genetics ; Sequence Alignment ; }, abstract = {The intra/inter-genomic comparative mapping-based phylogenetic footprinting identified 5 paralogous and 656 orthologous genome-wide CNMS markers in the upstream sequences of chickpea genes. These CNMS markers revealed a high-degree of gene-based syntenic relationship between chickpea and Medicago genomes while minimum between chickpea and Vitis genomes. The time of divergence and duplication estimated using CNMS markers highlight the expected phylogenetic relationships between chickpea and six dicot (legume) species as well as occurrence of ancient genome (approximately 53 Mya) with small-scale recent segmental (approximately 10 Mya) duplication events in chickpea. A wider level of functional molecular diversity (14 to 88 percent) and admixed population genetic structure was detected among desi, kabuli and wild genotypes by genic CNMS markers at a genome-wide scale suggesting their utility in large-scale genetic analysis in chickpea. The subfunctionalization at the cis-regulatory element region and TFBS (transcription factor binding site) motif levels in the upstream sequences of CNMS marker-associated orthologous genes than the paralogues was predominant. Functional constraint might have considerable effect on these CNMScontaining regulatory elements controlling consistent orthologous gene expression in dicots. A rapid subfunctionalization based on diverge differential expression of paralogous CNMS marker-associated genes particularly those that underwent recent small-scale segmental duplication events in chickpea was apparent. The differential regulation of expression and subfunctionalization potential of Ultra CNMS marker-associated genes suggest their utility in deciphering the complex gene regulatory function as well as identification and targeted mapping of potential genes/QTLs governing vital agronomic traits in chickpea. The gene-based CNMS markers with desirable inherent genetic attributes like higher degree of comparative genome mapping, functional genetic diversity and differential gene regulatory expression potential can significantly propel the genomics-assisted chickpea crop improvement.}, }
@article {pmid26329415, year = {2015}, author = {Dagli, N and Dagli, R and Baroudi, K and Tarakji, B}, title = {Oral Paleomicrobiology: Study of Ancient Oral Microbiome.}, journal = {The journal of contemporary dental practice}, volume = {16}, number = {7}, pages = {588-594}, doi = {10.5005/jp-journals-10024-1726}, pmid = {26329415}, issn = {1526-3711}, mesh = {DNA, Bacterial/history ; Dental Calculus/*history/microbiology ; Dental Pulp/microbiology ; History, Ancient ; Humans ; *Microbiota ; *Paleodontology ; Paleontology ; }, abstract = {BACKGROUND: Paleomicrobiology is a special branch of micropaleontology concerned with the study of bacterial fossils. We have used the term 'oral paleomicrobiology', as in this review we have focused on the ancient oral microflora. Recently, dental calculus and dental pulp have been identified as rich sources of ancient microbial DNA. Study of this ancient genetic material opens a new door to the ancient world. This review gives an overview of history of ancient DNA research, various techniques of analyzing ancient DNA in dental calculus and dental pulp, and the implications of the oral paleomicrobiology.<br><br>MATERIALS AND METHODS: A comprehensive literature search was performed in the following databases-pubmed, medline and google scholar for studies published before 10 April, 2015. The following keywords were used- 'ancient DNA', 'ancient oral flora, 'oral paleomicrobiology' and 'oral microbiome', '16S rRNA sequencing'. To obtain additional data, a manual search was performed using the reference lists of selected articles.<br><br>RESULT: As a result of literature search, 27 articles were found in pubmed, 12 in google scholar and one in medline. Eight more articles were selected from the reference list of selected articles.<br><br>CONCLUSION: The combination of microbiology and paleontology has brought a revolution in the study of human evolution and microbial communities. The naturally well-preserved samples of microbial DNA from dental pulp and microbial colonies trapped in dental calculus are a potential source of microbial genetic material, which will prove invaluable in resolving mysteries of the past. This may be a beginning of a new era of oral paleomicrobiology, which will contribute in our studies about prevention of disease by establishing symbiosis between human beings and their microbiome.}, }
@article {pmid26319403, year = {2015}, author = {Pontremoli, C and Mozzi, A and Forni, D and Cagliani, R and Pozzoli, U and Menozzi, G and Vertemara, J and Bresolin, N and Clerici, M and Sironi, M}, title = {Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2569-2584}, pmid = {26319403}, issn = {1759-6653}, mesh = {Adaptation, Biological/genetics ; Alleles ; Animals ; Carbohydrate Metabolism/genetics ; Dietary Carbohydrates/*metabolism ; *Evolution, Molecular ; Gorilla gorilla/genetics ; Humans ; Mammals/*genetics ; Microvilli/enzymology ; Pan troglodytes/genetics ; Protein Structure, Tertiary/genetics ; *Selection, Genetic ; Sucrase-Isomaltase Complex/genetics ; alpha-Glucosidases/genetics ; }, abstract = {Dietary shifts can drive molecular evolution in mammals and a major transition in human history, the agricultural revolution, favored carbohydrate consumption. We investigated the evolutionary history of nine genes encoding brush-border proteins involved in carbohydrate digestion/absorption. Results indicated widespread adaptive evolution in mammals, with several branches experiencing episodic selection, particularly strong in bats. Many positively selected sites map to functional protein regions (e.g., within glucosidase catalytic crevices), with parallel evolution at SI (sucrase-isomaltase) and MGAM (maltase-glucoamylase). In human populations, five genes were targeted by positive selection acting on noncoding variants within regulatory elements. Analysis of ancient DNA samples indicated that most derived alleles were already present in the Paleolithic. Positively selected variants at SLC2A5 (fructose transporter) were an exception and possibly spread following the domestication of specific fruit crops. We conclude that agriculture determined no major selective event at carbohydrate metabolism genes in humans, with implications for susceptibility to metabolic disorders.}, }
@article {pmid26310027, year = {2015}, author = {Druzhkova, AS and Vorobieva, NV and Trifonov, VA and Graphodatsky, AS}, title = {[Ancient DNA: Results and Prospects (the 30th Anniversary)].}, journal = {Genetika}, volume = {51}, number = {6}, pages = {627-643}, pmid = {26310027}, issn = {0016-6758}, mesh = {Animals ; DNA/*chemistry ; Evolution, Molecular ; *Fossils ; Humans ; Paleontology/*methods/trends ; Sequence Analysis, DNA/*methods/trends ; }, abstract = {Evolutionary genetics has reached a new level of research thanks to the opportunity to study the genomes of not only present-day but also of ancient organisms. The obtaining of reliable data when working with ancient DNA is possible only in the case of interdisciplinary collaboration between archaeologists, paleontologists, molecular geneticists, and bioinformaticians. Despite laborious and high-cost technologies, the results never cease to amaze and can not only fill the gaps in the knowledge of the evolutionary history of different species but can also review the existing ideas on population development and dynamics. In this review, we discuss the history of the development of investigative techniques in ancient DNA research and the most striking results of these studies, including the most recent achievements.}, }
@article {pmid26286644, year = {2016}, author = {Caliebe, A and Harder, M and Schuett, R and Krawczak, M and Nebel, A and von Wurmb-Schwark, N}, title = {The more the merrier? How a few SNPs predict pigmentation phenotypes in the Northern German population.}, journal = {European journal of human genetics : EJHG}, volume = {24}, number = {5}, pages = {739-747}, pmid = {26286644}, issn = {1476-5438}, mesh = {Adult ; Eye Color/*genetics ; Female ; Germany ; Guanine Nucleotide Exchange Factors/*genetics ; Hair Color/*genetics ; Humans ; Male ; Middle Aged ; *Phenotype ; *Polymorphism, Single Nucleotide ; Skin Pigmentation/*genetics ; Ubiquitin-Protein Ligases ; }, abstract = {Human pigmentation traits are of great interest to many research areas, from ancient DNA analysis to forensic science. We developed a gene-based predictive model for pigmentation phenotypes in a realistic target population for forensic case work from Northern Germany and compared our model with those brought forth by previous studies of genetically more heterogeneous populations. In doing so, we aimed at answering the following research questions: (1) do existing models allow good prediction of high-quality phenotypes in a genetically similar albeit more homogeneous population? (2) Would a model specifically set up for the more homogeneous population perform notably better than existing models? (3) Can the number of markers included in existing models be reduced without compromising their predictive capability in the more homogenous population? We investigated the association between eye, hair and skin colour and 12 candidate single-nucleotide polymorphisms (SNPs) from six genes. Our study comprised two samples of 300 and 100 individuals from Northern Germany. SNP rs12913832 in HERC2 was found to be strongly associated with blue eye colour (odds ratio=40.0, P<1.2 × 10(-4)) and to yield moderate predictive power (AUC: 77%; sensitivity: 90%, specificity: 63%, both at a 0.5 threshold for blue eye colour probability). SNP associations with hair and skin colour were weaker and genotypes less predictive. A comparison with two recently published sets of markers to predict eye and hair colour revealed that the consideration of additional SNPs with weak-to-moderate effect increased the predictive power for eye colour, but not for hair colour.}, }
@article {pmid26252497, year = {2015}, author = {Marcet-Houben, M and Gabaldón, T}, title = {Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage.}, journal = {PLoS biology}, volume = {13}, number = {8}, pages = {e1002220}, pmid = {26252497}, issn = {1545-7885}, mesh = {*Evolution, Molecular ; *Gene Duplication ; *Genome, Fungal ; *Hybridization, Genetic ; *Phylogeny ; Proteome/genetics ; Saccharomyces cerevisiae/*genetics ; }, abstract = {Whole-genome duplications have shaped the genomes of several vertebrate, plant, and fungal lineages. Earlier studies have focused on establishing when these events occurred and on elucidating their functional and evolutionary consequences, but we still lack sufficient understanding of how genome duplications first originated. We used phylogenomics to study the ancient genome duplication occurred in the yeast Saccharomyces cerevisiae lineage and found compelling evidence for the existence of a contemporaneous interspecies hybridization. We propose that the genome doubling was a direct consequence of this hybridization and that it served to provide stability to the recently formed allopolyploid. This scenario provides a mechanism for the origin of this ancient duplication and the lineage that originated from it and brings a new perspective to the interpretation of the origin and consequences of whole-genome duplications.}, }
@article {pmid26250679, year = {2015}, author = {Cooper, A and Turney, C and Hughen, KA and Brook, BW and McDonald, HG and Bradshaw, CJ}, title = {PALEOECOLOGY. Abrupt warming events drove Late Pleistocene Holarctic megafaunal turnover.}, journal = {Science (New York, N.Y.)}, volume = {349}, number = {6248}, pages = {602-606}, doi = {10.1126/science.aac4315}, pmid = {26250679}, issn = {1095-9203}, mesh = {Animals ; DNA/genetics/history/isolation &amp; purification ; *Extinction, Biological ; Fossils/history ; Global Warming/*history ; History, Ancient ; Humans ; Paleontology ; Population ; }, abstract = {The mechanisms of Late Pleistocene megafauna extinctions remain fiercely contested, with human impact or climate change cited as principal drivers. We compared ancient DNA and radiocarbon data from 31 detailed time series of regional megafaunal extinctions and replacements over the past 56,000 years with standard and new combined records of Northern Hemisphere climate in the Late Pleistocene. Unexpectedly, rapid climate changes associated with interstadial warming events are strongly associated with the regional replacement or extinction of major genetic clades or species of megafauna. The presence of many cryptic biotic transitions before the Pleistocene/Holocene boundary revealed by ancient DNA confirms the importance of climate change in megafaunal population extinctions and suggests that metapopulation structures necessary to survive such repeated and rapid climatic shifts were susceptible to human impacts.}, }
@article {pmid26250052, year = {2015}, author = {Huynen, L and Lambert, DM}, title = {A Concentrated Hydrochloric Acid-based Method for Complete Recovery of DNA from Bone.}, journal = {Journal of forensic sciences}, volume = {60}, number = {6}, pages = {1553-1557}, doi = {10.1111/1556-4029.12846}, pmid = {26250052}, issn = {1556-4029}, mesh = {Animals ; Birds/genetics ; Bone and Bones/*chemistry ; DNA/*isolation &amp; purification ; Forensic Genetics/*methods ; Hydrochloric Acid/*chemistry ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Silicon Dioxide ; }, abstract = {The successful extraction of DNA from historical or ancient animal bone is important for the analysis of discriminating genetic markers. Methods used currently rely on the digestion of bone with EDTA and proteinase K, followed by purification with phenol/chloroform and silica bed binding. We have developed a simple concentrated hydrochloric acid-based method that precludes the use of phenol/chloroform purification and can lead to a several-fold increase in DNA yield when compared to other commonly used methods. Concentrated hydrochloric acid was shown to dissolve most of the undigested bone and allowed the efficient recovery of DNA fragments <100 bases in length. This method should prove useful for the recovery of DNAs from highly degraded animal bone, such as that found in historical or ancient samples.}, }
@article {pmid26227633, year = {2015}, author = {Rawlence, NJ and Kennedy, M and Anderson, CN and Prost, S and Till, CE and Smith, IW and Scofield, RP and Tennyson, AJ and Hamel, J and Lalas, C and Matisoo-Smith, EA and Waters, JM}, title = {Geographically contrasting biodiversity reductions in a widespread New Zealand seabird.}, journal = {Molecular ecology}, volume = {24}, number = {18}, pages = {4605-4616}, doi = {10.1111/mec.13338}, pmid = {26227633}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; Birds/*genetics ; DNA, Mitochondrial/genetics ; Extinction, Biological ; Fossils ; *Genetic Variation ; Humans ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; New Zealand ; *Phylogeny ; Phylogeography ; Population Dynamics ; Radiometric Dating ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; }, abstract = {Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human-driven faunal declines.}, }
@article {pmid26216337, year = {2015}, author = {Samaniego Castruita, JA and Zepeda Mendoza, ML and Barnett, R and Wales, N and Gilbert, MT}, title = {Odintifier--A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing.}, journal = {BMC bioinformatics}, volume = {16}, number = {1}, pages = {232}, pmid = {26216337}, issn = {1471-2105}, mesh = {Ajuga/genetics/metabolism ; Algorithms ; Animals ; Computational Biology/*methods ; DNA/analysis/metabolism ; Genome, Chloroplast ; Genome, Mitochondrial ; Genomics ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Lions/genetics/metabolism ; Mitochondria/*genetics ; Plastids/*genetics ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Vitis/genetics/metabolism ; }, abstract = {BACKGROUND: Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny. The extent of the occurrence of these organellar-derived inserted sequences (odins) is still unknown, but if not accounted for in genomic and phylogenetic studies, they can be a source of error. However, if correctly identified, these inserted sequences can be used for evolutionary and comparative genomic studies. Although such insertions can be detected using various laboratory and bioinformatic strategies, there is currently no straightforward way to apply them as a standard organellar genome assembly on next-generation sequencing data. Furthermore, most current methods for identification of such insertions are unsuitable for use on non-model organisms or ancient DNA datasets.<br><br>RESULTS: We present a bioinformatic method that uses phasing algorithms to reconstruct both source and inserted organelle sequences. The method was tested in different shotgun and organellar-enriched DNA high-throughput sequencing (HTS) datasets from ancient and modern samples. Specifically, we used datasets from lions (Panthera leo ssp. and Panthera leo leo) to characterize insertions from mitochondrial origin, and from common grapevine (Vitis vinifera) and bugle (Ajuga reptans) to characterize insertions derived from plastid genomes. Comparison of the results against other available organelle genome assembly methods demonstrated that our new method provides an improvement in the sequence assembly.<br><br>CONCLUSION: Using datasets from a wide range of species and different levels of complexity we showed that our novel bioinformatic method based on phasing algorithms can be used to achieve the next two goals: i) reference-guided assembly of chloroplast/mitochondrial genomes from HTS data and ii) identification and simultaneous assembly of odins. This method represents the first application of haplotype phasing for automatic detection of odins and reference-based organellar genome assembly.}, }
@article {pmid26213269, year = {2015}, author = {de la Fuente, C and Galimany, J and Kemp, BM and Judd, K and Reyes, O and Moraga, M}, title = {Ancient marine hunter-gatherers from Patagonia and Tierra Del Fuego: Diversity and differentiation using uniparentally inherited genetic markers.}, journal = {American journal of physical anthropology}, volume = {158}, number = {4}, pages = {719-729}, doi = {10.1002/ajpa.22815}, pmid = {26213269}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Archaeology ; Argentina ; Chile ; Female ; Genetic Markers/*genetics ; Haplotypes ; Humans ; Indians, South American/*genetics ; Male ; }, abstract = {OBJECTIVES: The human population history from Patagonia and Tierra del Fuego has been of great interest in the context of the American peopling. Different sources of evidence have contributed to the characterization of the local populations, but some main questions about their history remain unsolved. Among the native populations, two marine hunter-gatherers groups inhabited the Patagonian channels below the 478S: Kawéskar and Yámana. Regardless of their geographical proximity and cultural resemblance, their languages were mutually unintelligible. In this study we aim to evaluate the genetic diversity of uniparental genetic markers in both groups and to test if there is a high genetic differentiation between them, mirroring their linguistic differences.<br><br>MATERIAL AND METHODS: Ancient DNA was extracted from 37 samples from both populations. We compared their genetic variability of their mitochondrial lineages and Y-STR as well as with other modern native populations from the area and further north.<br><br>RESULTS AND DISCUSSION: We observed an important differentiation in their maternal lineages: while Kaw&#xe9;skar shows a high frequency of D (80%), Y&#xe1;mana shows a high frequency of C (90%). The analysis of paternal lineages reveals the presence of only Q1a2a1a1 and little variation was found between individuals. Both groups show very low levels of genetic diversity compared with modern populations. We also notice shared and unique mitochondrial DNA variants between modern and ancient samples of Kaw&#xe9;skar and Y&#xe1;mana.}, }
@article {pmid26210385, year = {2015}, author = {Witas, HW and Donoghue, HD and Kubiak, D and Lewandowska, M and Gładykowska-Rzeczycka, JJ}, title = {Molecular studies on ancient M. tuberculosis and M. leprae: methods of pathogen and host DNA analysis.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {34}, number = {9}, pages = {1733-1749}, pmid = {26210385}, issn = {1435-4373}, mesh = {Archaeology ; Biological Evolution ; DNA, Bacterial/genetics ; Europe ; Genetic Predisposition to Disease ; Genome, Bacterial/*genetics ; Humans ; Leprosy/*diagnosis/microbiology ; Molecular Typing/methods ; Mycobacterium leprae/*genetics ; Mycobacterium tuberculosis/*genetics ; Tuberculosis/*diagnosis/microbiology ; }, abstract = {Humans have evolved alongside infectious diseases for millennia. Despite the efforts to reduce their incidence, infectious diseases still pose a tremendous threat to the world population. Fast development of molecular techniques and increasing risk of new epidemics have resulted in several studies that look to the past in order to investigate the origin and evolution of infectious diseases. Tuberculosis and leprosy have become frequent targets of such studies, owing to the persistence of their molecular biomarkers in ancient material and the characteristic skeletal lesions each disease may cause. This review examines the molecular methods used to screen for the presence of M. tuberculosis and M. leprae ancient DNA (aDNA) and their differentiation in ancient human remains. Examples of recent studies, mainly from Europe, that employ the newest techniques of molecular analysis are also described. Moreover, we present a specific approach based on assessing the likely immunological profile of historic populations, in order to further elucidate the influence of M. tuberculosis and M. leprae on historical human populations.}, }
@article {pmid26200455, year = {2015}, author = {Álvarez-Sandoval, BA and Manzanilla, LR and González-Ruiz, M and Malgosa, A and Montiel, R}, title = {Genetic Evidence Supports the Multiethnic Character of Teopancazco, a Neighborhood Center of Teotihuacan, Mexico (AD 200-600).}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132371}, pmid = {26200455}, issn = {1932-6203}, mesh = {Adult ; Anthropology, Cultural/*methods ; DNA, Mitochondrial/*analysis ; Female ; Genetic Variation ; Genetics, Population ; Human Migration ; Humans ; Indians, North American/*ethnology/*genetics ; Male ; Mexico/ethnology ; Phylogeography ; Principal Component Analysis ; Young Adult ; }, abstract = {Multiethnicity in Teopancazco, Teotihuacan, is supported by foreign individuals found in the neighborhood center as well as by the diversity observed in funerary rituals at the site. Studies of both stable and strontium isotopes as well as paleodietary analysis, suggest that the population of Teopancazco was composed by three population groups: people from Teotihuacan, people from nearby sites (Tlaxcala-Hidalgo-Puebla), and people from afar, including the coastal plains. In an attempt to understand the genetic dynamics in Teopancazco we conducted an ancient DNA (aDNA) analysis based on mtDNA. Our results show that the level of genetic diversity is consistent with the multiethnicity phenomenon at the neighborhood center. Levels of genetic diversity at different time periods of Teopancazco's history show that multiethnicity was evident since the beginning and lasted until the collapse of the neighborhood center. However, a PCA and a Neighbor-Joining tree suggested the presence of a genetically differentiated group (buried at the Transitional phase) compared to the population from the initial phase (Tlamimilolpa) as well as the population from the final phase (Xolalpan) of the history of Teopancazco. Genetic studies showed no differences in genetic diversity between males and females in the adult population of Teopancazco, this data along with ample archaeological evidence, suggest a neolocal post-marital pattern of residence in Teopancazco. Nevertheless, genetic analyses on the infant population showed that the males are significantly more heterogeneous than the females suggesting a possible differential role in cultural practices by sex in the infant sector. Regarding interpopulation analysis, we found similar indices of genetic diversity between Teopancazco and heterogeneous native groups, which support the multiethnic character of Teopancazco. Finally, our data showed a close genetic relationship between Teopancazco and populations from the "Teotihuacan corridor" and from Oaxaca and the Maya region, in agreement with previous archaeological evidence.}, }
@article {pmid26170006, year = {2015}, author = {Guselnikov, SV and Grayfer, L and De Jesús Andino, F and Rogozin, IB and Robert, J and Taranin, AV}, title = {Retention of duplicated ITAM-containing transmembrane signaling subunits in the tetraploid amphibian species Xenopus laevis.}, journal = {Developmental and comparative immunology}, volume = {53}, number = {1}, pages = {158-168}, pmid = {26170006}, issn = {1879-0089}, support = {R24 AI059830/AI/NIAID NIH HHS/United States ; Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; R24-AI-059830/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Evolution, Molecular ; HEK293 Cells ; Humans ; Immunoreceptor Tyrosine-Based Activation Motif/*genetics ; Molecular Sequence Data ; Receptors, Antigen, T-Cell, alpha-beta/*genetics/immunology ; Receptors, IgG/*genetics/immunology ; Sequence Alignment ; Signal Transduction/genetics/*immunology ; *Tetraploidy ; Xenopus laevis ; }, abstract = {The ITAM-bearing transmembrane signaling subunits (TSS) are indispensable components of activating leukocyte receptor complexes. The TSS-encoding genes map to paralogous chromosomal regions, which are thought to arise from ancient genome tetraploidization(s). To assess a possible role of tetraploidization in the TSS evolution, we studied TSS and other functionally linked genes in the amphibian species Xenopus laevis whose genome was duplicated about 40 MYR ago. We found that X. laevis has retained a duplicated set of sixteen TSS genes, all except one being transcribed. Furthermore, duplicated TCRα loci and genes encoding TSS-coupling protein kinases have also been retained. No clear evidence for functional divergence of the TSS paralogs was obtained from gene expression and sequence analyses. We suggest that the main factor of maintenance of duplicated TSS genes in X. laevis was a protein dosage effect and that this effect might have facilitated the TSS set expansion in early vertebrates.}, }
@article {pmid26169594, year = {2015}, author = {Hofman, CA and Rick, TC and Fleischer, RC and Maldonado, JE}, title = {Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene.}, journal = {Trends in ecology &amp; evolution}, volume = {30}, number = {9}, pages = {540-549}, doi = {10.1016/j.tree.2015.06.008}, pmid = {26169594}, issn = {1872-8383}, mesh = {Animals ; Archaeology ; Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; Genomics ; Human Activities ; Humans ; Plants/genetics ; }, abstract = {There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.}, }
@article {pmid26159228, year = {2015}, author = {Brandão, MM and Spoladore, L and Faria, LC and Rocha, AS and Silva-Filho, MC and Palazzo, R}, title = {Ancient DNA sequence revealed by error-correcting codes.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {12051}, pmid = {26159228}, issn = {2045-2322}, mesh = {Algorithms ; Arabidopsis/enzymology/genetics ; Bayes Theorem ; Codon ; DNA/*analysis/chemistry ; Evolution, Molecular ; Malate Dehydrogenase/classification/genetics ; *Models, Genetic ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.}, }
@article {pmid26156780, year = {2015}, author = {Mouttham, N and Klunk, J and Kuch, M and Fourney, R and Poinar, H}, title = {Surveying the repair of ancient DNA from bones via high-throughput sequencing.}, journal = {BioTechniques}, volume = {59}, number = {1}, pages = {19-25}, doi = {10.2144/000114307}, pmid = {26156780}, issn = {1940-9818}, mesh = {Animals ; Bone and Bones/*chemistry ; DNA/*chemistry ; *DNA Damage ; DNA Repair Enzymes/*chemistry ; Fossils ; High-Throughput Nucleotide Sequencing/*methods ; Mammoths/*genetics ; }, abstract = {DNA damage in the form of abasic sites, chemically altered nucleotides, and strand fragmentation is the foremost limitation in obtaining genetic information from many ancient samples. Upon cell death, DNA continues to endure various chemical attacks such as hydrolysis and oxidation, but repair pathways found in vivo no longer operate. By incubating degraded DNA with specific enzyme combinations adopted from these pathways, it is possible to reverse some of the post-mortem nucleic acid damage prior to downstream analyses such as library preparation, targeted enrichment, and high-throughput sequencing. Here, we evaluate the performance of two available repair protocols on previously characterized DNA extracts from four mammoths. Both methods use endonucleases and glycosylases along with a DNA polymerase-ligase combination. PreCR Repair Mix increases the number of molecules converted to sequencing libraries, leading to an increase in endogenous content and a decrease in cytosine-to-thymine transitions due to cytosine deamination. However, the effects of Nelson Repair Mix on repair of DNA damage remain inconclusive.}, }
@article {pmid26153924, year = {2015}, author = {Ferrando, A and Manunza, A and Jordana, J and Capote, J and Pons, A and Pais, J and Delgado, T and Atoche, P and Cabrera, B and Martínez, A and Landi, V and Delgado, JV and Argüello, A and Vidal, O and Lalueza-Fox, C and Ramírez, O and Amills, M}, title = {A mitochondrial analysis reveals distinct founder effect signatures in Canarian and Balearic goats.}, journal = {Animal genetics}, volume = {46}, number = {4}, pages = {452-456}, doi = {10.1111/age.12302}, pmid = {26153924}, issn = {1365-2052}, mesh = {Animals ; Animals, Domestic/genetics ; DNA, Mitochondrial/*genetics ; *Founder Effect ; Gene Pool ; Genetic Drift ; *Genetics, Population ; Goats/*genetics ; Haplotypes ; Islands ; Molecular Sequence Data ; Sequence Analysis, DNA ; Spain ; }, abstract = {In the course of human migrations, domestic animals often have been translocated to islands with the aim of assuring food availability. These founder events are expected to leave a genetic footprint that may be recognised nowadays. Herewith, we have examined the mitochondrial diversity of goat populations living in the Canarian and Balearic archipelagos. Median-joining network analysis produced very distinct network topologies for these two populations. Indeed, a majority of Canarian goats shared a single ancestral haplotype that segregated in all sampled islands, suggesting a single founder effect followed by a stepping-stone pattern of diffusion. This haplotype also was present in samples collected from archaeological assemblies at Gran Canaria and Lanzarote, making evident its widespread distribution in ancient times. In stark contrast, goats from Majorca and Ibiza did not share any mitochondrial haplotypes, indicating the occurrence of two independent founder events. Furthermore, in Majorcan goats, we detected the segregation of the mitochondrial G haplogroup that has only been identified in goats from Egypt, Iran and Turkey. This finding suggests the translocation of Asian and/or African goats to Majorca, possibly as a consequence of the Phoenician and Carthaginian colonisations of this island.}, }
@article {pmid26141130, year = {2015}, author = {Paris, HS}, title = {Origin and emergence of the sweet dessert watermelon, Citrullus lanatus.}, journal = {Annals of botany}, volume = {116}, number = {2}, pages = {133-148}, pmid = {26141130}, issn = {1095-8290}, mesh = {Africa ; Citrullus/classification/*physiology ; Europe ; Fruit ; Israel ; Terminology as Topic ; }, abstract = {BACKGROUND AND AIMS: Watermelons, Citrullus species (Cucurbitaceae), are native to Africa and have been cultivated since ancient times. The fruit flesh of wild watermelons is watery, but typically hard-textured, pale-coloured and bland or bitter. The familiar sweet dessert watermelons, C. lanatus, featuring non-bitter, tender, well-coloured flesh, have a narrow genetic base, suggesting that they originated from a series of selection events in a single ancestral population. The objective of the present investigation was to determine where dessert watermelons originated and the time frame during which sweet dessert watermelons emerged.<br><br>KEY FINDINGS: Archaeological remains of watermelons, mostly seeds, that date from 5000 years ago have been found in northeastern Africa. An image of a large, striped, oblong fruit on a tray has been found in an Egyptian tomb that dates to at least 4000 years ago. The Greek word pepon, Latin pepo and Hebrew avattiah of the first centuries CE were used for the same large, thick-rinded, wet fruit which, evidently, was the watermelon. Hebrew literature from the end of the second century CE and Latin literature from the beginning of the sixth century CE present watermelons together with three sweet fruits: figs, table grapes and pomegranates. Wild and primitive watermelons have been observed repeatedly in Sudan and neighbouring countries of northeastern Africa.<br><br>CONCLUSIONS: The diverse evidence, combined, indicates that northeastern Africa is the centre of origin of the dessert watermelon, that watermelons were domesticated for water and food there over 4000 years ago, and that sweet dessert watermelons emerged in Mediterranean lands by approximately 2000 years ago. Next-generation ancient-DNA sequencing and state-of-the-art genomic analysis offer opportunities to rigorously assess the relationships among ancient and living wild and primitive watermelons from northeastern Africa, modern sweet dessert watermelons and other Citrullus taxa.}, }
@article {pmid26137993, year = {2016}, author = {Jones, MR and Good, JM}, title = {Targeted capture in evolutionary and ecological genomics.}, journal = {Molecular ecology}, volume = {25}, number = {1}, pages = {185-202}, pmid = {26137993}, issn = {1365-294X}, support = {R01 GM098536/GM/NIGMS NIH HHS/United States ; R01 HD073439/HD/NICHD NIH HHS/United States ; R01GM098536/GM/NIGMS NIH HHS/United States ; R01HD73439/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Chromosome Mapping ; Ecology/*methods ; *Genetics, Population ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Phenotype ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome-partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole-genome sequencing in ecological and evolutionary genomic studies. High-throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome-partitioning approaches in the light of the increasing accessibility of whole-genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole-genome sequencing.}, }
@article {pmid26134828, year = {2015}, author = {Seguin-Orlando, A and Gamba, C and Sarkissian, C and Ermini, L and Louvel, G and Boulygina, E and Sokolov, A and Nedoluzhko, A and Lorenzen, ED and Lopez, P and McDonald, HG and Scott, E and Tikhonov, A and Stafford, TW and Alfarhan, AH and Alquraishi, SA and Al-Rasheid, KAS and Shapiro, B and Willerslev, E and Prokhortchouk, E and Orlando, L}, title = {Pros and cons of methylation-based enrichment methods for ancient DNA.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {11826}, pmid = {26134828}, issn = {2045-2322}, mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Methylation/*genetics ; Fossils ; Mammoths/*genetics ; Ursidae/*genetics ; }, abstract = {The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.}, }
@article {pmid26122166, year = {2015}, author = {Möst, M and Oexle, S and Marková, S and Aidukaite, D and Baumgartner, L and Stich, HB and Wessels, M and Martin-Creuzburg, D and Spaak, P}, title = {Population genetic dynamics of an invasion reconstructed from the sediment egg bank.}, journal = {Molecular ecology}, volume = {24}, number = {16}, pages = {4074-4093}, doi = {10.1111/mec.13298}, pmid = {26122166}, issn = {1365-294X}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Daphnia/*genetics ; Gene Frequency ; Genetic Markers ; Genetic Variation ; *Genetics, Population ; Genotype ; Geologic Sediments ; Germany ; Inbreeding ; Introduced Species ; Lakes ; Microsatellite Repeats ; Models, Genetic ; Molecular Sequence Data ; *Ovum ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Switzerland ; }, abstract = {Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as 'European D. pulicaria' originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations.}, }
@article {pmid26117294, year = {2015}, author = {Choimet, M and Tourrette, A and Drouet, C}, title = {Adsorption of nucleotides on biomimetic apatite: The case of cytidine 5' monophosphate (CMP).}, journal = {Journal of colloid and interface science}, volume = {456}, number = {}, pages = {132-137}, doi = {10.1016/j.jcis.2015.06.021}, pmid = {26117294}, issn = {1095-7103}, mesh = {Adsorption ; Animals ; Apatites/*chemistry ; Biomimetic Materials/chemistry ; *Biomimetics ; Bone and Bones/chemistry ; Calcification, Physiologic ; Cytidine Monophosphate/*chemistry ; DNA/chemistry ; Dentin ; Durapatite/chemistry ; Humans ; Kinetics ; Male ; Middle Aged ; Nanoparticles/chemistry ; Nucleotides/*chemistry ; Phosphates ; RNA/chemistry ; Rats ; Time Factors ; X-Ray Diffraction ; }, abstract = {The chemical interaction between DNA macromolecules and hard tissues in vertebrate is of foremost importance in paleogenetics, as bones and teeth represent a major substrate for the genetic material after cell death. Recently, the empirical hypothesis of DNA "protection" over time thanks to its adsorption on hard tissues was revisited from a physico-chemical viewpoint. In particular, the existence of a strong interaction between phosphate groups of DNA backbone and the surface of apatite nanocrystals (mimicking bone/dentin mineral) was evidenced on an experimental basis. In the field of nanomedicine, DNA or RNA can be used for gene transport into cells, and apatite nanocarriers then appear promising. In order to shed some more light on interactions between DNA molecules and apatite, the present study focuses on the adsorption of a "model" nucleotide, cytidine 5' monophosphate (CMP), on a carbonated biomimetic apatite sample. The follow-up of CMP kinetics of adsorption pointed out the rapidity of interaction with stabilization reached within few minutes. The adsorption isotherm could be realistically fitted to the Sips model (Langmuir-Freundlich) suggesting the influence of surface heterogeneities and adsorption cooperativity in the adsorption process. The desorption study pointed out the reversible character of CMP adsorption on biomimetic apatite. This contribution is intended to prove helpful in view of better apprehending the molecular interaction of DNA fragments and apatite compounds, independently of the application domain, such as bone diagenesis or nanomedicine. This study may also appear informative for researchers interested in the origins of life on Earth and the occurrence and behavior of primitive biomolecules.}, }
@article {pmid26086078, year = {2015}, author = {Pinhasi, R and Fernandes, D and Sirak, K and Novak, M and Connell, S and Alpaslan-Roodenberg, S and Gerritsen, F and Moiseyev, V and Gromov, A and Raczky, P and Anders, A and Pietrusewsky, M and Rollefson, G and Jovanovic, M and Trinhhoang, H and Bar-Oz, G and Oxenham, M and Matsumura, H and Hofreiter, M}, title = {Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129102}, pmid = {26086078}, issn = {1932-6203}, mesh = {Archaeology ; DNA/*isolation &amp; purification ; DNA Damage ; Ear, Inner/*chemistry ; *Fossils ; Humans ; Petrous Bone/*chemistry ; Sequence Analysis, DNA/methods ; }, abstract = {The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (~ 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.}, }
@article {pmid26083419, year = {2015}, author = {Marsolier-Kergoat, MC and Palacio, P and Berthonaud, V and Maksud, F and Stafford, T and Bégouën, R and Elalouf, JM}, title = {Hunting the Extinct Steppe Bison (Bison priscus) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128267}, pmid = {26083419}, issn = {1932-6203}, mesh = {Animals ; Bison/classification/*genetics ; Bone and Bones/metabolism ; Carbon Radioisotopes/chemistry ; Caves ; DNA, Mitochondrial/analysis/genetics ; Extinction, Biological ; Fossils ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Despite the abundance of fossil remains for the extinct steppe bison (Bison priscus), an animal that was painted and engraved in numerous European Paleolithic caves, a complete mitochondrial genome sequence has never been obtained for this species. In the present study we collected bone samples from a sector of the Trois-Frères Paleolithic cave (Ariège, France) that formerly functioned as a pitfall and was sealed before the end of the Pleistocene. Screening the DNA content of the samples collected from the ground surface revealed their contamination by Bos DNA. However, a 19,000-year-old rib collected on a rock apart the pathway delineated for modern visitors was devoid of such contaminants and reproducibly yielded Bison priscus DNA. High-throughput shotgun sequencing combined with conventional PCR analysis of the rib DNA extract enabled to reconstruct a complete mitochondrial genome sequence of 16,318 bp for the extinct steppe bison with a 10.4-fold coverage. Phylogenetic analyses robustly established the position of the Bison priscus mitochondrial genome as basal to the clade delineated by the genomes of the modern American Bison bison. The extinct steppe bison sequence, which exhibits 93 specific polymorphisms as compared to the published Bison bison mitochondrial genomes, provides an additional resource for the study of Bovinae specimens. Moreover this study of ancient DNA delineates a new research pathway for the analysis of the Magdalenian Trois-Frères cave.}, }
@article {pmid26081994, year = {2015}, author = {Damgaard, PB and Margaryan, A and Schroeder, H and Orlando, L and Willerslev, E and Allentoft, ME}, title = {Improving access to endogenous DNA in ancient bones and teeth.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {11184}, pmid = {26081994}, issn = {2045-2322}, mesh = {Archaeology ; *Bone and Bones ; *DNA, Mitochondrial ; Fossils ; Humans ; *Tooth ; }, abstract = {Poor DNA preservation is the most limiting factor in ancient genomic research. In the majority of ancient bones and teeth, endogenous DNA molecules represent a minor fraction of the whole DNA extract, rendering shot-gun sequencing inefficient for obtaining genomic data. Based on ancient human bone samples from temperate and tropical environments, we show that an EDTA-based enzymatic 'pre-digestion' of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we observe an asymptotic increase in endogenous DNA content, with a 2.7-fold average increase reached at 1 hour. We repeat the experiment using a brief pre-digestion (15 or 30 mins) on 21 ancient bones and teeth from a variety of archaeological contexts and observe an improvement in 16 of these. We here advocate the implementation of a brief pre-digestion step as a standard procedure in ancient DNA extractions. Finally, we demonstrate on 14 ancient teeth that by targeting the outer layer of the roots we obtain up to 14 times more endogenous DNA than when using the inner dentine. Our presented methods are likely to increase the proportion of ancient samples that are suitable for genome-scale characterization.}, }
@article {pmid26062506, year = {2015}, author = {Novembre, J}, title = {Human evolution: ancient DNA steps into the language debate.}, journal = {Nature}, volume = {522}, number = {7555}, pages = {164-165}, pmid = {26062506}, issn = {1476-4687}, mesh = {Asian People/*genetics ; Cultural Evolution/*history ; *Fossils ; Genome, Human/*genetics ; *Genomics ; *Grassland ; Human Migration/*history ; Humans ; Language/*history ; Male ; White People/*genetics ; }, }
@article {pmid26057710, year = {2015}, author = {Muñoz-Moreno, R and Galindo, I and Cuesta-Geijo, M&#xc1; and Barrado-Gil, L and Alonso, C}, title = {Host cell targets for African swine fever virus.}, journal = {Virus research}, volume = {209}, number = {}, pages = {118-127}, doi = {10.1016/j.virusres.2015.05.026}, pmid = {26057710}, issn = {1872-7492}, mesh = {African Swine Fever Virus/*physiology ; Animals ; *Host-Pathogen Interactions ; Swine ; *Virus Replication ; }, abstract = {Viruses are strict intracellular pathogens that require the cellular environment to complete a successful infection. Among them, African swine fever virus (ASFV) is an evolutionary ancient DNA virus, endemic in Africa, which is nowadays causing an emergent disease in Europe with a potential high economic impact in the pig industry. It is well known that host-cell components are critical crossroads mapping the virus path for a productive infection, some of them at the endocytic pathway. Considering that ASFV infectious cycle strongly relies in several factors from the host cell, the study of virus-host interactions remains crucial as they will reveal the obstacles, routes and tracks, hints and the target waypoint in the virus journey to destination.}, }
@article {pmid26055157, year = {2015}, author = {Orlando, L and Gilbert, MT and Willerslev, E}, title = {Reconstructing ancient genomes and epigenomes.}, journal = {Nature reviews. Genetics}, volume = {16}, number = {7}, pages = {395-408}, pmid = {26055157}, issn = {1471-0064}, mesh = {Animals ; DNA/*genetics/*history ; Epigenomics/*methods/trends ; Genomics/*methods/trends ; High-Throughput Nucleotide Sequencing/*methods/trends ; History, Ancient ; Humans ; }, abstract = {Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.}, }
@article {pmid26053041, year = {2015}, author = {Hervella, M and Rotea, M and Izagirre, N and Constantinescu, M and Alonso, S and Ioana, M and Lazăr, C and Ridiche, F and Soficaru, AD and Netea, MG and de-la-Rua, C}, title = {Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128810}, pmid = {26053041}, issn = {1932-6203}, mesh = {DNA, Mitochondrial/*genetics ; *Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes/genetics ; Humans ; Multivariate Analysis ; Principal Component Analysis ; Romania ; Time Factors ; }, abstract = {The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations.}, }
@article {pmid26050523, year = {2015}, author = {Springer, MS and Signore, AV and Paijmans, JL and Vélez-Juarbe, J and Domning, DP and Bauer, CE and He, K and Crerar, L and Campos, PF and Murphy, WJ and Meredith, RW and Gatesy, J and Willerslev, E and MacPhee, RD and Hofreiter, M and Campbell, KL}, title = {Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia.}, journal = {Molecular phylogenetics and evolution}, volume = {91}, number = {}, pages = {178-193}, doi = {10.1016/j.ympev.2015.05.022}, pmid = {26050523}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; Dental Enamel Proteins/genetics ; Fossils ; Genes ; Phylogeny ; Sequence Analysis, DNA ; Sirenia/anatomy &amp; histology/*classification/genetics ; }, abstract = {The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean=98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans.}, }
@article {pmid26039408, year = {2015}, author = {Allentoft, ME and Heller, R and Holdaway, RN and Bunce, M}, title = {Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site.}, journal = {Heredity}, volume = {115}, number = {6}, pages = {481-487}, pmid = {26039408}, issn = {1365-2540}, mesh = {Animals ; Bone and Bones ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Female ; *Fossils ; Genetics, Population ; Haplotypes ; Likelihood Functions ; *Microsatellite Repeats ; New Zealand ; Palaeognathae/*genetics ; Sequence Analysis, DNA ; }, abstract = {By analysing ancient DNA (aDNA) from 74 (14)C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA, coupled with overlapping radiocarbon ages. The observed rXY values in the four dyads exceeded a conservative cutoff value for potential relatives obtained from simulated data. In three of the four dyads, the kinship was further supported by observing shared and rare mitochondrial haplotypes. Simulations demonstrated that the proportion of observed dyads above the cutoff value was at least 20 times higher than expected in a randomly mating population with temporal sampling, also when introducing population structure in the simulations. We conclude that the results must reflect social structure in the moa population and we discuss the implications for future aDNA research.}, }
@article {pmid26037535, year = {2015}, author = {Heintzman, PD and Zazula, GD and Cahill, JA and Reyes, AV and MacPhee, RD and Shapiro, B}, title = {Genomic Data from Extinct North American Camelops Revise Camel Evolutionary History.}, journal = {Molecular biology and evolution}, volume = {32}, number = {9}, pages = {2433-2440}, doi = {10.1093/molbev/msv128}, pmid = {26037535}, issn = {1537-1719}, mesh = {Animals ; Bayes Theorem ; Camelus/*genetics ; DNA, Mitochondrial/genetics ; Extinction, Biological ; Fossils ; Genetic Speciation ; *Genome, Mitochondrial ; Models, Genetic ; Molecular Sequence Data ; North America ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Recent advances in paleogenomic technologies have enabled an increasingly detailed understanding of the evolutionary relationships of now-extinct mammalian taxa. However, a number of enigmatic Quaternary species have never been characterized with molecular data, often because available fossils are rare or are found in environments that are not optimal for DNA preservation. Here, we analyze paleogenomic data extracted from bones attributed to the late Pleistocene western camel, Camelops cf. hesternus, a species that was distributed across central and western North America until its extinction approximately 13,000 years ago. Despite a modal sequence length of only around 35 base pairs, we reconstructed high-coverage complete mitochondrial genomes and low-coverage partial nuclear genomes for each specimen. We find that Camelops is sister to African and Asian bactrian and dromedary camels, to the exclusion of South American camelids (llamas, guanacos, alpacas, and vicuñas). These results contradict previous morphology-based phylogenetic models for Camelops, which suggest instead a closer relationship between Camelops and the South American camelids. The molecular data imply a Late Miocene divergence of the Camelops clade from lineages that separately gave rise to the extant camels of Eurasia. Our results demonstrate the increasing capacity of modern paleogenomic methods to resolve evolutionary relationships among distantly related lineages.}, }
@article {pmid26026577, year = {2015}, author = {Hassanin, A}, title = {The role of Pleistocene glaciations in shaping the evolution of polar and brown bears. Evidence from a critical review of mitochondrial and nuclear genome analyses.}, journal = {Comptes rendus biologies}, volume = {338}, number = {7}, pages = {494-501}, doi = {10.1016/j.crvi.2015.04.008}, pmid = {26026577}, issn = {1768-3238}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Female ; Genome ; History, Ancient ; *Ice Cover ; Male ; Ursidae/*genetics ; }, abstract = {In this report, I review recent molecular studies dealing with the origin and evolution of polar bears (Ursus maritimus), with special emphasis on their relationships with brown bears (U. arctos). On the basis of mitochondrial and nuclear data, different hypotheses have been proposed, including rapid morphological differentiation of U. maritimus, genetic introgression from U. arctos into U. maritimus, or inversely from U. maritimus into U. arctos, involving either male- or female-mediated gene flow. In the light of available molecular and eco-ethological data, I suggest, firstly, that all divergences among major clades of large bears can be linked to glacial periods, secondly, that polar bears diverged from brown bears before 530 thousand years ago (ka), during one of the three glacial marine isotope stages (MIS) 14, 15.2 or 16, and, thirdly, that genetic introgression had occurred from female polar bears into brown bear populations during at least two glacial periods, at 340 ± 10 ka (MIS 10) in western Europe, and at 155 ± 5 ka (MIS 6) on the ABC islands of southeastern Alaska, and probably also in Beringia and Ireland based on ancient DNA sequences.}, }
@article {pmid26020526, year = {2015}, author = {Huynh, MD and Page, JT and Richardson, BA and Udall, JA}, title = {Insights into transcriptomes of big and low sagebrush.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0127593}, pmid = {26020526}, issn = {1932-6203}, mesh = {*Artemisia/genetics/metabolism ; *Evolution, Molecular ; Gene Duplication/*physiology ; Genes, Plant/*physiology ; *Phylogeny ; Plant Proteins/genetics/metabolism ; Species Specificity ; Transcriptome/*physiology ; }, abstract = {We report the sequencing and assembly of three transcriptomes from Big (Artemisia tridentata ssp. wyomingensis and A. tridentata ssp. tridentata) and Low (A. arbuscula ssp. arbuscula) sagebrush. The sequence reads are available in the Sequence Read Archive of NCBI. We demonstrate the utilities of these transcriptomes for gene discovery and phylogenomic analysis. An assembly of 61,883 transcripts followed by transcript identification by the program TRAPID revealed 16 transcripts directly related to terpene synthases, proteins critical to the production of multiple secondary metabolites in sagebrush. A putative terpene synthase was identified in two of our sagebrush samples. Using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. By applying a constant mutation rate to the data we estimate that these three ancient duplications occurred about 18, 34 and 60 million years ago. These transcriptomes offer a foundation for future studies of sagebrush, including inferences in chemical defense and the identification of species and subspecies of sagebrush for restoration and preservation of the threatened sage-grouse.}, }
@article {pmid26018528, year = {2015}, author = {Lee, EJ and Merriwether, DA and Kasparov, AK and Nikolskiy, PA and Sotnikova, MV and Pavlova, EY and Pitulko, VV}, title = {Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0125759}, pmid = {26018528}, issn = {1932-6203}, mesh = {Animals ; Arctic Regions ; Canidae/*genetics ; *DNA, Mitochondrial/genetics ; Dogs/genetics ; *Fossils ; Phylogeny ; Siberia ; }, abstract = {Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP) to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool.}, }
@article {pmid26016479, year = {2015}, author = {Smith, RW and Monroe, C and Bolnick, DA}, title = {Detection of Cytosine methylation in ancient DNA from five native american populations using bisulfite sequencing.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0125344}, pmid = {26016479}, issn = {1932-6203}, mesh = {CpG Islands/genetics ; Cytosine/*metabolism ; DNA Methylation/*genetics/physiology ; Humans ; Indians, North American/*genetics ; Retroelements/genetics ; Sequence Analysis, DNA ; Sulfites/*chemistry ; }, abstract = {While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/μL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches.}, }
@article {pmid25999485, year = {2015}, author = {Gibbons, A}, title = {Human evolution. Ancient DNA pinpoints Paleolithic liaison in Europe.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6237}, pages = {847}, doi = {10.1126/science.348.6237.847}, pmid = {25999485}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; DNA/*genetics ; Europe ; *Fossils ; Humans ; *Mandible ; Neanderthals/*genetics ; }, }
@article {pmid25998652, year = {2015}, author = {Oh, CS and Koh, BJ and Yoo, DS and Park, JB and Min, SR and Kim, YS and Lee, SS and Ge, J and Seo, SB and Shin, DH}, title = {Joseon funerary texts tested using ancient DNA analysis of a Korean mummy.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {298}, number = {6}, pages = {1191-1207}, doi = {10.1002/ar.23142}, pmid = {25998652}, issn = {1932-8494}, mesh = {Asian People ; *Funeral Rites ; Humans ; *Mummies ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {In Korea, ancient DNA (aDNA) analysis has been applied to investigations into the genetic affiliations of mummies found in Joseon Dynasty tombs (1392-1910 CE), becoming now indispensable tool for researches studying human remains from archaeological sites. In the course of our recent examinations on a Korean mummy of Joseon Dynasty, we discovered many teeth contained in a pouch. And in fact, the historical literature on the topic of Joseon funerals contain general accounts of pouches in which an individual's lost teeth were collected over the course of a lifetime and, after death, placed in the coffin with the body. To test the veracity of the historical texts, the present study undertook aDNA analyses and compared the results between specifically questioned (Q) samples (teeth) and known (K) samples (brain and bone) from the mummy to ensure that they came from the same individual. Although the Q-K comparison of autosomal short tandem repeat results did not show full concordance due to allelic drop-outs in some loci, our statistical calculation indicated that the teeth in the pouch are highly likely those of the mummy. Additionally, Q-K comparison of mitochondrial DNA sequence results showed 100% matches between samples. There results, in short, could not gainsay the conjecture that the teeth samples originated from the person buried in the tomb; and if so, he must have kept his teeth for a long time after their loss. As the application of aDNA analysis to Korean mummy studies develops, there will be other opportunities to test historical documents, particularly those referring to funerary rites.}, }
@article {pmid25998650, year = {2015}, author = {Kreissl Lonfat, BM and Kaufmann, IM and Rühli, F}, title = {A code of ethics for evidence-based research with ancient human remains.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {298}, number = {6}, pages = {1175-1181}, doi = {10.1002/ar.23126}, pmid = {25998650}, issn = {1932-8494}, mesh = {*Codes of Ethics ; *Ethics, Research ; Humans ; *Mummies ; }, abstract = {As clinical research constantly advances and the concept of evolution becomes a strong and influential part of basic medical research, the absence of a discourse that deals with the use of ancient human remains in evidence-based research is becoming unbearable. While topics such as exhibition and excavation of human remains are established ethical fields of discourse, when faced with instrumentalization of ancient human remains for research (i.e., ancient DNA extractions for disease marker analyses) the answers from traditional ethics or even more practical fields of bio-ethics or more specific biomedical ethics are rare to non-existent. The Centre for Evolutionary Medicine at the University of Zurich solved their needs for discursive action through the writing of a self-given code of ethics which was written in dialogue with the researchers at the Institute and was published online in Sept. 2011: http://evolutionäremedizin.ch/coe/. The philosophico-ethical basis for this a code of conduct and ethics and the methods are published in this article.}, }
@article {pmid25998631, year = {2015}, author = {Zimmerman, MR and Gleeson, M}, title = {PUM I Revisited: Tradeoffs in Preservation and Discovery.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {298}, number = {6}, pages = {949-953}, doi = {10.1002/ar.23133}, pmid = {25998631}, issn = {1932-8494}, mesh = {*Autopsy ; Humans ; Magnetic Resonance Imaging ; Mummies/*pathology ; Skin Diseases/*pathology ; }, abstract = {An Egyptian mummy designated PUM I (Pennsylvania University Museum) was subjected to a complete autopsy in 1972. Forty-one years later, the senior author (MZ) was invited back to the Penn Museum to identify several packages of material that had been preserved with the mummy joining the project conservator (MG) in the evaluation of these remains. A summary of the 1972 examination reviews the dating of the mummy, about 3,000 years ago. The mummy was poorly preserved and the only significant pathology was a rare skin disease, subcorneal pustular dermatosis, which was not identified by modern medicine until 1956. The review of PUM 1, as the mummy is stabilized during conservation at the Penn Museum (previously called the Pennsylvania University Museum), generates a discussion for researchers who embark on the study of mummified remains. There have been major advances in the study of mummies since 1972, including computed tomography (CT) scanning, with much less invasive endoscopically guided biopsies, analysis for ancient DNA (aDNA), nuclear magnetic resonance technology, chemical analysis, and paleoserology. The value of complete autopsy must now be balanced against preservation of a complete mummy by less invasive techniques that are tissue sampled through guided technology. Indeed it is unlikely that these regions of the skin of PUM 1 would have been sampled and studied if these new tools of analysis had been available and applied.}, }
@article {pmid25994097, year = {2015}, author = {Gaul, JS and Winter, E and Grossschmidt, K}, title = {Ancient pathogens in museal dry bone specimens: analysis of paleocytology and aDNA.}, journal = {Wiener medizinische Wochenschrift (1946)}, volume = {165}, number = {7-8}, pages = {133-139}, pmid = {25994097}, issn = {1563-258X}, mesh = {Austria ; Bone and Bones/*microbiology/*pathology ; DNA, Bacterial/*genetics/*history ; History, Ancient ; Humans ; Museums/*history ; Paleopathology/*history ; Treponema pallidum/*genetics ; Treponemal Infections/*genetics/*history ; }, abstract = {Bone samples investigated in this study derive from the pathologic-anatomical collection of the Natural History Museum of Vienna. In order to explore the survival of treponemes and treponemal ancient DNA in museal dry bone specimens, we analyzed three individuals known to have been infected with Treponema pallidum pallidum. No reproducible evidence of surviving pathogen's ancient DNA (aDNA) was obtained, despite the highly sensitive extraction and amplification techniques (TPP15 and arp). Additionally, decalcification fluid of bone sections was smear stained with May-Gruenwald-Giemsa. The slides were examined using direct light microscope and dark field illumination. Remnants of spirochetal structures were detectable in every smear. Our results demonstrate that aDNA is unlikely to survive, but spirochetal remains are stainable and thus detectable.}, }
@article {pmid25992976, year = {2015}, author = {Niemi, M and Bläuer, A and Iso-Touru, T and Harjula, J and Nyström Edmark, V and Rannamäe, E and Lõugas, L and Sajantila, A and Lidén, K and Taavitsainen, JP}, title = {Temporal fluctuation in North East Baltic Sea region cattle population revealed by mitochondrial and Y-chromosomal DNA analyses.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0123821}, pmid = {25992976}, issn = {1932-6203}, mesh = {Animals ; Animals, Domestic/genetics ; Baltic States ; Base Sequence ; Bone and Bones/cytology ; Breeding ; Cattle/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation/*genetics ; Haplotypes/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Radiometric Dating ; Sequence Analysis, DNA/veterinary ; Y Chromosome/*genetics ; }, abstract = {BACKGROUND: Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies.<br><br>RESULTS: Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples).<br><br>CONCLUSIONS: The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle.}, }
@article {pmid25992635, year = {2015}, author = {Higgins, D and Rohrlach, AB and Kaidonis, J and Townsend, G and Austin, JJ}, title = {Differential nuclear and mitochondrial DNA preservation in post-mortem teeth with implications for forensic and ancient DNA studies.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0126935}, pmid = {25992635}, issn = {1932-6203}, mesh = {Cell Nucleus/*genetics ; DNA/*genetics ; DNA, Mitochondrial/*genetics ; *Forensic Genetics ; Humans ; Microsatellite Repeats/genetics ; *Postmortem Changes ; Tooth/*metabolism ; }, abstract = {Major advances in genetic analysis of skeletal remains have been made over the last decade, primarily due to improvements in post-DNA-extraction techniques. Despite this, a key challenge for DNA analysis of skeletal remains is the limited yield of DNA recovered from these poorly preserved samples. Enhanced DNA recovery by improved sampling and extraction techniques would allow further advancements. However, little is known about the post-mortem kinetics of DNA degradation and whether the rate of degradation varies between nuclear and mitochondrial DNA or across different skeletal tissues. This knowledge, along with information regarding ante-mortem DNA distribution within skeletal elements, would inform sampling protocols facilitating development of improved extraction processes. Here we present a combined genetic and histological examination of DNA content and rates of DNA degradation in the different tooth tissues of 150 human molars over short-medium post-mortem intervals. DNA was extracted from coronal dentine, root dentine, cementum and pulp of 114 teeth via a silica column method and the remaining 36 teeth were examined histologically. Real time quantification assays based on two nuclear DNA fragments (67 bp and 156 bp) and one mitochondrial DNA fragment (77 bp) showed nuclear and mitochondrial DNA degraded exponentially, but at different rates, depending on post-mortem interval and soil temperature. In contrast to previous studies, we identified differential survival of nuclear and mtDNA in different tooth tissues. Furthermore histological examination showed pulp and dentine were rapidly affected by loss of structural integrity, and pulp was completely destroyed in a relatively short time period. Conversely, cementum showed little structural change over the same time period. Finally, we confirm that targeted sampling of cementum from teeth buried for up to 16 months can provide a reliable source of nuclear DNA for STR-based genotyping using standard extraction methods, without the need for specialised equipment or large-volume demineralisation steps.}, }
@article {pmid25970602, year = {2015}, author = {Inskip, SA and Taylor, GM and Zakrzewski, SR and Mays, SA and Pike, AW and Llewellyn, G and Williams, CM and Lee, OY and Wu, HH and Minnikin, DE and Besra, GS and Stewart, GR}, title = {Osteological, biomolecular and geochemical examination of an early anglo-saxon case of lepromatous leprosy.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0124282}, pmid = {25970602}, issn = {1932-6203}, support = {MR/K012118/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Carbon Radioisotopes ; Fibula/microbiology/pathology ; *Genes, Bacterial ; *Genome, Bacterial ; Genotype ; History, Medieval ; Humans ; Leprosy, Lepromatous/*history/microbiology/pathology ; Lipids/isolation &amp; purification ; Male ; Metatarsal Bones/microbiology/pathology ; Mycobacterium leprae/classification/*genetics/isolation &amp; purification/metabolism ; Osteology ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Talus/microbiology/pathology ; United Kingdom ; }, abstract = {We have examined a 5th to 6th century inhumation from Great Chesterford, Essex, UK. The incomplete remains are those of a young male, aged around 21-35 years at death. The remains show osteological evidence of lepromatous leprosy (LL) and this was confirmed by lipid biomarker analysis and ancient DNA (aDNA) analysis, which provided evidence for both multi-copy and single copy loci from the Mycobacterium leprae genome. Genotyping showed the strain belonged to the 3I lineage, but the Great Chesterford isolate appeared to be ancestral to 3I strains found in later medieval cases in southern Britain and also continental Europe. While a number of contemporaneous cases exist, at present, this case of leprosy is the earliest radiocarbon dated case in Britain confirmed by both aDNA and lipid biomarkers. Importantly, Strontium and Oxygen isotope analysis suggest that the individual is likely to have originated from outside Britain. This potentially sheds light on the origins of the strain in Britain and its subsequent spread to other parts of the world, including the Americas where the 3I lineage of M. leprae is still found in some southern states of America.}, }
@article {pmid25963373, year = {2015}, author = {Racimo, F and Sankararaman, S and Nielsen, R and Huerta-Sánchez, E}, title = {Evidence for archaic adaptive introgression in humans.}, journal = {Nature reviews. Genetics}, volume = {16}, number = {6}, pages = {359-371}, pmid = {25963373}, issn = {1471-0064}, support = {R01HG003229-09/HG/NHGRI NIH HHS/United States ; R01 GM040282/GM/NIGMS NIH HHS/United States ; R01 HG003229/HG/NHGRI NIH HHS/United States ; R01&#x2011;GM40282/GM/NIGMS NIH HHS/United States ; K99 GM111744/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Animals ; Evolution, Molecular ; Gene Flow ; Genome, Human ; Haplotypes ; Humans ; Linkage Disequilibrium ; Markov Chains ; *Models, Genetic ; Neanderthals/genetics ; Phylogeny ; Selection, Genetic ; }, abstract = {As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments - a process known as adaptive introgression. Within the past few years, a series of studies have identified genomic regions that show strong evidence for archaic adaptive introgression. Here, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans and to determine whether positive selection has acted on these fragments. We review recently reported examples of adaptive introgression, grouped by selection pressure, and consider the level of supporting evidence for each. Finally, we discuss challenges and recommendations for inferring selection on introgressed regions.}, }
@article {pmid25944642, year = {2015}, author = {Olalde, I and Capote, J and Del-Arco, MC and Atoche, P and Delgado, T and González-Anton, R and Pais, J and Amills, M and Lalueza-Fox, C and Ramírez, O}, title = {Ancient DNA sheds light on the ancestry of pre-hispanic Canarian pigs.}, journal = {Genetics, selection, evolution : GSE}, volume = {47}, number = {1}, pages = {40}, pmid = {25944642}, issn = {1297-9686}, mesh = {Animals ; Cytochromes b/genetics ; DNA/chemistry ; Genetic Variation ; Haplotypes ; Spain ; Sus scrofa/genetics ; Swine/*genetics ; }, abstract = {BACKGROUND: Canarian Black (CB) pigs belong to an autochthonous and endangered breed, which is spread throughout the Canarian archipelago. It is commonly accepted that they represent a relic of the pig populations that were bred by the Berbers in North Africa over millennia. It is important to note that the geographic isolation of the Canary Islands has preserved this genetic legacy intact from foreign introgressions until the Spanish conquest of the archipelago in the 15(th) century. Ten years ago, it was demonstrated that, in CB pigs, the frequency of the Asian A2 cytochrome-b haplogroup reached 73%. The current work aimed at investigating whether this observation is explained by either a recent or an ancient introgression of CB pigs with Far Eastern pigs.<br><br>RESULTS: Genetic analyses of 23 ancient samples from pre-hispanic Canarian pigs (420 to 2500 years before present) showed that Near Eastern and Far Eastern genetic signatures were totally absent in the primitive Canarian pre-hispanic pigs. Indeed, the haplotypes detected in these pigs were closely related to those of North African and European wild boars.<br><br>CONCLUSIONS: Our results demonstrate that the high frequency of the Far Eastern mitochondrial cytochrome B A2 haplotype in modern Canarian Black pigs probably corresponds to a relatively recent introgression with British breeds.}, }
@article {pmid25938511, year = {2015}, author = {Zhao, YB and Zhang, Y and Zhang, QC and Li, HJ and Cui, YQ and Xu, Z and Jin, L and Zhou, H and Zhu, H}, title = {Ancient DNA reveals that the genetic structure of the northern Han Chinese was shaped prior to 3,000 years ago.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0125676}, pmid = {25938511}, issn = {1932-6203}, mesh = {Asian People/*genetics ; Base Sequence ; DNA, Mitochondrial/*history ; Ethnicity/*genetics ; Geography ; Haplotypes ; History, Ancient ; Humans ; Molecular Sequence Data ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; }, abstract = {The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area.}, }
@article {pmid25928633, year = {2015}, author = {Rivollat, M and Mendisco, F and Pemonge, MH and Safi, A and Saint-Marc, D and Brémond, A and Couture-Veschambre, C and Rottier, S and Deguilloux, MF}, title = {When the waves of European Neolithization met: first paleogenetic evidence from early farmers in the southern Paris Basin.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0125521}, pmid = {25928633}, issn = {1932-6203}, mesh = {Archaeology/*methods ; DNA, Mitochondrial/genetics ; Europe ; Farmers/*statistics &amp; numerical data ; France ; Haplotypes/genetics ; Humans ; Molecular Sequence Data ; Paris ; White People ; }, abstract = {An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.}, }
@article {pmid25925186, year = {2015}, author = {Oh, CS and Seo, M and Hong, JH and Chai, JY and Oh, SW and Park, JB and Shin, DH}, title = {Ancient mitochondrial DNA analyses of ascaris eggs discovered in coprolites from joseon tomb.}, journal = {The Korean journal of parasitology}, volume = {53}, number = {2}, pages = {237-242}, pmid = {25925186}, issn = {1738-0006}, mesh = {Adult ; Animals ; Ascariasis/diagnosis/history/*parasitology ; Ascaris/classification/genetics/*isolation &amp; purification ; Base Sequence ; Cytochromes b/genetics ; DNA Primers/genetics ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics/history ; Female ; Fossils/history/parasitology ; History, Ancient ; Humans ; Male ; Molecular Sequence Data ; Mummies/history/*parasitology ; Ovum/chemistry/classification ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Analysis of ancient DNA (aDNA) extracted from Ascaris is very important for understanding the phylogenetic lineage of the parasite species. When aDNAs obtained from a Joseon tomb (SN2-19-1) coprolite in which Ascaris eggs were identified were amplified with primers for cytochrome b (cyt b) and 18S small subunit ribosomal RNA (18S rRNA) gene, the outcome exhibited Ascaris specific amplicon bands. By cloning, sequencing, and analysis of the amplified DNA, we obtained information valuable for comprehending genetic lineage of Ascaris prevalent among pre-modern Joseon peoples.}, }
@article {pmid25912776, year = {2015}, author = {Coulson-Thomas, YM and Norton, AL and Coulson-Thomas, VJ and Florencio-Silva, R and Ali, N and Elmrghni, S and Gil, CD and Sasso, GR and Dixon, RA and Nader, HB}, title = {DNA and bone structure preservation in medieval human skeletons.}, journal = {Forensic science international}, volume = {251}, number = {}, pages = {186-194}, doi = {10.1016/j.forsciint.2015.04.005}, pmid = {25912776}, issn = {1872-6283}, mesh = {Adult ; Bone and Bones/*chemistry/*ultrastructure ; Chromosomes, Human, Y ; Collagen Type III/analysis ; DNA/*isolation &amp; purification ; DNA Fingerprinting ; DNA Primers ; Female ; History, Medieval ; Humans ; Immunohistochemistry ; Male ; Microsatellite Repeats ; Microscopy, Electron, Transmission ; Osteocalcin/analysis ; Osteocytes/cytology ; Real-Time Polymerase Chain Reaction ; Sex Determination Analysis ; Tooth/chemistry ; }, abstract = {Morphological and ultrastructural data from archaeological human bones are scarce, particularly data that have been correlated with information on the preservation of molecules such as DNA. Here we examine the bone structure of macroscopically well-preserved medieval human skeletons by transmission electron microscopy and immunohistochemistry, and the quantity and quality of DNA extracted from these skeletons. DNA technology has been increasingly used for analyzing physical evidence in archaeological forensics; however, the isolation of ancient DNA is difficult since it is highly degraded, extraction yields are low and the co-extraction of PCR inhibitors is a problem. We adapted and optimised a method that is frequently used for isolating DNA from modern samples, Chelex(®) 100 (Bio-Rad) extraction, for isolating DNA from archaeological human bones and teeth. The isolated DNA was analysed by real-time PCR using primers targeting the sex determining region on the Y chromosome (SRY) and STR typing using the AmpFlSTR(®) Identifiler PCR Amplification kit. Our results clearly show the preservation of bone matrix in medieval bones and the presence of intact osteocytes with well preserved encapsulated nuclei. In addition, we show how effective Chelex(®) 100 is for isolating ancient DNA from archaeological bones and teeth. This optimised method is suitable for STR typing using kits aimed specifically at degraded and difficult DNA templates since amplicons of up to 250bp were successfully amplified.}, }
@article {pmid25912182, year = {2015}, author = {Kim, K and Bazarragchaa, M and Brenner, CH and Choi, BS and Kim, KY}, title = {Extensive evaluation of DNA polymerase performance for highly degraded human DNA samples.}, journal = {Forensic science international}, volume = {251}, number = {}, pages = {171-178}, doi = {10.1016/j.forsciint.2015.04.001}, pmid = {25912182}, issn = {1872-6283}, mesh = {*DNA Degradation, Necrotic ; DNA-Directed DNA Polymerase/*genetics ; Electrophoresis, Agar Gel ; Forensic Genetics ; Humans ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Highly degraded human DNA is commonly encountered in the forensic studies. Despite many efforts, the poor quality and quantity of the DNA often result in unsuccessful DNA analysis. There has been no extensive evaluation of DNA polymerase performance for the successful PCR of highly degraded DNA samples. We evaluated the most efficient DNA polymerases, based on real-time PCR and agarose gel electrophoresis analyses for a single copy gene amplification, with 200 ancient DNA (aDNA) samples of various origins. Nine commercially available DNA polymerases were tested, which included enzymes that are reportedly effective for PCR-inhibitory samples. The first screening test for the polymerases with 20 aDNA samples showed that Pico Maxx HF, FastStart Taq, and Ex Taq HS DNA polymerases were the most effective. Further tests with 180 aDNA samples showed that AmpliTaq Gold (control) amplified PCR products from 52 aDNA samples, PicoMaxx HF from 62, FastStart Taq from 64, and Ex Taq HS from 65. The use of two or more of Ex Taq HS, FastStart Taq, and PicoMaxx HF resulted in a significantly higher success rate than that of AmpliTaq Gold alone. With 37 positive samples tested in duplicate, Ex Taq HS showed the highest reproducibility (13 samples) and AmpliTaq Gold, the lowest (four samples); this difference was significant. The data also showed preferential amplification by the enzymes; Ex Taq HS exclusively produced amplification from two samples, FastStart Taq from one, and PicoMaxx HF from one. We suggest that the initial use of these three DNA polymerases will increase the probability of successfully amplifying DNA from highly degraded human DNA samples.}, }
@article {pmid25904660, year = {2015}, author = {Brace, S and Turvey, ST and Weksler, M and Hoogland, ML and Barnes, I}, title = {Unexpected evolutionary diversity in a recently extinct Caribbean mammal radiation.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1807}, pages = {20142371}, pmid = {25904660}, issn = {1471-2954}, mesh = {Animals ; Arvicolinae/*genetics ; *Biological Evolution ; Caribbean Region ; DNA, Mitochondrial/genetics ; Extinction, Biological ; Fossils ; Islands ; Phylogeny ; Phylogeography ; }, abstract = {Identifying general patterns of colonization and radiation in island faunas is often hindered by past human-caused extinctions. The insular Caribbean is one of the only complex oceanic-type island systems colonized by land mammals, but has witnessed the globally highest level of mammalian extinction during the Holocene. Using ancient DNA analysis, we reconstruct the evolutionary history of one of the Caribbean's now-extinct major mammal groups, the insular radiation of oryzomyine rice rats. Despite the significant problems of recovering DNA from prehistoric tropical archaeological material, it was possible to identify two discrete Late Miocene colonizations of the main Lesser Antillean island chain from mainland South America by oryzomyine lineages that were only distantly related. A high level of phylogenetic diversification was observed within oryzomyines across the Lesser Antilles, even between allopatric populations on the same island bank. The timing of oryzomyine colonization is closely similar to the age of several other Caribbean vertebrate taxa, suggesting that geomorphological conditions during the Late Miocene facilitated broadly simultaneous overwater waif dispersal of many South American lineages to the Lesser Antilles. These data provide an important baseline by which to further develop the Caribbean as a unique workshop for studying island evolution.}, }
@article {pmid25883677, year = {2015}, author = {McManus, KF}, title = {popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator.}, journal = {Source code for biology and medicine}, volume = {10}, number = {}, pages = {6}, pmid = {25883677}, issn = {1751-0473}, support = {T32 GM007276/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Sequencing and genotyping technology advancements have led to massive, growing repositories of spatially explicit genetic data and increasing quantities of temporal data (i.e., ancient DNA). These data will allow more complex and fine-scale inferences about population history than ever before; however, new methods are needed to test complex hypotheses.<br><br>RESULTS: This article presents popRange, a forward genetic simulator, which incorporates large-scale genetic data with stochastic spatially and temporally explicit demographic and selective models. Features such as spatially and temporally variable selection coefficients and demography are incorporated in a highly flexible manner. popRange is implemented as an R package and presented with an example simulation exploring a selected allele's trajectory in multiple subpopulations.<br><br>CONCLUSIONS: popRange allows researchers to evaluate and test complex scenarios by simulating large-scale data with complicated demographic and selective features. popRange is available for download at http://cran.r-project.org/web/packages/popRange/index.html.}, }
@article {pmid25863165, year = {2015}, author = {Freire, A and Araújo, A and Maldonado, A and Lobo, A and Garcia, J and Fonseca, AB and Leles, D}, title = {It is needless to rehydrate archeological samples to extract ancient DNA.}, journal = {Parasitology international}, volume = {64}, number = {5}, pages = {303-304}, doi = {10.1016/j.parint.2015.03.006}, pmid = {25863165}, issn = {1873-0329}, mesh = {Animals ; Archaeology ; DNA, Helminth/*isolation &amp; purification ; Desiccation ; Echinostoma/*genetics ; Feces/parasitology ; }, }
@article {pmid25849125, year = {2015}, author = {Demeter, F and Shackelford, L and Westaway, K and Duringer, P and Bacon, AM and Ponche, JL and Wu, X and Sayavongkhamdy, T and Zhao, JX and Barnes, L and Boyon, M and Sichanthongtip, P and Sénégas, F and Karpoff, AM and Patole-Edoumba, E and Coppens, Y and Braga, J}, title = {Early modern humans and morphological variation in Southeast Asia: fossil evidence from Tam Pa Ling, Laos.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0121193}, pmid = {25849125}, issn = {1932-6203}, mesh = {*Anthropology, Physical ; *Fossils ; Humans ; Laos ; Mandible/*anatomy &amp; histology ; }, abstract = {Little is known about the timing of modern human emergence and occupation in Eastern Eurasia. However a rapid migration out of Africa into Southeast Asia by at least 60 ka is supported by archaeological, paleogenetic and paleoanthropological data. Recent discoveries in Laos, a modern human cranium (TPL1) from Tam Pa Ling's cave, provided the first evidence for the presence of early modern humans in mainland Southeast Asia by 63-46 ka. In the current study, a complete human mandible representing a second individual, TPL 2, is described using discrete traits and geometric morphometrics with an emphasis on determining its population affinity. The TPL2 mandible has a chin and other discrete traits consistent with early modern humans, but it retains a robust lateral corpus and internal corporal morphology typical of archaic humans across the Old World. The mosaic morphology of TPL2 and the fully modern human morphology of TPL1 suggest that a large range of morphological variation was present in early modern human populations residing in the eastern Eurasia by MIS 3.}, }
@article {pmid25840859, year = {2015}, author = {Gómez-Robles, A and Bermúdez de Castro, JM and Martinón-Torres, M and Prado-Simón, L and Arsuaga, JL}, title = {A geometric morphometric analysis of hominin lower molars: Evolutionary implications and overview of postcanine dental variation.}, journal = {Journal of human evolution}, volume = {82}, number = {}, pages = {34-50}, doi = {10.1016/j.jhevol.2015.02.013}, pmid = {25840859}, issn = {1095-8606}, mesh = {Africa ; Animals ; Asia ; *Biological Evolution ; Classification ; Cuspid/*anatomy &amp; histology ; Europe ; Fossils ; History, Ancient ; Hominidae/*anatomy &amp; histology ; Molar/*anatomy &amp; histology ; }, abstract = {Lower molars have been extensively studied in the context of hominin evolution using classic and geometric morphometric analyses, 2D and 3D approaches, evaluations of the external (outer enamel surface) and internal anatomy (dentine, pulp chamber, and radicular canals), and studies of the crown and root variation. In this study, we present a 2D geometric morphometric analysis of the crown anatomy of lower first, second, and third molars of a broad sample of hominins, including Pliocene and Lower, Middle, and Upper Pleistocene species coming from Africa, Asia, and Europe. We show that shape variability increases from first to second and third molars. While first molars tend to retain a relatively stable 5-cusped conformation throughout the hominin fossil record, second and third molars show marked distal reductions in later Homo species. This trend to distal reduction is similar to that observed in previous studies of premolars and upper second and third molars, and points to a correlated reduction of distal areas across the whole postcanine dentition. Results on lower molar variation, as well as on other postcanine teeth, show certain trends in European Pleistocene populations from the Atapuerca sites. Middle Pleistocene hominins from Sima de los Huesos show Neanderthal affinities and strong dental reduction, especially in the most distal molars. The degree of dental reduction in this population is stronger than that observed in classic Neanderthals. Homo antecessor hominins from Gran Dolina-TD6 have primitive lower teeth that contrast with their more derived upper teeth. The evolutionary implications of these dental affinities are discussed in light of recent paleogenetic studies.}, }
@article {pmid25833851, year = {2015}, author = {Buckley, M}, title = {Ancient collagen reveals evolutionary history of the endemic South American 'ungulates'.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1806}, pages = {20142671}, pmid = {25833851}, issn = {1471-2954}, mesh = {Animals ; *Biological Evolution ; Chromatography, Liquid ; Collagen/*genetics ; Evolution, Molecular ; Mammals/*classification/*genetics ; Molecular Sequence Data ; Perissodactyla/classification/genetics ; Proteome ; Sequence Analysis, Protein ; South America ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tandem Mass Spectrometry ; }, abstract = {Since the late eighteenth century, fossils of bizarre extinct creatures have been described from the Americas, revealing a previously unimagined chapter in the history of mammals. The most bizarre of these are the 'native' South American ungulates thought to represent a group of mammals that evolved in relative isolation on South America, but with an uncertain affinity to any particular placental lineage. Many authors have considered them descended from Laurasian 'condylarths', which also includes the probable ancestors of perissodactyls and artiodactyls, whereas others have placed them either closer to the uniquely South American xenarthrans (anteaters, armadillos and sloths) or the basal afrotherians (e.g. elephants and hyraxes). These hypotheses have been debated owing to conflicting morphological characteristics and the hitherto inability to retrieve molecular information. Of the 'native' South American mammals, only the toxodonts and litopterns persisted until the Late Pleistocene-Early Holocene. Owing to known difficulties in retrieving ancient DNA (aDNA) from specimens from warm climates, this research presents a molecular phylogeny for both Macrauchenia patachonica (Litopterna) and Toxodon platensis (Notoungulata) recovered using proteomics-based (liquid chromatography-tandem mass spectrometry) sequencing analyses of bone collagen. The results place both taxa in a clade that is monophyletic with the perissodactyls, which today are represented by horses, rhinoceroses and tapirs.}, }
@article {pmid25831121, year = {2015}, author = {Galik, A and Mohandesan, E and Forstenpointner, G and Scholz, UM and Ruiz, E and Krenn, M and Burger, P}, title = {A sunken ship of the desert at the river Danube in Tulln, Austria.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0121235}, pmid = {25831121}, issn = {1932-6203}, support = {P 24706/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Austria ; Camelus/*genetics/physiology ; DNA, Mitochondrial/analysis/isolation &amp; purification ; History, 18th Century ; Male ; Polymorphism, Single Nucleotide ; Rivers ; Ships/history ; Skull/anatomy &amp; histology/metabolism ; }, abstract = {Rescue excavations recovered a skeleton that resurrect the contemporary dramatic history of Austria in the 17th century as troops besieged Vienna in the second Osmanic-Habsburg war. Unique for Central Europe is the evidence of a completely preserved camel skeleton uncovered in a large refuse pit. The male individual of slender stature indicates a few but characteristic pathological changes revealing not a beast of burden but probably a valuable riding animal. Anatomical and morphometrical analyses suggest a hybrid confirmed by the ancient DNA analyses resulting in the presence of a dromedary in the maternal and a Bactrian camel in the paternal line.}, }
@article {pmid25819157, year = {2015}, author = {Baker, O and Lee, OY and Wu, HH and Besra, GS and Minnikin, DE and Llewellyn, G and Williams, CM and Maixner, F and O'Sullivan, N and Zink, A and Chamel, B and Khawam, R and Coqueugniot, E and Helmer, D and Le Mort, F and Perrin, P and Gourichon, L and Dutailly, B and Pálfi, G and Coqueugniot, H and Dutour, O}, title = {Human tuberculosis predates domestication in ancient Syria.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {95 Suppl 1}, number = {}, pages = {S4-S12}, doi = {10.1016/j.tube.2015.02.001}, pmid = {25819157}, issn = {1873-281X}, support = {MR/K012118/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Agriculture/history ; Animals ; Animals, Domestic ; Anthropology, Medical ; Biomarkers/analysis ; Child ; Child, Preschool ; DNA, Bacterial/genetics ; History, Ancient ; Humans ; Infant ; Lipids/analysis ; Mycobacterium tuberculosis/genetics ; Paleopathology ; Syria ; Tuberculosis, Osteoarticular/genetics/*history ; Young Adult ; }, abstract = {The question of pre-neolithic tuberculosis is still open in paleopathological perspective. One of the major interests is to explore what type of infection could have existed around the early stage of animal domestication. Paleopathological lesions evoking skeletal TB were observed on five human skeletons coming from two PPNB sites in Syria, which belongs to the geographical cradle of agriculture. These sites represent respectively pre-domestication phase (Dja'de el Mughara, Northern Syria, 8800-8300 BCE cal.) and early domestication phase (Tell Aswad, Southern Syria, 8200-7600 BCE cal.). MicroCT scan analyses were performed on two specimens (one per site) and revealed microscopic changes in favor of TB infection. Detection of lipid biomarkers is positive for two specimens (one per site). Initial molecular analysis further indicates the presence of TB in one individual from Dja'de. Interestingly, no morphological evidence of TB was observed on animal remains of wild and newly domesticated species, discovered in these sites. These observations strongly suggest the presence of human tuberculosis before domestication and at its early stages.}, }
@article {pmid25819058, year = {2015}, author = {Sabbatani, S and Fiorini, S}, title = {[Mycobacterium infection in prehistoric humans: co-evolution in remote ages].}, journal = {Le infezioni in medicina}, volume = {23}, number = {1}, pages = {83-93}, pmid = {25819058}, issn = {2532-8689}, mesh = {Africa ; Ancient Lands ; Animal Husbandry/history ; Animals ; Cattle ; Cattle Diseases/*history/microbiology ; Cultural Evolution/history ; DNA, Bacterial/*history ; Emigration and Immigration/*history ; *Genome, Bacterial ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Medical Illustration/*history ; *Mycobacterium tuberculosis/genetics ; North America ; Paleopathology/history/methods ; Phylogeny ; Phylogeography ; Tuberculosis/*history ; }, abstract = {The introduction of agriculture and animal husbandry at the end of the Mesolithic era, despite enabling a significant demographic growth through an increase in food storage and availability, caused new infectious noxae to enter the pathocoenosis. However in the Palaeolithic era, hunter-gatherers were already in contact with infectious diseases of animal origin, albeit episodically. Modern biomedical technologies allow us to estimate, with better approximation, how long mankind has been in contact with Mycobacterium tuberculosis. Archaeological finds, including human and animal remains (especially the aurochs), are particularly studied by palaeopathologists, as mycobacteria frequently cause bone involvement and this characteristic is of particular interest for palaeopathological (even macroscopic) studies; the interest is to detect the ancient DNA of MT, which is the cause of bone tuberculosis in skeletal remains as well as in mummies. According to our present knowledge, palaeopathological findings, confirmed by molecular techniques, suggest that tuberculosis in human skeletons goes back at most to 9000 years ago, while, in a veterinary environment, the most ancient DNA of MTBC to be detected in an American bison dates back about 17,000 years. The possibility of discovering archaeological finds making even more ancient human remains available leaves opens up the possibility of dating back to previous eras the transmission of MTBC infection to mankind. Phylogenetic works examining the available materials (DNAa) suggest that Mycobacterium tuberculosis, the cause of tuberculosis infection in humans and cattle (Aurochs), would have had a co-evolutionary process. On the basis of recent phylogenetic studies, the MTBC genome would have had a wide span of time to reach a suitable adjustment, co-evolving in geographical environments both at high and low host density. It is likely that the strains that did not show this strong "flexibility" underwent extinction, in favour of more versatile, adaptable strains, that are able to infect susceptible hosts "always" and in any environmental condition.}, }
@article {pmid25808890, year = {2015}, author = {Szécsényi-Nagy, A and Brandt, G and Haak, W and Keerl, V and Jakucs, J and Möller-Rieker, S and Köhler, K and Mende, BG and Oross, K and Marton, T and Osztás, A and Kiss, V and Fecher, M and Pálfi, G and Molnár, E and Sebők, K and Czene, A and Paluch, T and Šlaus, M and Novak, M and Pećina-Šlaus, N and Ősz, B and Voicsek, V and Somogyi, K and Tóth, G and Kromer, B and Bánffy, E and Alt, KW}, title = {Tracing the genetic origin of Europe's first farmers reveals insights into their social organization.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1805}, pages = {}, pmid = {25808890}, issn = {1471-2954}, mesh = {Agriculture ; Archaeology ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Europe ; *Farmers ; Female ; Genetic Variation ; Humans ; Male ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Social Behavior ; Social Environment ; }, abstract = {Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis is yet unclear. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (seventh/sixth millennia BC) from the Carpathian Basin and southeastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early southeastern European and Carpathian Basin farming cultures on Central European populations of the sixth-fourth millennia BC. Comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through southeastern Europe and the Carpathian Basin into Central Europe. However, our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting a system of patrilineal descent and patrilocal residential rules among the early farmers.}, }
@article {pmid25808000, year = {2015}, author = {Gutiérrez-García, TA and Vázquez-Domínguez, E and Arroyo-Cabrales, J and Kuch, M and Enk, J and King, C and Poinar, HN}, title = {Correction to 'Ancient DNA and the tropics: a rodent's tale'.}, journal = {Biology letters}, volume = {11}, number = {3}, pages = {}, doi = {10.1098/rsbl.2015.0111}, pmid = {25808000}, issn = {1744-957X}, abstract = {The present erratum is in regards to our article entitled ‘Ancient DNA and the tropics: a rodent's tale’. We were made aware of problems with some of the ancient sequences submitted to GenBank and conducted a systematic review of all the files used in our study. We discovered that, unfortunately, an incorrect file was sent to GenBank and was also used in some of our downstream analyses. We immediately contacted GenBank, explained the situation and corrected the file. We have redone some analyses with the correct file and describe these changes below.}, }
@article {pmid25806829, year = {2015}, author = {Schwarz, R and Renhart, S and Gruber, H and Kli Mesch, W and Neuhuber, F and Cemper-Kiesslich, J}, title = {In naming the dead: Autosomal and Y-chromosomal STR typing on human skeletal remains from an 18th/19th century aristocratic crypt in Gallspach, Upper Austria.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {72}, number = {3}, pages = {335-346}, doi = {10.1127/anthranz/2015/0515}, pmid = {25806829}, issn = {0003-5548}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Austria/epidemiology ; Child ; Chromosomes, Human/*genetics ; Chromosomes, Human, Y/*genetics ; DNA/analysis/chemistry/genetics ; Female ; Forensic Anthropology ; Genotype ; Genotyping Techniques ; History, 18th Century ; History, 19th Century ; Humans ; Male ; Microsatellite Repeats/*genetics ; Middle Aged ; White People/*genetics/*history ; }, abstract = {Ancient DNA analyses have shown to be a powerful tool in the joint transdisciplinary assessment of archaeological records involving human remains. In this study we set out to identify single inhumations by synoptically evaluating the historical, archaeological, anthropological and molecular records on human remains from the crypt of the aristocratic family of Hoheneck (or: Hohenegg) dating to the 18(th) and 19(th) century AD. A total of 11 individuals were under investigation, yielding complete autosomal and Y-chromosomal STR profiles for 5 persons clearly showing a family group. DNA results, anthropological data and archaeological records taken together resulted in (almost) unambiguous correlation to historical records on the persons entombed in the crypt.}, }
@article {pmid25805042, year = {2015}, author = {Lari, M and Di Vincenzo, F and Borsato, A and Ghirotto, S and Micheli, M and Balsamo, C and Collina, C and De Bellis, G and Frisia, S and Giacobini, G and Gigli, E and Hellstrom, JC and Lannino, A and Modi, A and Pietrelli, A and Pilli, E and Profico, A and Ramirez, O and Rizzi, E and Vai, S and Venturo, D and Piperno, M and Lalueza-Fox, C and Barbujani, G and Caramelli, D and Manzi, G}, title = {The Neanderthal in the karst: First dating, morphometric, and paleogenetic data on the fossil skeleton from Altamura (Italy).}, journal = {Journal of human evolution}, volume = {82}, number = {}, pages = {88-94}, doi = {10.1016/j.jhevol.2015.02.007}, pmid = {25805042}, issn = {1095-8606}, mesh = {Animals ; Base Sequence ; *Caves ; DNA/analysis ; *Fossils ; History, Ancient ; Italy ; Molecular Sequence Data ; *Neanderthals ; Paleontology/*methods ; Phylogeny ; Scapula/chemistry ; *Skeleton/chemistry ; }, abstract = {In 1993, a fossil hominin skeleton was discovered in the karst caves of Lamalunga, near Altamura, in southern Italy. Despite the fact that this specimen represents one of the most extraordinary hominin specimens ever found in Europe, for the last two decades our knowledge of it has been based purely on the documented on-site observations. Recently, the retrieval from the cave of a fragment of bone (part of the right scapula) allowed the first dating of the individual, the quantitative analysis of a diagnostic morphological feature, and a preliminary paleogenetic characterization of this hominin skeleton from Altamura. Overall, the results concur in indicating that it belongs to the hypodigm of Homo neanderthalensis, with some phenetic peculiarities that appear consistent with a chronology ranging from 172 ± 15 ka to 130.1 ± 1.9 ka. Thus, the skeleton from Altamura represents the most ancient Neanderthal from which endogenous DNA has ever been extracted.}, }
@article {pmid25799987, year = {2015}, author = {Welker, F and Collins, MJ and Thomas, JA and Wadsley, M and Brace, S and Cappellini, E and Turvey, ST and Reguero, M and Gelfo, JN and Kramarz, A and Burger, J and Thomas-Oates, J and Ashford, DA and Ashton, PD and Rowsell, K and Porter, DM and Kessler, B and Fischer, R and Baessmann, C and Kaspar, S and Olsen, JV and Kiley, P and Elliott, JA and Kelstrup, CD and Mullin, V and Hofreiter, M and Willerslev, E and Hublin, JJ and Orlando, L and Barnes, I and MacPhee, RD}, title = {Ancient proteins resolve the evolutionary history of Darwin's South American ungulates.}, journal = {Nature}, volume = {522}, number = {7554}, pages = {81-84}, pmid = {25799987}, issn = {1476-4687}, mesh = {Amino Acid Sequence ; Animals ; Bone and Bones/chemistry ; Cattle ; Collagen Type I/*chemistry/genetics ; Female ; *Fossils ; Mammals/*classification ; Perissodactyla/classification ; *Phylogeny ; Placenta ; Pregnancy ; Proteomics ; South America ; }, abstract = {No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much like 180 years ago, it is no clearer whether they had one origin or several, arose before or after the Cretaceous/Palaeogene transition 66.2 million years ago, or are more likely to belong with the elephants and sirenians of superorder Afrotheria than with the euungulates (cattle, horses, and allies) of superorder Laurasiatheria. Morphology-based analyses have proved unconvincing because convergences are pervasive among unrelated ungulate-like placentals. Approaches using ancient DNA have also been unsuccessful, probably because of rapid DNA degradation in semitropical and temperate deposits. Here we apply proteomic analysis to screen bone samples of the Late Quaternary South American native ungulate taxa Toxodon (Notoungulata) and Macrauchenia (Litopterna) for phylogenetically informative protein sequences. For each ungulate, we obtain approximately 90% direct sequence coverage of type I collagen α1- and α2-chains, representing approximately 900 of 1,140 amino-acid residues for each subunit. A phylogeny is estimated from an alignment of these fossil sequences with collagen (I) gene transcripts from available mammalian genomes or mass spectrometrically derived sequence data obtained for this study. The resulting consensus tree agrees well with recent higher-level mammalian phylogenies. Toxodon and Macrauchenia form a monophyletic group whose sister taxon is not Afrotheria or any of its constituent clades as recently claimed, but instead crown Perissodactyla (horses, tapirs, and rhinoceroses). These results are consistent with the origin of at least some South American native ungulates from 'condylarths', a paraphyletic assembly of archaic placentals. With ongoing improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics such as that achieved by genomics, but with the possibility of reaching much further back in time.}, }
@article {pmid25799293, year = {2015}, author = {Anagnostou, P and Capocasa, M and Milia, N and Sanna, E and Battaggia, C and Luzi, D and Destro Bisol, G}, title = {When data sharing gets close to 100%: what human paleogenetics can teach the open science movement.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0121409}, pmid = {25799293}, issn = {1932-6203}, mesh = {Chromosomes, Human, Y/genetics ; DNA/*genetics ; Humans ; *Information Dissemination ; Mitochondria/genetics ; *Paleontology ; Polymorphism, Genetic ; Publications ; *Science ; Surveys and Questionnaires ; }, abstract = {This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals' editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers' awareness of the importance of openness and transparency for scientific progress may complement stakeholders' policies in achieving very high sharing rates. Second, widespread data sharing does not necessarily coincide with a prevalent use of practices which maximize data findability, accessibility, useability and preservation. A detailed look at the different ways in which data are released can be very useful to detect failures to adopt the best sharing modalities and understand how to correct them. Third and finally, the case of human paleogenetics tells us that a widespread awareness of the importance of Open Science may be important to build reliable scientific practices even in the presence of complex experimental challenges.}, }
@article {pmid25788902, year = {2015}, author = {Gargani, M and Pariset, L and Lenstra, JA and De Minicis, E and ,  and Valentini, A}, title = {Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle.}, journal = {Frontiers in genetics}, volume = {6}, number = {}, pages = {68}, pmid = {25788902}, issn = {1664-8021}, abstract = {Analysis of DNA from archeological remains is a valuable tool to interpret the history of ancient animal populations. So far most studies of ancient DNA target mitochondrial DNA (mtDNA), which reveals maternal lineages, but only partially the relationships of current breeds and ancient populations. In this study we explore the feasibility of nuclear DNA analysis. DNA was extracted from 1000-years old cattle bone collected from Ferento, an archeological site in central Italy. Amplification of 15 microsatellite FAO-recommended markers with PCR products yielded genotypes for four markers. Expected heterozygosity was comparable with values of modern breeds, but observed heterozygosity was underestimated due to allelic loss. Genetic distances suggested a position intermediate between (1) Anatolian, Balkan, Sicilian and South-Italian cattle and (2) the Iberian, North-European and Central-European cattle, but also a clear relationship with two central-Italian breeds, Chianina and Romagnola. This suggests that these breeds are derived from medieval cattle living in the same area. Our results illustrate the potential of ancient DNA for reconstructing the history of local cattle husbandry.}, }
@article {pmid25773651, year = {2015}, author = {Donoghue, HD and Spigelman, M and O'Grady, J and Szikossy, I and Pap, I and Lee, OY and Wu, HH and Besra, GS and Minnikin, DE}, title = {Ancient DNA analysis - An established technique in charting the evolution of tuberculosis and leprosy.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {95 Suppl 1}, number = {}, pages = {S140-4}, doi = {10.1016/j.tube.2015.02.020}, pmid = {25773651}, issn = {1873-281X}, mesh = {Bacterial Typing Techniques ; Coinfection/complications/genetics/history ; DNA, Bacterial/*analysis/genetics ; *Evolution, Molecular ; Genome, Bacterial ; History, Ancient ; Humans ; Leprosy/complications/*genetics/history ; Molecular Typing/methods ; Mycobacterium leprae/*genetics ; Mycobacterium tuberculosis/*genetics ; Nucleic Acid Amplification Techniques ; Paleopathology/methods ; Polymerase Chain Reaction ; Tuberculosis/complications/*genetics/history ; }, abstract = {Many tuberculosis and leprosy infections are latent or paucibacillary, suggesting a long time-scale for host and pathogen co-existence. Palaeopathology enables recognition of archaeological cases and PCR detects pathogen ancient DNA (aDNA). Mycobacterium tuberculosis and Mycobacterium leprae cell wall lipids are more stable than aDNA and restrict permeability, thereby possibly aiding long-term persistence of pathogen aDNA. Amplification of aDNA, using specific PCR primers designed for short fragments and linked to fluorescent probes, gives good results, especially when designed to target multi-copy loci. Such studies have confirmed tuberculosis and leprosy, including co-infections. Many tuberculosis cases have non-specific or no visible skeletal pathology, consistent with the natural history of this disease. M. tuberculosis and M. leprae are obligate parasites, closely associated with their human host following recent clonal distribution. Therefore genotyping based on single nucleotide polymorphisms (SNPs) can indicate their origins, spread and phylogeny. Knowledge of extant genetic lineages at particular times in past human populations can be obtained from well-preserved specimens where molecular typing is possible, using deletion analysis, microsatellite analysis and whole genome sequencing. Such studies have identified non-bovine tuberculosis from a Pleistocene bison from 17,500 years BP, human tuberculosis from 9000 years ago and leprosy from over 2000 years ago.}, }
@article {pmid25771204, year = {2015}, author = {Molnár, E and Donoghue, HD and Lee, OY and Wu, HH and Besra, GS and Minnikin, DE and Bull, ID and Llewellyn, G and Williams, CM and Spekker, O and Pálfi, G}, title = {Morphological and biomolecular evidence for tuberculosis in 8th century AD skeletons from Bélmegyer-Csömöki domb, Hungary.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {95 Suppl 1}, number = {}, pages = {S35-41}, doi = {10.1016/j.tube.2015.02.032}, pmid = {25771204}, issn = {1873-281X}, support = {MR/K012118/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Aged ; Biomarkers/analysis ; Chromatography, High Pressure Liquid ; DNA, Bacterial/genetics ; Female ; History, Medieval ; Humans ; Hungary ; Lipids/analysis ; Male ; Middle Aged ; Mycobacterium tuberculosis/genetics ; Mycolic Acids/analysis ; Nucleic Acid Amplification Techniques ; Paleopathology ; Polymerase Chain Reaction ; Tuberculosis, Osteoarticular/genetics/history/*pathology ; Young Adult ; }, abstract = {Macromorphological analysis of skeletons, from 20 selected graves of the 8th century AD Bélmegyer-Csömöki domb, revealed 19 cases of possible skeletal tuberculosis. Biomolecular analyses provided general support for such diagnoses, including the individual without pathology, but the data did not show coherent consistency over the range of biomarkers examined. Amplification of ancient DNA fragments found evidence for the Mycobacterium tuberculosis complex DNA only in five graves. In contrast, varying degrees of lipid biomarker presence were recorded in all except two of the skeletons, though most lipid components appeared to be somewhat degraded. Mycobacterial mycolic acid biomarkers were absent in five cases, but the weak, possibly degraded profiles for the remainder were smaller and inconclusive for either tuberculosis or leprosy. The most positive lipid biomarker evidence for tuberculosis was provided by mycolipenic acid, with 13 clear cases, supported by five distinct possible cases. Combinations of mycocerosic acids were present in all but three graves, but in one case a tuberculosis-leprosy co-infection was indicated. In two specimens with pathology, no lipid biomarker evidence was recorded, but one of these specimens provided M. tuberculosis complex DNA fragments.}, }
@article {pmid25771203, year = {2015}, author = {Spigelman, M and Donoghue, HD and Abdeen, Z and Ereqat, S and Sarie, I and Greenblatt, CL and Pap, I and Szikossy, I and Hershkovitz, I and Bar-Gal, GK and Matheson, C}, title = {Evolutionary changes in the genome of Mycobacterium tuberculosis and the human genome from 9000 years BP until modern times.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {95 Suppl 1}, number = {}, pages = {S145-9}, doi = {10.1016/j.tube.2015.02.022}, pmid = {25771203}, issn = {1873-281X}, mesh = {Animals ; Cation Transport Proteins/genetics ; Cattle ; Disease Resistance/genetics ; *Evolution, Molecular ; Genetic Predisposition to Disease/genetics/history ; Genome, Bacterial/*genetics ; Genome, Human/*genetics ; Genotype ; History, 18th Century ; History, 19th Century ; History, Ancient ; Host-Pathogen Interactions/genetics ; Humans ; Mummies ; Mycobacterium tuberculosis/*genetics ; Paleopathology ; Tuberculosis/*genetics/history ; }, abstract = {The demonstration of Mycobacterium tuberculosis DNA in ancient skeletons gives researchers an insight into its evolution. Findings of the last two decades sketched the biological relationships between the various species of tubercle bacilli, the time scale involved, their possible origin and dispersal. This paper includes the available evidence and on-going research. In the submerged Eastern Mediterranean Neolithic village of Atlit Yam (9000 BP), a human lineage of M. tuberculosis, defined by the TbD1 deletion in its genome, was demonstrated. An infected infant at the site provides an example of active tuberculosis in a human with a naïve immune system. Over 4000 years later tuberculosis was found in Jericho. Urbanization increases population density encouraging M. tuberculosis/human co-evolution. As susceptible humans die of tuberculosis, survivors develop genetic resistance to disease. Thus in 18th century Hungarian mummies from Vác, 65% were positive for tuberculosis yet a 95-year-old woman had clearly survived a childhood Ghon lesion. Whole genome studies are in progress, to detect changes over the millennia both in bacterial virulence and also host susceptibility/resistance genes that determine the NRAMP protein and Killer Cell Immunoglobulin-like Receptors (KIRs). This paper surveys present evidence and includes initial findings.}, }
@article {pmid25770088, year = {2015}, author = {Karmin, M and Saag, L and Vicente, M and Wilson Sayres, MA and Järve, M and Talas, UG and Rootsi, S and Ilumäe, AM and Mägi, R and Mitt, M and Pagani, L and Puurand, T and Faltyskova, Z and Clemente, F and Cardona, A and Metspalu, E and Sahakyan, H and Yunusbayev, B and Hudjashov, G and DeGiorgio, M and Loogväli, EL and Eichstaedt, C and Eelmets, M and Chaubey, G and Tambets, K and Litvinov, S and Mormina, M and Xue, Y and Ayub, Q and Zoraqi, G and Korneliussen, TS and Akhatova, F and Lachance, J and Tishkoff, S and Momynaliev, K and Ricaut, FX and Kusuma, P and Razafindrazaka, H and Pierron, D and Cox, MP and Sultana, GN and Willerslev, R and Muller, C and Westaway, M and Lambert, D and Skaro, V and Kovačevic, L and Turdikulova, S and Dalimova, D and Khusainova, R and Trofimova, N and Akhmetova, V and Khidiyatova, I and Lichman, DV and Isakova, J and Pocheshkhova, E and Sabitov, Z and Barashkov, NA and Nymadawa, P and Mihailov, E and Seng, JW and Evseeva, I and Migliano, AB and Abdullah, S and Andriadze, G and Primorac, D and Atramentova, L and Utevska, O and Yepiskoposyan, L and Marjanovic, D and Kushniarevich, A and Behar, DM and Gilissen, C and Vissers, L and Veltman, JA and Balanovska, E and Derenko, M and Malyarchuk, B and Metspalu, A and Fedorova, S and Eriksson, A and Manica, A and Mendez, FL and Karafet, TM and Veeramah, KR and Bradman, N and Hammer, MF and Osipova, LP and Balanovsky, O and Khusnutdinova, EK and Johnsen, K and Remm, M and Thomas, MG and Tyler-Smith, C and Underhill, PA and Willerslev, E and Nielsen, R and Metspalu, M and Villems, R and Kivisild, T}, title = {A recent bottleneck of Y chromosome diversity coincides with a global change in culture.}, journal = {Genome research}, volume = {25}, number = {4}, pages = {459-466}, pmid = {25770088}, issn = {1549-5469}, support = {261213/ERC_/European Research Council/International ; 098051/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R01 GM113657/GM/NIGMS NIH HHS/United States ; BB/H005854/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Base Sequence ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genetic Variation/genetics ; Genetics, Population ; Haplotypes/genetics ; Humans ; Male ; Models, Genetic ; Phylogeny ; Racial Groups/*genetics ; Sequence Analysis, DNA ; }, abstract = {It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.}, }
@article {pmid25762573, year = {2015}, author = {Der Sarkissian, C and Vilstrup, JT and Schubert, M and Seguin-Orlando, A and Eme, D and Weinstock, J and Alberdi, MT and Martin, F and Lopez, PM and Prado, JL and Prieto, A and Douady, CJ and Stafford, TW and Willerslev, E and Orlando, L}, title = {Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids.}, journal = {Biology letters}, volume = {11}, number = {3}, pages = {}, pmid = {25762573}, issn = {1744-957X}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Equidae/*classification/genetics ; Evolution, Molecular ; *Fossils ; *Genome, Mitochondrial ; North America ; Phylogeny ; Sequence Analysis, DNA ; South America ; }, abstract = {Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hippidion could have diverged from the lineage leading to modern equids before 10 Ma. In contrast, a much later divergence date, with Hippidion nesting within modern equids, was indicated by partial ancient mitochondrial DNA sequences. Here, we characterized eight Hippidion complete mitochondrial genomes at 3.4-386.3-fold coverage using target-enrichment capture and next-generation sequencing. Our dataset reveals that the two morphospecies sequenced (H. saldiasi and H. principale) formed a monophyletic clade, basal to extant and extinct Equus lineages. This contrasts with previous genetic analyses and supports Hippidion as a distinct genus, in agreement with palaeontological models. We date the Hippidion split from Equus at 5.6-6.5 Ma, suggesting an early divergence in North America prior to the colonization of South America, after the formation of the Panamanian Isthmus 3.5 Ma and the Great American Biotic Interchange.}, }
@article {pmid25757334, year = {2014}, author = {Dovgerd, AP and Zharkov, DO}, title = {[Application of repair enzymes to improve the quality of degraded DNA templates for PCR amplification].}, journal = {Prikladnaia biokhimiia i mikrobiologiia}, volume = {50}, number = {3}, pages = {264-272}, doi = {10.7868/s0555109914030210}, pmid = {25757334}, issn = {0555-1099}, mesh = {Animals ; Bacterial Proteins/*chemistry ; Bacteriophage T4/chemistry ; Cattle ; DNA Damage ; DNA Glycosylases/chemistry ; DNA Ligase ATP ; DNA Ligases/chemistry ; *DNA Repair ; DNA, Bacterial/*chemistry ; DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry ; Escherichia coli/chemistry ; Humans ; Pancreas/chemistry/enzymology ; Plasmids/*chemistry ; Polymerase Chain Reaction/*methods ; Polynucleotide 5'-Hydroxyl-Kinase/chemistry ; Ribonucleases/chemistry ; Taq Polymerase/chemistry ; Viral Proteins/*chemistry ; }, abstract = {PCR amplification of severely degraded DNA, including ancient DNA, forensic samples, and preparations from deeply processed foodstuffs, is a serious problem. Living organisms have a set of enzymes to repair lesions in their DNA. In this work, we have developed and characterized model systems of degraded high-molecular-weight DNA with a predominance of different types of damage. It was shown that depurination and oxidation of the model plasmid DNA template led to a decrease in the PCR efficiency. A set of enzymes performing a full cycle of excision repair of some lesions was determined. The treatment of model-damaged substrates with this set of enzymes resulted in an increased PCR product yield as compared with that of the unrepaired samples.}, }
@article {pmid25755263, year = {2015}, author = {Schroeder, H and Ávila-Arcos, MC and Malaspinas, AS and Poznik, GD and Sandoval-Velasco, M and Carpenter, ML and Moreno-Mayar, JV and Sikora, M and Johnson, PL and Allentoft, ME and Samaniego, JA and Haviser, JB and Dee, MW and Stafford, TW and Salas, A and Orlando, L and Willerslev, E and Bustamante, CD and Gilbert, MT}, title = {Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {12}, pages = {3669-3673}, pmid = {25755263}, issn = {1091-6490}, support = {R00 GM104158/GM/NIGMS NIH HHS/United States ; F32 HG007342/HG/NHGRI NIH HHS/United States ; K99 GM104158/GM/NIGMS NIH HHS/United States ; R01 GM090087/GM/NIGMS NIH HHS/United States ; T15 LM007033/LM/NLM NIH HHS/United States ; 5F32HG007342/HG/NHGRI NIH HHS/United States ; }, mesh = {Africa/ethnology ; Algorithms ; Archaeology ; Bayes Theorem ; Black People/genetics ; Caribbean Region/ethnology ; Chromosomes, Human, Y/genetics ; Cluster Analysis ; DNA, Mitochondrial/genetics ; *Enslaved Persons ; Enslavement ; Ethnicity/genetics ; Genetic Markers ; *Genetics, Population ; Genome, Human ; *Genome-Wide Association Study ; Haplotypes ; Humans ; Likelihood Functions ; Principal Component Analysis ; Probability ; Sequence Analysis, DNA ; }, abstract = {Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.}, }
@article {pmid25754539, year = {2015}, author = {Xue, HR and Yamaguchi, N and Driscoll, CA and Han, Y and Bar-Gal, GK and Zhuang, Y and Mazak, JH and Macdonald, DW and O'Brien, SJ and Luo, SJ}, title = {Genetic ancestry of the extinct Javan and Bali tigers.}, journal = {The Journal of heredity}, volume = {106}, number = {3}, pages = {247-257}, pmid = {25754539}, issn = {1465-7333}, mesh = {Animals ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Gene Flow ; *Genetics, Population ; Haplotypes ; *Phylogeny ; Sequence Analysis, DNA ; Tigers/*genetics ; }, abstract = {The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating little or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers.}, }
@article {pmid25754342, year = {2015}, author = {Mokrousov, I}, title = {Mycobacterium tuberculosis phylogeography in the context of human migration and pathogen's pathobiology: Insights from Beijing and Ural families.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {95 Suppl 1}, number = {}, pages = {S167-76}, doi = {10.1016/j.tube.2015.02.031}, pmid = {25754342}, issn = {1873-281X}, mesh = {Africa/epidemiology ; Beijing/ethnology ; Genotype ; Global Health ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Ancient ; *Human Migration ; Humans ; Japan/epidemiology ; Mycobacterium tuberculosis/*genetics ; Oceania/epidemiology ; Phylogeography ; Prevalence ; Russia/ethnology ; South America/epidemiology ; Tuberculosis/ethnology/*genetics/history ; }, abstract = {Here, I review the population structure and phylogeography of the two contrasting families of Mycobacterium tuberculosis, Beijing and Ural, in the context of strain pathobiology and human history and migration. Proprietary database (12-loci MIRU-VNTR profiles of 3067 Beijing genotype isolates) was subjected to phylogenetic and statistical analysis. The highest rate (90%) and diversity (HGI 0.80-0.95) of the Beijing genotype in North China suggest it to be its area of origin. Under VNTR-based MDS analysis the interpopulation genetic distances correlated with geography over uninterrupted landmasses. In contrast, large water distances together with long time generated remarkable outliers. Weak and less expected affinities of the distant M. tuberculosis populations may reflect hidden epidemiological links due to unknown migration. Association with drug-resistance or increased virulence/transmissibility along with particular human migration flows shape global dissemination of some Beijing clones. The paucity of data on the Ural genotype prevents from high-resolution analysis that was mainly based on the available spoligotyping data. The North/East Pontic area marked with the highest prevalence of the Ural family may have been the area of its origin and primary dispersal in Eurasia. Ural strains are not marked by increased pathogenic capacities, increased transmissibility and association with drug resistance (but most recent reports describe an alarming increase of MDR Ural strains in some parts of eastern Europe and northwestern Russia). Large-scale SNP or WGS population-based studies targeting strains from indigenous populations and, eventually, analysis of ancient DNA will better test these hypotheses. Host genetics factors likely play the most prominent role in differential dissemination of particular M. tuberculosis genotypes.}, }
@article {pmid25754341, year = {2015}, author = {Lösch, S and Kim, MR and Dutour, O and Courtaud, P and Maixner, F and Romon, T and Sola, C and Zink, A}, title = {Evidence for tuberculosis in 18th/19th century slaves in Anse Sainte-Marguerite (Guadeloupe - French Western Indies).}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {95 Suppl 1}, number = {}, pages = {S65-8}, doi = {10.1016/j.tube.2015.02.006}, pmid = {25754341}, issn = {1873-281X}, mesh = {Actins/genetics ; Adolescent ; Adult ; Black People/genetics ; Child ; DNA, Bacterial/genetics ; Enslaved Persons/*history ; Female ; Guadeloupe ; History, 18th Century ; History, 19th Century ; Humans ; Male ; Mycobacterium tuberculosis/genetics ; Nucleic Acid Amplification Techniques ; Paleopathology ; Polymerase Chain Reaction ; Tuberculosis, Osteoarticular/*history ; Young Adult ; }, abstract = {During the American colonization in the 18th and 19th century, Africans were captured and shipped to America. Harsh living and working conditions often led to chronic diseases and high mortality rates. Slaves in the Caribbean were forced to work mainly on sugar plantations. They were buried in cemeteries like Anse Sainte-Marguerite on the isle of Grande-Terre (Guadeloupe) which was examined by archaeologists and physical anthropologists. Morphological studies on osseous remains of 148 individuals revealed 15 cases with signs for bone tuberculosis and a high frequency of periosteal reactions which indicates early stages of the disease. 11 bone samples from these cemeteries were analysed for ancient DNA. The samples were extracted with established procedures and examined for the cytoplasmic multicopy β-actin gene and Mycobacterium tuberculosis complex DNA (IS 6110) by PCR. An amplification product for M. tuberculosis with the size of 123 bp was obtained. Sequencing confirmed the result. This study shows evidence of M. tuberculosis complex DNA in a Caribbean slave population.}, }
@article {pmid25753251, year = {2015}, author = {Alter, SE and Meyer, M and Post, K and Czechowski, P and Gravlund, P and Gaines, C and Rosenbaum, HC and Kaschner, K and Turvey, ST and van der Plicht, J and Shapiro, B and Hofreiter, M}, title = {Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100.}, journal = {Molecular ecology}, volume = {24}, number = {7}, pages = {1510-1522}, doi = {10.1111/mec.13121}, pmid = {25753251}, issn = {1365-294X}, support = {310763/ERC_/European Research Council/International ; }, mesh = {Animals ; Arctic Regions ; Atlantic Ocean ; *Climate Change ; DNA, Mitochondrial/genetics ; Ecosystem ; Fossils ; *Genetic Variation ; Haplotypes ; Models, Biological ; Molecular Sequence Data ; Phylogeography ; Population Dynamics ; Sequence Analysis, DNA ; Whales/*genetics ; }, abstract = {Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.}, }
@article {pmid25741209, year = {2014}, author = {Nesheva, D}, title = {Aspects of ancient mitochondrial DNA analysis in different populations for understanding human evolution.}, journal = {Balkan journal of medical genetics : BJMG}, volume = {17}, number = {1}, pages = {5-14}, pmid = {25741209}, issn = {1311-0160}, abstract = {The evolution of modern humans is a long and difficult process which started from their first appearance and continues to the present day. The study of the genetic origin of populations can help to determine population kinship and to better understand the gradual changes of the gene pool in space and time. Mitochondrial DNA (mtDNA) is a proper tool for the determination of the origin of populations due to its high evolutionary importance. Ancient mitochondrial DNA retrieved from museum specimens, archaeological finds and fossil remains can provide direct evidence for population origins and migration processes. Despite the problems with contaminations and authenticity of ancient mitochondrial DNA, there is a developed set of criteria and platforms for obtaining authentic ancient DNA. During the last two decades, the application of different methods and techniques for analysis of ancient mitochondrial DNA gave promising results. Still, the literature is relatively poor with information for the origin of human populations. Using comprehensive phylogeographic and population analyses we can observe the development and formation of the contemporary populations. The aim of this study was to shed light on human migratory processes and the formation of populations based on available ancient mtDNA data.}, }
@article {pmid25735209, year = {2015}, author = {Pansu, J and Giguet-Covex, C and Ficetola, GF and Gielly, L and Boyer, F and Zinger, L and Arnaud, F and Poulenard, J and Taberlet, P and Choler, P}, title = {Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA.}, journal = {Molecular ecology}, volume = {24}, number = {7}, pages = {1485-1498}, doi = {10.1111/mec.13136}, pmid = {25735209}, issn = {1365-294X}, mesh = {Agriculture ; Climate Change ; DNA Barcoding, Taxonomic ; DNA, Plant/genetics ; *Ecosystem ; Geologic Sediments/*analysis ; High-Throughput Nucleotide Sequencing ; Humans ; *Lakes ; Plants/*classification/genetics ; Population Dynamics ; }, abstract = {Paleoenvironmental studies are essential to understand biodiversity changes over long timescales and to assess the relative importance of anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA) is an emerging tool in the field of paleoecology and has proven to be a complementary approach to the use of pollen and macroremains for investigating past community changes. SedaDNA-based reconstructions of ancient environments often rely on indicator taxa or expert knowledge, but quantitative ecological analyses might provide more objective information. Here, we analysed sedaDNA to investigate plant community trajectories in the catchment of a high-elevation lake in the Alps over the last 6400 years. We combined data on past and present plant species assemblages along with sedimentological and geochemical records to assess the relative impact of human activities through pastoralism, and abiotic factors (temperature and soil evolution). Over the last 6400 years, we identified significant variation in plant communities, mostly related to soil evolution and pastoral activities. An abrupt vegetational change corresponding to the establishment of an agropastoral landscape was detected during the Late Holocene, approximately 4500 years ago, with the replacement of mountain forests and tall-herb communities by heathlands and grazed lands. Our results highlight the importance of anthropogenic activities in mountain areas for the long-term evolution of local plant assemblages. SedaDNA data, associated with other paleoenvironmental proxies and present plant assemblages, appear to be a relevant tool for reconstruction of plant cover history. Their integration, in conjunction with classical tools, offers interesting perspectives for a better understanding of long-term ecosystem dynamics under the influence of human-induced and environmental drivers.}, }
@article {pmid25731166, year = {2015}, author = {Haak, W and Lazaridis, I and Patterson, N and Rohland, N and Mallick, S and Llamas, B and Brandt, G and Nordenfelt, S and Harney, E and Stewardson, K and Fu, Q and Mittnik, A and Bánffy, E and Economou, C and Francken, M and Friederich, S and Pena, RG and Hallgren, F and Khartanovich, V and Khokhlov, A and Kunst, M and Kuznetsov, P and Meller, H and Mochalov, O and Moiseyev, V and Nicklisch, N and Pichler, SL and Risch, R and Rojo Guerra, MA and Roth, C and Szécsényi-Nagy, A and Wahl, J and Meyer, M and Krause, J and Brown, D and Anthony, D and Cooper, A and Alt, KW and Reich, D}, title = {Massive migration from the steppe was a source for Indo-European languages in Europe.}, journal = {Nature}, volume = {522}, number = {7555}, pages = {207-211}, pmid = {25731166}, issn = {1476-4687}, support = {/HHMI_/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Cultural Evolution/*history ; Europe/ethnology ; Genome, Human/genetics ; *Grassland ; History, Ancient ; Human Migration/*history ; Humans ; Language/*history ; Male ; Polymorphism, Genetic/genetics ; Population Dynamics ; Russia ; }, abstract = {We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian. By ∼6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.}, }
@article {pmid25726364, year = {2015}, author = {Hershkovitz, I and Donoghue, HD and Minnikin, DE and May, H and Lee, OY and Feldman, M and Galili, E and Spigelman, M and Rothschild, BM and Bar-Gal, GK}, title = {Tuberculosis origin: The Neolithic scenario.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {95 Suppl 1}, number = {}, pages = {S122-6}, doi = {10.1016/j.tube.2015.02.021}, pmid = {25726364}, issn = {1873-281X}, mesh = {Adult ; Animals ; Biomarkers/analysis ; Cattle ; Chromatography, High Pressure Liquid ; DNA, Bacterial/analysis/genetics ; Female ; History, Ancient ; Humans ; Infant ; Lipids/analysis ; Male ; Mycobacterium tuberculosis/genetics ; Mycolic Acids/analysis ; Paleopathology/*methods ; Tuberculosis, Osteoarticular/genetics/*history/pathology ; }, abstract = {This paper follows the dramatic changes in scientific research during the last 20 years regarding the relationship between the Mycobacterium tuberculosis complex and its hosts - bovids and/or humans. Once the M. tuberculosis and Mycobacterium bovis genomes were sequenced, it became obvious that the old story of M. bovis evolving into the human pathogen should be reversed, as M. tuberculosis is more ancestral than M. bovis. Nevertheless, the timescale and geographical origin remained an enigma. In the current study human and cattle bone samples were examined for evidence of tuberculosis from the site of Atlit-Yam in the Eastern Mediterranean, dating from 9250 to 8160 (calibrated) years ago. Strict precautions were used to prevent contamination in the DNA analysis, and independent centers used to confirm authenticity of findings. DNA from five M. tuberculosis genetic loci was detected and had characteristics consistent with extant genetic lineages. High performance liquid chromatography was used as an independent method of verification and it directly detected mycolic acid lipid biomarkers, specific for the M. tuberculosis complex. These, together with pathological changes detected in some of the bones, confirm the presence of the disease in the Levantine populations during the Pre-pottery Neolithic C period, more than 8000 years ago.}, }
@article {pmid25722413, year = {2015}, author = {Smith, O and Momber, G and Bates, R and Garwood, P and Fitch, S and Pallen, M and Gaffney, V and Allaby, RG}, title = {Archaeology. Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago.}, journal = {Science (New York, N.Y.)}, volume = {347}, number = {6225}, pages = {998-1001}, doi = {10.1126/science.1261278}, pmid = {25722413}, issn = {1095-9203}, mesh = {DNA, Plant/genetics/*history ; Fossils ; Geologic Sediments/chemistry ; History, Ancient ; Triticum/anatomy &amp; histology/genetics/*history ; United Kingdom ; }, abstract = {The Mesolithic-to-Neolithic transition marked the time when a hunter-gatherer economy gave way to agriculture, coinciding with rising sea levels. Bouldnor Cliff, is a submarine archaeological site off the Isle of Wight in the United Kingdom that has a well-preserved Mesolithic paleosol dated to 8000 years before the present. We analyzed a core obtained from sealed sediments, combining evidence from microgeomorphology and microfossils with sedimentary ancient DNA (sedaDNA) analyses to reconstruct floral and faunal changes during the occupation of this site, before it was submerged. In agreement with palynological analyses, the sedaDNA sequences suggest a mixed habitat of oak forest and herbaceous plants. However, they also provide evidence of wheat 2000 years earlier than mainland Britain and 400 years earlier than proximate European sites. These results suggest that sophisticated social networks linked the Neolithic front in southern Europe to the Mesolithic peoples of northern Europe.}, }
@article {pmid25711463, year = {2015}, author = {Hubbard, AR and Guatelli-Steinberg, D and Irish, JD}, title = {Do nuclear DNA and dental nonmetric data produce similar reconstructions of regional population history? An example from modern coastal Kenya.}, journal = {American journal of physical anthropology}, volume = {157}, number = {2}, pages = {295-304}, doi = {10.1002/ajpa.22714}, pmid = {25711463}, issn = {1096-8644}, mesh = {Adult ; Anthropology, Physical ; Black People/*genetics/*statistics &amp; numerical data ; Female ; Genetics, Population ; Humans ; Kenya/epidemiology ; Male ; Microsatellite Repeats/genetics ; Phenotype ; Tooth/*anatomy &amp; histology ; }, abstract = {This study investigates whether variants in dental morphology and nuclear DNA provide similar patterns of intergroup affinity among regional populations using biological distance (biodistance) estimates. Many biodistance studies of archaeological populations use skeletal variants in lieu of ancient DNA, based on the widely accepted assumption of a strong correlation between phenetic- and genetic-based affinities. Within studies of dental morphology, this assumption has been well supported by research on a global scale but remains unconfirmed at a more geographically restricted scale. Paired genetic (42 microsatellite loci) and dental (nine crown morphology traits) data were collected from 295 individuals among four contemporary Kenyan populations, two of which are known ethnically as "Swahili" and two as "Taita;" all have well-documented population histories. The results indicate that biodistances based on genetic data are correlated with those obtained from dental morphology. Specifically, both distance matrices indicate that the closest affinities are between population samples within each ethnic group. Both also identify greater divergence among samples from the different ethnic groups. However, for this particular study the genetic data may provide finer resolution at detecting overall among-population relationships.}, }
@article {pmid25700511, year = {2015}, author = {Kemp, BM and Lindo, J and Bolnick, DA and Malhi, RS and Chatters, JC}, title = {Anthropology. Response to Comment on "Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans".}, journal = {Science (New York, N.Y.)}, volume = {347}, number = {6224}, pages = {835}, doi = {10.1126/science.1261188}, pmid = {25700511}, issn = {1095-9203}, mesh = {*Biological Evolution ; Humans ; Indians, North American/*genetics ; *Skeleton ; }, abstract = {Prüfer and Meyer raise concerns over the mitochondrial DNA (mtDNA) results we reported for the Hoyo Negro individual, citing failure of a portion of these data to conform to their expectations of ancient DNA (aDNA). Because damage patterns in aDNA vary, outright rejection of our findings on this basis is unwarranted, especially in light of our other observations.}, }
@article {pmid25700495, year = {2015}, author = {Balter, M and Gibbons, A}, title = {Ancient DNA. Indo-European languages tied to herders.}, journal = {Science (New York, N.Y.)}, volume = {347}, number = {6224}, pages = {814-815}, doi = {10.1126/science.347.6224.814}, pmid = {25700495}, issn = {1095-9203}, mesh = {DNA/genetics/*history ; DNA Fingerprinting/methods ; Europe ; Genome, Human/*genetics ; Grassland ; History, Ancient ; *Human Migration ; Humans ; India ; Language/*history ; Skeleton ; }, }
@article {pmid25680828, year = {2015}, author = {Donoghue, HD and Michael Taylor, G and Marcsik, A and Molnár, E and Pálfi, G and Pap, I and Teschler-Nicola, M and Pinhasi, R and Erdal, YS and Velemínsky, P and Likovsky, J and Belcastro, MG and Mariotti, V and Riga, A and Rubini, M and Zaio, P and Besra, GS and Lee, OY and Wu, HH and Minnikin, DE and Bull, ID and O'Grady, J and Spigelman, M}, title = {A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {31}, number = {}, pages = {250-256}, doi = {10.1016/j.meegid.2015.02.001}, pmid = {25680828}, issn = {1567-7257}, support = {MR/K012118/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Europe/epidemiology ; Female ; Genotype ; History, Medieval ; *Human Migration ; Humans ; Leprosy/*epidemiology/history/*transmission ; Male ; Middle Aged ; *Models, Statistical ; Mycobacterium leprae/genetics ; Paleopathology ; Young Adult ; }, abstract = {Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th-11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th-8th century Northern Italy, 7th-11th century Hungary, 8th-9th century Austria, the Slavic Greater Moravian Empire of the 9th-10th century and 8th-10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor.}, }
@article {pmid25673485, year = {2015}, author = {Shaw, KJ and Brown, KA and Brown, TA and Haswell, SJ}, title = {Sex identification of ancient DNA samples using a microfluidic device.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1274}, number = {}, pages = {93-98}, doi = {10.1007/978-1-4939-2353-3_8}, pmid = {25673485}, issn = {1940-6029}, mesh = {Animals ; Bone and Bones/chemistry ; DNA/*chemistry ; DNA Fingerprinting/*methods ; Female ; Humans ; Male ; Microfluidic Analytical Techniques/*methods ; }, abstract = {Ancient DNA is the name given to the degraded, fragmented, and chemically damaged biomolecules that can be recovered from archaeological remains of plants, animals, and humans. Where ancient human DNA has survived at archaeological sites, it can give valuable information and is especially useful for its potential to identify kinship, population affinities, pathogens, and biological sex. Here, we describe the operation of a microfluidic device for the sex identification of ancient DNA samples using an efficient sample handling process. DNA is extracted from powdered bone samples and abasic sites labeled with biotin. Streptavidin-coated superparamagnetic particles are used to isolate the labeled DNA prior to amplification of the Amelogenin sex marker.}, }
@article {pmid25667090, year = {2014}, author = {Zink, A and Wann, LS and Thompson, RC and Keller, A and Maixner, F and Allam, AH and Finch, CE and Frohlich, B and Kaplan, H and Lombardi, GP and Sutherland, ML and Sutherland, JD and Watson, L and Cox, SL and Miyamoto, MI and Narula, J and Stewart, AF and Thomas, GS and Krause, J}, title = {Genomic correlates of atherosclerosis in ancient humans.}, journal = {Global heart}, volume = {9}, number = {2}, pages = {203-209}, doi = {10.1016/j.gheart.2014.03.2453}, pmid = {25667090}, issn = {2211-8179}, mesh = {Atherosclerosis/diagnostic imaging/*genetics ; Egypt ; *Genomics ; Humans ; Imaging, Three-Dimensional ; Italy ; *Mummies ; Tomography, X-Ray Computed ; }, abstract = {Paleogenetics offers a unique opportunity to study human evolution, population dynamics, and disease evolution in situ. Although histologic and computed x-ray tomographic investigations of ancient mummies have clearly shown that atherosclerosis has been present in humans for more than 5,000 years, limited data are available on the presence of genetic predisposition for cardiovascular disease in ancient human populations. In a previous whole-genome study of the Tyrolean Iceman, a 5,300-year-old glacier mummy from the Alps, an increased risk for coronary heart disease was detected. The Iceman's genome revealed several single nucleotide polymorphisms that are linked with cardiovascular disease in genome-wide association studies. Future genetic studies of ancient humans from various geographic origins and time periods have the potential to provide more insights into the presence and possible changes of genetic risk factors in our ancestors. The study of ancient humans and a better understanding of the interaction between environmental and genetic influences on the development of heart diseases may lead to a more effective prevention and treatment of the most common cause of death in the modern world.}, }
@article {pmid25655399, year = {2015}, author = {Gering, E and Johnsson, M and Willis, P and Getty, T and Wright, D}, title = {Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs.}, journal = {Molecular ecology}, volume = {24}, number = {9}, pages = {2112-2124}, doi = {10.1111/mec.13096}, pmid = {25655399}, issn = {1365-294X}, mesh = {Animals ; *Biological Evolution ; Breeding ; Chickens/*genetics ; Color ; DNA, Mitochondrial/genetics ; Feathers ; Gene Pool ; *Genetics, Population ; Genotype ; Hawaii ; *Hybridization, Genetic ; Introduced Species ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Vocalization, Animal ; }, abstract = {A major goal of invasion genetics is to determine how establishment histories shape non-native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D-loop &amp; whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancient DNA sequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNA clade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increased G. gallus density on Kauai within the last few decades. SNPs obtained from whole-genome sequencing were consistent with historic admixture between Kauai's divergent (G. gallus) lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feral G. gallus descend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.}, }
@article {pmid25649153, year = {2015}, author = {Novo, SP and Leles, D and Bianucci, R and Araujo, A}, title = {Leishmania tarentolae molecular signatures in a 300 hundred-years-old human Brazilian mummy.}, journal = {Parasites &amp; vectors}, volume = {8}, number = {}, pages = {72}, pmid = {25649153}, issn = {1756-3305}, mesh = {Bone Marrow/parasitology ; Brazil ; DNA, Protozoan/genetics ; History, 18th Century ; History, 19th Century ; Humans ; Leishmania/classification/genetics/*isolation &amp; purification ; Leishmaniasis/history/*parasitology ; Male ; Mummies/history/*parasitology ; }, abstract = {BACKGROUND: L. tarentolae, the lizard-infecting species of Old World geckos, has been classified as non-pathogenic to man. While it has been demonstrated that L. tarentolae is capable of infecting human phagocytic cells and to differentiate into amastigote-like forms, there is no clear evidence for its efficient replication within macrophages. Here we provide first evidence for L. tarentolae ancient DNA sequences from bone marrow and intestines of a 300yo adult male.<br><br>METHODS: We identified molecular signatures of Leishmania tarentolae, the lizard-infecting species of Old World geckos, in hard and soft tissue biopsies from a Brazilian mummy (A74) uncovered in Itacambira (Brazil) and dating to the Colonial Period (end of 18th/beginning of the 19th century).<br><br>RESULTS: Our results imply that efficient replication of the parasite occurred within human macrophage and to lead to a systemic spread and visceralization in this individual. The ancient sequences show a 100% similarity with those of isolated L. tarentolae parasites grown on artificial nutrient media and a 99% similarity with two modern sequences isolated from reptiles.<br><br>CONCLUSIONS: De facto, our findings re-open the debate about the potential survival of ancient L. tarentolae strain within human macrophage and its ability to spread systemically. They also raise ecological issues since it is unknown whether this parasite circulates in the reptilian reservoir in modern day Brazil or not. Investigations on fossil fauna and arthropods are needed to shed light on the interactions between saurian Leishmania and lizards in Brazil's remote and recent past.}, }
@article {pmid25646523, year = {2015}, author = {Evin, A and Flink, LG and Bălăşescu, A and Popovici, D and Andreescu, R and Bailey, D and Mirea, P and Lazăr, C and Boroneanţ, A and Bonsall, C and Strand Vidarsdottir, U and Brehard, S and Tresset, A and Cucchi, T and Larson, G and Dobney, K}, title = {Correction to 'Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania'.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1664}, pages = {20150018}, doi = {10.1098/rstb.2015.0018}, pmid = {25646523}, issn = {1471-2970}, }
@article {pmid25640964, year = {2015}, author = {Emerson, BC and Hickerson, MJ}, title = {Lack of support for the time-dependent molecular evolution hypothesis.}, journal = {Molecular ecology}, volume = {24}, number = {4}, pages = {702-709}, doi = {10.1111/mec.13070}, pmid = {25640964}, issn = {1365-294X}, mesh = {Animals ; *Evolution, Molecular ; Genetics, Population ; Humans ; *Models, Genetic ; *Mutation Rate ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {There is increasing momentum surrounding the hypothesis that rates of molecular evolution between individuals within contemporary populations are high, and that these rates decrease as a function of time, perhaps over several millions of years, before reaching stationarity. The implications of this are powerful, potentially reshaping our view of how climate history impacts upon both species distribution patterns and the geographic structuring of genetic variation within species. However, our assessment of the hypothesis reveals a lack of theoretical support and empirical evidence for hypothesized magnitudes of time-dependent rates of molecular evolution, with much of the apparent rate changes coming from artefacts and biases inherent in the methods of rate estimation. Our assessment also reveals a problem with how serial sampling is implemented for mutation rate estimation using ancient DNA samples, rendering published estimates unreliable.}, }
@article {pmid25637221, year = {2015}, author = {Murat, F and Zhang, R and Guizard, S and Gavranović, H and Flores, R and Steinbach, D and Quesneville, H and Tannier, E and Salse, J}, title = {Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.}, journal = {Genome biology and evolution}, volume = {7}, number = {3}, pages = {735-749}, pmid = {25637221}, issn = {1759-6653}, mesh = {Chromosomes, Plant ; Crops, Agricultural/*genetics ; *Evolution, Molecular ; Gene Duplication ; *Gene Order ; *Genome, Plant ; Genomics ; *Karyotype ; Magnoliopsida/classification/*genetics ; Phylogeny ; Polyploidy ; Synteny ; }, abstract = {We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, "DicotSyntenyViewer" (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids.}, }
@article {pmid25636226, year = {2015}, author = {Hassanin, A and Khouider, S and Gembu, GC and Goodman, SM and Kadjo, B and Nesi, N and Pourrut, X and Nakouné, E and Bonillo, C}, title = {The comparative phylogeography of fruit bats of the tribe Scotonycterini (Chiroptera, Pteropodidae) reveals cryptic species diversity related to African Pleistocene forest refugia.}, journal = {Comptes rendus biologies}, volume = {338}, number = {3}, pages = {197-211}, doi = {10.1016/j.crvi.2014.12.003}, pmid = {25636226}, issn = {1768-3238}, mesh = {Africa ; Animals ; Base Sequence ; Bayes Theorem ; Chiroptera/*classification/genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Female ; *Forests ; Gene Flow ; Haplotypes ; Introns/genetics ; Male ; *Phylogeny ; Phylogeography ; Species Specificity ; }, abstract = {The hypothesis of Pleistocene forest refugia was tested using comparative phylogeography of Scotonycterini, a fruit bat tribe endemic to Africa containing four species: Scotonycteris zenkeri, Casinycteris argynnis, C. campomaanensis, and C. ophiodon. Patterns of genetic structure were assessed using 105 Scotonycterini (including material from three holotypes) collected at 37 localities, and DNA sequences from the mitochondrial cytochrome b gene (1140 nt) and 12 nuclear introns (9641 nt). Phylogenetic trees and molecular dating were inferred by Bayesian methods. Multilocus analyses were performed using supermatrix, SuperTRI, and *BEAST approaches. Mitochondrial analyses reveal strong phylogeographical structure in Scotonycteris, with four divergent haplogroups (4.9-8.7%), from Upper Guinea, Cameroon, western Equatorial Africa, and eastern Democratic Republic of the Congo (DRC). In C. argynnis, we identify two mtDNA haplogroups corresponding to western and eastern Equatorial Africa (1.4-2.1%). In C. ophiodon, the mtDNA haplotypes from Cameroon and Ivory Coast differ by only 1.3%. Nuclear analyses confirm the validity of the recently described C. campomaanensis and indicate that western and eastern populations of C. argynnis are not fully isolated. All mtDNA clusters detected in Scotonycteris are found to be monophyletic based on the nuclear dataset, except in eastern DRC. In the nuclear tree, the clade from western Equatorial Africa is closely related to individuals from eastern DRC, whereas in the mitochondrial tree it appears to be the sister-group of the Cameroon clade. Migrate-n analyses support gene flow from western Equatorial Africa to eastern DRC. Molecular dating indicates that Pleistocene forest refugia have played an important role in shaping the evolution of Scotonycterini, with two phases of allopatric speciation at approximately 2.7 and 1.6 Mya, resulting from isolation in three main forest areas corresponding to Upper Guinea, Cameroon, and Equatorial Africa. Two cryptic species and two subspecies are described herein in the genus Scotonycteris. Female philopatry and male biased dispersal are supported for the smallest taxa, i.e., the three species of Scotonycteris and C. argynnis. The Congo, Ntem, and Sanaga rivers are identified as biogeographic barriers to the dispersal of Scotonycteris during interglacial periods. A greater capacity for long-distance dispersal is inferred for the largest species, C. ophiodon.}, }
@article {pmid25619123, year = {2015}, author = {Perry, GH and Orlando, L}, title = {Ancient DNA and human evolution.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {1-3}, doi = {10.1016/j.jhevol.2014.12.002}, pmid = {25619123}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; *DNA/analysis/genetics ; Fossils ; Hominidae/*genetics ; Humans ; *Paleontology ; }, }
@article {pmid25613391, year = {2015}, author = {Parks, M and Lambert, D}, title = {Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {19}, pmid = {25613391}, issn = {1471-2164}, mesh = {Base Composition ; Computational Biology ; *Computer Simulation ; DNA/genetics/*metabolism ; DNA Damage/*genetics ; High-Throughput Nucleotide Sequencing ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Massively parallel sequencing platforms, featuring high throughput and relatively short read lengths, are well suited to ancient DNA (aDNA) studies. Variant identification from short-read alignment could be hindered, however, by low DNA concentrations common to historic samples, which constrain sequencing depths, and post-mortem DNA damage patterns.<br><br>RESULTS: We simulated pairs of sequences to act as reference and sample genomes at varied GC contents and divergence levels. Short-read sequence pools were generated from sample sequences, and subjected to varying levels of "post-mortem" damage by adjusting levels of fragmentation and fragmentation biases, transition rates at sequence ends, and sequencing depths. Mapping of sample read pools to reference sequences revealed several trends, including decreased alignment success with increased read length and decreased variant recovery with increased divergence. Variants were generally called with high accuracy, however identification of SNPs (single-nucleotide polymorphisms) was less accurate for high damage/low divergence samples. Modest increases in sequencing depth resulted in rapid gains in total variant recovery, and limited improvements to recovery of heterozygous variants.<br><br>CONCLUSIONS: This in silico study suggests aDNA-associated damage patterns minimally impact variant call accuracy and recovery from short-read alignment, while modest increases in sequencing depth can greatly improve variant recovery.}, }
@article {pmid25601038, year = {2015}, author = {Marciniak, S and Klunk, J and Devault, A and Enk, J and Poinar, HN}, title = {Ancient human genomics: the methodology behind reconstructing evolutionary pathways.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {21-34}, doi = {10.1016/j.jhevol.2014.11.003}, pmid = {25601038}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; DNA/analysis/genetics ; *Fossils ; *Genomics ; *High-Throughput Nucleotide Sequencing ; Hominidae/*genetics ; Humans ; }, abstract = {High-throughput sequencing (HTS) has radically altered approaches to human evolutionary research. Recent contributions highlight that HTS is able to reach depths of the human lineage previously thought to be impossible. In this paper, we outline the methodological advances afforded by recent developments in DNA recovery, data output, scalability, speed, and resolution of the current sequencing technology. We review and critically evaluate the 'DNA pipeline' for ancient samples: from DNA extraction, to constructing immortalized sequence libraries, to enrichment strategies (e.g., polymerase chain reaction [PCR] and hybridization capture), and finally, to bioinformatic analyses of sequence data. We argue that continued evaluations and improvements to this process are essential to ensure sequence data validity. Also, we highlight the role of contamination and authentication in ancient DNA-HTS, which is particularly relevant to ancient human genomics, since sequencing the genomes of hominins such as Homo erectus and Homo heidelbergensis may soon be within the realm of possibility.}, }
@article {pmid25598858, year = {2014}, author = {Steinrücken, M and Bhaskar, A and Song, YS}, title = {A NOVEL SPECTRAL METHOD FOR INFERRING GENERAL DIPLOID SELECTION FROM TIME SERIES GENETIC DATA.}, journal = {The annals of applied statistics}, volume = {8}, number = {4}, pages = {2203-2222}, pmid = {25598858}, issn = {1932-6157}, support = {R01 GM094402/GM/NIGMS NIH HHS/United States ; }, abstract = {The increased availability of time series genetic variation data from experimental evolution studies and ancient DNA samples has created new opportunities to identify genomic regions under selective pressure and to estimate their associated fitness parameters. However, it is a challenging problem to compute the likelihood of non-neutral models for the population allele frequency dynamics, given the observed temporal DNA data. Here, we develop a novel spectral algorithm to analytically and efficiently integrate over all possible frequency trajectories between consecutive time points. This advance circumvents the limitations of existing methods which require fine-tuning the discretization of the population allele frequency space when numerically approximating requisite integrals. Furthermore, our method is flexible enough to handle general diploid models of selection where the heterozygote and homozygote fitness parameters can take any values, while previous methods focused on only a few restricted models of selection. We demonstrate the utility of our method on simulated data and also apply it to analyze ancient DNA data from genetic loci associated with coat coloration in horses. In contrast to previous studies, our exploration of the full fitness parameter space reveals that a heterozygote-advantage form of balancing selection may have been acting on these loci.}, }
@article {pmid25577019, year = {2015}, author = {Allaby, RG and Kistler, L and Gutaker, RM and Ware, R and Kitchen, JL and Smith, O and Clarke, AC}, title = {Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant-hominin co-evolution back to the Pliocene.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {150-157}, doi = {10.1016/j.jhevol.2014.10.014}, pmid = {25577019}, issn = {1095-8606}, support = {BB/G0177941//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological/*genetics ; Agriculture ; Animals ; Archaeology ; *Biological Evolution ; DNA, Plant/genetics ; Genome, Plant/*genetics ; Genomics/*methods ; Hominidae ; Humans ; Plant Physiological Phenomena/*genetics ; Plants/*genetics ; }, abstract = {The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plant-hominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plant-hominin co-evolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage.}, }
@article {pmid25563409, year = {2015}, author = {Perry, GH and Kistler, L and Kelaita, MA and Sams, AJ}, title = {Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {55-63}, doi = {10.1016/j.jhevol.2014.10.018}, pmid = {25563409}, issn = {1095-8606}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA/analysis/genetics ; DNA Copy Number Variations ; Feeding Behavior/*physiology ; Fossils ; Genetic Variation ; Genomics ; Hominidae/*genetics/*physiology ; Humans ; Molecular Sequence Data ; Myosin Heavy Chains/genetics ; Neanderthals ; Paleontology ; Phenotype ; Receptors, G-Protein-Coupled/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Taste Receptors, Type 2 ; }, abstract = {Nuclear genome sequence data from Neandertals, Denisovans, and archaic anatomically modern humans can be used to complement our understanding of hominin evolutionary biology and ecology through i) direct inference of archaic hominin phenotypes, ii) indirect inference of those phenotypes by identifying the effects of previously-introgressed alleles still present among modern humans, or iii) determining the evolutionary timing of relevant hominin-specific genetic changes. Here we review and reanalyze published Neandertal and Denisovan genome sequence data to illustrate an example of the third approach. Specifically, we infer the timing of five human gene presence/absence changes that may be related to particular hominin-specific dietary changes and discuss these results in the context of our broader reconstructions of hominin evolutionary ecology. We show that pseudogenizing (gene loss) mutations in the TAS2R62 and TAS2R64 bitter taste receptor genes and the MYH16 masticatory myosin gene occurred after the hominin-chimpanzee divergence but before the divergence of the human and Neandertal/Denisovan lineages. The absence of a functional MYH16 protein may explain our relatively reduced jaw muscles; this gene loss may have followed the adoption of cooking behavior. In contrast, salivary amylase gene (AMY1) duplications were not observed in the Neandertal and Denisovan genomes, suggesting a relatively recent origin for the AMY1 copy number gains that are observed in modern humans. Thus, if earlier hominins were consuming large quantities of starch-rich underground storage organs, as previously hypothesized, then they were likely doing so without the digestive benefits of increased salivary amylase production. Our most surprising result was the observation of a heterozygous mutation in the first codon of the TAS2R38 bitter taste receptor gene in the Neandertal individual, which likely would have resulted in a non-functional protein and inter-individual PTC (phenylthiocarbamide) taste sensitivity variation, as also observed in both humans and chimpanzees.}, }
@article {pmid25559298, year = {2015}, author = {Warinner, C and Speller, C and Collins, MJ and Lewis, CM}, title = {Ancient human microbiomes.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {125-136}, pmid = {25559298}, issn = {1095-8606}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM089886/GM/NIGMS NIH HHS/United States ; R01 GM089886)/GM/NIGMS NIH HHS/United States ; }, mesh = {Dental Calculus/microbiology ; Diet ; Feces/microbiology ; Health/history ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Humans ; Metagenomics ; *Microbiota ; *Paleontology ; }, abstract = {Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.}, }
@article {pmid25556846, year = {2015}, author = {Matisoo-Smith, E}, title = {Ancient DNA and the human settlement of the Pacific: a review.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {93-104}, doi = {10.1016/j.jhevol.2014.10.017}, pmid = {25556846}, issn = {1095-8606}, mesh = {Archaeology ; DNA/analysis/*genetics ; *Evolution, Molecular ; History, Ancient ; Human Migration/*history ; Humans ; Polynesia ; }, abstract = {The Pacific region provides unique opportunities to study human evolution including through analyses of ancient DNA. While some of the earliest studies involving ancient DNA from skeletal remains focused on Pacific samples, in the following 25 years, several factors meant that little aDNA research, particularly research focused on human populations, has emerged. This paper briefly presents the genetic evidence for population origins, reviews what ancient DNA work has been undertaken to address human history and evolution in the Pacific region, and argues that the future is bright but research requires a collaborative approach between academic disciplines but also with local communities.}, }
@article {pmid25546319, year = {2015}, author = {Gao, SZ and Zhang, Y and Wei, D and Li, HJ and Zhao, YB and Cui, YQ and Zhou, H}, title = {Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age.}, journal = {American journal of physical anthropology}, volume = {157}, number = {1}, pages = {71-80}, doi = {10.1002/ajpa.22690}, pmid = {25546319}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Asian People/*genetics ; China ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; Female ; *Human Migration ; Humans ; Male ; Microsatellite Repeats/genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Xinjiang is at the crossroads between East and West Eurasia, and it harbors a relatively complex genetic history. In order to better understand the population movements and interactions in this region, mitochondrial and Y chromosome analyses on 40 ancient human remains from the Tianshanbeilu site in eastern Xinjiang were performed. Twenty-nine samples were successfully assigned to specific mtDNA haplogroups, including the west Eurasian maternal lineages of U and W and the east Eurasian maternal lineages of A, C, D, F, G, Z, M7, and M10. In the male samples, two Y chromosome haplogroups, C* and N1 (xN1a, N1c), were successfully assigned. Our mitochondrial and Y-chromosomal DNA analyses combined with the archaeological studies revealed that the Di-qiang populations from the Hexi Corridor had migrated to eastern Xinjiang and admixed with the Eurasian steppe populations in the early Bronze Age.}, }
@article {pmid25532803, year = {2015}, author = {Witt, KE and Judd, K and Kitchen, A and Grier, C and Kohler, TA and Ortman, SG and Kemp, BM and Malhi, RS}, title = {DNA analysis of ancient dogs of the Americas: identifying possible founding haplotypes and reconstructing population histories.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {105-118}, doi = {10.1016/j.jhevol.2014.10.012}, pmid = {25532803}, issn = {1095-8606}, mesh = {Americas ; Animals ; DNA, Mitochondrial/*genetics ; *Databases, Genetic ; Dogs/*genetics ; *Evolution, Molecular ; Female ; Genetic Variation/genetics ; Haplotypes/*genetics ; Humans ; }, abstract = {As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) of mitochondrial DNA (mtDNA) to indicate that prior to European contact the dogs of Native Americans originated in Eurasia. In this study, we summarize past DNA studies of both humans and dogs to discuss their population histories in the Americas. We then sequenced a portion of the mtDNA HVR of 42 pre-Columbian dogs from three sites located in Illinois, coastal British Columbia, and Colorado, and identify four novel dog mtDNA haplotypes. Next, we analyzed a dataset comprised of all available ancient dog sequences from the Americas to infer the pre-Columbian population history of dogs in the Americas. Interestingly, we found low levels of genetic diversity for some populations consistent with the possibility of deliberate breeding practices. Furthermore, we identified multiple putative founding haplotypes in addition to dog haplotypes that closely resemble those of wolves, suggesting admixture with North American wolves or perhaps a second domestication of canids in the Americas. Notably, initial effective population size estimates suggest at least 1000 female dogs likely existed in the Americas at the time of the first known canid burial, and that population size increased gradually over time before stabilizing roughly 1200 years before present.}, }
@article {pmid25532802, year = {2015}, author = {Harkins, KM and Stone, AC}, title = {Ancient pathogen genomics: insights into timing and adaptation.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {137-149}, doi = {10.1016/j.jhevol.2014.11.002}, pmid = {25532802}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; Bacteria/*genetics/pathogenicity ; Bacterial Infections/history/microbiology ; *Biological Evolution ; DNA/genetics ; *Genomics ; History, Ancient ; Humans ; Parasites/*genetics/pathogenicity ; Parasitic Diseases/history/parasitology ; }, abstract = {Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.}, }
@article {pmid25532801, year = {2015}, author = {Burrell, AS and Disotell, TR and Bergey, CM}, title = {The use of museum specimens with high-throughput DNA sequencers.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {35-44}, pmid = {25532801}, issn = {1095-8606}, support = {UL1 TR000038/TR/NCATS NIH HHS/United States ; UL1 TR001445/TR/NCATS NIH HHS/United States ; P30CA016087/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; DNA/analysis/genetics ; Fossils ; High-Throughput Nucleotide Sequencing/*methods ; Metagenomics/*methods ; Museums ; Paleontology/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists' ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials.}, }
@article {pmid25532800, year = {2015}, author = {Ermini, L and Der Sarkissian, C and Willerslev, E and Orlando, L}, title = {Major transitions in human evolution revisited: a tribute to ancient DNA.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {4-20}, doi = {10.1016/j.jhevol.2014.06.015}, pmid = {25532800}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; *DNA/analysis/genetics ; Fossils ; Genome, Human/genetics ; *Genomics ; Hominidae/*genetics ; Humans ; Paleontology/*methods ; }, abstract = {The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.}, }
@article {pmid25526902, year = {2015}, author = {Llamas, B and Brotherton, P and Mitchell, KJ and Templeton, JE and Thomson, VA and Metcalf, JL and Armstrong, KN and Kasper, M and Richards, SM and Camens, AB and Lee, MS and Cooper, A}, title = {Late pleistocene Australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies.}, journal = {Molecular biology and evolution}, volume = {32}, number = {3}, pages = {574-584}, doi = {10.1093/molbev/msu338}, pmid = {25526902}, issn = {1537-1719}, mesh = {Animals ; Caves ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Fossils ; Macropodidae/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Tasmania ; }, abstract = {Understanding the evolution of Australia's extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39-52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania. Using low-stringency hybridization and high-throughput sequencing, we were able to retrieve mitochondrial sequences from two extinct megafaunal macropodid species. The two specimens, Simosthenurus occidentalis (giant short-faced kangaroo) and Protemnodon anak (giant wallaby), have been radiocarbon dated to 46-50 and 40-45 ka, respectively. This is significantly older than any Australian fossil that has previously yielded DNA sequence information. Processing the raw sequence data from these samples posed a bioinformatic challenge due to the poor preservation of DNA. We explored several approaches in order to maximize the signal-to-noise ratio in retained sequencing reads. Our findings demonstrate the critical importance of adopting stringent processing criteria when distant outgroups are used as references for mapping highly fragmented DNA. Based on the most stringent nucleotide data sets (879 bp for S. occidentalis and 2,383 bp for P. anak), total-evidence phylogenetic analyses confirm that macropodids consist of three primary lineages: Sthenurines such as Simosthenurus (extinct short-faced kangaroos), the macropodines (all other wallabies and kangaroos), and the enigmatic living banded hare-wallaby Lagostrophus fasciatus (Lagostrophinae). Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.}, }
@article {pmid25525220, year = {2014}, author = {Gibbons, A}, title = {Ancient DNA. The thoroughly bred horse.}, journal = {Science (New York, N.Y.)}, volume = {346}, number = {6216}, pages = {1439}, doi = {10.1126/science.346.6216.1439}, pmid = {25525220}, issn = {1095-9203}, mesh = {Animals ; Animals, Domestic/*genetics ; Bone and Bones/chemistry ; *Breeding ; DNA/*genetics/isolation &amp; purification ; Horses/*genetics ; }, }
@article {pmid25523037, year = {2015}, author = {Kistler, L and Ratan, A and Godfrey, LR and Crowley, BE and Hughes, CE and Lei, R and Cui, Y and Wood, ML and Muldoon, KM and Andriamialison, H and McGraw, JJ and Tomsho, LP and Schuster, SC and Miller, W and Louis, EE and Yoder, AD and Malhi, RS and Perry, GH}, title = {Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {45-54}, doi = {10.1016/j.jhevol.2014.06.016}, pmid = {25523037}, issn = {1095-8606}, mesh = {Animals ; *Body Size/genetics/physiology ; DNA/analysis/genetics ; *Extinction, Biological ; Fossils ; Genomics/*methods ; *Lemur/classification/genetics/physiology ; Madagascar ; Paleontology/*methods ; Phylogeny ; }, abstract = {Humans first arrived on Madagascar only a few thousand years ago. Subsequent habitat destruction and hunting activities have had significant impacts on the island's biodiversity, including the extinction of megafauna. For example, we know of 17 recently extinct 'subfossil' lemur species, all of which were substantially larger (body mass ∼11-160 kg) than any living population of the ∼100 extant lemur species (largest body mass ∼6.8 kg). We used ancient DNA and genomic methods to study subfossil lemur extinction biology and update our understanding of extant lemur conservation risk factors by i) reconstructing a comprehensive phylogeny of extinct and extant lemurs, and ii) testing whether low genetic diversity is associated with body size and extinction risk. We recovered complete or near-complete mitochondrial genomes from five subfossil lemur taxa, and generated sequence data from population samples of two extinct and eight extant lemur species. Phylogenetic comparisons resolved prior taxonomic uncertainties and confirmed that the extinct subfossil species did not comprise a single clade. Genetic diversity estimates for the two sampled extinct species were relatively low, suggesting small historical population sizes. Low genetic diversity and small population sizes are both risk factors that would have rendered giant lemurs especially susceptible to extinction. Surprisingly, among the extant lemurs, we did not observe a relationship between body size and genetic diversity. The decoupling of these variables suggests that risk factors other than body size may have as much or more meaning for establishing future lemur conservation priorities.}, }
@article {pmid25512547, year = {2014}, author = {Schubert, M and Jónsson, H and Chang, D and Der Sarkissian, C and Ermini, L and Ginolhac, A and Albrechtsen, A and Dupanloup, I and Foucal, A and Petersen, B and Fumagalli, M and Raghavan, M and Seguin-Orlando, A and Korneliussen, TS and Velazquez, AM and Stenderup, J and Hoover, CA and Rubin, CJ and Alfarhan, AH and Alquraishi, SA and Al-Rasheid, KA and MacHugh, DE and Kalbfleisch, T and MacLeod, JN and Rubin, EM and Sicheritz-Ponten, T and Andersson, L and Hofreiter, M and Marques-Bonet, T and Gilbert, MT and Nielsen, R and Excoffier, L and Willerslev, E and Shapiro, B and Orlando, L}, title = {Prehistoric genomes reveal the genetic foundation and cost of horse domestication.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {52}, pages = {E5661-9}, pmid = {25512547}, issn = {1091-6490}, support = {260372/ERC_/European Research Council/International ; }, mesh = {Animals ; Animals, Domestic/*genetics ; Cardiovascular System/anatomy &amp; histology ; Dogs ; *Evolution, Molecular ; Genome/*physiology ; Hindlimb/anatomy &amp; histology/physiology ; Horses/anatomy &amp; histology/*genetics ; Humans ; Inbreeding ; Russia ; }, abstract = {The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the "cost of domestication" hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.}, }
@article {pmid25505436, year = {2014}, author = {Boeckx, C and Benítez-Burraco, A}, title = {Globularity and language-readiness: generating new predictions by expanding the set of genes of interest.}, journal = {Frontiers in psychology}, volume = {5}, number = {}, pages = {1324}, pmid = {25505436}, issn = {1664-1078}, abstract = {This study builds on the hypothesis put forth in Boeckx and Benítez-Burraco (2014), according to which the developmental changes expressed at the levels of brain morphology and neural connectivity that resulted in a more globular braincase in our species were crucial to understand the origins of our language-ready brain. Specifically, this paper explores the links between two well-known 'language-related' genes like FOXP2 and ROBO1 implicated in vocal learning and the initial set of genes of interest put forth in Boeckx and Benítez-Burraco (2014), with RUNX2 as focal point. Relying on the existing literature, we uncover potential molecular links that could be of interest to future experimental inquiries into the biological foundations of language and the testing of our initial hypothesis. Our discussion could also be relevant for clinical linguistics and for the interpretation of results from paleogenomics.}, }
@article {pmid25493538, year = {2015}, author = {Roca, AL and Ishida, Y and Brandt, AL and Benjamin, NR and Zhao, K and Georgiadis, NJ}, title = {Elephant natural history: a genomic perspective.}, journal = {Annual review of animal biosciences}, volume = {3}, number = {}, pages = {139-167}, doi = {10.1146/annurev-animal-022114-110838}, pmid = {25493538}, issn = {2165-8110}, mesh = {Animals ; DNA/genetics ; Elephants/classification/*genetics ; Female ; Fossils ; *Genome ; Genomics ; Male ; Mammoths/genetics ; Phylogeography ; Species Specificity ; }, abstract = {We review DNA-based studies of elephants and recently extinct proboscideans. The evidence indicates that little or no nuclear gene flow occurs between African savanna elephants (Loxodonta africana) and African forest elephants (Loxodonta cyclotis), establishing that they comprise separate species. In all elephant species, males disperse, whereas females remain with their natal social group, leading to discordance in the phylogeography of nuclear and mitochondrial DNA patterns. Improvements in ancient DNA methods have permitted sequences to be generated from an increasing number of proboscidean fossils and have definitively established that the Asian elephant (Elephas maximus) is the closest living relative of the extinct woolly mammoth (Mammuthus primigenius). DNA-based methods have been developed to determine the geographic provenance of confiscated ivory in an effort to aid the conservation of elephants.}, }
@article {pmid25487342, year = {2015}, author = {Rohland, N and Harney, E and Mallick, S and Nordenfelt, S and Reich, D}, title = {Partial uracil-DNA-glycosylase treatment for screening of ancient DNA.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130624}, pmid = {25487342}, issn = {1471-2970}, mesh = {Base Sequence ; DNA/*genetics/history ; DNA Barcoding, Taxonomic/methods ; *Fossils ; *Gene Library ; Genetic Testing/*methods ; Genetics, Population/methods ; History, Ancient ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA/*methods ; Uracil-DNA Glycosidase/*chemistry ; }, abstract = {The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 ancient human samples.}, }
@article {pmid25487341, year = {2015}, author = {Harkins, KM and Buikstra, JE and Campbell, T and Bos, KI and Johnson, ED and Krause, J and Stone, AC}, title = {Screening ancient tuberculosis with qPCR: challenges and opportunities.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130622}, pmid = {25487341}, issn = {1471-2970}, mesh = {Bone and Bones/*chemistry ; DNA Primers/genetics ; DNA, Bacterial/*genetics/history ; *Fossils ; History, Ancient ; Humans ; Mycobacterium tuberculosis/*genetics ; Paleopathology/*methods/trends ; Real-Time Polymerase Chain Reaction/*methods ; }, abstract = {The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the Mycobacterium tuberculosis complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies.}, }
@article {pmid25487340, year = {2015}, author = {Evin, A and Flink, LG and Bălăşescu, A and Popovici, D and Andreescu, R and Bailey, D and Mirea, P and Lazăr, C and Boroneanţ, A and Bonsall, C and Vidarsdottir, US and Brehard, S and Tresset, A and Cucchi, T and Larson, G and Dobney, K}, title = {Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130616}, pmid = {25487340}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; Body Weights and Measures ; DNA/*genetics/history ; *Fossils ; History, Ancient ; Humans ; *Hybridization, Genetic ; Paleontology/*methods ; Romania ; Sus scrofa/*anatomy &amp; histology/*genetics ; Tooth/anatomy &amp; histology/chemistry ; }, abstract = {Current evidence suggests that pigs were first domesticated in Eastern Anatolia during the ninth millennium cal BC before dispersing into Europe with Early Neolithic farmers from the beginning of the seventh millennium. Recent ancient DNA (aDNA) research also indicates the incorporation of European wild boar into domestic stock during the Neolithization process. In order to establish the timing of the arrival of domestic pigs into Europe, and to test hypotheses regarding the role European wild boar played in the domestication process, we combined a geometric morphometric analysis (allowing us to combine tooth size and shape) of 449 Romanian ancient teeth with aDNA analysis. Our results firstly substantiate claims that the first domestic pigs in Romania possessed the same mtDNA signatures found in Neolithic pigs in west and central Anatolia. Second, we identified a significant proportion of individuals with large molars whose tooth shape matched that of archaeological (likely) domestic pigs. These large 'domestic shape' specimens were present from the outset of the Romanian Neolithic (6100-5500 cal BC) through to later prehistory, suggesting a long history of admixture between introduced domestic pigs and local wild boar. Finally, we confirmed a turnover in mitochondrial lineages found in domestic pigs, possibly coincident with human migration into Anatolia and the Levant that occurred in later prehistory.}, }
@article {pmid25487339, year = {2015}, author = {Mendisco, F and Pemonge, MH and Leblay, E and Romon, T and Richard, G and Courtaud, P and Deguilloux, MF}, title = {Where are the Caribs? Ancient DNA from ceramic period human remains in the Lesser Antilles.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130388}, pmid = {25487339}, issn = {1471-2970}, mesh = {Base Sequence ; Cloning, Molecular ; Complementarity Determining Regions/genetics ; DNA/*genetics/history ; DNA, Mitochondrial/genetics ; Ethnicity/*genetics ; *Fossils ; Haplotypes/genetics ; History, Ancient ; Humans ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques/methods ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Sequence Analysis, DNA ; West Indies ; }, abstract = {The identity and history of the indigenous groups who occupied the Lesser Antilles during the ceramic periods remain highly controversial. Although recent archaeological evidence has challenged hypotheses concerning the organization of human groups in this region, more biological data are needed to fully inform the discussion. Our study provides, to our knowledge, the first palaeogenetic data for Late Ceramic groups of the Guadeloupe archipelago, yielding crucial information concerning the identities of these groups. Despite the generally poor DNA preservation in the tested remains, we were able to retrieve Hypervariable Region 1 sequences from 11 individuals and mitochondrial single-nucleotide polymorphisms from 13 individuals. These novel data provide interesting preliminary results in favour of a common origin for all Saladoid Caribbean communities, i.e. the first ceramic groups of the region, as well as for a local continuity between the Saladoid and post-Saladoid groups. A combination of the genetic data obtained and several pieces of cultural evidence allows us to propose that two different groups inhabited the Guadeloupe archipelago during the Late Ceramic period, with the possible occupation of the La Désirade and Marie-Galante islands by groups affiliated with the Taíno communities. The working hypotheses proposed here appear consistent with recent archaeological evidence.}, }
@article {pmid25487338, year = {2015}, author = {Der Sarkissian, C and Allentoft, ME and Ávila-Arcos, MC and Barnett, R and Campos, PF and Cappellini, E and Ermini, L and Fernández, R and da Fonseca, R and Ginolhac, A and Hansen, AJ and Jónsson, H and Korneliussen, T and Margaryan, A and Martin, MD and Moreno-Mayar, JV and Raghavan, M and Rasmussen, M and Velasco, MS and Schroeder, H and Schubert, M and Seguin-Orlando, A and Wales, N and Gilbert, MT and Willerslev, E and Orlando, L}, title = {Ancient genomics.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130387}, pmid = {25487338}, issn = {1471-2970}, mesh = {Animals ; DNA/*genetics/*history ; Genomics/*methods/trends ; High-Throughput Nucleotide Sequencing/*methods/trends ; History, Ancient ; Humans ; }, abstract = {The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.}, }
@article {pmid25487337, year = {2015}, author = {Ludwig, A and Reissmann, M and Benecke, N and Bellone, R and Sandoval-Castellanos, E and Cieslak, M and Fortes, GG and Morales-Muñiz, A and Hofreiter, M and Pruvost, M}, title = {Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130386}, pmid = {25487337}, issn = {1471-2970}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; DNA/genetics/history ; DNA Mutational Analysis/veterinary ; DNA Primers/genetics ; Europe ; Eye Diseases, Hereditary/genetics/*veterinary ; Fossils ; Gene Frequency ; Genetic Diseases, X-Linked/genetics/*veterinary ; *Genetic Variation ; Hair Color/*genetics ; History, Ancient ; History, Medieval ; Horse Diseases/*genetics/*history ; Horses ; Molecular Sequence Data ; Myopia/genetics/*veterinary ; Night Blindness/genetics/*veterinary ; Polymorphism, Single Nucleotide/genetics ; *Selection, Genetic ; TRPM Cation Channels/*genetics ; }, abstract = {Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.}, }
@article {pmid25487336, year = {2015}, author = {Keyser, C and Hollard, C and Gonzalez, A and Fausser, JL and Rivals, E and Alexeev, AN and Riberon, A and Crubézy, E and Ludes, B}, title = {The ancient Yakuts: a population genetic enigma.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130385}, pmid = {25487336}, issn = {1471-2970}, mesh = {Base Sequence ; Bone and Bones/chemistry ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics/history ; Ethnicity/*genetics/*history ; *Fossils ; Genetics, Population ; Haplotypes/genetics ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Likelihood Functions ; Male ; Microsatellite Repeats/genetics ; Molecular Sequence Data ; Pedigree ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Siberia ; }, abstract = {This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages.}, }
@article {pmid25487335, year = {2015}, author = {Krzewińska, M and Bjørnstad, G and Skoglund, P and Olason, PI and Bill, J and Götherström, A and Hagelberg, E}, title = {Mitochondrial DNA variation in the Viking age population of Norway.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130384}, pmid = {25487335}, issn = {1471-2970}, mesh = {Base Sequence ; Bone and Bones/chemistry ; DNA, Mitochondrial/*genetics/history ; Female ; *Fossils ; Genetic Markers/*genetics ; *Genetic Variation ; Haplotypes/genetics ; History, Medieval ; Human Migration/*history ; Humans ; Molecular Sequence Data ; Norway ; Nucleic Acid Amplification Techniques ; Sequence Alignment ; Sequence Analysis, DNA ; Tooth/chemistry ; }, abstract = {The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.}, }
@article {pmid25487334, year = {2015}, author = {Pedersen, MW and Overballe-Petersen, S and Ermini, L and Sarkissian, CD and Haile, J and Hellstrom, M and Spens, J and Thomsen, PF and Bohmann, K and Cappellini, E and Schnell, IB and Wales, NA and Carøe, C and Campos, PF and Schmidt, AM and Gilbert, MT and Hansen, AJ and Orlando, L and Willerslev, E}, title = {Ancient and modern environmental DNA.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130383}, pmid = {25487334}, issn = {1471-2970}, mesh = {*Biodiversity ; DNA/*genetics/history ; Geologic Sediments/*chemistry ; History, Ancient ; Metagenomics/*methods/trends ; Water/*chemistry ; }, abstract = {DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.}, }
@article {pmid25487333, year = {2015}, author = {Parducci, L and Väliranta, M and Salonen, JS and Ronkainen, T and Matetovici, I and Fontana, SL and Eskola, T and Sarala, P and Suyama, Y}, title = {Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130382}, pmid = {25487333}, issn = {1471-2970}, mesh = {Base Sequence ; DNA, Plant/classification/*genetics/history ; Finland ; *Fossils ; Geologic Sediments/*chemistry ; History, Ancient ; Molecular Sequence Data ; Multiplex Polymerase Chain Reaction ; Pollen/*genetics ; Russia ; Sequence Analysis, DNA/methods ; Soil/*chemistry ; }, abstract = {We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected Quercus spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.}, }
@article {pmid25487332, year = {2015}, author = {Parks, M and Subramanian, S and Baroni, C and Salvatore, MC and Zhang, G and Millar, CD and Lambert, DM}, title = {Ancient population genomics and the study of evolution.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130381}, pmid = {25487332}, issn = {1471-2970}, mesh = {Animals ; Antarctic Regions ; *Biological Evolution ; DNA/*genetics/history ; *Fossils ; History, Ancient ; Metagenomics/*methods ; Spheniscidae/*genetics ; }, abstract = {Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.}, }
@article {pmid25487331, year = {2015}, author = {Teasdale, MD and van Doorn, NL and Fiddyment, S and Webb, CC and O'Connor, T and Hofreiter, M and Collins, MJ and Bradley, DG}, title = {Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130379}, pmid = {25487331}, issn = {1471-2970}, mesh = {Animals ; Base Sequence ; DNA/*genetics/history ; England ; *Fossils ; High-Throughput Nucleotide Sequencing/*methods/trends ; History, 17th Century ; History, 18th Century ; Livestock/*genetics ; Mass Spectrometry ; Molecular Sequence Data ; Sequence Alignment ; Sheep ; Skin/*chemistry ; Species Specificity ; }, abstract = {Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.}, }
@article {pmid25487330, year = {2015}, author = {Cui, Y and Song, L and Wei, D and Pang, Y and Wang, N and Ning, C and Li, C and Feng, B and Tang, W and Li, H and Ren, Y and Zhang, C and Huang, Y and Hu, Y and Zhou, H}, title = {Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130378}, pmid = {25487330}, issn = {1471-2970}, mesh = {Archaeology/*methods ; Asian People/*genetics ; Base Sequence ; Burial/*history ; China ; Chromosomes, Human, Y/*genetics ; Collagen/chemistry ; DNA, Mitochondrial/*genetics/history ; *Genetic Techniques ; History, Medieval ; Humans ; Microsatellite Repeats/genetics ; Molecular Sequence Data ; Oxygen Isotopes/analysis ; Pedigree ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Tritium/analysis ; }, abstract = {The Yuan Dynasty (AD 1271-1368) was the first dynasty in Chinese history where a minority ethnic group (Mongols) ruled. Few cemeteries containing Mongolian nobles have been found owing to their tradition of keeping burial grounds secret and their lack of historical records. Archaeological excavations at the Shuzhuanglou site in the Hebei province of China led to the discovery of 13 skeletons in six separate tombs. The style of the artefacts and burials indicate the cemetery occupants were Mongol nobles. However, the origin, relationships and status of the chief occupant (M1m) are unclear. To shed light on the identity of the principal occupant and resolve the kin relationships between individuals, a multidisciplinary approach was adopted, combining archaeological information, stable isotope data and molecular genetic data. Analysis of autosomal, mitochondrial and Y-chromosomal DNA show that some of the occupants were related. The available evidence strongly suggests that the principal occupant may have been the Mongol noble Korguz. Our study demonstrates the power of a multidisciplinary approach in elucidating information about the inhabitants of ancient historical sites.}, }
@article {pmid25487329, year = {2015}, author = {Allaby, RG and Gutaker, R and Clarke, AC and Pearson, N and Ware, R and Palmer, SA and Kitchen, JL and Smith, O}, title = {Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130377}, pmid = {25487329}, issn = {1471-2970}, support = {BB/G0177941//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Biological/*genetics/physiology ; Computational Biology/*methods ; Crops, Agricultural/*genetics/physiology ; Egypt ; *Environment ; *Evolution, Molecular ; Genomics/*methods ; Geography ; Hordeum/genetics ; *Models, Genetic ; Paleontology/*methods ; Selection, Genetic ; }, abstract = {Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.}, }
@article {pmid25487328, year = {2015}, author = {Warinner, C and Speller, C and Collins, MJ}, title = {A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130376}, pmid = {25487328}, issn = {1471-2970}, support = {097829/Z/11/A//Wellcome Trust/United Kingdom ; }, mesh = {Archaeology/*methods/trends ; Dental Calculus/*microbiology ; *Fossils ; High-Throughput Nucleotide Sequencing/methods/trends ; Humans ; Microbiological Techniques/*methods/trends ; Microbiota/*genetics ; Paleodontology/*methods/trends ; }, abstract = {The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.}, }
@article {pmid25487327, year = {2015}, author = {Bos, KI and Jäger, G and Schuenemann, VJ and Vågene, &#xc5;J and Spyrou, MA and Herbig, A and Nieselt, K and Krause, J}, title = {Parallel detection of ancient pathogens via array-based DNA capture.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130375}, pmid = {25487327}, issn = {1471-2970}, mesh = {Bacteria/*genetics/*pathogenicity ; Bone and Bones/chemistry ; DNA, Bacterial/*genetics/isolation &amp; purification ; *Fossils ; Gene Library ; *Genetic Techniques ; Genetic Testing ; High-Throughput Nucleotide Sequencing/*methods ; Mycobacterium leprae/genetics ; }, abstract = {DNA capture coupled with next generation sequencing is highly suitable for the study of ancient pathogens. Screening for pathogens can, however, be meticulous when assays are restricted to the enrichment of single organisms, which is common practice. Here, we report on an array-based DNA capture screening technique for the parallel detection of nearly 100 pathogens that could have potentially left behind molecular signatures in preserved ancient tissues. We demonstrate the sensitivity of our method through evaluation of its performance with a library known to harbour ancient Mycobacterium leprae DNA. This rapid and economical technique will be highly useful for the identification of historical diseases that are difficult to characterize based on archaeological information alone.}, }
@article {pmid25487325, year = {2015}, author = {Malmström, H and Linderholm, A and Skoglund, P and Storå, J and Sjödin, P and Gilbert, MT and Holmlund, G and Willerslev, E and Jakobsson, M and Lidén, K and Götherström, A}, title = {Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130373}, pmid = {25487325}, issn = {1471-2970}, mesh = {Agriculture/history ; Base Sequence ; Computational Biology ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics/history ; Gene Flow ; *Genetic Variation ; Genetics, Population ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Human Migration/*history ; Humans ; Models, Genetic ; Molecular Sequence Data ; Population Dynamics ; Real-Time Polymerase Chain Reaction ; Sweden ; }, abstract = {The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.}, }
@article {pmid25487324, year = {2015}, author = {Hagelberg, E and Hofreiter, M and Keyser, C}, title = {Introduction. Ancient DNA: the first three decades.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130371}, pmid = {25487324}, issn = {1471-2970}, mesh = {DNA/*genetics/history ; *Evolution, Molecular ; *Fossils ; Genetic Techniques/*history ; History, 20th Century ; History, 21st Century ; History, Ancient ; }, }
@article {pmid25476244, year = {2015}, author = {Weyrich, LS and Dobney, K and Cooper, A}, title = {Ancient DNA analysis of dental calculus.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {119-124}, doi = {10.1016/j.jhevol.2014.06.018}, pmid = {25476244}, issn = {1095-8606}, mesh = {Archaeology ; DNA, Bacterial/*genetics ; Dental Calculus/history/*microbiology ; Diet ; Evolution, Molecular ; History, Ancient ; Humans ; Microbiota/genetics ; Oral Health/history ; }, abstract = {Dental calculus (calcified tartar or plaque) is today widespread on modern human teeth around the world. A combination of soft starchy foods, changing acidity of the oral environment, genetic pre-disposition, and the absence of dental hygiene all lead to the build-up of microorganisms and food debris on the tooth crown, which eventually calcifies through a complex process of mineralisation. Millions of oral microbes are trapped and preserved within this mineralised matrix, including pathogens associated with the oral cavity and airways, masticated food debris, and other types of extraneous particles that enter the mouth. As a result, archaeologists and anthropologists are increasingly using ancient human dental calculus to explore broad aspects of past human diet and health. Most recently, high-throughput DNA sequencing of ancient dental calculus has provided valuable insights into the evolution of the oral microbiome and shed new light on the impacts of some of the major biocultural transitions on human health throughout history and prehistory. Here, we provide a brief historical overview of archaeological dental calculus research, and discuss the current approaches to ancient DNA sampling and sequencing. Novel applications of ancient DNA from dental calculus are discussed, highlighting the considerable scope of this new research field for evolutionary biology and modern medicine.}, }
@article {pmid25468443, year = {2015}, author = {Bíró, A and Fehér, T and Bárány, G and Pamjav, H}, title = {Testing Central and Inner Asian admixture among contemporary Hungarians.}, journal = {Forensic science international. Genetics}, volume = {15}, number = {}, pages = {121-126}, doi = {10.1016/j.fsigen.2014.11.007}, pmid = {25468443}, issn = {1878-0326}, mesh = {Asian People/*genetics ; Haplotypes ; Humans ; Hungary ; Polymorphism, Single Nucleotide ; }, abstract = {Historically, the Carpathian Basin was the final destination for many nomadic peoples who migrated westward from Inner and Central Asia towards Europe. Proto-Hungarians (Steppe Magyars) were among those who came from the East, the Eurasian Steppe in the early middle ages. In order to detect the paternal genetic contribution from nomadic Steppe tribes, we tested 966 samples from Central Asian (Uzbekistan, Kazakhstan), Inner Asian (Mongolians and Buryats in Mongolia) and Hungarian-speaking European (Hungarian, Sekler and Csango) populations. We constructed median-joining networks of certain haplogroups in Hungarian-speaking European, and Altaic-speaking Central and Inner Asian populations. We estimated that the possible paternal genetic contribution from the above described populations among contemporary Hungarian speaking populations ranged between 5% and 7.4%. It is lowest among Hungarians from Hungary (5.1%), while higher among Hungarian-speaking groups in Romania, notably Sekler (7.4%) and Csango (6.3%). However, these results represent only an upper limit. Actual Central/Inner Asian admixture might be somewhat lower as some of the related lineages may have come from a common third source. The main haplogroups responsible for the Central/Inner Asian admixture among Hungarians are J2*-M172 (xM47, M67, M12), J2-L24, R1a-Z93; Q-M242 and E-M78. Earlier studies showed very limited Uralic genetic influence among Hungarians, and based on the present study, Altaic/Turkic genetic contribution is also not significant, although significantly higher than the Uralic one. The conclusion of this study is that present-day Hungarian speakers are genetically very similar to neighbouring populations, isolated Hungarian speaking groups having relatively higher presence of Central and Inner Asian genetic elements. At the same time, the reliable historical and genetic conclusions require an extension of the study to a significantly larger database with deep haplogroup resolution, including ancient DNA data.}, }
@article {pmid25467114, year = {2015}, author = {Brandt, G and Szécsényi-Nagy, A and Roth, C and Alt, KW and Haak, W}, title = {Human paleogenetics of Europe--the known knowns and the known unknowns.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {73-92}, doi = {10.1016/j.jhevol.2014.06.017}, pmid = {25467114}, issn = {1095-8606}, mesh = {*Archaeology ; Chromosomes, Human/genetics ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Europe ; Genetic Variation/*genetics ; Humans ; *Paleontology ; }, abstract = {The number of ancient human DNA studies has drastically increased in recent years. This results in a substantial record of mitochondrial sequences available from many prehistoric sites across Western Eurasia, but also growing Y-chromosome and autosomal sequence data. We review the current state of research with specific emphasis on the Holocene population events that likely have shaped the present-day genetic variation in Europe. We reconcile observations from the genetic data with hypotheses about the peopling and settlement history from anthropology and archaeology for various key regions, and also discuss the data in light of evidence from related disciplines, such as modern human genetics, climatology and linguistics.}, }
@article {pmid25467111, year = {2015}, author = {Sams, AJ and Hawks, J and Keinan, A}, title = {The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {64-72}, pmid = {25467111}, issn = {1095-8606}, support = {R01 GM108805/GM/NIGMS NIH HHS/United States ; R01GM108805/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical ; DNA/analysis/*genetics ; Europe ; *Evolution, Molecular ; Genetics, Population/*methods ; Humans ; Male ; Neanderthals/*genetics ; Selection, Genetic ; }, abstract = {The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles.}, }
@article {pmid25466970, year = {2015}, author = {Rothe, J and Melisch, C and Powers, N and Geppert, M and Zander, J and Purps, J and Spors, B and Nagy, M}, title = {Genetic research at a fivefold children's burial from medieval Berlin.}, journal = {Forensic science international. Genetics}, volume = {15}, number = {}, pages = {90-97}, doi = {10.1016/j.fsigen.2014.10.022}, pmid = {25466970}, issn = {1878-0326}, mesh = {Child ; Chromosomes, Human, Y ; DNA, Mitochondrial/genetics ; Family ; *Funeral Rites ; *Genetics, Medical ; Germany ; History, Medieval ; Humans ; }, abstract = {Berlin originated from the two twin cities Berlin and Cölln, which both were founded at the beginning of the 13th century. However the real date of their foundation as well as the origin of the first settlers is still unknown. On the Berlin site the historic city center is still visible in the Nikolaiviertel, but the medieval origin of Cölln disappeared almost completely. In 2007 a large scale excavation, which comprised an area of about 1700m(2) of the historical center of the St. Peters church, recovers the remains of Cölln's first citizens and span a period of 500 years of medieval population. Here we present the first genetic analysis of a fivefold children's burial from excavations in Berlin. The genetic data unveiled next to ancestry and eye color data also the kinship and the gender of the five individuals. Together with the archeological context the new gained information help to shed more light on the possible reasons for this burial.}, }
@article {pmid25463753, year = {2015}, author = {Hailer, F and James, HF and Olson, SL and Fleischer, RC}, title = {Distinct and extinct: genetic differentiation of the Hawaiian eagle.}, journal = {Molecular phylogenetics and evolution}, volume = {83}, number = {}, pages = {40-43}, doi = {10.1016/j.ympev.2014.11.005}, pmid = {25463753}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Eagles/*classification ; Extinction, Biological ; Fossils ; Haplotypes ; Hawaii ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Eagles currently occur in the Hawaiian Islands only as vagrants, but Quaternary bones of Haliaeetus eagles have been found on three of the major islands. A previous study of a ∼3500-year-old skeleton from Maui found its mtDNA more similar to White-tailed (H. albicilla) than to Bald (H. leucocephalus) Eagles, but low intraspecific resolution of the markers and lack of comparative data from mainland populations precluded assessment of whether the individual was part of the diversity found in Eurasia, or whether it represented an endemic Hawaiian lineage. Using ancient DNA techniques, we sequenced part of the rapidly evolving mtDNA control region from the same specimen, and compared it to published range-wide control region data from White-tailed Eagles and newly generated sequences from Bald Eagles. Phylogenetic analyses indicated that the Hawaiian eagle represents a distinct (>3% divergent) mtDNA lineage most closely related to those of extant White-tailed Eagles. Based on fossil calibration, we estimate that the Hawaiian mtDNA lineage diverged from mainland sequences around the Middle Pleistocene. Although not clearly differentiated morphologically from mainland forms, the Hawaiian eagle thus likely constituted an isolated, resident population in the Hawaiian archipelago for more than 100,000 years, where it was the largest terrestrial predator.}, }
@article {pmid25453080, year = {2015}, author = {Carrigan, MA and Uryasev, O and Frye, CB and Eckman, BL and Myers, CR and Hurley, TD and Benner, SA}, title = {Hominids adapted to metabolize ethanol long before human-directed fermentation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {2}, pages = {458-463}, pmid = {25453080}, issn = {1091-6490}, support = {P51 OD011133/OD/NIH HHS/United States ; R01 AA017723/AA/NIAAA NIH HHS/United States ; R01AA017723/AA/NIAAA NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Alcohol Dehydrogenase/classification/genetics/metabolism ; Amino Acid Sequence ; Animals ; Diet ; Ethanol/*metabolism ; Evolution, Molecular ; Fermentation/genetics ; Fruit/metabolism ; Genetic Variation ; Hominidae/*genetics/*metabolism ; Humans ; Kinetics ; Molecular Sequence Data ; Phylogeny ; Primates/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate-ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol.}, }
@article {pmid25447174, year = {2014}, author = {Zouganelis, GD and Ogden, R and Nahar, N and Runfola, V and Bonab, M and Ardalan, A and Radford, D and Barnett, R and Larson, G and Hildred, A and Jones, M and Scarlett, G}, title = {An old dog and new tricks: Genetic analysis of a Tudor dog recovered from the Mary Rose wreck.}, journal = {Forensic science international}, volume = {245}, number = {}, pages = {51-57}, doi = {10.1016/j.forsciint.2014.10.001}, pmid = {25447174}, issn = {1872-6283}, mesh = {Accidents ; Animals ; *Body Remains ; DNA/isolation &amp; purification ; DNA Fingerprinting/*veterinary ; Dogs/*genetics ; Glucose Transport Proteins, Facilitative/genetics ; History, Medieval ; Homozygote ; Male ; Microsatellite Repeats ; Polymorphism, Single Nucleotide ; *Ships ; }, abstract = {The Tudor warship the Mary Rose sank in the Solent waters between Portsmouth and the Isle of Wight on the 19th of July 1545, whilst engaging a French invasion fleet. The ship was rediscovered in 1971 and between 1979 and 1982 the entire contents of the ship were excavated resulting in the recovery of over 25,000 objects, including the skeleton of a small to medium sized dog referred to as the Mary Rose Dog (MRD). Here we report the extraction and analysis of both mitochondrial and genomic DNA from a tooth of this animal. Our results show that the MRD was a young male of a terrier type most closely related to modern Jack Russell Terriers with a light to dark brown coat colour. Interestingly, given the antiquity of the sample, the dog was heterozygotic for the SLC2A9 gene variant that leads to hyperuricosuria when found in modern homozygotic animals. These findings help shed light on a notable historical artefact from an important period in the development of modern dog breeds.}, }
@article {pmid25433485, year = {2014}, author = {Han, L and Zhu, S and Ning, C and Cai, D and Wang, K and Chen, Q and Hu, S and Yang, J and Shao, J and Zhu, H and Zhou, H}, title = {Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {246}, pmid = {25433485}, issn = {1471-2148}, mesh = {Animals ; Animals, Domestic ; Archaeology ; China ; Cytochromes b/genetics ; DNA, Mitochondrial/analysis/*genetics ; Equidae/*classification/*genetics ; Horses/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {BACKGROUND: The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced.<br><br>RESULTS: Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age.<br><br>CONCLUSIONS: This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.}, }
@article {pmid25422439, year = {2014}, author = {Xiang, H and Gao, J and Yu, B and Zhou, H and Cai, D and Zhang, Y and Chen, X and Wang, X and Hofreiter, M and Zhao, X}, title = {Early Holocene chicken domestication in northern China.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {49}, pages = {17564-17569}, pmid = {25422439}, issn = {1091-6490}, mesh = {Animal Husbandry/*history ; Animals ; Archaeology/methods ; Bayes Theorem ; *Biological Evolution ; Bone and Bones ; Chickens/*genetics ; China ; DNA, Mitochondrial/*analysis ; Gene Pool ; Geography ; Haplotypes ; History, Ancient ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; }, abstract = {Chickens represent by far the most important poultry species, yet the number, locations, and timings of their domestication have remained controversial for more than a century. Here we report ancient mitochondrial DNA sequences from the earliest archaeological chicken bones from China, dating back to ∼ 10,000 B.P. The results clearly show that all investigated bones, including the oldest from the Nanzhuangtou site, are derived from the genus Gallus, rather than any other related genus, such as Phasianus. Our analyses also suggest that northern China represents one region of the earliest chicken domestication, possibly dating as early as 10,000 y B.P. Similar to the evidence from pig domestication, our results suggest that these early domesticated chickens contributed to the gene pool of modern chicken populations. Moreover, our results support the idea that multiple members of the genus Gallus, specifically Gallus gallus and Gallus sonneratii contributed to the gene pool of the modern domestic chicken. Our results provide further support for the growing evidence of an early mixed agricultural complex in northern China.}, }
@article {pmid25418693, year = {2015}, author = {Reynolds, AW and Raff, JA and Bolnick, DA and Cook, DC and Kaestle, FA}, title = {Ancient DNA from the Schild site in Illinois: Implications for the Mississippian transition in the Lower Illinois River Valley.}, journal = {American journal of physical anthropology}, volume = {156}, number = {3}, pages = {434-448}, doi = {10.1002/ajpa.22668}, pmid = {25418693}, issn = {1096-8644}, mesh = {DNA, Mitochondrial/*genetics ; Female ; *Genetics, Population ; Haplotypes ; *Human Migration ; Humans ; Illinois ; Male ; Mississippi ; Paleontology ; Rivers ; }, abstract = {Archaeologists have long debated whether rapid cultural change in the archaeological record is due to in situ developments, migration of a new group into the region, or the spread of new cultural practices into an area through existing social networks, with the local peoples adopting and adapting practices from elsewhere as they see fit (acculturation). Researchers have suggested each of these explanations for the major cultural transition that occurred at the beginning of the Mississippian period (AD 1050) across eastern North America. In this study, we used ancient DNA to test competing hypotheses of migration and acculturation for the culture change that occurred between the Late Woodland (AD 400-1050) and Mississippian (AD 1050-1500) periods in the Lower Illinois River Valley. We obtained sequences of the first hypervariable segment of the mitochondrial genome (mtDNA) from 39 individuals (17 Late Woodland, 22 Mississippian) interred in the Schild cemetery in western Illinois, and compared these lineages to ancient mtDNA lineages present at other sites in the region. Computer simulations were used to test a null hypothesis of population continuity from Late Woodland to Mississippian times at the Schild site and to investigate the possibility of gene flow from elsewhere in the region. Our results suggest that the Late Woodland to Mississippian cultural transition at Schild was not due to an influx of people from elsewhere. Instead, it is more likely that the transition to Mississippian cultural practices at this site was due to a process of acculturation.}, }
@article {pmid25413709, year = {2015}, author = {Hofreiter, M and Paijmans, JL and Goodchild, H and Speller, CF and Barlow, A and Fortes, GG and Thomas, JA and Ludwig, A and Collins, MJ}, title = {The future of ancient DNA: Technical advances and conceptual shifts.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {37}, number = {3}, pages = {284-293}, doi = {10.1002/bies.201400160}, pmid = {25413709}, issn = {1521-1878}, mesh = {Animals ; DNA/*genetics/isolation &amp; purification ; DNA Damage ; Genome ; *High-Throughput Nucleotide Sequencing ; Humans ; Multilocus Sequence Typing ; Temperature ; }, abstract = {Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.}, }
@article {pmid25378462, year = {2014}, author = {Seguin-Orlando, A and Korneliussen, TS and Sikora, M and Malaspinas, AS and Manica, A and Moltke, I and Albrechtsen, A and Ko, A and Margaryan, A and Moiseyev, V and Goebel, T and Westaway, M and Lambert, D and Khartanovich, V and Wall, JD and Nigst, PR and Foley, RA and Lahr, MM and Nielsen, R and Orlando, L and Willerslev, E}, title = {Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years.}, journal = {Science (New York, N.Y.)}, volume = {346}, number = {6213}, pages = {1113-1118}, doi = {10.1126/science.aaa0114}, pmid = {25378462}, issn = {1095-9203}, mesh = {DNA/*genetics/history ; Europe ; Fossils ; Genome, Human/*genetics ; Genomics ; History, Ancient ; Humans ; Male ; Siberia ; White People/*genetics/history ; }, abstract = {The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.}, }
@article {pmid25357228, year = {2015}, author = {Søe, MJ and Nejsum, P and Fredensborg, BL and Kapel, CM}, title = {DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement.}, journal = {The Journal of parasitology}, volume = {101}, number = {1}, pages = {57-63}, doi = {10.1645/14-650.1}, pmid = {25357228}, issn = {1937-2345}, mesh = {Animals ; Ascariasis/*history ; Ascaris/classification/genetics/isolation &amp; purification ; Cattle ; Cattle Diseases/*history/parasitology ; DNA Fingerprinting ; Denmark ; Fasciola hepatica/classification/genetics/isolation &amp; purification ; Fascioliasis/*history ; History, Medieval ; Humans ; Molecular Sequence Data ; Ovum/classification ; Paleopathology ; Sheep ; Sheep Diseases/*history/parasitology ; Trichuriasis/*history ; Trichuris/classification/genetics/isolation &amp; purification ; }, abstract = {Ancient parasite eggs were recovered from environmental samples collected at a Viking-age settlement in Viborg, Denmark, dated 1018-1030 A.D. Morphological examination identified Ascaris sp., Trichuris sp., and Fasciola sp. eggs, but size and shape did not allow species identification. By carefully selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura , using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology. The identification of T. trichiura eggs indicates that human fecal material is present and, hence, that the Ascaris sp. haplotype 07 was most likely a human variant in Viking-age Denmark. The location of the F. hepatica finding suggests that sheep or cattle are the most likely hosts. Further, we sequenced the Ascaris sp. 18S rRNA gene in recent isolates from humans and pigs of global distribution and show that this is not a suited marker for species-specific identification. Finally, we discuss ancient parasitism in Denmark and the implementation of aDNA analysis methods in paleoparasitological studies. We argue that when employing species-specific identification, soil samples offer excellent opportunities for studies of human parasite infections and of human and animal interactions of the past.}, }
@article {pmid25348509, year = {2014}, author = {Mainali, HR and Chapman, P and Dhaubhadel, S}, title = {Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max).}, journal = {BMC plant biology}, volume = {14}, number = {}, pages = {282}, pmid = {25348509}, issn = {1471-2229}, mesh = {Cyclophilins/*genetics ; Databases, Genetic ; Fabaceae/*genetics ; Genome, Plant/*genetics ; Genome-Wide Association Study ; Introns/genetics ; *Multigene Family ; Open Reading Frames/genetics ; Organ Specificity ; Peptidylprolyl Isomerase/*genetics ; Plant Proteins/genetics ; Protein Structure, Tertiary ; Glycine max/*genetics ; Untranslated Regions/genetics ; }, abstract = {BACKGROUND: Cyclophilins (CYPs) belong to the immunophilin superfamily, and have peptidyl-prolyl cis-trans isomerase (PPIase) activity. PPIase catalyzes cis- and trans-rotamer interconversion of the peptidyl-prolyl amide bond of peptides, a rate-limiting step in protein folding. Studies have demonstrated the importance of many PPIases in plant biology, but no genome-wide analysis of the CYP gene family has been conducted for a legume species.<br><br>RESULTS: Here we performed a comprehensive database survey and identified a total of 62 CYP genes, located on 18 different chromosomes in the soybean genome (GmCYP1 to GmCYP62), of which 10 are multi- and 52 are single-domain proteins. Most of the predicted GmCYPs clustered together in pairs, reflecting the ancient genome duplication event. Analysis of gene structure revealed the presence of introns in protein-coding regions as well as in 5' and 3' untranslated regions, and that their size, abundance and distribution varied within the gene family. Expression analysis of GmCYP genes in soybean tissues displayed their differential tissue specific expression patterns.<br><br>CONCLUSIONS: Overall, we have identified 62 CYP genes in the soybean genome, the largest CYP gene family known to date. This is the first genome-wide study of the CYP gene family of a legume species. The expansion of GmCYP genes in soybean, and their distribution pattern on the chromosomes strongly suggest genome-wide segmental and tandem duplications.}, }
@article {pmid25346253, year = {2014}, author = {Martínez de la Escalera, G and Antoniades, D and Bonilla, S and Piccini, C}, title = {Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems.}, journal = {Molecular ecology}, volume = {23}, number = {23}, pages = {5791-5802}, doi = {10.1111/mec.12979}, pmid = {25346253}, issn = {1365-294X}, mesh = {Chlorophyll/analysis ; Chlorophyll A ; Cyanobacteria/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Fresh Water/*microbiology ; Geologic Sediments/microbiology ; Lakes/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Saxitoxin/genetics ; Sequence Analysis, DNA ; Uruguay ; *Water Microbiology ; }, abstract = {Ancient DNA (aDNA) analysis of lake sediments is a promising tool for detecting shifts in past microbial assemblages in response to changing environmental conditions. We examined sediment core samples from subtropical, freshwater Laguna Blanca (Uruguay), which has been severely affected by cultural eutrophication since 1960 and where cyanobacterial blooms, particularly those of the saxitoxin-producer Cylindrospermopsis raciborskii, have been reported since the 1990s. Samples corresponding to ~1846, 1852, 2000 and 2007 AD were selected to perform denaturing gradient gel electrophoresis (DGGE) analysis of the 16S-23S rRNA intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic assemblage composition. Each stratum showed different ITS patterns, but the composition of 21st century samples was clearly different than those of mid-19th century. This compositional change was correlated with shifts in sediment organic matter and chlorophyll a content, which were significantly higher in recent samples. The presence of saxitoxin-producing cyanobacteria was addressed by quantitative real-time PCR of the sxtU gene involved in toxin biosynthesis. This gene was present only in recent samples, for which clone libraries and ITS sequencing indicated the presence of Cyanobacteria. Phylogenetic analyses identified C. raciborskii only in the 2000 sample, shortly after several years when blooms were recorded in the lake. These data suggest the utility of aDNA for the reconstruction of microbial assemblage shifts in subtropical lakes, at least on centennial scales. The application of aDNA analysis to genes involved in cyanotoxin synthesis extends the applicability of molecular techniques in palaeolimnological studies to include key microbial community characteristics of great scientific and social interest.}, }
@article {pmid25337992, year = {2014}, author = {Juras, A and Dabert, M and Kushniarevich, A and Malmström, H and Raghavan, M and Kosicki, JZ and Metspalu, E and Willerslev, E and Piontek, J}, title = {Ancient DNA reveals matrilineal continuity in present-day Poland over the last two millennia.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110839}, pmid = {25337992}, issn = {1932-6203}, mesh = {Base Sequence ; Consensus Sequence ; DNA, Mitochondrial/*genetics ; Female ; *Haplotypes ; History, Ancient ; Humans ; Phylogeny ; Poland ; Sequence Analysis, DNA ; White People/*genetics ; }, abstract = {While numerous ancient human DNA datasets from across Europe have been published till date, modern-day Poland in particular, remains uninvestigated. Besides application in the reconstruction of continent-wide human history, data from this region would also contribute towards our understanding of the history of the Slavs, whose origin is hypothesized to be in East or Central Europe. Here, we present the first population-scale ancient human DNA study from the region of modern-day Poland by establishing mitochondrial DNA profiles for 23 samples dated to 200 BC - 500 AD (Roman Iron Age) and for 20 samples dated to 1000-1400 AD (Medieval Age). Our results show that mitochondrial DNA sequences from both periods belong to haplogroups that are characteristic of contemporary West Eurasia. Haplotype sharing analysis indicates that majority of the ancient haplotypes are widespread in some modern Europeans, including Poles. Notably, the Roman Iron Age samples share more rare haplotypes with Central and Northeast Europeans, whereas the Medieval Age samples share more rare haplotypes with East-Central and South-East Europeans, primarily Slavic populations. Our data demonstrates genetic continuity of certain matrilineages (H5a1 and N1a1a2) in the area of present-day Poland from at least the Roman Iron Age until present. As such, the maternal gene pool of present-day Poles, Czechs and Slovaks, categorized as Western Slavs, is likely to have descended from inhabitants of East-Central Europe during the Roman Iron Age.}, }
@article {pmid25327646, year = {2015}, author = {Ficetola, GF and Pansu, J and Bonin, A and Coissac, E and Giguet-Covex, C and De Barba, M and Gielly, L and Lopes, CM and Boyer, F and Pompanon, F and Rayé, G and Taberlet, P}, title = {Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data.}, journal = {Molecular ecology resources}, volume = {15}, number = {3}, pages = {543-556}, doi = {10.1111/1755-0998.12338}, pmid = {25327646}, issn = {1755-0998}, mesh = {DNA Barcoding, Taxonomic/*methods/*standards ; *Diagnostic Errors ; *Environmental Microbiology ; Metagenomics/*methods/*standards ; }, abstract = {Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false-positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false-positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.}, }
@article {pmid25323386, year = {2014}, author = {Hou, W and Dong, H and Li, G and Yang, J and Coolen, MJ and Liu, X and Wang, S and Jiang, H and Wu, X and Xiao, H and Lian, B and Wan, Y}, title = {Identification of photosynthetic plankton communities using sedimentary ancient DNA and their response to late-Holocene climate change on the Tibetan Plateau.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {6648}, pmid = {25323386}, issn = {2045-2322}, mesh = {China ; Climate Change ; Cyanobacteria/*genetics/growth &amp; development ; DNA/*genetics/isolation &amp; purification ; *Ecosystem ; Geologic Sediments/microbiology ; Photosynthesis/genetics ; Plankton/*genetics/isolation &amp; purification/physiology ; Tibet ; }, abstract = {Sediments from Tibetan lakes in NW China are potentially sensitive recorders of climate change and its impact on ecosystem function. However, the important plankton members in many Tibetan Lakes do not make and leave microscopically diagnostic features in the sedimentary record. Here we established a taxon-specific molecular approach to specifically identify and quantify sedimentary ancient DNA (sedaDNA) of non-fossilized planktonic organisms preserved in a 5-m sediment core from Kusai Lake spanning the last 3100 years. The reliability of the approach was validated with multiple independent genetic markers. Parallel analyses of the geochemistry of the core and paleo-climate proxies revealed that Monsoon strength-driven changes in nutrient availability, temperature, and salinity as well as orbitally-driven changes in light intensity were all responsible for the observed temporal changes in the abundance of two dominant phytoplankton groups in the lake, Synechococcus (cyanobacteria) and Isochrysis (haptophyte algae). Collectively our data show that global and regional climatic events exhibited a strong influence on the paleoecology of phototrophic plankton in Kusai Lake.}, }
@article {pmid25294605, year = {2014}, author = {Lindgreen, S and Krogh, A and Pedersen, JS}, title = {SNPest: a probabilistic graphical model for estimating genotypes.}, journal = {BMC research notes}, volume = {7}, number = {}, pages = {698}, pmid = {25294605}, issn = {1756-0500}, mesh = {Computer Simulation ; Diploidy ; Escherichia coli/*genetics ; Gene Frequency ; Genetic Association Studies ; *Genome, Bacterial ; *Genome, Human ; Genotype ; Haploidy ; *High-Throughput Nucleotide Sequencing ; Humans ; *Models, Statistical ; Phenotype ; *Polymorphism, Single Nucleotide ; Probability ; Reproducibility of Results ; Software Design ; }, abstract = {BACKGROUND: As the use of next-generation sequencing technologies is becoming more widespread, the need for robust software to help with the analysis is growing as well. A key challenge when analyzing sequencing data is the prediction of genotypes from the reads, i.e. correct inference of the underlying DNA sequences that gave rise to the sequenced fragments. For diploid organisms, the genotyper should be able to predict both alleles in the individual. Variations between the individual and the population can then be analyzed by looking for SNPs (single nucleotide polymorphisms) in order to investigate diseases or phenotypic features. To perform robust and high confidence genotyping and SNP calling, methods are needed that take the technology specific limitations into account and can model different sources of error. As an example, ancient DNA poses special challenges as the data is often shallow and subject to errors induced by post mortem damage.<br><br>FINDINGS: We present a novel approach to the genotyping problem where a probabilistic framework describing the process from sampling to sequencing is implemented as a graphical model. This makes it possible to model technology specific errors and other sources of variation that can affect the result. The inferred genotype is given a posterior probability to signify the confidence in the result. SNPest has already been used to genotype large scale projects such as the first ancient human genome published in 2010.<br><br>CONCLUSIONS: We compare the performance of SNPest to a number of other widely used genotypers on both real and simulated data, covering both haploid and diploid genomes. We investigate the effects of read depth, of removing adapters before mapping and genotyping, of using different mapping tools, and of using the correct model in the genotyping process. We show that the performance of SNPest is comparable to existing methods, and we also illustrate cases where SNPest has an advantage over other methods, e.g. when dealing with simulated ancient DNA.}, }
@article {pmid25277105, year = {2014}, author = {Schneider, E and El Hajj, N and Haaf, T}, title = {Epigenetic information from ancient DNA provides new insights into human evolution. Commentary on Gokhman D et al. (2014): Reconstructing the DNA methylation maps of the Neanderthal and the Denisovan. Science 344:523-527.}, journal = {Brain, behavior and evolution}, volume = {84}, number = {3}, pages = {169-171}, doi = {10.1159/000365650}, pmid = {25277105}, issn = {1421-9743}, mesh = {Animals ; *DNA Methylation ; *Epigenesis, Genetic ; *Evolution, Molecular ; *Genome, Human ; Humans ; Neanderthals/*genetics ; }, }
@article {pmid25260035, year = {2014}, author = {Brandt, L&#xd8; and Schmidt, AL and Mannering, U and Sarret, M and Kelstrup, CD and Olsen, JV and Cappellini, E}, title = {Species identification of archaeological skin objects from Danish bogs: comparison between mass spectrometry-based peptide sequencing and microscopy-based methods.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e106875}, pmid = {25260035}, issn = {1932-6203}, mesh = {*Archaeology ; Denmark ; Geography ; Mass Spectrometry ; Microscopy ; Peptides/chemistry ; Skin/*chemistry ; }, abstract = {Denmark has an extraordinarily large and well-preserved collection of archaeological skin garments found in peat bogs, dated to approximately 920 BC - AD 775. These objects provide not only the possibility to study prehistoric skin costume and technologies, but also to investigate the animal species used for the production of skin garments. Until recently, species identification of archaeological skin was primarily performed by light and scanning electron microscopy or the analysis of ancient DNA. However, the efficacy of these methods can be limited due to the harsh, mostly acidic environment of peat bogs leading to morphological and molecular degradation within the samples. We compared species assignment results of twelve archaeological skin samples from Danish bogs using Mass Spectrometry (MS)-based peptide sequencing, against results obtained using light and scanning electron microscopy. While it was difficult to obtain reliable results using microscopy, MS enabled the identification of several species-diagnostic peptides, mostly from collagen and keratins, allowing confident species discrimination even among taxonomically close organisms, such as sheep and goat. Unlike previous MS-based methods, mostly relying on peptide fingerprinting, the shotgun sequencing approach we describe aims to identify the complete extracted ancient proteome, without preselected specific targets. As an example, we report the identification, in one of the samples, of two peptides uniquely assigned to bovine foetal haemoglobin, indicating the production of skin from a calf slaughtered within the first months of its life. We conclude that MS-based peptide sequencing is a reliable method for species identification of samples from bogs. The mass spectrometry proteomics data were deposited in the ProteomeXchange Consortium with the dataset identifier PXD001029.}, }
@article {pmid25231926, year = {2015}, author = {Scorrano, G and Valentini, F and Martínez-Labarga, C and Rolfo, MF and Fiammenghi, A and Lo Vetro, D and Martini, F and Casoli, A and Ferraris, G and Palleschi, G and Palleschi, A and Rickards, O}, title = {Methodological strategies to assess the degree of bone preservation for ancient DNA studies.}, journal = {Annals of human biology}, volume = {42}, number = {1}, pages = {10-19}, doi = {10.3109/03014460.2014.954614}, pmid = {25231926}, issn = {1464-5033}, mesh = {Bone and Bones/*cytology/*metabolism ; DNA/*analysis/chemistry/genetics ; *Fossils ; Humans ; }, abstract = {BACKGROUND: Archaeological bones contain only small amounts of DNA due to post-mortem DNA degradation and the changes endogenous DNA is subjected to during diagenesis. An important step before undertaking such time-consuming and costly analyses as ancient DNA investigation is to predict the presence of DNA in ancient samples. To date, the leading screening method has been amino acid racemization; however, other analytical techniques can also be used to assess the degree of bone preservation.<br><br>AIM: The aim of the present study was to relate the presence of DNA with bone preservation in order to select samples potentially suitable for ancient DNA analysis.<br><br>SUBJECTS AND METHODS: Bones collected from several archaeological sites, different locations (cave, rockshelter or sub divo) and diachronic periods were selected for analytical and spectroscopic analysis in order to correlate bone tissue preservation with the presence of DNA. Different techniques were combined to assess the degree of preservation of organic and inorganic components.<br><br>RESULTS: As determined by different analytical methods, preservation of the inorganic component was best associated with the presence of DNA.<br><br>CONCLUSION: Evaluation of the bone preservation state may be an efficient step to predict the presence of DNA in ancient samples prior to aDNA analysis.}, }
@article {pmid25212860, year = {2014}, author = {Morris, AG and Heinze, A and Chan, EK and Smith, AB and Hayes, VM}, title = {First ancient mitochondrial human genome from a prepastoralist southern African.}, journal = {Genome biology and evolution}, volume = {6}, number = {10}, pages = {2647-2653}, pmid = {25212860}, issn = {1759-6653}, mesh = {Africa ; *Fossils ; Genome, Mitochondrial/*genetics ; Humans ; Phylogeny ; }, abstract = {The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semidesert regions of Namibia and Botswana, whereas archeological, historical, and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. No genetic data have been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa prepastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330-year-old male skeleton, confirmed through osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that prepastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.}, }
@article {pmid25207979, year = {2014}, author = {Cano, RJ and Rivera-Perez, J and Toranzos, GA and Santiago-Rodriguez, TM and Narganes-Storde, YM and Chanlatte-Baik, L and García-Roldán, E and Bunkley-Williams, L and Massey, SE}, title = {Paleomicrobiology: revealing fecal microbiomes of ancient indigenous cultures.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e106833}, pmid = {25207979}, issn = {1932-6203}, support = {R25 GM061151/GM/NIGMS NIH HHS/United States ; 5R25GM061151-12/GM/NIGMS NIH HHS/United States ; }, mesh = {Diet ; Feces/*microbiology/parasitology ; Humans ; *Microbiology ; *Microbiota ; *Paleontology ; *Population Groups ; Puerto Rico/ethnology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations.}, }
@article {pmid25204303, year = {2015}, author = {Ramírez, O and Burgos-Paz, W and Casas, E and Ballester, M and Bianco, E and Olalde, I and Santpere, G and Novella, V and Gut, M and Lalueza-Fox, C and Saña, M and Pérez-Enciso, M}, title = {Genome data from a sixteenth century pig illuminate modern breed relationships.}, journal = {Heredity}, volume = {114}, number = {2}, pages = {175-184}, pmid = {25204303}, issn = {1365-2540}, mesh = {Alleles ; Animals ; *Breeding ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; *Genome ; Genotype ; Male ; Phylogeography ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Sequence Alignment ; Sequence Analysis, DNA ; Spain ; Sus scrofa/*genetics ; }, abstract = {Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.}, }
@article {pmid25190770, year = {2014}, author = {Gibbons, A}, title = {Ancient DNA. Three-part ancestry for Europeans.}, journal = {Science (New York, N.Y.)}, volume = {345}, number = {6201}, pages = {1106-1107}, doi = {10.1126/science.345.6201.1106}, pmid = {25190770}, issn = {1095-9203}, mesh = {DNA/*genetics ; Genome, Human ; Humans ; White People/*genetics ; }, }
@article {pmid25168683, year = {2014}, author = {Pickrell, JK and Reich, D}, title = {Toward a new history and geography of human genes informed by ancient DNA.}, journal = {Trends in genetics : TIG}, volume = {30}, number = {9}, pages = {377-389}, pmid = {25168683}, issn = {0168-9525}, support = {F32 GM103098/GM/NIGMS NIH HHS/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Africa ; DNA/*genetics/*history ; Evolution, Molecular ; *Genetics, Population ; *Genome, Human ; *Geography ; History, Ancient ; Humans ; Phenotype ; Selection, Genetic/*genetics ; }, abstract = {Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture, and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world's human populations. In light of this we argue that it is time to critically reevaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.}, }
@article {pmid25162694, year = {2014}, author = {Jaeger, LH and Iñiguez, AM}, title = {Molecular paleoparasitological hybridization approach as effective tool for diagnosing human intestinal parasites from scarce archaeological remains.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e105910}, pmid = {25162694}, issn = {1932-6203}, mesh = {Animals ; Anthropology/methods ; Ascaris/classification/*genetics ; Brazil ; Cemeteries ; DNA, Helminth/*genetics/isolation &amp; purification ; Enterobius/classification/*genetics ; Exhumation ; Helminthiasis/diagnosis/*history/parasitology ; History, 18th Century ; Humans ; Hybridization, Genetic ; Intestinal Diseases, Parasitic/diagnosis/*history/parasitology ; Parasitology/methods ; Strongyloides stercoralis/classification/*genetics ; Trichuris/classification/*genetics ; }, abstract = {Paleoparasitology is the science that uses parasitological techniques for diagnosing parasitic diseases in the past. Advances in molecular biology brought new insights into this field allowing the study of archaeological material. However, due to technical limitations a proper diagnosis and confirmation of the presence of parasites is not always possible, especially in scarce and degraded archaeological remains. In this study, we developed a Molecular Paleoparasitological Hybridization (MPH) approach using ancient DNA (aDNA) hybridization to confirm and complement paleoparasitological diagnosis. Eight molecular targets from four helminth parasites were included: Ascaris sp., Trichuris trichiura, Enterobius vermicularis, and Strongyloides stercoralis. The MPH analysis using 18th century human remains from Praça XV cemetery (CPXV), Rio de Janeiro, Brazil, revealed for the first time the presence E. vermicularis aDNA (50%) in archaeological sites of Brazil. Besides, the results confirmed T. trichiura and Ascaris sp. infections. The prevalence of infection by Ascaris sp. and E. vermicularis increased considerably when MPH was applied. However, a lower aDNA detection of T. trichiura (40%) was observed when compared to the diagnosis by paleoparasitological analysis (70%). Therefore, based on these data, we suggest a combination of Paleoparasitological and MPH approaches to verify the real panorama of intestinal parasite infection in human archeological samples.}, }
@article {pmid25158691, year = {2014}, author = {Wang, GZ and Marini, S and Ma, X and Yang, Q and Zhang, X and Zhu, Y}, title = {Improvement of Dscam homophilic binding affinity throughout Drosophila evolution.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {186}, pmid = {25158691}, issn = {1471-2148}, support = {R01 AA020401/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Brain/cytology/metabolism ; Cell Adhesion Molecules/*genetics/*metabolism ; Drosophila/*genetics/*metabolism ; Drosophila Proteins/*genetics/*metabolism ; *Evolution, Molecular ; Exons/genetics ; Genetic Variation ; Genomics ; Neural Cell Adhesion Molecules/genetics/metabolism ; Neurons/cytology/metabolism ; Protein Binding ; Protein Isoforms/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is known that thousands of isoforms bind themselves through specific homophilic interactions, a process which provides the basis for cellular self-recognition. Detailed biochemical studies of specific isoforms strongly suggest that homophilic binding, i.e. the formation of homodimers by identical Dscam1 isomers, is of great importance for the self-avoidance of neurons. Due to experimental limitations, it is currently impossible to measure the homophilic binding affinities for all 19,000 potential isoforms.<br><br>RESULTS: Here we reconstructed the DNA sequences of an ancestral Dscam form (which likely existed approximately 40&#x2009;~&#x2009;50 million years ago) using a comparative genomic approach. On the basis of this sequence, we established a working model to predict the self-binding affinities of all isoforms in both the current and the ancestral genome, using machine-learning methods. Detailed computational analysis was performed to compare the self-binding affinities of all isoforms present in these two genomes. Our results revealed that 1) isoforms containing newly derived variable domains exhibit higher self-binding affinities than those with conserved domains, and 2) current isoforms display higher self-binding affinities than their counterparts in the ancient genome. As thousands of Dscam isoforms are needed for the self-avoidance of the neuron, we propose that an increase in self-binding affinity provides the basis for the successful evolution of the arthropod brain.<br><br>CONCLUSIONS: Our data presented here provide an excellent model for future experimental studies of the binding behavior of Dscam isoforms. The results of our analysis indicate that evolution favored the rise of novel variable domains thanks to their higher self-binding affinities, rather than selection merely on the basis of simple expansion of isoform diversity, as that this particular selection process would have established the powerful mechanisms required for neuronal self-avoidance. Thus, we reveal here a new molecular mechanism for the successful evolution of arthropod brains.}, }
@article {pmid25143190, year = {2014}, author = {Overballe-Petersen, S and Willerslev, E}, title = {Horizontal transfer of short and degraded DNA has evolutionary implications for microbes and eukaryotic sexual reproduction.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {10}, pages = {1005-1010}, pmid = {25143190}, issn = {1521-1878}, mesh = {Animals ; Bacteria/*genetics ; *Biological Evolution ; DNA/*genetics ; DNA Damage/*genetics ; Eukaryota/*genetics ; *Gene Transfer, Horizontal ; Humans ; Reproduction/*genetics ; }, abstract = {Horizontal gene transfer in the form of long DNA fragments has changed our view of bacterial evolution. Recently, we discovered that such processes may also occur with the massive amounts of short and damaged DNA in the environment, and even with truly ancient DNA. Although it presently remains unclear how often it takes place in nature, horizontal gene transfer of short and damaged DNA opens up the possibility for genetic exchange across distinct species in both time and space. In this essay, we speculate on the potential evolutionary consequences of this phenomenon. We argue that it may challenge basic assumptions in evolutionary theory; that it may have distant origins in life's history; and that horizontal gene transfer should be viewed as an evolutionary strategy not only preceding but causally underpinning the evolution of sexual reproduction.}, }
@article {pmid25130911, year = {2014}, author = {Zhao, YB and Zhang, Y and Li, HJ and Cui, YQ and Zhu, H and Zhou, H}, title = {Ancient DNA evidence reveals that the Y chromosome haplogroup Q1a1 admixed into the Han Chinese 3,000 years ago.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {26}, number = {6}, pages = {813-821}, doi = {10.1002/ajhb.22604}, pmid = {25130911}, issn = {1520-6300}, mesh = {Asian People/*genetics ; China ; Chromosomes, Human, Y/*genetics ; Genetics, Population ; *Haplotypes ; Humans ; Male ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: Y chromosome haplogroup Q1a1 is found almost only in Han Chinese populations. However, it has not been found in ancient Han Chinese samples until now. Thus, the origin of haplogroup Q1a1 in Han Chinese is still obscure. This study attempts to provide answer to this question, and to uncover the origin and paternal genetic structure of the ancestors of the Han Chinese.<br><br>METHODS: Eighty-nine ancient human remains that were excavated from the presumed geographic source of the Han Chinese and dated to approximately 3,000 years ago were treated by the amelogenin gene polymerase chain reaction test, to determine their sex. Then, Y chromosome single nucleotide polymorphisms were subsequently analyzed from the samples detected as male.<br><br>RESULTS: Samples from 27 individuals were successfully amplified. Their haplotypes could be attributed to haplogroups N, O*, O2a, O3a, and Q1a1. Analyses showed that the assigned haplogroup of each sample is correlated to the suspected social status and observed burial custom associated with the sample.<br><br>CONCLUSIONS: The origins of the observed haplotypes and their distribution in present day Han Chinese and in the samples suggest that haplogroup Q1a1 was probably introduced into the Han Chinese population approximately 3,000 years ago.}, }
@article {pmid25129844, year = {2014}, author = {Jeong, C and Di Rienzo, A}, title = {Adaptations to local environments in modern human populations.}, journal = {Current opinion in genetics &amp; development}, volume = {29}, number = {}, pages = {1-8}, pmid = {25129844}, issn = {1879-0380}, support = {R01 HL119577/HL/NHLBI NIH HHS/United States ; UL1 TR000430/TR/NCATS NIH HHS/United States ; R01HL119577/HL/NHLBI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; *Environment ; Evolution, Molecular ; Genetic Variation/*genetics ; Genetics, Population ; Humans ; Phenotype ; Polymorphism, Single Nucleotide ; Selection, Genetic/*genetics ; Skin Pigmentation/genetics ; }, abstract = {After leaving sub-Saharan Africa around 50000-100000 years ago, anatomically modern humans have quickly occupied extremely diverse environments. Human populations were exposed to further environmental changes resulting from cultural innovations, such as the spread of farming, which gave rise to new selective pressures related to pathogen exposures and dietary shifts. In addition to changing the frequency of individual adaptive alleles, natural selection may also shape the overall genetic architecture of adaptive traits. Here, we review recent advances in understanding the genetic architecture of adaptive human phenotypes based on insights from the studies of lactase persistence, skin pigmentation and high-altitude adaptation. These adaptations evolved in parallel in multiple human populations, providing a chance to investigate independent realizations of the evolutionary process. We suggest that the outcome of adaptive evolution is often highly variable even under similar selective pressures. Finally, we highlight a growing need for detecting adaptations that did not follow the classical sweep model and for incorporating new sources of genetic evidence such as information from ancient DNA.}, }
@article {pmid25111840, year = {2014}, author = {Herman, JS and McDevitt, AD and Kawałko, A and Jaarola, M and Wójcik, JM and Searle, JB}, title = {Land-bridge calibration of molecular clocks and the post-glacial Colonization of Scandinavia by the Eurasian field vole Microtus agrestis.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e103949}, pmid = {25111840}, issn = {1932-6203}, mesh = {Animals ; *Arvicolinae/genetics ; Calibration ; *Evolution, Molecular ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeography ; Scandinavian and Nordic Countries ; }, abstract = {Phylogeography interprets molecular genetic variation in a spatial and temporal context. Molecular clocks are frequently used to calibrate phylogeographic analyses, however there is mounting evidence that molecular rates decay over the relevant timescales. It is therefore essential that an appropriate rate is determined, consistent with the temporal scale of the specific analysis. This can be achieved by using temporally spaced data such as ancient DNA or by relating the divergence of lineages directly to contemporaneous external events of known time. Here we calibrate a Eurasian field vole (Microtus agrestis) mitochondrial genealogy from the well-established series of post-glacial geophysical changes that led to the formation of the Baltic Sea and the separation of the Scandinavian peninsula from the central European mainland. The field vole exhibits the common phylogeographic pattern of Scandinavian colonization from both the north and the south, however the southernmost of the two relevant lineages appears to have originated in situ on the Scandinavian peninsula, or possibly in the adjacent island of Zealand, around the close of the Younger Dryas. The mitochondrial substitution rate and the timescale for the genealogy are closely consistent with those obtained with a previous calibration, based on the separation of the British Isles from mainland Europe. However the result here is arguably more certain, given the level of confidence that can be placed in one of the central assumptions of the calibration, that field voles could not survive the last glaciation of the southern part of the Scandinavian peninsula. Furthermore, the similarity between the molecular clock rate estimated here and those obtained by sampling heterochronous (ancient) DNA (including that of a congeneric species) suggest that there is little disparity between the measured genetic divergence and the population divergence that is implicit in our land-bridge calibration.}, }
@article {pmid25106086, year = {2014}, author = {Wann, S and Thomas, GS}, title = {What can ancient mummies teach us about atherosclerosis?.}, journal = {Trends in cardiovascular medicine}, volume = {24}, number = {7}, pages = {279-284}, doi = {10.1016/j.tcm.2014.06.005}, pmid = {25106086}, issn = {1873-2615}, mesh = {Atherosclerosis/diagnostic imaging/ethnology/genetics/*history ; Autopsy ; Cultural Characteristics/history ; Genetic Predisposition to Disease ; History, Ancient ; Humans ; Life Style/ethnology/history ; Mummies/diagnostic imaging/*history ; Phenotype ; Risk Factors ; Tomography, X-Ray Computed ; Vascular Calcification/diagnostic imaging/ethnology/genetics/*history ; Whole Body Imaging ; }, abstract = {Ancient mummies have captivated a wide variety of audiences for centuries. In order to better understand the evolution and causative features of atherosclerosis, the Horus group is applying modern scientific methods to study ancient mummies. We have used CT scanning to detect calcification in arteries as an indication of the presence of atherosclerosis, and are correlating these results with cultural and lifestyle features of various populations of ancient people as represented by their ancient mummified remains. We are also pursuing related studies of ancient DNA to define genotypes associated with atherosclerotic phenotypes.}, }
@article {pmid25100869, year = {2014}, author = {Renaud, G and Stenzel, U and Kelso, J}, title = {leeHom: adaptor trimming and merging for Illumina sequencing reads.}, journal = {Nucleic acids research}, volume = {42}, number = {18}, pages = {e141}, pmid = {25100869}, issn = {1362-4962}, mesh = {*Algorithms ; Bayes Theorem ; Likelihood Functions ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {The sequencing of libraries containing molecules shorter than the read length, such as in ancient or forensic applications, may result in the production of reads that include the adaptor, and in paired reads that overlap one another. Challenges for the processing of such reads are the accurate identification of the adaptor sequence and accurate reconstruction of the original sequence most likely to have given rise to the observed read(s). We introduce an algorithm that removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. Our algorithm is faster, and provides a more accurate reconstruction of the original sequence for both simulated and ancient DNA data sets, than other approaches. leeHom is released under the GPLv3 and is freely available from: https://bioinf.eva.mpg.de/leehom/}, }
@article {pmid25098828, year = {2014}, author = {Álvarez-Sandoval, BA and Manzanilla, LR and Montiel, R}, title = {Sex determination in highly fragmented human DNA by high-resolution melting (HRM) analysis.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e104629}, pmid = {25098828}, issn = {1932-6203}, mesh = {Adult ; Amelogenin/*genetics ; Chromosomes, Human, X/*genetics ; Chromosomes, Human, Y/*genetics ; DNA/*genetics ; Female ; Humans ; Male ; Real-Time Polymerase Chain Reaction/*methods ; Sex Determination Analysis/*methods ; }, abstract = {Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp) of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM). HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design.}, }
@article {pmid25082857, year = {2014}, author = {Jiao, Y and Li, J and Tang, H and Paterson, AH}, title = {Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots.}, journal = {The Plant cell}, volume = {26}, number = {7}, pages = {2792-2802}, pmid = {25082857}, issn = {1532-298X}, mesh = {*Evolution, Molecular ; Gene Duplication ; Genome, Plant/*genetics ; Genomics ; Magnoliopsida/*genetics ; Phylogeny ; Polyploidy ; Sequence Alignment ; Sequence Analysis, DNA ; Synteny ; }, abstract = {Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [Sorghum bicolor], banana, and oil palm [Elaeis guineensis]) and two eudicot (grape [Vitis vinifera] and sacred lotus [Nelumbo nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy events than either approach individually, a principle that is exemplified in the disambiguation of a WGD series of rho (ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the alpha (α)-beta (β)-gamma (γ) series previously revealed in the Arabidopsis thaliana lineage.}, }
@article {pmid25081630, year = {2014}, author = {Gansauge, MT and Meyer, M}, title = {Selective enrichment of damaged DNA molecules for ancient genome sequencing.}, journal = {Genome research}, volume = {24}, number = {9}, pages = {1543-1549}, pmid = {25081630}, issn = {1549-5469}, mesh = {Animals ; Base Sequence ; DNA Contamination ; Deoxyuracil Nucleotides/*chemistry/genetics ; *Genome ; Humans ; Molecular Sequence Data ; Neanderthals/*genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; }, abstract = {Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA--the presence of deoxyuracils--for selective enrichment of endogenous DNA against a complex background of contamination during DNA library preparation. By applying the method to Neanderthal DNA extracts that are heavily contaminated with present-day human DNA, we show that the fraction of useful sequence information increases ∼ 10-fold and that the resulting sequences are more efficiently depleted of human contamination than when using purely computational approaches. Furthermore, we show that U selection can lead to a four- to fivefold increase in the proportion of endogenous DNA sequences relative to those of microbial contaminants in some samples. U selection may thus help to lower the costs for ancient genome sequencing of nonhuman samples also.}, }
@article {pmid25079126, year = {2013}, author = {Brody, AJ and King, RJ}, title = {Letter to the editor: Genetics and the archaeology of ancient Israel.}, journal = {Human biology}, volume = {85}, number = {6}, pages = {925-940}, doi = {10.3378/027.085.0606}, pmid = {25079126}, issn = {1534-6617}, mesh = {Chromosomes, Human, Y/genetics ; Emigration and Immigration/history ; Ethnicity/*genetics/history ; Genetics, Population/history ; Haplotypes ; History, Ancient ; Humans ; Israel/ethnology ; Middle East/ethnology ; }, abstract = {This letter is a call for DNA testing on ancient skeletal materials from the southern Levant to begin a database of genetic information of the inhabitants of this crossroads region. In this region, during the Iron I period traditionally dated to circa 1200-1000 BCE, archaeologists and biblical historians view the earliest presence of a group that called itself Israel. They lived in villages in the varied hill countries of the region, contemporary with urban settlements in the coastal plains, inland valleys, and central hill country attributed to varied indigenous groups collectively called Canaanite. The remnants of Egyptian imperial presence in the region lasted until around 1150 BCE, postdating the arrival of an immigrant group from the Aegean called the Philistines circa 1175 BCE. The period that follows in the southern Levant is marked by the development of territorial states throughout the region, circa 1000-800 BCE. These patrimonial kingdoms, including the United Kingdom of Israel and the divided kingdoms of northern Israel and Judah, coalesced varied peoples under central leadership and newly founded administrative and religious bureaucracies. Ancient DNA testing will give us a further refined understanding of the individuals who peopled the region of the southern Levant throughout its varied archaeological and historic periods and provide scientific data that will support, refute, or nuance our sociohistoric reconstruction of ancient group identities. These social identities may or may not map onto genetic data, but without sampling of ancient DNA we may never know. A database of ancient DNA will also allow for comparisons with modern DNA samples collected throughout the greater region and the Mediterranean littoral, giving a more robust understanding of the long historical trajectories of regional human genetics and the genetics of varied ancestral groups of today's Jewish populations and other cultural groups in the modern Middle East and Mediterranean.}, }
@article {pmid25059709, year = {2014}, author = {Veeramah, KR and Novembre, J}, title = {Demographic events and evolutionary forces shaping European genetic diversity.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {9}, pages = {a008516}, pmid = {25059709}, issn = {1943-0264}, support = {R01 HG005226/HG/NHGRI NIH HHS/United States ; R01 HG007089/HG/NHGRI NIH HHS/United States ; R01-HG005226/HG/NHGRI NIH HHS/United States ; R01-HG007089/HG/NHGRI NIH HHS/United States ; }, mesh = {Biological Evolution ; DNA, Mitochondrial/genetics ; Europe ; Evolution, Molecular ; *Genetic Variation ; *Genetics, Population ; Geography ; *Human Migration ; Humans ; Selection, Genetic ; White People ; }, abstract = {Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease.}, }
@article {pmid25052335, year = {2014}, author = {Schibler, J and Elsner, J and Schlumbaum, A}, title = {Incorporation of aurochs into a cattle herd in Neolithic Europe: single event or breeding?.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {5798}, pmid = {25052335}, issn = {2045-2322}, mesh = {Animals ; *Archaeology ; *Breeding ; Cattle/*genetics ; DNA, Mitochondrial/*genetics ; Europe ; *Evolution, Molecular ; Female ; *Genome, Mitochondrial ; Haplotypes/*genetics ; History, Ancient ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Domestication is an ongoing process continuously changing the lives of animals and humans and the environment. For the majority of European cattle (Bos taurus) genetic and archaeozoological evidence support initial domestication ca. 11'000 BP in the Near East from few founder aurochs (Bos primigenius) belonging to the mitochondrial DNA T macro-haplogroup. Gene flow between wild European aurochs of P haplogroup and domestic cattle of T haplogroup, coexisting over thousands of years, appears to have been sporadic. We report archaeozoological and ancient DNA evidence for the incorporation of wild stock into a domestic cattle herd from a Neolithic lake-dwelling in Switzerland. A complete metacarpus of a small and compact adult bovid is morphologically and genetically a female. With withers height of ca. 112 cm, it is comparable in size with small domestic cattle from contemporaneous sites in the area. The bone is directly dated to 3360-3090 cal BC and associated to the Horgen culture, a period of the secondary products revolution. The cow possessed a novel mtDNA P haplotype variant of the European aurochs. We argue this is either a single event or, based on osteological characteristics of the Horgen cattle, a rare instance of intentional breeding with female aurochs.}, }
@article {pmid25047956, year = {2014}, author = {Guo, L and Chen, Y and Ye, N and Dai, X and Yang, W and Yin, T}, title = {Differential retention and expansion of the ancestral genes associated with the paleopolyploidies in modern rosid plants, as revealed by analysis of the extensins super-gene family.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {612}, pmid = {25047956}, issn = {1471-2164}, mesh = {Arabidopsis/*genetics ; Carica/*genetics ; Databases, Genetic ; *Genes, Plant ; Glycoproteins/classification/genetics/metabolism ; Phylogeny ; Plant Proteins/classification/genetics/metabolism ; Polyploidy ; Populus/*genetics ; Vitis/*genetics ; }, abstract = {BACKGROUND: All modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods.<br><br>RESULTS: The majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common &#x3b3;-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene.<br><br>CONCLUSIONS: Our analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species.}, }
@article {pmid25047803, year = {2014}, author = {Lin, Y and Cheng, Y and Jin, J and Jin, X and Jiang, H and Yan, H and Cheng, B}, title = {Genome duplication and gene loss affect the evolution of heat shock transcription factor genes in legumes.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102825}, pmid = {25047803}, issn = {1932-6203}, mesh = {Cajanus/genetics ; DNA-Binding Proteins/*genetics ; *Evolution, Molecular ; Fabaceae/*genetics ; *Gene Duplication ; Genes, Plant ; Genome, Plant ; Heat Shock Transcription Factors ; Lotus/genetics ; Medicago truncatula/genetics ; *Polyploidy ; Glycine max/genetics ; Transcription Factors/*genetics ; }, abstract = {Whole-genome duplication events (polyploidy events) and gene loss events have played important roles in the evolution of legumes. Here we show that the vast majority of Hsf gene duplications resulted from whole genome duplication events rather than tandem duplication, and significant differences in gene retention exist between species. By searching for intraspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found that genome duplications accounted for 42 of 46 Hsf-containing segments in Glycine max, while paired segments were rarely identified in Lotus japonicas, Medicago truncatula and Cajanus cajan. However, by comparing interspecies microsynteny, we determined that the great majority of Hsf-containing segments in Lotus japonicas, Medicago truncatula and Cajanus cajan show extensive conservation with the duplicated regions of Glycine max. These segments formed 17 groups of orthologous segments. These results suggest that these regions shared ancient genome duplication with Hsf genes in Glycine max, but more than half of the copies of these genes were lost. On the other hand, the Glycine max Hsf gene family retained approximately 75% and 84% of duplicated genes produced from the ancient genome duplication and recent Glycine-specific genome duplication, respectively. Continuous purifying selection has played a key role in the maintenance of Hsf genes in Glycine max. Expression analysis of the Hsf genes in Lotus japonicus revealed their putative involvement in multiple tissue-/developmental stages and responses to various abiotic stimuli. This study traces the evolution of Hsf genes in legume species and demonstrates that the rates of gene gain and loss are far from equilibrium in different species.}, }
@article {pmid25047360, year = {2015}, author = {Hervella, M and Iñiguez, MG and Izagirre, N and Anta, A and de-la-Rúa, C}, title = {Nondestructive methods for recovery of biological material from human teeth for DNA extraction.}, journal = {Journal of forensic sciences}, volume = {60}, number = {1}, pages = {136-141}, doi = {10.1111/1556-4029.12568}, pmid = {25047360}, issn = {1556-4029}, mesh = {Cuspid ; DNA Fingerprinting ; DNA, Mitochondrial/*isolation &amp; purification ; Dental Pulp/chemistry ; Forensic Dentistry ; Humans ; Molar, Third ; Polymerase Chain Reaction ; Specimen Handling/*methods ; Tooth Root/*chemistry ; }, abstract = {The extraction of DNA from human skeletal remains applied to forensic, and evolutionary studies do not exclude risks, which are to be evaluated when working with unique specimens that could be damaged or even destroyed. In the present study were evaluated several nondestructive methods for recovering DNA instead of the most currently used pulverization method. Three different procedures to access inside the dental pieces (occlusal perforation, cervical perforation, and cervical cut) have been compared with the aim of recovering as many cell remains as possible to carry out a DNA extraction. Given the DNA quantitation results, a method was proposed that consists of a cervical cut to facilitate the access to the pulp cavity and a subsequent filing of the root canals down to the apex of the dental root. This methodology allows the recovery of both mitochondrial and nuclear DNA, with the minimum deterioration for the dental pieces.}, }
@article {pmid25027719, year = {2014}, author = {Heupink, TH and van Grouw, H and Lambert, DM}, title = {The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {136}, pmid = {25027719}, issn = {1471-2148}, mesh = {Animals ; Biological Evolution ; Birds/*classification/genetics ; Columbidae/anatomy &amp; histology/*classification/*genetics ; Extinction, Biological ; Feathers/chemistry ; Molecular Sequence Data ; Museums ; Phylogeny ; }, abstract = {BACKGROUND: The closely related and extinct Dodo (Raphus cucullatus) and Rodrigues Solitaire (Pezophaps solitaria), both in the subfamily Raphinae, are members of a clade of morphologically very diverse pigeons. Genetic analyses have revealed that the Nicobar Pigeon (Caloenas nicobarica) is the closest living relative of these birds, thereby highlighting their ancestors' remarkable migration and morphological evolution. The Spotted Green Pigeon (Caloenas maculata) was described in 1783 and showed some similarities to the Nicobar Pigeon. Soon however the taxon fell into obscurity, as it was regarded as simply an abnormal form of the Nicobar Pigeon. The relationship between both taxa has occasionally been questioned, leading some ornithologists to suggest that the two may in fact be different taxa. Today only one of the original two specimens survives and nothing is known about the origin of the taxon. Due to its potential close relationship, the Spotted Green Pigeon may hold clues to the historical migration, isolation and morphological evolution of the Dodo and its kindred.<br><br>RESULTS: We use ancient DNA methodologies to investigate the phylogeny and authenticity of the Spotted Green Pigeon. A novel extraction method with the ability to retain and purify heavily fragmented DNA is used to investigate two feathers from the sole surviving specimen. Maximum Likelihood phylogenetic analyses reveal that the Spotted Green Pigeon is a unique lineage and together with the Nicobar Pigeon, is basal to the Dodo and Rodrigues Solitaire.<br><br>CONCLUSIONS: The distance observed for the Spotted Green Pigeon and Nicobar Pigeon is larger than that observed within other Pigeon species, indicating that the Spotted Green pigeon is a unique taxon, thereby also indicating it is a genuine addition to the list of extinct species. The phylogenetic placement of the Spotted Green Pigeon indicates that the ancestors of both Caloenas and therefore Raphinae displayed and shared the following traits: ability of flight, semi-terrestrial habits and an affinity towards islands. This set of traits supports the stepping stone hypothesis, which states that the Raphinae got to their respective localities by island hopping from India or Southeast Asia.}, }
@article {pmid25016250, year = {2014}, author = {Hollard, C and Keyser, C and Giscard, PH and Tsagaan, T and Bayarkhuu, N and Bemmann, J and Crubézy, E and Ludes, B}, title = {Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers.}, journal = {Forensic science international. Genetics}, volume = {12}, number = {}, pages = {199-207}, doi = {10.1016/j.fsigen.2014.05.012}, pmid = {25016250}, issn = {1878-0326}, mesh = {Asia ; Chromosomes, Human, Y ; DNA, Mitochondrial/*genetics ; Europe ; Female ; Genetic Markers ; Humans ; Male ; Microsatellite Repeats ; }, abstract = {The Altai Mountains have been a long-term boundary zone between the Eurasian Steppe populations and South and East Asian populations. To disentangle some of the historical population movements in this area, 14 ancient human specimens excavated in the westernmost part of the Mongolian Altai were studied. Thirteen of them were dated from the Middle to the End of the Bronze Age and one of them to the Eneolithic period. The environmental conditions encountered in this region led to the good preservation of DNA in the human remains. Therefore, a multi-markers approach was adopted for the genetic analysis of identity, ancestry and phenotype markers. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages. To go further in the search of the origin of these ancient specimens, phenotypical characters (i.e. hair and eye color) were determined. For this purpose, we adapted the HIrisPlex assay recently described to MALDI-TOF mass spectrometry. In addition, some ancestry informative markers were analyzed with this assay. The results revealed mixed phenotypes among this group confirming the probable admixed ancestry of the studied Altaian population at the Middle Bronze Age. The good results obtained from ancient DNA samples suggest that this approach might be relevant for forensic casework too.}, }
@article {pmid24993353, year = {2014}, author = {Smith, O and Clapham, AJ and Rose, P and Liu, Y and Wang, J and Allaby, RG}, title = {Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {5559}, pmid = {24993353}, issn = {2045-2322}, support = {DTA BBG0177941//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Crops, Agricultural/genetics/history/virology ; *DNA Methylation ; Evolution, Molecular ; Gene-Environment Interaction ; Genetic Loci ; Genome, Plant ; History, 15th Century ; History, 16th Century ; History, Ancient ; History, Medieval ; Hordeum/*genetics/history/virology ; Host-Pathogen Interactions ; Humans ; Mosaic Viruses/physiology ; Plant Diseases/virology ; }, abstract = {Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE - 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis in ancient DNA.}, }
@article {pmid24979787, year = {2014}, author = {Fehren-Schmitz, L and Haak, W and Mächtle, B and Masch, F and Llamas, B and Cagigao, ET and Sossna, V and Schittek, K and Isla Cuadrado, J and Eitel, B and Reindel, M}, title = {Climate change underlies global demographic, genetic, and cultural transitions in pre-Columbian southern Peru.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {26}, pages = {9443-9448}, pmid = {24979787}, issn = {1091-6490}, mesh = {Archaeology/methods ; Base Sequence ; Bayes Theorem ; Climate Change/*history ; Computer Simulation ; Cultural Evolution/*history ; DNA, Mitochondrial/isolation &amp; purification ; Droughts/*history ; Haplotypes/genetics ; History, 15th Century ; History, Ancient ; History, Medieval ; Human Migration/*history ; Humans ; Models, Genetic ; Molecular Sequence Data ; Peru ; Population Dynamics/*history ; Sequence Analysis, DNA ; }, abstract = {Several archaeological studies in the Central Andes have pointed at the temporal coincidence of climatic fluctuations (both long- and short-term) and episodes of cultural transition and changes of socioeconomic structures throughout the pre-Columbian period. Although most scholars explain the connection between environmental and cultural changes by the impact of climatic alterations on the capacities of the ecosystems inhabited by pre-Columbian cultures, direct evidence for assumed demographic consequences is missing so far. In this study, we address directly the impact of climatic changes on the spatial population dynamics of the Central Andes. We use a large dataset of pre-Columbian mitochondrial DNA sequences from the northern Rio Grande de Nasca drainage (RGND) in southern Peru, dating from ∼840 BC to 1450 AD. Alternative demographic scenarios are tested using Bayesian serial coalescent simulations in an approximate Bayesian computational framework. Our results indicate migrations from the lower coastal valleys of southern Peru into the Andean highlands coincident with increasing climate variability at the end of the Nasca culture at ∼640 AD. We also find support for a back-migration from the highlands to the coast coincident with droughts in the southeastern Andean highlands and improvement of climatic conditions on the coast after the decline of the Wari and Tiwanaku empires (∼1200 AD), leading to a genetic homogenization in the RGND and probably southern Peru as a whole.}, }
@article {pmid24979776, year = {2014}, author = {Hung, CM and Shaner, PJ and Zink, RM and Liu, WC and Chu, TC and Huang, WS and Li, SH}, title = {Drastic population fluctuations explain the rapid extinction of the passenger pigeon.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {29}, pages = {10636-10641}, pmid = {24979776}, issn = {1091-6490}, mesh = {Animals ; Chromosome Mapping ; Columbidae/*physiology ; *Extinction, Biological ; Food Supply ; Genome/genetics ; Geography ; Markov Chains ; Population Density ; Population Dynamics ; Quercus/physiology ; United States ; }, abstract = {To assess the role of human disturbances in species' extinction requires an understanding of the species population history before human impact. The passenger pigeon was once the most abundant bird in the world, with a population size estimated at 3-5 billion in the 1800s; its abrupt extinction in 1914 raises the question of how such an abundant bird could have been driven to extinction in mere decades. Although human exploitation is often blamed, the role of natural population dynamics in the passenger pigeon's extinction remains unexplored. Applying high-throughput sequencing technologies to obtain sequences from most of the genome, we calculated that the passenger pigeon's effective population size throughout the last million years was persistently about 1/10,000 of the 1800's estimated number of individuals, a ratio 1,000-times lower than typically found. This result suggests that the passenger pigeon was not always super abundant but experienced dramatic population fluctuations, resembling those of an "outbreak" species. Ecological niche models supported inference of drastic changes in the extent of its breeding range over the last glacial-interglacial cycle. An estimate of acorn-based carrying capacity during the past 21,000 y showed great year-to-year variations. Based on our results, we hypothesize that ecological conditions that dramatically reduced population size under natural conditions could have interacted with human exploitation in causing the passenger pigeon's rapid demise. Our study illustrates that even species as abundant as the passenger pigeon can be vulnerable to human threats if they are subject to dramatic population fluctuations, and provides a new perspective on the greatest human-caused extinction in recorded history.}, }
@article {pmid24977469, year = {2014}, author = {Sankaranarayanan, K and Lowenstein, TK and Timofeeff, MN and Schubert, BA and Lum, JK}, title = {Characterization of ancient DNA supports long-term survival of Haloarchaea.}, journal = {Astrobiology}, volume = {14}, number = {7}, pages = {553-560}, pmid = {24977469}, issn = {1557-8070}, mesh = {Base Sequence ; California ; DNA, Archaeal/*genetics ; DNA, Ribosomal/*genetics ; Euryarchaeota/genetics/physiology ; Halobacteriaceae/genetics/physiology ; Halorubrum/*genetics/physiology ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacteria and archaea isolated from crystals of halite 10(4) to 10(8) years old suggest long-term survival of halophilic microorganisms, but the results are controversial. Independent verification of the authenticity of reputed living prokaryotes in ancient salt is required because of the high potential for environmental and laboratory contamination. Low success rates of prokaryote cultivation from ancient halite, however, hamper direct replication experiments. In such cases, culture-independent approaches that use the polymerase chain reaction (PCR) and sequencing of 16S ribosomal DNA are a robust alternative. Here, we use amplification, cloning, and sequencing of 16S ribosomal DNA to investigate the authenticity of halophilic archaea cultured from subsurface halite, Death Valley, California, 22,000 to 34,000 years old. We recovered 16S ribosomal DNA sequences that are identical, or nearly so (>99%), to two strains, Natronomonas DV462A and Halorubrum DV427, which were previously isolated from the same halite interval. These results provide the best independent support to date for the long-term survival of halophilic archaea in ancient halite. PCR-based approaches are sensitive to small amounts of DNA and could allow investigation of even older halites, 10(6) to 10(8) years old, from which microbial cultures have been reported. Such studies of microbial life in ancient salt are particularly important as we search for microbial signatures in similar deposits on Mars and elsewhere in the Solar System.}, }
@article {pmid24974206, year = {2014}, author = {Malaspinas, AS and Tange, O and Moreno-Mayar, JV and Rasmussen, M and DeGiorgio, M and Wang, Y and Valdiosera, CE and Politis, G and Willerslev, E and Nielsen, R}, title = {bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).}, journal = {Bioinformatics (Oxford, England)}, volume = {30}, number = {20}, pages = {2962-2964}, pmid = {24974206}, issn = {1367-4811}, mesh = {Genetics, Population ; Genome, Human/genetics ; Genomics/*methods ; Genotype ; Humans ; Phylogeography/*methods ; *Software ; }, abstract = {SUMMARY: We present bammds, a practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional scaling algorithm. Our tool is aimed at determining the ancestry of unknown samples-typical of ancient DNA data-particularly when only low amounts of data are available for those samples.<br><br>The software package is available under GNU General Public License v3 and is freely available together with test datasets https://savannah.nongnu.org/projects/bammds/. It is using R (http://www.r-project.org/), parallel (http://www.gnu.org/software/parallel/), samtools (https://github.com/samtools/samtools).<br><br>CONTACT: bammds-users@nongnu.org<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid24964386, year = {2015}, author = {Molak, M and Suchard, MA and Ho, SY and Beilman, DW and Shapiro, B}, title = {Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA.}, journal = {Molecular ecology resources}, volume = {15}, number = {1}, pages = {81-86}, pmid = {24964386}, issn = {1755-0998}, support = {R01 AI107034/AI/NIAID NIH HHS/United States ; R01 HG006139/HG/NHGRI NIH HHS/United States ; }, mesh = {Bayes Theorem ; Calibration ; DNA/*chemistry/*genetics ; *Fossils ; *Phylogeny ; Radiometric Dating/*methods/standards ; }, abstract = {Studies of DNA from ancient samples provide a valuable opportunity to gain insight into past evolutionary and demographic processes. Bayesian phylogenetic methods can estimate evolutionary rates and timescales from ancient DNA sequences, with the ages of the samples acting as calibrations for the molecular clock. Sample ages are often estimated using radiocarbon dating, but the associated measurement error is rarely taken into account. In addition, the total uncertainty quantified by converting radiocarbon dates to calendar dates is typically ignored. Here, we present a tool for incorporating both of these sources of uncertainty into Bayesian phylogenetic analyses of ancient DNA. This empirical calibrated radiocarbon sampler (ECRS) integrates the age uncertainty for each ancient sequence over the calibrated probability density function estimated for its radiocarbon date and associated error. We use the ECRS to analyse three ancient DNA data sets. Accounting for radiocarbon-dating and calibration error appeared to have little impact on estimates of evolutionary rates and related parameters for these data sets. However, analyses of other data sets, particularly those with few or only very old radiocarbon dates, might be more sensitive to using artificially precise sample ages and should benefit from use of the ECRS.}, }
@article {pmid24963058, year = {2014}, author = {Kim, C and Wang, X and Lee, TH and Jakob, K and Lee, GJ and Paterson, AH}, title = {Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates.}, journal = {The Plant cell}, volume = {26}, number = {6}, pages = {2420-2429}, pmid = {24963058}, issn = {1532-298X}, abstract = {Multiple polyploidizations with divergent consequences in the grass subtribe Saccharinae provide a singular opportunity to study in situ adaptation of a genome to the duplicated state, heretofore known primarily from paleogenomics. We show that allopolyploidy in a common Miscanthus-Saccharum ancestor ∼3.8 to 4.6 million years ago closely coincides in time with their divergence from the Sorghum lineage. Subsequent Saccharum-specific autopolyploidy may have created pseudo-paralogous chromosome groups with random pairing within a group but infrequent pairing between groups. High chromosome number may reduce differentiation among Saccharum pseudo-paralogs by increasing opportunities for recombinations, with the lower chromosome numbers of Miscanthus favoring the return to disomic inheritance. The widespread tendency of plant chromosome numbers to recursively return to a narrow range following genome duplication appears to be occurring now in Saccharum spontaneum based on rich polymorphism for chromosome number among genotypes, with past reductions indicated by condensations of two ancestral chromosomes in Miscanthus (now n = 19) and perhaps as many as 10 in the Narenga-Sclerostachya clade (n = 15).}, }
@article {pmid24962720, year = {2014}, author = {Mendisco, F and Keyser, C and Seldes, V and Rivolta, C and Mercolli, P and Cruz, P and Nielsen, AE and Crubezy, E and Ludes, B}, title = {Genetic diversity of a late prehispanic group of the Quebrada de Humahuaca, northwestern Argentina.}, journal = {Annals of human genetics}, volume = {78}, number = {5}, pages = {367-380}, doi = {10.1111/ahg.12075}, pmid = {24962720}, issn = {1469-1809}, mesh = {Archaeology/methods ; Argentina ; Base Sequence ; *Biological Evolution ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; *Fossils ; *Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; History, Medieval ; Humans ; Indians, South American/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {This palaeogenetic study focused on the analysis of a late prehispanic Argentinean group from the Humahuaca valley, with the main aim of reconstructing its (micro)evolutionary history. The Humahuaca valley, a natural passageway from the eastern plains to the highlands, was the living environment of Andean societies whose cultural but especially biological diversity is still poorly understood. We analyzed the DNA extracted from 39 individuals who populated this upper valley during the Regional Development period (RDP) (between the 11th and 15th centuries CE), to determine their maternal and paternal genetic ancestry. Some mitochondrial and Y-chromosomal haplotypes specific to the Andean region are consistent with an origin in the highlands of Central Andes. On the other hand, a significant genetic affinity with contemporary admixed communities of the Chaco area was detected. Expectedly, recent demographic events, such as the expansion of the Inca Empire or the European colonization, have changed the original mitochondrial gene pool of the ancient Humahuaca Valley community. Finally, we identified a particular geographical organization of the prehispanic populations of Northwestern Argentina. Our results suggest that the communities of the region were divided between two different spheres of interaction, which is consistent with assumptions made by means of craniometric traits.}, }
@article {pmid24955890, year = {2014}, author = {Alawi, M and Schneider, B and Kallmeyer, J}, title = {A procedure for separate recovery of extra- and intracellular DNA from a single marine sediment sample.}, journal = {Journal of microbiological methods}, volume = {104}, number = {}, pages = {36-42}, doi = {10.1016/j.mimet.2014.06.009}, pmid = {24955890}, issn = {1872-8359}, mesh = {Analytic Sample Preparation Methods/*methods ; DNA/genetics/*isolation &amp; purification ; Geologic Sediments/*chemistry ; Oceans and Seas ; Polymerase Chain Reaction ; Soil/chemistry ; }, abstract = {Extracellular DNA (eDNA) is a ubiquitous biological compound in aquatic sediment and soil. Previous studies suggested that eDNA plays an important role in biogeochemical element cycling, horizontal gene transfer and stabilization of biofilm structures. Previous methods for eDNA extraction were either not suitable for oligotrophic sediments or only allowed quantification but no genetic analyses. Our procedure is based on cell detachment and eDNA liberation from sediment particles by sequential washing with an alkaline sodium phosphate buffer followed by a separation of cells and eDNA. The separated eDNA is then bound onto silica particles and purified, whereas the intracellular DNA from the separated cells is extracted using a commercial kit. The method provides extra- and intracellular DNA of high purity that is suitable for downstream applications like PCR. Extracellular DNA was extracted from organic-rich shallow sediment of the Baltic Sea, glacially influenced sediment of the Barents Sea and from the oligotrophic South Pacific Gyre. The eDNA concentration in these samples varied from 23 to 626ngg(-1) wet weight sediment. A number of experiments were performed to verify each processing step. Although extraction efficiency is higher than other published methods, it is not fully quantitative.}, }
@article {pmid24951394, year = {2014}, author = {Fordham, DA and Brook, BW and Moritz, C and Nogués-Bravo, D}, title = {Better forecasts of range dynamics using genetic data.}, journal = {Trends in ecology &amp; evolution}, volume = {29}, number = {8}, pages = {436-443}, doi = {10.1016/j.tree.2014.05.007}, pmid = {24951394}, issn = {1872-8383}, mesh = {*Biodiversity ; *Climate Change ; *Databases, Genetic ; *Ecosystem ; *Models, Biological ; *Phylogeography ; }, abstract = {The spatiotemporal response of species to past global change must be understood for adaptive management and to make useful predictions. Characteristics of past population dynamics are imprinted in genes, yet these molecular 'log books' are just beginning to be used to improve forecasts of biotic responses to climate change. This is despite there now being robust quantitative frameworks to incorporate such information. A tighter integration of genetic data into models of species range dynamics should lead to more robust and validated predictions of the response of demographic and evolutionary processes to large-scale environmental change. The use of these multidisciplinary methods will help conservation scientists to better connect theory to the on-ground design and implementation of effective measures to protect biodiversity.}, }
@article {pmid24939468, year = {2014}, author = {Skoglund, P and Sjödin, P and Skoglund, T and Lascoux, M and Jakobsson, M}, title = {Investigating population history using temporal genetic differentiation.}, journal = {Molecular biology and evolution}, volume = {31}, number = {9}, pages = {2516-2527}, pmid = {24939468}, issn = {1537-1719}, mesh = {Algorithms ; Animals ; Computational Biology/methods ; Genetic Drift ; *Genetic Variation ; Humans ; *Phylogeny ; Population Dynamics ; Sampling Studies ; }, abstract = {The rapid advance of sequencing technology, coupled with improvements in molecular methods for obtaining genetic data from ancient sources, holds the promise of producing a wealth of genomic data from time-separated individuals. However, the population-genetic properties of time-structured samples have not been extensively explored. Here, we consider the implications of temporal sampling for analyses of genetic differentiation and use a temporal coalescent framework to show that complex historical events such as size reductions, population replacements, and transient genetic barriers between populations leave a footprint of genetic differentiation that can be traced through history using temporal samples. Our results emphasize explicit consideration of the temporal structure when making inferences and indicate that genomic data from ancient individuals will greatly increase our ability to reconstruct population history.}, }
@article {pmid24924490, year = {2014}, author = {McLeod, BA and Frasier, TR and Lucas, Z}, title = {Assessment of the extirpated Maritimes walrus using morphological and ancient DNA analysis.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99569}, pmid = {24924490}, issn = {1932-6203}, mesh = {Animals ; Canada ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Discriminant Analysis ; *Extinction, Biological ; Female ; Geography ; Haplotypes ; Male ; Mandible/anatomy &amp; histology ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Sequence Analysis, DNA/*methods ; Skull/anatomy &amp; histology ; Walruses/*anatomy &amp; histology/*genetics ; }, abstract = {Species biogeography is a result of complex events and factors associated with climate change, ecological interactions, anthropogenic impacts, physical geography, and evolution. To understand the contemporary biogeography of a species, it is necessary to understand its history. Specimens from areas of localized extinction are important, as extirpation of species from these areas may represent the loss of unique adaptations and a distinctive evolutionary trajectory. The walrus (Odobenus rosmarus) has a discontinuous circumpolar distribution in the arctic and subarctic that once included the southeastern Canadian Maritimes region. However, exploitation of the Maritimes population during the 16th-18th centuries led to extirpation, and the species has not inhabited areas south of 55°N for ∼250 years. We examined genetic and morphological characteristics of specimens from the Maritimes, Atlantic (O. r. rosmarus) and Pacific (O. r. divergens) populations to test the hypothesis that the first group was distinctive. Analysis of Atlantic and Maritimes specimens indicated that most skull and mandibular measurements were significantly different between the Maritimes and Atlantic groups and discriminant analysis of principal components confirmed them as distinctive groups, with complete isolation of skull features. The Maritimes walrus appear to have been larger animals, with larger and more robust tusks, skulls and mandibles. The mtDNA control region haplotypes identified in Maritimes specimens were unique to the region and a greater average number of nucleotide differences were found between the regions (Atlantic and Maritimes) than within either group. Levels of diversity (h and π) were lower in the Maritimes, consistent with other studies of species at range margins. Our data suggest that the Maritimes walrus was a morphologically and genetically distinctive group that was on a different evolutionary path from other walrus found in the north Atlantic.}, }
@article {pmid24924389, year = {2014}, author = {Bennett, EA and Massilani, D and Lizzo, G and Daligault, J and Geigl, EM and Grange, T}, title = {Library construction for ancient genomics: single strand or double strand?.}, journal = {BioTechniques}, volume = {56}, number = {6}, pages = {289-90, 292-6, 298, passim}, doi = {10.2144/000114176}, pmid = {24924389}, issn = {1940-9818}, mesh = {Animals ; Cattle ; DNA/*genetics ; DNA, Single-Stranded/*genetics ; *Gene Library ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mammoths ; Paleontology/*methods ; Pan troglodytes ; Sequence Analysis, DNA/methods ; }, abstract = {A novel method of library construction that takes advantage of a single-stranded DNA ligase has been recently described and used to generate high-resolution genomes from ancient DNA samples. While this method is effective and appears to recover a greater fraction of endogenous ancient material, there has been no direct comparison of results from different library construction methods on a diversity of ancient DNA samples. In addition, the single-stranded method is limited by high cost and lengthy preparation time and is restricted to the Illumina sequencing platform. Here we present in-depth comparisons of the different available library construction methods for DNA purified from 16 ancient and modern faunal and human remains, covering a range of different taphonomic and climatic conditions. We further present a DNA purification method for ancient samples that permits the concentration of a large volume of dissolved extract with minimal manipulation and methodological improvements to the single-stranded method to render it more economical and versatile, in particular to expand its use to both the Illumina and the Ion Torrent sequencing platforms. We show that the single-stranded library construction method improves the relative recovery of endogenous to exogenous DNA for most, but not all, of our ancient extracts.}, }
@article {pmid24923666, year = {2014}, author = {Huynen, L and Gill, BJ and Doyle, A and Millar, CD and Lambert, DM}, title = {Identification, classification, and growth of moa chicks (Aves: Dinornithiformes) from the genus Euryapteryx.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99929}, pmid = {24923666}, issn = {1932-6203}, mesh = {Animals ; Birds/anatomy &amp; histology/classification/genetics/growth &amp; development ; Bone Development ; Bone and Bones/anatomy &amp; histology/diagnostic imaging ; Cloning, Molecular ; DNA, Mitochondrial/*analysis/genetics ; Environment ; New Zealand ; Palaeognathae/anatomy &amp; histology/*classification/*genetics/*growth &amp; development ; Paleontology ; Radiography ; Radiometric Dating ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The analysis of growth in extinct organisms is difficult. The general lack of skeletal material from a range of developmental states precludes determination of growth characteristics. For New Zealand's extinct moa we have available to us a selection of rare femora at different developmental stages that have allowed a preliminary determination of the early growth of this giant flightless bird. We use a combination of femora morphometrics, ancient DNA, and isotope analysis to provide information on the identification, classification, and growth of extinct moa from the genus Euryapteryx.<br><br>RESULTS: Using ancient DNA, we identify a number of moa chick bones for the species Euryapteryx curtus, Dinornis novaezealandiae, and Anomalopteryx didiformis, and the first chick bone for Pachyornis geranoides. Isotope analysis shows that &#x2202;15N levels vary between the two known size classes of Euryapteryx, with the larger size class having reduced levels of &#x2202;15N. A growth series for femora of the two size classes of Euryapteryx shows that early femora growth characteristics for both classes are almost identical. Morphometric, isotopic, and radiographic analysis of the smallest Euryapteryx bones suggests that one of these femora is from a freshly hatched moa at a very early stage of development.<br><br>CONCLUSION: Using morphometric, isotopic, and ancient DNA analyses have allowed the determination of a number of characteristics of rare moa chick femora. For Euryapteryx the analyses suggest that the smaller sized class II Euryapteryx is identical in size and growth to the extant Darwin's rhea.}, }
@article {pmid24906487, year = {2014}, author = {Motley, ST and Picuri, JM and Crowder, CD and Minich, JJ and Hofstadler, SA and Eshoo, MW}, title = {Improved multiple displacement amplification (iMDA) and ultraclean reagents.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {443}, pmid = {24906487}, issn = {1471-2164}, mesh = {DNA/analysis ; *DNA Contamination ; Ethylene Oxide/pharmacology ; Genome, Bacterial ; Genome, Human ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Indicators and Reagents ; Polymerase Chain Reaction ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Next-generation sequencing sample preparation requires nanogram to microgram quantities of DNA; however, many relevant samples are comprised of only a few cells. Genomic analysis of these samples requires a whole genome amplification method that is unbiased and free of exogenous DNA contamination. To address these challenges we have developed protocols for the production of DNA-free consumables including reagents and have improved upon multiple displacement amplification (iMDA).<br><br>RESULTS: A specialized ethylene oxide treatment was developed that renders free DNA and DNA present within Gram positive bacterial cells undetectable by qPCR. To reduce DNA contamination in amplification reagents, a combination of ion exchange chromatography, filtration, and lot testing protocols were developed. Our multiple displacement amplification protocol employs a second strand-displacing DNA polymerase, improved buffers, improved reaction conditions and DNA free reagents. The iMDA protocol, when used in combination with DNA-free laboratory consumables and reagents, significantly improved efficiency and accuracy of amplification and sequencing of specimens with moderate to low levels of DNA. The sensitivity and specificity of sequencing of amplified DNA prepared using iMDA was compared to that of DNA obtained with two commercial whole genome amplification kits using 10 fg (~1-2 bacterial cells worth) of bacterial genomic DNA as a template. Analysis showed >99% of the iMDA reads mapped to the template organism whereas only 0.02% of the reads from the commercial kits mapped to the template. To assess the ability of iMDA to achieve balanced genomic coverage, a non-stochastic amount of bacterial genomic DNA (1 pg) was amplified and sequenced, and data obtained were compared to sequencing data obtained directly from genomic DNA. The iMDA DNA and genomic DNA sequencing had comparable coverage 99.98% of the reference genome at &#x2265;1X coverage and 99.9% at &#x2265;5X coverage while maintaining both balance and representation of the genome.<br><br>CONCLUSIONS: The iMDA protocol in combination with DNA-free laboratory consumables, significantly improved the ability to sequence specimens with low levels of DNA. iMDA has broad utility in metagenomics, diagnostics, ancient DNA analysis, pre-implantation embryo screening, single-cell genomics, whole genome sequencing of unculturable organisms, and forensic applications for both human and microbial targets.}, }
@article {pmid24901650, year = {2014}, author = {Fernández, E and Pérez-Pérez, A and Gamba, C and Prats, E and Cuesta, P and Anfruns, J and Molist, M and Arroyo-Pardo, E and Turbón, D}, title = {Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands.}, journal = {PLoS genetics}, volume = {10}, number = {6}, pages = {e1004401}, pmid = {24901650}, issn = {1553-7404}, mesh = {Agriculture ; Archaeology ; Base Sequence ; Cyprus ; DNA, Mitochondrial/*genetics ; Ethnicity/*genetics ; Europe ; Gene Frequency ; Gene Pool ; Genetics, Population ; Greece, Ancient ; Haplotypes/genetics ; History, Ancient ; *Human Migration ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; Principal Component Analysis ; Sequence Analysis, DNA ; Skeleton ; }, abstract = {The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700-6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.}, }
@article {pmid24899841, year = {2014}, author = {Scheel, DM and Slater, GJ and Kolokotronis, SO and Potter, CW and Rotstein, DS and Tsangaras, K and Greenwood, AD and Helgen, KM}, title = {Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology.}, journal = {ZooKeys}, volume = {}, number = {409}, pages = {1-33}, pmid = {24899841}, issn = {1313-2989}, abstract = {Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M. tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and "New World monk seals" (Hawaiian and Caribbean) is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals (Monachus and Neomonachus) represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.}, }
@article {pmid24899682, year = {2014}, author = {Gutiérrez-García, TA and Vázquez-Domínguez, E and Arroyo-Cabrales, J and Kuch, M and Enk, J and King, C and Poinar, HN}, title = {Ancient DNA and the tropics: a rodent's tale.}, journal = {Biology letters}, volume = {10}, number = {6}, pages = {}, pmid = {24899682}, issn = {1744-957X}, mesh = {Animals ; Arvicolinae/*genetics ; Cytochromes b/genetics ; DNA/genetics ; *Evolution, Molecular ; *Fossils ; Mexico ; Phylogeny ; Sequence Analysis, DNA ; Time Factors ; Tropical Climate ; }, abstract = {Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient DNA from rodent jawbones identified as Ototylomys phyllotis, found in Holocene and Late Pleistocene stratigraphic layers from Loltún, a humid tropical cave located in the Yucatan peninsula. We extracted DNA and amplified six short overlapping fragments of the cytochrome b gene, totalling 666 bp, which represents an unprecedented success considering tropical ancient DNA samples. We performed genetic, phylogenetic and divergence time analyses, combining sequences from ancient and modern O. phyllotis, in order to assess the ancestry of the Loltún samples. Results show that all ancient samples fall into a unique clade that diverged prior to the divergence of the modern O. phyllotis, supporting it as a distinct Pleistocene form of the Ototylomys genus. Hence, this rodent's tale suggests that the sister group to modern O. phyllotis arose during the Miocene-Pliocene, diversified during the Pleistocene and went extinct in the Holocene.}, }
@article {pmid24885927, year = {2014}, author = {Huynen, L and Suzuki, T and Ogura, T and Watanabe, Y and Millar, CD and Hofreiter, M and Smith, C and Mirmoeini, S and Lambert, DM}, title = {Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes).}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {75}, pmid = {24885927}, issn = {1471-2148}, mesh = {Animals ; Atrial Natriuretic Factor/genetics ; Avian Proteins/*genetics/metabolism ; *Biological Evolution ; Chickens ; Fibroblast Growth Factor 10/genetics ; *Flight, Animal ; Forelimb/*embryology ; Humans ; Mice ; New Zealand ; Palaeognathae/*genetics/physiology ; Struthioniformes/embryology ; T-Box Domain Proteins/*genetics/metabolism ; }, abstract = {BACKGROUND: The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures.<br><br>RESULTS: To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.<br><br>CONCLUSIONS: The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa's remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.}, }
@article {pmid24865457, year = {2014}, author = {Sandoval-Castellanos, E and Palkopoulou, E and Dalén, L}, title = {Back to BaySICS: a user-friendly program for Bayesian Statistical Inference from Coalescent Simulations.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e98011}, pmid = {24865457}, issn = {1932-6203}, mesh = {*Bayes Theorem ; *Computer Simulation ; *Genetics, Population ; Humans ; Markov Chains ; *Models, Theoretical ; Population Groups/genetics ; *Software ; }, abstract = {Inference of population demographic history has vastly improved in recent years due to a number of technological and theoretical advances including the use of ancient DNA. Approximate Bayesian computation (ABC) stands among the most promising methods due to its simple theoretical fundament and exceptional flexibility. However, limited availability of user-friendly programs that perform ABC analysis renders it difficult to implement, and hence programming skills are frequently required. In addition, there is limited availability of programs able to deal with heterochronous data. Here we present the software BaySICS: Bayesian Statistical Inference of Coalescent Simulations. BaySICS provides an integrated and user-friendly platform that performs ABC analyses by means of coalescent simulations from DNA sequence data. It estimates historical demographic population parameters and performs hypothesis testing by means of Bayes factors obtained from model comparisons. Although providing specific features that improve inference from datasets with heterochronous data, BaySICS also has several capabilities making it a suitable tool for analysing contemporary genetic datasets. Those capabilities include joint analysis of independent tables, a graphical interface and the implementation of Markov-chain Monte Carlo without likelihoods.}, }
@article {pmid24855267, year = {2014}, author = {Mitchell, KJ and Llamas, B and Soubrier, J and Rawlence, NJ and Worthy, TH and Wood, J and Lee, MS and Cooper, A}, title = {Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution.}, journal = {Science (New York, N.Y.)}, volume = {344}, number = {6186}, pages = {898-900}, doi = {10.1126/science.1251981}, pmid = {24855267}, issn = {1095-9203}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA/*genetics ; Flight, Animal ; Fossils ; Molecular Sequence Data ; New Zealand ; Palaeognathae/*classification/genetics ; Phylogeny ; Struthioniformes/*classification/genetics ; }, abstract = {The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.}, }
@article {pmid24847315, year = {2014}, author = {Killelea, T and Ralec, C and Bossé, A and Henneke, G}, title = {PCR performance of a thermostable heterodimeric archaeal DNA polymerase.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {195}, pmid = {24847315}, issn = {1664-302X}, abstract = {DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR), cDNA cloning, genome sequencing, and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased performance and broadened substrate spectra. At present, there is a great demand for such enzymes in applications, e.g., forensics or paleogenomics. Current major limitations hinge on the inability of conventional PCR enzymes, such as Taq, to amplify degraded or low amounts of template DNA. Besides, a wide range of PCR inhibitors can also impede reactions of nucleic acid amplification. Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. Proficient proof-reading Pab-polD enzyme could also extend a primer containing up to two mismatches at the 3' primer termini. Overall, we found valuable biochemical properties in Pab-polD compared to the conventional Taq, which makes the enzyme ideally suited for cutting-edge PCR-applications.}, }
@article {pmid24838416, year = {2014}, author = {Grunenwald, A and Keyser, C and Sautereau, AM and Crubézy, E and Ludes, B and Drouet, C}, title = {Novel contribution on the diagenetic physicochemical features of bone and teeth minerals, as substrates for ancient DNA typing.}, journal = {Analytical and bioanalytical chemistry}, volume = {406}, number = {19}, pages = {4691-4704}, doi = {10.1007/s00216-014-7863-z}, pmid = {24838416}, issn = {1618-2650}, mesh = {Aged, 80 and over ; Anthropology, Physical/methods ; Bone and Bones/*chemistry ; Calcium/*analysis ; DNA Fingerprinting/*methods ; Female ; Humans ; Male ; Middle Aged ; Phosphates/*analysis ; Spectroscopy, Fourier Transform Infrared/*methods ; Tooth/*chemistry ; X-Ray Diffraction/*methods ; }, abstract = {The extraction of DNA from skeletal remains is a major step in archeological or forensic contexts. However, diagenesis of mineralized tissues often compromises this task although bones and teeth may represent preservation niches allowing DNA to persist over a wide timescale. This exceptional persistence is not only explained on the basis of complex organo-mineral interactions through DNA adsorption on apatite crystals composing the mineral part of bones and teeth but is also linked to environmental factors such as low temperatures and/or a dry environment. The preservation of the apatite phase itself, as an adsorption substrate, is another crucial factor susceptible to significantly impact the retrieval of DNA. With the view to bring physicochemical evidence of the preservation or alteration of diagenetic biominerals, we developed here an analytical approach on various skeletal specimens (ranging from ancient archeological samples to recent forensic specimens), allowing us to highlight several diagenetic indices so as to better apprehend the complexity of bone diagenesis. Based on complementary techniques (X-ray diffraction (XRD), Fourier transform infrared (FTIR), calcium and phosphate titrations, SEM-EDX, and gravimetry), we have identified specific indices that allow differentiating 11 biological samples, primarily according to the crystallinity and maturation state of the apatite phase. A good correlation was found between FTIR results from the analysis of the v3(PO4) and v4(PO4) vibrational domains and XRD-based crystallinity features. A maximal amount of information has been sought from this analytical approach, by way of optimized posttreatment of the data (spectral subtraction and enhancement of curve-fitting parameters). The good overall agreement found between all techniques leads to a rather complete picture of the diagenetic changes undergone by these 11 skeletal specimens. Although the heterogeneity and scarcity of the studied samples did not allow us to seek direct correlations with DNA persistence, the physicochemical parameters described in this work permit a fine differentiation of key properties of apatite crystals among post mortem samples. As a perspective, this analytical approach could be extended to more numerous sets of specimens so as to draw statistical relationships between mineral and molecular conservation.}, }
@article {pmid24827440, year = {2014}, author = {Collins, CJ and Rawlence, NJ and Prost, S and Anderson, CN and Knapp, M and Scofield, RP and Robertson, BC and Smith, I and Matisoo-Smith, EA and Chilvers, BL and Waters, JM}, title = {Extinction and recolonization of coastal megafauna following human arrival in New Zealand.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1786}, pages = {}, pmid = {24827440}, issn = {1471-2954}, mesh = {*Animal Distribution ; Animals ; Archaeology ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Fossils ; Humans ; Molecular Sequence Data ; New Zealand ; Phylogeny ; Polymerase Chain Reaction ; Radiometric Dating ; Sea Lions/genetics/physiology ; Sequence Analysis, DNA ; Spheniscidae/genetics/physiology ; }, abstract = {Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage (Phocarctos spp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction-replacement event in penguins (Megadyptes spp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction.}, }
@article {pmid24825849, year = {2014}, author = {Baker, AJ and Haddrath, O and McPherson, JD and Cloutier, A}, title = {Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites.}, journal = {Molecular biology and evolution}, volume = {31}, number = {7}, pages = {1686-1696}, doi = {10.1093/molbev/msu153}, pmid = {24825849}, issn = {1537-1719}, mesh = {Adaptation, Physiological ; Animals ; Bayes Theorem ; Evolution, Molecular ; Genome ; Likelihood Functions ; Models, Genetic ; Palaeognathae/anatomy &amp; histology/*classification/*genetics/physiology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {One of the most startling discoveries in avian molecular phylogenetics is that the volant tinamous are embedded in the flightless ratites, but this topology remains controversial because recent morphological phylogenies place tinamous as the closest relative of a monophyletic ratite clade. Here, we integrate new phylogenomic sequences from 1,448 nuclear DNA loci totaling almost 1 million bp from the extinct little bush moa, Chilean tinamou, and emu with available sequences from ostrich, elegant crested tinamou, four neognaths, and the green anole. Phylogenetic analysis using standard homogeneous models and heterogeneous models robust to common topological artifacts recovered compelling support for ratite paraphyly with the little bush moa closest to tinamous within ratites. Ratite paraphyly was further corroborated by eight independent CR1 retroposon insertions. Analysis of morphological characters reinterpreted on a 27-gene paleognath topology indicates that many characters are convergent in the ratites, probably as the result of adaptation to a cursorial life style.}, }
@article {pmid24803574, year = {2014}, author = {Wendland, J and Walther, A}, title = {Chromosome number reduction in Eremothecium coryli by two telomere-to-telomere fusions.}, journal = {Genome biology and evolution}, volume = {6}, number = {5}, pages = {1186-1198}, pmid = {24803574}, issn = {1759-6653}, mesh = {Biological Evolution ; Centromere/genetics ; *Chromosomes, Fungal ; DNA Transposable Elements ; Eremothecium/*genetics ; *Genome, Fungal ; Molecular Sequence Data ; *Telomere ; }, abstract = {The genus Eremothecium belongs to the Saccharomyces complex of pre-whole-genome duplication (WGD) yeasts and contains both dimorphic and filamentous species. We established the 9.1-Mb draft genome of Eremothecium coryli, which encodes 4,682 genes, 186 tRNA genes, and harbors several Ty3 transposons as well as more than 60 remnants of transposition events (LTRs). The initial de novo assembly resulted in 19 scaffolds, which were assembled based on synteny to other Eremothecium genomes into six chromosomes. Interestingly, we identified eight E. coryli loci that bear centromeres in the closely related species E. cymbalariae. Two of these E. coryli loci, CEN1 and CEN8, however, lack conserved DNA elements and did not convey centromere function in a plasmid stability assay. Correspondingly, using a comparative genomics approach we identified two telomere-to-telomere fusion events in E. coryli as the cause of chromosome number reduction from eight to six chromosomes. Finally, with the genome sequences of E. coryli, E. cymbalariae, and Ashbya gossypii a reconstruction of three complete chromosomes of an Eremothecium ancestor revealed that E. coryli is more syntenic to this ancestor than the other Eremothecium species.}, }
@article {pmid24801631, year = {2014}, author = {Baca, M and Molak, M and Sobczyk, M and Węgleński, P and Stankovic, A}, title = {Locals, resettlers, and pilgrims: a genetic portrait of three pre-Columbian Andean populations.}, journal = {American journal of physical anthropology}, volume = {154}, number = {3}, pages = {402-412}, doi = {10.1002/ajpa.22524}, pmid = {24801631}, issn = {1096-8644}, mesh = {Cemeteries ; DNA, Mitochondrial/genetics ; Female ; Genetic Variation/*genetics ; *Genetics, Population ; Haplotypes ; Human Migration ; Humans ; Indians, South American/*genetics ; Male ; Microsatellite Repeats ; Peru ; Sex Determination Analysis ; }, abstract = {The common practice of resettlement and the development of administrative and ceremonial systems shaped the population landscape of the Andean region under the Inca rule. The area surrounding Coropuna and Solimana volcanoes, in the Arequipa region (Peru), carried a high-density, multiethnic population. We studied the genetic variation among three pre-Columbian populations from three functionally diverse archaeological sites excavated in this region. By analyzing the genetic composition of a large ceremonial center (Acchaymarca), an isolated pastoral settlement (Tompullo 2), and an agricultural settlement characterized by architectural features rare in the region (Puca), we investigated the patterns of population movements and the distribution of genetic diversity. We obtained mitochondrial DNA sequences for 25 individuals and autosomal microsatellite profiles for 20 individuals from Acchaymarca and Puca sites. These were compared with previously published genetic data for Tompullo 2 and other pre-Columbian populations. We found differences among the genetic portraits of the three populations, congruent with the archaeologically described functions and characteristics of the sites. The Acchaymarca population had the highest genetic diversity and possessed the lowest number of unique mtDNA haplotypes. The Tompullo 2 population exhibited the lowest level of genetic diversity. The Puca population was distinct from the other two populations owing to a high frequency of haplogroup A haplotypes, what potentially explains the non-local character of the burial architecture. Our analyses of microsatellite data suggest that gene flow between sites was mostly mediated by females, which is consistent with ethnohistorical knowledge of the social organization of the pre-Columbian communities.}, }
@article {pmid24786081, year = {2014}, author = {Gokhman, D and Lavi, E and Prüfer, K and Fraga, MF and Riancho, JA and Kelso, J and Pääbo, S and Meshorer, E and Carmel, L}, title = {Reconstructing the DNA methylation maps of the Neandertal and the Denisovan.}, journal = {Science (New York, N.Y.)}, volume = {344}, number = {6183}, pages = {523-527}, doi = {10.1126/science.1250368}, pmid = {24786081}, issn = {1095-9203}, mesh = {Animals ; *DNA Methylation ; *Epigenesis, Genetic ; *Evolution, Molecular ; *Genome, Human ; Humans ; Neanderthals/*genetics ; }, abstract = {Ancient DNA sequencing has recently provided high-coverage archaic human genomes. However, the evolution of epigenetic regulation along the human lineage remains largely unexplored. We reconstructed the full DNA methylation maps of the Neandertal and the Denisovan by harnessing the natural degradation processes of methylated and unmethylated cytosines. Comparing these ancient methylation maps to those of present-day humans, we identified ~2000 differentially methylated regions (DMRs). Particularly, we found substantial methylation changes in the HOXD cluster that may explain anatomical differences between archaic and present-day humans. Additionally, we found that DMRs are significantly more likely to be associated with diseases. This study provides insight into the epigenetic landscape of our closest evolutionary relatives and opens a window to explore the epigenomes of extinct species.}, }
@article {pmid24780138, year = {2014}, author = {Leles, D and Cascardo, P and Freire, Ados S and Maldonado, A and Sianto, L and Araújo, A}, title = {Insights about echinostomiasis by paleomolecular diagnosis.}, journal = {Parasitology international}, volume = {63}, number = {4}, pages = {646-649}, doi = {10.1016/j.parint.2014.04.005}, pmid = {24780138}, issn = {1873-0329}, mesh = {Animals ; Base Sequence ; Brazil ; DNA, Ribosomal Spacer/genetics ; Echinostoma/*genetics/*isolation &amp; purification ; Echinostomiasis/*parasitology ; Electron Transport Complex IV/genetics ; Feces/parasitology ; Helminth Proteins/genetics ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Alignment ; }, abstract = {Echinostomiasis is a zoonosis caused by intestinal trematodes and transmitted by the ingestion of mollusks, crustaceans, fish, amphibians, and reptiles, either raw or poorly cooked. Today human infection is endemic in Southeast Asia and the Far East, but has been reported more recently in other regions of the world. Interestingly eggs identified as Echinostoma sp. were found in coprolites from a mummified body human in Brazil, dated 560 ± 40 BP (before present). However, the specific diagnosis based on morphology of the eggs has not been resolved at the species level. As a follow-up to the previous finding, the current study now aims to standardize the methodology for molecular diagnosis and apply it to the coprolite, using current Echinostoma paraensei-positive feces as the reference, and also the same fecal material dried in a stove as an experimental coprolite model. Isolated eggs of E. paraensei and adult worm were included to verify the sensibility and as positive control, respectively. An adult worm of E. luisreyi was used for comparison. PCR using primers in-house for ITS1 region (126 bp) and cox1 (123 bp) of Echinostoma spp. and subsequent nucleotide sequencing were performed. This is the first molecular paleoparasitological diagnosis for echinostomiasis. The methodology was able to amplify specific DNA fragments for the genus Echinostoma sp. in all samples: adult worm, feces, and a single egg of the parasite, in both the experimental coprolite and archaeological sample. Additionally we observed that ancient DNA can also be retrieved without rehydrating the material. The nucleotide sequences from E. paraensei and E. luisreyi are very similar in the fragment analyzed that difficult the differentiation these species, but DNA sequence analysis recovered in the parasite found in the mummy showed more similarity with the species E. paraensei.}, }
@article {pmid24753608, year = {2014}, author = {Girdland Flink, L and Allen, R and Barnett, R and Malmström, H and Peters, J and Eriksson, J and Andersson, L and Dobney, K and Larson, G}, title = {Establishing the validity of domestication genes using DNA from ancient chickens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {17}, pages = {6184-6189}, pmid = {24753608}, issn = {1091-6490}, mesh = {Animals ; Animals, Domestic/*genetics ; Chickens/*genetics ; DNA/*genetics/*history ; DNA, Mitochondrial/genetics ; Europe ; Geography ; Haplotypes/genetics ; History, Ancient ; Humans ; Molecular Sequence Data ; Reproducibility of Results ; }, abstract = {Modern domestic plants and animals are subject to human-driven selection for desired phenotypic traits and behavior. Large-scale genetic studies of modern domestic populations and their wild relatives have revealed not only the genetic mechanisms underlying specific phenotypic traits, but also allowed for the identification of candidate domestication genes. Our understanding of the importance of these genes during the initial stages of the domestication process traditionally rests on the assumption that robust inferences about the past can be made on the basis of modern genetic datasets. A growing body of evidence from ancient DNA studies, however, has revealed that ancient and even historic populations often bear little resemblance to their modern counterparts. Here, we test the temporal context of selection on specific genetic loci known to differentiate modern domestic chickens from their extant wild ancestors. We extracted DNA from 80 ancient chickens excavated from 12 European archaeological sites, dated from ∼ 280 B.C. to the 18th century A.D. We targeted three unlinked genetic loci: the mitochondrial control region, a gene associated with yellow skin color (β-carotene dioxygenase 2), and a putative domestication gene thought to be linked to photoperiod and reproduction (thyroid-stimulating hormone receptor, TSHR). Our results reveal significant variability in both nuclear genes, suggesting that the commonality of yellow skin in Western breeds and the near fixation of TSHR in all modern chickens took place only in the past 500 y. In addition, mitochondrial variation has increased as a result of recent admixture with exotic breeds. We conclude by emphasizing the perils of inferring the past from modern genetic data alone.}, }
@article {pmid24753607, year = {2014}, author = {Castellano, S and Parra, G and Sánchez-Quinto, FA and Racimo, F and Kuhlwilm, M and Kircher, M and Sawyer, S and Fu, Q and Heinze, A and Nickel, B and Dabney, J and Siebauer, M and White, L and Burbano, HA and Renaud, G and Stenzel, U and Lalueza-Fox, C and de la Rasilla, M and Rosas, A and Rudan, P and Brajković, D and Kucan, &#x17d; and Gušic, I and Shunkov, MV and Derevianko, AP and Viola, B and Meyer, M and Kelso, J and Andrés, AM and Pääbo, S}, title = {Patterns of coding variation in the complete exomes of three Neandertals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {18}, pages = {6666-6671}, pmid = {24753607}, issn = {1091-6490}, mesh = {Amino Acid Substitution ; Animals ; Croatia ; DNA/genetics ; *Exome ; Gene Frequency ; *Genetic Variation ; Humans ; Neanderthals/*genetics ; Paleontology ; Phylogeny ; Polymorphism, Single Nucleotide ; Siberia ; Spain ; }, abstract = {We present the DNA sequence of 17,367 protein-coding genes in two Neandertals from Spain and Croatia and analyze them together with the genome sequence recently determined from a Neandertal from southern Siberia. Comparisons with present-day humans from Africa, Europe, and Asia reveal that genetic diversity among Neandertals was remarkably low, and that they carried a higher proportion of amino acid-changing (nonsynonymous) alleles inferred to alter protein structure or function than present-day humans. Thus, Neandertals across Eurasia had a smaller long-term effective population than present-day humans. We also identify amino acid substitutions in Neandertals and present-day humans that may underlie phenotypic differences between the two groups. We find that genes involved in skeletal morphology have changed more in the lineage leading to Neandertals than in the ancestral lineage common to archaic and modern humans, whereas genes involved in behavior and pigmentation have changed more on the modern human lineage.}, }
@article {pmid24744352, year = {2014}, author = {Pennisi, E}, title = {Epigenetics. Ancient DNA holds clues to gene activity in extinct humans.}, journal = {Science (New York, N.Y.)}, volume = {344}, number = {6181}, pages = {245-246}, doi = {10.1126/science.344.6181.245}, pmid = {24744352}, issn = {1095-9203}, mesh = {Animals ; Bone and Bones/anatomy &amp; histology ; DNA/*genetics ; *DNA Methylation ; *Epigenesis, Genetic ; Extinction, Biological ; Female ; *Fossils ; Gene Silencing ; *Genome ; *Genome, Human ; Humans ; Neanderthals/*genetics ; Sequence Analysis, DNA ; }, }
@article {pmid24730667, year = {2014}, author = {Pawłowska, J and Lejzerowicz, F and Esling, P and Szczuciński, W and Zajączkowski, M and Pawlowski, J}, title = {Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium.}, journal = {Geobiology}, volume = {12}, number = {4}, pages = {277-288}, doi = {10.1111/gbi.12087}, pmid = {24730667}, issn = {1472-4669}, mesh = {Biodiversity ; DNA/analysis ; Foraminifera/*genetics ; *Fossils ; Metagenomics ; }, abstract = {Recent palaeogenetic studies have demonstrated the occurrence of preserved ancient DNA (aDNA) in various types of fossilised material. Environmental aDNA sequences assigned to modern species have been recovered from marine sediments dating to the Pleistocene. However, the match between the aDNA and the fossil record still needs to be evaluated for the environmental DNA approaches to be fully exploited. Here, we focus on foraminifera in sediments up to one thousand years old retrieved from the Hornsund fjord (Svalbard). We compared the diversity of foraminiferal microfossil assemblages with the diversity of aDNA sequenced from subsurface sediment samples using both cloning and high-throughput sequencing (HTS). Our study shows that 57% of the species archived in the fossil record were also detected in the aDNA data. However, the relative abundance of aDNA sequence reads and fossil specimens differed considerably. We also found a limited match between the stratigraphic occurrence of some fossil species and their aDNA sequences, especially in the case of rare taxa. The aDNA data comprised a high proportion of non-fossilised monothalamous species, which are known to dominate in modern foraminiferal communities of the Svalbard region. Our results confirm the relevance of HTS for studying past micro-eukaryotic diversity and provide insight into its ability to reflect fossil assemblages. Palaeogenetic studies including aDNA analyses of non-fossilised groups expand the range of palaeoceanographical proxies and therefore may increase the accuracy of palaeoenvironmental reconstructions.}, }
@article {pmid24722405, year = {2014}, author = {Schubert, M and Ermini, L and Der Sarkissian, C and Jónsson, H and Ginolhac, A and Schaefer, R and Martin, MD and Fernández, R and Kircher, M and McCue, M and Willerslev, E and Orlando, L}, title = {Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.}, journal = {Nature protocols}, volume = {9}, number = {5}, pages = {1056-1082}, pmid = {24722405}, issn = {1750-2799}, mesh = {Computational Biology/*methods ; Genome/*genetics ; High-Throughput Nucleotide Sequencing ; Likelihood Functions ; Metagenomics/*methods ; Paleontology/*methods ; *Phylogeny ; Phytophthora infestans/genetics ; Polymorphism, Single Nucleotide/*genetics ; *Software ; }, abstract = {Next-generation sequencing technologies have revolutionized the field of paleogenomics, allowing the reconstruction of complete ancient genomes and their comparison with modern references. However, this requires the processing of vast amounts of data and involves a large number of steps that use a variety of computational tools. Here we present PALEOMIX (http://geogenetics.ku.dk/publications/paleomix), a flexible and user-friendly pipeline applicable to both modern and ancient genomes, which largely automates the in silico analyses behind whole-genome resequencing. Starting with next-generation sequencing reads, PALEOMIX carries out adapter removal, mapping against reference genomes, PCR duplicate removal, characterization of and compensation for postmortem damage, SNP calling and maximum-likelihood phylogenomic inference, and it profiles the metagenomic contents of the samples. As such, PALEOMIX allows for a series of potential applications in paleogenomics, comparative genomics and metagenomics. Applying the PALEOMIX pipeline to the three ancient and seven modern Phytophthora infestans genomes as described here takes 5 d using a 16-core server.}, }
@article {pmid24709029, year = {2014}, author = {Barta, JL and Monroe, C and Crockford, SJ and Kemp, BM}, title = {Mitochondrial DNA preservation across 3000-year-old northern fur seal ribs is not related to bone density: Implications for forensic investigations.}, journal = {Forensic science international}, volume = {239}, number = {}, pages = {11-18}, doi = {10.1016/j.forsciint.2014.02.029}, pmid = {24709029}, issn = {1872-6283}, mesh = {Animals ; *Bone Density ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; Forensic Anthropology ; Fur Seals/*genetics ; Polymerase Chain Reaction ; Ribs/*chemistry ; }, abstract = {While recent forensic research has focused on determining which skeletal elements are superior in their preservation of DNA over the long term, little focus has been placed on measuring intra-element variation. Moreover, there is a general belief that dense (cortical) bone material will contain better-preserved DNA than does spongy (cancellous) bone. To address these ideas, quantitative PCR was used to estimate the degree of mitochondrial DNA (mtDNA) preservation variance across sections of 19 northern fur seal ribs (Callorhinus ursinus) that date to ∼3000 years before present. Further, we developed a measure called the "density index" that was used to gauge the relative densities of the rib sections studied here to determine if density was an appropriate predictor of preservation. The average preservation among the samples was significantly different (ANOVA, p=1.9×10(-9)) with only 15% of the total variance observed within samples. However, 12 of the 19 specimens (∼63.2%) exhibited at least an order of magnitude difference in mtDNA preservation across the whole. Regression of the amount of mtDNA extracted per gram of bone material against the density index of the bone from which it was extracted demonstrates no relationship between these variables (R(2)=0.03, p=0.28).}, }
@article {pmid24706482, year = {2014}, author = {Orlando, L}, title = {A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins: using the latest advances in ancient genomics, the mitochondrial genome sequence of a 400,000-year-old hominin has been deciphered.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {6}, pages = {598-605}, doi = {10.1002/bies.201400018}, pmid = {24706482}, issn = {1521-1878}, mesh = {Animals ; Base Sequence ; DNA Damage/genetics ; Genome, Mitochondrial/*genetics ; Genomics/*methods ; Hominidae/*genetics ; *Phylogeny ; Time Factors ; }, abstract = {By combining state-of-the-art approaches in ancient genomics, Meyer and co-workers have reconstructed the mitochondrial sequence of an archaic hominin that lived at Sierra de Atapuerca, Spain about 400,000 years ago. This achievement follows recent advances in molecular anthropology that delivered the genome sequence of younger archaic hominins, such as Neanderthals and Denisovans. Molecular phylogenetic reconstructions placed the Atapuercan as a sister group to Denisovans, although its morphology suggested closer affinities with Neanderthals. In addition to possibly challenging our interpretation of the fossil record, this study confirms that genomic information can be recovered from extremely damaged DNA molecules, even in the presence of significant levels of human contamination. Together with the recent characterization of a 700,000-year-old horse genome, this study opens the Middle Pleistocene to genomics, thereby extending the scope of ancient DNA to the last million years.}, }
@article {pmid24702983, year = {2014}, author = {Stringer, C}, title = {Why we are not all multiregionalists now.}, journal = {Trends in ecology &amp; evolution}, volume = {29}, number = {5}, pages = {248-251}, doi = {10.1016/j.tree.2014.03.001}, pmid = {24702983}, issn = {1872-8383}, mesh = {Animals ; *Biological Evolution ; Gene Flow ; Genetic Speciation ; Genetics, Population ; Hominidae/genetics ; Humans/genetics ; *Hybridization, Genetic ; Neanderthals ; }, abstract = {Recent revelations that human genomes contain DNA introgressed through interbreeding with archaic populations outside of Africa have led to reassessments of models for the origins of our species. The fact that small portions of the DNA of recent Homo sapiens derive from ancient populations in more than one region of the world makes our origins 'multiregional', but does that mean that the multiregional model of modern human origins has been proved correct? The extent of archaic assimilation in living humans remains modest, and fossil evidence outside of Africa shows little sign of the long-term morphological continuity through to recent humans expected from the multiregional model. Thus, rather than multiregionalism, a recent African origin (RAO) model for modern humans is still supported by the data.}, }
@article {pmid24690312, year = {2014}, author = {Barnett, R and Yamaguchi, N and Shapiro, B and Ho, SY and Barnes, I and Sabin, R and Werdelin, L and Cuisin, J and Larson, G}, title = {Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis.}, journal = {BMC evolutionary biology}, volume = {14}, number = {1}, pages = {70}, pmid = {24690312}, issn = {1471-2148}, mesh = {Africa, Eastern ; Animals ; Asia ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Endangered Species ; *Fossils ; Lions/*classification/*genetics ; *Phylogeography ; }, abstract = {BACKGROUND: Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations.<br><br>RESULTS: We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East.<br><br>CONCLUSIONS: We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.}, }
@article {pmid24689878, year = {2014}, author = {Hoban, S}, title = {An overview of the utility of population simulation software in molecular ecology.}, journal = {Molecular ecology}, volume = {23}, number = {10}, pages = {2383-2401}, doi = {10.1111/mec.12741}, pmid = {24689878}, issn = {1365-294X}, mesh = {*Computer Simulation ; Ecology/*methods ; Genetics, Population/*methods ; Population Dynamics ; *Software ; Stochastic Processes ; }, abstract = {Stochastic simulation software that simultaneously model genetic, population and environmental processes can inform many topics in molecular ecology. These include forecasting species and community response to environmental change, inferring dispersal ecology, revealing cryptic mating, quantifying past population dynamics, assessing in situ management options and monitoring neutral and adaptive biodiversity change. Advances in population demographic-genetic simulation software, especially with respect to individual life history, landscapes and genetic processes, are transforming and expanding the ways that molecular data can be used. The aim of this review is to explain the roles that such software can play in molecular ecology studies (whether as a principal component or a supporting function) so that researchers can decide whether, when and precisely how simulations can be incorporated into their work. First, I use seven case studies to demonstrate how simulations are employed, their specific advantage/necessity and what alternative or complementary (nonsimulation) approaches are available. I also explain how simulations can be integrated with existing spatial, environmental, historical and genetic data sets. I next describe simulation features that may be of interest to molecular ecologists, such as spatial and behavioural considerations and species' interactions, to provide guidance on how particular simulation capabilities can serve particular needs. Lastly, I discuss the prospect of simulation software in emerging challenges (climate change, biodiversity monitoring, population exploitation) and opportunities (genomics, ancient DNA), in order to emphasize that the scope of simulation-based work is expanding. I also suggest practical considerations, priorities and elements of best practice. This should accelerate the uptake of simulation approaches and firmly embed them as a versatile tool in the molecular ecologist's toolbox.}, }
@article {pmid24675822, year = {2014}, author = {Idziak, D and Hazuka, I and Poliwczak, B and Wiszynska, A and Wolny, E and Hasterok, R}, title = {Insight into the karyotype evolution of brachypodium species using comparative chromosome barcoding.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e93503}, pmid = {24675822}, issn = {1932-6203}, mesh = {Biological Evolution ; *Brachypodium/classification/genetics ; Chromosomes, Artificial, Bacterial ; Chromosomes, Plant/*chemistry ; DNA Barcoding, Taxonomic ; DNA, Plant/classification/*genetics ; *Genome, Plant ; Genomic Library ; In Situ Hybridization, Fluorescence ; *Karyotype ; Karyotyping ; *Phylogeny ; Ploidies ; }, abstract = {Paleogenomic studies based on bioinformatic analyses of DNA sequences have enabled unprecedented insight into the evolution of grass genomes. They have revealed that nested chromosome fusions played an important role in the divergence of modern grasses. Nowadays, studies on karyotype evolution based on the sequence analysis can also be effectively complemented by the fine-scale cytomolecular approach. In this work, we studied the karyotype evolution of small genome grasses using BAC-FISH based comparative chromosome barcoding in four Brachypodium species: diploid B. distachyon (2n = 10) and B. sylvaticum (2n = 18), diploid (2n = 18) and allopolyploid (2n = 28) B. pinnatum as well as B. phoenicoides (2n = 28). Using BAC clones derived from the B. distachyon genomic libraries for the chromosomes Bd2 and Bd3, we identified the descending dysploidy events that were common for diploids with x = 9 and B. distachyon as well as two nested chromosome fusions that were specific only for B. distachyon. We suggest that dysploidy events that are shared by different lineages of the genus had already appeared in their common ancestor. We also show that additional structural rearrangements, such as translocations and duplications, contributed to increasing genome diversification in the species analysed. No chromosomes structured exactly like Bd2 and Bd3 were found in B. pinnatum (2n = 28) and B. phoenicoides. The structure of Bd2 and Bd3 homeologues belonging to the two genomes in the allopolyploids resembled the structure of their counterparts in the 2n = 18 diploids. These findings reinforce the hypothesis which excludes B. distachyon as a potential parent for Eurasian perennial Brachypodium allopolyploids. Our cytomolecular data elucidate some mechanisms of the descending dysploidy in monocots and enable reconstructions of the evolutionary events which shaped the extant karyotypes in both the genus Brachypodium and in grasses as a whole.}, }
@article {pmid24665960, year = {2014}, author = {Longenecker, K and Chan, YL and Toonen, RJ and Carlon, DB and Hunt, TL and Friedlander, AM and Demartini, EE}, title = {Archaeological evidence of validity of fish populations on unexploited reefs as proxy targets for modern populations.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {28}, number = {5}, pages = {1322-1330}, doi = {10.1111/cobi.12287}, pmid = {24665960}, issn = {1523-1739}, mesh = {Animals ; Archaeology ; *Conservation of Natural Resources ; *Coral Reefs ; Cytochromes b/genetics/metabolism ; Fish Proteins/genetics/metabolism ; Hawaii ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Perciformes/genetics/*physiology ; Population Density ; Sequence Analysis, DNA ; }, abstract = {Reef-fish management and conservation is hindered by a lack of information on fish populations prior to large-scale contemporary human impacts. As a result, relatively pristine sites are often used as conservation baselines for populations near sites affected by humans. This space-for-time approach can only be validated by sampling assemblages through time. We used archaeological remains to evaluate whether the remote, uninhabited Northwestern Hawaiian Islands (NWHI) might provide a reasonable proxy for a lightly exploited baseline in the Main Hawaiian Islands (MHI). We used molecular and morphological techniques to describe the taxonomic and size composition of the scarine parrotfish catches present in 2 archaeological assemblages from the MHI, compared metrics of these catches with modern estimates of reproductive parameters to evaluate whether catches represented by the archaeological material were consistent with sustainable fishing, and evaluated overlap between size structures represented by the archaeological material and modern survey data from the MHI and the NWHI to assess whether a space-for-time substitution is reasonable. The parrotfish catches represented by archaeological remains were consistent with sustainable fishing because they were dominated by large, mature individuals whose average size remained stable from prehistoric (AD approximately 1400-1700) through historic (AD 1700-1960) periods. The ancient catches were unlike populations in the MHI today. Overlap between the size structure of ancient MHI catches and modern survey data from the NWHI or the MHI was an order of magnitude greater for the NWHI comparison, a result that supports the validity of using the NWHI parrotfish data as a proxy for the MHI before accelerated, heavy human impacts in modern times.}, }
@article {pmid24661631, year = {2014}, author = {Lagerholm, VK and Sandoval-Castellanos, E and Ehrich, D and Abramson, NI and Nadachowski, A and Kalthoff, DC and Germonpré, M and Angerbjörn, A and Stewart, JR and Dalén, L}, title = {On the origin of the Norwegian lemming.}, journal = {Molecular ecology}, volume = {23}, number = {8}, pages = {2060-2071}, doi = {10.1111/mec.12698}, pmid = {24661631}, issn = {1365-294X}, mesh = {Animals ; Arvicolinae/*genetics ; Bayes Theorem ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Fossils ; Genetic Variation ; Genetics, Population ; Models, Genetic ; Molecular Sequence Data ; Norway ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The Pleistocene glacial cycles resulted in significant changes in species distributions, and it has been discussed whether this caused increased rates of population divergence and speciation. One species that is likely to have evolved during the Pleistocene is the Norwegian lemming (Lemmus lemmus). However, the origin of this species, both in terms of when and from what ancestral taxon it evolved, has been difficult to ascertain. Here, we use ancient DNA recovered from lemming remains from a series of Late Pleistocene and Holocene sites to explore the species' evolutionary history. The results revealed considerable genetic differentiation between glacial and contemporary samples. Moreover, the analyses provided strong support for a divergence time prior to the Last Glacial Maximum (LGM), therefore likely ruling out a postglacial colonization of Scandinavia. Consequently, it appears that the Norwegian lemming evolved from a small population that survived the LGM in an ice-free Scandinavian refugium.}, }
@article {pmid24646515, year = {2014}, author = {Wilder, BT and Betancourt, JL and Epps, CW and Crowhurst, RS and Mead, JI and Ezcurra, E}, title = {Local extinction and unintentional rewilding of bighorn sheep (Ovis canadensis) on a desert island.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e91358}, pmid = {24646515}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/classification/*genetics ; Base Sequence ; *Conservation of Natural Resources ; DNA, Mitochondrial/*genetics ; Extinction, Biological ; Feces/chemistry ; Female ; Introduced Species ; Islands ; Male ; Mexico ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Sheep, Bighorn/classification/*genetics ; }, abstract = {Bighorn sheep (Ovis canadensis) were not known to live on Tiburón Island, the largest island in the Gulf of California and Mexico, prior to the surprisingly successful introduction of 20 individuals as a conservation measure in 1975. Today, a stable island population of ∼500 sheep supports limited big game hunting and restocking of depleted areas on the Mexican mainland. We discovered fossil dung morphologically similar to that of bighorn sheep in a dung mat deposit from Mojet Cave, in the mountains of Tiburón Island. To determine the origin of this cave deposit we compared pellet shape to fecal pellets of other large mammals, and extracted DNA to sequence mitochondrial DNA fragments at the 12S ribosomal RNA and control regions. The fossil dung was 14C-dated to 1476-1632 calendar years before present and was confirmed as bighorn sheep by morphological and ancient DNA (aDNA) analysis. 12S sequences closely or exactly matched known bighorn sheep sequences; control region sequences exactly matched a haplotype described in desert bighorn sheep populations in southwest Arizona and southern California and showed subtle differentiation from the extant Tiburón population. Native desert bighorn sheep previously colonized this land-bridge island, most likely during the Pleistocene, when lower sea levels connected Tiburón to the mainland. They were extirpated sometime in the last ∼1500 years, probably due to inherent dynamics of isolated populations, prolonged drought, and (or) human overkill. The reintroduced population is vulnerable to similar extinction risks. The discovery presented here refutes conventional wisdom that bighorn sheep are not native to Tiburón Island, and establishes its recent introduction as an example of unintentional rewilding, defined here as the introduction of a species without knowledge that it was once native and has since gone locally extinct.}, }
@article {pmid24639531, year = {2014}, author = {Allentoft, ME and Heller, R and Oskam, CL and Lorenzen, ED and Hale, ML and Gilbert, MT and Jacomb, C and Holdaway, RN and Bunce, M}, title = {Extinct New Zealand megafauna were not in decline before human colonization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {13}, pages = {4922-4927}, pmid = {24639531}, issn = {1091-6490}, mesh = {Animals ; Bayes Theorem ; Birds/genetics/*physiology ; Calibration ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Genetic Variation ; Geography ; Humans ; Molecular Sequence Data ; New Zealand ; Time Factors ; }, abstract = {The extinction of New Zealand's moa (Aves: Dinornithiformes) followed the arrival of humans in the late 13th century and was the final event of the prehistoric Late Quaternary megafauna extinctions. Determining the state of the moa populations in the pre-extinction period is fundamental to understanding the causes of the event. We sampled 281 moa individuals and combined radiocarbon dating with ancient DNA analyses to help resolve the extinction debate and gain insights into moa biology. The samples, which were predominantly from the last 4,000 years preceding the extinction, represent four sympatric moa species excavated from five adjacent fossil deposits. We characterized the moa assemblage using mitochondrial DNA and nuclear microsatellite markers developed specifically for moa. Although genetic diversity differed significantly among the four species, we found that the millennia preceding the extinction were characterized by a remarkable degree of genetic stability in all species, with no loss of heterozygosity and no shifts in allele frequencies over time. The extinction event itself was too rapid to be manifested in the moa gene pools. Contradicting previous claims of a decline in moa before Polynesian settlement in New Zealand, our findings indicate that the populations were large and stable before suddenly disappearing. This interpretation is supported by approximate Bayesian computation analyses. Our analyses consolidate the disappearance of moa as the most rapid, human-facilitated megafauna extinction documented to date.}, }
@article {pmid24639505, year = {2014}, author = {Thomson, VA and Lebrasseur, O and Austin, JJ and Hunt, TL and Burney, DA and Denham, T and Rawlence, NJ and Wood, JR and Gongora, J and Girdland Flink, L and Linderholm, A and Dobney, K and Larson, G and Cooper, A}, title = {Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {13}, pages = {4826-4831}, pmid = {24639505}, issn = {1091-6490}, mesh = {*Animal Migration ; Animals ; Base Pairing/genetics ; Bayes Theorem ; Chickens/*genetics ; DNA/*genetics ; Genome, Mitochondrial/genetics ; Geography ; Haplotypes/genetics ; Humans ; Locus Control Region/genetics ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Polynesia ; Time Factors ; }, abstract = {The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken.}, }
@article {pmid24634719, year = {2014}, author = {Gold, DA and Robinson, J and Farrell, AB and Harris, JM and Thalmann, O and Jacobs, DK}, title = {Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits.}, journal = {Ecology and evolution}, volume = {4}, number = {4}, pages = {329-336}, pmid = {24634719}, issn = {2045-7758}, support = {T32 HG002536/HG/NHGRI NIH HHS/United States ; }, abstract = {Fossil-bearing asphalt deposits are an understudied and potentially significant source of ancient DNA. Previous attempts to extract DNA from skeletons preserved at the Rancho La Brea tar pits in Los Angeles, California, have proven unsuccessful, but it is unclear whether this is due to a lack of endogenous DNA, or if the problem is caused by asphalt-mediated inhibition. In an attempt to test these hypotheses, a recently recovered Columbian mammoth (Mammuthus columbi) skeleton with an unusual pattern of asphalt impregnation was studied. Ultimately, none of the bone samples tested successfully amplified M. columbi DNA. Our work suggests that reagents typically used to remove asphalt from ancient samples also inhibit DNA extraction. Ultimately, we conclude that the probability of recovering ancient DNA from fossils in asphalt deposits is strongly (perhaps fatally) hindered by the organic compounds that permeate the bones and that at the Rancho La Brea tar pits, environmental conditions might not have been ideal for the general preservation of genetic material.}, }
@article {pmid24623098, year = {2014}, author = {Briggs, DE and Summons, RE}, title = {Ancient biomolecules: their origins, fossilization, and role in revealing the history of life.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {5}, pages = {482-490}, doi = {10.1002/bies.201400010}, pmid = {24623098}, issn = {1521-1878}, mesh = {Animals ; Arthropods/anatomy &amp; histology ; Biomarkers/metabolism ; DNA/metabolism ; *Fossils ; Macromolecular Substances/*metabolism ; Melanins/metabolism ; Time Factors ; }, abstract = {The discovery of traces of a blood meal in the abdomen of a 50-million-year-old mosquito reminds us of the insights that the chemistry of fossils can provide. Ancient DNA is the best known fossil molecule. It is less well known that new fossil targets and a growing database of ancient gene sequences are paralleled by discoveries on other classes of organic molecules. New analytical tools, such as the synchrotron, reveal traces of the original composition of arthropod cuticles that are more than 400 my old. Pigments such as melanin are readily fossilized, surviving virtually unaltered for ∼200 my. Other biomarkers provide evidence of microbial processes in ancient sediments, and have been used to reveal the presence of demosponges, for example, more than 635 mya, long before their spicules appear in the fossil record. Ancient biomolecules are a powerful complement to fossil remains in revealing the history of life.}, }
@article {pmid24617463, year = {2016}, author = {Merheb, M and Vaiedelich, S and Maniguet, T and Hänni, C}, title = {Mitochondrial DNA, restoring Beethovens music.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {355-359}, doi = {10.3109/19401736.2014.895988}, pmid = {24617463}, issn = {2470-1408}, mesh = {Animals ; Cattle/genetics ; DNA, Mitochondrial/*genetics/*history/isolation &amp; purification ; History, 17th Century ; Music/*history ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sheep/genetics ; }, abstract = {Great ancient composers have endured many obstacles and constraints which are very difficult to understand unless we perform the restoration process of ancient music. Species identification in leather used during manufacturing is the key step to start such a restoration process in order to produce a facsimile of a museum piano. Our study reveals the species identification in the leather covering the hammer head in a piano created by Erard in 1802. This is the last existing piano similar to the piano that Beethoven used with its leather preserved in its original state. The leather sample was not present in a homogeneous piece, yet combined with glue. Using a DNA extraction method that avoids PCR inhibitors; we discovered that sheep and cattle are the origin of the combination. To identify the species in the leather, we focused on the amounts of mitochondrial DNA in both leather and glue and results have led us to the conclusion that the leather used to cover the hammer head in this piano was made of cattle hide.}, }
@article {pmid24616928, year = {2014}, author = {Rühli, FJ and Ikram, S}, title = {Purported medical diagnoses of Pharaoh Tutankhamun, c. 1325 BC-.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {65}, number = {1}, pages = {51-63}, doi = {10.1016/j.jchb.2013.08.006}, pmid = {24616928}, issn = {1618-1301}, mesh = {Adolescent ; Egypt, Ancient ; History, Ancient ; Homicide ; Humans ; Male ; Metabolic Diseases/diagnosis/mortality ; Mummies/diagnostic imaging/*history/pathology ; Tomography, X-Ray Computed ; Wounds and Injuries/diagnosis/mortality ; Young Adult ; }, abstract = {King Tutankhamun is one of the most famous rulers of antiquity,thus it is not surprising that a plethora of scientific studies have put forth possible medical diagnoses and causes of his death. Diseases(autologous or infectious), metabolic disorders, trauma (possibly even murder-related), or tumorous conditions have been postulated, frequently only based on secondary data sources. The aim of this article is to critically review all these diagnoses. Since the initial examination of the mummy in the mid 1920s by Howard Carter and others, several dozens of medical diagnoses based on various levels of evidence have been proposed. While some studies did not support any sign of a major disease, others suggested diseases whose existence cannot be proven with the little tissue that is preserved for study. In the last c. five years new examinations of the mummy were performed by computed tomography and ancient DNA analyses,now allowing not only to exclude certain diagnoses that had been postulated earlier, but also to arrive at new theories with a higher degree of certainty concerning the state of health and the early death of this most famous ruler.}, }
@article {pmid24616518, year = {2014}, author = {Wilde, S and Timpson, A and Kirsanow, K and Kaiser, E and Kayser, M and Unterländer, M and Hollfelder, N and Potekhina, ID and Schier, W and Thomas, MG and Burger, J}, title = {Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {13}, pages = {4832-4837}, pmid = {24616518}, issn = {1091-6490}, mesh = {Alleles ; Antigens, Neoplasm/genetics ; Eye Color/*genetics ; Gene Frequency/genetics ; Hair Color/*genetics ; Humans ; Membrane Transport Proteins/genetics ; Polymorphism, Single Nucleotide/genetics ; *Selection, Genetic ; Skin Pigmentation/*genetics ; Time Factors ; White People/*genetics ; }, abstract = {Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways--HERC2, SLC45A2, and TYR--using allele frequency estimates from Eneolithic, Bronze Age, and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied, with point estimates of selection ranging from around 2-10% per generation. Our results provide direct evidence that strong selection favoring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 y.}, }
@article {pmid24614677, year = {2014}, author = {Rawlence, NJ and Till, CE and Scofield, RP and Tennyson, AJ and Collins, CJ and Lalas, C and Loh, G and Matisoo-Smith, E and Waters, JM and Spencer, HG and Kennedy, M}, title = {Strong phylogeographic structure in a sedentary seabird, the Stewart Island Shag (Leucocarbo chalconotus).}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90769}, pmid = {24614677}, issn = {1932-6203}, mesh = {Animals ; Base Pairing/genetics ; Charadriiformes/*genetics ; Cluster Analysis ; DNA, Mitochondrial/genetics ; *Islands ; Molecular Sequence Data ; New Zealand ; Phylogeny ; *Phylogeography ; Principal Component Analysis ; }, abstract = {New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups (Otago and Foveaux Strait) that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one), and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi). Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal co-ordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades.}, }
@article {pmid24612293, year = {2014}, author = {Der Sarkissian, C and Ermini, L and Jónsson, H and Alekseev, AN and Crubezy, E and Shapiro, B and Orlando, L}, title = {Shotgun microbial profiling of fossil remains.}, journal = {Molecular ecology}, volume = {23}, number = {7}, pages = {1780-1798}, doi = {10.1111/mec.12690}, pmid = {24612293}, issn = {1365-294X}, mesh = {Animals ; DNA/isolation &amp; purification ; DNA Damage ; *Fossils ; Horses/genetics/*microbiology ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; Siberia ; }, abstract = {Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next-generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using a shotgun sequencing approach. In future, it may be possible to correlate, for example, the accumulation of postmortem DNA damage with the presence and/or abundance of particular microbes.}, }
@article {pmid24608104, year = {2014}, author = {Star, B and Nederbragt, AJ and Hansen, MH and Skage, M and Gilfillan, GD and Bradbury, IR and Pampoulie, C and Stenseth, NC and Jakobsen, KS and Jentoft, S}, title = {Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e89676}, pmid = {24608104}, issn = {1932-6203}, mesh = {Animals ; *Artifacts ; DNA/*genetics ; DNA, Single-Stranded/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting of reverse complementary sequence at the 5' and 3'-ends of sequencing reads. The palindromic sequences themselves have specific properties - the bases at the 5'-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3'-end. The terminal 3' bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA), which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3'-end of DNA strands, with the 5'-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA) datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias.}, }
@article {pmid24586848, year = {2014}, author = {Panzer, S and Peschel, O and Haas-Gebhard, B and Bachmeier, BE and Pusch, CM and Nerlich, AG}, title = {Reconstructing the life of an unknown (ca. 500 years-old South American Inca) mummy--multidisciplinary study of a Peruvian Inca mummy suggests severe Chagas disease and ritual homicide.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e89528}, pmid = {24586848}, issn = {1932-6203}, mesh = {Adult ; *Ceremonial Behavior ; Chagas Disease/*parasitology ; *Craniocerebral Trauma ; DNA/*analysis ; Female ; Hair/chemistry ; History, Medieval ; *Homicide ; Humans ; Image Processing, Computer-Assisted ; Mummies/history/*parasitology/pathology ; Paleopathology ; South America ; Tomography, X-Ray Computed ; Trypanosoma cruzi/pathogenicity ; Young Adult ; }, abstract = {The paleopathological, paleoradiological, histological, molecular and forensic investigation of a female mummy (radiocarbon dated 1451-1642 AD) provides circumstantial evidence for massive skull trauma affecting a young adult female individual shortly before death along with chronic infection by Trypanosoma cruzi (Chagas disease). The mummy (initially assumed to be a German bog body) was localized by stable isotope analysis to South America at/near the Peruvian/Northern Chilean coast line. This is further supported by New World camelid fibers attached to her plaits, typical Inca-type skull deformation and the type of Wormian bone at her occiput. Despite an only small transverse wound of the supraorbital region computed tomography scans show an almost complete destruction of face and frontal skull bones with terrace-like margins, but without evidence for tissue reaction. The type of destruction indicates massive blunt force applied to the center of the face. Stable isotope analysis indicates South American origin: Nitrogen and hydrogen isotope patterns indicate an extraordinarily high marine diet along with C4-plant alimentation which fits best to the coastal area of Pacific South America. A hair strand over the last ten months of her life indicates a shift to a more "terrestric" nutrition pattern suggesting either a move from the coast or a change in her nutrition. Paleoradiology further shows extensive hypertrophy of the heart muscle and a distended large bowel/rectum. Histologically, in the rectum wall massive fibrosis alternates with residual smooth muscle. The latter contains multiple inclusions of small intracellular parasites as confirmed by immunohistochemical and molecular ancient DNA analysis to represent a chronic Trypanosoma cruzi infection. This case shows a unique paleopathological setting with massive blunt force trauma to the skull nurturing the hypothesis of a ritual homicide as previously described in South American mummies in an individual that suffered from severe chronic Chagas disease.}, }
@article {pmid24577840, year = {2014}, author = {Martin, MD and Ho, SY and Wales, N and Ristaino, JB and Gilbert, MT}, title = {Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant new world phytophthora infestans.}, journal = {Molecular biology and evolution}, volume = {31}, number = {6}, pages = {1414-1420}, doi = {10.1093/molbev/msu086}, pmid = {24577840}, issn = {1537-1719}, mesh = {Americas ; Bayes Theorem ; DNA, Mitochondrial/*analysis ; Evolution, Molecular ; History, 19th Century ; Ireland ; Phylogeny ; Phylogeography ; Phytophthora infestans/*classification/genetics/*isolation &amp; purification ; Plant Diseases/history/*parasitology ; Solanum tuberosum/*parasitology ; Starvation/history ; United Kingdom ; }, abstract = {The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in recent decades. Recently, complete P. infestans mitogenome sequences from 19th-century herbarium specimens were shown to belong to a unique lineage (HERB-1) predicted to be rare or extinct in modern times. We report 44 additional P. infestans mitogenomes: four from 19th-century Europe, three from 1950s UK, and 37 from modern populations across the New World. We use phylogenetic analyses to identify the HERB-1 lineage in modern populations from both Mexico and South America, and to demonstrate distinct mitochondrial haplotypes were present in 19th-century Europe, with this lineage initially diversifying 75 years before the first reports of potato late blight.}, }
@article {pmid24573854, year = {2014}, author = {Müller, R and Roberts, CA and Brown, TA}, title = {Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1781}, pages = {20133236}, pmid = {24573854}, issn = {1471-2954}, mesh = {Base Sequence ; Bone and Bones/chemistry ; Cluster Analysis ; Europe ; *Evolution, Molecular ; Genetic Variation/*genetics ; Genotype ; Humans ; Molecular Sequence Data ; Mycobacterium tuberculosis/*genetics ; Phylogeny ; Polymorphism, Genetic/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second-nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth-nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis.}, }
@article {pmid24568772, year = {2013}, author = {Carpenter, ML and Buenrostro, JD and Valdiosera, C and Schroeder, H and Allentoft, ME and Sikora, M and Rasmussen, M and Gravel, S and Guillén, S and Nekhrizov, G and Leshtakov, K and Dimitrova, D and Theodossiev, N and Pettener, D and Luiselli, D and Sandoval, K and Moreno-Estrada, A and Li, Y and Wang, J and Gilbert, MT and Willerslev, E and Greenleaf, WJ and Bustamante, CD}, title = {Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries.}, journal = {American journal of human genetics}, volume = {93}, number = {5}, pages = {852-864}, pmid = {24568772}, issn = {1537-6605}, support = {F32 HG007342/HG/NHGRI NIH HHS/United States ; U01 HG005715/HG/NHGRI NIH HHS/United States ; HG003220/HG/NHGRI NIH HHS/United States ; HG005715/HG/NHGRI NIH HHS/United States ; }, mesh = {Adolescent ; Bone and Bones ; Child ; DNA/chemistry/genetics/*isolation &amp; purification ; *Fossils ; Gene Library ; *Genomics ; Hair ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Humans ; Male ; *Mummies ; Nucleic Acid Hybridization ; Principal Component Analysis ; RNA/genetics ; Sequence Analysis, DNA/*methods ; Tooth ; }, abstract = {Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062-147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217-73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.}, }
@article {pmid24568097, year = {2014}, author = {Campana, MG and Robles García, N and Rühli, FJ and Tuross, N}, title = {False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing.}, journal = {BMC research notes}, volume = {7}, number = {}, pages = {111}, pmid = {24568097}, issn = {1756-0500}, mesh = {Adolescent ; Adult ; Bacteria/classification/*genetics ; Bacterial Infections/genetics/history/microbiology ; Child, Preschool ; False Positive Reactions ; Female ; Genome, Human/genetics ; High-Throughput Nucleotide Sequencing/*methods ; History, 16th Century ; Humans ; Male ; Metagenome/genetics ; Mexico ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Soil Microbiology ; Virus Diseases/genetics/history/virology ; Viruses/classification/*genetics ; Young Adult ; }, abstract = {BACKGROUND: Identification of historic pathogens is challenging since false positives and negatives are a serious risk. Environmental non-pathogenic contaminants are ubiquitous. Furthermore, public genetic databases contain limited information regarding these species. High-throughput sequencing may help reliably detect and identify historic pathogens.<br><br>RESULTS: We shotgun-sequenced 8 16th-century Mixtec individuals from the site of Teposcolula Yucundaa (Oaxaca, Mexico) who are reported to have died from the huey cocoliztli ('Great Pestilence' in Nahautl), an unknown disease that decimated native Mexican populations during the Spanish colonial period, in order to identify the pathogen. Comparison of these sequences with those deriving from the surrounding soil and from 4 precontact individuals from the site found a wide variety of contaminant organisms that confounded analyses. Without the comparative sequence data from the precontact individuals and soil, false positives for Yersinia pestis and rickettsiosis could have been reported.<br><br>CONCLUSIONS: False positives and negatives remain problematic in ancient DNA analyses despite the application of high-throughput sequencing. Our results suggest that several studies claiming the discovery of ancient pathogens may need further verification. Additionally, true single molecule sequencing's short read lengths, inability to sequence through DNA lesions, and limited ancient-DNA-specific technical development hinder its application to palaeopathology.}, }
@article {pmid24550262, year = {2014}, author = {Nair, P}, title = {Sequencing ancient DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {7}, pages = {2401}, pmid = {24550262}, issn = {1091-6490}, mesh = {DNA/*genetics ; Humans ; *Mummies ; Sequence Analysis, DNA/*methods ; }, }
@article {pmid24531081, year = {2014}, author = {Enk, JM and Devault, AM and Kuch, M and Murgha, YE and Rouillard, JM and Poinar, HN}, title = {Ancient whole genome enrichment using baits built from modern DNA.}, journal = {Molecular biology and evolution}, volume = {31}, number = {5}, pages = {1292-1294}, doi = {10.1093/molbev/msu074}, pmid = {24531081}, issn = {1537-1719}, mesh = {Animals ; DNA/genetics/isolation &amp; purification ; Elephants/genetics ; Fossils ; *Genome ; Genomics/*methods ; History, Ancient ; Mammoths/*genetics ; Sequence Alignment/methods ; Sequence Analysis, DNA/*methods ; }, abstract = {We report metrics from complete genome capture of nuclear DNA from extinct mammoths using biotinylated RNAs transcribed from an Asian elephant DNA extract. Enrichment of the nuclear genome ranged from 1.06- to 18.65-fold, to an apparent maximum threshold of ∼80% on-target. This projects an order of magnitude less costly complete genome sequencing from long-dead organisms, even when a reference genome is unavailable for bait design.}, }
@article {pmid24528593, year = {2014}, author = {Walsh, S and Chaitanya, L and Clarisse, L and Wirken, L and Draus-Barini, J and Kovatsi, L and Maeda, H and Ishikawa, T and Sijen, T and de Knijff, P and Branicki, W and Liu, F and Kayser, M}, title = {Developmental validation of the HIrisPlex system: DNA-based eye and hair colour prediction for forensic and anthropological usage.}, journal = {Forensic science international. Genetics}, volume = {9}, number = {}, pages = {150-161}, doi = {10.1016/j.fsigen.2013.12.006}, pmid = {24528593}, issn = {1878-0326}, mesh = {Alleles ; Blood Chemical Analysis ; DNA/*genetics/isolation &amp; purification ; Eye Color/*genetics ; *Forensic Genetics ; Genotype ; Hair/chemistry ; Hair Color/*genetics ; Heterozygote ; Humans ; Polymorphism, Single Nucleotide ; Saliva/chemistry ; Semen/chemistry ; }, abstract = {Forensic DNA Phenotyping or 'DNA intelligence' tools are expected to aid police investigations and find unknown individuals by providing information on externally visible characteristics of unknown suspects, perpetrators and missing persons from biological samples. This is especially useful in cases where conventional DNA profiling or other means remain non-informative. Recently, we introduced the HIrisPlex system, capable of predicting both eye and hair colour from DNA. In the present developmental validation study, we demonstrate that the HIrisPlex assay performs in full agreement with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines providing an essential prerequisite for future HIrisPlex applications to forensic casework. The HIrisPlex assay produces complete profiles down to only 63 pg of DNA. Species testing revealed human specificity for a complete HIrisPlex profile, while only non-human primates showed the closest full profile at 20 out of the 24 DNA markers, in all animals tested. Rigorous testing of simulated forensic casework samples such as blood, semen, saliva stains, hairs with roots as well as extremely low quantity touch (trace) DNA samples, produced complete profiles in 88% of cases. Concordance testing performed between five independent forensic laboratories displayed consistent reproducible results on varying types of DNA samples. Due to its design, the assay caters for degraded samples, underlined here by results from artificially degraded DNA and from simulated casework samples of degraded DNA. This aspect was also demonstrated previously on DNA samples from human remains up to several hundreds of years old. With this paper, we also introduce enhanced eye and hair colour prediction models based on enlarged underlying databases of HIrisPlex genotypes and eye/hair colour phenotypes (eye colour: N = 9188 and hair colour: N = 1601). Furthermore, we present an online web-based system for individual eye and hair colour prediction from full and partial HIrisPlex DNA profiles. By demonstrating that the HIrisPlex assay is fully compatible with the SWGDAM guidelines, we provide the first forensically validated DNA test system for parallel eye and hair colour prediction now available to forensic laboratories for immediate casework application, including missing person cases. Given the robustness and sensitivity described here and in previous work, the HIrisPlex system is also suitable for analysing old and ancient DNA in anthropological and evolutionary studies.}, }
@article {pmid24522580, year = {2014}, author = {Callaway, E}, title = {Ancient genome stirs ethics debate.}, journal = {Nature}, volume = {506}, number = {7487}, pages = {142-143}, doi = {10.1038/506142a}, pmid = {24522580}, issn = {1476-4687}, mesh = {Asia/ethnology ; Child ; *Ethics, Research ; Genome, Human/*genetics ; Humans ; Indians, North American/classification/*genetics/psychology ; Male ; Montana ; Negotiating ; Phylogeny ; }, }
@article {pmid24516122, year = {2014}, author = {Kistler, L and Montenegro, A and Smith, BD and Gifford, JA and Green, RE and Newsom, LA and Shapiro, B}, title = {Transoceanic drift and the domestication of African bottle gourds in the Americas.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {8}, pages = {2937-2941}, pmid = {24516122}, issn = {1091-6490}, mesh = {Africa ; Agriculture/*history ; Americas ; Asia ; Base Sequence ; Bayes Theorem ; Computer Simulation ; Cucurbitaceae/*genetics/physiology ; *Demography ; History, Ancient ; Human Migration/*history ; Humans ; Models, Genetic ; Molecular Sequence Data ; Oceans and Seas ; *Phylogeny ; Plastids/genetics ; Sequence Analysis, DNA ; *Water Movements ; }, abstract = {Bottle gourd (Lagenaria siceraria) was one of the first domesticated plants, and the only one with a global distribution during pre-Columbian times. Although native to Africa, bottle gourd was in use by humans in east Asia, possibly as early as 11,000 y ago (BP) and in the Americas by 10,000 BP. Despite its utilitarian importance to diverse human populations, it remains unresolved how the bottle gourd came to be so widely distributed, and in particular how and when it arrived in the New World. A previous study using ancient DNA concluded that Paleoindians transported already domesticated gourds to the Americas from Asia when colonizing the New World [Erickson et al. (2005) Proc Natl Acad Sci USA 102(51):18315-18320]. However, this scenario requires the propagation of tropical-adapted bottle gourds across the Arctic. Here, we isolate 86,000 base pairs of plastid DNA from a geographically broad sample of archaeological and living bottle gourds. In contrast to the earlier results, we find that all pre-Columbian bottle gourds are most closely related to African gourds, not Asian gourds. Ocean-current drift modeling shows that wild African gourds could have simply floated across the Atlantic during the Late Pleistocene. Once they arrived in the New World, naturalized gourd populations likely became established in the Neotropics via dispersal by megafaunal mammals. These wild populations were domesticated in several distinct New World locales, most likely near established centers of food crop domestication.}, }
@article {pmid24503968, year = {2014}, author = {Der Sarkissian, C and Brotherton, P and Balanovsky, O and Templeton, JE and Llamas, B and Soubrier, J and Moiseyev, V and Khartanovich, V and Cooper, A and Haak, W and , }, title = {Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e87612}, pmid = {24503968}, issn = {1932-6203}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Cluster Analysis ; *DNA, Mitochondrial ; Europe ; Genetics, Population ; *Genome, Mitochondrial ; Geography ; *Haplotypes ; Humans ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; White People/*genetics ; }, abstract = {The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. Three individuals from the 7,500 year old Mesolithic site of Yuzhnyy Oleni Ostrov, Western Russia, could be assigned to haplogroup C1 based on mitochondrial hypervariable region I sequences. However, hypervariable region I data alone could not provide enough resolution to establish the phylogenetic relationship of these Mesolithic haplotypes with haplogroup C1 mitochondrial DNA sequences found today in populations of Europe, Asia and the Americas. In order to obtain high-resolution data and shed light on the origin of this European Mesolithic C1 haplotype, we target-enriched and sequenced the complete mitochondrial genome of one Yuzhnyy Oleni Ostrov C1 individual. The updated phylogeny of C1 haplogroups indicated that the Yuzhnyy Oleni Ostrov haplotype represents a new distinct clade, provisionally coined "C1f". We show that all three C1 carriers of Yuzhnyy Oleni Ostrov belong to this clade. No haplotype closely related to the C1f sequence could be found in the large current database of ancient and present-day mitochondrial genomes. Hence, we have discovered past human mitochondrial diversity that has not been observed in modern-day populations so far. The lack of positive matches in modern populations may be explained by under-sampling of rare modern C1 carriers or by demographic processes, population extinction or replacement, that may have impacted on populations of Northeast Europe since prehistoric times.}, }
@article {pmid24499916, year = {2014}, author = {Willerslev, E and Davison, J and Moora, M and Zobel, M and Coissac, E and Edwards, ME and Lorenzen, ED and Vestergård, M and Gussarova, G and Haile, J and Craine, J and Gielly, L and Boessenkool, S and Epp, LS and Pearman, PB and Cheddadi, R and Murray, D and Bråthen, KA and Yoccoz, N and Binney, H and Cruaud, C and Wincker, P and Goslar, T and Alsos, IG and Bellemain, E and Brysting, AK and Elven, R and Sønstebø, JH and Murton, J and Sher, A and Rasmussen, M and Rønn, R and Mourier, T and Cooper, A and Austin, J and Möller, P and Froese, D and Zazula, G and Pompanon, F and Rioux, D and Niderkorn, V and Tikhonov, A and Savvinov, G and Roberts, RG and MacPhee, RD and Gilbert, MT and Kjær, KH and Orlando, L and Brochmann, C and Taberlet, P}, title = {Fifty thousand years of Arctic vegetation and megafaunal diet.}, journal = {Nature}, volume = {506}, number = {7486}, pages = {47-51}, pmid = {24499916}, issn = {1476-4687}, mesh = {Animals ; Arctic Regions ; *Biodiversity ; Bison/physiology ; Cold Climate ; *Diet ; Freezing ; *Herbivory ; High-Throughput Nucleotide Sequencing ; Horses/physiology ; Mammoths/physiology ; *Nematoda/classification/genetics/isolation &amp; purification ; *Plants/classification/genetics ; Poaceae/genetics/growth &amp; development ; Soil ; Time Factors ; Yukon Territory ; }, abstract = {Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25-15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.}, }
@article {pmid24497031, year = {2014}, author = {Sjödin, P and Skoglund, P and Jakobsson, M}, title = {Assessing the maximum contribution from ancient populations.}, journal = {Molecular biology and evolution}, volume = {31}, number = {5}, pages = {1248-1260}, doi = {10.1093/molbev/msu059}, pmid = {24497031}, issn = {1537-1719}, mesh = {Animals ; Computer Simulation ; DNA, Mitochondrial/genetics/history ; *Evolution, Molecular ; Fossils ; Gene Flow ; Gene Frequency ; Genetic Drift ; *Genetics, Population ; History, Ancient ; Humans ; Mammoths/genetics ; *Models, Genetic ; Scandinavian and Nordic Countries ; Siberia ; }, abstract = {Ancestral relationships between populations separated by time represent an often neglected dimension in population genetics, a field which historically has focused on analysis of spatially distributed samples from the same point in time. Models are usually straightforward when two time-separated populations are assumed to be completely isolated from all other populations. However, this is usually an unrealistically stringent assumption when there is gene flow with other populations. Here, we investigate continuity in the presence of gene flow from unknown populations. This setup allows a more nuanced treatment of questions regarding population continuity in terms of "level of contribution" from a particular ancient population to a more recent population. We propose a statistical framework which makes use of a biallelic marker sampled at two different points in time to assess population contribution, and present two different interpretations of the concept. We apply the approach to published data from a prehistoric human population in Scandinavia (Malmström H, Gilbert MTP, Thomas MG, Brandström M, Storå J, Molnar P, Andersen PK, Bendixen C, Holmlund G, Götherström A, et al. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol. 19:1758-1762) and Pleistocene woolly mammoth (Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG. 2007. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol. 17:1072-1075; Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Gröcke DR, Matheus P, Zazula G, et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326).}, }
@article {pmid24478305, year = {2014}, author = {de Bruyn, M and Pinsky, ML and Hall, B and Koch, P and Baroni, C and Hoelzel, AR}, title = {Rapid increase in southern elephant seal genetic diversity after a founder event.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1779}, pages = {20133078}, pmid = {24478305}, issn = {1471-2954}, mesh = {Adaptation, Biological/genetics ; Animals ; Bayes Theorem ; Biological Evolution ; Extinction, Biological ; Female ; *Founder Effect ; Genetic Drift ; Population Dynamics ; Seals, Earless/*genetics ; }, abstract = {Genetic diversity provides the raw material for populations to respond to changing environmental conditions. The evolution of diversity within populations is based on the accumulation of mutations and their retention or loss through selection and genetic drift, while migration can also introduce new variation. However, the extent to which population growth and sustained large population size can lead to rapid and significant increases in diversity has not been widely investigated. Here, we assess this empirically by applying approximate Bayesian computation to a novel ancient DNA dataset that spans the life of a southern elephant seal (Mirounga leonina) population, from initial founding approximately 7000 years ago to eventual extinction within the past millennium. We find that rapid population growth and sustained large population size can explain substantial increases in population genetic diversity over a period of several hundred generations, subsequently lost when the population went to extinction. Results suggest that the impact of diversity introduced through migration was relatively minor. We thus demonstrate, by examining genetic diversity across the life of a population, that environmental change could generate the raw material for adaptive evolution over a very short evolutionary time scale through rapid establishment of a large, stable population.}, }
@article {pmid24476670, year = {2014}, author = {Vernot, B and Akey, JM}, title = {Resurrecting surviving Neandertal lineages from modern human genomes.}, journal = {Science (New York, N.Y.)}, volume = {343}, number = {6174}, pages = {1017-1021}, doi = {10.1126/science.1245938}, pmid = {24476670}, issn = {1095-9203}, mesh = {Animals ; Genetic Variation ; *Genome, Human ; Humans ; Hybridization, Genetic ; Indians, North American/genetics ; Neanderthals/*genetics ; Sequence Analysis, DNA ; }, abstract = {Anatomically modern humans overlapped and mated with Neandertals such that non-African humans inherit ~1 to 3% of their genomes from Neandertal ancestors. We identified Neandertal lineages that persist in the DNA of modern humans, in whole-genome sequences from 379 European and 286 East Asian individuals, recovering more than 15 gigabases of introgressed sequence that spans ~20% of the Neandertal genome (false discovery rate = 5%). Analyses of surviving archaic lineages suggest that there were fitness costs to hybridization, admixture occurred both before and after divergence of non-African modern humans, and Neandertals were a source of adaptive variation for loci involved in skin phenotypes. Our results provide a new avenue for paleogenomics studies, allowing substantial amounts of population-level DNA sequence information to be obtained from extinct groups, even in the absence of fossilized remains.}, }
@article {pmid24475182, year = {2014}, author = {Wales, N and Andersen, K and Cappellini, E and Avila-Arcos, MC and Gilbert, MT}, title = {Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86827}, pmid = {24475182}, issn = {1932-6203}, mesh = {Analysis of Variance ; Base Sequence ; Botany/*methods ; DNA, Plant/*isolation &amp; purification ; DNA-Directed DNA Polymerase/metabolism ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques/*methods ; Paleontology/*methods ; Plants/*genetics ; }, abstract = {Ancient DNA (aDNA) recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities.}, }
@article {pmid24471807, year = {2014}, author = {Myšková, E and Ditrich, O and Sak, B and Kváč, M and Cymbalak, T}, title = {Detection of ancient DNA of Encephalitozoon intestinalis (Microsporidia) in archaeological material.}, journal = {The Journal of parasitology}, volume = {100}, number = {3}, pages = {356-359}, doi = {10.1645/13-232.1}, pmid = {24471807}, issn = {1937-2345}, mesh = {Animals ; Base Sequence ; Czech Republic ; DNA, Fungal/chemistry/history/*isolation &amp; purification ; Encephalitozoon/*genetics/isolation &amp; purification ; Encephalitozoonosis/*history ; History, 18th Century ; History, 19th Century ; Humans ; Molecular Sequence Data ; }, abstract = {Ancient DNA (aDNA) of Encephalitozoon intestinalis (Microsporidia, Fungi) was detected in archaeological material originated from New Town of Prague (Czech Republic) with the use of molecular methods. Microsporidial aDNA was found in 3 samples originating from 2 objects, in a well/cesspit (samples from layers from the 18th century) and in a well from the 18th/19th century. The ability to use molecular methods to detect microsporidia extends the range of paleoparasitological inquiry, and could contribute to a better understanding of parasites shared between human and animals.}, }
@article {pmid24469802, year = {2014}, author = {Skoglund, P and Northoff, BH and Shunkov, MV and Derevianko, AP and Pääbo, S and Krause, J and Jakobsson, M}, title = {Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {6}, pages = {2229-2234}, pmid = {24469802}, issn = {1091-6490}, mesh = {Animals ; DNA, Mitochondrial/genetics/*isolation &amp; purification ; Humans ; Molecular Sequence Data ; Neanderthals/*genetics ; Siberia ; }, abstract = {One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation-summarized in a postmortem degradation score-which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material.}, }
@article {pmid24465990, year = {2014}, author = {Krüttli, A and Bouwman, A and Akgül, G and Della Casa, P and Rühli, F and Warinner, C}, title = {Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86251}, pmid = {24465990}, issn = {1932-6203}, mesh = {Alleles ; Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; Gene Frequency ; Germany ; History, Medieval ; Humans ; Lactase/*genetics ; Lactose Intolerance/*genetics/history ; Male ; Milk ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications.}, }
@article {pmid24461411, year = {2014}, author = {Brundin, M and Figdor, D and Johansson, A and Sjögren, U}, title = {Preservation of bacterial DNA by human dentin.}, journal = {Journal of endodontics}, volume = {40}, number = {2}, pages = {241-245}, doi = {10.1016/j.joen.2013.08.025}, pmid = {24461411}, issn = {1878-3554}, mesh = {Blood ; Blood Proteins/metabolism ; Coculture Techniques ; Collagen/drug effects/metabolism ; Culture Media ; DNA, Bacterial/analysis/*metabolism ; Dentin/drug effects/*microbiology ; Deoxyribonuclease I/metabolism ; Edetic Acid/pharmacology ; Endopeptidase K/pharmacology ; Eubacterium/genetics ; Fusobacterium nucleatum/*genetics ; Humans ; Humidity ; Microbial Consortia ; Peptostreptococcus/genetics ; Polymerase Chain Reaction/methods ; Prevotella intermedia/genetics ; Protein Binding ; Temperature ; Time Factors ; Water ; }, abstract = {INTRODUCTION: The capacity of dentin and collagen to bind DNA and protect against spontaneous and nuclease-induced degradation was evaluated individually and by the incubation of DNA with nuclease-producing bacteria in a mixed culture.<br><br>METHODS: Extracted Fusobacterium nucleatum DNA was incubated with dentin shavings or collagen for 90 minutes. The DNA-bound substrates were incubated in different media (water, sera, and DNase I) for up to 3 months. Amplifiable DNA was released from dentin using EDTA,or from collagen using proteinase K, and evaluated by polymerase chain reaction (PCR). The stability of dentin-bound DNA was also assessed in a mixed culture (Parvimonas micra and Pseudoramibacter alactolyticus) containing a DNase-producing species, Prevotella intermedia. Samples were analyzed for amplifiable DNA.<br><br>RESULTS: In water, dentin-bound DNA was recoverable by PCR at 3 months compared with no detectable DNA after 4 weeks in controls (no dentin). DNA bound to collagen was detectable by PCR after 3 months of incubation in water. In 10% human sera, amplifiable DNA was detectable at 3 months when dentin bound and in controls (no dentin). In mixed bacterial culture, dentin-bound DNA was recoverable throughout the experimental period (3 months), compared with no recoverable F. nucleatum DNA within 24 hours in controls (no dentin).<br><br>CONCLUSIONS: There is a strong binding affinity between DNA and dentin, and between DNA and serum proteins or collagen. These substrates preserve DNA against natural decomposition and protect DNA from nuclease activity, factors that may confound molecular analysis of the endodontic microbiota yet favor paleomicrobiological studies of ancient DNA.}, }
@article {pmid24458647, year = {2014}, author = {Shapiro, B and Hofreiter, M}, title = {A paleogenomic perspective on evolution and gene function: new insights from ancient DNA.}, journal = {Science (New York, N.Y.)}, volume = {343}, number = {6169}, pages = {1236573}, doi = {10.1126/science.1236573}, pmid = {24458647}, issn = {1095-9203}, mesh = {Animals ; Classification ; Columbidae/genetics ; DNA/*genetics ; *Evolution, Molecular ; Extinction, Biological ; Genomics/*trends ; Hominidae/genetics ; Humans ; Mammoths/genetics ; Mastodons/genetics ; Paleontology/*trends ; }, abstract = {The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events.}, }
@article {pmid24450980, year = {2014}, author = {Shapiro, B and Ho, SY}, title = {Ancient hyaenas highlight the old problem of estimating evolutionary rates.}, journal = {Molecular ecology}, volume = {23}, number = {3}, pages = {499-501}, doi = {10.1111/mec.12621}, pmid = {24450980}, issn = {1365-294X}, mesh = {Animals ; *Biological Evolution ; Hyaenidae/*genetics ; *Phylogeny ; }, abstract = {Phylogenetic analyses of ancient DNA data can provide a timeline for evolutionary change even in the absence of fossils. The power to infer the evolutionary rate is, however, highly dependent on the number and age of samples, the information content of the sequence data and the demographic history of the sampled population. In this issue of Molecular Ecology, Sheng et al. (2014) analysed mitochondrial DNA sequences isolated from a combination of ancient and present-day hyaenas, including three Pleistocene samples from China. Using an evolutionary rate inferred from the ages of the ancient sequences, they recalibrated the timing of hyaena diversification and suggest a much more recent evolutionary history than was believed previously. Their results highlight the importance of accurately estimating the evolutionary rate when inferring timescales of geographical and evolutionary diversification.}, }
@article {pmid24448642, year = {2014}, author = {Sverrisdóttir, O&#xd3; and Timpson, A and Toombs, J and Lecoeur, C and Froguel, P and Carretero, JM and Arsuaga Ferreras, JL and Götherström, A and Thomas, MG}, title = {Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe.}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {975-983}, doi = {10.1093/molbev/msu049}, pmid = {24448642}, issn = {1537-1719}, mesh = {Calcium/*metabolism ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; France ; Gene Frequency ; Genetic Drift ; Humans ; Intestinal Absorption/*genetics ; Lactase/*genetics ; Models, Genetic ; Polymorphism, Single Nucleotide ; *Selection, Genetic ; Sequence Analysis, DNA ; Spain ; }, abstract = {Lactase persistence (LP) is a genetically determined trait whereby the enzyme lactase is expressed throughout adult life. Lactase is necessary for the digestion of lactose--the main carbohydrate in milk--and its production is downregulated after the weaning period in most humans and all other mammals studied. Several sources of evidence indicate that LP has evolved independently, in different parts of the world over the last 10,000 years, and has been subject to strong natural selection in dairying populations. In Europeans, LP is strongly associated with, and probably caused by, a single C to T mutation 13,910 bp upstream of the lactase (LCT) gene (-13,910*T). Despite a considerable body of research, the reasons why LP should provide such a strong selective advantage remain poorly understood. In this study, we examine one of the most widely cited hypotheses for selection on LP--that fresh milk consumption supplemented the poor vitamin D and calcium status of northern Europe's early farmers (the calcium assimilation hypothesis). We do this by testing for natural selection on -13,910*T using ancient DNA data from the skeletal remains of eight late Neolithic Iberian individuals, whom we would not expect to have poor vitamin D and calcium status because of relatively high incident UVB light levels. None of the eight samples successfully typed in the study had the derived T-allele. In addition, we reanalyze published data from French Neolithic remains to both test for population continuity and further examine the evolution of LP in the region. Using simulations that accommodate genetic drift, natural selection, uncertainty in calibrated radiocarbon dates, and sampling error, we find that natural selection is still required to explain the observed increase in allele frequency. We conclude that the calcium assimilation hypothesis is insufficient to explain the spread of LP in Europe.}, }
@article {pmid24438205, year = {2014}, author = {Thèves, C and Biagini, P and Crubézy, E}, title = {The rediscovery of smallpox.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {20}, number = {3}, pages = {210-218}, doi = {10.1111/1469-0691.12536}, pmid = {24438205}, issn = {1469-0691}, mesh = {Animals ; Biological Evolution ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; Humans ; Smallpox/diagnosis/epidemiology/*history/virology ; Variola virus/genetics/isolation &amp; purification ; }, abstract = {Smallpox is an infectious disease that is unique to humans, caused by a poxvirus. It is one of the most lethal of diseases; the virus variant Variola major has a mortality rate of 30%. People surviving this disease have life-long consequences, but also assured immunity. Historically, smallpox was recognized early in human populations. This led to prevention attempts--variolation, quarantine, and the isolation of infected subjects--until Jenner's discovery of the first steps of vaccination in the 18th century. After vaccination campaigns throughout the 19th and 20th centuries, the WHO declared the eradication of smallpox in 1980. With the development of microscopy techniques, the structural characterization of the virus began in the early 20th century. In 1990, the genomes of different smallpox viruses were determined; viruses could be classified in order to investigate their origin, diffusion, and evolution. To study the evolution and possible re-emergence of this viral pathogen, however, researchers can only use viral genomes collected during the 20th century. Cases of smallpox in ancient periods are sometimes well documented, so palaeomicrobiology and, more precisely, the study of ancient smallpox viral strains could be an exceptional opportunity. The analysis of poxvirus fragmented genomes could give new insights into the genetic evolution of the poxvirus. Recently, small fragments of the poxvirus genome were detected. With the genetic information obtained, a new phylogeny of smallpox virus was described. The interest in conducting studies on ancient strains is discussed, in order to explore the natural history of this disease.}, }
@article {pmid24417407, year = {2014}, author = {Zhan, SH and Glick, L and Tsigenopoulos, CS and Otto, SP and Mayrose, I}, title = {Comparative analysis reveals that polyploidy does not decelerate diversification in fish.}, journal = {Journal of evolutionary biology}, volume = {27}, number = {2}, pages = {391-403}, doi = {10.1111/jeb.12308}, pmid = {24417407}, issn = {1420-9101}, mesh = {Animals ; *Biodiversity ; Fishes/*genetics ; *Genetic Speciation ; Phylogeny ; *Polyploidy ; }, abstract = {While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life.}, }
@article {pmid24403343, year = {2014}, author = {Ólafsdóttir, G&#xc1; and Westfall, KM and Edvardsson, R and Pálsson, S}, title = {Historical DNA reveals the demographic history of Atlantic cod (Gadus morhua) in medieval and early modern Iceland.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1777}, pages = {20132976}, pmid = {24403343}, issn = {1471-2954}, mesh = {Animals ; Climate ; Cytochromes b/genetics/metabolism ; Demography ; Ecosystem ; Fish Proteins/genetics/metabolism ; Gadus morhua/*classification/*genetics/physiology ; Iceland ; Mitochondrial Proteins/*genetics/metabolism ; Molecular Sequence Data ; Polymerase Chain Reaction ; Population Dynamics ; Sequence Analysis, DNA ; Spine/chemistry ; Synaptophysin/genetics/metabolism ; Time Factors ; }, abstract = {Atlantic cod (Gadus morhua) vertebrae from archaeological sites were used to study the history of the Icelandic Atlantic cod population in the time period of 1500-1990. Specifically, we used coalescence modelling to estimate population size and fluctuations from the sequence diversity at the cytochrome b (cytb) and Pantophysin I (PanI) loci. The models are consistent with an expanding population during the warm medieval period, large historical effective population size (NE), a marked bottleneck event at 1400-1500 and a decrease in NE in early modern times. The model results are corroborated by the reduction of haplotype and nucleotide variation over time and pairwise population distance as a significant portion of nucleotide variation partitioned across the 1550 time mark. The mean age of the historical fished stock is high in medieval times with a truncation in age in early modern times. The population size crash coincides with a period of known cooling in the North Atlantic, and we conclude that the collapse may be related to climate or climate-induced ecosystem change.}, }
@article {pmid24403338, year = {2014}, author = {Metcalf, JL and Prost, S and Nogués-Bravo, D and DeChaine, EG and Anderson, C and Batra, P and Araújo, MB and Cooper, A and Guralnick, RP}, title = {Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1777}, pages = {20132782}, pmid = {24403338}, issn = {1471-2954}, mesh = {Animals ; *Biological Evolution ; Bison/genetics/*physiology ; Canada ; *Climate ; DNA, Mitochondrial/*genetics ; Demography ; *Food Chain ; Fossils ; Humans ; Models, Genetic ; Population Density ; United States ; }, abstract = {One of the grand goals of historical biogeography is to understand how and why species' population sizes and distributions change over time. Multiple types of data drawn from disparate fields, combined into a single modelling framework, are necessary to document changes in a species's demography and distribution, and to determine the drivers responsible for change. Yet truly integrated approaches are challenging and rarely performed. Here, we discuss a modelling framework that integrates spatio-temporal fossil data, ancient DNA, palaeoclimatological reconstructions, bioclimatic envelope modelling and coalescence models in order to statistically test alternative hypotheses of demographic and potential distributional changes for the iconic American bison (Bison bison). Using different assumptions about the evolution of the bioclimatic niche, we generate hypothetical distributional and demographic histories of the species. We then test these demographic models by comparing the genetic signature predicted by serial coalescence against sequence data derived from subfossils and modern populations. Our results supported demographic models that include both climate and human-associated drivers of population declines. This synthetic approach, integrating palaeoclimatology, bioclimatic envelopes, serial coalescence, spatio-temporal fossil data and heterochronous DNA sequences, improves understanding of species' historical biogeography by allowing consideration of both abiotic and biotic interactions at the population level.}, }
@article {pmid26260087, year = {2015}, author = {Korlević, P and Gerber, T and Gansauge, MT and Hajdinjak, M and Nagel, S and Aximu-Petri, A and Meyer, M}, title = {Reducing microbial and human contamination in DNA extractions from ancient bones and teeth.}, journal = {BioTechniques}, volume = {59}, number = {2}, pages = {87-93}, doi = {10.2144/000114320}, pmid = {26260087}, issn = {1940-9818}, mesh = {Bacteria ; Bone and Bones ; *DNA Contamination ; Decontamination/methods ; *Fossils ; Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; *Paleodontology/methods ; Tooth ; }, abstract = {Although great progress has been made in improving methods for generating DNA sequences from ancient biological samples, many, if not most, samples are still not amenable for analyses due to overwhelming contamination with microbial or modern human DNA. Here we explore different DNA decontamination procedures for ancient bones and teeth for use prior to DNA library preparation and high-throughput sequencing. Two procedures showed promising results: (i) the release of surface-bound DNA by phosphate buffer and (ii) the removal of DNA contamination by sodium hypochlorite treatment. Exposure to phosphate removes on average 64% of the microbial DNA from bone powder but only 37% of the endogenous DNA (from the organism under study), increasing the percentage of informative sequences by a factor of two on average. An average 4.6-fold increase, in one case reaching 24-fold, is achieved by sodium hypochlorite treatment, albeit at the expense of destroying 63% of the endogenous DNA preserved in the bone. While both pretreatment methods described here greatly reduce the cost of genome sequencing from ancient material due to efficient depletion of microbial DNA, we find that the removal of human DNA contamination remains a challenging problem.}, }
@article {pmid24372820, year = {2014}, author = {Boessenkool, S and McGlynn, G and Epp, LS and Taylor, D and Pimentel, M and Gizaw, A and Nemomissa, S and Brochmann, C and Popp, M}, title = {Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {28}, number = {2}, pages = {446-455}, doi = {10.1111/cobi.12195}, pmid = {24372820}, issn = {1523-1739}, mesh = {*Altitude ; *Biodiversity ; Conservation of Natural Resources/*methods ; DNA, Plant/*analysis ; *Fossils ; Geologic Sediments/*analysis ; Plants/classification/*genetics ; Rwanda ; }, abstract = {Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited.}, }
@article {pmid24357323, year = {2013}, author = {, }, title = {The Amborella genome and the evolution of flowering plants.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6165}, pages = {1241089}, doi = {10.1126/science.1241089}, pmid = {24357323}, issn = {1095-9203}, mesh = {Conservation of Natural Resources ; Contig Mapping ; *Evolution, Molecular ; Flowers/*genetics ; Gene Duplication ; Genetic Variation ; *Genome, Plant ; Metagenomics/statistics &amp; numerical data ; Molecular Sequence Annotation ; Multigene Family ; New Caledonia ; Phylogeny ; Sequence Analysis, DNA ; Tracheophyta/classification/*genetics/*growth &amp; development ; }, abstract = {Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications.}, }
@article {pmid24355295, year = {2014}, author = {Rai, N and Taher, N and Singh, M and Chaubey, G and Jha, AN and Singh, L and Thangaraj, K}, title = {Relic excavated in western India is probably of Georgian Queen Ketevan.}, journal = {Mitochondrion}, volume = {14}, number = {1}, pages = {1-6}, doi = {10.1016/j.mito.2013.12.002}, pmid = {24355295}, issn = {1872-8278}, mesh = {Bone and Bones/*chemistry ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; Female ; *Forensic Anthropology ; *Fossils ; Genotyping Techniques ; Haplotypes ; Humans ; India ; Sequence Analysis, DNA ; }, abstract = {History has well documented the execution of Queen Ketevan of Georgia by the Persian Emperor of modern day Iran. Based on historical records, in 1624 two Augustinian friars unearthed the queen's remains and one of them brought the relic to the St. Augustine convent in Goa, India. We carried out ancient DNA analysis on the human bone remains excavated from the St. Augustine convent by sequencing and genotyping of the mitochondrial DNA. The investigations of the remains revealed a unique mtDNA haplogroup U1b, which is absent in India, but present in Georgia and surrounding regions. Since our genetic analysis corroborates archaeological and literary evidence, it is likely that the excavated bone belongs to Queen Ketevan of Georgia.}, }
@article {pmid24352233, year = {2014}, author = {Dohm, JC and Minoche, AE and Holtgräwe, D and Capella-Gutiérrez, S and Zakrzewski, F and Tafer, H and Rupp, O and Sörensen, TR and Stracke, R and Reinhardt, R and Goesmann, A and Kraft, T and Schulz, B and Stadler, PF and Schmidt, T and Gabaldón, T and Lehrach, H and Weisshaar, B and Himmelbauer, H}, title = {The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).}, journal = {Nature}, volume = {505}, number = {7484}, pages = {546-549}, pmid = {24352233}, issn = {1476-4687}, mesh = {Beta vulgaris/*genetics ; Biofuels/supply &amp; distribution ; Carbohydrate Metabolism ; Chromosomes, Plant/genetics ; Crops, Agricultural/*genetics ; Ethanol/metabolism ; Genome, Plant/*genetics ; Genomics ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Spinacia oleracea/genetics ; }, abstract = {Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.}, }
@article {pmid24344679, year = {2013}, author = {Enk, J and Rouillard, JM and Poinar, H}, title = {Quantitative PCR as a predictor of aligned ancient DNA read counts following targeted enrichment.}, journal = {BioTechniques}, volume = {55}, number = {6}, pages = {300-309}, doi = {10.2144/000114114}, pmid = {24344679}, issn = {1940-9818}, mesh = {Animals ; DNA, Mitochondrial/chemistry ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mammoths/*genetics ; Nucleic Acid Amplification Techniques ; RNA, Ribosomal/genetics ; Real-Time Polymerase Chain Reaction/*methods ; }, abstract = {Targeted DNA enrichment through hybridization capture (EHC) is rapidly replacing PCR as the method of choice for enrichment prior to genomic resequencing. This is especially true in the case of ancient DNA (aDNA) from long-dead organisms, where targets tend to be highly fragmented and outnumbered by contaminant DNA. However, the behavior of EHC using aDNA has been quite variable, making success difficult to predict and preventing efficient sample equilibration during multiplexed sequencing runs. Here, we evaluate whether quantitative PCR (qPCR) measurements of aDNA samples correlate with on-target read counts before and after EHC. Our data indicate that not only do simple target qPCRs correlate strongly with high-throughput sequencing (HTS) data but that certain sample characteristics, such as overall target abundance as well as experimental parameters (e.g., bait concentration and secondary structure propensity), consistently influenced enrichment of our diverse set of aDNA samples. Taken together, our results should help guide experimental design, screening strategies, and multiplexed sample equilibration, increasing yield and reducing the expected and actual cost of aDNA EHC high-throughput sequencing projects in the future.}, }
@article {pmid24337269, year = {2013}, author = {Curry, A}, title = {Ancient DNA. Fossilized teeth offer mouthful on ancient microbiome.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6164}, pages = {1303}, doi = {10.1126/science.342.6164.1303}, pmid = {24337269}, issn = {1095-9203}, mesh = {DNA, Bacterial/*isolation &amp; purification ; Dental Calculus/*microbiology ; *Fossils ; Humans ; *Microbiota ; Paleodontology ; Spirochaetales/classification/genetics/isolation &amp; purification ; Tetracycline Resistance/genetics ; Tooth/*microbiology ; }, }
@article {pmid24335981, year = {2014}, author = {Meiri, M and Lister, AM and Collins, MJ and Tuross, N and Goebel, T and Blockley, S and Zazula, GD and van Doorn, N and Dale Guthrie, R and Boeskorov, GG and Baryshnikov, GF and Sher, A and Barnes, I}, title = {Faunal record identifies Bering isthmus conditions as constraint to end-Pleistocene migration to the New World.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1776}, pages = {20132167}, pmid = {24335981}, issn = {1471-2954}, mesh = {Alaska ; Animal Migration/*physiology ; Animals ; Base Sequence ; Bayes Theorem ; Carbon Radioisotopes/analysis ; *Climate ; Collagen/genetics ; Deer/*genetics ; History, Ancient ; Humans ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Oceans and Seas ; Oxygen Isotopes/analysis ; *Phylogeny ; Sequence Analysis, DNA ; Siberia ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tritium/analysis ; }, abstract = {Human colonization of the New World is generally believed to have entailed migrations from Siberia across the Bering isthmus. However, the limited archaeological record of these migrations means that details of the timing, cause and rate remain cryptic. Here, we have used a combination of ancient DNA, 14C dating, hydrogen and oxygen isotopes, and collagen sequencing to explore the colonization history of one of the few other large mammals to have successfully migrated into the Americas at this time: the North American elk (Cervus elaphus canadensis), also known as wapiti. We identify a long-term occupation of northeast Siberia, far beyond the species's current Old World distribution. Migration into North America occurred at the end of the last glaciation, while the northeast Siberian source population became extinct only within the last 500 years. This finding is congruent with a similar proposed delay in human colonization, inferred from modern human mitochondrial DNA, and suggestions that the Bering isthmus was not traversable during parts of the Late Pleistocene. Our data imply a fundamental constraint in crossing Beringia, placing limits on the age and mode of human settlement in the Americas, and further establish the utility of ancient DNA in palaeontological investigations of species histories.}, }
@article {pmid24334485, year = {2013}, author = {Benítez-Burraco, A and Barceló-Coblijn, L}, title = {Paleogenomics, hominin interbreeding and language evolution.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {91}, number = {}, pages = {239-244}, doi = {10.4436/jass.91012}, pmid = {24334485}, issn = {2037-0644}, mesh = {Animals ; *Biological Evolution ; *Genomics ; *Hominidae ; Humans ; Hybridization, Genetic ; *Language ; *Paleontology ; }, }
@article {pmid24331083, year = {2014}, author = {Benazzi, S and Peresani, M and Talamo, S and Fu, Q and Mannino, MA and Richards, MP and Hublin, JJ}, title = {A reassessment of the presumed Neandertal remains from San Bernardino Cave, Italy.}, journal = {Journal of human evolution}, volume = {66}, number = {}, pages = {89-94}, doi = {10.1016/j.jhevol.2013.09.009}, pmid = {24331083}, issn = {1095-8606}, mesh = {Animals ; Carbon Isotopes/analysis ; Caves ; Chronology as Topic ; DNA, Mitochondrial/*genetics ; Fossils ; Humans/classification ; Italy ; Mass Spectrometry ; Molar/*anatomy &amp; histology/*chemistry ; Molecular Sequence Data ; Neanderthals/*classification ; Nitrogen Isotopes/analysis ; Paleodontology ; Phylogeny ; Radiometric Dating ; Sequence Analysis, DNA ; Sequence Homology ; Tooth Root/*anatomy &amp; histology ; }, abstract = {In 1986-1987, three human remains were unearthed from macro-unit II of San Bernardino Cave (Berici Hills, Veneto, Italy), a deposit containing a late Mousterian lithic assemblage. The human remains (a distal phalanx, a lower right third molar and a lower right second deciduous incisor) do not show diagnostic morphological features that could be used to determine whether they were from Homo neanderthalensis or Homo sapiens. Despite being of small size, and thus more similar to recent H. sapiens, the specimens were attributed to Neandertals, primarily because they were found in Mousterian layers. We carried out a taxonomic reassessment of the lower right third molar (LRM3; San Bernardino 4) using digital morphometric analysis of the root, ancient DNA analysis, carbon and nitrogen isotope analyses, and direct accelerator mass spectrometry (AMS) radiocarbon dating of dentine collagen. Mitochondrial DNA analysis and root morphology show that the molar belongs to a modern human and not to a Neandertal. Carbon 14 ((14)C) dating of the molar attributes it to the end of the Middle Ages (1420-1480 cal AD, 2 sigma). Carbon and nitrogen isotope analyses suggest that the individual in question had a diet similar to that of Medieval Italians. These results show that the molar, as well as the other two human remains, belong to recent H. sapiens and were introduced in the Mousterian levels post-depositionally.}, }
@article {pmid24320717, year = {2014}, author = {Sheng, GL and Soubrier, J and Liu, JY and Werdelin, L and Llamas, B and Thomson, VA and Tuke, J and Wu, LJ and Hou, XD and Chen, QJ and Lai, XL and Cooper, A}, title = {Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta.}, journal = {Molecular ecology}, volume = {23}, number = {3}, pages = {522-533}, doi = {10.1111/mec.12576}, pmid = {24320717}, issn = {1365-294X}, mesh = {Animals ; Asia ; Bayes Theorem ; *Biological Evolution ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Europe ; Fossils ; Genetics, Population ; Hyaenidae/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The living hyena species (spotted, brown, striped and aardwolf) are remnants of a formerly diverse group of more than 80 fossil species, which peaked in diversity in the Late Miocene (about 7-8 Ma). The fossil history indicates an African origin, and morphological and ancient DNA data have confirmed that living spotted hyenas (Crocuta crocuta) of Africa were closely related to extinct Late Pleistocene cave hyenas from Europe and Asia. The current model used to explain the origins of Eurasian cave hyena populations invokes multiple migrations out of Africa between 3.5-0.35 Ma. We used mitochondrial DNA sequences from radiocarbon-dated Chinese Pleistocene hyena specimens to examine the origin of Asian populations, and temporally calibrate the evolutionary history of spotted hyenas. Our results support a far more recent evolutionary timescale (430-163 kya) and suggest that extinct and living spotted hyena populations originated from a widespread Eurasian population in the Late Pleistocene, which was only subsequently restricted to Africa. We developed statistical tests of the contrasting population models and their fit to the fossil record. Coalescent simulations and Bayes Factor analysis support the new radiocarbon-calibrated timescale and Eurasian origins model. The new Eurasian biogeographic scenario proposed for the hyena emphasizes the role of the vast steppe grasslands of Eurasia in contrast to models only involving Africa. The new methodology for combining genetic and geological data to test contrasting models of population history will be useful for a wide range of taxa where ancient and historic genetic data are available.}, }
@article {pmid24299399, year = {2013}, author = {Smith, KL and Hale, JM and Gay, L and Kearney, M and Austin, JJ and Parris, KM and Melville, J}, title = {Spatio-temporal changes in the structure of an Australian frog hybrid zone: a 40-year perspective.}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {12}, pages = {3442-3454}, doi = {10.1111/evo.12140}, pmid = {24299399}, issn = {1558-5646}, mesh = {Animals ; Anura/*genetics ; *Genetic Speciation ; Phylogeography ; }, abstract = {Spatio-temporal studies of hybrid zones provide an opportunity to test evolutionary hypotheses of hybrid zone maintenance and movement. We conducted a landscape genetics study on a classic hybrid zone of the south-eastern Australian frogs, Litoria ewingii and Litoria paraewingi. This hybrid zone has been comprehensively studied since the 1960s, providing the unique opportunity to directly assess changes in hybrid zone structure across time. We compared both mtDNA and male advertisement call data from two time periods (present and 1960s). Clinal analysis of the coincidence (same center) and concordance (same width) of these traits indicated that the center of the hybrid zone has shifted 1 km south over the last 40 years, although the width of the zone and the rate of introgression remained unchanged. The low frequency of hybrids, the strong concordance of clines within a time period, and the small but significant movement across the study period despite significant anthropogenic changes through the region, suggest the hybrid zone is a tension zone located within a low-density trough. Hybrid zone movement has not been considered common in the past but our findings highlight that it should be considered a crucial component to our understanding of evolution.}, }
@article {pmid24288018, year = {2013}, author = {Murray, DC and Haile, J and Dortch, J and White, NE and Haouchar, D and Bellgard, MI and Allcock, RJ and Prideaux, GJ and Bunce, M}, title = {Scrapheap challenge: a novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {3371}, pmid = {24288018}, issn = {2045-2322}, mesh = {Archaeology/methods ; Australia ; Bone and Bones/*physiology ; DNA/*genetics ; Fossils ; }, abstract = {Highly fragmented and morphologically indistinct fossil bone is common in archaeological and paleontological deposits but unfortunately it is of little use in compiling faunal assemblages. The development of a cost-effective methodology to taxonomically identify bulk bone is therefore a key challenge. Here, an ancient DNA methodology using high-throughput sequencing is developed to survey and analyse thousands of archaeological bones from southwest Australia. Fossils were collectively ground together depending on which of fifteen stratigraphical layers they were excavated from. By generating fifteen synthetic blends of bulk bone powder, each corresponding to a chronologically distinct layer, samples could be collectively analysed in an efficient manner. A diverse range of taxa, including endemic, extirpated and hitherto unrecorded taxa, dating back to c.46,000 years BP was characterized. The method is a novel, cost-effective use for unidentifiable bone fragments and a powerful molecular tool for surveying fossils that otherwise end up on the taxonomic "scrapheap".}, }
@article {pmid24266987, year = {2014}, author = {Heintzman, PD and Elias, SA and Moore, K and Paszkiewicz, K and Barnes, I}, title = {Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera).}, journal = {Molecular ecology resources}, volume = {14}, number = {3}, pages = {606-615}, doi = {10.1111/1755-0998.12205}, pmid = {24266987}, issn = {1755-0998}, mesh = {Animals ; Coleoptera/classification/*genetics ; DNA/*genetics ; DNA Contamination ; DNA, Mitochondrial/genetics ; Molecular Sequence Data ; Museums ; Phylogeny ; Preservation, Biological ; Sequence Analysis, DNA ; }, abstract = {DNA preserved in degraded beetle (Coleoptera) specimens, including those derived from dry-stored museum and ancient permafrost-preserved environments, could provide a valuable resource for researchers interested in species and population histories over timescales from decades to millenia. However, the potential of these samples as genetic resources is currently unassessed. Here, using Sanger and Illumina shotgun sequence data, we explored DNA preservation in specimens of the ground beetle Amara alpina, from both museum and ancient environments. Nearly all museum specimens had amplifiable DNA, with the maximum amplifiable fragment length decreasing with age. Amplification of DNA was only possible in 45% of ancient specimens. Preserved mitochondrial DNA fragments were significantly longer than those of nuclear DNA in both museum and ancient specimens. Metagenomic characterization of extracted DNA demonstrated that parasite-derived sequences, including Wolbachia and Spiroplasma, are recoverable from museum beetle specimens. Ancient DNA extracts contained beetle DNA in amounts comparable to museum specimens. Overall, our data demonstrate that there is great potential for both museum and ancient specimens of beetles in future genetic studies, and we see no reason why this would not be the case for other orders of insect.}, }
@article {pmid24248361, year = {2013}, author = {Overballe-Petersen, S and Harms, K and Orlando, LA and Mayar, JV and Rasmussen, S and Dahl, TW and Rosing, MT and Poole, AM and Sicheritz-Ponten, T and Brunak, S and Inselmann, S and de Vries, J and Wackernagel, W and Pybus, OG and Nielsen, R and Johnsen, PJ and Nielsen, KM and Willerslev, E}, title = {Bacterial natural transformation by highly fragmented and damaged DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {49}, pages = {19860-19865}, pmid = {24248361}, issn = {1091-6490}, mesh = {Acinetobacter/*genetics ; Animals ; Base Sequence ; DNA/genetics/*metabolism ; DNA Damage/*genetics ; DNA Primers/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Mammoths/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; Transformation, Bacterial/*genetics ; }, abstract = {DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often <100 bp) and may persist in the environment for more than half a million years. Fragmented DNA is recognized as nutrient source for microbes, but not as potential substrate for bacterial evolution. Here, we show that fragmented DNA molecules (≥ 20 bp) that additionally may contain abasic sites, cross-links, or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake of DNA from a 43,000-y-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations generated by uptake of short DNA fragments escape mismatch repair. Moreover, double-nucleotide polymorphisms appear more common among genomes of transformable than nontransformable bacteria. Our findings reveal that short and damaged, including truly ancient, DNA molecules, which are present in large quantities in the environment, can be acquired by bacteria through natural transformation. Our findings open for the possibility that natural genetic exchange can occur with DNA up to several hundreds of thousands years old.}, }
@article {pmid24243191, year = {2014}, author = {Mutou, C and Tanaka, K and Ishikawa, R}, title = {DNA extraction from rice endosperm (including a protocol for extraction of DNA from ancient seed samples).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1099}, number = {}, pages = {7-15}, doi = {10.1007/978-1-62703-715-0_2}, pmid = {24243191}, issn = {1940-6029}, mesh = {Chemical Fractionation/methods ; DNA, Plant/chemistry/*isolation &amp; purification ; Endosperm/*chemistry/genetics ; Oryza/*chemistry/genetics ; Seeds/*chemistry/genetics ; }, abstract = {Deoxyribonucleic acid (DNA) extracted from endosperm can be effectively used for rapid genotyping using seed tissue, to evaluate seed quality from packaged grains and to determine the purity of milled grains. Methods outlined here are optimal procedures to isolate DNA from endosperm tissue of modern rice grains and of aged rice remains preserved between 50 and 100 years. The extracted DNA can be used to amplify regions of chloroplast genomic DNA (ctDNA), mitochondrial genomic DNA (mtDNA), and nuclear genomic DNA using standard PCR protocols. In addition, we describe an optimal procedure to process archaeological grain specimens, aged for a couple of thousand years, to isolate DNA from these ancient samples, referred to here as ancient DNA (aDNA). The aDNA can be successfully amplified by PCR using appropriate primer pairs designed specifically for aDNA amplification.}, }
@article {pmid24233697, year = {2013}, author = {Pennisi, E}, title = {Ancient DNA. Old dogs teach a new lesson about canine origins.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6160}, pages = {785-786}, doi = {10.1126/science.342.6160.785}, pmid = {24233697}, issn = {1095-9203}, mesh = {Animals ; Animals, Domestic/*genetics ; Dogs/*genetics ; Genome, Mitochondrial/*genetics ; }, }
@article {pmid24226751, year = {2014}, author = {Müller, R and Roberts, CA and Brown, TA}, title = {Biomolecular identification of ancient Mycobacterium tuberculosis complex DNA in human remains from Britain and continental Europe.}, journal = {American journal of physical anthropology}, volume = {153}, number = {2}, pages = {178-189}, doi = {10.1002/ajpa.22417}, pmid = {24226751}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Bone and Bones/microbiology ; DNA, Bacterial/*isolation &amp; purification ; Europe ; Female ; Forensic Anthropology ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, Ancient ; History, Medieval ; Humans ; Male ; Middle Aged ; Mycobacterium tuberculosis/*genetics/*isolation &amp; purification ; Tuberculosis/*history/microbiology ; United Kingdom ; Young Adult ; }, abstract = {Tuberculosis is known to have afflicted humans throughout history and re-emerged towards the end of the 20th century, to an extent that it was declared a global emergency in 1993. The aim of this study was to apply a rigorous analytical regime to the detection of Mycobacterium tuberculosis complex (MTBC) DNA in 77 bone and tooth samples from 70 individuals from Britain and continental Europe, spanning the 1st-19th centuries AD. We performed the work in dedicated ancient DNA facilities designed to prevent all types of modern contamination, we checked the authenticity of all products obtained by the polymerase chain reaction, and we based our conclusions on up to four replicate experiments for each sample, some carried out in an independent laboratory. We identified 12 samples that, according to our strict criteria, gave definite evidence for the presence of MTBC DNA, and another 22 that we classified as "probable" or "possible." None of the definite samples came from vertebrae displaying lesions associated with TB. Instead, eight were from ribs displaying visceral new bone formation, one was a tooth from a skeleton with rib lesions, one was taken from a skeleton with endocranial lesions, one from an individual with lesions to the sacrum and sacroiliac joint and the last was from an individual with no lesions indicative of TB or possible TB. Our results add to information on the past temporal and geographical distribution of TB and affirm the suitability of ribs for studying ancient TB.}, }
@article {pmid24205269, year = {2013}, author = {Seguin-Orlando, A and Schubert, M and Clary, J and Stagegaard, J and Alberdi, MT and Prado, JL and Prieto, A and Willerslev, E and Orlando, L}, title = {Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e78575}, pmid = {24205269}, issn = {1932-6203}, mesh = {Artifacts ; DNA Damage ; DNA, Bacterial/genetics ; *Gene Library ; *Genomics ; High-Throughput Nucleotide Sequencing/*methods ; }, abstract = {Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.}, }
@article {pmid24205173, year = {2013}, author = {Masson, M and Molnár, E and Donoghue, HD and Besra, GS and Minnikin, DE and Wu, HH and Lee, OY and Bull, ID and Pálfi, G}, title = {Osteological and biomolecular evidence of a 7000-year-old case of hypertrophic pulmonary osteopathy secondary to tuberculosis from neolithic hungary.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e78252}, pmid = {24205173}, issn = {1932-6203}, mesh = {Biomarkers/*metabolism ; DNA, Bacterial/genetics ; Humans ; Hungary ; Hypertrophy/genetics/*metabolism/microbiology/*pathology ; Male ; Mycobacterium tuberculosis/genetics ; Osteology/methods ; Paleopathology/methods ; Ribs/microbiology/pathology ; Spine/microbiology/pathology ; Tuberculosis/genetics/metabolism/microbiology/*pathology ; }, abstract = {Seventy-one individuals from the late Neolithic population of the 7000-year-old site of Hódmezővásárhely-Gorzsa were examined for their skeletal palaeopathology. This revealed numerous cases of infections and non-specific stress indicators in juveniles and adults, metabolic diseases in juveniles, and evidence of trauma and mechanical changes in adults. Several cases showed potential signs of tuberculosis, particularly the remains of the individual HGO-53. This is an important finding that has significant implications for our understanding of this community. The aim of the present study was to seek biomolecular evidence to confirm this diagnosis. HGO-53 was a young male with a striking case of hypertrophic pulmonary osteopathy (HPO), revealing rib changes and cavitations in the vertebral bodies. The initial macroscopic diagnosis of HPO secondary to tuberculosis was confirmed by analysis of Mycobacterium tuberculosis complex specific cell wall lipid biomarkers and corroborated by ancient DNA (aDNA) analysis. This case is the earliest known classical case of HPO on an adult human skeleton and is one of the oldest palaeopathological and palaeomicrobiological tuberculosis cases to date.}, }
@article {pmid24187523, year = {2013}, author = {Del Gaudio, S and Cirillo, A and Di Bernardo, G and Galderisi, U and Thanassoulas, T and Pitsios, T and Cipollaro, M}, title = {Preamplification procedure for the analysis of ancient DNA samples.}, journal = {TheScientificWorldJournal}, volume = {2013}, number = {}, pages = {734676}, pmid = {24187523}, issn = {1537-744X}, mesh = {Anthropology, Physical/*methods ; Base Sequence ; DNA/*genetics ; DNA Fingerprinting/*methods ; Forensic Genetics/*methods ; Greece ; Molecular Sequence Data ; Real-Time Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/methods ; Specimen Handling/*methods ; }, abstract = {In ancient DNA studies the low amount of endogenous DNA represents a limiting factor that often hampers the result achievement. In this study we extracted the DNA from nine human skeletal remains of different ages found in the Byzantine cemetery of Abdera Halkidiki and in the medieval cemetery of St. Spiridion in Rhodes (Greece). Real-time quantitative polymerase chain reaction (qPCR) was used to detect in the extracts the presence of PCR inhibitors and to estimate the DNA content. As mitochondrial DNA was detected in all samples, amplification of nuclear targets, as amelogenin and the polymorphism M470V of the transmembrane conductance regulator gene, yielded positive results in one case only. In an effort to improve amplification success, we applied, for the first time in ancient DNA, a preamplification strategy based on TaqMan PreAmp Master Mix. A comparison between results obtained from nonpreamplified and preamplified samples is reported. Our data, even if preliminary, show that the TaqMan PreAmp procedure may improve the sensitivity of qPCR analysis.}, }
@article {pmid24186332, year = {2013}, author = {Meiri, M and Huchon, D and Bar-Oz, G and Boaretto, E and Horwitz, LK and Maeir, AM and Sapir-Hen, L and Larson, G and Weiner, S and Finkelstein, I}, title = {Ancient DNA and population turnover in southern levantine pigs--signature of the sea peoples migration?.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {3035}, pmid = {24186332}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; *DNA ; DNA, Mitochondrial/genetics ; *Genetics, Population ; Geography ; Haplotypes ; *Human Migration ; Humans ; Israel ; Phylogeny ; Sus scrofa/*classification/*genetics ; }, abstract = {Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have the DNA sequences of European wild boars and domestic pigs. To understand how this anomaly evolved, we sequenced DNA from ancient and modern pigs from Israel. Pigs from Late Bronze Age (until ca. 1150 BCE) in Israel shared haplotypes of modern and ancient Near Eastern pigs. European haplotypes became dominant only during the Iron Age (ca. 900 BCE). This raises the possibility that European pigs were brought to the region by the Sea Peoples who migrated to the Levant at that time. Then, a complete genetic turnover took place, most likely because of repeated admixture between local and introduced European domestic pigs that went feral. Severe population bottlenecks likely accelerated this process. Introductions by humans have strongly affected the phylogeography of wild animals, and interpretations of phylogeography based on modern DNA alone should be taken with caution.}, }
@article {pmid24179194, year = {2013}, author = {Kaiser, J}, title = {Genetics. RNA helps resurrect ancient DNA.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6158}, pages = {543}, doi = {10.1126/science.342.6158.543}, pmid = {24179194}, issn = {1095-9203}, mesh = {Animals ; DNA/chemistry/*genetics/history ; *Genetic Code ; Genome, Human/*genetics ; History, Ancient ; Humans ; Mummies ; Peru ; RNA/chemical synthesis/*chemistry/genetics ; RNA Probes/chemical synthesis/*chemistry/genetics ; Sequence Analysis, DNA/*methods ; }, }
@article {pmid24167615, year = {2013}, author = {Bellone, RR and Holl, H and Setaluri, V and Devi, S and Maddodi, N and Archer, S and Sandmeyer, L and Ludwig, A and Foerster, D and Pruvost, M and Reissmann, M and Bortfeldt, R and Adelson, DL and Lim, SL and Nelson, J and Haase, B and Engensteiner, M and Leeb, T and Forsyth, G and Mienaltowski, MJ and Mahadevan, P and Hofreiter, M and Paijmans, JL and Gonzalez-Fortes, G and Grahn, B and Brooks, SA}, title = {Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e78280}, pmid = {24167615}, issn = {1932-6203}, support = {P30 CA014520/CA/NCI NIH HHS/United States ; R01 AR056087/AR/NIAMS NIH HHS/United States ; AR AR056087/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Female ; Horse Diseases/*genetics ; Horses ; Male ; *Mutagenesis, Insertional ; Night Blindness/*genetics/metabolism/*veterinary ; Retroelements ; Retroviridae/*genetics ; Skin Pigmentation/*genetics ; TRPM Cation Channels/*genetics/metabolism ; }, abstract = {Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ(2)=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ(2)=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.}, }
@article {pmid24164652, year = {2013}, author = {Pont, C and Murat, F and Guizard, S and Flores, R and Foucrier, S and Bidet, Y and Quraishi, UM and Alaux, M and Doležel, J and Fahima, T and Budak, H and Keller, B and Salvi, S and Maccaferri, M and Steinbach, D and Feuillet, C and Quesneville, H and Salse, J}, title = {Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {76}, number = {6}, pages = {1030-1044}, doi = {10.1111/tpj.12366}, pmid = {24164652}, issn = {1365-313X}, mesh = {Chromosomes, Plant/*genetics ; Conserved Sequence ; DNA, Plant/chemistry/genetics ; *Evolution, Molecular ; Genes, Dominant ; Genetic Markers ; Genome, Plant/*genetics ; *Genomics ; Models, Biological ; Polymorphism, Single Nucleotide ; Polyploidy ; Sequence Analysis, DNA ; Synteny/*genetics ; Triticum/*genetics ; }, abstract = {Bread wheat derives from a grass ancestor structured in seven protochromosomes followed by a paleotetraploidization to reach a 12 chromosomes intermediate and a neohexaploidization (involving subgenomes A, B and D) event that finally shaped the 21 modern chromosomes. Insights into wheat syntenome in sequencing conserved orthologous set (COS) genes unravelled differences in genomic structure (such as gene conservation and diversity) and genetical landscape (such as recombination pattern) between ancestral as well as recent duplicated blocks. Contrasted evolutionary plasticity is observed where the B subgenome appears more sensitive (i.e. plastic) in contrast to A as dominant (i.e. stable) in response to the neotetraploidization and D subgenome as supra-dominant (i.e. pivotal) in response to the neohexaploidization event. Finally, the wheat syntenome, delivered through a public web interface PlantSyntenyViewer at http://urgi.versailles.inra.fr/synteny-wheat, can be considered as a guide for accelerated dissection of major agronomical traits in wheat.}, }
@article {pmid24159019, year = {2013}, author = {Balter, M}, title = {Genomes. Ancient DNA links Native Americans with Europe.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6157}, pages = {409-410}, doi = {10.1126/science.342.6157.409}, pmid = {24159019}, issn = {1095-9203}, mesh = {Child, Preschool ; DNA/*genetics ; Genome, Human/*genetics ; Haplotypes ; Humans ; Indians, North American/*genetics ; Male ; Siberia/ethnology ; White People/*genetics ; }, }
@article {pmid24115443, year = {2013}, author = {Brandt, G and Haak, W and Adler, CJ and Roth, C and Szécsényi-Nagy, A and Karimnia, S and Möller-Rieker, S and Meller, H and Ganslmeier, R and Friederich, S and Dresely, V and Nicklisch, N and Pickrell, JK and Sirocko, F and Reich, D and Cooper, A and Alt, KW and , }, title = {Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6155}, pages = {257-261}, pmid = {24115443}, issn = {1095-9203}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Agriculture/history ; Base Sequence ; DNA, Mitochondrial/*genetics/history ; Europe ; *Genetic Drift ; *Genetic Variation ; History, Ancient ; Humans ; Molecular Sequence Data ; Population/*genetics ; Transients and Migrants ; }, abstract = {The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.}, }
@article {pmid24115417, year = {2013}, author = {Balter, M}, title = {Ancient DNA. Farming's tangled European roots.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6155}, pages = {181-182}, doi = {10.1126/science.342.6155.181}, pmid = {24115417}, issn = {1095-9203}, mesh = {Agriculture/*history/trends ; DNA, Mitochondrial/genetics/*history ; Europe ; History, Ancient ; Humans ; Middle East ; Paleontology ; Skeleton ; }, }
@article {pmid24098367, year = {2013}, author = {Ollivier, M and Tresset, A and Hitte, C and Petit, C and Hughes, S and Gillet, B and Duffraisse, M and Pionnier-Capitan, M and Lagoutte, L and Arbogast, RM and Balasescu, A and Boroneant, A and Mashkour, M and Vigne, JD and Hänni, C}, title = {Evidence of coat color variation sheds new light on ancient canids.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e75110}, pmid = {24098367}, issn = {1932-6203}, mesh = {Alleles ; Animals ; DNA, Mitochondrial/genetics ; Dogs/*anatomy &amp; histology/*genetics ; Hair Color/*genetics ; Molecular Sequence Data ; Mutation ; Wolves/*anatomy &amp; histology/*genetics ; }, abstract = {We have used a paleogenetics approach to investigate the genetic landscape of coat color variation in ancient Eurasian dog and wolf populations. We amplified DNA fragments of two genes controlling coat color, Mc1r (Melanocortin 1 Receptor) and CBD103 (canine-β-defensin), in respectively 15 and 19 ancient canids (dogs and wolf morphotypes) from 14 different archeological sites, throughout Asia and Europe spanning from ca. 12 000 B.P. (end of Upper Palaeolithic) to ca. 4000 B.P. (Bronze Age). We provide evidence of a new variant (R301C) of the Melanocortin 1 receptor (Mc1r) and highlight the presence of the beta-defensin melanistic mutation (CDB103-K locus) on ancient DNA from dog-and wolf-morphotype specimens. We show that the dominant K(B) allele (CBD103), which causes melanism, and R301C (Mc1r), the variant that may cause light hair color, are present as early as the beginning of the Holocene, over 10,000 years ago. These results underline the genetic diversity of prehistoric dogs. This diversity may have partly stemmed not only from the wolf gene pool captured by domestication but also from mutations very likely linked to the relaxation of natural selection pressure occurring in-line with this process.}, }
@article {pmid24092956, year = {2013}, author = {Michaelsen, A and Pinzari, F and Barbabietola, N and Piñar, G}, title = {Monitoring the effects of different conservation treatments on paper-infecting fungi.}, journal = {International biodeterioration &amp; biodegradation}, volume = {84}, number = {100}, pages = {333-341}, pmid = {24092956}, issn = {0964-8305}, support = {V 194/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Fungi are among the most degradative organisms inducing biodeterioration of paper-based items of cultural heritage. Appropriate conservation measures and restoration treatments to deal with fungal infections include mechanical, chemical, and biological methods, which entail effects on the paper itself and health hazards for humans. Three different conservation treatments, namely freeze-drying, gamma rays, and ethylene oxide fumigation, were compared and monitored to assess their short- (one month, T1) and long-term (one year, T2) effectiveness to inhibit fungal growth. After the inoculation with fungi possessing cellulose hydrolysis ability - Chaetomium globosum, Trichoderma viride, and Cladosporium cladosporioides - as single strains or as a mixture, different quality paper samples were treated and screened for fungal viability by culture-dependent and -independent techniques. Results derived from both strategies were contradictory. Both gamma irradiation and EtO fumigation showed full efficacy as disinfecting agents when evaluated with cultivation techniques. However, when using molecular analyses, the application of gamma rays showed a short-term reduction in DNA recovery and DNA fragmentation; the latter phenomenon was also observed in a minor degree in samples treated with freeze-drying. When RNA was used as an indicator of long-term fungal viability, differences in the RNA recovery from samples treated with freeze-drying or gamma rays could be observed in samples inoculated with the mixed culture. Only the treatment with ethylene oxide proved negative for both DNA and RNA recovery. Therefore, DNA fragmentation after an ethylene oxide treatment can hamper future paleogenetic and archaeological molecular studies on the objects.}, }
@article {pmid24082104, year = {2013}, author = {Wood, JR and Wilmshurst, JM and Richardson, SJ and Rawlence, NJ and Wagstaff, SJ and Worthy, TH and Cooper, A}, title = {Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {42}, pages = {16910-16915}, pmid = {24082104}, issn = {1091-6490}, mesh = {Animals ; Behavior, Animal/physiology ; *Ecosystem ; *Fossils ; Herbivory/*physiology ; New Zealand ; Palaeognathae/*physiology ; }, abstract = {Knowledge of extinct herbivore community structuring is essential for assessing the wider ecological impacts of Quaternary extinctions and determining appropriate taxon substitutes for rewilding. Here, we demonstrate the potential for coprolite studies to progress beyond single-species diet reconstructions to resolving community-level detail. The moa (Aves: Dinornithiformes) of New Zealand are an intensively studied group of nine extinct herbivore species, yet many details of their diets and community structuring remain unresolved. We provide unique insights into these aspects of moa biology through analyses of a multispecies coprolite assemblage from a rock overhang in a montane river valley in southern New Zealand. Using ancient DNA (aDNA), we identified 51 coprolites, which included specimens from four sympatric moa species. Pollen, plant macrofossils, and plant aDNA from the coprolites chronicle the diets and habitat preferences of these large avian herbivores during the 400 y before their extinction (∼1450 AD). We use the coprolite data to develop a paleoecological niche model in which moa species were partitioned based on both habitat (forest and valley-floor herbfield) and dietary preferences, the latter reflecting allometric relationships between body size, digestive efficiency, and nutritional requirements. Broad ecological niches occupied by South Island giant moa (Dinornis robustus) and upland moa (Megalapteryx didinus) may reflect sexual segregation and seasonal variation in habitat use, respectively. Our results show that moa lack extant ecological analogs, and their extinction represents an irreplaceable loss of function from New Zealand's terrestrial ecosystems.}, }
@article {pmid24069445, year = {2013}, author = {Seifert, L and Harbeck, M and Thomas, A and Hoke, N and Zöller, L and Wiechmann, I and Grupe, G and Scholz, HC and Riehm, JM}, title = {Strategy for sensitive and specific detection of Yersinia pestis in skeletons of the black death pandemic.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e75742}, pmid = {24069445}, issn = {1932-6203}, mesh = {Archaeology/methods ; Bacterial Proteins/genetics ; Bone and Bones/*microbiology ; DNA, Bacterial/genetics ; Germany ; Humans ; Plague/*diagnosis/epidemiology ; Plasmids/genetics ; Plasminogen Activators/genetics ; Polymerase Chain Reaction/methods ; Reproducibility of Results ; Sensitivity and Specificity ; Switzerland ; Yersinia pestis/*genetics ; }, abstract = {Yersinia pestis has been identified as the causative agent of the Black Death pandemic in the 14(th) century. However, retrospective diagnostics in human skeletons after more than 600 years are critical. We describe a strategy following a modern diagnostic algorithm and working under strict ancient DNA regime for the identification of medieval human plague victims. An initial screening and DNA quantification assay detected the Y. pestis specific pla gene of the high copy number plasmid pPCP1. Results were confirmed by conventional PCR and sequence analysis targeting both Y. pestis specific virulence plasmids pPCP1 and pMT1. All assays were meticulously validated according to human clinical diagnostics requirements (ISO 15189) regarding efficiency, sensitivity, specificity, and limit of detection (LOD). Assay specificity was 100% tested on 41 clinically relevant bacteria and 29 Y. pseudotuberculosis strains as well as for DNA of 22 Y. pestis strains and 30 previously confirmed clinical human plague samples. The optimized LOD was down to 4 gene copies. 29 individuals from three different multiple inhumations were initially assessed as possible victims of the Black Death pandemic. 7 samples (24%) were positive in the pPCP1 specific screening assay. Confirmation through second target pMT1 specific PCR was successful for 4 of the positive individuals (14%). A maximum of 700 and 560 copies per µl aDNA were quantified in two of the samples. Those were positive in all assays including all repetitions, and are candidates for future continuative investigations such as whole genome sequencing. We discuss that all precautions taken here for the work with aDNA are sufficient to prevent external sample contamination and fulfill the criteria of authenticity. With regard to retrospective diagnostics of a human pathogen and the uniqueness of ancient material we strongly recommend using a careful strategy and validated assays as presented in our study.}, }
@article {pmid24068852, year = {2012}, author = {Edwards, CJ and Soulsbury, CD and Statham, MJ and Ho, SY and Wall, D and Dolf, G and Iossa, G and Baker, PJ and Harris, S and Sacks, BN and Bradley, DG}, title = {Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles.}, journal = {Quaternary science reviews}, volume = {57}, number = {100}, pages = {95-104}, pmid = {24068852}, issn = {0277-3791}, support = {//Wellcome Trust/United Kingdom ; }, abstract = {Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.}, }
@article {pmid24068034, year = {2013}, author = {Rajaraman, A and Tannier, E and Chauve, C}, title = {FPSAC: fast phylogenetic scaffolding of ancient contigs.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {23}, pages = {2987-2994}, doi = {10.1093/bioinformatics/btt527}, pmid = {24068034}, issn = {1367-4811}, mesh = {Computer Simulation ; *Contig Mapping ; Evolution, Molecular ; *Genome, Bacterial ; *Phylogeny ; Plague/microbiology ; Sequence Analysis, DNA/*methods ; *Software ; Yersinia pestis/classification/*genetics ; }, abstract = {MOTIVATIONS: Recent progress in ancient DNA sequencing technologies and protocols has lead to the sequencing of whole ancient bacterial genomes, as illustrated by the recent sequence of the Yersinia pestis strain that caused the Black Death pandemic. However, sequencing ancient genomes raises specific problems, because of the decay and fragmentation of ancient DNA among others, making the scaffolding of ancient contigs challenging.<br><br>RESULTS: We show that computational paleogenomics methods aimed at reconstructing the organization of ancestral genomes from the comparison of extant genomes can be adapted to correct, order and orient ancient bacterial contigs. We describe the method FPSAC (fast phylogenetic scaffolding of ancient contigs) and apply it on a set of 2134 ancient contigs assembled from the recently sequenced Black Death agent genome. We obtain a unique scaffold for the whole chromosome of this ancient genome that allows to gain precise insights into the structural evolution of the Yersinia clade.}, }
@article {pmid24045113, year = {2013}, author = {Crespo, B and Lan-Chow-Wing, O and Rocha, A and Zanuy, S and Gómez, A}, title = {foxl2 and foxl3 are two ancient paralogs that remain fully functional in teleosts.}, journal = {General and comparative endocrinology}, volume = {194}, number = {}, pages = {81-93}, doi = {10.1016/j.ygcen.2013.08.016}, pmid = {24045113}, issn = {1095-6840}, mesh = {3' Untranslated Regions/genetics ; 5' Untranslated Regions/genetics ; Amino Acid Sequence ; Animals ; Bass/*genetics/*metabolism ; DNA, Complementary/genetics ; Female ; Fish Proteins/chemistry/*genetics/*metabolism ; Male ; Molecular Sequence Data ; Real-Time Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; }, abstract = {FOXL2 is a forkhead transcription factor involved in mammalian development and regulation of reproduction. Two foxl2 paralogs, foxl2a and foxl2b, have been described in various teleost species and were considered as fish-specific duplicates. Here, we report the isolation and characterization of foxl2a (foxl2) and foxl2b (foxl3) in European sea bass (Dicentrarchus labrax), together with the identification of these two genes in non-teleost genomes. Phylogenetic and synteny analyses indicate that these paralogs originated from an ancient genome duplication event that happened long before the teleost specific duplication. While foxl2/foxl2a has been maintained in most vertebrate lineages, foxl2b, which we propose to rename as foxl3, was repeatedly lost in tetrapods. Gonadal expression patterns of the sea bass genes point to a strong sexual dimorphism, and the mRNA levels of foxl2 in ovary and foxl3 in testis vary significantly during the reproductive cycle. When overexpressed in cultured ovarian follicular cells, foxl2 and foxl3 produced functional transcription factors able to control the expression of reproduction-related genes. Taken together, these data suggest that Foxl2 may play a conserved role in ovarian maturation, while Foxl3 could be involved in testis physiology.}, }
@article {pmid24040024, year = {2013}, author = {Witas, HW and Tomczyk, J and Jędrychowska-Dańska, K and Chaubey, G and Płoszaj, T}, title = {mtDNA from the early Bronze Age to the Roman period suggests a genetic link between the Indian subcontinent and Mesopotamian cradle of civilization.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e73682}, pmid = {24040024}, issn = {1932-6203}, mesh = {Archaeology ; Base Sequence ; *Civilization ; DNA, Mitochondrial/chemistry/classification/*genetics ; Emigration and Immigration ; Female ; Fossils ; Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes/*genetics ; Humans ; India ; Male ; Mesopotamia ; Pakistan ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Syria ; Tibet ; Time Factors ; Tooth/metabolism ; }, abstract = {Ancient DNA methodology was applied to analyse sequences extracted from freshly unearthed remains (teeth) of 4 individuals deeply deposited in slightly alkaline soil of the Tell Ashara (ancient Terqa) and Tell Masaikh (ancient Kar-Assurnasirpal) Syrian archaeological sites, both in the middle Euphrates valley. Dated to the period between 2.5 Kyrs BC and 0.5 Kyrs AD the studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Paleolithic and are absent in people living today in Syria. However, they are present in people inhabiting today's Tibet, Himalayas, India and Pakistan. We anticipate that the analysed remains from Mesopotamia belonged to people with genetic affinity to the Indian subcontinent since the distribution of identified ancient haplotypes indicates solid link with populations from the region of South Asia-Tibet (Trans-Himalaya). They may have been descendants of migrants from much earlier times, spreading the clades of the macrohaplogroup M throughout Eurasia and founding regional Mesopotamian groups like that of Terqa or just merchants moving along trade routes passing near or through the region. None of the successfully identified nuclear alleles turned out to be ΔF508 CFTR, LCT-13910T or Δ32 CCR5.}, }
@article {pmid24039876, year = {2013}, author = {Penney, D and Wadsworth, C and Fox, G and Kennedy, SL and Preziosi, RF and Brown, TA}, title = {Absence of ancient DNA in sub-fossil insect inclusions preserved in 'Anthropocene' Colombian copal.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e73150}, pmid = {24039876}, issn = {1932-6203}, mesh = {Amber/chemistry ; Animals ; Bees/genetics ; Biological Evolution ; *DNA ; Extinction, Biological ; *Fossils ; Insecta/*genetics ; Sequence Analysis, DNA ; }, abstract = {Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae) preserved in 'Anthropocene' Colombian copal, dated to 'post-Bomb' and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal.}, }
@article {pmid24035510, year = {2013}, author = {Haas, C and Shved, N and Rühli, FJ and Papageorgopoulou, C and Purps, J and Geppert, M and Willuweit, S and Roewer, L and Krawczak, M}, title = {Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jörg Jenatsch (1596-1639).}, journal = {Forensic science international. Genetics}, volume = {7}, number = {6}, pages = {610-617}, doi = {10.1016/j.fsigen.2013.08.006}, pmid = {24035510}, issn = {1878-0326}, mesh = {Base Sequence ; *Chromosomes, Human, Y ; DNA Primers ; *Forensic Anthropology ; History, 16th Century ; History, 17th Century ; Humans ; Male ; Pedigree ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Switzerland ; }, abstract = {Jörg Jenatsch was a Swiss defender of independence and a fighter for liberty in the 17th century. With the help of three living male members of the Jenatsch family, we successfully identified a skeleton exhumed from Chur cathedral as the remains of Jörg Jenatsch. Our conclusion was based upon complete Y-STR and Y-SNP profiles that could be generated by replicate analyses of a bone sample available to us. The skeleton and the three living family members carried the same Y-SNP haplogroup, but were discordant at three of 23 Y-STR loci. This notwithstanding, conservative biostatistical evaluation of the data suggests that the Chur skeleton is at least 20 times more likely than not to be Jörg Jenatsch.}, }
@article {pmid24026825, year = {2013}, author = {Palkopoulou, E and Dalén, L and Lister, AM and Vartanyan, S and Sablin, M and Sher, A and Edmark, VN and Brandström, MD and Germonpré, M and Barnes, I and Thomas, JA}, title = {Holarctic genetic structure and range dynamics in the woolly mammoth.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1770}, pages = {20131910}, pmid = {24026825}, issn = {1471-2954}, mesh = {*Animal Distribution ; Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Europe ; Evolution, Molecular ; Extinction, Biological ; Fossils ; *Genetic Variation ; Haplotypes ; Mammoths/genetics/metabolism/*physiology ; Molecular Sequence Data ; North America ; Phylogeny ; Polymerase Chain Reaction ; Population Dynamics ; Sequence Analysis, DNA ; Siberia ; }, abstract = {Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32-34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20-15 kyr BP, when a severe population size decline occurred.}, }
@article {pmid24024911, year = {2014}, author = {Wilmshurst, JM and Moar, NT and Wood, JR and Bellingham, PJ and Findlater, AM and Robinson, JJ and Stone, C}, title = {Use of pollen and ancient DNA as conservation baselines for offshore islands in New Zealand.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {28}, number = {1}, pages = {202-212}, doi = {10.1111/cobi.12150}, pmid = {24024911}, issn = {1523-1739}, mesh = {*Biodiversity ; Conservation of Natural Resources/*methods ; DNA, Plant/*analysis ; Ecosystem ; Human Activities ; Humans ; Islands ; Mass Spectrometry ; New Zealand ; Pollen/*chemistry ; Polymerase Chain Reaction ; Soil/chemistry ; }, abstract = {Islands play a key role globally in the conservation of endemic species. Many island reserves have been highly modified since human colonization, and their restoration and management usually occur without knowledge of their prehuman state. However, conservation paleoecology is increasingly being recognized as a tool that can help to inform both restoration and conservation of island reserves by providing prehuman vegetation baselines. Many of New Zealand's mammal-free offshore islands are foci for biological diversity conservation and, like many islands in the Polynesian region, were deforested following initial human settlement. Therefore, their current restoration, replanting, and management are guided either by historic vegetation descriptions or the occurrence of species on forested islands. We analyzed pollen and ancient DNA in soil cores from an offshore island in northern New Zealand. The result was a 2000-year record of vegetation change that began >1200 years before human settlement and spanned 550 years of human occupation and 180 years of forest succession since human occupation ceased. Between prehuman and contemporary forests there was nearly a complete species turnover including the extirpation of a dominant conifer and a palm tree. The podocarp-dominated forests were replaced by a native but novel angiosperm-dominated forest. There is no modern analog of the prehuman forests on any northern New Zealand island, and those islands that are forested are dominated by angiosperms which are assumed to be climax forests. The pollen and DNA evidence for conifer- and palm-rich forests in the prehuman era challenge this climax forest assumption. Prehuman vegetation records can thus help to inform future restoration of degraded offshore islands by informing the likely rate and direction of successional change; helping to determine whether natural rates of succession are preferable to more costly replanting programs; and providing past species lists if restoration replanting is desired.}, }
@article {pmid24019490, year = {2013}, author = {Dabney, J and Knapp, M and Glocke, I and Gansauge, MT and Weihmann, A and Nickel, B and Valdiosera, C and García, N and Pääbo, S and Arsuaga, JL and Meyer, M}, title = {Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {39}, pages = {15758-15763}, pmid = {24019490}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; Caves ; DNA/*genetics/isolation &amp; purification ; Genome, Mitochondrial/*genetics ; Molecular Sequence Data ; Phylogeny ; Time Factors ; Ursidae/*genetics ; }, abstract = {Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp.}, }
@article {pmid24018114, year = {2013}, author = {Gabillard, JC and Biga, PR and Rescan, PY and Seiliez, I}, title = {Revisiting the paradigm of myostatin in vertebrates: insights from fishes.}, journal = {General and comparative endocrinology}, volume = {194}, number = {}, pages = {45-54}, doi = {10.1016/j.ygcen.2013.08.012}, pmid = {24018114}, issn = {1095-6840}, mesh = {Animals ; Fishes/growth &amp; development/*metabolism ; Myostatin/genetics/*metabolism ; Vertebrates/growth &amp; development/*metabolism ; }, abstract = {In the last decade, myostatin (MSTN), a member of the TGFβ superfamily, has emerged as a strong inhibitor of muscle growth in mammals. In fish many studies reveal a strong conservation of mstn gene organization, sequence, and protein structures. Because of ancient genome duplication, teleostei may have retained two copies of mstn genes and even up to four copies in salmonids due to additional genome duplication event. In sharp contrast to mammals, the different fish mstn orthologs are widely expressed with a tissue-specific expression pattern. Quantification of mstn mRNA in fish under different physiological conditions, demonstrates that endogenous expression of mstn paralogs is rarely related to fish muscle growth rate. In addition, attempts to inhibit MSTN activity did not consistently enhance muscle growth as in mammals. In vitro, MSTN stimulates myotube atrophy and inhibits proliferation but not differentiation of myogenic cells as in mammals. In conclusion, given the strong mstn expression non-muscle tissues of fish, we propose a new hypothesis stating that fish MSTN functions as a general inhibitors of cell proliferation and cell growth to control tissue mass but is not specialized into a strong muscle regulator.}, }
@article {pmid24002647, year = {2013}, author = {Zhao, L and Lascoux, M and Overall, AD and Waxman, D}, title = {The characteristic trajectory of a fixing allele: a consequence of fictitious selection that arises from conditioning.}, journal = {Genetics}, volume = {195}, number = {3}, pages = {993-1006}, pmid = {24002647}, issn = {1943-2631}, mesh = {*Alleles ; Animals ; Gene Frequency ; Genetic Drift ; *Genetics, Population ; Humans ; *Models, Genetic ; Mutation ; Population Density ; *Selection, Genetic ; }, abstract = {This work is concerned with the historical progression, to fixation, of an allele in a finite population. This progression is characterized by the average frequency trajectory of alleles that achieve fixation before a given time, T. Under a diffusion analysis, the average trajectory, conditional on fixation by time T, is shown to be equivalent to the average trajectory in an unconditioned problem involving additional selection. We call this additional selection "fictitious selection"; it plays the role of a selective force in the unconditioned problem but does not exist in reality. It is a consequence of conditioning on fixation. The fictitious selection is frequency dependent and can be very large compared with any real selection that is acting. We derive an approximation for the characteristic trajectory of a fixing allele, when subject to real additive selection, from an unconditioned problem, where the total selection is a combination of real and fictitious selection. Trying to reproduce the characteristic trajectory from the action of additive selection, in an infinite population, can lead to estimates of the strength of the selection that deviate from the real selection by >1000% or have the opposite sign. Strong evolutionary forces may be invoked in problems where conditioning has been carried out, but these forces may largely be an outcome of the conditioning and hence may not have a real existence. The work presented here clarifies these issues and provides two useful tools for future analyses: the characteristic trajectory of a fixing allele and the force that primarily drives this, namely fictitious selection. These should prove useful in a number of areas of interest including coalescence with selection, experimental evolution, time series analyses of ancient DNA, game theory in finite populations, and the historical dynamics of selected alleles in wild populations.}, }
@article {pmid23994164, year = {2014}, author = {Mitchell, KJ and Wood, JR and Scofield, RP and Llamas, B and Cooper, A}, title = {Ancient mitochondrial genome reveals unsuspected taxonomic affinity of the extinct Chatham duck (Pachyanas chathamica) and resolves divergence times for New Zealand and sub-Antarctic brown teals.}, journal = {Molecular phylogenetics and evolution}, volume = {70}, number = {}, pages = {420-428}, doi = {10.1016/j.ympev.2013.08.017}, pmid = {23994164}, issn = {1095-9513}, mesh = {Animals ; Antarctic Regions ; DNA, Mitochondrial/genetics ; Ducks/classification/*genetics ; Female ; Fossils ; *Genome, Mitochondrial ; Humans ; Islands ; New Zealand ; *Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {The Chatham duck (Pachyanas chathamica) represented one of just three modern bird genera endemic to the Chatham archipelago (situated ~850 km east of New Zealand) but became extinct soon after humans first settled the islands (c. 13th-15th centuries AD). The taxonomic affinity of the Chatham duck remains largely unresolved; previous studies have tentatively suggested placements within both Tadornini (shelducks) and Anatini (dabbling ducks). Herein, we sequence a partial mitochondrial genome (excluding the D-loop) from the Chatham duck and discover that it was a phenotypically-divergent species within the genus Anas (Anatini). This conclusion is further supported by a re-examination of osteological characters. Our molecular analyses convincingly demonstrate that the Chatham duck is the most basal member of a sub-clade comprising the New Zealand and sub-Antarctic brown teals (the brown teal [A. chlorotis], Auckland Island teal [A. aucklandica] and Campbell Island teal [A. nesiotis]). Molecular clock calculations based on an ingroup fossil calibration support a divergence between the Chatham duck and its sister-taxa that is consistent with the estimated time of emergence of the Chatham Islands. Additionally, we find that mtDNA divergence between the two sub-Antarctic teal species (A. aucklandica and A. nesiotis) significantly pre-dates the last few glacial cycles, raising interesting questions about the timing of their dispersal to these islands, and the recent phylogeographic history of brown teal lineages in the region.}, }
@article {pmid23986765, year = {2013}, author = {Kim, DH and Parupalli, S and Azam, S and Lee, SH and Varshney, RK}, title = {Comparative sequence analysis of nitrogen fixation-related genes in six legumes.}, journal = {Frontiers in plant science}, volume = {4}, number = {}, pages = {300}, pmid = {23986765}, issn = {1664-462X}, abstract = {Legumes play an important role as food and forage crops in international agriculture especially in developing countries. Legumes have a unique biological process called nitrogen fixation (NF) by which they convert atmospheric nitrogen to ammonia. Although legume genomes have undergone polyploidization, duplication and divergence, NF-related genes, because of their essential functional role for legumes, might have remained conserved. To understand the relationship of divergence and evolutionary processes in legumes, this study analyzes orthologs and paralogs for selected 20 NF-related genes by using comparative genomic approaches in six legumes i.e., Medicago truncatula (Mt), Cicer arietinum, Lotus japonicus, Cajanus cajan (Cc), Phaseolus vulgaris (Pv), and Glycine max (Gm). Subsequently, sequence distances, numbers of synonymous substitutions per synonymous site (Ks) and non-synonymous substitutions per non-synonymous site (Ka) between orthologs and paralogs were calculated and compared across legumes. These analyses suggest the closest relationship between Gm and Cc and the highest distance between Mt and Pv in six legumes. Ks proportional plots clearly showed ancient genome duplication in all legumes, whole genome duplication event in Gm and also speciation pattern in different legumes. This study also reports some interesting observations e.g., no peak at Ks 0.4 in Gm-Gm, location of two independent genes next to each other in Mt and low Ks values for outparalogs for three genes as compared to other 12 genes. In summary, this study underlines the importance of NF-related genes and provides important insights in genome organization and evolutionary aspects of six legume species analyzed.}, }
@article {pmid23983221, year = {2013}, author = {Cheng, S and van den Bergh, E and Zeng, P and Zhong, X and Xu, J and Liu, X and Hofberger, J and de Bruijn, S and Bhide, AS and Kuelahoglu, C and Bian, C and Chen, J and Fan, G and Kaufmann, K and Hall, JC and Becker, A and Bräutigam, A and Weber, AP and Shi, C and Zheng, Z and Li, W and Lv, M and Tao, Y and Wang, J and Zou, H and Quan, Z and Hibberd, JM and Zhang, G and Zhu, XG and Xu, X and Schranz, ME}, title = {The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers.}, journal = {The Plant cell}, volume = {25}, number = {8}, pages = {2813-2830}, pmid = {23983221}, issn = {1532-298X}, mesh = {Brassicaceae/*genetics ; *Evolution, Molecular ; Flowers/genetics/growth &amp; development ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genome, Plant/*genetics ; MADS Domain Proteins/genetics/metabolism ; Molecular Sequence Annotation ; Phylogeny ; Physical Chromosome Mapping ; Polyploidy ; *Quantitative Trait, Heritable ; Reproduction/genetics ; Self-Incompatibility in Flowering Plants/genetics ; Sequence Analysis, DNA ; Synteny/genetics ; Time Factors ; }, abstract = {The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for minichromosome maintenance1, AGAMOUS, DEFICIENS and serum response factor) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical serine receptor kinase receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.}, }
@article {pmid23980394, year = {2013}, author = {Ovchinnikov, IV}, title = {Hominin evolution and gene flow in the Pleistocene Africa.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {70}, number = {2}, pages = {221-227}, doi = {10.1127/0003-5548/2013/0313}, pmid = {23980394}, issn = {0003-5548}, mesh = {Africa ; Animals ; Anthropology, Physical ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fossils ; *Gene Flow ; Genome, Mitochondrial/genetics ; Hominidae/*genetics ; Humans ; Phylogeny ; }, abstract = {Africa demonstrates a complex process of the hominin evolution with a series of adaptive radiations during several millions of years that led to diverse morphological forms. Recently, Hammer et al. (2011) and Harvati et al. (2011) provided integrated morphological and genetic evidence of interbreeding between modern humans and unknown archaic hominins in Africa as recently as 35,000 years ago. However, a genetic evidence of hybridization between hominin lineages during the Lower and Middle Pleistocene epochs is unknown and the direct retrieval of DNA from extinct lineages of African hominins remains elusive. The availability of both nuclear and mitochondrial genome sequences from modern humans, Neanderthals, and Denisovans allows collecting nuclear DNA sequences of mitochondrial origin (numts) inserted into the nuclear genome of the ancestral hominin lineages and drawing conclusions about the hominin evolution in the remote past. The mtDNA and numt analysis uncovered a deep division of mtDNA lineages that existed in African hominins in the Middle Pleistocene. The first cluster included the human and Neanderthal-like mtDNA sequences while the second consisted of DNA sequences that are known today as mtAncestor-1, a nuclear fossil of the mtDNA, and the Denisova mtDNA isolated from a bone and a tooth found in southern Siberia. The two groups initially diverged 610,000-1,110,000 years ago. Approximately 220,000 years after the primary split, the Denisova - mtAncestor-1 mtDNA lineages mixed with the mtDNA pool of an ancestral population of Neanderthals and modern humans. This admixture after the profound division is demonstrated by the transposition of the Denisova-like mtDNA sequence into the nuclear genome of an ancestor of Neanderthals and modern humans. This finding suggests the matrilineal genetic structure among the Middle Pleistocene hominins as well as the existence of gene flow between African hominin lineages. Through paleogenomic analyses, it is impossible to exclude the theory that population structure and gene flow in African hominins influenced the admixture pattern observed in the nuclear genomes of non-Africans.}, }
@article {pmid23971194, year = {2013}, author = {Zeyland, J and Wolko, L and Bocianowski, J and Szalata, M and Słomski, R and Dzieduszycki, AM and Ryba, M and Przystałowska, H and Lipiński, D}, title = {Complete mitochondrial genome of wild aurochs (Bos primigenius) reconstructed from ancient DNA.}, journal = {Polish journal of veterinary sciences}, volume = {16}, number = {2}, pages = {265-273}, doi = {10.2478/pjvs-2013-0037}, pmid = {23971194}, issn = {1505-1773}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Cattle/*genetics ; DNA/*genetics ; Female ; Fossils ; *Genome, Mitochondrial ; Molecular Sequence Data ; Poland ; Polymerase Chain Reaction/methods/veterinary ; }, abstract = {Extinct aurochs (Bos primigenius), accepted as the ancestor of domestic cattle, was one of the largest wild animals inhabiting Europe, Asia and North Africa. The gradual process of aurochs extinction finished in Poland in 1627, were the last recorded aurochs, a female, died. Some aspects of cattle domestication history and the distribution of aurochs genetic material among modern cattle breeds still remain unclear. Analyses of ancient DNA (aDNA) from bone sample deliver new genetic information about extinct wild aurochs as well as modern cattle phylogeny. DNA was extracted from a fragment of aurochs fossil bone found in the Pisz Forest, Poland. The sample was radiocarbon-dated to about 1500 yBP. The aDNA was used for Whole Genome Amplification in order to form a DNA bank. Auroch mitochondrial DNA sequences were amplified using sets of 41 primers overlapping the whole mtDNA, cloned and sequenced. The sequence of the whole mitochondrial genome was reconstructed and deposed in GenBank [GenBank:JQ437479]. Based on the phylogenetic analyses of the Bovine mitochondrial genomes, a phylogenetic tree was created. As expected, the tree clearly shows that the mtDNA sequence of the analyzed PWA (Polish Wild Aurochs) individual belongs to haplogroup P. In the course of the comparative mtDNA analysis we identified 30 nucleotide marker positions for haplogroup P and nine unique PWA differences compared to the two remaining haplotype P representatives. Our analysis provides the next step to the reconstruction of the demographic history of this extinct but still exciting species.}, }
@article {pmid23967453, year = {2013}, author = {Gugerli, F and Alvarez, N and Tinner, W}, title = {A deep dig––hindsight on Holocene vegetation composition from ancient environmental DNA.}, journal = {Molecular ecology}, volume = {22}, number = {13}, pages = {3433-3436}, doi = {10.1111/mec.12356}, pmid = {23967453}, issn = {1365-294X}, mesh = {Geologic Sediments/*analysis ; Lakes/*analysis ; Plants/*genetics ; Pollen/*chemistry ; }, abstract = {Want a glimpse at past vegetation? Studying pollen and other plant remains, which are preserved for example in lake sediments or mires for thousands of years, allows us to document regional occurrences of plant species over radiocarbon-dated time series. Such vegetation reconstructions derived from optical analyses of fossil samples are inherently incomplete because they only comprise taxa that contribute sufficient amounts of pollen, spores, macrofossil or other evidences. To complement optical analyses for paleoecological inference, molecular markers applied to ancient DNA (aDNA) may help in disclosing information hitherto inaccessible to biologists. Parducci et al. (2013) targeted aDNA from sediment cores of two lakes in the Scandes Mountains with generic primers in a meta-barcoding approach. When compared to palynological records from the same cores, respective taxon lists show remarkable differences in their compositions, but also in quantitative representation and in taxonomic resolution similar to a previous study (Jørgensen et al. 2012). While not free of assumptions that need critical and robust testing, notably the question of possible contamination, this study provides thrilling prospects to improve our knowledge about past vegetation composition, but also other organismic groups, stored as a biological treasure in the ground.}, }
@article {pmid23945688, year = {2013}, author = {Foote, AD and Newton, J and Ávila-Arcos, MC and Kampmann, ML and Samaniego, JA and Post, K and Rosing-Asvid, A and Sinding, MH and Gilbert, MT}, title = {Tracking niche variation over millennial timescales in sympatric killer whale lineages.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1768}, pages = {20131481}, pmid = {23945688}, issn = {1471-2954}, mesh = {Animals ; Diet ; Gene Flow ; Genetic Speciation ; Genetic Variation ; Genotype ; Homing Behavior ; Microsatellite Repeats ; *Models, Genetic ; North Sea ; Phylogeny ; Phylogeography ; Population Dynamics ; Predatory Behavior ; Whale, Killer/genetics/*physiology ; }, abstract = {Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue samples of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina. Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-individual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-individual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish.}, }
@article {pmid23927498, year = {2013}, author = {Meiri, M and Lister, AM and Higham, TF and Stewart, JR and Straus, LG and Obermaier, H and González Morales, MR and Marín-Arroyo, AB and Barnes, I}, title = {Late-glacial recolonization and phylogeography of European red deer (Cervus elaphus L.).}, journal = {Molecular ecology}, volume = {22}, number = {18}, pages = {4711-4722}, doi = {10.1111/mec.12420}, pmid = {23927498}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; *Climate Change ; DNA, Mitochondrial/genetics ; Deer/*genetics ; Europe ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Likelihood Functions ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Radiometric Dating ; Sequence Analysis, DNA ; }, abstract = {The Pleistocene was an epoch of extreme climatic and environmental changes. How individual species responded to the repeated cycles of warm and cold stages is a major topic of debate. For the European fauna and flora, an expansion-contraction model has been suggested, whereby temperate species were restricted to southern refugia during glacial times and expanded northwards during interglacials, including the present interglacial (Holocene). Here, we test this model on the red deer (Cervus elaphus) a large and highly mobile herbivore, using both modern and ancient mitochondrial DNA from the entire European range of the species over the last c. 40,000 years. Our results indicate that this species was sensitive to the effects of climate change. Prior to the Last Glacial Maximum (LGM) haplogroups restricted today to South-East Europe and Western Asia reached as far west as the UK. During the LGM, red deer was mainly restricted to southern refugia, in Iberia, the Balkans and possibly in Italy and South-Western Asia. At the end of the LGM, red deer expanded from the Iberian refugium, to Central and Northern Europe, including the UK, Belgium, Scandinavia, Germany, Poland and Belarus. Ancient DNA data cannot rule out refugial survival of red deer in North-West Europe through the LGM. Had such deer survived, though, they were replaced by deer migrating from Iberia at the end of the glacial. The Balkans served as a separate LGM refugium and were probably connected to Western Asia with genetic exchange between the two areas.}, }
@article {pmid23911317, year = {2013}, author = {Narlikar, GJ and Sundaramoorthy, R and Owen-Hughes, T}, title = {Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes.}, journal = {Cell}, volume = {154}, number = {3}, pages = {490-503}, pmid = {23911317}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; 097945/WT_/Wellcome Trust/United Kingdom ; 095062/WT_/Wellcome Trust/United Kingdom ; G1100021/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/*metabolism ; Animals ; *Chromatin Assembly and Disassembly ; DNA/metabolism ; Eukaryota/*metabolism ; Humans ; Nucleosomes/metabolism ; Transferases/metabolism ; }, abstract = {Chromatin provides both a means to accommodate a large amount of genetic material in a small space and a means to package the same genetic material in different chromatin states. Transitions between chromatin states are enabled by chromatin-remodeling ATPases, which catalyze a diverse range of structural transformations. Biochemical evidence over the last two decades suggests that chromatin-remodeling activities may have emerged by adaptation of ancient DNA translocases to respond to specific features of chromatin. Here, we discuss such evidence and also relate mechanistic insights to our understanding of how chromatin-remodeling enzymes enable different in vivo processes.}, }
@article {pmid23900768, year = {2013}, author = {Tassi, F and Ghirotto, S and Caramelli, D and Barbujani, G}, title = {Genetic evidence does not support an Etruscan origin in Anatolia.}, journal = {American journal of physical anthropology}, volume = {152}, number = {1}, pages = {11-18}, doi = {10.1002/ajpa.22319}, pmid = {23900768}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; Emigration and Immigration/*history ; *Genetic Variation ; Genetics, Population ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Italy ; Models, Statistical ; Turkey ; White People/*genetics ; }, abstract = {The debate on the origins of Etruscans, documented in central Italy between the eighth century BC and the first century AD, dates back to antiquity. Herodotus described them as a group of immigrants from Lydia, in Western Anatolia, whereas for Dionysius of Halicarnassus they were an indigenous population. Dionysius' view is shared by most modern archeologists, but the observation of similarities between the (modern) mitochondrial DNAs (mtDNAs) of Turks and Tuscans was interpreted as supporting an Anatolian origin of the Etruscans. However, ancient DNA evidence shows that only some isolates, and not the bulk of the modern Tuscan population, are genetically related to the Etruscans. In this study, we tested alternative models of Etruscan origins by Approximate Bayesian Computation methods, comparing levels of genetic diversity in the mtDNAs of modern and ancient populations with those obtained by millions of computer simulations. The results show that the observed genetic similarities between modern Tuscans and Anatolians cannot be attributed to an immigration wave from the East leading to the onset of the Etruscan culture in Italy. Genetic links between Tuscany and Anatolia do exist, but date back to a remote stage of prehistory, possibly but not necessarily to the spread of farmers during the Neolithic period.}, }
@article {pmid23900195, year = {2013}, author = {Kihana, M and Mizuno, F and Sawafuji, R and Wang, L and Ueda, S}, title = {Emulsion PCR-coupled target enrichment: an effective fishing method for high-throughput sequencing of poorly preserved ancient DNA.}, journal = {Gene}, volume = {528}, number = {2}, pages = {347-351}, doi = {10.1016/j.gene.2013.07.040}, pmid = {23900195}, issn = {1879-0038}, mesh = {DNA Damage ; DNA, Mitochondrial/*genetics ; Emulsions ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Polymerase Chain Reaction/*methods ; Preservation, Biological ; Sequence Analysis, DNA/*methods ; }, abstract = {Due to the difficulties in deep sequencing, high-throughput sequencing of ancient DNA has been limited to exceptionally well-preserved ancient materials. The primary factor is microbial attack popularly observed in the buried materials, and it causes drastic increase in relative ratio of microbial DNA in the extracted DNA. We present a unified strategy in which emulsion PCR is coupled with target enrichment followed by next-generation sequencing. The method made it possible to obtain efficiently non-duplicated reads mapped to target sequences of interest, and this can achieve deep and reliable sequencing of ancient DNA from typical materials, even though poorly preserved.}, }
@article {pmid23894505, year = {2013}, author = {Speller, CF and Burley, DV and Woodward, RP and Yang, DY}, title = {Ancient mtDNA analysis of early 16(th) century Caribbean cattle provides insight into founding populations of New World creole cattle breeds.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e69584}, pmid = {23894505}, issn = {1932-6203}, mesh = {Animals ; Breeding ; Caribbean Region ; Cattle/classification/*genetics ; DNA, Mitochondrial/*genetics ; Haplotypes/genetics ; Phylogeny ; Spain ; }, abstract = {The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15(th) to early 16(th) century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus) breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the 'African' haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16(th) century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of "African-derived American" haplotypes (AA/T1c1a1) in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle.}, }
@article {pmid23890658, year = {2013}, author = {Barta, JL and Monroe, C and Kemp, BM}, title = {Further evaluation of the efficacy of contamination removal from bone surfaces.}, journal = {Forensic science international}, volume = {231}, number = {1-3}, pages = {340-348}, doi = {10.1016/j.forsciint.2013.06.004}, pmid = {23890658}, issn = {1872-6283}, mesh = {Animals ; *DNA Contamination ; DNA, Mitochondrial/*isolation &amp; purification ; *Disinfectants ; Fur Seals/genetics ; Humans ; Real-Time Polymerase Chain Reaction ; Ribs/*chemistry ; *Sodium Hypochlorite ; Specimen Handling ; }, abstract = {Studies of low copy number (LCN) and degraded DNA are prone to contamination from exogenous DNA sources that in some cases out-compete endogenous DNA in PCR amplification, thus leading to false positives and/or aberrant results. Particularly problematic is contamination that is inadvertently deposited on the surfaces of bones through direct handling. Whereas some previous studies have shown that contamination removal is possible by subjecting samples to sodium hypochlorite prior to DNA extraction, others caution that such treatment can destroy a majority of the molecules endogenous to the sample. To further explore this topic, we experimentally contaminated ancient northern fur seal (Callorhinus ursinus) ribs with human DNA and treated them with sodium hypochlorite to remove that contamination. Our findings are consistent with previous studies that found sodium hypochlorite to be highly efficient (~81-99%) at contamination removal; however, there emerged no treatment capable of removing 100% of the contamination across all of the experiments. Moreover, the ability to estimate the degree of damage to endogenous northern fur seal molecules was compromised due to the inherent variability of preserved mtDNA across the bones, and the presence of co-extracted PCR inhibitors.}, }
@article {pmid23868176, year = {2013}, author = {Villanea, FA and Bolnick, DA and Monroe, C and Worl, R and Cambra, R and Leventhal, A and Kemp, BM}, title = {Brief communication: Evolution of a specific O allele (O1vG542A) supports unique ancestry of Native Americans.}, journal = {American journal of physical anthropology}, volume = {151}, number = {4}, pages = {649-657}, doi = {10.1002/ajpa.22292}, pmid = {23868176}, issn = {1096-8644}, mesh = {ABO Blood-Group System/*genetics ; Alaska ; *Alleles ; Base Sequence ; *Biological Evolution ; California ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Demography ; Gene Flow/*genetics ; Genetics, Population ; Haplotypes/genetics ; Humans ; Indians, North American/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {In this study, we explore the geographic and temporal distribution of a unique variant of the O blood group allele called O1v(G542A) , which has been shown to be shared among Native Americans but is rare in other populations. O1v(G542A) was previously reported in Native American populations in Mesoamerica and South America, and has been proposed as an ancestry informative marker. We investigated whether this allele is also found in the Tlingit and Haida, two contemporary indigenous populations from Alaska, and a pre-Columbian population from California. If O1v(G542A) is present in Na-Dene speakers (i.e., Tlingits), it would indicate that Na-Dene speaking groups share close ancestry with other Native American groups and support a Beringian origin of the allele, consistent with the Beringian Incubation Model. If O1v(G542A) is found in pre-Columbian populations, it would further support a Beringian origin of the allele, rather than a more recent introduction of the allele into the Americas via gene flow from one or more populations which have admixed with Native Americans over the past five centuries. We identified this allele in one Na-Dene population at a frequency of 0.11, and one ancient California population at a frequency of 0.20. Our results support a Beringian origin of O1v(G542A) , which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus. This result is consistent with the hypothesis that Na-Dene and other Native American populations primarily derive their ancestry from a single source population.}, }
@article {pmid23843972, year = {2013}, author = {Cui, Y and Lindo, J and Hughes, CE and Johnson, JW and Hernandez, AG and Kemp, BM and Ma, J and Cunningham, R and Petzelt, B and Mitchell, J and Archer, D and Cybulski, JS and Malhi, RS}, title = {Ancient DNA analysis of mid-holocene individuals from the Northwest Coast of North America reveals different evolutionary paths for mitogenomes.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e66948}, pmid = {23843972}, issn = {1932-6203}, mesh = {Adult ; Canada ; *Evolution, Molecular ; Female ; *Genome, Mitochondrial ; Haplotypes ; Humans ; Indians, North American/*genetics ; Male ; Molecular Sequence Data ; Mutation ; North America ; Phylogeny ; Young Adult ; }, abstract = {To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga'a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor-descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.}, }
@article {pmid23803770, year = {2013}, author = {Millar, CD and Lambert, DM}, title = {Ancient DNA: Towards a million-year-old genome.}, journal = {Nature}, volume = {499}, number = {7456}, pages = {34-35}, pmid = {23803770}, issn = {1476-4687}, mesh = {Animals ; *Evolution, Molecular ; Genome/*genetics ; Horses/*genetics ; *Phylogeny ; }, }
@article {pmid23795302, year = {2013}, author = {Birch, PR and Cooke, DE}, title = {The early days of late blight.}, journal = {eLife}, volume = {2}, number = {}, pages = {e00954}, pmid = {23795302}, issn = {2050-084X}, support = {BB/G015244/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; Phytophthora infestans/*pathogenicity ; Solanum tuberosum/*microbiology ; *Starvation ; }, abstract = {Large-scale DNA sequencing of samples of foliage collected in the 19th century from plants infected with late blight has shown that the potato famines of the 1840s were triggered by a single clonal lineage of Phytophthora infestans, called HERB-1, which persisted for at least 50 years.}, }
@article {pmid23792062, year = {2013}, author = {Anastasiou, E and Mitchell, PD}, title = {Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations.}, journal = {Gene}, volume = {528}, number = {1}, pages = {33-40}, doi = {10.1016/j.gene.2013.06.017}, pmid = {23792062}, issn = {1879-0038}, mesh = {Bacterial Infections/genetics/microbiology ; Communicable Diseases/*genetics ; DNA/genetics/isolation &amp; purification ; Fossils ; Genetics, Population/*methods ; Humans ; Mummies ; Paleopathology/*methods ; Parasitic Diseases/genetics/parasitology ; Virus Diseases/genetics/virology ; }, abstract = {The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future.}, }
@article {pmid23792014, year = {2013}, author = {Anastasiou, E and Mitchell, PD}, title = {Evolutionary anthropology and genes: investigating the genetics of human evolution from excavated skeletal remains.}, journal = {Gene}, volume = {528}, number = {1}, pages = {27-32}, doi = {10.1016/j.gene.2013.06.011}, pmid = {23792014}, issn = {1879-0038}, mesh = {Animals ; Anthropology/*methods ; Cell Nucleus/genetics ; DNA/analysis/*genetics/isolation &amp; purification ; DNA, Mitochondrial/analysis/genetics/isolation &amp; purification ; *Evolution, Molecular ; Fossils ; Genetics, Population/methods ; Hominidae/*genetics ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {The development of molecular tools for the extraction, analysis and interpretation of DNA from the remains of ancient organisms (paleogenetics) has revolutionised a range of disciplines as diverse as the fields of human evolution, bioarchaeology, epidemiology, microbiology, taxonomy and population genetics. The paper draws attention to some of the challenges associated with the extraction and interpretation of ancient DNA from archaeological material, and then reviews the influence of paleogenetics on the field of human evolution. It discusses the main contributions of molecular studies to reconstructing the evolutionary and phylogenetic relationships between extinct hominins (human ancestors) and anatomically modern humans. It also explores the evidence for evolutionary changes in the genetic structure of anatomically modern humans in recent millennia. This breadth of research has led to discoveries that would never have been possible using traditional approaches to human evolution.}, }
@article {pmid23741619, year = {2013}, author = {Yoshida, K and Schuenemann, VJ and Cano, LM and Pais, M and Mishra, B and Sharma, R and Lanz, C and Martin, FN and Kamoun, S and Krause, J and Thines, M and Weigel, D and Burbano, HA}, title = {The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine.}, journal = {eLife}, volume = {2}, number = {}, pages = {e00731}, pmid = {23741619}, issn = {2050-084X}, mesh = {DNA, Mitochondrial/genetics ; Genes, Fungal ; Haplotypes ; Humans ; Ireland ; Phytophthora infestans/genetics/*pathogenicity ; Solanum tuberosum/*microbiology ; *Starvation ; }, abstract = {Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the 19th century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the 20th century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity. DOI:http://dx.doi.org/10.7554/eLife.00731.001.}, }
@article {pmid23729639, year = {2013}, author = {Dabney, J and Meyer, M and Pääbo, S}, title = {Ancient DNA damage.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {5}, number = {7}, pages = {}, pmid = {23729639}, issn = {1943-0264}, mesh = {DNA/*chemistry ; *DNA Damage ; DNA Fragmentation ; Deamination ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Under favorable conditions DNA can survive for thousands of years in the remains of dead organisms. The DNA extracted from such remains is invariably degraded to a small average size by processes that at least partly involve depurination. It also contains large amounts of deaminated cytosine residues that are accumulated toward the ends of the molecules, as well as several other lesions that are less well characterized.}, }
@article {pmid23703035, year = {2013}, author = {Fortes, GG and Speller, CF and Hofreiter, M and King, TE}, title = {Phenotypes from ancient DNA: approaches, insights and prospects.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {8}, pages = {690-695}, doi = {10.1002/bies.201300036}, pmid = {23703035}, issn = {1521-1878}, mesh = {Archaeology/methods ; DNA/*genetics ; DNA Fingerprinting ; DNA, Mitochondrial/*genetics ; Eye Color ; Fossils ; Genome, Human ; Hair ; Humans ; Paleontology/methods ; *Phenotype ; Pigmentation/*genetics ; Polymorphism, Single Nucleotide ; }, abstract = {The great majority of phenotypic characteristics are complex traits, complicating the identification of the genes underlying their expression. However, both methodological and theoretical progress in genome-wide association studies have resulted in a much better understanding of the underlying genetics of many phenotypic traits, including externally visible characteristics (EVCs) such as eye and hair color. Consequently, it has become possible to predict EVCs from human samples lacking phenotypic information. Predicting EVCs from genetic evidence is clearly appealing for forensic applications involving the personal identification of human remains. Now, a recent paper has reported the genetic determination of eye and hair color in samples up to 800 years old. The ability to predict EVCs from ancient human remains opens up promising perspectives for ancient DNA research, as this could allow studies to directly address archaeological and evolutionary questions related to the temporal and geographical origins of the genetic variants underlying phenotypes.}, }
@article {pmid23697340, year = {2013}, author = {Jaeger, LH and de Souza, SM and Dias, OF and Iñiguez, AM}, title = {Mycobacterium tuberculosis complex in remains of 18th-19th century slaves, Brazil.}, journal = {Emerging infectious diseases}, volume = {19}, number = {5}, pages = {837-839}, pmid = {23697340}, issn = {1080-6059}, mesh = {Adolescent ; Adult ; Base Sequence ; *Black People ; Brazil/epidemiology ; DNA, Bacterial/classification/*genetics/isolation &amp; purification ; DNA, Mitochondrial/classification/*genetics/isolation &amp; purification ; Forensic Anthropology ; Haplotypes ; History, 18th Century ; History, 19th Century ; Humans ; Male ; Molecular Sequence Data ; Mycobacterium tuberculosis/classification/*genetics/isolation &amp; purification ; Paleopathology ; Social Problems ; Tuberculosis/ethnology/history/*microbiology ; }, }
@article {pmid23694692, year = {2013}, author = {Porter, TM and Golding, GB and King, C and Froese, D and Zazula, G and Poinar, HN}, title = {Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility.}, journal = {Molecular ecology resources}, volume = {13}, number = {5}, pages = {798-810}, doi = {10.1111/1755-0998.12124}, pmid = {23694692}, issn = {1755-0998}, mesh = {Animals ; *Biodiversity ; Chloroplast Proteins/genetics ; Cluster Analysis ; Electron Transport Complex IV/genetics ; *Fossils ; Introns ; Plants ; Prokaryotic Cells ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil ; }, abstract = {DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1 and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, sequenced control reactions were used to produce a contaminant library that was used to filter similar sequences from sample libraries. Contaminant filtering resulted in the removal of 1% of reads or 0.3% of operational taxonomic units. We found similar richness, overlap, abundance and taxonomic diversity from the 12S, 16S and trnL markers from each soil core. Jaccard dissimilarity across the two soil cores was highest for metazoan taxa detected by the 12S and cox1 markers. Taxonomic community distances were similar for each marker across the two soil cores when the chi-squared metric was used; however, the 12S and cox1 markers did not cluster well when the Goodall similarity metric was used. A comparison of plant macrofossil vs. read abundance corroborates previous work that suggests eastern Beringia was dominated by grasses and forbs during cold stages of the Pleistocene, a habitat that is restricted to isolated sites in the present-day Yukon.}, }
@article {pmid23688345, year = {2013}, author = {Ramírez, O and Gómez-Díaz, E and Olalde, I and Illera, JC and Rando, JC and González-Solís, J and Lalueza-Fox, C}, title = {Population connectivity buffers genetic diversity loss in a seabird.}, journal = {Frontiers in zoology}, volume = {10}, number = {1}, pages = {28}, pmid = {23688345}, issn = {1742-9994}, abstract = {BACKGROUND: Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems' threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory's shearwater (Calonectris borealis).<br><br>FINDINGS: We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia.<br><br>CONCLUSIONS: Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.}, }
@article {pmid23658776, year = {2013}, author = {Zaremba-Niedźwiedzka, K and Andersson, SG}, title = {No ancient DNA damage in Actinobacteria from the Neanderthal bone.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e62799}, pmid = {23658776}, issn = {1932-6203}, mesh = {Actinobacteria/classification/*genetics ; Animals ; Bacterial Proteins/classification/*genetics ; Bone and Bones/*microbiology ; Collagenases/classification/*genetics ; Fossils ; *Genes, Bacterial ; Genes, rRNA ; Neanderthals/genetics/*microbiology ; Paleontology ; Phylogeny ; }, abstract = {BACKGROUND: The Neanderthal genome was recently sequenced using DNA extracted from a 38,000-year-old fossil. At the start of the project, the fraction of mammalian and bacterial DNA in the sample was estimated to be <6% and 9%, respectively. Treatment with restriction enzymes prior to sequencing increased the relative proportion of mammalian DNA to 15%, but the large majority of sequences remain uncharacterized.<br><br>PRINCIPAL FINDINGS: Our taxonomic profiling of 3.95 Gb of Neanderthal DNA isolated from the Vindija Neanderthal Vi33.16 fossil showed that 90% of about 50,000 rRNA gene sequence reads were of bacterial origin, of which Actinobacteria accounted for more than 75%. Actinobacteria also represented more than 80% of the PCR-amplified 16S rRNA gene sequences from a cave sediment sample taken from the same G layer as the Neanderthal bone. However, phylogenetic analyses did not identify any sediment clones that were closely related to the bone-derived sequences. We analysed the patterns of nucleotide differences in the individual sequence reads compared to the assembled consensus sequences of the rRNA gene sequences. The typical ancient nucleotide substitution pattern with a majority of C to T changes indicative of DNA damage was observed for the Neanderthal rRNA gene sequences, but not for the Streptomyces-like rRNA gene sequences.<br><br>CONCLUSIONS/SIGNIFICANCE: Our analyses suggest that the Actinobacteria, and especially members of the Streptomycetales, contribute the majority of sequences in the DNA extracted from the Neanderthal fossil Vi33.16. The bacterial DNA showed no signs of damage, and we hypothesize that it was derived from bacteria that have been enriched inside the bone. The bioinformatic approach used here paves the way for future studies of microbial compositions and patterns of DNA damage in bacteria from archaeological bones. Such studies can help identify targeted measures to increase the relative amount of endogenous DNA in the sample.}, }
@article {pmid23658525, year = {2013}, author = {Harbeck, M and Seifert, L and Hänsch, S and Wagner, DM and Birdsell, D and Parise, KL and Wiechmann, I and Grupe, G and Thomas, A and Keim, P and Zöller, L and Bramanti, B and Riehm, JM and Scholz, HC}, title = {Yersinia pestis DNA from skeletal remains from the 6(th) century AD reveals insights into Justinianic Plague.}, journal = {PLoS pathogens}, volume = {9}, number = {5}, pages = {e1003349}, pmid = {23658525}, issn = {1553-7374}, mesh = {Base Sequence ; Bone and Bones/*microbiology ; DNA, Bacterial/*genetics ; Female ; Genotype ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 19th Century ; History, 20th Century ; History, Medieval ; Humans ; Male ; Molecular Sequence Data ; Pandemics/*history ; *Phylogeny ; *Plague/epidemiology/etiology/genetics/history/microbiology ; Yersinia pestis/*genetics ; }, abstract = {Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19(th) and 20(th) centuries, during which plague was spread around the world, and the second pandemic of the 14(th)-17(th) centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6(th)-8(th) centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics.}, }
@article {pmid23658006, year = {2013}, author = {Lejzerowicz, F and Esling, P and Majewski, W and Szczuciński, W and Decelle, J and Obadia, C and Arbizu, PM and Pawlowski, J}, title = {Ancient DNA complements microfossil record in deep-sea subsurface sediments.}, journal = {Biology letters}, volume = {9}, number = {4}, pages = {20130283}, pmid = {23658006}, issn = {1744-957X}, mesh = {Atlantic Ocean ; DNA, Protozoan/*analysis ; Foraminifera/classification/genetics/metabolism ; *Fossils ; Geologic Sediments/*analysis ; Molecular Sequence Data ; Rhizaria/classification/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on Foraminifera and Radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropalaeontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian small subunit rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the last glacial maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.}, }
@article {pmid23657158, year = {2013}, author = {Ruiz-Núñez, B and Pruimboom, L and Dijck-Brouwer, DA and Muskiet, FA}, title = {Lifestyle and nutritional imbalances associated with Western diseases: causes and consequences of chronic systemic low-grade inflammation in an evolutionary context.}, journal = {The Journal of nutritional biochemistry}, volume = {24}, number = {7}, pages = {1183-1201}, doi = {10.1016/j.jnutbio.2013.02.009}, pmid = {23657158}, issn = {1873-4847}, mesh = {Brain/growth &amp; development/metabolism ; Glucose/metabolism ; Humans ; Inflammation/*etiology/metabolism ; Insulin Resistance ; *Life Style ; *Nutritional Status ; }, abstract = {In this review, we focus on lifestyle changes, especially dietary habits, that are at the basis of chronic systemic low grade inflammation, insulin resistance and Western diseases. Our sensitivity to develop insulin resistance traces back to our rapid brain growth in the past 2.5 million years. An inflammatory reaction jeopardizes the high glucose needs of our brain, causing various adaptations, including insulin resistance, functional reallocation of energy-rich nutrients and changing serum lipoprotein composition. The latter aims at redistribution of lipids, modulation of the immune reaction, and active inhibition of reverse cholesterol transport for damage repair. With the advent of the agricultural and industrial revolutions, we have introduced numerous false inflammatory triggers in our lifestyle, driving us to a state of chronic systemic low grade inflammation that eventually leads to typically Western diseases via an evolutionary conserved interaction between our immune system and metabolism. The underlying triggers are an abnormal dietary composition and microbial flora, insufficient physical activity and sleep, chronic stress and environmental pollution. The disturbance of our inflammatory/anti-inflammatory balance is illustrated by dietary fatty acids and antioxidants. The current decrease in years without chronic disease is rather due to "nurture" than "nature," since less than 5% of the typically Western diseases are primary attributable to genetic factors. Resolution of the conflict between environment and our ancient genome might be the only effective manner for "healthy aging," and to achieve this we might have to return to the lifestyle of the Paleolithic era as translated to the 21st century culture.}, }
@article {pmid23645967, year = {2013}, author = {Cleeland, LM and Reichard, MV and Tito, RY and Reinhard, KJ and Lewis, CM}, title = {Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular Approach.}, journal = {Journal of archaeological science}, volume = {40}, number = {7}, pages = {3060-3066}, pmid = {23645967}, issn = {0305-4403}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; R01 HG005172/HG/NHGRI NIH HHS/United States ; }, abstract = {This paper reports an approach to the identification of prehistoric parasitic infection, which integrates traditional morphological methods with molecular methods. The approach includes the strengths of each method while mitigating the limitations. Demonstrating the efficacy of this approach, we provide a case study from a 1,400 year old desiccated fecal sample from La Cueva de los Muertos Chiquitos, archaeological site, near Rio Zape, Durango, Mexico. Traditionally prepared microscope slides were processed via microscopy and tentative ascarids were identified. Information regarding the parasites' developmental stage was recorded. DNA was then extracted directly from the slide material. From this DNA extract, a small segment of the 18S ribosomal RNA gene variant that is specific to Ascaris, and its phylogenetically close relatives, was targeted for PCR amplification and sequencing. Phylogenetic analysis of the DNA sequence best matched a member of physalopterids, rather than ascarids, with a single exception of a match to Contracaecum spiculigerum. Subsequent extractions, amplifications and sequencing of the original rehydrated coprolite material confirmed these results. The C. spiculigerum sequence represented a phylogenetic anomaly and subsequent analysis determined the sequence was an error in the BLAST database, likely attributable to misidentification of juvenile specimens prior to sequencing and submission. Physaloptera are a difficult genus to identify morphologically and can carry major health burdens. They may be underreported in humans, in part, because of morphological similarities to the more common human parasites belonging to ascarids. We conclude that integrating traditional morphological methods with molecular methods can help resolve this issue, in both contemporary and prehistoric populations.}, }
@article {pmid23628961, year = {2013}, author = {Stadler, T and Yang, Z}, title = {Dating phylogenies with sequentially sampled tips.}, journal = {Systematic biology}, volume = {62}, number = {5}, pages = {674-688}, doi = {10.1093/sysbio/syt030}, pmid = {23628961}, issn = {1076-836X}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Algorithms ; Bayes Theorem ; Evolution, Molecular ; Genetic Speciation ; HIV-2/classification/genetics ; Influenza A virus/classification/genetics ; Markov Chains ; *Models, Genetic ; Monte Carlo Method ; *Phylogeny ; Simian Immunodeficiency Virus/classification/genetics ; Time ; }, abstract = {We develop a Bayesian Markov chain Monte Carlo (MCMC) algorithm for estimating divergence times using sequentially sampled molecular sequences. This type of data is commonly collected during viral epidemics and is sometimes available from different species in ancient DNA studies. We derive the distribution of ages of nodes in the tree under a birth-death-sequential-sampling (BDSS) model and use it as the prior for divergence times in the dating analysis. We implement the prior in the MCMCtree program in the PAML package for divergence dating. The BDSS prior is very flexible and, with different parameters, can generate trees of very different shapes, suitable for examining the sensitivity of posterior time estimates. We apply the method to a data set of SIV/HIV-2 genes in comparison with a likelihood-based dating method, and to a data set of influenza H1 genes from different hosts in comparison with the Bayesian program BEAST. We examined the impact of tree topology on time estimates and suggest that multifurcating consensus trees should be avoided in dating analysis. We found posterior time estimates for old nodes to be sensitive to the priors on times and rates and suggest that previous Bayesian dating studies may have produced overconfident estimates.}, }
@article {pmid23622484, year = {2013}, author = {Kaminiwa, J and Honda, K and Sugano, Y and Yano, S and Nishi, T and Sekine, Y}, title = {Vanadium accelerates polymerase chain reaction and expands the applicability of forensic DNA testing.}, journal = {Journal of forensic and legal medicine}, volume = {20}, number = {4}, pages = {326-333}, doi = {10.1016/j.jflm.2012.09.006}, pmid = {23622484}, issn = {1878-7487}, mesh = {Chromosomes, Human, Y ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/genetics ; Humans ; Microsatellite Repeats ; *Multiplex Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction ; Vanadium Compounds/*chemistry ; }, abstract = {Polymerase chain reaction (PCR) has been rapidly established as one of the most widely used techniques in molecular biology. Because most DNA analysis is PCR-based, the analysis of unamplifiable DNA of poor quality or low quantity is nearly impossible. However, we observed that if an appropriate concentration of vanadium chloride is added to the standard reaction mixture, the enzymatic amplification of DNA could be enhanced. Using multiplex PCR with the addition of vanadium, DNA typing was possible from even trace amounts of DNA that we were unable to amplify using normal reaction conditions. This method might be an effective tool for not only criminal investigations and ancient DNA analysis, but also for nearly all fields using DNA technology.}, }
@article {pmid23613487, year = {2013}, author = {Jónsson, H and Ginolhac, A and Schubert, M and Johnson, PL and Orlando, L}, title = {mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.}, journal = {Bioinformatics (Oxford, England)}, volume = {29}, number = {13}, pages = {1682-1684}, pmid = {23613487}, issn = {1367-4811}, mesh = {Bayes Theorem ; Cytosine/metabolism ; *DNA Damage ; Deamination ; Fossils ; *High-Throughput Nucleotide Sequencing ; Humans ; *Sequence Analysis, DNA ; *Software ; }, abstract = {MOTIVATION: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples.<br><br>RESULTS: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (&#x3bb;), nick frequency (&#x3bd;) and cytosine deamination rates in both double-stranded regions () and overhangs (). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols.<br><br>AVAILABILITY: mapDamage 2.0 is available at ginolhac.github.io/mapDamage/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk/publications/mapdamage2.0/).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid23597751, year = {2013}, author = {Monroe, C and Grier, C and Kemp, BM}, title = {Evaluating the efficacy of various thermo-stable polymerases against co-extracted PCR inhibitors in ancient DNA samples.}, journal = {Forensic science international}, volume = {228}, number = {1-3}, pages = {142-153}, doi = {10.1016/j.forsciint.2013.02.029}, pmid = {23597751}, issn = {1872-6283}, mesh = {Animals ; DNA, Mitochondrial/genetics ; DNA-Directed DNA Polymerase/*genetics ; Enzyme Inhibitors ; Paleontology ; *Polymerase Chain Reaction ; Salmon/*genetics ; }, abstract = {DNA from ancient and forensic specimens is often co-extracted with unknown amounts of unknown PCR inhibitors, which can lead to underestimated DNA concentrations, allelic drop-out, and/or false-negative results. It is not surprising, in this case, that numerous methods have been developed to remove PCR inhibitors or subdue their effects. One simple and cost effective approach could be the adoption of a polymerase that overcomes or is less affected by PCR inhibitors. In this study, nine different polymerases were evaluated for their efficacy against PCR inhibitors co-extracted with DNA from 63 ancient salmon vertebrae. These samples were excavated from two archeological sites located at the Dionisio Point locality on the northern end of Galiano Island in coastal southwestern British Columbia, Canada and date to 700-1000 and 1300-1500 years before present. Previously, DNA extracts from samples studied from this locality were determined to be largely inhibited to PCR amplification. In the present study, Omni Klentaq LA (DNA Polymerase Technology, Inc.) outperformed the other 8 polymerases in two measures: (1) its success in genetic species identification of these vertebrae, and (2) its ability to amplify an ancient DNA positive control when spiked with a volume of potentially inhibited extract from the vertebrae.}, }
@article {pmid23596858, year = {2012}, author = {Lecomte, D and Plu, I and Froment, A}, title = {[Modern biology, imagery and forensic medicine: contributions and limitations in examination of skeletal remains].}, journal = {Bulletin de l'Academie nationale de medecine}, volume = {196}, number = {6}, pages = {1103-15; discussion 1116}, pmid = {23596858}, issn = {0001-4079}, mesh = {Adult ; Age Determination by Skeleton ; Anthropometry/*methods ; Blood Stains ; Body Height ; Bone and Bones/chemistry ; Cause of Death ; Child ; DNA/genetics ; Face ; Female ; Forensic Anthropology/methods ; Forensic Medicine/*methods ; Humans ; Image Processing, Computer-Assisted ; Imaging, Three-Dimensional/*methods ; Male ; Radiometric Dating ; Sex Characteristics ; *Skeleton ; Time Factors ; Tomography, X-Ray Computed/methods ; }, abstract = {Forensic examination is often requested when skeletal remains are discovered. Detailed visual observation can provide much information, such as the human or animal origin, sex, age, stature, and ancestry, and approximate time since death. New three-dimensional imaging techniques can provide further information (osteometry, facial reconstruction). Bone chemistry, and particularly measurement of stable or unstable carbon and nitrogen isotopes, yields information on diet and time since death, respectively. Genetic analyses of ancient DNA are also developing rapidly. Although seldom used in a judicial context, these modern anthropologic techniques are nevertheless available for the most complex cases.}, }
@article {pmid23596284, year = {2013}, author = {Cenci, A and Combes, MC and Lashermes, P}, title = {Differences in evolution rates among eudicotyledon species observed by analysis of protein divergence.}, journal = {The Journal of heredity}, volume = {104}, number = {4}, pages = {459-464}, doi = {10.1093/jhered/est025}, pmid = {23596284}, issn = {1465-7333}, mesh = {Coffea/genetics ; Databases, Protein ; *Evolution, Molecular ; Genetic Variation/*physiology ; Genome, Plant ; Solanum lycopersicum/genetics ; Magnoliopsida/*genetics ; Mimulus/genetics ; *Mutation Rate ; Phylogeny ; Plant Proteins/*genetics ; Sequence Homology ; Species Specificity ; Vitis/genetics ; }, abstract = {Genome evolution rates can vary considerably among plants. In particular, a correlation has often been reported between the evolution rate and annual/perennial habit, possibly associated with differences in generation time. For example, among the rosid species whose genome is fully sequenced, Vitis vinifera, a perennial species, was shown to have the genome that evolved the slowest. In order to extend knowledge of evolution rates to the asterid clade, one of the two major clades of core eudicotyledonous, the protein evolution rates in three asterid species, one perennial (Coffea canephora) and two annual species (Solanum lycopersicum and Mimulus guttatus), were investigated and compared with V. vinifera. Significant differences were observed among these species, and the proteins that evolved the most slowly were those of V. vinifera. Among the species belonging to the asterid clade, C. canephora appears to have evolved more slowly than the others. These findings are consistent with a correlation between perennial habit and slow evolution rates. The C. canephora genome seems to be an appropriate model for paleogenomic studies of asterids.}, }
@article {pmid23590114, year = {2013}, author = {Pósa, A and Maixner, F and Lovász, G and Molnár, E and Bereczki, Z and Perrin, P and Zink, A and Pálfi, G}, title = {Revision of tuberculous lesions in the Bácsalmás-Oalmás series--preliminary morphological and biomolecular studies.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {70}, number = {1}, pages = {83-100}, doi = {10.1127/0003-5548/2012/0260}, pmid = {23590114}, issn = {0003-5548}, mesh = {Adult ; Bone and Bones/chemistry/*microbiology/*pathology ; Child ; DNA, Bacterial/analysis/isolation &amp; purification ; Female ; History, 16th Century ; History, 17th Century ; Humans ; Hungary ; Infant ; Male ; Molecular Typing ; Mycobacterium tuberculosis/genetics/*isolation &amp; purification ; Paleopathology ; Polymerase Chain Reaction ; Tuberculosis, Osteoarticular/*history/microbiology/pathology ; }, abstract = {Previous investigations carried out in some parts of the 16th-17th century AD series of Bácsalmás-Oalmás (southern Hungary) have already provided interesting paleopathological cases of tuberculosis (e.g. Molnár &amp; Pálfi 1994). These studies were essentially based on macromorphological analysis, biomolecular methods were used only in a few cases (e.g. Haas et al. 2000). From a macromorphological point of view, former investigations have only considered 'classical' tuberculosis (TB) alterations (advanced-stage lesions in common skeletal locations). However, due to the recent development of diagnostic criteria in the field of the paleopathology of infectious diseases, new approaches have been introduced in the identification of skeletal TB lesions (Pálfi et al. 1999, Maczel 2003). Molecular methods for the detection of mycobacterial aDNA have also been developed considerably in the last few years (e.g. Donoghue 2008, Donoghue 2011). The good state of preservation of the material, the important chronological period of the series and the relative high prevalence of TB reported in preliminary studies encouraged us to carry out a revision of TB-related lesions in the complete Bácsalmás-Oalmás series. A five year international research program--including both macroscopic and biomolecular studies of the series--was recently started. The present paper summarizes the results ofa pilot project conducted to optimize the further systematic paleopathological and paleomicrobial studies. Skeletal material of 205 individuals was chosen forthe macromorphological test-investigation, which was focused both on classical/advanced stage skeletal TB alterations (tuberculous spondylitis, tuberculous arthritis) and atypical/early-stage TB lesions (rib lesions, superficial vertebral changes, endocranial alterations, early-stage spondylodiscitis). In addition, the association of possible stress factors (long bone periostitis, cribra orbitalia, cribra cranii) were also considered. Paleomicrobiological analysis was used to study the presence of Mycobacterium tuberculosis ancient DNA (aDNA) in morphologically positive and negative cases. A comparative paleomicrobial analysis was carried out on different samples, to test the presence of MTB DNA in different skeletal regions.}, }
@article {pmid23590113, year = {2013}, author = {Oh, CS and Lee, SJ and Lee, SD and Kim, MJ and Kim, YS and Lim, DS and Shin, DH}, title = {Amplification of DNA remnants in mummified human brains from medieval Joseon tombs of Korea.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {70}, number = {1}, pages = {57-81}, doi = {10.1127/0003-5548/2012/0225}, pmid = {23590113}, issn = {0003-5548}, mesh = {Base Sequence ; Brain/anatomy &amp; histology/pathology ; *Brain Chemistry ; DNA/*analysis/*genetics/isolation &amp; purification ; DNA, Mitochondrial/genetics ; Female ; Femur/chemistry ; Humans ; Male ; Microsatellite Repeats ; Middle Aged ; Molecular Sequence Data ; *Mummies ; Polymerase Chain Reaction ; Republic of Korea ; Young Adult ; }, abstract = {Recently, a number of mummified brains obtained from the remains of medieval Joseon Koreans have been subjected to biological investigations. Although the morphology of the organs had been perfectly maintained on gross examination, we still do not know how well biomolecules such as DNA were preserved. In the present study, the preservation status of remnant DNA in mummified brain tissue was determined by means of comparisons with corresponding DNA taken from the femurs of the same subjects. Quantifiler analysis revealed that DNA from the mummified brain was less fragmented than that contained in the femurs. The better preservation status of the brain DNA was shown also in MiniFiler assays: the number of short tandem repeat (STR) locus profiles for the mummified brain was far higher than in the case of the femur bones. In the case of the mtDNA analysis, longer DNA fragments (821 bp) could be successfully amplified with brain samples, whereas only shorter PCR amplicons (221-263 bp) were seen with the femur samples. Indeed mummified brain tissue, if discovered in amounts suitable for ancient DNA analysis, promises to be the preferred source for genetic analysis of individuals from pre-modern Korean tombs.}, }
@article {pmid23575681, year = {2013}, author = {Foote, AD and Kaschner, K and Schultze, SE and Garilao, C and Ho, SY and Post, K and Higham, TF and Stokowska, C and van der Es, H and Embling, CB and Gregersen, K and Johansson, F and Willerslev, E and Gilbert, MT}, title = {Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {1677}, pmid = {23575681}, issn = {2041-1723}, mesh = {Animals ; Bowhead Whale/*genetics ; *Climate Change ; DNA/*genetics ; *Ecosystem ; Models, Theoretical ; }, abstract = {The climatic changes of the glacial cycles are thought to have been a major driver of population declines and species extinctions. However, studies to date have focused on terrestrial fauna and there is little understanding of how marine species responded to past climate change. Here we show that a true Arctic species, the bowhead whale (Balaena mysticetus), shifted its range and tracked its core suitable habitat northwards during the rapid climate change of the Pleistocene-Holocene transition. Late Pleistocene lineages survived into the Holocene and effective female population size increased rapidly, concurrent with a threefold increase in core suitable habitat. This study highlights that responses to climate change are likely to be species specific and difficult to predict. We estimate that the core suitable habitat of bowhead whales will be almost halved by the end of this century, potentially influencing future population dynamics.}, }
@article {pmid23555726, year = {2013}, author = {Buckley, M}, title = {A molecular phylogeny of Plesiorycteropus reassigns the extinct mammalian order 'Bibymalagasia'.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59614}, pmid = {23555726}, issn = {1932-6203}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Collagen/chemistry/metabolism ; *Extinction, Biological ; Fossils ; Mammals/*classification/metabolism ; Molecular Sequence Data ; *Phylogeny ; Proteomics ; }, abstract = {Madagascar is well known for its diverse fauna and flora, being home to many species not found anywhere else in the world. However, its biodiversity in the recent past included a range of extinct enigmatic fauna, such as elephant birds, giant lemurs and dwarfed hippopotami. The 'Malagasy aardvark' (Plesiorycteropus) has remained one of Madagascar's least well-understood extinct species since its discovery in the 19(th) century. Initially considered a close relative of the aardvark (Orycteropus) within the order Tubulidentata, more recent morphological analyses challenged this placement on the grounds that the identifiably derived traits supporting this allocation were adaptations to digging rather than shared ancestry. Because the skeletal evidence showed many morphological traits diagnostic of different eutherian mammal orders, they could not be used to resolve its closest relatives. As a result, the genus was tentatively assigned its own taxonomic order 'Bibymalagasia', yet how this order relates to other eutherian mammal orders remains unclear despite numerous morphological investigations. This research presents the first known molecular sequence data for Plesiorycteropus, obtained from the bone protein collagen (I), which places the 'Malagasy aardvark' as more closely related to tenrecs than aardvarks. More specifically, Plesiorycteropus was recovered within the order Tenrecoidea (golden moles and tenrecs) within Afrotheria, suggesting that the taxonomic order 'Bibymalagasia' is obsolete. This research highlights the potential for collagen sequencing in investigating the phylogeny of extinct species as a viable alternative to ancient DNA (aDNA) sequencing, particularly in cases where aDNA cannot be recovered.}, }
@article {pmid23553074, year = {2013}, author = {Khairat, R and Ball, M and Chang, CC and Bianucci, R and Nerlich, AG and Trautmann, M and Ismail, S and Shanab, GM and Karim, AM and Gad, YZ and Pusch, CM}, title = {First insights into the metagenome of Egyptian mummies using next-generation sequencing.}, journal = {Journal of applied genetics}, volume = {54}, number = {3}, pages = {309-325}, pmid = {23553074}, issn = {2190-3883}, mesh = {Base Sequence ; Biopsy ; Egypt, Ancient ; Embalming/history/*methods ; Gene Library ; History, Ancient ; Humans ; *Metagenome ; Molecular Sequence Data ; *Mummies ; Phylogeny ; Plasmodium falciparum/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Temperature ; Toxoplasma/genetics ; }, abstract = {We applied, for the first time, next-generation sequencing (NGS) technology on Egyptian mummies. Seven NGS datasets obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC-124AD) and two unearthed pre-contact Bolivian lowland skeletons were generated and characterised. The datasets were contrasted to three recently published NGS datasets obtained from cold-climate regions, i.e. the Saqqaq, the Denisova hominid and the Alpine Iceman. Analysis was done using one million reads of each newly generated or published dataset. Blastn and megablast results were analysed using MEGAN software. Distinct NGS results were replicated by specific and sensitive polymerase chain reaction (PCR) protocols in ancient DNA dedicated laboratories. Here, we provide unambiguous identification of authentic DNA in Egyptian mummies. The NGS datasets showed variable contents of endogenous DNA harboured in tissues. Three of five mummies displayed a human DNA proportion comparable to the human read count of the Saqqaq permafrost-preserved specimen. Furthermore, a metagenomic signature unique to mummies was displayed. By applying a "bacterial fingerprint", discrimination among mummies and other remains from warm areas outside Egypt was possible. Due to the absence of an adequate environment monitoring, a bacterial bloom was identified when analysing different biopsies from the same mummies taken after a lapse of time of 1.5 years. Plant kingdom representation in all mummy datasets was unique and could be partially associated with their use in embalming materials. Finally, NGS data showed the presence of Plasmodium falciparum and Toxoplasma gondii DNA sequences, indicating malaria and toxoplasmosis in these mummies. We demonstrate that endogenous ancient DNA can be extracted from mummies and serve as a proper template for the NGS technique, thus, opening new pathways of investigation for future genome sequencing of ancient Egyptian individuals.}, }
@article {pmid23505210, year = {2013}, author = {Prost, S and Guralnick, RP and Waltari, E and Fedorov, VB and Kuzmina, E and Smirnov, N and van Kolfschoten, T and Hofreiter, M and Vrieling, K}, title = {Losing ground: past history and future fate of Arctic small mammals in a changing climate.}, journal = {Global change biology}, volume = {19}, number = {6}, pages = {1854-1864}, doi = {10.1111/gcb.12157}, pmid = {23505210}, issn = {1354-1013}, mesh = {Animals ; Arctic Regions ; *Climate Change ; Mammals/*physiology ; Models, Theoretical ; }, abstract = {According to the IPCC, the global average temperature is likely to increase by 1.4-5.8 °C over the period from 1990 to 2100. In Polar regions, the magnitude of such climatic changes is even larger than in temperate and tropical biomes. This amplified response is particularly worrisome given that the so-far moderate warming is already impacting Arctic ecosystems. Predicting species responses to rapid warming in the near future can be informed by investigating past responses, as, like the rest of the planet, the Arctic experienced recurrent cycles of temperature increase and decrease (glacial-interglacial changes) in the past. In this study, we compare the response of two important prey species of the Arctic ecosystem, the collared lemming and the narrow-skulled vole, to Late Quaternary climate change. Using ancient DNA and Ecological Niche Modeling (ENM), we show that the two species, which occupy similar, but not identical ecological niches, show markedly different responses to climatic and environmental changes within broadly similar habitats. We empirically demonstrate, utilizing coalescent model-testing approaches, that collared lemming populations decreased substantially after the Last Glacial Maximum; a result consistent with distributional loss over the same period based on ENM results. Given this strong association, we projected the current niche onto future climate conditions based on IPCC 4.0 scenarios, and forecast accelerating loss of habitat along southern range boundaries with likely associated demographic consequences. Narrow-skulled vole distribution and demography, by contrast, was only moderately impacted by past climatic changes, but predicted future changes may begin to affect their current western range boundaries. Our work, founded on multiple lines of evidence suggests a future of rapidly geographically shifting Arctic small mammal prey communities, some of whom are on the edge of existence, and whose fate may have ramifications for the whole Arctic food web and ecosystem.}, }
@article {pmid23505017, year = {2013}, author = {Prost, S and Klietmann, J and van Kolfschoten, T and Guralnick, RP and Waltari, E and Vrieling, K and Stiller, M and Nagel, D and Rabeder, G and Hofreiter, M and Sommer, RS}, title = {Effects of late quaternary climate change on Palearctic shrews.}, journal = {Global change biology}, volume = {19}, number = {6}, pages = {1865-1874}, doi = {10.1111/gcb.12153}, pmid = {23505017}, issn = {1354-1013}, mesh = {Animals ; Arctic Regions ; *Climate Change ; Cluster Analysis ; DNA/genetics ; Models, Theoretical ; Shrews/genetics/*physiology ; }, abstract = {The Late Quaternary was a time of rapid climatic oscillations and drastic environmental changes. In general, species can respond to such changes by behavioral accommodation, distributional shifts, ecophenotypic modifications (nongenetic), evolution (genetic) or ultimately face local extinction. How those responses manifested in the past is essential for properly predicting future ones especially as the current warm phase is further intensified by rising levels of atmospheric carbon dioxide. Here, we use ancient DNA (aDNA) and morphological features in combination with ecological niche modeling (ENM) to investigate genetic and nongenetic responses of Central European Palearctic shrews to past climatic change. We show that a giant form of shrew, previously described as an extinct Pleistocene Sorex species, represents a large ecomorph of the common shrew (Sorex araneus), which was replaced by populations from a different gene-pool and with different morphology after the Pleistocene Holocene transition. We also report the presence of the cold-adapted tundra shrew (S. tundrensis) in Central Europe. This species is currently restricted to Siberia and was hitherto unknown as an element of the Pleistocene fauna of Europe. Finally, we show that there is no clear correlation between climatic oscillations within the last 50 000 years and body size in shrews and conclude that a special nonanalogous situation with regard to biodiversity and food supply in the Late Glacial may have caused the observed large body size.}, }
@article {pmid23495672, year = {2013}, author = {Fulton, TL and Norris, RW and Graham, RW and Semken, HA and Shapiro, B}, title = {Ancient DNA supports southern survival of Richardson's collared lemming (Dicrostonyx richardsoni) during the last glacial maximum.}, journal = {Molecular ecology}, volume = {22}, number = {9}, pages = {2540-2548}, doi = {10.1111/mec.12267}, pmid = {23495672}, issn = {1365-294X}, mesh = {Animals ; Arctic Regions ; Arvicolinae/*classification/*genetics ; Canada ; DNA/genetics/*isolation &amp; purification ; DNA, Mitochondrial/genetics/*isolation &amp; purification ; Ecosystem ; Fossils ; Genetic Variation ; Haplotypes ; Ice Cover/chemistry ; Iowa ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; South Dakota ; }, abstract = {Collared lemmings (genus Dicrostonyx) are circumpolar Arctic arvicoline rodents associated with tundra. However, during the last glacial maximum (LGM), Dicrostonyx lived along the southern ice margin of the Laurentide ice sheet in communities comprising both temperate and boreal species. To better understand these communities and the fate of these southern individuals, we compare mitochondrial cytochrome b sequence data from three LGM-age Dicrostonyx fossils from south of the Laurentide ice sheet to sequences from modern Dicrostonyx sampled from across their present-day range. We test whether the Dicrostonyx populations from LGM-age continental USA became extinct at the Pleistocene-Holocene transition ~11000 years ago or, alternatively, if they belong to an extant species whose habitat preferences can be used to infer the palaeoclimate along the glacial margin. Our results indicate that LGM-age Dicrostonyx from Iowa and South Dakota belong to Dicrostonyx richardsoni, which currently lives in a temperate tundra environment west of Hudson Bay, Canada. This suggests a palaeoclimate south of the Laurentide ice sheet that contains elements similar to the more temperate shrub tundra characteristic of extant D. richardsoni habitat, rather than the very cold, dry tundra of the Northern Arctic. While more data are required to determine whether or not the LGM southern population is ancestral to extant D. richardsoni, it seems most probable that the species survived the LGM in a southern refugium.}, }
@article {pmid23493070, year = {2013}, author = {Gansauge, MT and Meyer, M}, title = {Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA.}, journal = {Nature protocols}, volume = {8}, number = {4}, pages = {737-748}, pmid = {23493070}, issn = {1750-2799}, mesh = {Biotinylation ; DNA Primers ; DNA, Single-Stranded/*chemistry ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; }, abstract = {This protocol describes a method for converting short single-stranded and double-stranded DNA into libraries compatible with high-throughput sequencing using Illumina technology. This method has primarily been developed to improve sequence retrieval from ancient DNA, but it is also applicable to the sequencing of short or degraded DNA from other sources, and it can also be used for sequencing oligonucleotides. Single-stranded library preparation is performed by ligating a biotinylated adapter oligonucleotide to the 3' ends of heat-denatured DNA. The resulting strands are then immobilized on streptavidin-coated beads and copied with a polymerase. A second adapter is attached by blunt-end ligation, and library preparation is completed by PCR amplification. We estimate that intact DNA strands are recovered in the library with ∼50% efficiency. Libraries can be generated from up to 12 DNA or oligonucleotide samples in parallel within 2 d.}, }
@article {pmid23483925, year = {2013}, author = {Druzhkova, AS and Thalmann, O and Trifonov, VA and Leonard, JA and Vorobieva, NV and Ovodov, ND and Graphodatsky, AS and Wayne, RK}, title = {Ancient DNA analysis affirms the canid from Altai as a primitive dog.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e57754}, pmid = {23483925}, issn = {1932-6203}, mesh = {Animals ; Asia ; Base Sequence ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; Extinction, Biological ; Genome, Mitochondrial/genetics ; Geography ; Likelihood Functions ; Models, Genetic ; Phylogeny ; Wolves/genetics ; }, abstract = {The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication.}, }
@article {pmid23462995, year = {2013}, author = {Austin, JJ and Soubrier, J and Prevosti, FJ and Prates, L and Trejo, V and Mena, F and Cooper, A}, title = {The origins of the enigmatic Falkland Islands wolf.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {1552}, pmid = {23462995}, issn = {2041-1723}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Falkland Islands ; Fossils ; Geography ; Humans ; Time Factors ; Wolves/*genetics ; }, abstract = {The origins of the extinct Falkland Islands wolf (FIW), Dusicyon australis, have remained a mystery since it was first recorded by Europeans in the seventeenth century. It is the only terrestrial mammal on the Falkland Islands (also known as the Malvinas Islands), which lie ~460 km from Argentina, leading to suggestions of either human-mediated transport or overwater dispersal. Previous studies used ancient DNA from museum specimens to suggest that the FIW diverged from its closest living relative, the South American maned wolf (Chrysocyon brachyurus) around 7 Ma, and colonized the islands ~330 ka by unknown means. Here we retrieve ancient DNA from subfossils of an extinct mainland relative, Dusicyon avus, and reveal the FIW lineage became isolated only 16 ka (8-31 ka), during the last glacial phase. Submarine terraces, formed on the Argentine coastal shelf by low sea-stands during this period, suggest that the FIW colonized via a narrow, shallow marine strait, potentially while it was frozen over.}, }
@article {pmid23459685, year = {2013}, author = {Der Sarkissian, C and Balanovsky, O and Brandt, G and Khartanovich, V and Buzhilova, A and Koshel, S and Zaporozhchenko, V and Gronenborn, D and Moiseyev, V and Kolpakov, E and Shumkin, V and Alt, KW and Balanovska, E and Cooper, A and Haak, W and , }, title = {Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.}, journal = {PLoS genetics}, volume = {9}, number = {2}, pages = {e1003296}, pmid = {23459685}, issn = {1553-7404}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; DNA, Mitochondrial/*genetics ; Europe ; *Gene Flow ; *Genetic Variation ; Genetics, Population ; *Genome, Mitochondrial ; Genotype ; Haplotypes ; Humans ; Population Dynamics ; Russia ; Scandinavian and Nordic Countries ; Siberia ; White People/genetics ; }, abstract = {North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans.}, }
@article {pmid23453014, year = {2013}, author = {Lindahl, T}, title = {My journey to DNA repair.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {11}, number = {1}, pages = {2-7}, pmid = {23453014}, issn = {2210-3244}, mesh = {Animals ; DNA Damage ; DNA Glycosylases/history/metabolism ; DNA Ligases/history/metabolism ; *DNA Repair ; Exodeoxyribonucleases/history/metabolism ; History, 20th Century ; History, 21st Century ; Humans ; United Kingdom ; }, abstract = {I completed my medical studies at the Karolinska Institute in Stockholm but have always been devoted to basic research. My longstanding interest is to understand fundamental DNA repair mechanisms in the fields of cancer therapy, inherited human genetic disorders and ancient DNA. I initially measured DNA decay, including rates of base loss and cytosine deamination. I have discovered several important DNA repair proteins and determined their mechanisms of action. The discovery of uracil-DNA glycosylase defined a new category of repair enzymes with each specialized for different types of DNA damage. The base excision repair pathway was first reconstituted with human proteins in my group. Cell-free analysis for mammalian nucleotide excision repair of DNA was also developed in my laboratory. I found multiple distinct DNA ligases in mammalian cells, and led the first genetic and biochemical work on DNA ligases I, III and IV. I discovered the mammalian exonucleases DNase III (TREX1) and IV (FEN1). Interestingly, expression of TREX1 was altered in some human autoimmune diseases. I also showed that the mutagenic DNA adduct O(6)-methylguanine (O(6)mG) is repaired without removing the guanine from DNA, identifying a surprising mechanism by which the methyl group is transferred to a residue in the repair protein itself. A further novel process of DNA repair discovered by my research group is the action of AlkB as an iron-dependent enzyme carrying out oxidative demethylation.}, }
@article {pmid23451203, year = {2013}, author = {Wood, JR and Wilmshurst, JM and Rawlence, NJ and Bonner, KI and Worthy, TH and Kinsella, JM and Cooper, A}, title = {A megafauna's microfauna: gastrointestinal parasites of New Zealand's extinct moa (Aves: Dinornithiformes).}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e57315}, pmid = {23451203}, issn = {1932-6203}, support = {R01 CA031615/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Birds/*parasitology ; DNA Primers ; *Extinction, Biological ; Gastrointestinal Tract/*parasitology ; New Zealand ; Polymerase Chain Reaction ; }, abstract = {WE PERFORM THE FIRST MULTIDISCIPLINARY STUDY OF PARASITES FROM AN EXTINCT MEGAFAUNAL CLADE USING COPROLITES FROM THE NEW ZEALAND MOA (AVES: Dinornithiformes). Ancient DNA and microscopic analyses of 84 coprolites deposited by four moa species (South Island giant moa, Dinornis robustus; little bush moa, Anomalopteryx didiformis; heavy-footed moa, Pachyornis elephantopus; and upland moa, Megalapteryx didinus) reveal an array of gastrointestinal parasites including coccidians (Cryptosporidium and members of the suborder Eimeriorina), nematodes (Heterakoidea, Trichostrongylidae, Trichinellidae) and a trematode (Echinostomida). Parasite eggs were most prevalent and diverse in coprolites from lowland sites, where multiple sympatric moa species occurred and host density was therefore probably higher. Morphological and phylogenetic evidence supports a possible vicariant Gondwanan origin for some of the moa parasites. The discovery of apparently host-specific parasite taxa suggests paleoparasitological studies of megafauna coprolites may provide useful case-studies of coextinction.}, }
@article {pmid23437111, year = {2013}, author = {Hung, CM and Lin, RC and Chu, JH and Yeh, CF and Yao, CJ and Li, SH}, title = {The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56301}, pmid = {23437111}, issn = {1932-6203}, mesh = {Animals ; Base Pairing/genetics ; Base Sequence ; Columbidae/*genetics ; DNA/genetics ; DNA Contamination ; *Extinction, Biological ; Gene Frequency/genetics ; Genome, Mitochondrial/*genetics ; Metagenome/genetics ; Postmortem Changes ; Sequence Analysis, DNA/*methods ; }, abstract = {The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.}, }
@article {pmid23437078, year = {2013}, author = {Vilstrup, JT and Seguin-Orlando, A and Stiller, M and Ginolhac, A and Raghavan, M and Nielsen, SC and Weinstock, J and Froese, D and Vasiliev, SK and Ovodov, ND and Clary, J and Helgen, KM and Fleischer, RC and Cooper, A and Shapiro, B and Orlando, L}, title = {Mitochondrial phylogenomics of modern and ancient equids.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e55950}, pmid = {23437078}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Fossils ; Genome, Mitochondrial/*genetics ; *Genomics ; Horses/*genetics ; *Phylogeny ; Selection, Genetic/genetics ; Time Factors ; }, abstract = {The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).}, }
@article {pmid23407348, year = {2013}, author = {Wang, CC and Yan, S and Yao, C and Huang, XY and Ao, X and Wang, Z and Han, S and Jin, L and Li, H}, title = {Ancient DNA of Emperor CAO Cao's granduncle matches those of his present descendants: a commentary on present Y chromosomes reveal the ancestry of Emperor CAO Cao of 1800 years ago.}, journal = {Journal of human genetics}, volume = {58}, number = {4}, pages = {238-239}, doi = {10.1038/jhg.2013.5}, pmid = {23407348}, issn = {1435-232X}, mesh = {*Chromosomes, Human, Y ; Humans ; }, }
@article {pmid23405111, year = {2013}, author = {Baker, DM and Weigt, L and Fogel, M and Knowlton, N}, title = {Ancient DNA from coral-hosted Symbiodinium reveal a static mutualism over the last 172 years.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e55057}, pmid = {23405111}, issn = {1932-6203}, mesh = {Adaptation, Psychological/physiology ; Animals ; Anthozoa/*genetics ; Biological Evolution ; DNA/*genetics ; DNA, Ribosomal/genetics ; Dinoflagellida/*genetics ; Ecology ; Environment ; Genotype ; Oceans and Seas ; Phylogeny ; Symbiosis/genetics ; Temperature ; }, abstract = {Ancient DNA (aDNA) provides powerful evidence for detecting the genetic basis for adaptation to environmental change in many taxa. Among the greatest of changes in our biosphere within the last century is rapid anthropogenic ocean warming. This phenomenon threatens corals with extinction, evidenced by the increasing observation of widespread mortality following mass bleaching events. There is some evidence and conjecture that coral-dinoflagellate symbioses change partnerships in response to changing external conditions over ecological and evolutionary timescales. Until now, we have been unable to ascertain the genetic identity of Symbiodinium hosted by corals prior to the rapid global change of the last century. Here, we show that Symbiodinium cells recovered from dry, century old specimens of 6 host species of octocorals contain sufficient DNA for amplification of the ITS2 subregion of the nuclear ribosomal DNA, commonly used for genotyping within this genus. Through comparisons with modern specimens sampled from similar locales we show that symbiotic associations among several species have been static over the last century, thereby suggesting that adaptive shifts to novel symbiont types is not common among these gorgonians, and perhaps, symbiotic corals in general.}, }
@article {pmid23372650, year = {2013}, author = {Pilli, E and Modi, A and Serpico, C and Achilli, A and Lancioni, H and Lippi, B and Bertoldi, F and Gelichi, S and Lari, M and Caramelli, D}, title = {Monitoring DNA contamination in handled vs. directly excavated ancient human skeletal remains.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e52524}, pmid = {23372650}, issn = {1932-6203}, mesh = {Archaeology/methods/standards ; *Artifacts ; Bone and Bones/chemistry ; Burial ; DNA/*analysis ; *DNA Contamination ; DNA, Mitochondrial ; *Fossils ; Hair/chemistry ; Humans ; Polymerase Chain Reaction ; Specimen Handling/*standards ; Tooth/*chemistry ; }, abstract = {Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14(th) century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as "virgin samples" (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called "lab samples"(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from "lab samples" are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the "virgin samples" set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between "lab" and "virgin" samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history.}, }
@article {pmid23350155, year = {2012}, author = {Fromm-Dornieden, C and Pepperl, J and Herrmann, B and Hummel, S}, title = {Multiplex analysis of genetic markers related to body mass index (BMI) and bone mineral density (BMD).}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {69}, number = {4}, pages = {423-438}, doi = {10.1127/0003-5548/2012/0161}, pmid = {23350155}, issn = {0003-5548}, mesh = {Adult ; Alpha-Ketoglutarate-Dependent Dioxygenase FTO ; Aromatase/genetics ; Base Sequence ; *Body Mass Index ; Bone Density/*genetics ; Cemeteries ; DNA ; Female ; Genetic Markers/*genetics ; Genotyping Techniques/*methods ; Germany ; History, Medieval ; Humans ; Interleukin-6/genetics ; Low Density Lipoprotein Receptor-Related Protein-5/genetics ; Male ; *Microsatellite Repeats ; Molecular Sequence Data ; Paleopathology ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Proteins/genetics ; }, abstract = {The multiplex analysis system described here allows simultaneous typing of one short tandem repeat (STR) and three single nucleotide polymorphisms (SNPs) that are associated with obesity and/or osteoporosis. Genes that are related to a high body mass index (BMI) and/or a high bone mineral density (BMD) are presumed to give an advantage in surviving famines. This analysis system makes it possible to genotype the (TTTA)n polymorphism of CYP19 and three SNPs, namely the rs1800795 polymorphism of IL6, the rs373 6228 polymorphism of LRP5 and the rs993 9609 polymorphism of FTO, in a single PCR amplification in recent and ancient DNA samples. Furthermore, it allows a synchronous authentication of the results with the (TATC)n polymorphism of D13S317, the (TCTA)n polymorphism of D21S11 and the (TTTC)n polymorphism of FGA in a partial genetic fingerprinting. For this purpose, PCR products for fragment-length analysis, as well as those for sequence analysis, were amplified together. After amplification, the PCR product was split into two aliquots. The first aliquot was used for fragment-length analysis and the second one for sequence analysis. The analysis system described here has been optimized for analysing ancient samples, since only minimal amounts of material are available.}, }
@article {pmid23341875, year = {2013}, author = {McCallum, J and Hall, S and Lissone, I and Anderson, J and Huynen, L and Lambert, DM}, title = {Highly informative ancient DNA 'snippets' for New Zealand moa.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e50732}, pmid = {23341875}, issn = {1932-6203}, mesh = {Animals ; Bone and Bones/anatomy &amp; histology ; DNA, Mitochondrial/*genetics ; Extinction, Biological ; Haplotypes/genetics ; New Zealand ; Nucleic Acid Conformation ; Nucleotides/genetics ; Palaeognathae/anatomy &amp; histology/*genetics ; }, abstract = {BACKGROUND: Analysis of ancient DNA has provided invaluable information on past ecologies, ancient populations, and extinct species. We used a short snippet of highly variable mitochondrial control region sequence from New Zealand's moa to characterise a large number of bones previously intractable to DNA analysis as well as bone fragments from swamps to gain information about the haplotype diversity and phylogeography that existed in five moa species.<br><br>By targeting such 'snippets', we show that moa populations differed substantially in geographic structure that is likely to be related to population mobility and history. We show that populations of Pachyornis geranoides, Dinornis novaezealandiae, and Dinornis robustus were highly structured and some appear to have occupied the same geographic location for hundreds of thousands of years. In contrast, populations of the moa Anomalopteryx didiformis and Euryapteryx curtus were widespread, with specific populations of the latter occupying both the North and South Islands of New Zealand. We further show that for a specific area, in this case a North Island swamp, complete haplotype diversity and even sex can be recovered from collections of small, often discarded, bone fragments.<br><br>CONCLUSIONS/SIGNIFICANCE: Short highly variable mitochondrial 'snippets' allow successful typing of environmentally damaged and fragmented skeletal material, and can provide useful information about ancient population diversity and structure without the need to sample valuable, whole bones often held by museums.}, }
@article {pmid23339395, year = {2013}, author = {Niemi, M and Bläuer, A and Iso-Touru, T and Nyström, V and Harjula, J and Taavitsainen, JP and Storå, J and Lidén, K and Kantanen, J}, title = {Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland: comparison with contemporary sheep breeds.}, journal = {Genetics, selection, evolution : GSE}, volume = {45}, number = {1}, pages = {2}, pmid = {23339395}, issn = {1297-9686}, mesh = {Animals ; Animals, Inbred Strains ; Base Sequence ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Finland ; *Genetic Variation ; Haplotypes ; Molecular Sequence Data ; Phylogeny ; Population/genetics ; SOXB1 Transcription Factors/genetics ; Sheep/*genetics ; Y Chromosome/*genetics ; }, abstract = {BACKGROUND: Several molecular and population genetic studies have focused on the native sheep breeds of Finland. In this work, we investigated their ancestral sheep populations from Iron Age, Medieval and Post-Medieval periods by sequencing a partial mitochondrial DNA D-loop and the 5'-promoter region of the SRY gene. We compared the maternal (mitochondrial DNA haplotypes) and paternal (SNP oY1) genetic diversity of ancient sheep in Finland with modern domestic sheep populations in Europe and Asia to study temporal changes in genetic variation and affinities between ancient and modern populations.<br><br>RESULTS: A 523-bp mitochondrial DNA sequence was successfully amplified for 26 of 36 sheep ancient samples i.e. five, seven and 14 samples representative of Iron Age, Medieval and Post-Medieval sheep, respectively. Genetic diversity was analyzed within the cohorts. This ancient dataset was compared with present-day data consisting of 94 animals from 10 contemporary European breeds and with GenBank DNA sequence data to carry out a haplotype sharing analysis. Among the 18 ancient mitochondrial DNA haplotypes identified, 14 were present in the modern breeds. Ancient haplotypes were assigned to the highly divergent ovine haplogroups A and B, haplogroup B being the major lineage within the cohorts. Only two haplotypes were detected in the Iron Age samples, while the genetic diversity of the Medieval and Post-Medieval cohorts was higher. For three of the ancient DNA samples, Y-chromosome SRY gene sequences were amplified indicating that they originated from rams. The SRY gene of these three ancient ram samples contained SNP G-oY1, which is frequent in modern north-European sheep breeds.<br><br>CONCLUSIONS: Our study did not reveal any sign of major population replacement of native sheep in Finland since the Iron Age. Variations in the availability of archaeological remains may explain differences in genetic diversity estimates and patterns within the cohorts rather than demographic events that occurred in the past. Our ancient DNA results fit well with the genetic context of domestic sheep as determined by analyses of modern north-European sheep breeds.}, }
@article {pmid23321233, year = {2013}, author = {Brundin, M and Figdor, D and Sundqvist, G and Sjögren, U}, title = {DNA binding to hydroxyapatite: a potential mechanism for preservation of microbial DNA.}, journal = {Journal of endodontics}, volume = {39}, number = {2}, pages = {211-216}, doi = {10.1016/j.joen.2012.09.013}, pmid = {23321233}, issn = {1878-3554}, mesh = {Adult ; Base Pairing/genetics ; Blood ; Chelating Agents/chemistry ; DNA, Bacterial/analysis/*chemistry ; Deoxyribonuclease I/chemistry ; Durapatite/*chemistry ; Edetic Acid/chemistry ; Electrophoresis, Agar Gel ; Fusobacterium nucleatum/genetics ; Humans ; *Immobilized Nucleic Acids ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Temperature ; Time Factors ; Water/chemistry ; }, abstract = {INTRODUCTION: Molecular methods are increasingly being deployed for analysis of the microbial flora in the root canal. Such methods are based on the assumption that recovered DNA is associated with the active endodontic infection, yet paleomicrobiology research is based on the recovery of ancient DNA from centuries-old tooth and bone samples, which points to considerable longevity of the DNA molecule in these tissues. The main component of dentin and bone is the mineral hydroxyapatite. This study assessed DNA binding to hydroxyapatite and whether this binding affinity stabilizes the DNA molecule in various media.<br><br>METHODS: DNA was extracted from Fusobacterium nucleatum and added to ceramic hydroxyapatite for 90 minutes. The DNA-bound hydroxyapatite was incubated in different media (ie, water, sera, and DNase I) for up to 3 months. At predetermined intervals, the recovery of detectable DNA was assessed by releasing the DNA from the hydroxyapatite using EDTA and evaluating the presence of DNA by gel electrophoresis and polymerase chain reaction (PCR) amplification.<br><br>RESULTS: When incubated with hydroxyapatite, nonamplified DNA was detectable after 3 months in water, sera, and DNase I. In contrast, DNA incubated in the same media (without hydroxyapatite) decomposed to levels below the detection level of PCR within 3 weeks, with the exception of DNA in sera in which PCR revealed a weak positive amplification product.<br><br>CONCLUSIONS: These results confirm a specific binding affinity of hydroxyapatite for DNA. Hydroxyapatite-bound DNA is more resistant to decay and less susceptible to degradation by serum and nucleases, which may account for the long-term persistence of DNA in bone and tooth.}, }
@article {pmid23317428, year = {2013}, author = {Draus-Barini, J and Walsh, S and Pośpiech, E and Kupiec, T and Głąb, H and Branicki, W and Kayser, M}, title = {Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains.}, journal = {Investigative genetics}, volume = {4}, number = {1}, pages = {3}, pmid = {23317428}, issn = {2041-2223}, abstract = {BACKGROUND: DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing persons, disaster victims or family relationships. They may also provide useful information towards unravelling controversies that surround famous historical individuals. Retrieving information about a deceased person's externally visible characteristics can be informative in both types of DNA analyses. Recently, we demonstrated that human eye and hair colour can be reliably predicted from DNA using the HIrisPlex system. Here we test the feasibility of the novel HIrisPlex system at establishing eye and hair colour of deceased individuals from skeletal remains of various post-mortem time ranges and storage conditions.<br><br>METHODS: Twenty-one teeth between 1 and approximately 800 years of age and 5 contemporary bones were subjected to DNA extraction using standard organic protocol followed by analysis using the HIrisPlex system.<br><br>RESULTS: Twenty-three out of 26 bone DNA extracts yielded the full 24 SNP HIrisPlex profile, therefore successfully allowing model-based eye and hair colour prediction. HIrisPlex analysis of a tooth from the Polish general W&#x142;adys&#x142;aw Sikorski (1881 to 1943) revealed blue eye colour and blond hair colour, which was positively verified from reliable documentation. The partial profiles collected in the remaining three cases (two contemporary samples and a 14th century sample) were sufficient for eye colour prediction.<br><br>CONCLUSIONS: Overall, we demonstrate that the HIrisPlex system is suitable, sufficiently sensitive and robust to successfully predict eye and hair colour from ancient and contemporary skeletal remains. Our findings, therefore, highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including ancient DNA studies, for the prediction of eye and hair colour of deceased individuals.}, }
@article {pmid23315957, year = {2013}, author = {Mendez, FL and Watkins, JC and Hammer, MF}, title = {Neandertal origin of genetic variation at the cluster of OAS immunity genes.}, journal = {Molecular biology and evolution}, volume = {30}, number = {4}, pages = {798-801}, doi = {10.1093/molbev/mst004}, pmid = {23315957}, issn = {1537-1719}, mesh = {2',5'-Oligoadenylate Synthetase/*genetics ; Animals ; Evolution, Molecular ; Genetic Loci/*immunology ; Genetic Speciation ; Gorilla gorilla/genetics ; Haplotypes ; Humans ; Linkage Disequilibrium ; Models, Genetic ; Multigene Family ; Neanderthals/*genetics ; Pan troglodytes/genetics ; Phylogeography ; *Polymorphism, Single Nucleotide ; }, abstract = {Analyses of ancient DNA from extinct humans reveal signals of at least two independent hybridization events in the history of non-African populations. To date, there are very few examples of specific genetic variants that have been rigorously identified as introgressive. Here, we survey DNA sequence variation in the OAS gene cluster on chromosome 12 and provide strong evidence that a haplotype extending for ~185 kb introgressed from Neandertals. This haplotype is nearly restricted to Eurasians and is estimated to have diverged from the Neandertal sequence ~125 kya. Despite the potential for novel functional variation, the observed frequency of this haplotype is consistent with neutral introgression. This is the second locus in the human genome, after STAT2, carrying distinct haplotypes that appear to have introgressed separately from both Neandertals and Denisova.}, }
@article {pmid23314239, year = {2013}, author = {Bouwman, A and Rühli, F}, title = {Advances in ancient DNA research can help radiological interpretations of archaeological diseases.}, journal = {Skeletal radiology}, volume = {42}, number = {6}, pages = {751-752}, pmid = {23314239}, issn = {1432-2161}, mesh = {Archaeology/*methods ; DNA, Bacterial/*genetics ; Forensic Genetics/*methods ; History, Ancient ; Mycobacterium tuberculosis/*genetics ; Radiography ; Radiology/*methods ; Tuberculosis/*diagnostic imaging/*genetics/history ; }, }
@article {pmid23308128, year = {2013}, author = {García-Robledo, C and Erickson, DL and Staines, CL and Erwin, TL and Kress, WJ}, title = {Tropical plant-herbivore networks: reconstructing species interactions using DNA barcodes.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e52967}, pmid = {23308128}, issn = {1932-6203}, mesh = {Animals ; Coleoptera/*physiology ; *DNA Barcoding, Taxonomic ; DNA, Plant/*genetics/*isolation &amp; purification ; *Herbivory ; Plant Leaves/genetics ; Plants/*genetics ; }, abstract = {Plants and their associated insect herbivores, represent more than 50% of all known species on earth. The first step in understanding the mechanisms generating and maintaining this important component of biodiversity is to identify plant-herbivore associations. In this study we determined insect-host plant associations for an entire guild of insect herbivores using plant DNA extracted from insect gut contents. Over two years, in a tropical rain forest in Costa Rica (La Selva Biological Station), we recorded the full diet breadth of rolled-leaf beetles, a group of herbivores that feed on plants in the order Zingiberales. Field observations were used to determine the accuracy of diet identifications using a three-locus DNA barcode (rbcL, trnH-psbA and ITS2). Using extraction techniques for ancient DNA, we obtained high-quality sequences for two of these loci from gut contents (rbcL and ITS2). Sequences were then compared to a comprehensive DNA barcode library of the Zingiberales. The rbcL locus identified host plants to family (success/sequence = 58.8%) and genus (success/sequence = 47%). For all Zingiberales except Heliconiaceae, ITS2 successfully identified host plants to genus (success/sequence = 67.1%) and species (success/sequence = 61.6%). Kindt's sampling estimates suggest that by collecting ca. four individuals representing each plant-herbivore interaction, 99% of all host associations included in this study can be identified to genus. For plants that amplified ITS2, 99% of the hosts can be identified to species after collecting at least four individuals representing each interaction. Our study demonstrates that host plant identifications at the species-level using DNA barcodes are feasible, cost-effective, and reliable, and that reconstructing plant-herbivore networks with these methods will become the standard for a detailed understanding of these interactions.}, }
@article {pmid23298497, year = {2012}, author = {Poma, A and Carlucci, G and Fontecchio, G}, title = {Immunogenetics and HPLC analyses contribute to understanding the etiopathology of rheumatoid arthritis through studies on ancient human remains.}, journal = {International journal of immunopathology and pharmacology}, volume = {25}, number = {4}, pages = {1075-1082}, doi = {10.1177/039463201202500424}, pmid = {23298497}, issn = {0394-6320}, mesh = {Arthritis, Psoriatic/etiology/genetics ; Arthritis, Rheumatoid/*etiology/genetics ; Chromatography, High Pressure Liquid/*methods ; DNA/*analysis ; HLA-DRB1 Chains/genetics ; Humans ; Immunogenetics/*methods ; *Paleopathology ; }, abstract = {Genetic investigations on ancient human remains affected by rheumatological pathologies are a research field of particular interest for identifying origins and the etiopathology of diseases, especially those having an autoimmune background such as rheumatoid arthritis (RA). We wish to demonstrate how reliable studies concerning this topic require collaboration between multiple disciplines, usually starting from paleopathologic observations up to immunogenetic screening, even involving analytical chemistry. Here, we focused our investigation on the skeleton of Cardinal Carlo de'Medici (1595-1666) for whom RA and psoriatic arthritis (PsA) were postulated after paleopathologic examination. RA susceptibility is linked to specific HLA alleles belonging to DRB1 04 locus, such as DRB1 0401, while Cw 0602 and DRB1 07 predispose to PsA. Thus, we genotyped the Cardinal?s remains to search for RA or PsA risk genes. Ancient DNA is often subjected to hydrolysis followed by fragmentation. For this reason, all immunogenetic tests were preceded by an original RP-HPLC-FL method able to inform on the ancient DNA preservation and the extent of contamination, with the purpose of avoiding the risk of false positive results. After DNA isolation from a piece of bone from the Cardinal, PCR-SSP and reverse-SSO hybridization assays were applied to perform genomic HLA-typing. RP-HPLC-FL analysis revealed a good preservation of DNA without contamination by exogenous genomes. Molecular tests assigned to the Cardinal the genotype DRB1 0401/1102 for HLA-DRB locus and Cw 04/ 12 for HLA-C locus, data that support a genetic predisposition for RA but not for PsA. This multidisciplinary study has allowed us: (i) to ascertain that the remains undoubtedly belonged to the specific subject, Cardinal Carlo de?Medici; (ii) to sustain that the subject suffered from RA rather then that PsA, and (iii) to state that RA was already widespread in Europe at the Renaissance age, despite some authors claiming that the disease was introduced to the Old Continent from America after colonization during the 18th century.}, }
@article {pmid23295167, year = {2013}, author = {Liu, H and Tian, X and Zhang, Y and Wang, C and Jiang, H}, title = {The discovery of Artemisia annua L. in the Shengjindian cemetery, Xinjiang, China and its implications for early uses of traditional Chinese herbal medicine qinghao.}, journal = {Journal of ethnopharmacology}, volume = {146}, number = {1}, pages = {278-286}, doi = {10.1016/j.jep.2012.12.044}, pmid = {23295167}, issn = {1872-7573}, mesh = {*Artemisia annua/genetics/ultrastructure ; Cemeteries ; China ; DNA, Plant/analysis ; *Drugs, Chinese Herbal ; Flowers/genetics/ultrastructure ; Microscopy, Electron, Scanning ; Phylogeny ; Plant Stems/genetics/ultrastructure ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Artemisia annua L., with the ancient name of qinghao, is a traditional Chinese herbal medicine. It has appeared in many ancient Chinese medical manuscripts, which describe its uses to include treatment of wounds, alleviating intermittent fevers, as well as enhancing the brightness of eyes and even improving longevity.<br><br>MATERIALS AND METHODS: A sheaf of plant remains, including stalks and inflorescence intentionally placed in the corner of a tomb, have been recovered from the Shengjindian cemetery (about 2400-2000 BP on the basis of (14)C dating), Turpan, Xinjiang, China. The morphology of these materials was examined using a stereomicroscope and a scanning electron microscope. Ancient DNA was also extracted from these remains.<br><br>RESULTS: By comparing the morphological and DNA characteristics with modern specimens, these plant remains were identified to belong to Artemisia annua L. Owing to its strong fragrance, these plant remains are suggested as serving to disguise the odor of the deceased.<br><br>CONCLUSIONS: This is the first material archaeological evidence to date despite numerous records of A. annua in ancient Chinese texts as herbal medicine qinghao, though it seems to have been employed as odor suppressant, not for medical purpose.}, }
@article {pmid26000423, year = {2013}, author = {Garrigos, YE and Hugueny, B and Koerner, K and Ibañez, C and Bonillo, C and Pruvost, P and Causse, R and Cruaud, C and Gaubert, P}, title = {Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae).}, journal = {Zootaxa}, volume = {3640}, number = {}, pages = {373-394}, doi = {10.11646/zootaxa.3640.3.3}, pmid = {26000423}, issn = {1175-5326}, mesh = {Animal Structures/anatomy &amp; histology ; Animals ; DNA/*genetics ; Evolution, Molecular ; Female ; Killifishes/anatomy &amp; histology/*classification/*genetics ; Male ; Museums ; Phylogeny ; Preservation, Biological ; }, abstract = {Specimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. Although fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of DNA, few ancient DNA protocols have been applied to such material. In this study, we describe a non-invasive Guanidine-based (GuSCN) ancient DNA extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus Orestias (Cyprinodontidae: Teleostei). The latter regroups pupfishes endemic to the inter-Andean basin that have been considered as a 'species flock', and for which the morphology-based taxonomic delimitations have been hotly debated. We extracted DNA from the type specimens of Orestias kept at the Muséum National d'Histoire Naturelle of Paris, France, including the extinct species O. cuvieri. We then built the first molecular (control region [CR] and rhodopsin [RH]) phylogeny including historical and recently collected representatives of all the Orestias complexes as recognized by Parenti (1984a): agassizii, cuvieri, gilsoni and mulleri. Our ancient DNA extraction protocol was validated after PCR amplification through an approach based on fragment-by-fragment chimera detection. After optimization, we were able to amplify < 200 bp fragments from both mitochondrial and nuclear DNA (CR and RH, respectively) from probably formalin-fixed type specimens bathed entirely in the extraction fluid. Most of the individuals exhibited few modifications of their external structures after GuSCN bath. Our approach combining type material and 'fresh' specimens allowed us to taxonomically delineate four clades recovered from the well-resolved CR tree into four redefined complexes: agassizii (sensu stricto, i.e. excluding luteus-like species), luteus, cuvieri and gilsoni. The mulleri complex is polyphyletic. Our phylogenetic analyses based on both mitochondrial and nuclear DNA revealed a main, deep dichotomy within the genus Orestias, separating the agassizii complex from a clade grouped under shallow dichotomies as (luteus, (cuvieri, gilsoni)). This 'deep and shallow' diversification pattern could fit within a scenario of ancient divergence between the agassizii complex and the rest of Orestias, followed by a recent diversification or adaptive radiation within each complex during the Pleistocene, in- and outside the Lake Titicaca. We could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. As a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for Orestias. Although not included in our phylogenetic analysis, the syntype of O. jussiei could not be assigned to the agassizii complex as newly defined. The CR sequence of the extinct O. cuvieri was recovered within the cuvieri clade (same haplotype as one representative of O. pentlandii), so the mtDNA of the former species might still be represented in the wild.}, }
@article {pmid25807700, year = {2013}, author = {De Angelis, F and Scorrano, G and Rickards, O}, title = {[Ancient DNA: principles and methodologies].}, journal = {Medicina nei secoli}, volume = {25}, number = {1}, pages = {51-83}, pmid = {25807700}, issn = {0394-9001}, mesh = {Archaeology/*methods ; DNA/analysis/*genetics ; Humans ; Paleontology/*methods ; Sequence Analysis, DNA ; }, abstract = {Paleogenetics is providing increasing evidence about the biological characteristics of ancient populations. This paper examines the guiding principles and methodologies to the study of ancient DNA with constant references to the state of the art in this fascinating disciplin.}, }
@article {pmid24861860, year = {2013}, author = {Gerbault, P}, title = {The onset of lactase persistence in Europe.}, journal = {Human heredity}, volume = {76}, number = {3-4}, pages = {154-161}, doi = {10.1159/000360136}, pmid = {24861860}, issn = {1423-0062}, mesh = {Dairying ; Demography ; Europe ; Humans ; Lactase/*genetics ; *Quantitative Trait, Heritable ; Selection, Genetic ; }, abstract = {The genomic region containing the lactase (LCT) gene shows one of the strongest signals of positive selection in Europeans, detectable using a range of approaches including haplotype length, linked microsatellite variation and population-differentiation-based tests. Lactase is the enzyme that carries out the digestion of the milk sugar lactose. Its expression decreases at some point after the weaning period is over in most mammals and in around 68% of all living adult humans. However, in some humans, particularly those from populations with a history of dairying, lactase is expressed throughout adulthood. This trait is called lactase persistence (LP), and in people of European ancestry, it is associated with a single mutation (-13910*T). Evidence from the detection of dairy fat residues in potsherds, and allele frequencies in ancient DNA samples suggest that LP arose after dairying practices had developed. However, the reasons why LP may have been advantageous are still debated, and the respective contribution of demography and natural selection remains to be disentangled. This paper discusses various studies, from archaeology to population genetics, that have shed some light on the subject by investigating the evolution of LP in Europe.}, }
@article {pmid24861859, year = {2013}, author = {Currat, M and Silva, NM}, title = {Investigating European genetic history through computer simulations.}, journal = {Human heredity}, volume = {76}, number = {3-4}, pages = {142-153}, doi = {10.1159/000360162}, pmid = {24861859}, issn = {1423-0062}, mesh = {*Computer Simulation ; DNA/genetics ; Europe ; *Genetic Variation ; Genetics, Population/*history ; History, Ancient ; Humans ; White People/*genetics ; }, abstract = {BACKGROUND/AIMS: The genetic diversity of Europeans has been shaped by various evolutionary forces including their demographic history. Genetic data can thus be used to draw inferences on the population history of Europe using appropriate statistical methods such as computer simulation, which constitutes a powerful tool to study complex models.<br><br>METHODS: Here, we focus on spatially explicit simulation, a method which takes population movements over space and time into account. We present its main principles and then describe a series of studies using this approach that we consider as particularly significant in the context of European prehistory.<br><br>RESULTS AND CONCLUSION: All simulation studies agree that ancient demographic events played a significant role in the establishment of the European gene pool; but while earlier works support a major genetic input from the Near East during the Neolithic transition, the most recent ones revalue positively the contribution of pre-Neolithic hunter-gatherers and suggest a possible impact of very ancient demographic events. This result of a substantial genetic continuity from pre-Neolithic times to the present challenges some recent studies analyzing ancient DNA. We discuss the possible reasons for this discrepancy and identify future lines of investigation in order to get a better understanding of European evolution.}, }
@article {pmid24861858, year = {2013}, author = {Barbujani, G}, title = {Genetic evidence for prehistoric demographic changes in Europe.}, journal = {Human heredity}, volume = {76}, number = {3-4}, pages = {133-141}, doi = {10.1159/000357957}, pmid = {24861858}, issn = {1423-0062}, mesh = {*Demography ; Europe ; Founder Effect ; *Genetics, Population ; Humans ; Models, Biological ; Time Factors ; }, abstract = {OBJECTIVES: Two main models have been proposed to explain the origins of the patterns of genetic variation in Europe, one emphasizing Paleolithic and the other Neolithic immigration from the Southeast. In this paper, I summarize how the models developed and how they can help address some open questions.<br><br>METHODS: The rationale of the methods traditionally supporting the Neolithic and the Paleolithic models is discussed, and the evidence supporting either of them is reviewed.<br><br>RESULTS: Ancient DNA evidence proves for good that the studies traditionally supporting the Paleolithic model had serious methodological flaws. This does not imply that the alternative model is right, but rather calls for further analyses explicitly testing the two models against the genomic information now available.<br><br>CONCLUSIONS: Questions that need to be addressed include whether the two main models differ enough to be discriminated by analyses of modern DNA diversity, and to what extent inferences from ancient mitochondrial DNA can be trusted in the absence of sufficient datasets of ancient nuclear DNA. The time seems ripe for the construction of a more complex (and hence more realistic) model, incorporating the possibility of different processes affecting different geographic locations at different times.}, }
@article {pmid24861857, year = {2013}, author = {Deguilloux, MF and Mendisco, F}, title = {Ancient DNA: A window to the past of Europe.}, journal = {Human heredity}, volume = {76}, number = {3-4}, pages = {121-132}, doi = {10.1159/000356933}, pmid = {24861857}, issn = {1423-0062}, mesh = {Biological Evolution ; DNA/*genetics ; Europe ; Gene Pool ; Geography ; History, Ancient ; Humans ; Time Factors ; }, abstract = {OBJECTIVES: The history of European populations is characterised by numerous migrations or demographic events that are likely to have had major impacts on the European gene pool patterns. This paper will focus on how ancient DNA (aDNA) data contribute to our understanding of past population dynamics in Europe.<br><br>METHODS: Technological challenges of the palaeogenetic approach will be discussed. With these limitations in mind, it will be shown that the acquisition of aDNA now permits a glimpse of how human genetic diversity has changed, spatially and temporally, in Europe, from the Palaeolithic through to the present day.<br><br>RESULTS: Although early modern human DNA sequences come only from rare exceptionally well-preserved specimens, genetic samples of a reasonable size are becoming available for the Mesolithic and the Neolithic periods, permitting a discussion of regional variation in the inferred mode of the spread of farming. Palaeogenetic data collected for ancient and more recent periods regularly demonstrate genetic discontinuity between past and present populations.<br><br>CONCLUSIONS: The results indicate that only large diachronic aDNA datasets from throughout Europe will permit researchers to reliably identify all demographic and evolutionary events that shaped the modern European gene pool.}, }
@article {pmid23274747, year = {2012}, author = {Hawks, J}, title = {Dynamics of genetic and morphological variability within Neandertals.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {90}, number = {}, pages = {81-87}, doi = {10.4436/jass.90019}, pmid = {23274747}, issn = {2037-0644}, mesh = {Animals ; *Anthropology, Physical ; Archaeology ; Biological Evolution ; DNA, Mitochondrial ; Europe ; Genetic Variation ; Neanderthals/*anatomy &amp; histology/*genetics ; Population Dynamics ; Tool Use Behavior ; }, abstract = {Paleogenomics may suggest changes to the way anthropologists have discussed the dynamics and morphological diversity among Neandertals. Genetic comparisons show that later Neandertals had relatively low autosomal genetic variation compared to recent humans. The known mitochondrial sample from Neandertals covers a broader geographic and temporal range, and shows greater diversity. This review addresses how genetic data compare to morphological and archaeological evidence about Neandertal variation and dynamics. Traditional views emphasized the morphological differences between western and eastern Neandertal populations, and between early and later Neandertals. Genomes broadly support these groupings, without resolving the outstanding question of the affinities of specimens from southwest Asia. However, the pattern of genetic variation appears to reject a long, in situ transformation of Neandertal groups over time, suggesting instead a more rapid process of regional dispersal and partial population replacement. Archaeological indicators sample dynamics on a much finer timescale than morphological or genetic evidence, and point to dispersal and turnover among Neandertals on a regional scale. In this way, genetic evidence may provide a bridge between the timescales relevant to morphological and archaeological comparisons. New ways of looking at the morphology of Neandertals may yield a better picture of their interactions and movements.}, }
@article {pmid23249313, year = {2012}, author = {Wang, H and Chen, L and Ge, B and Zhang, Y and Zhu, H and Zhou, H}, title = {Genetic data suggests that the Jinggouzi people are associated with the Donghu, an ancient nomadic group of North China.}, journal = {Human biology}, volume = {84}, number = {4}, pages = {365-378}, doi = {10.3378/027.084.0402}, pmid = {23249313}, issn = {1534-6617}, mesh = {Asian People/*genetics ; China ; DNA, Mitochondrial ; Female ; Genetic Markers ; Genotyping Techniques ; *Haplotypes ; *Human Migration ; Humans ; Male ; Phylogeography ; Polymorphism, Single Nucleotide ; *Transients and Migrants ; }, abstract = {Nomadic populations have played a significant role in the history of not only China but also in many nations worldwide. Because they had no written language, an important aspect in the study of these people is the discovery of their tombs. It has been generally accepted that Xiongnu was the first empire created by a nomadic tribe in the 3rd century BC. However, little population genetic information is available concerning the Donghu, another flourishing nomadic tribe at the same period because of the restriction of materials until the Jinggouzi site was excavated. In order to test the genetic characteristics of ancient people in this site and to explore the relationship between Jinggouzis and Donghus, two uniparentally inherited markers were analyzed from 42 human remains in this site, which was located in northern China, dated approximately 2500 years ago. With ancient DNA technology, four mtDNA haplogroups (D, G, C, and M10) and one Y chromosome haplogroup (C) were identified using mitochondrial DNA and Y-chromosome single nucleotide polymorphisms. Those haplogroups are common in North Asia and East Asia. The Jinggouzi people were genetically closest to the Xianbeis in ancient populations and to the Oroqens among extant populations, who were all pastoralists. This might indicate that ancient Jinggouzi people were nomads. Meanwhile, according to the genetic data and the evidences in archaeology, we inferred that Jinggouzi people were associated with Donghu. It is of much value to trace the history of the Donghu tribe and this might show some insight into the ancient nomadic society.}, }
@article {pmid23201231, year = {2013}, author = {Lowery, RK and Herrera, K and Uribe, G and Reguiero, M and Herrera, RJ}, title = {Sub-population structure evident in forensic Y-STR profiles from Armenian geographical groups.}, journal = {Legal medicine (Tokyo, Japan)}, volume = {15}, number = {2}, pages = {85-90}, doi = {10.1016/j.legalmed.2012.10.003}, pmid = {23201231}, issn = {1873-4162}, mesh = {Armenia ; *Chromosomes, Human, Y ; DNA Fingerprinting ; Gene Frequency ; Genetic Variation ; *Genetics, Population ; Genotype ; Haplotypes ; Humans ; *Microsatellite Repeats ; Multiplex Polymerase Chain Reaction ; Phylogeography ; Principal Component Analysis ; }, abstract = {Over the course of its long history, Armenia has acted as both a source of numerous indigenous cultures and as a recipient of foreign invasions. As a result of this complex history among populations, the gene pool of the Armenian population may contain traces of historically well-documented ancient migrations. Furthermore, the regions within the historical boundaries of Armenia possess unique demographic histories, having hosted both autochthonous and specific exogenous genetic influences. In the present study, we analyze the Armenian population sub-structure utilizing 17 Y-chromosome short tandem repeat (Y-STR) loci of 412 Armenians from four geographically and anthropologically well-defined groups (Ararat Valley, Gardman, Lake Van and Sasun). To place the genetic composition of Armenia in a regional and historic context, we have compared the Y-STR profiles from these four Armenian collections to 18 current-day Eurasian populations and two ancient DNA collections. Our results illustrate regional trends in Armenian paternal lineages and locale-specific patterns of affinities with neighboring regions. Additionally, we observe a phylogenetic relationship between the Northern Caucasus and the group from Sasun, which offers an explanation for the genetic divergence of this group from other three Armenian collections. These findings highlight the importance of analyzing both general populations as well as geographically defined sub-populations when utilizing Y-STRs for forensic analyses and population genetics studies.}, }
@article {pmid23185018, year = {2012}, author = {Brace, S and Palkopoulou, E and Dalén, L and Lister, AM and Miller, R and Otte, M and Germonpré, M and Blockley, SP and Stewart, JR and Barnes, I}, title = {Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {50}, pages = {20532-20536}, pmid = {23185018}, issn = {1091-6490}, mesh = {Animals ; *Arvicolinae/classification/genetics ; Biodiversity ; Climate Change ; DNA, Mitochondrial/genetics ; *Ecosystem ; Europe ; Evolution, Molecular ; *Extinction, Biological ; Fossils ; Molecular Sequence Data ; Paleontology ; Phylogeny ; Population Dynamics ; }, abstract = {The Late Pleistocene global extinction of many terrestrial mammal species has been a subject of intensive scientific study for over a century, yet the relative contributions of environmental changes and the global expansion of humans remain unresolved. A defining component of these extinctions is a bias toward large species, with the majority of small-mammal taxa apparently surviving into the present. Here, we investigate the population-level history of a key tundra-specialist small mammal, the collared lemming (Dicrostonyx torquatus), to explore whether events during the Late Pleistocene had a discernible effect beyond the large mammal fauna. Using ancient DNA techniques to sample across three sites in North-West Europe, we observe a dramatic reduction in genetic diversity in this species over the last 50,000 y. We further identify a series of extinction-recolonization events, indicating a previously unrecognized instability in Late Pleistocene small-mammal populations, which we link with climatic fluctuations. Our results reveal climate-associated, repeated regional extinctions in a keystone prey species across the Late Pleistocene, a pattern likely to have had an impact on the wider steppe-tundra community, and one that is concordant with environmental change as a major force in structuring Late Pleistocene biodiversity.}, }
@article {pmid23180580, year = {2013}, author = {Gill, MS and Lemey, P and Faria, NR and Rambaut, A and Shapiro, B and Suchard, MA}, title = {Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.}, journal = {Molecular biology and evolution}, volume = {30}, number = {3}, pages = {713-724}, pmid = {23180580}, issn = {1537-1719}, support = {T32 AI007370/AI/NIAID NIH HHS/United States ; R01 GM086887/GM/NIGMS NIH HHS/United States ; R01 HG006139/HG/NHGRI NIH HHS/United States ; 260864/ERC_/European Research Council/International ; 5T32AI007370-22/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; Bayes Theorem ; Computer Simulation ; Evolution, Molecular ; Genes, Viral ; *Genetic Loci ; Genetic Speciation ; HIV-1/genetics ; Humans ; Markov Chains ; *Models, Genetic ; Monte Carlo Method ; Mutation ; Population Density ; Population Dynamics ; Statistics, Nonparametric ; }, abstract = {Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a Gaussian Markov random field (GMRF) model for a single gene locus. Here, we present a generalization of the GMRF model that allows for the analysis of multilocus sequence data. Using simulated data, we demonstrate the improved performance of our method to recover true population trajectories and the time to the most recent common ancestor (TMRCA). We analyze a multilocus alignment of HIV-1 CRF02_AG gene sequences sampled from Cameroon. Our results are consistent with HIV prevalence data and uncover some aspects of the population history that go undetected in Bayesian parametric estimation. Finally, we recover an older and more reconcilable TMRCA for a classic ancient DNA data set.}, }
@article {pmid23180578, year = {2013}, author = {Ottoni, C and Flink, LG and Evin, A and Geörg, C and De Cupere, B and Van Neer, W and Bartosiewicz, L and Linderholm, A and Barnett, R and Peters, J and Decorte, R and Waelkens, M and Vanderheyden, N and Ricaut, FX and Cakirlar, C and Cevik, O and Hoelzel, AR and Mashkour, M and Karimlu, AF and Seno, SS and Daujat, J and Brock, F and Pinhasi, R and Hongo, H and Perez-Enciso, M and Rasmussen, M and Frantz, L and Megens, HJ and Crooijmans, R and Groenen, M and Arbuckle, B and Benecke, N and Vidarsdottir, US and Burger, J and Cucchi, T and Dobney, K and Larson, G}, title = {Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics.}, journal = {Molecular biology and evolution}, volume = {30}, number = {4}, pages = {824-832}, pmid = {23180578}, issn = {1537-1719}, mesh = {Animal Distribution ; Animals ; Animals, Domestic/genetics ; Asia ; DNA, Mitochondrial/*genetics ; Europe ; Humans ; Molar/*anatomy &amp; histology ; Phylogeography ; Sequence Analysis, DNA ; Sus scrofa/*genetics ; Swine/genetics ; }, abstract = {Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ~8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.}, }
@article {pmid23171292, year = {2013}, author = {Bellemain, E and Davey, ML and Kauserud, H and Epp, LS and Boessenkool, S and Coissac, E and Geml, J and Edwards, M and Willerslev, E and Gussarova, G and Taberlet, P and Haile, J and Brochmann, C}, title = {Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost.}, journal = {Environmental microbiology}, volume = {15}, number = {4}, pages = {1176-1189}, doi = {10.1111/1462-2920.12020}, pmid = {23171292}, issn = {1462-2920}, mesh = {Animals ; Arctic Regions ; Ascomycota/genetics ; DNA Barcoding, Taxonomic ; DNA, Fungal/*analysis ; *Ecosystem ; Endophytes/genetics ; *Fossils ; Fungi/*classification/*genetics ; Genetic Variation/*genetics ; *High-Throughput Nucleotide Sequencing ; Insecta/microbiology ; Plants/microbiology ; Siberia ; Species Specificity ; }, abstract = {The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty-six sediment samples dated 16 000-32 000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 ± 3811 (mean ± SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 16 000-32 000 bp. However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one-third of the OTUs are presumed plant-associates (pathogens, saprotrophs and endophytes) typical of graminoid- and forb-rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.}, }
@article {pmid23170222, year = {2012}, author = {Elizabeth Alter, S and Rosenbaum, HC and Postma, LD and Whitridge, P and Gaines, C and Weber, D and Egan, MG and Lindsay, M and Amato, G and Dueck, L and Brownell, RL and Heide-Jørgensen, MP and Laidre, KL and Caccone, G and Hancock, BL}, title = {Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus).}, journal = {Ecology and evolution}, volume = {2}, number = {11}, pages = {2895-2911}, pmid = {23170222}, issn = {2045-7758}, abstract = {Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range-wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay-Davis Strait, Hudson Bay-Foxe Basin, Bering-Beaufort-Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period.}, }
@article {pmid23138153, year = {2013}, author = {Guy, PL}, title = {Ancient RNA? RT-PCR of 50-year-old RNA identifies peach latent mosaic viroid.}, journal = {Archives of virology}, volume = {158}, number = {3}, pages = {691-694}, doi = {10.1007/s00705-012-1527-0}, pmid = {23138153}, issn = {1432-8798}, mesh = {Nucleic Acid Conformation ; Plant Diseases/virology ; Plant Leaves/virology ; *Preservation, Biological ; Prunus/*virology ; *RNA, Viral ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; Time Factors ; Viroids/*genetics ; }, abstract = {The preservation of macromolecules is at best haphazard. Modern techniques have improved the detection of ancient DNA and proteins, but there is little information on the preservation of RNA. Fifty-year-old dried leaf material showing symptoms of peach calico disease was used successfully in RT-PCRs to amplify peach latent mosaic viroid (PLMVd) RNA and the mRNA for the large subunit of ribulose 1,5-bisphosphate carboxylase (rubisco). These results indicate that naked RNA may be preserved, under suitable conditions, for at least 50 years. The results are discussed in the context of ancient DNA and proteins and the process of fossilization.}, }
@article {pmid23091009, year = {2012}, author = {Bouwman, AS and Kennedy, SL and Müller, R and Stephens, RH and Holst, M and Caffell, AC and Roberts, CA and Brown, TA}, title = {Genotype of a historic strain of Mycobacterium tuberculosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {45}, pages = {18511-18516}, pmid = {23091009}, issn = {1091-6490}, mesh = {Bacterial Typing Techniques ; Base Sequence ; England ; Female ; Genome, Bacterial/genetics ; Genotype ; Humans ; Molecular Sequence Data ; Mycobacterium tuberculosis/*genetics ; Oligonucleotides/genetics ; *Paleontology ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The use of ancient DNA in paleopathological studies of tuberculosis has largely been restricted to confirmation of disease identifications made by skeletal analysis; few attempts at obtaining genotype data from archaeological samples have been made because of the need to perform different PCRs for each genetic locus being studied in an ancient DNA extract. We used a next generation sequencing approach involving hybridization capture directed at specific polymorphic regions of the Mycobacterium tuberculosis genome to identify a detailed genotype for a historic strain of M. tuberculosis from an individual buried in the 19th century St. George's Crypt, Leeds, West Yorkshire, England. We obtained 664,500 sequencing by oligonucleotide ligation and detection (SOLiD) reads that mapped to the targeted regions of the M. tuberculosis genome; the coverage included 218 of 247 SNPs, 10 of 11 insertion/deletion regions, and the repeat elements IS1081 and IS6110. The accuracy of the SOLiD data was checked by conventional PCRs directed at 11 SNPs and two insertion/deletions. The data placed the historic strain of M. tuberculosis in a group that is uncommon today, but it is known to have been present in North America in the early 20th century. Our results show the use of hybridization capture followed by next generation sequencing as a means of obtaining detailed genotypes of ancient varieties of M. tuberculosis, potentially enabling meaningful comparisons between strains from different geographic locations and different periods in the past.}, }
@article {pmid23076995, year = {2012}, author = {Mata-Míguez, J and Overholtzer, L and Rodríguez-Alegría, E and Kemp, BM and Bolnick, DA}, title = {The genetic impact of Aztec imperialism: ancient mitochondrial DNA evidence from Xaltocan, Mexico.}, journal = {American journal of physical anthropology}, volume = {149}, number = {4}, pages = {504-516}, doi = {10.1002/ajpa.22152}, pmid = {23076995}, issn = {1096-8644}, mesh = {Adult ; Bayes Theorem ; Bone and Bones/chemistry ; Child ; Child, Preschool ; DNA, Mitochondrial/analysis/*genetics ; Genetic Variation ; Haplotypes/genetics ; History, Medieval ; Humans ; Indians, Central American/*genetics/*history ; Infant ; Infant, Newborn ; Mexico ; Middle Aged ; Phylogeny ; Tooth/chemistry ; }, abstract = {In AD 1428, the city-states of Tenochtitlan, Texcoco, and Tlacopan formed the Triple Alliance, laying the foundations of the Aztec empire. Although it is well documented that the Aztecs annexed numerous polities in the Basin of Mexico over the following years, the demographic consequences of this expansion remain unclear. At the city-state capital of Xaltocan, 16th century documents suggest that the site's conquest and subsequent incorporation into the Aztec empire led to a replacement of the original Otomí population, whereas archaeological evidence suggests that some of the original population may have remained at the town under Aztec rule. To help address questions about Xaltocan's demographic history during this period, we analyzed ancient DNA from 25 individuals recovered from three houses rebuilt over time and occupied between AD 1240 and 1521. These individuals were divided into two temporal groups that predate and postdate the site's conquest. We determined the mitochondrial DNA haplogroup of each individual and identified haplotypes based on 372 base pair sequences of first hypervariable region. Our results indicate that the residents of these houses before and after the Aztec conquest have distinct haplotypes that are not closely related, and the mitochondrial compositions of the temporal groups are statistically different. Altogether, these results suggest that the matrilines present in the households were replaced following the Aztec conquest. This study therefore indicates that the Aztec expansion may have been associated with significant demographic and genetic changes within Xaltocan.}, }
@article {pmid23066327, year = {2012}, author = {Gasbarrini, G and Rickards, O and Martínez-Labarga, C and Pacciani, E and Chilleri, F and Laterza, L and Marangi, G and Scaldaferri, F and Gasbarrini, A}, title = {Origin of celiac disease: how old are predisposing haplotypes?.}, journal = {World journal of gastroenterology}, volume = {18}, number = {37}, pages = {5300-5304}, pmid = {23066327}, issn = {2219-2840}, mesh = {Archaeology/methods ; Celiac Disease/*diagnosis/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Female ; *Genetic Predisposition to Disease ; Genotype ; HLA Antigens/metabolism ; HLA-DQ Antigens/genetics ; *Haplotypes ; Humans ; Italy ; Malabsorption Syndromes/genetics ; Polymorphism, Genetic ; Risk ; }, abstract = {We recently presented the case of a first century AD young woman, found in the archaeological site of Cosa, showing clinical signs of malnutrition, such as short height, osteoporosis, dental enamel hypoplasia and cribra orbitalia, indirect sign of anemia, all strongly suggestive for celiac disease (CD). However, whether these findings were actually associated to CD was not shown based on genetic parameters. To investigate her human leukocyte antigen (HLA) class II polymorphism, we extracted DNA from a bone sample and a tooth and genotyped HLA using three HLA-tagging single nucleotide polymorphisms for DQ8, DQ2.2 and DQ2.5, specifically associated to CD. She displayed HLA DQ 2.5, the haplotype associated to the highest risk of CD. This is the first report showing the presence of a HLA haplotype compatible for CD in archaeological specimens.}, }
@article {pmid23052219, year = {2013}, author = {Lacan, M and Keyser, C and Crubézy, E and Ludes, B}, title = {Ancestry of modern Europeans: contributions of ancient DNA.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {70}, number = {14}, pages = {2473-2487}, pmid = {23052219}, issn = {1420-9071}, mesh = {Animals ; DNA, Mitochondrial/analysis/*genetics ; Genetics, Population ; Genome ; Haplotypes ; History, Ancient ; Humans ; Neanderthals/genetics ; Paleopathology ; White People/*genetics/history ; }, abstract = {Understanding the peopling history of Europe is crucial to comprehend the origins of modern populations. Of course, the analysis of current genetic data offers several explanations about human migration patterns which occurred on this continent, but it fails to explain precisely the impact of each demographic event. In this context, direct access to the DNA of ancient specimens allows the overcoming of recent demographic phenomena, which probably highly modified the constitution of the current European gene pool. In recent years, several DNA studies have been successfully conducted from ancient human remains thanks to the improvement of molecular techniques. They have brought new fundamental information on the peopling of Europe and allowed us to refine our understanding of European prehistory. In this review, we will detail all the ancient DNA studies performed to date on ancient European DNA from the Middle Paleolithic to the beginning of the protohistoric period.}, }
@article {pmid23025275, year = {2012}, author = {Wood, JR and Wilmshurst, JM and Worthy, TH and Holzapfel, AS and Cooper, A}, title = {A lost link between a flightless parrot and a parasitic plant and the potential role of coprolites in conservation paleobiology.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {26}, number = {6}, pages = {1091-1099}, doi = {10.1111/j.1523-1739.2012.01931.x}, pmid = {23025275}, issn = {1523-1739}, mesh = {Animals ; Balanophoraceae/*physiology ; *Conservation of Natural Resources ; DNA/analysis ; Diet ; *Endangered Species ; Feces/chemistry ; *Food Chain ; *Fossils ; New Zealand ; Parrots/*physiology ; Plant Dispersal ; Pollen/chemistry ; Polymerase Chain Reaction ; }, abstract = {Late Quaternary extinctions and population fragmentations have severely disrupted animal-plant interactions globally. Detection of disrupted interactions often relies on anachronistic plant characteristics, such as spines in the absence of large herbivores or large fruit without dispersers. However, obvious anachronisms are relatively uncommon, and it can be difficult to prove a direct link between the anachronism and a particular faunal taxon. Analysis of coprolites (fossil feces) provides a novel way of exposing lost interactions between animals (depositors) and consumed organisms. We analyzed ancient DNA to show that a coprolite from the South Island of New Zealand was deposited by the rare and threatened kakapo (Strigops habroptilus), a large, nocturnal, flightless parrot. When we analyzed the pollen and spore content of the coprolite, we found pollen from the cryptic root-parasite Dactylanthus taylorii. The relatively high abundance (8.9% of total pollen and spores) of this zoophilous pollen type in the coprolite supports the hypothesis of a former direct feeding interaction between kakapo and D. taylorii. The ranges of both species have contracted substantially since human settlement, and their present distributions no longer overlap. Currently, the lesser short-tailed bat (Mystacina tuberculata) is the only known native pollinator of D. taylorii, but our finding raises the possibility that birds, and other small fauna, could have once fed on and pollinated the plant. If confirmed, through experimental work and observations, this finding may inform conservation of the plant. For example, it may be possible to translocate D. taylorii to predator-free offshore islands that lack bats but have thriving populations of endemic nectar-feeding birds. The study of coprolites of rare or extinct taxonomic groups provides a unique way forward to expand existing knowledge of lost plant and animal interactions and to identify pollination and dispersal syndromes. This approach of linking paleobiology with neoecology offers significant untapped potential to help inform conservation and restoration plans.}, }
@article {pmid23024187, year = {2013}, author = {Molak, M and Lorenzen, ED and Shapiro, B and Ho, SY}, title = {Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages.}, journal = {Molecular biology and evolution}, volume = {30}, number = {2}, pages = {253-262}, doi = {10.1093/molbev/mss232}, pmid = {23024187}, issn = {1537-1719}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; Ursidae ; }, abstract = {In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.}, }
@article {pmid22976345, year = {2012}, author = {Hajdu, T and Donoghue, HD and Bernert, Z and Fóthi, E and Kővári, I and Marcsik, A}, title = {A case of spinal tuberculosis from the middle ages in Transylvania (Romania).}, journal = {Spine}, volume = {37}, number = {25}, pages = {E1598-601}, doi = {10.1097/BRS.0b013e31827300dc}, pmid = {22976345}, issn = {1528-1159}, mesh = {Adult ; Base Sequence ; *DNA, Bacterial/isolation &amp; purification ; History, Medieval ; Humans ; Hungary ; Male ; Middle Aged ; Molecular Sequence Data ; *Mycobacterium tuberculosis/genetics ; Paleopathology ; Polymerase Chain Reaction ; Romania ; Sequence Analysis, DNA ; *Spine/microbiology/pathology ; Spondylitis/diagnosis/*history/microbiology ; Tuberculosis, Spinal/complications/diagnosis/*history/microbiology ; }, abstract = {STUDY DESIGN: Case report.<br><br>OBJECTIVE: To characterize the paleopathology presented in the skeleton of a 45- to 50-year-old man indicative of tuberculous spondylitis and to confirm by the detection of ancient DNA.<br><br>SUMMARY OF BACKGROUND DATA: Tuberculosis (TB) is an infectious disease prevalent in both present and ancient human populations. The disease is primarily located within the lungs; although characteristic bone lesions can lead to a clear diagnosis, skeletal TB occurs in only 5% to 6% of TB infections, even in historical cases. In addition, the visual appearance of human skeletal remains may be influenced by the environmental conditions at the burial site. However, it is important to recognize ancient skeletal TB because it can provide important data on the history of Mycobacterium tuberculosis and give a unique opportunity for physicians to observe the natural outcome of the infection of the preantibiotic era.<br><br>METHODS: Paleopathological analysis was carried out using careful visual observation supported by ancient DNA analysis. Approximately 60 mg of bone powder from rib fragments was examined and DNA from the M. tuberculosis complex was detected by polymerase chain reaction (PCR) targeting specific genetic loci of the IS6110 and IS1081 regions.<br><br>RESULTS: The skeleton is part of a human osteoarchaeological collection (n = 274) from the 12th- to 13th-century Transylvanian archaeological site of Peteni, in modern-day Romania. The individual, a 45- to 50-year-old man, showed gross pathology typical of tuberculous spondylitis. The paleopathological diagnosis was supported by analysis for M. tuberculosis complex ancient DNA.<br><br>CONCLUSIONS: This case demonstrates that TB was present in Transylvania (Romania) during the 12th and 13th centuries and adds to the growing body of knowledge on the history of this disease.}, }
@article {pmid22958530, year = {2012}, author = {Sweet, MJ and Scriven, LA and Singleton, I}, title = {Microsatellites for microbiologists.}, journal = {Advances in applied microbiology}, volume = {81}, number = {}, pages = {169-207}, doi = {10.1016/B978-0-12-394382-8.00005-8}, pmid = {22958530}, issn = {0065-2164}, mesh = {Bacteria/genetics ; DNA ; *DNA Primers ; Fungi/genetics ; Genetic Markers ; *Microsatellite Repeats ; Sequence Analysis, DNA ; }, abstract = {Microsatellites are repeating sequences of 2-6base pairs of DNA. Currently, they are used as molecular markers in many organisms, specifically in genetic studies analyzing kinship and population structure. In addition, they can be used to study gene duplication and/or deletion. Although they are used in studies on microorganisms including fungi, bacteria, protists, and archaea, it appears that these genetic markers are not being utilized to their full microbiological potential. Microsatellites have many advantages over other genetic markers currently in use as they are in general species specific, and therefore, cross-contamination by nontarget organisms is rare. Furthermore, microsatellites are suitable for use with fast and cheap DNA extraction methods, with ancient DNA or DNA from hair and fecal samples used in noninvasive sampling, making them widely available as a genetic marker. Microsatellites have already proven to be a useful tool for evolutionary studies of pathogenic microorganisms such as Candida albicans and Helicobacter pylori, and the onset of new sequencing techniques (such as 454, PACBIO, and mini-ion sequencing) means the ability to detect such markers will become less time consuming and cheaper, thus further expanding their potential to answer important microbial ecology questions.}, }
@article {pmid22939251, year = {2012}, author = {Birchler, JA}, title = {Insights from paleogenomic and population studies into the consequences of dosage sensitive gene expression in plants.}, journal = {Current opinion in plant biology}, volume = {15}, number = {5}, pages = {544-548}, doi = {10.1016/j.pbi.2012.08.005}, pmid = {22939251}, issn = {1879-0356}, mesh = {Aneuploidy ; Chromosomes, Plant/genetics ; *Evolution, Molecular ; *Gene Dosage ; *Gene Duplication ; Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Genomics ; Models, Genetic ; Plants/*genetics ; Polyploidy ; }, abstract = {Classical studies of plant phenotypes of individuals with whole or partial genome dosage changes led to the concept of genomic balance. Subsequent studies of gene expression in ploidy and aneuploidy series showed a greater number of modulations in aneuploid plants than with whole genome changes leading to the idea that gene expression processes were modulated by stoichiometric changes of interacting regulatory factors. Recent studies of genomic sequences and copy number variants in populations reveal different fates of duplicate genes depending on whole genome or segmental duplication. Following polyploidy formation, members of macromolecular complexes persist in the evolutionary lineage longer than random genes and a complementary pattern is found for segmental duplications in that there is an underrepresentation of members of macromolecular complexes. These and other studies described suggest there are negative fitness consequences when an imbalance occurs for members of macromolecular complexes including regulatory functions.}, }
@article {pmid22937219, year = {2012}, author = {Giosan, L and Coolen, MJ and Kaplan, JO and Constantinescu, S and Filip, F and Filipova-Marinova, M and Kettner, AJ and Thom, N}, title = {Early anthropogenic transformation of the Danube-Black Sea system.}, journal = {Scientific reports}, volume = {2}, number = {}, pages = {582}, pmid = {22937219}, issn = {2045-2322}, mesh = {Black Sea ; *Conservation of Natural Resources ; Ecosystem ; Environmental Monitoring ; Europe, Eastern ; Food Chain ; Geography ; *Geologic Sediments ; Humans ; *Rivers ; Salinity ; *Seawater ; }, abstract = {Over the last century humans have altered the export of fluvial materials leading to significant changes in morphology, chemistry, and biology of the coastal ocean. Here we present sedimentary, paleoenvironmental and paleogenetic evidence to show that the Black Sea, a nearly enclosed marine basin, was affected by land use long before the changes of the Industrial Era. Although watershed hydroclimate was spatially and temporally variable over the last ~3000 years, surface salinity dropped systematically in the Black Sea. Sediment loads delivered by Danube River, the main tributary of the Black Sea, significantly increased as land use intensified in the last two millennia, which led to a rapid expansion of its delta. Lastly, proliferation of diatoms and dinoflagellates over the last five to six centuries, when intensive deforestation occurred in Eastern Europe, points to an anthropogenic pulse of river-borne nutrients that radically transformed the food web structure in the Black Sea.}, }
@article {pmid22936748, year = {2012}, author = {Gibbons, A}, title = {Ancient DNA. A crystal-clear view of an extinct girl's genome.}, journal = {Science (New York, N.Y.)}, volume = {337}, number = {6098}, pages = {1028-1029}, doi = {10.1126/science.337.6098.1028}, pmid = {22936748}, issn = {1095-9203}, mesh = {Animals ; DNA, Single-Stranded/*genetics/history/*isolation &amp; purification ; Evolution, Molecular ; Female ; *Fossils ; Genome, Human/*genetics ; History, Ancient ; Humans ; Sequence Analysis, DNA/history/*methods ; }, }
@article {pmid22923880, year = {2012}, author = {Kurushima, JD and Ikram, S and Knudsen, J and Bleiberg, E and Grahn, RA and Lyons, LA}, title = {Cats of the Pharaohs: Genetic Comparison of Egyptian Cat Mummies to their Feline Contemporaries.}, journal = {Journal of archaeological science}, volume = {39}, number = {10}, pages = {3217-3223}, pmid = {22923880}, issn = {0305-4403}, support = {R24 OD010928/OD/NIH HHS/United States ; R24 RR016094/RR/NCRR NIH HHS/United States ; }, abstract = {The ancient Egyptians mummified an abundance of cats during the Late Period (664 - 332 BC). The overlapping morphology and sizes of developing wildcats and domestic cats confounds the identity of mummified cat species. Genetic analyses should support mummy identification and was conducted on two long bones and a mandible of three cats that were mummified by the ancient Egyptians. The mummy DNA was extracted in a dedicated ancient DNA laboratory at the University of California - Davis, then directly sequencing between 246 and 402 bp of the mtDNA control region from each bone. When compared to a dataset of wildcats (Felis silvestris silvestris, F. s. tristrami, and F. chaus) as well as a previously published worldwide dataset of modern domestic cat samples, including Egypt, the DNA evidence suggests the three mummies represent common contemporary domestic cat mitotypes prevalent in modern Egypt and the Middle East. Divergence estimates date the origin of the mummies' mitotypes to between two and 7.5 thousand years prior to their mummification, likely prior to or during Egyptian Predyanstic and Early Dynastic Periods. These data are the first genetic evidence supporting that the ancient Egyptians used domesticated cats, F. s. catus, for votive mummies, and likely implies cats were domesticated prior to extensive mummification of cats.}, }
@article {pmid22905156, year = {2012}, author = {Thornton, EK and Emery, KF and Steadman, DW and Speller, C and Matheny, R and Yang, D}, title = {Earliest Mexican Turkeys (Meleagris gallopavo) in the Maya Region: implications for pre-Hispanic animal trade and the timing of turkey domestication.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42630}, pmid = {22905156}, issn = {1932-6203}, mesh = {Animals ; Animals, Domestic/*genetics ; Archaeology ; Bone and Bones/pathology ; DNA/genetics ; Diffusion ; Female ; Geography ; Male ; Mexico ; Models, Genetic ; Molecular Sequence Data ; Polymorphism, Genetic ; Turkeys/*genetics/*physiology ; }, abstract = {Late Preclassic (300 BC-AD 100) turkey remains identified at the archaeological site of El Mirador (Petén, Guatemala) represent the earliest evidence of the Mexican turkey (Meleagris gallopavo) in the ancient Maya world. Archaeological, zooarchaeological, and ancient DNA evidence combine to confirm the identification and context. The natural pre-Hispanic range of the Mexican turkey does not extend south of central Mexico, making the species non-local to the Maya area where another species, the ocellated turkey (Meleagris ocellata), is indigenous. Prior to this discovery, the earliest evidence of M. gallopavo in the Maya area dated to approximately one thousand years later. The El Mirador specimens therefore represent previously unrecorded Preclassic exchange of animals from northern Mesoamerica to the Maya cultural region. As the earliest evidence of M. gallopavo found outside its natural geographic range, the El Mirador turkeys also represent the earliest indirect evidence for Mesoamerican turkey rearing or domestication. The presence of male, female and sub-adult turkeys, and reduced flight morphology further suggests that the El Mirador turkeys were raised in captivity. This supports an argument for the origins of turkey husbandry or at least captive rearing in the Preclassic.}, }
@article {pmid22889475, year = {2012}, author = {Pinhasi, R and Thomas, MG and Hofreiter, M and Currat, M and Burger, J}, title = {The genetic history of Europeans.}, journal = {Trends in genetics : TIG}, volume = {28}, number = {10}, pages = {496-505}, doi = {10.1016/j.tig.2012.06.006}, pmid = {22889475}, issn = {0168-9525}, support = {263441/ERC_/European Research Council/International ; }, mesh = {Animals ; *Biological Evolution ; Bone and Bones/anatomy &amp; histology/metabolism ; Fossils ; Genetic Variation ; Humans ; White People/*genetics ; }, abstract = {The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data.}, }
@article {pmid22876319, year = {2012}, author = {Shepherd, LD and Worthy, TH and Tennyson, AJ and Scofield, RP and Ramstad, KM and Lambert, DM}, title = {Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp.) and a recently extinct lineage of spotted kiwi.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42384}, pmid = {22876319}, issn = {1932-6203}, mesh = {Adenosine Triphosphatases/genetics ; Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Genetic Variation ; Haplotypes ; Palaeognathae/classification/*genetics ; Phylogeny ; Phylogeography ; Sequence Alignment ; }, abstract = {The little spotted kiwi (Apteryx owenii) is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis), with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii) formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species) survived on the South Island mainland until more recently than previously thought.}, }
@article {pmid22848352, year = {2012}, author = {Storey, AA and Athens, JS and Bryant, D and Carson, M and Emery, K and deFrance, S and Higham, C and Huynen, L and Intoh, M and Jones, S and Kirch, PV and Ladefoged, T and McCoy, P and Morales-Muñiz, A and Quiroz, D and Reitz, E and Robins, J and Walter, R and Matisoo-Smith, E}, title = {Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e39171}, pmid = {22848352}, issn = {1932-6203}, mesh = {Animals ; Chickens/*genetics ; DNA, Mitochondrial/*genetics ; *Fossils ; Haplotypes/*genetics ; Humans ; }, abstract = {Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testing.}, }
@article {pmid22847014, year = {2012}, author = {Gismondi, A and Rolfo, MF and Leonardi, D and Rickards, O and Canini, A}, title = {Identification of ancient Olea europaea L. and Cornus mas L. seeds by DNA barcoding.}, journal = {Comptes rendus biologies}, volume = {335}, number = {7}, pages = {472-479}, doi = {10.1016/j.crvi.2012.05.004}, pmid = {22847014}, issn = {1768-3238}, mesh = {Agriculture/*history ; Archaeology/*methods ; Caves ; Cornus/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Plant/*analysis/isolation &amp; purification ; Databases, Genetic ; *Fossils ; *Genes, Plant ; History, Ancient ; Italy ; Microscopy, Electron, Scanning ; Olea/classification/*genetics ; Polymerase Chain Reaction/methods ; Seeds/*chemistry/ultrastructure ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The analysis of ancient DNA (aDNA) provides archaeologists and anthropologists with innovative, scientific and accurate data to study and understand the past. In this work, ancient seeds, found in the "Mora Cavorso" archaeological site (Latium, Central Italy), were analyzed to increase information about Italian Neolithic populations (plant use, agriculture, diet, trades, customs and ecology). We performed morphological and genetic techniques to identify fossil botanical species. In particular, this study also suggests and emphasizes the use of DNA barcode method for ancient plant sample analysis. Scanning electron microscope (SEM) observations showed seed compact structure and irregular surface but they did not permit a precise nor empirical classification: so, a molecular approach was necessary. DNA was extracted from ancient seeds and then it was used, as template, for PCR amplifications of standardized barcode genes. Although aDNA could be highly degraded by the time, successful PCR products were obtained, sequenced and compared to nucleotide sequence databases. Positive outcomes (supported by morphological comparison with modern seeds, geographical distribution and historical data) indicated that seeds could be identified as belonging to two plant species: Olea europaea L. and Cornus mas L.}, }
@article {pmid22844851, year = {2012}, author = {Campbell, KL and Hofreiter, M}, title = {New life for ancient DNA.}, journal = {Scientific American}, volume = {307}, number = {2}, pages = {46-51}, doi = {10.1038/scientificamerican0812-46}, pmid = {22844851}, issn = {0036-8733}, mesh = {Animals ; Cold Climate ; *DNA/chemistry/genetics ; Elephants/genetics ; Extinction, Biological ; Fossils ; Genetic Techniques ; Hemoglobins/genetics ; Mammoths/*blood/*genetics ; Sequence Analysis, DNA/veterinary ; }, }
@article {pmid22844071, year = {2012}, author = {Welch, AJ and Wiley, AE and James, HF and Ostrom, PH and Stafford, TW and Fleischer, RC}, title = {Ancient DNA reveals genetic stability despite demographic decline: 3,000 years of population history in the endemic Hawaiian petrel.}, journal = {Molecular biology and evolution}, volume = {29}, number = {12}, pages = {3729-3740}, doi = {10.1093/molbev/mss185}, pmid = {22844071}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Birds/*genetics ; Bone and Bones/chemistry ; Carbon Radioisotopes/analysis ; Computer Simulation ; DNA, Mitochondrial/*genetics/history ; *Endangered Species ; *Fossils ; Gene Flow/genetics ; *Genetic Variation ; Genetics, Population/methods ; Hawaii ; History, Ancient ; Mass Spectrometry ; Models, Genetic ; Molecular Sequence Data ; Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {In the Hawaiian Islands, human colonization, which began approximately 1,200 to 800 years ago, marks the beginning of a period in which nearly 75% of the endemic avifauna became extinct and the population size and range of many additional species declined. It remains unclear why some species persisted whereas others did not. The endemic Hawaiian petrel (Pterodroma sandwichensis) has escaped extinction, but colonies on two islands have been extirpated and populations on remaining islands have contracted. We obtained mitochondrial DNA sequences from 100 subfossil bones, 28 museum specimens, and 289 modern samples to investigate patterns of gene flow and temporal changes in the genetic diversity of this endangered species over the last 3,000 years, as Polynesians and then Europeans colonized the Hawaiian Islands. Genetic differentiation was found to be high between both modern and ancient petrel populations. However, gene flow was substantial between the extirpated colonies on Oahu and Molokai and modern birds from the island of Lanai. No significant reductions in genetic diversity occurred over this period, despite fears in the mid-1900s that this species may have been extinct. Simulations show that even a decline to a stable effective population size of 100 individuals would result in the loss of only 5% of the expected heterozygosity. Simulations also show that high levels of genetic diversity may be retained due to the long generation time of this species. Such decoupling between population size and genetic diversity in long-lived species can have important conservation implications. It appears that a pattern of dispersal from declining colonies, in addition to long generation time, may have allowed the Hawaiian petrel to escape a severe genetic bottleneck, and the associated extinction vortex, and persist despite a large population decline after human colonization.}, }
@article {pmid22820205, year = {2012}, author = {Jones, BR and Rajaraman, A and Tannier, E and Chauve, C}, title = {ANGES: reconstructing ANcestral GEnomeS maps.}, journal = {Bioinformatics (Oxford, England)}, volume = {28}, number = {18}, pages = {2388-2390}, doi = {10.1093/bioinformatics/bts457}, pmid = {22820205}, issn = {1367-4811}, mesh = {Chromosome Mapping/*methods ; Evolution, Molecular ; Genomics/*methods ; *Software ; }, abstract = {SUMMARY: ANGES is a suite of Python programs that allows reconstructing ancestral genome maps from the comparison of the organization of extant-related genomes. ANGES can reconstruct ancestral genome maps for multichromosomal linear genomes and unichromosomal circular genomes. It implements methods inspired from techniques developed to compute physical maps of extant genomes. Examples of cereal, amniote, yeast or bacteria ancestral genomes are provided, computed with ANGES.<br><br>AVAILABILITY: ANGES is freely available for download at http://paleogenomics.irmacs.sfu.ca/ANGES/. Documentation and examples are available together with the package.<br><br>CONTACT: cedric.chauve@sfu.ca.}, }
@article {pmid22777774, year = {2012}, author = {Hollemeyer, K and Altmeyer, W and Heinzle, E and Pitra, C}, title = {Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry combined with multidimensional scaling, binary hierarchical cluster tree and selected diagnostic masses improves species identification of Neolithic keratin sequences from furs of the Tyrolean Iceman Oetzi.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {26}, number = {16}, pages = {1735-1745}, doi = {10.1002/rcm.6277}, pmid = {22777774}, issn = {1097-0231}, mesh = {Amino Acid Sequence ; Animals ; Anthropology ; Austria ; Canidae ; Cattle ; *Clothing ; Cluster Analysis ; Deer ; Goats ; Hair/*chemistry ; Humans ; Italy ; Keratins/*chemistry ; Male ; Molecular Sequence Data ; Moles ; Mummies ; Shoes ; Species Specificity ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; }, abstract = {The identification of fur origins from the 5300-year-old Tyrolean Iceman's accoutrement is not yet complete, although definite identification is essential for the socio-cultural context of his epoch. Neither have all potential samples been identified so far, nor there has a consensus been reached on the species identified using the classical methods. Archaeological hair often lacks analyzable hair scale patterns in microscopic analyses and polymer chain reaction (PCR)-based techniques are often inapplicable due to the lack of amplifiable ancient DNA. To overcome these drawbacks, a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method was used exclusively based on hair keratins. Thirteen fur specimens from his accoutrement were analyzed after tryptic digest of native hair. Peptide mass fingerprints (pmfs) from ancient samples and from reference species mostly occurring in the Alpine surroundings at his lifetime were compared to each other using multidimensional scaling and binary hierarchical cluster tree analysis. Both statistical methods highly reflect spectral similarities among pmfs as close zoological relationships. While multidimensional scaling was useful to discriminate specimens on the zoological order level, binary hierarchical cluster tree reached the family or subfamily level. Additionally, the presence and/or absence of order, family and/or species-specific diagnostic masses in their pmfs allowed the identification of mammals mostly down to single species level. Red deer was found in his shoe vamp, goat in the leggings, cattle in his shoe sole and at his quiver's closing flap as well as sheep and chamois in his coat. Canid species, like grey wolf, domestic dog or European red fox, were discovered in his leggings for the first time, but could not be differentiated to species level. This is widening the spectrum of processed fur-bearing species to at least one member of the Canidae family. His fur cap was allocated to a carnivore species, but differentiation between brown bear and a canid species could not be made with certainty.}, }
@article {pmid22768206, year = {2012}, author = {Wood, JR and Wilmshurst, JM and Wagstaff, SJ and Worthy, TH and Rawlence, NJ and Cooper, A}, title = {High-resolution coproecology: using coprolites to reconstruct the habits and habitats of New Zealand's extinct upland moa (Megalapteryx didinus).}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e40025}, pmid = {22768206}, issn = {1932-6203}, mesh = {Animals ; Caves ; DNA, Plant/genetics ; *Ecosystem ; *Extinction, Biological ; *Fossils ; Humans ; New Zealand ; Palaeognathae/*classification/genetics ; Plants/classification/genetics ; Pollen/genetics ; Radiometric Dating ; Species Specificity ; }, abstract = {Knowledge about the diet and ecology of extinct herbivores has important implications for understanding the evolution of plant defence structures, establishing the influences of herbivory on past plant community structure and composition, and identifying pollination and seed dispersal syndromes. The flightless ratite moa (Aves: Dinornithiformes) were New Zealand's largest herbivores prior to their extinction soon after initial human settlement. Here we contribute to the knowledge of moa diet and ecology by reporting the results of a multidisciplinary study of 35 coprolites from a subalpine cave (Euphrates Cave) on the South Island of New Zealand. Ancient DNA analysis and radiocarbon dating revealed the coprolites were deposited by the extinct upland moa (Megalapteryx didinus), and span from at least 6,368±31 until 694±30 (14)C years BP; the approximate time of their extinction. Using pollen, plant macrofossil, and ancient DNA analyses, we identified at least 67 plant taxa from the coprolites, including the first evidence that moa fed on the nectar-rich flowers of New Zealand flax (Phormium) and tree fuchsia (Fuchsia excorticata). The plant assemblage from the coprolites reflects a highly-generalist feeding ecology for upland moa, including browsing and grazing across the full range of locally available habitats (spanning southern beech (Nothofagus) forest to tussock (Chionochloa) grassland). Intact seeds in the coprolites indicate that upland moa may have been important dispersal agents for several plant taxa. Plant taxa with putative anti-browse adaptations were also identified in the coprolites. Clusters of coprolites (based on pollen assemblages, moa haplotypes, and radiocarbon dates), probably reflect specimens deposited at the same time by individual birds, and reveal the necessity of suitably large sample sizes in coprolite studies to overcome potential biases in diet interpretation.}, }
@article {pmid22748318, year = {2012}, author = {Sánchez-Quinto, F and Schroeder, H and Ramirez, O and Avila-Arcos, MC and Pybus, M and Olalde, I and Velazquez, AM and Marcos, ME and Encinas, JM and Bertranpetit, J and Orlando, L and Gilbert, MT and Lalueza-Fox, C}, title = {Genomic affinities of two 7,000-year-old Iberian hunter-gatherers.}, journal = {Current biology : CB}, volume = {22}, number = {16}, pages = {1494-1499}, doi = {10.1016/j.cub.2012.06.005}, pmid = {22748318}, issn = {1879-0445}, mesh = {Base Sequence ; *DNA, Mitochondrial ; *Fossils ; *Genome, Human ; *Genome, Mitochondrial ; History, Ancient ; Humans ; Molecular Sequence Data ; Spain ; }, abstract = {The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic is poorly understood, both due to the scarcity of human remains from that period and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain). The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.}, }
@article {pmid22705825, year = {2013}, author = {Paijmans, JL and Gilbert, MT and Hofreiter, M}, title = {Mitogenomic analyses from ancient DNA.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {2}, pages = {404-416}, doi = {10.1016/j.ympev.2012.06.002}, pmid = {22705825}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/analysis ; Extinction, Biological ; Genetics, Population ; *Genome, Mitochondrial ; Nucleic Acid Hybridization/methods ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; }, abstract = {The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences (mitogenomes). Such studies were initially limited to analyses of extant organisms, but developments in both DNA sequencing technologies and general methodological aspects related to working with degraded DNA have resulted in complete mitogenomes becoming increasingly popular for ancient DNA studies as well. To date, at least 124 partially or fully assembled mitogenomes from more than 20 species have been obtained, and, given the rapid progress in sequencing technology, this number is likely to dramatically increase in the future. The increased information content offered by analysing full mitogenomes has yielded major progress with regard to both the phylogenetic positions of extinct species, as well as resolving population genetics questions in both extinct and extant species.}, }
@article {pmid22697611, year = {2012}, author = {Rizzi, E and Lari, M and Gigli, E and De Bellis, G and Caramelli, D}, title = {Ancient DNA studies: new perspectives on old samples.}, journal = {Genetics, selection, evolution : GSE}, volume = {44}, number = {1}, pages = {21}, pmid = {22697611}, issn = {1297-9686}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA Damage ; DNA, Mitochondrial/analysis/*genetics ; *Evolution, Molecular ; Extinction, Biological ; Genome, Human ; Humans ; Mitochondria/genetics ; Polymerase Chain Reaction/methods/standards ; Sequence Analysis, DNA/*methods ; Time Factors ; }, abstract = {In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.}, }
@article {pmid22674514, year = {2012}, author = {Huynen, L and Millar, CD and Lambert, DM}, title = {Resurrecting ancient animal genomes: the extinct moa and more.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {34}, number = {8}, pages = {661-669}, doi = {10.1002/bies.201200040}, pmid = {22674514}, issn = {1521-1878}, mesh = {Animals ; Cell Nucleus/chemistry/genetics ; Chromosomes, Mammalian/chemistry/genetics ; DNA/chemistry/genetics/isolation &amp; purification ; *Extinction, Biological ; Genome/*genetics ; Hair/cytology ; Hemoglobins/chemistry/genetics ; Mammoths/*genetics ; Oxygen/chemistry ; RNA/chemistry/genetics ; Sequence Analysis, DNA ; }, abstract = {Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals.}, }
@article {pmid22673687, year = {2012}, author = {Bánffy, E and Brandt, G and Alt, KW}, title = {'Early Neolithic' graves of the Carpathian Basin are in fact 6000 years younger-appeal for real interdisciplinarity between archaeology and ancient DNA research.}, journal = {Journal of human genetics}, volume = {57}, number = {7}, pages = {467-9; author reply 470-1}, doi = {10.1038/jhg.2012.36}, pmid = {22673687}, issn = {1435-232X}, mesh = {Asian People/*genetics ; DNA, Mitochondrial/*chemistry ; *Haplotypes ; Humans ; *Polymorphism, Single Nucleotide ; }, }
@article {pmid22666489, year = {2012}, author = {Boyer, S and Brown, SD and Collins, RA and Cruickshank, RH and Lefort, MC and Malumbres-Olarte, J and Wratten, SD}, title = {Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e38215}, pmid = {22666489}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; DNA/*chemistry/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Ribosomal/chemistry/genetics ; Digestion ; Genetic Markers/genetics ; Mollusca/physiology ; Oligochaeta/classification/genetics ; }, abstract = {DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp), amplification fails when the DNA molecule is degraded into smaller fragments. However, relevant information for specimen identification may not be evenly distributed along the barcoding region, and a shorter target can be sufficient for identification purposes. This study proposes a new, widely applicable, method to compare the performance of all potential 'mini-barcodes' for a given molecular marker and to objectively select the shortest and most informative one. Our method is based on a sliding window analysis implemented in the new R package SPIDER (Species IDentity and Evolution in R). This method is applicable to any taxon and any molecular marker. Here, it was tested on earthworm DNA that had been degraded through digestion by carnivorous landsnails. A 100 bp region of 16 S rDNA was selected as the shortest informative fragment (mini-barcode) required for accurate specimen identification. Corresponding primers were designed and used to amplify degraded earthworm (prey) DNA from 46 landsnail (predator) faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative region of the gene they aim to amplify from degraded DNA. The method and tools provided here, can be particularly useful (1) when dealing with degraded DNA for which only small fragments can be amplified, (2) for cases where no consensus has yet been reached on the appropriate barcode gene, or (3) to allow direct analysis of short reads derived from massively parallel sequencing without the need for bioinformatic consolidation.}, }
@article {pmid22665278, year = {2012}, author = {Alquezar-Planas, DE and Fordyce, SL}, title = {Roche genome sequencer FLX based high-throughput sequencing of ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {888}, number = {}, pages = {109-118}, doi = {10.1007/978-1-61779-870-2_7}, pmid = {22665278}, issn = {1940-6029}, mesh = {Animals ; Biological Specimen Banks ; Chromosome Mapping ; DNA/*analysis/chemistry ; DNA Fragmentation ; Extinction, Biological ; Gene Library ; *Genome ; *High-Throughput Nucleotide Sequencing/instrumentation/methods ; Humans ; Mammoths/genetics ; Neanderthals/genetics ; Nucleic Acid Amplification Techniques/*methods ; *Sequence Analysis, DNA/instrumentation/methods ; Ursidae/genetics ; }, abstract = {Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred to as "ancient DNA," using the Roche GS FLX 454 platform.}, }
@article {pmid22643842, year = {2012}, author = {Do, H and Dobrovic, A}, title = {Dramatic reduction of sequence artefacts from DNA isolated from formalin-fixed cancer biopsies by treatment with uracil- DNA glycosylase.}, journal = {Oncotarget}, volume = {3}, number = {5}, pages = {546-558}, pmid = {22643842}, issn = {1949-2553}, mesh = {*Artifacts ; Biopsy ; *DNA Mutational Analysis/standards ; Diagnostic Errors/prevention &amp; control ; Fixatives/adverse effects/*chemistry ; Formaldehyde/adverse effects/*chemistry ; Genes, erbB-1/genetics ; Humans ; Mutation/genetics ; Neoplasms/*diagnosis/genetics ; Precision Medicine ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins B-raf/genetics ; Proto-Oncogene Proteins c-akt/genetics ; Proto-Oncogene Proteins p21(ras) ; Sequence Analysis, DNA ; Substrate Specificity/genetics ; Tissue Fixation/*methods ; Uracil-DNA Glycosidase/*metabolism ; ras Proteins/genetics ; }, abstract = {Non-reproducible sequence artefacts are frequently detected in DNA from formalinfixed and paraffin-embedded (FFPE) tissues. However, no rational strategy has been developed for reduction of sequence artefacts from FFPE DNA as the underlying causes of the artefacts are poorly understood. As cytosine deamination to uracil is a common form of DNA damage in ancient DNA, we set out to examine whether treatment of FFPE DNA with uracil-DNA glycosylase (UDG) would lead to the reduction of C>T (and G>A) sequence artefacts. Heteroduplex formation in high resolution melting (HRM)-based assays was used for the detection of sequence variants in FFPE DNA samples. A set of samples that gave false positive HRM results for screening for the E17K mutation in exon 4 of the AKT1 gene were chosen for analysis. Sequencing of these samples showed multiple non-reproducible C:G>T:A artefacts. Treatment of the FFPE DNA with UDG prior to PCR amplification led to a very marked reduction of the sequence artefacts as indicated by both HRM and sequencing analysis, indicating that uracil lesions are the major cause of sequence artefacts. Similar results were shown for the BRAF V600 region in the same sample set and EGFR exon 19 in another sample set. UDG treatment specifically suppressed the formation of artefacts in FFPE DNA as it did not affect the detection of true KRAS codon 12 and true EGFR exon 19 and 20 mutations. We conclude that uracil in FFPE DNA leads to a significant proportion of sequence artefacts. These can be minimised by a simple UDG pretreatment which can be readily carried out, in the same tube, as the PCR immediately prior to commencing thermal cycling. HRM is a convenient way of monitoring both the degree of damage and the effectiveness of the UDG treatment. These findings have immediate and important implications for cancer diagnostics where FFPE DNA is used as the primary genetic material for mutational studies guiding personalised medicine strategies and where simple effective strategies to detect mutations are required.}, }
@article {pmid22622227, year = {2012}, author = {Goldman, AD and Landweber, LF}, title = {Oxytricha as a modern analog of ancient genome evolution.}, journal = {Trends in genetics : TIG}, volume = {28}, number = {8}, pages = {382-388}, pmid = {22622227}, issn = {0168-9525}, support = {R01 GM059708/GM/NIGMS NIH HHS/United States ; GM59708/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Cell Division ; DNA Replication ; *Genome, Protozoan ; Genomic Instability ; Oxytricha/cytology/*genetics/metabolism ; }, abstract = {Several independent lines of evidence suggest that the modern genetic system was preceded by the 'RNA world' in which RNA genes encoded RNA catalysts. Current gaps in our conceptual framework of early genetic systems make it difficult to imagine how a stable RNA genome may have functioned and how the transition to a DNA genome could have taken place. Here we use the single-celled ciliate, Oxytricha, as an analog to some of the genetic and genomic traits that may have been present in organisms before and during the establishment of a DNA genome. Oxytricha and its close relatives have a unique genome architecture involving two differentiated nuclei, one of which encodes the genome on small, linear nanochromosomes. While its unique genomic characteristics are relatively modern, some physiological processes related to the genomes and nuclei of Oxytricha may exemplify primitive states of the developing genetic system.}, }
@article {pmid22615879, year = {2012}, author = {Hervella, M and Plantinga, TS and Alonso, S and Ferwerda, B and Izagirre, N and Fontecha, L and Fregel, R and van der Meer, JW and de-la-Rúa, C and Netea, MG}, title = {The loss of functional caspase-12 in Europe is a pre-neolithic event.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e37022}, pmid = {22615879}, issn = {1932-6203}, mesh = {Alleles ; Caspase 12/genetics/*physiology ; Europe ; Genetics, Population ; Genotype ; History, Ancient ; Humans ; Sepsis/enzymology/genetics ; }, abstract = {BACKGROUND: Caspase-12 (CASP12) modulates the susceptibility to sepsis. In humans, the "C" allele at CASP12 rs497116 has been associated with an increased risk of sepsis. Instead, the derived "T" allele encodes for an inactive caspase-12. Interestingly, Eurasians are practically fixed for the inactive variant, whereas in Sub-Saharan Africa the active variant is still common (~24%). This marked structure has been explained as a function of the selective advantage that the inactive caspase-12 confers by increasing resistance to infection. As regards to both when positive selection started acting and as to the speed with which fixation was achieved in Eurasia, estimates depend on the method and assumptions used, and can vary substantially. Using experimental evidence, we propose that, least in Eurasia, the increase in the frequency of the T allele might be related to the selective pressure exerted by the increase in zoonotic diseases transmission caused by the interplay between increased human population densities and a closer contact with animals during the Neolithic. METHODOLOG/PRINCIPAL FINDINGS: We genotyped CASP12 rs497116 in prehistoric individuals from 6 archaeological sites from the North of the Iberian Peninsula that date from Late Upper Paleolithic to Late Neolithic. DNA extraction was done from teeth lacking cavities or breakages using standard anti-contamination procedures, including processing of the samples in a positive pressure, ancient DNA-only chamber, quantitation of DNAs by qPCR, duplication, replication, genotyping of associated animals, or cloning of PCR products. Out of 50, 24 prehistoric individuals could finally be genotyped for rs497116. Only the inactive form of CASP12 was found.<br><br>CONCLUSIONS/SIGNIFICANCE: We demonstrate that the loss of caspase-12 in Europe predates animal domestication and that consequently CASP12 loss is unlikely to be related to the impact of zoonotic infections transmitted by livestock.}, }
@article {pmid22590727, year = {2012}, author = {Jørgensen, T and Haile, J and Möller, P and Andreev, A and Boessenkool, S and Rasmussen, M and Kienast, F and Coissac, E and Taberlet, P and Brochmann, C and Bigelow, NH and Andersen, K and Orlando, L and Gilbert, MT and Willerslev, E}, title = {A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability.}, journal = {Molecular ecology}, volume = {21}, number = {8}, pages = {1989-2003}, doi = {10.1111/j.1365-294x.2011.05287.x}, pmid = {22590727}, issn = {1365-294X}, mesh = {DNA, Plant/*analysis ; Ecosystem ; *Fossils ; Geologic Sediments/*chemistry ; History, Ancient ; *Ice ; Plants/classification/genetics ; *Pollen ; Siberia ; }, abstract = {Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared with the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46-12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping and, in combination, reveal more detailed information on plant palaeocommunities than can be achieved by each individual approach. SedaDNA and macrofossils share greater overlap in plant identifications than with pollen, suggesting that sedaDNA is local in origin. These two proxies also permit identification to lower taxonomic levels than pollen, enabling investigation into temporal changes in species composition and the determination of indicator species to describe environmental changes. Combining data from all three proxies reveals an area continually dominated by a mosaic vegetation of tundra-steppe, pioneer and wet-indicator plants. Such vegetational stability is unexpected, given the severe climate changes taking place in the Northern Hemisphere during this time, with changes in average annual temperatures of >22 °C. This may explain the abundance of ice-age mammals such as horse and bison in Taymyr Peninsula during the Pleistocene and why it acted as a refugium for the last mainland woolly mammoth. Our finding reveals the benefits of combining sedaDNA, pollen and macrofossil for palaeovegetational reconstruction and adds to the increasing evidence suggesting large areas of the Northern Hemisphere remained ecologically stable during the Late Pleistocene.}, }
@article {pmid22590499, year = {2012}, author = {Alter, SE and Newsome, SD and Palumbi, SR}, title = {Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: insights from ancient DNA and stable isotopes.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e35039}, pmid = {22590499}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Ecosystem ; *Evolution, Molecular ; Genetic Variation/physiology ; Isotopes ; Pacific Ocean ; Population Dynamics ; Whales/*physiology ; }, abstract = {Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.}, }
@article {pmid22574660, year = {2012}, author = {Schubert, M and Ginolhac, A and Lindgreen, S and Thompson, JF and Al-Rasheid, KA and Willerslev, E and Krogh, A and Orlando, L}, title = {Improving ancient DNA read mapping against modern reference genomes.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {178}, pmid = {22574660}, issn = {1471-2164}, mesh = {DNA Damage/genetics ; Fossils ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA.<br><br>RESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%.<br><br>CONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material.}, }
@article {pmid22574620, year = {2012}, author = {Ginolhac, A and Vilstrup, J and Stenderup, J and Rasmussen, M and Stiller, M and Shapiro, B and Zazula, G and Froese, D and Steinmann, KE and Thompson, JF and Al-Rasheid, KA and Gilbert, TM and Willerslev, E and Orlando, L}, title = {Improving the performance of true single molecule sequencing for ancient DNA.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {177}, pmid = {22574620}, issn = {1471-2164}, support = {RC2 HG005598/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; DNA/*genetics ; DNA, Mitochondrial/genetics ; *Fossils ; Genome/genetics ; Horses/*genetics ; Nucleotidases/metabolism ; Nucleotides/genetics ; Phylogeny ; Sequence Analysis, DNA/*methods/*standards ; }, abstract = {BACKGROUND: Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase.<br><br>RESULTS: We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existence of molecular preservation niches in large bone crystals from which DNA could be preferentially extracted.<br><br>CONCLUSIONS: We propose DNA phosphatase treatment as a mechanism to increase sequence coverage of ancient genomes when using Helicos tSMS as a sequencing platform. Together with mild denaturation temperatures that favor access to endogenous ancient templates over modern DNA contaminants, this simple preparation procedure can improve overall Helicos tSMS performance when damaged DNA templates are targeted.}, }
@article {pmid22572206, year = {2012}, author = {Herridge, VL and Lister, AM}, title = {Extreme insular dwarfism evolved in a mammoth.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1741}, pages = {3193-3200}, pmid = {22572206}, issn = {1471-2954}, mesh = {Animals ; *Biological Evolution ; Body Size ; *Dwarfism/genetics ; Elephants/*classification/genetics/physiology ; *Fossils ; Mammoths/*classification/genetics/*physiology ; Species Specificity ; }, abstract = {The insular dwarfism seen in Pleistocene elephants has come to epitomize the island rule; yet our understanding of this phenomenon is hampered by poor taxonomy. For Mediterranean dwarf elephants, where the most extreme cases of insular dwarfism are observed, a key systematic question remains unresolved: are all taxa phyletic dwarfs of a single mainland species Palaeoloxodon antiquus (straight-tusked elephant), or are some referable to Mammuthus (mammoths)? Ancient DNA and geochronological evidence have been used to support a Mammuthus origin for the Cretan 'Palaeoloxodon' creticus, but these studies have been shown to be flawed. On the basis of existing collections and recent field discoveries, we present new, morphological evidence for the taxonomic status of 'P'. creticus, and show that it is indeed a mammoth, most probably derived from Early Pleistocene Mammuthus meridionalis or possibly Late Pliocene Mammuthus rumanus. We also show that Mammuthus creticus is smaller than other known insular dwarf mammoths, and is similar in size to the smallest dwarf Palaeoloxodon species from Sicily and Malta, making it the smallest mammoth species known to have existed. These findings indicate that extreme insular dwarfism has evolved to a similar degree independently in two elephant lineages.}, }
@article {pmid22567153, year = {2012}, author = {Montiel, R and Solórzano, E and Díaz, N and Álvarez-Sandoval, BA and González-Ruiz, M and Cañadas, MP and Simões, N and Isidro, A and Malgosa, A}, title = {Neonate human remains: a window of opportunity to the molecular study of ancient syphilis.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e36371}, pmid = {22567153}, issn = {1932-6203}, mesh = {Archaeology/methods ; DNA, Mitochondrial/genetics ; Humans ; Infant, Newborn ; Spain ; Syphilis/*genetics ; }, abstract = {Ancient DNA (aDNA) analysis can be a useful tool in bacterial disease diagnosis in human remains. However, while the recovery of Mycobacterium spp. has been widely successful, several authors report unsuccessful results regarding ancient treponemal DNA, casting doubts on the usefulness of this technique for the diagnosis of ancient syphilis. Here, we present results from an analysis of four newborn specimens recovered from the crypt of "La Ermita de la Soledad" (XVI-XVII centuries), located in the province of Huelva in the southwest of Spain. We extracted and analyzed aDNA in three independent laboratories, following specific procedures generally practiced in the aDNA field, including cloning of the amplified DNA fragments and sequencing of several clones. This is the most ancient case, reported to date, from which detection of DNA from T. pallidum subspecies pallidum has been successful in more than one individual, and we put forward a hypothesis to explain this result, taking into account the course of the disease in neonate individuals.}, }
@article {pmid22563371, year = {2012}, author = {Hervella, M and Izagirre, N and Alonso, S and Fregel, R and Alonso, A and Cabrera, VM and de la Rúa, C}, title = {Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e34417}, pmid = {22563371}, issn = {1932-6203}, mesh = {Agriculture ; Archaeology ; DNA, Mitochondrial/*genetics/history ; Europe ; Genetic Heterogeneity ; Genetic Variation ; Genetics, Population/classification ; Haplotypes ; History, Ancient ; Humans ; *Models, Theoretical ; Phylogeny ; Spain ; }, abstract = {BACKGROUND/PRINCIPAL FINDINGS: The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe.<br><br>METHODOLOGY/SIGNIFICANCE: Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples) and replication of the results (43% of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe.<br><br>CONCLUSION: The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study) suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different impact on the various geographic regions, and thus contradicts the more simplistic total acculturation and replacement models proposed so far to explain Neolithisation.}, }
@article {pmid22552938, year = {2012}, author = {Lee, EJ and Makarewicz, C and Renneberg, R and Harder, M and Krause-Kyora, B and Müller, S and Ostritz, S and Fehren-Schmitz, L and Schreiber, S and Müller, J and von Wurmb-Schwark, N and Nebel, A}, title = {Emerging genetic patterns of the European Neolithic: perspectives from a late Neolithic Bell Beaker burial site in Germany.}, journal = {American journal of physical anthropology}, volume = {148}, number = {4}, pages = {571-579}, doi = {10.1002/ajpa.22074}, pmid = {22552938}, issn = {1096-8644}, mesh = {Anthropology, Physical ; *Cemeteries ; Cultural Evolution ; DNA, Mitochondrial/genetics ; Emigration and Immigration ; Germany ; Haplotypes ; History, Ancient ; Humans ; Male ; White People/*genetics/*history ; }, abstract = {The transition from hunting and gathering to agriculture in Europe is associated with demographic changes that may have shifted the human gene pool of the region as a result of an influx of Neolithic farmers from the Near East. However, the genetic composition of populations after the earliest Neolithic, when a diverse mosaic of societies that had been fully engaged in agriculture for some time appeared in central Europe, is poorly known. At this period during the Late Neolithic (ca. 2,800-2,000 BC), regionally distinctive burial patterns associated with two different cultural groups emerge, Bell Beaker and Corded Ware, and may reflect differences in how these societies were organized. Ancient DNA analyses of human remains from the Late Neolithic Bell Beaker site of Kromsdorf, Germany showed distinct mitochondrial haplotypes for six individuals, which were classified under the haplogroups I1, K1, T1, U2, U5, and W5, and two males were identified as belonging to the Y haplogroup R1b. In contrast to other Late Neolithic societies in Europe emphasizing maintenance of biological relatedness in mortuary contexts, the diversity of maternal haplotypes evident at Kromsdorf suggests that burial practices of Bell Beaker communities operated outside of social norms based on shared maternal lineages. Furthermore, our data, along with those from previous studies, indicate that modern U5-lineages may have received little, if any, contribution from the Mesolithic or Neolithic mitochondrial gene pool.}, }
@article {pmid22524324, year = {2012}, author = {Baca, M and Doan, K and Sobczyk, M and Stankovic, A and Węgleński, P}, title = {Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community.}, journal = {BMC genetics}, volume = {13}, number = {}, pages = {30}, pmid = {22524324}, issn = {1471-2156}, mesh = {*Archaeology ; Burial ; DNA/*analysis ; DNA, Mitochondrial/analysis ; *Family ; Genetics, Population ; Humans ; Indians, South American/*genetics ; Male ; Microsatellite Repeats/immunology ; Peru ; }, abstract = {BACKGROUND: A detailed genetic study of the pre-Columbian population inhabiting the Tompullo 2 archaeological site (department Arequipa, Peru) was undertaken to resolve the kin relationships between individuals buried in six different chullpas. Kin relationships were an important factor shaping the social organization in the pre-Columbian Andean communities, centering on the ayllu, a group of relatives that shared a common land and responsibilities. The aim of this study was to evaluate whether this Andean model of a social organization had an influence on mortuary practices, in particular to determine whether chullpas served as family graves.<br><br>RESULTS: The remains of forty-one individuals were analyzed with both uniparental (mtDNA, Y-chromosome) and biparental (autosomal microsatellites) markers. Reproducible HVRI sequences, autosomal and Y chromosomal STR profiles were obtained for 24, 16 and 11 individuals, respectively. Mitochondrial DNA diversity was comparable to that of ancient and contemporary Andean populations. The Tompullo 2 population exhibited the closest relationship with the modern population from the same region. A kinship analysis revealed complex pattern of relations within and between the graves. However mean relatedness coefficients regarding the pairs of individuals buried in the same grave were significantly higher than those regarding pairs buried in different graves. The Y chromosome profiles of 11 males suggest that only members of one male line were buried in the same grave.<br><br>CONCLUSIONS: Genetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site was organized into extended family groups that were buried in different graves. This finding is in congruence with known models of social organization of Andean communities.}, }
@article {pmid22516743, year = {2012}, author = {Overballe-Petersen, S and Orlando, L and Willerslev, E}, title = {Next-generation sequencing offers new insights into DNA degradation.}, journal = {Trends in biotechnology}, volume = {30}, number = {7}, pages = {364-368}, doi = {10.1016/j.tibtech.2012.03.007}, pmid = {22516743}, issn = {1879-3096}, mesh = {Animals ; DNA/analysis/chemistry/*genetics ; DNA Damage/*genetics ; Fossils ; Horses ; Humans ; Mammals ; *Models, Genetic ; Nucleic Acid Conformation ; Sequence Analysis, DNA/*methods ; }, abstract = {The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation rates that previously were obtained only from extrapolations of results from in vitro kinetic experiments performed over short timescales. For example, recent next-generation sequencing of ancient DNA reveals purine bases as one of the main targets of postmortem hydrolytic damage, through base elimination and strand breakage. It also shows substantially increased rates of DNA base-loss at guanosine. In this review, we argue that the latter results from an electron resonance structure unique to guanosine rather than adenosine having an extra resonance structure over guanosine as previously suggested.}, }
@article {pmid22479540, year = {2012}, author = {Sawyer, S and Krause, J and Guschanski, K and Savolainen, V and Pääbo, S}, title = {Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e34131}, pmid = {22479540}, issn = {1932-6203}, mesh = {Animals ; Base Composition ; DNA/*genetics ; DNA Damage ; *DNA Fragmentation ; DNA, Mitochondrial/*genetics ; Gene Library ; Gorilla gorilla ; Humans ; Paleontology/methods ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5'-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.}, }
@article {pmid22470432, year = {2012}, author = {Yegorov, S and Good, S}, title = {Using paleogenomics to study the evolution of gene families: origin and duplication history of the relaxin family hormones and their receptors.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e32923}, pmid = {22470432}, issn = {1932-6203}, mesh = {Animals ; *Evolution, Molecular ; Gene Duplication ; *Genomics ; Humans ; Phylogeny ; Receptors, G-Protein-Coupled/*genetics/metabolism ; Receptors, Peptide/*genetics/metabolism ; Relaxin/*genetics/metabolism ; }, abstract = {Recent progress in the analysis of whole genome sequencing data has resulted in the emergence of paleogenomics, a field devoted to the reconstruction of ancestral genomes. Ancestral karyotype reconstructions have been used primarily to illustrate the dynamic nature of genome evolution. In this paper, we demonstrate how they can also be used to study individual gene families by examining the evolutionary history of relaxin hormones (RLN/INSL) and relaxin family peptide receptors (RXFP). Relaxin family hormones are members of the insulin superfamily, and are implicated in the regulation of a variety of primarily reproductive and neuroendocrine processes. Their receptors are G-protein coupled receptors (GPCR's) and include members of two distinct evolutionary groups, an unusual characteristic. Although several studies have tried to elucidate the origins of the relaxin peptide family, the evolutionary origin of their receptors and the mechanisms driving the diversification of the RLN/INSL-RXFP signaling systems in non-placental vertebrates has remained elusive. Here we show that the numerous vertebrate RLN/INSL and RXFP genes are products of an ancestral receptor-ligand system that originally consisted of three genes, two of which apparently trace their origins to invertebrates. Subsequently, diversification of the system was driven primarily by whole genome duplications (WGD, 2R and 3R) followed by almost complete retention of the ligand duplicates in most vertebrates but massive loss of receptor genes in tetrapods. Interestingly, the majority of 3R duplicates retained in teleosts are potentially involved in neuroendocrine regulation. Furthermore, we infer that the ancestral AncRxfp3/4 receptor may have been syntenically linked to the AncRln-like ligand in the pre-2R genome, and show that syntenic linkages among ligands and receptors have changed dynamically in different lineages. This study ultimately shows the broad utility, with some caveats, of incorporating paleogenomics data into understanding the evolution of gene families.}, }
@article {pmid22457070, year = {2012}, author = {Frith, MC and Mori, R and Asai, K}, title = {A mostly traditional approach improves alignment of bisulfite-converted DNA.}, journal = {Nucleic acids research}, volume = {40}, number = {13}, pages = {e100}, pmid = {22457070}, issn = {1362-4962}, mesh = {DNA/chemistry ; *DNA Methylation ; Genome, Human ; Humans ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment/*methods ; *Sequence Analysis, DNA ; *Sulfites ; }, abstract = {Cytosines in genomic DNA are sometimes methylated. This affects many biological processes and diseases. The standard way of measuring methylation is to use bisulfite, which converts unmethylated cytosines to thymines, then sequence the DNA and compare it to a reference genome sequence. We describe a method for the critical step of aligning the DNA reads to the correct genomic locations. Our method builds on classic alignment techniques, including likelihood-ratio scores and spaced seeds. In a realistic benchmark, our method has a better combination of sensitivity, specificity and speed than nine other high-throughput bisulfite aligners. This study enables more accurate and rational analysis of DNA methylation. It also illustrates how to adapt general-purpose alignment methods to a special case with distorted base patterns: this should be informative for other special cases such as ancient DNA and AT-rich genomes.}, }
@article {pmid22456883, year = {2012}, author = {Bon, C and Berthonaud, V and Maksud, F and Labadie, K and Poulain, J and Artiguenave, F and Wincker, P and Aury, JM and Elalouf, JM}, title = {Coprolites as a source of information on the genome and diet of the cave hyena.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1739}, pages = {2825-2830}, pmid = {22456883}, issn = {1471-2954}, mesh = {Animals ; DNA/genetics/isolation &amp; purification ; Diet/*veterinary ; Feces/*chemistry ; Fossils ; *Genome ; Hyaenidae/*genetics/*physiology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {We performed high-throughput sequencing of DNA from fossilized faeces to evaluate this material as a source of information on the genome and diet of Pleistocene carnivores. We analysed coprolites derived from the extinct cave hyena (Crocuta crocuta spelaea), and sequenced 90 million DNA fragments from two specimens. The DNA reads enabled a reconstruction of the cave hyena mitochondrial genome with up to a 158-fold coverage. This genome, and those sequenced from extant spotted (Crocuta crocuta) and striped (Hyaena hyaena) hyena specimens, allows for the establishment of a robust phylogeny that supports a close relationship between the cave and the spotted hyena. We also demonstrate that high-throughput sequencing yields data for cave hyena multi-copy and single-copy nuclear genes, and that about 50 per cent of the coprolite DNA can be ascribed to this species. Analysing the data for additional species to indicate the cave hyena diet, we retrieved abundant sequences for the red deer (Cervus elaphus), and characterized its mitochondrial genome with up to a 3.8-fold coverage. In conclusion, we have demonstrated the presence of abundant ancient DNA in the coprolites surveyed. Shotgun sequencing of this material yielded a wealth of DNA sequences for a Pleistocene carnivore and allowed unbiased identification of diet.}, }
@article {pmid22452428, year = {2012}, author = {Pinhasi, R and von Cramon-Taubadel, N}, title = {A craniometric perspective on the transition to agriculture in Europe.}, journal = {Human biology}, volume = {84}, number = {1}, pages = {45-66}, doi = {10.3378/027.084.0102}, pmid = {22452428}, issn = {1534-6617}, mesh = {Agriculture/*history/statistics &amp; numerical data ; Cephalometry/*instrumentation/methods ; *Culture ; DNA/analysis/genetics ; Demography ; Europe ; Genetics, Population/statistics &amp; numerical data ; History, Ancient ; Humans ; Models, Theoretical ; Skull ; }, abstract = {Debates surrounding the nature of the Neolithic demographic transition in Europe have historically centered on two opposing models: a "demic" diffusion model whereby incoming farmers from the Near East and Anatolia effectively replaced or completely assimilated indigenous Mesolithic foraging communities, and an "indigenist" model resting on the assumption that ideas relating to agriculture and animal domestication diffused from the Near East but with little or no gene flow. The extreme versions of these dichotomous models were heavily contested primarily on the basis of archeological and modern genetic data. However, in recent years a growing acceptance has arisen of the likelihood that both processes were ongoing throughout the Neolithic transition and that a more complex, regional approach is required to fully understand the change from a foraging to a primarily agricultural mode of subsistence in Europe. Craniometric data were particularly useful for testing these more complex scenarios, as they can reliably be employed as a proxy for the genetic relationships among Mesolithic and Neolithic populations. In contrast, modern genetic data assume that modern European populations accurately reflect the genetic structure of Europe at the time of the Neolithic transition, while ancient DNA data are still not geographically or temporally detailed enough to test continent-wide processes. Here, with particular emphasis on the role of craniometric analyses, we review the current state of knowledge regarding the cultural and biological nature of the Neolithic transition in Europe.}, }
@article {pmid22427878, year = {2012}, author = {McMenamin, SK and Hadly, EA}, title = {Ancient DNA assessment of tiger salamander population in Yellowstone National Park.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e32763}, pmid = {22427878}, issn = {1932-6203}, mesh = {Ambystoma/*genetics ; Analysis of Variance ; Animals ; Base Sequence ; Bayes Theorem ; Computer Simulation ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Fossils ; *Genetic Variation ; Haplotypes/genetics ; Models, Genetic ; Molecular Sequence Data ; Mutation Rate ; Population Density ; Sequence Analysis, DNA ; Wyoming ; }, abstract = {Recent data indicates that blotched tiger salamanders (Ambystoma tigrinum melanostictum) in northern regions of Yellowstone National Park are declining due to climate-related habitat changes. In this study, we used ancient and modern mitochondrial haplotype diversity to model the effective size of this amphibian population through recent geological time and to assess past responses to climatic changes in the region. Using subfossils collected from a cave in northern Yellowstone, we analyzed >700 base pairs of mitochondrial sequence from 16 samples ranging in age from 100 to 3300 years old and found that all shared an identical haplotype. Although mitochondrial diversity was extremely low within the living population, we still were able to detect geographic subdivision within the local area. Using serial coalescent modelling with Bayesian priors from both modern and ancient genetic data we simulated a range of probable population sizes and mutation rates through time. Our simulations suggest that regional mitochondrial diversity has remained relatively constant even through climatic fluctuations of recent millennia.}, }
@article {pmid22427842, year = {2012}, author = {Fu, Q and Rudan, P and Pääbo, S and Krause, J}, title = {Complete mitochondrial genomes reveal neolithic expansion into Europe.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e32473}, pmid = {22427842}, issn = {1932-6203}, mesh = {Agriculture/*history ; Base Sequence ; Bayes Theorem ; Computational Biology ; *Cultural Evolution ; DNA, Mitochondrial/*genetics ; *Demography ; Emigration and Immigration/*history ; Europe ; Evolution, Molecular ; Haplotypes/genetics ; History, Ancient ; Humans ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; *Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.}, }
@article {pmid22427706, year = {2012}, author = {Mourier, T and Ho, SY and Gilbert, MT and Willerslev, E and Orlando, L}, title = {Statistical guidelines for detecting past population shifts using ancient DNA.}, journal = {Molecular biology and evolution}, volume = {29}, number = {9}, pages = {2241-2251}, doi = {10.1093/molbev/mss094}, pmid = {22427706}, issn = {1537-1719}, mesh = {Animals ; Computer Simulation ; *DNA, Mitochondrial ; Genetics, Population ; Guidelines as Topic ; Humans ; *Models, Genetic ; *Models, Statistical ; Polymorphism, Single Nucleotide ; Population Dynamics ; }, abstract = {Populations carry a genetic signal of their demographic past, providing an opportunity for investigating the processes that shaped their evolution. Our ability to infer population histories can be enhanced by including ancient DNA data. Using serial-coalescent simulations and a range of both quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast post-bottleneck recoveries. In contrast, nuclear SNPs can detect bottlenecks followed by rapid recovery, although bottlenecks involving reduction of less than half the population are generally detected with low power unless extensive genetic information from ancient individuals is available. Our results provide useful guidelines for scaling sampling schemes and for optimizing our ability to infer past population dynamics. In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when based solely on mitochondrial information.}, }
@article {pmid22422765, year = {2012}, author = {Bollongino, R and Burger, J and Powell, A and Mashkour, M and Vigne, JD and Thomas, MG}, title = {Modern taurine cattle descended from small number of near-eastern founders.}, journal = {Molecular biology and evolution}, volume = {29}, number = {9}, pages = {2101-2104}, doi = {10.1093/molbev/mss092}, pmid = {22422765}, issn = {1537-1719}, mesh = {Animals ; Cattle/*genetics ; DNA, Mitochondrial/*genetics ; Female ; *Founder Effect ; Models, Genetic ; Mutation Rate ; Population Dynamics ; }, abstract = {Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago. However, while modern mitochondrial DNA (mtDNA) variation indicates early Holocene founding event(s), a lack of ancient DNA data from the region of origin, variation in mutation rate estimates, and limited application of appropriate inference methodologies have resulted in uncertainty on the number of animals first domesticated. A large number would be expected if cattle domestication was a technologically straightforward and unexacting region-wide phenomenon, while a smaller number would be consistent with a more complex and challenging process. We report mtDNA sequences from 15 Neolithic to Iron Age Iranian domestic cattle and, in conjunction with modern data, use serial coalescent simulation and approximate Bayesian computation to estimate that around 80 female aurochs were initially domesticated. Such a low number is consistent with archaeological data indicating that initial domestication took place in a restricted area and suggests the process was constrained by the difficulty of sustained managing and breeding of the wild progenitors of domestic cattle.}, }
@article {pmid22363563, year = {2012}, author = {Pagès, M and Chevret, P and Gros-Balthazard, M and Hughes, S and Alcover, JA and Hutterer, R and Rando, JC and Michaux, J and Hänni, C}, title = {Paleogenetic analyses reveal unsuspected phylogenetic affinities between mice and the extinct Malpaisomys insularis, an endemic rodent of the Canaries.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31123}, pmid = {22363563}, issn = {1932-6203}, mesh = {Animals ; Artifacts ; Biological Evolution ; DNA/genetics ; *Extinction, Biological ; Fossils ; Geography ; Likelihood Functions ; Mice/*genetics ; Molecular Sequence Data ; Mutation/genetics ; *Paleontology ; *Phylogeny ; Polymerase Chain Reaction ; Rodentia/*genetics ; Sequence Analysis, DNA ; Spain ; Time Factors ; Tooth/anatomy &amp; histology ; }, abstract = {BACKGROUND: The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14(th) century when the Europeans reached the archipelago. Studies to determine Malpaisomys' phylogenetic affinities, based on morphological characters, remained inconclusive because morphological changes experienced by this insular rodent make phylogenetic investigations a real challenge. Over 20 years since its first description, Malpaisomys' phylogenetic position remains enigmatic.<br><br>In this study, we resolved this issue using molecular characters. Mitochondrial and nuclear markers were successfully amplified from subfossils of three lava mouse samples. Molecular phylogenetic reconstructions revealed, without any ambiguity, unsuspected relationships between Malpaisomys and extant mice (genus Mus, Murinae). Moreover, through molecular dating we estimated the origin of the Malpaisomys/mouse clade at 6.9 Ma, corresponding to the maximal age at which the archipelago was colonised by the Malpaisomys ancestor via natural rafting.<br><br>CONCLUSION/SIGNIFICANCE: This study reconsiders the derived morphological characters of Malpaisomys in light of this unexpected molecular finding. To reconcile molecular and morphological data, we propose to consider Malpaisomys insularis as an insular lineage of mouse.}, }
@article {pmid22357937, year = {2012}, author = {Heupink, TH and van den Hoff, J and Lambert, DM}, title = {King penguin population on Macquarie Island recovers ancient DNA diversity after heavy exploitation in historic times.}, journal = {Biology letters}, volume = {8}, number = {4}, pages = {586-589}, pmid = {22357937}, issn = {1744-957X}, mesh = {Animals ; *Conservation of Natural Resources ; DNA, Mitochondrial/analysis/*genetics ; Extinction, Biological ; Fossils ; *Genetic Variation ; Genetics, Population/methods ; Geography ; Mitochondria/genetics ; Population Dynamics ; Radiometric Dating ; Sequence Analysis, DNA ; Spheniscidae/*genetics ; Time Factors ; }, abstract = {Historically, king penguin populations on Macquarie Island have suffered greatly from human exploitation. Two large colonies on the island were drastically reduced to a single small colony as a result of harvesting for the blubber oil industry. However, recent conservation efforts have resulted in the king penguin population expanding in numbers and range to recolonize previous as well as new sites. Ancient DNA methods were used to estimate past genetic diversity and combined with studies of modern populations, we are now able to compare past levels of variation with extant populations on northern Macquarie Island. The ancient and modern populations are closely related and show a similar level of genetic diversity. These results suggest that the king penguin population has recovered past genetic diversity in just 80 years owing to conservation efforts, despite having seen the brink of extinction.}, }
@article {pmid22355593, year = {2011}, author = {Avila-Arcos, MC and Cappellini, E and Romero-Navarro, JA and Wales, N and Moreno-Mayar, JV and Rasmussen, M and Fordyce, SL and Montiel, R and Vielle-Calzada, JP and Willerslev, E and Gilbert, MT}, title = {Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA.}, journal = {Scientific reports}, volume = {1}, number = {}, pages = {74}, pmid = {22355593}, issn = {2045-2322}, mesh = {DNA, Plant/genetics/*isolation &amp; purification ; Plants/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA.}, }
@article {pmid22334578, year = {2012}, author = {Palmer, SA and Clapham, AJ and Rose, P and Freitas, FO and Owen, BD and Beresford-Jones, D and Moore, JD and Kitchen, JL and Allaby, RG}, title = {Archaeogenomic evidence of punctuated genome evolution in Gossypium.}, journal = {Molecular biology and evolution}, volume = {29}, number = {8}, pages = {2031-2038}, doi = {10.1093/molbev/mss070}, pmid = {22334578}, issn = {1537-1719}, mesh = {*Evolution, Molecular ; Genome, Plant/*genetics ; Genomics/*methods ; Gossypium/*genetics ; Metagenome/genetics ; *Paleontology ; Repetitive Sequences, Nucleic Acid/genetics ; Species Specificity ; }, abstract = {Transposable elements (TEs) are drivers of evolution resulting in episodic surges of genetic innovation and genomic reorganization (Oliver KR, Greene WK. 2009. TEs: powerful facilitators of evolution. Bioessays 31:703-714.), but there is little evidence of the timescale in which this process has occurred (Gingerich PD. 2009. Rates of evolution. Ann Rev Ecol Evol Syst. 40:657-675.). The paleontological and archaeological records provide direct evidence for how evolution has proceeded in the past, which can be accessed through ancient DNA to examine genomes using high-throughput sequencing technologies (Palmer SA, Smith O, Allaby RG. 2011. The blossoming of plant archaeogenetics. Ann Anat. 194:146-156.). In this study, we report shotgun sequencing of four archaeological samples of cotton using the GS 454 FLX platform, which enabled reconstruction of the TE composition of these past genomes and species identification. From this, a picture of lineage specific evolutionary patterns emerged, even over the relatively short timescale of a few thousand years. Genomic stability was observed between South American Gossypium barbadense samples separated by over 2,000 miles and 3,000 years. In contrast, the TE composition of ancient Nubian cotton, identified as G. herbaceum, differed dramatically from that of modern G. herbaceum and resembled closely the A genome of the New World tetraploids. Our analysis has directly shown that considerable genomic reorganization has occurred within the history of a domesticated plant species while genomic stability has occurred in closely related species. A pattern of episodes of rapid change and periods of stability is expected of punctuated evolution. This observation is important to understanding the process of evolution under domestication.}, }
@article {pmid22313406, year = {2012}, author = {Dabney, J and Meyer, M}, title = {Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries.}, journal = {BioTechniques}, volume = {52}, number = {2}, pages = {87-94}, doi = {10.2144/000113809}, pmid = {22313406}, issn = {1940-9818}, mesh = {Base Composition/*genetics ; Buffers ; DNA-Directed DNA Polymerase/*genetics ; *Gene Library ; Humans ; Nucleic Acid Amplification Techniques/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {High-throughput sequencing technologies frequently necessitate the use of PCR for sequencing library amplification. PCR is a sometimes enigmatic process and is known to introduce biases. Here we perform a simple amplification-sequencing assay using 10 commercially available polymerase-buffer systems to amplify libraries prepared from both modern and ancient DNA. We compare the performance of the polymerases with respect to a previously uncharacterized template length bias, as well as GC-content bias, and find that simply avoiding certain polymerase can dramatically decrease the occurrence of both. For amplification of ancient DNA, we found that some commonly used polymerases strongly bias against amplification of endogenous DNA in favor of GC-rich microbial contamination, in our case reducing the fraction of endogenous sequences to almost half.}, }
@article {pmid22312053, year = {2012}, author = {Achtman, M}, title = {Insights from genomic comparisons of genetically monomorphic bacterial pathogens.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {367}, number = {1590}, pages = {860-867}, pmid = {22312053}, issn = {1471-2970}, mesh = {Epidemics/*history ; *Evolution, Molecular ; *Genetic Variation ; Genetics, Population/*methods ; Genome, Bacterial/*genetics ; History, 19th Century ; History, Ancient ; History, Medieval ; Humans ; Phylogeography ; Plague/*epidemiology/microbiology ; Polymorphism, Single Nucleotide/genetics ; Selection, Genetic ; Yersinia pestis/*genetics/*pathogenicity ; }, abstract = {Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called 'genetically monomorphic bacteria'. It has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. The genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. Some genetically monomorphic lineages have evolved in the last decades, e.g. antibiotic-resistant Staphylococcus aureus, whereas others have evolved over several millennia, e.g. the cause of plague, Yersinia pestis. Based on recent results, it is now possible to reconstruct the sources and the history of pandemic waves of plague by a combined analysis of phylogeographic signals in Y. pestis plus polymorphisms found in ancient DNA. Different from historical accounts based exclusively on human disease, Y. pestis evolved in China, or the vicinity, and has spread globally on multiple occasions. These routes of transmission can be reconstructed from the genealogy, most precisely for the most recent pandemic that was spread from Hong Kong in multiple independent waves in 1894.}, }
@article {pmid22307722, year = {2012}, author = {Deguilloux, MF and Leahy, R and Pemonge, MH and Rottier, S}, title = {European neolithization and ancient DNA: an assessment.}, journal = {Evolutionary anthropology}, volume = {21}, number = {1}, pages = {24-37}, doi = {10.1002/evan.20341}, pmid = {22307722}, issn = {1520-6505}, mesh = {Agriculture ; Anthropology, Physical ; DNA/*genetics ; *Emigration and Immigration ; Humans ; *Phylogeography ; White People/*genetics ; }, abstract = {Neolithic processes underlying the distribution of genetic diversity among European populations have been the subject of intense debate since the first genetic data became available. However, patterns observed in the current European gene pool are the outcome of Paleolithic and Neolithic processes, overlaid with four millennia of further developments. This observation encouraged paleogeneticists to contribute to the debate by directly comparing genetic variation from the ancient inhabitants of Europe to their contemporary counterparts. Pre-Neolithic and Neolithic paleogenetic data are becoming increasingly available for north and northwest European populations. Despite the numerous problems inherent in the paleogenetic approach, the accumulation of ancient DNA datasets offers new perspectives from which to interpret the interactions between hunter-gatherer and farming communities. In light of information emerging from diverse disciplines, including recent paleogenetic studies, the most plausible model explaining the movement of Neolithic pioneer groups in central Europe is that of leapfrog migration.}, }
@article {pmid22280839, year = {2012}, author = {Salse, J}, title = {In silico archeogenomics unveils modern plant genome organisation, regulation and evolution.}, journal = {Current opinion in plant biology}, volume = {15}, number = {2}, pages = {122-130}, doi = {10.1016/j.pbi.2012.01.001}, pmid = {22280839}, issn = {1879-0356}, mesh = {Archaeology/*methods ; *Evolution, Molecular ; Genome, Plant/*genetics ; Genomics/*methods ; }, abstract = {Increasing access to plant genome sequences as well as high resolution gene-based genetic maps have recently offered the opportunity to compare modern genomes and model their evolutionary history from their reconstructed founder ancestors on an unprecedented scale. In silico paleogenomic data have revealed the evolutionary forces that have shaped present-day genomes and allowed us to gain insight into how they are organised and regulated today.}, }
@article {pmid22276161, year = {2012}, author = {Llamas, B and Holland, ML and Chen, K and Cropley, JE and Cooper, A and Suter, CM}, title = {High-resolution analysis of cytosine methylation in ancient DNA.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30226}, pmid = {22276161}, issn = {1932-6203}, mesh = {Animals ; Bison/genetics ; Cytosine/*metabolism ; DNA Methylation/*genetics ; Epigenesis, Genetic/genetics ; Genome/genetics ; Mammals ; Retroelements/genetics ; }, abstract = {Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to participate in the rapid adaptation of species to changes in environment. Any direct test of this hypothesis would require the ability to measure epigenetic states over evolutionary timescales. Here we describe the first single-base resolution of cytosine methylation patterns in an ancient mammalian genome, by bisulphite allelic sequencing of loci from late Pleistocene Bison priscus remains. Retrotransposons and the differentially methylated regions of imprinted loci displayed methylation patterns identical to those derived from fresh bovine tissue, indicating that methylation patterns are preserved in the ancient DNA. Our findings establish the biochemical stability of methylated cytosines over extensive time frames, and provide the first direct evidence that cytosine methylation patterns are retained in DNA from ancient specimens. The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution.}, }
@article {pmid22268568, year = {2012}, author = {Oh, CS and Lee, SJ and Park, JB and Lee, SD and Seo, SB and Kim, HY and Kim, J and Kim, YS and Shin, DH}, title = {Autosomal short tandem repeat analysis of ancient DNA by coupled use of mini- and conventional STR kits.}, journal = {Journal of forensic sciences}, volume = {57}, number = {3}, pages = {820-825}, doi = {10.1111/j.1556-4029.2011.02044.x}, pmid = {22268568}, issn = {1556-4029}, mesh = {DNA/isolation &amp; purification ; *DNA Degradation, Necrotic ; DNA Fingerprinting/*instrumentation/methods ; Femur/chemistry ; Genotyping Techniques/instrumentation/methods ; History, 16th Century ; History, 18th Century ; Humans ; *Microsatellite Repeats ; Polymerase Chain Reaction ; }, abstract = {Multiplex autosomal short tandem repeat (STR) genotyping enables researchers to obtain genetic information from ancient human samples. In this study, we tested newly developed AmpFℓSTR(®) MiniFiler™ kit for autosomal STR analysis of ancient DNA (aDNA), using human femurs (n = 8) collected from medieval Korean tombs. After extracting aDNA from the bones, autosomal STR analyses were repeated for each sample using the AmpFℓSTR(®) MiniFiler™ and Identifiler™ kits. Whereas only 21.87% of larger-sized loci profiles could be obtained with the Identifiler™ kit, 75% of the same loci profiles were determined by MiniFiler™ kit analysis. This very successful amplification of large-sized STR markers from highly degraded aDNA suggests that the MiniFiler™ kit could be a useful complement to conventional STR kit analysis of ancient samples.}, }
@article {pmid22247504, year = {2012}, author = {Basu, A and Chatterjee, S and Chatterjee, S and Das Gupta, SK}, title = {Evolutionary link between the mycobacterial plasmid pAL5000 replication protein RepB and the extracytoplasmic function family of σ factors.}, journal = {Journal of bacteriology}, volume = {194}, number = {6}, pages = {1331-1341}, pmid = {22247504}, issn = {1098-5530}, mesh = {Bacterial Proteins/*genetics ; Binding Sites ; DNA Mutational Analysis ; DNA, Bacterial/metabolism ; *Evolution, Molecular ; Helix-Turn-Helix Motifs ; Mycobacterium/*genetics ; Phylogeny ; *Plasmids ; Protein Binding ; Sigma Factor/*genetics ; }, abstract = {Mycobacterial plasmid pAL5000 represents a family of plasmids found mostly in the Actinobacteria. It replicates using two plasmid-encoded proteins, RepA and RepB. While BLAST searches indicate that RepA is a replicase family protein, the evolutionary connection of RepB cannot be established, as no significant homologous partner (E < 10(-3)) outside the RepB family can be identified. To obtain insight into the structure-function and evolutionary connections of RepB, an investigation was undertaken using homology modeling, phylogenetic, and mutational analysis methods. The results indicate that although they are synthesized from the same operon, the phylogenetic affinities of RepA and RepB differ. Thus, the operon may have evolved through random breaking and joining events. Homology modeling predicted the presence of a three-helical helix-turn-helix domain characteristic of region 4 of extracytoplasmic function (ECF) σ factors in the C-terminal region of RepB. At the N-terminal region, there is a helical stretch, which may be distantly related to region 3 of σ factors. Mutational analysis identified two arginines indispensable for RepB activity, one each located within the C- and N-terminal conserved regions. Apart from analyzing the domain organization of the protein, the significance of the presence of a highly conserved A/T-rich element within the RepB binding site was investigated. Mutational analysis revealed that although this motif does not bind RepB, its integrity is important for efficient DNA-protein interactions and replication to occur. The present investigation unravels the possibility that RepB-like proteins and their binding sites represent ancient DNA-protein interaction modules.}, }
@article {pmid22237796, year = {2013}, author = {Kim, KY and Kwon, Y and Bazarragchaa, M and Park, AJ and Bang, H and Lee, WB and Lee, J and Lee, KH and Kim, BJ and Kim, K}, title = {A real-time PCR-based amelogenin Y allele dropout assessment model in gender typing of degraded DNA samples.}, journal = {International journal of legal medicine}, volume = {127}, number = {1}, pages = {55-61}, pmid = {22237796}, issn = {1437-1596}, mesh = {Alleles ; Amelogenin/*genetics ; *Chromosomes, Human, Y ; *DNA Degradation, Necrotic ; Female ; Forensic Genetics ; Humans ; Humic Substances ; Male ; *Real-Time Polymerase Chain Reaction ; Sex Determination Analysis/*methods ; }, abstract = {Allelic dropout due to stochastic variation in degraded small quantity DNA appears to be one of the most serious genotyping errors. Most methods require PCR replication to address this problem. The small amounts of valuable samples are often a limitation for such replications. We report a real-time PCR-based amelogonin Y (AMELY) allele dropout estimation model in an AMEL-based gender typing. We examined 915 replicates of AMELY-positive modern male DNA with varying amounts of DNA and humic acid. A male-specific AMEL fragment (AMELy) dropped out in 143 genuine male replicates, leading to gender typing errors. By graphing a scatter plot of the crossing point versus the end cycle fluorescence of the male replicates, a standard graph model for the estimation of the AMELy allele dropout was constructed with the dropout-prone and dropout-free zones. This model was then applied to ancient DNA (aDNA) samples. Nine samples identified as female were found in the dropout-prone zone; with higher DNA concentrations, six were shifted to the dropout-free zone. Among them, two female identifications were converted to male. All the aDNA gender was confirmed by sex-determination region Y marker amplification. Our data suggest that this model could be a basic approach for securing AMELy allele dropout-safe data from the stochastic variation of degraded inhibitory DNA samples.}, }
@article {pmid22237538, year = {2012}, author = {Ho, SY}, title = {Phylogenetic analysis of ancient DNA using BEAST.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {229-241}, doi = {10.1007/978-1-61779-516-9_24}, pmid = {22237538}, issn = {1940-6029}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; DNA/*genetics ; Fossils ; Mammoths/*genetics ; Monte Carlo Method ; *Mutation Rate ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Under exceptional circumstances, it is possible to obtain DNA sequences from samples that are up to hundreds of thousands of years old. These data provide an opportunity to look directly at past genetic diversity, to trace the evolutionary process through time, and to infer demographic and phylogeographic trends. Ancient DNA (aDNA) data sets have some degree of intrinsic temporal structure because the sequences have been obtained from samples of different ages. When analyzing these data sets, it is usually necessary to take the sampling times into account. A number of phylogenetic methods have been designed with this purpose in mind. Here I describe the steps involved in Bayesian phylogenetic analysis of aDNA data. I outline a procedure that can be used to co-estimate the genealogical relationships, mutation rate, evolutionary timescale, and demographic history of the study species in a single analytical framework. A number of modifications to the methodology can be made in order to deal with complicating factors such as postmortem damage, sequences from undated samples, and data sets with low information content.}, }
@article {pmid22237537, year = {2012}, author = {Kircher, M}, title = {Analysis of high-throughput ancient DNA sequencing data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {197-228}, doi = {10.1007/978-1-61779-516-9_23}, pmid = {22237537}, issn = {1940-6029}, mesh = {Base Sequence ; DNA/*genetics ; *Fossils ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Molecular Sequence Data ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {Advances in sequencing technologies have dramatically changed the field of ancient DNA (aDNA). It is now possible to generate an enormous quantity of aDNA sequence data both rapidly and inexpensively. As aDNA sequences are generally short in length, damaged, and at low copy number relative to coextracted environmental DNA, high-throughput approaches offer a tremendous advantage over traditional sequencing approaches in that they enable a complete characterization of an aDNA extract. However, the particular qualities of aDNA also present specific limitations that require careful consideration in data analysis. For example, results of high-throughout analyses of aDNA libraries may include chimeric sequences, sequencing error and artifacts, damage, and alignment ambiguities due to the short read lengths. Here, I describe typical primary data analysis workflows for high-throughput aDNA sequencing experiments, including (1) separation of individual samples in multiplex experiments; (2) removal of protocol-specific library artifacts; (3) trimming adapter sequences and merging paired-end sequencing data; (4) base quality score filtering or quality score propagation during data analysis; (5) identification of endogenous molecules from an environmental background; (6) quantification of contamination from other DNA sources; and (7) removal of clonal amplification products or the compilation of a consensus from clonal amplification products, and their exploitation for estimation of library complexity.}, }
@article {pmid22237536, year = {2012}, author = {Horn, S}, title = {Case study: enrichment of ancient mitochondrial DNA by hybridization capture.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {189-195}, doi = {10.1007/978-1-61779-516-9_22}, pmid = {22237536}, issn = {1940-6029}, mesh = {Animals ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; *Fossils ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Rodentia/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {In ancient DNA studies focusing on estimating population histories, genetic markers are sequenced from a large number of samples belonging to the same species. Targeting loci of interest using traditional PCR can be time-consuming, in particular when samples are not well preserved and multiple overlapping fragments are required. Here, I describe the process of generating DNA libraries from ancient DNA (aDNA) extracts for high-throughput sequencing. I use a serial in-solution DNA hybridization approach with subsequent bead capture to enrich libraries for the target locus, in this case the mitochondrial control region of ancient beavers (Castor fiber). The resulting sequencing reads are run through quality control filters to obtain reliable consensus sequences. Using these sequences, I construct a phylogenetic tree, which agrees with previously published data regarding phylogeographic relationships among beavers.}, }
@article {pmid22237535, year = {2012}, author = {Horn, S}, title = {Target enrichment via DNA hybridization capture.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {177-188}, doi = {10.1007/978-1-61779-516-9_21}, pmid = {22237535}, issn = {1940-6029}, mesh = {Animals ; DNA/*genetics/*isolation &amp; purification ; Fossils ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Nucleic Acid Hybridization/*methods ; }, abstract = {Recent advances in high-throughput DNA sequencing technologies have allowed entire nuclear genomes to be shotgun sequenced from ancient DNA (aDNA) extracts. Nonetheless, targeted analyses of specific genomic loci will remain an important tool for future aDNA studies. DNA capture via hybridization allows the efficient exploitation of current high-throughput sequencing for population genetic analyses using aDNA samples. Specifically, hybridization capture allows larger data sets to be generated for multiple target loci as well as for multiple samples in parallel. "Bait" molecules are used to select target regions from DNA libraries for sequencing. Here we present a brief overview of the currently available hybridization capture protocols using either an in-solution or a solid-phase (immobilized) approach. While it is possible to purchase ready-made kits for this purpose, I present a protocol that allows users to generate their own custom bait to be used for hybridization capture.}, }
@article {pmid22237534, year = {2012}, author = {Stiller, M}, title = {Case study: targeted high-throughput sequencing of mitochondrial genomes from extinct cave bears via direct multiplex PCR sequencing (DMPS).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {171-176}, doi = {10.1007/978-1-61779-516-9_20}, pmid = {22237534}, issn = {1940-6029}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Extinction, Biological ; Fossils ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Multiplex Polymerase Chain Reaction/*methods ; Ursidae/*genetics ; }, abstract = {Here I describe the use of a recently developed technique for targeted high-throughput sequencing of highly degraded DNA by direct multiplex PCR sequencing (DMPS) that was used to amplify 31 near-complete mitochondrial genomes of the extinct cave bear (Ursus spelaeus). DMPS couples multiplex PCR with the generation of barcoded sequencing libraries to be sequenced in parallel on a high-throughput sequencing platform. DMPS makes it possible to generate large amounts of targeted DNA sequence data simultaneously from multiple degraded samples such as fossil remains. In this chapter, I describe an experiment that uses DMPS with different primer sets and on both modern and ancient DNA templates.}, }
@article {pmid22237533, year = {2012}, author = {Knapp, M and Stiller, M and Meyer, M}, title = {Generating barcoded libraries for multiplex high-throughput sequencing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {155-170}, doi = {10.1007/978-1-61779-516-9_19}, pmid = {22237533}, issn = {1940-6029}, mesh = {Base Sequence ; DNA/chemistry/*genetics ; DNA Barcoding, Taxonomic ; Fossils ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Multiplex Polymerase Chain Reaction/methods ; }, abstract = {Molecular barcoding is an essential tool to use the high throughput of next generation sequencing platforms optimally in studies involving more than one sample. Various barcoding strategies allow for the incorporation of short recognition sequences (barcodes) into sequencing libraries, either by ligation or polymerase chain reaction (PCR). Here, we present two approaches optimized for generating barcoded sequencing libraries from low copy number extracts and amplification products typical of ancient DNA studies.}, }
@article {pmid22237532, year = {2012}, author = {Briggs, AW and Heyn, P}, title = {Preparation of next-generation sequencing libraries from damaged DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {143-154}, doi = {10.1007/978-1-61779-516-9_18}, pmid = {22237532}, issn = {1940-6029}, mesh = {DNA/chemistry/*genetics ; DNA Damage ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Uracil/chemistry ; }, abstract = {Next-generation sequencing (NGS) has revolutionized ancient DNA research, especially when combined with high-throughput target enrichment methods. However, attaining high sequencing depth and accuracy from samples often remains problematic due to the damaged state of ancient DNA, in particular the extremely low copy number of ancient DNA and the abundance of uracil residues derived from cytosine deamination that lead to miscoding errors. It is therefore critical to use a highly efficient procedure for conversion of a raw DNA extract into an adaptor-ligated sequencing library, and equally important to reduce errors from uracil residues. We present a protocol for NGS library preparation that allows highly efficient conversion of DNA fragments into an adaptor-ligated form. The protocol incorporates an option to remove the vast majority of uracil miscoding lesions as part of the library preparation process. The procedure requires only two spin column purification steps and no gel purification or bead handling. Starting from an aliquot of DNA extract, a finished, highly amplified library can be generated in 5 h, or under 3 h if uracil removal is not required.}, }
@article {pmid22237531, year = {2012}, author = {Stiller, M and Fulton, TL}, title = {Multiplex PCR amplification of ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {133-141}, doi = {10.1007/978-1-61779-516-9_17}, pmid = {22237531}, issn = {1940-6029}, mesh = {Animals ; DNA/*genetics ; DNA Primers/genetics ; Electrophoresis, Agar Gel/methods ; *Fossils ; Multiplex Polymerase Chain Reaction/*methods ; }, abstract = {Multiplex PCR allows the simultaneous amplification of up to dozens of target fragments in a single PCR. It is therefore a powerful tool to obtain many kilobases of continuous sequence from minute amounts of ancient DNA (aDNA), which usually must be amplified in multiple short and overlapping fragments. Because significantly less template is required compared to amplifying each fragment separately, multiplex PCR is particularly beneficial when the fossil material itself, or access to the fossil material, is limited. The recently refined two-step multiplex PCR protocol consists of a first-step reaction (the actual multiplex PCR) that then acts as the template for the second-step PCR. During the second step, nested primers are used in individual amplification reactions. Although the same set of primers can be used in both steps, using a nested set in the second step adds an additional level of selectivity and specificity, minimizing PCR artifacts. This is particularly important when complex mixtures of template DNA, such as aDNA extracts, are amplified.}, }
@article {pmid22237530, year = {2012}, author = {Bunce, M and Oskam, CL and Allentoft, ME}, title = {Quantitative real-time PCR in aDNA research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {121-132}, doi = {10.1007/978-1-61779-516-9_16}, pmid = {22237530}, issn = {1940-6029}, mesh = {Base Sequence ; Benzothiazoles ; DNA/*genetics ; Diamines ; Fluorescent Dyes/analysis ; *Fossils ; Models, Molecular ; Molecular Sequence Data ; Organic Chemicals/analysis ; Quinolines ; Real-Time Polymerase Chain Reaction/economics/*methods ; }, abstract = {Quantitative real-time PCR (qPCR) is a technique that is widely used in the field of ancient DNA (aDNA). Quantitative PCR can be used to optimize aDNA extraction methodologies, to detect PCR inhibition, and to quantify aDNA libraries for use in high-throughput sequencing. In this chapter, we outline factors that need to be considered when developing efficient SYBR Green qPCR assays. We describe how to setup qPCR standards of known copy number and provide some useful tips regarding interpretation of qPCR data generated from aDNA templates.}, }
@article {pmid22237529, year = {2012}, author = {Fulton, TL and Stiller, M}, title = {PCR amplification, cloning, and sequencing of ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {111-119}, doi = {10.1007/978-1-61779-516-9_15}, pmid = {22237529}, issn = {1940-6029}, mesh = {Animals ; Cloning, Molecular/*methods ; DNA/*genetics/isolation &amp; purification/metabolism ; DNA-Directed DNA Polymerase/metabolism ; Electrophoresis, Agar Gel/methods ; *Fossils ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {PCR amplification of DNA is routine in modern molecular biology. However, the application of PCR to ancient DNA (aDNA) experiments often requires significant modification to standard protocols. The degraded nature of most aDNA fragments requires targeting shorter fragments, performing replicate amplifications, incorporating multiple negative controls, combating PCR inhibition, using specific DNA polymerases to deal with damaged bases, working in a separate aDNA facility, and modifying the PCR recipe to deal with damaged and low copy-number target DNA. In this chapter, we describe how and why these procedures are implemented, discuss aDNA-specific troubleshooting methodology, and suggest modifications to commercial cloning and sequencing procedures to reduce the expense of PCR product cloning.}, }
@article {pmid22237528, year = {2012}, author = {Mohandesan, E and Prost, S and Hofreiter, M}, title = {Case study: using a nondestructive DNA extraction method to generate mtDNA sequences from historical chimpanzee specimens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {101-110}, doi = {10.1007/978-1-61779-516-9_14}, pmid = {22237528}, issn = {1940-6029}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics/*isolation &amp; purification ; Mitochondria/genetics ; Museums ; Paleontology/methods ; Pan troglodytes/*genetics ; Phylogeny ; Phylogeography ; Polymerase Chain Reaction/methods ; }, abstract = {A major challenge for ancient DNA (aDNA) studies using museum specimens is that sampling procedures usually involve at least the partial destruction of each specimen used, such as the removal of skin, pieces of bone, or a tooth. Recently, a nondestructive DNA extraction method was developed for the extraction of amplifiable DNA fragments from museum specimens without appreciable damage to the specimen. Here, we examine the utility of this method by attempting DNA extractions from historic (older than 70 years) chimpanzee specimens. Using this method, we PCR-amplified part of the mitochondrial HVR-I region from 65% (56/86) of the specimens from which we attempted DNA extraction. However, we found a high incidence of multiple sequences in individual samples, suggesting substantial cross-contamination among samples, most likely originating from storage and handling in the museums. Consequently, reproducible sequences could be reconstructed from only 79% (44/56) of the successfully extracted samples, even after multiple extractions and amplifications. This resulted in an overall success rate of just over half (44/86 of samples, or 51% success), from which 39 distinct HVR-I haplotypes were recovered. We found a high incidence of C to T changes, arguing for both low concentrations of and substantial damage to the endogenous DNA. This chapter highlights both the potential and the limitations of nondestructive DNA extraction from museum specimens.}, }
@article {pmid22237526, year = {2012}, author = {Letts, B and Shapiro, B}, title = {Case study: ancient DNA recovered from pleistocene-age remains of a Florida armadillo.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {87-92}, doi = {10.1007/978-1-61779-516-9_12}, pmid = {22237526}, issn = {1940-6029}, mesh = {Animals ; Armadillos/*genetics ; Base Sequence ; Cloning, Molecular/methods ; DNA, Mitochondrial/chemistry/genetics/*isolation &amp; purification ; Florida ; *Fossils ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {Warm, humid regions are not ideal for long-term DNA preservation. Consequently, little ancient DNA research has been carried out involving taxa that lived in, for example, tropical and subtropical regions. Those studies that have isolated ancient DNA from warm environments have mostly been limited to the most recent several thousand years. Here, we discuss an ancient DNA experiment in which we attempt to amplify mitochondrial DNA from remains of armadillo, glyptodont, and pampathere from sites in Florida, USA, all believed to be around 10,000-12,000 years old. We were successful in recovering DNA from only one of these samples. However, based on the amount and distribution of DNA damage, the ancient DNA recovered was well-preserved despite the age and preservation environment. In this case study chapter, we discuss the experimental procedure we used to characterize the DNA from the Floridian samples, focusing on challenges of working with ancient specimens from warm environments and steps taken to confirm the authenticity of the recovered sequence.}, }
@article {pmid22237524, year = {2012}, author = {Kistler, L}, title = {Ancient DNA extraction from plants.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {71-79}, doi = {10.1007/978-1-61779-516-9_10}, pmid = {22237524}, issn = {1940-6029}, mesh = {Cetrimonium ; Cetrimonium Compounds/chemistry ; Chloroform/chemistry ; DNA, Plant/*isolation &amp; purification ; *Fossils ; Plants/*genetics ; Thiazoles/chemistry ; }, abstract = {A variety of protocols for DNA extraction from archaeological and paleobotanical plant specimens have been proposed. This is not surprising given the range of taxa and tissue types that may be preserved and the variety of conditions in which that preservation may take place. Commercially available DNA extraction kits can be used to recover ancient plant DNA, but modifications to standard approaches are often necessary to improve yield. In this chapter, I describe two protocols for extracting DNA from small amounts of ancient plant tissue. The CTAB protocol, which I recommend for use with single seeds, utilizes an incubation period in extraction buffer and subsequent chloroform extraction followed by DNA purification and suspension. The PTB protocol, which I recommend for use with gourd rind and similar tissues, utilizes an overnight incubation of pulverized tissue in extraction buffer, removal of the tissue by centrifugation, and DNA extraction from the buffer using commercial plant DNA extraction kits.}, }
@article {pmid22237523, year = {2012}, author = {Oskam, CL and Bunce, M}, title = {DNA extraction from fossil eggshell.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {65-70}, doi = {10.1007/978-1-61779-516-9_9}, pmid = {22237523}, issn = {1940-6029}, mesh = {Animals ; Birds/genetics ; DNA/*isolation &amp; purification ; Egg Shell/*chemistry ; *Fossils ; Hot Temperature ; Silicon Dioxide/chemistry ; }, abstract = {Avian eggshell fragments recovered from both paleontological and archaeological deposits contain a cache of well-preserved ancient DNA. Here, we describe an extraction protocol that has been optimized to maximize the recovery of ancient DNA from fossil eggshell and minimize the co-purification of PCR inhibitors. In this method, fossil eggshell fragments are powdered, then digested and heated to release DNA from the calcite matrix. The digest then undergoes a concentration step before purification and washing using silica columns. The method has been used to recover aDNA from the eggshell of many avian species including moa, elephant birds, and emu, up to 19,000 years old.}, }
@article {pmid22237522, year = {2012}, author = {Haile, J}, title = {Ancient DNA extraction from soils and sediments.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {57-63}, doi = {10.1007/978-1-61779-516-9_8}, pmid = {22237522}, issn = {1940-6029}, mesh = {DNA/*isolation &amp; purification ; Geologic Sediments/*chemistry ; Paleontology/*methods ; Soil/*chemistry ; }, abstract = {DNA contained in soils and sediments can provide novel insights into past environments and ecosystems. In this chapter, I describe an efficient and effective technique to extract total DNA from sediments in a manner that minimizes the coextraction of PCR-inhibitory compounds. I describe two different approaches: one that is suitable for large (up to 10 g wet weight) amounts of substrate, and a second that is more appropriate for small (up to 0.5 g) amounts of substrate. Finally, I discuss some of the obstacles that may be encountered in the process of extracting DNA from soils and sediments and suggest approaches to circumvent some common problems.}, }
@article {pmid22237521, year = {2012}, author = {Clack, AA and Macphee, RD and Poinar, HN}, title = {Case study: ancient sloth DNA recovered from hairs preserved in paleofeces.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {51-56}, doi = {10.1007/978-1-61779-516-9_7}, pmid = {22237521}, issn = {1940-6029}, mesh = {Animals ; Base Sequence ; DNA/chemistry/genetics/*isolation &amp; purification ; Feces/*chemistry ; *Fossils ; Hair/*chemistry/metabolism ; Molecular Sequence Data ; Sequence Alignment ; Sloths/*genetics ; }, abstract = {Ancient hair, which has proved to be an excellent source of well-preserved ancient DNA, is often preserved in paleofeces. Here, we separate and wash hair shafts preserved in a paleofecal specimen believed to be from a Darwin's ground sloth, Mylodon darwinii. After extracting DNA from the recovered and cleaned hair using a protocol optimized for DNA extraction from keratinous substrates, we amplify 12S and 16S rDNA sequences from the DNA extract. As expected, the recovered sequences most closely match previously published sequences of M. darwinii. Our results demonstrate that hair preserved in paleofeces, even from temperate cave environments, is an effective source of ancient DNA.}, }
@article {pmid22237518, year = {2012}, author = {Fulton, TL and Wagner, SM and Shapiro, B}, title = {Case study: recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {29-35}, doi = {10.1007/978-1-61779-516-9_4}, pmid = {22237518}, issn = {1940-6029}, mesh = {Animals ; Cell Nucleus/genetics ; Columbidae/*genetics ; DNA/genetics/*isolation &amp; purification ; Dithiothreitol/chemistry ; *Extinction, Biological ; Phylogeny ; Silicon Dioxide/chemistry ; }, abstract = {A variety of DNA extraction methods have been employed successfully to extract DNA from museum specimens. Toe pads are a common source of ancient DNA in birds, as they are generally not an informative character and can be removed without significant destruction of precious specimens. However, the DNA in these tissues is often highly degraded, both by natural postmortem decay and due to treatment by preservatives. In this case study chapter, we describe the use of both a commercial DNA extraction method and a silica-based method to extract ancient DNA from desiccated toe pads from the extinct passenger pigeon, Ectopistes migratorius. Successful amplification of nuclear DNA was achieved from both methods, representing the first nuclear DNA sequence recovered from this extinct species. We describe simple modifications to both protocols that we employed during the DNA extraction process.}, }
@article {pmid22237516, year = {2012}, author = {Barnett, R and Larson, G}, title = {A phenol-chloroform protocol for extracting DNA from ancient samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {13-19}, doi = {10.1007/978-1-61779-516-9_2}, pmid = {22237516}, issn = {1940-6029}, mesh = {Chelating Agents/chemistry ; Chloroform/*chemistry ; DNA/*isolation &amp; purification ; Genetic Techniques ; Paleontology/*methods ; Phenol/*chemistry ; }, abstract = {The myriad downstream applications of ancient DNA (aDNA) analysis all ultimately require that sequence data are generated from extracts of ancient material. DNA extraction from tissues known to contain preserved biomolecules (e.g. teeth, hair, tissue, bone) relies on subtle modifications of a basic technique that has been in use for nearly two decades. Multiple DNA extraction protocols have been introduced, with varying levels of success depending on tissue type and the long-term preservation environment to which the ancient tissue was exposed. Here, we describe the phenol-chloroform method for extracting aDNA from any tissue type. This commonly employed method allows for the recovery of total nucleic acid content with minimal loss of low molecular weight double-stranded DNA.}, }
@article {pmid22237515, year = {2012}, author = {Fulton, TL}, title = {Setting up an ancient DNA laboratory.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {1-11}, doi = {10.1007/978-1-61779-516-9_1}, pmid = {22237515}, issn = {1940-6029}, mesh = {Animals ; *DNA/chemistry/genetics/isolation &amp; purification ; Fossils ; *Genetic Techniques ; Humans ; *Laboratories ; Paleontology/*methods ; }, abstract = {Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential for contamination of ancient samples and DNA extracts with modern DNA is considerable. To minimize the risk associated with working with ancient DNA, experimental protocols specific to handling ancient specimens have been introduced. Here, I outline the challenges associated with working with ancient DNA and describe guidelines for setting up a new ancient DNA laboratory. I also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination with exogenous sources of DNA.}, }
@article {pmid22235141, year = {2012}, author = {Ishida, Y and Roca, AL and Fratpietro, S and Greenwood, AD}, title = {Successful genotyping of microsatellites in the woolly mammoth.}, journal = {The Journal of heredity}, volume = {103}, number = {3}, pages = {459-464}, doi = {10.1093/jhered/esr139}, pmid = {22235141}, issn = {1465-7333}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Speciation ; Genotyping Techniques ; Heterozygote ; Likelihood Functions ; Mammoths/*genetics ; Microsatellite Repeats/*genetics ; Phylogeny ; Printers' Marks ; Sequence Analysis, DNA ; Tandem Repeat Sequences/genetics ; }, abstract = {Genetic analyses using ancient DNA from Pleistocene and early Holocene fossils have largely relied on mitochondrial DNA (mtDNA) sequences. Among woolly mammoths, Mammuthus primigenius, mtDNA analyses have identified 2 distinct clades (I and II) that diverged 1-2 Ma. Here, we establish that microsatellite markers can be effective on Pleistocene samples, successfully genotyping woolly mammoth specimens at 2 loci. Although significant differentiation at the 2 microsatellite loci was not detected between 16 clade I and 4 clade II woolly mammoths, our results demonstrate that the nuclear population structure of Pleistocene species can be examined using fast-evolving nuclear microsatellite markers.}, }
@article {pmid22194840, year = {2011}, author = {Brown, SK and Pedersen, NC and Jafarishorijeh, S and Bannasch, DL and Ahrens, KD and Wu, JT and Okon, M and Sacks, BN}, title = {Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Y chromosomes illuminates dog origins.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e28496}, pmid = {22194840}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/genetics ; Asia, Southeastern ; Breeding ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; Female ; Genetic Variation ; Geography ; Haplotypes ; Male ; Microsatellite Repeats ; Middle East ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Rural Population ; Wolves/genetics ; Y Chromosome/*genetics ; }, abstract = {Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.}, }
@article {pmid22192823, year = {2011}, author = {Lalueza-Fox, C and Gilbert, MT}, title = {Paleogenomics of archaic hominins.}, journal = {Current biology : CB}, volume = {21}, number = {24}, pages = {R1002-9}, doi = {10.1016/j.cub.2011.11.021}, pmid = {22192823}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Demography ; *Evolution, Molecular ; Fossils ; Gene Flow ; Genetic Variation ; Genome, Human ; Hominidae/anatomy &amp; histology/*genetics/physiology ; Humans/anatomy &amp; histology/genetics/physiology ; Neanderthals/anatomy &amp; histology/*genetics/physiology ; Phylogeny ; Species Specificity ; }, abstract = {In order to understand the genetic basis for the evolutionary success of modern humans, it is necessary to compare their genetic makeup to that of closely related species. Unfortunately, our closest living relatives, the chimpanzees, are evolutionarily quite distant. With the advent of ancient DNA study and more recently paleogenomics - the study of the genomes of ancient organisms - it has become possible to compare human genomes to those of much more closely related groups. Our closest known relatives are the Neanderthals, which evolved and lived in Europe and Western Asia, from about 600,000 years ago until their disappearance around 30,000 years ago following the expansion of anatomically modern humans into their range. The closely related Denisovans are only known by virtue of their DNA, which has been extracted from bone fragments dating around 30,000 to 50,000 years ago found in a single Siberian cave. Analyses of Neanderthal and Denisovan nuclear and mitochondrial genomes have revealed surprising insights into these archaic humans as well as our own species. The genomes provide a preliminary catalogue of derived amino acids that are specific to all extant modern humans, thus offering insights into the functional differences between the three lineages. In addition, the genomes provide evidence of gene flow between the three lineages after anatomically modern humans left Africa, drastically changing our view of human evolution.}, }
@article {pmid22188739, year = {2012}, author = {Gravlund, P and Aaris-Sørensen, K and Hofreiter, M and Meyer, M and Bollback, JP and Noe-Nygaard, N}, title = {Ancient DNA extracted from Danish aurochs (Bos primigenius): genetic diversity and preservation.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {103-111}, doi = {10.1016/j.aanat.2011.10.011}, pmid = {22188739}, issn = {1618-0402}, mesh = {Animals ; Bone and Bones/chemistry ; Cattle/*genetics ; Cloning, Molecular ; Collagen/chemistry/genetics ; DNA/*genetics ; DNA Primers ; Denmark ; Environment ; Europe ; *Genetic Variation ; Genetics, Population ; Geography ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Specimen Handling ; }, abstract = {We extracted DNA from 39 Danish aurochs specimens and successfully amplified and sequenced a 252 base pair long fragment of the multivariable region I of the mitochondrial control region from 11 specimens. The sequences from these specimens dated back to 9830-2865 14Cyr BP and represent the first study of genetic variation of Danish aurochs. In addition, for all specimens we address correlations between the ability to obtain DNA sequences and various parameters such as the age of the sample, the collagen content, the museum storage period, Danish geography and whether the specimens were found in an archeological or geological context. We find that aurochs from southern Scandinavia display a star-shaped population genetic structure, that is indicative of a local and relatively recent diversification from a few ancestral haplotypes that may have originated in the ancestral Western European population before migration northwards during the retreat of the glaciers. Scenarios suggesting several invasions of genetically distinct aurochs are not supported by these analyses. Rather, our results suggest that a single continuous migration northward occurred. Our findings also suggest, although with only limited support, that aurochs in Northwestern Europe underwent a population expansion beginning shortly after the retreat of the glacial ice from Denmark and had a stable population size until the population decline that must have occurred prior to extinction. The absence of haplotypes similar to modern domestic cattle in our aurochs suggests that introgression between these species must have been limited, if it occurred at all. We found that the successful recovery of genetic material for PCR amplification correlates with sample age and local geographic conditions. However, contrary to other studies, we found no significant correlation between length of time in museum storage or the type of the locality in which a specimen was discovered (archeological or geological) and amplification success. Finally, we found large variances in our estimates of collagen content preventing an evaluation of this as an indicator of preservation quality.}, }
@article {pmid22183740, year = {2012}, author = {Bolnick, DA and Bonine, HM and Mata-Míguez, J and Kemp, BM and Snow, MH and LeBlanc, SA}, title = {Nondestructive sampling of human skeletal remains yields ancient nuclear and mitochondrial DNA.}, journal = {American journal of physical anthropology}, volume = {147}, number = {2}, pages = {293-300}, doi = {10.1002/ajpa.21647}, pmid = {22183740}, issn = {1096-8644}, mesh = {Archaeology/*methods ; Bone and Bones/*chemistry ; DNA/*isolation &amp; purification ; DNA, Mitochondrial/*isolation &amp; purification ; Humans ; North America ; Polymerase Chain Reaction ; Tooth/*chemistry ; }, abstract = {Museum curators and living communities are sometimes reluctant to permit ancient DNA (aDNA) studies of human skeletal remains because the extraction of aDNA usually requires the destruction of at least some skeletal material. Whether these views stem from a desire to conserve precious materials or an objection to destroying ancestral remains, they limit the potential of aDNA research. To help address concerns about destructive analysis and to minimize damage to valuable specimens, we describe a nondestructive method for extracting DNA from ancient human remains. This method can be used with both teeth and bone, but it preserves the structural integrity of teeth much more effectively than that of bone. Using this method, we demonstrate that it is possible to extract both mitochondrial and nuclear DNA from human remains dating between 300 BC and 1600 AD. Importantly, the method does not expose the remains to hazardous chemicals, allowing them to be safely returned to curators, custodians, and/or owners of the samples. We successfully amplified mitochondrial DNA from 90% of the individuals tested, and we were able to analyze 1-9 nuclear loci in 70% of individuals. We also show that repeated nondestructive extractions from the same tooth can yield amplifiable mitochondrial and nuclear DNA. The high success rate of this method and its ability to yield DNA from samples spanning a wide geographic and temporal range without destroying the structural integrity of the sampled material may make possible the genetic study of skeletal collections that are not available for destructive analysis.}, }
@article {pmid22154270, year = {2012}, author = {Pruvost, M and Reissmann, M and Benecke, N and Ludwig, A}, title = {From genes to phenotypes - evaluation of two methods for the SNP analysis in archaeological remains: pyrosequencing and competitive allele specific PCR (KASPar).}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {74-81}, doi = {10.1016/j.aanat.2011.10.007}, pmid = {22154270}, issn = {1618-0402}, mesh = {Alleles ; Animals ; *Archaeology ; Bone and Bones/chemistry ; DNA/*genetics ; DNA Primers ; Hair Color/genetics ; Horses/*genetics ; Phenotype ; Polymerase Chain Reaction/*methods ; Polymorphism, Single Nucleotide/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Siberia ; Specimen Handling ; }, abstract = {The amplification length of the DNA fragments is one major limitation of most paleogenetic analyses. Routinely, only fragments below 200 bp can be amplified, significantly reducing the content of genetic information. Although overlapping PCR strategies and next generation sequencing techniques have strongly improved data mining recently, these methods are still expensive and time consuming. In contrast, SNP analyses are easy to handle, fast and cheap. In this study, we compare two methods of SNP detection as to efficiency, cost and reliability for their use in ancient DNA applications: pyrosequencing and competitive allele specific PCR (KASPar). Our sample set consisted of 16 horse bones from two Scythian graves (600-800 BC). In conclusion, both approaches produced reliable results for most allelic patterns. But an indel of 11 bp (ASIP) could not be detected in the KASPar approach and produced problems in the pyrosequencing method (70% success rate). In such cases, we recommend checking allelic distribution using a gel approach or capillary sequencing. Overall, in comparison with the traditional mode of ancient DNA investigations (PCR, cloning, capillary sequencing), both approaches are superior for SNP analyses especially of large sample sets.}, }
@article {pmid22117930, year = {2012}, author = {Gamba, C and Fernández, E and Tirado, M and Deguilloux, MF and Pemonge, MH and Utrilla, P and Edo, M and Molist, M and Rasteiro, R and Chikhi, L and Arroyo-Pardo, E}, title = {Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers.}, journal = {Molecular ecology}, volume = {21}, number = {1}, pages = {45-56}, doi = {10.1111/j.1365-294X.2011.05361.x}, pmid = {22117930}, issn = {1365-294X}, mesh = {Agriculture/history ; Archaeology ; DNA, Mitochondrial/genetics/*history ; Genetic Drift ; Haplotypes/*genetics ; History, Ancient ; Humans ; Middle East ; Phylogeography/history ; Spain ; }, abstract = {The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations-N* and X1-are found at higher frequencies in our Early Neolithic population (∼31%). Genetic differentiation between Early and Middle Neolithic populations was significant (F(ST) ∼0.13, P<10(-5)), suggesting that genetic drift played an important role at this time. To improve our understanding of the Neolithic demographic processes, we used a Bayesian coalescence-based simulation approach to identify the most likely of three demographic scenarios that might explain the genetic data. The three scenarios were chosen to reflect archaeological knowledge and previous genetic studies using similar inferential approaches. We found that models that ignore population structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East.}, }
@article {pmid22106429, year = {2012}, author = {Barney, A and Martelli, S and Serrurier, A and Steele, J}, title = {Articulatory capacity of Neanderthals, a very recent and human-like fossil hominin.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {367}, number = {1585}, pages = {88-102}, pmid = {22106429}, issn = {1471-2970}, mesh = {Animals ; Biological Evolution ; Computer Simulation ; *Fossils ; Humans ; Hyoid Bone/diagnostic imaging ; Language ; Larynx/*anatomy &amp; histology/physiology ; Neanderthals/anatomy &amp; histology/*physiology ; Regression Analysis ; Selection, Genetic ; Skull/diagnostic imaging ; Speech ; *Speech Acoustics ; Tomography, X-Ray Computed ; }, abstract = {Scientists seek to use fossil and archaeological evidence to constrain models of the coevolution of human language and tool use. We focus on Neanderthals, for whom indirect evidence from tool use and ancient DNA appears consistent with an adaptation to complex vocal-auditory communication. We summarize existing arguments that the articulatory apparatus for speech had not yet come under intense positive selection pressure in Neanderthals, and we outline some recent evidence and analyses that challenge such arguments. We then provide new anatomical results from our own attempt to reconstruct vocal tract (VT) morphology in Neanderthals, and document our simulations of the acoustic and articulatory potential of this reconstructed Neanderthal VT. Our purpose in this paper is not to polarize debate about whether or not Neanderthals were human-like in all relevant respects, but to contribute to the development of methods that can be used to make further incremental advances in our understanding of the evolution of speech based on fossil and archaeological evidence.}, }
@article {pmid22103443, year = {2012}, author = {Cappellini, E and Jensen, LJ and Szklarczyk, D and Ginolhac, A and da Fonseca, RA and Stafford, TW and Holen, SR and Collins, MJ and Orlando, L and Willerslev, E and Gilbert, MT and Olsen, JV}, title = {Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins.}, journal = {Journal of proteome research}, volume = {11}, number = {2}, pages = {917-926}, doi = {10.1021/pr200721u}, pmid = {22103443}, issn = {1535-3907}, mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Elephants ; Femur/*chemistry ; *Fossils ; Mammoths/*metabolism ; Molecular Sequence Data ; Proteins/*chemistry/classification ; Proteome/analysis/chemistry ; Proteomics/*methods ; Sequence Analysis, Protein ; Serum Albumin/chemistry ; Siberia ; Tandem Mass Spectrometry ; }, abstract = {We used high-sensitivity, high-resolution tandem mass spectrometry to shotgun sequence ancient protein remains extracted from a 43 000 year old woolly mammoth (Mammuthus primigenius) bone preserved in the Siberian permafrost. For the first time, 126 unique protein accessions, mostly low-abundance extracellular matrix and plasma proteins, were confidently identified by solid molecular evidence. Among the best characterized was the carrier protein serum albumin, presenting two single amino acid substitutions compared to extant African (Loxodonta africana) and Indian (Elephas maximus) elephants. Strong evidence was observed of amino acid modifications due to post-mortem hydrolytic and oxidative damage. A consistent subset of this permafrost bone proteome was also identified in more recent Columbian mammoth (Mammuthus columbi) samples from temperate latitudes, extending the potential of the approach described beyond subpolar environments. Mass spectrometry-based ancient protein sequencing offers new perspectives for future molecular phylogenetic inference and physiological studies on samples not amenable to ancient DNA investigation. This approach therefore represents a further step into the ongoing integration of different high-throughput technologies for identification of ancient biomolecules, unleashing the field of paleoproteomics.}, }
@article {pmid22101653, year = {2011}, author = {Molak, M and Ho, SY}, title = {Evaluating the impact of post-mortem damage in ancient DNA: a theoretical approach.}, journal = {Journal of molecular evolution}, volume = {73}, number = {3-4}, pages = {244-255}, pmid = {22101653}, issn = {1432-1432}, mesh = {Algorithms ; Animals ; Base Sequence ; Bayes Theorem ; Computer Simulation ; *DNA Degradation, Necrotic ; *Fossils ; Kinetics ; Models, Chemical ; Postmortem Changes ; Temperature ; Time Factors ; }, abstract = {The growth of ancient DNA research has offered exceptional opportunities and raised great expectations, but has also presented some considerable challenges. One of the ongoing issues is the impact of post-mortem damage in DNA molecules. Nucleotide alterations and DNA strand breakages lead to a significant decrease in the quantity of DNA molecules of useful length in a sample and to errors in the final DNA sequences obtained. We present a model of age-dependent DNA damage and quantify the influence of that damage on subsequent steps in the sequencing process, including the polymerase chain reaction and cloning. Calculations using our model show that deposition conditions, rather than the age of a sample, have the greatest influence on the level of DNA damage. In turn, this affects the probability of interpreting an erroneous (possessing damage-derived mutations) sequence as being authentic. We also evaluated the effect of post-mortem damage on real data sets using a Bayesian phylogenetic approach. According to our study, damage-derived sequence alterations appear to have little impact on the final DNA sequences. This indicates the effectiveness of current methods for sequence authentication and validation.}, }
@article {pmid22065436, year = {2011}, author = {Briggs, AW}, title = {Rapid retrieval of DNA target sequences by primer extension capture.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {772}, number = {}, pages = {145-154}, doi = {10.1007/978-1-61779-228-1_8}, pmid = {22065436}, issn = {1940-6029}, mesh = {Base Sequence ; DNA Primers/*metabolism ; Gene Library ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {There is a widespread need for methods to enrich DNA samples for sequences of interest prior to high-throughput sequencing and to reduce the costs associated with a shotgun approach. While useful for targeting megabase-sized regions in a few samples, hybridization capture approaches such as those using microarrays currently involve bulky handling steps, long incubation times, and high per-sample costs. In contrast, the primer extension capture (PEC) method allows direct selection of small genomic regions from DNA sources within 2 h, with low costs for use with parallel samples. PEC promises useful applications in studies such as ancient DNA or forensic sequencing, taxonomic surveying of metagenomic samples, or genomic mapping of repetitive elements.}, }
@article {pmid22048313, year = {2011}, author = {Lorenzen, ED and Nogués-Bravo, D and Orlando, L and Weinstock, J and Binladen, J and Marske, KA and Ugan, A and Borregaard, MK and Gilbert, MT and Nielsen, R and Ho, SY and Goebel, T and Graf, KE and Byers, D and Stenderup, JT and Rasmussen, M and Campos, PF and Leonard, JA and Koepfli, KP and Froese, D and Zazula, G and Stafford, TW and Aaris-Sørensen, K and Batra, P and Haywood, AM and Singarayer, JS and Valdes, PJ and Boeskorov, G and Burns, JA and Davydov, SP and Haile, J and Jenkins, DL and Kosintsev, P and Kuznetsova, T and Lai, X and Martin, LD and McDonald, HG and Mol, D and Meldgaard, M and Munch, K and Stephan, E and Sablin, M and Sommer, RS and Sipko, T and Scott, E and Suchard, MA and Tikhonov, A and Willerslev, R and Wayne, RK and Cooper, A and Hofreiter, M and Sher, A and Shapiro, B and Rahbek, C and Willerslev, E}, title = {Species-specific responses of Late Quaternary megafauna to climate and humans.}, journal = {Nature}, volume = {479}, number = {7373}, pages = {359-364}, pmid = {22048313}, issn = {1476-4687}, support = {R01 HG003229/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; *Biota ; Bison ; Climate Change/*history ; DNA, Mitochondrial/analysis/genetics ; Europe ; *Extinction, Biological ; Fossils ; Genetic Variation ; Geography ; History, Ancient ; Horses ; Human Activities/*history ; Humans ; Mammals/genetics/*physiology ; Mammoths ; Molecular Sequence Data ; Population Dynamics ; Reindeer ; Siberia ; Species Specificity ; Time Factors ; }, abstract = {Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.}, }
@article {pmid22042855, year = {2011}, author = {Lacan, M and Keyser, C and Ricaut, FX and Brucato, N and Tarrús, J and Bosch, A and Guilaine, J and Crubézy, E and Ludes, B}, title = {Ancient DNA suggests the leading role played by men in the Neolithic dissemination.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {45}, pages = {18255-18259}, pmid = {22042855}, issn = {1091-6490}, mesh = {Cell Nucleus/genetics ; Chromosomes, Human, Y ; DNA/*genetics ; *Fossils ; History, Ancient ; Humans ; Male ; Mitochondria/genetics ; *Role ; }, abstract = {The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA extracted from human remains excavated in a Spanish funeral cave dating from the beginning of the fifth millennium B.C. Thanks to a "multimarkers" approach based on the analysis of mitochondrial and nuclear DNA (autosomes and Y-chromosome), we obtained information on the early Neolithic funeral practices and on the biogeographical origin of the inhumed individuals. No close kinship was detected. Maternal haplogroups found are consistent with pre-Neolithic settlement, whereas the Y-chromosomal analyses permitted confirmation of the existence in Spain approximately 7,000 y ago of two haplogroups previously associated with the Neolithic transition: G2a and E1b1b1a1b. These results are highly consistent with those previously found in Neolithic individuals from French Late Neolithic individuals, indicating a surprising temporal genetic homogeneity in these groups. The high frequency of G2a in Neolithic samples in western Europe could suggest, furthermore, that the role of men during Neolithic dispersal could be greater than currently estimated.}, }
@article {pmid22008209, year = {2011}, author = {Chan, YL and Hadly, EA}, title = {Genetic variation over 10,000 years in Ctenomys: comparative phylochronology provides a temporal perspective on rarity, environmental change and demography.}, journal = {Molecular ecology}, volume = {20}, number = {22}, pages = {4592-4605}, doi = {10.1111/j.1365-294X.2011.05295.x}, pmid = {22008209}, issn = {1365-294X}, mesh = {Animals ; Ecosystem ; *Environment ; Fossils ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; Models, Genetic ; Phylogeny ; Rodentia/*genetics ; Sequence Analysis, DNA ; }, abstract = {An understanding of how ecological traits influence past species response to environmental change can aid our future predictions of species persistence. We used ancient DNA and serial coalescent modelling in a hypothesis-testing framework to reveal differences in temporal genetic variation over 10,000 years for two species of subterranean rodents that currently differ in rarity (abundance, range size and habitat specificity) and mating system, but that reside in the same volcanically active region. Comparative phylochronologic analyses indicated little genetic change and suggest genetic stability in the solitary widespread Ctenomys haigi over thousands of years. In contrast, we found a pattern of haplotypic turnover in the rare and currently endangered Ctenomys sociabilis. Serial coalescent modelling indicated that the best-fit models of microevolutionary change included gene flow between isolated populations for this species. Although C. haigi and C. sociabilis are congeners that share many life history traits, they have behavioural, habitat-preference and population-size differences that may have resulted in contrasting patterns of temporal variation during periods of environmental change.}, }
@article {pmid22000492, year = {2012}, author = {Hughey, JR and Du, M and Li, Q and Michalodimitrakis, M and Stamatoyannopoulos, G}, title = {A search for β thalassemia mutations in 4000 year old ancient DNAs of Minoan Cretans.}, journal = {Blood cells, molecules &amp; diseases}, volume = {48}, number = {1}, pages = {7-10}, pmid = {22000492}, issn = {1096-0961}, support = {R56 DK045365/DK/NIDDK NIH HHS/United States ; T32 GM007454/GM/NIGMS NIH HHS/United States ; R90 HG004152-01/HG/NHGRI NIH HHS/United States ; R37 DK045365/DK/NIDDK NIH HHS/United States ; DK 045365/DK/NIDDK NIH HHS/United States ; R01 DK045365/DK/NIDDK NIH HHS/United States ; GM 007454/GM/NIGMS NIH HHS/United States ; R90 HG004152/HG/NHGRI NIH HHS/United States ; }, mesh = {DNA/chemistry/*genetics ; Exons ; *Fossils ; Greece ; HeLa Cells ; Heterozygote ; Humans ; Introns/*genetics ; *Mutation ; Phylogeography ; Polymorphism, Single Nucleotide ; RNA Splicing ; beta-Globins/chemistry/*genetics ; beta-Thalassemia/*genetics ; }, abstract = {Ancient DNA methodologies can be applied in the investigation of the genetics of extinct populations. A search for beta thalassemia mutations was performed on 49 Minoan individuals from the Bronze Age who were living in the island of Crete approximately 4000 Years Before Present (YBP). Standard precautionary measures were employed in the laboratory to ensure authenticity of the DNA extracted from the ancient bones, resulting in the successful analysis of DNA of 24 Minoans. DNA sequencing focused on the Intervening Sequence 1 (IVS-1) of the beta globin gene and its splicing junctions. 63% of the thalassemia mutations observed among modern Cretans reside in beta IVS-1. None of the Minoan individuals carried one of the IVS-1 mutations known to cause beta thalassemia; however, only one was expected to be observed if the average frequency of beta thalassemia heterozygotes in the Minoan population was the same with that of modern day Cretans (7.6%). One individual contained a C to G substitution in position 91 of the IVS-1, located 40 bp 5' to the intron 1/exon 2 junction. Functional studies indicated that the mutation did not affect mRNA splicing or stability, and most likely represented an innocent single nucleotide polymorphism.}, }
@article {pmid21993626, year = {2011}, author = {Bos, KI and Schuenemann, VJ and Golding, GB and Burbano, HA and Waglechner, N and Coombes, BK and McPhee, JB and DeWitte, SN and Meyer, M and Schmedes, S and Wood, J and Earn, DJ and Herring, DA and Bauer, P and Poinar, HN and Krause, J}, title = {A draft genome of Yersinia pestis from victims of the Black Death.}, journal = {Nature}, volume = {478}, number = {7370}, pages = {506-510}, pmid = {21993626}, issn = {1476-4687}, support = {R24 HD044943/HD/NICHD NIH HHS/United States ; /CAPMC/CIHR/Canada ; }, mesh = {Chromosomes, Bacterial/genetics ; Contig Mapping ; Dental Pulp/microbiology ; Evolution, Molecular ; Genome, Bacterial/*genetics ; History, Medieval ; Humans ; London/epidemiology ; Molecular Sequence Data ; Phylogeny ; Plague/epidemiology/*microbiology/transmission ; Plasmids/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Virulence/genetics ; Yersinia pestis/classification/*genetics/*isolation &amp; purification ; }, abstract = {Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348-1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347-1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.}, }
@article {pmid21990065, year = {2011}, author = {Casas-Vargas, A and Gómez, A and Briceño, I and Díaz-Matallana, M and Bernal, JE and Rodríguez, JV}, title = {High genetic diversity on a sample of pre-Columbian bone remains from Guane territories in northwestern Colombia.}, journal = {American journal of physical anthropology}, volume = {146}, number = {4}, pages = {637-649}, doi = {10.1002/ajpa.21626}, pmid = {21990065}, issn = {1096-8644}, mesh = {Americas ; Anthropology, Physical ; Bone and Bones/*chemistry ; Colombia ; DNA, Mitochondrial/analysis/*genetics ; Emigration and Immigration ; *Genetic Variation ; Haplotypes ; History, Medieval ; Humans ; Indians, South American/*genetics/history ; Phylogeography ; Principal Component Analysis ; }, abstract = {Ancient DNA was recovered from 17 individuals found in a rock shelter in the district of "La Purnia" (Santander, Colombia). This region is the homeland of pre-Columbian Guane, whom spread over the "Río Suarez" to the "Río de Oro", and were surrounded to the west by the Central Andes, south and east by foothills of Eastern Andes, and north by the "Chicamocha" river canyon. Guanes established in a region that straddles the Andes and the northern Amazon basin, possibly making it an unavoidable conduit for people moving to and from South America. We amplified mtDNA hypervariable region I (HVI) segments from ancient bone remains, and the resulting sequences were compared with both ancient and modern mitochondrial haplogroups from American and non-American populations. Samples showed a distribution of 35% for haplogroup A, 41% for haplogroup B and 24% for haplogroup D. Nine haplotypes were found in 17 samples, indicating an unusually high genetic diversity on a single site ancient population. Among them, three haplotypes have not been previously found in America, two are shared in Asia, and one is a private haplotype. Despite geographical barriers that eventually isolated them, an important influence of gene flow from neighboring pre-Columbian communities, mainly Muiscas, could explain the high genetic polymorphism of this community before the Spanish conquest, and argues against Guanes as being a genetic isolate.}, }
@article {pmid21988749, year = {2012}, author = {Boessenkool, S and Epp, LS and Haile, J and Bellemain, E and Edwards, M and Coissac, E and Willerslev, E and Brochmann, C}, title = {Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA.}, journal = {Molecular ecology}, volume = {21}, number = {8}, pages = {1806-1815}, doi = {10.1111/j.1365-294X.2011.05306.x}, pmid = {21988749}, issn = {1365-294X}, mesh = {Animals ; DNA/analysis/isolation &amp; purification ; *DNA Contamination ; DNA Primers/*genetics ; *Fossils ; Geologic Sediments/chemistry ; Humans ; Ice ; Perissodactyla/classification/*genetics ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/methods ; Siberia ; }, abstract = {Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results because of competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA, we first optimized the design and concentration of blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe the first retrieval of woolly rhinoceros (Coelodonta antiquitatis) DNA from ancient permafrost cores. In contrast, reactions without blocking primer resulted in complete dominance by human DNA sequences. These results demonstrate that in ancient environmental analyses, the PCR can be biased towards the amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified.}, }
@article {pmid21968286, year = {2012}, author = {Plantinga, TS and Ioana, M and Alonso, S and Izagirre, N and Hervella, M and Joosten, LA and van der Meer, JW and de la Rúa, C and Netea, MG}, title = {The evolutionary history of TLR4 polymorphisms in Europe.}, journal = {Journal of innate immunity}, volume = {4}, number = {2}, pages = {168-175}, pmid = {21968286}, issn = {1662-8128}, mesh = {Europe ; *Evolution, Molecular ; Genetic Drift ; Genetic Predisposition to Disease ; Haplotypes ; Humans ; Immunity, Innate/*genetics ; *Polymorphism, Single Nucleotide ; Toll-Like Receptor 4/*genetics ; White People/genetics ; }, abstract = {Infections exert important evolutionary pressures shaping the human genome, especially on genes involved in host defense. A crucial step for host defense is recognition of pathogens by pattern recognition receptors on innate immune cells, among which Toll-like receptor 4 (TLR4) is one of the best known. Genetic variation in TLR4 (Asp299Gly, Thr399Ile) has been recently described. Haplotype frequencies of these polymorphisms differ among African, Asian and European populations, suggesting evolutionary pressures exerted by local infections. The TLR4 299Gly/399Ile haplotype, characteristic mainly of European populations, has relatively high frequency in the Iberian peninsula. This region is also described as refuge area during the last glacial maximum 20,000 years ago, from which repopulation of Europe took place. We speculate that a genetic bottleneck in the Iberian peninsula could have promoted the increased frequency of this haplotype by genetic drift. This hypothesis is supported by three arguments: (1) the West-East gradient of prevalence in the haplotype among European populations; (2) ancient DNA from Neolithic burials in the Iberian peninsula, dated 6,600-4,500 years before present, confirmed the relatively high frequency of this haplotype in the region, and (3) no functional differences between this haplotype and wild-type TLR4 have been found. In contrast, the disappearance of the 299Gly/399Thr haplotype in Europe is most likely due to negative selection due to sepsis. In conclusion, differences in distribution of TLR4 polymorphisms Asp299Gly and Thr399Ile in European populations are most likely due to a combination of population migration events combined with selection due to sepsis.}, }
@article {pmid24137623, year = {2011}, author = {Gilbert, MT}, title = {The mummy returns… and sheds new light on old questions.}, journal = {Molecular ecology}, volume = {20}, number = {20}, pages = {4195-4198}, doi = {10.1111/j.1365-294x.2011.05265.x}, pmid = {24137623}, issn = {1365-294X}, mesh = {Alligators and Crocodiles/*genetics ; Animals ; DNA/*genetics ; *Evolution, Molecular ; *Genetic Speciation ; Humans ; }, abstract = {Whether as the ancient Egyptian crocodile-god Sobek, a terrifying predator of African waterways, or simply as a premium handbag leather, the Nile crocodile (Crocodylus niloticus) has long held the fascination of mankind. Despite 200 years of study, however, uncertainty remains as to its taxonomy. While resolving such issues are key to understanding the origins and biogeography of the so-called true crocodiles of genus Crocodylus, given widespread ongoing range contraction, such issues are paramount for design of future conservation strategies. In this issue of Molecular Ecology, Hekkala et al. (2011) apply analysis of modern, historic and ancient DNA (aDNA) to the questions, with far-reaching implications. First they demonstrate that, as currently described, the Nile crocodile is paraphyletic, with individuals from the east and western clades separated by a number of New World crocodile species. The consequences of this finding are as important for conservation efforts as for their impact on crocodile taxonomy. Furthermore, they strike at the heart of the long-standing debate over whether aDNA analysis of ancient Egyptian mummies is scientifically sound.}, }
@article {pmid21953438, year = {2011}, author = {Adachi, N and Shinoda, K and Umetsu, K and Kitano, T and Matsumura, H and Fujiyama, R and Sawada, J and Tanaka, M}, title = {Mitochondrial DNA analysis of Hokkaido Jomon skeletons: remnants of archaic maternal lineages at the southwestern edge of former Beringia.}, journal = {American journal of physical anthropology}, volume = {146}, number = {3}, pages = {346-360}, doi = {10.1002/ajpa.21561}, pmid = {21953438}, issn = {1096-8644}, mesh = {Anthropology, Physical ; *Asian People ; Bone and Bones/chemistry ; DNA, Mitochondrial/*analysis ; Genetics, Population ; Haplotypes ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Siberia ; *Skeleton ; Tooth/chemistry ; }, abstract = {To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present.}, }
@article {pmid21951625, year = {2012}, author = {Jørgensen, T and Kjaer, KH and Haile, J and Rasmussen, M and Boessenkool, S and Andersen, K and Coissac, E and Taberlet, P and Brochmann, C and Orlando, L and Gilbert, MT and Willerslev, E}, title = {Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding.}, journal = {Molecular ecology}, volume = {21}, number = {8}, pages = {1980-1988}, doi = {10.1111/j.1365-294X.2011.05278.x}, pmid = {21951625}, issn = {1365-294X}, mesh = {Arctic Regions ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/analysis ; DNA, Plant ; *Fossils ; Geologic Sediments/*chemistry ; Greenland ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; Ice ; *Ice Cover ; Plants/*genetics ; Species Specificity ; }, abstract = {Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in 'oceans' of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen's Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km(2) of ice-free land that was established in the early Holocene. We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528 ± 75 cal year BP) using meta-barcoding of plant DNA recovered from the nunatak sediments (sedaDNA). Our results show that several of the plant species detected with sedaDNA are described from earlier vegetation surveys on the nunataks (in 1878, 1967 and 2009). In 1967, a much higher biodiversity was detected than from any other of the studied periods. While this may be related to differences in sampling efforts for the oldest period, it is not the case when comparing the 1967 and 2009 levels where the botanical survey was exhaustive. As no animals and humans are found on the nunataks, this change in diversity over a period of just 42 years must relate to environmental changes probably being climate-driven. This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate.}, }
@article {pmid21938002, year = {2011}, author = {Li, H and Zhao, X and Zhao, Y and Li, C and Si, D and Zhou, H and Cui, Y}, title = {Genetic characteristics and migration history of a bronze culture population in the West Liao-River valley revealed by ancient DNA.}, journal = {Journal of human genetics}, volume = {56}, number = {12}, pages = {815-822}, doi = {10.1038/jhg.2011.102}, pmid = {21938002}, issn = {1435-232X}, mesh = {Asian People/*genetics/history ; China ; Chromosomes, Human, Y ; DNA/chemistry ; DNA, Mitochondrial/chemistry ; Emigration and Immigration/*history ; Female ; Geography ; History, Ancient ; Humans ; Male ; Polymorphism, Single Nucleotide ; Population/genetics ; Sequence Analysis, DNA ; }, abstract = {In order to study the genetic characteristics of the Lower Xiajiadian culture (LXC) population, a main bronze culture branch in northern China dated 4500-3500 years ago, two uniparentally inherited markers, mitochondrial DNA and Y-chromosome single-nucleotide polymorphisms (Y-SNPs), were analyzed on 14 human remains excavated from the Dadianzi site. The 14 sequences, which contained 13 haplotypes, were assigned to 9 haplogroups, and Y-SNP typing of 5 male individuals assigned them to haplogroups N (M231) and O3 (M122). The results indicate that the LXC population mainly included people carrying haplogroups from northern Asia who had lived in this region since the Neolithic period, as well as genetic evidence of immigration from the Central Plain. Later in the Bronze Age, part of the population migrated to the south away from a cooler climate, which ultimately influenced the gene pool in the Central Plain. Thus, climate change is an important factor, which drove the population migration during the Bronze Age in northern China. Based on these results, the local genetic continuity did not seem to be affected by outward migration, although more data are needed especially from other ancient populations to determine the influence of return migration on genetic continuity.}, }
@article {pmid21926069, year = {2012}, author = {Crandall, ED and Sbrocco, EJ and Deboer, TS and Barber, PH and Carpenter, KE}, title = {Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf Following the Last Glacial Maximum.}, journal = {Molecular biology and evolution}, volume = {29}, number = {2}, pages = {707-719}, doi = {10.1093/molbev/msr227}, pmid = {21926069}, issn = {1537-1719}, mesh = {Animals ; Aquatic Organisms/*genetics ; Arthropods/genetics ; *Biological Evolution ; Bivalvia/genetics ; DNA/genetics ; Echinodermata/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; Ice Cover ; Mitochondria/genetics ; Models, Genetic ; Mutation Rate ; Phylogeny ; Phylogeography/*methods ; Time Factors ; }, abstract = {The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 My and are typically 0.5-2% per lineage per million years. Recently, calibrations made with ancient DNA (aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting ∼18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two-epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3-6.6% per lineage per million years), lending additional support to the hypothesis of calibration time dependency for molecular rates.}, }
@article {pmid21913177, year = {2011}, author = {Raff, JA and Bolnick, DA and Tackney, J and O'Rourke, DH}, title = {Ancient DNA perspectives on American colonization and population history.}, journal = {American journal of physical anthropology}, volume = {146}, number = {4}, pages = {503-514}, doi = {10.1002/ajpa.21594}, pmid = {21913177}, issn = {1096-8644}, mesh = {American Indian or Alaska Native/*genetics/*history ; Americas ; Analysis of Variance ; DNA, Mitochondrial/*genetics ; Emigration and Immigration/*history ; Haplotypes ; History, 21st Century ; History, Ancient ; Humans ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; }, abstract = {Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history.}, }
@article {pmid21906195, year = {2011}, author = {Hekkala, E and Shirley, MH and Amato, G and Austin, JD and Charter, S and Thorbjarnarson, J and Vliet, KA and Houck, ML and Desalle, R and Blum, MJ}, title = {An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile.}, journal = {Molecular ecology}, volume = {20}, number = {20}, pages = {4199-4215}, doi = {10.1111/j.1365-294X.2011.05245.x}, pmid = {21906195}, issn = {1365-294X}, mesh = {Africa ; Alligators and Crocodiles/*genetics ; Animals ; DNA/*genetics ; Egypt, Ancient ; *Evolution, Molecular ; *Genetic Speciation ; Haplotypes ; History, Ancient ; Humans ; Mummies/history ; Phylogeography ; Sequence Alignment ; }, abstract = {The Nile crocodile (Crocodylus niloticus) is an ancient icon of both cultural and scientific interest. The species is emblematic of the great civilizations of the Nile River valley and serves as a model for international wildlife conservation. Despite its familiarity, a centuries-long dispute over the taxonomic status of the Nile crocodile remains unresolved. This dispute not only confounds our understanding of the origins and biogeography of the 'true crocodiles' of the crown genus Crocodylus, but also complicates conservation and management of this commercially valuable species. We have taken a total evidence approach involving phylogenetic analysis of mitochondrial and nuclear markers, as well as karyotype analysis of chromosome number and structure, to assess the monophyletic status of the Nile crocodile. Samples were collected from throughout Africa, covering all major bioregions. We also utilized specimens from museum collections, including mummified crocodiles from the ancient Egyptian temples at Thebes and the Grottes de Samoun, to reconstruct the genetic profiles of extirpated populations. Our analyses reveal a cryptic evolutionary lineage within the Nile crocodile that elucidates the biogeographic history of the genus and clarifies long-standing arguments over the species' taxonomic identity and conservation status. An examination of crocodile mummy haplotypes indicates that the cryptic lineage corresponds to an earlier description of C. suchus and suggests that both African Crocodylus lineages historically inhabited the Nile River. Recent survey efforts indicate that C. suchus is declining or extirpated throughout much of its distribution. Without proper recognition of this cryptic species, current sustainable use-based management policies for the Nile crocodile may do more harm than good.}, }
@article {pmid21904610, year = {2011}, author = {García-Garcerà, M and Gigli, E and Sanchez-Quinto, F and Ramirez, O and Calafell, F and Civit, S and Lalueza-Fox, C}, title = {Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e24161}, pmid = {21904610}, issn = {1932-6203}, mesh = {Animals ; DNA/*genetics ; *Fossils ; Genomics/*methods ; Humans ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. METHODOLOGY/PRINCIPALS FINDINGS: To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants.<br><br>CONCLUSIONS: We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5' and 3' ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.}, }
@article {pmid21896337, year = {2012}, author = {Jaeger, LH and Leles, D and Lima, Vdos S and da Silva, Lda P and Dias, O and Iñiguez, AM}, title = {Mycobacterium tuberculosis complex detection in human remains: tuberculosis spread since the 17th century in Rio de Janeiro, Brazil.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {12}, number = {4}, pages = {642-648}, doi = {10.1016/j.meegid.2011.08.021}, pmid = {21896337}, issn = {1567-7257}, mesh = {Brazil/epidemiology ; DNA, Bacterial/history ; DNA, Mitochondrial/history ; History, 17th Century ; Humans ; Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Nucleic Acid Hybridization ; Tuberculosis/epidemiology/*history ; }, abstract = {Paleogenetic analysis for tuberculosis (TB) was conducted on bone and sediment samples dating from the 17th to 19th centuries from the archeological site of Nossa Senhora do Carmo Church in Rio de Janeiro, Brazil. Forty samples were analyzed, corresponding to 32 individuals from 28 burials, 22 of primary type and 6 of secondary type. The samples were collected following strict paleogenetic investigation guidelines and submitted to ancient DNA (aDNA) extraction. In order to detect TB infection, aDNA hybridizations with the molecular targets of Mycobacterium tuberculosis complex (MTC) IS6110 and IS1081 were applied. Additionally, the ancestry of individuals was assessed by human mitochondrial DNA (mtDNA) analysis of hypervariable segment I (HVS-I) sequence polymorphisms. The results of aDNA hybridizations demonstrated varying levels of MTC intensity in 17/32 individuals (53.1%), using the IS6110 target. The IS1081 MTC target showed lower sensitivity, confirming TB positivity in 10/32 (31.2%) individuals. The mtDNA analysis allowed the recovery of HVS-I sequences in 23/32 individuals (71.8%). The majority of these individuals (21/23, 91.3%) were of European ancestry, especially in primary burials. Haplogroups U, J, V, T, K, N, H and R, were identified with haplogroup U being the most frequent at 6/23 (26.1%). African and Amerindian mtDNA haplogroups were observed in two individuals in secondary burials. In spite of the ecclesiastic and aristocratic bias of the population of the study, human ancestry analysis revealed the prominent contribution of Europeans in the introduction or spread of TB in the New World.}, }
@article {pmid21881561, year = {2011}, author = {D'Costa, VM and King, CE and Kalan, L and Morar, M and Sung, WW and Schwarz, C and Froese, D and Zazula, G and Calmels, F and Debruyne, R and Golding, GB and Poinar, HN and Wright, GD}, title = {Antibiotic resistance is ancient.}, journal = {Nature}, volume = {477}, number = {7365}, pages = {457-461}, pmid = {21881561}, issn = {1476-4687}, support = {MOP-79488//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/enzymology/genetics ; Bayes Theorem ; Crystallography, X-Ray ; DNA, Chloroplast/genetics ; Freezing ; Genes, Bacterial/*genetics ; Genes, Mitochondrial/genetics ; Genes, Plant/genetics ; Geologic Sediments/microbiology ; History, Ancient ; Hydrogen Bonding ; *Metagenomics ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Siberia ; Vancomycin Resistance/drug effects/*genetics ; Vertebrates/genetics ; beta-Lactamases/genetics ; }, abstract = {The discovery of antibiotics more than 70 years ago initiated a period of drug innovation and implementation in human and animal health and agriculture. These discoveries were tempered in all cases by the emergence of resistant microbes. This history has been interpreted to mean that antibiotic resistance in pathogenic bacteria is a modern phenomenon; this view is reinforced by the fact that collections of microbes that predate the antibiotic era are highly susceptible to antibiotics. Here we report targeted metagenomic analyses of rigorously authenticated ancient DNA from 30,000-year-old Beringian permafrost sediments and the identification of a highly diverse collection of genes encoding resistance to β-lactam, tetracycline and glycopeptide antibiotics. Structure and function studies on the complete vancomycin resistance element VanA confirmed its similarity to modern variants. These results show conclusively that antibiotic resistance is a natural phenomenon that predates the modern selective pressure of clinical antibiotic use.}, }
@article {pmid21876128, year = {2011}, author = {Franchini, LF and López-Leal, R and Nasif, S and Beati, P and Gelman, DM and Low, MJ and de Souza, FJ and Rubinstein, M}, title = {Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {37}, pages = {15270-15275}, pmid = {21876128}, issn = {1091-6490}, support = {R01 DK068400/DK/NIDDK NIH HHS/United States ; R01 DK068400-07/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; DK068400/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Enhancer Elements, Genetic/*genetics ; *Evolution, Molecular ; Female ; Gene Expression Regulation, Developmental ; Genes, Reporter/genetics ; Humans ; Mammals/*genetics ; Mice ; Mice, Transgenic ; Molecular Sequence Data ; Neurons/cytology/*metabolism ; Phylogeny ; Placenta/metabolism ; Pregnancy ; Pro-Opiomelanocortin/genetics ; Retroelements/*genetics ; Time Factors ; }, abstract = {The proopiomelanocortin gene (POMC) is expressed in a group of neurons present in the arcuate nucleus of the hypothalamus. Neuron-specific POMC expression in mammals is conveyed by two distal enhancers, named nPE1 and nPE2. Previous transgenic mouse studies showed that nPE1 and nPE2 independently drive reporter gene expression to POMC neurons. Here, we investigated the evolutionary mechanisms that shaped not one but two neuron-specific POMC enhancers and tested whether nPE1 and nPE2 drive identical or complementary spatiotemporal expression patterns. Sequence comparison among representative genomes of most vertebrate classes and mammalian orders showed that nPE1 is a placental novelty. Using in silico paleogenomics we found that nPE1 originated from the exaptation of a mammalian-apparent LTR retrotransposon sometime between the metatherian/eutherian split (147 Mya) and the placental mammal radiation (≈ 90 Mya). Thus, the evolutionary origin of nPE1 differs, in kind and time, from that previously demonstrated for nPE2, which was exapted from a CORE-short interspersed nucleotide element (SINE) retroposon before the origin of prototherians, 166 Mya. Transgenic mice expressing the fluorescent markers tomato and EGFP driven by nPE1 or nPE2, respectively, demonstrated coexpression of both reporter genes along the entire arcuate nucleus. The onset of reporter gene expression guided by nPE1 and nPE2 was also identical and coincidental with the onset of Pomc expression in the presumptive mouse diencephalon. Thus, the independent exaptation of two unrelated retroposons into functional analogs regulating neuronal POMC expression constitutes an authentic example of convergent molecular evolution of cell-specific enhancers.}, }
@article {pmid21863017, year = {2011}, author = {Lippold, S and Knapp, M and Kuznetsova, T and Leonard, JA and Benecke, N and Ludwig, A and Rasmussen, M and Cooper, A and Weinstock, J and Willerslev, E and Shapiro, B and Hofreiter, M}, title = {Discovery of lost diversity of paternal horse lineages using ancient DNA.}, journal = {Nature communications}, volume = {2}, number = {}, pages = {450}, pmid = {21863017}, issn = {2041-1723}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; *Genetic Variation ; Horses/*classification/*genetics ; Male ; Molecular Sequence Data ; Phylogeny ; Y Chromosome/*genetics ; }, abstract = {Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA from eight ancient wild horses and one 2,800-year-old domesticated horse. Both ancient and modern domestic horses form a separate branch from the ancient wild horses, with the Przewalski horse at its base. Our methodology establishes the feasibility of re-sequencing long ancient nuclear DNA fragments and demonstrates the power of ancient Y chromosome DNA sequence data to provide insights into the evolutionary history of populations.}, }
@article {pmid21855309, year = {2012}, author = {Campos, PF and Craig, OE and Turner-Walker, G and Peacock, E and Willerslev, E and Gilbert, MT}, title = {DNA in ancient bone - where is it located and how should we extract it?.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {7-16}, doi = {10.1016/j.aanat.2011.07.003}, pmid = {21855309}, issn = {1618-0402}, mesh = {Aging ; Animals ; Bone Development ; Bone and Bones/*chemistry ; Collagen/chemistry ; DNA/*chemistry/*genetics/isolation &amp; purification ; DNA, Mitochondrial/chemistry/genetics ; Dogs ; Durapatite/chemistry ; Fossils ; Oceans and Seas ; Paleontology ; Polymerase Chain Reaction ; Tooth/chemistry ; }, abstract = {Despite the widespread use of bones in ancient DNA (aDNA) studies, relatively little concrete information exists in regard to how the DNA in mineralised collagen degrades, or where it survives in the material's architecture. While, at the macrostructural level, physical exclusion of microbes and other external contaminants may be an important feature, and, at the ultrastructural level, the adsorption of DNA to hydroxyapatite and/or binding of DNA to Type I collagen may stabilise the DNA, the relative contribution of each, and what other factors may be relevant, are unclear. There is considerable variation in the quality of DNA retrieved from bones and teeth. This is in part due to various environmental factors such as temperature, proximity to free water or oxygen, pH, salt content, and exposure to radiation, all of which increase the rate of DNA decay. For example, bone specimens from sites at high latitudes usually yield better quality DNA than samples from temperate regions, which in turn yield better results than samples from tropical regions. However, this is not always the case, and rates of success of DNA recovery from apparently similar sites are often strikingly different. The question arises as to whether this may be due to post-collection preservation or just an artefact of the extraction methods used in these different studies? In an attempt to resolve these questions, we examine the efficacy of DNA extraction methods, and the quality and quantity of DNA recovered from both artificially degraded, and genuinely ancient, but well preserved, bones. In doing so we offer hypotheses relevant to the DNA degradation process itself, and to where and how the DNA is actually preserved in ancient bone.}, }
@article {pmid21846735, year = {2011}, author = {Ouangraoua, A and Tannier, E and Chauve, C}, title = {Reconstructing the architecture of the ancestral amniote genome.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {19}, pages = {2664-2671}, doi = {10.1093/bioinformatics/btr461}, pmid = {21846735}, issn = {1367-4811}, mesh = {Animals ; Biological Evolution ; Birds/genetics ; Chromosomes/*genetics ; *Evolution, Molecular ; Genetic Linkage ; Genome/*genetics ; Mammals/genetics ; Synteny ; Vertebrates/*genetics ; }, abstract = {MOTIVATION: The ancestor of birds and mammals lived approximately 300 million years ago. Inferring its genome organization is key to understanding the differentiated evolution of these two lineages. However, detecting traces of its chromosomal organization in its extant descendants is difficult due to the accumulation of molecular evolution since birds and mammals lineages diverged.<br><br>RESULTS: We address several methodological issues for the detection and assembly of ancestral genomic features of ancient vertebrate genomes, which encompass adjacencies, contiguous segments, syntenies and double syntenies in the context of a whole genome duplication. Using generic, but stringent, methods for all these problems, some of them new, we analyze 15 vertebrate genomes, including 12 amniotes and 3 teleost fishes, and infer a high-resolution genome organization of the amniote ancestral genome, composed of 39 ancestral linkage groups at a resolution of 100 kb. We extensively discuss the validity and robustness of the method to variations of data and parameters. We introduce a support value for each of the groups, and show that 36 out of 39 have maximum support.<br><br>CONCLUSIONS: Single methodological principle cannot currently be used to infer the organization of the amniote ancestral genome, and we demonstrate that it is possible to gather several principles into a computational paleogenomics pipeline. This strategy offers a solid methodological base for the reconstruction of ancient vertebrate genomes.<br><br>AVAILABILITY: Source code, in C++ and Python, is available at http://www.cecm.sfu.ca/~cchauve/SUPP/AMNIOTE2010/<br><br>CONTACT: cedric.chauve@sfu.ca<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid21834072, year = {2011}, author = {Marshall, C and Tench, PA and Cook, DC and Kaestle, FA}, title = {Brief communication: Conjoined twins at angel mounds? an ancient DNA perspective.}, journal = {American journal of physical anthropology}, volume = {146}, number = {1}, pages = {138-142}, doi = {10.1002/ajpa.21557}, pmid = {21834072}, issn = {1096-8644}, mesh = {*Anthropology, Physical ; Burial/*history ; DNA, Mitochondrial/*genetics ; Femur ; Haplotypes ; History, Medieval ; Humans ; Indiana ; Infant ; *Twins, Conjoined ; }, abstract = {Conjoined twins are born when a single fertilized egg partially splits into two fetuses. A hypothetical case of infant conjoined twins from Angel Mounds, a Middle Mississippian site (A.D. 1050-1400) on the Ohio River near Evansville, Indiana, was discovered in 1941. Morphological analysis does not rule out the field interpretation of this double burial as twins. Ancient mitochondrial DNA recovered from both infants demonstrates that they were not maternal relatives, and hence that they cannot have been conjoined twins.}, }
@article {pmid21833713, year = {2011}, author = {Malenica, N and Simon, S and Besendorfer, V and Maletić, E and Kontić, JK and Pejić, I}, title = {Whole genome amplification and microsatellite genotyping of herbarium DNA revealed the identity of an ancient grapevine cultivar.}, journal = {Die Naturwissenschaften}, volume = {98}, number = {9}, pages = {763-772}, pmid = {21833713}, issn = {1432-1904}, mesh = {*Genome, Plant ; Genotyping Techniques ; Microsatellite Repeats/*genetics ; Species Specificity ; Vitis/classification/*genetics ; }, abstract = {Reconstruction of the grapevine cultivation history has advanced tremendously during the last decade. Identification of grapevine cultivars by using microsatellite DNA markers has mostly become a routine. The parentage of several renowned grapevine cultivars, like Cabernet Sauvignon and Chardonnay, has been elucidated. However, the assembly of a complete grapevine genealogy is not yet possible because missing links might no longer be in cultivation or are even extinct. This problem could be overcome by analyzing ancient DNA from grapevine herbarium specimens and other historical remnants of once cultivated varieties. Here, we present the first successful genotyping of a grapevine herbarium specimen and the identification of the corresponding grapevine cultivar. Using a set of nine grapevine microsatellite markers, in combination with a whole genome amplification procedure, we found the 90-year-old Tribidrag herbarium specimen to display the same microsatellite profile as the popular American cultivar Zinfandel. This work, together with information from several historical documents, provides a new clue of Zinfandel cultivation in Croatia as early as the beginning of fifteenth century, under the native name Tribidrag. Moreover, it emphasizes substantial information potential of existing grapevine and other herbarium collections worldwide.}, }
@article {pmid21833062, year = {2011}, author = {Callaway, E}, title = {Ancient DNA reveals secrets of human history.}, journal = {Nature}, volume = {476}, number = {7359}, pages = {136-137}, pmid = {21833062}, issn = {1476-4687}, mesh = {Animals ; DNA/*analysis/*genetics ; Genetic Predisposition to Disease ; Genome, Human/*genetics ; Genomics ; Hominidae/genetics/physiology ; Humans ; *Phylogeny ; *Phylogeography ; }, }
@article {pmid21822975, year = {2012}, author = {Barabaschi, D and Guerra, D and Lacrima, K and Laino, P and Michelotti, V and Urso, S and Valè, G and Cattivelli, L}, title = {Emerging knowledge from genome sequencing of crop species.}, journal = {Molecular biotechnology}, volume = {50}, number = {3}, pages = {250-266}, pmid = {21822975}, issn = {1559-0305}, mesh = {Biodiversity ; Chromosome Mapping ; Cloning, Molecular ; Crops, Agricultural/*genetics ; DNA Transposable Elements ; Evolution, Molecular ; *Genome, Plant ; Haplotypes ; Hybridization, Genetic ; Phylogeny ; Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA ; }, abstract = {Extensive insights into the genome composition, organization, and evolution have been gained from the plant genome sequencing and annotation ongoing projects. The analysis of crop genomes provided surprising evidences with important implications in plant origin and evolution: genome duplication, ancestral re-arrangements and unexpected polyploidization events opened new doors to address fundamental questions related to species proliferation, adaptation, and functional modulations. Detailed paleogenomic analysis led to many speculation on how chromosomes have been shaped over time in terms of gene content and order. The completion of the genome sequences of several major crops, prompted to a detailed identification and annotation of transposable elements: new hypothesis related to their composition, chromosomal distribution, insertion models, amplification rate, and evolution patterns are coming up. Availability of full genome sequence of several crop species as well as from many accessions within species is providing new keys for biodiversity exploitation and interpretation. Re-sequencing is enabling high-throughput genotyping to identify a wealth of SNP and afterward to produce haplotype maps necessary to accurately associate molecular variation to phenotype. Conservation genomics is emerging as a powerful tool to explain adaptation, genetic drift, natural selection, hybridization and to estimate genetic variation, fitness and population's viability.}, }
@article {pmid21820882, year = {2012}, author = {Geigl, EM and Grange, T}, title = {Eurasian wild asses in time and space: morphological versus genetic diversity.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {88-102}, doi = {10.1016/j.aanat.2011.06.002}, pmid = {21820882}, issn = {1618-0402}, mesh = {Animals ; Asia ; Bone and Bones/chemistry ; DNA/chemistry/genetics ; DNA, Mitochondrial/genetics ; Equidae/*anatomy &amp; histology/*genetics ; Europe ; Fossils ; Horses ; Paleontology ; Sequence Analysis, DNA ; Tooth/anatomy &amp; histology ; }, abstract = {The Equidae have a long evolutionary history that has interested palaeontologists for a long time. Their morphology-based taxonomy, however, is a matter of controversy. Since most equid species are now extinct, the phylogenetic tree based on genetic data can be established only imperfectly via deduction of present day genomes and little is known about the past genetic diversity of these species. Recent studies of ancient DNA preserved in fossil bones have led to a simplification of the phylogenetic tree and the classification system. The situation is still particularly unclear for the wild asses whose geographical distribution in the Pleistocene and the early Holocene stretched from Northern Africa to Eurasia before they became endangered or extinct. Therefore, we performed a phylogeographic study of bone remains of wild asses covering their former geographic range over the past 100,000 years based on the analysis of ancient mitochondrial DNA. Here, we will not show but rather discuss our results calling the morphology-based classification into question and indicating that morphological criteria alone can be an unreliable index in inferring various equid species. Indeed, the diversity of mitochondrial lineages in populations with similar morphology along with genetic signatures shared between morphologically distinct animals reveal a significant morphological plasticity among Equus species. The classification of palaeontological species based on morphological and genetic criteria will be discussed.}, }
@article {pmid21803858, year = {2011}, author = {Orlando, L and Ginolhac, A and Raghavan, M and Vilstrup, J and Rasmussen, M and Magnussen, K and Steinmann, KE and Kapranov, P and Thompson, JF and Zazula, G and Froese, D and Moltke, I and Shapiro, B and Hofreiter, M and Al-Rasheid, KA and Gilbert, MT and Willerslev, E}, title = {True single-molecule DNA sequencing of a pleistocene horse bone.}, journal = {Genome research}, volume = {21}, number = {10}, pages = {1705-1719}, pmid = {21803858}, issn = {1549-5469}, support = {R44 HG005279/HG/NHGRI NIH HHS/United States ; R44 HG005279-02/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bone and Bones/chemistry ; Chromosome Mapping ; DNA/chemistry/isolation &amp; purification ; DNA Damage ; DNA Fragmentation ; Fossils ; High-Throughput Nucleotide Sequencing/instrumentation/*methods ; Horses/*genetics ; Sequence Analysis, DNA/instrumentation/*methods ; }, abstract = {Second-generation sequencing platforms have revolutionized the field of ancient DNA, opening access to complete genomes of past individuals and extinct species. However, these platforms are dependent on library construction and amplification steps that may result in sequences that do not reflect the original DNA template composition. This is particularly true for ancient DNA, where templates have undergone extensive damage post-mortem. Here, we report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing libraries of ancient DNA molecules, as required for second-generation sequencing, introduce biases into the data that reduce the efficiency of the sequencing process and limit our ability to fully explore the molecular complexity of ancient DNA extracts. We demonstrate that simple modifications to the standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by threefold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates, indicating the presence of 3'-sequence overhangs. Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third-generation sequencing approaches.}, }
@article {pmid21799731, year = {2011}, author = {Redrejo-Rodríguez, M and Saint-Pierre, C and Couve, S and Mazouzi, A and Ishchenko, AA and Gasparutto, D and Saparbaev, M}, title = {New insights in the removal of the hydantoins, oxidation product of pyrimidines, via the base excision and nucleotide incision repair pathways.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e21039}, pmid = {21799731}, issn = {1932-6203}, mesh = {Base Sequence ; DNA/*genetics/*metabolism ; DNA Glycosylases/metabolism ; *DNA Repair ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; HeLa Cells ; Humans ; Hydantoins/*metabolism ; Kinetics ; Oligodeoxyribonucleotides/chemistry/*metabolism ; Oxidation-Reduction ; Pyrimidines/*metabolism ; Thymine/analogs &amp; derivatives/metabolism ; Urea/metabolism ; }, abstract = {BACKGROUND: Oxidative damage to DNA, if not repaired, can be both miscoding and blocking. These genetic alterations can lead to mutations and/or cell death, which in turn cause cancer and aging. Oxidized DNA bases are substrates for two overlapping repair pathways: base excision (BER) and nucleotide incision repair (NIR). Hydantoin derivatives such as 5-hydroxyhydantoin (5OH-Hyd) and 5-methyl-5-hydroxyhydantoin (5OH-5Me-Hyd), major products of cytosine and thymine oxidative degradation pathways, respectively, have been detected in cancer cells and ancient DNA. Hydantoins are blocking lesions for DNA polymerases and excised by bacterial and yeast DNA glycosylases in the BER pathway. However little is known about repair of pyrimidine-derived hydantoins in human cells.<br><br>Here, using both denaturing PAGE and MALDI-TOF MS analyses we report that the bacterial, yeast and human AP endonucleases can incise duplex DNA 5' next to 5OH-Hyd and 5OH-5Me-Hyd thus initiating the NIR pathway. We have fully reconstituted the NIR pathway for these lesions in vitro using purified human proteins. Depletion of Nfo in E. coli and APE1 in HeLa cells abolishes the NIR activity in cell-free extracts. Importantly, a number of redundant DNA glycosylase activities can excise hydantoin residues, including human NTH1, NEIL1 and NEIL2 and the former protein being a major DNA glycosylase activity in HeLa cells extracts.<br><br>CONCLUSIONS/SIGNIFICANCE: This study demonstrates that both BER and NIR pathways can compete and/or back-up each other to remove hydantoin DNA lesions in vivo.}, }
@article {pmid21781037, year = {2011}, author = {Tran, TN and Aboudharam, G and Raoult, D and Drancourt, M}, title = {Beyond ancient microbial DNA: nonnucleotidic biomolecules for paleomicrobiology.}, journal = {BioTechniques}, volume = {50}, number = {6}, pages = {370-380}, doi = {10.2144/000113689}, pmid = {21781037}, issn = {1940-9818}, mesh = {Bacterial Proteins/analysis ; Bone and Bones/microbiology ; DNA, Bacterial/*analysis ; *Fossils ; History, Ancient ; Humans ; Immunoassay ; Lipids/analysis ; Mass Spectrometry ; Microbiological Techniques ; Paleontology/*methods ; Polymerase Chain Reaction ; Proteomics ; }, abstract = {Identifying the causes of past epidemics depends on the specific detection of pathogens in buried individuals; this field of research is known as paleomicrobiology, an emerging field that has benefited from technological advances in microbiology. For almost 15 years, the detection, identification, and characterization of microbes in ancient environmental and human specimens emerged on the basis of ancient DNA (aDNA) analyses. aDNA limitations due to potential contamination by modern DNA and altered aDNA led to the development of alternative methods for the detection and characterization of nonnucleotidic biomolecules, including mycolic acids (of ancient mycobacteria) and proteins. Accordingly, immunohistochemistry, immunochromatography, and enzyme-linked immunosorbent assay techniques have been developed for the specific detection of microbes from ancient human and environmental specimens. Protein analysis by mass spectrometry, a standard for ancient animal identification, has also recently emerged as a technique for ancient mycobacteria detection, while immuno-PCR is yet another promising technique. As with aDNA, strict protocols must be enforced to ensure authenticity of the data. Here we review the analysis of nonnucleotidic biomolecules from ancient microbes and the ability of these analyses to complement aDNA analyses, which opens new opportunities for identification of ancient microbes as well as new avenues to potentially resolve controversies regarding the cause of some historical pandemics and study the coevolution of microbes and hosts.}, }
@article {pmid21774815, year = {2011}, author = {Teacher, AG and Thomas, JA and Barnes, I}, title = {Modern and ancient red fox (Vulpes vulpes) in Europe show an unusual lack of geographical and temporal structuring, and differing responses within the carnivores to historical climatic change.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {214}, pmid = {21774815}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Carnivora/classification/*genetics ; Climate Change/*history ; Cytochromes b/genetics ; Europe ; *Evolution, Molecular ; Foxes/classification/*genetics ; History, Ancient ; Molecular Sequence Data ; Phylogeny ; Phylogeography/history ; Wolves/classification/genetics ; }, abstract = {BACKGROUND: Despite phylogeographical patterns being well characterised in a large number of species, and generalised patterns emerging, the carnivores do not all appear to show consistent trends. While some species tend to fit with standard theoretical phylogeographic expectations (e.g. bears), others show little obvious modern phylogeographic structure (e.g. wolves). In this study we briefly review these studies, and present a new phylogeographical study of the red fox (Vulpes vulpes) throughout Europe, using a combination of ancient DNA sequences obtained from museum specimens, and modern sequences collated from GenBank. We used cytochrome b (250 bp) and the mitochondrial control region (268 bp) to elucidate both current and historical phylogeographical patterning.<br><br>RESULTS: We found evidence for slight isolation by distance in modern populations, as well as differentiation associated with time, both of which can likely be attributed to random genetic drift. Despite high sequence diversity (11.2% cytochrome b, 16.4% control region), no evidence for spatial structure (from Bayesian trees) is found either in modern samples or ancient samples for either gene, and Bayesian skyline plots suggested little change in the effective population size over the past 40,000 years.<br><br>CONCLUSIONS: It is probable that the high dispersal ability and adaptability of the red fox has contributed to the lack of observable differentiation, which appears to have remained consistent over tens of thousands of years. Generalised patterns of how animals are thought to have responded to historical climatic change are not necessarily valid for all species, and so understanding the differences between species will be critical for predicting how species will be affected by future climatic change.}, }
@article {pmid21765907, year = {2011}, author = {Thèves, C and Senescau, A and Vanin, S and Keyser, C and Ricaut, FX and Alekseev, AN and Dabernat, H and Ludes, B and Fabre, R and Crubézy, E}, title = {Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e21733}, pmid = {21765907}, issn = {1932-6203}, mesh = {Bacteria/*classification/*genetics ; Bacterial Typing Techniques/*methods ; Base Sequence ; Bone and Bones/microbiology ; *Cause of Death ; DNA/genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Environmental Microbiology ; Fossils ; Freezing ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Male ; Molecular Typing/*methods ; Phylogeny ; Reproducibility of Results ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Siberia ; }, abstract = {Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17(th) to the 19(th) century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity ≥ 95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17(th) century to the early 18(th) century.}, }
@article {pmid21753768, year = {2011}, author = {Sato, T and Razhev, D and Amano, T and Masuda, R}, title = {Genetic features of ancient West Siberian people of the Middle Ages, revealed by mitochondrial DNA haplogroup analysis.}, journal = {Journal of human genetics}, volume = {56}, number = {8}, pages = {602-608}, doi = {10.1038/jhg.2011.68}, pmid = {21753768}, issn = {1435-232X}, mesh = {Archaeology/methods ; DNA, Mitochondrial/chemistry/classification/*genetics ; Genetic Variation ; Genetics, Population/*methods ; Geography ; Haplotypes/*genetics ; Humans ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Principal Component Analysis ; Sequence Analysis, DNA ; Siberia ; }, abstract = {In order to investigate the genetic features of ancient West Siberian people of the Middle Ages, we studied ancient DNA from bone remains excavated from two archeological sites in West Siberia: Saigatinsky 6 (eighth to eleventh centuries) and Zeleny Yar (thirteenth century). Polymerase chain reaction amplification and nucleotide sequencing of mitochondrial DNA (mtDNA) succeeded for 9 of 67 specimens examined, and the sequences were assigned to mtDNA haplogroups B4, C4, G2, H and U. This distribution pattern of mtDNA haplogroups in medieval West Siberian people was similar to those previously reported in modern populations living in West Siberia, such as the Mansi, Ket and Nganasan. Exact tests of population differentiation showed no significant differences between the medieval people and modern populations in West Siberia. The findings suggest that some medieval West Siberian people analyzed in the present study are included in direct ancestral lineages of modern populations native to West Siberia.}, }
@article {pmid21738691, year = {2011}, author = {Montero-Pau, J and Ramos-Rodríguez, E and Serra, M and Gómez, A}, title = {Long-term coexistence of rotifer cryptic species.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e21530}, pmid = {21738691}, issn = {1932-6203}, mesh = {Animals ; Ecosystem ; Lakes ; Population Dynamics ; Rotifera/*growth &amp; development ; }, abstract = {Despite their high morphological similarity, cryptic species often coexist in aquatic habitats presenting a challenge in the framework of niche differentiation theory and coexistence mechanisms. Here we use a rotifer species complex inhabiting highly unpredictable and fluctuating salt lakes to gain insights into the mechanisms involved in stable coexistence in cryptic species. We combined molecular barcoding surveys of planktonic populations and paleogenetic analysis of diapausing eggs to reconstruct the current and historical coexistence dynamics of two highly morphologically similar rotifer species, B. plicatilis and B. manjavacas. In addition, we carried out laboratory experiments using clones isolated from eight lakes where both species coexist to explore their clonal growth responses to salinity, a challenging, highly variable and unpredictable condition in Mediterranean salt lakes. We show that both species have co-occurred in a stable way in one lake, with population fluctuations in which no species was permanently excluded. The seasonal occurrence patterns of the plankton in two lakes agree with laboratory experiments showing that both species differ in their optimal salinity. These results suggest that stable species coexistence is mediated by differential responses to salinity and its fluctuating regime. We discuss the role of fluctuating salinity and a persistent diapausing egg banks as a mechanism for species coexistence in accordance with the 'storage effect'.}, }
@article {pmid21738625, year = {2011}, author = {Winters, M and Barta, JL and Monroe, C and Kemp, BM}, title = {To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e21247}, pmid = {21738625}, issn = {1932-6203}, mesh = {Animals ; Cloning, Molecular/*methods ; DNA/*analysis ; Humans ; }, abstract = {The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from "modern" DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be "gold standards" in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones.To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous.}, }
@article {pmid21732320, year = {2011}, author = {Galeta, P and Sládek, V and Sosna, D and Bruzek, J}, title = {Modeling neolithic dispersal in central Europe: demographic implications.}, journal = {American journal of physical anthropology}, volume = {146}, number = {1}, pages = {104-115}, doi = {10.1002/ajpa.21572}, pmid = {21732320}, issn = {1096-8644}, mesh = {Agriculture ; Anthropology, Physical ; Cephalometry ; DNA/analysis/genetics ; *Emigration and Immigration ; Europe ; Female ; History, Ancient ; Humans ; *Models, Biological ; Parity ; Population Dynamics/*history ; Regression Analysis ; Stochastic Processes ; Survival Analysis ; }, abstract = {On the basis of new examination of ancient DNA and craniometric analyses, Neolithic dispersal in Central Europe has been recently explained as reflecting colonization or at least a major influx of near eastern farmers. Given the fact that Neolithic dispersal in Central Europe was very rapid and extended into a large area, colonization would have to be associated with high population growth and fertility rates of an expanding Neolithic population. We built three demographic models to test whether the growth and fertility rates of Neolithic farmers were high enough to allow them to colonize Central Europe without admixture with foragers. The principle of the models is based on stochastic population projections. Our results demonstrate that colonization is an unlikely explanation for the Neolithic dispersal in Central Europe, as the majority of fertility and growth rate estimates obtained in all three models are higher than levels expected in the early Neolithic population. On the basis of our models, we derived that colonization would be possible only if (1) more than 37% of women survived to mean age at childbearing, (2) Neolithic expansion in Central Europe lasted more than 150 years, and (3) the population of farmers grew in the entire settled area. These settings, however, represent very favorable demographic conditions that seem unlikely given current archaeological and demographic evidence. Therefore, our results support the view that Neolithic dispersal in Central Europe involved admixture of expanding farmers with local foragers. We estimate that the admixture contribution from foragers may have been between 55% and 72%.}, }
@article {pmid21685079, year = {2011}, author = {Gavranović, H and Chauve, C and Salse, J and Tannier, E}, title = {Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {13}, pages = {i257-65}, pmid = {21685079}, issn = {1367-4811}, mesh = {Animals ; Biological Evolution ; *Evolution, Molecular ; *Genome ; Humans ; Magnoliopsida/genetics ; Mammals/genetics ; }, abstract = {MOTIVATION: Ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. Most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of DNA segments present in exactly one exemplar in every considered species. Complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. It follows that some ancestors are inaccessible by these methods, such as the proto-monocotyledon whose evolution involved massive gene loss following a whole genome duplication.<br><br>RESULTS: We propose a mapping approach based on the combinatorial notion of 'sandwich consecutive ones matrix', which explicitly takes gene losses into account. We introduce combinatorial optimization problems related to this concept, and propose a heuristic solver and a lower bound on the optimal solution. We use these results to propose a configuration for the proto-chromosomes of the monocot ancestor, and study the accuracy of this configuration. We also use our method to reconstruct the ancestral boreoeutherian genomes, which illustrates that the framework we propose is not specific to plant paleogenomics but is adapted to reconstruct any ancestral genome from extant genomes with heterogeneous marker content.<br><br>AVAILABILITY: Upon request to the authors.<br><br>CONTACT: haris.gavranovic@gmail.com; eric.tannier@inria.fr.}, }
@article {pmid21659319, year = {2011}, author = {Ginolhac, A and Rasmussen, M and Gilbert, MT and Willerslev, E and Orlando, L}, title = {mapDamage: testing for damage patterns in ancient DNA sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {15}, pages = {2153-2155}, doi = {10.1093/bioinformatics/btr347}, pmid = {21659319}, issn = {1367-4811}, mesh = {Base Sequence ; Computational Biology/methods ; *DNA Contamination ; DNA Damage/*genetics ; DNA Restriction Enzymes ; Genome, Human ; Humans ; Paleontology ; Reference Standards ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {SUMMARY: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequencing reads that could be advantageously used to argue for sequence validity. mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences.<br><br>The Perl script mapDamage is freely available with documentation and example files at http://geogenetics.ku.dk/all_literature/mapdamage/. The script requires prior installation of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems.}, }
@article {pmid21658464, year = {2011}, author = {Taylor, GM and Donoghue, HD}, title = {Multiple loci variable number tandem repeat (VNTR) analysis (MLVA) of Mycobacterium leprae isolates amplified from European archaeological human remains with lepromatous leprosy.}, journal = {Microbes and infection}, volume = {13}, number = {11}, pages = {923-929}, doi = {10.1016/j.micinf.2011.05.003}, pmid = {21658464}, issn = {1769-714X}, mesh = {Adult ; Archaeology/*methods ; Child ; Female ; Humans ; Leprosy, Lepromatous/*microbiology ; Male ; Middle Aged ; *Minisatellite Repeats ; *Molecular Typing ; Mycobacterium leprae/*classification/*genetics ; Polymorphism, Genetic ; *White People ; }, abstract = {Molecular typing methods based on polymorphisms in single nucleotides and short tandem repeat motifs have been developed as epidemiological typing tools for Mycobacterium leprae. We have used a variable number tandem repeat method based on three variable loci to identify strain variation in archaeological cases of lepromatous leprosy. The panel of polymorphic loci used revealed unique profiles in five cases of leprosy, including those with identical SNP type and subtype. These were also different from profiles of three previously studied lepromatous skeletons. Whilst examination with SNP typing provides evidence for disease origins, dissemination and phylogeny, tandem repeat typing may be useful for studying cases from within a defined area or community where SNP types may be identical due to geographical constraints. We envisage the technique may be useful in studying contemporaneous burials such as those associated with leprosaria and will prove invaluable in authentication of ancient DNA analyses.}, }
@article {pmid21655320, year = {2011}, author = {Feuillie, C and Merheb, MM and Gillet, B and Montagnac, G and Daniel, I and Hänni, C}, title = {A novel SERRS sandwich-hybridization assay to detect specific DNA target.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e17847}, pmid = {21655320}, issn = {1932-6203}, mesh = {DNA/*analysis ; Nucleic Acid Hybridization/*methods ; Polymerase Chain Reaction ; Spectrum Analysis, Raman ; }, abstract = {In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR). In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method) with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.}, }
@article {pmid21652193, year = {2012}, author = {Foote, AD and Hofreiter, M and Morin, PA}, title = {Ancient DNA from marine mammals: studying long-lived species over ecological and evolutionary timescales.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {112-120}, doi = {10.1016/j.aanat.2011.04.010}, pmid = {21652193}, issn = {1618-0402}, mesh = {Animals ; Antarctic Regions ; *Biological Evolution ; DNA/*genetics ; Ecology ; Environment ; Genetic Markers ; Genetic Variation ; Mammals/*genetics ; Marine Biology/*methods ; Otters ; Paleontology ; Phylogeny ; Seals, Earless ; Walruses ; Whales ; }, abstract = {Marine mammals have long generation times and broad, difficult to sample distributions, which makes inferring evolutionary and demographic changes using field studies of extant populations challenging. However, molecular analyses from sub-fossil or historical materials of marine mammals such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) approaches provide an opportunity for investigating such changes over evolutionary and ecological timescales. Here, we review the application of aDNA techniques to the study of marine mammals. Most of the studies have focused on detecting changes in genetic diversity following periods of exploitation and environmental change. To date, these studies have shown that even small sample sizes can provide useful information on historical genetic diversity. Ancient DNA has also been used in investigations of changes in distribution and range of marine mammal species; we review these studies and discuss the limitations of such 'presence only' studies. Combining aDNA data with stable isotopes can provide further insights into changes in ecology and we review past studies and suggest future potential applications. We also discuss studies reconstructing inter- and intra-specific phylogenies from aDNA sequences and discuss how aDNA sequences could be used to estimate mutation rates. Finally, we highlight some of the problems of aDNA studies on marine mammals, such as obtaining sufficient sample sizes and calibrating for the marine reservoir effect when radiocarbon-dating such wide-ranging species.}, }
@article {pmid21651551, year = {2011}, author = {de Bruyn, M and Parenti, LR and Carvalho, GR}, title = {Successful extraction of DNA from archived alcohol-fixed white-eye fish specimens using an ancient DNA protocol.}, journal = {Journal of fish biology}, volume = {78}, number = {7}, pages = {2074-2079}, doi = {10.1111/j.1095-8649.2011.02975.x}, pmid = {21651551}, issn = {1095-8649}, mesh = {Animals ; Beloniformes/*genetics ; Conservation of Natural Resources/methods ; Cyprinodontiformes/*genetics ; DNA/chemistry/*isolation &amp; purification ; Fixatives/chemistry ; Genetic Techniques ; }, abstract = {A protocol used routinely for rapid ancient DNA extraction was applied to fish tissue archived over 80 years ago. The method proved successful, whereas other extraction protocols failed. Researchers working on DNA from older archived fish samples are encouraged to continue to concentrate their efforts on 'white-eye' specimens, which indicate an alcohol-based fixative and are thus likely to yield viable DNA.}, }
@article {pmid21641784, year = {2012}, author = {Tsangaras, K and Greenwood, AD}, title = {Museums and disease: using tissue archive and museum samples to study pathogens.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {58-73}, doi = {10.1016/j.aanat.2011.04.003}, pmid = {21641784}, issn = {1618-0402}, mesh = {Animals ; Ascariasis/history/parasitology ; Bacteria/*genetics ; Bacterial Infections/*history/*microbiology ; DNA, Bacterial/genetics ; Disease/*history ; Enterobiasis/history/parasitology ; History, Ancient ; Humans ; Malaria/history/parasitology ; *Museums ; Mycobacterium/genetics ; Mycobacterium Infections/history/microbiology ; Mycoses/*history/*microbiology ; Parasitic Diseases/*history/*parasitology ; Phytophthora infestans ; Plague/history/microbiology ; Plant Diseases/history/microbiology ; Plasmodium falciparum/genetics ; Trypanosomiasis/history/parasitology ; Virus Diseases/*history/*virology ; Yersinia pestis/genetics ; }, abstract = {Molecular studies of archival and fossil samples have traditionally focused on the nucleic acids derived from the host species. However, there has recently been an increase in ancient DNA research on the identification and characterization of infectious agents within the hosts. The study of pathogens from the past provides great opportunities for discovering the causes of historical infection events, characterizing host-microorganism co-evolution and directly investigating the evolution of specific pathogens. Several research teams have been able to isolate and characterize a variety of different bacterial, parasite and viral microorganisms. However, this emerging field is not without obstacles. The diagenetic processes that make ancient DNA research generally difficult are also impediments to ancient pathogen research and perhaps more so given that their DNA may represent an even rarer proportion of the remaining nucleic acids in a fossil sample than host DNA. However, studies performed under controlled conditions and following stringent ancient DNA protocols can and have yielded reliable and often surprising results. This article reviews the advantages, problems, and failures of ancient microbiological research.}, }
@article {pmid21641192, year = {2012}, author = {Hofreiter, M}, title = {Special issue ancient DNA.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {1-2}, doi = {10.1016/j.aanat.2011.04.011}, pmid = {21641192}, issn = {1618-0402}, mesh = {Animals ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Equidae ; Humans ; Paleontology/*methods ; Plants/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods/trends ; }, }
@article {pmid21640569, year = {2012}, author = {Clack, AA and MacPhee, RD and Poinar, HN}, title = {Mylodon darwinii DNA sequences from ancient fecal hair shafts.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {26-30}, doi = {10.1016/j.aanat.2011.05.001}, pmid = {21640569}, issn = {1618-0402}, mesh = {Animals ; Caves ; Chloroform ; DNA/*chemistry/genetics ; DNA Primers ; DNA, Mitochondrial/chemistry/genetics ; Environment ; Feces/*chemistry ; Fossils ; Hair/*chemistry ; Molecular Sequence Data ; Paleontology/methods ; Phenols ; Phylogeny ; Pilot Projects ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sloths/*genetics ; Solvents ; South America ; }, abstract = {Preserved hair has been increasingly used as an ancient DNA source in high throughput sequencing endeavors, and it may actually offer several advantages compared to more traditional ancient DNA substrates like bone. However, cold environments have yielded the most informative ancient hair specimens, while its preservation, and thus utility, in temperate regions is not well documented. Coprolites could represent a previously underutilized preservation substrate for hairs, which, if present therein, represent macroscopic packages of specific cells that are relatively simple to separate, clean and process. In this pilot study, we report amplicons 147-152 base pairs in length (w/primers) from hair shafts preserved in a south Chilean coprolite attributed to Darwin's extinct ground sloth, Mylodon darwinii. Our results suggest that hairs preserved in coprolites from temperate cave environments can serve as an effective source of ancient DNA. This bodes well for potential molecular-based population and phylogeographic studies on sloths, several species of which have been understudied despite leaving numerous coprolites in caves across of the Americas.}, }
@article {pmid21639832, year = {2011}, author = {Klyosov, AA}, title = {Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history".}, journal = {Biochemistry. Biokhimiia}, volume = {76}, number = {5}, pages = {517-533}, doi = {10.1134/S0006297911050026}, pmid = {21639832}, issn = {1608-3040}, mesh = {Biology/instrumentation/*methods ; Chemistry/history/*methods ; DNA/*genetics ; *Genealogy and Heraldry ; Genetics, Population/history/*methods ; History, Ancient ; Humans ; *Phylogeny ; White People/ethnology/genetics/history ; }, abstract = {This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the foundation for "molecular history", in which the principal tool is high-technology analysis of DNA molecules of both our contemporaries and excavated ancient DNA samples, along with their biological kinetics.}, }
@article {pmid21628562, year = {2011}, author = {Lacan, M and Keyser, C and Ricaut, FX and Brucato, N and Duranthon, F and Guilaine, J and Crubézy, E and Ludes, B}, title = {Ancient DNA reveals male diffusion through the Neolithic Mediterranean route.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {24}, pages = {9788-9791}, pmid = {21628562}, issn = {1091-6490}, mesh = {DNA/*analysis/genetics ; DNA, Mitochondrial/analysis/genetics ; *Emigration and Immigration ; Europe ; *Fossils ; France ; Genetics, Population ; Geography ; Humans ; Mediterranean Region ; Polymerase Chain Reaction ; Population Dynamics ; Time Factors ; White People/*genetics ; }, abstract = {The Neolithic is a key period in the history of the European settlement. Although archaeological and present-day genetic data suggest several hypotheses regarding the human migration patterns at this period, validation of these hypotheses with the use of ancient genetic data has been limited. In this context, we studied DNA extracted from 53 individuals buried in a necropolis used by a French local community 5,000 y ago. The relatively good DNA preservation of the samples allowed us to obtain autosomal, Y-chromosomal, and/or mtDNA data for 29 of the 53 samples studied. From these datasets, we established close parental relationships within the necropolis and determined maternal and paternal lineages as well as the absence of an allele associated with lactase persistence, probably carried by Neolithic cultures of central Europe. Our study provides an integrative view of the genetic past in southern France at the end of the Neolithic period. Furthermore, the Y-haplotype lineages characterized and the study of their current repartition in European populations confirm a greater influence of the Mediterranean than the Central European route in the peopling of southern Europe during the Neolithic transition.}, }
@article {pmid21616909, year = {2010}, author = {Gould, BA and León, B and Buffen, AM and Thompson, LG}, title = {Evidence of a high-Andean, mid-Holocene plant community: An ancient DNA analysis of glacially preserved remains.}, journal = {American journal of botany}, volume = {97}, number = {9}, pages = {1579-1584}, doi = {10.3732/ajb.1000058}, pmid = {21616909}, issn = {0002-9122}, abstract = {PREMISE OF THE STUDY: Around the world, tropical glaciers and ice caps are retreating at unprecedented rates because of climate change. In at least one location, along the margin of the Quelccaya Ice Cap in southeastern Peru, ancient plant remains have been continually uncovered since 2002. We used genetic analysis to identify plants that existed at these sites during the mid-Holocene. •<br><br>METHODS: We examined remains between 4576 and 5222 yr old, using PCR amplification, cloning, and sequencing of a fragment of the chloroplast trnL intron. We then matched these sequences to sequences in GenBank. &#x2022;<br><br>KEY RESULTS: We found evidence of at least five taxa characteristic of wetlands, which occur primarily at lower elevations in the region today. &#x2022;<br><br>CONCLUSIONS: A diverse community most likely existed at these locations the last time they were ice-free and thus has the potential to reestablish with time. This is the first genetic analysis of vegetation uncovered by receding glacial ice, and it may become one of many as ancient plant materials are newly uncovered in a changing climate.}, }
@article {pmid21596538, year = {2012}, author = {Malmström, H and Vretemark, M and Tillmar, A and Durling, MB and Skoglund, P and Gilbert, MT and Willerslev, E and Holmlund, G and Götherström, A}, title = {Finding the founder of Stockholm - a kinship study based on Y-chromosomal, autosomal and mitochondrial DNA.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {138-145}, doi = {10.1016/j.aanat.2011.03.014}, pmid = {21596538}, issn = {1618-0402}, mesh = {Adult ; Algorithms ; Chromosomes, Human, Y/*genetics ; Cloning, Molecular ; DNA/chemistry ; DNA Primers ; DNA, Mitochondrial/*genetics ; Family ; Female ; Gene Dosage ; Humans ; Male ; Paleodontology ; Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Sweden ; Tooth/chemistry ; }, abstract = {Historical records claim that Birger Magnusson (died 1266), famous regent of Sweden and the founder of Stockholm, was buried in Varnhem Abbey in Västergötland. After being lost for centuries, his putative grave was rediscovered during restoration work in the 1920s. Morphological analyses of the three individuals in the grave concluded that the older male, the female and the younger male found in the grave were likely to be Birger, his second wife Mechtild of Holstein and his son Erik from a previous marriage. More recent evaluations of the data from the 1920s seriously questioned these conclusions, ultimately leading to the reopening and reexamination of the grave in 2002. Ancient DNA-analyses were performed to investigate if the relationship between the three individuals matched what we would expect if the individuals were Birger, Erik and Mechtild. We used pyrosequencing of Y-chromosomal and autosomal SNPs and compared the results with haplogroup frequencies of modern Swedes to investigate paternal relations. Possible maternal kinship was investigated by deep FLX-sequencing of overlapping mtDNA amplicons. The authenticity of the sequences was examined using data from independent extractions, massive clonal data, the c-statistics, and real-time quantitative data. We show that the males carry the same Y-chromosomal haplogroup and thus we cannot reject a father-son type of relation. Further, as shown by the mtDNA analyses, none of the individuals are maternally related. We conclude that the graves indeed belong to Birger, Erik and Mechtild, or to three individuals with the exact same kind of biological relatedness.}, }
@article {pmid21596537, year = {2012}, author = {Allentoft, ME and Rawlence, NJ}, title = {Moa's Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {36-51}, doi = {10.1016/j.aanat.2011.04.002}, pmid = {21596537}, issn = {1618-0402}, mesh = {Animals ; Biodiversity ; Bone and Bones/chemistry ; Cell Nucleus/chemistry/genetics ; Classification ; DNA/*genetics/isolation &amp; purification ; DNA, Mitochondrial/chemistry/genetics ; *Extinction, Biological ; Feathers ; Fossils ; Genome ; Models, Genetic ; New Zealand ; Palaeognathae/*genetics ; Sequence Analysis, DNA ; }, abstract = {The moa (Aves: Dinornithiformes) of New Zealand represent one of the extinct iconic taxa that define the field of ancient DNA (aDNA), and after almost two decades of genetic scrutiny of bones, feathers, coprolites, mummified tissue, eggshell, and sediments, our knowledge of these prehistoric giants has increased significantly. Thanks to molecular and morphological-based research, the insights that have been obtained into moa phylogenetics, phylogeography, and palaeobiology exceeds that of any other extinct taxon. This review documents the strengths of applying a multidisciplinary approach when studying extinct taxa but also shows that cross-disciplinary controversies still remain at the most fundamental levels, with highly conflicting interpretations derived from aDNA and morphology. Moa species diversity, for example, is still heavily debated, as well as their relationship with other ratites and the mode of radiation. In addition to increasing our knowledge on a lineage of extinct birds, further insights into these aspects can clarify some of the basal splits in avian evolution, and the evolutionary implications of the breakup of the prehistoric supercontinent Gondwana. Did a flightless moa ancestor drift away on proto New Zealand (Moa's Ark) or did a volant ancestor arrive by flight? Here we provide an overview of 19 years of aDNA research on moa, critically assess the attempts and controversies in placing the moa lineage among palaeognath birds, and discuss the factors that facilitated the extensive radiation of moa. Finally, we identify the most obvious gaps in the current knowledge to address the future potential research areas in moa genetics.}, }
@article {pmid21592108, year = {2011}, author = {Li, H and Gu, S and Han, Y and Xu, Z and Pakstis, AJ and Jin, L and Kidd, JR and Kidd, KK}, title = {Diversification of the ADH1B gene during expansion of modern humans.}, journal = {Annals of human genetics}, volume = {75}, number = {4}, pages = {497-507}, pmid = {21592108}, issn = {1469-1809}, support = {P01 GM057672/GM/NIGMS NIH HHS/United States ; R01 AA009379/AA/NIAAA NIH HHS/United States ; AA009379/AA/NIAAA NIH HHS/United States ; GM057672/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa ; Alcohol Dehydrogenase/*genetics ; Americas ; Asian People/genetics ; China ; Europe ; Asia, Eastern ; Gene Frequency ; *Genetics, Population ; Haplotypes ; Humans ; Middle East ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Time Factors ; }, abstract = {A variant allele, ADH1B*48His, also known as ADH1B*2, at the human Alcohol Dehydrogenase 1B gene (ADH1B) is strongly associated with alcoholism in some populations and has an unusual geographic distribution. Strong evidence implies selection has increased the frequency of this allele in some East Asian populations but does not fully explain its geographic pattern. We have studied haplotypes of 10 single nucleotide polymorphisms (SNPs) and two short tandem repeat polymorphisms (STRPs) in the ADH1B region in 2,206 individuals from a worldwide set of populations. These SNPs and STRPs define nine common haplogroups most of which have distinct geographic patterns. The haplogroups H5 and H6, both with the derived ADH1B*48His allele, appear restricted to the Middle East and East Asia, respectively. The positively selected H7 is derived from H6 by a new regulatory region variant defining SNP rs3811801 restricted to East Asia. Age estimates of the haplogroups based on the STRPs also agree with the time of the migration events estimated by other studies. H7 is estimated to have expanded recently, around 2,800 years ago, and ancient DNA samples from North China confirm its presence about that time. The dating of the H7 expansion may help understand the selective force on the ADH1B gene.}, }
@article {pmid21565110, year = {2010}, author = {Sønstebø, JH and Gielly, L and Brysting, AK and Elven, R and Edwards, M and Haile, J and Willerslev, E and Coissac, E and Rioux, D and Sannier, J and Taberlet, P and Brochmann, C}, title = {Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate.}, journal = {Molecular ecology resources}, volume = {10}, number = {6}, pages = {1009-1018}, doi = {10.1111/j.1755-0998.2010.02855.x}, pmid = {21565110}, issn = {1755-0998}, abstract = {Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13-158 bp) and variable region with highly conserved flanking sequences. For taxonomic reference, a whole trnL intron sequence database was constructed from recently collected material of 842 species, representing all widespread and/or ecologically important taxa of the species-poor arctic flora. The P6 loop alone allowed identification of all families, most genera (>75%) and one-third of the species, thus providing much higher taxonomic resolution than pollen records. The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high-throughput parallel pyrosequencing of permafrost-preserved DNA and reconstruction of two plant communities from the last glacial period. Our approach opens new possibilities for DNA-based assessment of ancient as well as modern biodiversity of many groups of organisms using environmental samples.}, }
@article {pmid21565088, year = {2010}, author = {Navascués, M and Depaulis, F and Emerson, BC}, title = {Combining contemporary and ancient DNA in population genetic and phylogeographical studies.}, journal = {Molecular ecology resources}, volume = {10}, number = {5}, pages = {760-772}, doi = {10.1111/j.1755-0998.2010.02895.x}, pmid = {21565088}, issn = {1755-0998}, abstract = {The analysis of ancient DNA in a population genetic or phylogeographical framework is an emerging field, as traditional analytical tools were largely developed for the purpose of analysing data sampled from a single time point. Markov chain Monte Carlo approaches have been successfully developed for the analysis of heterochronous sequence data from closed panmictic populations. However, attributing genetic differences between temporal samples to mutational events between time points requires the consideration of other factors that may also result in genetic differentiation. Geographical effects are an obvious factor for species exhibiting geographical structuring of genetic variation. The departure from a closed panmictic model require researchers to either exploit software developed for the analysis of isochronous data, take advantage of simulation approaches using algorithms developed for heterochronous data, or explore approximate Bayesian computation. Here, we review statistical approaches employed and available software for the joint analysis of ancient and modern DNA, and where appropriate we suggest how these may be further developed.}, }
@article {pmid21565072, year = {2010}, author = {Rohland, N and Siedel, H and Hofreiter, M}, title = {A rapid column-based ancient DNA extraction method for increased sample throughput.}, journal = {Molecular ecology resources}, volume = {10}, number = {4}, pages = {677-683}, doi = {10.1111/j.1755-0998.2009.02824.x}, pmid = {21565072}, issn = {1755-0998}, abstract = {Genetic analyses using museum specimens and ancient DNA from fossil samples are becoming increasingly important in phylogenetic and especially population genetic studies. Recent progress in ancient DNA sequencing technologies has substantially increased DNA sequence yields and, in combination with barcoding methods, has enabled large-scale studies using any type of DNA. Moreover, more and more studies now use nuclear DNA sequences in addition to mitochondrial ones. Unfortunately, nuclear DNA is, due to its much lower copy number in living cells compared to mitochondrial DNA, much more difficult to obtain from low-quality samples. Therefore, a DNA extraction method that optimizes DNA yields from low-quality samples and at the same time allows processing many samples within a short time frame is immediately required. In fact, the major bottleneck in the analysis process using samples containing low amounts of degraded DNA now lies in the extraction of samples, as column-based methods using commercial kits are fast but have proven to give very low yields, while more efficient methods are generally very time-consuming. Here, we present a method that combines the high DNA yield of batch-based silica extraction with the time-efficiency of column-based methods. Our results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method. Thus, this method is suited for harvesting the power of high-throughput sequencing using the DNA preserved in the millions of paleontological and museums specimens.}, }
@article {pmid21558445, year = {2011}, author = {Hartnup, K and Huynen, L and Te Kanawa, R and Shepherd, LD and Millar, CD and Lambert, DM}, title = {Ancient DNA recovers the origins of Māori feather cloaks.}, journal = {Molecular biology and evolution}, volume = {28}, number = {10}, pages = {2741-2750}, doi = {10.1093/molbev/msr107}, pmid = {21558445}, issn = {1537-1719}, mesh = {Animals ; Anthropology, Cultural ; *Clothing ; DNA/*analysis/genetics ; DNA, Mitochondrial/analysis/genetics ; Feathers/*chemistry ; Female ; Haplotypes ; History, 18th Century ; History, 19th Century ; Humans ; Male ; Models, Genetic ; New Zealand ; Palaeognathae/*genetics ; Phylogeography ; Sex Determination Analysis ; Travel ; }, abstract = {Feather cloaks ("kakahu"), particularly those adorned with kiwi feathers, are treasured items or "taonga" to the Māori people of "Aotearoa"/New Zealand. They are considered iconic expression of Māori culture. Despite their status, much of our knowledge of the materials used to construct cloaks, the provenance of cloaks, and the origins of cloak making itself, has been lost. We used ancient DNA methods to recover mitochondrial DNA sequences from 849 feather samples taken from 109 cloaks. We show that almost all (>99%) of the cloaks were constructed using feathers from North Island brown kiwi. Molecular sexing of nuclear DNA recovered from 92 feather cloak samples also revealed that the sex ratio of birds deviated from a ratio of 1:1 observed in reference populations. Additionally, we constructed a database of 185 mitochondrial control region DNA sequences of kiwi feathers comprising samples collected from 26 North Island locations together with data available from the literature. Genetic subdivision (G(ST)), nucleotide subdivision (N(ST)) and Spatial Analysis of Molecular Variants (SAMOVA) analyses revealed high levels of genetic structuring in North Island brown kiwi. Together with sequence data from previously studied ancient and modern kiwi samples, we were able to determine the geographic provenance of 847 cloak feathers from 108 cloaks. A surprising proportion (15%) of cloaks were found to contain feathers from different geographic locations, providing evidence of kiwi trading among Māori tribes or organized hunting trips into other tribal areas. Our data also suggest that the east of the North Island of New Zealand was the most prolific of all kiwi cloak making areas, with over 50% of all cloaks analyzed originating from this region. Similar molecular approaches have the potential to discover a wealth of lost information from artifacts of endemic cultures worldwide.}, }
@article {pmid21558193, year = {2010}, author = {Kuraku, S}, title = {Palaeophylogenomics of the vertebrate ancestor--impact of hidden paralogy on hagfish and lamprey gene phylogeny.}, journal = {Integrative and comparative biology}, volume = {50}, number = {1}, pages = {124-129}, doi = {10.1093/icb/icq044}, pmid = {21558193}, issn = {1557-7023}, mesh = {Animals ; Bone Morphogenetic Proteins/genetics ; CDX2 Transcription Factor ; *Evolution, Molecular ; Gene Dosage ; Gene Duplication ; Genome ; Hagfishes/*genetics ; Homeodomain Proteins/genetics ; Lampreys/*genetics ; *Phylogeny ; Receptors, Retinoic Acid/genetics ; Trans-Activators/genetics ; Transcription Factors/genetics ; }, abstract = {In dissecting the transition from invertebrates to vertebrates at the molecular level, whole-genome duplications are recognized as a key event. This gave rise to more copies of genes in jawed vertebrates (gnathostomes), such as the four Hox clusters in the human, compared to the single ancestral cluster in invertebrates. To date, as the most early-branching lineages in vertebrates, cyclostomes (hagfishes and lampreys) have been used for comparative analyses of gene regulations and functions. However, assignment of orthology/paralogy for cyclostomes' genes is not unambiguously demonstrated. Thus, there is a high degree of incongruence in tree topologies between gene families, although whole genome duplications postulate uniform patterns in gene phylogeny. In this review, we demonstrate how expansion of an ancient genome before the cyclostome-gnathostome split, followed by reciprocal gene loss, can cause this incongruence. This is sometimes referred to as 'hidden paralogy'.}, }
@article {pmid21531123, year = {2012}, author = {Palmer, SA and Smith, O and Allaby, RG}, title = {The blossoming of plant archaeogenetics.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {146-156}, doi = {10.1016/j.aanat.2011.03.012}, pmid = {21531123}, issn = {1618-0402}, mesh = {Agriculture ; Biological Evolution ; Crops, Agricultural/genetics ; DNA, Plant/genetics ; Ecology ; Ethnobotany ; Genomics ; *Paleontology ; Plants/*genetics ; Selection, Genetic ; }, abstract = {Recent years have seen a broadening range of studies undertaken in the field of plant archaeogenetics as the field has entered a new stage of maturity. There has been a movement towards a more functional understanding of plant evolution that has been facilitated by sequencing technologies and increasingly powerful genomic annotation. Studies have progressed to consideration of genes of pertinent function, metagenomics and investigation of the genetic basis of domestication traits coupled with human agricultural selection. Recent applications of high-throughput sequencing have facilitated archaeogenomic investigations and allowed increasingly fragmented DNA to be retrieved and characterised. While these developments are leading to the selective resequencing of targeted genomic regions in archaeobotanical samples, they have also opened up new avenues of opportunity in terms of the accessibility of biomolecules. Material once thought to be void of useful quantities of ancient DNA is now being accessed in the light of diagenetic information thrown up by HTS. The amount of archaeobotanical material that can be utilised and the work that is possible with that material are both increasing making it likely that a fertile period of plant archaeogenetics is underway.}, }
@article {pmid21529992, year = {2011}, author = {de Bruyn, M and Hoelzel, AR and Carvalho, GR and Hofreiter, M}, title = {Faunal histories from Holocene ancient DNA.}, journal = {Trends in ecology &amp; evolution}, volume = {26}, number = {8}, pages = {405-413}, doi = {10.1016/j.tree.2011.03.021}, pmid = {21529992}, issn = {1872-8383}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Climate Change ; DNA/*analysis ; *Fossils ; *Genetic Variation ; Population Dynamics ; }, abstract = {Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.}, }
@article {pmid21525906, year = {2011}, author = {Marchant, J}, title = {Ancient DNA: Curse of the Pharaoh's DNA.}, journal = {Nature}, volume = {472}, number = {7344}, pages = {404-406}, pmid = {21525906}, issn = {1476-4687}, mesh = {Animals ; Cold Climate ; DNA/*analysis/*genetics/isolation &amp; purification ; DNA, Mitochondrial/genetics ; Egypt ; Female ; Hot Temperature ; Humans ; Male ; *Mummies ; Reproducibility of Results ; *Sequence Analysis, DNA/methods/standards/trends ; Y Chromosome/genetics ; }, }
@article {pmid21514120, year = {2012}, author = {Knapp, M and Clarke, AC and Horsburgh, KA and Matisoo-Smith, EA}, title = {Setting the stage - building and working in an ancient DNA laboratory.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {3-6}, doi = {10.1016/j.aanat.2011.03.008}, pmid = {21514120}, issn = {1618-0402}, mesh = {Animals ; Biological Evolution ; DNA/chemistry/*genetics ; Humans ; Laboratories/organization &amp; administration ; Paleontology/*methods/organization &amp; administration ; Plants/chemistry/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Specimen Handling ; }, abstract = {With the introduction of next generation high throughput sequencing in 2005 and the resulting revolution in genetics, ancient DNA research has rapidly developed from an interesting but marginal field within evolutionary biology into one that can contribute significantly to our understanding of evolution in general and the development of our own species in particular. While the amount of sequence data available from ancient human, other animal and plant remains has increased dramatically over the past five years, some key limitations of ancient DNA research remain. Most notably, reduction of contamination and the authentication of results are of utmost importance. A number of studies have addressed different aspects of sampling, DNA extraction and DNA manipulation in order to establish protocols that most efficiently generate reproducible and authentic results. As increasing numbers of researchers from different backgrounds become interested in using ancient DNA technology to address key questions, the need for practical guidelines on how to construct and use an ancient DNA facility arises. The aim of this article is therefore to provide practical tips for building a state-of-the-art ancient DNA facility. It is intended to help researchers new to the field of ancient DNA research generally, and those considering the application of next generation sequencing, in their planning process.}, }
@article {pmid21501956, year = {2012}, author = {Schlumbaum, A and van Glabeke, S and Roldan-Ruiz, I}, title = {Towards the onset of fruit tree growing north of the Alps: ancient DNA from waterlogged apple (Malus sp.) seed fragments.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {194}, number = {1}, pages = {157-162}, doi = {10.1016/j.aanat.2011.03.004}, pmid = {21501956}, issn = {1618-0402}, mesh = {Agriculture/history ; Biomarkers/analysis ; Cell Nucleus/chemistry ; Chloroplasts/chemistry/genetics ; Cloning, Molecular ; DNA, Intergenic/chemistry/genetics ; DNA, Plant/*chemistry ; Endoribonucleases/genetics ; Europe ; France ; History, Ancient ; Malus/*chemistry ; Mutation/physiology ; Nucleotidyltransferases/genetics ; Paleontology ; Polymerase Chain Reaction ; Ribosomes/chemistry ; Seeds/chemistry ; Trees/*physiology ; }, abstract = {Wild apples (Malus sp.) have been a major food source in the northern Alpine region since prehistory and their use is well understood. The onset of deliberate fruit tree growing in the area is, however, less clear. It is generally assumed that horticulture was practised in Roman times, but it might be even earlier. In the archaeological record seed testa and pericarp remains are particularly frequent at sites with waterlogged preservation such as lakeshore settlements or wells, pits and ditches, but the distinction between wild and domestic plants is not morphologically possible. With waterlogged remains being one main source of information about past fruit cultivation, we have tested the feasibility of analysing ancient DNA from waterlogged preserved bulk samples of testa fragments. We studied apple seeds from three Neolithic and three Roman sites with waterlogged preservation in the Alpine foreland. Chloroplast markers failed in all samples, but nuclear ITS1 (internal transcribed spacer region 1) of the ribosomal DNA was successfully typed in two Roman samples from the site Oedenburg/Biesheim-Kunheim (Haut-Rhin, F). The retrieved ITS1 sequences are identical to each other and are shared with wild Malus sylvestris and Malus sieversii, and with domestic apple cultivars, supporting the potential of using waterlogged remains for identifying the genetic status of apple diachronically.}, }
@article {pmid21494561, year = {2011}, author = {Heupink, TH and Huynen, L and Lambert, DM}, title = {Ancient DNA suggests dwarf and 'giant' emu are conspecific.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e18728}, pmid = {21494561}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Body Size/*genetics ; Brain/anatomy &amp; histology ; DNA/*genetics ; Dromaiidae/anatomy &amp; histology/*classification/*genetics ; Extinction, Biological ; Fossils ; Geography ; Haplotypes/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Species Specificity ; Tasmania ; Time Factors ; }, abstract = {BACKGROUND: The King Island Emu (Dromaius ater) of Australia is one of several extinct emu taxa whose taxonomic relationship to the modern Emu (D. novaehollandiae) is unclear. King Island Emu were mainly distinguished by their much smaller size and a reported darker colour compared to modern Emu.<br><br>METHODOLOGY AND RESULTS: We investigated the evolutionary relationships between the King Island and modern Emu by the recovery of both nuclear and mitochondrial DNA sequences from sub-fossil remains. The complete mitochondrial control (1,094 bp) and cytochrome c oxidase subunit I (COI) region (1,544 bp), as well as a region of the melanocortin 1 receptor gene (57 bp) were sequenced using a multiplex PCR approach. The results show that haplotypes for King Island Emu fall within the diversity of modern Emu.<br><br>CONCLUSIONS: These data show the close relationship of these emu when compared to other congeneric bird species and indicate that the King Island and modern Emu share a recent common ancestor. King Island emu possibly underwent insular dwarfism as a result of phenotypic plasticity. The close relationship between the King Island and the modern Emu suggests it is most appropriate that the former should be considered a subspecies of the latter. Although both taxa show a close genetic relationship they differ drastically in size. This study also suggests that rates of morphological and neutral molecular evolution are decoupled.}, }
@article {pmid21478875, year = {2011}, author = {Jiao, Y and Wickett, NJ and Ayyampalayam, S and Chanderbali, AS and Landherr, L and Ralph, PE and Tomsho, LP and Hu, Y and Liang, H and Soltis, PS and Soltis, DE and Clifton, SW and Schlarbaum, SE and Schuster, SC and Ma, H and Leebens-Mack, J and dePamphilis, CW}, title = {Ancestral polyploidy in seed plants and angiosperms.}, journal = {Nature}, volume = {473}, number = {7345}, pages = {97-100}, pmid = {21478875}, issn = {1476-4687}, mesh = {*Evolution, Molecular ; Genome, Plant/*genetics ; Genomics ; Magnoliopsida/*classification/*genetics ; Phylogeny ; *Polyploidy ; }, abstract = {Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications-one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.}, }
@article {pmid21453001, year = {2011}, author = {Hofreiter, M}, title = {Drafting human ancestry: what does the Neanderthal genome tell us about hominid evolution? Commentary on Green et al. (2010).}, journal = {Human biology}, volume = {83}, number = {1}, pages = {1-11}, doi = {10.3378/027.083.0101}, pmid = {21453001}, issn = {1534-6617}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial ; Gene Flow ; Genome, Human/*genetics ; History, Ancient ; Hominidae/*genetics ; Humans ; *Sequence Analysis, DNA ; }, abstract = {Ten years after the first draft versions of the human genome were announced, technical progress in both DNA sequencing and ancient DNA analyses has allowed a research team around Ed Green and Svante Pääbo to complete this task from infinitely more difficult hominid samples: a few pieces of bone originating from our closest, albeit extinct, relatives, the Neanderthals. Pulling the Neanderthal sequences out of a sea of contaminating environmental DNA impregnating the bones and at the same time avoiding the problems of contamination with modern human DNA is in itself a remarkable accomplishment. However, the crucial question in the long run is, what can we learn from such genomic data about hominid evolution?}, }
@article {pmid21418639, year = {2011}, author = {Castroviejo-Fisher, S and Skoglund, P and Valadez, R and Vilà, C and Leonard, JA}, title = {Vanishing native American dog lineages.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {73}, pmid = {21418639}, issn = {1471-2148}, mesh = {Americas ; Animals ; DNA, Mitochondrial/genetics ; Dogs/*classification/*genetics ; *Endangered Species ; Genetic Variation ; Genetics, Population ; Haplotypes ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Dogs were an important element in many native American cultures at the time Europeans arrived. Although previous ancient DNA studies revealed the existence of unique native American mitochondrial sequences, these have not been found in modern dogs, mainly purebred, studied so far.<br><br>RESULTS: We identified many previously undescribed mitochondrial control region sequences in 400 dogs from rural and isolated areas as well as street dogs from across the Americas. However, sequences of native American origin proved to be exceedingly rare, and we estimate that the native population contributed only a minor fraction of the gene pool that constitutes the modern population.<br><br>CONCLUSIONS: The high number of previously unidentified haplotypes in our sample suggests that a lot of unsampled genetic variation exists in non-breed dogs. Our results also suggest that the arrival of European colonists to the Americas may have led to an extensive replacement of the native American dog population by the dogs of the invaders.}, }
@article {pmid21398675, year = {2011}, author = {Excoffier, L and Foll, M}, title = {fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios.}, journal = {Bioinformatics (Oxford, England)}, volume = {27}, number = {9}, pages = {1332-1334}, doi = {10.1093/bioinformatics/btr124}, pmid = {21398675}, issn = {1367-4811}, mesh = {Bayes Theorem ; *Biological Evolution ; *Computer Simulation ; Genetic Markers ; Genomics/*methods ; Markov Chains ; *Models, Genetic ; Recombination, Genetic ; *Software ; }, abstract = {MOTIVATION: Genetic studies focus on increasingly larger genomic regions of both extant and ancient DNA, and there is a need for simulation software to match these technological advances. We present here a new coalescent-based simulation program fastsimcoal, which is able to quickly simulate a variety of genetic markers scattered over very long genomic regions with arbitrary recombination patterns under complex evolutionary scenarios.<br><br>fastsimcoal is a C++ program compiled for Windows, MacOsX and Linux platforms. It is freely available at cmpg.unibe.ch/software/fastsimcoal/, together with its detailed user manual and example input files.}, }
@article {pmid21392386, year = {2011}, author = {Magyari, EK and Major, A and Bálint, M and Nédli, J and Braun, M and Rácz, I and Parducci, L}, title = {Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {66}, pmid = {21392386}, issn = {1471-2148}, mesh = {DNA Primers ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; Europe ; Evolution, Molecular ; Fossils ; *Genetic Variation ; *Genetics, Population ; Phylogeny ; Picea/*genetics ; Pollen/genetics ; Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site.<br><br>RESULTS: We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci.Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact.<br><br>CONCLUSION: Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient populations and the loss of ancient allele types detected in the extant individuals were likely due to the repeated bottlenecks during the Holocene; however our limited sample size did not allow us to exclude sampling effect.This study demonstrates how past population size changes inferred from PAR records can be efficiently used in combination with ancient DNA studies. The joint application of palaeoecological and population genetics analyses proved to be a powerful tool to understand the influence of past population demographic changes on the haplotype diversity and genetic composition of forest tree species.}, }
@article {pmid21355972, year = {2011}, author = {Gramain, A and Díaz, GC and Demergasso, C and Lowenstein, TK and McGenity, TJ}, title = {Archaeal diversity along a subterranean salt core from the Salar Grande (Chile).}, journal = {Environmental microbiology}, volume = {13}, number = {8}, pages = {2105-2121}, doi = {10.1111/j.1462-2920.2011.02435.x}, pmid = {21355972}, issn = {1462-2920}, mesh = {Archaea/*classification/genetics/*physiology ; Bacteriological Techniques ; *Biodiversity ; Chile ; *Environmental Microbiology ; Halobacterium/classification/genetics ; Halococcus/genetics/physiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salts ; }, abstract = {The Salar Grande in the Coastal Range of Northern Chile is a fossil evaporitic basin filled with almost pure halite (95% NaCl average). It is assumed that the basin has not received input of brines since the Pliocene (5.3 to 1.8 million years). Below 1 m the halite has remained undissolved since this time, whereas the upper layer has been dissolved and recrystallized by dripping fogs and occasional rainfall. We compared the archaeal community at different depths using both nested PCR and cultivation. The upper 10 cm of halite crust contained diverse haloarchaeal species, including several from new genera, but their provenance is unknown. For samples deeper in the core, a new and rigorous procedure for chemically sterilizing the surface of single halite crystals was developed. These halite crystals contained only species of the genus Halobacterium (Hbt.). Halobacterium salinarum-like sequences were detected by PCR, and evidence that they were from ancient DNA include: comparison with numerous negative controls; detection of 16S rRNA sequence differences in non-conserved regions, indicating genuine evolutionary mutations rather than PCR-cloning artefacts; independent isolation of Hbt. salinarum from ancient halite; and diverse mechanisms possessed by this species for minimizing radiation damage and thus enhancing its potential for long-term survival. Haloarchaea related to Hbt. noricense were obtained from enrichment cultures from ≈ 0.4 and 15.4 m depth. We investigated Hbt. noricense strain A1 and found that when trapped inside halite crystals its recovery was as rapid after 27 months of entombment as at day 0, faring much better than other extreme halophiles. A biogeographical investigation showed that Hbt. noricense-like organisms were: commonly found in surface-sterilized ancient halite, associated with salt mines, in halite crusts, and, despite a much more intense search, only rarely detected in surface environments. We conclude that some Halobacterium species are specialists at long-term survival in halite.}, }
@article {pmid21352905, year = {2011}, author = {Lin, L and Tang, H and Compton, RO and Lemke, C and Rainville, LK and Wang, X and Rong, J and Rana, MK and Paterson, AH}, title = {Comparative analysis of Gossypium and Vitis genomes indicates genome duplication specific to the Gossypium lineage.}, journal = {Genomics}, volume = {97}, number = {5}, pages = {313-320}, doi = {10.1016/j.ygeno.2011.02.007}, pmid = {21352905}, issn = {1089-8646}, mesh = {Chromosome Duplication/*genetics ; Chromosome Mapping ; Chromosomes, Artificial, Bacterial ; DNA Transposable Elements ; *Evolution, Molecular ; Genes, Plant ; Genome, Plant/*genetics ; Gossypium/*genetics ; Sequence Analysis, DNA ; Vitis/*genetics ; }, abstract = {Genetic mapping studies have suggested that diploid cotton (Gossypium) might be an ancient polyploid. However, further evidence is lacking due to the complexity of the genome and the lack of sequence resources. Here, we used the grape (Vitis vinifera) genome as an out-group in two different approaches to further explore evidence regarding ancient genome duplication (WGD) event(s) in the diploid Gossypium lineage and its (their) effects: a genome-level alignment analysis and a local-level sequence component analysis. Both studies suggest that at least one round of genome duplication occurred in the Gossypium lineage. Also, gene densities in corresponding regions from Gossypium raimondii, V. vinifera, Arabidopsis thaliana and Carica papaya genomes are similar, despite the huge difference in their genome sizes and the different number of WGDs each genome has experienced. These observations fit the model that differences in plant genome sizes are largely explained by transposon insertions into heterochromatic regions.}, }
@article {pmid21304955, year = {2011}, author = {Allentoft, ME and Oskam, C and Houston, J and Hale, ML and Gilbert, MT and Rasmussen, M and Spencer, P and Jacomb, C and Willerslev, E and Holdaway, RN and Bunce, M}, title = {Profiling the dead: generating microsatellite data from fossil bones of extinct megafauna--protocols, problems, and prospects.}, journal = {PloS one}, volume = {6}, number = {1}, pages = {e16670}, pmid = {21304955}, issn = {1932-6203}, mesh = {Animals ; Bone and Bones ; DNA Primers ; DNA, Mitochondrial/*isolation &amp; purification ; Egg Shell ; Extinction, Biological ; *Fossils ; Microsatellite Repeats/*genetics ; Palaeognathae ; Research Design ; }, abstract = {We present the first set of microsatellite markers developed exclusively for an extinct taxon. Microsatellite data have been analysed in thousands of genetic studies on extant species but the technology can be problematic when applied to low copy number (LCN) DNA. It is therefore rarely used on substrates more than a few decades old. Now, with the primers and protocols presented here, microsatellite markers are available to study the extinct New Zealand moa (Aves: Dinornithiformes) and, as with single nucleotide polymorphism (SNP) technology, the markers represent a means by which the field of ancient DNA can (preservation allowing) move on from its reliance on mitochondrial DNA. Candidate markers were identified using high throughput sequencing technology (GS-FLX) on DNA extracted from fossil moa bone and eggshell. From the 'shotgun' reads, >60 primer pairs were designed and tested on DNA from bones of the South Island giant moa (Dinornis robustus). Six polymorphic loci were characterised and used to assess measures of genetic diversity. Because of low template numbers, typical of ancient DNA, allelic dropout was observed in 36-70% of the PCR reactions at each microsatellite marker. However, a comprehensive survey of allelic dropout, combined with supporting quantitative PCR data, allowed us to establish a set of criteria that maximised data fidelity. Finally, we demonstrated the viability of the primers and the protocols, by compiling a full Dinornis microsatellite dataset representing fossils of c. 600-5000 years of age. A multi-locus genotype was obtained from 74 individuals (84% success rate), and the data showed no signs of being compromised by allelic dropout. The methodology presented here provides a framework by which to generate and evaluate microsatellite data from samples of much greater antiquity than attempted before, and opens new opportunities for ancient DNA research.}, }
@article {pmid21302275, year = {2011}, author = {Gamba, C and Fernández, E and Tirado, M and Pastor, F and Arroyo-Pardo, E}, title = {Brief communication: Ancient nuclear DNA and kinship analysis: the case of a medieval burial in San Esteban Church in Cuellar (Segovia, Central Spain).}, journal = {American journal of physical anthropology}, volume = {144}, number = {3}, pages = {485-491}, doi = {10.1002/ajpa.21451}, pmid = {21302275}, issn = {1096-8644}, mesh = {*Anthropology, Physical ; Cemeteries ; Computational Biology ; DNA/*genetics ; Female ; Genetic Markers/genetics ; Humans ; Male ; Minisatellite Repeats/genetics ; *Pedigree ; Polymerase Chain Reaction ; *Sequence Analysis, DNA ; Spain ; }, abstract = {The aim of this work was to investigate a very common situation in the archaeological and anthropological context: the study of a burial site containing several individuals, probably related genetically, using ancient DNA techniques. We used available ancient DNA and forensic protocols to obtain reliable results on archaeological material. The results also enabled molecular sex determination to be compared with osteological data. Specifically, a modified ancient DNA extraction method combined with the amplification of nuclear markers with the AmpFlSTR®MiniFiler™ kit(Applied Biosystems) was used. Seven medieval individuals buried in four niches dated in the 15th Century at San Esteban Church in Cuellar (Segovia, Central Spain) were analyzed by the proposed method, and four of seven provided complete autosomal short tandem repeat (STRs) profiles. Kinship analyses comprising paternity and sibship relations were carried out with pedigree-specific software used in forensic casework. A 99.98% paternity probability was established between two individuals, although lower percentages (68%) were obtained in other cases, and some hypothetical kinship relations were excluded. The overall results could eventually provide evidence for reconstructing the historical record.}, }
@article {pmid21298665, year = {2011}, author = {Mendisco, F and Keyser, C and Hollard, C and Seldes, V and Nielsen, AE and Crubézy, E and Ludes, B}, title = {Application of the iPLEX™ Gold SNP genotyping method for the analysis of Amerindian ancient DNA samples: benefits for ancient population studies.}, journal = {Electrophoresis}, volume = {32}, number = {3-4}, pages = {386-393}, doi = {10.1002/elps.201000483}, pmid = {21298665}, issn = {1522-2683}, mesh = {DNA/*analysis/genetics ; DNA, Mitochondrial/*analysis/genetics ; Fossils ; Gene Frequency/genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Genotype ; Humans ; Indians, North American/*genetics ; Microsatellite Repeats/*genetics ; Polymerase Chain Reaction/methods ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; }, abstract = {Important developments in the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique have generated new perspectives regarding SNP genotyping, which are particularly promising for ancient population-based studies. The main aim of the present study was to investigate the application of a MALDI-TOF MS-based SNP genotyping technique, called iPLEX(®) Gold, to analyze Amerindian ancient DNA samples. The first objective was to test the sensitivity of the method, which is recommended for DNA quantities between 10 and 5 ng, for ancient biological samples containing DNA molecules that were degraded and present in minute quantities. The second objective was to detail the advantages of this technique for studies on ancient populations. Two multiplexes were designed, allowing the major Amerindian mitochondrial and Y haplogroups to be determined simultaneously. This analysis has never been described before. Results demonstrated the reliability and accuracy of the method; data were obtained for both mitochondrial and nuclear DNA using picogram (pg) quantities of nucleic acid. This technique has the advantages of both MS and minisequencing techniques; thus, it should be included in the protocols for future ancient DNA studies.}, }
@article {pmid21296909, year = {2011}, author = {Ho, SY and Lanfear, R and Phillips, MJ and Barnes, I and Thomas, JA and Kolokotronis, SO and Shapiro, B}, title = {Bayesian estimation of substitution rates from ancient DNA sequences with low information content.}, journal = {Systematic biology}, volume = {60}, number = {3}, pages = {366-375}, doi = {10.1093/sysbio/syq099}, pmid = {21296909}, issn = {1076-836X}, mesh = {Animals ; *Artifacts ; Bayes Theorem ; Calibration ; DNA/*genetics ; *Evolution, Molecular ; Mammals/genetics ; Models, Genetic ; Palaeognathae/genetics ; Zea mays/genetics ; }, }
@article {pmid21272315, year = {2011}, author = {Anderson-Carpenter, LL and McLachlan, JS and Jackson, ST and Kuch, M and Lumibao, CY and Poinar, HN}, title = {Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {30}, pmid = {21272315}, issn = {1471-2148}, mesh = {DNA, Plant/*genetics ; *Fossils ; Geologic Sediments/*analysis ; Great Lakes Region ; Molecular Sequence Data ; Phylogeny ; Plants/classification/*genetics ; }, abstract = {BACKGROUND: Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes.<br><br>RESULTS: We successfully sequenced DNA from 64 samples (out of 126) comprised of bulk sediment and seeds, leaf fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10 copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments < 2000 years old, but we were able to successfully amplify DNA from samples up to 4600 years old. DNA sequences matched the taxonomic identity of the macrofossil from which they were extracted 79% of the time. Exceptions suggest that DNA molecules from surrounding nearby sediments may permeate or adhere to macrofossils in sediments.<br><br>CONCLUSIONS: An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights into the genetic consequences of long-term environmental change. The low DNA copy numbers we found in fossil material and the discovery of multiple sequence variants from single macrofossil extractions highlight the need for careful experimental and laboratory protocols. Further application of these protocols should lead to better understanding of the ecological and evolutionary consequences of environmental change.}, }
@article {pmid21225205, year = {2010}, author = {Gijón Botella, H and Afonso Vargas, JA and Arnay de la Rosa, M and Leles, D and González Reimers, E and Vicente, AC and Iñiguez, AM}, title = {Paleoparasitologic, paleogenetic and paleobotanic analysis of XVIII century coprolites from the church La Concepción in Santa Cruz de Tenerife, Canary Islands, Spain.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {105}, number = {8}, pages = {1054-1056}, doi = {10.1590/s0074-02762010000800017}, pmid = {21225205}, issn = {1678-8060}, mesh = {Animals ; Ascaris/*isolation &amp; purification ; DNA, Helminth ; DNA, Mitochondrial ; *Feces/chemistry/parasitology ; *Fossils ; Fruit ; Humans ; *Moraceae ; *Paleontology ; Polymerase Chain Reaction ; Seeds ; Silicates/*analysis ; Spain ; }, abstract = {We present the results of a paleoparasitologic, paleogenetic and paleobotanic analysis of coprolites recovered during the excavation of the church La Concepción in Santa Cruz de Tenerife. Coprolites (n = 4) were rehydrated and a multidisciplinary analysis was conducted. The paleobotanic analysis showed numerous silicates, seeds and fruits of the family Moraceae. In the paleoparasitologic study, Ascaris sp. eggs (n = 344) were identified. The paleogenetic results confirmed the Ascaris sp. infection as well as the European origin of human remains. These findings contribute to our knowledge of ancient helminthes infections and are the first paleoparasitological record of Ascaris sp. infection in Spain.}, }
@article {pmid21224890, year = {2011}, author = {Ottoni, C and Ricaut, FX and Vanderheyden, N and Brucato, N and Waelkens, M and Decorte, R}, title = {Mitochondrial analysis of a Byzantine population reveals the differential impact of multiple historical events in South Anatolia.}, journal = {European journal of human genetics : EJHG}, volume = {19}, number = {5}, pages = {571-576}, pmid = {21224890}, issn = {1476-5438}, mesh = {DNA, Mitochondrial/genetics ; *Genes, Mitochondrial ; *Genetics, Population ; Humans ; Molecular Sequence Data ; Turkey ; }, abstract = {The archaeological site of Sagalassos is located in Southwest Turkey, in the western part of the Taurus mountain range. Human occupation of its territory is attested from the late 12th millennium BP up to the 13th century AD. By analysing the mtDNA variation in 85 skeletons from Sagalassos dated to the 11th-13th century AD, this study attempts to reconstruct the genetic signature potentially left in this region of Anatolia by the many civilizations, which succeeded one another over the centuries until the mid-Byzantine period (13th century BC). Authentic ancient DNA data were determined from the control region and some SNPs in the coding region of the mtDNA in 53 individuals. Comparative analyses with up to 157 modern populations allowed us to reconstruct the origin of the mid-Byzantine people still dwelling in dispersed hamlets in Sagalassos, and to detect the maternal contribution of their potential ancestors. By integrating the genetic data with historical and archaeological information, we were able to attest in Sagalassos a significant maternal genetic signature of Balkan/Greek populations, as well as ancient Persians and populations from the Italian peninsula. Some contribution from the Levant has been also detected, whereas no contribution from Central Asian population could be ascertained.}, }
@article {pmid21209838, year = {2010}, author = {Ramirez, O and Illera, JC and Rando, JC and Gonzalez-Solis, J and Alcover, JA and Lalueza-Fox, C}, title = {Ancient DNA of the extinct lava shearwater (Puffinus olsoni) from the Canary Islands reveals incipient differentiation within the P. puffinus complex.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e16072}, pmid = {21209838}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Birds/*genetics/*physiology ; Bone and Bones/pathology ; DNA/*genetics ; DNA, Mitochondrial/*genetics ; Ecosystem ; *Extinction, Biological ; Genetic Variation ; Geography ; Haplotypes ; History, Ancient ; Mitochondria/metabolism ; Models, Genetic ; Phylogeny ; Predatory Behavior ; Spain ; }, abstract = {BACKGROUND: The loss of species during the Holocene was, dramatically more important on islands than on continents. Seabirds from islands are very vulnerable to human-induced alterations such as habitat destruction, hunting and exotic predators. For example, in the genus Puffinus (family Procellariidae) the extinction of at least five species has been recorded during the Holocene, two of them coming from the Canary Islands.<br><br>We used bones of the two extinct Canary shearwaters (P. olsoni and P. holeae) to obtain genetic data, for use in providing insights into the differentiation process within the genus Puffinus. Although mitochondrial DNA (mtDNA) cytochrome b sequences were successfully retrieved from four Holocene specimens of the extinct Lava shearwater (P. olsoni) from Fuerteventura (Canary Islands), the P. holeae specimens yielded no DNA. Only one haplotype was detected in P. olsoni, suggesting a low genetic diversity within this species.<br><br>CONCLUSIONS: The phylogenetic analyses based on the DNA data reveal that: (i) the "Puffinus puffinus complex", an assemblage of species defined using osteological characteristics (P. puffinus, P. olsoni, P. mauretanicus, P. yelkouan and probably P. holeae), shows unresolved phylogenetic relationships; (ii) despite the differences in body size and proportions, P. olsoni and the extant P. puffinus are sister species. Several hypotheses can be considered to explain the incipient differentiation between P. olsoni and P. puffinus.}, }
@article {pmid21149707, year = {2010}, author = {Brodie, ED}, title = {How an ancient genome duplication electrified modern fish.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {51}, pages = {21953-21954}, pmid = {21149707}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Electric Organ/*physiology ; Evolution, Molecular ; Fish Proteins/*genetics ; Fishes/*genetics ; Gene Duplication/*genetics ; Genome-Wide Association Study ; Humans ; Molecular Sequence Data ; Sodium Channels/*genetics ; }, }
@article {pmid21103372, year = {2010}, author = {Maricic, T and Whitten, M and Pääbo, S}, title = {Multiplexed DNA sequence capture of mitochondrial genomes using PCR products.}, journal = {PloS one}, volume = {5}, number = {11}, pages = {e14004}, pmid = {21103372}, issn = {1932-6203}, mesh = {DNA, Mitochondrial/chemistry/*genetics ; Forensic Genetics/methods ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Humans ; Polymerase Chain Reaction/instrumentation/*methods ; Reproducibility of Results ; Sequence Analysis, DNA/instrumentation/*methods ; }, abstract = {BACKGROUND: To utilize the power of high-throughput sequencers, target enrichment methods have been developed. The majority of these require reagents and equipment that are only available from commercial vendors and are not suitable for the targets that are a few kilobases in length.<br><br>We describe a novel and economical method in which custom made long-range PCR products are used to capture complete human mitochondrial genomes from complex DNA mixtures. We use the method to capture 46 complete mitochondrial genomes in parallel and we sequence them on a single lane of an Illumina GA(II) instrument.<br><br>CONCLUSIONS/SIGNIFICANCE: This method is economical and simple and particularly suitable for targets that can be amplified by PCR and do not contain highly repetitive sequences such as mtDNA. It has applications in population genetics and forensics, as well as studies of ancient DNA.}, }
@article {pmid21091812, year = {2011}, author = {Organ, CL and Canoville, A and Reisz, RR and Laurin, M}, title = {Paleogenomic data suggest mammal-like genome size in the ancestral amniote and derived large genome size in amphibians.}, journal = {Journal of evolutionary biology}, volume = {24}, number = {2}, pages = {372-380}, doi = {10.1111/j.1420-9101.2010.02176.x}, pmid = {21091812}, issn = {1420-9101}, mesh = {Amphibians/*genetics ; Animals ; *Biological Evolution ; *Fossils ; Genome/*genetics ; *Genomics ; Models, Genetic ; Multivariate Analysis ; Osteocytes/cytology ; Time Factors ; }, abstract = {An unsolved question in evolutionary genomics is whether amniote genomes have been expanding or contracting since the common ancestor of this diverse group. Here, we report on the polarity of amniote genome size evolution using genome size estimates for 14 extinct tetrapod genera from the Paleozoic and early Mesozoic Eras using osteocyte lacunae size as a correlate. We find substantial support for a phylogenetically controlled regression model relating genome size to osteocyte lacunae size (P of slopes <0.01, r[2]=0.65, phylogenetic signal λ=0.83). Genome size appears to have been homogeneous across Paleozoic crown-tetrapod lineages (average haploid genome size 2.9-3.7 pg) with values similar to those of extant mammals. The differentiation in genome size and underlying architecture among extant tetrapod lineages likely evolved in the Mesozoic and Cenozoic Eras, with expansion in amphibians, contractions along the diapsid lineage, and no directional change within the synapsid lineage leading to mammals.}, }
@article {pmid21085689, year = {2010}, author = {Haak, W and Balanovsky, O and Sanchez, JJ and Koshel, S and Zaporozhchenko, V and Adler, CJ and Der Sarkissian, CS and Brandt, G and Schwarz, C and Nicklisch, N and Dresely, V and Fritsch, B and Balanovska, E and Villems, R and Meller, H and Alt, KW and Cooper, A and , }, title = {Ancient DNA from European early neolithic farmers reveals their near eastern affinities.}, journal = {PLoS biology}, volume = {8}, number = {11}, pages = {e1000536}, pmid = {21085689}, issn = {1545-7885}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Agriculture ; DNA, Mitochondrial/*genetics ; *Emigration and Immigration ; Europe ; *Fossils ; Humans ; }, abstract = {In Europe, the Neolithic transition (8,000-4,000 B.C.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500-4,900 calibrated B.C.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500-4,900 calibrated B.C.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic.}, }
@article {pmid21085688, year = {2010}, author = {Robinson, R}, title = {Ancient DNA indicates farmers, not just farming, spread West.}, journal = {PLoS biology}, volume = {8}, number = {11}, pages = {e1000535}, doi = {10.1371/journal.pbio.1000535}, pmid = {21085688}, issn = {1545-7885}, mesh = {*Agriculture ; DNA, Mitochondrial/*genetics ; *Emigration and Immigration ; Europe ; Humans ; }, }
@article {pmid20927390, year = {2010}, author = {Champlot, S and Berthelot, C and Pruvost, M and Bennett, EA and Grange, T and Geigl, EM}, title = {An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications.}, journal = {PloS one}, volume = {5}, number = {9}, pages = {}, pmid = {20927390}, issn = {1932-6203}, mesh = {DNA/*chemistry/genetics ; *DNA Contamination ; Decontamination/*methods ; Endonucleases/chemistry ; Gamma Rays ; Indicators and Reagents/*analysis/radiation effects ; Polymerase Chain Reaction/*instrumentation ; Ultraviolet Rays ; }, abstract = {BACKGROUND: PCR amplification of minute quantities of degraded DNA for ancient DNA research, forensic analyses, wildlife studies and ultrasensitive diagnostics is often hampered by contamination problems. The extent of these problems is inversely related to DNA concentration and target fragment size and concern (i) sample contamination, (ii) laboratory surface contamination, (iii) carry-over contamination, and (iv) contamination of reagents.<br><br>Here we performed a quantitative evaluation of current decontamination methods for these last three sources of contamination, and developed a new procedure to eliminate contaminating DNA contained in PCR reagents. We observed that most current decontamination methods are either not efficient enough to degrade short contaminating DNA molecules, rendered inefficient by the reagents themselves, or interfere with the PCR when used at doses high enough to eliminate these molecules. We also show that efficient reagent decontamination can be achieved by using a combination of treatments adapted to different reagent categories. Our procedure involves &#x3b3;- and UV-irradiation and treatment with a mutant recombinant heat-labile double-strand specific DNase from the Antarctic shrimp Pandalus borealis. Optimal performance of these treatments is achieved in narrow experimental conditions that have been precisely analyzed and defined herein.<br><br>CONCLUSIONS/SIGNIFICANCE: There is not a single decontamination method valid for all possible contamination sources occurring in PCR reagents and in the molecular biology laboratory and most common decontamination methods are not efficient enough to decontaminate short DNA fragments of low concentration. We developed a versatile multistrategy decontamination procedure for PCR reagents. We demonstrate that this procedure allows efficient reagent decontamination while preserving the efficiency of PCR amplification of minute quantities of DNA.}, }
@article {pmid20889726, year = {2011}, author = {Shapiro, B and Ho, SY and Drummond, AJ and Suchard, MA and Pybus, OG and Rambaut, A}, title = {A Bayesian phylogenetic method to estimate unknown sequence ages.}, journal = {Molecular biology and evolution}, volume = {28}, number = {2}, pages = {879-887}, pmid = {20889726}, issn = {1537-1719}, support = {R01 GM083603/GM/NIGMS NIH HHS/United States ; R01 GM083983/GM/NIGMS NIH HHS/United States ; R01 GM086887/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Bison/genetics ; Computer Simulation ; DNA, Mitochondrial/genetics ; Dengue Virus/genetics ; *Models, Genetic ; *Phylogeny ; Time ; }, abstract = {Heterochronous data sets comprise molecular sequences sampled at different points in time. If the temporal range of the sampled sequences is large relative to the rate of mutation, the sampling times can directly calibrate evolutionary rates to calendar time. Here, we extend this calibration process to provide a full probabilistic method that utilizes temporal information in heterochronous data sets to estimate sampling times (leaf-ages) for sequenced for which this information unavailable. Our method is similar to relaxing the constraints of the molecular clock on specific lineages within a phylogenetic tree. Using a combination of synthetic and empirical data sets, we demonstrate that the method estimates leaf-ages reliably and accurately. Potential applications of our approach include incorporating samples of uncertain or radiocarbon-infinite age into ancient DNA analyses, evaluating the temporal signal in a particular sequence or data set, and exploring the reliability of sequence ages that are somehow contentious.}, }
@article {pmid20880988, year = {2012}, author = {Benner, SA and Kim, HJ and Yang, Z}, title = {Setting the stage: the history, chemistry, and geobiology behind RNA.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {4}, number = {1}, pages = {a003541}, pmid = {20880988}, issn = {1943-0264}, mesh = {Animals ; Humans ; *Molecular Biology ; *Origin of Life ; RNA/*physiology ; *Synthetic Biology ; }, abstract = {No community-accepted scientific methods are available today to guide studies on what role RNA played in the origin and early evolution of life on Earth. Further, a definition-theory for life is needed to develop hypotheses relating to the "RNA First" model for the origin of life. Four approaches are currently at various stages of development of such a definition-theory to guide these studies. These are (a) paleogenetics, in which inferences about the structure of past life are drawn from the structure of present life; (b) prebiotic chemistry, in which hypotheses with experimental support are sought that get RNA from organic and inorganic species possibly present on early Earth; (c) exploration, hoping to encounter life independent of terran life, which might contain RNA; and (d) synthetic biology, in which laboratories attempt to reproduce biological behavior with unnatural chemical systems.}, }
@article {pmid20876790, year = {2010}, author = {Murat, F and Xu, JH and Tannier, E and Abrouk, M and Guilhot, N and Pont, C and Messing, J and Salse, J}, title = {Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution.}, journal = {Genome research}, volume = {20}, number = {11}, pages = {1545-1557}, pmid = {20876790}, issn = {1549-5469}, mesh = {Brachypodium/genetics ; Chromosomes, Plant ; *Evolution, Molecular ; Genetic Speciation ; *Genome, Plant/genetics ; Karyotyping/methods ; Models, Biological ; Oryza/genetics ; Phylogeny ; Poaceae/*genetics ; Recombination, Genetic/*physiology ; Sorghum/genetics ; Synteny ; Zea mays/genetics ; }, abstract = {The comparison of the chromosome numbers of today's species with common reconstructed paleo-ancestors has led to intense speculation of how chromosomes have been rearranged over time in mammals. However, similar studies in plants with respect to genome evolution as well as molecular mechanisms leading to mosaic synteny blocks have been lacking due to relevant examples of evolutionary zooms from genomic sequences. Such studies require genomes of species that belong to the same family but are diverged to fall into different subfamilies. Our most important crops belong to the family of the grasses, where a number of genomes have now been sequenced. Based on detailed paleogenomics, using inference from n = 5-12 grass ancestral karyotypes (AGKs) in terms of gene content and order, we delineated sequence intervals comprising a complete set of junction break points of orthologous regions from rice, maize, sorghum, and Brachypodium genomes, representing three different subfamilies and different polyploidization events. By focusing on these sequence intervals, we could show that the chromosome number variation/reduction from the n = 12 common paleo-ancestor was driven by nonrandom centric double-strand break repair events. It appeared that the centromeric/telomeric illegitimate recombination between nonhomologous chromosomes led to nested chromosome fusions (NCFs) and synteny break points (SBPs). When intervals comprising NCFs were compared in their structure, we concluded that SBPs (1) were meiotic recombination hotspots, (2) corresponded to high sequence turnover loci through repeat invasion, and (3) might be considered as hotspots of evolutionary novelty that could act as a reservoir for producing adaptive phenotypes.}, }
@article {pmid20874761, year = {2010}, author = {Campos, PF and Kristensen, T and Orlando, L and Sher, A and Kholodova, MV and Götherström, A and Hofreiter, M and Drucker, DG and Kosintsev, P and Tikhonov, A and Baryshnikov, GF and Willerslev, E and Gilbert, MT}, title = {Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene.}, journal = {Molecular ecology}, volume = {19}, number = {22}, pages = {4863-4875}, doi = {10.1111/j.1365-294X.2010.04826.x}, pmid = {20874761}, issn = {1365-294X}, mesh = {Animals ; Antelopes/classification/*genetics ; Asia, Central ; *Base Sequence ; Bayes Theorem ; Climate ; DNA, Mitochondrial/*genetics ; *Fossils ; *Genetic Variation ; Phylogeny ; Population Dynamics ; }, abstract = {Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49,500 (14) C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40,400 to 10,250 (14) C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.}, }
@article {pmid20872803, year = {2011}, author = {Deguilloux, MF and Pemonge, MH and Dubut, V and Hughes, S and Hänni, C and Chollet, L and Conte, E and Murail, P}, title = {Human ancient and extant mtDNA from the Gambier Islands (French polynesia): evidence for an early Melanesian maternal contribution and new perspectives into the settlement of easternmost Polynesia.}, journal = {American journal of physical anthropology}, volume = {144}, number = {2}, pages = {248-257}, doi = {10.1002/ajpa.21398}, pmid = {20872803}, issn = {1096-8644}, mesh = {Humans ; Anthropology/methods ; *DNA, Mitochondrial/genetics ; Emigration and Immigration ; *Fossils ; Genetic Markers/genetics ; Genetic Variation ; Melanesia ; Polynesia ; Sequence Analysis, DNA ; *Pacific Island People/genetics ; }, abstract = {Molecular anthropology has been widely used to infer the origin and processes of the colonization of Polynesia. However, there are still a lack of representative geographical studies of Eastern Polynesia and unchallenged genetic data about ancient Polynesian people. The absence of both of these elements prevents an accurate description of the demographic processes of internal dispersion within the Polynesian triangle. This study provides a twofold analysis of ancient and modern mtDNA in the eastern part of French Polynesia: the Gambier Islands. The paleogenetic analyses conducted on burials of the Temoe Atoll (14(th) -17(th) centuries) represent the first fully authenticated ancient human sequences from Polynesia. The identification of the "Melanesian" Q1 mtDNA lineage in ancient human remains substantiates the Near Oceanic contribution to the early gene pool of this region. Modern samples originate from Mangareva Island. Genealogical investigations enable us to reliably identify the conservation of the Melanesian component in Easternmost Polynesia, despite recent European colonization. Finally, the identification of rare mutations in sequences belonging to haplogroup B4a1a1a provides new perspectives to the debate on the internal peopling of the Polynesian region. Altogether, the results laid out in our study put the emphasis on the necessity of controlled sampling when discussing the internal settlement of Polynesia.}, }
@article {pmid20872743, year = {2011}, author = {Zhao, YB and Li, HJ and Li, SN and Yu, CC and Gao, SZ and Xu, Z and Jin, L and Zhu, H and Zhou, H}, title = {Ancient DNA evidence supports the contribution of Di-Qiang people to the han Chinese gene pool.}, journal = {American journal of physical anthropology}, volume = {144}, number = {2}, pages = {258-268}, doi = {10.1002/ajpa.21399}, pmid = {20872743}, issn = {1096-8644}, mesh = {Analysis of Variance ; Asian People/*genetics ; Base Sequence ; Bone and Bones/chemistry ; China ; Chromosomes, Human, Y ; Cluster Analysis ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Female ; *Fossils ; Gene Pool ; Humans ; Male ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Tooth/chemistry ; }, abstract = {Han Chinese is the largest ethnic group in the world. During its development, it gradually integrated with many neighboring populations. To uncover the origin of the Han Chinese, ancient DNA analysis was performed on the remains of 46 humans (1700 to 1900 years ago) excavated from the Taojiazhai site in Qinghai province, northwest of China, where the Di-Qiang populations had previously lived. In this study, eight mtDNA haplogroups (A, B, D, F, M*, M10, N9a, and Z) and one Y-chromosome haplogroup (O3) were identified. All analyses show that the Taojiazhai population presents close genetic affinity to Tibeto-Burman populations (descendants of Di-Qiang populations) and Han Chinese, suggesting that the Di-Qiang populations may have contributed to the Han Chinese genetic pool.}, }
@article {pmid20865042, year = {2010}, author = {Suzuki, K and Takigawa, W and Tanigawa, K and Nakamura, K and Ishido, Y and Kawashima, A and Wu, H and Akama, T and Sue, M and Yoshihara, A and Mori, S and Ishii, N}, title = {Detection of Mycobacterium leprae DNA from archaeological skeletal remains in Japan using whole genome amplification and polymerase chain reaction.}, journal = {PloS one}, volume = {5}, number = {8}, pages = {e12422}, pmid = {20865042}, issn = {1932-6203}, mesh = {*Archaeology ; Base Sequence ; *Cadaver ; DNA, Bacterial/*genetics/isolation &amp; purification ; Genome, Bacterial ; Humans ; Japan ; Molecular Sequence Data ; Mycobacterium leprae/genetics/*isolation &amp; purification ; Polymerase Chain Reaction/*methods ; Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Identification of pathogen DNA from archaeological human remains is a powerful tool in demonstrating that the infectious disease existed in the past. However, it is very difficult to detect trace amounts of DNA remnants attached to the human skeleton, especially from those buried in a humid atmosphere with a relatively high environmental temperature such as in Asia.<br><br>Here we demonstrate Mycobacterium leprae DNA from archaeological skeletal remains in Japan by polymerase chain reaction, DNA sequencing and single nucleotide polymorphism (SNP) analysis. In addition, we have established a highly sensitive method of detecting DNA using a combination of whole genome amplification and polymerase chain reaction, or WGA-PCR, which provides superior sensitivity and specificity in detecting DNA from trace amounts of skeletal materials.<br><br>CONCLUSION/SIGNIFICANCE: We have detected M. leprae DNA in archaeological skeletal remains for the first time in the Far East. Its SNP genotype corresponded to type 1; the first detected case worldwide of ancient M. leprae DNA. We also developed a highly sensitive method to detect ancient DNA by utilizing whole genome amplification.}, }
@article {pmid20851541, year = {2011}, author = {Luptáková, L and Bábelová, A and Omelka, R and Kolena, B and Vondráková, M and Bauerová, M}, title = {Sex determination of early medieval individuals through nested PCR using a new primer set in the SRY gene.}, journal = {Forensic science international}, volume = {207}, number = {1-3}, pages = {1-5}, doi = {10.1016/j.forsciint.2010.08.012}, pmid = {20851541}, issn = {1872-6283}, mesh = {Amelogenin/genetics ; Chromosomes, Human, X ; Chromosomes, Human, Y ; DNA Primers ; Female ; Forensic Genetics/methods ; History, Medieval ; Humans ; Male ; Polymerase Chain Reaction/*methods ; Sex Determination Analysis/*methods ; Sex-Determining Region Y Protein/*genetics ; Slovakia ; }, abstract = {One of the first questions asked about excavated human skeletal remains is the sex. As the morphological sex determination is complicated in cases involving fragmentary bones and in skeletons from infants and children, the development of DNA-based techniques has led to improvements in sex determination. This study is focused on sex determination from ancient DNA obtained from 25 skeletons found in Middle Aged burials in western Slovakia. We performed separate amplifications of DXZ4 repetitive satellite sequences on the X chromosome, and SRY gene - testis determined factor on the Y chromosome, using nested PCR. Our results showed that DXZ4 was amplified in the case of 23 individuals. With newly designed internal and external primer sets for SRY detection with internal PCR products in lengths of 102 bp and 85 bp we succeeded in detecting the SRY locus in 9 samples. Finally, the gender was determined in 23 individuals (14 females and 9 males). In 20 samples, the gender was determined by morphological and molecular methods. Sex determination of 17 samples using nested PCR matched the morphological one, providing evidence of the authenticity and ancient origin of the PCR amplifications. The DXZ4/SRY nested PCR method represents a useful technique in sex determination of medieval human remains and it is a critical addition to anthropological studies.}, }
@article {pmid20812797, year = {2010}, author = {Fletcher, A}, title = {Genuine fakes.}, journal = {Politics and the life sciences : the journal of the Association for Politics and the Life Sciences}, volume = {29}, number = {1}, pages = {48-60}, doi = {10.2990/29_1_48}, pmid = {20812797}, issn = {1471-5457}, mesh = {Animals ; Australia ; Biotechnology/*ethics ; Cloning, Organism/*ethics/history ; *Extinction, Biological ; Fraud/history ; History, 20th Century ; History, 21st Century ; Humans ; Program Development ; Science/*ethics ; Scientific Misconduct/ethics/*history ; Tasmania ; *Tigers ; }, abstract = {This case study of the Australian Museum's Thylacine Cloning Project analyzes a frame dispute that emerged during public communication of a scientific project, which lasted from 1999 to 2005, and was premised on the idea of resurrecting an extinct species. In choosing the Tasmanian tiger--an iconic Australian marsupial officially declared extinct in 1986--the promoters of the cloning project ensured extensive media coverage. However, the popular and scientific attention generated by the idea of bringing back an extinct species challenged the Museum's efforts to frame the project in terms of scientific progress. The project repeatedly shifted from science to spectacle, as multiple stakeholders used the mass media to negotiate the scientific feasibility of trying to reverse extinction through the application of advanced biotechnology. The case study findings are relevant both to the emerging social issues surrounding the use of paleogenomics in wildlife conservation, and to the theoretical development of frame analysis as applied to scientific controversies.}, }
@article {pmid20805485, year = {2010}, author = {Huynen, L and Gill, BJ and Millar, CD and Lambert, DM}, title = {Ancient DNA reveals extreme egg morphology and nesting behavior in New Zealand's extinct moa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {37}, pages = {16201-16206}, pmid = {20805485}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; DNA/*genetics ; Egg Shell/chemistry/metabolism ; *Extinction, Biological ; Female ; Male ; *Nesting Behavior ; New Zealand ; Palaeognathae/anatomy &amp; histology/classification/*genetics/physiology ; *Phylogeny ; }, abstract = {New Zealand's extinct flightless moa radiated rapidly into a large number of morphologically diverse species, which produced an equally large range of egg morphologies. The exact number of moa species, as well as the characteristics of the eggs they laid, remains contentious. Moreover, like most extinct species, we understand little about their nesting and incubation habits. We used a modified ancient DNA extraction procedure to recover exogenous mitochondrial and nuclear DNA from the inside and outside surfaces of moa eggs. We used sequences from the inside of 69 eggshells to directly assign these remains to seven of the 10 currently recognized moa species. In addition we were able to assign, to the species level, six of the rare reconstructed "whole" eggs. These molecular results enabled us to identify two distinct lineages within the genus Euryapteryx. Members of these lineages differed in eggshell thickness, with one lineage being characterized by a relatively thin eggshell. Unexpectedly, several thin-shelled eggs were also shown to belong to the heaviest moa of the genera Dinornis, Euryapteryx and Emeus, making these, to our knowledge, the most fragile of all avian eggs measured to date. Moreover, sex-specific DNA recovered from the outer surfaces of eggshells belonging to species of Dinornis and Euryapteryx suggest that these very thin eggs were likely to have been incubated by the lighter males. The thin nature of the eggshells of these larger species of moa, even if incubated by the male, suggests that egg breakage in these species would have been common if the typical contact method of avian egg incubation was used.}, }
@article {pmid20717990, year = {2011}, author = {Deguilloux, MF and Soler, L and Pemonge, MH and Scarre, C and Joussaume, R and Laporte, L}, title = {News from the west: ancient DNA from a French megalithic burial chamber.}, journal = {American journal of physical anthropology}, volume = {144}, number = {1}, pages = {108-118}, doi = {10.1002/ajpa.21376}, pmid = {20717990}, issn = {1096-8644}, mesh = {Adult ; Archaeology ; Base Sequence ; Cemeteries ; Child ; DNA, Mitochondrial/*genetics ; *Emigration and Immigration ; France ; Haplotypes ; History, Ancient ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Genetic ; White People/*genetics/history ; Young Adult ; }, abstract = {Recent paleogenetic studies have confirmed that the spread of the Neolithic across Europe was neither genetically nor geographically uniform. To extend existing knowledge of the mitochondrial European Neolithic gene pool, we examined six samples of human skeletal material from a French megalithic long mound (c.4200 cal BC). We retrieved HVR-I sequences from three individuals and demonstrated that in the Neolithic period the mtDNA haplogroup N1a, previously only known in central Europe, was as widely distributed as western France. Alternative scenarios are discussed in seeking to explain this result, including Mesolithic ancestry, Neolithic demic diffusion, and long-distance matrimonial exchanges. In light of the limited Neolithic ancient DNA (aDNA) data currently available, we observe that all three scenarios appear equally consistent with paleogenetic and archaeological data. In consequence, we advocate caution in interpreting aDNA in the context of the Neolithic transition in Europe. Nevertheless, our results strengthen conclusions demonstrating genetic discontinuity between modern and ancient Europeans whether through migration, demographic or selection processes, or social practices.}, }
@article {pmid20703243, year = {2010}, author = {Sato, T and Kazuta, H and Amano, T and Ono, H and Ishida, H and Kodera, H and Matsumura, H and Yoneda, M and Dodo, Y and Masuda, R}, title = {Polymorphisms and allele frequencies of the ABO blood group gene among the Jomon, Epi-Jomon and Okhotsk people in Hokkaido, northern Japan, revealed by ancient DNA analysis.}, journal = {Journal of human genetics}, volume = {55}, number = {10}, pages = {691-696}, doi = {10.1038/jhg.2010.90}, pmid = {20703243}, issn = {1435-232X}, mesh = {ABO Blood-Group System/*genetics ; Alleles ; Archaeology ; Asian People/*genetics ; Ethnicity/*genetics ; *Gene Frequency ; History, Ancient ; Humans ; Japan ; *Polymorphism, Genetic ; Principal Component Analysis ; }, abstract = {To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon/ Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon/Epi-Jomon and Okhotsk people were compared with those of the modern Asian, European and Oceanic populations. The genetic relationships inferred from principal component analyses indicated that both Jomon/Epi-Jomon and Okhotsk people are included in the same group as modern Asian populations. However, the genetic characteristics of these ancient populations in Hokkaido were significantly different from each other, which is in agreement with the conclusions from mitochondrial DNA and ABCC11 gene analyses that were previously reported.}, }
@article {pmid20700629, year = {2010}, author = {den Tex, RJ and Maldonado, JE and Thorington, R and Leonard, JA}, title = {Nuclear copies of mitochondrial genes: another problem for ancient DNA.}, journal = {Genetica}, volume = {138}, number = {9-10}, pages = {979-984}, pmid = {20700629}, issn = {1573-6857}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA Primers ; DNA Transposable Elements ; DNA, Mitochondrial/*genetics ; Gene Amplification ; *Genes, Mitochondrial ; Sciuridae/*genetics ; }, abstract = {The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.}, }
@article {pmid20667880, year = {2011}, author = {Kimura, B and Marshall, FB and Chen, S and Rosenbom, S and Moehlman, PD and Tuross, N and Sabin, RC and Peters, J and Barich, B and Yohannes, H and Kebede, F and Teclai, R and Beja-Pereira, A and Mulligan, CJ}, title = {Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication.}, journal = {Proceedings. Biological sciences}, volume = {278}, number = {1702}, pages = {50-57}, pmid = {20667880}, issn = {1471-2954}, mesh = {Africa, Northern ; Animals ; Animals, Domestic/*genetics ; Base Sequence ; *Biological Evolution ; Body Weights and Measures ; Bone and Bones/chemistry ; Cluster Analysis ; DNA, Mitochondrial/genetics ; Demography ; Endangered Species ; Equidae/*genetics ; Feces/chemistry ; Geography ; Haplotypes/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Skin/chemistry ; Species Specificity ; }, abstract = {Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.}, }
@article {pmid20649402, year = {2010}, author = {Kemp, BM and Glenn Smith, D}, title = {Ancient DNA methodology: thoughts from Brian M. Kemp and David Glenn Smith on "Mitochondrial DNA of protohistoric remains of an Arikara population from South Dakota".}, journal = {Human biology}, volume = {82}, number = {2}, pages = {227-238}, doi = {10.3378/027.082.0207}, pmid = {20649402}, issn = {1534-6617}, mesh = {Animals ; DNA, Mitochondrial/*analysis ; Gene Amplification ; Genetic Variation ; Genetics, Population ; History, Ancient ; Humans ; Indians, North American/genetics/*history ; Phylogeny ; Polymerase Chain Reaction ; South Dakota ; }, }
@article {pmid20649397, year = {2010}, author = {Bennett, CC and Kaestle, FA}, title = {Investigation of ancient DNA from Western Siberia and the Sargat culture.}, journal = {Human biology}, volume = {82}, number = {2}, pages = {143-156}, doi = {10.3378/027.082.0202}, pmid = {20649397}, issn = {1534-6617}, mesh = {*Culture ; DNA, Mitochondrial/analysis/genetics/*history ; Feasibility Studies ; Female ; Gene Amplification ; Gene Flow ; Genetic Variation ; Genetics, Population/*methods ; Haplotypes/*genetics ; History, Ancient ; Humans ; Mutation ; Prevalence ; Siberia ; }, abstract = {Mitochondrial DNA from 14 archaeological samples at the Ural State University in Yekaterinburg, Russia, was extracted to test the feasibility of ancient DNA work on their collection. These samples come from a number of sites that fall into two groupings. Seven samples are from three sites, dating to the 8th-12th century AD, that belong to a northern group of what are thought to be Ugrians, who lived along the Ural Mountains in northwestern Siberia. The remaining seven samples are from two sites that belong to a southern group representing the Sargat culture, dating between roughly the 5th century BC and the 5th century AD, from southwestern Siberia near the Ural Mountains and the present-day Kazakhstan border. The samples are derived from several burial types, including kurgan burials. They also represent a number of different skeletal elements and a range of observed preservation. The northern sites repeatedly failed to amplify after multiple extraction and amplification attempts, but the samples from the southern sites were successfully extracted and amplified. The sequences obtained from the southern sites support the hypothesis that the Sargat culture was a potential zone of intermixture between native Ugrian and/or Siberian populations and steppe peoples from the south, possibly early Iranian or Indo-Iranian, which has been previously suggested by archaeological analysis.}, }
@article {pmid26242595, year = {2010}, author = {Stray, JE and Shewale, JG}, title = {Extraction of DNA from Human Remains.}, journal = {Forensic science review}, volume = {22}, number = {2}, pages = {177-185}, pmid = {26242595}, issn = {1042-7201}, abstract = {Improvements to analytical methods have made it possible for highly discriminative genotypic information to be gleaned from smaller and smaller amounts of sample material. This fact makes it practical to genotype samples or remains consisting of bone and tooth-samples that likely would not have yielded interpretable genotypic results a short time ago. In parallel, there have been improvements to protocols specifically designed to recover DNA from very old calcified tissues, i.e., ancient or compromised nature. This review discusses the current best practices for isolating and purifying DNA from bones and teeth with a focus on the processes of lysis and DNA purification linked together to yield DNA from these challenging samples. The mitochondrial and genomic DNA recovered from more recently developed techniques for isolation from skeletal remains and teeth, even very old samples, is surprisingly amenable to genotypic analysis.}, }
@article {pmid20587499, year = {2010}, author = {Heyn, P and Stenzel, U and Briggs, AW and Kircher, M and Hofreiter, M and Meyer, M}, title = {Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA.}, journal = {Nucleic acids research}, volume = {38}, number = {16}, pages = {e161}, pmid = {20587499}, issn = {1362-4962}, mesh = {*DNA Damage ; *DNA-Directed DNA Polymerase ; Fossils ; Genomics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; Templates, Genetic ; }, abstract = {Although the last few years have seen great progress in DNA sequence retrieval from fossil specimens, some of the characteristics of ancient DNA remain poorly understood. This is particularly true for blocking lesions, i.e. chemical alterations that cannot be bypassed by DNA polymerases and thus prevent amplification and subsequent sequencing of affected molecules. Some studies have concluded that the vast majority of ancient DNA molecules carry blocking lesions, suggesting that the removal, repair or bypass of blocking lesions might dramatically increase both the time depth and geographical range of specimens available for ancient DNA analysis. However, previous studies used very indirect detection methods that did not provide conclusive estimates on the frequency of blocking lesions in endogenous ancient DNA. We developed a new method, polymerase extension profiling (PEP), that directly reveals occurrences of polymerase stalling on DNA templates. By sequencing thousands of single primer extension products using PEP methodology, we have for the first time directly identified blocking lesions in ancient DNA on a single molecule level. Although we found clear evidence for blocking lesions in three out of four ancient samples, no more than 40% of the molecules were affected in any of the samples, indicating that such modifications are far less frequent in ancient DNA than previously thought.}, }
@article {pmid20579289, year = {2010}, author = {Osada, N and Uno, Y and Mineta, K and Kameoka, Y and Takahashi, I and Terao, K}, title = {Ancient genome-wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M. mulatta.}, journal = {Molecular ecology}, volume = {19}, number = {14}, pages = {2884-2895}, doi = {10.1111/j.1365-294X.2010.04687.x}, pmid = {20579289}, issn = {1365-294X}, mesh = {Animals ; Comparative Genomic Hybridization ; Cytochrome P-450 Enzyme System/genetics ; Evolution, Molecular ; Female ; Genetics, Population ; Genome ; *Hybridization, Genetic ; Macaca fascicularis/*genetics ; Macaca mulatta/*genetics ; Male ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Macaca fascicularis and Macaca mulatta are two of the most commonly used laboratory macaques, yet their genetic differences at a genome-wide level remain unclear. We analysed the multilocus DNA sequence data of 54 autosomal loci obtained from M. fascicularis samples from three different geographic origins and M. mulatta samples of Burmese origin. M. fascicularis shows high nucleotide diversity, four to five times higher than humans, and a strong geographic population structure between Indonesian-Malaysian and Philippine macaques. The pattern of divergence and polymorphism between M. fascicularis and M. mulatta shows a footprint of genetic exchange not only within their current hybrid zone but also across a wider range for more than 1 million years. However, genetic admixture may not be a random event in the genome. Whereas randomly selected genic and intergenic regions have the same evolutionary dynamics between the species, some cytochrome oxidase P450 (CYP) genes (major chemical metabolizing genes and potential target genes for local adaptation) have a significantly larger species divergence than other genes. By surveying CYP3A5 gene sequences of more than a hundred macaques, we identified three nonsynonymous single nucleotide polymorphisms that were highly differentiated between the macaques. The mosaic pattern of species divergence in the genomes may be a consequence of genetic differentiation under ecological adaptation and may be a salient feature in the genomes of nascent species under parapatry.}, }
@article {pmid20576738, year = {2010}, author = {Shi, T and Huang, H and Barker, MS}, title = {Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales.}, journal = {Annals of botany}, volume = {106}, number = {3}, pages = {497-504}, pmid = {20576738}, issn = {1095-8290}, mesh = {Actinidia/*genetics ; *Biological Evolution ; Expressed Sequence Tags ; *Gene Duplication ; *Genome, Plant ; Phylogeny ; }, abstract = {BACKGROUND AND AIMS: To assess the number and phylogenetic distribution of large-scale genome duplications in the ancestry of Actinidia, publicly available expressed sequenced tags (ESTs) for members of the Actinidiaceae and related Ericales, including tea (Camellia sinensis), were analysed.<br><br>METHODS: Synonymous divergences (K(s)) were calculated for all duplications within gene families and examined for evidence of large-scale duplication events. Phylogenetic comparisons for a selection of orthologues among several related species in Ericales and two outgroups permitted placement of duplication events in relation to lineage divergences. Gene ontology (GO) categories were analysed for each whole-genome duplication (WGD) and the whole transcriptome.<br><br>KEY RESULTS: Evidence for three ancient WGDs in Actinidia was found. Analyses of paleologue GO categories indicated a different pattern of retained genes for each genome duplication, but a pattern consistent with the dosage-balance hypothesis among all retained paleologues.<br><br>CONCLUSIONS: This study provides evidence for one independent WGD in the ancestry of Actinidia (Ad-alpha), a WGD shared by Actinidia and Camellia (Ad-beta), and the well-established At-gamma WGD that occurred prior to the divergence of all taxa examined. More ESTs in other taxa are needed to elucidate which groups in Ericales share the Ad-beta or Ad-alpha duplications and their impact on diversification.}, }
@article {pmid20565819, year = {2010}, author = {Pagès, M and Chaval, Y and Herbreteau, V and Waengsothorn, S and Cosson, JF and Hugot, JP and Morand, S and Michaux, J}, title = {Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {184}, pmid = {20565819}, issn = {1471-2148}, mesh = {Animals ; Asia, Southeastern ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Likelihood Functions ; *Phylogeny ; Rats/*classification/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe.<br><br>RESULTS: We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria.<br><br>CONCLUSIONS: Using a recently developed methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals. Most of the species expected within the area were retrieved but new putative species limits were also indicated, in particular within Berylmys and Rattus genera, where future taxonomic studies should be directed. Our study lays the foundations to better investigate rodent-born diseases in South East Asia and illustrates the relevance of evolutionary studies for health and medical sciences.}, }
@article {pmid20525589, year = {2009}, author = {Debruyne, R and Poinar, HN}, title = {Time dependency of molecular rates in ancient DNA data sets, a sampling artifact?.}, journal = {Systematic biology}, volume = {58}, number = {3}, pages = {348-360}, doi = {10.1093/sysbio/syp028}, pmid = {20525589}, issn = {1076-836X}, mesh = {Animals ; *Artifacts ; Bayes Theorem ; Bison/genetics ; Calibration ; *Evolution, Molecular ; Hominidae/genetics ; Mammoths/genetics ; Models, Genetic ; *Time ; }, }
@article {pmid20523724, year = {2010}, author = {Prost, S and Smirnov, N and Fedorov, VB and Sommer, RS and Stiller, M and Nagel, D and Knapp, M and Hofreiter, M}, title = {Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus.}, journal = {PloS one}, volume = {5}, number = {5}, pages = {e10447}, pmid = {20523724}, issn = {1932-6203}, mesh = {Animals ; Arctic Regions ; Arvicolinae/*genetics ; *Climate ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Demography ; Gene Flow/genetics ; *Global Warming ; Haplotypes/genetics ; Ice Cover ; Models, Genetic ; Phylogeny ; Russia ; Time Factors ; }, abstract = {BACKGROUND: Global temperature increased by approximately half a degree (Celsius) within the last 150 years. Even this moderate warming had major impacts on Earth's ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographical distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus), which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia) to see if climate warming events after the Last Glacial Maximum had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with a cold and dry climate.<br><br>RESULTS: Using three dimensional network reconstructions we found a dramatic decline in genetic diversity following the LGM. Model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (B&#xf8;lling/Aller&#xf8;d) warming phase at 14.5 kyrs BP.<br><br>CONCLUSION: Our results show that previous climate warming events had a strong influence on genetic diversity and population size of collared lemmings. Due to its already severely compromised genetic diversity a similar population reduction as a result of the predicted future climate change could completely abolish the remaining genetic diversity in this population. Local population extinctions of collared lemmings would have severe effects on the arctic ecosystem, as collared lemmings are a key species in the trophic interactions and ecosystem processes in the Arctic.}, }
@article {pmid20514346, year = {2010}, author = {Snow, MH and Durand, KR and Smith, DG}, title = {Ancestral Puebloan mtDNA in Context of the Greater Southwest.}, journal = {Journal of archaeological science}, volume = {37}, number = {7}, pages = {1635-1645}, pmid = {20514346}, issn = {0305-4403}, support = {R24 RR005090/RR/NCRR NIH HHS/United States ; R24 RR005090-03/RR/NCRR NIH HHS/United States ; }, abstract = {Ancient DNA (aDNA) was extracted from the human remains of seventy-three individuals from the Tommy and Mine Canyon sites (dated to PI-II and PIII, respectively), located on the B-Square Ranch in the Middle San Juan region of New Mexico. The mitochondrial DNA (mtDNA) haplogroups of forty-eight (65.7%) of these samples were identified, and their frequency distributions were compared with those of other prehistoric and modern populations from the Greater Southwest and Mexico. The haplogroup frequency distributions for the two sites were statistically significantly different from each other, with the Mine Canyon site exhibiting an unusually high frequency of haplogroup A for a Southwestern population, indicating the possible influence of migration or other evolutionary forces. However, both sites exhibited a relatively high frequency of haplogroup B, typical of Southwestern populations, suggesting continuity in the Southwest, as has been hypothesized by others (S. Carlyle 2003; Carlyle, et al. 2000; Kemp 2006; Malhi, et al. 2003; Smith, et al. 2000). The first hypervariable region of twenty-three individuals (31.5%) was also sequenced to confirm haplogroup assignments and compared with other sequences from the region. This comparison further strengthens the argument for population continuity in the Southwest without a detectable influence from Mesoamerica.}, }
@article {pmid20514042, year = {2010}, author = {Wolinsky, H}, title = {History in a single hair.}, journal = {EMBO reports}, volume = {11}, number = {6}, pages = {427-430}, pmid = {20514042}, issn = {1469-3178}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; Extinction, Biological ; Fossils ; Genomics/methods ; Geologic Sediments ; Hair/*metabolism ; History, Ancient ; Humans ; Inuit/genetics ; Mammoths/genetics ; *Museums ; Paleontology/*methods ; Sequence Analysis, DNA/economics/*methods ; }, abstract = {Museums are treasure troves of ancient DNA. Modern extraction and sequencing technology is key to putting the secrets of genetic history to use}, }
@article {pmid20498832, year = {2010}, author = {Lari, M and Rizzi, E and Milani, L and Corti, G and Balsamo, C and Vai, S and Catalano, G and Pilli, E and Longo, L and Condemi, S and Giunti, P and Hänni, C and De Bellis, G and Orlando, L and Barbujani, G and Caramelli, D}, title = {The microcephalin ancestral allele in a Neanderthal individual.}, journal = {PloS one}, volume = {5}, number = {5}, pages = {e10648}, pmid = {20498832}, issn = {1932-6203}, mesh = {*Alleles ; Cell Cycle Proteins ; Cytoskeletal Proteins ; DNA, Mitochondrial/genetics ; *Fossils ; Genetic Loci/genetics ; Humans ; Nerve Tissue Proteins/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The high frequency (around 0.70 worldwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal.<br><br>Here we report the first PCR amplification and high-throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination.<br><br>CONCLUSIONS/SIGNIFICANCE: The MCPH1 genotype of the Monti Lessini (MLS) Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA.}, }
@article {pmid20492755, year = {2010}, author = {Eliásová, I and Mazura, I and Smejtek, L}, title = {DNA analysis of ancient skeletal remains.}, journal = {Folia biologica}, volume = {56}, number = {2}, pages = {47-50}, pmid = {20492755}, issn = {0015-5500}, mesh = {Archaeology/*methods ; Base Sequence ; Bone and Bones/*chemistry ; DNA/*analysis ; Female ; History, Ancient ; Humans ; Male ; Microsatellite Repeats ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Non-Governmental Organization Archaia (http://www.archaia.cz) carried out the rescue archaeological research at Knezeves near Prague in 1998. Most of dating objects in Knezeves come from the period of Late and Final Bronze Age. The approximately 3,000 years old set, which included 11 human remains from three settlement features, was collected for the study. First, gender was determined according to anthropological characteristics. Ancient DNA from bones was extracted by the phenol-chloroform procedure and N-phenacetylthiazolum bromide reagent. Polymerase chain reaction amplification of AMEL XY, part of amelogenin gene, with subsequent polyacrylamide gel electrophoresis and Short Tandem Repeats analysis followed. DNA profiles of skeletal remains were obtained by the fragmentation analysis of autosomal short tandem repeat markers. Genetic profiles showed us whether individuals from Knezeves were in mutual relationship (parent - descendant). The congruence of results in sex determination supported reliability of genetic methods, which are suitable for sex determination of fragmental and subadult skeletal remains.}, }
@article {pmid20463713, year = {2010}, author = {Dalton, R}, title = {Ancient DNA set to rewrite human history.}, journal = {Nature}, volume = {465}, number = {7295}, pages = {148-149}, pmid = {20463713}, issn = {1476-4687}, mesh = {Animals ; Climate ; *Emigration and Immigration ; *Evolution, Molecular ; Fossils ; Genome, Human/genetics ; Greenland ; History, Ancient ; Hominidae/*genetics ; Humans ; Inuit/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, }
@article {pmid20456521, year = {2010}, author = {Lim, DS and Oh, CS and Lee, SJ and Shin, DH}, title = {Auto-fluorescence emitted from the cell residues preserved in human tissues of medieval Korean mummies.}, journal = {Journal of anatomy}, volume = {217}, number = {1}, pages = {67-75}, pmid = {20456521}, issn = {1469-7580}, mesh = {Cartilage/cytology ; Cartilage, Articular/ultrastructure ; Chondrocytes/ultrastructure ; *Fluorescence ; Humans ; Kidney/cytology ; Lung/cytology ; Microdissection/methods ; Microscopy, Confocal ; Microscopy, Electron, Scanning ; Microscopy, Fluorescence/methods ; Mummies/*pathology ; Paleopathology ; }, abstract = {As a significant association has been established between residual ancient DNA (aDNA) and histological preservation, the morphological identification or confirmation of preserved cell residue in ancient tissues would greatly facilitate aDNA studies and enhance the definitiveness of their conclusions. However, morphological differentiation of cell residue from other tissue structures has always been difficult, even for experienced histologists, due to the severe degradation of cells over long burial durations. In the present study, using a fluorescence microscopy equipped with a specific type of filter set (excitation filter, 510-550 nm; dichroic mirror, 570 nm; emission filter, approximately 590 nm), we found that certain structures in well-preserved mummified tissues emitted auto-fluorescence. Those structures were actually cell residues (e.g. fragmented DNA), laser capture microdissection and Quantifiler kit analysis having shown that preservation of nuclear DNA correlates with auto-fluorescence emission in laser capture microdissection-captured areas. Detection of auto-fluorescence could be an effective means of identifying cell residues in ancient tissue, enabling selection of the well-preserved samples necessary in successful aDNA studies.}, }
@article {pmid20448179, year = {2010}, author = {Burbano, HA and Hodges, E and Green, RE and Briggs, AW and Krause, J and Meyer, M and Good, JM and Maricic, T and Johnson, PL and Xuan, Z and Rooks, M and Bhattacharjee, A and Brizuela, L and Albert, FW and de la Rasilla, M and Fortea, J and Rosas, A and Lachmann, M and Hannon, GJ and Pääbo, S}, title = {Targeted investigation of the Neandertal genome by array-based sequence capture.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5979}, pages = {723-725}, pmid = {20448179}, issn = {1095-9203}, support = {P01 CA013106/CA/NCI NIH HHS/United States ; P01 CA013106-38/CA/NCI NIH HHS/United States ; P01 CA013106-39/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Amino Acid Substitution ; Animals ; Fossils ; Genes ; *Genome ; *Genome, Human ; Hominidae/*genetics ; Humans ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis/*methods ; Pan troglodytes/genetics ; Proteins/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {It is now possible to perform whole-genome shotgun sequencing as well as capture of specific genomic regions for extinct organisms. However, targeted resequencing of large parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of approximately 99.8% microbial DNA. Using this approach, we have sequenced approximately 14,000 protein-coding positions inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals.}, }
@article {pmid20448165, year = {2010}, author = {Pennisi, E}, title = {Paleogenetics. Computer kid makes good.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5979}, pages = {683}, doi = {10.1126/science.328.5979.683}, pmid = {20448165}, issn = {1095-9203}, mesh = {Algorithms ; Animals ; *Computational Biology ; Genome ; Genome, Human ; History, 21st Century ; Hominidae/*genetics ; Humans ; *Sequence Analysis, DNA ; *Software ; }, }
@article {pmid20448164, year = {2010}, author = {Pennisi, E}, title = {Paleogenetics. Cloned Neandertals still in the realm of sci-fi.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5979}, pages = {682-683}, doi = {10.1126/science.328.5979.682}, pmid = {20448164}, issn = {1095-9203}, mesh = {Animals ; *Cloning, Organism/ethics ; *Extinction, Biological ; *Fossils ; Genome ; Genome, Human ; Hominidae/*genetics ; Humans ; }, }
@article {pmid20448163, year = {2010}, author = {Gibbons, A}, title = {Paleogenetics. Close encounters of the prehistoric kind.}, journal = {Science (New York, N.Y.)}, volume = {328}, number = {5979}, pages = {680-684}, doi = {10.1126/science.328.5979.680}, pmid = {20448163}, issn = {1095-9203}, mesh = {Animals ; Asian People/genetics ; Black People/genetics ; Extinction, Biological ; Female ; *Fossils ; Gene Flow ; *Genome ; *Genome, Human ; Hominidae/anatomy &amp; histology/*genetics/physiology ; Humans ; Mutation ; Pan troglodytes/genetics ; Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA ; White People/genetics ; }, }
@article {pmid20441577, year = {2010}, author = {Prüfer, K and Stenzel, U and Hofreiter, M and Pääbo, S and Kelso, J and Green, RE}, title = {Computational challenges in the analysis of ancient DNA.}, journal = {Genome biology}, volume = {11}, number = {5}, pages = {R47}, pmid = {20441577}, issn = {1474-760X}, mesh = {Animals ; Base Sequence ; Computational Biology/*methods ; Computer Simulation ; DNA/*analysis/*genetics ; Databases, Nucleic Acid ; *Extinction, Biological ; Genetic Variation ; Humans ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.}, }
@article {pmid20428686, year = {2010}, author = {Oh, CS and Seo, M and Lim, NJ and Lee, SJ and Lee, EJ and Lee, SD and Shin, DH}, title = {Paleoparasitological report on Ascaris aDNA from an ancient East Asian sample.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {105}, number = {2}, pages = {225-228}, doi = {10.1590/s0074-02762010000200020}, pmid = {20428686}, issn = {1678-8060}, mesh = {Animals ; Ascaris lumbricoides/*genetics/isolation &amp; purification ; Cytochromes b/genetics ; DNA, Helminth/*genetics/isolation &amp; purification ; Humans ; Mummies/*parasitology ; Polymerase Chain Reaction ; Republic of Korea ; }, abstract = {In this study, Ascaris DNA was extracted and sequenced from a medieval archaeological sample in Korea. While Ascaris eggs were confirmed to be of human origin by archaeological evidence, it was not possible to pinpoint the exact species due to close genetic relationships among them. Despite this shortcoming, this is the first Ascaris ancient DNA (aDNA) report from a medieval Asian country and thus will expand the scope of Ascaris aDNA research.}, }
@article {pmid20414896, year = {2010}, author = {Shapiro, B and Hofreiter, M}, title = {Analysis of ancient human genomes: using next generation sequencing, 20-fold coverage of the genome of a 4,000-year-old human from Greenland has been obtained.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {32}, number = {5}, pages = {388-391}, doi = {10.1002/bies.201000026}, pmid = {20414896}, issn = {1521-1878}, mesh = {Archaeology ; DNA, Mitochondrial/genetics ; Fossils ; Genome, Human/*genetics ; Greenland ; Humans ; Sequence Analysis, DNA/*methods ; }, abstract = {High-capacity sequencing technologies have dramatically reduced both the cost and time required to generate complete human genome sequences. Besides expanding our knowledge about existing diversity, the nature of these technologies makes it possible to extend knowledge in yet another dimension: time. Recently, the complete genome sequence of a 4,000-year-old human from the Saqqaq culture of Greenland was determined to 20-fold coverage. These data make it possible to investigate the population affinities of this enigmatic culture and, by identifying several phenotypic traits of this individual, provide a limited glimpse into how these people may have looked. While undoubtedly a milestone in ancient DNA research, the cost to generate an ancient genome, even from such an exceptionally preserved specimen, remains out of reach for most. Nonetheless, recently developed DNA capture methods, already applied to Neanderthal and fossil human mitochondrial DNA, may soon make large-scale genome-wide analysis of ancient human diversity a reality, providing a fresh look at human population history.}, }
@article {pmid20404179, year = {2010}, author = {Larson, G and Liu, R and Zhao, X and Yuan, J and Fuller, D and Barton, L and Dobney, K and Fan, Q and Gu, Z and Liu, XH and Luo, Y and Lv, P and Andersson, L and Li, N}, title = {Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {17}, pages = {7686-7691}, pmid = {20404179}, issn = {1091-6490}, mesh = {Agriculture/*history ; *Animal Migration ; Animals ; Base Sequence ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; Demography ; *Evolution, Molecular ; Asia, Eastern ; *Fossils ; Geography ; Haplotypes/genetics ; History, Ancient ; Humans ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; *Sus scrofa ; }, abstract = {The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as "cryptic domestication," given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.}, }
@article {pmid20346116, year = {2010}, author = {Mona, S and Catalano, G and Lari, M and Larson, G and Boscato, P and Casoli, A and Sineo, L and Di Patti, C and Pecchioli, E and Caramelli, D and Bertorelle, G}, title = {Population dynamic of the extinct European aurochs: genetic evidence of a north-south differentiation pattern and no evidence of post-glacial expansion.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {83}, pmid = {20346116}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; *Genetics, Population ; Geography ; Haplotypes ; Italy ; Phylogeny ; Population Dynamics ; Ruminants/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The aurochs (Bos primigenius) was a large bovine that ranged over almost the entirety of the Eurasian continent and North Africa. It is the wild ancestor of the modern cattle (Bos taurus), and went extinct in 1627 probably as a consequence of human hunting and the progressive reduction of its habitat. To investigate in detail the genetic history of this species and to compare the population dynamics in different European areas, we analysed Bos primigenius remains from various sites across Italy.<br><br>RESULTS: Fourteen samples provided ancient DNA fragments from the mitochondrial hypervariable region. Our data, jointly analysed with previously published sequences, support the view that Italian aurochsen were genetically similar to modern bovine breeds, but very different from northern/central European aurochsen. Bayesian analyses and coalescent simulations indicate that the genetic variation pattern in both Italian and northern/central European aurochsen is compatible with demographic stability after the last glaciation. We provide evidence that signatures of population expansion can erroneously arise in stable aurochsen populations when the different ages of the samples are not taken into account.<br><br>CONCLUSIONS: Distinct groups of aurochsen probably inhabited Italy and northern/central Europe after the last glaciation, respectively. On the contrary, Italian and Fertile Crescent aurochsen likely shared several mtDNA sequences, now common in modern breeds. We argue that a certain level of genetic homogeneity characterized aurochs populations in Southern Europe and the Middle East, and also that post-glacial recolonization of northern and central Europe advanced, without major demographic expansions, from eastern, and not southern, refugia.}, }
@article {pmid20345871, year = {2010}, author = {Witas, HW and Jedrychowska-Dańska, K and Zawicki, P}, title = {Changes in frequency of IDDM-associated HLA DQB, CTLA4 and INS alleles.}, journal = {International journal of immunogenetics}, volume = {37}, number = {3}, pages = {155-158}, doi = {10.1111/j.1744-313X.2010.00896.x}, pmid = {20345871}, issn = {1744-313X}, mesh = {Alleles ; Antigens, CD/*genetics ; CTLA-4 Antigen ; DNA/genetics/isolation &amp; purification ; Diabetes Mellitus, Type 1/*genetics/history/immunology ; Gene Frequency ; Genotype ; HLA-DQ Antigens/*genetics ; HLA-DQ beta-Chains ; History, Medieval ; Humans ; Insulin/*genetics ; Poland ; }, abstract = {The incidence of type 1 diabetes is increasing worldwide. In Poland, the number of cases tripled during the last two decades. The aim of this study was to test the hypothesis that the increase may be at least partly explained by a shift in predisposing alleles' frequencies - resulting from treating the otherwise lethal disease, generally better health care as well as selective pressure imposed by pathogens affecting humankind throughout history. The source of DNA was skeletal remains of 232 individuals excavated in four burial sites, dating back to 11th-14th centuries. With all necessary precautions required in ancient DNA analysis, frequencies of HLA DQB(57), CTLA4+49A/G and INS -23A/T alleles were assessed and compared with available data, characterising contemporary Polish population. Frequency of HLA DQB(57-Asp) protective allele is much higher in present-day population of Poland (50.6%) than in the group of 155 medieval specimens successfully typed for this polymorphism (28.4%, P < 0.001). Out of 86 medieval individuals typed for CTLA4+49A/G, 29.1% were homozygous for the predisposing G allele, which is significantly more than contemporarily - 7.6% (P < 0.001). No statistically significant difference was found in alleles and genotypes frequencies of INS-23A/T polymorphic site. Contrary to the initial assumptions, genetic predisposition towards type 1 diabetes, conferred by HLA DQB(57), CTLA4+49A/G and INS -23A/T alleles is much lower contemporarily than it was approximately 700 years before present. This suggests involvement of other than genetic factors in the fast growing incidence of the disease.}, }
@article {pmid20339040, year = {2010}, author = {Balter, M}, title = {Human evolution. Ancient DNA from Siberia fingers a possible new human lineage.}, journal = {Science (New York, N.Y.)}, volume = {327}, number = {5973}, pages = {1566-1567}, doi = {10.1126/science.327.5973.1566-b}, pmid = {20339040}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/chemistry/*genetics ; Finger Phalanges ; Genome, Mitochondrial ; Hominidae/*classification/genetics ; Humans ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Siberia ; Time ; }, }
@article {pmid20335279, year = {2010}, author = {Stiller, M and Baryshnikov, G and Bocherens, H and Grandal d'Anglade, A and Hilpert, B and Münzel, SC and Pinhasi, R and Rabeder, G and Rosendahl, W and Trinkaus, E and Hofreiter, M and Knapp, M}, title = {Withering away--25,000 years of genetic decline preceded cave bear extinction.}, journal = {Molecular biology and evolution}, volume = {27}, number = {5}, pages = {975-978}, doi = {10.1093/molbev/msq083}, pmid = {20335279}, issn = {1537-1719}, mesh = {Animals ; Competitive Behavior ; Ecosystem ; *Extinction, Biological ; Female ; History, Ancient ; Humans ; Population Density ; Ursidae/classification/*genetics/*physiology ; }, abstract = {The causes of the late Pleistocene megafaunal extinctions are still enigmatic. Although the fossil record can provide approximations for when a species went extinct, the timing of its disappearance alone cannot resolve the causes and mode of the decline preceding its extinction. However, ancient DNA analyses can reveal population size changes over time and narrow down potential causes of extinction. Here, we present an ancient DNA study comparing late Pleistocene population dynamics of two closely related species, cave and brown bears. We found that the decline of cave bears started approximately 25,000 years before their extinction, whereas brown bear population size remained constant. We conclude that neither the effects of climate change nor human hunting alone can be responsible for the decline of the cave bear and suggest that a complex of factors including human competition for cave sites lead to the cave bear's extinction.}, }
@article {pmid20333229, year = {2010}, author = {Roulin, A and Chaparro, C and Piégu, B and Jackson, S and Panaud, O}, title = {Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rices.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {132-139}, pmid = {20333229}, issn = {1759-6653}, abstract = {Rice is one of the most important crops, feeding more than half of the world population. There are two cultivated species, the African rice Oryza glaberrima and the Asian rice O. sativa. Although the African species is gradually replaced by O. sativa in most of African rice agrosystems, this species represents an important reservoir of genes of agronomical interest. Their exploitation for the development of modern African rice varieties requires a good understanding of the genetic relationships between the two cultivated species. We took advantage of the recent availability of the sequence of the chromosome 3 short arm of O. glaberrima to estimate the date of radiation between O. glaberrima and O. sativa lineages, using all the long terminal repeat (LTR)-retrotransposons as paleogenomic markers. We first demonstrated that in two distinct lineages, LTR-retrotransposons mutate at the same rate. Based on LTR-retrotransposons shared by both species in orthologous position, we then estimated that O. glaberrima and O. sativa progenitors diverged 1.2 Ma. This constitutes one of the first studies using such a large sample of transposable elements to reconstruct the phylogeny of species. Given the number of genome sequencing projects, there is no doubt that such approach will allow to resolve phylogenetic incongruities. The application of this method to other plant genomes will also facilitate further understanding of evolution of LTR-retrotransposons and eventually of the whole genome in divergent plant lineages.}, }
@article {pmid20306303, year = {2011}, author = {Kim, NY and Lee, HY and Park, MJ and Yang, WI and Shin, KJ}, title = {A genetic investigation of Korean mummies from the Joseon Dynasty.}, journal = {Molecular biology reports}, volume = {38}, number = {1}, pages = {115-121}, pmid = {20306303}, issn = {1573-4978}, mesh = {ABO Blood-Group System/genetics ; Adult ; Child ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/*genetics ; Electrophoresis ; Female ; Genotype ; Humans ; Male ; Microsatellite Repeats/genetics ; *Mummies ; Polymorphism, Single Nucleotide/genetics ; Pregnancy ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {Two Korean mummies (Danwoong-mirra and Yoon-mirra) found in medieval tombs in the central region of the Korean peninsula were genetically investigated by analysis of mitochondrial DNA (mtDNA), Y-chromosomal short tandem repeat (Y-STR) and the ABO gene. Danwoong-mirra is a male child mummy and Yoon-mirra is a pregnant female mummy, dating back about 550 and 450 years, respectively. DNA was extracted from soft tissues or bones. mtDNA, Y-STR and the ABO gene were amplified using a small size amplicon strategy and were analyzed according to the criteria of ancient DNA analysis to ensure that authentic DNA typing results were obtained from these ancient samples. Analysis of mtDNA hypervariable region sequence and coding region single nucleotide polymorphism (SNP) information revealed that Danwoong-mirra and Yoon-mirra belong to the East Asian mtDNA haplogroups D4 and M7c, respectively. The Y-STRs were analyzed in the male child mummy (Danwoong-mirra) using the AmpFlSTR® Yfiler PCR Amplification Kit and an in-house Y-miniplex plus system, and could be characterized in 4 loci with small amplicon size. The analysis of ABO gene SNPs using multiplex single base extension methods revealed that the ABO blood types of Danwoong-mirra and Yoon-mirra are AO01 and AB, respectively. The small size amplicon strategy and the authentication process in the present study will be effectively applicable to future genetic analyses of various forensic and ancient samples.}, }
@article {pmid20229501, year = {2010}, author = {Woide, D and Zink, A and Thalhammer, S}, title = {Technical note: PCR analysis of minimum target amount of ancient DNA.}, journal = {American journal of physical anthropology}, volume = {142}, number = {2}, pages = {321-327}, doi = {10.1002/ajpa.21268}, pmid = {20229501}, issn = {1096-8644}, mesh = {Actins/genetics ; Amelogenin/genetics ; DNA/analysis/*isolation &amp; purification ; Egypt ; Electrophoresis, Polyacrylamide Gel ; Haversian System/chemistry ; Humans ; Microdissection/methods ; *Mummies ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {The study of ancient DNA plays an important role in archaeological and palaeontological research as well as in pathology and forensics. Here, we present a new tool for ancient DNA analysis, which overcomes contamination problems, DNA degradation, and the negative effects of PCR inhibitors while reducing the amount of starting target material in the picogram range. Ancient bone samples from four Egyptian mummies were examined by combining laser microdissection, conventional DNA extraction, and low-volume PCR. Initially, several bone particles (osteons) in the micrometer range were extracted by laser microdissection. Subsequently, ancient DNA amplification was performed to verify our extraction method. Amelogenin and beta-actin gene specific fragments were amplified via low-volume PCR in a total reaction volume of 1 microl. Results of microdissected mummy DNA samples were compared to mummy DNA, which was extracted using a standard DNA extraction method based on pulverization of bone material. Our results highlight the combination of laser microdissection and low-volume PCR as a promising new technique in ancient DNA analysis.}, }
@article {pmid20219731, year = {2010}, author = {Oskam, CL and Haile, J and McLay, E and Rigby, P and Allentoft, ME and Olsen, ME and Bengtsson, C and Miller, GH and Schwenninger, JL and Jacomb, C and Walter, R and Baynes, A and Dortch, J and Parker-Pearson, M and Gilbert, MT and Holdaway, RN and Willerslev, E and Bunce, M}, title = {Fossil avian eggshell preserves ancient DNA.}, journal = {Proceedings. Biological sciences}, volume = {277}, number = {1690}, pages = {1991-2000}, pmid = {20219731}, issn = {1471-2954}, mesh = {Animals ; Australia ; Birds/*genetics ; *DNA/analysis/chemistry/genetics/isolation &amp; purification ; *DNA, Mitochondrial/analysis/chemistry/genetics/isolation &amp; purification ; Dromaiidae/genetics ; Ducks/genetics ; Egg Shell/*chemistry ; Extinction, Biological ; *Fossils ; Madagascar ; Microscopy, Confocal/methods ; Molecular Sequence Data ; New Zealand ; Paleontology ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Strigiformes/genetics ; }, abstract = {Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.}, }
@article {pmid20212118, year = {2010}, author = {Campos, PF and Willerslev, E and Sher, A and Orlando, L and Axelsson, E and Tikhonov, A and Aaris-Sørensen, K and Greenwood, AD and Kahlke, RD and Kosintsev, P and Krakhmalnaya, T and Kuznetsova, T and Lemey, P and MacPhee, R and Norris, CA and Shepherd, K and Suchard, MA and Zazula, GD and Shapiro, B and Gilbert, MT}, title = {Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {12}, pages = {5675-5680}, pmid = {20212118}, issn = {1091-6490}, support = {R01 GM086887/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA/*genetics/history ; DNA, Mitochondrial/genetics/history ; Extinction, Biological ; *Fossils ; Genetic Variation ; History, Ancient ; Humans ; Molecular Sequence Data ; Phylogeny ; Population Dynamics ; Ruminants/*genetics ; }, abstract = {The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at approximately 45,000 radiocarbon years before present ((14)C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 (14)C YBP, recontracted at ca. 18,000 (14)C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations.}, }
@article {pmid20196813, year = {2010}, author = {Kuhn, TS and McFarlane, KA and Groves, P and Mooers, A&#xd8; and Shapiro, B}, title = {Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon.}, journal = {Molecular ecology}, volume = {19}, number = {7}, pages = {1312-1323}, doi = {10.1111/j.1365-294X.2010.04565.x}, pmid = {20196813}, issn = {1365-294X}, mesh = {Animals ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genetics, Population ; Genotype ; Microsatellite Repeats ; Reindeer/*genetics ; Sequence Analysis, DNA ; Yukon Territory ; }, abstract = {The long-term persistence of forest-dwelling caribou (Rangifer tarandus caribou) will probably be determined by management and conservation decisions. Understanding the evolutionary relationships between modern caribou herds, and how these relationships have changed through time will provide key information for the design of appropriate management strategies. To explore these relationships, we amplified microsatellite and mitochondrial markers from modern caribou from across the Southern Yukon, Canada, as well as mitochondrial DNA from Holocene specimens recovered from alpine ice patches in the same region. Our analyses identify a genetically distinct group of caribou composed of herds from the Southern Lakes region that may warrant special management consideration. We also identify a partial genetic replacement event occurring 1000 years before present, coincident with the deposition of the White River tephra and the Medieval Warm Period. These results suggest that, in the face of increasing anthropogenic pressures and climate variability, maintaining the ability of caribou herds to expand in numbers and range may be more important than protecting the survival of any individual, isolated sedentary forest-dwelling herd.}, }
@article {pmid20194164, year = {2010}, author = {Petren, K and Grant, PR and Grant, BR and Clack, AA and Lescano, NV}, title = {Multilocus genotypes from Charles Darwin's finches: biodiversity lost since the voyage of the Beagle.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1543}, pages = {1009-1018}, pmid = {20194164}, issn = {1471-2970}, mesh = {Animals ; *Biodiversity ; DNA/chemistry/genetics ; Ecuador ; Finches/*genetics ; Genetic Variation ; Genotype ; Microsatellite Repeats ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Genetic analysis of museum specimens offers a direct window into a past that can predate the loss of extinct forms. We genotyped 18 Galápagos finches collected by Charles Darwin and companions during the voyage of the Beagle in 1835, and 22 specimens collected in 1901. Our goals were to determine if significant genetic diversity has been lost since the Beagle voyage and to determine the genetic source of specimens for which the collection locale was not recorded. Using 'ancient' DNA techniques, we quantified variation at 14 autosomal microsatellite loci. Assignment tests showed several museum specimens genetically matched recently field-sampled birds from their island of origin. Some were misclassified or were difficult to classify. Darwin's exceptionally large ground finches (Geospiza magnirostris) from Floreana and San Cristóbal were genetically distinct from several other currently existing populations. Sharp-beaked ground finches (Geospiza difficilis) from Floreana and Isabela were also genetically distinct. These four populations are currently extinct, yet they were more genetically distinct from congeners than many other species of Darwin's finches are from each other. We conclude that a significant amount of the finch biodiversity observed and collected by Darwin has been lost since the voyage of the Beagle.}, }
@article {pmid20193133, year = {2010}, author = {Kim, AJ and Kim, K and Choi, JH and Choi, EH and Jung, YJ and Min, NY and Lkhagvasuren, G and Rhee, S and Kim, JH and Noh, M and Park, AJ and Kim, KY and Kang, Y and Lee, KH and Kim, KC}, title = {Mitochondrial DNA analysis of ancient human bones excavated from Nukdo island, S.Korea.}, journal = {BMB reports}, volume = {43}, number = {2}, pages = {133-139}, doi = {10.5483/bmbrep.2010.43.2.133}, pmid = {20193133}, issn = {1976-670X}, mesh = {Bone and Bones/chemistry ; DNA, Mitochondrial/chemistry/*classification ; Haplotypes ; Humans ; Phylogeny ; Principal Component Analysis ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {We have performed analyses using ancient DNA extracted from 25 excavated human bones, estimating around the 1(st) century B.C. Ancient human bones were obtained from Nukdo Island, which is located off of the Korean peninsula of East Asia. We made concerted efforts to extract ancient DNA of high quality and to obtain reproducible PCR products, as this was a primary consideration for this extensive kind of undertaking. We performed PCR amplifications for several regions of the mitochondrial DNA, and could determine mitochondrial haplogroups for 21 ancient DNA samples. Genetic information from mitochondrial DNA belonged to super-haplogroup M, haplogroup D or its sub-haplogroups (D4 or D4b), which are distinctively found in East Asians, including Koreans or Japanese. The dendrogram and principal component analysis based on haplogroup frequencies revealed that the Nukdo population was close to those of the East Asians and clearly distinguished from populations shown in the other regions. Considering that Nukdo is geologically isolated in the southern part of them Korean peninsula and is a site of commercial importance with neighboring countries, these results may reflect genetic continuity for the habitation and migration of ethnic groups who had lived in a particular area in the past. Therefore, we suggest that phylogenetic analyses of ancient DNA have significant advantages for clarifying the origins and migrations of ethnic groups, or human races.}, }
@article {pmid20186156, year = {2010}, author = {Zhao, YB and Li, HJ and Cai, DW and Li, CX and Zhang, QC and Zhu, H and Zhou, H}, title = {Ancient DNA from nomads in 2500-year-old archeological sites of Pengyang, China.}, journal = {Journal of human genetics}, volume = {55}, number = {4}, pages = {215-218}, doi = {10.1038/jhg.2010.8}, pmid = {20186156}, issn = {1435-232X}, mesh = {Archaeology ; China ; DNA, Mitochondrial/classification/*genetics ; Asia, Eastern/ethnology ; Female ; *Fossils ; Haplotypes ; Humans ; Male ; Phylogeny ; Polymorphism, Single Nucleotide ; Siberia/ethnology ; *Transients and Migrants ; }, abstract = {Six human remains (dating approximately 2500 years ago) were excavated from Pengyang, China, an area occupied by both ancient nomadic and farming people. The funerary objects found with these remains suggested they were nomads. To further confirm their ancestry, we analyzed both the maternal lineages and paternal lineages of the ancient DNA. From the mitochondrial DNA, six haplotypes were identified as three haplogroups: C, D4 and M10. The haplotype-sharing populations and phylogenetic analyses revealed that these individuals were closely associated with the ancient Xiongnu and modern northern Asians. Single-nucleotide polymorphism analysis of Y chromosomes from four male samples that were typed as haplogroup Q indicated that these people had originated in Siberia. These results show that these ancient people from Pengyang present a close genetic affinity to nomadic people, indicating that northern nomads had reached the Central Plain area of China nearly 2500 years ago.}, }
@article {pmid20159872, year = {2010}, author = {Hawass, Z and Gad, YZ and Ismail, S and Khairat, R and Fathalla, D and Hasan, N and Ahmed, A and Elleithy, H and Ball, M and Gaballah, F and Wasef, S and Fateen, M and Amer, H and Gostner, P and Selim, A and Zink, A and Pusch, CM}, title = {Ancestry and pathology in King Tutankhamun's family.}, journal = {JAMA}, volume = {303}, number = {7}, pages = {638-647}, doi = {10.1001/jama.2010.121}, pmid = {20159872}, issn = {1538-3598}, mesh = {Cause of Death ; Clubfoot ; Consanguinity ; *DNA Fingerprinting ; Egypt, Ancient ; Female ; History, Ancient ; Humans ; Malaria, Falciparum/genetics/*pathology ; Male ; Microsatellite Repeats ; Mummies/*pathology ; Osteonecrosis/*pathology ; Pedigree ; }, abstract = {CONTEXT: The New Kingdom in ancient Egypt, comprising the 18th, 19th, and 20th dynasties, spanned the mid-16th to the early 11th centuries bc. The late 18th dynasty, which included the reigns of pharaohs Akhenaten and Tutankhamun, was an extraordinary time. The identification of a number of royal mummies from this era, the exact relationships between some members of the royal family, and possible illnesses and causes of death have been matters of debate.<br><br>OBJECTIVES: To introduce a new approach to molecular and medical Egyptology, to determine familial relationships among 11 royal mummies of the New Kingdom, and to search for pathological features attributable to possible murder, consanguinity, inherited disorders, and infectious diseases.<br><br>DESIGN: From September 2007 to October 2009, royal mummies underwent detailed anthropological, radiological, and genetic studies as part of the King Tutankhamun Family Project. Mummies distinct from Tutankhamun's immediate lineage served as the genetic and morphological reference. To authenticate DNA results, analytical steps were repeated and independently replicated in a second ancient DNA laboratory staffed by a separate group of personnel. Eleven royal mummies dating from circa 1410-1324 bc and suspected of being kindred of Tutankhamun and 5 royal mummies dating to an earlier period, circa 1550-1479 bc, were examined.<br><br>MAIN OUTCOME MEASURES: Microsatellite-based haplotypes in the mummies, generational segregation of alleles within possible pedigree variants, and correlation of identified diseases with individual age, archeological evidence, and the written historical record.<br><br>RESULTS: Genetic fingerprinting allowed the construction of a 5-generation pedigree of Tutankhamun's immediate lineage. The KV55 mummy and KV35YL were identified as the parents of Tutankhamun. No signs of gynecomastia and craniosynostoses (eg, Antley-Bixler syndrome) or Marfan syndrome were found, but an accumulation of malformations in Tutankhamun's family was evident. Several pathologies including K&#xf6;hler disease II were diagnosed in Tutankhamun; none alone would have caused death. Genetic testing for STEVOR, AMA1, or MSP1 genes specific for Plasmodium falciparum revealed indications of malaria tropica in 4 mummies, including Tutankhamun's. These results suggest avascular bone necrosis in conjunction with the malarial infection as the most likely cause of death in Tutankhamun. Walking impairment and malarial disease sustained by Tutankhamun is supported by the discovery of canes and an afterlife pharmacy in his tomb.<br><br>CONCLUSION: Using a multidisciplinary scientific approach, we showed the feasibility of gathering data on Pharaonic kinship and diseases and speculated about individual causes of death.}, }
@article {pmid20140213, year = {2010}, author = {Li, G and Ma, J and Zhang, L}, title = {Greedy selection of species for ancestral state reconstruction on phylogenies: elimination is better than insertion.}, journal = {PloS one}, volume = {5}, number = {2}, pages = {e8985}, pmid = {20140213}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; *Evolution, Molecular ; Genome/genetics ; Humans ; Mammals/classification/*genetics ; *Models, Genetic ; Mutagenesis, Insertional ; *Phylogeny ; Sequence Deletion ; Species Specificity ; }, abstract = {Accurate reconstruction of ancestral character states on a phylogeny is crucial in many genomics studies. We study how to select species to achieve the best reconstruction of ancestral character states on a phylogeny. We first show that the marginal maximum likelihood has the monotonicity property that more taxa give better reconstruction, but the Fitch method does not have it even on an ultrametric phylogeny. We further validate a greedy approach for species selection using simulation. The validation tests indicate that backward greedy selection outperforms forward greedy selection. In addition, by applying our selection strategy, we obtain a set of the ten most informative species for the reconstruction of the genomic sequence of the so-called boreoeutherian ancestor of placental mammals. This study has broad relevance in comparative genomics and paleogenomics since limited research resources do not allow researchers to sequence the large number of descendant species required to reconstruct an ancestral sequence.}, }
@article {pmid20100333, year = {2010}, author = {Crubézy, E and Amory, S and Keyser, C and Bouakaze, C and Bodner, M and Gibert, M and Röck, A and Parson, W and Alexeev, A and Ludes, B}, title = {Human evolution in Siberia: from frozen bodies to ancient DNA.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {25}, pmid = {20100333}, issn = {1471-2148}, support = {L 397/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Chromosomes, Human, Y/genetics ; DNA/genetics ; DNA, Mitochondrial/genetics ; Female ; *Genetics, Population ; Humans ; Male ; Siberia ; }, abstract = {BACKGROUND: The Yakuts contrast strikingly with other populations from Siberia due to their cattle- and horse-breeding economy as well as their Turkic language. On the basis of ethnological and linguistic criteria as well as population genetic studies, it has been assumed that they originated from South Siberian populations. However, many questions regarding the origins of this intriguing population still need to be clarified (e.g. the precise origin of paternal lineages and the admixture rate with indigenous populations). This study attempts to better understand the origins of the Yakuts by performing genetic analyses on 58 mummified frozen bodies dated from the 15th to the 19th century, excavated from Yakutia (Eastern Siberia).<br><br>RESULTS: High quality data were obtained for the autosomal STRs, Y-chromosomal STRs and SNPs and mtDNA due to exceptional sample preservation. A comparison with the same markers on seven museum specimens excavated 3 to 15 years ago showed significant differences in DNA quantity and quality. Direct access to ancient genetic data from these molecular markers combined with the archaeological evidence, demographical studies and comparisons with 166 contemporary individuals from the same location as the frozen bodies helped us to clarify the microevolution of this intriguing population.<br><br>CONCLUSION: We were able to trace the origins of the male lineages to a small group of horse-riders from the Cis-Ba&#xef;kal area. Furthermore, mtDNA data showed that intermarriages between the first settlers with Evenks women led to the establishment of genetic characteristics during the 15th century that are still observed today.}, }
@article {pmid20080189, year = {2010}, author = {Papageorgopoulou, C and Rentsch, K and Raghavan, M and Hofmann, MI and Colacicco, G and Gallien, V and Bianucci, R and Rühli, F}, title = {Preservation of cell structures in a medieval infant brain: a paleohistological, paleogenetic, radiological and physico-chemical study.}, journal = {NeuroImage}, volume = {50}, number = {3}, pages = {893-901}, doi = {10.1016/j.neuroimage.2010.01.029}, pmid = {20080189}, issn = {1095-9572}, mesh = {Brain/diagnostic imaging/*pathology ; Brain Chemistry ; Cerebral Hemorrhage/history/pathology ; DNA/analysis ; Fatty Acids/analysis ; France ; Gas Chromatography-Mass Spectrometry ; History, Medieval ; Humans ; Infant ; Magnetic Resonance Imaging ; Neurons/pathology ; Organ Size ; Paleopathology ; Tomography, X-Ray Computed ; }, abstract = {Cerebral tissues from archaeological human remains are extremely rare findings. Hereby, we report a multidisciplinary study of a unique case of a left cerebral hemisphere from a 13th century AD child, found in north-western France. The cerebral tissue-reduced by ca. 80% of its original weight-had been fixed in formalin since its discovery. However, it fully retained its gross anatomical characteristics such as sulci, and gyri; the frontal, temporal and occipital lobe as well as grey and white matter could be readily recognised. Neuronal remains near the hippocampus area and Nissl bodies from the motor cortex area were observed (Nissl, Klüver-Barrera staining). Also, computed tomography (CT) and magnetic resonance imaging (T1, proton density, ultra short echo time sequences) were feasible. They produced high quality morpho-diagnostic images. Both histological and radiological examinations could not confirm the pathologist's previously suggested diagnosis of cerebral haemorrhage as the cause of death. Reproducible cloned mtDNA sequences were recovered from the skeleton but not from the brain itself. This was most likely due to the combined effect of formaldehyde driven DNA-DNA and/or DNA-protein cross-linking, plus hydrolytic fragmentation of the DNA. The chemical profile of the brain tissue, from gas-chromatography/mass-spectroscopy analysis, suggested adipocerous formation as the main aetiology of the mummification process. The hereby presented child brain is a unique paleo-case of well-preserved neuronal cellular tissue, which is a conditio sine qua non for any subsequent study addressing wider perspectives in neuroscience research, such as the evolution of brain morphology and pathology.}, }
@article {pmid20072618, year = {2010}, author = {Olivieri, C and Ermini, L and Rizzi, E and Corti, G and Bonnal, R and Luciani, S and Marota, I and De Bellis, G and Rollo, F}, title = {Characterization of nucleotide misincorporation patterns in the iceman's mitochondrial DNA.}, journal = {PloS one}, volume = {5}, number = {1}, pages = {e8629}, pmid = {20072618}, issn = {1932-6203}, mesh = {DNA, Mitochondrial/*genetics ; *Fossils ; *Freezing ; Humans ; Nucleotides/*metabolism ; *Paleontology ; }, abstract = {BACKGROUND: The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation ("miscoding lesions") has been the object of extensive investigations.<br><br>To improve our knowledge regarding the nature and incidence of ancient DNA nucleotide misincorporations, we have utilized 6,859 (629,975 bp) mitochondrial (mt) DNA sequences obtained from the 5,350-5,100-years-old, freeze-desiccated human mummy popularly known as the Tyrolean Iceman or Otzi. To generate the sequences, we have applied a mixed PCR/pyrosequencing procedure allowing one to obtain a particularly high sequence coverage. As a control, we have produced further 8,982 (805,155 bp) mtDNA sequences from a contemporary specimen using the same system and starting from the same template copy number of the ancient sample. From the analysis of the nucleotide misincorporation rate in ancient, modern, and putative contaminant sequences, we observed that the rate of misincorporation is significantly lower in modern and putative contaminant sequence datasets than in ancient sequences. In contrast, type 2 transitions represent the vast majority (85%) of the observed nucleotide misincorporations in ancient sequences.<br><br>CONCLUSIONS/SIGNIFICANCE: This study provides a further contribution to the knowledge of nucleotide misincorporation patterns in DNA sequences obtained from freeze-preserved archeological specimens. In the Iceman system, ancient sequences can be clearly distinguished from contaminants on the basis of nucleotide misincorporation rates. This observation confirms a previous identification of the ancient mummy sequences made on a purely phylogenetical basis. The present investigation provides further indication that the majority of ancient DNA damage is reflected by type 2 (cytosine-->thymine/guanine-->adenine) transitions and that type 1 transitions are essentially PCR artifacts.}, }
@article {pmid20059556, year = {2010}, author = {Panieri, G and Lugli, S and Manzi, V and Roveri, M and Schreiber, BC and Palinska, KA}, title = {Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene, Italy.}, journal = {Geobiology}, volume = {8}, number = {2}, pages = {101-111}, doi = {10.1111/j.1472-4669.2009.00230.x}, pmid = {20059556}, issn = {1472-4669}, mesh = {*Calcium Sulfate/chemistry ; Crystallization ; Cyanobacteria/*classification/genetics ; DNA, Bacterial/analysis/isolation &amp; purification ; Evolution, Molecular ; *Fossils ; *Genes, rRNA ; Geologic Sediments/microbiology ; Italy ; Microscopy, Electron, Scanning ; *Paleontology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Sodium Selenite ; }, abstract = {Earth scientists have searched for signs of microscopic life in ancient samples of permafrost, ice, deep-sea sediments, amber, salt and chert. Until now, evidence of cyanobacteria has not been reported in any studies of ancient DNA older than a few thousand years. Here, we investigate morphologically, biochemically and genetically primary evaporites deposited in situ during the late Miocene (Messinian) Salinity Crisis from the north-eastern Apennines of Italy. The evaporites contain fossilized bacterial structures having identical morphological forms as modern microbes. We successfully extracted and amplified genetic material belonging to ancient cyanobacteria from gypsum crystals dating back to 5.910-5.816 Ma, when the Mediterranean became a giant hypersaline brine pool. This finding represents the oldest ancient cyanobacterial DNA to date. Our clone library and its phylogenetic comparison with present cyanobacterial populations point to a marine origin for the depositional basin. This investigation opens the possibility of including fossil cyanobacterial DNA into the palaeo-reconstruction of various environments and could also be used to quantify the ecological importance of cyanobacteria through geological time. These genetic markers serve as biosignatures providing important clues about ancient life and begin a new discussion concerning the debate on the origin of late Miocene evaporites in the Mediterranean.}, }
@article {pmid20045327, year = {2010}, author = {Krause, J and Briggs, AW and Kircher, M and Maricic, T and Zwyns, N and Derevianko, A and Pääbo, S}, title = {A complete mtDNA genome of an early modern human from Kostenki, Russia.}, journal = {Current biology : CB}, volume = {20}, number = {3}, pages = {231-236}, doi = {10.1016/j.cub.2009.11.068}, pmid = {20045327}, issn = {1879-0445}, mesh = {DNA, Mitochondrial/*genetics/*history/isolation &amp; purification ; Evolution, Molecular ; Fossils ; *Genome, Human ; *Genome, Mitochondrial ; History, Ancient ; Humans ; Polymerase Chain Reaction ; Russia ; }, abstract = {The recovery of DNA sequences from early modern humans (EMHs) could shed light on their interactions with archaic groups such as Neandertals and their relationships to current human populations. However, such experiments are highly problematic because present-day human DNA frequently contaminates bones [1, 2]. For example, in a recent study of mitochondrial (mt) DNA from Neolithic European skeletons, sequence variants were only taken as authentic if they were absent or rare in the present population, whereas others had to be discounted as possible contamination [3, 4]. This limits analysis to EMH individuals carrying rare sequences and thus yields a biased view of the ancient gene pool. Other approaches of identifying contaminating DNA, such as genotyping all individuals who have come into contact with a sample, restrict analyses to specimens where this is possible [5, 6] and do not exclude all possible sources of contamination. By studying mtDNA in Neandertal remains, where contamination and endogenous DNA can be distinguished by sequence, we show that fragmentation patterns and nucleotide misincorporations can be used to gauge authenticity of ancient DNA sequences. We use these features to determine a complete mtDNA sequence from a approximately 30,000-year-old EMH from the Kostenki 14 site in Russia.}, }
@article {pmid24710043, year = {2010}, author = {Knapp, M and Hofreiter, M}, title = {Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives.}, journal = {Genes}, volume = {1}, number = {2}, pages = {227-243}, pmid = {24710043}, issn = {2073-4425}, abstract = {The invention of next-generation-sequencing has revolutionized almost all fields of genetics, but few have profited from it as much as the field of ancient DNA research. From its beginnings as an interesting but rather marginal discipline, ancient DNA research is now on its way into the centre of evolutionary biology. In less than a year from its invention next-generation-sequencing had increased the amount of DNA sequence data available from extinct organisms by several orders of magnitude. Ancient DNA research is now not only adding a temporal aspect to evolutionary studies and allowing for the observation of evolution in real time, it also provides important data to help understand the origins of our own species. Here we review progress that has been made in next-generation-sequencing of ancient DNA over the past five years and evaluate sequencing strategies and future directions.}, }
@article {pmid20041847, year = {2009}, author = {King, C and Debruyne, R and Kuch, M and Schwarz, C and Poinar, H}, title = {A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts.}, journal = {BioTechniques}, volume = {47}, number = {5}, pages = {941-949}, doi = {10.2144/000113244}, pmid = {20041847}, issn = {1940-9818}, mesh = {*Algorithms ; Computer Simulation ; DNA/*genetics/*isolation &amp; purification ; *Models, Genetic ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; }, abstract = {Inhibition is problematic in many applications of PCR, particularly those involving degraded or low amounts of template DNA, when simply diluting the extract is undesirable. Two basic approaches to monitoring inhibition in such samples using real-time or quantitative PCR (qPCR) have been proposed. The first method analyzes the quantification cycle (Cq) deviation of a spiked internal positive control. The second method considers variations in reaction efficiency based on the slopes of individual amplification plots. In combining these methods, we observed increased Cq values together with reduced amplification efficiencies in some samples, as expected; however, deviations from this pattern in other samples support the use of both measurements. Repeat inhibition testing enables optimization of PCR facilitator combinations and sample dilution such that DNA yields and/or quantitative accuracy can be maximized in subsequent PCR runs. Although some trends were apparent within sample types, differences in inhibition levels, optimal reactions conditions, and expected recovery of DNA under these conditions suggest that all samples be routinely tested with this approach.}, }
@article {pmid20033124, year = {2010}, author = {Cappellini, E and Gilbert, MT and Geuna, F and Fiorentino, G and Hall, A and Thomas-Oates, J and Ashton, PD and Ashford, DA and Arthur, P and Campos, PF and Kool, J and Willerslev, E and Collins, MJ}, title = {A multidisciplinary study of archaeological grape seeds.}, journal = {Die Naturwissenschaften}, volume = {97}, number = {2}, pages = {205-217}, pmid = {20033124}, issn = {1432-1904}, mesh = {Agriculture/history/methods ; Archaeology ; Climate ; DNA, Plant/genetics/isolation &amp; purification ; History, Medieval ; Mediterranean Region ; Plant Proteins/genetics ; Polymerase Chain Reaction/methods ; Seeds/*physiology ; Sequence Homology, Nucleic Acid ; Vitis/classification/genetics/*physiology ; Water Supply ; Wine ; }, abstract = {We report here the first integrated investigation of both ancient DNA and proteins in archaeobotanical samples: medieval grape (Vitis vinifera L.) seeds, preserved by anoxic waterlogging, from an early medieval (seventh-eighth century A.D.) Byzantine rural settlement in the Salento area (Lecce, Italy) and a late (fourteenth-fifteenth century A.D.) medieval site in York (England). Pyrolysis gas chromatography mass spectrometry documented good carbohydrate preservation, whilst amino acid analysis revealed approximately 90% loss of the original protein content. In the York sample, mass spectrometry-based sequencing identified several degraded ancient peptides. Nuclear microsatellite locus (VVS2, VVMD5, VVMD7, ZAG62 and ZAG79) analysis permitted a tentative comparison of the genetic profiles of both the ancient samples with the modern varieties. The ability to recover microsatellite DNA has potential to improve biomolecular analysis on ancient grape seeds from archaeological contexts. Although the investigation of five microsatellite loci cannot assign the ancient samples to any geographic region or modern cultivar, the results allow speculation that the material from York was not grown locally, whilst the remains from Supersano could represent a trace of contacts with the eastern Mediterranean.}, }
@article {pmid20028723, year = {2010}, author = {Briggs, AW and Stenzel, U and Meyer, M and Krause, J and Kircher, M and Pääbo, S}, title = {Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA.}, journal = {Nucleic acids research}, volume = {38}, number = {6}, pages = {e87}, pmid = {20028723}, issn = {1362-4962}, mesh = {Animals ; CpG Islands ; Cytosine/chemistry ; *DNA Methylation ; DNA Repair ; Deamination ; Deoxyribonuclease (Pyrimidine Dimer) ; Hominidae/genetics ; Humans ; Mammoths/genetics ; Oligonucleotides/chemistry ; Sequence Analysis, DNA/*methods ; Uracil-DNA Glycosidase ; }, abstract = {DNA sequences determined from ancient organisms have high error rates, primarily due to uracil bases created by cytosine deamination. We use synthetic oligonucleotides, as well as DNA extracted from mammoth and Neandertal remains, to show that treatment with uracil-DNA-glycosylase and endonuclease VIII removes uracil residues from ancient DNA and repairs most of the resulting abasic sites, leaving undamaged parts of the DNA fragments intact. Neandertal DNA sequences determined with this protocol have greatly increased accuracy. In addition, our results demonstrate that Neandertal DNA retains in vivo patterns of CpG methylation, potentially allowing future studies of gene inactivation and imprinting in ancient organisms.}, }
@article {pmid20018740, year = {2009}, author = {Haile, J and Froese, DG and Macphee, RD and Roberts, RG and Arnold, LJ and Reyes, AV and Rasmussen, M and Nielsen, R and Brook, BW and Robinson, S and Demuro, M and Gilbert, MT and Munch, K and Austin, JJ and Cooper, A and Barnes, I and Möller, P and Willerslev, E}, title = {Ancient DNA reveals late survival of mammoth and horse in interior Alaska.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {52}, pages = {22352-22357}, pmid = {20018740}, issn = {1091-6490}, mesh = {Alaska ; Animals ; DNA/*genetics/*history/isolation &amp; purification ; *Extinction, Biological ; Fossils ; Geologic Sediments/chemistry ; History, Ancient ; Horses/*genetics ; Humans ; Mammoths/*genetics ; Models, Biological ; }, abstract = {Causes of late Quaternary extinctions of large mammals ("megafauna") continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000-13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinct are offset, however, by the improbability of finding and dating the remains of the last-surviving members of populations that were restricted in numbers or confined to refugia. Here we report an alternative approach to detect 'ghost ranges' of dwindling populations, based on recovery of ancient DNA from perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later than indicated from macrofossil surveys. These results contradict claims that Holocene survival of mammoths in Beringia was restricted to ecologically isolated high-latitude islands. More importantly, our finding that mammoth and horse overlapped with humans for several millennia in the region where people initially entered the Americas challenges theories that megafaunal extinction occurred within centuries of human arrival or were due to an extraterrestrial impact in the late Pleistocene.}, }
@article {pmid20007379, year = {2009}, author = {Orlando, L and Metcalf, JL and Alberdi, MT and Telles-Antunes, M and Bonjean, D and Otte, M and Martin, F and Eisenmann, V and Mashkour, M and Morello, F and Prado, JL and Salas-Gismondi, R and Shockey, BJ and Wrinn, PJ and Vasil'ev, SK and Ovodov, ND and Cherry, MI and Hopwood, B and Male, D and Austin, JJ and Hänni, C and Cooper, A}, title = {Revising the recent evolutionary history of equids using ancient DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {51}, pages = {21754-21759}, pmid = {20007379}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; DNA/*genetics ; Fossils ; Horses/classification/*genetics ; Molecular Sequence Data ; }, abstract = {The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.}, }
@article {pmid19966307, year = {2010}, author = {Tang, H and Bowers, JE and Wang, X and Paterson, AH}, title = {Angiosperm genome comparisons reveal early polyploidy in the monocot lineage.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {1}, pages = {472-477}, pmid = {19966307}, issn = {1091-6490}, mesh = {Algorithms ; Chromosomes, Plant ; DNA Repeat Expansion ; Edible Grain/*genetics ; Evolution, Molecular ; *Gene Duplication ; Genes, Plant ; *Genome, Plant ; Magnoliopsida/*genetics ; Models, Genetic ; Molecular Sequence Data ; Oryza/genetics ; Phylogeny ; *Polyploidy ; Sorghum/genetics ; Synteny ; }, abstract = {Although the timing and extent of a whole-genome duplication occurring in the common lineage of most modern cereals are clear, the existence or extent of more ancient genome duplications in cereals and perhaps other monocots has been hinted at, but remain unclear. We present evidence of additional duplication blocks of deeper hierarchy than the pancereal rho (rho) duplication, covering at least 20% of the cereal transcriptome. These more ancient duplicated regions, herein called sigma, are evident in both intragenomic and intergenomic analyses of rice and sorghum. Resolution of such ancient duplication events improves the understanding of the early evolutionary history of monocots and the origins and expansions of gene families. Comparisons of syntenic blocks reveal clear structural similarities in putatively homologous regions of monocots (rice) and eudicots (grapevine). Although the exact timing of the sigma-duplication(s) is unclear because of uncertainties of the molecular clock assumption, our data suggest that it occurred early in the monocot lineage after its divergence from the eudicot clade.}, }
@article {pmid19955482, year = {2010}, author = {Ghirotto, S and Mona, S and Benazzo, A and Paparazzo, F and Caramelli, D and Barbujani, G}, title = {Inferring genealogical processes from patterns of Bronze-Age and modern DNA variation in Sardinia.}, journal = {Molecular biology and evolution}, volume = {27}, number = {4}, pages = {875-886}, doi = {10.1093/molbev/msp292}, pmid = {19955482}, issn = {1537-1719}, mesh = {DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Gene Flow ; *Genealogy and Heraldry ; Humans ; Italy ; Population Density ; }, abstract = {The ancient inhabitants of a region are often regarded as ancestral, and hence genetically related, to the modern dwellers (for instance, in studies of admixture), but so far, this assumption has not been tested empirically using ancient DNA data. We studied mitochondrial DNA (mtDNA) variation in Sardinia, across a time span of 2,500 years, comparing 23 Bronze-Age (nuragic) mtDNA sequences with those of 254 modern individuals from two regions, Ogliastra (a likely genetic isolate) and Gallura, and considering the possible impact of gene flow from mainland Italy. To understand the genealogical relationships between past and present populations, we developed seven explicit demographic models; we tested whether these models can account for the levels and patterns of genetic diversity in the data and which one does it best. Extensive simulation based on a serial coalescent algorithm allowed us to compare the posterior probability of each model and estimate the relevant evolutionary (mutation and migration rates) and demographic (effective population sizes, times since population splits) parameters, by approximate Bayesian computations. We then validated the analyses by investigating how well parameters estimated from the simulated data can reproduce the observed data set. We show that a direct genealogical continuity between Bronze-Age Sardinians and the current people of Ogliastra, but not Gallura, has a much higher probability than any alternative scenarios and that genetic diversity in Gallura evolved largely independently, owing in part to gene flow from the mainland.}, }
@article {pmid19943892, year = {2010}, author = {Lira, J and Linderholm, A and Olaria, C and Brandström Durling, M and Gilbert, MT and Ellegren, H and Willerslev, E and Lidén, K and Arsuaga, JL and Götherström, A}, title = {Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses.}, journal = {Molecular ecology}, volume = {19}, number = {1}, pages = {64-78}, doi = {10.1111/j.1365-294X.2009.04430.x}, pmid = {19943892}, issn = {1365-294X}, mesh = {Animals ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Horses/*genetics ; *Phylogeny ; Population Density ; Sequence Alignment ; Sequence Analysis, DNA ; Spain ; }, abstract = {Multiple geographical regions have been proposed for the domestication of Equus caballus. It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern Iberian horses supports this suggestion. To test this hypothesis, we analysed mitochondrial DNA from 22 ancient Iberian horse remains belonging to the Neolithic, the Bronze Age and the Middle Ages, against previously published sequences. Only the medieval Iberian sequence appeared in the D1 group. Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other ancient domesticates using nonparametric bootstrapping analyses. We conclude that the excessive clustering of Bronze Age horses in the Lusitano group C, the observed nucleotide diversity and the local continuity from wild Neolithic Iberian to modern Iberian horses, could be explained by the use of local wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times.}, }
@article {pmid19943747, year = {2009}, author = {Chamberlain, A}, title = {Archaeological demography.}, journal = {Human biology}, volume = {81}, number = {2-3}, pages = {275-286}, doi = {10.3378/027.081.0309}, pmid = {19943747}, issn = {1534-6617}, mesh = {*Archaeology ; Demography ; Ecology ; Fertility ; Humans ; *Population Density ; Population Growth ; Time Factors ; }, abstract = {Archaeological demography investigates the structure and dynamics of past human populations using evidence from traces of human activities and remnants of material culture in the archaeological record. Research in this field is interdisciplinary, incorporating findings from anthropology, paleogenetics, and human ecology but with a remit that extends beyond the primarily biological focus of paleodemography. Important questions addressed by archaeological demography include the establishment of methods for inferring past population structure, the timing of the emergence of modern human demographic systems, the relative importance of attritional and catastrophic patterns of mortality, and the search for adaptive explanations for demographic transitions, colonization events, and population extinctions. Archaeological evidence, including the extent of settlements and site catchment areas as well as measures of the exploitation, consumption, and discard of materials and artifacts, have traditionally been used as proxies for estimating past population size and density. In recent years this evidence has been supplemented by increasingly large data sets compiled from radiocarbon dating programs. These data sets have been used to investigate demographic waves of advance during continental-scale periods of colonization and cultural change and to detect episodes of population decline, extinction, and hiatuses in settlement history. By considering studies of human genetic diversity that indicate temporary but drastic reductions in effective population size, I hypothesize that catastrophic mortality may have had an important role in long-term population processes and may have limited long-term rates of growth, particularly in prehistoric populations.}, }
@article {pmid19933156, year = {2010}, author = {Bemer, M and Gordon, J and Weterings, K and Angenent, GC}, title = {Divergence of recently duplicated M{gamma}-type MADS-box genes in Petunia.}, journal = {Molecular biology and evolution}, volume = {27}, number = {2}, pages = {481-495}, doi = {10.1093/molbev/msp279}, pmid = {19933156}, issn = {1537-1719}, mesh = {Blotting, Southern ; Chromosome Walking ; Evolution, Molecular ; Gene Duplication ; In Situ Hybridization ; Likelihood Functions ; MADS Domain Proteins/*chemistry/classification ; Petunia/*genetics ; Phylogeny ; Plant Proteins/classification/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {The MADS-box transcription factor family has expanded considerably in plants via gene and genome duplications and can be subdivided into type I and MIKC-type genes. The two gene classes show a different evolutionary history. Whereas the MIKC-type genes originated during ancient genome duplications, as well as during more recent events, the type I loci appear to experience high turnover with many recent duplications. This different mode of origin also suggests a different fate for the type I duplicates, which are thought to have a higher chance to become silenced or lost from the genome. To get more insight into the evolution of the type I MADS-box genes, we isolated nine type I genes from Petunia, which belong to the Mgamma subclass, and investigated the divergence of their coding and regulatory regions. The isolated genes could be subdivided into two categories: two genes were highly similar to Arabidopsis Mgamma-type genes, whereas the other seven genes showed less similarity to Arabidopsis genes and originated more recently. Two of the recently duplicated genes were found to contain deleterious mutations in their coding regions, and expression analysis revealed that a third paralog was silenced by mutations in its regulatory region. However, in addition to the three genes that were subjected to nonfunctionalization, we also found evidence for neofunctionalization of one of the Petunia Mgamma-type genes. Our study shows a rapid divergence of recently duplicated Mgamma-type MADS-box genes and suggests that redundancy among type I paralogs may be less common than expected.}, }
@article {pmid19918991, year = {2010}, author = {Carnese, FR and Mendisco, F and Keyser, C and Dejean, CB and Dugoujon, JM and Bravi, CM and Ludes, B and Crubézy, E}, title = {Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta, Argentina).}, journal = {American journal of physical anthropology}, volume = {141}, number = {3}, pages = {452-462}, doi = {10.1002/ajpa.21165}, pmid = {19918991}, issn = {1096-8644}, mesh = {Argentina ; Burial/methods ; Chromosomes, Human, Y/*genetics ; DNA/*genetics/isolation &amp; purification ; DNA, Mitochondrial/genetics ; Gene Expression Profiling/methods ; Genetic Markers ; Genetic Variation ; Genetics, Medical/methods ; Humans ; Male ; Microsatellite Repeats/genetics ; Museums ; Paleontology/*methods ; Polymerase Chain Reaction/methods ; South America ; }, abstract = {Ancient DNA recovered from 21 individuals excavated from burial sites in the Pampa Grande (PG) region (Salta province) of North-Western Argentina (NWA) was analyzed using various genetic markers (mitochondrial DNA, autosomal STRs, and Y chromosomal STRs). The results were compared to ancient and modern DNA from various populations in the Andean and North Argentinean regions, with the aim of establishing their relationships with PG. The mitochondrial haplogroup frequencies described (11% A, 47% B, and 42% D) presented values comparable to those found for the ancient Andean populations from Peru and San Pedro de Atacama. On the other hand, mitochondrial and Y chromosomal haplotypes were specific to PG, as they did not match any other of the South American populations studied. The described genetic diversity indicates homogeneity in the genetic structure of the ancient Andean populations, which was probably facilitated by the intense exchange network in the Andean zone, in particular among Tiwanaku, San Pedro de Atacama, and NWA. The discovery of haplotypes unique to PG could be due to a loss of genetic diversity caused by recent events affecting the autochthonous populations (establishment of the Inca Empire in the region, colonization by the Europeans).}, }
@article {pmid19864251, year = {2010}, author = {Brotherton, P and Sanchez, JJ and Cooper, A and Endicott, P}, title = {Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX.}, journal = {Nucleic acids research}, volume = {38}, number = {2}, pages = {e7}, pmid = {19864251}, issn = {1362-4962}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Base Sequence ; Genotype ; Hominidae/*genetics ; Humans ; Molecular Sequence Data ; Museums ; Nucleic Acid Amplification Techniques/*methods ; Polymerase Chain Reaction ; *Polymorphism, Single Nucleotide ; Reproducibility of Results ; *Sequence Analysis, DNA ; }, abstract = {The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples, the pervasive presence of highly PCR-amplifiable human DNA contaminants in the vast majority of samples can lead to the creation of recombinant hybrids and other non-authentic artefacts. The resulting PCR-generated sequences can then be difficult, if not impossible, to authenticate. In contrast, single primer extension (SPEX)-based approaches can genotype single nucleotide polymorphisms from ancient fragments of DNA as accurately as modern DNA. A single SPEX-type assay can amplify just one of the duplex DNA strands at target loci and generate a multi-fold depth-of-coverage, with non-authentic recombinant hybrids reduced to undetectable levels. Crucially, SPEX-type approaches can preferentially access genetic information from damaged and degraded endogenous ancient DNA templates over modern human DNA contaminants. The development of SPEX-type assays offers the potential for highly accurate, quantitative genotyping from ancient hominin samples.}, }
@article {pmid19847306, year = {2009}, author = {Watson, CL and Lockwood, DN}, title = {Single nucleotide polymorphism analysis of European archaeological M. leprae DNA.}, journal = {PloS one}, volume = {4}, number = {10}, pages = {e7547}, pmid = {19847306}, issn = {1932-6203}, mesh = {Archaeology/methods ; Bacterial Typing Techniques/methods ; Base Sequence ; DNA Fingerprinting ; DNA, Bacterial/*genetics ; Europe ; Genotype ; Humans ; Leprosy/*microbiology ; Molecular Sequence Data ; Mycobacterium leprae/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; *Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Leprosy was common in Europe eight to twelve centuries ago but molecular confirmation of this has been lacking. We have extracted M. leprae ancient DNA (aDNA) from medieval bones and single nucleotide polymorphism (SNP) typed the DNA, this provides insight into the pattern of leprosy transmission in Europe and may assist in the understanding of M. leprae evolution.<br><br>METHODS AND FINDINGS: Skeletons have been exhumed from 3 European countries (the United Kingdom, Denmark and Croatia) and are dated around the medieval period (476 to 1350 A.D.). we tested for the presence of 3 previously identified single nucleotide polymorphisms (SNPs) in 10 aDNA extractions. M. leprae aDNA was extracted from 6 of the 10 bone samples. SNP analysis of these 6 extractions were compared to previously analysed European SNP data using the same PCR assays and were found to be the same. Testing for the presence of SNPs in M. leprae DNA extracted from ancient bone samples is a novel approach to analysing European M. leprae DNA and the findings concur with the previously published data that European M. leprae strains fall in to one group (SNP group 3).<br><br>CONCLUSIONS: These findings support the suggestion that the M. leprae genome is extremely stable and show that archaeological M. leprae DNA can be analysed to gain detailed information about the genotypic make-up of European leprosy, which may assist in the understanding of leprosy transmission worldwide.}, }
@article {pmid19846765, year = {2009}, author = {Decker, JE and Pires, JC and Conant, GC and McKay, SD and Heaton, MP and Chen, K and Cooper, A and Vilkki, J and Seabury, CM and Caetano, AR and Johnson, GS and Brenneman, RA and Hanotte, O and Eggert, LS and Wiener, P and Kim, JJ and Kim, KS and Sonstegard, TS and Van Tassell, CP and Neibergs, HL and McEwan, JC and Brauning, R and Coutinho, LL and Babar, ME and Wilson, GA and McClure, MC and Rolf, MM and Kim, J and Schnabel, RD and Taylor, JF}, title = {Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {44}, pages = {18644-18649}, pmid = {19846765}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Breeding ; Cattle ; DNA/analysis/genetics ; *Extinction, Biological ; Fossils ; Genomics/*methods ; Genotype ; *Phylogeny ; Ruminants/*genetics ; }, abstract = {The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve, and 11 of the 15 possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used a high-throughput assay with 54,693 SNP loci developed for Bos taurus taurus to rapidly genotype 678 individuals representing 61 Pecoran species. We produced a highly resolved phylogeny for this diverse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a method to amplify and screen genomic information from extinct species, and place Bison priscus within the Bovidae. The quality of genotype calls and the placement of samples within a well-supported phylogeny may provide an important test for validating the fidelity and integrity of ancient samples. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.}, }
@article {pmid19796837, year = {2009}, author = {Podlaha, O and Zhang, J}, title = {Processed pseudogenes: the 'fossilized footprints' of past gene expression.}, journal = {Trends in genetics : TIG}, volume = {25}, number = {10}, pages = {429-434}, pmid = {19796837}, issn = {0168-9525}, support = {R01 GM067030/GM/NIGMS NIH HHS/United States ; R01 GM067030-06A2/GM/NIGMS NIH HHS/United States ; R01 GM080285/GM/NIGMS NIH HHS/United States ; R01 GM080285-03/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Embryo, Mammalian/metabolism ; Evolution, Molecular ; Fossils ; Gene Expression Profiling/*methods ; Germ Cells/metabolism ; Humans ; Mice ; Pseudogenes/*genetics ; Time Factors ; }, abstract = {Although our knowledge of the genes and genomes of extinct organisms is improving as a result of progress in sequencing ancient DNA, the transcriptomes of extinct organisms remain inaccessible, owing to the rapid degradation of messenger RNA after death. We provide empirical evidence that gene expression levels in the reproductive tissues of mice and during early mouse development correlate highly with the rate of inherited retroposition: the source of processed pseudogenes in the genome. Thus, processed pseudogenes might serve as fossilized footprints of the expression of their parent genes, shedding light on ancient transcriptomes that could provide significant insights into the evolution of gene expression.}, }
@article {pmid19793751, year = {2010}, author = {Donoghue, HD and Lee, OY and Minnikin, DE and Besra, GS and Taylor, JH and Spigelman, M}, title = {Tuberculosis in Dr Granville's mummy: a molecular re-examination of the earliest known Egyptian mummy to be scientifically examined and given a medical diagnosis.}, journal = {Proceedings. Biological sciences}, volume = {277}, number = {1678}, pages = {51-56}, pmid = {19793751}, issn = {1471-2954}, support = {G0802079/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {DNA, Bacterial/chemistry/genetics ; Egypt ; Female ; Femur/microbiology ; Humans ; Lung/microbiology ; Middle Aged ; Mummies/*microbiology ; Mycobacterium tuberculosis/genetics/*isolation &amp; purification ; Mycolic Acids/analysis ; Polymerase Chain Reaction ; Tuberculosis, Pulmonary/*diagnosis ; }, abstract = {'Dr Granville's mummy' was described to the Royal Society of London in 1825 and was the first ancient Egyptian mummy to be subjected to a scientific autopsy. The remains are those of a woman, Irtyersenu, aged about 50, from the necropolis of Thebes and dated to about 600 BC. Augustus Bozzi Granville (1783-1872), an eminent physician and obstetrician, described many organs still in situ and attributed the cause of death to a tumour of the ovary. However, subsequent histological investigations indicate that the tumour is a benign cystadenoma. Histology of the lungs demonstrated a potentially fatal pulmonary exudate and earlier studies attempted to associate this with particular disease conditions. Palaeopathology and ancient DNA analyses show that tuberculosis was widespread in ancient Egypt, so a systematic search for tuberculosis was made, using specific DNA and lipid biomarker analyses. Clear evidence for Mycobacterium tuberculosis complex DNA was obtained in lung tissue and gall bladder samples, based on nested PCR of the IS6110 locus. Lung and femurs were positive for specific M. tuberculosis complex cell-wall mycolic acids, demonstrated by high-performance liquid chromatography of pyrenebutyric acid-pentafluorobenzyl mycolates. Therefore, tuberculosis is likely to have been the major cause of death of Irtyersenu.}, }
@article {pmid22649615, year = {2009}, author = {Grigorenko, AP and Borinskaya, SA and Yankovsky, NK and Rogaev, EI}, title = {Achievements and peculiarities in studies of ancient DNA and DNA from complicated forensic specimens.}, journal = {Acta naturae}, volume = {1}, number = {3}, pages = {58-69}, pmid = {22649615}, issn = {2075-8251}, abstract = {Studies of ancient DNA specimens started 25 years ago. At that time short mitochondrial DNA (mtDNA) fragments were the main targets in ancient DNA studies. The last three years were especially productive in the development of new methods of DNA purification and analysis. Complete mtDNA molecules and relatively large fragments of nuclear DNA are the targets of ancient DNA studies today. Ancient DNA studies allowed us to study organisms that went extinct more than ten thousand years ago, to reconstruct their phenotypic traits and evolution. Ancient DNA analyses can help understand the development of ancient human populations and how they migrated. A new evolutionary hypothesis and reconstruction of the biota history have been re-created from recent ancient DNA data. Some peculiarities and problems specific to the study of ancient DNA were revealed, such as very limited amounts of DNA available for study, the short length of the DNA fragments, breaks and chemical modifications in DNA molecules that result in "postmortem" mutations or complete blockage of DNA replication in vitro. The same specific features of DNA analysis were revealed for specimens from complicated forensic cases that result in the lack of experimental data or interpretation problems.. Here, we list the specific features of ancient DNA methodology and describe some achievements in fundamental and applied research of ancient DNA, including our own work in the field.}, }
@article {pmid19788938, year = {2010}, author = {Ho, SY and Gilbert, MT}, title = {Ancient mitogenomics.}, journal = {Mitochondrion}, volume = {10}, number = {1}, pages = {1-11}, doi = {10.1016/j.mito.2009.09.005}, pmid = {19788938}, issn = {1872-8278}, mesh = {Animals ; DNA, Mitochondrial/*analysis/genetics ; *Fossils ; Genomics/*methods ; Humans ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field.}, }
@article {pmid19781941, year = {2009}, author = {Malmström, H and Gilbert, MT and Thomas, MG and Brandström, M and Storå, J and Molnar, P and Andersen, PK and Bendixen, C and Holmlund, G and Götherström, A and Willerslev, E}, title = {Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians.}, journal = {Current biology : CB}, volume = {19}, number = {20}, pages = {1758-1762}, doi = {10.1016/j.cub.2009.09.017}, pmid = {19781941}, issn = {1879-0445}, mesh = {Agriculture/*history ; Anthropology, Physical ; DNA, Mitochondrial/chemistry ; Emigration and Immigration/*history ; Genetic Variation ; History, Ancient ; Humans ; Scandinavian and Nordic Countries ; }, abstract = {The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1-3]. Of particular interest is whether population replacement or cultural exchange was responsible [3-5]. Scandinavia holds a unique place in this debate, for it maintained one of the last major hunter-gatherer complexes in Neolithic Europe, the Pitted Ware culture [6]. Intriguingly, these late hunter-gatherers existed in parallel to early farmers for more than a millennium before they vanished some 4,000 years ago [7, 8]. The prolonged coexistence of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.}, }
@article {pmid19781880, year = {2010}, author = {Farrugia, A and Keyser, C and Ludes, B}, title = {Efficiency evaluation of a DNA extraction and purification protocol on archival formalin-fixed and paraffin-embedded tissue.}, journal = {Forensic science international}, volume = {194}, number = {1-3}, pages = {e25-8}, doi = {10.1016/j.forsciint.2009.09.004}, pmid = {19781880}, issn = {1872-6283}, mesh = {Chloroform ; DNA/*isolation &amp; purification ; DNA Degradation, Necrotic ; DNA Fingerprinting ; *Fixatives ; Forensic Genetics/methods ; *Formaldehyde ; Humans ; Liver/pathology ; Myocardium/pathology ; *Paraffin Embedding ; Phenol ; Polymerase Chain Reaction ; Solvents ; Tandem Repeat Sequences ; }, abstract = {Formalin-fixed and paraffin-embedded tissue (FF-PET) is an invaluable resource for retrospective molecular genetic studies, but the extraction of high-quality genomic DNA from FF-PET is still a problematic issue. Despite the range of DNA extraction methods currently in use, the association of phenol-chloroform extraction and silica-based purification protocols, reported in ancient DNA studies on archaeological bones, has, to our knowledge, not been used for DNA extraction from FF-PET yet. The present study compared the efficiency of three DNA extraction and purification protocols from two different FF-PET substrates, heart and liver, by using quantitative PCR and multiplex amplification. We showed that the method, using phenol-chloroform and the QIAamp DNA mini Kit (Qiagen), was the most effective DNA extraction and purification method and that the DNA quantity extracted from liver is statistically more important than that extracted from heart. Autosomal STR typing by multiplex amplifications gave partial allelic profiles with only small size products (less than 300 bases) amplified, suggesting that DNA extracted from FF-PET was degraded. In conclusion, the protocol presented here, previously described in studies on ancient bones, should find application in different molecular studies involving FF-PET material.}, }
@article {pmid19747392, year = {2009}, author = {Roca, AL and Ishida, Y and Nikolaidis, N and Kolokotronis, SO and Fratpietro, S and Stewardson, K and Hensley, S and Tisdale, M and Boeskorov, G and Greenwood, AD}, title = {Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {232}, pmid = {19747392}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Elephants/*genetics ; *Extinction, Biological ; Fibroblast Growth Factor 5/*genetics ; Fossils ; *Genetic Variation ; *Hair ; Humans ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Like humans, the living elephants are unusual among mammals in being sparsely covered with hair. Relative to extant elephants, the extinct woolly mammoth, Mammuthus primigenius, had a dense hair cover and extremely long hair, which likely were adaptations to its subarctic habitat. The fibroblast growth factor 5 (FGF5) gene affects hair length in a diverse set of mammalian species. Mutations in FGF5 lead to recessive long hair phenotypes in mice, dogs, and cats; and the gene has been implicated in hair length variation in rabbits. Thus, FGF5 represents a leading candidate gene for the phenotypic differences in hair length notable between extant elephants and the woolly mammoth. We therefore sequenced the three exons (except for the 3' UTR) and a portion of the promoter of FGF5 from the living elephantid species (Asian, African savanna and African forest elephants) and, using protocols for ancient DNA, from a woolly mammoth.<br><br>RESULTS: Between the extant elephants and the mammoth, two single base substitutions were observed in FGF5, neither of which alters the amino acid sequence. Modeling of the protein structure suggests that the elephantid proteins fold similarly to the human FGF5 protein. Bioinformatics analyses and DNA sequencing of another locus that has been implicated in hair cover in humans, type I hair keratin pseudogene (KRTHAP1), also yielded negative results. Interestingly, KRTHAP1 is a pseudogene in elephantids as in humans (although fully functional in non-human primates).<br><br>CONCLUSION: The data suggest that the coding sequence of the FGF5 gene is not the critical determinant of hair length differences among elephantids. The results are discussed in the context of hairlessness among mammals and in terms of the potential impact of large body size, subarctic conditions, and an aquatic ancestor on hair cover in the Proboscidea.}, }
@article {pmid19744143, year = {2009}, author = {Lei, CZ and Su, R and Bower, MA and Edwards, CJ and Wang, XB and Weining, S and Liu, L and Xie, WM and Li, F and Liu, RY and Zhang, YS and Zhang, CM and Chen, H}, title = {Multiple maternal origins of native modern and ancient horse populations in China.}, journal = {Animal genetics}, volume = {40}, number = {6}, pages = {933-944}, doi = {10.1111/j.1365-2052.2009.01950.x}, pmid = {19744143}, issn = {1365-2052}, mesh = {Animals ; China ; DNA, Mitochondrial/analysis ; Horses/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A-G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China (c. 4000-2000a bp) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A-G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.}, }
@article {pmid19735451, year = {2009}, author = {Navascués, M and Emerson, BC}, title = {Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods.}, journal = {Molecular ecology}, volume = {18}, number = {21}, pages = {4390-4397}, doi = {10.1111/j.1365-294X.2009.04333.x}, pmid = {19735451}, issn = {1365-294X}, mesh = {Bayes Theorem ; Computer Simulation ; *Evolution, Molecular ; Gene Flow ; *Genetics, Population ; Markov Chains ; *Models, Genetic ; Monte Carlo Method ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The increasing ability to extract and sequence DNA from noncontemporaneous tissue offers biologists the opportunity to analyse ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. In this study, we provide a critical assessment of Bayesian Markov chain Monte Carlo (MCMC) analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates because of model misspecification when the data come from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However, when model misspecification is only mild, then the 95% highest posterior density intervals provide adequate frequentist coverage of the true rates.}, }
@article {pmid19729623, year = {2009}, author = {Balter, M}, title = {Archaeology. Ancient DNA says Europe's first farmers came from afar.}, journal = {Science (New York, N.Y.)}, volume = {325}, number = {5945}, pages = {1189}, doi = {10.1126/science.325_1189}, pmid = {19729623}, issn = {1095-9203}, mesh = {Agriculture/*history ; Archaeology ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Europe ; History, Ancient ; Humans ; Sequence Analysis, DNA ; Skull/*chemistry ; }, }
@article {pmid19720678, year = {2009}, author = {Salse, J and Abrouk, M and Murat, F and Quraishi, UM and Feuillet, C}, title = {Improved criteria and comparative genomics tool provide new insights into grass paleogenomics.}, journal = {Briefings in bioinformatics}, volume = {10}, number = {6}, pages = {619-630}, doi = {10.1093/bib/bbp037}, pmid = {19720678}, issn = {1477-4054}, mesh = {*Biological Evolution ; Chromosome Mapping/*trends ; *Evolution, Molecular ; Genome, Plant/*genetics ; Genomics/*methods ; Paleontology/methods ; Poaceae/*genetics ; Quantitative Trait Loci/*genetics ; }, abstract = {In the past decade, a number of bioinformatics tools have been developed to perform comparative genomics studies in plants and animals. However, most of the publicly available and user friendly tools lack common standards for the identification of robust orthologous relationships between genomes leading non-specialists to often over interpret the results of large scale comparative sequence analyses. Recently, we have established a number of improved parameters and tools to define significant relationships between genomes as a basis to develop paleogenomics studies in grasses. Here, we describe our approaches and propose the development of community-based standards that can be used in comparative genomic studies to (i) identify robust sets of orthologous gene pairs, (ii) derive complete sets of chromosome to chromosome relationships within and between genomes and (iii) model common paleo-ancestor genome structures. The rice and sorghum genome sequences are used to exemplify step-by-step a methodology that should allow users to perform accurate comparative genome analyses in their favourite species. Finally, we describe two applications for accurate gene annotation and synteny-based cloning of agronomically important traits.}, }
@article {pmid19714212, year = {2009}, author = {Bradley, RK and Holmes, I}, title = {Evolutionary triplet models of structured RNA.}, journal = {PLoS computational biology}, volume = {5}, number = {8}, pages = {e1000483}, pmid = {19714212}, issn = {1553-7358}, support = {R01 GM076705/GM/NIGMS NIH HHS/United States ; GM076705/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Base Sequence ; Computational Biology/*methods ; Computer Simulation ; Evolution, Molecular ; Likelihood Functions ; Markov Chains ; Models, Statistical ; Phylogeny ; RNA/*chemistry ; Sequence Analysis, RNA ; Software ; }, abstract = {The reconstruction and synthesis of ancestral RNAs is a feasible goal for paleogenetics. This will require new bioinformatics methods, including a robust statistical framework for reconstructing histories of substitutions, indels and structural changes. We describe a "transducer composition" algorithm for extending pairwise probabilistic models of RNA structural evolution to models of multiple sequences related by a phylogenetic tree. This algorithm draws on formal models of computational linguistics as well as the 1985 protosequence algorithm of David Sankoff. The output of the composition algorithm is a multiple-sequence stochastic context-free grammar. We describe dynamic programming algorithms, which are robust to null cycles and empty bifurcations, for parsing this grammar. Example applications include structural alignment of non-coding RNAs, propagation of structural information from an experimentally-characterized sequence to its homologs, and inference of the ancestral structure of a set of diverged RNAs. We implemented the above algorithms for a simple model of pairwise RNA structural evolution; in particular, the algorithms for maximum likelihood (ML) alignment of three known RNA structures and a known phylogeny and inference of the common ancestral structure. We compared this ML algorithm to a variety of related, but simpler, techniques, including ML alignment algorithms for simpler models that omitted various aspects of the full model and also a posterior-decoding alignment algorithm for one of the simpler models. In our tests, incorporation of basepair structure was the most important factor for accurate alignment inference; appropriate use of posterior-decoding was next; and fine details of the model were least important. Posterior-decoding heuristics can be substantially faster than exact phylogenetic inference, so this motivates the use of sum-over-pairs heuristics where possible (and approximate sum-over-pairs). For more exact probabilistic inference, we discuss the use of transducer composition for ML (or MCMC) inference on phylogenies, including possible ways to make the core operations tractable.}, }
@article {pmid19714206, year = {2009}, author = {Itan, Y and Powell, A and Beaumont, MA and Burger, J and Thomas, MG}, title = {The origins of lactase persistence in Europe.}, journal = {PLoS computational biology}, volume = {5}, number = {8}, pages = {e1000491}, pmid = {19714206}, issn = {1553-7358}, mesh = {Alleles ; Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Diet ; Europe ; Evolution, Molecular ; Gene Frequency ; Genetic Markers ; Geography ; Haplotypes ; Humans ; Lactase/*chemistry/genetics/physiology ; Lactose/metabolism ; *Polymorphism, Genetic ; Vitamin D/metabolism ; }, abstract = {Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (-13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the--13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and unlinked genetic markers in Europe and western Asia's geographic space. Using data on--13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the--13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe.}, }
@article {pmid19706486, year = {2009}, author = {Salse, J and Abrouk, M and Bolot, S and Guilhot, N and Courcelle, E and Faraut, T and Waugh, R and Close, TJ and Messing, J and Feuillet, C}, title = {Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {35}, pages = {14908-14913}, pmid = {19706486}, issn = {1091-6490}, mesh = {Animals ; *Chromosomes, Plant ; *Evolution, Molecular ; Flowers/genetics ; Genome, Plant ; Poaceae/*genetics ; Seeds/genetics ; Time Factors ; }, abstract = {Paleogenomics seeks to reconstruct ancestral genomes from the genes of today's species. The characterization of paleo-duplications represented by 11,737 orthologs and 4,382 paralogs identified in five species belonging to three of the agronomically most important subfamilies of grasses, that is, Ehrhartoideae (rice) Panicoideae (sorghum, maize), and Pooideae (wheat, barley), permitted us to propose a model for an ancestral genome with a minimal size of 33.6 Mb structured in five proto-chromosomes containing at least 9,138 predicted proto-genes. It appears that only four major evolutionary shuffling events (alpha, beta, gamma, and delta) explain the divergence of these five cereal genomes during their evolution from a common paleo-ancestor. Comparative analysis of ancestral gene function with rice as a reference indicated that five categories of genes were preferentially modified during evolution. Furthermore, alignments between the five grass proto-chromosomes and the recently identified seven eudicot proto-chromosomes indicated that additional very active episodes of genome rearrangements and gene mobility occurred during angiosperm evolution. If one compares the pace of primate evolution of 90 million years (233 species) to 60 million years of the Poaceae (10,000 species), change in chromosome structure through speciation has accelerated significantly in plants.}, }
@article {pmid19675005, year = {2010}, author = {Steeves, TE and Holdaway, RN and Hale, ML and McLay, E and McAllan, IA and Christian, M and Hauber, ME and Bunce, M}, title = {Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea.}, journal = {Biology letters}, volume = {6}, number = {1}, pages = {94-97}, pmid = {19675005}, issn = {1744-957X}, mesh = {Animals ; Base Sequence ; Birds/anatomy &amp; histology/*classification/*genetics ; Body Weights and Measures ; Bone and Bones/*anatomy &amp; histology ; DNA/*genetics ; *Fossils ; Haplotypes/genetics ; Molecular Sequence Data ; Pacific Islands ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Ancient DNA has revolutionized the way in which evolutionary biologists research both extinct and extant taxa, from the inference of evolutionary history to the resolution of taxonomy. Here, we present, to our knowledge, the first study to report the rediscovery of an 'extinct' avian taxon, the Tasman booby (Sula tasmani), using classical palaeontological data combined with ancient and modern DNA data. Contrary to earlier work, we show an overlap in size between fossil and modern birds in the North Tasman Sea (classified currently as S. tasmani and Sula dactylatra fullagari, respectively). In addition, we show that Holocene fossil birds have mitochondrial control region sequences that are identical to those found in modern birds. These results indicate that the Tasman booby is not an extinct taxon: S. dactylatra fullagari O'Brien &amp; Davies, 1990 is therefore a junior synonym of Sula tasmani van Tets, Meredith, Fullagar &amp; Davidson, 1988 and all North Tasman Sea boobies should be known as S. d. tasmani. In addition to reporting the rediscovery of an extinct avian taxon, our study highlights the need for researchers to be cognizant of multidisciplinary approaches to understanding taxonomy and past biodiversity.}, }
@article {pmid19661919, year = {2009}, author = {Green, RE and Briggs, AW and Krause, J and Prüfer, K and Burbano, HA and Siebauer, M and Lachmann, M and Pääbo, S}, title = {The Neandertal genome and ancient DNA authenticity.}, journal = {The EMBO journal}, volume = {28}, number = {17}, pages = {2494-2502}, pmid = {19661919}, issn = {1460-2075}, mesh = {Animals ; Base Sequence ; DNA/*chemistry ; DNA, Mitochondrial/chemistry ; Evolution, Molecular ; Fossils ; Genetic Variation ; *Genome ; Hominidae/*genetics ; Humans ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Recent advances in high-thoughput DNA sequencing have made genome-scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the authenticity of the DNA sequences retrieved. We discuss how these difficulties can be addressed, particularly with regard to analyses of the Neandertal genome. We argue that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination. Indirect measures, such as the extent of DNA fragmentation, nucleotide misincorporations, or comparison of derived allele frequencies in different fragment size classes, are unreliable. Fortunately, interim approaches based on mtDNA differences between Neandertals and current humans, detection of male contamination through Y chromosomal sequences, and repeated sequencing from the same fossil to detect autosomal contamination allow initial large-scale sequencing of Neandertal genomes. This will result in the discovery of fixed differences in the nuclear genome between Neandertals and current humans that can serve as future direct assays for contamination. For analyses of other fossil hominins, which may become possible in the future, we suggest a similar 'boot-strap' approach in which interim approaches are applied until sufficient data for more definitive direct assays are acquired.}, }
@article {pmid19652647, year = {2009}, author = {Van de Peer, Y and Maere, S and Meyer, A}, title = {The evolutionary significance of ancient genome duplications.}, journal = {Nature reviews. Genetics}, volume = {10}, number = {10}, pages = {725-732}, pmid = {19652647}, issn = {1471-0064}, mesh = {*Evolution, Molecular ; *Gene Duplication ; *Genome, Human ; Humans ; }, abstract = {Many organisms are currently polyploid, or have a polyploid ancestry and now have secondarily 'diploidized' genomes. This finding is surprising because retained whole-genome duplications (WGDs) are exceedingly rare, suggesting that polyploidy is usually an evolutionary dead end. We argue that ancient genome doublings could probably have survived only under very specific conditions, but that, whenever established, they might have had a pronounced impact on species diversification, and led to an increase in biological complexity and the origin of evolutionary novelties.}, }
@article {pmid19650916, year = {2009}, author = {Zhang, XC and Cannon, SB and Stacey, G}, title = {Evolutionary genomics of LysM genes in land plants.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {183}, pmid = {19650916}, issn = {1471-2148}, mesh = {Amino Acid Motifs ; *Evolution, Molecular ; Gene Duplication ; Genes, Plant ; Genomics ; *Phylogeny ; Plant Proteins/*genetics ; Plants/*genetics ; Sequence Alignment ; Synteny ; }, abstract = {BACKGROUND: The ubiquitous LysM motif recognizes peptidoglycan, chitooligosaccharides (chitin) and, presumably, other structurally-related oligosaccharides. LysM-containing proteins were first shown to be involved in bacterial cell wall degradation and, more recently, were implicated in perceiving chitin (one of the established pathogen-associated molecular patterns) and lipo-chitin (nodulation factors) in flowering plants. However, the majority of LysM genes in plants remain functionally uncharacterized and the evolutionary history of complex LysM genes remains elusive.<br><br>RESULTS: We show that LysM-containing proteins display a wide range of complex domain architectures. However, only a simple core architecture is conserved across kingdoms. Each individual kingdom appears to have evolved a distinct array of domain architectures. We show that early plant lineages acquired four characteristic architectures and progressively lost several primitive architectures. We report plant LysM phylogenies and associated gene, protein and genomic features, and infer the relative timing of duplications of LYK genes.<br><br>CONCLUSION: We report a domain architecture catalogue of LysM proteins across all kingdoms. The unique pattern of LysM protein domain architectures indicates the presence of distinctive evolutionary paths in individual kingdoms. We describe a comparative and evolutionary genomics study of LysM genes in plant kingdom. One of the two groups of tandemly arrayed plant LYK genes likely resulted from an ancient genome duplication followed by local genomic rearrangement, while the origin of the other groups of tandemly arrayed LYK genes remains obscure. Given the fact that no animal LysM motif-containing genes have been functionally characterized, this study provides clues to functional characterization of plant LysM genes and is also informative with regard to evolutionary and functional studies of animal LysM genes.}, }
@article {pmid19650893, year = {2009}, author = {Fregel, R and Gomes, V and Gusmão, L and González, AM and Cabrera, VM and Amorim, A and Larruga, JM}, title = {Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {181}, pmid = {19650893}, issn = {1471-2148}, mesh = {Black People/*genetics ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; *Gene Pool ; *Genetics, Population ; Humans ; Male ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Spain ; White People/*genetics ; }, abstract = {BACKGROUND: The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th-18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times.<br><br>RESULTS: Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th-18th centuries than today.<br><br>CONCLUSION: The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.}, }
@article {pmid19640497, year = {2009}, author = {Hofreiter, M and Stewart, J}, title = {Ecological change, range fluctuations and population dynamics during the Pleistocene.}, journal = {Current biology : CB}, volume = {19}, number = {14}, pages = {R584-94}, doi = {10.1016/j.cub.2009.06.030}, pmid = {19640497}, issn = {1879-0445}, mesh = {Animals ; *Biodiversity ; *Climate ; *Ecosystem ; Extinction, Biological ; *Fossils ; *Genetic Variation ; *Genetics, Population ; Geography ; History, Ancient ; *Population Dynamics ; }, abstract = {Apart from the current human-induced climate change, the Holocene is notable for its stable climate. In contrast, the preceding age, the Pleistocene, was a time of intensive climatic fluctuations, with temperature changes of up to 15 degrees C occurring within a few decades. These climatic changes have substantially influenced both animal and plant populations. Until recently, the prevailing opinion about the effect of these climatic fluctuations on species in Europe was that populations survived glacial maxima in southern refugia and that populations died out outside these refugia. However, some of the latest studies of modern population genetics, the fossil record and especially ancient DNA reveal a more complex picture. There is now strong evidence for additional local northern refugia for a large number of species, including both plants and animals. Furthermore, population genetic analyses using ancient DNA have shown that genetic diversity and its geographical structure changed more often and in more unpredictable ways during the Pleistocene than had been inferred. Taken together, the Pleistocene is now seen as an extremely dynamic era, with rapid and large climatic fluctuations and correspondingly variable ecology. These changes were accompanied by similarly fast and sometimes dramatic changes in population size and extensive gene flow mediated by population movements. Thus, the Pleistocene is an excellent model case for the effects of rapid climate change, as we experience at the moment, on the ecology of plants and animals.}, }
@article {pmid19639639, year = {2010}, author = {Fehren-Schmitz, L and Reindel, M and Cagigao, ET and Hummel, S and Herrmann, B}, title = {Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis.}, journal = {American journal of physical anthropology}, volume = {141}, number = {2}, pages = {208-221}, doi = {10.1002/ajpa.21135}, pmid = {19639639}, issn = {1096-8644}, mesh = {Base Sequence ; Cluster Analysis ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; *Fossils ; *Genetic Variation ; Haplotypes/genetics ; History, Ancient ; History, Medieval ; Humans ; Molecular Sequence Data ; Peru ; Phylogeny ; *Population Dynamics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021-16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups.}, }
@article {pmid19636374, year = {2009}, author = {Seabrook-Davison, M and Huynen, L and Lambert, DM and Brunton, DH}, title = {Ancient DNA resolves identity and phylogeny of New Zealand's extinct and living quail (Coturnix sp.).}, journal = {PloS one}, volume = {4}, number = {7}, pages = {e6400}, pmid = {19636374}, issn = {1932-6203}, mesh = {Animals ; Coturnix/*genetics ; DNA/*genetics ; *Extinction, Biological ; *Phylogeny ; }, abstract = {BACKGROUND: The New Zealand quail, Coturnix novaezealandiae, was widespread throughout New Zealand until its rapid extinction in the 1870's. To date, confusion continues to exist concerning the identity of C. novaezealandiae and its phylogenetic relationship to Coturnix species in neighbouring Australia, two of which, C. ypsilophora and C. pectoralis, were introduced into New Zealand as game birds. The Australian brown quail, C. ypsilophora, was the only species thought to establish with current populations distributed mainly in the northern part of the North Island of New Zealand. Owing to the similarities between C. ypsilophora, C. pectoralis, and C. novaezealandiae, uncertainty has arisen over whether the New Zealand quail is indeed extinct, with suggestions that remnant populations of C. novaezealandiae may have survived on offshore islands.<br><br>Using fresh and historical samples of Coturnix sp. from New Zealand and Australia, DNA analysis of selected mitochondrial regions was carried out to determine phylogenetic relationships and species status. Results show that Coturnix sp. specimens from the New Zealand mainland and offshore island Tiritiri Matangi are not the New Zealand quail but are genetically identical to C. ypsilophora from Australia and can be classified as the same species. Furthermore, cytochrome b and COI barcoding analysis of the New Zealand quail and Australia's C. pectoralis, often confused in museum collections, show that they are indeed separate species that diverged approximately 5 million years ago (mya). Gross morphological analysis of these birds suggests a parallel loss of sustained flight with very little change in other phenotypic characters such as plumage or skeletal structure.<br><br>CONCLUSION/SIGNIFICANCE: Ancient DNA has proved invaluable for the detailed analysis and identification of extinct and morphologically cryptic taxa such as that of quail and can provide insights into the timing of evolutionary changes that influence morphology.}, }
@article {pmid19623249, year = {2009}, author = {Palmer, SA and Moore, JD and Clapham, AJ and Rose, P and Allaby, RG}, title = {Archaeogenetic evidence of ancient nubian barley evolution from six to two-row indicates local adaptation.}, journal = {PloS one}, volume = {4}, number = {7}, pages = {e6301}, pmid = {19623249}, issn = {1932-6203}, mesh = {*Adaptation, Physiological ; *Archaeology ; *Biological Evolution ; DNA, Plant/genetics ; Hordeum/*genetics/physiology ; Molecular Sequence Data ; }, abstract = {BACKGROUND: Archaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years.<br><br>METHODOLOGY AND FINDINGS: We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure.<br><br>CONCLUSIONS: The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures.}, }
@article {pmid19617246, year = {2010}, author = {Alakoç, YD and Aka, PS and Eğin, Y and Akar, N}, title = {Factor V Leiden in an Urartian, dating back to 1000 BC.}, journal = {Clinical and applied thrombosis/hemostasis : official journal of the International Academy of Clinical and Applied Thrombosis/Hemostasis}, volume = {16}, number = {6}, pages = {679-683}, doi = {10.1177/1076029609338045}, pmid = {19617246}, issn = {1938-2723}, mesh = {Activated Protein C Resistance/genetics ; Archaeology ; DNA/chemistry/*genetics ; Factor V/*genetics/metabolism ; *Fossils ; Genetic Testing ; Humans ; Point Mutation ; Tooth/*chemistry ; Turkey ; }, abstract = {Factor V Leiden (FVL) is the most common monogenic disorder that causes activated protein C (APC) resistance, creating hyper-coagulation. The mutation shows an uneven geographic distribution, significantly high in European populations. The mutation is believed to have originated approximately 20 000 years ago probably from a geographic region close to Anatolia. This fact makes it noteworthy to search for the mutation in ancient populations that once lived in this area. One of these civilizations, Urartu was centered around Van Lake in Eastern Turkey. The archeological remains from the excavations of the region are dated back to 1000 BC. Teeth, taken from the excavations of Van Yoncatepe fortress, were taken into DNA analysis considering all the precautions for ancient DNA analysis. Multiplex STR (Short Tandem Repeats) analysis were performed both to determine the gender of the samples and to conclude that the samples are preserved from modern DNA contamination. After getting an 80% amplification success for amelogenin, a melting curve analysis using lightcycler was performed to determine the FVL genotype of each sample. Of the 60 samples, 1 gave a positive amplification result for FV gene and was found to be heterozygous. To date, the age of this mutation was estimated based on statistical calculations using haplotype frequencies; here for the first time, we report FVL in an ancient population of 3000 years.}, }
@article {pmid19608918, year = {2009}, author = {Briggs, AW and Good, JM and Green, RE and Krause, J and Maricic, T and Stenzel, U and Lalueza-Fox, C and Rudan, P and Brajkovic, D and Kucan, Z and Gusic, I and Schmitz, R and Doronichev, VB and Golovanova, LV and de la Rasilla, M and Fortea, J and Rosas, A and Pääbo, S}, title = {Targeted retrieval and analysis of five Neandertal mtDNA genomes.}, journal = {Science (New York, N.Y.)}, volume = {325}, number = {5938}, pages = {318-321}, doi = {10.1126/science.1174462}, pmid = {19608918}, issn = {1095-9203}, mesh = {Animals ; Bayes Theorem ; DNA Primers ; DNA, Mitochondrial/analysis/*genetics/isolation &amp; purification ; Evolution, Molecular ; Female ; *Fossils ; Gene Library ; Genetic Variation ; Genome, Human ; *Genome, Mitochondrial ; Geography ; Hominidae/*genetics ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; Population Density ; *Sequence Analysis, DNA ; }, abstract = {Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes.}, }
@article {pmid19608883, year = {2009}, author = {Pennisi, E}, title = {Ancient DNA. Sequencing Neandertal mitochondrial genomes by the half-dozen.}, journal = {Science (New York, N.Y.)}, volume = {325}, number = {5938}, pages = {252}, doi = {10.1126/science.325_252}, pmid = {19608883}, issn = {1095-9203}, mesh = {Animals ; Biological Evolution ; Bone and Bones ; DNA, Mitochondrial/genetics ; Female ; *Fossils ; Gene Library ; Genetic Variation ; Genome, Human ; *Genome, Mitochondrial ; Hominidae/*genetics ; Humans ; Male ; Population Density ; *Sequence Analysis, DNA/economics ; }, }
@article {pmid19607845, year = {2009}, author = {Sánchez, R and Grau, R}, title = {An algebraic hypothesis about the primeval genetic code architecture.}, journal = {Mathematical biosciences}, volume = {221}, number = {1}, pages = {60-76}, doi = {10.1016/j.mbs.2009.07.001}, pmid = {19607845}, issn = {1879-3134}, mesh = {Acinetobacter baumannii/genetics ; Algorithms ; Amino Acids/genetics ; Animals ; Base Pairing/genetics ; *Evolution, Molecular ; Fourier Analysis ; Genetic Code/*genetics ; Genome, Mitochondrial/genetics ; Humans ; Influenza A Virus, H5N1 Subtype/genetics ; Methanococcus/genetics ; *Models, Genetic ; Mutation/genetics ; Phylogeny ; Protein Biosynthesis/genetics ; RNA, Messenger/genetics ; RNA, Transfer/genetics ; Transcription, Genetic/genetics ; }, abstract = {A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvement of a primeval DNA repair system could make possible the transition from ancient to modern genetic codes. Our results suggest that the Watson-Crick base pairing G identical with C and A=U and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the latter. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences. The phylogenetic analyses achieved with metrics defined in the N-dimensional vector space (B(3))(N) of DNA sequences and with the new evolutionary model presented here also suggest that an ancient DNA coding sequence with five or more bases does not contradict the expected evolutionary history.}, }
@article {pmid19570784, year = {2009}, author = {Rawlence, NJ and Wood, JR and Armstrong, KN and Cooper, A}, title = {DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1672}, pages = {3395-3402}, pmid = {19570784}, issn = {0962-8452}, mesh = {Animals ; Base Sequence ; Birds/*genetics/*physiology ; DNA, Mitochondrial/*analysis/*genetics ; Extinction, Biological ; Feathers/*physiology ; Pigments, Biological ; }, abstract = {Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather 'vane' which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains.}, }
@article {pmid19570745, year = {2009}, author = {Guimaraes, S and Ghirotto, S and Benazzo, A and Milani, L and Lari, M and Pilli, E and Pecchioli, E and Mallegni, F and Lippi, B and Bertoldi, F and Gelichi, S and Casoli, A and Belle, EM and Caramelli, D and Barbujani, G}, title = {Genealogical discontinuities among Etruscan, Medieval, and contemporary Tuscans.}, journal = {Molecular biology and evolution}, volume = {26}, number = {9}, pages = {2157-2166}, doi = {10.1093/molbev/msp126}, pmid = {19570745}, issn = {1537-1719}, mesh = {Computer Simulation ; Consensus Sequence ; DNA, Mitochondrial/genetics ; Demography ; Female ; Gene Regulatory Networks ; *Genealogy and Heraldry ; Genetic Variation ; History, 15th Century ; History, 21st Century ; History, Medieval ; Humans ; Italy ; Male ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Reproducibility of Results ; Sample Size ; White People/*genetics/*history ; }, abstract = {The available mitochondrial DNA (mtDNA) data do not point to clear genetic relationships between current Tuscans and the Bronze-Age inhabitants of Tuscany, the Etruscans. To understand how and when such a genetic discontinuity may have arisen, we extracted and typed the mtDNAs of 27 medieval Tuscans from an initial sample of 61, spanning a period between the 10th and 15th century AD. We then tested by serial coalescent simulation various models describing the genealogical relationships among past and current inhabitants of Tuscany, the latter including three samples (from Murlo, Volterra, and Casentino) that were recently claimed to be of Etruscan descent. Etruscans and medieval Tuscans share three mitochondrial haplotypes but fall in distinct branches of the mitochondrial genealogy in the only model that proved compatible with the data. Under that model, contemporary people of Tuscany show clear genetic relationships with Medieval people, but not with the Etruscans, along the female lines. No evidence of excess mutation was found in the Etruscan DNAs by a Bayesian test, and so there is no reason to suspect that these results are biased by systematic contamination of the ancient sequences or laboratory artefacts. Extensive demographic changes before AD 1000 are thus the simplest explanation for the differences between the contemporary and the Bronze-Age mtDNAs of Tuscany. Accordingly, genealogical continuity between ancient and modern populations of the same area does not seem a safe general assumption, but rather a hypothesis that, when possible, should be tested using ancient DNA analysis.}, }
@article {pmid19545382, year = {2009}, author = {Endicott, P and Sanchez, JJ and Pichler, I and Brotherton, P and Brooks, J and Egarter-Vigl, E and Cooper, A and Pramstaller, P}, title = {Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman.}, journal = {BMC genetics}, volume = {10}, number = {}, pages = {29}, pmid = {19545382}, issn = {1471-2156}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Biological Evolution ; Bone and Bones/chemistry ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Humans ; Polymerase Chain Reaction/*methods ; *Polymorphism, Genetic ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman.<br><br>RESULTS: The multiplex assay developed for this study was able to confirm that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups.<br><br>CONCLUSION: The new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of a priori risks would significantly improve the credibility of results.}, }
@article {pmid19523150, year = {2009}, author = {Di Bernardo, G and Del Gaudio, S and Galderisi, U and Cascino, A and Cipollaro, M}, title = {Ancient DNA and family relationships in a Pompeian house.}, journal = {Annals of human genetics}, volume = {73}, number = {Pt 4}, pages = {429-437}, doi = {10.1111/j.1469-1809.2009.00520.x}, pmid = {19523150}, issn = {1469-1809}, mesh = {Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Family ; Female ; Humans ; Male ; Middle Aged ; *Paleontology ; Pedigree ; Skeleton ; Young Adult ; }, abstract = {Archaeological, anthropological and pathological data suggest that thirteen skeletons found in a house at the Pompeii archaeological site, dated to 79 A.D., belong to one family. To verify this and to identify the relationships between these individuals, we analyzed DNA extracted from bone specimens. Specifically, hypervariable segment 1 (HVS1) of the human mitochondrial DNA (mtDNA) control region was amplified in two overlapping polymerase chain reactions and the sequences were compared to the revised Cambridge Reference Sequence. As independent controls, other polymorphic sites in HVS1, HVS2 and in the coding region were analyzed. We also amplified some short tandem repeats of the thirteen specimens. This study revealed that six of the thirteen individuals are indeed closely related.}, }
@article {pmid19508981, year = {2009}, author = {Zhao, F and Qi, J and Schuster, SC}, title = {Tracking the past: interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius.}, journal = {Genome research}, volume = {19}, number = {8}, pages = {1384-1392}, pmid = {19508981}, issn = {1088-9051}, mesh = {Animals ; Chromosome Mapping ; Chromosomes, Mammalian/genetics ; Computer Simulation ; DNA Transposable Elements/genetics ; Evolution, Molecular ; *Extinction, Biological ; Genome/genetics ; Genomics/methods ; Humans ; Interspersed Repetitive Sequences/*genetics ; Mammals/classification/*genetics ; Models, Genetic ; Opossums ; Paleontology ; *Phylogeny ; Retroelements/genetics ; Time Factors ; }, abstract = {The woolly mammoth (Mammuthus primigenius) died out about several thousand years ago, yet recent paleogenomic studies have successfully recovered genetic information from both the mitochondrial and nuclear genomes of this extinct species. Mammoths belong to Afrotheria, a group of mammals exhibiting extreme morphological diversity and large genome sizes. In this study, we found that the mammoth genome contains a larger proportion of interspersed repeats than any other mammalian genome reported so far, in which the proliferation of the RTE family of retrotransposons (covering 12% of the genome) may be the main reason for an increased genome size. Phylogenetic analysis showed that RTEs in mammoth are closely related to the family BovB/RTE. The incongruence of the reconstructed RTE phylogeny indicates that RTEs in mammoth may be acquired through an ancient lateral gene transfer event. A recent proliferation of SINEs was also found in the probocidean lineage, whereas the Afrotherian-wide SINEs in mammoth have undergone a rather flat and stepwise expansion. Comparisons of the transposable elements (TEs) between mammoth and other mammals may shed light on the evolutionary history of TEs in various mammalian lineages.}, }
@article {pmid19493899, year = {2009}, author = {Collins, MJ and Penkman, KE and Rohland, N and Shapiro, B and Dobberstein, RC and Ritz-Timme, S and Hofreiter, M}, title = {Is amino acid racemization a useful tool for screening for ancient DNA in bone?.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1669}, pages = {2971-2977}, pmid = {19493899}, issn = {0962-8452}, mesh = {Amino Acids/*chemistry ; Animals ; Archaeology ; Bison ; Bone and Bones/*chemistry ; DNA/*chemistry ; Paleontology/methods ; Protein Denaturation ; }, abstract = {Many rare and valuable ancient specimens now carry the scars of ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02-0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that d/l Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx d/l is not a useful screening technique for ancient DNA from bone.}, }
@article {pmid19461892, year = {2009}, author = {Ramírez, O and Gigli, E and Bover, P and Alcover, JA and Bertranpetit, J and Castresana, J and Lalueza-Fox, C}, title = {Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine.}, journal = {PloS one}, volume = {4}, number = {5}, pages = {e5670}, pmid = {19461892}, issn = {1932-6203}, mesh = {Amino Acid Substitution ; Animals ; Base Pairing ; *Climate ; *Extinction, Biological ; Genome/genetics ; *Genomics ; Goats/*genetics ; Likelihood Functions ; Mediterranean Islands ; Paleontology/*methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; Spain ; }, abstract = {BACKGROUND: Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. METHODOLOGY/PRINCIPALS FINDINGS: A DNA extraction of a approximately 6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous.<br><br>CONCLUSIONS: A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.}, }
@article {pmid19454219, year = {2009}, author = {Colotte, M and Couallier, V and Tuffet, S and Bonnet, J}, title = {Simultaneous assessment of average fragment size and amount in minute samples of degraded DNA.}, journal = {Analytical biochemistry}, volume = {388}, number = {2}, pages = {345-347}, doi = {10.1016/j.ab.2009.02.003}, pmid = {19454219}, issn = {1096-0309}, mesh = {Animals ; DNA/*analysis/genetics/*metabolism ; DNA Fragmentation ; Forensic Genetics/methods ; Humans ; Polymerase Chain Reaction/*methods ; }, abstract = {There is currently no method allowing routine characterization of minute amounts of degraded DNA samples such as those encountered in forensic science, archived tissues, ancient DNA, extracellular or stool DNA, and processed food. Here we describe and directly validate such a method based, on the one hand, on a generalized DNA random fragmentation model and, on the other, on two quantitative polymerase chain reaction (PCR) experiments using two different target sizes. The model also makes it possible to determine the minimum sample amount, the minimum mass average fragment size, and the maximum degradation time necessary to obtain a positive PCR.}, }
@article {pmid19449030, year = {2009}, author = {Keyser, C and Bouakaze, C and Crubézy, E and Nikolaev, VG and Montagnon, D and Reis, T and Ludes, B}, title = {Ancient DNA provides new insights into the history of south Siberian Kurgan people.}, journal = {Human genetics}, volume = {126}, number = {3}, pages = {395-410}, pmid = {19449030}, issn = {1432-1203}, mesh = {Asian People/classification/*genetics ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; Gene Pool ; Geography ; Haplotypes/*genetics ; History, Ancient ; Humans ; Male ; Pigmentation ; Polymorphism, Single Nucleotide ; Siberia ; Tandem Repeat Sequences ; }, abstract = {To help unravel some of the early Eurasian steppe migration movements, we determined the Y-chromosomal and mitochondrial haplotypes and haplogroups of 26 ancient human specimens from the Krasnoyarsk area dated from between the middle of the second millennium BC. to the fourth century AD. In order to go further in the search of the geographic origin and physical traits of these south Siberian specimens, we also typed phenotype-informative single nucleotide polymorphisms. Our autosomal, Y-chromosomal and mitochondrial DNA analyses reveal that whereas few specimens seem to be related matrilineally or patrilineally, nearly all subjects belong to haplogroup R1a1-M17 which is thought to mark the eastward migration of the early Indo-Europeans. Our results also confirm that at the Bronze and Iron Ages, south Siberia was a region of overwhelmingly predominant European settlement, suggesting an eastward migration of Kurgan people across the Russo-Kazakh steppe. Finally, our data indicate that at the Bronze and Iron Age timeframe, south Siberians were blue (or green)-eyed, fair-skinned and light-haired people and that they might have played a role in the early development of the Tarim Basin civilization. To the best of our knowledge, no equivalent molecular analysis has been undertaken so far.}, }
@article {pmid19440242, year = {2009}, author = {Depaulis, F and Orlando, L and Hänni, C}, title = {Using classical population genetics tools with heterochroneous data: time matters!.}, journal = {PloS one}, volume = {4}, number = {5}, pages = {e5541}, pmid = {19440242}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Computer Simulation ; DNA, Mitochondrial/genetics ; *Databases, Genetic ; Evolution, Molecular ; Genetic Variation ; Genetics, Population/*methods ; Phylogeny ; Polymorphism, Genetic/genetics ; Ursidae/genetics ; }, abstract = {BACKGROUND: New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations.<br><br>We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony (approximately 10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism theta, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22-130 thousand years ago (KYA)).<br><br>CONCLUSIONS/SIGNIFICANCE: Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically considering heterochroneous models when analyzing heterochroneous samples covering a large time scale.}, }
@article {pmid19415315, year = {2009}, author = {Bouakaze, C and Keyser, C and Crubézy, E and Montagnon, D and Ludes, B}, title = {Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis.}, journal = {International journal of legal medicine}, volume = {123}, number = {4}, pages = {315-325}, pmid = {19415315}, issn = {1437-1596}, mesh = {Antigens, Neoplasm/genetics ; Antiporters/genetics ; DNA Degradation, Necrotic ; DNA Fingerprinting ; Eye Color/*genetics ; Forensic Anthropology ; Genotype ; Guanine Nucleotide Exchange Factors/genetics ; Hair Color/*genetics ; Humans ; Intramolecular Oxidoreductases/genetics ; Membrane Transport Proteins/genetics ; Polymerase Chain Reaction ; *Polymorphism, Single Nucleotide ; Racial Groups/*genetics ; Receptor, Melanocortin, Type 1/genetics ; Skin Pigmentation/*genetics ; Ubiquitin-Protein Ligases ; }, abstract = {In the present study, a multiplexed genotyping assay for ten single nucleotide polymorphisms (SNPs) located within six pigmentation candidate genes was developed on modern biological samples and applied to DNA retrieved from 25 archeological human remains from southern central Siberia dating from the Bronze and Iron Ages. SNP genotyping was successful for the majority of ancient samples and revealed that most probably had typical European pigment features, i.e., blue or green eye color, light hair color and skin type, and were likely of European individual ancestry. To our knowledge, this study reports for the first time the multiplexed typing of autosomal SNPs on aged and degraded DNA. By providing valuable information on pigment traits of an individual and allowing individual biogeographical ancestry estimation, autosomal SNP typing can improve ancient DNA studies and aid human identification in some forensic casework situations when used to complement conventional molecular markers.}, }
@article {pmid19390039, year = {2009}, author = {Ludwig, A and Pruvost, M and Reissmann, M and Benecke, N and Brockmann, GA and Castaños, P and Cieslak, M and Lippold, S and Llorente, L and Malaspinas, AS and Slatkin, M and Hofreiter, M}, title = {Coat color variation at the beginning of horse domestication.}, journal = {Science (New York, N.Y.)}, volume = {324}, number = {5926}, pages = {485}, pmid = {19390039}, issn = {1095-9203}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Husbandry/*history ; Animals ; Biological Evolution ; Breeding ; DNA ; Europe ; Genetic Variation ; Hair Color/*genetics ; History, Ancient ; Horses/*genetics ; Siberia ; }, abstract = {The transformation of wild animals into domestic ones available for human nutrition was a key prerequisite for modern human societies. However, no other domestic species has had such a substantial impact on the warfare, transportation, and communication capabilities of human societies as the horse. Here, we show that the analysis of ancient DNA targeting nuclear genes responsible for coat coloration allows us to shed light on the timing and place of horse domestication. We conclude that it is unlikely that horse domestication substantially predates the occurrence of coat color variation, which was found to begin around the third millennium before the common era.}, }
@article {pmid19367332, year = {2009}, author = {Fabre, V and Condemi, S and Degioanni, A}, title = {Genetic evidence of geographical groups among Neanderthals.}, journal = {PloS one}, volume = {4}, number = {4}, pages = {e5151}, pmid = {19367332}, issn = {1932-6203}, mesh = {Animals ; Anthropology, Physical ; Asia, Western ; Base Sequence ; Computational Biology ; Computer Simulation ; DNA, Mitochondrial ; Demography ; Emigration and Immigration ; Europe ; *Genetic Variation ; *Genetics, Population ; Geography ; Hominidae/*genetics ; Humans ; Models, Genetic ; Phylogeny ; *Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {The Neanderthals are a well-distinguished Middle Pleistocene population which inhabited a vast geographical area extending from Europe to western Asia and the Middle East. Since the 1950s paleoanthropological studies have suggested variability in this group. Different sub-groups have been identified in western Europe, in southern Europe and in the Middle East. On the other hand, since 1997, research has been published in paleogenetics, carried out on 15 mtDNA sequences from 12 Neanderthals. In this paper we used a new methodology derived from different bioinformatic models based on data from genetics, demography and paleoanthropology. The adequacy of each model was measured by comparisons between simulated results (obtained by BayesianSSC software) and those estimated from nucleotide sequences (obtained by DNAsp4 software). The conclusions of this study are consistent with existing paleoanthropological research and show that Neanderthals can be divided into at least three groups: one in western Europe, a second in the Southern area and a third in western Asia. Moreover, it seems from our results that the size of the Neanderthal population was not constant and that some migration occurred among the demes.}, }
@article {pmid19352435, year = {2009}, author = {Marrone, A and Ballantyne, J}, title = {Changes in dry state hemoglobin over time do not increase the potential for oxidative DNA damage in dried blood.}, journal = {PloS one}, volume = {4}, number = {4}, pages = {e5110}, pmid = {19352435}, issn = {1932-6203}, mesh = {DNA/*metabolism ; *DNA Damage ; Hemoglobins/*chemistry/metabolism ; Humans ; Hydroxyl Radical/metabolism ; *Oxidative Stress ; }, abstract = {BACKGROUND: Hemoglobin (Hb) is the iron-containing oxygen transport protein present in the red blood cells of vertebrates. Ancient DNA and forensic scientists are particularly interested in Hb reactions in the dry state because both regularly encounter aged, dried bloodstains. The DNA in such stains may be oxidatively damaged and, in theory, may be deteriorated by the presence of Hb. To understand the nature of the oxidative systems potentially available to degrade DNA in the presence of dried Hb, we need to determine what molecular species Hb forms over time. These species will determine what type of iron (i.e. Fe(2+)/Fe(3+)/Fe(4+)) is available to participate in further chemical reactions. The availability of "free" iron will affect the ability of the system to undergo Fenton-type reactions which generate the highly reactive hydroxyl radical (OH*). The OH* can directly damage DNA.<br><br>Oxygenated Hb (oxyHb) converts over time to oxidized Hb (metHb), but this happens more quickly in the dry state than in the hydrated state, as shown by monitoring stabilized oxyHb. In addition, dry state oxyHb converts into at least one other unknown species other than metHb. Although "free" iron was detectable as both Fe(2+) and Fe(3+) in dry and hydrated oxyHb and metHb, the amount of ions detected did not increase over time. There was no evidence that Hb becomes more prone to generating OH* as it ages in either the hydrated or dry states.<br><br>CONCLUSIONS: The Hb molecule in the dried state undergoes oxidative changes and releases reactive Fe(II) cations. These changes, however, do not appear to increase the ability of Hb to act as a more aggressive Fenton reagent over time. Nevertheless, the presence of Hb in the vicinity of DNA in dried bloodstains creates the opportunity for OH*-induced oxidative damage to the deoxyribose sugar and the DNA nucleobases.}, }
@article {pmid19337382, year = {2009}, author = {Thomsen, PF and Elias, S and Gilbert, MT and Haile, J and Munch, K and Kuzmina, S and Froese, DG and Sher, A and Holdaway, RN and Willerslev, E}, title = {Non-destructive sampling of ancient insect DNA.}, journal = {PloS one}, volume = {4}, number = {4}, pages = {e5048}, pmid = {19337382}, issn = {1932-6203}, mesh = {Animals ; DNA/*genetics ; Fossils ; Insecta/*genetics ; Polymerase Chain Reaction ; Species Specificity ; }, abstract = {BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil) dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from non-frozen sediments deposited 3280-1800 years ago -- an alternative approach that also does not involve destruction of valuable material.<br><br>The success of the methodological approaches are tested by PCR and sequencing of COI and 16S mitochondrial DNA (mtDNA) fragments of 77-204 base pairs (-bp) in size using species-specific and general insect primers.<br><br>CONCLUSION/SIGNIFICANCE: The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient biodiversity.}, }
@article {pmid19324622, year = {2009}, author = {Hendy, MD and Woodhams, MD and Dodd, A}, title = {Modelling mitochondrial site polymorphisms to infer the number of segregating units and mutation rate.}, journal = {Biology letters}, volume = {5}, number = {3}, pages = {397-400}, pmid = {19324622}, issn = {1744-9561}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Mitochondria/*genetics ; *Models, Genetic ; *Polymorphism, Genetic ; }, abstract = {We present a mathematical model of mitochondrial inheritance evolving under neutral evolution to interpret the heteroplasmies observed at some sites. A comparison of the levels of heteroplasmies transmitted from mother to her offspring allows us to estimate the number N(x) of inherited mitochondrial genomes (segregating units). The model demonstrates the necessity of accounting for both the multiplicity of an unknown number N(x), and the threshold , below which heteroplasmy cannot be detected reliably, in order to estimate the mitochondrial mutation rate mu(m) in the maternal line of descent. Our model is applicable to pedigree studies of any eukaryotic species where site heteroplasmies are observed in regions of the mitochondria, provided neutrality can be assumed. The model is illustrated with an analysis of site heteroplasmies in the first hypervariable region of mitochondrial sequence data sampled from Adélie penguin families, providing an estimate N(x) and mu(m). This estimate of mu(m) was found to be consistent with earlier estimates from ancient DNA analysis.}, }
@article {pmid19317662, year = {2009}, author = {Allentoft, M and Schuster, SC and Holdaway, R and Hale, M and McLay, E and Oskam, C and Gilbert, MT and Spencer, P and Willerslev, E and Bunce, M}, title = {Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data.}, journal = {BioTechniques}, volume = {46}, number = {3}, pages = {195-200}, doi = {10.2144/000113086}, pmid = {19317662}, issn = {0736-6205}, mesh = {*Algorithms ; Animals ; Base Sequence ; Chromosome Mapping/*methods ; Extinction, Biological ; *Fossils ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; Palaeognathae/*genetics ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {Genetic variation in microsatellites is rarely examined in the field of ancient DNA (aDNA) due to the low quantity of nuclear DNA in the fossil record together with the lack of characterized nuclear markers in extinct species. 454 sequencing platforms provide a new high-throughput technology capable of generating up to 1 gigabases per run as short (200-400-bp) read lengths. 454 data were generated from the fossil bone of an extinct New Zealand moa (Aves: Dinornithiformes). We identified numerous short tandem repeat (STR) motifs, and here present the successful isolation and characterization of one polymorphic microsatellite (Moa_MS2). Primers designed to flank this locus amplified all three moa species tested here. The presented method proved to be a fast and efficient way of identifying microsatellite markers in ancient DNA templates and, depending on biomolecule preservation, has the potential of enabling high-resolution population genetic studies of extinct taxa. As sequence read lengths of the 454 platforms and its competitors (e.g., the SOLEXA and SOLiD platforms) increase, this approach will become increasingly powerful in identifying microsatellites in extinct (and extant) organisms, and will afford new opportunities to study past biodiversity and extinction processes.}, }
@article {pmid19302360, year = {2009}, author = {Barnett, R and Shapiro, B and Barnes, I and Ho, SY and Burger, J and Yamaguchi, N and Higham, TF and Wheeler, HT and Rosendahl, W and Sher, AV and Sotnikova, M and Kuznetsova, T and Baryshnikov, GF and Martin, LD and Harington, CR and Burns, JA and Cooper, A}, title = {Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity.}, journal = {Molecular ecology}, volume = {18}, number = {8}, pages = {1668-1677}, doi = {10.1111/j.1365-294X.2009.04134.x}, pmid = {19302360}, issn = {1365-294X}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fossils ; Genetic Variation ; *Genetics, Population ; Geography ; Lions/classification/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions.}, }
@article {pmid19294688, year = {2009}, author = {Xu, Z and Zhang, F and Xu, B and Tan, J and Li, S and Jin, L}, title = {Improving the sensitivity of negative controls in ancient DNA extractions.}, journal = {Electrophoresis}, volume = {30}, number = {8}, pages = {1282-1285}, doi = {10.1002/elps.200800473}, pmid = {19294688}, issn = {1522-2683}, mesh = {Archaeology ; Bacteriophage lambda/chemistry/genetics ; Bone and Bones/chemistry ; *DNA/chemistry/isolation &amp; purification ; DNA, Viral/chemistry ; Drug Contamination ; Humans ; Poly A/*chemistry ; Polymerase Chain Reaction ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Tooth/chemistry ; }, abstract = {Much attention has been paid on ancient DNA (aDNA) studies, and negative control was used as one of the stringent quality assurance criteria in order to detect potential contamination. However, the results of some aDNA studies showed the evidence of contamination despite their negative controls failed to do so. Using lambda DNA to mock extraneous contaminating DNA, our study showed that aDNA had a property of improving the efficiency of extraction including contaminating DNA, while negative controls had low sensitivity to detect contamination. To circumvent this problem, carrier DNA such as poly(dA) is suggested to be introduced into aDNA extraction.}, }
@article {pmid19281471, year = {2009}, author = {Ramakrishnan, U and Hadly, EA}, title = {Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies.}, journal = {Molecular ecology}, volume = {18}, number = {7}, pages = {1310-1330}, doi = {10.1111/j.1365-294X.2009.04092.x}, pmid = {19281471}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; *Evolution, Molecular ; Fossils ; Gene Flow ; Genetic Variation ; *Genetics, Population ; Markov Chains ; *Models, Genetic ; Monte Carlo Method ; Population Density ; Population Dynamics ; Sequence Analysis, DNA/*methods ; }, abstract = {The evolutionary history of a population involves changes in size, movements and selection pressures through time. Reconstruction of population history based on modern genetic data tends to be averaged over time or to be biased by generally reflecting only recent or extreme events, leaving many population historic processes undetected. Temporal genetic data present opportunities to reveal more complex population histories and provide important insights into what processes have influenced modern genetic diversity. Here we provide a synopsis of methods available for the analysis of ancient genetic data. We review 29 ancient DNA studies, summarizing the analytical methods and general conclusions for each study. Using the serial coalescent and a model-testing approach, we then re-analyse data from two species represented by these data sets in a common interpretive framework. Our analyses show that phylochronologic data can reveal more about population history than modern data alone, thus revealing 'cryptic' population processes, and enable us to determine whether simple or complex models best explain the data. Our re-analyses point to the need for novel methods that consider gene flow, multiple populations and population size in reconstruction of population history. We conclude that population genetic samples over large temporal and geographical scales, when analysed using more complex models and the serial coalescent, are critical to understand past population dynamics and provide important tools for reconstructing the evolutionary process.}, }
@article {pmid21564674, year = {2009}, author = {Lawrence, HA and Millar, CD and Imber, MJ and Crockett, DE and Robins, JH and Scofield, RP and Taylor, GA and Lambert, DM}, title = {Molecular evidence for the identity of the Magenta petrel.}, journal = {Molecular ecology resources}, volume = {9}, number = {2}, pages = {458-461}, doi = {10.1111/j.1755-0998.2008.02370.x}, pmid = {21564674}, issn = {1755-098X}, abstract = {A lone petrel was shot from the decks of an Italian warship (the 'Magenta') while it was sailing the South Pacific Ocean in 1867, far from land. The species, unknown to science, was named the 'Magenta petrel' (Procellariiformes, Procellariidae, Pterodroma magentae). No other specimens of this bird were collected and the species it represented remained a complete enigma for over 100 years. We compared DNA sequence of the mitochondrial cytochrome b gene from the Magenta petrel to that of other petrels using phylogenetic methods and ancient DNA techniques. Our results strongly suggest that the Magenta petrel specimen is a Chatham Island taiko. Furthermore, given the collection location of the Magenta petrel, our finding indicates that the Chatham Island taiko forages far into the Pacific Ocean (near South America). This has implications for the conservation of the taiko, one of the world's rarest seabirds.}, }
@article {pmid19222749, year = {2009}, author = {Sommer, RS and Lindqvist, C and Persson, A and Bringsøe, H and Rhodin, AG and Schneeweiss, N and Siroký, P and Bachmann, L and Fritz, U}, title = {Unexpected early extinction of the European pond turtle (Emys orbicularis) in Sweden and climatic impact on its Holocene range.}, journal = {Molecular ecology}, volume = {18}, number = {6}, pages = {1252-1262}, doi = {10.1111/j.1365-294X.2009.04096.x}, pmid = {19222749}, issn = {1365-294X}, mesh = {Animals ; Base Sequence ; *Climate ; *Extinction, Biological ; Molecular Sequence Data ; Radiometric Dating ; Sequence Analysis, DNA ; Sweden ; Turtles/*genetics ; }, abstract = {Using ancient DNA sequences of subfossil European pond turtles (Emys orbicularis) from Britain, Central and North Europe and accelerator mass spectrometry radiocarbon dating for turtle remains from most Swedish sites, we provide evidence for a Holocene range expansion of the pond turtle from the southeastern Balkans into Britain, Central Europe and Scandinavia, according to the 'grasshopper pattern' of Hewitt. Northeastern Europe and adjacent Asia were colonized from another refuge located further east. With increasing annual mean temperatures, pond turtles reached southern Sweden approximately 9800 years ago. Until approximately 5500 years ago, rising temperatures facilitated a further range expansion up to Ostergötland, Sweden (approximately 58 degrees 30'N). However, around 5500 years ago pond turtle records suddenly terminate in Sweden, some 1500 years before the Holocene thermal maximum ended in Scandinavia and distinctly earlier than previously thought. This extinction coincides with a temporary cooling oscillation during the Holocene thermal maximum and is likely related to lower summer temperatures deteriorating reproductive success. Although climatic conditions improved later again, recolonization of Sweden from southern source populations was prevented by the Holocene submergence of the previous land connection via the Danish Straits that occurred approximately 8500 years ago.}, }
@article {pmid19215875, year = {2009}, author = {Gibbon, V and Paximadis, M and Strkalj, G and Ruff, P and Penny, C}, title = {Novel methods of molecular sex identification from skeletal tissue using the amelogenin gene.}, journal = {Forensic science international. Genetics}, volume = {3}, number = {2}, pages = {74-79}, doi = {10.1016/j.fsigen.2008.10.007}, pmid = {19215875}, issn = {1878-0326}, mesh = {Amelogenin/*genetics ; Base Sequence ; Bone and Bones/chemistry ; Chromosomes, Human, X/chemistry ; Chromosomes, Human, Y/chemistry ; Forensic Genetics/methods ; Humans ; Molecular Sequence Data ; Paleontology/methods ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Sequence Homology, Nucleic Acid ; Sex Determination Analysis/*methods ; Sex Determination by Skeleton/*methods ; }, abstract = {Sex identification from skeletal material is of vital importance in order to reconstruct the demographic variables of an individual in forensic genetics and ancient DNA (aDNA) analysis. When the use of conventional methods of sex identification are impossible, molecular analysis of the X and Y chromosomes provides an expedient solution. Two novel systems of molecular sex identification suitable for skeletal material using the amelogenin gene are described, beginning in intron 2-3, spanning exon 3 and ending in intron 3-4. This area was optimal for sexing, as it includes 14 sex-specific polymorphic regions in addition to an indel (insertion or deletion of nucleotides). Once optimised and working with 100% efficiency on the controls, these procedures were applied to a collection of miscellaneous archaeological skeletons (ex situ) sourced from the Raymond Dart Collection of Human Skeletons (Dart Collection). This collection was used to optimise these techniques for skeletal remains derived from an archaeological context. These methods produced 46.66% sex results for the ex situ sample, which is within the normal range for aDNA studies. These new techniques are optimal for sex identification, with both the inherent control of isolating many sex-specific features and combined with the use of sensitive micro-fluidic electrophoresis.}, }
@article {pmid19214468, year = {2009}, author = {Martín-González, A and Wierzchos, J and Gutiérrez, JC and Alonso, J and Ascaso, C}, title = {Microbial Cretaceous park: biodiversity of microbial fossils entrapped in amber.}, journal = {Die Naturwissenschaften}, volume = {96}, number = {5}, pages = {551-564}, pmid = {19214468}, issn = {1432-1904}, mesh = {*Amber ; Animals ; Bacteria/classification/genetics ; *Biodiversity ; Biological Evolution ; Biology ; DNA/genetics ; DNA Repair ; Ecosystem ; Eukaryota/classification/genetics/pathogenicity ; *Fossils ; Fungi/classification/genetics ; Gene Amplification ; Paleontology ; Plant Roots/microbiology ; Spores, Bacterial/classification/pathogenicity ; Spores, Fungal/pathogenicity/physiology ; Viruses/classification/genetics/pathogenicity ; }, abstract = {Microorganisms are the most ancient cells on this planet and they include key phyla for understanding cell evolution and Earth history, but, unfortunately, their microbial records are scarce. Here, we present a critical review of fossilized prokaryotic and eukaryotic microorganisms entrapped in Cretaceous ambers (but not exclusively from this geological period) obtained from deposits worldwide. Microbiota in ambers are rather diverse and include bacteria, fungi, and protists. We comment on the most important microbial records from the last 25 years, although it is not an exhaustive bibliographic compilation. The most frequently reported eukaryotic microfossils are shells of amoebae and protists with a cell wall or a complex cortex. Likewise, diverse dormant stages (palmeloid forms, resting cysts, spores, etc.) are abundant in ambers. Besides, viral and protist pathogens have been identified inside insects entrapped in amber. The situation regarding filamentous bacteria and fungi is quite confusing because in some cases, the same record was identified consecutively as a member of these phylogenetically distant groups. To avoid these identification errors in the future, we propose to apply a more resolute microscopic and analytical method in amber studies. Also, we discuss the most recent findings about ancient DNA repair and bacterial survival in remote substrates, which support the real possibility of ancient DNA amplification and bacterial resuscitation from Cretaceous resins.}, }
@article {pmid19148284, year = {2009}, author = {Helgason, A and Lalueza-Fox, C and Ghosh, S and Sigurethardóttir, S and Sampietro, ML and Gigli, E and Baker, A and Bertranpetit, J and Arnadóttir, L and Thornorsteinsdottir, U and Stefánsson, K}, title = {Sequences from first settlers reveal rapid evolution in Icelandic mtDNA pool.}, journal = {PLoS genetics}, volume = {5}, number = {1}, pages = {e1000343}, pmid = {19148284}, issn = {1553-7404}, mesh = {DNA, Mitochondrial/*chemistry ; *Evolution, Molecular ; *Gene Pool ; *Genetics, Population ; Geography ; Humans ; Iceland ; Sequence Analysis, DNA ; }, abstract = {A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA) control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples.}, }
@article {pmid19142238, year = {2009}, author = {Driscoll, CA and Yamaguchi, N and Bar-Gal, GK and Roca, AL and Luo, S and Macdonald, DW and O'Brien, SJ}, title = {Mitochondrial phylogeography illuminates the origin of the extinct caspian tiger and its relationship to the amur tiger.}, journal = {PloS one}, volume = {4}, number = {1}, pages = {e4125}, pmid = {19142238}, issn = {1932-6203}, support = {N01CO12400/CA/NCI NIH HHS/United States ; N01-CO-12400/CO/NCI NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; Asia, Central ; *Biological Evolution ; China ; DNA, Mitochondrial/*genetics ; Extinction, Biological ; Geography ; Haplotypes ; *Phylogeny ; Siberia ; Tigers/classification/*genetics ; }, abstract = {The Caspian tiger (Panthera tigris virgata) flourished in Central Asian riverine forest systems in a range disjunct from that of other tigers, but was driven to extinction in 1970 prior to a modern molecular evaluation. For over a century naturalists puzzled over the taxonomic validity, placement, and biogeographic origin of this enigmatic animal. Using ancient-DNA (aDNA) methodology, we generated composite mtDNA haplotypes from twenty wild Caspian tigers from throughout their historic range sampled from museum collections. We found that Caspian tigers carry a major mtDNA haplotype differing by only a single nucleotide from the monomorphic haplotype found across all contemporary Amur tigers (P. t. altaica). Phylogeographic analysis with extant tiger subspecies suggests that less than 10,000 years ago the Caspian/Amur tiger ancestor colonized Central Asia via the Gansu Corridor (Silk Road) from eastern China then subsequently traversed Siberia eastward to establish the Amur tiger in the Russian Far East. The conservation implications of these findings are far reaching, as the observed genetic depletion characteristic of modern Amur tigers likely reflects these founder migrations and therefore predates human influence. Also, due to their evolutionary propinquity, living Amur tigers offer an appropriate genetic source should reintroductions to the former range of the Caspian tiger be implemented.}, }
@article {pmid21628192, year = {2009}, author = {Soltis, DE and Albert, VA and Leebens-Mack, J and Bell, CD and Paterson, AH and Zheng, C and Sankoff, D and Depamphilis, CW and Wall, PK and Soltis, PS}, title = {Polyploidy and angiosperm diversification.}, journal = {American journal of botany}, volume = {96}, number = {1}, pages = {336-348}, doi = {10.3732/ajb.0800079}, pmid = {21628192}, issn = {0002-9122}, abstract = {Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.}, }
@article {pmid19108732, year = {2008}, author = {Lalueza-Fox, C and Gigli, E and de la Rasilla, M and Fortea, J and Rosas, A and Bertranpetit, J and Krause, J}, title = {Genetic characterization of the ABO blood group in Neandertals.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {342}, pmid = {19108732}, issn = {1471-2148}, mesh = {ABO Blood-Group System/*genetics ; Animals ; Hominidae/*genetics ; Male ; Molecular Sequence Data ; Polymorphism, Genetic ; Spain ; }, abstract = {BACKGROUND: The high polymorphism rate in the human ABO blood group gene seems to be related to susceptibility to different pathogens. It has been estimated that all genetic variation underlying the human ABO alleles appeared along the human lineage, after the divergence from the chimpanzee lineage. A paleogenetic analysis of the ABO blood group gene in Neandertals allows us to directly test for the presence of the ABO alleles in these extinct humans.<br><br>RESULTS: We have analysed two male Neandertals that were retrieved under controlled conditions at the El Sidron site in Asturias (Spain) and that appeared to be almost free of modern human DNA contamination. We find a human specific diagnostic deletion for blood group O (O01 haplotype) in both Neandertal individuals.<br><br>CONCLUSION: These results suggest that the genetic change responsible for the O blood group in humans predates the human and Neandertal divergence. A potential selective event associated with the emergence of the O allele may have therefore occurred after humans separated from their common ancestor with chimpanzees and before the human-Neandertal population divergence.}, }
@article {pmid19104042, year = {2009}, author = {Premo, LS and Hublin, JJ}, title = {Culture, population structure, and low genetic diversity in Pleistocene hominins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {1}, pages = {33-37}, pmid = {19104042}, issn = {1091-6490}, mesh = {Animal Migration ; Animals ; Computer Simulation ; *Culture ; *Genetic Variation ; *Hominidae ; Humans ; Population Density ; *Population Dynamics ; }, abstract = {Paleogenomic research has shown that modern humans, Neanderthals, and their most recent common ancestor have displayed less genetic diversity than living great apes. The traditional interpretation that low levels of genetic diversity in modern humans resulted from a relatively recent demographic bottleneck cannot account for similarly low levels of genetic diversity in Middle Pleistocene hominins. A more parsimonious hypothesis proposes that the effective population size of the human lineage has been low for more than 500,000 years, but the mechanism responsible for suppressing genetic diversity in Pleistocene hominin populations without similarly affecting that of their hominoid contemporaries remains unknown. Here we use agent-based simulation to study the effect of culturally mediated migration on neutral genetic diversity in structured populations. We show that, in populations structured by culturally mediated migration, selection can suppress neutral genetic diversity over thousands of generations, even in the absence of bottlenecks or expansions in census population size. In other words, selection could have suppressed the effective population size of Pleistocene hominins for as long as the degree of cultural similarity between regionally differentiated groups played an important role in mediating intraspecific gene flow.}, }
@article {pmid19092297, year = {2008}, author = {Marini, F and Carbonell Sala, S and Falchetti, A and Caramelli, D and Brandi, ML}, title = {The genetic ascertainment of multiple endocrine neoplasia type 1 syndrome by ancient DNA analysis.}, journal = {Journal of endocrinological investigation}, volume = {31}, number = {10}, pages = {905-909}, pmid = {19092297}, issn = {1720-8386}, mesh = {Adult ; Child ; DNA, Mitochondrial/analysis ; Female ; Femur/chemistry ; Forensic Anthropology/*methods ; Haplotypes ; Humans ; Male ; Microsatellite Repeats/genetics ; Multiple Endocrine Neoplasia Type 1/*genetics ; Pedigree ; }, abstract = {Multiple endocrine neoplasia type 1 (MEN1) is a rare autosomal dominant inherited endocrine cancer syndrome characterised by parathyroid, pancreas, and anterior pituitary tumors. The disease responsible gene, MEN1, was identified in 1997 and localizes to chromosome 11q13 in a minimal 600 kb interval between PYGM and D11S449 loci. About 10-20% of MEN1 patients do not have any mutation in the coding region and/or in the exon-intron junctions of the MEN1 gene. In this case, familial haplotype analysis of the 11q13 region, in at least two generations of affected members, is the only possible genetic ascertainment of the disease. We performed a microsatellite haplotype analysis at 11q13 region in 8 living and 1 deceased member of a MEN1 Italian family without any detected germline mutation of the MEN1 gene. The application of forensic techniques for ancient DNA analysis made it possible to identify the familial disease-associated haplotype and demonstrated that MEN1 disease haplotype family history can be reconstructed even when one or more family members are deceased. Identification of MEN1 disease haplotype is helpful in the clinical management of patients and relatives in families without any mutation of the MEN1 gene. Genetic screening allows the identification of individuals who are at risk before the development of clinical symptoms, limiting invasive annual cancer surveillance only to genetically positive individuals and making it possible to avoid further clinical screenings in non-carriers.}, }
@article {pmid19083823, year = {2008}, author = {Fondevila, M and Phillips, C and Naveran, N and Fernandez, L and Cerezo, M and Salas, A and Carracedo, A and Lareu, MV}, title = {Case report: identification of skeletal remains using short-amplicon marker analysis of severely degraded DNA extracted from a decomposed and charred femur.}, journal = {Forensic science international. Genetics}, volume = {2}, number = {3}, pages = {212-218}, doi = {10.1016/j.fsigen.2008.02.005}, pmid = {19083823}, issn = {1878-0326}, mesh = {Alleles ; Benchmarking ; DNA/*analysis/genetics/isolation &amp; purification ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/genetics ; Femur/*chemistry ; Forensic Anthropology/*methods ; Genetic Markers ; Genotype ; Humans ; Likelihood Functions ; Microsatellite Repeats ; Nuclear Family ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Sensitivity and Specificity ; }, abstract = {Applying two extraction protocols to isolate DNA from a charred femur recovered after a major forest fire, a range of established and recently developed forensic marker sets that included mini-STRs and SNPs were used to type the sample and confirm identity by comparison to a claimed daughter of the deceased. Identification of the remains suggested that the individual had been dead for 10 years and the DNA was therefore likely to be severely degraded from the combined effects of decomposition and exposure to very high temperatures. We used new marker sets specifically developed to analyze degraded DNA comprising both reduced-length amplicon STR sets and autosomal SNP multiplexes, giving an opportunity to assess the ability of each approach to successfully type highly degraded material from a challenging case. The results also suggest a modified ancient DNA extraction procedure offers improved typing success from degraded skeletal material.}, }
@article {pmid19083805, year = {2008}, author = {Anderung, C and Persson, P and Bouwman, A and Elburg, R and Götherström, A}, title = {Fishing for ancient DNA.}, journal = {Forensic science international. Genetics}, volume = {2}, number = {2}, pages = {104-107}, doi = {10.1016/j.fsigen.2007.09.004}, pmid = {19083805}, issn = {1878-0326}, mesh = {Animals ; Biotinylation ; Bone and Bones/chemistry ; Cattle ; DNA/*analysis/chemistry/*isolation &amp; purification ; DNA Primers/metabolism ; Edetic Acid/chemistry/pharmacology ; Female ; *Fossils ; *History, Ancient ; Magnetics ; Nucleic Acid Amplification Techniques ; Paleontology ; Polymerase Chain Reaction ; Silicon Dioxide/chemistry/economics ; Time Factors ; Tooth/chemistry ; }, abstract = {The major problems concerning ancient DNA studies are related to the amount of extractable DNA and the precautions needed to avoid contamination. From the very first step of the analyses, the DNA extraction, these problems must be confronted. There are several extraction methods available for DNA in ancient tissue; several of them are complicated and time consuming, and none of the methods have reached an acceptance level such that they are routinely used on a widespread basis. Here we investigate the efficiency of two methods, one based on magnetic separation of the targeted molecules, and one based on silica binding. The efficiency rate of these two on the material studied seems to be identical. The silica binding method has the benefit of relative simplicity, but the magnetic separation technique also has advantages. For example, it is possible to reuse the extract several times for different loci, and it is possible to concentrate all extracted DNA from one locus into one PCR.}, }
@article {pmid19067486, year = {2008}, author = {Yan, H and Talbert, PB and Lee, HR and Jett, J and Henikoff, S and Chen, F and Jiang, J}, title = {Intergenic locations of rice centromeric chromatin.}, journal = {PLoS biology}, volume = {6}, number = {11}, pages = {e286}, pmid = {19067486}, issn = {1545-7885}, mesh = {Base Sequence ; Binding Sites ; Centromere/*genetics/metabolism ; Chromatin/*genetics/metabolism ; Chromatin Immunoprecipitation ; *Chromosome Mapping ; Chromosomes, Plant ; Gene Duplication ; Histones/*metabolism ; Oryza/*genetics ; }, abstract = {Centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis. Plant and animal centromeres are typically located in megabase-sized arrays of tandem satellite repeats, making their precise mapping difficult. However, some rice centromeres are largely embedded in nonsatellite DNA, providing an excellent model to study centromere structure and evolution. We used chromatin immunoprecipitation and 454 sequencing to define the boundaries of nine of the 12 centromeres of rice. Centromere regions from chromosomes 8 and 9 were found to share synteny, most likely reflecting an ancient genome duplication. For four centromeres, we mapped discrete subdomains of binding by the centromeric histone variant CENH3. These subdomains were depleted in both intact and nonfunctional genes relative to interspersed subdomains lacking CENH3. The intergenic location of rice centromeric chromatin resembles the situation for human neocentromeres and supports a model of the evolution of centromeres from gene-poor regions.}, }
@article {pmid19067027, year = {2009}, author = {Lamers, R and Hayter, S and Matheson, CD}, title = {Postmortem miscoding lesions in sequence analysis of human ancient mitochondrial DNA.}, journal = {Journal of molecular evolution}, volume = {68}, number = {1}, pages = {40-55}, pmid = {19067027}, issn = {0022-2844}, mesh = {Adenine/chemistry ; Cytosine/chemistry ; DNA Damage/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Guanine/analogs &amp; derivatives/chemistry ; Humans ; Sequence Analysis ; Thymine/chemistry ; }, abstract = {Genetic miscoding lesions can cause inaccuracies during the interpretation of ancient DNA sequence data. In this study, genetic miscoding lesions were identified and assessed by cloning and direct sequencing of degraded, amplified mitochondrial DNA (mtDNA) extracted from human remains. Forty-two individuals, comprising nine collections from five geographic locations, were analyzed for the presence of DNA damage that can affect the generation of a correct mtDNA profile. In agreement with previous studies, high levels (56.5% of all damage sites) of proposed hydrolytic damage products were observed. Among these, type 2 transitions (cytosine --> thymine or guanine --> adenine), which are highly indicative of hydrolytic deamination, were observed in 50% of all misincorporations that occurred. In addition to hydrolytic damage products, oxidative damage products were also observed in this study and were responsible for approximately 43.5% of all misincorporations. This level of misincorporation is in contrast to previous studies characterizing miscoding lesions from the analysis of bone and teeth, where few to no oxidative damage products were observed. Of all the oxidative damage products found in this study, type 2 transversions (cytosine --> adenine/guanine --> thymine or cytosine --> guanine/guanine --> cytosine), which are commonly formed through the generation of 8-hydroxyguanine, accounted for 30.3% of all genetic miscoding lesions observed. This study identifies the previously unreported presence of oxidative DNA damage and proposes that damage to degraded DNA templates is highly specific in type, correlating with the geographic location and the taphonomic conditions of the depositional environment from which the remains are recovered.}, }
@article {pmid19043689, year = {2009}, author = {Ottoni, C and Koon, HE and Collins, MJ and Penkman, KE and Rickards, O and Craig, OE}, title = {Preservation of ancient DNA in thermally damaged archaeological bone.}, journal = {Die Naturwissenschaften}, volume = {96}, number = {2}, pages = {267-278}, pmid = {19043689}, issn = {0028-1042}, mesh = {Animals ; Archaeology ; Bone and Bones/*chemistry ; Cattle ; DNA/analysis/*genetics/isolation &amp; purification ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; *Fossils ; History, Medieval ; Polymerase Chain Reaction ; Preservation, Biological/methods ; }, abstract = {Evolutionary biologists are increasingly relying on ancient DNA from archaeological animal bones to study processes such as domestication and population dispersals. As many animal bones found on archaeological sites are likely to have been cooked, the potential for DNA preservation must be carefully considered to maximise the chance of amplification success. Here, we assess the preservation of mitochondrial DNA in a medieval cattle bone assemblage from Coppergate, York, UK. These bones have variable degrees of thermal alterations to bone collagen fibrils, indicative of cooking. Our results show that DNA preservation is not reliant on the presence of intact collagen fibrils. In fact, a greater number of template molecules could be extracted from bones with damaged collagen. We conclude that moderate heating of bone may enhance the retention of DNA fragments. Our results also indicate that ancient DNA preservation is highly variable, even within a relatively recent assemblage from contexts conducive to organic preservation, and that diagenetic parameters based on protein diagenesis are not always useful for predicting ancient DNA survival.}, }
@article {pmid19020620, year = {2008}, author = {Miller, W and Drautz, DI and Ratan, A and Pusey, B and Qi, J and Lesk, AM and Tomsho, LP and Packard, MD and Zhao, F and Sher, A and Tikhonov, A and Raney, B and Patterson, N and Lindblad-Toh, K and Lander, ES and Knight, JR and Irzyk, GP and Fredrikson, KM and Harkins, TT and Sheridan, S and Pringle, T and Schuster, SC}, title = {Sequencing the nuclear genome of the extinct woolly mammoth.}, journal = {Nature}, volume = {456}, number = {7220}, pages = {387-390}, doi = {10.1038/nature07446}, pmid = {19020620}, issn = {1476-4687}, support = {R01 HG002238/HG/NHGRI NIH HHS/United States ; HG002238/HG/NHGRI NIH HHS/United States ; }, mesh = {Africa ; Animals ; Cell Nucleus/*genetics ; Conserved Sequence/genetics ; Elephants/anatomy &amp; histology/*genetics ; *Evolution, Molecular ; *Extinction, Biological ; Female ; *Fossils ; Genome/*genetics ; *Genomics ; Hair/metabolism ; Humans ; India ; Male ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {In 1994, two independent groups extracted DNA from several Pleistocene epoch mammoths and noted differences among individual specimens. Subsequently, DNA sequences have been published for a number of extinct species. However, such ancient DNA is often fragmented and damaged, and studies to date have typically focused on short mitochondrial sequences, never yielding more than a fraction of a per cent of any nuclear genome. Here we describe 4.17 billion bases (Gb) of sequence from several mammoth specimens, 3.3 billion (80%) of which are from the woolly mammoth (Mammuthus primigenius) genome and thus comprise an extensive set of genome-wide sequence from an extinct species. Our data support earlier reports that elephantid genomes exceed 4 Gb. The estimated divergence rate between mammoth and African elephant is half of that between human and chimpanzee. The observed number of nucleotide differences between two particular mammoths was approximately one-eighth of that between one of them and the African elephant, corresponding to a separation between the mammoths of 1.5-2.0 Myr. The estimated probability that orthologous elephant and mammoth amino acids differ is 0.002, corresponding to about one residue per protein. Differences were discovered between mammoth and African elephant in amino-acid positions that are otherwise invariant over several billion years of combined mammalian evolution. This study shows that nuclear genome sequencing of extinct species can reveal population differences not evident from the fossil record, and perhaps even discover genetic factors that affect extinction.}, }
@article {pmid19018271, year = {2008}, author = {Lawrence, HA and Scofield, RP and Crockett, DE and Millar, CD and Lambert, DM}, title = {Ancient genetic variation in one of the world's rarest seabirds.}, journal = {Heredity}, volume = {101}, number = {6}, pages = {543-547}, doi = {10.1038/hdy.2008.85}, pmid = {19018271}, issn = {1365-2540}, mesh = {Animals ; Birds/*genetics ; DNA, Mitochondrial/genetics ; *Genetic Variation ; Geography ; Haplotypes ; }, abstract = {The Chatham Island Taiko (Tchaik, Pterodroma magentae) is one of the world's rarest seabirds. In the past there were millions of breeding pairs of Taiko and it was the most abundant burrowing petrel on Chatham Island. The present population consists of just 120-150 birds, including only 8-15 breeding pairs. Surprisingly high genetic variation was revealed by DNA sequencing of almost every known adult Taiko (N=90). Given the massive population decline, genetic variation may have been even larger in the past. Therefore, we investigated past genetic diversity by sequencing regions of the mitochondrial cytochrome b gene in 44 ancient Taiko bones. We identified a total of 12 haplotypes in Taiko. Eight haplotypes were revealed in the ancient DNA: four were unique to the bones and four corresponded to those found in the modern Taiko population. Surprisingly, despite the critically endangered status of the Taiko, no significant reduction in mitochondrial DNA haplotype diversity was observed between ancient samples (N=44) and modern adult Taiko (N=90). The modern population may have however lost four haplotypes present in the ancient populations.}, }
@article {pmid19015520, year = {2008}, author = {Haak, W and Brandt, G and de Jong, HN and Meyer, C and Ganslmeier, R and Heyd, V and Hawkesworth, C and Pike, AW and Meller, H and Alt, KW}, title = {Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {47}, pages = {18226-18231}, pmid = {19015520}, issn = {1091-6490}, mesh = {Adult ; *Anthropology ; *Bone and Bones ; Child ; DNA/*genetics ; *Fossils ; Funeral Rites ; Germany ; History, Ancient ; Humans ; Molecular Sequence Data ; *Social Behavior ; Strontium Isotopes/*analysis ; }, abstract = {In 2005 four outstanding multiple burials were discovered near Eulau, Germany. The 4,600-year-old graves contained groups of adults and children buried facing each other. Skeletal and artifactual evidence and the simultaneous interment of the individuals suggest the supposed families fell victim to a violent event. In a multidisciplinary approach, archaeological, anthropological, geochemical (radiogenic isotopes), and molecular genetic (ancient DNA) methods were applied to these unique burials. Using autosomal, mitochondrial, and Y-chromosomal markers, we identified genetic kinship among the individuals. A direct child-parent relationship was detected in one burial, providing the oldest molecular genetic evidence of a nuclear family. Strontium isotope analyses point to different origins for males and children versus females. By this approach, we gain insight into a Late Stone Age society, which appears to have been exogamous and patrilocal, and in which genetic kinship seems to be a focal point of social organization.}, }
@article {pmid19002248, year = {2008}, author = {Tito, RY and Macmil, S and Wiley, G and Najar, F and Cleeland, L and Qu, C and Wang, P and Romagne, F and Leonard, S and Ruiz, AJ and Reinhard, K and Roe, BA and Lewis, CM}, title = {Phylotyping and functional analysis of two ancient human microbiomes.}, journal = {PloS one}, volume = {3}, number = {11}, pages = {e3703}, pmid = {19002248}, issn = {1932-6203}, mesh = {Bacteria/classification/isolation &amp; purification ; DNA, Bacterial/analysis ; Evolution, Molecular ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Geography ; Humans ; Metagenome/*genetics ; Mexico ; *Phylogeny ; }, abstract = {BACKGROUND: The Human Microbiome Project (HMP) is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas.<br><br>We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases.<br><br>CONCLUSIONS/SIGNIFICANCE: We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today.}, }
@article {pmid19001634, year = {2009}, author = {Rambaut, A and Ho, SY and Drummond, AJ and Shapiro, B}, title = {Accommodating the effect of ancient DNA damage on inferences of demographic histories.}, journal = {Molecular biology and evolution}, volume = {26}, number = {2}, pages = {245-248}, doi = {10.1093/molbev/msn256}, pmid = {19001634}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Bison/*genetics ; *DNA Damage ; *Evolution, Molecular ; *Fossils ; Genetics, Population ; Models, Genetic ; }, abstract = {DNA sequences extracted from ancient remains are increasingly used to generate large population data sets, often spanning tens of thousands of years of population history. Bayesian coalescent methods such as those implemented in the software package BEAST can be used to estimate the demographic history of these populations, sometimes resulting in complex scenarios of fluctuations in population size, which can be correlated with the timing of environmental events, such as glaciations. Recently, however, Axelsson et al. (Axelsson E, Willerslev E, Gilbert MTP, Nielsen R. 2008. The effect of ancient DNA damage on inferences of demographic histories. Mol Biol Evol 25:2181-2187.) claimed that many of these complex demographic trends are likely to be the result of postmortem DNA damage, a problem that they investigate by removing all sites involving transitions from ancient sequences prior to analysis. When this solution is applied to a previously published data set of Pleistocene bison, they show that the demographic signal of population expansion and decline disappears. Although some apparently segregating mutations in ancient sequences may be due to postmortem damage, we argue that discarding the data will result in loss of power to detect patterns of population change. Instead, to accommodate this problem, we implement a model in which sequences are the result of a joint process of molecular evolution and postmortem DNA damage within a probabilistic inference framework. Through simulation, we demonstrate the ability of this model to accurately recover evolutionary parameters, demographic history, and DNA damage rates. When this model is applied to the bison data set, we find that the rate of DNA damage is significant but low and that the reconstruction of population size history is nearly identical to previously published estimates.}, }
@article {pmid18985148, year = {2008}, author = {Wyatt, KB and Campos, PF and Gilbert, MT and Kolokotronis, SO and Hynes, WH and DeSalle, R and Ball, SJ and Daszak, P and MacPhee, RD and Greenwood, AD}, title = {Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease.}, journal = {PloS one}, volume = {3}, number = {11}, pages = {e3602}, pmid = {18985148}, issn = {1932-6203}, mesh = {Animals ; Chimera/genetics/parasitology ; Crosses, Genetic ; DNA, Protozoan/analysis/isolation &amp; purification ; *Disease Transmission, Infectious/history/veterinary ; *Extinction, Biological ; Genetic Predisposition to Disease ; History, 18th Century ; History, 19th Century ; Indian Ocean ; Mammals/genetics/parasitology ; Micronesia ; Models, Biological ; Phylogeny ; Population Dynamics ; *Rats/genetics/parasitology/physiology ; Trypanosoma/genetics/pathogenicity ; Trypanosomiasis/genetics/parasitology/transmission/veterinary ; }, abstract = {It is now widely accepted that novel infectious disease can be a leading cause of serious population decline and even outright extinction in some invertebrate and vertebrate groups (e.g., amphibians). In the case of mammals, however, there are still no well-corroborated instances of such diseases having caused or significantly contributed to the complete collapse of species. A case in point is the extinction of the endemic Christmas Island rat (Rattus macleari): although it has been argued that its disappearance ca. AD 1900 may have been partly or wholly caused by a pathogenic trypanosome carried by fleas hosted on recently-introduced black rats (Rattus rattus), no decisive evidence for this scenario has ever been adduced. Using ancient DNA methods on samples from museum specimens of these rodents collected during the extinction window (AD 1888-1908), we were able to resolve unambiguously sequence evidence of murid trypanosomes in both endemic and invasive rats. Importantly, endemic rats collected prior to the introduction of black rats were devoid of trypanosome signal. Hybridization between endemic and black rats was also previously hypothesized, but we found no evidence of this in examined specimens, and conclude that hybridization cannot account for the disappearance of the endemic species. This is the first molecular evidence for a pathogen emerging in a naïve mammal species immediately prior to its final collapse.}, }
@article {pmid18955696, year = {2008}, author = {Bon, C and Caudy, N and de Dieuleveult, M and Fosse, P and Philippe, M and Maksud, F and Beraud-Colomb, E and Bouzaid, E and Kefi, R and Laugier, C and Rousseau, B and Casane, D and van der Plicht, J and Elalouf, JM}, title = {Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {45}, pages = {17447-17452}, pmid = {18955696}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Bone and Bones/*chemistry ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; *Extinction, Biological ; France ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques/methods ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Ursidae/classification/*genetics ; }, abstract = {Retrieving a large amount of genetic information from extinct species was demonstrated feasible, but complete mitochondrial genome sequences have only been deciphered for the moa, a bird that became extinct a few hundred years ago, and for Pleistocene species, such as the woolly mammoth and the mastodon, both of which could be studied from animals embedded in permafrost. To enlarge the diversity of mitochondrial genomes available for Pleistocene species, we turned to the cave bear (Ursus spelaeus), whose only remains consist of skeletal elements. We collected bone samples from the Paleolithic painted cave of Chauvet-Pont d'Arc (France), which displays the earliest known human drawings, and contains thousands of bear remains. We selected a cave bear sternebra, radiocarbon dated to 32,000 years before present, from which we generated overlapping DNA fragments assembling into a 16,810-base pair mitochondrial genome. Together with the first mitochondrial genome for the brown bear western lineage, this study provides a statistically secured molecular phylogeny assessing the cave bear as a sister taxon to the brown bear and polar bear clade, with a divergence inferred to 1.6 million years ago. With the first mitochondrial genome for a Pleistocene carnivore to be delivered, our study establishes the Chauvet-Pont d'Arc Cave as a new reservoir for Paleogenetic studies. These molecular data enable establishing the chronology of bear speciation, and provide a helpful resource to rescue for genetic analysis archeological samples initially diagnosed as devoid of amplifiable DNA.}, }
@article {pmid18951391, year = {2009}, author = {Adachi, N and Shinoda, K and Umetsu, K and Matsumura, H}, title = {Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American.}, journal = {American journal of physical anthropology}, volume = {138}, number = {3}, pages = {255-265}, doi = {10.1002/ajpa.20923}, pmid = {18951391}, issn = {1096-8644}, mesh = {Asia ; Bone and Bones/*anatomy &amp; histology ; DNA Primers ; DNA, Mitochondrial/*genetics ; Humans ; Indians, North American/*genetics ; Japan ; NADH Dehydrogenase/genetics ; Phylogeny ; RNA, Transfer, Arg/genetics ; Siberia ; Skeleton ; }, abstract = {Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America.}, }
@article {pmid18925940, year = {2008}, author = {Faure, E}, title = {Could FIV zoonosis responsible of the breakdown of the pathocenosis which has reduced the European CCR5-Delta32 allele frequencies?.}, journal = {Virology journal}, volume = {5}, number = {}, pages = {119}, pmid = {18925940}, issn = {1743-422X}, mesh = {Animals ; Cats ; Ethnicity ; Europe ; *Gene Frequency ; Genetics, Population ; Humans ; Immunodeficiency Virus, Feline/*growth &amp; development ; Lentivirus Infections/*transmission ; Receptors, CCR5/*genetics ; Selection, Genetic ; *Sequence Deletion ; Zoonoses/*transmission ; }, abstract = {BACKGROUND: In Europe, the north-south downhill cline frequency of the chemokine receptor CCR5 allele with a 32-bp deletion (CCR5-Delta32) raises interesting questions for evolutionary biologists. We had suggested first that, in the past, the European colonizers, principally Romans, might have been instrumental of a progressively decrease of the frequencies southwards. Indeed, statistical analyses suggested strong negative correlations between the allele frequency and historical parameters including the colonization dates by Mediterranean civilisations. The gene flows from colonizers to native populations were extremely low but colonizers are responsible of the spread of several diseases suggesting that the dissemination of parasites in naive populations could have induced a breakdown rupture of the fragile pathocenosis changing the balance among diseases. The new equilibrium state has been reached through a negative selection of the null allele.<br><br>RESULTS: Most of the human diseases are zoonoses and cat might have been instrumental in the decrease of the allele frequency, because its diffusion through Europe was a gradual process, due principally to Romans; and that several cat zoonoses could be transmitted to man. The possible implication of a feline lentivirus (FIV) which does not use CCR5 as co-receptor is discussed. This virus can infect primate cells in vitro and induces clinical signs in macaque. Moreover, most of the historical regions with null or low frequency of CCR5-Delta32 allele coincide with historical range of the wild felid species which harbor species-specific FIVs.<br><br>CONCLUSION: We proposed the hypothesis that the actual European CCR5 allelic frequencies are the result of a negative selection due to a disease spreading. A cat zoonosis, could be the most plausible hypothesis. Future studies could provide if CCR5 can play an antimicrobial role in FIV pathogenesis. Moreover, studies of ancient DNA could provide more evidences regarding the implications of zoonoses in the actual CCR5-Delta32 distribution.}, }
@article {pmid18853361, year = {2008}, author = {Munch, K and Boomsma, W and Huelsenbeck, JP and Willerslev, E and Nielsen, R}, title = {Statistical assignment of DNA sequences using Bayesian phylogenetics.}, journal = {Systematic biology}, volume = {57}, number = {5}, pages = {750-757}, doi = {10.1080/10635150802422316}, pmid = {18853361}, issn = {1076-836X}, support = {R01 GM069801/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Computer Simulation ; DNA/*genetics ; Insecta/genetics ; *Models, Genetic ; *Models, Statistical ; *Phylogeny ; Plants/genetics ; }, abstract = {We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all false assignment based on best Blast hit. However, the most important advance of the method is that it provides statistically meaningful measures of confidence. We apply the method to a re-analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA.}, }
@article {pmid18852900, year = {2008}, author = {Bollongino, R and Elsner, J and Vigne, JD and Burger, J}, title = {Y-SNPs do not indicate hybridisation between European aurochs and domestic cattle.}, journal = {PloS one}, volume = {3}, number = {10}, pages = {e3418}, pmid = {18852900}, issn = {1932-6203}, mesh = {Animals ; Cattle/*genetics ; Europe ; Gene Frequency ; *Genetics, Population ; Haplotypes ; History, Ancient ; Hybridization, Genetic ; Male ; *Phylogeny ; *Polymorphism, Single Nucleotide ; *Y Chromosome ; }, abstract = {BACKGROUND: Previous genetic studies of modern and ancient mitochondrial DNA have confirmed the Near Eastern origin of early European domestic cattle. However, these studies were not able to test whether hybridisation with male aurochs occurred post-domestication. To address this issue, Götherström and colleagues (2005) investigated the frequencies of two Y-chromosomal haplotypes in extant bulls. They found a significant influence of wild aurochs males on domestic populations thus challenging the common view on early domestication and Neolithic stock-rearing. To test their hypothesis, we applied these Y-markers on Neolithic bone specimens from various European archaeological sites.<br><br>METHODS AND FINDINGS: Here, we have analysed the ancient DNA of 59 Neolithic skeletal samples. After initial molecular sexing, two segregating Y-SNPs were identified in 13 bulls. Strikingly, our results do not support the hypothesis that these markers distinguish European aurochs from domesticated cattle.<br><br>CONCLUSIONS: The model of a rapid introduction of domestic cattle into Central Europe without significant crossbreeding with local wild cattle remains unchallenged.}, }
@article {pmid18842688, year = {2009}, author = {Kuraku, S and Meyer, A and Kuratani, S}, title = {Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after?.}, journal = {Molecular biology and evolution}, volume = {26}, number = {1}, pages = {47-59}, doi = {10.1093/molbev/msn222}, pmid = {18842688}, issn = {1537-1719}, mesh = {Animals ; *Gene Duplication ; Genes, Homeobox ; *Genome ; Hagfishes/*genetics ; Lampreys/*genetics ; Molecular Sequence Data ; Opsonin Proteins/genetics ; *Phylogeny ; Receptors, Retinoic Acid/genetics ; Synteny ; Vertebrates/*genetics ; }, abstract = {Two rounds of whole-genome duplications are thought to have played an important role in the establishment of gene repertoires in vertebrates. These events occurred during chordate evolution after the split of the urochordate and cephalochordate lineages but before the radiation of extant gnathostomes (jawed vertebrates). During this interval, diverse agnathans (jawless fishes), including cyclostomes (hagfishes and lampreys), diverged. However, there is no solid evidence for the timing of these genome duplications in relation to the divergence of cyclostomes from the gnathostome lineage. We conducted cDNA sequencing in diverse early vertebrates for members of homeobox-containing (Dlx and ParaHox) and other gene families that would serve as landmarks for genome duplications. Including these new sequences, we performed a molecular phylogenetic census using the maximum likelihood method for 55 gene families. In most of these gene families, we detected many more gene duplications before the cyclostome-gnathostome split, than after. Many of these gene families (e.g., visual opsins, RAR, Notch) have multiple paralogs in conserved, syntenic genomic regions that must have been generated by large-scale duplication events. Taken together, this indicates that the genome duplications occurred before the cyclostome-gnathostome split. We propose that the redundancy in gene repertoires possessed by all vertebrates, including hagfishes and lampreys, was introduced primarily by genome duplications. Apart from subsequent lineage-specific modifications, these ancient genome duplication events might serve generally to distinguish vertebrates from invertebrates at the genomic level.}, }
@article {pmid18833341, year = {2008}, author = {Xu, Z and Zhang, F and Xu, B and Tan, J and Li, S and Li, C and Zhou, H and Zhu, H and Zhang, J and Duan, Q and Jin, L}, title = {Mitochondrial DNA evidence for a diversified origin of workers building First Emperor of China.}, journal = {PloS one}, volume = {3}, number = {10}, pages = {e3275}, pmid = {18833341}, issn = {1932-6203}, mesh = {Base Sequence ; China ; Cloning, Molecular ; DNA Primers ; DNA, Mitochondrial/*genetics ; History, Ancient ; Humans ; Molecular Sequence Data ; *Occupations ; Polymorphism, Restriction Fragment Length ; Sequence Homology, Nucleic Acid ; }, abstract = {Variant studies on ancient DNA have attempted to reveal individual origin. Here, based on cloning sequencing and polymerase chain reaction-restriction fragment length polymorphisms, we analyzed polymorphisms in the first hypervariable region and coding regions of mitochondrial DNA of 19 human bone remains which were excavated from a tomb near the Terra Cotta Warriors and dated some 2,200 years before present. With the aim of shedding light on origins of these samples who were supposed to be workers building the mausoleum for the First Emperor of China, we compared them with 2,164 mtDNA profiles from 32 contemporary Chinese populations at both population and individual levels. Our results showed that mausoleum-building workers may be derived from very diverse sources of origin.}, }
@article {pmid18799009, year = {2008}, author = {Bachmann, L and Däubl, B and Lindqvist, C and Kruckenhauser, L and Teschler-Nicola, M and Haring, E}, title = {PCR diagnostics of Mycobacterium tuberculosis in historic human long bone remains from 18th century burials in Kaiserebersdorf, Austria.}, journal = {BMC research notes}, volume = {1}, number = {}, pages = {83}, pmid = {18799009}, issn = {1756-0500}, abstract = {UNLABELLED: In the present pilot study we applied recently published protocols for detecting Mycobacterium tuberculosis in human remains. We screened long bones from an 18th century cemetery and skulls from the anatomical "Weisbach collection" (19th century). In addition, besides the study of abundance of tuberculosis in inmates of the poorhouse itself, we were interested to test whether in this particular instance tuberculosis can be identified from cortical bones, which are rarely affected by tuberculosis, but mostly better preserved than the vertebral bodies or epiphyses.<br><br>METHOD: The DNA extractions from the bone samples were obtained following established ancient DNA protocols. Subsequently extracts were subjected to a series of PCR amplifications using primer pairs published previously 12. PCR products of the expected size were subsequently sequenced.<br><br>RESULTS: Only primers targeting the repetitive IS6110 insertion sequence yielded PCR products of appropriate size. In one sample only (skull sample WB354 of the "Weisbach collection") sequence analysis revealed an authentic M. tuberculosis sequence that matched to a reference sequence from GenBank.<br><br>CONCLUSION: With a variety of established PCR approaches we failed to detect M. tuberculosis DNA in historic human femurs from an 18th century cemetery relating to a poor house in Kaiserebersdorf, Austria. Our data may indicate that in this particular case, thoracic or lumbar vertebrae, i.e. bones that are severely affected by the disease, would be more suitable for molecular diagnostics than long bones. However, the unpredictable state of DNA preservation in bones from museum collections does not allow any general recommendation of any type of bone.}, }
@article {pmid18790087, year = {2008}, author = {Faure, E and Royer-Carenzi, M}, title = {Is the European spatial distribution of the HIV-1-resistant CCR5-Delta32 allele formed by a breakdown of the pathocenosis due to the historical Roman expansion?.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {8}, number = {6}, pages = {864-874}, doi = {10.1016/j.meegid.2008.08.007}, pmid = {18790087}, issn = {1567-1348}, mesh = {Analysis of Variance ; Demography ; Evolution, Molecular ; Gene Flow ; *Gene Frequency ; Geography ; HIV Infections/*genetics/immunology ; *HIV-1 ; History, Ancient ; Humans ; Immunity, Innate/*genetics ; Linear Models ; *Mutation ; Receptors, CCR5/*genetics ; Roman World/history ; Selection, Genetic ; White People/*genetics/history ; }, abstract = {We studied the possible effects of the expansion of ancient Mediterranean civilizations during the five centuries before and after Christ on the European distribution of the mutant allele for the chemokine receptor gene CCR5 which has a 32-bp deletion (CCR5-Delta32). There is a strong evidence for the unitary origin of the CCR5-Delta32 mutation, this it is found principally in Europe and Western Asia, with generally a north-south downhill cline frequency. Homozygous carriers of this mutation show a resistance to HIV-1 infection and a slower progression towards AIDS. However, HIV has clearly emerged too recently to have been the selective force on CCR5. Our analyses showed strong negative correlations in Europe between the allele frequency and two historical parameters, i.e. the first colonization dates by the great ancient Mediterranean civilizations, and the distances from the Northern frontiers of the Roman Empire in its greatest expansion. Moreover, other studies have shown that the deletion frequencies in both German Bronze Age and Swedish Neolithic populations were similar to those found in the corresponding modern populations, and this deletion has been found in ancient DNA of around 7000 years ago, suggesting that in the past, the deletion frequency could have been relatively high in European populations. In addition, in West Nile virus pathogenesis, CCR5 plays an antimicrobial role showing that host genetic factors are highly pathogen-specific. Our results added to all these previous data suggest that the actual European allele frequency distribution might not be due to genes spreading, but to a negative selection resulting in the spread of pathogens principally during Roman expansion. Indeed, as gene flows from colonizers to European native populations were extremely low, the mutational changes might be associated with vulnerability to imported infections. To date, the nature of the parasites remains unknown; however, zoonoses could be incriminated.}, }
@article {pmid18776461, year = {2008}, author = {Kranaster, R and Marx, A}, title = {New strategies for DNA polymerase library screening.}, journal = {Nucleic acids symposium series (2004)}, volume = {}, number = {52}, pages = {477-478}, doi = {10.1093/nass/nrn242}, pmid = {18776461}, issn = {1746-8272}, mesh = {DNA Primers ; DNA-Directed DNA Polymerase/*genetics/*metabolism ; *Gene Library ; Mutation ; Oligonucleotide Array Sequence Analysis/*methods ; }, abstract = {Engineered enzymes are of increasing importance for a plethora of biotechnical applications. Especially DNA polymerases are workhorses in biochemical technologies in particular the polymerase chain reaction (PCR), cDNA cloning procedures, genome sequencing and in diagnostic applications. DNA polymerase mutant libraries can be used for the screening of non-standard reaction conditions or substrates e.g. the efficient amplification of difficult templates like ancient DNA. We are convinced that these fascinating enzymes can be optimized and custom-made for a specific application to result in more robust and reliable systems. To our knowledge, all known screening methods for DNA polymerase mutants are focused and thus limited to the screening of a single reaction or one new function. We developed improved strategies for multiplexed DNA polymerase screening that will be presented.}, }
@article {pmid18776392, year = {2008}, author = {Yamamoto, J and Loakes, D and Masutani, C and Simmyo, S and Urabe, K and Hanaoka, F and Holliger, P and Iwai, S}, title = {Translesion synthesis across the (6-4) photoproduct and its Dewar valence isomer by the Y-family and engineered DNA polymerases.}, journal = {Nucleic acids symposium series (2004)}, volume = {}, number = {52}, pages = {339-340}, doi = {10.1093/nass/nrn171}, pmid = {18776392}, issn = {1746-8272}, support = {MC_U105178804/MRC_/Medical Research Council/United Kingdom ; }, mesh = {DNA/biosynthesis/chemistry ; DNA-Directed DNA Polymerase/genetics/*metabolism ; Humans ; Isomerism ; Mutation ; Protein Engineering ; Pyrimidine Dimers/*chemistry ; Thermus/enzymology ; DNA Polymerase iota ; }, abstract = {We analyzed the translesion synthesis across the UV-induced lesions, the (6-4) photoproduct and its Dewar valence isomer, by using human DNA polymerases eta and iota in vitro. The primer extension experiments revealed that pol eta tended to incorporate dG opposite the 3' component of both lesions, but the incorporation efficiency for the Dewar isomer was higher than that for the (6-4) photoproduct. On the other hand, pol iota was likely to incorporate dA opposite the 3' components of the (6-4) photoproduct and its Dewar isomer with a similar efficiency. Elongation after the incorporation opposite the UV lesions was not observed for these Y-family polymerases. We further analyzed the bypass ability of an engineered polymerase developed from Thermus DNA polymerase for the amplification of ancient DNA. This polymerase could bypass the Dewar isomer more efficiently than the (6-4) photoproduct.}, }
@article {pmid18771918, year = {2008}, author = {Debruyne, R and Chu, G and King, CE and Bos, K and Kuch, M and Schwarz, C and Szpak, P and Gröcke, DR and Matheus, P and Zazula, G and Guthrie, D and Froese, D and Buigues, B and de Marliave, C and Flemming, C and Poinar, D and Fisher, D and Southon, J and Tikhonov, AN and MacPhee, RD and Poinar, HN}, title = {Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths.}, journal = {Current biology : CB}, volume = {18}, number = {17}, pages = {1320-1326}, doi = {10.1016/j.cub.2008.07.061}, pmid = {18771918}, issn = {0960-9822}, mesh = {Animals ; Asia ; Biodiversity ; DNA, Mitochondrial/*chemistry ; Extinction, Biological ; *Fossils ; Geography ; Haplotypes ; Mammals/*genetics ; North America ; *Phylogeny ; Population Dynamics ; }, abstract = {Although the iconic mammoth of the Late Pleistocene, the woolly mammoth (Mammuthus primigenius), has traditionally been regarded as the end point of a single anagenetically evolving lineage, recent paleontological and molecular studies have shown that successive allopatric speciation events must have occurred within Pleistocene Mammuthus in Asia, with subsequent expansion and hybridization between nominal taxa [1, 2]. However, the role of North American mammoth populations in these events has not been adequately explored from an ancient-DNA standpoint. To undertake this task, we analyzed mtDNA from a large data set consisting of mammoth samples from across Holarctica (n = 160) and representing most of radiocarbon time. Our evidence shows that, during the terminal Pleistocene, haplotypes originating in and characteristic of New World populations replaced or succeeded those endemic to Asia and western Beringia. Also, during the Last Glacial Maximum, mammoth populations do not appear to have suffered an overall decline in diversity, despite differing responses on either side of the Bering land bridge. In summary, the "Out-of-America" hypothesis holds that the dispersal of North American woolly mammoths into other parts of Holarctica created major phylogeographic structuring within Mammuthus primigenius populations, shaping the last phase of their evolutionary history before their demise.}, }
@article {pmid18702302, year = {2008}, author = {Fedorova, SA and Stepanov, AD and Adoian, M and Parik, J and Argunov, VA and Ozawa, T and Khusnutdinova, EK and Villems, R}, title = {[Phylogenetic analysis of ancient mitochondrial DNA lineages of human remains found in Yakutia].}, journal = {Molekuliarnaia biologiia}, volume = {42}, number = {3}, pages = {445-453}, pmid = {18702302}, issn = {0026-8984}, mesh = {Asian People/ethnology/*genetics ; DNA, Mitochondrial/*genetics ; Haplotypes/genetics ; Humans ; Paleontology ; *Phylogeny ; Siberia ; }, abstract = {Molecular genetic analysis of ancient human remains are mostly based on mitochondrial DNA due to its better preservation in human skeletons in comparison with nuclear DNA. We investigated mtDNA extracted from human skeletons found in graves in Yakutia to determine their haplotypes and to compare them with lineages of modern populations. Ancient DNA was extracted from fragments of three skeletons of Yakut graves at At-Dabaan, Ojuluun and Jaraama sites (dating XVIII century) and two skeletons of Neolithic graves at Kerdugen site found in central Yakutia (Churapchinsky, Kangalassky and Megino-Kangalassky districts of Yakutia). Five different haplotypes belonging to specific Asian haplogroups were identified. Lineages of mtDNA of Yakut graves belong to haplo-groups C4a, D5a2 and B5b. Our results indicate the continuity of mitochondrial lineages in the Yakut gene pool during the last 300 years. Haplotypes of two humans from Kerdugen site graves belong to haplogroups A4 and G2a/D. We compared these haplotypes with that of 40,000 Eurasian individuals, 900 of them from Yakutia. No exact matches were found in Paleoasian populations of Chukchi, Eskimos, Koryaks and Itelmen. Phylogenetically close haplotypes (+/- 1 mutation) were found in populations of Yakuts and Evenks, as well as in some populations of China, Southern and Western Siberia.}, }
@article {pmid18701071, year = {2008}, author = {Nikonov, SS and Brown, BM and Davis, JA and Zuniga, FI and Bragin, A and Pugh, EN and Craft, CM}, title = {Mouse cones require an arrestin for normal inactivation of phototransduction.}, journal = {Neuron}, volume = {59}, number = {3}, pages = {462-474}, pmid = {18701071}, issn = {1097-4199}, support = {EY016453/EY/NEI NIH HHS/United States ; R01 EY002660-30/EY/NEI NIH HHS/United States ; R01 EY015851-02/EY/NEI NIH HHS/United States ; R01 EY015851-04/EY/NEI NIH HHS/United States ; EY02660/EY/NEI NIH HHS/United States ; GM799102/GM/NIGMS NIH HHS/United States ; R01 EY016453/EY/NEI NIH HHS/United States ; F31 GM079910/GM/NIGMS NIH HHS/United States ; R01 EY015851-03/EY/NEI NIH HHS/United States ; EY015851/EY/NEI NIH HHS/United States ; R01 EY015851-01A2/EY/NEI NIH HHS/United States ; R01 EY002660/EY/NEI NIH HHS/United States ; EY03040/EY/NEI NIH HHS/United States ; }, mesh = {Analysis of Variance ; Animals ; Arrestin/classification/deficiency/*metabolism ; Electrophysiology ; Light ; Membrane Potentials/genetics/radiation effects ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Microscopy, Confocal ; Reaction Time/physiology ; Retina/cytology ; Retinal Cone Photoreceptor Cells/*physiology ; Rod Opsins/pharmacology ; Vision, Ocular/*physiology/radiation effects ; }, abstract = {Arrestins are proteins that arrest the activity of G protein-coupled receptors (GPCRs). While it is well established that normal inactivation of photoexcited rhodopsin, the GPCR of rod phototransduction, requires arrestin (Arr1), it has been controversial whether the same requirement holds for cone opsin inactivation. Mouse cone photoreceptors express two distinct visual arrestins: Arr1 and Arr4. By means of recordings from cones of mice with one or both arrestins knocked out, this investigation establishes that a visual arrestin is required for normal cone inactivation. Arrestin-independent inactivation is 70-fold more rapid in cones than in rods, however. Dual arrestin expression in cones could be a holdover from ancient genome duplication events that led to multiple isoforms of arrestin, allowing evolutionary specialization of one form while the other maintains the basic function.}, }
@article {pmid18692462, year = {2008}, author = {Clark, AG}, title = {Genome sequences from extinct relatives.}, journal = {Cell}, volume = {134}, number = {3}, pages = {388-389}, doi = {10.1016/j.cell.2008.07.026}, pmid = {18692462}, issn = {1097-4172}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Fossils ; Hominidae/*genetics ; Humans ; Sequence Analysis, DNA ; }, abstract = {Next-generation sequencing methods use massively parallel detection of short sequencing reactions, making them ideal for the analysis of ancient DNA. In this issue, Green et al. (2008) exploit this feature to infer the complete mitochondrial genome sequence of one Neanderthal and place bounds on its time of common ancestry with modern humans.}, }
@article {pmid18684136, year = {2008}, author = {Leonard, JA}, title = {Ancient DNA applications for wildlife conservation.}, journal = {Molecular ecology}, volume = {17}, number = {19}, pages = {4186-4196}, doi = {10.1111/j.1365-294X.2008.03891.x}, pmid = {18684136}, issn = {0962-1083}, mesh = {Animals ; Animals, Wild/*genetics ; Birds/genetics ; Breeding/methods/standards ; Climate ; *Conservation of Natural Resources ; DNA/*genetics ; Fishes/genetics ; Gene Flow ; Genetic Drift ; *Genetic Variation ; Greenhouse Effect ; Humans ; Mammals/genetics ; Population Density ; Social Responsibility ; }, abstract = {Ancient DNA analyses of historical, archaeological and paleontological remains can contribute important information for the conservation of populations and species that cannot be obtained any other way. In addition to ancient DNA analyses involving a single or few individuals, population level studies are now possible. Biases inherent in estimating population parameters and history from modern genetic diversity are exaggerated when populations are small or have been heavily impacted by recent events, as is common for many endangered species. Going directly back in time to study past populations removes many of the assumptions that undermine conclusions based only on recent populations. Accurate characterization of historic population size, levels of gene flow and relationships with other populations are fundamental to developing appropriate conservation and management plans. The incorporation of ancient DNA into conservation genetics holds a lot of potential, if it is employed responsibly.}, }
@article {pmid18664258, year = {2008}, author = {Ludwig, A and Arndt, U and Lippold, S and Benecke, N and Debus, L and King, TL and Matsumura, S}, title = {Tracing the first steps of American sturgeon pioneers in Europe.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {221}, pmid = {18664258}, issn = {1471-2148}, mesh = {Animals ; Atlantic Ocean ; Base Sequence ; Chimera/genetics ; DNA, Mitochondrial/*genetics ; Europe ; *Evolution, Molecular ; Fishes/*genetics ; *Genetics, Population ; Haplotypes ; *Microsatellite Repeats ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: A Baltic population of Atlantic sturgeon was founded approximately 1,200 years ago by migrants from North America, but after centuries of persistence, the population was extirpated in the 1960s, mainly as a result of over-harvest and habitat alterations. As there are four genetically distinct groups of Atlantic sturgeon inhabiting North American rivers today, we investigated the genetic provenance of the historic Baltic population by ancient DNA analyses using mitochondrial and nuclear markers.<br><br>RESULTS: The phylogeographic signal obtained from multilocus microsatellite DNA genotypes and mitochondrial DNA control region haplotypes, when compared to existing baseline datasets from extant populations, allowed for the identification of the region-of-origin of the North American Atlantic sturgeon founders. Moreover, statistical and simulation analyses of the multilocus genotypes allowed for the calculation of the effective number of individuals that originally founded the European population of Atlantic sturgeon. Our findings suggest that the Baltic population of A. oxyrinchus descended from a relatively small number of founders originating from the northern extent of the species' range in North America.<br><br>CONCLUSION: These results demonstrate that the most northerly distributed North American A. oxyrinchus colonized the Baltic Sea approximately 1,200 years ago, suggesting that Canadian specimens should be the primary source of broodstock used for restoration in Baltic rivers. This study illustrates the great potential of patterns obtained from ancient DNA to identify population-of-origin to investigate historic genotype structure of extinct populations.}, }
@article {pmid18663216, year = {2008}, author = {Gongora, J and Rawlence, NJ and Mobegi, VA and Jianlin, H and Alcalde, JA and Matus, JT and Hanotte, O and Moran, C and Austin, JJ and Ulm, S and Anderson, AJ and Larson, G and Cooper, A}, title = {Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {30}, pages = {10308-10313}, pmid = {18663216}, issn = {1091-6490}, mesh = {Animals ; Asia ; Base Sequence ; Chickens/*genetics ; Chile ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; Europe ; *Genetic Variation ; Haplotypes/genetics ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Genetic ; Polynesia ; Sequence Analysis, DNA ; }, abstract = {European chickens were introduced into the American continents by the Spanish after their arrival in the 15th century. However, there is ongoing debate as to the presence of pre-Columbian chickens among Amerindians in South America, particularly in relation to Chilean breeds such as the Araucana and Passion Fowl. To understand the origin of these populations, we have generated partial mitochondrial DNA control region sequences from 41 native Chilean specimens and compared them with a previously generated database of approximately 1,000 domestic chicken sequences from across the world as well as published Chilean and Polynesian ancient DNA sequences. The modern Chilean sequences cluster closely with haplotypes predominantly distributed among European, Indian subcontinental, and Southeast Asian chickens, consistent with a European genetic origin. A published, apparently pre-Columbian, Chilean specimen and six pre-European Polynesian specimens also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing no support for a Polynesian introduction of chickens to South America. In contrast, sequences from two archaeological sites on Easter Island group with an uncommon haplogroup from Indonesia, Japan, and the Philippines [corrected] and may represent a genetic signature of an early Polynesian dispersal. Modeling of the potential marine carbon contribution to the Chilean archaeological specimen casts further doubt on claims for pre-Columbian chickens, and definitive proof will require further analyses of ancient DNA sequences and radiocarbon and stable isotope data from archaeological excavations within both Chile and Polynesia.}, }
@article {pmid18662376, year = {2008}, author = {Krause, J and Unger, T and Noçon, A and Malaspinas, AS and Kolokotronis, SO and Stiller, M and Soibelzon, L and Spriggs, H and Dear, PH and Briggs, AW and Bray, SC and O'Brien, SJ and Rabeder, G and Matheus, P and Cooper, A and Slatkin, M and Pääbo, S and Hofreiter, M}, title = {Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {220}, pmid = {18662376}, issn = {1471-2148}, support = {MC_U105131672/MRC_/Medical Research Council/United Kingdom ; R01-GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Extinction, Biological ; Fossils ; *Genetic Speciation ; *Genome, Mitochondrial ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Ursidae/classification/*genetics ; }, abstract = {BACKGROUND: Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods.<br><br>RESULTS: We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus Ursus. The sun bear is the sister taxon to both the American and Asian black bears, and this clade is the sister clade of cave bear, brown bear and polar bear confirming a recent study on bear mitochondrial genomes.<br><br>CONCLUSION: Sequences from extinct bears represent the third and fourth Pleistocene species for which complete mitochondrial genomes have been sequenced. Moreover, the cave bear specimen demonstrates that mitogenomic studies can be applied to Pleistocene fossils that have not been preserved in permafrost, and therefore have a broad application within ancient DNA research. Molecular dating of the mtDNA divergence times suggests a rapid radiation of bears in both the Old and New Worlds around 5 million years ago, at the Miocene-Pliocene boundary. This coincides with major global changes, such as the Messinian crisis and the first opening of the Bering Strait, and suggests a global influence of such events on species radiations.}, }
@article {pmid18661472, year = {2009}, author = {Fu, Y and Xie, C and Xu, X and Li, C and Zhang, Q and Zhou, H and Zhu, H}, title = {Ancient DNA analysis of human remains from the Upper Capital City of Kublai Khan.}, journal = {American journal of physical anthropology}, volume = {138}, number = {1}, pages = {23-29}, doi = {10.1002/ajpa.20894}, pmid = {18661472}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Archaeology/methods ; Asian People/*genetics ; Cemeteries ; China ; Climate ; DNA/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Female ; Genetics, Population ; Humans ; Male ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Seasons ; Tooth/anatomy &amp; histology ; Young Adult ; }, abstract = {Analysis of DNA from human archaeological remains is a powerful tool for reconstructing ancient events in human history. To help understand the origin of the inhabitants of Kublai Khan's Upper Capital in Inner Mongolia, we analyzed mitochondrial DNA (mtDNA) polymorphisms in 21 ancient individuals buried in the Zhenzishan cemetery of the Upper Capital. MtDNA coding and noncoding region polymorphisms identified in the ancient individuals were characteristic of the Asian mtDNA haplogroups A, B, N9a, C, D, Z, M7b, and M. Phylogenetic analysis of the ancient mtDNA sequences, and comparison with extant reference populations, revealed that the maternal lineages of the population buried in the Zhenzishan cemetery are of Asian origin and typical of present-day Han Chinese, despite the presence of typical European morphological features in several of the skeletons.}, }
@article {pmid18653730, year = {2008}, author = {Axelsson, E and Willerslev, E and Gilbert, MT and Nielsen, R}, title = {The effect of ancient DNA damage on inferences of demographic histories.}, journal = {Molecular biology and evolution}, volume = {25}, number = {10}, pages = {2181-2187}, doi = {10.1093/molbev/msn163}, pmid = {18653730}, issn = {1537-1719}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Bison/*genetics ; *DNA Damage ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Models, Genetic ; Phylogeny ; Polymerase Chain Reaction ; Population Density ; Sequence Analysis, DNA ; }, abstract = {The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution.}, }
@article {pmid18644108, year = {2008}, author = {Mendizabal, I and Sandoval, K and Berniell-Lee, G and Calafell, F and Salas, A and Martínez-Fuentes, A and Comas, D}, title = {Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {213}, pmid = {18644108}, issn = {1471-2148}, mesh = {Chromosomes, Human, Y/*genetics ; Cuba/ethnology ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Male ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Racial Groups/genetics ; }, abstract = {BACKGROUND: Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals.<br><br>RESULTS: The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively.<br><br>CONCLUSION: While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.}, }
@article {pmid18627611, year = {2008}, author = {Greiss, S and Schumacher, B and Grandien, K and Rothblatt, J and Gartner, A}, title = {Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {334}, pmid = {18627611}, issn = {1471-2164}, support = {//Cancer Research UK/United Kingdom ; }, mesh = {Animals ; *Apoptosis ; Caenorhabditis elegans/*genetics/*radiation effects ; Caenorhabditis elegans Proteins/*genetics/*radiation effects ; *DNA Damage ; Gene Expression Profiling ; Gene Expression Regulation ; Oligonucleotide Array Sequence Analysis ; RNA, Helminth/genetics/radiation effects ; Repressor Proteins/genetics/radiation effects ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic ; Tumor Suppressor Protein p53/*genetics/*radiation effects ; }, abstract = {BACKGROUND: In contrast to the three mammalian p53 family members, p53, which is generally involved in DNA damage responses, and p63 and p73 which are primarily needed for developmental regulation, cep-1 encodes for the single C. elegans p53-like gene. cep-1 acts as a transcription activator in a primordial p53 pathway that involves CEP-1 activation and the CEP-1 dependent transcriptional induction of the worm BH3 only domain encoding genes egl-1 and ced-13 to induce germ cell apoptosis. EGL-1 and CED-13 proteins inactivate Bcl-2 like CED-9 to trigger CED-4 and CED-3 caspase dependent germ cell apoptosis. To address the function of p53 in global transcriptional regulation we investigate genome-wide transcriptional responses upon DNA damage and cep-1 deficiency.<br><br>RESULTS: Examining C. elegans expression profiles using whole genome Affymetrix GeneChip arrays, we found that 83 genes were induced more than two fold upon ionizing radiation (IR). None of these genes, with exception of an ATP ribosylase homolog, encode for known DNA repair genes. Using two independent cep-1 loss of function alleles we did not find genes regulated by cep-1 in the absence of IR. Among the IR-induced genes only three are dependent on cep-1, namely egl-1, ced-13 and a novel C. elegans specific gene. The majority of IR-induced genes appear to be involved in general stress responses, and qRT-PCR experiments indicate that they are mainly expressed in somatic tissues. Interestingly, we reveal an extensive overlap of gene expression changes occurring in response to DNA damage and in response to bacterial infection. Furthermore, many genes induced by IR are also transcriptionally regulated in longevity mutants suggesting that DNA damage and aging induce an overlapping stress response.<br><br>CONCLUSION: We performed genome-wide gene expression analyses which indicate that only a surprisingly small number of genes are regulated by CEP-1 and that DNA damage induced apoptosis via the transcriptional induction of BH3 domain proteins is likely to be an ancient DNA damage response function of the p53 family. Interestingly, although the apoptotic response to DNA damage is regulated through the transcriptional activity of CEP-1, other DNA damage responses do not appear to be regulated on the transcriptional level and do not require the p53 like gene cep-1.}, }
@article {pmid18618657, year = {2008}, author = {Halverson, MS and Bolnick, DA}, title = {An ancient DNA test of a founder effect in Native American ABO blood group frequencies.}, journal = {American journal of physical anthropology}, volume = {137}, number = {3}, pages = {342-347}, doi = {10.1002/ajpa.20887}, pmid = {18618657}, issn = {1096-8644}, mesh = {ABO Blood-Group System/*genetics ; DNA/*chemistry ; Disease Outbreaks ; *Founder Effect ; Genetic Drift ; *Genetic Variation ; Genotype ; History, Ancient ; Humans ; Indians, North American/*genetics/history ; Selection, Genetic ; Sequence Analysis, DNA ; White People/genetics ; }, abstract = {Anthropologists have assumed that reduced genetic diversity in extant Native Americans is due to a founder effect that occurred during the initial peopling of the Americas. However, low diversity could also be the result of subsequent historical events, such as the population decline following European contact. In this study, we show that autosomal DNA from ancient Native American skeletal remains can be used to investigate the low level of ABO blood group diversity in the Americas. Extant Native Americans exhibit a high frequency of blood type O, which may reflect a founder effect, genetic drift associated with the historical population decline, or natural selection in response to the smallpox epidemics that occurred following European contact. To help distinguish between these possibilities, we determined the ABO genotypes of 15 precontact individuals from eastern North America. The precontact ABO frequencies were not significantly different from those observed in extant Native Americans from the same region, but they did differ significantly from the ABO frequencies in extant Siberian populations. Studies of other precontact populations are needed to better test the three hypotheses for low ABO blood group diversity in the Americas, but our findings are most consistent with the hypothesis of a founder effect during the initial settlement of this continent.}, }
@article {pmid18576944, year = {2008}, author = {Mardis, ER}, title = {Next-generation DNA sequencing methods.}, journal = {Annual review of genomics and human genetics}, volume = {9}, number = {}, pages = {387-402}, doi = {10.1146/annurev.genom.9.081307.164359}, pmid = {18576944}, issn = {1527-8204}, mesh = {Chromatin Immunoprecipitation/methods ; Fossils ; Gene Expression Profiling/methods ; Genome, Human ; Genomics/methods ; Humans ; RNA, Untranslated/genetics ; Sequence Analysis, DNA/instrumentation/*methods/trends ; }, abstract = {Recent scientific discoveries that resulted from the application of next-generation DNA sequencing technologies highlight the striking impact of these massively parallel platforms on genetics. These new methods have expanded previously focused readouts from a variety of DNA preparation protocols to a genome-wide scale and have fine-tuned their resolution to single base precision. The sequencing of RNA also has transitioned and now includes full-length cDNA analyses, serial analysis of gene expression (SAGE)-based methods, and noncoding RNA discovery. Next-generation sequencing has also enabled novel applications such as the sequencing of ancient DNA samples, and has substantially widened the scope of metagenomic analysis of environmentally derived samples. Taken together, an astounding potential exists for these technologies to bring enormous change in genetic and biological research and to enhance our fundamental biological knowledge.}, }
@article {pmid18535754, year = {2008}, author = {Wang, H}, title = {Comparative analysis of period genes in teleost fish genomes.}, journal = {Journal of molecular evolution}, volume = {67}, number = {1}, pages = {29-40}, pmid = {18535754}, issn = {0022-2844}, mesh = {Animals ; Circadian Rhythm/*genetics ; *Evolution, Molecular ; Exons ; Eye Proteins/classification/*genetics ; Fish Proteins/classification/*genetics ; Fishes/genetics ; Gene Duplication ; Gene Order ; Genome ; Period Circadian Proteins ; Phylogeny ; RNA Splice Sites ; Synteny ; Zebrafish Proteins/metabolism ; }, abstract = {Period (Per) is a canonical circadian clock gene. The fruit fly, an invertebrate, has one per gene, while the human, a tetrapod vertebrate, has three Per genes. Per1, Per2, and Per3 of the tetrapods were generated from two rounds of ancient genome duplications from the ancestral chordate Per gene. Searching for five teleost fish genomes in a combination of phylogenetic, splicing site, and syntenic analyses revealed that zebrafish have two per1 genes, per1a and per1b, one per2, and one per3; medaka, fugu, and tetraodon each have two per2 genes, per2a and per2b, one per1, and one per3; sticklebacks also have per2a, per2b, and one per1 but lack per3; and per1a/per1b in zebrafish and per2a/per2b in madaka, fugu, tetraodon, and stickleback are ancient duplicates. While the dN/dS ratios of the five fish per duplicates are all <1, suggesting that they likely have been subject to purifying selection, the Tajima relative rate test showed that zebrafish per1a/per1b and fugu and medaka per2a/per2b have asymmetric evolutionary rates, implicating that one of these duplicates might have been under positive selection or relaxed functional constraint. Further, in situ hybridization showed that zebrafish per1a and per1b clearly have distinct patterns of temporal and spatial expression. These results support the notion that extra copies of teleost per genes were generated from the fish-specific genome duplication, and divergent resolution after the duplication resulted in retention of different per duplicates in different fish, most of which have diverged significantly.}, }
@article {pmid21798156, year = {2008}, author = {Wang, H}, title = {Comparative analysis of teleost fish genomes reveals preservation of different ancient clock duplicates in different fishes.}, journal = {Marine genomics}, volume = {1}, number = {2}, pages = {69-78}, doi = {10.1016/j.margen.2008.06.003}, pmid = {21798156}, issn = {1874-7787}, abstract = {Clock (Circadian locomotor output cycle kaput) was the first vertebrate circadian clock gene identified in a mouse forward genetics mutagenesis screen. It encodes a bHLH-PAS protein that is highly conserved throughout evolution. Tetrapods also have the second Clock gene, Clock2 or Npas2 (Neuronal PAS domain protein 2). Conversely, the fruit fly, an invertebrate, has only one clock gene. Interrogation of the five teleost fish genome databases revealed that the zebrafish and the Japanese pufferfish (fugu) each have three clock genes, whereas the green spotted pufferfish (tetraodon), the Japanese medaka fish and the three-spine stickleback each have two clock genes. Phylogenetic and splice site analyses indicated that zebrafish and fugu each have two clock1 genes, clock1a and clock1b and one clock2; tetraodon also have clock1a and clock1b but do not have clock2; and medaka and stickleback each have clock1b and one clock2. Genome neighborhood analysis further showed that clock1a/clock1b in zebrafish, fugu and tetraodon is an ancient duplicate. While the dN/dS ratios of these three fish clock duplicates are all <1, indicating that purifying selection has acted upon them; the Tajima relative rate test showed that all three fish clock duplicates have asymmetric evolutionary rates, implicating that one of these duplicates have been under positive selection or relaxed functional constraint. These results support the view that teleost fish clock genes were generated from an ancient genome-wide duplication, and differential gene loss after the duplication resulted in retention of different ancient duplicates in different teleost fishes, which could have contributed to the evolution of the distinct fish circadian clock mechanisms.}, }
@article {pmid18511664, year = {2008}, author = {Balter, M}, title = {Genetics. Ancient DNA from frozen hair may untangle Eskimo roots.}, journal = {Science (New York, N.Y.)}, volume = {320}, number = {5880}, pages = {1146-1147}, doi = {10.1126/science.320.5880.1146b}, pmid = {18511664}, issn = {1095-9203}, mesh = {Asian People/genetics ; *DNA, Mitochondrial ; Emigration and Immigration ; Freezing ; Genetic Markers ; Greenland ; Hair/*chemistry ; History, Ancient ; Humans ; Inuit/*genetics ; Male ; }, }
@article {pmid18509537, year = {2008}, author = {Melchior, L and Kivisild, T and Lynnerup, N and Dissing, J}, title = {Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years.}, journal = {PloS one}, volume = {3}, number = {5}, pages = {e2214}, pmid = {18509537}, issn = {1932-6203}, mesh = {Archaeology ; Base Sequence ; *Bone and Bones ; DNA, Mitochondrial/*genetics ; Denmark ; *Fossils ; Haplotypes ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Given the relative abundance of modern human DNA and the inherent impossibility for incontestable proof of authenticity, results obtained on ancient human DNA have often been questioned. The widely accepted rules regarding ancient DNA work mainly affect laboratory procedures, however, pre-laboratory contamination occurring during excavation and archaeological-/anthropological handling of human remains as well as rapid degradation of authentic DNA after excavation are major obstacles.<br><br>We avoided some of these obstacles by analyzing DNA from ten Viking Age subjects that at the time of sampling were untouched by humans for 1,000 years. We removed teeth from the subjects prior to handling by archaeologists and anthropologists using protective equipment. An additional tooth was removed after standard archaeological and anthropological handling. All pre-PCR work was carried out in a "clean- laboratory" dedicated solely to ancient DNA work. Mitochondrial DNA was extracted and overlapping fragments spanning the HVR-1 region as well as diagnostic sites in the coding region were PCR amplified, cloned and sequenced. Consistent results were obtained with the "unhandled" teeth and there was no indication of contamination, while the latter was the case with half of the "handled" teeth. The results allowed the unequivocal assignment of a specific haplotype to each of the subjects, all haplotypes being compatible in their character states with a phylogenetic tree drawn from present day European populations. Several of the haplotypes are either infrequent or have not been observed in modern Scandinavians. The observation of haplogroup I in the present study (<2% in modern Scandinavians) supports our previous findings of a pronounced frequency of this haplogroup in Viking and Iron Age Danes.<br><br>CONCLUSION: The present work provides further evidence that retrieval of ancient human DNA is a possible task provided adequate precautions are taken and well-considered sampling is applied.}, }
@article {pmid18501471, year = {2008}, author = {Millar, CD and Huynen, L and Subramanian, S and Mohandesan, E and Lambert, DM}, title = {New developments in ancient genomics.}, journal = {Trends in ecology &amp; evolution}, volume = {23}, number = {7}, pages = {386-393}, doi = {10.1016/j.tree.2008.04.002}, pmid = {18501471}, issn = {0169-5347}, mesh = {Animals ; *Biological Evolution ; *Ecology ; Genomics/economics/*methods ; Humans ; Phenotype ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA/economics/*methods ; }, abstract = {Ancient DNA research is on the crest of a 'third wave' of progress due to the introduction of a new generation of DNA sequencing technologies. Here we review the advantages and disadvantages of the four new DNA sequencers that are becoming available to researchers. These machines now allow the recovery of orders of magnitude more DNA sequence data, albeit as short sequence reads. Hence, the potential reassembly of complete ancient genomes seems imminent, and when used to screen libraries of ancient sequences, these methods are cost effective. This new wealth of data is also likely to herald investigations into the functional properties of extinct genes and gene complexes and will improve our understanding of the biological basis of extinct phenotypes.}, }
@article {pmid18494363, year = {2008}, author = {O'Corry-Crowe, G}, title = {Climate change and the molecular ecology of Arctic marine mammals.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {18}, number = {2 Suppl}, pages = {S56-76}, doi = {10.1890/06-0795.1}, pmid = {18494363}, issn = {1051-0761}, mesh = {Animals ; *Climate ; *Ecology ; *Mammals/genetics ; *Marine Biology ; }, abstract = {Key to predicting likely consequences of future climate change for Arctic marine mammals is developing a detailed understanding of how these species use their environment today and how they were affected by past climate-induced environmental change. Genetic analyses are uniquely placed to address these types of questions. Molecular genetic approaches are being used to determine distribution and migration patterns, dispersal and breeding behavior, population structure and abundance over time, and the effects of past and present climate change in Arctic marine mammals. A review of published studies revealed that population subdivision, dispersal, and gene flow in Arctic marine mammals was shaped primarily by evolutionary history, geography, sea ice, and philopatry to predictable, seasonally available resources. A meta-analysis of data from 38 study units across seven species found significant relationships between neutral genetic diversity and population size and climate region, revealing that small, isolated subarctic populations tend to harbor lower diversity than larger Arctic populations. A few small populations had substantially lower diversity than others. By contrast, other small populations retain substantial neutral diversity despite extensive population declines in the 19th and 20th centuries. The evolutionary and contemporary perspectives gained from these studies can be used to model the consequences of different climate projections for individual behavior and population structure and ultimately individual fitness and population viability. Future research should focus on: (1) the use of ancient-DNA techniques to directly reconstruct population histories through the analysis of historical and prehistorical material, (2) the use of genomic technologies to identify, map, and survey genes that directly influence fitness, (3) long-term studies to monitor populations and investigate evolution in contemporary time, (4) further Arctic-wide, multispecies analyses, preferably across different taxa and trophic levels, and (5) the use of genetic parameters in population and species risk analyses.}, }
@article {pmid18493600, year = {2008}, author = {Pask, AJ and Behringer, RR and Renfree, MB}, title = {Resurrection of DNA function in vivo from an extinct genome.}, journal = {PloS one}, volume = {3}, number = {5}, pages = {e2240}, pmid = {18493600}, issn = {1932-6203}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; CA16672/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; DNA/*genetics ; *Extinction, Biological ; *Genome ; Marsupialia/*genetics ; Mice ; Mice, Transgenic ; }, abstract = {There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine), obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.}, }
@article {pmid18442367, year = {2008}, author = {Orlando, L and Calvignac, S and Schnebelen, C and Douady, CJ and Godfrey, LR and Hänni, C}, title = {DNA from extinct giant lemurs links archaeolemurids to extant indriids.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {121}, pmid = {18442367}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; DNA/*genetics ; DNA Primers ; Evolution, Molecular ; *Extinction, Biological ; *Fossils ; Genetic Speciation ; Lemur/classification/*genetics ; Madagascar ; Models, Genetic ; Monte Carlo Method ; Phylogeny ; Sequence Analysis, DNA ; Strepsirhini/classification/*genetics ; }, abstract = {BACKGROUND: Although today 15% of living primates are endemic to Madagascar, their diversity was even greater in the recent past since dozens of extinct species have been recovered from Holocene excavation sites. Among them were the so-called "giant lemurs" some of which weighed up to 160 kg. Although extensively studied, the phylogenetic relationships between extinct and extant lemurs are still difficult to decipher, mainly due to morphological specializations that reflect ecology more than phylogeny, resulting in rampant homoplasy.<br><br>RESULTS: Ancient DNA recovered from subfossils recently supported a sister relationship between giant "sloth" lemurs and extant indriids and helped to revise the phylogenetic position of Megaladapis edwardsi among lemuriformes, but several taxa - such as the Archaeolemuridae - still await analysis. We therefore used ancient DNA technology to address the phylogenetic status of the two archaeolemurid genera (Archaeolemur and Hadropithecus). Despite poor DNA preservation conditions in subtropical environments, we managed to recover 94- to 539-bp sequences for two mitochondrial genes among 5 subfossil samples.<br><br>CONCLUSION: This new sequence information provides evidence for the proximity of Archaeolemur and Hadropithecus to extant indriids, in agreement with earlier assessments of their taxonomic status (Primates, Indrioidea) and in contrast to recent suggestions of a closer relationship to the Lemuridae made on the basis of analyses of dental developmental and postcranial characters. These data provide new insights into the evolution of the locomotor apparatus among lemurids and indriids.}, }
@article {pmid18440082, year = {2008}, author = {Shapiro, B}, title = {Engineered polymerases amplify the potential of ancient DNA.}, journal = {Trends in biotechnology}, volume = {26}, number = {6}, pages = {285-287}, doi = {10.1016/j.tibtech.2008.03.005}, pmid = {18440082}, issn = {0167-7799}, mesh = {Animals ; Biotechnology/*methods ; DNA/*chemistry ; DNA-Directed DNA Polymerase/*chemistry/*genetics ; Fossils ; *Genetic Techniques ; Humans ; Protein Engineering/*methods ; Sequence Analysis, DNA/methods ; }, abstract = {The generation of genomic data from mammoths and Neanderthals has reinvigorated discussion about whether extinct species could be brought back within the foreseeable future. However, post-mortem DNA decay rapidly reduces the number and quality of surviving DNA fragments, consequently increasing rates of sequencing error and forming a significant obstacle to accurate sequence reconstruction. Recent work has shown that it is possible to engineer a polymerase capable of using even highly damaged fragments as template sequences.}, }
@article {pmid18428729, year = {2004}, author = {Goode, M and Rodrigo, AG}, title = {Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences.}, journal = {Current protocols in bioinformatics}, volume = {Chapter 6}, number = {}, pages = {Unit 6.8}, doi = {10.1002/0471250953.bi0608s05}, pmid = {18428729}, issn = {1934-340X}, mesh = {*Algorithms ; Base Sequence ; DNA Mutational Analysis/*methods ; *Evolution, Molecular ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {The PEBBLE (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) application is a relative newcomer to the field of phylogenetic applications. Although designed as a customizable generalist application, PEBBLE was initially developed to implement procedures for the analysis of sequences associated with different sampling times, e.g., rapidly evolving viral genes sampled over the course of infection, or ancient DNA sequences. The basic protocol describes the use of PEBBLE to infer a phylogenetic tree using the sUPGMA algorithm, and the inference of substitution rate parameters using maximum likelihood. The alternate and support protocols describe the simulation capabilities of PEBBLE, and general use of the PEBBLE application, respectively.}, }
@article {pmid18428264, year = {2001}, author = {Holland, MM and Huffine, EF}, title = {Molecular analysis of the human mitochondrial DNA control region for forensic identity testing.}, journal = {Current protocols in human genetics}, volume = {Chapter 14}, number = {}, pages = {Unit 14.7}, doi = {10.1002/0471142905.hg1407s26}, pmid = {18428264}, issn = {1934-8258}, mesh = {DNA, Mitochondrial/*genetics ; Female ; Forensic Genetics/*methods ; Genetics, Medical ; Genome, Mitochondrial ; Humans ; Male ; Pedigree ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {This unit on mitochondrial DNA (mtDNA) highlights methods used to perform mtDNA sequence analysis on highly degraded biological material. The focus is on applications to forensic casework, and a number of case examples are provided. However, the laboratory working with ancient DNA, or any basic research laboratory, will benefit from this information.}, }
@article {pmid18426903, year = {2008}, author = {Blow, MJ and Zhang, T and Woyke, T and Speller, CF and Krivoshapkin, A and Yang, DY and Derevianko, A and Rubin, EM}, title = {Identification of ancient remains through genomic sequencing.}, journal = {Genome research}, volume = {18}, number = {8}, pages = {1347-1353}, pmid = {18426903}, issn = {1088-9051}, support = {R01 HG004123/HG/NHGRI NIH HHS/United States ; HG 004123/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; DNA/analysis/isolation &amp; purification ; *Fossils ; Genomics/*methods ; Incisor/chemistry ; *Phylogeny ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; }, abstract = {Studies of ancient DNA have been hindered by the preciousness of remains, the small quantities of undamaged DNA accessible, and the limitations associated with conventional PCR amplification. In these studies, we developed and applied a genomewide adapter-mediated emulsion PCR amplification protocol for ancient mammalian samples estimated to be between 45,000 and 69,000 yr old. Using 454 Life Sciences (Roche) and Illumina sequencing (formerly Solexa sequencing) technologies, we examined over 100 megabases of DNA from amplified extracts, revealing unbiased sequence coverage with substantial amounts of nonredundant nuclear sequences from the sample sources and negligible levels of human contamination. We consistently recorded over 500-fold increases, such that nanogram quantities of starting material could be amplified to microgram quantities. Application of our protocol to a 50,000-yr-old uncharacterized bone sample that was unsuccessful in mitochondrial PCR provided sufficient nuclear sequences for comparison with extant mammals and subsequent phylogenetic classification of the remains. The combined use of emulsion PCR amplification and high-throughput sequencing allows for the generation of large quantities of DNA sequence data from ancient remains. Using such techniques, even small amounts of ancient remains with low levels of endogenous DNA preservation may yield substantial quantities of nuclear DNA, enabling novel applications of ancient DNA genomics to the investigation of extinct phyla.}, }
@article {pmid18426745, year = {2008}, author = {Ho, SY and Larson, G and Edwards, CJ and Heupink, TH and Lakin, KE and Holland, PW and Shapiro, B}, title = {Correlating Bayesian date estimates with climatic events and domestication using a bovine case study.}, journal = {Biology letters}, volume = {4}, number = {4}, pages = {370-374}, pmid = {18426745}, issn = {1744-9561}, mesh = {Animals ; Bayes Theorem ; Cattle/classification/*genetics ; *Climate ; *Evolution, Molecular ; Haplotypes ; *Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {The tribe Bovini contains a number of commercially and culturally important species, such as cattle. Understanding their evolutionary time scale is important for distinguishing between post-glacial and domestication-associated population expansions, but estimates of bovine divergence times have been hindered by a lack of reliable calibration points. We present a Bayesian phylogenetic analysis of 481 mitochondrial D-loop sequences, including 228 radiocarbon-dated ancient DNA sequences, using a multi-demographic coalescent model. By employing the radiocarbon dates as internal calibrations, we co-estimate the bovine phylogeny and divergence times in a relaxed-clock framework. The analysis yields evidence for significant population expansions in both taurine and zebu cattle, European aurochs and yak clades. The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence.}, }
@article {pmid18420593, year = {2008}, author = {Mateiu, LM and Rannala, BH}, title = {Bayesian inference of errors in ancient DNA caused by postmortem degradation.}, journal = {Molecular biology and evolution}, volume = {25}, number = {7}, pages = {1503-1511}, doi = {10.1093/molbev/msn095}, pmid = {18420593}, issn = {1537-1719}, mesh = {Algorithms ; Animals ; Base Sequence ; *Bayes Theorem ; DNA/*analysis/genetics ; *DNA Damage ; DNA Fragmentation ; Fossils ; Horses/genetics ; Humans ; Markov Chains ; Mathematics ; *Models, Genetic ; *Models, Statistical ; Molecular Sequence Data ; Sequence Analysis, DNA/methods ; Spheniscidae/genetics ; }, abstract = {Methods for extracting and amplifying sequences using ancient DNA (aDNA) can be prone to errors caused by postmortem modifications of the DNA strand. A new statistical method is developed for predicting errors in aDNA sequences caused by such processes. In addition to the canonical DNA substitution model parameters, a discrete Markov chain is used to describe nucleotide substitutions occurring via postmortem degradation of the aDNA sequences. A computer program, BYPASSR-degr, was developed implementing the method and was used in subsequent analyses of simulated data sets under the new model. Simulation studies show that the new method can be powerful and accurate in identifying damaged sites. The method is applied to analyze aDNA sequences of Etruscans, Adélie penguins, and horses. No significant signals of degradation were observed at any sites of the aDNA sequences we analyzed.}, }
@article {pmid18410293, year = {2008}, author = {Shepherd, LD and Lambert, DM}, title = {Ancient DNA and conservation: lessons from the endangered kiwi of New Zealand.}, journal = {Molecular ecology}, volume = {17}, number = {9}, pages = {2174-2184}, doi = {10.1111/j.1365-294X.2008.03749.x}, pmid = {18410293}, issn = {1365-294X}, mesh = {Animals ; *Conservation of Natural Resources ; DNA/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Extinction, Biological ; Genetic Variation ; Haplotypes ; New Zealand ; Palaeognathae/*genetics ; Population Density ; Sequence Analysis, DNA ; }, abstract = {Conservation genetics typically seeks to map the distribution of contemporary genetic variation across space, and to use the resulting genetic parameters to infer any likely short-term evolutionary consequences for rare and endangered species. Recent developments in the study of ancient DNA now enable the extension of genetic variation studies backwards in time and provide a context by which to interpret contemporary levels of genetic variation, in addition to any patterns of genetic change over time. Ancient DNA research can also help to determine past levels of genetic diversity, identify species' boundaries and reveal former ranges among morphologically cryptic taxa. Ancient DNA sequence data for the New Zealand kiwi (Apteryx spp.) are presented and we show that most ancient populations of rowi and tokoeka exhibited private mitochondrial DNA haplotypes. Moreover, we illustrate that the extinction of these populations has led to the loss of considerable genetic variation. We also use ancient DNA methodology to determine past species distributions for brown kiwi and great spotted kiwi whose bones are morphologically indistinguishable.}, }
@article {pmid18398561, year = {2008}, author = {Orlando, L and Male, D and Alberdi, MT and Prado, JL and Prieto, A and Cooper, A and Hänni, C}, title = {Ancient DNA clarifies the evolutionary history of American Late Pleistocene equids.}, journal = {Journal of molecular evolution}, volume = {66}, number = {5}, pages = {533-538}, pmid = {18398561}, issn = {0022-2844}, mesh = {Animals ; DNA, Mitochondrial/chemistry/*genetics ; Equidae/classification/*genetics ; *Evolution, Molecular ; Fossils ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Hippidions are past members of the equid lineage which appeared in the South American fossil record around 2.5 Ma but then became extinct during the great late Pleistocene megafaunal extinction. According to fossil records and numerous dental, cranial, and postcranial characters, Hippidion and Equus lineages were expected to cluster in two distinct phylogenetic groups that diverged at least 10 MY, long before the emergence of the first Equus. However, the first DNA sequence information retrieved from Hippidion fossils supported a striking different phylogeny, with hippidions nesting inside a paraphyletic group of Equus. This result indicated either that the currently accepted phylogenetic tree of equids was incorrect regarding the timing of the evolutionary split between Hippidion and Equus or that the taxonomic identification of the hippidion fossils used for DNA analysis needed to be reexamined (and attributed to another extinct South American member of the equid lineage). The most likely candidate for the latter explanation is Equus (Amerhippus) neogeus. Here, we show by retrieving new ancient mtDNA sequences that hippidions and Equus (Amerhippus) neogeus were members of two distinct lineages. Furthermore, using a rigorous phylogenetic approach, we demonstrate that while formerly the largest equid from Southern America, Equus (Amerhippus) was just a member of the species Equus caballus. This new data increases the known phenotypic plasticity of horses and consequently casts doubt on the taxonomic validity of the subgenus Equus (Amerhippus).}, }
@article {pmid18363668, year = {2008}, author = {Calvignac, S and Hughes, S and Tougard, C and Michaux, J and Thevenot, M and Philippe, M and Hamdine, W and Hänni, C}, title = {Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times.}, journal = {Molecular ecology}, volume = {17}, number = {8}, pages = {1962-1970}, doi = {10.1111/j.1365-294X.2008.03631.x}, pmid = {18363668}, issn = {1365-294X}, mesh = {Africa, Northern ; Animals ; Base Sequence ; Cytochromes b/chemistry/genetics ; DNA, Mitochondrial/*chemistry/genetics ; *Extinction, Biological ; *Fossils ; Genetic Variation/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Ursidae/*genetics ; }, abstract = {The genetic diversity of present-day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35,000 years. However, the post-last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.}, }
@article {pmid18350170, year = {2008}, author = {Groenenberg, DS and Beintema, AJ and Dekker, RW and Gittenberger, E}, title = {Ancient DNA elucidates the controversy about the flightless island hens (Gallinula sp.) of Tristan da Cunha.}, journal = {PloS one}, volume = {3}, number = {3}, pages = {e1835}, pmid = {18350170}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; DNA/*genetics ; DNA Primers ; Galliformes/classification/*genetics ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {A persistent controversy surrounds the flightless island hen of Tristan da Cunha, Gallinula nesiotis. Some believe that it became extinct by the end of the 19th century. Others suppose that it still inhabits Tristan. There is no consensus about Gallinula comeri, the name introduced for the flightless moorhen from the nearby island of Gough. On the basis of DNA sequencing of both recently collected and historical material, we conclude that G. nesiotis and G. comeri are different taxa, that G. nesiotis indeed became extinct, and that G. comeri now inhabits both islands. This study confirms that among gallinules seemingly radical adaptations (such as the loss of flight) can readily evolve in parallel on different islands, while conspicuous changes in other morphological characters fail to occur.}, }
@article {pmid18327505, year = {2008}, author = {Leles, D and Araújo, A and Ferreira, LF and Vicente, AC and Iñiguez, AM}, title = {Molecular paleoparasitological diagnosis of Ascaris sp. from coprolites: new scenery of ascariasis in pre-Colombian South America times.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {103}, number = {1}, pages = {106-108}, doi = {10.1590/s0074-02762008005000004}, pmid = {18327505}, issn = {0074-0276}, mesh = {Animals ; *Ascariasis/diagnosis/history ; Ascaris/*genetics/isolation &amp; purification ; Cytochromes b/chemistry/*genetics ; DNA, Helminth/chemistry/genetics/*isolation &amp; purification ; Feces/*parasitology ; History, Ancient ; Humans ; Paleopathology/*methods ; Polymerase Chain Reaction ; Sensitivity and Specificity ; Sequence Analysis, DNA ; South America ; }, abstract = {Paleoparasitological studies using microscopy showed that Ascarisand Trichuris trichiura are the human intestinal parasites most found in archaeological sites. However, in pre-Columbian South American archaeological sites, Ascaris is rare. In this work we standardized a molecular methodology for Ascaris diagnosis directly from ancient DNA retrieved from coprolites. Using cythochrome b gene (142 bp) target, ancient DNA sequences were retrieved from South American samples, negative by microscopy. Moreover, the methodology applied was sensitive enough to detect ancient DNA extracted from 30 Ascaris eggs from an European coprolite. These results revealed a new scenery for the paleodistribution of Ascaris in South America.}, }
@article {pmid18322457, year = {2008}, author = {Relethford, JH}, title = {Genetic evidence and the modern human origins debate.}, journal = {Heredity}, volume = {100}, number = {6}, pages = {555-563}, doi = {10.1038/hdy.2008.14}, pmid = {18322457}, issn = {1365-2540}, mesh = {Animals ; *Biological Evolution ; DNA/genetics ; Emigration and Immigration ; Fossils ; Genetic Variation ; *Hominidae ; Humans ; Models, Genetic ; Phylogeny ; }, abstract = {A continued debate in anthropology concerns the evolutionary origin of 'anatomically modern humans' (Homo sapiens sapiens). Different models have been proposed to examine the related questions of (1) where and when anatomically modern humans first appeared and (2) the genetic and evolutionary relationship between modern humans and earlier human populations. Genetic data have been increasingly used to address these questions. Genetic data on living human populations have been used to reconstruct the evolutionary history of the human species by considering how global patterns of human variation could be produced given different evolutionary scenarios. Of particular interest are gene trees that reconstruct the time and place of the most recent common ancestor of humanity for a given haplotype and the analysis of regional differences in genetic diversity. Ancient DNA has also allowed a direct assessment of genetic variation in European Neandertals. Together with the fossil record, genetic data provide insight into the origin of modern humans. The evidence points to an African origin of modern humans dating back to 200,000 years followed by later expansions of moderns out of Africa across the Old World. What is less clear is what happened when these early modern humans met preexisting 'archaic human' populations outside of Africa. At present, it is difficult to distinguish between a model of total genetic replacement and a model that includes some degree of genetic mixture.}, }
@article {pmid18318449, year = {2008}, author = {Sutlovic, D and Gamulin, S and Definis-Gojanovic, M and Gugic, D and Andjelinovic, S}, title = {Interaction of humic acids with human DNA: proposed mechanisms and kinetics.}, journal = {Electrophoresis}, volume = {29}, number = {7}, pages = {1467-1472}, doi = {10.1002/elps.200700699}, pmid = {18318449}, issn = {0173-0835}, mesh = {DNA/*chemistry ; Electrophoresis, Agar Gel ; Humans ; *Humic Substances ; Reverse Transcriptase Polymerase Chain Reaction ; Spectrophotometry, Ultraviolet ; }, abstract = {Human DNA quantification by quantitative real-time PCR (QRT-PCR) has gained great importance in forensic DNA and ancient DNA studies. However, in such samples, DNA quantification is impaired by the frequently present humic acid (HA). We have previously shown that the addition of synthetic HA inhibits QRT-PCR. In this study we investigated the possible mechanisms of HA interaction with human DNA, and kinetics of QRT-PCR inhibition. In QRT-PCR with pure human DNA and no HA added, VMAX was 40. With DNA sample containing 4 microg/mL of HA, VMAX was 30.30 while the addition of extra Taq polymerase to the same sample changed VMAX into 38.91, amplifying between 80 and 90% of input DNA. The KM/VMAX ratio in all the samples remained constant, indicating that the mechanism of HA inhibition of QRT-PCR is uncompetitive by nature. Moreover, HA shifts the human DNA melting temperature point (Tm) from 75 to 87 degrees C and inhibits DNase I-mediated DNA cleavage, most probably affecting the enzyme's activity.}, }
@article {pmid18297799, year = {2007}, author = {Priskin, K and Tömöry, G and Bogácsi-Szabó, E and Csányi, B and Raskó, I}, title = {Mitochondrial DNA control region analysis of a late Neolithic aurochs (Bos primigenius Boj. 1827) from the Carpathian Basin.}, journal = {Acta biologica Hungarica}, volume = {58 Suppl}, number = {}, pages = {131-137}, doi = {10.1556/ABiol.58.2007.Suppl.10}, pmid = {18297799}, issn = {0236-5383}, mesh = {Animals ; Cattle ; DNA, Mitochondrial/*genetics ; Polymerase Chain Reaction ; }, abstract = {Bos primigenius, the wild aurochs is believed to be the ancestor of European domestic cattle, Bos taurus. The geography and climate of the Great Hungarian Plain were well suited for these large grazing animals in the Late Neolithic. Till now, there are just a few aurochs mtDNA fragments available from two geographically restricted area, the British Isles and Italy. To increase our knowledge about the genetics of the European aurochsen livestock, and to investigate the phylogenetic position of a late Neolithic aurochs, excavated from the Carpathian Basin, mitochondrial DNA was extracted from a fragment of corpus mandibulae using ancient-DNA techniques and a portion of mitochondrial hypervariable region was amplified by PCR. The resulting sequence was aligned with GenBank sequences of 11 aurochsen. Our new sequence is identical with the sequence of two British aurochs. The 6000-year-old Hungarian aurochs shows a mtDNA sequence pattern, that occurs only among 6-12,000-year-old North European aurochsen, and it does not occur among modern, domesticated cattle.}, }
@article {pmid18296697, year = {2008}, author = {Calvignac, S and Terme, JM and Hensley, SM and Jalinot, P and Greenwood, AD and Hänni, C}, title = {Ancient DNA identification of early 20th century simian T-cell leukemia virus type 1.}, journal = {Molecular biology and evolution}, volume = {25}, number = {6}, pages = {1093-1098}, doi = {10.1093/molbev/msn054}, pmid = {18296697}, issn = {1537-1719}, mesh = {Animals ; Cercopithecinae/*virology ; DNA, Viral/genetics/history/*isolation &amp; purification ; *Evolution, Molecular ; *Genetic Variation ; History, 20th Century ; Phylogeny ; Proviruses/classification/genetics/*isolation &amp; purification ; Simian T-lymphotropic virus 1/classification/genetics/*isolation &amp; purification ; Terminal Repeat Sequences ; }, abstract = {The molecular identification of proviruses from ancient tissues (and particularly from bones) remains a contentious issue. It can be expected that the copy number of proviruses will be low, which magnifies the risk of contamination with retroviruses from exogenous sources. To assess the feasibility of paleoretrovirological studies, we attempted to identify proviruses from early 20th century bones of museum specimens while following a strict ancient DNA methodology. Simian T-cell leukemia virus type 1 sequences were successfully obtained and authenticated from a Chlorocebus pygerythrus specimen. This represents the first clear evidence that it will be possible to use museum specimens to better characterize simian and human T-tropic retrovirus genetic diversity and analyze their origin and evolution, in greater detail.}, }
@article {pmid18281273, year = {2008}, author = {Burridge, CP and Craw, D and Fletcher, D and Waters, JM}, title = {Geological dates and molecular rates: fish DNA sheds light on time dependency.}, journal = {Molecular biology and evolution}, volume = {25}, number = {4}, pages = {624-633}, doi = {10.1093/molbev/msm271}, pmid = {18281273}, issn = {1537-1719}, mesh = {Animals ; Calibration ; DNA/*genetics ; *Evolution, Molecular ; Fishes/*genetics ; Fresh Water ; *Geology ; History, Ancient ; Mutation/genetics ; New Zealand ; Time Factors ; }, abstract = {Knowledge of DNA evolution is central to our understanding of biological history, but how fast does DNA change? Previously, pedigree and ancient DNA studies--focusing on evolution in the short term--have yielded molecular rate estimates substantially faster than those based on deeper phylogenies. It has recently been suggested that short-term, elevated molecular rates decay exponentially over 1-2 Myr to long-term, phylogenetic rates, termed "time dependency of molecular rates." This transition has potential to confound molecular inferences of demographic parameters and dating of many important evolutionary events. Here, we employ a novel approach--geologically dated changes in river drainages and isolation of fish populations--to document rates of mitochondrial DNA change over a range of temporal scales. This method utilizes precise spatiotemporal disruptions of linear freshwater systems and hence avoids many of the limitations associated with typical DNA calibration methods involving fossil data or island formation. Studies of freshwater-limited fishes across the South Island of New Zealand have revealed that genetic relationships reflect past, rather than present, drainage connections. Here, we use this link between drainage geology and genetics to calibrate rates of molecular evolution across nine events ranging in age from 0.007 Myr (Holocene) to 5.0 Myr (Pliocene). Molecular rates of change in galaxiid fishes from calibration points younger than 200 kyr were faster than those based on older calibration points. This study provides conclusive evidence of time dependency in molecular rates as it is based on a robust calibration system that was applied to closely related taxa, and analyzed using a consistent and rigorous methodology. The time dependency observed here appears short-lived relative to previous suggestions (1-2 Myr), which has bearing on the accuracy of molecular inferences drawn from processes operating within the Quaternary and mechanisms invoked to explain the decay of rates with time.}, }
@article {pmid18257014, year = {2008}, author = {Kim, K and Kim, KY and Jeon, E and Togloom, A and Cho, YO and Lee, MS and Lkhagvasuren, G and Choi, JH and Tumen, D and Ja Park, A and Kim, KC and Park, KW and Kim, JH and Noh, M and Yoo, KJ and Lee, KH}, title = {Technical note: improved ancient DNA purification for PCR using ion-exchange columns.}, journal = {American journal of physical anthropology}, volume = {136}, number = {1}, pages = {114-121}, doi = {10.1002/ajpa.20782}, pmid = {18257014}, issn = {1096-8644}, mesh = {Bone and Bones ; Chromatography, Ion Exchange ; DNA/*isolation &amp; purification ; Forensic Anthropology/*methods ; Humans ; Polymerase Chain Reaction/*methods ; }, abstract = {A novel method of ancient DNA (aDNA) purification was developed using ion-exchange columns to improve PCR-amplifiable DNA extraction from ancient bone samples. Thirteen PCR-resistant ancient bone samples aged 500-3,300 years were tested to extract aDNA using a recently reported, silica-based aDNA extraction method and an ion-exchange column method for the further purification. The PCR success rates of the aDNA extracts were evaluated for the amplification ability of the fragments of mitochondrial DNA, a high-copy DNA, and amelogenin, a low-copy DNA. The results demonstrate that the further purification of silica-based aDNA extracts using ion-exchange columns considerably improved PCR amplification. We suggest that the ion-exchange column-based method will be useful for the improvement of PCR-amplifiable aDNA extraction, particularly from the poorly preserved, PCR-resistant, ancient samples.}, }
@article {pmid18225581, year = {2007}, author = {Schlott, T and Eiffert, H and Schmidt-Schultz, T and Gebhardt, M and Parzinger, H and Schultz, M}, title = {Detection and analysis of cancer genes amplified from bone material of a Scythian royal burial in Arzhan near Tuva, Siberia.}, journal = {Anticancer research}, volume = {27}, number = {6B}, pages = {4117-4119}, pmid = {18225581}, issn = {0250-7005}, mesh = {Anthropology, Physical/methods ; Bone and Bones/*chemistry ; DNA Repair ; DNA, Neoplasm/analysis/*genetics ; Gene Amplification ; *Genes, p53 ; Humans ; Male ; Prostatic Neoplasms/*genetics ; Sequence Analysis, DNA/methods ; Siberia ; Transcription Factor CHOP/*genetics ; Tumor Suppressor Protein p14ARF/*genetics ; }, abstract = {Molecular paleopathology has become an emerging field that helps to characterize molecular markers of past disease. Especially highly sensitive genetic techniques such as PCR are an important means of unraveling changes in ancient DNA extracted from bone tissue, teeth and mummified soft tissue. In the present study, excavated bone material from the skeleton of a Scythian sovereign, morphologically and immunohistochemically suspicious of a metastatic prostate carcinoma, was analyzed by PCR for amplifiable human gene sequences. Short sequences of the human GADD153 DNA repair gene and p53 tumor suppressor gene were detectable which revealed the absence of mutations according to the data of automatic sequencing. Using bisulfite-treated DNA from the bone, methylation-specific PCR detected hypermethylated promoter sequences of the p14ARF tumor suppressor gene. In summary, these data show that it is possible: a) to amply short human DNA stretches from 2,500-year-old bone material, b) to detect tumorigenetically important genes within this DNA, c) to detect epigenetically modified DNA in ancient bone material. The finding of hypermethylated p14ARF sequences merits attention because this may indicate an intraosseal neoplastic process and may corroborate the hypothesis of prostate cancer.}, }
@article {pmid18200550, year = {2008}, author = {Muffato, M and Roest Crollius, H}, title = {Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {30}, number = {2}, pages = {122-134}, doi = {10.1002/bies.20707}, pmid = {18200550}, issn = {0265-9247}, mesh = {Animals ; Evolution, Molecular ; Genomics/*methods ; Models, Genetic ; Phylogeny ; Vertebrates/classification/*genetics ; }, abstract = {Knowledge of the structure of ancestral genomes provides the basis of a new framework to better represent and interpret results from genomic and evolutionary studies. Because these ancestors lived tens of hundreds of million years ago, this knowledge will inevitably take the form of abstract representations, reconstructed on the basis both of experimental evidence collected on extant genomes and of our understanding of evolutionary processes. This is the field of Paleogenomics, a young discipline that is providing an increasingly precise picture of our ancestral vertebrate genomes based on cytogenetic data, genome sequences and new algorithmic developments. Many recent studies have focused on the ancestral placental mammal and teleost fish genomes, although the outlines of even more distant pre-vertebrate ancestors are being reported.}, }
@article {pmid18175620, year = {2006}, author = {Verginelli, F and Capelli, C and Coia, V and Musiani, M and Falchetti, M and Ottini, L and Palmirotta, R and Tagliacozzo, A and Mazzorin, Ide G and Mariani-Costantini, R}, title = {[The origins of dogs: archaeozoology, genetics, and ancient DNA].}, journal = {Medicina nei secoli}, volume = {18}, number = {3}, pages = {741-754}, pmid = {18175620}, issn = {0394-9001}, mesh = {Animals ; DNA, Mitochondrial/genetics/*history ; Dogs/*genetics ; *Evolution, Molecular ; Fossils ; History, Ancient ; Wolves/*genetics ; }, abstract = {The domestication of the dog from the wolf was a key step in the pathway that led to the Neolithic revolution. The earliest fossil dogs, dated to the end of the last glacial period (17,000 to 12,000 years ago), have been found in Russia, Germany and the Middle East. No dogs are represented in the naturalistic art of the European Upper Palaeolithic, suggesting that dogs were introduced at a later date. Genetic studies of extant dog and wolf mitochondrial DNA sequences were interpreted in favour of multiple dog founding events as early as 135-76,000 years ago, or of a single origin in East Asia, 40,000 or 15,000 years ago. Our study included mitochondrial DNA sequences from Italian fossil bones attributed to three Late Pleistocene-Early Holocene wolves (dated from a15,000 to a10,000 14C years ago) and two dogs, dated to a4000 and a3000 14C years ago respectively. Taking paleogeography into account, our phylogenetic data point to a contribution of European wolves to the three major dog clades, in agreement with archaeozoological data. Our phylogeographic studies also suggest genetic differentiation of dogs and wolves related to isolation by geographic distance, supporting multicentric origins of dogs from wolves throughout their vast range of sympatry.}, }
@article {pmid18175619, year = {2006}, author = {Rollo, F and Ermini, L and Luciani, S and Marota, I and Olivieri, C}, title = {Studies on the preservation of the intestinal microbiota's DNA in human mummies from cold environments.}, journal = {Medicina nei secoli}, volume = {18}, number = {3}, pages = {725-740}, pmid = {18175619}, issn = {0394-9001}, mesh = {Cold Climate ; DNA, Bacterial/analysis/*history ; History, Ancient ; Humans ; Intestines/*microbiology ; Male ; Molecular Biology/*methods ; Mummies/*history ; Paleopathology/methods ; }, abstract = {Analysis of ancient microorganism DNA represents one of the newest and most promising branches of molecular archaeology. In particular, microbial DNA associated with human remains can provide direct evidence of the occurrence and frequency of infectious diseases in historic times. Human mummies represent very interesting subjects for palaeomicrobiological investigations as they retain soft tissues. Recently reports on the identification of ancient bacterial pathogens in human mummies by DNA analysis are steadily becoming more numerous. However, despite this favourable trend, the analysis of ancient microbial DNA is still a contentious issue. As a model system, we studied the preservation of the intestinal microbiota's DNA in two naturally freeze-dried human mummies found on the Alps. This kind of mummy is an ideal subject for ancient DNA investigations. The first is a male body historically dated 1918 A.D. while the second is the famous Tyrolean Iceman (3.350-3.100 BC).}, }
@article {pmid18175618, year = {2006}, author = {Gilbert, MT and Willerslev, E}, title = {Authenticity in ancient DNA studies.}, journal = {Medicina nei secoli}, volume = {18}, number = {3}, pages = {701-723}, pmid = {18175618}, issn = {0394-9001}, mesh = {DNA/*analysis/classification/history ; *Fossils ; History, Ancient ; Humans ; Reproducibility of Results ; Specimen Handling/history/methods ; }, abstract = {Ancient DNA studies represent a powerful tool that can be used to obtain genetic insights into the past. However, despite the publication of large numbers of apparently successful ancient DNA studies, a number of problems exist with the field that are often ignored. Therefore, questions exist as to how reliable the conclusions of many of the published studies are. In this paper we outline first the problems associated with aDNA studies, and secondly present potential guidelines designed so as to enable non-specialist readers the opportunity to critically assess the quality of aDNA publications.}, }
@article {pmid18174420, year = {2008}, author = {Buckley, M and Walker, A and Ho, SY and Yang, Y and Smith, C and Ashton, P and Oates, JT and Cappellini, E and Koon, H and Penkman, K and Elsworth, B and Ashford, D and Solazzo, C and Andrews, P and Strahler, J and Shapiro, B and Ostrom, P and Gandhi, H and Miller, W and Raney, B and Zylber, MI and Gilbert, MT and Prigodich, RV and Ryan, M and Rijsdijk, KF and Janoo, A and Collins, MJ}, title = {Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry".}, journal = {Science (New York, N.Y.)}, volume = {319}, number = {5859}, pages = {33; author reply 33}, pmid = {18174420}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; 076905/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Bone and Bones/*chemistry ; Collagen/*chemistry ; *Dinosaurs ; *Elephants ; *Fossils ; Mass Spectrometry ; Phylogeny ; }, abstract = {We used authentication tests developed for ancient DNA to evaluate claims by Asara et al. (Reports, 13 April 2007, p. 280) of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon samples pass these tests, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of alpha1(I) collagen sequences with amphibians rather than birds suggest that T. rex does not.}, }
@article {pmid21585717, year = {2008}, author = {Mitchell, D and McAllister, P and Stick, K and Hauser, L}, title = {Sperm contamination in archived and contemporary herring samples.}, journal = {Molecular ecology resources}, volume = {8}, number = {1}, pages = {50-55}, doi = {10.1111/j.1471-8286.2007.01840.x}, pmid = {21585717}, issn = {1755-098X}, abstract = {Studies using archived scales and otoliths to examine ancient fish populations have become increasingly common, despite many methodological challenges in ancient DNA research. Here, we describe a case of DNA contamination in both modern and historical samples of Pacific herring (Clupea pallasii), where the source of the contamination is likely from milt spillage during collection. We describe a series of experiments to remove contamination using pre-extraction wash treatments. Though contamination was easily removed from contemporary fin clippings, no method was successful at removing contamination from historical scales. We discuss the implications of our findings to the genetic analysis of archived samples.}, }
@article {pmid18162443, year = {2008}, author = {Zawicki, P and Witas, HW}, title = {HIV-1 protecting CCR5-Delta32 allele in medieval Poland.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {8}, number = {2}, pages = {146-151}, doi = {10.1016/j.meegid.2007.11.003}, pmid = {18162443}, issn = {1567-1348}, mesh = {Acquired Immunodeficiency Syndrome/*genetics/history ; Alleles ; Base Sequence ; Gene Frequency ; Genetic Predisposition to Disease ; *HIV-1 ; Heterozygote ; *History, Medieval ; Humans ; Immunity, Innate/*genetics ; Molecular Sequence Data ; Mutant Proteins/physiology ; Poland ; Receptors, CCR5/*genetics/*history ; }, abstract = {CCR5-Delta32 is the mutation in the chemokine receptor CCR5 that gives its homozygous carriers nearly complete protections from HIV-1 infection. Restricted almost exclusively to Europe, the mutation is thought to have originated in the continent and risen in frequency to the present-day value of approximately 10% due to a selective advantage it gave its carriers. The mutation bearing allele was initially calculated to be approximately 1000 years old and pandemic diseases, such as Bubonic Plague or smallpox were postulated to have selected it. However, new reports appear, that question these hypotheses. Data from ancient DNA (aDNA) studies prove the mutation to be much older, as suggested by calculations based on newer genetic maps. In order to investigate if the plagues of the last millennium selected the allele, and add to the discussion on CCR5-Delta32 origin and age, we searched for the mutation in aDNA isolated from individuals whose skeletal remains were collected at archaeological sites in Poland, dated back to 11-14th centuries. The calculated mean frequency of the allele in medieval Poland (5.06% as compared to contemporary 10.26%), implies its longer than previously believed presence in European populations, and suggests that historic pandemics had little effect on its present-day frequency.}, }
@article {pmid18084031, year = {2008}, author = {Meyer, M and Briggs, AW and Maricic, T and Höber, B and Höffner, B and Krause, J and Weihmann, A and Pääbo, S and Hofreiter, M}, title = {From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing.}, journal = {Nucleic acids research}, volume = {36}, number = {1}, pages = {e5}, pmid = {18084031}, issn = {1362-4962}, mesh = {Animals ; Fossils ; Gene Library ; Hominidae/genetics ; Humans ; Pan paniscus/genetics ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Current efforts to recover the Neandertal and mammoth genomes by 454 DNA sequencing demonstrate the sensitivity of this technology. However, routine 454 sequencing applications still require microgram quantities of initial material. This is due to a lack of effective methods for quantifying 454 sequencing libraries, necessitating expensive and labour-intensive procedures when sequencing ancient DNA and other poor DNA samples. Here we report a 454 sequencing library quantification method based on quantitative PCR that effectively eliminates these limitations. We estimated both the molecule numbers and the fragment size distributions in sequencing libraries derived from Neandertal DNA extracts, SAGE ditags and bonobo genomic DNA, obtaining optimal sequencing yields without performing any titration runs. Using this method, 454 sequencing can routinely be performed from as little as 50 pg of initial material without titration runs, thereby drastically reducing costs while increasing the scope of sample throughput and protocol development on the 454 platform. The method should also apply to Illumina/Solexa and ABI/SOLiD sequencing, and should therefore help to widen the accessibility of all three platforms.}, }
@article {pmid18039829, year = {2008}, author = {Manske, AK and Henssge, U and Glaeser, J and Overmann, J}, title = {Subfossil 16S rRNA gene sequences of green sulfur bacteria in the Black Sea and their implications for past photic zone anoxia.}, journal = {Applied and environmental microbiology}, volume = {74}, number = {3}, pages = {624-632}, pmid = {18039829}, issn = {1098-5336}, mesh = {Chlorobi/*classification/genetics/growth &amp; development ; Chlorobium/classification/genetics/growth &amp; development ; DNA, Bacterial/analysis/isolation &amp; purification ; *Fossils ; Genes, rRNA ; Geologic Sediments/microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Seawater/*microbiology ; *Sequence Analysis, DNA ; }, abstract = {The Black Sea is the largest extant anoxic water body on Earth. Its oxic-anoxic boundary is located at a depth of 100 m and is populated by a single phylotype of marine green sulfur bacteria. This organism, Chlorobium sp. strain BS-1, is extraordinarily low light adapted and can therefore serve as an indicator of deep photic zone anoxia (A. K. Manske, J. Glaeser, M. M. M. Kuypers, and J. Overmann, Appl. Environ. Microbiol. 71:8049-8060, 2005). In the present study, two sediment cores were retrieved from the bottom of the Black Sea at depths of 2,006 and 2,162 m and were analyzed for the presence of subfossil DNA sequences of BS-1 using ancient-DNA methodology. Using optimized cultivation media, viable cells of the BS-1 phylotype were detected only at the sediment surface and not in deeper layers. In contrast, green sulfur bacterial 16S rRNA gene fragments were amplified from all the sediment layers investigated, including turbidites. After separation by denaturing gradient gel electrophoresis and sequencing, 14 different sequence types were distinguished. The sequence of BS-1 represented only a minor fraction of the amplification products and was found in 6 of 22 and 4 of 26 samples from the 2,006- and 2,162-m stations, respectively. Besides the sequences of BS-1, three additional phylotypes of the marine clade of green sulfur bacteria were detected. However, the majority of sequences clustered with groups from freshwater habitats. Our results suggest that a considerable fraction of green sulfur bacterial chemofossils did not originate in a low-light marine chemocline environment and therefore were likely to have an allochthonous origin. Thus, analysis of subfossil DNA sequences permits a more differentiated interpretation and reconstruction of past environmental conditions if specific chemofossils of stenoec species, like Chlorobium sp. strain BS-1, are employed.}, }
@article {pmid17981113, year = {2007}, author = {McIntosh, KB and Warner, JR}, title = {Yeast ribosomes: variety is the spice of life.}, journal = {Cell}, volume = {131}, number = {3}, pages = {450-451}, doi = {10.1016/j.cell.2007.10.028}, pmid = {17981113}, issn = {0092-8674}, support = {CA13330/CA/NCI NIH HHS/United States ; GM25532/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA-Binding Proteins/biosynthesis/genetics ; Gene Expression Regulation, Fungal ; Humans ; RNA Transport ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/biosynthesis/genetics ; Ribosomal Proteins/genetics/metabolism ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/cytology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/biosynthesis/genetics ; Sequence Homology, Amino Acid ; }, abstract = {In the budding yeast Saccharomyces cerevisiae, 59 of the 79 cytoplasmic ribosomal proteins are encoded by two genes, stemming from an ancient genome duplication event. Komili et al. (2007) now report that these paralogous genes are not functionally equivalent, suggesting the possible existence of a "ribosome code."}, }
@article {pmid17966429, year = {2007}, author = {Vergnaud, G and Li, Y and Gorgé, O and Cui, Y and Song, Y and Zhou, D and Grissa, I and Dentovskaya, SV and Platonov, ME and Rakin, A and Balakhonov, SV and Neubauer, H and Pourcel, C and Anisimov, AP and Yang, R}, title = {Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA.}, journal = {Advances in experimental medicine and biology}, volume = {603}, number = {}, pages = {327-338}, doi = {10.1007/978-0-387-72124-8_30}, pmid = {17966429}, issn = {0065-2598}, mesh = {Base Sequence ; DNA, Bacterial/*genetics/*history ; Disease Outbreaks/history ; Evolution, Molecular ; Genes, Bacterial ; History, Ancient ; Humans ; Interspersed Repetitive Sequences ; Molecular Sequence Data ; Phylogeny ; Plague/epidemiology/*history/microbiology ; Species Specificity ; Yersinia pestis/classification/*genetics/pathogenicity ; Yersinia pseudotuberculosis/classification/genetics ; }, abstract = {The precise nature of the pathogen having caused early plague pandemics is uncertain. Although Yersinia pestis is a likely candidate for all three plague pandemics, the very rare direct evidence that can be deduced from ancient DNA (aDNA) analysis is controversial. Moreover, which of the three biovars, Antiqua, Medievalis or Orientalis, was associated with these pandemics is still debated. There is a need for phylogenetic analysis performed on Y. pestis strains isolated from countries from which plague probably arose and is still endemic. In addition there exist technical difficulties inherent to aDNA investigations and a lack of appropriate genetic targets. The recently described CRISPRs (clustered regularly interspaced short palindromic repeats) may represent such a target. CRISPR loci consist of a succession of highly conserved regions separated by specific "spacers" usually of viral origin. To be of use, data describing the mechanisms of evolution and diversity of CRISPRs in Y. pestis, its closest neighbors, and other species which might contaminate ancient DNA, are necessary. The investigation of closely related Y. pestis isolates has revealed recent mutation events in which elements constituting CRISPRs were acquired or lost, providing essential insight on their evolution. Rules deduced represent the basis for subsequent interpretation. In the present study, the CRISPR loci from representative Y. pestis and Yersinia pseudotuberculosis strains were investigated by PCR amplification and sequence analysis. The investigation of this wider panel of strains, including other subspecies or ecotypes within Y. pestis and also Y. pseudotuberculosis strains provides a database of the existing CRISPR spacers and helps predict the expected CRISPR structure of the Y. pestis ancestor. This knowledge will open the way to the development of a spoligotyping assay, in which spacers can be amplified even from highly degraded DNA samples. The data obtained show that CRISPR analysis can provide a very powerful typing tool, adapted to the systematic, large-scale genotyping of Y. pestis isolates, and the creation of international typing databases. In addition, CRISPRs do constitute a very promising new tool and genetic target to investigate ancient DNA. The corresponding genetic targets are small (<70bp), present in multiple copies (usually more than 10), highly conserved and specific. In addition, the assay can be run in any laboratory. Interpretation of the data is not dependent on accurate sequence data.}, }
@article {pmid17963478, year = {2007}, author = {Poole, AM and Willerslev, E}, title = {Can identification of a fourth domain of life be made from sequence data alone, and could it be done on Mars?.}, journal = {Astrobiology}, volume = {7}, number = {5}, pages = {801-814}, doi = {10.1089/ast.2006.0094}, pmid = {17963478}, issn = {1531-1074}, mesh = {Artifacts ; Equipment Contamination ; Exobiology ; *Life ; *Mars ; *Phylogeny ; Polymerase Chain Reaction ; *Sequence Analysis, DNA ; }, abstract = {A central question in astrobiology is whether life exists elsewhere in the universe. If so, is it related to Earth life? Technologies exist that enable identification of DNA- or RNA-based microbial life directly from environmental samples here on Earth. Such technologies could, in principle, be applied to the search for life elsewhere; indeed, efforts are underway to initiate such a search. However, surveying for nucleic acid-based life on other planets, if attempted, must be carried out with caution, owing to the risk of contamination by Earth-based life. Here we argue that the null hypothesis must be that any DNA discovered and sequenced from samples taken elsewhere in the universe are Earth-based contaminants. Experience from studies of low-biomass ancient DNA demonstrates that some results, by their very nature, will not enable complete rejection of the null hypothesis. In terms of eliminating contamination as an explanation of the data, there may be value in identification of sequences that lie outside the known diversity of the three domains of life. We therefore have examined whether a fourth domain could be readily identified from environmental DNA sequence data alone. We concluded that, even on Earth, this would be far from trivial, and we illustrate this point by way of examples drawn from the literature. Overall, our conclusions do not bode well for planned PCR-based surveys for life on Mars, and we argue that other independent biosignatures will be essential in corroborating any claims for the presence of life based on nucleic acid sequences.}, }
@article {pmid17962526, year = {2007}, author = {Culotta, E}, title = {Genetics. Ancient DNA reveals Neandertals with red hair, fair complexions.}, journal = {Science (New York, N.Y.)}, volume = {318}, number = {5850}, pages = {546-547}, doi = {10.1126/science.318.5850.546}, pmid = {17962526}, issn = {1095-9203}, mesh = {Animals ; Forkhead Transcription Factors/genetics ; Hair Color/*genetics ; Hominidae/*genetics ; Humans ; Point Mutation ; Polymerase Chain Reaction ; Receptor, Melanocortin, Type 1/*genetics/metabolism ; Skin Pigmentation/*genetics ; }, }
@article {pmid17955361, year = {2007}, author = {McCloskey, ML and Stöger, R and Hansen, RS and Laird, CD}, title = {Encoding PCR products with batch-stamps and barcodes.}, journal = {Biochemical genetics}, volume = {45}, number = {11-12}, pages = {761-767}, doi = {10.1007/s10528-007-9114-x}, pmid = {17955361}, issn = {0006-2928}, support = {GM 53805/GM/NIGMS NIH HHS/United States ; HD 02274/HD/NICHD NIH HHS/United States ; }, mesh = {Fragile X Mental Retardation Protein/*genetics ; Humans ; Oligonucleotides/chemistry/*genetics ; *Polymerase Chain Reaction/methods ; Quantitative Trait Loci/*genetics ; Sensitivity and Specificity ; }, abstract = {Polymerase chain reaction (PCR) has become the mainstay of DNA sequence analysis. Yet there is always uncertainty concerning the source of the template DNA that gave rise to a particular PCR product. The risks of contamination, biased amplification, and product redundancy are especially high when limited amounts of template DNA are used. We have developed and applied molecular encoding principles to solve this source-uncertainty problem for DNA sequences generated by standard PCR. Batch-stamps specify the date and sample identity, and barcodes detect template redundancy. Our approach thus enables classification of each PCR-derived sequence as valid, contaminant, or redundant, and provides a measure of sequence diversity. We recommend that batch-stamps and barcodes be used when amplifying irreplaceable DNAs and cDNAs available for forensic, clinical, single cell, and ancient DNA analyses.}, }
@article {pmid17922573, year = {2007}, author = {Santangelo, AM and de Souza, FS and Franchini, LF and Bumaschny, VF and Low, MJ and Rubinstein, M}, title = {Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene.}, journal = {PLoS genetics}, volume = {3}, number = {10}, pages = {1813-1826}, pmid = {17922573}, issn = {1553-7404}, support = {R01 DK068400/DK/NIDDK NIH HHS/United States ; DK68400/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Computational Biology ; Consensus Sequence ; *Conserved Sequence ; Embryonic Development/genetics ; Enhancer Elements, Genetic/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Developmental ; Genomics ; Mammals/*genetics ; Mice ; Mice, Transgenic ; Molecular Sequence Data ; Neurons/*metabolism ; Opossums/genetics ; Paleontology ; Pro-Opiomelanocortin/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Deletion ; Short Interspersed Nucleotide Elements/*genetics ; }, abstract = {The proopiomelanocortin gene (POMC) is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5' distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE) retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution.}, }
@article {pmid17901335, year = {2007}, author = {Gilbert, MT and Tomsho, LP and Rendulic, S and Packard, M and Drautz, DI and Sher, A and Tikhonov, A and Dalén, L and Kuznetsova, T and Kosintsev, P and Campos, PF and Higham, T and Collins, MJ and Wilson, AS and Shidlovskiy, F and Buigues, B and Ericson, PG and Germonpré, M and Götherström, A and Iacumin, P and Nikolaev, V and Nowak-Kemp, M and Willerslev, E and Knight, JR and Irzyk, GP and Perbost, CS and Fredrikson, KM and Harkins, TT and Sheridan, S and Miller, W and Schuster, SC}, title = {Whole-genome shotgun sequencing of mitochondria from ancient hair shafts.}, journal = {Science (New York, N.Y.)}, volume = {317}, number = {5846}, pages = {1927-1930}, doi = {10.1126/science.1146971}, pmid = {17901335}, issn = {1095-9203}, support = {HG002238/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Bone and Bones/chemistry ; DNA Damage ; DNA, Mitochondrial/chemistry/genetics/*history ; Elephants/*genetics ; Genes, Mitochondrial ; *Genome ; *Hair/chemistry/ultrastructure ; History, Ancient ; Mitochondria/*genetics ; Molecular Sequence Data ; Preservation, Biological ; *Sequence Analysis, DNA ; Siberia ; Temperature ; }, abstract = {Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.}, }
@article {pmid17894859, year = {2007}, author = {Martin, N and Ruedi, EA and Leduc, R and Sun, FJ and Caetano-Anollés, G}, title = {Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event?.}, journal = {Biology direct}, volume = {2}, number = {}, pages = {23}, pmid = {17894859}, issn = {1745-6150}, mesh = {Chromosomes, Fungal ; *Gene Duplication ; Gene Order ; *Genome, Fungal ; Kluyveromyces/genetics ; Phylogeny ; Saccharomyces cerevisiae/classification/*genetics ; *Synteny ; }, abstract = {BACKGROUND: Recent comparative genomic studies claim local syntenic gene-interleaving relationships in Ashbya gossypii and Kluyveromyces waltii are compelling evidence for an ancient whole-genome duplication event in Saccharomyces cerevisiae. We here test, using Hannenhalli-Pevzner rearrangement algorithms that address the multiple genome rearrangement problem, whether syntenic patterns are proof of paleopolyploidization.<br><br>RESULTS: We focus on (1) pairwise comparison of gene arrangement sequences in A. gossypii and S. cerevisiae, (2) reconstruction of gene arrangements ancestral to A. gossypii, S. cerevisiae, and K. waltii, (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets. The existence of syntenic patterns between ancestral gene sets and A. gossypii, S. cerevisiae, and K. waltii, and other evidence, suggests that gene-interleaving relationships are the natural consequence of topological rearrangements in chromosomes and that a more gradual scenario of genome evolution involving segmental duplication and recombination constitutes a more parsimonious explanation. Furthermore, phylogenetic trees reconstructed under alternative hypotheses placed the putative whole-genome duplication event after the divergence of the S. cerevisiae and K. waltii lineages, but in the lineage leading to K. waltii. This is clearly incompatible with an ancient genome duplication event in S. cerevisiae.<br><br>CONCLUSION: Because the presence of syntenic patterns appears to be a condition that is necessary, but not sufficient, to support the existence of the whole-genome duplication event, our results prompt careful re-evaluation of paleopolyploidization in the yeast lineage and the evolutionary meaning of syntenic patterns.}, }
@article {pmid17855556, year = {2007}, author = {Larson, G and Albarella, U and Dobney, K and Rowley-Conwy, P and Schibler, J and Tresset, A and Vigne, JD and Edwards, CJ and Schlumbaum, A and Dinu, A and Balaçsescu, A and Dolman, G and Tagliacozzo, A and Manaseryan, N and Miracle, P and Van Wijngaarden-Bakker, L and Masseti, M and Bradley, DG and Cooper, A}, title = {Ancient DNA, pig domestication, and the spread of the Neolithic into Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {39}, pages = {15276-15281}, pmid = {17855556}, issn = {0027-8424}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Agriculture ; Animals ; Asia ; Biometry ; DNA, Mitochondrial/*genetics ; Europe ; Geography ; History, Ancient ; Markov Chains ; Molecular Sequence Data ; Monte Carlo Method ; Regression Analysis ; Sequence Analysis, DNA ; Sus scrofa ; Swine ; }, abstract = {The Neolithic Revolution began 11,000 years ago in the Near East and preceded a westward migration into Europe of distinctive cultural groups and their agricultural economies, including domesticated animals and plants. Despite decades of research, no consensus has emerged about the extent of admixture between the indigenous and exotic populations or the degree to which the appearance of specific components of the "Neolithic cultural package" in Europe reflects truly independent development. Here, through the use of mitochondrial DNA from 323 modern and 221 ancient pig specimens sampled across western Eurasia, we demonstrate that domestic pigs of Near Eastern ancestry were definitely introduced into Europe during the Neolithic (potentially along two separate routes), reaching the Paris Basin by at least the early 4th millennium B.C. Local European wild boar were also domesticated by this time, possibly as a direct consequence of the introduction of Near Eastern domestic pigs. Once domesticated, European pigs rapidly replaced the introduced domestic pigs of Near Eastern origin throughout Europe. Domestic pigs formed a key component of the Neolithic Revolution, and this detailed genetic record of their origins reveals a complex set of interactions and processes during the spread of early farmers into Europe.}, }
@article {pmid17767734, year = {2007}, author = {Paffetti, D and Vettori, C and Caramelli, D and Vernesi, C and Lari, M and Paganelli, A and Paule, L and Giannini, R}, title = {Unexpected presence of Fagus orientalis complex in Italy as inferred from 45,000-year-old DNA pollen samples from Venice lagoon.}, journal = {BMC evolutionary biology}, volume = {7 Suppl 2}, number = {Suppl 2}, pages = {S6}, pmid = {17767734}, issn = {1471-2148}, mesh = {Base Sequence ; Cloning, Molecular ; DNA, Chloroplast/*genetics ; Fagus/classification/*genetics ; *Fossils ; Haplotypes ; Italy ; *Phylogeny ; Pollen/*genetics ; Polymerase Chain Reaction ; Sequence Alignment ; }, abstract = {BACKGROUND: Phylogeographic analyses on the Western Euroasiatic Fagus taxa (F. orientalis, F. sylvatica, F. taurica and F. moesiaca) is available, however, the subdivision of Fagus spp. is unresolved and there is no consensus on the phylogeny and on the identification (both with morphological than molecular markers) of Fagus Eurasiatic taxa. For the first time molecular analyses of ancient pollen, dated at least 45,000 years ago, were used in combination with the phylogeny analysis on current species, to identify the Fagus spp. present during the Last Interglacial period in Italy. In this work we aim at testing if the trnL-trnF chloroplast DNA (cpDNA) region, that has been previously proved efficient in discriminating different Quercus taxa, can be employed in distinguishing the Fagus species and in identifying the ancient pollen.<br><br>RESULTS: 86 populations from 4 Western Euroasistic taxa were sampled, and sequenced for the trnL-trnF region to verify the efficiency of this cpDNA region in identifying the Fagus spp.. Furthermore, Fagus crenata (2 populations), Fagus grandifolia (2 populations), Fagus japonica, Fagus hayatae, Quercus species and Castanea species were analysed to better resolve the phylogenetic inference. Our results show that this cpDNA region harbour some informative sites that allow to infer relationships among the species within the Fagaceae family. In particular, few specific and fixed mutations were able to discriminate and identify all the different Fagus species. Considering a short fragment of 176 base pairs within the trnL intron, 2 transversions were found able in distinguishing the F. orientalis complex taxa (F. orientalis, F. taurica and F. moesiaca) from the remaining Fagus spp. (F. sylvatica, F. japonica, F. hayataea, F. crenata and F. grandifolia). This permits to analyse this fragment also in ancient samples, where DNA is usually highly degraded. The sequences data indicate that the DNA recovered from ancient pollen belongs to the F. orientalis complex since it displays the informative sites characteristic of this complex.<br><br>CONCLUSION: The ancient DNA sequences demonstrate for the first time that, in contrast to current knowledge based on palynological and macrofossil data, the F. orientalis complex was already present during the Tyrrhenian period in what is now the Venice lagoon (Italy). This is a new and important insight considering that nowadays West Europe is not the natural area of Fagus orientalis complex, and up to now nobody has hypothesized the presence during the Last Interglacial period of F. orientalis complex in Italy.}, }
@article {pmid17785261, year = {2007}, author = {Ho, SY and Kolokotronis, SO and Allaby, RG}, title = {Elevated substitution rates estimated from ancient DNA sequences.}, journal = {Biology letters}, volume = {3}, number = {6}, pages = {702-705}, pmid = {17785261}, issn = {1744-9561}, mesh = {*Bayes Theorem ; Computer Simulation ; *Evolution, Molecular ; *Models, Genetic ; Mutation ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which are not directly accessible via modern DNA. They are particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing the difficult task of choosing independent calibration points. The substitution rates obtained from such datasets have typically been high, falling between the rates estimated from pedigrees and species phylogenies. Many of these estimates have been made using a Bayesian phylogenetic method that explicitly accommodates heterochronous data. Stimulated by recent criticism of this method, we present a comprehensive simulation study that validates its performance. For datasets of moderate size, it produces accurate estimates of rates, while appearing robust to assumptions about demographic history. We then analyse a large collection of 749 ancient and 727 modern DNA sequences from 19 species of animals, plants and bacteria. Our new estimates confirm that the substitution rates estimated from ancient DNA sequences are elevated above long-term phylogenetic levels.}, }
@article {pmid25869168, year = {2007}, author = {Graham, EA}, title = {DNA reviews: Ancient DNA.}, journal = {Forensic science, medicine, and pathology}, volume = {3}, number = {3}, pages = {221-225}, pmid = {25869168}, issn = {1547-769X}, abstract = {The rapid development, success, and occasional failures of forensic DNA profiling are highly publicised, and as a consequence are well known to the scientific and public communities alike. Over the same period of time that forensic DNA typing has accelerated onto the scene, another related discipline has been born and has made equally, or perhaps, even more groundbreaking achievements in the same arena; that is the science of (bio)molecular archaeology. This review describes the extreme complications of ancient DNA analysis and highlights some of the major achievements that have been accomplished in this field. The nature of DNA degradation and possible solutions to this problem are discussed.}, }
@article {pmid17715147, year = {2007}, author = {Brotherton, P and Endicott, P and Sanchez, JJ and Beaumont, M and Barnett, R and Austin, J and Cooper, A}, title = {Novel high-resolution characterization of ancient DNA reveals C &gt; U-type base modification events as the sole cause of post mortem miscoding lesions.}, journal = {Nucleic acids research}, volume = {35}, number = {17}, pages = {5717-5728}, pmid = {17715147}, issn = {1362-4962}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adenosine/chemistry ; Animals ; Cytosine/chemistry ; DNA/chemistry ; *DNA Damage ; DNA Fragmentation ; DNA Primers ; *Fossils ; Guanine/chemistry ; Humans ; Nucleic Acid Amplification Techniques/*methods ; Polymerase Chain Reaction ; *Sequence Analysis, DNA ; Taq Polymerase ; Templates, Genetic ; Uracil/chemistry ; }, abstract = {Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy.}, }
@article {pmid17715061, year = {2007}, author = {Briggs, AW and Stenzel, U and Johnson, PL and Green, RE and Kelso, J and Prüfer, K and Meyer, M and Krause, J and Ronan, MT and Lachmann, M and Pääbo, S}, title = {Patterns of damage in genomic DNA sequences from a Neandertal.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {37}, pages = {14616-14621}, pmid = {17715061}, issn = {0027-8424}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; R01-GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophage T4/enzymology ; Base Sequence ; Computer Simulation ; Cytosine/metabolism ; DNA/genetics/history ; *DNA Damage ; DNA-Directed DNA Polymerase/metabolism ; Deamination ; *Genome ; Genomic Library ; History, Ancient ; Humans ; Likelihood Functions ; Models, Biological ; Molecular Sequence Data ; Paleontology/*methods ; Polymerase Chain Reaction ; Reference Standards ; *Sequence Analysis, DNA ; Templates, Genetic ; }, abstract = {High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms.}, }
@article {pmid17687362, year = {2007}, author = {Gilbert, MT and Willerslev, E}, title = {Rescuing ancient DNA.}, journal = {Nature biotechnology}, volume = {25}, number = {8}, pages = {872-874}, doi = {10.1038/nbt0807-872}, pmid = {17687362}, issn = {1087-0156}, mesh = {DNA/*genetics ; DNA Damage/*genetics ; DNA Fingerprinting/*methods ; *Fossils ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; }, }
@article {pmid17683536, year = {2007}, author = {Rensing, SA and Ick, J and Fawcett, JA and Lang, D and Zimmer, A and Van de Peer, Y and Reski, R}, title = {An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {130}, pmid = {17683536}, issn = {1471-2148}, mesh = {Bryopsida/*genetics/*metabolism ; *Evolution, Molecular ; *Gene Duplication ; Genome, Plant/*genetics ; Metabolic Networks and Pathways/*genetics ; Phylogeny ; Polyploidy ; }, abstract = {BACKGROUND: Analyses of complete genomes and large collections of gene transcripts have shown that most, if not all seed plants have undergone one or more genome duplications in their evolutionary past.<br><br>RESULTS: In this study, based on a large collection of EST sequences, we provide evidence that the haploid moss Physcomitrella patens is a paleopolyploid as well. Based on the construction of linearized phylogenetic trees we infer the genome duplication to have occurred between 30 and 60 million years ago. Gene Ontology and pathway association of the duplicated genes in P. patens reveal different biases of gene retention compared with seed plants.<br><br>CONCLUSION: Metabolic genes seem to have been retained in excess following the genome duplication in P. patens. This might, at least partly, explain the versatility of metabolism, as described for P. patens and other mosses, in comparison to other land plants.}, }
@article {pmid17661290, year = {2007}, author = {Veiga-Crespo, P and Blasco, L and Poza, M and Villa, TG}, title = {Putative ancient microorganisms from amber nuggets.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {10}, number = {2}, pages = {117-122}, pmid = {17661290}, issn = {1139-6709}, mesh = {Amber/*chemistry ; Amino Acid Transport Systems/genetics ; Animals ; Bacillus/*classification/genetics/isolation &amp; purification ; *Biological Evolution ; DNA/genetics/isolation &amp; purification ; *Fossils ; Microscopy, Electron, Transmission ; *Paleontology ; Paramecium/*classification/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Analysis, DNA ; Symporters/genetics ; }, abstract = {Evolutionary microbiology studies based on the isolation of ancient DNA and/or microbial samples are scarce due to the difficulty of finding well preserved biological specimens. However, amber is a fossil resin with natural preserving properties for microbial cells and DNA. The visualization by transmission electron microscopy of different microorganism-like specimens found in amber nuggets from both the Miocene and the Cretaceous periods was accompanied by studies of ancient DNA obtained from the nuggets. After the design of specific primers based on the present sequences of both genes in Saccharomyces cerevisiae, the ancestral AGP2 sequence from the Miocene, as well as the 18S rRNA from the Cretaceous, were amplified.}, }
@article {pmid17658954, year = {2007}, author = {Wei, F and Coe, E and Nelson, W and Bharti, AK and Engler, F and Butler, E and Kim, H and Goicoechea, JL and Chen, M and Lee, S and Fuks, G and Sanchez-Villeda, H and Schroeder, S and Fang, Z and McMullen, M and Davis, G and Bowers, JE and Paterson, AH and Schaeffer, M and Gardiner, J and Cone, K and Messing, J and Soderlund, C and Wing, RA}, title = {Physical and genetic structure of the maize genome reflects its complex evolutionary history.}, journal = {PLoS genetics}, volume = {3}, number = {7}, pages = {e123}, pmid = {17658954}, issn = {1553-7404}, mesh = {Chromosome Mapping ; Chromosomes, Artificial, Bacterial/genetics ; Chromosomes, Plant/genetics ; DNA Fingerprinting ; DNA, Plant/genetics ; Edible Grain/genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Rearrangement ; *Genome, Plant ; Oryza/genetics ; Phylogeny ; Species Specificity ; Zea mays/*genetics ; }, abstract = {Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a framework for genome sequencing, we constructed a sequence-ready fingerprinted contig-based physical map that covers 93.5% of the genome, of which 86.1% is aligned to the genetic map. The fingerprinted contig map contains 25,908 genic markers that enabled us to align nearly 73% of the anchored maize genome to the rice genome. The distribution pattern of expressed sequence tags correlates to that of recombination. In collinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, yet maize has a 6-fold genome size expansion. This can be explained by the fact that most rice regions correspond to two regions in maize as a result of its recent polyploid origin. Inversions account for the majority of chromosome structural variations during subsequent maize diploidization. We also find clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes.}, }
@article {pmid17657509, year = {2007}, author = {Li, H and Huang, Y and Mustavich, LF and Zhang, F and Tan, JZ and Wang, LE and Qian, J and Gao, MH and Jin, L}, title = {Y chromosomes of prehistoric people along the Yangtze River.}, journal = {Human genetics}, volume = {122}, number = {3-4}, pages = {383-388}, pmid = {17657509}, issn = {0340-6717}, mesh = {Asian People/*genetics ; China ; Chromosomes, Human, Y/*genetics ; DNA/genetics/history/isolation &amp; purification ; Evolution, Molecular ; Fossils ; Fresh Water ; Genetic Markers ; Genetic Variation ; Haplotypes ; History, Ancient ; Humans ; Male ; Polymorphism, Single Nucleotide ; }, abstract = {The ability to extract mitochondrial and nuclear DNA from ancient remains has enabled the study of ancient DNA, a legitimate field for over 20 years now. Recently, Y chromosome genotyping has begun to be applied to ancient DNA. The Y chromosome haplogroup in East Asia has since caught the attention of molecular anthropologists, as it is one of the most ethnic-related genetic markers of the region. In this paper, the Y chromosome haplogroup of DNA from ancient East Asians was examined, in order to genetically link them to modern populations. Fifty-six human remains were sampled from five archaeological sites, primarily along the Yangtze River. Strict criteria were followed to eliminate potential contamination. Five SNPs from the Y chromosome were successfully amplified from most of the samples, with at least 62.5% of the samples belonging to the O haplogroup, similar to the frequency for modern East Asian populations. A high frequency of O1 was found in Liangzhu Culture sites around the mouth of the Yangtze River, linking this culture to modern Austronesian and Daic populations. A rare haplogroup, O3d, was found at the Daxi site in the middle reaches of the Yangtze River, indicating that the Daxi people might be the ancestors of modern Hmong-Mien populations, which show only small traces of O3d today. Noticeable genetic segregation was observed among the prehistoric cultures, demonstrating the genetic foundation of the multiple origins of the Chinese Civilization.}, }
@article {pmid17641642, year = {2007}, author = {Rohland, N and Hofreiter, M}, title = {Ancient DNA extraction from bones and teeth.}, journal = {Nature protocols}, volume = {2}, number = {7}, pages = {1756-1762}, doi = {10.1038/nprot.2007.247}, pmid = {17641642}, issn = {1750-2799}, mesh = {Animals ; Bone and Bones/*chemistry ; Centrifugation/methods ; DNA/genetics/*isolation &amp; purification ; *Fossils ; Freezing ; Indicators and Reagents ; Polymerase Chain Reaction/methods ; Silicon Dioxide/isolation &amp; purification ; Tooth/*chemistry ; }, abstract = {This method is designed to maximize recovery of PCR-amplifiable DNA from ancient bone and teeth specimens and at the same time to minimize co-extraction of substances that inhibit PCR. This is achieved by a combination of DNA extraction from bone powder using a buffer consisting solely of EDTA and proteinase K, and purification of the DNA by binding to silica in the presence of high concentrations of guanidinium thiocyanate. All steps are performed at room temperature (20-23 degrees C), thereby reducing further degradation of the already damaged and fragile ancient DNA and providing an optimal trade-off between DNA release and degradation. Furthermore, the purification step removes most of the various types of PCR inhibitors present in ancient bone samples, thereby optimizing the amount of ancient DNA available for subsequent enzymatic manipulation, such as PCR amplification. The protocol presented here allows DNA extraction from ancient bone and teeth with a minimum of working steps and equipment and yields DNA extracts within 2 working days.}, }
@article {pmid17632524, year = {2007}, author = {d'Abbadie, M and Hofreiter, M and Vaisman, A and Loakes, D and Gasparutto, D and Cadet, J and Woodgate, R and Pääbo, S and Holliger, P}, title = {Molecular breeding of polymerases for amplification of ancient DNA.}, journal = {Nature biotechnology}, volume = {25}, number = {8}, pages = {939-943}, pmid = {17632524}, issn = {1087-0156}, support = {MC_U105178804/MRC_/Medical Research Council/United Kingdom ; U.1051.03.006(78804)/MRC_/Medical Research Council/United Kingdom ; /ImNIH/Intramural NIH HHS/United States ; }, mesh = {DNA/*genetics ; DNA Damage/*genetics ; DNA Fingerprinting/*methods ; DNA-Directed DNA Polymerase/*chemistry/genetics ; Forensic Genetics/methods ; Fossils ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/*methods ; Specimen Handling/*methods ; }, abstract = {In the absence of repair, lesions accumulate in DNA. Thus, DNA persisting in specimens of paleontological, archaeological or forensic interest is inevitably damaged. We describe a strategy for the recovery of genetic information from damaged DNA. By molecular breeding of polymerase genes from the genus Thermus (Taq (Thermus aquaticus), Tth (Thermus thermophilus) and Tfl (Thermus flavus)) and compartmentalized self-replication selection, we have evolved polymerases that can extend single, double and even quadruple mismatches, process non-canonical primer-template duplexes and bypass lesions found in ancient DNA, such as hydantoins and abasic sites. Applied to the PCR amplification of 47,000-60,000-year-old cave bear DNA, these outperformed Taq DNA polymerase by up to 150% and yielded amplification products at sample dilutions at which Taq did not. Our results demonstrate that engineered polymerases can expand the recovery of genetic information from Pleistocene specimens and may benefit genetic analysis in paleontology, archeology and forensic medicine.}, }
@article {pmid17626351, year = {2007}, author = {Seo, M and Guk, SM and Kim, J and Chai, JY and Bok, GD and Park, SS and Oh, CS and Kim, MJ and Yil, YS and Shin, MH and Kang, IU and Shin, DH}, title = {Paleoparasitological report on the stool from a Medieval child mummy in Yangju, Korea.}, journal = {The Journal of parasitology}, volume = {93}, number = {3}, pages = {589-592}, doi = {10.1645/GE-905R3.1}, pmid = {17626351}, issn = {0022-3395}, mesh = {Animals ; Ascariasis/history ; Ascaris lumbricoides/isolation &amp; purification ; Clonorchiasis/history ; Clonorchis sinensis/isolation &amp; purification ; Feces/parasitology ; Helminthiasis/*history ; History, 15th Century ; Humans ; Mummies/*parasitology ; Trichuriasis/history ; Trichuris/isolation &amp; purification ; }, abstract = {Previous studies have successfully shown evidence for parasitic infections in human remains from various archaeological sites. However, in the case of Korea, since there have been very few paleoparasitological reports published, pre-20th century parasitic infection patterns remain obscure. Therefore, in order to partly fill this gap, we are reporting on a case of paleoparasitic infection from the feces of a 15th century child mummy from Yangju, Korea. In the course of the present study, we found the eggs of Clonorchis sinensis, Ascaris lumbricoides, and Trichuris trichiura in the feces of the mummy. Trichuris trichiura eggs were found in far greater numbers than other parasite eggs; in fact, intact bipolar plugs were clearly observed and even the larvae were still visible in some eggs. The eggs of C. sinensis and A. lumbricoides were also well preserved, though not in as great a number. Since we could find a number of well-preserved larvae-containing eggs, we are encouraged that successful extraction, amplification, and sequence determination of ancient DNA from the paleoparasite eggs might be possible in future studies. With additional paleoparasitological investigation using feces from Korean mummies, we hope that a history of parasite infection in Korea will be reconstructed.}, }
@article {pmid17615317, year = {2007}, author = {Curry, A}, title = {Profile: Eske Willerslev. Ancient DNA's intrepid explorer.}, journal = {Science (New York, N.Y.)}, volume = {317}, number = {5834}, pages = {36-37}, doi = {10.1126/science.317.5834.36}, pmid = {17615317}, issn = {1095-9203}, mesh = {Animals ; Climate ; DNA/*analysis/history/isolation &amp; purification ; Denmark ; Genetics/history ; Greenland ; History, 20th Century ; History, 21st Century ; History, Ancient ; Ice Cover/*chemistry ; Plants/genetics ; }, }
@article {pmid17610332, year = {2007}, author = {Witas, HW and Jedrychowska-Dańska, K and Zawicki, P}, title = {Extremely high frequency of autoimmune-predisposing alleles in medieval specimens.}, journal = {Journal of Zhejiang University. Science. B}, volume = {8}, number = {7}, pages = {512-514}, pmid = {17610332}, issn = {1673-1581}, mesh = {Alleles ; Antigens, CD/genetics ; Antigens, Differentiation/genetics ; Autoimmune Diseases/genetics/*history/immunology ; CTLA-4 Antigen ; DNA/genetics/isolation &amp; purification ; Gene Frequency ; Genotype ; HLA-DQ Antigens/genetics ; HLA-DQ beta-Chains ; History, Medieval ; Humans ; Poland ; Tooth/chemistry ; }, abstract = {The precise etiology and reasons for the increase in incidence of autoimmune disorders still remain unclear, and although both genetic and environmental factors have been proven to shape individual predisposition, it is not known which of the factors, if not both, is responsible for the boom observed during the last decades. In order to establish whether a higher frequency of autoimmune-predisposing alleles may explain this increase we took advantage of ancient DNA methodology to establish the genetic predisposition, conferred by cytotoxic T lymphocyte associated antigen-4 (CTLA4) +49A/G and human leukocyte antigens (HLA) DQB1(57), in population inhabiting Poland in the Middle Ages. After successful typing of 42 individuals from a 12th approximately 14th's century archeological burial site, we found that frequencies of the predisposing alleles in the medieval population were higher than they are at present, suggesting thus that the recently observed incidence increase results most probably from factors of other than genetic nature.}, }
@article {pmid17596126, year = {2007}, author = {Svensson, EM and Anderung, C and Baubliene, J and Persson, P and Malmström, H and Smith, C and Vretemark, M and Daugnora, L and Götherström, A}, title = {Tracing genetic change over time using nuclear SNPs in ancient and modern cattle.}, journal = {Animal genetics}, volume = {38}, number = {4}, pages = {378-383}, doi = {10.1111/j.1365-2052.2007.01620.x}, pmid = {17596126}, issn = {0268-9146}, mesh = {Alleles ; Animals ; Breeding ; Cattle/*genetics ; *Evolution, Molecular ; Gene Frequency ; Genetic Markers ; Heterozygote ; *Polymorphism, Single Nucleotide ; }, abstract = {Ancient DNA has the potential of adding the dimension of time to genetic studies. With a suitable sample set it should be possible to follow genetic changes over time as they occur. To date, only a limited number of ancient DNA studies that cover a large time span have been published, and all of these studies have used mitochondrial DNA. Here, we explore SNP typing as a way to access ancient coding nuclear genes. By targeting fragments of minimal size, we typed three polymorphic sites in 111 ancient cattle remains spanning some 4000 years. We showed that there has been a decrease in heterozygosity over time, especially since the late Middle Ages. We conclude that SNPs can be used to generate a time series for nuclear markers from ancient material, and thereby to study selection on genes over time.}, }
@article {pmid17593420, year = {2007}, author = {Helgason, A and Pálsson, S and Lalueza-Fox, C and Ghosh, S and Sigurdardóttir, S and Baker, A and Hrafnkelsson, B and Arnadóttir, L and Thorsteinsdóttir, U and Stefánsson, K}, title = {A statistical approach to identify ancient template DNA.}, journal = {Journal of molecular evolution}, volume = {65}, number = {1}, pages = {92-102}, pmid = {17593420}, issn = {0022-2844}, mesh = {DNA/*analysis/metabolism ; *DNA Damage ; Data Interpretation, Statistical ; Humans ; Mitochondria/*genetics/metabolism ; *Models, Statistical ; *Postmortem Changes ; }, abstract = {One of the key problems in the study of ancient DNA is that of authenticating sequences obtained from PCR amplifications of highly degraded samples. Contamination of ancient samples and postmortem damage to endogenous DNA templates are the major obstacles facing researchers in this task. In particular, the authentication of sequences obtained from ancient human remains is thought by many to be rather challenging. We propose a novel approach, based on the c statistic, that can be employed to help identify the sequence motif of an endogenous template, based on a sample of sequences that reflect the nucleotide composition of individual template molecules obtained from ancient tissues (such as cloned products from a PCR amplification). The c statistic exploits as information the most common form of postmortem damage observed among clone sequences in ancient DNA studies, namely, lesion-induced substitutions caused by cytosine deamination events. Analyses of simulated sets of templates with miscoding lesions and real sets of clone sequences from the literature indicate that the c-based approach is highly effective in identifying endogenous sequence motifs, even when they are not present among the sampled clones. The proposed approach is likely to be of general use to researchers working with DNA from ancient tissues, particularly from human remains, where authentication of results has been most challenging.}, }
@article {pmid17576599, year = {2007}, author = {Mimida, N and Kidou, S and Kotoda, N}, title = {Constitutive expression of two apple (Malus x domestica Borkh.) homolog genes of LIKE HETEROCHROMATIN PROTEIN1 affects flowering time and whole-plant growth in transgenic Arabidopsis.}, journal = {Molecular genetics and genomics : MGG}, volume = {278}, number = {3}, pages = {295-305}, pmid = {17576599}, issn = {1617-4615}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/growth &amp; development ; Base Sequence ; Chromosomal Proteins, Non-Histone/*genetics ; DNA Primers/genetics ; DNA, Complementary/genetics/isolation &amp; purification ; DNA, Plant/genetics/isolation &amp; purification ; Flowers/genetics/growth &amp; development ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; *Genes, Plant ; Malus/*genetics ; Molecular Sequence Data ; Mutation ; Phenotype ; Phylogeny ; Plant Proteins/*genetics ; Plants, Genetically Modified ; Sequence Homology, Amino Acid ; }, abstract = {Fruit trees, such as apple (Malus x domestica Borkh.), are woody perennial plants with a long juvenile phase. The biological analysis for the regulation of flowering time provides insights into the reduction of juvenile phase and the acceleration of breeding in fruit trees. In Arabidopsis, LIKE HETEROCHROMATIN PROTEIN1 (LHP1) is involved in epigenetic silencing of the target genes such as flowering genes. We isolated and characterized twin apple LHP1 homolog genes, MdLHP1a and MdLHP1b. These genes may have been generated as a result of ancient genome duplication. Although the putative MdLHP1 proteins showed lower similarity to any other known plant LHP1 homologs, a chromo domain, a chromo shadow domain, and the nuclear localization signal motifs were highly conserved among them. RT-PCR analysis showed that MdLHP1a and MdLHP1b were expressed constantly in developing shoot apices of apple trees throughout the growing season. Constitutive expression of MdLHP1a or MdLHP1b could compensate for the pleiotropic phenotype of lhp1/tfl2 mutant, suggesting that apple LHP1 homolog genes are involved in the regulation of flowering time and whole-plant growth. Based on these results, LHP1 homolog genes might have rapidly evolved among plant species, but the protein functions were conserved, at least between Arabidopsis and apple.}, }
@article {pmid17556540, year = {2007}, author = {Storey, AA and Ramírez, JM and Quiroz, D and Burley, DV and Addison, DJ and Walter, R and Anderson, AJ and Hunt, TL and Athens, JS and Huynen, L and Matisoo-Smith, EA}, title = {Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {25}, pages = {10335-10339}, pmid = {17556540}, issn = {0027-8424}, mesh = {Animals ; Archaeology/*methods ; Base Sequence ; Carbon/*analysis ; Carbon Radioisotopes/*chemistry ; Chickens ; Chile ; DNA/*analysis/*chemistry ; DNA, Mitochondrial/analysis/chemistry ; Fossils ; Geography ; History, Ancient ; Molecular Sequence Data ; Polymerase Chain Reaction ; Polynesia ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Two issues long debated among Pacific and American prehistorians are (i) whether there was a pre-Columbian introduction of chicken (Gallus gallus) to the Americas and (ii) whether Polynesian contact with South America might be identified archaeologically, through the recovery of remains of unquestionable Polynesian origin. We present a radiocarbon date and an ancient DNA sequence from a single chicken bone recovered from the archaeological site of El Arenal-1, on the Arauco Peninsula, Chile. These results not only provide firm evidence for the pre-Columbian introduction of chickens to the Americas, but strongly suggest that it was a Polynesian introduction.}, }
@article {pmid17540861, year = {2007}, author = {Jackson, DJ and Macis, L and Reitner, J and Degnan, BM and Wörheide, G}, title = {Sponge paleogenomics reveals an ancient role for carbonic anhydrase in skeletogenesis.}, journal = {Science (New York, N.Y.)}, volume = {316}, number = {5833}, pages = {1893-1895}, doi = {10.1126/science.1141560}, pmid = {17540861}, issn = {1095-9203}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bicarbonates/metabolism ; *Calcification, Physiologic ; Calcium Carbonate/analysis/metabolism ; Carbonic Anhydrases/chemistry/*genetics/*metabolism ; Computational Biology ; Evolution, Molecular ; Gene Duplication ; Genes ; Genomics ; Molecular Sequence Data ; Porifera/anatomy &amp; histology/enzymology/*genetics/*physiology ; Recombinant Proteins/chemistry/metabolism ; }, abstract = {Sponges (phylum Porifera) were prolific reef-building organisms during the Paleozoic and Mesozoic approximately 542 to 65 million years ago. These ancient animals inherited components of the first multicellular skeletogenic toolkit from the last common ancestor of the Metazoa. Using a paleogenomics approach, including gene- and protein-expression techniques and phylogenetic reconstruction, we show that a molecular component of this toolkit was the precursor to the alpha-carbonic anhydrases (alpha-CAs), a gene family used by extant animals in a variety of fundamental physiological processes. We used the coralline demosponge Astrosclera willeyana, a "living fossil" that has survived from the Mesozoic, to provide insight into the evolution of the ability to biocalcify, and show that the alpha-CA family expanded from a single ancestral gene through several independent gene-duplication events in sponges and eumetazoans.}, }
@article {pmid19083754, year = {2007}, author = {Loreille, OM and Diegoli, TM and Irwin, JA and Coble, MD and Parsons, TJ}, title = {High efficiency DNA extraction from bone by total demineralization.}, journal = {Forensic science international. Genetics}, volume = {1}, number = {2}, pages = {191-195}, doi = {10.1016/j.fsigen.2007.02.006}, pmid = {19083754}, issn = {1878-0326}, mesh = {Bone Demineralization Technique/*methods ; Bone and Bones/*chemistry ; DNA/*genetics/*isolation &amp; purification ; DNA, Mitochondrial/genetics/isolation &amp; purification ; Forensic Genetics/*methods ; Humans ; Microsatellite Repeats ; Tooth/chemistry ; }, abstract = {In historical cases, missing persons' identification, mass disasters, and ancient DNA investigations, bone and teeth samples are often the only, and almost always the best, biological material available for DNA typing. This is because of the physical and chemical barrier that the protein:mineral matrix of bone poses to environmental deterioration and biological attack. Most bone extraction protocols utilized in the forensic community involve an incubation period of bone powder in extraction buffer for proteinase digestion, followed by the collection of the supernatant, and the disposal of large quantities of undissolved bone powder. Here we present an extremely efficient protocol for recovery of DNA by complete demineralization, resulting in full physical dissolution of the bone sample. This is performed in a manner that retains and concentrates all the reagent volume, for complete DNA recovery. For our study, we selected 14 challenging bone samples. The bones were extracted side-by-side with our new demineralization protocol and the standard extraction protocol in use at AFDIL. A real-time quantification assay based on the amplification of a 143 bp mtDNA fragment showed that this new demineralization protocol significantly enhances the quantity of DNA that can be extracted and amplified from degraded skeletal remains. We have used this technique to successfully recover authentic DNA sequences from extremely challenging samples that failed repeatedly using the standard protocol.}, }
@article {pmid17534642, year = {2007}, author = {Bouakaze, C and Keyser, C and Amory, S and Crubézy, E and Ludes, B}, title = {First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA.}, journal = {International journal of legal medicine}, volume = {121}, number = {6}, pages = {493-499}, pmid = {17534642}, issn = {0937-9827}, mesh = {Alleles ; Asian People/*genetics ; Bone and Bones/metabolism ; Chromosomes, Human, Y/*genetics ; Evolution, Molecular ; Female ; *Haplotypes ; Humans ; Male ; Paleontology/*methods ; Polymerase Chain Reaction/methods ; Polymorphism, Single Nucleotide/*genetics ; *Postmortem Changes ; Sequence Analysis, DNA ; Siberia ; }, abstract = {In the present study, a set of 13 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) selected for the identification of the most frequent Asian Y-haplogroups was included in an allele-specific primer extension assay. Single nucleotide polymorphism (SNP) genotyping was accomplished by co-amplification of these 13 DNA fragments within 2 multiplex PCRs followed by detection with 1 minisequencing reaction using the SNaPshottrade mark Multiplex kit and analysis of extension products by capillary electrophoresis. First developed on modern samples, the assay was optimized for the analysis of 11 ancient DNA (aDNA) samples from the Krasnoyarsk region (southern Siberia) that were dated from 5,500-1,800 years before present (YBP). SNP typing was successful for most of them, which were all assigned to Y-haplogroup R1a1 except one. These results show that SNPs are well-suited for the analysis of aged and degraded DNA samples. Moreover, we found that the SNaPshot minisequencing methodology is a convenient, robust, and efficient method for SNP typing. To our knowledge, this study reports the first successful investigation of Y-SNPs on aDNA samples. The potential use of Y-SNPs in both evolutionary and forensic fields is also discussed.}, }
@article {pmid17510332, year = {2007}, author = {Pennisi, E}, title = {Ancient DNA. No sex please, we're Neandertals.}, journal = {Science (New York, N.Y.)}, volume = {316}, number = {5827}, pages = {967}, doi = {10.1126/science.316.5827.967a}, pmid = {17510332}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; *Fossils ; Gene Flow ; Genome ; Genome, Human ; Hominidae/*genetics ; Humans ; *Hybridization, Genetic ; Polymorphism, Single Nucleotide ; *Sexual Behavior ; }, }
@article {pmid17506489, year = {2007}, author = {Gao, SZ and Yang, YD and Xu, Y and Zhang, QC and Zhu, H and Zhou, H}, title = {Tracing the genetic history of the Chinese people: mitochondrial DNA analysis of aneolithic population from the Lajia site.}, journal = {American journal of physical anthropology}, volume = {133}, number = {4}, pages = {1128-1136}, doi = {10.1002/ajpa.20623}, pmid = {17506489}, issn = {0002-9483}, mesh = {Asian People/genetics/*history ; China ; DNA, Mitochondrial/*chemistry/classification ; Female ; Haplotypes ; History, Ancient ; Humans ; Male ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; }, abstract = {Ancient DNA analysis was conducted on the dental remains of specimens from the Lajia site, dating back 3,800-4,000 years. The Lajia site is located in Minhe county, Qinghai province, in northwestern China. Archaeological studies link Lajia to the late period of the Qijia culture, one of the most important Neolithic civilizations of the upper Yellow River region, the cradle of Chinese civilization. Excavations at the site revealed that the inhabitants died in their houses as the result of a sudden flood. The Lajia site provides a rare chance to study the putative families, all of whom died at the same instant. Possible maternal familial relationships were investigated through mitochondrial DNA (mtDNA) sequence analysis. Twelve sequences from individuals found in one house were assigned to only five haplotypes, consistent with a possible close kinship. Results from analyses of RFLP typing and HVI motifs suggest that the Lajia people belonged to the haplogroups B, C, D, M*, and M10. This study, combined with archaeological and anthropological investigations, provides a better understanding of the genetic history of the Chinese people.}, }
@article {pmid17476775, year = {2007}, author = {Lia, VV and Confalonieri, VA and Ratto, N and Hernández, JA and Alzogaray, AM and Poggio, L and Brown, TA}, title = {Microsatellite typing of ancient maize: insights into the history of agriculture in southern South America.}, journal = {Proceedings. Biological sciences}, volume = {274}, number = {1609}, pages = {545-554}, pmid = {17476775}, issn = {0962-8452}, mesh = {Crops, Agricultural/classification/*genetics ; Genotype ; Geography ; *Microsatellite Repeats ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; South America ; Zea mays/classification/*genetics ; }, abstract = {Archaeological maize specimens from Andean sites of southern South America, dating from 400 to 1400 years before present, were tested for the presence of ancient DNA and three microsatellite loci were typed in the specimens that gave positive results. Genotypes were also obtained for 146 individuals corresponding to modern landraces currently cultivated in the same areas and for 21 plants from Argentinian lowland races. Sequence analysis of cloned ancient DNA products revealed a high incidence of substitutions appearing in only one clone, with transitions prevalent. In the archaeological specimens, there was no evidence of polymorphism at any one of the three microsatellite loci: each exhibited a single allelic variant, identical to the most frequent allele found in contemporary populations belonging to races Amarillo Chico, Amarillo Grande, Blanco and Altiplano. Affiliation between ancient specimens and a set of races from the Andean complex was further supported by assignment tests. The striking genetic uniformity displayed by the ancient specimens and their close relationship with the Andean complex suggest that the latter gene pool has predominated in the western regions of southern South America for at least the past 1400 years. The results support hypotheses suggesting that maize cultivation initially spread into South America via a highland route, rather than through the lowlands.}, }
@article {pmid17466066, year = {2007}, author = {Kolokotronis, SO and Macphee, RD and Greenwood, AD}, title = {Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {67}, pmid = {17466066}, issn = {1471-2148}, mesh = {Animals ; Cloning, Molecular ; Complementarity Determining Regions/*genetics ; DNA Transposable Elements/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Haplotypes ; Paleontology ; Phylogeny ; Polymerase Chain Reaction ; Ruminants/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Nuclear insertions of mitochondrial sequences (NuMts) have been identified in a wide variety of organisms. Trafficking of genetic material from the mitochondria to the nucleus has occurred frequently during mammalian evolution and can lead to the production of a large pool of sequences with varying degrees of homology to organellar mitochondrial DNA (mtDNA) sequences. This presents both opportunities and challenges for forensics, population genetics, evolutionary genetics, conservation biology and the study of DNA from ancient samples. Here we present a case in which difficulties in ascertaining the organellar mtDNA sequence from modern samples hindered their comparison to ancient DNA sequences.<br><br>RESULTS: We obtained mitochondrial hypervariable region (HVR) sequences from six ancient samples of tundra muskox (Ovibos moschatus) that were reproducible but distinct from modern muskox sequences reported previously. Using the same PCR primers applied to the ancient specimens and the primers used to generate the modern muskox DNA sequences in a previous study, we failed to definitively identify the organellar sequence from the two modern muskox samples tested. Instead of anticipated sequence homogeneity, we obtained multiple unique sequences from both hair and blood of one modern specimen. Sequencing individual clones of a >1 kb PCR fragment from modern samples did not alleviate the problem as there was not a consistent match across the entire length of the sequences to Ovibos when compared to sequences in GenBank.<br><br>CONCLUSION: In specific taxa, due to nuclear insertions some regions of the mitochondrial genome may not be useful for the characterization of modern or ancient DNA.}, }
@article {pmid17456457, year = {2007}, author = {Nichols, C and Herman, J and Gaggiotti, OE and Dobney, KM and Parsons, K and Hoelzel, AR}, title = {Genetic isolation of a now extinct population of bottlenose dolphins (Tursiops truncatus).}, journal = {Proceedings. Biological sciences}, volume = {274}, number = {1618}, pages = {1611-1616}, pmid = {17456457}, issn = {0962-8452}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bayes Theorem ; Bottle-Nosed Dolphin/*genetics ; Conservation of Natural Resources ; DNA Primers ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Fossils ; Gene Frequency ; *Genetics, Population ; Genotype ; Likelihood Functions ; Microsatellite Repeats/genetics ; Models, Genetic ; United Kingdom ; }, abstract = {A number of dolphin species, though highly mobile, show genetic structure among parapatric and sometimes sympatric populations. However, little is known about the temporal patterns of population structure for these species. Here, we apply Bayesian inference and data from ancient DNA to assess the structure and dynamics of bottlenose dolphin (Tursiops truncatus) populations in the coastal waters of the UK. We show that regional population structure in UK waters is consistent with earlier studies suggesting local habitat dependence for this species in the Mediterranean Sea and North Atlantic. One genetically differentiated UK population went extinct at least 100 years ago and has not been replaced. The data indicate that this was a local extinction, and not a case of historical range shift or contraction. One possible interpretation is a declining metapopulation and conservation need for this species in the UK.}, }
@article {pmid17456455, year = {2007}, author = {Xie, CZ and Li, CX and Cui, YQ and Zhang, QC and Fu, YQ and Zhu, H and Zhou, H}, title = {Evidence of ancient DNA reveals the first European lineage in Iron Age Central China.}, journal = {Proceedings. Biological sciences}, volume = {274}, number = {1618}, pages = {1597-1601}, pmid = {17456455}, issn = {0962-8452}, mesh = {Base Sequence ; China ; DNA Primers ; DNA, Mitochondrial/*genetics ; Emigration and Immigration/*history ; Female ; Femur/anatomy &amp; histology/*chemistry ; *Fossils ; Haplotypes/genetics ; History, Medieval ; Humans ; Male ; Molecular Sequence Data ; Sequence Analysis, DNA ; Tooth/anatomy &amp; histology/*chemistry ; White People/genetics ; }, abstract = {Various studies on ancient DNA have attempted to reconstruct population movement in Asia, with much interest focused on determining the arrival of European lineages in ancient East Asia. Here, we discuss our analysis of the mitochondrial DNA of human remains excavated from the Yu Hong tomb in Taiyuan, China, dated 1400 years ago. The burial style of this tomb is characteristic of Central Asia at that time. Our analysis shows that Yu Hong belonged to the haplogroup U5, one of the oldest western Eurasian-specific haplogroups, while his wife can be classified as haplogroup G, the type prevalent in East Asia. Our findings show that this man with European lineage arrived in Taiyuan approximately 1400 years ago, and most probably married a local woman. Haplogroup U5 was the first west Eurasian-specific lineage to be found in the central part of ancient China, and Taiyuan may be the easternmost location of the discovered remains of European lineage in ancient China.}, }
@article {pmid17443966, year = {2007}, author = {Orlando, L and Pagés, M and Calvignac, S and Hughes, S and Hänni, C}, title = {Does the 43 bp sequence from an 800,000 year old cretan dwarf elephantid really rewrite the textbook on mammoths?.}, journal = {Biology letters}, volume = {3}, number = {1}, pages = {57-9; discussion 60-3}, pmid = {17443966}, issn = {1744-9561}, mesh = {Animals ; Base Sequence ; Bone and Bones/chemistry ; DNA Primers ; DNA, Mitochondrial/analysis/*genetics ; Elephants/*genetics ; *Fossils ; Mediterranean Islands ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Pigmy elephants inhabited the islands from the Mediterranean region during the Pleistocene period but became extinct in the course of the Holocene. Despite striking distinctive anatomical characteristics related to insularity, some similarities with the lineage of extant Asian elephants have suggested that pigmy elephants could be most probably seen as members of the genus Elephas. Poulakakis et al (2006) have recently challenged this view by recovering a short mtDNA sequence from an 800 000 year old fossil of the Cretan pigmy elephant (Elephas creticus). According to the authors of this study, a deep taxonomic revision of Cretan dwarf elephants would be needed, as the sequence exhibits clear affinities with woolly mammoth haplotypes. However, we point here many aspects that seriously weaken the strength of the ancient DNA evidence reported.}, }
@article {pmid17443965, year = {2007}, author = {Binladen, J and Gilbert, MT and Willerslev, E}, title = {800,000 year old mammoth DNA, modern elephant DNA or PCR artefact?.}, journal = {Biology letters}, volume = {3}, number = {1}, pages = {55-6; discussion 60-3}, pmid = {17443965}, issn = {1744-9561}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Base Sequence ; Bone and Bones/chemistry ; DNA Primers ; DNA, Mitochondrial/analysis/*genetics ; Elephants/*genetics ; *Fossils ; Mediterranean Islands ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Poulakakis and colleagues (Poulakakis et al. 2006: Biol. Lett. 2, 451-454), report the recovery of 'authentic' mammoth DNA from an 800,000-year-old fragment of bone excavated on the island of Crete. In light of results from other ancient DNA studies that indicate how DNA survival is unlikely in samples, which are recovered from warm environments and are relatively old (e.g. more than 100,000 years), these findings come as a great surprise. Here, we show that problems exist with the methodological approaches used in the study. First, the nested PCR technique as reported is nonsensical--one of the second round 'nested' primers falls outside the amplicon of the first round PCR. More worryingly, the binding region of one of the first round primers (Elcytb320R) falls within the short 43 base pair reported mammoth sequence, specifically covering two of the three reportedly diagnostic Elephas polymorphisms. Finally, we demonstrate using a simple BLAST search in GenBank that the claimed 'uniquely derived character state' for mammoths is in fact also found within modern elephants.}, }
@article {pmid17420452, year = {2007}, author = {Dalén, L and Nyström, V and Valdiosera, C and Germonpré, M and Sablin, M and Turner, E and Angerbjörn, A and Arsuaga, JL and Götherström, A}, title = {Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {16}, pages = {6726-6729}, pmid = {17420452}, issn = {0027-8424}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; *Ecosystem ; *Fossils ; Foxes/*genetics ; Molecular Sequence Data ; *Natural History ; Scandinavian and Nordic Countries ; *Sequence Analysis, DNA ; }, abstract = {How species respond to an increased availability of habitat, for example at the end of the last glaciation, has been well established. In contrast, little is known about the opposite process, when the amount of habitat decreases. The hypothesis of habitat tracking predicts that species should be able to track both increases and decreases in habitat availability. The alternative hypothesis is that populations outside refugia become extinct during periods of unsuitable climate. To test these hypotheses, we used ancient DNA techniques to examine genetic variation in the arctic fox (Alopex lagopus) through an expansion/contraction cycle. The results show that the arctic fox in midlatitude Europe became extinct at the end of the Pleistocene and did not track the habitat when it shifted to the north. Instead, a high genetic similarity between the extant populations in Scandinavia and Siberia suggests an eastern origin for the Scandinavian population at the end of the last glaciation. These results provide new insights into how species respond to climate change, since they suggest that populations are unable to track decreases in habitat avaliability. This implies that arctic species may be particularly vulnerable to increases in global temperatures.}, }
@article {pmid17409720, year = {2007}, author = {Sakahira, F and Niimi, M}, title = {Ancient DNA analysis of the Japanese sea lion (Zalophus californianus japonicus Peters, 1866): preliminary results using mitochondrial control-region sequences.}, journal = {Zoological science}, volume = {24}, number = {1}, pages = {81-85}, doi = {10.2108/zsj.24.81}, pmid = {17409720}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; DNA Primers/genetics ; DNA, Mitochondrial/genetics/isolation &amp; purification ; Japan ; Molecular Sequence Data ; *Phylogeny ; Sea Lions/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {In this study, we successfully extracted ancient DNA from skeletal remains of the Japanese sea lion-a species that is practically extinct-from archaeological sites and determined a partial sequence of its mitochondrial DNA control region. A molecular phylogenetic tree constructed by the neighbor-joining (NJ) method showed that the sequences from Japanese sea lions clustered together, with a high bootstrap value, and that this cluster was closest to the California sea lion cluster. The distinctly divergent cluster of Japanese sea lions reflected the morphological classification of these animals as a distinct species of the genus Zalophus; however, proximity to the California sea lion cluster simultaneously implied conformation with the traditional classification of these animals as a subspecies of Zalophus californianus. The average amount of nucleotide substitution between the Japanese and California sea lions was 7.02%. The Japanese and California sea lions were estimated to have diverged 2.2 million years ago, i.e., in the late Pliocene Epoch. This is the first report on a genetic analysis of the Japanese sea lion.}, }
@article {pmid17406424, year = {2006}, author = {Sanchez, JJ and Endicott, P}, title = {Developing multiplexed SNP assays with special reference to degraded DNA templates.}, journal = {Nature protocols}, volume = {1}, number = {3}, pages = {1370-1378}, doi = {10.1038/nprot.2006.247}, pmid = {17406424}, issn = {1750-2799}, mesh = {DNA/*genetics ; Electrophoresis, Capillary/methods ; Genetic Testing/*methods ; Polymorphism, Single Nucleotide/*genetics ; }, abstract = {This protocol describes a single nucleotide polymorphism (SNP) genotyping strategy for highly degraded DNA, using a two-stage multiplex whereby multiple fragments are first amplified in a single exponential reaction and the products of this PCR are added to a linear single-base-extension reaction. It utilizes the analytical power of a capillary electrophoresis system to simultaneously type all the target sites. The protocol is specifically written for use with severely fragmented templates, typical of ancient DNA, and can be adapted to widely used detection platforms. The addition of the single-phase genotyping step avoids the need for the re-amplification and cloning of PCR products, while providing its own controls for the detection of contamination and allelic drop-out. This protocol can facilitate the routine analysis of up to 52 SNP markers (haploid or diploid) in 96 samples in a single day, and is recommended for the authentication of data in all areas of DNA research (population and medical genetics, forensics, ancient DNA).}, }
@article {pmid17406302, year = {2006}, author = {Römpler, H and Dear, PH and Krause, J and Meyer, M and Rohland, N and Schöneberg, T and Spriggs, H and Stiller, M and Hofreiter, M}, title = {Multiplex amplification of ancient DNA.}, journal = {Nature protocols}, volume = {1}, number = {2}, pages = {720-728}, doi = {10.1038/nprot.2006.84}, pmid = {17406302}, issn = {1750-2799}, support = {MC_U105131672/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Archaeology/methods ; DNA/*analysis/*genetics ; Laboratories ; Paleontology/methods ; Polymerase Chain Reaction/instrumentation/*methods ; Reproducibility of Results ; Templates, Genetic ; Time Factors ; }, abstract = {This method is designed to assemble long, continuous DNA sequences using minimal amounts of fragmented ancient DNA as template. This is achieved by a two-step approach. In the first step, multiple fragments are simultaneously amplified in a single multiplex reaction. Subsequently, each of the generated fragments is amplified individually using a single primer pair, in a standard simplex (monoplex) PCR. The ability to amplify multiple fragments simultaneously in the first step allows the generation of large amounts of sequence from rare template DNA, whereas the second nested step increases specificity and decreases amplification of contaminating DNA. In contrast to current protocols using many template-consuming simplex PCRs, the method described allows amplification of several kilobases of sequence in just one reaction. It thus combines optimal template usage with a high specificity and can be performed within a day.}, }
@article {pmid17395598, year = {2007}, author = {Ho, SY and Heupink, TH and Rambaut, A and Shapiro, B}, title = {Bayesian estimation of sequence damage in ancient DNA.}, journal = {Molecular biology and evolution}, volume = {24}, number = {6}, pages = {1416-1422}, doi = {10.1093/molbev/msm062}, pmid = {17395598}, issn = {0737-4038}, mesh = {Animals ; *Bayes Theorem ; Bison/genetics ; Computer Simulation ; DNA Damage/*genetics ; *Fossils ; Lions/genetics ; Models, Genetic ; *Sequence Analysis, DNA ; }, abstract = {DNA extracted from archaeological and paleontological remains is usually damaged by biochemical processes postmortem. Some of these processes lead to changes in the structure of the DNA molecule, which can result in the incorporation of incorrect nucleotides during polymerase chain reaction. These base misincorporations, or miscoding lesions, can lead to the inclusion of spurious additional mutations in ancient DNA (aDNA) data sets. This has the potential to affect the outcome of phylogenetic and population genetic analyses, including estimates of mutation rates and genetic diversity. We present a novel model, termed the delta model, which estimates the amount of damage in DNA data and accounts for its effects in a Bayesian phylogenetic framework. The ability of the delta model to estimate damage is first investigated using a simulation study. The model is then applied to 13 aDNA data sets. The amount of damage in these data sets is shown to be significant but low (about 1 damaged base per 750 nt), suggesting that precautions for limiting the influence of damaged sites, such as cloning and enzymatic treatment, are worthwhile. The results also suggest that relatively high rates of mutation previously estimated from aDNA data are not entirely an artifact of sequence damage and are likely to be due to other factors such as the persistence of transient polymorphisms. The delta model appears to be particularly useful for placing upper credibility limits on the amount of sequence damage in an alignment, and this capacity might be beneficial for future aDNA studies or for the estimation of sequencing errors in modern DNA.}, }
@article {pmid17390541, year = {2007}, author = {Rohland, N and Hofreiter, M}, title = {Comparison and optimization of ancient DNA extraction.}, journal = {BioTechniques}, volume = {42}, number = {3}, pages = {343-352}, doi = {10.2144/000112383}, pmid = {17390541}, issn = {0736-6205}, mesh = {Animals ; Bone and Bones/metabolism ; Buffers ; DNA/*analysis/chemistry/isolation &amp; purification ; Edetic Acid/chemistry/pharmacology ; Endopeptidase K/pharmacology ; Fossils ; Hydrogen-Ion Concentration ; Paleontology ; Polymerase Chain Reaction/methods ; Salts/pharmacology ; Sequence Analysis, DNA/*methods ; Serum Albumin, Bovine/metabolism ; Silicon Dioxide/chemistry ; Ursidae ; }, abstract = {Ancient DNA analyses rely on the extraction of the tiny amounts of DNA remaining in samples that are hundreds to tens of thousands of years old. Despite the critical role extraction efficiency plays in this field of research, no study has comprehensively compared ancient DNA extraction techniques to date. There are a wide range of methods currently in use, which rely on such disparate principles as spin columns, alcohol precipitation, or binding to silica. We have compared a number of these methods using quantitative PCR and then optimized each step of the most promising method. We found that most chemicals routinely added to ancient DNA extraction buffers do not increase, and sometimes even decrease, DNA yields. Consequently, our optimized method uses a buffer consisting solely of EDTA and proteinase K for bone digestion and binding DNA to silica via guanidinium thiocyanate for DNA purification. In a comparison with published methods, this minimalist approach, on average, outperforms all other methods in terms of DNA yields as measured using quantitative PCR. We also found that the addition of bovine serum albumin (BSA) to the PCR helps to overcome inhibitors in ancient DNA extracts. Finally, we observed a marked difference in the performance between different types of DNA polymerases, as measured by amplification success.}, }
@article {pmid17389894, year = {2007}, author = {Foley, RA and Lahr, MM}, title = {Ancient DNA closes on human uniqueness: the base nature of Neanderthals.}, journal = {Heredity}, volume = {98}, number = {4}, pages = {187-188}, doi = {10.1038/sj.hdy.6800953}, pmid = {17389894}, issn = {0018-067X}, mesh = {Africa ; Animals ; DNA/*genetics/isolation &amp; purification ; Evolution, Molecular ; Hominidae/*genetics ; Humans ; }, }
@article {pmid17379733, year = {2007}, author = {Taylor, GM and Murphy, E and Hopkins, R and Rutland, P and Chistov, Y}, title = {First report of Mycobacterium bovis DNA in human remains from the Iron Age.}, journal = {Microbiology (Reading, England)}, volume = {153}, number = {Pt 4}, pages = {1243-1249}, doi = {10.1099/mic.0.2006/002154-0}, pmid = {17379733}, issn = {1350-0872}, mesh = {Animals ; Cattle ; DNA, Bacterial/history/*isolation &amp; purification ; Female ; History, Ancient ; Humans ; Male ; Mycobacterium bovis/*genetics/isolation &amp; purification ; Polymerase Chain Reaction ; Siberia ; Spine/*microbiology/pathology ; Tuberculosis, Spinal/*history/microbiology/pathology ; }, abstract = {Tuberculosis has plagued humankind since prehistoric times, as is evident from characteristic lesions on human skeletons dating back to the Neolithic period. The disease in man is due predominantly to infection with either Mycobacterium tuberculosis or Mycobacterium bovis, both members of the M. tuberculosis (MTB) complex. A number of studies have shown that when conditions permit, surviving mycobacterial DNA may be amplified from bone by PCR. Such ancient DNA (aDNA) analyses are subject to stringent tests of authenticity and, when feasible, are invariably limited by DNA fragmentation. Using PCRs based on single-nucleotide polymorphic loci and regions of difference (RDs) in the MTB complex, a study was made of five Iron Age individuals with spinal lesions recovered from the cemetery of Aymyrlyg, South Siberia. A sensitive screening PCR for MTB complex mycobacteria was positive in four out of the five cases. Genotyping evidence indicated that all four cases were due to infection with M. bovis rather than M. tuberculosis and the data were consistent with the proposed phylogenetic model of the MTB complex. This is believed to be the first report of M. bovis causing Pott's disease in archaeological human remains. The study shows that genotyping of ancestral strains of MTB complex mycobacteria from contexts of known date provides information which allows the phylogeny of the model to be tested. Moreover, it shows that loss of DNA from RD4, which defines classic M. bovis, had already occurred from the genome over 2000 years before the present.}, }
@article {pmid17360422, year = {2007}, author = {Burger, J and Kirchner, M and Bramanti, B and Haak, W and Thomas, MG}, title = {Absence of the lactase-persistence-associated allele in early Neolithic Europeans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {10}, pages = {3736-3741}, pmid = {17360422}, issn = {0027-8424}, mesh = {*Alleles ; Bone and Bones/metabolism ; DNA, Mitochondrial/genetics ; Emigration and Immigration ; Europe ; Genetics, Population ; History, Ancient ; Humans ; Lactase/*genetics ; Lactose/metabolism ; Lactose Intolerance/*genetics ; Polymorphism, Single Nucleotide ; Tandem Repeat Sequences ; Tooth/metabolism ; White People/*genetics/history ; }, abstract = {Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk. Some have argued for the "culture-historical hypothesis," whereby LP alleles were rare until the advent of dairying early in the Neolithic but then rose rapidly in frequency under natural selection. Others favor the "reverse cause hypothesis," whereby dairying was adopted in populations with preadaptive high LP allele frequencies. Analysis based on the conservation of lactase gene haplotypes indicates a recent origin and high selection coefficients for LP, although it has not been possible to say whether early Neolithic European populations were lactase persistent at appreciable frequencies. We developed a stepwise strategy for obtaining reliable nuclear ancient DNA from ancient skeletons, based on (i) the selection of skeletons from archaeological sites that showed excellent biomolecular preservation, (ii) obtaining highly reproducible human mitochondrial DNA sequences, and (iii) reliable short tandem repeat (STR) genotypes from the same specimens. By applying this experimental strategy, we have obtained high-confidence LP-associated genotypes from eight Neolithic and one Mesolithic human remains, using a range of strict criteria for ancient DNA work. We did not observe the allele most commonly associated with LP in Europeans, thus providing evidence for the culture-historical hypothesis, and indicating that LP was rare in early European farmers.}, }
@article {pmid17360400, year = {2007}, author = {Larson, G and Cucchi, T and Fujita, M and Matisoo-Smith, E and Robins, J and Anderson, A and Rolett, B and Spriggs, M and Dolman, G and Kim, TH and Thuy, NT and Randi, E and Doherty, M and Due, RA and Bollt, R and Djubiantono, T and Griffin, B and Intoh, M and Keane, E and Kirch, P and Li, KT and Morwood, M and Pedriña, LM and Piper, PJ and Rabett, RJ and Shooter, P and Van den Bergh, G and West, E and Wickler, S and Yuan, J and Cooper, A and Dobney, K}, title = {Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {12}, pages = {4834-4839}, pmid = {17360400}, issn = {0027-8424}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animal Migration ; Animals ; Asia, Southeastern ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; *Geography ; Haplotypes ; History, Ancient ; Molecular Sequence Data ; Oceania ; *Phylogeny ; Principal Component Analysis ; Swine/*genetics ; }, abstract = {Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called "wild" pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region.}, }
@article {pmid17320326, year = {2007}, author = {Caramelli, D and Lalueza-Fox, C and Capelli, C and Lari, M and Sampietro, ML and Gigli, E and Milani, L and Pilli, E and Guimaraes, S and Chiarelli, B and Marin, VT and Casoli, A and Stanyon, R and Bertranpetit, J and Barbujani, G}, title = {Genetic analysis of the skeletal remains attributed to Francesco Petrarca.}, journal = {Forensic science international}, volume = {173}, number = {1}, pages = {36-40}, doi = {10.1016/j.forsciint.2007.01.020}, pmid = {17320326}, issn = {1872-6283}, mesh = {*DNA Fingerprinting ; DNA, Mitochondrial/*analysis ; Exhumation ; *Famous Persons ; History, Ancient ; Humans ; Italy ; Male ; Molar ; Polymerase Chain Reaction ; Ribs ; Sequence Analysis, DNA ; Sex Determination Analysis ; }, abstract = {We report on the mitochondrial DNA (mtDNA) analysis of the supposed remains of Francesco Petrarca exhumed in November 2003, from the S. Maria Assunta church, in Arquà Padua (Italy) where he died in 1374. The optimal preservation of the remains allowed the retrieval of sufficient mtDNA for genetic analysis. DNA was extracted from a rib and a tooth and mtDNA sequences were determined in multiple clones using the strictest criteria currently available for validation of ancient DNA sequences, including independent replication. MtDNA sequences from the tooth and rib were not identical, suggesting that they belonged to different individuals. Indeed, molecular gender determination showed that the postcranial remains belonged to a male while the skull belonged to a female. Historical records indicated that the remains were violated in 1630, possibly by thieves. These results are consistent with morphological investigations and confirm the importance of integrating molecular and morphological approaches in investigating historical remains.}, }
@article {pmid17308804, year = {2006}, author = {Marinho, AN and Miranda, NC and Braz, V and Ribeiro-Dos-Santos, AK and de Souza, SM}, title = {Paleogenetic and taphonomic analysis of human bones from Moa, Beirada, and Zé Espinho Sambaquis, Rio de Janeiro, Brazil.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {101 Suppl 2}, number = {}, pages = {15-23}, doi = {10.1590/s0074-02762006001000004}, pmid = {17308804}, issn = {0074-0276}, mesh = {*Archaeology ; *Bone and Bones ; Brazil ; DNA, Mitochondrial/*genetics ; *Fossils ; Humans ; Paleontology/methods ; }, abstract = {The present paper discusses mtDNA and taphonomy of human remains from Moa, Beirada, and Zé Espinho sambaquis of Saquarema, state of Rio de Janeiro, Brazil. New human bone dating by 14C-AMS for Moa archeological site (3810+50 BP - GX-31826-AMS) is included. Preservation of microscopic lamellae and DNA is not related to the macroscopic integrity of the bones. Results here suggest that the preservation of amplifiable DNA fragments may have relation to the preservation of the lamellar arrangement as indicated by optical microscopic examination (polarized light). In 13 human bone fragments from Moa, Beirada, and Zé Espinho it was possible to sequence mtDNA from the 3 individuals of Moa, and from 1 of 4 individuals of Beirada, whose bones also show extensive areas with preserved lamellar structures. The 6 human bone fragments of Zé Espinho and 3 of the 4 fragments of Beirada showed extensive destruction of cortical microstructure represented by cavities, intrusive minerals, and agglomerated microscopic bodies of fungi and bacteria; it was not possible to extract mtDNA from these samples. The results support the hypothesis that the preservation of the microscopic osteon organization is a good predictor for DNA preservation. It was also confirmed the C haplogroup antiquity in Brazil.}, }
@article {pmid17278619, year = {2006}, author = {Bennett, CC and Kaestle, FA}, title = {Reanalysis of Eurasian population history: ancient DNA evidence of population affinities.}, journal = {Human biology}, volume = {78}, number = {4}, pages = {413-440}, doi = {10.1353/hub.2006.0052}, pmid = {17278619}, issn = {0018-7143}, mesh = {Asian People/*genetics ; China ; DNA, Mitochondrial/*analysis ; *Genetics, Population ; Humans ; Mongolia ; }, abstract = {Mitochondrial hypervariable region I genetic data from ancient populations at two sites in Asia-Linzi in Shandong (northern China) and Egyin Gol in Mongolia-were reanalyzed to detect population affinities. Data from 51 modern populations were used to generate distance measures (Fst's) to the two ancient populations. The tests first analyzed relationships at the regional level and then compiled the top regional matches for an overall comparison to the two probe populations. The reanalysis showed that the Egyin Gol and Linzi populations have clear distinctions in genetic affinity. The Egyin Gol population as a whole appears to bear close affinities with modern populations of northern East Asia. The Linzi population seems to have some genetic affinities with the West, as suggested by the original analysis, although the original attribution of "European-like" seems to be misleading. We suggest that the Linzi individuals are potentially related to early Iranians, who are thought to have been widespread in parts of Central Eurasia and the steppe regions in the first millennium B.C., although some significant admixture between a number of populations of varying origin cannot be ruled out. We also examine the effect of sequence length on this type of genetic data analysis and discuss the results of previous studies on the Linzi sample.}, }
@article {pmid17255122, year = {2007}, author = {Malmström, H and Svensson, EM and Gilbert, MT and Willerslev, E and Götherström, A and Holmlund, G}, title = {More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA.}, journal = {Molecular biology and evolution}, volume = {24}, number = {4}, pages = {998-1004}, doi = {10.1093/molbev/msm015}, pmid = {17255122}, issn = {0737-4038}, mesh = {Animals ; Bone and Bones/metabolism ; Cattle ; DNA/*analysis/genetics ; DNA, Mitochondrial/analysis/genetics ; Dogs ; Fossils ; *Haplotypes ; Humans ; Polymerase Chain Reaction/methods ; Specimen Handling/methods ; Tooth/metabolism ; }, abstract = {Authentication of ancient human DNA results is an exceedingly difficult challenge due to the presence of modern contaminant DNA sequences. Nevertheless, the field of ancient human genetics generates huge scientific and public interest, and thus researchers are rarely discouraged by problems concerning the authenticity of such data. Although several methods have been developed to the purpose of authenticating ancient DNA (aDNA) results, while they are useful in faunal research, most of the methods have proven complicated to apply to ancient human DNA. Here, we investigate in detail the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing so, we also produce data that describes the efficiency of bleach incubation of bone powder and its relative detrimental effects on contaminant and authentic ancient DNA. We note that bleach treatment is significantly more detrimental to contaminant than to authentic aDNA in the bleached bone powder. Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination. This asymmetrical behavior of authentic and contaminant DNA can be used to identify authentic haplotypes in human aDNA studies.}, }
@article {pmid17255121, year = {2007}, author = {Haile, J and Holdaway, R and Oliver, K and Bunce, M and Gilbert, MT and Nielsen, R and Munch, K and Ho, SY and Shapiro, B and Willerslev, E}, title = {Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?.}, journal = {Molecular biology and evolution}, volume = {24}, number = {4}, pages = {982-989}, doi = {10.1093/molbev/msm016}, pmid = {17255121}, issn = {0737-4038}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Birds/genetics ; DNA/*analysis/genetics ; Evolution, Molecular ; Geography ; Geologic Sediments/*analysis ; New Zealand ; Paleontology/*methods ; Plants/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sheep/metabolism ; Time Factors ; }, abstract = {In recent years, several studies have reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even in the absence of macrofossils) in order to obtain genetic "profiles" from past environments. One of the hazards associated with this approach, particularly in nonfrozen environments, is the potential for vertical migration of aDNA across strata. To assess the extent of this problem, we extracted aDNA from sediments up to 3300 years old at 2 cave sites in the North Island of New Zealand. These sites are ideal for this purpose as the presence or absence of DNA from nonindigenous fauna (such as sheep) in sediments deposited prior to European settlement can serve as an indicator of DNA movement. Additionally, these strata are well defined and dated. DNA from sheep was found in strata that also contained moa DNA, indicating that genetic material had migrated downwards. Quantitative polymerase chain reaction analyses demonstrated that the amount of sheep DNA decreased as the age of sediments increased. Our results suggest that sedimentary aDNA is unlikely to be deposited from wind-borne DNA and that physical remains of organisms or their ejecta need to have been incorporated in the sediments for their DNA to be detected. Our study indicates that DNA from sediments can still offer a rich source of information on past environments, provided that the risk from vertical migration can be controlled for.}, }
@article {pmid17227428, year = {2007}, author = {Coolen, MJ and Overmann, J}, title = {217 000-year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment.}, journal = {Environmental microbiology}, volume = {9}, number = {1}, pages = {238-249}, doi = {10.1111/j.1462-2920.2006.01134.x}, pmid = {17227428}, issn = {1462-2912}, mesh = {Benzopyrans ; Carotenoids ; Chlorobi/*classification/*genetics ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/analysis/genetics ; Ecosystem ; Fossils ; Geologic Sediments/chemistry/*microbiology ; Humic Substances/*microbiology ; Mediterranean Sea ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; }, abstract = {Deep-sea sediments of the eastern Mediterranean harbour a series of dark, organic carbon-rich layers, so-called sapropels. Within these layers, the carotenoid isorenieratene was detected. Since it is specific for the obligately anaerobic phototrophic green sulfur bacteria, the presence of isorenieratene may suggest that extended water column anoxia occurred in the ancient Mediterranean Sea during periods of sapropel formation. Only three carotenoids (isorenieratene, beta-isorenieratene and chlorobactene) are typical for green sulfur bacteria and thus do not permit to differentiate between the approximately 80 known phylotypes. In order to reconstruct the paleoecological conditions in more detail, we searched for fossil 16S rRNA gene sequences of green sulfur bacteria employing ancient DNA methodology. 540 bp-long fossil sequences could indeed be amplified from up to 217 000-year-old sapropels. In addition, such sequences were also recovered from carbon-lean intermediate sediment layers deposited during times of an entirely oxic water column. Unexpectedly, however, all the recovered 16S rRNA gene sequences grouped with freshwater or brackish, rather than truly marine, types of green sulfur bacteria. It is therefore feasible that the molecular remains of green sulfur bacteria originated from populations which thrived in adjacent freshwater or estuarine coastal environments rather than from an indigenous pelagic population.}, }
@article {pmid17219208, year = {2007}, author = {Stein, N and Prasad, M and Scholz, U and Thiel, T and Zhang, H and Wolf, M and Kota, R and Varshney, RK and Perovic, D and Grosse, I and Graner, A}, title = {A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {114}, number = {5}, pages = {823-839}, pmid = {17219208}, issn = {0040-5752}, mesh = {Chromosome Mapping ; Consensus Sequence ; DNA, Plant/genetics ; Evolution, Molecular ; Expressed Sequence Tags ; Gene Duplication ; Gene Order ; Genome, Plant ; Genomics ; Hordeum/*genetics ; Minisatellite Repeats ; Oryza/genetics ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide ; Species Specificity ; Transcription, Genetic ; }, abstract = {An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identification of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.}, }
@article {pmid17218991, year = {2006}, author = {Endicott, P and Metspalu, M and Stringer, C and Macaulay, V and Cooper, A and Sanchez, JJ}, title = {Multiplexed SNP typing of ancient DNA clarifies the origin of Andaman mtDNA haplogroups amongst South Asian tribal populations.}, journal = {PloS one}, volume = {1}, number = {1}, pages = {e81}, pmid = {17218991}, issn = {1932-6203}, mesh = {Asian People/*genetics/history ; DNA, Mitochondrial/*genetics ; Genetics, Population ; History, 19th Century ; History, Ancient ; Humans ; India ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Single Nucleotide ; }, abstract = {The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately, significantly reducing the amount of errors appearing in published data sets. To show the sensitivity of this technique for screening mtDNA genomic sequence data, 20 historic samples of the enigmatic Andaman Islanders and 12 modern samples from three Indian tribal populations (Chenchu, Lambadi and Lodha) were genotyped for 20 coding region sites after provisional haplogroup assignment with control region sequences. The genotype data from the historic samples significantly revise the topologies for the Andaman M31 and M32 mtDNA lineages by rectifying conflicts in published data sets. The new Indian data extend the distribution of the M31a lineage to South Asia, challenging previous interpretations of mtDNA phylogeography. This genetic connection between the ancestors of the Andamanese and South Asian tribal groups approximately 30 kya has important implications for the debate concerning migration routes and settlement patterns of humans leaving Africa during the late Pleistocene, and indicates the need for more detailed genotyping strategies. The methodology serves as a low-cost, high-throughput model for the production and authentication of data from modern or ancient DNA, and demonstrates the value of museum collections as important records of human genetic diversity.}, }
@article {pmid17210911, year = {2007}, author = {Pruvost, M and Schwarz, R and Correia, VB and Champlot, S and Braguier, S and Morel, N and Fernandez-Jalvo, Y and Grange, T and Geigl, EM}, title = {Freshly excavated fossil bones are best for amplification of ancient DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {3}, pages = {739-744}, pmid = {17210911}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Bone and Bones/*metabolism ; Cattle ; DNA/analysis/*genetics/*isolation &amp; purification ; *Fossils ; Microscopy, Electron, Scanning ; Mitochondria/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Time Factors ; }, abstract = {Despite the enormous potential of analyses of ancient DNA for phylogeographic studies of past populations, the impact these analyses, most of which are performed with fossil samples from natural history museum collections, has been limited to some extent by the inefficient recovery of ancient genetic material. Here we show that the standard storage conditions and/or treatments of fossil bones in these collections can be detrimental to DNA survival. Using a quantitative paleogenetic analysis of 247 herbivore fossil bones up to 50,000 years old and originating from 60 different archeological and paleontological contexts, we demonstrate that freshly excavated and nontreated unwashed bones contain six times more DNA and yield twice as many authentic DNA sequences as bones treated with standard procedures. This effect was even more pronounced with bones from one Neolithic site, where only freshly excavated bones yielded results. Finally, we compared the DNA content in the fossil bones of one animal, a approximately 3,200-year-old aurochs, excavated in two separate seasons 57 years apart. Whereas the washed museum-stored fossil bones did not permit any DNA amplification, all recently excavated bones yielded authentic aurochs sequences. We established that during the 57 years when the aurochs bones were stored in a collection, at least as much amplifiable DNA was lost as during the previous 3,200 years of burial. This result calls for a revision of the postexcavation treatment of fossil bones to better preserve the genetic heritage of past life forms.}, }
@article {pmid19430604, year = {2007}, author = {Orlando, L and Hänni, C and Douady, CJ}, title = {Mammoth and elephant phylogenetic relationships: Mammut americanum, the missing outgroup.}, journal = {Evolutionary bioinformatics online}, volume = {3}, number = {}, pages = {45-51}, pmid = {19430604}, issn = {1176-9343}, abstract = {At the morphological level, the woolly mammoth has most often been considered as the sister-species of Asian elephants, but at the DNA level, different studies have found support for proximity with African elephants. Recent reports have increased the available sequence data and apparently solved the discrepancy, finding mammoths to be most closely related to Asian elephants. However, we demonstrate here that the three competing topologies have similar likelihood, bayesian and parsimony supports. The analysis further suggests the inadequacy of using Sirenia or Hyracoidea as outgroups. We therefore argue that orthologous sequences from the extinct American mastodon will be required to definitively solve this long-standing question.}, }
@article {pmid17169982, year = {2007}, author = {Taberlet, P and Coissac, E and Pompanon, F and Gielly, L and Miquel, C and Valentini, A and Vermat, T and Corthier, G and Brochmann, C and Willerslev, E}, title = {Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding.}, journal = {Nucleic acids research}, volume = {35}, number = {3}, pages = {e14}, pmid = {17169982}, issn = {1362-4962}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Base Sequence ; Conserved Sequence ; DNA Primers ; DNA, Chloroplast/*chemistry ; Databases, Nucleic Acid ; *Introns ; Molecular Sequence Data ; Plants/*classification/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trnL (UAA) intron (254-767 bp) and of a shorter fragment of this intron (the P6 loop, 10-143 bp) amplified with highly conserved primers. The main limitation of the whole trnL intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trnL intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.}, }
@article {pmid17167798, year = {2007}, author = {Göbbel, L and Schultka, R and Klunker, R and Stock, K and Helm, J and Olsson, L and Opitz, JM and Gerlach, A and Tönnies, H}, title = {Nuchal cystic hygroma in five fetuses from 1819 to 1826 in the Meckel-anatomical collections at the University of Halle, Germany.}, journal = {American journal of medical genetics. Part A}, volume = {143A}, number = {2}, pages = {119-128}, doi = {10.1002/ajmg.a.31488}, pmid = {17167798}, issn = {1552-4825}, mesh = {DNA/analysis/genetics ; Developmental Biology ; Female ; Fetal Diseases/genetics/*pathology ; Fetus/abnormalities ; Germany ; History, 19th Century ; Humans ; Lymphangioma, Cystic/genetics/*pathology ; Male ; Museums ; Neck/pathology ; Nucleic Acid Hybridization ; Skull/pathology ; }, abstract = {The Anatomical collection of the Department of Anatomy and Cell Biology, Medical School of the University of Halle, Germany, comprises more than 8,000 specimens. Around 600 of them show congenital anomalies. The collection of abnormal human and animal fetuses began as the private collection of Johann Friedrich Meckel the Elder (1724-1774), his son Philipp Friedrich Theodor Meckel (1755-1803) and his grandson Johann Friedrich Meckel the Younger (1781-1833). Meckel the Younger founded the systematic science of developmental pathology. Radiographical techniques, computer tomographic (CT) methods, magnetic resonance imaging (MRI), and comparative genomic hybridization (CGH) were used to diagnose abnormal human fetuses in the Meckel-anatomical collections. Cystic hygroma colli was found in five of the human fetuses originally described by JF Meckel the Younger in 1826 and one of his students in 1819 [Hencke, 1819]. CGH analyses were used to test whether the observed cystic hygroma colli could be caused by chromosomal aneuploidies. CGH-ratio profiles of all chromosomes were apparently normal. PCR-based sex determination tests on ancient DNA were used to determine the fetal gonosomal constitution. It is likely that the Meckel specimens are among the oldest fetuses in which Ullrich-Turner "phenotype" has been diagnosed.}, }
@article {pmid17148432, year = {2006}, author = {Fleischer, RC and Kirchman, JJ and Dumbacher, JP and Bevier, L and Dove, C and Rotzel, NC and Edwards, SV and Lammertink, M and Miglia, KJ and Moore, WS}, title = {Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers.}, journal = {Biology letters}, volume = {2}, number = {3}, pages = {466-469}, pmid = {17148432}, issn = {1744-9561}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Birds/*genetics/*physiology ; Conservation of Natural Resources ; Cuba ; DNA, Mitochondrial/metabolism ; Ecology ; Likelihood Functions ; Models, Biological ; North America ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {We used ancient DNA analysis of seven museum specimens of the endangered North American ivory-billed woodpecker (Campephilus principalis) and three specimens of the species from Cuba to document their degree of differentiation and their relationships to other Campephilus woodpeckers. Analysis of these mtDNA sequences reveals that the Cuban and North American ivory bills, along with the imperial woodpecker (Campephilus imperialis) of Mexico, are a monophyletic group and are roughly equidistant genetically, suggesting each lineage may be a separate species. Application of both internal and external rate calibrations indicates that the three lineages split more than one million years ago, in the Mid-Pleistocene. We thus can exclude the hypothesis that Native Americans introduced North American ivory-billed woodpeckers to Cuba. Our sequences of all three woodpeckers also provide an important DNA barcoding resource for identification of non-invasive samples or remains of these critically endangered and charismatic woodpeckers.}, }
@article {pmid17148428, year = {2006}, author = {Poulakakis, N and Parmakelis, A and Lymberakis, P and Mylonas, M and Zouros, E and Reese, DS and Glaberman, S and Caccone, A}, title = {Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids.}, journal = {Biology letters}, volume = {2}, number = {3}, pages = {451-454}, pmid = {17148428}, issn = {1744-9561}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA/metabolism ; DNA, Mitochondrial/*genetics ; Elephants/*classification/*genetics ; *Fossils ; Genome/*genetics ; Mediterranean Region ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10,000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cytb) DNA fragments from 4200 to 800,000 y.a. specimens from island and mainland samples, including pygmy and normal-sized forms. The short DNA sequence (43 bp) retrieved from the 800,000 y.a. sample is one of the oldest DNA fragment ever retrieved. Duplication of the experiments in two laboratories, the occurrence of three diagnostic sites and the results of the phylogenetic analyses strongly support its authenticity. Our results challenge the prevailing view that pygmy elephantids of the eastern Mediterranean originated exclusively from Elephas, suggesting independent histories of dwarfism and the presence of both pygmy mammoths and elephant-like taxa on these islands. Based on our molecular data, the origin of the Tilos and Cyprus elephantids from a lineage within the genus Elephas is confirmed, while the DNA sequence from the Cretan sample falls clearly within the mammoth clade. Thus, the name Mammuthus creticus rather than Elephas creticus, seems to be justified for this form. Our findings also suggest a need to re-evaluate the evolutionary history of the Sicilian/Maltese species, traditionally included in the genus Elephas.}, }
@article {pmid17148352, year = {2006}, author = {Bollongino, R and Edwards, CJ and Alt, KW and Burger, J and Bradley, DG}, title = {Early history of European domestic cattle as revealed by ancient DNA.}, journal = {Biology letters}, volume = {2}, number = {1}, pages = {155-159}, pmid = {17148352}, issn = {1744-9561}, mesh = {Animals ; Animals, Domestic/*genetics ; *Archaeology ; Bone and Bones/chemistry ; Cattle/*genetics ; DNA Mutational Analysis ; DNA, Mitochondrial/analysis ; Europe ; Genetics, Population ; Mutation ; }, abstract = {We present an extensive ancient DNA analysis of mainly Neolithic cattle bones sampled from archaeological sites along the route of Neolithic expansion, from Turkey to North-Central Europe and Britain. We place this first reasonable population sample of Neolithic cattle mitochondrial DNA sequence diversity in context to illustrate the continuity of haplotype variation patterns from the first European domestic cattle to the present. Interestingly, the dominant Central European pattern, a starburst phylogeny around the modal sequence, T3, has a Neolithic origin, and the reduced diversity within this cluster in the ancient samples accords with their shorter history of post-domestic accumulation of mutation.}, }
@article {pmid17148223, year = {2005}, author = {Chan, YL and Lacey, EA and Pearson, OP and Hadly, EA}, title = {Ancient DNA reveals Holocene loss of genetic diversity in a South American rodent.}, journal = {Biology letters}, volume = {1}, number = {4}, pages = {423-426}, pmid = {17148223}, issn = {1744-9561}, mesh = {Animals ; Biodiversity ; Climate ; Cytochromes b/genetics ; Fossils ; *Genetic Variation ; Geography ; Haplotypes ; Phylogeny ; Rodentia/*genetics ; Sequence Analysis, DNA ; South America ; }, abstract = {Understanding how animal populations have evolved in response to palaeoenvironmental conditions is essential for predicting the impact of future environmental change on current biodiversity. Analyses of ancient DNA provide a unique opportunity to track population responses to prehistoric environments. We explored the effects of palaeoenvironmental change on the colonial tuco-tuco (Ctenomys sociabilis), a highly endemic species of Patagonian rodent that is currently listed as threatened by the IUCN. By combining surveys of modern genetic variation from throughout this species' current geographic range with analyses of DNA samples from fossil material dating back to 10,000 ybp, we demonstrate a striking decline in genetic diversity that is concordant with environmental events in the study region. Our results highlight the importance of non-anthropogenic factors in loss of diversity, including reductions in smaller mammals such as rodents.}, }
@article {pmid17148190, year = {2005}, author = {Leonard, JA and Rohland, N and Glaberman, S and Fleischer, RC and Caccone, A and Hofreiter, M}, title = {A rapid loss of stripes: the evolutionary history of the extinct quagga.}, journal = {Biology letters}, volume = {1}, number = {3}, pages = {291-295}, pmid = {17148190}, issn = {1744-9561}, mesh = {Adaptation, Biological/*physiology ; Africa ; Animals ; Base Sequence ; Climate ; DNA, Mitochondrial/*genetics/history ; Equidae/*classification/genetics/physiology ; *Extinction, Biological ; History, Ancient ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; }, abstract = {Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga (Equus quagga) museum skin, an extinct South African equid (Higuchi et al. 1984 Nature312, 282-284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.}, }
@article {pmid17146600, year = {2007}, author = {Hebsgaard, MB and Wiuf, C and Gilbert, MT and Glenner, H and Willerslev, E}, title = {Evaluating Neanderthal genetics and phylogeny.}, journal = {Journal of molecular evolution}, volume = {64}, number = {1}, pages = {50-60}, pmid = {17146600}, issn = {0022-2844}, mesh = {Animals ; Artifacts ; Bayes Theorem ; *DNA, Mitochondrial ; Hominidae/genetics/*physiology ; Humans ; *Phylogeny ; Polymerase Chain Reaction ; }, abstract = {The retrieval of Neanderthal (Homo neanderthalsensis) mitochondrial DNA is thought to be among the most significant ancient DNA contributions to date, allowing conflicting hypotheses on modern human (Homo sapiens) evolution to be tested directly. Recently, however, both the authenticity of the Neanderthal sequences and their phylogenetic position outside contemporary human diversity have been questioned. Using Bayesian inference and the largest dataset to date, we find strong support for a monophyletic Neanderthal clade outside the diversity of contemporary humans, in agreement with the expectations of the Out-of-Africa replacement model of modern human origin. From average pairwise sequence differences, we obtain support for claims that the first published Neanderthal sequence may include errors due to postmortem damage in the template molecules for PCR. In contrast, we find that recent results implying that the Neanderthal sequences are products of PCR artifacts are not well supported, suffering from inadequate experimental design and a presumably high percentage (>68%) of chimeric sequences due to "jumping PCR" events.}, }
@article {pmid17135318, year = {2007}, author = {Hu, JM and Fu, HC and Lin, CH and Su, HJ and Yeh, HH}, title = {Reassortment and concerted evolution in banana bunchy top virus genomes.}, journal = {Journal of virology}, volume = {81}, number = {4}, pages = {1746-1761}, pmid = {17135318}, issn = {0022-538X}, mesh = {Asia ; Babuvirus/*genetics ; Base Sequence ; Capsid Proteins/genetics ; DNA Helicases/genetics ; DNA-Binding Proteins/genetics ; *Evolution, Molecular ; *Genome, Viral ; Molecular Sequence Data ; Open Reading Frames/genetics ; Pacific Islands ; Phylogeny ; Sequence Alignment ; Trans-Activators/genetics ; Viral Proteins/genetics ; }, abstract = {The nanovirus Banana bunchy top virus (BBTV) has six standard components in its genome and occasionally contains components encoding additional Rep (replication initiation protein) genes. Phylogenetic network analysis of coding sequences of DNA 1 and 3 confirmed the two major groups of BBTV, a Pacific and an Asian group, but show evidence of web-like phylogenies for some genes. Phylogenetic analysis of 102 major common regions (CR-Ms) from all six components showed a possible concerted evolution within the Pacific group, which is likely due to recombination in this region. The CR-M of additional Rep genes is close to that of DNA 1 and 2. Comparison of tree topologies constructed with DNA 1 and DNA 3 coding sequences of 14 BBTV isolates showed distinct phylogenetic histories based on Kishino-Hasegawa and Shimodaira-Hasegawa tests. The results of principal component analysis of amino acid and codon usages indicate that DNA 1 and 3 have a codon bias different from that of all other genes of nanoviruses, including all currently known additional Rep genes of BBTV, which suggests a possible ancient genome reassortment event between distinctive nanoviruses.}, }
@article {pmid17124866, year = {2007}, author = {Benner, SA and Sassi, SO and Gaucher, EA}, title = {Molecular paleoscience: systems biology from the past.}, journal = {Advances in enzymology and related areas of molecular biology}, volume = {75}, number = {}, pages = {1-132, xi}, doi = {10.1002/9780471224464.ch1}, pmid = {17124866}, issn = {0065-258X}, mesh = {Animals ; Biological Evolution ; History, 20th Century ; History, 21st Century ; Humans ; Molecular Biology/history/*methods ; Paleontology/*methods ; Systems Biology/*history ; }, abstract = {Experimental paleomolecular biology, paleobiochemistry, and paleogenetics are closely related emerging fields that infer the sequences of ancient genes and proteins from now-extinct organisms, and then resurrect them for study in the laboratory. The goal of paleogenetics is to use information from natural history to solve the conundrum of modern genomics: How can we understand deeply the function of biomolecular structures uncovered and described by modern chemical biology? Reviewed here are the first 20 cases where biomolecular resurrections have been achieved. These show how paleogenetics can lead to an understanding of the function of biomolecules, analyze changing function, and put meaning to genomic sequences, all in ways that are not possible with traditional molecular biological studies.}, }
@article {pmid17120261, year = {2006}, author = {Alonso, A and Albarran, C and Martín, P and García, P and Capilla, J and García, O and de la Rua, C and Izaguirre, N and Pereira, F and Pereira, L and Amorim, A and Sancho, M}, title = {Usefulness of microchip electrophoresis for the analysis of mitochondrial DNA in forensic and ancient DNA studies.}, journal = {Electrophoresis}, volume = {27}, number = {24}, pages = {5101-5109}, doi = {10.1002/elps.200600331}, pmid = {17120261}, issn = {0173-0835}, mesh = {Animals ; Bone and Bones/chemistry ; Cattle ; Cytochromes b/genetics ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/*analysis/genetics ; Dogs ; Electrophoresis, Microchip/*methods ; Forensic Anthropology/*methods ; Forensic Genetics/*methods ; Hair/chemistry ; Haplotypes ; Humans ; Mice ; RNA, Ribosomal, 16S/genetics ; Rats ; Receptors, Vasoactive Intestinal Peptide, Type II/genetics ; Receptors, Vasoactive Intestinal Polypeptide, Type I/genetics ; Sequence Analysis, DNA ; }, abstract = {We evaluate the usefulness of a commercially available microchip CE (MCE) device in different genetic identification studies performed with mitochondrial DNA (mtDNA) targets, including the haplotype analysis of HVR1 and HVR2 and the study of interspecies diversity of cytochrome b (Cyt b) and 16S ribosomal RNA (16S rRNA) mitochondrial genes in forensic and ancient DNA samples. The MCE commercial system tested in this study proved to be a fast and sensitive detection method of length heteroplasmy in cytosine stretches produced by 16 189T>C transitions in HVR1 and by 309.1 and 309.2 C-insertions in HVR2. Moreover, the quantitative analysis of PCR amplicons performed by LIF allowed normalizing the amplicon input in the sequencing reactions, improving the overall quality of sequence data. These quantitative data in combination with the quantification of genomic mtDNA by real-time PCR has been successfully used to evaluate the PCR efficiency and detection limit of full sequencing methods of different mtDNA targets. The quantification of amplicons also provided a method for the rapid evaluation of PCR efficiency of multiplex-PCR versus singleplex-PCR to amplify short HV1 amplicons (around 100 bp) from severely degraded ancient DNA samples. The combination of human-specific (Cyt b) and universal (16S rRNA) mtDNA primer sets in a single PCR reaction followed by MCE detection offers a very rapid and simple screening test to differentiate between human and nonhuman hair forensic samples. This method was also very efficient with degraded DNA templates from forensic hair and bone samples, because of its applicability to detect small amplicon sizes. Future possibilities of MCE in forensic DNA typing, including nuclear STRs and SNP profiling are suggested.}, }
@article {pmid17111181, year = {2007}, author = {Tiedemann, R and Moll, K and Paulus, KB and Scheer, M and Williot, P and Bartel, R and Gessner, J and Kirschbaum, F}, title = {Atlantic sturgeons (Acipenser sturio, Acipenser oxyrinchus): American females successful in Europe.}, journal = {Die Naturwissenschaften}, volume = {94}, number = {3}, pages = {213-217}, pmid = {17111181}, issn = {0028-1042}, mesh = {Animals ; Atlantic Ocean ; Canada ; DNA Primers ; DNA, Mitochondrial/genetics ; *Ecosystem ; Europe ; Female ; Fishes/classification/*genetics ; Major Histocompatibility Complex ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; }, abstract = {Recent molecular data on the maternally inherited mitochondrial (mt) DNA have challenged the traditional view that the now extinct Baltic sturgeon population belonged to the European sturgeon Acipenser sturio. Instead, there is evidence that American sea sturgeon Acipenser oxyrinchus historically immigrated into the Baltic Sea. In this study, we test the hypothesis that A. oxyrinchus introgressed into, rather than replaced, the A. sturio population in the Baltic. We established four single nucleotide polymorphisms (SNPs) in the nuclear MHC II antigen gene with a species-specific SNP pattern. Using an ancient DNA approach and two independent lines of molecular evidence (sequencing of allele-specific clones, SNaPshot), we detected both A. sturio and A. oxyrinchus alleles in the available museum material of the now extinct Baltic sturgeon population. The hybrid nature of the Baltic population was further confirmed by very high levels of heterozygosity. It had been previously postulated that the immigration of the cold-adapted A. oxyrinchus into the Baltic occurred during the Medieval Little Ice Age, when temperature likely dropped below the degree inducing spawning in A. sturio. Under this scenario, our new findings suggest that the genetic mosaic pattern in the Baltic sturgeon population (oxyrinchus mtDNA, sturio and oxyrinchus MHC alleles) is possibly caused by sex-biased introgression where spawning was largely restricted to immigrating American females, while fertilization was predominantly achieved by abundant local European males. The hybrid nature of the former Baltic sturgeon population should be taken into account in the current reintroduction measures.}, }
@article {pmid17110569, year = {2006}, author = {Noonan, JP and Coop, G and Kudaravalli, S and Smith, D and Krause, J and Alessi, J and Chen, F and Platt, D and Pääbo, S and Pritchard, JK and Rubin, EM}, title = {Sequencing and analysis of Neanderthal genomic DNA.}, journal = {Science (New York, N.Y.)}, volume = {314}, number = {5802}, pages = {1113-1118}, pmid = {17110569}, issn = {1095-9203}, support = {HL066681/HL/NHLBI NIH HHS/United States ; F32 GM074367/GM/NIGMS NIH HHS/United States ; R01 HG002772-1/HG/NHGRI NIH HHS/United States ; R01 HG002772-01/HG/NHGRI NIH HHS/United States ; 1-F32-GM074367/GM/NIGMS NIH HHS/United States ; R01 HG002772/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Bone and Bones ; Cell Nucleus ; DNA/*genetics/isolation &amp; purification ; DNA, Mitochondrial ; *Fossils ; Gene Pool ; Genome ; Genome, Human ; Genomic Library ; History, Ancient ; Hominidae/*genetics ; Humans ; Male ; Molecular Sequence Data ; Pan troglodytes/genetics ; Polymerase Chain Reaction ; Sequence Alignment ; *Sequence Analysis, DNA/methods ; Time ; }, abstract = {Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. These results enabled us to calculate the human-Neanderthal divergence time based on multiple randomly distributed autosomal loci. Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor approximately 706,000 years ago, and that the human and Neanderthal ancestral populations split approximately 370,000 years ago, before the emergence of anatomically modern humans. Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics.}, }
@article {pmid17110550, year = {2006}, author = {Balter, M}, title = {Paleogenetics. A Neandertal legacy?.}, journal = {Science (New York, N.Y.)}, volume = {314}, number = {5802}, pages = {1071}, doi = {10.1126/science.314.5802.1071}, pmid = {17110550}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Cell Cycle Proteins ; Cytoskeletal Proteins ; Evolution, Molecular ; Genome, Human ; History, Ancient ; Hominidae/*genetics ; Humans ; Nerve Tissue Proteins/genetics ; Paleontology ; Selection, Genetic ; Sexual Behavior ; tau Proteins/genetics ; }, }
@article {pmid17110549, year = {2006}, author = {Pennisi, E}, title = {Paleogenetics. The dawn of Stone Age genomics.}, journal = {Science (New York, N.Y.)}, volume = {314}, number = {5802}, pages = {1068-1071}, doi = {10.1126/science.314.5802.1068}, pmid = {17110549}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Bone and Bones ; Cell Nucleus ; DNA/genetics/history/*isolation &amp; purification ; DNA, Mitochondrial ; Equipment Contamination ; *Fossils ; Genome, Human ; Genomics/methods ; History, Ancient ; Hominidae/*genetics ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, }
@article {pmid17103428, year = {2006}, author = {Stojanowski, CM and Schillaci, MA}, title = {Phenotypic approaches for understanding patterns of intracemetery biological variation.}, journal = {American journal of physical anthropology}, volume = {Suppl 43}, number = {}, pages = {49-88}, doi = {10.1002/ajpa.20517}, pmid = {17103428}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Archaeology/*methods ; Child ; Culture ; Dentition ; Family ; Female ; *Genetic Variation ; History, 15th Century ; History, Ancient ; History, Medieval ; Humans ; Indians, North American ; Male ; Models, Theoretical ; *Mortuary Practice ; *Phenotype ; Residence Characteristics ; Skull ; Social Environment ; United States ; }, abstract = {This paper reviews studies of phenotypic inheritance and microevolutionary processes in archaeological populations using data on cranial and dental phenotypic variation, often referred to as paleogenetics or biodistance analysis. The estimation of biological distances between populations, or among individuals within populations, is one component of bioarchaeological research on past populations. In this overview, five approaches that focus on morphological variation within cemeteries are summarized: kinship and cemetery structure analysis, postmarital residence analysis, sample aggregate phenotypic variability, temporal microchronology, and age-structured phenotypic variation. Previous research, theoretical justifications, and methods are outlined for each topic. Case studies are presented that illustrate these theoretical and methodological bases, as well as demonstrate the kinds of inferences possible using these approaches. Kinship and cemetery structure analysis seeks to identify the members of family groups within larger cemeteries or determine whether cemeteries were kin-structured. Analysis of sex-specific phenotypic variation allows estimation of postmarital residence practices, which is important for understanding other aspects of prehistoric social organization. Analysis of aggregate phenotypic variability can be used to infer site formation processes or cemetery catchment area. The study of temporal microchronologies can be used to evaluate provisional archaeological chronologies or study microevolutionary processes such as adaptive selection or changing patterns of gene flow. Finally, age-structured phenotypic variation can be reflective of selection processes within populations or it can be used as a measure of morbidity, growth arrest, and early mortality within past populations. Use of phenotypic data as a genotypic proxy is theoretically sound, even at small scales of analysis.}, }
@article {pmid17095693, year = {2006}, author = {Bottjer, DJ and Davidson, EH and Peterson, KJ and Cameron, RA}, title = {Paleogenomics of echinoderms.}, journal = {Science (New York, N.Y.)}, volume = {314}, number = {5801}, pages = {956-960}, doi = {10.1126/science.1132310}, pmid = {17095693}, issn = {1095-9203}, support = {RR-15044/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Calcification, Physiologic/genetics ; Calcium Carbonate/analysis ; Echinodermata/*genetics/physiology ; *Fossils ; *Genes ; *Genomics ; Lectins, C-Type/chemistry/genetics/physiology ; Phylogeny ; Protein Structure, Tertiary ; Proteins/chemistry/genetics/physiology ; Strongylocentrotus purpuratus/chemistry/classification/*genetics/physiology ; }, abstract = {Paleogenomics propels the meaning of genomic studies back through hundreds of millions of years of deep time. Now that the genome of the echinoid Strongylocentrotus purpuratus is sequenced, the operation of its genes can be interpreted in light of the well-understood echinoderm fossil record. Characters that first appear in Early Cambrian forms are still characteristic of echinoderms today. Key genes for one of these characters, the biomineralized tissue stereom, can be identified in the S. purpuratus genome and are likely to be the same genes that were involved with stereom formation in the earliest echinoderms some 520 million years ago.}, }
@article {pmid17015310, year = {2006}, author = {Mergeay, J and Verschuren, D and De Meester, L}, title = {Invasion of an asexual American water flea clone throughout Africa and rapid displacement of a native sibling species.}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1603}, pages = {2839-2844}, pmid = {17015310}, issn = {0962-8452}, mesh = {Africa ; Animals ; Daphnia/genetics/*physiology ; Extinction, Biological ; Fresh Water ; Genetic Variation ; Genotype ; Microsatellite Repeats ; Mitochondrial Proteins/genetics ; Population Dynamics ; RNA, Ribosomal/genetics ; *Reproduction, Asexual ; }, abstract = {The huge ecological and economic impact of biological invasions creates an urgent need for knowledge of traits that make invading species successful and factors helping indigenous populations to resist displacement by invading species or genotypes. High genetic diversity is generally considered to be advantageous in both processes. Combined with sex, it allows rapid evolution and adaptation to changing environments. We combined paleogenetic analysis with continent-wide survey of genetic diversity at nuclear and mitochondrial loci to reconstruct the invasion history of a single asexual American water flea clone (hybrid Daphnia pulexxDaphnia pulicaria) in Africa. Within 60 years of the original introduction of this invader, it displaced the genetically diverse, sexual population of native D. pulex in Lake Naivasha (Kenya), despite a formidable numerical advantage of the local population and continuous replenishment from a large dormant egg bank. Currently, the invading clone has spread throughout the range of native African D. pulex, where it appears to be the only occurring genotype. The absence of genetic variation did not hamper either the continent-wide establishment of this exotic lineage or the effective displacement of an indigenous and genetically diverse sibling species.}, }
@article {pmid16978181, year = {2006}, author = {McGahern, AM and Edwards, CJ and Bower, MA and Heffernan, A and Park, SD and Brophy, PO and Bradley, DG and MacHugh, DE and Hill, EW}, title = {Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses.}, journal = {Animal genetics}, volume = {37}, number = {5}, pages = {498-502}, doi = {10.1111/j.1365-2052.2006.01506.x}, pmid = {16978181}, issn = {0268-9146}, mesh = {Animals ; DNA, Mitochondrial/*chemistry ; *Fossils ; *Genetic Variation ; Haplotypes ; Horses/*genetics ; Ireland ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Equine mitochondrial DNA sequence variation was investigated in three indigenous Irish horse populations (Irish Draught Horse, Kerry Bog Pony and Connemara Pony) and, for context, in 69 other horse populations. There was no evidence of Irish Draught Horse or Connemara Pony sequence clustering, although the majority of Irish Draught Horse sequences (47%) were assigned to haplogroup D. Conversely, 31% of the Kerry Bog Pony sequences were assigned to the rare haplogroup E. In addition to the extant population analyses, ancient DNA sequences were generated from three out of four Irish archaeological specimens, all of which were assigned to haplogroup A.}, }
@article {pmid16950265, year = {2006}, author = {Iñiguez, AM and Reinhard, K and Carvalho Gonçalves, ML and Ferreira, LF and Araújo, A and Paulo Vicente, AC}, title = {SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in pre-Columbian human coprolites.}, journal = {International journal for parasitology}, volume = {36}, number = {13}, pages = {1419-1425}, doi = {10.1016/j.ijpara.2006.07.005}, pmid = {16950265}, issn = {0020-7519}, mesh = {Animals ; Base Sequence ; DNA, Helminth/genetics ; Enterobiasis/*history/parasitology ; Enterobius/classification/genetics/*isolation &amp; purification ; History, Ancient ; Humans ; Molecular Sequence Data ; Paleopathology/*methods ; Polymerase Chain Reaction/methods ; RNA, Helminth/*genetics ; RNA, Spliced Leader/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Enterobius vermicularis, pinworm, is one of the most common helminths worldwide, infecting nearly a billion people at all socio-economic levels. In prehistoric populations the paleoparasitological findings show a pinworm homogeneous distribution among hunter-gatherers in North America, intensified with the advent of agriculture. This same increase also occurred in the transition from nomad hunter-gatherers to sedentary farmers in South America, although E. vermicularis infection encompasses only the ancient Andean peoples, with no record among the pre-Colombian populations in the South American lowlands. However, the outline of pinworm paleoepidemiology has been supported by microscopic finding of eggs recovered from coprolites. Since molecular techniques are precise and sensitive in detecting pathogen ancient DNA (aDNA), and also could provide insights into the parasite evolutionary history, in this work we have performed a molecular paleoparasitological study of E. vermicularis. aDNA was recovered and pinworm 5S rRNA spacer sequences were determined from pre-Columbian coprolites (4110 BC-AD 900) from four different North and South American archaeological sites. The sequence analysis confirmed E. vermicularis identity and revealed a similarity among ancient and modern sequences. Moreover, polymorphisms were identified at the relative positions 160, 173 and 180, in independent coprolite samples from Tulán, San Pedro de Atacama, Chile (1080-950 BC). We also verified the presence of peculiarities (Splicing leader (SL1) RNA sequence, spliced donor site, the Sm antigen biding site, and RNA secondary structure) which characterise the SL1 RNA gene. The analysis shows that the SL1 RNA gene of contemporary pinworms was present in pre-Columbian E. vermicularis by 6110 years ago. We were successful in detecting E. vermicularis aDNA even in coprolites without direct microscopic evidence of the eggs, improving the diagnosis of helminth infections in the past and further pinworm paleoepidemiological studies.}, }
@article {pmid16938852, year = {2006}, author = {Stiller, M and Green, RE and Ronan, M and Simons, JF and Du, L and He, W and Egholm, M and Rothberg, JM and Keates, SG and Ovodov, ND and Antipina, EE and Baryshnikov, GF and Kuzmin, YV and Vasilevski, AA and Wuenschell, GE and Termini, J and Hofreiter, M and Jaenicke-Després, V and Pääbo, S}, title = {Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {37}, pages = {13578-13584}, pmid = {16938852}, issn = {0027-8424}, mesh = {Animals ; *Artifacts ; Base Sequence ; Cytosine/*chemistry ; Evolution, Molecular ; Guanine/*chemistry ; Molecular Sequence Data ; Paleontology/*methods ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; Templates, Genetic ; Wolves/genetics ; }, abstract = {Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. Using a massively parallel sequencing method that allows large numbers of single DNA strands to be sequenced, we show that modifications of C, as well as to a lesser extent of G, residues cause such misincorporations. Experiments where oligonucleotides containing modified bases are used as templates in amplification reactions suggest that both of these types of misincorporations can be caused by deamination of the template bases. New DNA sequencing methods in conjunction with knowledge of misincorporation processes have now, in principle, opened the way for the determination of complete genomes from organisms that became extinct during and after the last glaciation.}, }
@article {pmid16930594, year = {2006}, author = {Macqueen, DJ and Johnston, IA}, title = {A novel salmonid myoD gene is distinctly regulated during development and probably arose by duplication after the genome tetraploidization.}, journal = {FEBS letters}, volume = {580}, number = {21}, pages = {4996-5002}, doi = {10.1016/j.febslet.2006.08.016}, pmid = {16930594}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; Cell Differentiation ; Embryo, Nonmammalian/cytology ; Evolution, Molecular ; *Gene Duplication ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genome/*genetics ; Likelihood Functions ; Molecular Sequence Data ; Muscle Fibers, Fast-Twitch/cytology ; Muscle Fibers, Slow-Twitch/cytology ; MyoD Protein/chemistry/*genetics ; Phylogeny ; Polymerase Chain Reaction ; *Polyploidy ; Salmonidae/embryology/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {A novel myoD paralogue was characterised in Salmo salar (smyoD1c) and S. trutta (btmyoD1c). SmyoD1c had 78.2/90.6% protein sequence identity to smyoD1a/smyoD1b, respectively. Each paralogue was differentially expressed throughout somitogenesis. In adult fish, smyoD1a was the predominant gene expressed in fast muscle, whereas smyoD1c was 2-3 times upregulated in slow muscle compared to smyoD1a/1b. A maximum likelihood analysis indicated that myoD1c arose by duplication of myoD1b after the salmonid tetraploidization. Another myoD paralogue (myoD2) is present in at least some teleosts, reflecting a more ancient genome duplication. To accommodate these findings we propose a simplified teleost-myoD nomenclature.}, }
@article {pmid16920744, year = {2007}, author = {Gilbert, MT and Binladen, J and Miller, W and Wiuf, C and Willerslev, E and Poinar, H and Carlson, JE and Leebens-Mack, JH and Schuster, SC}, title = {Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.}, journal = {Nucleic acids research}, volume = {35}, number = {1}, pages = {1-10}, pmid = {16920744}, issn = {1362-4962}, support = {R01 HG002238/HG/NHGRI NIH HHS/United States ; HG002238/HG/NHGRI NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *DNA Damage ; DNA, Chloroplast/chemistry ; DNA-Directed DNA Polymerase ; Data Interpretation, Statistical ; Elephants/genetics ; *Fossils ; Genomics/methods ; *Polymerase Chain Reaction ; Templates, Genetic ; }, abstract = {Although ancient DNA (aDNA) miscoding lesions have been studied since the earliest days of the field, their nature remains a source of debate. A variety of conflicting hypotheses exist about which miscoding lesions constitute true aDNA damage as opposed to PCR polymerase amplification error. Furthermore, considerable disagreement and speculation exists on which specific damage events underlie observed miscoding lesions. The root of the problem is that it has previously been difficult to assemble sufficient data to test the hypotheses, and near-impossible to accurately determine the specific strand of origin of observed damage events. With the advent of emulsion-based clonal amplification (emPCR) and the sequencing-by-synthesis technology this has changed. In this paper we demonstrate how data produced on the Roche GS20 genome sequencer can determine miscoding lesion strands of origin, and subsequently be interpreted to enable characterization of the aDNA damage behind the observed phenotypes. Through comparative analyses on 390,965 bp of modern chloroplast and 131,474 bp of ancient woolly mammoth GS20 sequence data we conclusively demonstrate that in this sample at least, a permafrost preserved specimen, Type 2 (cytosine-->thymine/guanine-->adenine) miscoding lesions represent the overwhelming majority of damage-derived miscoding lesions. Additionally, we show that an as yet unidentified guanine-->adenine analogue modification, not the conventionally argued cytosine-->uracil deamination, underpins a significant proportion of Type 2 damage. How widespread these implications are for aDNA will become apparent as future studies analyse data recovered from a wider range of substrates.}, }
@article {pmid16917897, year = {2006}, author = {Ricaut, FX and Bellatti, M and Lahr, MM}, title = {Ancient mitochondrial DNA from Malaysian hair samples: some indications of Southeast Asian population movements.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {18}, number = {5}, pages = {654-667}, doi = {10.1002/ajhb.20535}, pmid = {16917897}, issn = {1042-0533}, mesh = {Anthropology, Physical ; Asia, Southeastern ; Asian People/*genetics/history ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; History, Ancient ; Humans ; *Phylogeny ; }, abstract = {The late Pleistocene and early Holocene population history of Southeast Asia is not well-known. Our study provides new data on mitochondrial DNA (mtDNA) lineages of the aboriginal inhabitants of the Malay Peninsula, and through an extensive comparison to the known mtDNA diversity in Southeast and East Asia, provides some new insights into the origins and historical geography of certain mtDNA lineages in the region. We extracted DNA from hair samples (dating back 100 years) preserved in the Duckworth Collection and belonging to two Peninsular Malaysian individuals identified as "Negrito." Ancient DNA was analyzed by sequencing hypervariable region I (HVS-I) of the mtDNA control region and the mtDNA region V length polymorphism. The results show that the maternal lineages of these individuals belong to a recently defined haplogroup B sub-branch called B4c2. A comparison of mitochondrial haplotypes and haplogroups with those of 10,349 East Asian individuals indicates their very restricted geographical distribution (southwestern China, Southeast Asia Peninsula, and Indonesia). Recalculation of the B4c2 age across all of East Asia (approximately 13,000 years) and in different subregions/populations suggests its rapid diffusion in Southeast Asia between the end of the Last Glacial Maximum and the Neolithic expansion of the Holocene.}, }
@article {pmid16911807, year = {2006}, author = {Deagle, BE and Eveson, JP and Jarman, SN}, title = {Quantification of damage in DNA recovered from highly degraded samples--a case study on DNA in faeces.}, journal = {Frontiers in zoology}, volume = {3}, number = {}, pages = {11}, pmid = {16911807}, issn = {1742-9994}, abstract = {BACKGROUND: Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (lambda) can be estimated by determining the rate of decline.<br><br>RESULTS: The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean lambda(predator) = 0.0106 per nucleotide; mean lambda(prey) = 0.0176 per nucleotide). This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples.<br><br>CONCLUSION: We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will allow researchers to measure template quality in order to evaluate alternate sources of DNA, different methods of sample preservation and different DNA extraction protocols. The technique could also be applied to study the process of DNA decay.}, }
@article {pmid16856347, year = {2006}, author = {Zhang, HQ and Yang, ZQ and Liu, FE and Zhang, J and Zhao, WM}, title = {[Homologous amelogenin gene test of archaeological samples].}, journal = {Fa yi xue za zhi}, volume = {22}, number = {3}, pages = {213-216}, pmid = {16856347}, issn = {1004-5619}, mesh = {Alleles ; Amelogenin/*genetics ; Archaeology ; Bone and Bones/*chemistry/metabolism ; Chromosomes, Human, X ; Chromosomes, Human, Y ; DNA/*analysis/genetics/isolation &amp; purification ; DNA Primers ; Dental Enamel Proteins/*genetics ; Female ; Gene Amplification ; Humans ; Male ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Sex Determination Analysis/*methods ; Tooth/*chemistry/metabolism ; }, abstract = {OBJECTIVE: Based on the sequence differences of Amelogenin homologous gene in the X and Y chromosomes, a pair of specific primers was designed to identify the sex of archaeological samples.<br><br>METHODS: Ancient DNA fragments were extracted from the bones and teeth of sacrificial slaves with an improved method that combines phenol-chloroform extraction, silicon dioxide adsorption with ultrafiltration concentration. The polyacrylamide gel electrophoresis (PAGE) was used to detect PCR products.<br><br>RESULTS: Seven in sixteen samples from eight graves showed positive results and the targeted segments were visible: a male with two bands of 106bp (Amel-X) and 112 bp (Amel-Y), while a female with only one band of 106 bp (Amel-X). Ancient DNA analyzing results from tooth samples are more marked than that from bones.<br><br>CONCLUSION: The improved extraction method is more effective for ancient DNA extraction, which reduced the PCR inhibitors and lowered experimental costs. The sex determination technology based on Amelogenin homologous gene is an important and feasible method in the molecular archaeological research.}, }
@article {pmid16839727, year = {2007}, author = {Amory, S and Keyser, C and Crubézy, E and Ludes, B}, title = {STR typing of ancient DNA extracted from hair shafts of Siberian mummies.}, journal = {Forensic science international}, volume = {166}, number = {2-3}, pages = {218-229}, doi = {10.1016/j.forsciint.2006.05.042}, pmid = {16839727}, issn = {0379-0738}, mesh = {Bone and Bones/chemistry ; Chromosomes, Human, Y ; DNA/*isolation &amp; purification ; DNA Fingerprinting/*methods ; Female ; Genotype ; Hair/*chemistry ; Humans ; Male ; *Mummies ; Polymerase Chain Reaction ; Siberia ; *Tandem Repeat Sequences ; Tooth/chemistry ; }, abstract = {The aim of this study was to determine if ancient hair shafts could be suitable for nuclear DNA analysis and to develop an efficient and straightforward protocol for DNA extraction and STR typing of ancient specimens. The developed method was validated on modern and forensic samples and then successfully applied on ancient hairs collected from Siberian mummies dating from the 16th to the early 19th centuries. In parallel extractions including or excluding a washing step were performed at least two times for each sample in order to evaluate the influence on the quantity of nuclear DNA yielded and on the typing efficiency. Twelve ancient individuals were analyzed through our approach and full and reliable profiles were obtained for four of them. These profiles were validated by comparison with those obtained from bone and teeth DNA extracted from the same ancient specimens. The present study demonstrates that the washing step cannot be considered as deleterious for DNA retrieval since the same results were obtained by the two approaches. This finding challenges the hypothesis that recoverable nuclear DNA is only found on the outer surface of hair shafts and provides evidence that nuclear DNA can be successfully extracted from ancient hair shafts. The method described here constitutes a promising way for non-invasive investigations in ancient DNA analysis for precious or historical samples as well as forensic casework analyses.}, }
@article {pmid16809622, year = {2006}, author = {Sampietro, ML and Gilbert, MT and Lao, O and Caramelli, D and Lari, M and Bertranpetit, J and Lalueza-Fox, C}, title = {Tracking down human contamination in ancient human teeth.}, journal = {Molecular biology and evolution}, volume = {23}, number = {9}, pages = {1801-1807}, doi = {10.1093/molbev/msl047}, pmid = {16809622}, issn = {0737-4038}, mesh = {DNA, Mitochondrial/*analysis ; *Haplotypes ; History, Ancient ; Humans ; Paleodontology/*standards ; *Specimen Handling ; Tooth/*chemistry/pathology ; }, abstract = {DNA contamination arising from the manipulation of ancient calcified tissue samples is a poorly understood, yet fundamental, problem that affects the reliability of ancient DNA (aDNA) studies. We have typed the mitochondrial DNA hypervariable region I of the only 6 people involved in the excavation, washing, and subsequent anthropological and genetic study of 23 Neolithic remains excavated from Granollers (Barcelona, Spain) and searched for their presence among the 572 clones generated during the aDNA analyses of teeth from these samples. Of the cloned sequences, 17.13% could be unambiguously identified as contaminants, with those derived from the people involved in the retrieval and washing of the remains present in higher frequencies than those of the anthropologist and genetic researchers. This finding confirms, for the first time, previous hypotheses that teeth samples are most susceptible to contamination at their initial excavation. More worrying, the cloned contaminant sequences exhibit substitutions that can be attributed to DNA damage after the contamination event, and we demonstrate that the level of such damage increases with time: contaminants that are >10 years old have approximately 5 times more damage than those that are recent. Furthermore, we demonstrate that in this data set, the damage rate of the old contaminant sequences is indistinguishable from that of the endogenous DNA sequences. As such, the commonly used argument that miscoding lesions observed among cloned aDNA sequences can be used to support data authenticity is misleading in scenarios where the presence of old contaminant sequences is possible. We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results are accurate.}, }
@article {pmid16809513, year = {2006}, author = {Ammerman, AJ and Pinhasi, R and Bánffy, E}, title = {Comment on "Ancient DNA from the first European farmers in 7500-year-old Neolithic sites".}, journal = {Science (New York, N.Y.)}, volume = {312}, number = {5782}, pages = {1875; author reply 1875}, doi = {10.1126/science.1123984}, pmid = {16809513}, issn = {1095-9203}, mesh = {Agriculture/*history ; Culture ; DNA, Mitochondrial/*genetics/history ; Europe ; Female ; History, Ancient ; Humans ; Male ; Sample Size ; White People/*genetics/history ; }, abstract = {On the basis of analysis of ancient DNA from early European farmers, Haak et al. (Reports, 11 November 2005, p. 1016) argued for the Paleolithic ancestry of modern Europeans. We stress that the study is more limited in scope than the authors claim, in part because not all of the skeletal samples date to the time of the Neolithic transition in a given area of Europe.}, }
@article {pmid16702560, year = {2006}, author = {Belle, EM and Ramakrishnan, U and Mountain, JL and Barbujani, G}, title = {Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {21}, pages = {8012-8017}, pmid = {16702560}, issn = {0027-8424}, support = {P01 GM028428/GM/NIGMS NIH HHS/United States ; GM028428/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Founder Effect ; Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Italy ; Likelihood Functions ; Mutation ; Phylogeny ; Time Factors ; }, abstract = {The Etruscans, the only preclassical European population that has been genetically characterized so far, share only two haplotypes with their modern geographic counterparts, the Tuscans, who, nonetheless, appear to be their closest relatives. We modeled 10 demographic scenarios spanning the last 2,500 years and tested by serial coalescent simulation whether any are consistent with the patterns of genetic diversity observed within and between the Etruscan and the modern Tuscan populations. Models in which the Etruscans are the direct ancestors of modern Tuscans appear compatible with the observed data only when they also include a very high mutation rate and an ancient founder effect. A better fit was obtained when the ancient and the modern samples were extracted from two independently evolving populations, connected by little migration. Simulated and observed parameters were also similar for a scenario in which the ancient samples came from a subset, e.g., a social elite, genetically differentiated from the bulk of the Etruscan population. In principle, these results may be biased by factors such as gross and systematic errors in the ancient DNA sequences and failure to sample suitable modern individuals. If neither proves to be the case, this study strongly suggests that either the mitochondrial mutation rate is much higher than currently believed or the Etruscans left very few modern mitochondrial descendants.}, }
@article {pmid16702410, year = {2006}, author = {Cui, L and Wall, PK and Leebens-Mack, JH and Lindsay, BG and Soltis, DE and Doyle, JJ and Soltis, PS and Carlson, JE and Arumuganathan, K and Barakat, A and Albert, VA and Ma, H and dePamphilis, CW}, title = {Widespread genome duplications throughout the history of flowering plants.}, journal = {Genome research}, volume = {16}, number = {6}, pages = {738-749}, pmid = {16702410}, issn = {1088-9051}, mesh = {Cycadopsida/genetics ; Evolution, Molecular ; *Gene Duplication ; *Genome, Plant ; Magnoliopsida/*genetics ; Models, Genetic ; Models, Statistical ; Phylogeny ; Polyploidy ; }, abstract = {Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for species representing the basal-most extant flowering plant lineages. We found evidence for episodes of ancient genome-wide duplications in the basal angiosperm lineages including Nuphar advena (yellow water lily: Nymphaeaceae) and the magnoliids Persea americana (avocado: Lauraceae), Liriodendron tulipifera (tulip poplar: Magnoliaceae), and Saruma henryi (Aristolochiaceae). In addition, we detected independent genome duplications in the basal eudicot Eschscholzia californica (California poppy: Papaveraceae) and the basal monocot Acorus americanus (Acoraceae), both of which were distinct from duplications documented for ancestral grass (Poaceae) and core eudicot lineages. Among gymnosperms, we found equivocal evidence for ancient polyploidy in Welwitschia mirabilis (Gnetales) and no evidence for polyploidy in pine, although gymnosperms generally have much larger genomes than the angiosperms investigated. Cross-species sequence divergence estimates suggest that synonymous substitution rates in the basal angiosperms are less than half those previously reported for core eudicots and members of Poaceae. These lower substitution rates permit inference of older duplication events. We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella.}, }
@article {pmid16701432, year = {2005}, author = {Gilbert, MT and Bandelt, HJ and Hofreiter, M and Barnes, I}, title = {Assessing ancient DNA studies.}, journal = {Trends in ecology &amp; evolution}, volume = {20}, number = {10}, pages = {541-544}, doi = {10.1016/j.tree.2005.07.005}, pmid = {16701432}, issn = {0169-5347}, abstract = {The study of ancient DNA has the potential to make significant and unique contributions to ecology and evolution. However, the techniques used contain inherent problems, particularly with regards to the generation of authentic and useful data. The solution currently advocated to reduce contamination and artefactual results is to adopt criteria for authentication. Nevertheless, these criteria are not foolproof, and we believe that they have, in practice, replaced the use of thought and prudence when designing and executing ancient DNA studies. We argue here that researchers in this field must take a more cognitive and self-critical approach. Specifically, in place of checking criteria off lists, researchers must explain, in sufficient enough detail to dispel doubt, how the data were obtained, and why they should be believed to be authentic.}, }
@article {pmid16690747, year = {2006}, author = {Beja-Pereira, A and Caramelli, D and Lalueza-Fox, C and Vernesi, C and Ferrand, N and Casoli, A and Goyache, F and Royo, LJ and Conti, S and Lari, M and Martini, A and Ouragh, L and Magid, A and Atash, A and Zsolnai, A and Boscato, P and Triantaphylidis, C and Ploumi, K and Sineo, L and Mallegni, F and Taberlet, P and Erhardt, G and Sampietro, L and Bertranpetit, J and Barbujani, G and Luikart, G and Bertorelle, G}, title = {The origin of European cattle: evidence from modern and ancient DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {21}, pages = {8113-8118}, pmid = {16690747}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Breeding ; Cattle ; DNA, Mitochondrial/analysis/*genetics ; Europe ; Genetic Variation ; Genetics, Population ; Geography ; Molecular Sequence Data ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Cattle domestication from wild aurochsen was among the most important innovations during the Neolithic agricultural revolution. The available genetic and archaeological evidence points to at least two major sites of domestication in India and in the Near East, where zebu and the taurine breeds would have emerged independently. Under this hypothesis, all present-day European breeds would be descended from cattle domesticated in the Near East and subsequently spread during the diffusion of herding and farming lifestyles. We present here previously undescribed genetic evidence in contrast with this view, based on mtDNA sequences from five Italian aurochsen dated between 7,000 and 17,000 years B.P. and >1,000 modern cattle from 51 breeds. Our data are compatible with local domestication events in Europe and support at least some levels of introgression from the aurochs in Italy. The distribution of genetic variation in modern cattle suggest also that different south European breeds were affected by introductions from northern Africa. If so, the European cattle may represent a more variable and valuable genetic resource than previously realized, and previous simple hypotheses regarding the domestication process and the diffusion of selected breeds should be revised.}, }
@article {pmid16687224, year = {2007}, author = {Dissing, J and Binladen, J and Hansen, A and Sejrsen, B and Willerslev, E and Lynnerup, N}, title = {The last Viking King: a royal maternity case solved by ancient DNA analysis.}, journal = {Forensic science international}, volume = {166}, number = {1}, pages = {21-27}, doi = {10.1016/j.forsciint.2006.03.020}, pmid = {16687224}, issn = {0379-0738}, mesh = {Base Sequence ; DNA, Mitochondrial/analysis/*history ; Denmark ; Female ; Forensic Medicine ; History, Ancient ; Humans ; Male ; Molecular Sequence Data ; Mothers ; Polymerase Chain Reaction ; Tooth/chemistry ; White People/*genetics ; }, abstract = {The last of the Danish Viking Kings, Sven Estridsen, died in a.d. 1074 and is entombed in Roskilde Cathedral with other Danish kings and queens. Sven's mother, Estrid, is entombed in a pillar across the chancel. However, while there is no reasonable doubt about the identity of Sven, there have been doubts among historians whether the woman entombed was indeed Estrid. To shed light on this problem, we have extracted and analysed mitochondrial DNA (mtDNA) from pulp of teeth from each of the two royals. Four overlapping DNA-fragments covering about 400bp of hypervariable region 1 (HVR-1) of the D-loop were PCR amplified, cloned and a number of clones with each segment were sequenced. Also a segment containing the H/non-H specific nucleotide 7028 was sequenced. Consensus sequences were determined and D-loop results were replicated in an independent laboratory. This allowed the assignment of King Sven Estridsen to haplogroup H; Estrid's sequence differed from that of Sven at two positions in HVR-1, 16093T-->C and 16304T-->C, indicating that she belongs to subgroup H5a. Given the maternal inheritance of mtDNA, offspring will have the same mtDNA sequence as their mother with the exception of rare cases where the sequence has been altered by a germ line mutation. Therefore, the observation of two sequence differences makes it highly unlikely that the entombed woman was the mother of Sven. In addition, physical examination of the skeleton and the teeth strongly indicated that this woman was much younger (approximately 35 years) at the time of death than the 70 years history records tell. Although the entombed woman cannot be the Estrid, she may well be one of Sven's two daughters-in-law who were also called Estrid and who both became queens.}, }
@article {pmid16687118, year = {2006}, author = {Debruyne, R and Barriel, V}, title = {[Biological evolution and ancient DNA].}, journal = {Medecine sciences : M/S}, volume = {22}, number = {5}, pages = {502-506}, doi = {10.1051/medsci/2006225502}, pmid = {16687118}, issn = {0767-0974}, mesh = {Animals ; *Evolution, Molecular ; }, abstract = {Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.}, }
@article {pmid16649656, year = {2006}, author = {Chelomina, GN}, title = {[Ancient DNA].}, journal = {Genetika}, volume = {42}, number = {3}, pages = {293-309}, pmid = {16649656}, issn = {0016-6758}, mesh = {Animals ; DNA/chemistry/*classification/*genetics ; *Evolution, Molecular ; *Fossils ; Humans ; *Phylogeny ; }, abstract = {The review is devoted to molecular genetic studies of ancient DNA. The problems of DNA preservation and modification after cell death, as well as techniques of working with ancient DNA, including its retrieval, removal of inhibitors, PCR amplification, and phylogenetic analysis, are discussed in detail. The possibilities are considered of using ancient DNA in resolving issues of systematics and evolution of various animal taxa, population genetics of humans and rare species, taxonomic identification and paleontological reconstructions, geographic origin of populations, microbiological analysis of paleontological and archeological finds, as well as some humanitarian aspects of its use.}, }
@article {pmid16636697, year = {2006}, author = {Chan, YL and Anderson, CN and Hadly, EA}, title = {Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA.}, journal = {PLoS genetics}, volume = {2}, number = {4}, pages = {e59}, pmid = {16636697}, issn = {1553-7404}, mesh = {Animals ; Bayes Theorem ; DNA/*chemistry ; DNA, Mitochondrial ; Gene Frequency ; Genetic Variation ; Inbreeding ; Mammals ; *Models, Genetic ; Models, Statistical ; Population ; Population Density ; Rodentia ; }, abstract = {In this first application of the approximate Bayesian computation approach using the serial coalescent, we demonstrated the estimation of historical demographic parameters from ancient DNA. We estimated the timing and severity of a population bottleneck in an endemic subterranean rodent, Ctenomys sociabilis, over the last 10,000 y from two cave sites in northern Patagonia, Argentina. Understanding population bottlenecks is important in both conservation and evolutionary biology. Conservation implications include the maintenance of genetic variation, inbreeding, fixation of mildly deleterious alleles, and loss of adaptive potential. Evolutionary processes are impacted because of the influence of small populations in founder effects and speciation. We found a decrease from a female effective population size of 95,231 to less than 300 females at 2,890 y before present: a 99.7% decline. Our study demonstrates the persistence of a species depauperate in genetic diversity for at least 2,000 y and has implications for modes of speciation in the incredibly diverse rodent genus Ctenomys. Our approach shows promise for determining demographic parameters for other species with ancient and historic samples and demonstrates the power of such an approach using ancient DNA.}, }
@article {pmid16623087, year = {2006}, author = {Witas, HW and Jatczak, I and Jedrychowska-Dańska, K and Zadzińska, E and Wrzesińska, A and Wrzesiński, J and Nadolski, J}, title = {Sequence of deltaF508 CFTR allele identified at present is lacking in medieval specimens from Central Poland. Preliminary results.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {64}, number = {1}, pages = {41-49}, pmid = {16623087}, issn = {0003-5548}, mesh = {Adult ; Child ; Cystic Fibrosis/*epidemiology/*genetics/history ; Cystic Fibrosis Transmembrane Conductance Regulator/*genetics ; Female ; Gene Frequency ; Genetic Predisposition to Disease/*epidemiology/*genetics/history ; History, Medieval ; Humans ; Incidence ; Male ; Pilot Projects ; Poland/epidemiology ; Sequence Analysis, DNA ; }, abstract = {deltaF508 is the most common (70%) among over 1000 mutations of the gene encoding ATP-regulated chloride channel, namely CFTR--cystic fibrosis transmembrane regulator. The time which passed from the calculated mutation event was anticipated on the basis of the frequency of contemporary haplotypes, but not on its direct identification. The presence of three base pairs deletion in the ancient DNA (aDNA) isolated from skeletal remains of the Middle Ages origin was investigated. Teeth excavated in the area of three sites located in Central Poland were processed for a DNA. 6 out of 82 samples did not produce amplificable fragments of DNA. Although the number of specimens analyzed was sufficient to confirm the presence of the rare mutation, the deltaF508 CFTR sequence was not found in the remains of individuals living back 35 - 45 generations. The absence of the mutated allele in the particular geographic region cannot state for the status of mutated allele throughout the country, especially at times when migrations were limited and movements of people were more area restricted than at present days.}, }
@article {pmid16608680, year = {2006}, author = {Donoghue, HD and Spigelman, M}, title = {Comment. Pathogenic microbial ancient DNA: a problem or an opportunity?.}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1587}, pages = {641-2; discussion 643}, pmid = {16608680}, issn = {0962-8452}, mesh = {DNA, Bacterial/chemistry/*genetics ; *Evolution, Molecular ; Humans ; *Paleontology ; Sequence Analysis, DNA ; Specimen Handling ; }, }
@article {pmid16596944, year = {2005}, author = {Bogácsi-Szabó, E and Kalmár, T and Csányi, B and Tömöry, G and Czibula, A and Priskin, K and Horváth, F and Downes, CS and Raskó, I}, title = {Mitochondrial DNA of ancient Cumanians: culturally Asian steppe nomadic immigrants with substantially more western Eurasian mitochondrial DNA lineages.}, journal = {Human biology}, volume = {77}, number = {5}, pages = {639-662}, pmid = {16596944}, issn = {0018-7143}, mesh = {Asian People/*genetics ; Complementarity Determining Regions/genetics ; DNA, Mitochondrial/*genetics ; Electrophoresis, Polyacrylamide Gel ; Forensic Anthropology ; *Genetic Variation ; Genetics, Population/*methods ; Geography ; Haplotypes/genetics ; Humans ; Hungary ; Molecular Sequence Data ; *Population Dynamics ; *Transients and Migrants ; White People/*genetics ; }, abstract = {The Cumanians were originally Asian pastoral nomads who in the 13th century migrated to Hungary. We have examined mitochondrial DNA from members of the earliest Cumanian population in Hungary from two archeologically well-documented excavations and from 74 modern Hungarians from different rural locations in Hungary. Haplogroups were defined based on HVS I sequences and examinations of haplogroup-associated polymorphic sites of the protein coding region and of HVS II. To exclude contamination, some ancient DNA samples were cloned. A database was created from previously published mtDNA HVS I sequences (representing 2,615 individuals from different Asian and European populations) and 74 modem Hungarian sequences from the present study. This database was used to determine the relationships between the ancient Cumanians, modern Hungarians, and Eurasian populations and to estimate the genetic distances between these populations. We attempted to deduce the genetic trace of the migration of Cumanians. This study is the first ancient DNA characterization of an eastern pastoral nomad population that migrated into Europe. The results indicate that, while still possessing a Central Asian steppe culture, the Cumanians received a large admixture of maternal genes from more westerly populations before arriving in Hungary. A similar dilution of genetic, but not cultural, factors may have accompanied the settlement of other Asian nomads in Europe.}, }
@article {pmid16596603, year = {2006}, author = {Bouwman, AS and Chilvers, ER and Brown, KA and Brown, TA}, title = {Brief communication: identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNA.}, journal = {American journal of physical anthropology}, volume = {131}, number = {3}, pages = {428-431}, doi = {10.1002/ajpa.20411}, pmid = {16596603}, issn = {0002-9483}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bone and Bones/*chemistry ; DNA/*isolation &amp; purification ; DNA Primers ; England ; Fossils ; Greece, Ancient ; History, Ancient ; Humans ; Tibia/chemistry ; }, abstract = {We present a method to distinguish authentic ancient DNA from contaminating DNA in a human bone. This is achieved by taking account of the spatial distribution of the various sequence families within the bone and the extent of degradation of the template DNAs, as revealed by the error content of the sequences. To demonstrate the veracity of the method, we handled two ancient human tibiae in order to contaminate them with modern DNA, and then subjected segments of the bones to various decontaminating treatments, including removal of the outer 1-2 mm, before extracting DNA, cloning, and obtaining a total of 107 mitochondrial DNA sequences. Sequences resulting from the deliberate contamination were located exclusively in the outer 1-2 mm of the bones, and only one of these 27 sequences contained an error that could be ascribed to DNA degradation. A second, much smaller set of relatively error-free sequences, which we ascribe to contamination during excavation or curation, was also located exclusively in the outer 1-2 mm. In contrast, a family of 72 sequences, displaying extensive degradation products but identifiable as haplogroup U5a1a, was distributed throughout one of the bones and represents the authentic ancient DNA content of this specimen.}, }
@article {pmid16596591, year = {2006}, author = {Keyser-Tracqui, C and Crubézy, E and Pamzsav, H and Varga, T and Ludes, B}, title = {Population origins in Mongolia: genetic structure analysis of ancient and modern DNA.}, journal = {American journal of physical anthropology}, volume = {131}, number = {2}, pages = {272-281}, doi = {10.1002/ajpa.20429}, pmid = {16596591}, issn = {0002-9483}, mesh = {Chromosomes, Human, Y/chemistry ; DNA, Mitochondrial/analysis/*history ; Female ; Genealogy and Heraldry ; *Genetics, Population ; History, 21st Century ; History, Ancient ; Humans ; Male ; Mongolia ; Tandem Repeat Sequences ; }, abstract = {In the present study, nuclear (autosomal and Y-chromosome short tandem repeats) and mitochondrial (hypervariable region I) ancient DNA data previously obtained from a 2,300-year-old Xiongnu population of the Egyin Gol Valley (south of Lake Baikal in northern Mongolia) (Keyser-Tracqui et al. 2003 Am. J. Hum. Genet. 73:247-260) were compared with data from two contemporary Mongolian populations: one from the same location (Egyin Gol Valley plus a perimeter of less than 100 km around the valley), and one from the whole of Mongolia. The principal objective of this comparative analysis was to assess the likelihood that genetic continuity exists between ancient and present-day Mongolian populations. Since the ancient Xiongnu sample might have been composed of some of the ancestors of the present-day Yakuts, data from a present-day Yakut population, as well as published data from Turkish populations, were also included in the comparative analysis. The main result of our study was the genetic similarity observed among Mongolian samples from different periods and geographic areas. This result supports the hypothesis that the succession over time of different Turkic and Mongolian tribes in the current territory of Mongolia resulted in cultural rather than genetic exchanges. Furthermore, it appears that the Yakuts probably did not find their origin among the Xiongnu tribes, as we previously hypothesized.}, }
@article {pmid16582426, year = {2006}, author = {Hansen, AJ and Mitchell, DL and Wiuf, C and Paniker, L and Brand, TB and Binladen, J and Gilichinsky, DA and Rønn, R and Willerslev, E}, title = {Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments.}, journal = {Genetics}, volume = {173}, number = {2}, pages = {1175-1179}, pmid = {16582426}, issn = {0016-6731}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Cross-Linking Reagents ; DNA/chemistry/*genetics/*isolation &amp; purification ; DNA Damage ; DNA Repair ; DNA, Bacterial/chemistry/genetics/isolation &amp; purification ; *Fossils ; Freezing ; Geologic Sediments/microbiology ; Nucleic Acid Amplification Techniques ; Siberia ; Time Factors ; }, abstract = {Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10,000 to 400,000 years in age. Despite optimal preservation conditions, we found the sedimentary DNA to be severely modified by interstrand crosslinks; single- and double-stranded breaks; and freely exposed sugar, phosphate, and hydroxyl groups. Intriguingly, interstrand crosslinks were found to accumulate approximately 100 times faster than single-stranded breaks, suggesting that crosslinking rather than depurination is the primary limiting factor for ancient DNA amplification under frozen conditions. The results question the reliability of the commonly used models relying on depurination kinetics for predicting the long-term survival of DNA under permafrost conditions and suggest that new strategies for repair of ancient DNA must be considered if the yield of amplifiable DNA from permafrost sediments is to be significantly increased. Using the obtained rate constant for interstrand crosslinks the maximal survival time of amplifiable 120-bp fragments of bacterial 16S ribosomal DNA was estimated to be approximately 400,000 years. Additionally, a clear relationship was found between DNA damage and sample age, contradicting previously raised concerns about the possible leaching of free DNA molecules between permafrost layers.}, }
@article {pmid16507168, year = {2006}, author = {Casneuf, T and De Bodt, S and Raes, J and Maere, S and Van de Peer, Y}, title = {Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana.}, journal = {Genome biology}, volume = {7}, number = {2}, pages = {R13}, pmid = {16507168}, issn = {1474-760X}, mesh = {Amino Acid Substitution ; Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics ; Codon/genetics ; *Gene Duplication ; *Gene Expression Regulation, Plant ; *Genetic Variation ; *Genome, Plant ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; }, abstract = {BACKGROUND: Genome analyses have revealed that gene duplication in plants is rampant. Furthermore, many of the duplicated genes seem to have been created through ancient genome-wide duplication events. Recently, we have shown that gene loss is strikingly different for large- and small-scale duplication events and highly biased towards the functional class to which a gene belongs. Here, we study the expression divergence of genes that were created during large- and small-scale gene duplication events by means of microarray data and investigate both the influence of the origin (mode of duplication) and the function of the duplicated genes on expression divergence.<br><br>RESULTS: Duplicates that have been created by large-scale duplication events and that can still be found in duplicated segments have expression patterns that are more correlated than those that were created by small-scale duplications or those that no longer lie in duplicated segments. Moreover, the former tend to have highly redundant or overlapping expression patterns and are mostly expressed in the same tissues, while the latter show asymmetric divergence. In addition, a strong bias in divergence of gene expression was observed towards gene function and the biological process genes are involved in.<br><br>CONCLUSION: By using microarray expression data for Arabidopsis thaliana, we show that the mode of duplication, the function of the genes involved, and the time since duplication play important roles in the divergence of gene expression and, therefore, in the functional divergence of genes after duplication.}, }
@article {pmid16488882, year = {2006}, author = {McDonald, JP and Hall, A and Gasparutto, D and Cadet, J and Ballantyne, J and Woodgate, R}, title = {Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs.}, journal = {Nucleic acids research}, volume = {34}, number = {4}, pages = {1102-1111}, pmid = {16488882}, issn = {1362-4962}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/*enzymology ; Archaeal Proteins/classification/genetics/metabolism ; Base Sequence ; Cloning, Molecular ; DNA/*biosynthesis ; DNA Damage ; DNA Fingerprinting ; DNA Polymerase beta/classification/genetics/*metabolism ; Enzyme Stability ; Genes, Archaeal ; Humans ; K562 Cells ; Molecular Sequence Data ; Paleontology ; Phylogeny ; *Polymerase Chain Reaction ; Sulfolobaceae/genetics ; *Temperature ; Templates, Genetic ; }, abstract = {For many years, Taq polymerase has served as the stalwart enzyme in the PCR amplification of DNA. However, a major limitation of Taq is its inability to amplify damaged DNA, thereby restricting its usefulness in forensic applications. In contrast, Y-family DNA polymerases, such as Dpo4 from Sulfolobus solfataricus, can traverse a wide variety of DNA lesions. Here, we report the identification and characterization of five novel thermostable Dpo4-like enzymes from Acidianus infernus, Sulfolobus shibatae, Sulfolobus tengchongensis, Stygiolobus azoricus and Sulfurisphaera ohwakuensis, as well as two recombinant chimeras that have enhanced enzymatic properties compared with the naturally occurring polymerases. The Dpo4-like polymerases are moderately processive, can substitute for Taq in PCR and can bypass DNA lesions that normally block Taq. Such properties make the Dpo4-like enzymes ideally suited for the PCR amplification of damaged DNA samples. Indeed, by using a blend of Taq and Dpo4-like enzymes, we obtained a PCR amplicon from ultraviolet-irradiated DNA that was largely unamplifyable with Taq alone. The inclusion of thermostable Dpo4-like polymerases in PCRs, therefore, augments the recovery and analysis of lesion-containing DNA samples, such as those commonly found in forensic or ancient DNA molecular applications.}, }
@article {pmid16485299, year = {2006}, author = {Shinoda, K and Adachi, N and Guillen, S and Shimada, I}, title = {Mitochondrial DNA analysis of ancient Peruvian highlanders.}, journal = {American journal of physical anthropology}, volume = {131}, number = {1}, pages = {98-107}, doi = {10.1002/ajpa.20408}, pmid = {16485299}, issn = {0002-9483}, mesh = {DNA, Mitochondrial/*chemistry/classification ; *Fossils ; Haplotypes ; Humans ; Peru ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {Ancient DNA recovered from 57 individuals excavated by Hiram Bingham at the rural communities of Paucarcancha, Patallacta, and Huata near the famed Inca royal estate and ritual site of Machu Picchu was analyzed by polymerase chain reaction, and the results were compared with ancient and modern DNA from various Central Andean areas to test their hypothesized indigenous highland origins. The control and coding regions of the mitochondrial DNA (mtDNA) of 35 individuals in this group were sequenced, and the haplogroups of each individual were determined. The frequency data for the haplogroups of these samples show clear proximity to those of modern Quechua and Aymara populations in the Peruvian and Bolivian highlands, and contrast with those of pre-Hispanic individuals of the north coast of Peru that we defined previously. Our study suggests a strong genetic affinity between sampled late pre-Hispanic individuals and modern Andean highlanders. A previous analysis of the Machu Picchu osteological collection suggests that the residents there were a mixed group of natives from various coastal and highland regions relocated by the Inca state for varied purposes. Overall, our study indicates that the sampled individuals from Paucarcancha and Patallacta were indigenous highlanders who provided supportive roles for nearby Machu Picchu.}, }
@article {pmid16452924, year = {2006}, author = {Hunter, P}, title = {Ancient DNA research goes nuclear. A new technique to extract sequence data from nuclear DNA may reveal exciting new insights into evolution and phylogeny.}, journal = {EMBO reports}, volume = {7}, number = {2}, pages = {136-139}, pmid = {16452924}, issn = {1469-221X}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*chemistry ; DNA/*analysis ; *Evolution, Molecular ; *Fossils ; Humans ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {A new technique to extract sequence data from nuclear DNA may reveal exciting new insights into evolution and phylogeny}, }
@article {pmid16448215, year = {2006}, author = {Cooper, A}, title = {The year of the mammoth.}, journal = {PLoS biology}, volume = {4}, number = {3}, pages = {e78}, pmid = {16448215}, issn = {1545-7885}, mesh = {Animals ; DNA/analysis/genetics ; Elephants/classification/*genetics ; Humans ; Time Factors ; }, abstract = {Three recently published studies that independently sequenced the mitochondrial genomes of the long extinct mammoth are examined here, along with the state-of-the-art technologies used to study ancient DNA.}, }
@article {pmid16425179, year = {2006}, author = {Alzualde, A and Izagirre, N and Alonso, S and Alonso, A and Albarrán, C and Azkarate, A and de la Rúa, C}, title = {Insights into the "isolation" of the Basques: mtDNA lineages from the historical site of Aldaieta (6th-7th centuries AD).}, journal = {American journal of physical anthropology}, volume = {130}, number = {3}, pages = {394-404}, doi = {10.1002/ajpa.20375}, pmid = {16425179}, issn = {0002-9483}, mesh = {Base Sequence ; Complementarity Determining Regions/chemistry ; DNA, Mitochondrial/*chemistry ; *Genetic Variation ; Genetics, Population ; Haplotypes/*genetics ; History, Medieval ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Spain ; Tooth/chemistry ; White People/genetics/*history ; }, abstract = {We analyzed the hypervariable region I (HVR-I) sequence variability of the mitochondrial DNA (mtDNA) of individuals buried at Aldaieta (6th-7th centuries AD) in order to find out more about the biosocial implications of this cemetery. The results, fully authenticated by means of diverse criteria (analysis of duplicates, replication in an independent laboratory, quantification of target DNA, and sequencing and cloning of polymerase chain reaction products), suggest that Aldaieta largely consists of autochthonous individuals who shared common funereal customs with the late Ancient North Pyrenean cemeteries of Western Europe (the Reihengräberfelder), a cultural influence possibly accompanied by a certain genetic flow. Furthermore, the distribution of mtDNA lineages in the cemetery highlighted the existence of a significant number of family relationships, supporting the belief that it was a stable settlement and not a group that had haphazardly settled in the area. Finally, this paper stresses the importance of ancient DNA data for reconstructing the biological history of human populations, rendering it possible to verify certain hypotheses based solely on current population data. The presence at Aldaieta of an mtDNA lineage originating in Northwest Africa testifies to the existence of contact between the Iberian Peninsula and Northwest Africa prior to the Moorish occupation. Both this latter discovery and the high frequency of haplogroup J at the Aldaieta cemetery raise questions about the generally accepted belief that, since ancient times, the influence of other human groups has been very scarce in the Basque Country.}, }
@article {pmid16404145, year = {2005}, author = {Kim, JH and Oh, JH and Song, JH and Jeon, JT and Han, SH and Jung, YH and Oh, MY}, title = {Molecular genetic analysis of ancient cattle bones excavated from archaeological sites in Jeju, Korea.}, journal = {Molecules and cells}, volume = {20}, number = {3}, pages = {325-330}, pmid = {16404145}, issn = {1016-8478}, mesh = {Animals ; Base Sequence ; *Bone and Bones ; Cattle/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Korea ; Molecular Biology ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; }, abstract = {Ancient cattle bones were excavated from archaeological sites in Jeju, Korea. We used molecular genetic techniques to identify the species and establish its relationship to extant cattle breeds. Ancient DNA was extracted from four sources: a humerus (Gonae site, A.D. 700-800), two fragments of radius, and a tooth (Kwakji site, A.D. 0-900). The mitochondrial DNA (mtDNA) D-loop regions were cloned, sequenced, and compared with previously reported sequences of various cattle breeds (9 Asian, 8 European, and 3 African). The results revealed that these bones were of the breed, Bos taurus, and a phylogenetic tree indicated that the four cattle bones formed a monophyletic group with Jeju native black cattle. However, the patterns of sequence variation and reports from archaeological sites suggest that a few wild cattle, with a different maternal lineage, may have existed on Jeju Island. Our results will contribute to further studies of the origin of Jeju native cattle and the possible existence of local wild cattle.}, }
@article {pmid16401685, year = {2006}, author = {Clarke, AC and Burtenshaw, MK and McLenachan, PA and Erickson, DL and Penny, D and , }, title = {Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria).}, journal = {Molecular biology and evolution}, volume = {23}, number = {5}, pages = {893-900}, doi = {10.1093/molbev/msj092}, pmid = {16401685}, issn = {0737-4038}, mesh = {Cell Nucleus/genetics ; Chloroplasts/genetics ; Cucurbita/*genetics ; DNA/metabolism ; Evolution, Molecular ; Genes, Plant ; Genetic Markers ; Genetics ; Genetics, Population ; Genotype ; Geography ; Phylogeny ; Plants/*genetics ; Polymerase Chain Reaction ; Polynesia ; }, abstract = {The origin of the Polynesian bottle gourd (Lagenaria siceraria), an important crop species in prehistoric Polynesia, has remained elusive. Most recently, a South American origin has been favored as the bottle gourd could have been introduced from this continent with the sweet potato by Polynesian voyagers around A.D. 1,000. To test the hypothesis of an American origin for the Polynesian bottle gourd, we developed seven markers specific to bottle gourd (two chloroplast and five nuclear). The nuclear markers were developed using a new technique where polymorphic inter simple sequence repeat (ISSR) markers are converted into single-locus polymerase chain reaction and sequencing markers--an approach that will be useful for developing markers in other taxa. All seven markers were sequenced in 36 cultivars of bottle gourd from Asia, the Americas, and Polynesia. The results support a dual origin for the Polynesian bottle gourd: the chloroplast markers are exclusively of Asian origin, but the nuclear markers show alleles originating in both the Americas and Asia. Because hybridization of Polynesian bottle gourds with post-European introductions cannot be excluded, ancient DNA from archaeological material will be useful for further elucidating the prehistoric movements of this species in Polynesia. This work has implications not only for the dispersal of the Polynesian bottle gourd but also for the domestication and dispersal of the species as a whole.}, }
@article {pmid16388133, year = {2005}, author = {Zhang, L and Wu, Q}, title = {Single gene retrieval from thermally degraded DNA.}, journal = {Journal of biosciences}, volume = {30}, number = {5}, pages = {599-604}, pmid = {16388133}, issn = {0250-5991}, mesh = {Air ; DNA/genetics/isolation &amp; purification/*metabolism ; Electrophoresis, Agar Gel/methods ; Genes ; Hot Temperature/*adverse effects ; Nitrogen ; Polymerase Chain Reaction/methods ; Reactive Oxygen Species/metabolism ; Synechococcus/chemistry/genetics ; Time Factors ; }, abstract = {To simulate single gene retrieval from ancient DNA, several related factors have been investigated. By monitoring a 889 bp polymerase chain reaction (PCR) product and genomic DNA degradation, we find that heat and oxygen (especially heat) are both crucial factors influencing DNA degradation. The heat influence, mainly represented by temperature and heating time, affects the DNA degradation via DNA depurination followed by cleavage of nearby phosphodiesters. The heating time influence is temperature-dependent. By reactive oxygen species (ROS) scavenging and 1,3-diphenyl-isobenzofuran (DPBF) bleaching experiments the influence of oxygen on DNA thermal degradation was shown to occur via a singlet oxygen pathway. A comparative study of the thermal degradation of cellular DNA and isolated DNA showed that cellular lipids can aggravate DNA thermal degradation. These results confirm the possibility of gene amplification from thermally degraded DNA. They can be used to evaluate the feasibility of the retrieval of single gene from ancient remains.}, }
@article {pmid16373545, year = {2005}, author = {Gibbons, A}, title = {Ancient DNA. New methods yield mammoth samples.}, journal = {Science (New York, N.Y.)}, volume = {310}, number = {5756}, pages = {1889}, doi = {10.1126/science.310.5756.1889a}, pmid = {16373545}, issn = {1095-9203}, mesh = {Animals ; DNA ; DNA, Mitochondrial ; Elephants/*genetics ; Female ; History, Ancient ; Sequence Analysis, DNA/methods ; Specimen Handling ; }, }
@article {pmid16368896, year = {2006}, author = {Poinar, HN and Schwarz, C and Qi, J and Shapiro, B and Macphee, RD and Buigues, B and Tikhonov, A and Huson, DH and Tomsho, LP and Auch, A and Rampp, M and Miller, W and Schuster, SC}, title = {Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.}, journal = {Science (New York, N.Y.)}, volume = {311}, number = {5759}, pages = {392-394}, doi = {10.1126/science.1123360}, pmid = {16368896}, issn = {1095-9203}, support = {HG02238/HG/NHGRI NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Base Composition ; Computational Biology ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Dogs/genetics ; Elephants/*genetics ; *Fossils ; Gene Library ; Genome ; *Genomics ; Humans ; Mandible/*chemistry ; *Paleontology ; Polymerase Chain Reaction ; Sequence Alignment ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Siberia ; }, abstract = {We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.}, }
@article {pmid16362058, year = {2006}, author = {Krause, J and Dear, PH and Pollack, JL and Slatkin, M and Spriggs, H and Barnes, I and Lister, AM and Ebersberger, I and Pääbo, S and Hofreiter, M}, title = {Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae.}, journal = {Nature}, volume = {439}, number = {7077}, pages = {724-727}, doi = {10.1038/nature04432}, pmid = {16362058}, issn = {1476-4687}, support = {MC_U105131672/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Africa ; Animals ; Asia ; DNA, Mitochondrial/*genetics ; Elephants/*classification/*genetics ; Evolution, Molecular ; *Fossils ; Genome/*genetics ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Time Factors ; }, abstract = {In studying the genomes of extinct species, two principal limitations are typically the small quantities of endogenous ancient DNA and its degraded condition, even though products of up to 1,600 base pairs (bp) have been amplified in rare cases. Using small overlapping polymerase chain reaction products, longer stretches of sequences or even whole mitochondrial genomes can be reconstructed, but this approach is limited by the number of amplifications that can be performed from rare samples. Thus, even from well-studied Pleistocene species such as mammoths, ground sloths and cave bears, no DNA sequences of more than about 1,000 bp have been reconstructed. Here we report the complete mitochondrial genome sequence of the Pleistocene woolly mammoth Mammuthus primigenius. We used about 200 mg of bone and a new approach that allows the simultaneous retrieval of multiple sequences from small amounts of degraded DNA. Our phylogenetic analyses show that the mammoth was more closely related to the Asian than to the African elephant. However, the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages.}, }
@article {pmid16356273, year = {2005}, author = {Hoelzel, AR}, title = {Ancient genomes.}, journal = {Genome biology}, volume = {6}, number = {12}, pages = {239}, pmid = {16356273}, issn = {1474-760X}, mesh = {Animals ; Cloning, Molecular ; Databases, Genetic ; Genome/*genetics ; History, Ancient ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Ursidae/*genetics ; }, abstract = {Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.}, }
@article {pmid16352716, year = {2005}, author = {Erickson, DL and Smith, BD and Clarke, AC and Sandweiss, DH and Tuross, N}, title = {An Asian origin for a 10,000-year-old domesticated plant in the Americas.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {51}, pages = {18315-18320}, pmid = {16352716}, issn = {0027-8424}, mesh = {Africa ; Agriculture/*history ; Americas ; Archaeology ; Asia ; *Cucurbitaceae/genetics/growth &amp; development ; DNA, Chloroplast/genetics ; Emigration and Immigration ; Genetic Markers/genetics ; Genotype ; History, Ancient ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Seeds/genetics ; Time Factors ; Water Movements ; }, abstract = {New genetic and archaeological approaches have substantially improved our understanding of the transition to agriculture, a major turning point in human history that began 10,000-5,000 years ago with the independent domestication of plants and animals in eight world regions. In the Americas, however, understanding the initial domestication of New World species has long been complicated by the early presence of an African enigma, the bottle gourd (Lagenaria siceraria). Indigenous to Africa, it reached East Asia by 9,000-8,000 before present (B.P.) and had a broad New World distribution by 8,000 B.P. Here we integrate genetic and archaeological approaches to address a set of long-standing core questions regarding the introduction of the bottle gourd into the Americas. Did it reach the New World directly from Africa or through Asia? Was it transported by humans or ocean currents? Was it wild or domesticated upon arrival? Fruit rind thickness values and accelerator mass spectrometer radiocarbon dating of archaeological specimens indicate that the bottle gourd was present in the Americas as a domesticated plant by 10,000 B.P., placing it among the earliest domesticates in the New World. Ancient DNA sequence analysis of archaeological bottle gourd specimens and comparison with modern Asian and African landraces identify Asia as the source of its introduction. We suggest that the bottle gourd and the dog, two "utility" species, were domesticated long before any food crops or livestock species, and that both were brought to the Americas by Paleoindian populations as they colonized the New World.}, }
@article {pmid16342258, year = {2006}, author = {Luciani, S and Fornaciari, G and Rickards, O and Labarga, CM and Rollo, F}, title = {Molecular characterization of a pre-Columbian mummy and in situ coprolite.}, journal = {American journal of physical anthropology}, volume = {129}, number = {4}, pages = {620-629}, doi = {10.1002/ajpa.20314}, pmid = {16342258}, issn = {0002-9483}, mesh = {Base Sequence ; DNA, Bacterial/*analysis/genetics/history ; DNA, Mitochondrial/analysis/chemistry/history ; Feces/*microbiology ; Haemophilus Infections/*history/microbiology ; Haemophilus parainfluenzae/*genetics/isolation &amp; purification ; Haplotypes ; History, Medieval ; Humans ; Indians, South American/classification/*genetics/*history ; Molecular Sequence Data ; Mummies/*microbiology ; Peru ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA/methods ; }, abstract = {The history of Homo sapiens dispersal around the world and inherent interpopulation contacts and conflicts has given rise to several transitions in his relationships with the natural world, with the final result of changes in the patterns of infectious disease (McMichael [2001] Ecosystem Health 7:107-115). Of particular interest, in this context, is the contact between Amerindians and Europeans that started at the end of the 15th century, and the resulting exchange of microbes. We successfully recovered ancient DNA from a pre-Columbian mummy from Cuzco (Peru), radiocarbon-dated to 980-1170 AD, for which consistent mtDNA amplifications and sequences were obtained. The analysis of mtDNA revealed that the mummy's haplogroup was characteristic of Native American populations. We also investigated a sample of feces directly isolated from the intestines of the mummy, using a polymerase chain reaction system designed to detect the broadest spectrum of bacterial DNAs. The analysis of results, following a criterion of "paleoecological consistency" (Rollo and Marota [1998] Philos. Trans. R. Soc. Lond. [Biol.] 354: 111-119), demonstrated that some vestiges of the original microbial flora of the feces were preserved. In particular, we were able to identify the DNA of Haemophylus parainfluenzae, thus suggesting that this recently recognized pathogen was present in precontact Native Americans.}, }
@article {pmid16332256, year = {2005}, author = {Lalueza-Fox, C and Castresana, J and Sampietro, L and Marquès-Bonet, T and Alcover, JA and Bertranpetit, J}, title = {Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {70}, pmid = {16332256}, issn = {1471-2148}, mesh = {Animals ; Biological Evolution ; Cloning, Molecular ; Cytochromes b/genetics ; DNA, Mitochondrial/chemistry ; DNA, Ribosomal/chemistry ; *Evolution, Molecular ; Fossils ; Goats/*genetics ; Likelihood Functions ; Mammals/*genetics ; Phylogeny ; Ruminants/*genetics ; Time Factors ; }, abstract = {BACKGROUND: Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean) that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs.<br><br>RESULTS: We have retrieved the complete mitochondrial cytochrome b gene (1,143 base pairs), plus fragments of the mitochondrial 12S gene and the nuclear 28S rDNA multi-copy gene from a well preserved Myotragus subfossil bone. The best resolved phylogenetic trees, obtained with the cytochrome b gene, placed Myotragus in a position basal to the Ovis group. Using the calibration provided by the isolation of Balearic Islands, we calculated that the initial radiation of caprines can be dated at 6.2 +/- 0.4 Mya. In addition, alpine and southern chamois, considered until recently the same species, split around 1.6 +/- 0.3 Mya, indicating that the two chamois species have been separated much longer than previously thought.<br><br>CONCLUSION: Since there are almost no extant endemic mammals in Mediterranean islands, the sequence of the extinct Balearic endemic Myotragus has been crucial for allowing us to use the Messinian crisis calibration point for dating the caprines phylogenetic tree.}, }
@article {pmid16323184, year = {2006}, author = {Mooder, KP and Schurr, TG and Bamforth, FJ and Bazaliiski, VI and Savel'ev, NA}, title = {Population affinities of Neolithic Siberians: a snapshot from prehistoric Lake Baikal.}, journal = {American journal of physical anthropology}, volume = {129}, number = {3}, pages = {349-361}, doi = {10.1002/ajpa.20247}, pmid = {16323184}, issn = {0002-9483}, mesh = {Anthropology, Physical ; DNA Primers ; DNA, Mitochondrial/*genetics/*history ; *Genetic Variation ; *Genetics, Population ; Haplotypes/genetics ; History, Ancient ; Humans ; Polymorphism, Single Nucleotide ; *Population Dynamics ; Principal Component Analysis ; Siberia ; }, abstract = {Archaeological evidence supports the inhabitation of the Lake Baikal region since the Paleolithic. Both metric and nonmetric osteological studies suggest that Neolithic Cis-Baikal populations are the ancestors of contemporary inhabitants of the region. To date, ancient DNA data have not been used to corroborate this biological continuity hypothesis. This study presents a temporal snapshot of the Cis-Baikal Neolithic by examining mtDNA diversity in two cemetery populations situated on the Angara River downstream of Lake Baikal. The 800 years separating the use of the two cemeteries is thought to represent a biocultural hiatus in the Cis-Baikal region, one that ended when a new group migrated into the area. To assess the likelihood that genetic continuity exists between these two Neolithic groups, we examined both mtDNA coding region and hypervariable region I (HVI) polymorphisms from skeletal remains excavated from both cemeteries (Lokomotiv and Ust'-Ida). The mtDNA haplogroup distributions of the two cemetery populations differ significantly, suggesting that they were biologically distinct groups. When the biological distance between these Neolithic groups is compared with modern Siberian and other East Eurasian groups, the posthiatus group (Serovo-Glazkovo) generally aligns with contemporary Siberians, while the prehiatus (Kitoi) individuals are significantly different from all but modern Kets and Shorians living in the Yenisey and Ob River basins to the west of Lake Baikal. These results suggest that the Lake Baikal region experienced a significant depopulation event during the sixth millennium BP, and was reoccupied by a new immigrant population some 800 years later.}, }
@article {pmid16323046, year = {2005}, author = {Bonatto, D and Brendel, M and Henriques, JA}, title = {In silico identification and analysis of new Artemis/Artemis-like sequences from fungal and metazoan species.}, journal = {The protein journal}, volume = {24}, number = {6}, pages = {399-411}, pmid = {16323046}, issn = {1572-3887}, mesh = {Amino Acid Sequence ; Animals ; Cluster Analysis ; Computational Biology ; DNA Damage ; DNA-Binding Proteins ; Endodeoxyribonucleases ; Endonucleases ; Fungal Proteins ; Humans ; *Models, Molecular ; Nuclear Proteins/chemistry/*genetics ; Phylogeny ; Recombination, Genetic ; Saccharomyces cerevisiae Proteins ; }, abstract = {The Artemis Group comprises mammalian proteins with important functions in the repair of ionizing radiation-induced DNA double-strand breaks and in the cleavage of DNA hairpin extremities generated during V(D)J recombination. Little is known about the presence of Artemis/Artemis-like proteins in non-mammalian species. We have characterized new Artemis/Artemis-like sequences from the genomes of some fungi and from non-mammalian metazoan species. An in-depth phylogenetic analysis of these new Artemis/Artemis-like sequences showed that they form a distinct clade within the Pso2p/Snm1p A and B Groups. Hydrophobic cluster analysis and three-dimensional modeling allowed to map and to compare conserved regions in these Artemis/Artemis-like proteins. The results indicate that Artemis probably belongs to an ancient DNA recombination mechanism that diversified with the evolution of multi-cellular eukaryotic lineage.}, }
@article {pmid16318358, year = {2005}, author = {Yonekawa, H}, title = {[PCR as a double-edged sword: ancient DNA and forensic science].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {50}, number = {14 Suppl}, pages = {1912-1916}, pmid = {16318358}, issn = {0039-9450}, mesh = {Animals ; DNA/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Forensic Sciences ; Humans ; Paleontology ; *Polymerase Chain Reaction ; }, }
@article {pmid16299392, year = {2006}, author = {Binladen, J and Wiuf, C and Gilbert, MT and Bunce, M and Barnett, R and Larson, G and Greenwood, AD and Haile, J and Ho, SY and Hansen, AJ and Willerslev, E}, title = {Assessing the fidelity of ancient DNA sequences amplified from nuclear genes.}, journal = {Genetics}, volume = {172}, number = {2}, pages = {733-741}, pmid = {16299392}, issn = {0016-6731}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*chemistry/*genetics ; *Fossils ; Mammals/genetics ; Molecular Sequence Data ; Palaeognathae/genetics ; Polymerase Chain Reaction/*methods ; *Sequence Analysis, DNA ; }, abstract = {To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine --> guanine and thymine --> cytosine) and type 2 transitions (cytosine --> thymine and guanine --> adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nuDNA sequences. We argue that the problems presented by postmortem damage, as well as problems with contamination from exogenous sources of conserved nuclear genes, allelic variation, and the reliance on single nucleotide polymorphisms, call for great caution in studies relying on ancient nuDNA sequences.}, }
@article {pmid16285089, year = {2005}, author = {Ottini, L and Lupi, R and Falchetti, M and Fornaciari, G and Mariani-Costantini, R and Angeletti, LR}, title = {[Molecular paleopathology: a novel perspective for biomedical history].}, journal = {Medicina nei secoli}, volume = {17}, number = {1}, pages = {181-191}, pmid = {16285089}, issn = {0394-9001}, mesh = {Communicable Diseases/*history/microbiology ; Genetic Diseases, Inborn/history ; History, Ancient ; Humans ; Molecular Biology/*history ; Neoplasms/genetics/*history ; Paleopathology/*history ; }, abstract = {Molecular paleopathology is an emerging field that is devoted to the detection, indentification and characterization of the molecular signatures in past diseases. When studied with modern molecular techniques, ancient human remains may yield direct informations on the diseases of ancient populations as well as the history of human diseases. Data concerning specific diseases of infectious, neoplastic and genetic origin can be obtained by molecular investigations of skeletal and mummified human remains. In particular, ancient DNA extracted from bone tissue, teeth and mummified soft tissue can be deeply analyzed by using PCR-based molecular techniques. Additionally, DNA of ancient pathogens, including bacteria, viruses and parasites, can be isolated from human remains and molecular diagnosis of infectious diseases can be made. Thus, molecular data, complemented by morphological and biochemical analyses, could help to reconstruct the epidemiology of past diseases and epidemics.}, }
@article {pmid16284177, year = {2005}, author = {Haak, W and Forster, P and Bramanti, B and Matsumura, S and Brandt, G and Tänzer, M and Villems, R and Renfrew, C and Gronenborn, D and Alt, KW and Burger, J}, title = {Ancient DNA from the first European farmers in 7500-year-old Neolithic sites.}, journal = {Science (New York, N.Y.)}, volume = {310}, number = {5750}, pages = {1016-1018}, doi = {10.1126/science.1118725}, pmid = {16284177}, issn = {1095-9203}, mesh = {Agriculture/*history ; Austria ; Base Sequence ; Computer Simulation ; Cultural Evolution ; DNA, Mitochondrial/chemistry/classification/*genetics/history ; Emigration and Immigration ; Europe ; Female ; Gene Frequency ; Genetic Drift ; Genetics, Population ; Germany ; Haplotypes ; History, Ancient ; Humans ; Hungary ; Male ; Molecular Sequence Data ; Population Dynamics ; White People/*genetics/history ; }, abstract = {The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans.}, }
@article {pmid16284157, year = {2005}, author = {Balter, M}, title = {Evolution. Ancient DNA yields clues to the puzzle of European origins.}, journal = {Science (New York, N.Y.)}, volume = {310}, number = {5750}, pages = {964-965}, doi = {10.1126/science.310.5750.964}, pmid = {16284157}, issn = {1095-9203}, mesh = {Agriculture/*history ; Chromosomes, Human, Y/genetics ; Cultural Evolution ; DNA, Mitochondrial/*analysis/genetics/history ; Emigration and Immigration ; Europe ; Female ; Genetics, Population ; Haplotypes ; History, Ancient ; Humans ; Male ; Population Dynamics ; White People/*genetics/history ; }, }
@article {pmid16275908, year = {2005}, author = {Shepherd, LD and Millar, CD and Ballard, G and Ainley, DG and Wilson, PR and Haynes, GD and Baroni, C and Lambert, DM}, title = {Microevolution and mega-icebergs in the Antarctic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {46}, pages = {16717-16722}, pmid = {16275908}, issn = {0027-8424}, mesh = {Animal Migration ; Antarctic Regions ; Base Sequence ; *Biological Evolution ; DNA Primers ; DNA, Satellite/genetics ; Fossils ; Gene Frequency ; *Ice ; Polymerase Chain Reaction ; Spheniscidae/*genetics/physiology ; }, abstract = {Microevolution is regarded as changes in the frequencies of genes in populations over time. Ancient DNA technology now provides an opportunity to demonstrate evolution over a geological time frame and to possibly identify the causal factors in any such evolutionary event. Using nine nuclear microsatellite DNA loci, we genotyped an ancient population of Adélie penguins (Pygoscelis adeliae) aged approximately 6,000 years B.P. Subfossil bones from this population were excavated by using an accurate stratigraphic method that allowed the identification of individuals even within the same layer. We compared the allele frequencies in the ancient population with those recorded from the modern population at the same site in Antarctica. We report significant changes in the frequencies of alleles between these two time points, hence demonstrating microevolutionary change. This study demonstrates a nuclear gene-frequency change over such a geological time frame. We discuss the possible causes of such a change, including the role of mutation, genetic drift, and the effects of gene mixing among different penguin populations. The latter is likely to be precipitated by mega-icebergs that act to promote migration among penguin colonies that typically show strong natal return.}, }
@article {pmid16219984, year = {2005}, author = {Kuehn, R and Ludt, CJ and Schroeder, W and Rottmann, O}, title = {Molecular phylogeny of Megaloceros giganteus--the giant deer or just a giant red deer?.}, journal = {Zoological science}, volume = {22}, number = {9}, pages = {1031-1044}, doi = {10.2108/zsj.22.1031}, pmid = {16219984}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; DNA Primers ; Deer/classification/*genetics ; *Fossils ; Gene Components ; Haplotypes/genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Two fragments of mitochondrial DNA (mtDNA) of the cytochrome b gene (137 bp and 167 bp) were successfully isolated and sequenced from antlers and bones of five specimens of the Giant Deer (Megaloceros giganteus) to examine the phylogenetic position of Megaloceros giganteus within the family Cervidae. This is the first report on ancient DNA (aDNA) sequences from Megaloceros giganteus. A phylogenetic analysis based on parameter-rich models describes the evolutionary relationships between five individuals of fossil Megaloceros giganteus and 37 individuals of 11 extant species of the family Cervidae. The results support a "Cervus-Megaloceros" clade. The phylogenetic positions of sympatric Megaloceros and Cervus elaphus specimens in particular indicate either that the Megaloceros mtDNA gene pool did not evolve for a substantial time period as an entity distinct from Cervus elaphus until its extinction, or that Megaloceros contributed mtDNA to Cervus elaphus or vice versa. The results of this study allow the conclusion that the European Megaloceros giganteus is more related to its modern regional counterparts of the species of Cervus elaphus than recent claims have suggested.}, }
@article {pmid16188276, year = {2006}, author = {Wang, Y and Li, W and Zhang, T and Ding, C and Lu, Z and Long, N and Rose, JP and Wang, BC and Lin, D}, title = {Reconstruction of ancient genome and gene order from complete microbial genome sequences.}, journal = {Journal of theoretical biology}, volume = {239}, number = {4}, pages = {494-498}, doi = {10.1016/j.jtbi.2005.08.013}, pmid = {16188276}, issn = {0022-5193}, support = {GM062407/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology ; *Evolution, Molecular ; *Gene Order ; *Genome, Bacterial ; *Models, Genetic ; }, abstract = {Microbial genome sequences provide us with the fossil records for inferring their origination and evolution. Assuming that current microbial genomes are the evolutionary results of ancient genomes or fragments and the neighboring genes in ancient genomes are more likely neighbors in current genomes, in this paper we proposed a paleontological algorithm and assembled the orthologous gene groups from 66 complete and current microbial genome sequences into a pseudo-ancient genome, which consists of continuous fragments of various sizes. We performed bootstrap resampling and correlation analyses and the results showed that the assembled ancient genome and fragments are statistically significant and the genes of the same fragment are inherently related and likely derived from common ancestors. This method provides a new computational tool for studying microbial genome structure and evolution.}, }
@article {pmid16182949, year = {2005}, author = {Kemp, BM and Smith, DG}, title = {Use of bleach to eliminate contaminating DNA from the surface of bones and teeth.}, journal = {Forensic science international}, volume = {154}, number = {1}, pages = {53-61}, doi = {10.1016/j.forsciint.2004.11.017}, pmid = {16182949}, issn = {0379-0738}, support = {RR00169/RR/NCRR NIH HHS/United States ; }, mesh = {DNA/chemistry/*isolation &amp; purification ; Disinfectants/*administration &amp; dosage ; Forensic Anthropology/*methods ; Fossils ; Humans ; Immersion ; Polymerase Chain Reaction ; Ribs/*chemistry ; Sodium Hypochlorite/*administration &amp; dosage ; Time Factors ; Tooth/chemistry ; }, abstract = {The extraction of DNA from archaeological or forensic skeletal remains can provide quite powerful data for analysis, but is plagued by a unique set of methodological problems. One of the most important methodological problems to overcome in such analyses is the presence of modern contamination on the surfaces of bones and teeth, which can lead to false positives and erroneous results unless it is removed before DNA extraction is initiated. Ancient DNA (aDNA) researchers and forensic scientists have employed a number of techniques to minimize such contamination. One such technique is the use of bleach (sodium hypochlorite--NaOCl) to "destroy" contaminating DNA. However, a consensus on the optimum concentration of sodium hypochlorite to be used and the amount of time the bone or tooth should be exposed to it has not emerged. The present study systematically approaches the issue by introducing contamination to ancient bones (from approximately 500 BP) and determining which of several sodium hypochlorite treatments best eliminates surface contamination. The elimination of surface contamination from bone requires immersion in at least 3.0% (w/v) sodium hypochlorite (approximately equal parts of commercial bleach and water) for at least 15 min. Endogenous DNA proved to be quite stable to even extreme sodium hypochlorite treatments (6% for 21 h), suggesting that DNA adsorbs to hydroxyapatite in the bone and that this process facilitates the preservation of DNA in ancient skeletal remains.}, }
@article {pmid16162675, year = {2005}, author = {Salamon, M and Tuross, N and Arensburg, B and Weiner, S}, title = {Relatively well preserved DNA is present in the crystal aggregates of fossil bones.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {39}, pages = {13783-13788}, pmid = {16162675}, issn = {0027-8424}, mesh = {Base Sequence ; Biodegradation, Environmental ; Bone and Bones/*chemistry ; Crystallization ; DNA/*analysis/metabolism ; *Fossils ; Genetics, Population ; Humans ; Molecular Sequence Data ; Paleontology ; Sequence Analysis, DNA ; }, abstract = {DNA from fossil human bones could provide invaluable information about population migrations, genetic relations between different groups and the spread of diseases. The use of ancient DNA from bones to study the genetics of past populations is, however, very often compromised by the altered and degraded state of preservation of the extracted material. The universally observed postmortem degradation, together with the real possibility of contamination with modern human DNA, makes the acquisition of reliable data, from humans in particular, very difficult. We demonstrate that relatively well preserved DNA is occluded within clusters of intergrown bone crystals that are resistant to disaggregation by the strong oxidant NaOCl. We obtained reproducible authentic sequences from both modern and ancient animal bones, including humans, from DNA extracts of crystal aggregates. The treatment with NaOCl also minimizes the possibility of modern DNA contamination. We thus demonstrate the presence of a privileged niche within fossil bone, which contains DNA in a better state of preservation than the DNA present in the total bone. This counterintuitive approach to extracting relatively well preserved DNA from bones significantly improves the chances of obtaining authentic ancient DNA sequences, especially from human bones.}, }
@article {pmid16138912, year = {2005}, author = {Sampietro, ML and Caramelli, D and Lao, O and Calafell, F and Comas, D and Lari, M and Agustí, B and Bertranpetit, J and Lalueza-Fox, C}, title = {The genetics of the pre-Roman Iberian Peninsula: a mtDNA study of ancient Iberians.}, journal = {Annals of human genetics}, volume = {69}, number = {Pt 5}, pages = {535-548}, doi = {10.1111/j.1529-8817.2005.00194.x}, pmid = {16138912}, issn = {0003-4800}, mesh = {Adult ; Bone and Bones/metabolism ; DNA/metabolism ; DNA Primers ; DNA, Mitochondrial/*genetics ; Fossils ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; *History, Ancient ; Humans ; Male ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Skeleton ; Spain ; }, abstract = {The Iberians developed a surprisingly sophisticated culture in the Mediterranean coast of the Iberian Peninsula from the 6th century BC until their conquest by the Romans in the 2nd century BC. They spoke and wrote a non-Indo-European language that still cannot be understood; their origins and relationships with other non-Indo-European peoples, like the Etruscans, are unclear, since their funerary practices were based on the cremation of bodies, and therefore anthropology has been unable to approach the study of this people. We have retrieved mitochondrial DNA (mtDNA) from a few of the scarce skeletal remains that have been preserved, some of them belonging to ritualistically executed individuals. The most stringent authentication criteria proposed for ancient DNA, such as independent replication, amino-acid analysis, quantitation of template molecules, multiple extractions and cloning of PCR products, have been followed to obtain reliable sequences from the mtDNA hypervariable region 1 (HVR1), as well as some haplogroup diagnostic SNPs. Phylogeographic analyses show that the haplogroup composition of the ancient Iberians was very similar to that found in modern Iberian Peninsula populations, suggesting a long-term genetic continuity since pre-Roman times. Nonetheless, there is less genetic diversity in the ancient Iberians than is found among modern populations, a fact that could reflect the small population size at the origin of the population sampled, and the heterogenic tribal structure of the Iberian society. Moreover, the Iberians were not especially closely related to the Etruscans, which points to considerable genetic heterogeneity in Pre-Roman Western Europe.}, }
@article {pmid16135448, year = {2002}, author = {Yang, SJ and Lai, XL and Tang, XH and Sheng, GL}, title = {[Experimental techniques for ancient DNA research].}, journal = {Yi chuan = Hereditas}, volume = {24}, number = {5}, pages = {551-554}, pmid = {16135448}, issn = {0253-9772}, abstract = {The development of modern molecular biological techniques makes it possible to study minimum DNA from ancient materials. During past decade,a lot of significant achievements on ancient DNA research have been made in many fields especially in molecular evolutionary biology. The nature of degradation and contamination of ancient DNA from ancient biological materials pose a dominating problem in ancient DNA research. Therefore,the experiments should be modified based on the modern molecular techniques and more factors should be considered when the results are analyzed. In this paper,authors review the general experimental protocols on sampling,extraction and amplification as well as authenticity of ancient DNA.}, }
@article {pmid16130455, year = {2005}, author = {Kühn, R and Ludt, C and Manhart, H and Peters, J and Neumair, E and Rottmann, O}, title = {Close genetic relationship of early neolithic cattle from Ziegelberg (Freising, Germany) with modern breeds.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {122 Suppl 1}, number = {}, pages = {36-44}, doi = {10.1111/j.1439-0388.2005.00507.x}, pmid = {16130455}, issn = {0931-2668}, mesh = {Animals ; Base Sequence ; Carbon Radioisotopes/analysis ; Cattle/*genetics ; Cluster Analysis ; DNA Primers ; DNA, Mitochondrial/genetics ; *Fossils ; Germany ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Sequence Alignment ; Sequence Analysis, DNA/veterinary ; }, abstract = {In 2003 a variety of crafts and bone specimens were found during excavations of a Neolithic settlement near Freising, the southernmost site of the Linear Pottery Culture in Bavaria. Six cattle bones were used to extract ancient DNA (aDNA). Applying nested and touchdown PCR, two fragments of the mitochondrial (mt) DNA control region could be amplified from specimen 533/III which yielded a total of 230 base pairs (bp). The sequence was compared with the homologous part of 40 extant breeds of Bos taurus and B. indicus and related species, such as Banteng (B. javanicus), Gaur (B. gaurus), the European bison (Bison bonasus) and the aurochs (B. primigenius). A neighbour joining tree was constructed based on the appropriate model of sequence evolution. The control region sequence of the 533/III cattle bone, whose age was determined by radiocarbon dating, clusters close to the extant European breeds, but distinctly apart from the basal aurochs and far distant from the B. indicus group. The archaeological and genetic analyses of Bos Ziegelberg demonstrate that domesticated cattle reached southern Bavaria at least 7000 years ago.}, }
@article {pmid16124858, year = {2005}, author = {Pakendorf, B and Stoneking, M}, title = {Mitochondrial DNA and human evolution.}, journal = {Annual review of genomics and human genetics}, volume = {6}, number = {}, pages = {165-183}, doi = {10.1146/annurev.genom.6.080604.162249}, pmid = {16124858}, issn = {1527-8204}, mesh = {DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Female ; Gene Dosage ; Genetic Variation ; Genetics, Population ; Genome, Human ; Humans ; Male ; Mutation ; Recombination, Genetic ; }, abstract = {Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history.}, }
@article {pmid16120801, year = {2005}, author = {Verginelli, F and Capelli, C and Coia, V and Musiani, M and Falchetti, M and Ottini, L and Palmirotta, R and Tagliacozzo, A and De Grossi Mazzorin, I and Mariani-Costantini, R}, title = {Mitochondrial DNA from prehistoric canids highlights relationships between dogs and South-East European wolves.}, journal = {Molecular biology and evolution}, volume = {22}, number = {12}, pages = {2541-2551}, doi = {10.1093/molbev/msi248}, pmid = {16120801}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; *DNA, Mitochondrial ; Dogs/*genetics ; Europe ; *Evolution, Molecular ; History, Ancient ; Molecular Sequence Data ; *Phylogeny ; Wolves/*genetics ; }, abstract = {The question of the origins of the dog has been much debated. The dog is descended from the wolf that at the end of the last glaciation (the archaeologically hypothesized period of dog domestication) was one of the most widespread among Holarctic mammals. Scenarios provided by genetic studies range from multiple dog-founding events to a single origin in East Asia. The earliest fossil dogs, dated approximately 17-12,000 radiocarbon ((14)C) years ago (YA), were found in Europe and in the Middle East. Ancient DNA (a-DNA) evidence could contribute to the identification of dog-founder wolf populations. To gain insight into the relationships between ancient European wolves and dogs we analyzed a 262-bp mitochondrial DNA control region fragment retrieved from five prehistoric Italian canids ranging in age from approximately 15,000 to approximately 3,000 (14)C YA. These canids were compared to a worldwide sample of 547 purebred dogs and 341 wolves. The ancient sequences were highly diverse and joined the three major clades of extant dog sequences. Phylogenetic investigations highlighted relationships between the ancient sequences and geographically widespread extant dog matrilines and between the ancient sequences and extant wolf matrilines of mainly East European origin. The results provide a-DNA support for the involvement of European wolves in the origins of the three major dog clades. Genetic data also suggest multiple independent domestication events. East European wolves may still reflect the genetic variation of ancient dog-founder populations.}, }
@article {pmid16102170, year = {2005}, author = {Mudge, J and Cannon, SB and Kalo, P and Oldroyd, GE and Roe, BA and Town, CD and Young, ND}, title = {Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana.}, journal = {BMC plant biology}, volume = {5}, number = {}, pages = {15}, pmid = {16102170}, issn = {1471-2229}, mesh = {Arabidopsis/*genetics ; Base Sequence ; Chromosome Mapping ; Conserved Sequence ; Evolution, Molecular ; Genes, Plant ; *Genome, Plant ; Medicago truncatula/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Glycine max/*genetics ; *Synteny ; Tandem Repeat Sequences ; }, abstract = {BACKGROUND: Recent genome sequencing enables mega-base scale comparisons between related genomes. Comparisons between animals, plants, fungi, and bacteria demonstrate extensive synteny tempered by rearrangements. Within the legume plant family, glimpses of synteny have also been observed. Characterizing syntenic relationships in legumes is important in transferring knowledge from model legumes to crops that are important sources of protein, fixed nitrogen, and health-promoting compounds.<br><br>RESULTS: We have uncovered two large soybean regions exhibiting synteny with M. truncatula and with a network of segmentally duplicated regions in Arabidopsis. In all, syntenic regions comprise over 500 predicted genes spanning 3 Mb. Up to 75% of soybean genes are colinear with M. truncatula, including one region in which 33 of 35 soybean predicted genes with database support are colinear to M. truncatula. In some regions, 60% of soybean genes share colinearity with a network of A. thaliana duplications. One region is especially interesting because this 500 kbp segment of soybean is syntenic to two paralogous regions in M. truncatula on different chromosomes. Phylogenetic analysis of individual genes within these regions demonstrates that one is orthologous to the soybean region, with which it also shows substantially denser synteny and significantly lower levels of synonymous nucleotide substitutions. The other M. truncatula region is inferred to be paralogous, presumably resulting from a duplication event preceding speciation.<br><br>CONCLUSION: The presence of well-defined M. truncatula segments showing orthologous and paralogous relationships with soybean allows us to explore the evolution of contiguous genomic regions in the context of ancient genome duplication and speciation events.}, }
@article {pmid16030148, year = {2005}, author = {Schueler, MG and Dunn, JM and Bird, CP and Ross, MT and Viggiano, L and ,  and Rocchi, M and Willard, HF and Green, ED}, title = {Progressive proximal expansion of the primate X chromosome centromere.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {30}, pages = {10563-10568}, pmid = {16030148}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Centromere/*genetics ; Chromosomes, Human, X/*genetics ; Cluster Analysis ; Conserved Sequence/genetics ; DNA Repeat Expansion/*genetics ; *Evolution, Molecular ; Humans ; Interspersed Repetitive Sequences/genetics ; Molecular Sequence Data ; *Phylogeny ; Primates/*genetics ; Sequence Analysis, DNA ; }, abstract = {Previous studies of the pericentromeric region of the human X chromosome short arm (Xp) revealed an age gradient from ancient DNA that contains expressed genes to recent human-specific DNA at the functional centromere. We analyzed the finished sequence of this human genomic region to investigate its evolutionary history. Phylogenetic analysis of >1,500 alpha-satellite monomers from the region revealed the presence of five physical domains, each containing monomers from a distinct phylogenetic clade. The most distal domain contains long interspersed nucleotide element repeats that were active >35 million years ago, whereas the four proximal domains contain more recently active long interspersed nucleotide element repeats. An out-of-register, unequal recombination (i.e., crossover) detected at the edge of the X chromosome-specific alpha-satellite array (DXZ1) may reflect the most recent of a series of punctuating events during evolution that resulted in a proximal physical expansion of the X centromere. The first 18 kb of this array has 97-99% pairwise identity among all 2-kb repeat units. To perform more detailed evolutionary comparisons, we sequenced the junction between the ancient DNA of Xp and the primate-specific alpha satellite in chimpanzee, gorilla, orangutan, vervet, macaque, and baboon. The striking conservation found in all cases supports the ancestral nature of the alpha satellite at this location. These studies demonstrate that the primate X centromere appears to have evolved through repeated expansion events occurring within the central, active region of centromeric DNA, with the newly added sequences then conferring centromere function.}, }
@article {pmid16029485, year = {2005}, author = {Parducci, L and Suyama, Y and Lascoux, M and Bennett, KD}, title = {Ancient DNA from pollen: a genetic record of population history in Scots pine.}, journal = {Molecular ecology}, volume = {14}, number = {9}, pages = {2873-2882}, doi = {10.1111/j.1365-294X.2005.02644.x}, pmid = {16029485}, issn = {0962-1083}, mesh = {Base Sequence ; Cluster Analysis ; DNA Primers ; *Demography ; Electrophoresis, Agar Gel ; *Fossils ; Gene Components ; Haplotypes/genetics ; Microsatellite Repeats/genetics ; Molecular Sequence Data ; Pinus sylvestris/*genetics ; Plastids/genetics ; Pollen/*genetics ; Population Dynamics ; Sequence Analysis, DNA ; Sweden ; }, abstract = {Assessments of plant population dynamics in space and time have depended on dated records of fossil pollen synthesized on a subcontinental scale. Genetic analyses of extant populations have revealed spatial relationships that are indicative of past spatial dynamics, but lack an explicit timescale. Synthesis of these data requires genetic analyses from abundant dated fossil material, and this has hitherto been lacking. Fossil pollen is the most abundant material with which to fill this data gap. Here we report genetic analyses of fossil pollen retrieved from Holtjärnen postglacial lake sediment in Sweden and show that plastid DNA is recoverable from Scots Pine and Norway spruce pollen grains that are 100 and 10 000 years old. By sequencing clones from two short plastid PCR products and by using multiple controls we show that the ancient sequences were endogenous to the fossil grains. Comparison of ancient sequences and those obtained from an extant population of Scots pine establishes the first genetic link between extant and fossil samples in this species, providing genetic continuity through time. The finding of one common haplotype present in modern, 100-year old and 10 000-year old samples suggests that it may have persisted near Holtjärnen throughout the postglacial period. This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time.}, }
@article {pmid16018264, year = {2005}, author = {Tian, CG and Xiong, YQ and Liu, TY and Sun, SH and Chen, LB and Chen, MS}, title = {Evidence for an ancient whole-genome duplication event in rice and other cereals.}, journal = {Yi chuan xue bao = Acta genetica Sinica}, volume = {32}, number = {5}, pages = {519-527}, pmid = {16018264}, issn = {0379-4172}, mesh = {Edible Grain/*genetics ; Evolution, Molecular ; *Gene Duplication ; Genes, Plant/genetics ; *Genome, Plant ; Models, Genetic ; Oryza/*genetics ; Phylogeny ; Polyploidy ; Time Factors ; }, abstract = {Gene duplication has been proposed as an accelerator of evolution. Ancient genome duplication events have been identified in diverse organisms, such as yeast, vertebrates, and Arabidopsis. Here, we have identified a whole genome duplication event (WGD) in the rice genome, which took place prior to the divergence of grasses about 70 million years ago (mya). A total of 117 duplicated blocks were detected, which are distributed on all 12 chromosomes and cover about 60% of the rice genome. About 20% genes on these duplicated segments are retained as duplicate pairs. In contrast, 60% of the transcription factor genes are retained as duplicates. The identification of a WGD in the ancestral grass genome will impact the study of grass genome evolution, and suggest that polyploidization and subsequent gene losses and chromosomal rearrangements have played an important role in the diversification of grasses.}, }
@article {pmid15980958, year = {2005}, author = {Alberdi, MT and Prado, JL and Prieto, A}, title = {Considerations on the paper "Morphological convergence in Hippidion and Equus (Amerhippus) South American equids elucidated by ancient DNA analysis'', by Ludovic Orlando, Véra Eisenmann, Frédéric Reynier, Paul Sondaar, Catherine Hänni.}, journal = {Journal of molecular evolution}, volume = {61}, number = {1}, pages = {145-147}, pmid = {15980958}, issn = {0022-2844}, mesh = {Animals ; *Biological Evolution ; Bone and Bones/anatomy &amp; histology ; *DNA, Mitochondrial ; Equidae/anatomy &amp; histology/*classification/genetics ; Fossils ; *Phylogeny ; South America ; Species Specificity ; Tooth/anatomy &amp; histology ; }, }
@article {pmid15974804, year = {2005}, author = {Weinstock, J and Willerslev, E and Sher, A and Tong, W and Ho, SY and Rubenstein, D and Storer, J and Burns, J and Martin, L and Bravi, C and Prieto, A and Froese, D and Scott, E and Xulong, L and Cooper, A}, title = {Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective.}, journal = {PLoS biology}, volume = {3}, number = {8}, pages = {e241}, pmid = {15974804}, issn = {1545-7885}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Base Sequence ; Bone and Bones/anatomy &amp; histology ; DNA, Mitochondrial/genetics ; Equidae/*classification/genetics ; *Evolution, Molecular ; Fossils ; Horses/classification/genetics ; Molecular Sequence Data ; North America ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; South America ; }, abstract = {The rich fossil record of horses has made them a classic example of evolutionary processes. However, while the overall picture of equid evolution is well known, the details are surprisingly poorly understood, especially for the later Pliocene and Pleistocene, c. 3 million to 0.01 million years (Ma) ago, and nowhere more so than in the Americas. There is no consensus on the number of equid species or even the number of lineages that existed in these continents. Likewise, the origin of the endemic South American genus Hippidion is unresolved, as is the phylogenetic position of the "stilt-legged" horses of North America. Using ancient DNA sequences, we show that, in contrast to current models based on morphology and a recent genetic study, Hippidion was phylogenetically close to the caballine (true) horses, with origins considerably more recent than the currently accepted date of c. 10 Ma. Furthermore, we show that stilt-legged horses, commonly regarded as Old World migrants related to the hemionid asses of Asia, were in fact an endemic North American lineage. Finally, our data suggest that there were fewer horse species in late Pleistocene North America than have been named on morphological grounds. Both caballine and stilt-legged lineages may each have comprised a single, wide-ranging species.}, }
@article {pmid15960847, year = {2005}, author = {Forsberg, R and Drummond, AJ and Hein, J}, title = {Tree measures and the number of segregating sites in time-structured population samples.}, journal = {BMC genetics}, volume = {6}, number = {}, pages = {35}, pmid = {15960847}, issn = {1471-2156}, support = {1-R01-GM60729-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Humans ; *Models, Genetic ; *Mutation ; Pedigree ; Probability ; Time ; }, abstract = {BACKGROUND: Time-structured genetic samples are a valuable source of information in population genetics because they provide several correlated observations of the underlying evolutionary processes. In this paper we study basic properties of the genetic variation in time-structured samples as reflected in the genealogies relating individuals and the number of segregating sites observed. Our emphasis is on "measurably evolving populations" i.e. populations from which it is possible to obtain time-structured samples that span a significant interval of evolutionary time.<br><br>RESULTS: We use results from the coalescent process to derive properties of time-structured samples. In the first section we extend existing results to attain measures on coalescent trees relating time-structured samples. These include the expected time to a most recent common ancestor, the expected total branch length and the expected length of branches subtending only ancient individuals. The effect of different sampling schemes on the latter measure is studied. In the second section we study the special case where the full sample consists of a group of contemporary extant samples and a group of contemporary ancient samples. As regards this case, we present results and applications concerning the probability distribution of the number of segregating sites where a mutation is unique to the ancient individuals and the number of segregating sites where a mutation is shared between ancient and extant individuals.<br><br>CONCLUSION: The methodology and results presented here is of use to the design and interpretation of ancient DNA experiments. Furthermore, the results may be useful in further development of statistical tests of e.g. population dynamics and selection, which include temporal information.}, }
@article {pmid15958782, year = {2005}, author = {Malmström, H and Storå, J and Dalén, L and Holmlund, G and Götherström, A}, title = {Extensive human DNA contamination in extracts from ancient dog bones and teeth.}, journal = {Molecular biology and evolution}, volume = {22}, number = {10}, pages = {2040-2047}, doi = {10.1093/molbev/msi195}, pmid = {15958782}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Bone and Bones/*chemistry ; DNA/*genetics/isolation &amp; purification ; DNA Primers ; DNA Probes ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; Drug Contamination ; Humans ; Polymerase Chain Reaction ; Species Specificity ; Templates, Genetic ; Tooth/*chemistry ; }, abstract = {Ancient DNA (aDNA) sequences, especially those of human origin, are notoriously difficult to analyze due to molecular damage and exogenous DNA contamination. Relatively few systematic studies have focused on this problem. Here we investigate the extent and origin of human DNA contamination in the most frequently used sources for aDNA studies, that is, bones and teeth from museum collections. To distinguish contaminant DNA from authentic DNA we extracted DNA from dog (Canis familiaris) specimens. We monitored the presence of a 148-bp human-specific and a 152-bp dog-specific mitochondrial DNA (mtDNA) fragment in DNA extracts as well as in negative controls. The total number of human and dog template molecules were quantified using real-time polymerase chain reaction (PCR), and the sequences were characterized by amplicon cloning and sequencing. Although standard precautions to avoid contamination were taken, we found that all samples from the 29 dog specimens contained human DNA, often at levels exceeding the amount of authentic ancient dog DNA. The level of contaminating human DNA was also significantly higher in the dog extracts than in the negative controls, and an experimental setup indicated that this was not caused by the carrier effect. This suggests that the contaminating human DNA mainly originated from the dog bones rather than from laboratory procedures. When cloned, fragments within a contaminated PCR product generally displayed several different sequences, although one haplotype was often found in majority. This leads us to believe that recognized criteria for authenticating aDNA cannot separate contamination from ancient human DNA the way they are presently used.}, }
@article {pmid15935940, year = {2005}, author = {Ricaut, FX and Keyser-Tracqui, C and Crubézy, E and Ludes, B}, title = {STR-genotyping from human medieval tooth and bone samples.}, journal = {Forensic science international}, volume = {151}, number = {1}, pages = {31-35}, doi = {10.1016/j.forsciint.2004.07.001}, pmid = {15935940}, issn = {0379-0738}, mesh = {Adult ; Amelogenin ; Bone and Bones/*pathology ; Child ; DNA/*analysis/chemistry ; DNA Fingerprinting/*methods ; Dental Enamel Proteins/*genetics ; Female ; Forensic Anthropology ; Genotype ; History, Medieval ; Humans ; Male ; Paleontology ; Polymerase Chain Reaction ; *Tandem Repeat Sequences ; Tooth Germ/pathology ; }, abstract = {We extracted the DNA contained in samples of bones and teeth from 10 skeletons excavated from the Gravette site (400-1000 AD, south of France). Ancient DNA was analysed by autosomal short tandem repeats (STRs). The DNA present in these ancient remains appeared very degraded, but nevertheless, better conserved in tooth than in bone samples. Moreover, we showed that the DNA extracted from ancient dental pulp was not exempt from polymerase chain reaction (PCR) inhibitors, which could result from extreme DNA fragmentation. An adapted protocol with a supplementary step of purification removed this inhibition.}, }
@article {pmid15933176, year = {2005}, author = {Pennisi, E}, title = {The biology of genomes meeting. Reading ancient DNA the community way.}, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5727}, pages = {1401}, doi = {10.1126/science.308.5727.1401a}, pmid = {15933176}, issn = {1095-9203}, mesh = {Animals ; DNA/*isolation &amp; purification ; *Fossils ; Paleontology/methods ; Ursidae/*genetics ; }, }
@article {pmid15933159, year = {2005}, author = {Noonan, JP and Hofreiter, M and Smith, D and Priest, JR and Rohland, N and Rabeder, G and Krause, J and Detter, JC and Pääbo, S and Rubin, EM}, title = {Genomic sequencing of Pleistocene cave bears.}, journal = {Science (New York, N.Y.)}, volume = {309}, number = {5734}, pages = {597-599}, doi = {10.1126/science.1113485}, pmid = {15933159}, issn = {1095-9203}, support = {T32 HL07279/HL/NHLBI NIH HHS/United States ; U1 HL66681B/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Cloning, Molecular ; Computational Biology ; DNA/genetics/history ; Dogs/genetics ; *Genome ; Genomic Library ; History, Ancient ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; *Sequence Analysis, DNA ; Ursidae/*genetics ; }, abstract = {Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries constructed with unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of approximately 1 megabase of sequence from each library showed that despite significant microbial contamination, 5.8 and 1.1% of clones contained cave bear inserts, yielding 26,861 base pairs of cave bear genome sequence. Comparison of cave bear and modern bear sequences revealed the evolutionary relationship of these lineages. The metagenomic approach used here establishes the feasibility of ancient DNA genome sequencing programs.}, }
@article {pmid15928096, year = {2005}, author = {Baker, AJ and Huynen, LJ and Haddrath, O and Millar, CD and Lambert, DM}, title = {Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: the giant moas of New Zealand.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {23}, pages = {8257-8262}, pmid = {15928096}, issn = {0027-8424}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; DNA, Mitochondrial/analysis/genetics ; Molecular Sequence Data ; New Zealand ; Palaeognathae/*classification/*genetics/physiology ; Phylogeny ; Regulatory Sequences, Nucleic Acid/genetics ; Time Factors ; }, abstract = {The tempo and mode of evolution of the extinct giant moas of New Zealand remain obscure because the number of lineages and their divergence times cannot be estimated reliably by using fossil bone characters only. We therefore extracted ancient DNA from 125 specimens and genetically typed them for a 658-bp mtDNA control region sequence. The sequences detected 14 monophyletic lineages, 9 of which correspond to currently recognized species. One of the newly detected lineages was a genetically divergent form of Megalapteryx originally described as a separate species, two more were lineages of Pachyornis in southern and northeastern New Zealand, and two were basal lineages of South Island Dinornis. When results from genetic typing and previous molecular sexing were combined, at least 33.6% of the specimens were incorrectly classified. We used longer sequences of the control region and nine other mtDNA genes totaling 2,814 base pairs to derive a strongly supported phylogeny of the 14 moa lineages. Molecular dating estimated the most recent common ancestor of moas existed after the Oligocene drowning of New Zealand. However, a cycle of lineage-splitting occurred approximately 4-10 million years ago, when the landmass was fragmented by tectonic and mountain-building events and general cooling of the climate. These events resulted in the geographic isolation of lineages and ecological specialization. The spectacular radiation of moa lineages involved significant changes in body size, shape, and mass and provides another example of the general influence of large-scale paleoenvironmental changes on vertebrate evolutionary history.}, }
@article {pmid15927295, year = {2005}, author = {Teletchea, F and Maudet, C and Hänni, C}, title = {Food and forensic molecular identification: update and challenges.}, journal = {Trends in biotechnology}, volume = {23}, number = {7}, pages = {359-366}, doi = {10.1016/j.tibtech.2005.05.006}, pmid = {15927295}, issn = {0167-7799}, mesh = {Animals ; Artifacts ; DNA/*analysis ; Food Analysis/*methods ; Forensic Medicine/*methods ; Genetic Markers ; Polymerase Chain Reaction ; Species Specificity ; }, abstract = {The need for accurate and reliable methods for animal species identification has steadily increased during past decades, particularly with the recent food scares and the overall crisis of biodiversity primarily resulting from the huge ongoing illegal traffic of endangered species. A relatively new biotechnological field, known as species molecular identification, based on the amplification and analysis of DNA, offers promising solutions. Indeed, despite the fact that retrieval and analysis of DNA in processed products is a real challenge, numerous technically consistent methods are now available and allow the detection of animal species in almost any organic substrate. However, this field is currently facing a turning point and should rely more on knowledge primarily from three fundamental fields--paleogenetics, molecular evolution and systematics.}, }
@article {pmid15923618, year = {2005}, author = {Li, B and Espinal, A and Cross, GA}, title = {Trypanosome telomeres are protected by a homologue of mammalian TRF2.}, journal = {Molecular and cellular biology}, volume = {25}, number = {12}, pages = {5011-5021}, pmid = {15923618}, issn = {0270-7306}, support = {R01 AI050614/AI/NIAID NIH HHS/United States ; AI50614/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Cycle/physiology ; Humans ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Protein Binding ; Protein Isoforms/genetics/*metabolism ; RNA Interference ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Telomere/*metabolism ; Telomeric Repeat Binding Protein 2/genetics/*metabolism ; Trypanosoma/*genetics/metabolism ; }, abstract = {Putative TTAGGG repeat-binding factor (TRF) homologues in the genomes of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major were identified. They have significant sequence similarity to higher eukaryotic TRFs in their C-terminal DNA-binding myb domains but only weak similarity in their N-terminal domains. T. brucei TRF (tbTRF) is essential and was shown to bind to duplex TTAGGG repeats. The RNA interference-mediated knockdown of tbTRF arrested bloodstream cells at G(2)/M and procyclic cells partly at S phase. Functionally, tbTRF resembles mammalian TRF2 more than TRF1, as knockdown diminished telomere single-stranded G-overhang signals. This suggests that tbTRF, like vertebrate TRF2, is essential for telomere end protection, and this also supports the hypothesis that TRF rather than Rap1 is the more ancient DNA-binding component of the telomere protein complex. Identification of the first T. brucei telomere DNA-binding protein and characterization of its function provide a new route to explore the roles of telomeres in pathogenesis of this organism. This work also establishes T. brucei as an attractive model for telomere biology.}, }
@article {pmid15922553, year = {2005}, author = {Wilsker, D and Probst, L and Wain, HM and Maltais, L and Tucker, PW and Moran, E}, title = {Nomenclature of the ARID family of DNA-binding proteins.}, journal = {Genomics}, volume = {86}, number = {2}, pages = {242-251}, doi = {10.1016/j.ygeno.2005.03.013}, pmid = {15922553}, issn = {0888-7543}, support = {CA31534/CA/NCI NIH HHS/United States ; CA53592/CA/NCI NIH HHS/United States ; HG00330/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Biological Evolution ; DNA/chemistry ; DNA-Binding Proteins/*chemistry/*classification/*genetics ; Evolution, Molecular ; Genome ; Humans ; International Cooperation ; Mice ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Terminology as Topic ; }, abstract = {The ARID is an ancient DNA-binding domain that is conserved throughout the evolution of higher eukaryotes. The ARID consensus sequence spans about 100 amino acid residues, and structural studies identify the major groove contact site as a modified helix-turn-helix motif. ARID-containing proteins exhibit a range of cellular functions, including participation in chromatin remodeling, and regulation of gene expression during cell growth, differentiation, and development. A subset of ARID family proteins binds DNA specifically at AT-rich sites; the remainder bind DNA nonspecifically. Orthologs to each of the seven distinct subfamilies of mammalian ARID-containing proteins are found in insect genomes, indicating the minimum age for the organization of these higher metazoan subfamilies. Many of these ancestral genes were duplicated and fixed over time to yield the 15 ARID-containing genes that are found in the human, mouse, and dog genomes. This paper describes a nomenclature, recommended by the Mouse Genomic Nomenclature Committee (MGNC) and accepted by the Human Genome Organization (HUGO) Gene Nomenclature Committee, for these mammalian ARID-containing genes that reflects this evolutionary history.}, }
@article {pmid15917500, year = {2005}, author = {Wirth, B and Louis, VL and Potier, S and Souciet, JL and Despons, L}, title = {Paleogenomics or the search for remnant duplicated copies of the yeast DUP240 gene family in intergenic areas.}, journal = {Molecular biology and evolution}, volume = {22}, number = {9}, pages = {1764-1771}, doi = {10.1093/molbev/msi170}, pmid = {15917500}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Intergenic/*genetics/history ; Evolution, Molecular ; *Gene Duplication ; Genome, Fungal ; History, Ancient ; Molecular Sequence Data ; Multigene Family/*genetics ; Open Reading Frames ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; Sequence Analysis, DNA ; Tandem Repeat Sequences ; }, abstract = {Duplication, resulting in gene redundancy, is well known to be a driving force of evolutionary change. Gene families are therefore useful targets for approaching genome evolution. To address the gene death process, we examined the fate of the 10-member-large S288C DUP240 family in 15 Saccharomyces cerevisiae strains. Using an original three-step method of analysis reported here, both slightly and highly degenerate DUP240 copies, called pseudo-open reading frames (ORFs) and relics, respectively, were detected in strain S288C. It was concluded that two previously annotated ORFs correspond, in fact, to pseudo-ORFs and three additional relics were identified in intergenic areas. Comparative intraspecies analysis of these degenerate DUP240 loci revealed that the two pseudo-ORFs are present in a nondegenerate state in some other strains. This suggests that within a given gene family different loci are the target of the gene erasure process, which is therefore strain dependent. Besides, the variable positions observed indicate that the relic sequence may diverge faster than the flanking regions. All in all, this study shows that short conserved protein motifs provide a useful tool for detecting and accurately mapping degenerate gene remnants. The present results also highlight the strong contribution of comparative genomics for gene relic detection because the possibility of finding short conserved protein motifs in intergenic regions (IRs) largely depends on the choice of the most closely related paralog or ortholog. By mapping new genetic components in previously annotated IRs, our study constitutes a further refinement step in the crucial stage of genome annotation and provides a strategy for retracing ancient chromosomal reshaping events and, hence, for deciphering genome history.}, }
@article {pmid15913935, year = {2006}, author = {Gilbert, MT and Menez, L and Janaway, RC and Tobin, DJ and Cooper, A and Wilson, AS}, title = {Resistance of degraded hair shafts to contaminant DNA.}, journal = {Forensic science international}, volume = {156}, number = {2-3}, pages = {208-212}, doi = {10.1016/j.forsciint.2005.02.021}, pmid = {15913935}, issn = {0379-0738}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Blood ; Cloning, Molecular ; DNA/*analysis ; DNA Fingerprinting ; DNA Primers ; Hair/*chemistry ; Humans ; Saliva ; }, abstract = {We have investigated the susceptibility of degraded human hair shaft samples to contamination by exogenous sources of DNA, including blood, saliva, skin cells, and purified DNA. The results indicate that on the whole hair shafts are either largely resistant to penetration by contaminant DNA, or extremely easy to successfully decontaminate. This pertains to samples that are both morphologically and biochemically degraded. We suggest that this resistance to the incorporation of contaminant DNA relates to the hydrophobic and impermeable nature of the keratin structures forming the hair shaft. Therefore, hair samples represent an important and underestimated source of DNA in both forensic and ancient DNA studies.}, }
@article {pmid15890939, year = {2005}, author = {López-Sánchez, P and Costas, JC and Naveira, HF}, title = {Paleogenomic record of the extinction of human endogenous retrovirus ERV9.}, journal = {Journal of virology}, volume = {79}, number = {11}, pages = {6997-7004}, pmid = {15890939}, issn = {0022-538X}, mesh = {Animals ; Base Sequence ; DNA Transposable Elements/genetics ; DNA, Viral/genetics/isolation &amp; purification ; Endogenous Retroviruses/classification/*genetics/isolation &amp; purification ; *Evolution, Molecular ; Genetic Variation ; *Genome, Human ; Humans ; Molecular Sequence Data ; Paleontology ; Pan troglodytes/genetics/virology ; Phylogeny ; Primates/genetics/virology ; Sequence Homology, Amino Acid ; Terminal Repeat Sequences ; Time Factors ; }, abstract = {An outstanding question of genome evolution is what stops the invasion of a host genome by transposable elements (TEs). The human genome, harboring the remnants of many extinct TE families, offers an extraordinary opportunity to investigate this problem. ERV9 is an endogenous retrovirus repeatedly mobilized during primate evolution, 15 to 6 million years ago (MYA), which left a trace of over a hundred provirus-like copies and at least 4,000 solitary long terminal repeats (LTRs) in the human genome. Then, its proliferation ceased for unknown reasons, and the family went extinct. We have made a detailed reconstruction of its last active subfamily, ERV9_XII, by examining 115 solitary LTRs from it. These insertions were grouped into 11 sets according to shared nucleotide variants, which could be placed in a sequential order of 10 to 6 MYA. At least 75% of the subfamily was produced 8 to 6 MYA, during a stage of intense proliferation. With new analytical tools, we show that the youngest and most prolific sets may have been produced by effectively instantaneous expansions of corresponding single-sequence variants. The extinction of this family apparently was not a consequence of its slow gradual degeneration, but the outcome of the fixation of specific restrictive alleles in the human-chimpanzee ancestral population. Three species-specific insertions (two in humans and one in chimpanzees) were identified, further supporting that extinction took place when these two species were beginning to diverge. These are the only fixed differences of this kind so far observed between humans and chimpanzees, apart from those belonging to the human endogenous retrovirus K family.}, }
@article {pmid15884675, year = {2005}, author = {Pruvost, M and Grange, T and Geigl, EM}, title = {Minimizing DNA contamination by using UNG-coupled quantitative real-time PCR on degraded DNA samples: application to ancient DNA studies.}, journal = {BioTechniques}, volume = {38}, number = {4}, pages = {569-575}, doi = {10.2144/05384ST03}, pmid = {15884675}, issn = {0736-6205}, mesh = {Base Sequence ; Bone and Bones/chemistry ; Cloning, Molecular ; DNA/*genetics ; DNA Glycosylases/genetics/*metabolism ; DNA Primers ; Escherichia coli/enzymology/genetics ; Fossils ; Nucleic Acid Amplification Techniques ; *Polymerase Chain Reaction ; Pyrophosphatases/genetics/metabolism ; Uracil-DNA Glycosidase ; }, abstract = {PCR analyses of ancient and degraded DNA suffer from their extreme sensitivity to contamination by modern DNA originating, in particular, from carryover contamination with previously amplified or cloned material. Any strategy for limiting carryover contamination would also have to be compatible with the particular requirements of ancient DNA analyses. These include the need (i) to amplify short PCR products due to template fragmentation; (ii) to clone PCR products in order to track possible base misincorporation resulting from damaged templates; and (iii) to avoid incomplete decontamination causing artifactual sequence transformation. Here we show that the enzymatic decontamination procedures based upon dUTP- and uracil-N-glycosylase (UNG) can be adapted to meet the specific requirements of ancient DNA research. Thus, efficiency can be improved to vastly reduce the amplification of fragments < or = 100 bp. Secondly, the use of an Escherichia coli strain deficient in both UNG and dUTPase allows for the cloning of uracil-containing PCR products and offers protection from plasmid DNA contamination, and, lastly, PCR products amplified from UNG-degraded material are free of misleading sequence modifications.}, }
@article {pmid15878988, year = {2005}, author = {Beauval, C and Maureille, B and Lacrampe-Cuyaubère, F and Serre, D and Peressinotto, D and Bordes, JG and Cochard, D and Couchoud, I and Dubrasquet, D and Laroulandie, V and Lenoble, A and Mallye, JB and Pasty, S and Primault, J and Rohland, N and Pääbo, S and Trinkaus, E}, title = {A late Neandertal femur from Les Rochers-de-Villeneuve, France.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {20}, pages = {7085-7090}, pmid = {15878988}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Carbon Radioisotopes ; DNA, Mitochondrial/*genetics ; Femur/*anatomy &amp; histology ; *Fossils ; France ; Hominidae/*anatomy &amp; histology/genetics ; Humans ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {In 2002, a Neandertal partial femoral diaphysis was discovered at Les Rochers-de-Villeneuve (Vienne, France). Radiocarbon dated to approximately 40,700 14C years before present, this specimen is one of the most recent Middle Paleolithic Neandertals. The diaphysis derives from an archeological level indicating alternating human and carnivore (mostly hyena) occupation of the cave, reinforcing the close proximity and probable competition of Middle Paleolithic humans with large carnivores for resources and space. Morphological aspects of the diaphysis and ancient DNA extracted from it indicate that it is aligned with the Neandertals and is distinct from early modern humans. However, its midshaft cortical bone distribution places it between other Middle Paleolithic Neandertals and the Châtelperronian Neandertal from La Roche-à-Pierrot, supporting a pattern of changing mobility patterns among late Middle Paleolithic Neandertals on the eve of modern human dispersals into Europe.}, }
@article {pmid15875564, year = {2005}, author = {Willerslev, E and Cooper, A}, title = {Ancient DNA.}, journal = {Proceedings. Biological sciences}, volume = {272}, number = {1558}, pages = {3-16}, pmid = {15875564}, issn = {0962-8452}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {DNA/chemistry/*genetics ; Evolution, Molecular ; *Fossils ; *Genetic Techniques ; Genetics, Population ; Paleontology/*methods ; Phylogeny ; Specimen Handling/*methods ; }, abstract = {In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.}, }
@article {pmid15870386, year = {2005}, author = {Bower, MA and Spencer, M and Matsumura, S and Nisbet, RE and Howe, CJ}, title = {How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence?.}, journal = {Nucleic acids research}, volume = {33}, number = {8}, pages = {2549-2556}, pmid = {15870386}, issn = {1362-4962}, mesh = {Cloning, Molecular ; *Consensus Sequence ; DNA Fingerprinting/*methods ; *Fossils ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Software ; Templates, Genetic ; }, abstract = {Forensic and ancient DNA (aDNA) extracts are mixtures of endogenous aDNA, existing in more or less damaged state, and contaminant DNA. To obtain the true aDNA sequence, it is not sufficient to generate a single direct sequence of the mixture, even where the authentic aDNA is the most abundant (e.g. 25% or more) in the component mixture. Only bacterial cloning can elucidate the components of this mixture. We calculate the number of clones that need to be sampled (for various mixture ratios) in order to be confident (at various levels of confidence) to have identified the major component. We demonstrate that to be >95% confident of identifying the most abundant sequence present at 70% in the ancient sample, 20 clones must be sampled. We make recommendations and offer a free-access web-based program, which constructs the most reliable consensus sequence from the user's input clone sequences and analyses the confidence limits for each nucleotide position and for the whole consensus sequence. Accepted authentication methods must be employed in order to assess the authenticity and endogeneity of the resulting consensus sequences (e.g. quantification and replication by another laboratory, blind testing, amelogenin sex versus morphological sex, the effective use of controls, etc.) and determine whether they are indeed aDNA.}, }
@article {pmid15866038, year = {2005}, author = {Hebsgaard, MB and Phillips, MJ and Willerslev, E}, title = {Geologically ancient DNA: fact or artefact?.}, journal = {Trends in microbiology}, volume = {13}, number = {5}, pages = {212-220}, doi = {10.1016/j.tim.2005.03.010}, pmid = {15866038}, issn = {0966-842X}, mesh = {Amber ; Archaeology ; DNA/chemistry/genetics/*isolation &amp; purification ; *Fossils ; Paleontology ; }, abstract = {Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup and insufficient authentication of results. Consequently, it remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales. To enhance the credibility of future studies and assist in discarding false-positive results, we propose a rigorous set of authentication criteria for work with geologically ancient DNA.}, }
@article {pmid15865963, year = {2005}, author = {Mulligan, CJ}, title = {Isolation and analysis of DNA from archaeological, clinical, and natural history specimens.}, journal = {Methods in enzymology}, volume = {395}, number = {}, pages = {87-103}, doi = {10.1016/S0076-6879(05)95007-6}, pmid = {15865963}, issn = {0076-6879}, mesh = {Archaeology ; Bone and Bones/chemistry ; Connective Tissue/chemistry ; DNA/genetics/*isolation &amp; purification ; DNA Damage ; DNA Fragmentation ; Drug Contamination ; Enzyme Inhibitors/isolation &amp; purification ; *Fossils ; Humans ; Methods ; Nucleic Acid Synthesis Inhibitors ; Polymerase Chain Reaction ; Tooth/chemistry ; }, abstract = {The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. Novel methods exist for the isolation, purification, and analysis of aDNA because these DNA templates are likely to be damaged, fragmented and?or associated with non-nucleic acid material. However, contamination of ancient specimens and DNA extracts with modern DNA is more widespread than is generally acknowledged and remains a significant problem in aDNA analysis. Studies of human aDNA are uniquely sensitive to contamination due to the continual presence of potential contamination sources. Meticulous authentication of results and careful selection of polymorphic markers capable of distinguishing between aDNA and probable DNA contaminants are critical to a successful aDNA study.}, }
@article {pmid15819905, year = {2005}, author = {Gugerli, F and Parducci, L and Petit, RJ}, title = {Ancient plant DNA: review and prospects.}, journal = {The New phytologist}, volume = {166}, number = {2}, pages = {409-418}, doi = {10.1111/j.1469-8137.2005.01360.x}, pmid = {15819905}, issn = {0028-646X}, mesh = {Biological Evolution ; DNA, Plant/*analysis/genetics ; Genetic Markers ; Paleontology/methods ; Phylogeny ; Plants/*genetics ; }, abstract = {Ancient DNA has received much attention since the mid-1980s, when the first sequence of an extinct animal species was recovered from a museum specimen. Since then, the majority of ancient DNA studies have focused predominantly on animal species, while studies in plant palaeogenetics have been rather limited, with the notable exception of cultivated species found in archaeological sites. Here, we outline the recent developments in the analysis of plant ancient DNA. We emphasize the trend from species identification to population-level investigation and highlight the potential and the difficulties in this field, related to DNA preservation and to risks of contamination. Further efforts towards the analysis of ancient DNA from the abundant store of fossil plant remains should provide new research opportunities in palaeoecology and phylogeography. In particular, intraspecific variation should be considered not only in cultivated plants but also in wild taxa if palaeogenetics is to become a fully emancipated field of plant research.}, }
@article {pmid15818384, year = {2005}, author = {Huynh, KD and Lee, JT}, title = {X-chromosome inactivation: a hypothesis linking ontogeny and phylogeny.}, journal = {Nature reviews. Genetics}, volume = {6}, number = {5}, pages = {410-418}, doi = {10.1038/nrg1604}, pmid = {15818384}, issn = {1471-0056}, mesh = {Animals ; *Dosage Compensation, Genetic ; *Models, Genetic ; Phylogeny ; X Chromosome/*genetics ; }, abstract = {In mammals, sex is determined by differential inheritance of a pair of dimorphic chromosomes: the gene-rich X chromosome and the gene-poor Y chromosome. To balance the unequal X-chromosome dosage between the XX female and XY male, mammals have adopted a unique form of dosage compensation in which one of the two X chromosomes is inactivated in the female. This mechanism involves a complex, highly coordinated sequence of events and is a very different strategy from those used by other organisms, such as the fruitfly and the worm. Why did mammals choose an inactivation mechanism when other, perhaps simpler, means could have been used? Recent data offer a compelling link between ontogeny and phylogeny. Here, we propose that X-chromosome inactivation and imprinting might have evolved from an ancient genome-defence mechanism that silences unpaired DNA.}, }
@article {pmid15801584, year = {2004}, author = {Parham, JF and Stuart, BL and Bour, R and Fritz, U}, title = {Evolutionary distinctiveness of the extinct Yunnan box turtle (Cuora yunnanensis) revealed by DNA from an old museum specimen.}, journal = {Proceedings. Biological sciences}, volume = {271 Suppl 6}, number = {Suppl 6}, pages = {S391-4}, pmid = {15801584}, issn = {0962-8452}, mesh = {Animals ; Base Sequence ; China ; DNA Primers ; DNA, Mitochondrial/genetics ; *Genetic Variation ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Museums ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Turtles/*genetics ; }, abstract = {Cuora yunnanensis is an extinct turtle known from 12 specimens collected from Yunnan, China, before 1908. We used ancient DNA methods to sequence 1723 base pairs of mitochondrial DNA from a museum specimen of C. yunnanensis. Unlike some rare 'species' recently described from the pet trade, C. yunnanensis represents a lineage that is distinct from other known turtles. Besides C. yunnanensis, two other valid species (C. mccordi, C. zhoui) are unknown in the wild but are supposedly from Yunnan. Intensive field surveys for surviving wild populations of these critically endangered species are urgently needed.}, }
@article {pmid15784742, year = {2005}, author = {Karanth, KP and Delefosse, T and Rakotosamimanana, B and Parsons, TJ and Yoder, AD}, title = {Ancient DNA from giant extinct lemurs confirms single origin of Malagasy primates.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {14}, pages = {5090-5095}, pmid = {15784742}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; DNA/*genetics/isolation &amp; purification ; DNA Primers/genetics ; *Evolution, Molecular ; Fossils ; Lemur/classification/*genetics ; Madagascar ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Primates/classification/*genetics ; Sequence Alignment ; }, abstract = {The living Malagasy lemurs constitute a spectacular radiation of >50 species that are believed to have evolved from a common ancestor that colonized Madagascar in the early Tertiary period. Yet, at least 15 additional Malagasy primate species, some of which were relative giants, succumbed to extinction within the past 2,000 years. Their existence in Madagascar is recorded predominantly in its Holocene subfossil record. To rigorously test the hypothesis that all endemic Malagasy primates constitute a monophyletic group and to determine the evolutionary relationships among living and extinct taxa, we have conducted an ancient DNA analysis of subfossil species. A total of nine subfossil individuals from the extinct genera Palaeopropithecus and Megaladapis yielded amplifiable DNA. Phylogenetic analysis of cytochrome b sequences derived from these subfossils corroborates the monophyly of endemic Malagasy primates. Our results support the close relationship of sloth lemurs to living indriids, as has been hypothesized on morphological grounds. In contrast, Megaladapis does not show a sister-group relationship with the living genus Lepilemur. Thus, the classification of the latter in the family Megaladapidae is misleading. By correlating the geographic location of subfossil specimens with relative amplification success, we reconfirm the global trend of increased success rates of ancient DNA recovery from nontropical localities.}, }
@article {pmid15756672, year = {2005}, author = {Ricaut, FX and Fedoseeva, A and Keyser-Tracqui, C and Crubézy, E and Ludes, B}, title = {Ancient DNA analysis of human neolithic remains found in northeastern Siberia.}, journal = {American journal of physical anthropology}, volume = {126}, number = {4}, pages = {458-462}, doi = {10.1002/ajpa.20257}, pmid = {15756672}, issn = {0002-9483}, mesh = {Base Sequence ; Bone and Bones/*chemistry ; DNA/*genetics ; DNA Primers ; DNA, Mitochondrial/genetics ; *Fossils ; Gene Frequency ; Geography ; Haplotypes/genetics ; Humans ; Polymorphism, Genetic ; Population Dynamics ; Sequence Analysis, DNA ; Siberia ; Tandem Repeat Sequences/genetics ; }, abstract = {We successfully extracted DNA from a bone sample of a Neolithic skeleton (dated 3,600 +/- 60 years BP) excavated in northeastern Yakutia (east Siberia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by sequencing of the hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The STR profile, the mitochondrial haplotype, and the haplogroup determined were compared with those of modern Eurasian and Native American populations. The results showed the affinity of this ancient skeleton with both east Siberian/Asian and Native American populations.}, }
@article {pmid15750025, year = {2005}, author = {Tönnies, H and Gerlach, A and Klunker, R and Schultka, R and Göbbel, L}, title = {First systematic CGH-based analyses of ancient DNA samples of malformed fetuses preserved in the Meckel Anatomical Collection in Halle/Saale (Germany).}, journal = {The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society}, volume = {53}, number = {3}, pages = {381-384}, doi = {10.1369/jhc.4B6427.2005}, pmid = {15750025}, issn = {0022-1554}, mesh = {Congenital Abnormalities/genetics ; DNA/*analysis/isolation &amp; purification ; Female ; Fetus/*abnormalities ; Humans ; In Situ Hybridization, Fluorescence ; Karyotyping ; Male ; Museums ; Nucleic Acid Hybridization ; Specimen Handling ; }, abstract = {We present the first data on our comparative genomic hybridization (CGH)-based strategy for the analysis of ancient DNA (aDNA) samples extracted from fetuses preserved in the Meckel Anatomical Collection in Halle, Germany. The collection contains numerous differently fixed ancient samples of fetal malformations collected from the middle of the 18th to the early 19th century. The main objective of this study is to establish a "standard" aDNA extraction and amplification protocol as a prerequisite for successful CGH analyses to detect or exclude chromosomal imbalances possibly causative for the malformations described for the fetuses.}, }
@article {pmid15748652, year = {2005}, author = {Mitchell, D and Willerslev, E and Hansen, A}, title = {Damage and repair of ancient DNA.}, journal = {Mutation research}, volume = {571}, number = {1-2}, pages = {265-276}, doi = {10.1016/j.mrfmmm.2004.06.060}, pmid = {15748652}, issn = {0027-5107}, support = {ES07784/ES/NIEHS NIH HHS/United States ; }, mesh = {DNA/chemistry/genetics ; *DNA Damage ; *DNA Repair ; Freezing ; Oxidative Stress ; }, abstract = {Under certain conditions small amounts of DNA can survive for long periods of time and can be used as polymerase chain reaction (PCR) substrates for the study of phylogenetic relationships and population genetics of extinct plants and animals, including hominids. Because of extensive DNA degradation, these studies are limited to species that lived within the past 10(4)-10(5) years (Late Pleistocene), although DNA sequences from 10(6) years have been reported. Ancient DNA (aDNA) has been used to study phylogenetic relationships of protists, fungi, algae, plants, and higher eukaryotes such as extinct horses, cave bears, the marsupial wolf, the moa, and Neanderthal. In the past few years, this technology has been extended to the study of infectious disease in ancient Egyptian and South American mummies, the dietary habits of ancient animals, and agricultural practices and population dynamics of early native Americans. Hence, ancient DNA contains information pertinent to numerous fields of study including evolution, population genetics, ecology, climatology, medicine, archeology, and behavior. The major obstacles to the study of aDNA are its extremely low yield, contamination with modern DNA, and extensive degradation. In the course of this review, we will discuss the current aDNA literature describing the importance of aDNA studies as they relate to important biological questions and the difficulties associated with extracting useful information from highly degraded and damaged substrates derived from limited sources. In addition, we will present some of our own preliminary and published data on mechanisms of DNA degradation and some speculative thoughts on strategies for repair and restoration of aDNA.}, }
@article {pmid15742001, year = {2005}, author = {Hedrick, P and Waits, L}, title = {What ancient DNA tells us.}, journal = {Heredity}, volume = {94}, number = {5}, pages = {463-464}, doi = {10.1038/sj.hdy.6800647}, pmid = {15742001}, issn = {0018-067X}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; *Fossils ; *Geography ; Humans ; Species Specificity ; }, }
@article {pmid15721248, year = {2005}, author = {Benner, SA and Ricardo, A}, title = {Planetary systems biology.}, journal = {Molecular cell}, volume = {17}, number = {4}, pages = {471-472}, doi = {10.1016/j.molcel.2005.02.005}, pmid = {15721248}, issn = {1097-2765}, mesh = {*Bacterial Physiological Phenomena ; Biodegradation, Environmental ; Environmental Pollutants/metabolism ; Enzymes/metabolism ; *Genetic Engineering ; *Microbiology ; Systems Theory ; }, abstract = {Combining paleogenetics, protein engineering, synthetic biology, and metabolic modeling, a planetary biology perspective is brought to bear on adaptive evolutionary events in ancient bacteria.}, }
@article {pmid15719062, year = {2005}, author = {Nicholls, H}, title = {Ancient DNA comes of age.}, journal = {PLoS biology}, volume = {3}, number = {2}, pages = {e56}, pmid = {15719062}, issn = {1545-7885}, mesh = {Animals ; DNA/*genetics/*standards ; DNA Repair/genetics ; *Evolution, Molecular ; *Fossils ; Humans/genetics ; Paleontology/*methods/standards ; Time ; }, abstract = {Ancient DNA enables researchers to study the genetics of populations in the past; despite difficulties in its extraction, aDNA reveals that evolution is even more complex than we had imagined}, }
@article {pmid15714514, year = {2005}, author = {Gilbert, MT and Barnes, I and Collins, MJ and Smith, C and Eklund, J and Goudsmit, J and Poinar, H and Cooper, A}, title = {Long-term survival of ancient DNA in Egypt: response to Zink and Nerlich (2003).}, journal = {American journal of physical anthropology}, volume = {128}, number = {1}, pages = {110-4; discussion 115-8}, doi = {10.1002/ajpa.20045}, pmid = {15714514}, issn = {0002-9483}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Archaeology/*methods ; DNA/*history ; Egypt, Ancient ; Embalming/history/methods ; History, Ancient ; Humans ; Humidity ; Nucleic Acid Amplification Techniques ; Temperature ; Time Factors ; }, }
@article {pmid15699220, year = {2005}, author = {Cordain, L and Eaton, SB and Sebastian, A and Mann, N and Lindeberg, S and Watkins, BA and O'Keefe, JH and Brand-Miller, J}, title = {Origins and evolution of the Western diet: health implications for the 21st century.}, journal = {The American journal of clinical nutrition}, volume = {81}, number = {2}, pages = {341-354}, doi = {10.1093/ajcn.81.2.341}, pmid = {15699220}, issn = {0002-9165}, mesh = {Acid-Base Equilibrium ; Agriculture/*methods ; *Biological Evolution ; Chronic Disease/epidemiology ; Diet/*trends ; Dietary Fiber/administration &amp; dosage ; Fatty Acids/administration &amp; dosage/analysis ; Food Analysis ; Food Handling/methods ; Glycemic Index ; Humans ; Potassium, Dietary/administration &amp; dosage ; Sodium, Dietary/administration &amp; dosage ; United States ; }, abstract = {There is growing awareness that the profound changes in the environment (eg, in diet and other lifestyle conditions) that began with the introduction of agriculture and animal husbandry approximately 10000 y ago occurred too recently on an evolutionary time scale for the human genome to adjust. In conjunction with this discordance between our ancient, genetically determined biology and the nutritional, cultural, and activity patterns of contemporary Western populations, many of the so-called diseases of civilization have emerged. In particular, food staples and food-processing procedures introduced during the Neolithic and Industrial Periods have fundamentally altered 7 crucial nutritional characteristics of ancestral hominin diets: 1) glycemic load, 2) fatty acid composition, 3) macronutrient composition, 4) micronutrient density, 5) acid-base balance, 6) sodium-potassium ratio, and 7) fiber content. The evolutionary collision of our ancient genome with the nutritional qualities of recently introduced foods may underlie many of the chronic diseases of Western civilization.}, }
@article {pmid15693628, year = {2004}, author = {Fedorov, A and Fedorova, L}, title = {Introns: mighty elements from the RNA world.}, journal = {Journal of molecular evolution}, volume = {59}, number = {5}, pages = {718-721}, pmid = {15693628}, issn = {0022-2844}, mesh = {Animals ; Evolution, Molecular ; Introns/*genetics ; Models, Genetic ; Origin of Life ; RNA/*genetics ; RNA Splicing/genetics ; }, abstract = {The discovery of RNA-based enzymatic activity by Thomas Cech's and Sidney Altman's laboratories was a momentous event that led Walter Gilbert to the concept of an "RNA world"--a primitive ancient stage of life that existed before the appearance of DNA and protein molecules. A year later, Gilbert formulated "the exon theory of genes," which hypothesized that introns are very ancient genetic elements present at the earliest stages of life in the RNA world. This theory has been fiercely debated and still has vigorous supporters and opponents. In this communication, we explore peculiarities in the RNA-protein world and their effect on intron-exon structures. We demonstrate that these peculiarities, which exist in the absence of DNA, could shed light on introns' original functions as well as the important role they might have played in the origin of life. For ancient DNA-lacking cells, a crucial problem existed in distinguishing two distinct subsets of RNAs: those messenger molecules coding for proteins and those heritable genetic molecules complementary to messenger RNAs that propagate the genetic information through generations. We propose that ancient introns could act as markers of RNA subsets, directing them to different functions.}, }
@article {pmid15689370, year = {2005}, author = {Yan, YL and Willoughby, J and Liu, D and Crump, JG and Wilson, C and Miller, CT and Singer, A and Kimmel, C and Westerfield, M and Postlethwait, JH}, title = {A pair of Sox: distinct and overlapping functions of zebrafish sox9 co-orthologs in craniofacial and pectoral fin development.}, journal = {Development (Cambridge, England)}, volume = {132}, number = {5}, pages = {1069-1083}, doi = {10.1242/dev.01674}, pmid = {15689370}, issn = {0950-1991}, support = {DE13834/DE/NIDCR NIH HHS/United States ; DE15201/DE/NIDCR NIH HHS/United States ; HD22486/HD/NICHD NIH HHS/United States ; R01RR10715/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Body Patterning ; Bone and Bones/embryology ; Cartilage/embryology ; Cell Death ; Chondrocytes/metabolism ; Ear/embryology ; Embryonic Development ; Evolution, Molecular ; Extremities ; Gene Deletion ; *Gene Expression Regulation, Developmental ; Genotype ; High Mobility Group Proteins/*biosynthesis/*physiology ; In Situ Hybridization ; In Situ Nick-End Labeling ; Models, Genetic ; Mutation ; Phenotype ; Protein Structure, Tertiary ; RNA, Messenger/metabolism ; SOX9 Transcription Factor ; Time Factors ; Transcription Factors/*biosynthesis/*physiology ; Zebrafish ; }, abstract = {Understanding how developmental systems evolve after genome amplification is important for discerning the origins of vertebrate novelties, including neural crest, placodes, cartilage and bone. Sox9 is important for the development of these features, and zebrafish has two co-orthologs of tetrapod SOX9 stemming from an ancient genome duplication event in the lineage of ray-fin fish. We have used a genotype-driven screen to isolate a mutation deleting sox9b function, and investigated its phenotype and genetic interactions with a sox9a null mutation. Analysis of mutant phenotypes strongly supports the interpretation that ancestral gene functions partitioned spatially and temporally between Sox9 co-orthologs. Distinct subsets of the craniofacial skeleton, otic placode and pectoral appendage express each gene, and are defective in each single mutant. The double mutant phenotype is additive or synergistic. Ears are somewhat reduced in each single mutant but are mostly absent in the double mutant. Loss-of-function animals from mutations and morpholino injections, and gain-of-function animals injected with sox9a and sox9b mRNAs showed that sox9 helps regulate other early crest genes, including foxd3, sox10, snai1b and crestin, as well as the cartilage gene col2a1 and the bone gene runx2a; however, tfap2a was nearly unchanged in mutants. Chondrocytes failed to stack in sox9a mutants, failed to attain proper numbers in sox9b mutants and failed in both morphogenetic processes in double mutants. Pleiotropy can cause mutations in single copy tetrapod genes, such as Sox9, to block development early and obscure later gene functions. By contrast, subfunction partitioning between zebrafish co-orthologs of tetrapod genes, such as sox9a and sox9b, can relax pleiotropy and reveal both early and late developmental gene functions.}, }
@article {pmid15681615, year = {2005}, author = {Gill, P and Curran, J and Elliot, K}, title = {A graphical simulation model of the entire DNA process associated with the analysis of short tandem repeat loci.}, journal = {Nucleic acids research}, volume = {33}, number = {2}, pages = {632-643}, pmid = {15681615}, issn = {1362-4962}, mesh = {*Computer Graphics ; Computer Simulation ; DNA/isolation &amp; purification ; Haploidy ; Heterozygote ; *Models, Statistical ; Monte Carlo Method ; Polymerase Chain Reaction/*methods ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Stochastic Processes ; *Tandem Repeat Sequences ; }, abstract = {The use of expert systems to interpret short tandem repeat DNA profiles in forensic, medical and ancient DNA applications is becoming increasingly prevalent as high-throughput analytical systems generate large amounts of data that are time-consuming to process. With special reference to low copy number (LCN) applications, we use a graphical model to simulate stochastic variation associated with the entire DNA process starting with extraction of sample, followed by the processing associated with the preparation of a PCR reaction mixture and PCR itself. Each part of the process is modelled with input efficiency parameters. Then, the key output parameters that define the characteristics of a DNA profile are derived, namely heterozygote balance (Hb) and the probability of allelic drop-out p(D). The model can be used to estimate the unknown efficiency parameters, such as pi(extraction). 'What-if' scenarios can be used to improve and optimize the entire process, e.g. by increasing the aliquot forwarded to PCR, the improvement expected to a given DNA profile can be reliably predicted. We demonstrate that Hb and drop-out are mainly a function of stochastic effect of pre-PCR molecular selection. Whole genome amplification is unlikely to give any benefit over conventional PCR for LCN.}, }
@article {pmid15660162, year = {2005}, author = {Bunce, M and Szulkin, M and Lerner, HR and Barnes, I and Shapiro, B and Cooper, A and Holdaway, RN}, title = {Ancient DNA provides new insights into the evolutionary history of New Zealand's extinct giant eagle.}, journal = {PLoS biology}, volume = {3}, number = {1}, pages = {e9}, pmid = {15660162}, issn = {1545-7885}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Body Size ; DNA/*genetics ; Eagles/*anatomy &amp; histology/classification/*genetics ; Ecosystem ; *Evolution, Molecular ; *Fossils ; Molecular Sequence Data ; New Zealand ; Paleontology/methods ; }, abstract = {Prior to human settlement 700 years ago New Zealand had no terrestrial mammals--apart from three species of bats--instead, approximately 250 avian species dominated the ecosystem. At the top of the food chain was the extinct Haast's eagle, Harpagornis moorei. H. moorei (10-15 kg; 2-3 m wingspan) was 30%-40% heavier than the largest extant eagle (the harpy eagle, Harpia harpyja), and hunted moa up to 15 times its weight. In a dramatic example of morphological plasticity and rapid size increase, we show that the H. moorei was very closely related to one of the world's smallest extant eagles, which is one-tenth its mass. This spectacular evolutionary change illustrates the potential speed of size alteration within lineages of vertebrates, especially in island ecosystems.}, }
@article {pmid15648848, year = {2004}, author = {Haak, W and Burger, J and Alt, KW}, title = {ABO genotyping by PCR-RFLP and cloning and sequencing.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {62}, number = {4}, pages = {397-410}, pmid = {15648848}, issn = {0003-5548}, mesh = {ABO Blood-Group System/*genetics ; Alleles ; Archaeology ; Blood Stains ; Chromosome Deletion ; *Cloning, Molecular ; DNA Transposable Elements ; Forensic Medicine ; History, Ancient ; Humans ; Phenotype ; *Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; Postmortem Changes ; Reproducibility of Results ; *Sequence Analysis, DNA ; Tooth/pathology ; }, abstract = {A refined PCR-RFLP based method was established to genotype ABO blood groups. The main objective of this study was to make the techniques also suitable for working with degraded DNA. Specific primer design was carried out to choose fragments shorter than 200 bp as necessary in forensic and archaeological applications. Four fragments of exon 6 and 7 of the ABO gene were amplified and digested by in total 7 restriction endonucleases. Particular attention was paid to the base changes at nucleotide positions 261(delG), 297, 526, 703, 721, 771, 796 and 1060(delC) in order to distinguish the six common alleles A101, A201, B, O01, O02 and O03. Furthermore, this method also enables determination of seven of the less frequent alleles: A104, A204, Ax02, Ax03, O05, O06 and O07. The method was applied successfully to a series of blood samples with known phenotypes and genotypes as well as DNA extracted from a thirty year old blood stain and an ancient tooth sample. However, working with ancient DNA requires additional cloning and sequencing of the RFLP-typing results due to DNA post mortem damages such as deaminations, which could lead to false typing results.}, }
@article {pmid15648845, year = {2004}, author = {Schilz, F and Hummel, S and Herrmann, B}, title = {Design of a multiplex PCR for genotyping 16 short tandem repeats in degraded DNA samples.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {62}, number = {4}, pages = {369-378}, pmid = {15648845}, issn = {0003-5548}, mesh = {Alleles ; Amelogenin ; Anthropology/methods ; Burial ; Chromosome Mapping ; Chromosomes, Human, X/genetics ; Chromosomes, Human, Y/genetics ; DNA Fingerprinting/methods ; Dental Enamel Proteins/*genetics ; Europe ; Genetic Markers/*genetics ; *Genotype ; History, Ancient ; Humans ; Paleopathology ; Polymerase Chain Reaction/*methods ; Reproducibility of Results ; Sex Determination Processes ; Tandem Repeat Sequences/*genetics ; }, abstract = {The molecular genotyping of individuals and reconstruction of kinship through short and high polymorphic DNA markers, so-called short tandem repeats (STR), has become an important and efficient method in anthropology and forensic science. The here introduced experimental design describes a multiplex PCR capable of simultaneously amplifying 16 STRs and the sex determinant locus amelogenin in a short fragment lengths range from 84 bp to 275 bp. Thus, the design depends predominantly on the routines for DNA typing of historical samples with highly degraded ancient DNA. It is shown, that the newly designed multiplex PCR is suitable for successful typing of both forensic and historical material.}, }
@article {pmid15633242, year = {2005}, author = {Zhang, Y and Xu, GH and Guo, XY and Fan, LJ}, title = {Two ancient rounds of polyploidy in rice genome.}, journal = {Journal of Zhejiang University. Science. B}, volume = {6}, number = {2}, pages = {87-90}, pmid = {15633242}, issn = {1673-1581}, mesh = {Biological Evolution ; Chromosome Mapping/*methods ; *Evolution, Molecular ; Genetic Variation/genetics ; *Genome, Plant ; Oryza/*genetics ; *Polyploidy ; }, abstract = {An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.}, }
@article {pmid15601889, year = {2005}, author = {Pineau, P and Henry, M and Suspène, R and Marchio, A and Dettai, A and Debruyne, R and Petit, T and Lécu, A and Moisson, P and Dejean, A and Wain-Hobson, S and Vartanian, JP}, title = {A universal primer set for PCR amplification of nuclear histone H4 genes from all animal species.}, journal = {Molecular biology and evolution}, volume = {22}, number = {3}, pages = {582-588}, doi = {10.1093/molbev/msi053}, pmid = {15601889}, issn = {0737-4038}, mesh = {Animals ; DNA Primers/*genetics ; Histones/*genetics ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {To control the quality of genomic DNA of samples from a wide variety of animals, a heminested PCR assay specifically targeting a nuclear gene has been developed. The histone H4 gene family comprises a small number of genes considered among the most conserved genes in living organisms. Tissue samples from necropsies and from cells belonging to 43 different species were studied, eight samples from invertebrates and 35 samples from vertebrates covering all classes. Ancient DNA samples from three Siberian woolly mammoths (Mammuthus primigenius) dating between 40,000 and 49,000 years before present were also tested for PCR amplification. Performance of HIST2H4 amplification were also compared with those of previously published universal PCRs (28S rRNA, 18S rRNA, and cytochrome b). Overall, 95% of species studied yielded an amplification product, including some old samples from gorilla and chimpanzees. The data indicate that the HIST2H4 amplimers are, thus, suitable for both DNA quality testing as well as species identification in the animal kingdom.}, }
@article {pmid15574820, year = {2004}, author = {Blanchette, M and Green, ED and Miller, W and Haussler, D}, title = {Reconstructing large regions of an ancestral mammalian genome in silico.}, journal = {Genome research}, volume = {14}, number = {12}, pages = {2412-2423}, pmid = {15574820}, issn = {1088-9051}, support = {P41 HG002371/HG/NHGRI NIH HHS/United States ; R01 HG002238/HG/NHGRI NIH HHS/United States ; 1P41HG02371/HG/NHGRI NIH HHS/United States ; HG-02238/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Computer Simulation ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; *Evolution, Molecular ; *Genetic Variation ; *Genome ; Likelihood Functions ; Mammals/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can expect to get 98% of the bases correct in reconstructing megabase-scale euchromatic regions of an eutherian ancestral genome from the genomes of approximately 20 optimally chosen modern mammals. Using actual genomic sequences from 19 extant mammals, we reconstruct 1.1 Mb of ancient genome sequence around the CFTR locus. Detailed examination suggests the reconstruction is accurate and that it allows us to identify features in modern species, such as remnants of ancient transposon insertions, that were not identified by direct analysis. Tracing the predicted evolutionary history of the bases in the reconstructed region, estimates are made of the amount of DNA turnover due to insertion, deletion, and substitution in the different placental mammalian lineages since the common eutherian ancestor, showing considerable variation between lineages. In coming years, such reconstructions may help in identifying and understanding the genetic features common to eutherian mammals and may shed light on the evolution of human or primate-specific traits.}, }
@article {pmid15570114, year = {2005}, author = {Capelli, C and Tschentscher, F}, title = {Protocols for ancient DNA typing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {297}, number = {}, pages = {265-278}, doi = {10.1385/1-59259-867-6:265}, pmid = {15570114}, issn = {1064-3745}, mesh = {Archaeology ; Cloning, Molecular ; DNA/classification/*genetics ; Fossils ; Humans ; Phylogeny ; Polymerase Chain Reaction/methods ; }, abstract = {Molecular analysis of fossil and archaeological remains has been established as a powerful tool in providing new insight in phylogenetic investigations. The overlapping set of molecular modifications and degradation that forensic samples share with archaeological specimen suggests the application of similar technical approaches to the respective biological material. Polymerase chain reaction is the molecular technique of choice for the retrieval of specimen deoxyribonucleic acid (DNA) molecules. Because of intrinsic sensitivity, potential contaminations from exogenous DNA sources must be monitored through the entire process by the introduction of multiple blank controls. Cloning and sequencing of polymerase chain reaction products often is the only way to discriminate between contaminations and endogenous sequences as well as to identify variable positions from nucleotide modifications/DNA polymerase errors. Phylogenetic analysis and investigations of the pattern of substitutions are an additional and necessary step to validate the retrieved sequence. Comparison with available related samples (modern or extinct) is critical to correctly validate the results and to avoid artifactual data.}, }
@article {pmid15570113, year = {2005}, author = {Keyser-Tracqui, C and Ludes, B}, title = {Methods for the study of ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {297}, number = {}, pages = {253-264}, doi = {10.1385/1-59259-867-6:253}, pmid = {15570113}, issn = {1064-3745}, mesh = {Archaeology ; DNA/*genetics/isolation &amp; purification ; *Forensic Medicine ; Fossils ; Genetic Markers ; Humans ; Polymerase Chain Reaction ; }, abstract = {Whereas the analysis of ancient DNA (aDNA) has become an increasingly popular mode of investigation in both archaeological and evolutionary studies, this approach is complicated by the degraded nature of ancient nucleic acids, the presence of enzymatic inhibitors in aDNA extracts, as well as the risk of contamination during either excavation or manipulation of samples. Despite these difficulties, numerous methods have been developed to optimize the recovery, study, and authentication of aDNA. In this article, we describe the procedures used in our laboratory to extract and amplify informative DNA segments from prehistoric or protohistoric human samples, as well as the precautions and strategies implemented to avoid or at least detect contaminations.}, }
@article {pmid15570098, year = {2005}, author = {Alonso, A and Martín, P}, title = {A real-time PCR protocol to determine the number of amelogenin (X-Y) gene copies from forensic DNA samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {297}, number = {}, pages = {31-44}, doi = {10.1385/1-59259-867-6:031}, pmid = {15570098}, issn = {1064-3745}, mesh = {Amelogenin ; Base Sequence ; DNA Primers ; Dental Enamel Proteins/*genetics ; Female ; *Forensic Medicine ; Humans ; Polymerase Chain Reaction/*methods ; }, abstract = {We present a fluorogenic real-time polymerase chain reaction (PCR) procedure to target a segment (106-112 base pairs [bp]) of the X-Y homologous amelogenin gene by measuring the 5' nuclease activity of the Taq deoxyribonucleic acid (DNA) polymerase using two (X-Fam-labeled and Y-Vic-labeled) specific Taqman MGB probes to enable simultaneous the detection of two specific PCR products (AMGY: 112-bp and AMGX: 106 bp) as they accumulate cycle by cycle during PCR. The method makes possible not only human nuclear DNA quantitation but also sex determination and has been applied to the analysis of low copy number DNA samples in forensic and ancient DNA studies. Specific quantification of human nuclear DNA is a recommended procedure in forensic casework as a way to adjust the DNA input on subsequent end-point PCR-based DNA typing approaches ensuring the optimal use of the limited amounts of nuclear DNA found in many forensic evidences. Nuclear DNA quantification also aids in the interpretation of the consistency of multiplex STR profiling data obtained from low copy number DNA samples.}, }
@article {pmid15568989, year = {2004}, author = {Pääbo, S and Poinar, H and Serre, D and Jaenicke-Despres, V and Hebler, J and Rohland, N and Kuch, M and Krause, J and Vigilant, L and Hofreiter, M}, title = {Genetic analyses from ancient DNA.}, journal = {Annual review of genetics}, volume = {38}, number = {}, pages = {645-679}, doi = {10.1146/annurev.genet.37.110801.143214}, pmid = {15568989}, issn = {0066-4197}, mesh = {Animals ; Animals, Domestic ; *Archaeology ; Behavior ; Cloning, Molecular ; DNA/*genetics/metabolism ; DNA Damage ; DNA, Mitochondrial/genetics ; Deamination ; Diet ; *Fossils ; Geologic Sediments ; Hominidae/genetics ; Humans ; Mummies ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.}, }
@article {pmid15567864, year = {2004}, author = {Shapiro, B and Drummond, AJ and Rambaut, A and Wilson, MC and Matheus, PE and Sher, AV and Pybus, OG and Gilbert, MT and Barnes, I and Binladen, J and Willerslev, E and Hansen, AJ and Baryshnikov, GF and Burns, JA and Davydov, S and Driver, JC and Froese, DG and Harington, CR and Keddie, G and Kosintsev, P and Kunz, ML and Martin, LD and Stephenson, RO and Storer, J and Tedford, R and Zimov, S and Cooper, A}, title = {Rise and fall of the Beringian steppe bison.}, journal = {Science (New York, N.Y.)}, volume = {306}, number = {5701}, pages = {1561-1565}, doi = {10.1126/science.1101074}, pmid = {15567864}, issn = {1095-9203}, mesh = {Alaska ; Animals ; Bayes Theorem ; *Bison/classification/genetics ; Canada ; China ; *Climate ; DNA, Mitochondrial/genetics ; Environment ; *Fossils ; Genetic Variation ; Genetics, Population ; Human Activities ; Humans ; North America ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Time ; }, abstract = {The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later.}, }
@article {pmid15564305, year = {2005}, author = {Anderson, CN and Ramakrishnan, U and Chan, YL and Hadly, EA}, title = {Serial SimCoal: a population genetics model for data from multiple populations and points in time.}, journal = {Bioinformatics (Oxford, England)}, volume = {21}, number = {8}, pages = {1733-1734}, doi = {10.1093/bioinformatics/bti154}, pmid = {15564305}, issn = {1367-4803}, mesh = {*Biological Evolution ; Chromosome Mapping/*methods ; Computer Graphics ; Computer Simulation ; DNA Mutational Analysis/*methods ; Genetic Variation/genetics ; *Genetics, Population ; *Models, Genetic ; Models, Statistical ; Sample Size ; Sequence Analysis, DNA/*methods ; *Software ; *User-Computer Interface ; }, abstract = {UNLABELLED: We present Serial SimCoal, a program that models population genetic data from multiple time points, as with ancient DNA data. An extension of SIMCOAL, it also allows simultaneous modeling of complex demographic histories, and migration between multiple populations. Further, we incorporate a statistical package to calculate relevant summary statistics, which, for the first time allows users to investigate the statistical power provided by, conduct hypothesis-testing with, and explore sample size limitations of ancient DNA data.<br><br>AVAILABILITY: Source code and Windows/Mac executables at http://www.stanford.edu/group/hadlylab/ssc.html<br><br>CONTACT: senka@stanford.edu.}, }
@article {pmid15539371, year = {2004}, author = {van Tuinen, M and Ramakrishnan, U and Hadly, EA}, title = {Studying the effect of environmental change on biotic evolution: past genetic contributions, current work and future directions.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {362}, number = {1825}, pages = {2795-2820}, doi = {10.1098/rsta.2004.1465}, pmid = {15539371}, issn = {1364-503X}, mesh = {Animals ; DNA/analysis/*genetics ; *Environment ; *Evolution, Molecular ; Gene Expression Profiling/*methods/trends ; Gene Expression Regulation/*genetics ; Genetic Variation/genetics ; Genetics, Population/*methods/trends ; Humans ; Models, Genetic ; Paleontology/*methods/trends ; Phylogeny ; }, abstract = {Evolutionary geneticists currently face a major scientific opportunity when integrating across the rapidly increasing amount of genetic data and existing biological scenarios based on ecology, fossils or climate models. Although genetic data acquisition and analysis have improved tremendously, several limitations remain. Here, we discuss the feedback between history and genetic variation in the face of environmental change with increasing taxonomic and temporal scale, as well as the major challenges that lie ahead. In particular, we focus on recent developments in two promising genetic methods, those of 'phylochronology' and 'molecular clocks'. With the advent of ancient DNA techniques, we can now directly sample the recent past. We illustrate this amazing and largely untapped utility of ancient DNA extracted from accurately dated localities with documented environmental changes. Innovative statistical analyses of these genetic data expose the direct effect of recent environmental change on genetic endurance, or maintenance of genetic variation. The 'molecular clock' (assumption of a linear relationship between genetic distance and evolutionary time) has been used extensively in phylogenetic studies to infer time and correlation between lineage divergence time and concurrent environmental change. Several studies at both population and species scale support a persuasive relationship between particular perturbation events and time of biotic divergence. However, we are still a way from gleaning an overall pattern to this relationship, which is a prerequisite to ultimately understanding the mechanisms by which past environments have shaped the evolutionary trajectory. Current obstacles include as-yet undecided reasons behind the frequent discrepancy between molecular and fossil time estimates, and the frequent lack of consideration of extensive confidence intervals around time estimates. We suggest that use and interpretation of both ancient DNA and molecular clocks is most effective when results are synthesized with palaeontological (fossil) and ecological (life history) information.}, }
@article {pmid15527985, year = {2004}, author = {Zhang, P and Min, W and Li, WH}, title = {Different age distribution patterns of human, nematode, and Arabidopsis duplicate genes.}, journal = {Gene}, volume = {342}, number = {2}, pages = {263-268}, doi = {10.1016/j.gene.2004.08.001}, pmid = {15527985}, issn = {0378-1119}, mesh = {Algorithms ; Animals ; Arabidopsis/*genetics ; Caenorhabditis elegans/*genetics ; Databases, Nucleic Acid ; Drosophila melanogaster/genetics ; Genes, Duplicate/*genetics ; Genetic Variation ; Genome ; Humans ; Models, Genetic ; Time Factors ; }, abstract = {We studied the age distribution of duplicate genes in each of four eukaryotic genomes: human, Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster. The four distributions differ greatly from each other, contrary to the previous proposal of a universal L-shaped distribution in all eukaryotic genomes studied. Indeed, only the distribution in humans is L-shaped. The distribution in Arabidopsis is consistent with the hypothesis of an ancient genome duplication with no recent burst of duplication events, while the distribution in C. elegans is nearly uniform. We also applied a nonparametric method to the human distribution to show that the rate of loss of duplicate genes decreases over time, contrary to the proposal of an exponential decay. One possible explanation of the decreasing rate of loss of duplicate genes over time could be rapid functional divergence between duplicate genes, providing an advantage for the retention of both duplicates.}, }
@article {pmid15510166, year = {2004}, author = {Van de Peer, Y}, title = {Computational approaches to unveiling ancient genome duplications.}, journal = {Nature reviews. Genetics}, volume = {5}, number = {10}, pages = {752-763}, doi = {10.1038/nrg1449}, pmid = {15510166}, issn = {1471-0056}, mesh = {Computational Biology/*methods ; *Evolution, Molecular ; *Gene Duplication ; *Genome ; Multigene Family/genetics ; Phylogeny ; Species Specificity ; }, abstract = {Recent analyses of complete genome sequences have revealed that many genomes have been duplicated in their evolutionary past. Such events have been associated with important biological transitions, major leaps in evolution and adaptive radiations of species. Here, we consider recently developed computational methods to detect such ancient large-scale gene duplication events. Several new approaches have been used to show that large-scale gene duplications are more common than previously thought.}, }
@article {pmid15476930, year = {2004}, author = {Chang, CL and Roh, J and Hsu, SY}, title = {Intermedin, a novel calcitonin family peptide that exists in teleosts as well as in mammals: a comparison with other calcitonin/intermedin family peptides in vertebrates.}, journal = {Peptides}, volume = {25}, number = {10}, pages = {1633-1642}, doi = {10.1016/j.peptides.2004.05.021}, pmid = {15476930}, issn = {0196-9781}, mesh = {Adrenomedullin ; Amino Acid Sequence ; Amyloid/physiology ; Animals ; Calcitonin/*physiology ; Calcitonin Gene-Related Peptide/physiology ; Conserved Sequence ; Evolution, Molecular ; Fishes ; Humans ; Islet Amyloid Polypeptide ; Mammals ; Molecular Sequence Data ; Peptide Hormones/*physiology ; Peptides/physiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Vertebrates ; }, abstract = {Endocrine regulation in vertebrates is critical for the adaptation and regulation of homeostasis. The G protein-coupled receptor (GPCR) signaling transduction system represents one of the most ancient forms of cell surface signaling. Recently, comparative sequence analysis has aided in the identification and pairing of a variety of ligand/GPCR signaling systems. Among the ligands of type II GPCRs, the calcitonin family peptides including calcitonin, alpha-calcitonin gene-related peptide (alphaCGRP), betaCGRP, adrenomedullin, and amylin are among the best studied hormones, and the founding member, calcitonin, was originally identified and isolated from teleosts. This unique group of peptides shares a conserved tertiary structure with an N-terminal disulfide-bridged ring. In mammals, these peptides signal through two closely related type II GPCRs and three unique receptor activity-modifying proteins. Recently, based on the analysis of multiple vertebrate genomes, we identified a novel calcitonin/CGRP family peptide named intermedin. Here we show that in humans the five paralogous family genes, calcitonin, CGRP, amylin, adrenomedullin, and intermedin, evolved before the emergence of modern vertebrates, and that teleost genomes carry multiple copies of these co-evolved hormone genes. Sequence comparison showed that each of these genes is highly conserved in different vertebrates and that multiple copies of these peptides in teleosts could be derived from ancient genome duplication and/or lineage-specific intragenic duplications. The present article provides an overview of the calcitonin/intermedin family peptides found in teleost and mammalian genomes, and describes their putative functions. In addition, we demonstrate that one of the intermedin orthologs deduced from the pufferfish (Fugu rubripes) genome shares a conserved signaling activity with mammalian intermedin. The combined results indicate that the physiology associated with each of these family peptides likely evolved during early vertebrate evolution and diverged to serve select physiological functions in different vertebrates.}, }
@article {pmid15468050, year = {2004}, author = {Di Bernardo, G and Del Gaudio, S and Galderisi, U and Cipollaro, M}, title = {2000 Year-old ancient equids: an ancient-DNA lesson from pompeii remains.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {302}, number = {6}, pages = {550-556}, doi = {10.1002/jez.b.21017}, pmid = {15468050}, issn = {1552-5007}, mesh = {Animals ; Base Sequence ; Bone and Bones/*anatomy &amp; histology ; DNA/*isolation &amp; purification ; DNA Primers ; DNA, Mitochondrial/genetics ; *Fossils ; Horses/anatomy &amp; histology/*genetics ; Italy ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Ancient DNA extracted from 2000 year-old equine bones was examined in order to amplify mitochondrial and nuclear DNA fragments. A specific equine satellite-type sequence representing 3.7%-11% of the entire equine genome, proved to be a suitable target to address the question of the presence of aDNA in ancient bones. The PCR strategy designed to investigate this specific target also allowed us to calculate the molecular weight of amplifiable DNA fragments. Sequencing of a 370 bp DNA fragment of mitochondrial control region allowed the comparison of ancient DNA sequences with those of modern horses to assess their genetic relationship. The 16S rRNA mitochondrial gene was also examined to unravel the post-mortem base modification feature and to test the status of Pompeian equids taxon on the basis of a Mae III restriction site polymorphism.}, }
@article {pmid15459281, year = {2004}, author = {Miner, BE and Stöger, RJ and Burden, AF and Laird, CD and Hansen, RS}, title = {Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR.}, journal = {Nucleic acids research}, volume = {32}, number = {17}, pages = {e135}, pmid = {15459281}, issn = {1362-4962}, support = {R01 GM053805/GM/NIGMS NIH HHS/United States ; P30 HD002274/HD/NICHD NIH HHS/United States ; HD 02274/HD/NICHD NIH HHS/United States ; R01 HD016659/HD/NICHD NIH HHS/United States ; HD 16659/HD/NICHD NIH HHS/United States ; GM 53805/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Fragile X Mental Retardation Protein ; Genome, Human ; Humans ; Male ; Molecular Sequence Data ; Nerve Tissue Proteins/genetics ; Polymerase Chain Reaction/*methods ; Promoter Regions, Genetic ; RNA-Binding Proteins/genetics ; Sequence Analysis, DNA/*methods ; Sulfites/*chemistry ; Templates, Genetic ; }, abstract = {PCR amplification of limited amounts of DNA template carries an increased risk of product redundancy and contamination. We use molecular barcoding to label each genomic DNA template with an individual sequence tag prior to PCR amplification. In addition, we include molecular 'batch-stamps' that effectively label each genomic template with a sample ID and analysis date. This highly sensitive method identifies redundant and contaminant sequences and serves as a reliable method for positive identification of desired sequences; we can therefore capture accurately the genomic template diversity in the sample analyzed. Although our application described here involves the use of hairpin-bisulfite PCR for amplification of double-stranded DNA, the method can readily be adapted to single-strand PCR. Useful applications will include analyses of limited template DNA for biomedical, ancient DNA and forensic purposes.}, }
@article {pmid15456130, year = {2004}, author = {Aĭtkhozhina, NA and Dzisiuk, NV and Liudvikova, EK}, title = {[Polymorphism of mitochondrial genome noncoding regions in the three Kazakh populations inhabited different areas of Kazakhstan and in the samples of DNA from ancient people of Kazakhstan Altai].}, journal = {Molekuliarnaia biologiia}, volume = {38}, number = {4}, pages = {592-601}, pmid = {15456130}, issn = {0026-8984}, mesh = {Base Sequence ; DNA Primers ; DNA, Mitochondrial/*genetics ; *Genetics, Population ; *Genome, Human ; Humans ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Russia ; }, abstract = {Polymorphism of major noncoding region of mitochondrial DNA (mtDNA D-loop, 528 bp in length) from the three modem kazakh populations and from DNA samples of ancient people inhabited modern Kazakhstani Altai were studied. PCR and RFLP analysis of 13 sites of restriction--BamHI, EcoRV, Sau3AI (1 restriction site), KpnI (2 sites), HaeIII (3 sites), RsaI (5 restriction sites), were carried out. The distribution of each site frequencies was determined. Nucleotide diversity (h) and genetic distance between different kazakh population and other populations of world were estimated. The same RFLP analysis of the mitochondrial DNA control region was carried out for the paleogenomic samples. It was shown that two samples of ancient mitochondrial DNA were monomorphous throughout all analyzed restriction sites.}, }
@article {pmid15389521, year = {2005}, author = {Cipollaro, M and Galderisi, U and Di Bernardo, G}, title = {Ancient DNA as a multidisciplinary experience.}, journal = {Journal of cellular physiology}, volume = {202}, number = {2}, pages = {315-322}, doi = {10.1002/jcp.20116}, pmid = {15389521}, issn = {0021-9541}, mesh = {Animals ; Archaeology ; *DNA/isolation &amp; purification ; DNA Damage ; DNA Repair ; DNA, Mitochondrial/genetics ; *Fossils ; Gene Amplification ; *Genetics ; Humans ; *Interdisciplinary Communication ; *Molecular Biology ; Phylogeny ; Science ; }, abstract = {Investigation into DNA from archeological remains offers an inestimable tool for unraveling the history of humankind. However, a series of basic and technical difficulties renders the analysis of ancient DNA (aDNA) molecules troublesome, depending either on their own peculiar characteristics or on the complexity of processes affecting the bone matrix over time, all compromising the preservation of ancient DNA. This review underlines the contribution of many different disciplines, in particular molecular biology and genetics, to overcome these obstacles. The role of each expertise is illustrated to appropriately address the questions arising in aDNA investigations.}, }
@article {pmid15363896, year = {2004}, author = {Seoighe, C and Gehring, C}, title = {Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome.}, journal = {Trends in genetics : TIG}, volume = {20}, number = {10}, pages = {461-464}, doi = {10.1016/j.tig.2004.07.008}, pmid = {15363896}, issn = {0168-9525}, mesh = {Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics ; *Evolution, Molecular ; *Gene Duplication ; Gene Order ; Genes, Duplicate/*genetics ; *Genome, Plant ; Proteome/*genetics ; }, abstract = {Multiple ancient genome duplications in Arabidopsis thaliana provide unique opportunities to assess factors that influence the fates of duplicated genes. We have found that genes retained in duplicate following one round of genome duplication are significantly more likely to be retained in duplicate again after a subsequent genome duplication. Genes retained in duplicate form a functionally biased set and include a significant over-representation of genes involved in the regulation of transcription.}, }
@article {pmid21238085, year = {1997}, author = {Austin, JJ and Smith, AB and Thomas, RH}, title = {Palaeontology in a molecular world: the search for authentic ancient DNA.}, journal = {Trends in ecology &amp; evolution}, volume = {12}, number = {8}, pages = {303-306}, doi = {10.1016/S0169-5347(97)01102-6}, pmid = {21238085}, issn = {0169-5347}, abstract = {The survival of ancient DNA in specimens up to several thousands of years old is established. However, there have been several claims concerning the recovery of geologically ancient DNA from fossil material many millions of years old. The authenticity of these fossil DNA sequences is questionable on theoretical and empirical grounds, and the existence of authentic geologically ancient DNA remains to be proven.}, }
@article {pmid21236781, year = {1994}, author = {Lister, AM}, title = {Ancient DNA: not quite Jurassic Park.}, journal = {Trends in ecology &amp; evolution}, volume = {9}, number = {3}, pages = {82-84}, doi = {10.1016/0169-5347(94)90199-6}, pmid = {21236781}, issn = {0169-5347}, }
@article {pmid24173437, year = {1972}, author = {Holmquist, R}, title = {Theoretical foundations for a quantitative approach to paleogenetics : Part II: Proteins.}, journal = {Journal of molecular evolution}, volume = {1}, number = {2}, pages = {134-149}, pmid = {24173437}, issn = {0022-2844}, abstract = {It is shown that simply counting the number of amino acid differences between two homologous present day proteins may underestimate the number of mutagenic events that have occurred by more than a factor of three. In a previous paper (Part I) it was shown how to correct quantitatively for multiple mutagenic events at the same base site and for back mutation at that site. In this paper formulas are derived to correct for multiple mutagenic events within the same codon triplet and for the degeneracy of the genetic code. These formulas are related to the often used concept of minimum mutation distance, and it is demonstrated that the latter underestimates the number of 3-base changes (per codon) by more than an order of magnitude. The formulas developed in this paper are shown to be capable of detectinga priori, and with statistical significance, the nonrandomness that is known from experiment to exist in theA fibrinopeptides of ox, reindeer, sheep, and goat; the formulas also show, with statistical significance, that the assumption of a single ancestral DNA does not suffice to explain the known number of amino acid differences which occur between pairs of these fibrinopeptides.More explicitly, the following problems are solved: 1. Consider a protein ofT amino acids which is coded by a polynucleotide ofL = 3 T individual nucleotide bases. Let exactlyX mutagenic events occur randomly along the length of this polynucleotide. After theX mutagenic events have occurred, a numberA, less than or equal toT, amino acid sites will differ from the corresponding sites in the ancestral protein. An explicit formula forN(A), the average number of amino acid substitutions that have occurred, is derived. 2. Because of chance identities, the number of amino acid differencesN(d) between two homologous present day proteins will be less thanN 1 (A) plusN 2 (A), where the subscripts refer to each homologue; a formula forN(d) is derived. 3. The limits of validity of the commonly used approximationN(A)=1/2N(d) are derived. 4. Formulas are given which permit the estimation of the proportion of amino acid substitutions which have occurred by one base, two base, and three base changes.}, }
@article {pmid15361933, year = {2004}, author = {Hadly, EA and Ramakrishnan, U and Chan, YL and van Tuinen, M and O'Keefe, K and Spaeth, PA and Conroy, CJ}, title = {Genetic response to climatic change: insights from ancient DNA and phylochronology.}, journal = {PLoS biology}, volume = {2}, number = {10}, pages = {e290}, pmid = {15361933}, issn = {1545-7885}, mesh = {Animals ; Arvicolinae ; Biological Evolution ; Climate ; DNA/chemistry/*genetics ; Ecology ; Environment ; Fossils ; Genetic Variation ; Genetics, Population ; Geography ; Greenhouse Effect ; Haplotypes ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Population Density ; Time Factors ; }, abstract = {Understanding how climatic change impacts biological diversity is critical to conservation. Yet despite demonstrated effects of climatic perturbation on geographic ranges and population persistence, surprisingly little is known of the genetic response of species. Even less is known over ecologically long time scales pertinent to understanding the interplay between microevolution and environmental change. Here, we present a study of population variation by directly tracking genetic change and population size in two geographically widespread mammal species (Microtus montanus and Thomomys talpoides) during late-Holocene climatic change. We use ancient DNA to compare two independent estimates of population size (ecological and genetic) and corroborate our results with gene diversity and serial coalescent simulations. Our data and analyses indicate that, with population size decreasing at times of climatic change, some species will exhibit declining gene diversity as expected from simple population genetic models, whereas others will not. While our results could be consistent with selection, independent lines of evidence implicate differences in gene flow, which depends on the life history strategy of species.}, }
@article {pmid15356622, year = {2004}, author = {Rivera, MC and Lake, JA}, title = {The ring of life provides evidence for a genome fusion origin of eukaryotes.}, journal = {Nature}, volume = {431}, number = {7005}, pages = {152-155}, doi = {10.1038/nature02848}, pmid = {15356622}, issn = {1476-4687}, mesh = {Bacteria/genetics ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome ; *Genomics/methods ; *Models, Genetic ; Organelles/genetics ; Photosynthesis ; *Phylogeny ; Prokaryotic Cells/metabolism ; Recombination, Genetic/*genetics ; Saccharomyces cerevisiae/genetics ; Schizosaccharomyces/genetics ; }, abstract = {Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteria.}, }
@article {pmid15336226, year = {2004}, author = {Donoghue, HD and Spigelman, M and Greenblatt, CL and Lev-Maor, G and Bar-Gal, GK and Matheson, C and Vernon, K and Nerlich, AG and Zink, AR}, title = {Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA.}, journal = {The Lancet. Infectious diseases}, volume = {4}, number = {9}, pages = {584-592}, doi = {10.1016/S1473-3099(04)01133-8}, pmid = {15336226}, issn = {1473-3099}, mesh = {Animals ; Biological Evolution ; Communicable Diseases/history/microbiology ; DNA, Bacterial/analysis/*history ; History, Ancient ; Humans ; Mummies ; Mycobacterium tuberculosis/*genetics ; Paleopathology ; Tuberculosis/*history/microbiology ; }, abstract = {During the past 10 years palaeomicrobiology, a new scientific discipline, has developed. The study of ancient pathogens by direct detection of their DNA has answered several historical questions and shown changes to pathogens over time. However, ancient DNA (aDNA) continues to be controversial and great care is needed to provide valid data. Here we review the most successful application of the technology, which is the study of tuberculosis. This has provided direct support for the current theory of Mycobacterium tuberculosis evolution, and suggests areas of investigation for the interaction of M tuberculosis with its host.}, }
@article {pmid15276848, year = {2004}, author = {Chang, MS and Benner, SA}, title = {Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments.}, journal = {Journal of molecular biology}, volume = {341}, number = {2}, pages = {617-631}, doi = {10.1016/j.jmb.2004.05.045}, pmid = {15276848}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Amino Acids/chemistry ; Animals ; *Databases, Protein ; *Genetic Variation ; Humans ; Models, Genetic ; Molecular Sequence Data ; Proteins/*chemistry/genetics ; Sequence Alignment/*methods ; *Sequence Deletion ; }, abstract = {To understand how protein segments are inserted and deleted during divergent evolution, a set of pairwise alignments contained exactly one gap, and therefore arising from the first insertion-deletion (indel) event in the time separating the homologs, was examined. The alignments showed that "structure breaking" amino acids (PGDNS) were preferred within and flanking gapped regions, as are two residues with hydrophilic side-chains (QE) that frequently occur at the surface of protein folds. Conversely, hydrophobic residues (FMILYVW) occur infrequently within and flanking the gapped region. These preferences are modestly different in protein pairs separated by an episode of adaptive evolution, than in pairs diverging under strong functional constraints. Surprisingly, regions near an indel have not evolved more rapidly than the sequence pair overall, showing no evidence that an indel event must be compensated by local amino acid replacement. The gap-lengths are best approximated by a Zipfian distribution, with the probability of a gap of length L decreasing as a function of L(-1.8). These features are largely independent of the length of the gap and the extent of divergence (measured by both silent and non-silent sequence changes) separating the two proteins. Surprisingly, amino acid repeats were discovered in more than a third of the polypeptide segments in and around the gap. These correspond to repeats in the DNA sequence. This suggests that a signature of the mechanism by which indels occur in the DNA sequence remains in the encoded protein sequences. These data suggest specific tools to score gap placement in an alignment. They also suggest tools that distinguish true indels from gaps created by mistaken gene finding, including under-predicted and over-predicted introns. By providing mechanisms to identify errors, the tools will enhance the value of genome sequence databases in support of integrated paleogenomics strategies used to extract functional information in a post-genomic environment.}, }
@article {pmid15261647, year = {2004}, author = {Zhang, Z and Gerstein, M}, title = {Large-scale analysis of pseudogenes in the human genome.}, journal = {Current opinion in genetics &amp; development}, volume = {14}, number = {4}, pages = {328-335}, doi = {10.1016/j.gde.2004.06.003}, pmid = {15261647}, issn = {0959-437X}, support = {NP50 HG02357-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; Gene Expression ; *Genome, Human ; Humans ; Molecular Sequence Data ; Pseudogenes/*genetics ; Retroelements/genetics ; }, abstract = {Pseudogenes are considered as genomic fossils: disabled copies of functional genes that were once active in the ancient genome. Recently, whole-genome computational approaches have revealed thousands of pseudogenes in the genomes of the human and other eukaryotes. Identification of these pseudogenes can improve the accuracy of gene annotation. It also offers new insight on the evolutionary history and the stability of the genome as a whole.}, }
@article {pmid15256564, year = {2004}, author = {Veiga-Crespo, P and Poza, M and Prieto-Alcedo, M and Villa, TG}, title = {Ancient genes of Saccharomyces cerevisiae.}, journal = {Microbiology (Reading, England)}, volume = {150}, number = {Pt 7}, pages = {2221-2227}, doi = {10.1099/mic.0.27000-0}, pmid = {15256564}, issn = {1350-0872}, mesh = {Amber ; Animals ; Base Sequence ; Conserved Sequence ; DNA, Fungal/analysis/isolation &amp; purification ; Evolution, Molecular ; *Fossils ; *Fungal Proteins ; *Genes, Fungal ; Insecta/*microbiology ; Membrane Transport Proteins/chemistry/genetics ; Mitochondrial Proton-Translocating ATPases/chemistry/genetics ; Molecular Sequence Data ; RNA, Ribosomal, 18S/chemistry/genetics ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/chemistry/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Amber is a plant resin mainly produced by coniferous trees that, after entrapping a variety of living beings, was subjected to a process of fossilization until it turned into yellowish, translucent stones. It is also one of the best sources of ancient DNA on which to perform studies on evolution. Here a method for the sterilization of amber that allows reliable ancient DNA extraction with no actual DNA contamination is described. Working with insects taken from amber, it was possible to amplify the ATP9, PGU1 and rRNA18S ancient genes of Saccharomyces cerevisiae corresponding to samples from the Miocene and Oligocene. After comparison of the current genes with their ancient (up to 35-40 million years) counterparts it was concluded that essential genes such as rRNA18S are highly conserved and that even normal 'house-keeping' genes, such as PGU1, are strikingly conserved along the millions of years that S. cerevisiae has evolved.}, }
@article {pmid15255049, year = {2004}, author = {Lalueza-Fox, C and Sampietro, ML and Gilbert, MT and Castri, L and Facchini, F and Pettener, D and Bertranpetit, J}, title = {Unravelling migrations in the steppe: mitochondrial DNA sequences from ancient central Asians.}, journal = {Proceedings. Biological sciences}, volume = {271}, number = {1542}, pages = {941-947}, pmid = {15255049}, issn = {0962-8452}, mesh = {DNA Primers ; DNA, Mitochondrial/*genetics ; Emigration and Immigration/*history ; *Fossils ; Geography ; Haplotypes/genetics ; *History, Ancient ; Humans ; Kazakhstan ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide/genetics ; Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {This study helps to clarify the debate on the Western and Eastern genetic influences in Central Asia. Thirty-six skeletal remains from Kazakhstan (Central Asia), excavated from different sites dating between the fifteenth century BC to the fifth century AD, have been analysed for the hypervariable control region (HVR-I) and haplogroup diagnostic single nucleotide polymorphisms (SNPs) of the mitochondrial DNA genome. Standard authentication criteria for ancient DNA studies, including multiple extractions, cloning of PCR products and independent replication, have been followed. The distribution of east and west Eurasian lineages through time in the region is concordant with the available archaeological information: prior to the thirteenth-seventh century BC, all Kazakh samples belong to European lineages; while later an arrival of east Eurasian sequences that coexisted with the previous west Eurasian genetic substratum can be detected. The presence of an ancient genetic substratum of European origin in West Asia may be related to the discovery of ancient mummies with European features in Xinjiang and to the existence of an extinct Indo-European language, Tocharian. This study demonstrates the usefulness of the ancient DNA in unravelling complex patterns of past human migrations so as to help decipher the origin of present-day admixed populations.}, }
@article {pmid15254256, year = {2004}, author = {Pusch, CM and Broghammer, M and Nicholson, GJ and Nerlich, AG and Zink, A and Kennerknecht, I and Bachmann, L and Blin, N}, title = {PCR-induced sequence alterations hamper the typing of prehistoric bone samples for diagnostic achondroplasia mutations.}, journal = {Molecular biology and evolution}, volume = {21}, number = {11}, pages = {2005-2011}, doi = {10.1093/molbev/msh208}, pmid = {15254256}, issn = {0737-4038}, mesh = {Achondroplasia/*genetics ; Biological Evolution ; Cloning, Molecular ; DNA/metabolism ; DNA Glycosylases ; DNA, Complementary/metabolism ; DNA, Mitochondrial/genetics ; Egypt ; *Evolution, Molecular ; Germany ; Humans ; Mummies ; *Mutation ; Paleopathology/*methods ; Phenotype ; Point Mutation ; Polymerase Chain Reaction/*methods ; Protein-Tyrosine Kinases/genetics ; Receptor, Fibroblast Growth Factor, Type 3 ; Receptors, Fibroblast Growth Factor/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; Specimen Handling ; Uracil-DNA Glycosidase ; }, abstract = {Achondroplasia (ACH) is a skeletal disorder (MIM100800) with an autosomal dominant Mendelian inheritance and complete penetrance. Here we report the screening of ancient bone samples for diagnostic ACH mutations. The diagnostic G-->A transition in the FGFR3 gene at cDNA position 1138 was detected in cloned polymerase chain reaction (PCR) products obtained from the dry mummy of the Semerchet tomb, Egypt (first dynasty, approximately 4,890-5,050 BP [before present]), and from an individual from Kirchheim, Germany (Merovingian period, approximately 1,300-1,500 BP), both of which had short stature. However, these mutations were also reproducibly observed in four ancient control samples from phenotypically healthy individuals (false-positives), rendering the reliable molecular typing of ancient bones for ACH impossible. The treatment of a false-positive DNA extract with uracil N-glycosylase (UNG) to minimize type 2 transitions (G-->A/C-->T) did not reduce the frequency of the false-positive diagnostic ACH mutations. Recently, it was suggested that ancient DNA extracts may induce mutations under PCR. Contemporary human template DNA from a phenotypically healthy individual was therefore spiked with an ancient DNA extract from a cave bear. Again, sequences with the diagnostic G-->A transition in the FGFR3 gene were observed, and it is likely that the false-positive G-->A transitions result from errors introduced during the PCR reaction. Amplifications in the presence of MnCl(2) indicate that position 1138 of the FGFR3 gene is particularly sensitive for mutations. Our data are in line with previously published results on the occurrence of nonrandom mutations in PCR products of contemporary human mitochondrial HVRI template DNA spiked with ancient DNA extracts.}, }
@article {pmid15250473, year = {2004}, author = {Terra, MA and Bello, AR and Bastos, OM and Amendoeira, MR and Coelho, JM and Ferreira, LF and Araújo, A}, title = {Detection of Toxoplasma gondii DNA by polymerase chain reaction in experimentally desiccated tissues.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {99}, number = {2}, pages = {185-188}, doi = {10.1590/s0074-02762004000200012}, pmid = {15250473}, issn = {0074-0276}, mesh = {Animals ; DNA, Protozoan/analysis/*isolation &amp; purification ; *Dissection ; Female ; Immunoenzyme Techniques ; Mice ; Mice, Inbred C57BL ; Polymerase Chain Reaction/*methods ; Toxoplasma/genetics/*isolation &amp; purification ; }, abstract = {Despite toxoplasmosis being a common infection among human and other warm-blooded animals worldwide, there are no findings about Toxoplasma gondii evolutionary forms in ancient populations. The molecular techniques used for amplification of genetic material have allowed recovery of ancient DNA (aDNA) from parasites contained in mummified tissues. The application of polymerase chain reaction (PCR) to paleoparasitological toxoplasmosis research becomes a promising option, since it might allow diagnosis, acquisition of paleoepidemiological data, access to toxoplasmosis information related origin, evolution, and distribution among the ancient populations. Furthermore, it makes possible the analysis of parasite aDNA aiming at phylogenetic studies. To standardize and evaluate PCR applicability to toxoplasmosis paleodiagnostic, an experimental mummification protocol was tested using desiccated tissues from mice infected with the ME49 strain cysts, the chronic infection group (CIG), or infected with tachyzoites (RH strain), the acute infection group (AIG). Tissues were subjected to DNA extraction followed by PCR amplification of T. gondii B1 gene. PCR recovered T. gondii DNA in thigh muscle, encephalon, heart, and lung samples. AIG presented PCR positivity in encephalon, lungs, hearts, and livers. Based on this results, we propose this molecular approach for toxoplasmosis research in past populations.}, }
@article {pmid15199524, year = {2004}, author = {Spencer, M and Howe, CJ}, title = {Authenticity of ancient-DNA results: a statistical approach.}, journal = {American journal of human genetics}, volume = {75}, number = {2}, pages = {240-250}, pmid = {15199524}, issn = {0002-9297}, mesh = {*Data Interpretation, Statistical ; Humans ; Likelihood Functions ; *Sequence Analysis, DNA ; Time Factors ; }, abstract = {Although there have been several papers recommending appropriate experimental designs for ancient-DNA studies, there have been few attempts at statistical analysis. We assume that we cannot decide whether a result is authentic simply by examining the sequence (e.g., when working with humans and domestic animals). We use a maximum-likelihood approach to estimate the probability that a positive result from a sample is (either partly or entirely) an amplification of DNA that was present in the sample before the experiment began. Our method is useful in two situations. First, we can decide in advance how many samples will be needed to achieve a given level of confidence. For example, to be almost certain (95% confidence interval 0.96-1.00, maximum-likelihood estimate 1.00) that a positive result comes, at least in part, from DNA present before the experiment began, we need to analyze at least five samples and controls, even if all samples and no negative controls yield positive results. Second, we can decide how much confidence to place in results that have been obtained already, whether or not there are positive results from some controls. For example, the risk that at least one negative control yields a positive result increases with the size of the experiment, but the effects of occasional contamination are less severe in large experiments.}, }
@article {pmid15182692, year = {2004}, author = {Cooper, A and Drummond, AJ and Willerslev, E}, title = {Ancient DNA: would the real Neandertal please stand up?.}, journal = {Current biology : CB}, volume = {14}, number = {11}, pages = {R431-3}, doi = {10.1016/j.cub.2004.05.037}, pmid = {15182692}, issn = {0960-9822}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Fossils ; Hominidae/*genetics ; Humans ; *Models, Genetic ; Time Factors ; }, abstract = {Mitochondrial DNA sequences recovered from eight Neandertal specimens cannot be detected in either early fossil Europeans or in modern populations. This indicates that, if Neandertals made any genetic contribution at all to modern humans, it must have been limited, though the extent of the contribution cannot be resolved at present.}, }
@article {pmid15152601, year = {2004}, author = {Rohland, N and Siedel, H and Hofreiter, M}, title = {Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens.}, journal = {BioTechniques}, volume = {36}, number = {5}, pages = {814-6, 818-21}, doi = {10.2144/04365ST05}, pmid = {15152601}, issn = {0736-6205}, mesh = {Animals ; Archaeology/*methods ; Base Sequence ; Bone and Bones/metabolism ; Chemical Fractionation/*methods ; DNA, Mitochondrial/analysis/*chemistry/genetics/*isolation &amp; purification ; Gene Expression Profiling ; Molecular Sequence Data ; *Museums ; Pan troglodytes ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA/methods ; Skin/metabolism ; Specimen Handling/*methods ; Tooth/metabolism ; }, abstract = {Museum specimens have provided the material for a large proportion of ancient DNA studies conducted during the last 20 years. However, a major drawback of the genetic analyses is that the specimens investigated are usually damaged, as parts of skin, bone, or a tooth have to be removed for DNA extraction. To get around these limitations, we have developed a nondestructive extraction method for bone, tooth, and skin samples. We found that it is possible to amplify mitochondrial DNA (mtDNA) sequences up to at least 414 bp long from samples up to 164 years old. Using this method, almost 90% (35 of 40) of the investigated samples yielded amplifiable mtDNA. Moreover, we found that repeated extractions of the same samples allowed amplifications of the expected length for all samples at least three times and for some samples up to at least five times. Thus this method opens up the possibility to repeatedly use museum collections for mtDNA analyses without damaging the specimens and thus without reducing the value of irreplaceable collections for morphological analyses.}, }
@article {pmid15118235, year = {2004}, author = {Nabata, D and Masuda, R and Takahashi, O and Nagata, J}, title = {Bottleneck effects on the sika deer Cervus nippon population in Hokkaido, revealed by ancient DNA analysis.}, journal = {Zoological science}, volume = {21}, number = {4}, pages = {473-481}, doi = {10.2108/zsj.21.473}, pmid = {15118235}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; DNA Primers ; DNA, Mitochondrial/genetics ; Deer/*genetics ; *Fossils ; *Founder Effect ; Genetic Drift ; Geography ; Haplotypes/genetics ; Japan ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Tandem Repeat Sequences/genetics ; }, abstract = {The population size of the sika deer Cervus nippon on Hokkaido Island of Japan had been remarkably reduced because of heavy hunting pressure since the beginning of Meiji Period and effects of heavy snow in 1879 and 1881. After that, the number of sika deer in Hokkaido has increased gradually due to the protection by the Hokkaido government. In the present study, in order to investigate the bottleneck effects, we analyzed ancient mitochondrial DNA (mtDNA) on sika deer bones excavated from archaeological sites just before Meiji Period. On 86 of 113 bones from 13 archaeological sites of Ainu Culture Period (17-19th centuries), 602 base-pair fragments of the mtDNA control region were successfully sequenced. Consequently, we found three new haplotypes (g-, h- and i-types) which had not been identified in modern sika deer. In addition, four haplotypes (a-, b-, c- and d-types) identified from modern sika deer were also found in the archaeological deer. The new haplotypes and previously reported hapoltypes from sika deer of Hokkaido were phylogenetically much closer to each other, compared with those of modern sika deer from Honshu, Kyushu and the Chinese continent. Geographical distribution patterns of haplotypes of the ancient population were different from those of the modern population in Hokkaido. Our findings indicated that their genetic diversity was reduced through the bottleneck and that population structures of sika deer were changed widely in Hokkaido due to genetic drift.}, }
@article {pmid15084676, year = {2004}, author = {Serre, D and Hofreiter, M and Pääbo, S}, title = {Mutations induced by ancient DNA extracts?.}, journal = {Molecular biology and evolution}, volume = {21}, number = {8}, pages = {1463-1467}, doi = {10.1093/molbev/msh139}, pmid = {15084676}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; DNA/*genetics ; DNA, Mitochondrial/*genetics ; *Fossils ; Humans ; Molecular Sequence Data ; Mutation/*genetics ; Plants/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {We have investigated whether some factor in ancient DNA extracts induces site-specific mutations in modern DNA. We find no evidence for higher mutation rates when extracts from three different Pleistocene mammals are added to modern DNA than when water or extraction blanks are added. We also fail to find evidence that any such factor affects ancient DNA sequences determined from the same extracts. This as well as the patterns of nucleotide substitutions seen in DNA sequences determined from hundreds of other specimens leads us to doubt that a previously unknown mutagenic factor can be a general feature of extracts from old tissues.}, }
@article {pmid15040907, year = {2004}, author = {Alonso, A and Martín, P and Albarrán, C and García, P and García, O and de Simón, LF and García-Hirschfeld, J and Sancho, M and de La Rúa, C and Fernández-Piqueras, J}, title = {Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies.}, journal = {Forensic science international}, volume = {139}, number = {2-3}, pages = {141-149}, doi = {10.1016/j.forsciint.2003.10.008}, pmid = {15040907}, issn = {0379-0738}, mesh = {Amelogenin ; Animals ; Cell Nucleus/genetics ; DNA/*analysis ; DNA Fingerprinting/*methods ; Dental Enamel Proteins/genetics ; Female ; Forensic Anthropology/methods ; *Gene Dosage ; Hominidae/genetics ; Humans ; Male ; Polymerase Chain Reaction/*methods ; Sex Determination Analysis ; Tandem Repeat Sequences ; Tooth Germ ; }, abstract = {We explore different designs to estimate both nuclear and mitochondrial human DNA (mtDNA) content based on the detection of the 5' nuclease activity of the Taq DNA polymerase using fluorogenic probes and a real-time quantitative PCR detection system. Human mtDNA quantification was accomplished by monitoring the real-time progress of the PCR-amplification of two different fragment sizes (113 and 287 bp) within the hypervariable region I (HV1) of the mtDNA control region, using two fluorogenic probes to specifically determine the mtDNA copy of each fragment size category. This mtDNA real-time PCR design has been used to assess the mtDNA preservation (copy number and degradation state) of DNA samples retrieved from 500 to 1500 years old human remains that showed low copy number and highly degraded mtDNA. The quantification of nuclear DNA was achieved by real-time PCR of a segment of the X-Y homologous amelogenin (AMG) gene that allowed the simultaneous estimation of a Y-specific fragment (AMGY: 112 bp) and a X-specific fragment (AMGX: 106 bp) making possible not only haploid or diploid DNA quantitation but also sex determination. The AMG real-time PCR design has been used to quantify a set of 57 DNA samples from 4-5 years old forensic bone remains with improved sensitivity compared with the slot-blot hybridization method. The potential utility of this technology to improve the quality of some PCR-based forensic and ancient DNA studies (microsatellite typing and mtDNA sequencing) is discussed.}, }
@article {pmid15022363, year = {2004}, author = {Ricaut, FX and Keyser-Tracqui, C and Cammaert, L and Crubézy, E and Ludes, B}, title = {Genetic analysis and ethnic affinities from two Scytho-Siberian skeletons.}, journal = {American journal of physical anthropology}, volume = {123}, number = {4}, pages = {351-360}, doi = {10.1002/ajpa.10323}, pmid = {15022363}, issn = {0002-9483}, mesh = {Adult ; Asia/ethnology ; Asian People/*genetics ; Child, Preschool ; DNA, Mitochondrial/analysis/genetics ; Ethnicity/*genetics ; *Fossils ; Genetic Variation/*genetics ; Humans ; Male ; Paleontology/methods ; Polymorphism, Genetic/genetics ; *Skeleton ; Tandem Repeat Sequences/genetics ; }, abstract = {We extracted DNA from two skeletons belonging to the Sytho-Siberian population, which were excavated from the Sebÿstei site (dating back 2,500 years) in the Altai Republic (Central Asia). Ancient DNA was analyzed by autosomal short tandem repeats (STRs) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these two skeletons were not close relatives. Moreover, their haplogroups were characteristic of Asian populations. Comparison with the haplogroup of 3,523 Asian and American individuals linked one skeleton with a putative ancestral paleo-Asiatic population and the other with Chinese populations. It appears that the genetic study of ancient populations of Central Asia brings important elements to the understanding of human population movements in Asia.}, }
@article {pmid15015132, year = {2004}, author = {Vernesi, C and Caramelli, D and Dupanloup, I and Bertorelle, G and Lari, M and Cappellini, E and Moggi-Cecchi, J and Chiarelli, B and Castrì, L and Casoli, A and Mallegni, F and Lalueza-Fox, C and Barbujani, G}, title = {The Etruscans: a population-genetic study.}, journal = {American journal of human genetics}, volume = {74}, number = {4}, pages = {694-704}, pmid = {15015132}, issn = {0002-9297}, mesh = {Bone and Bones/metabolism ; DNA, Mitochondrial/*analysis/*genetics/isolation &amp; purification ; Ethnicity/*genetics ; Europe/ethnology ; Evolution, Molecular ; *Fossils ; Genetic Variation/genetics ; Genetics, Population ; Haplotypes/genetics ; History, Ancient ; Humans ; Italy/ethnology ; Molecular Sequence Data ; *Phylogeny ; Reproducibility of Results ; Roman World ; }, abstract = {The origins of the Etruscans, a non-Indo-European population of preclassical Italy, are unclear. There is broad agreement that their culture developed locally, but the Etruscans' evolutionary and migrational relationships are largely unknown. In this study, we determined mitochondrial DNA sequences in multiple clones derived from bone samples of 80 Etruscans who lived between the 7th and the 3rd centuries b.c. In the first phase of the study, we eliminated all specimens for which any of nine tests for validation of ancient DNA data raised the suspicion that either degradation or contamination by modern DNA might have occurred. On the basis of data from the remaining 30 individuals, the Etruscans appeared as genetically variable as modern populations. No significant heterogeneity emerged among archaeological sites or time periods, suggesting that different Etruscan communities shared not only a culture but also a mitochondrial gene pool. Genetic distances and sequence comparisons show closer evolutionary relationships with the eastern Mediterranean shores for the Etruscans than for modern Italian populations. All mitochondrial lineages observed among the Etruscans appear typically European or West Asian, but only a few haplotypes were found to have an exact match in a modern mitochondrial database, raising new questions about the Etruscans' fate after their assimilation into the Roman state.}, }
@article {pmid15014140, year = {2004}, author = {Pusch, CM and Bachmann, L}, title = {Spiking of contemporary human template DNA with ancient DNA extracts induces mutations under PCR and generates nonauthentic mitochondrial sequences.}, journal = {Molecular biology and evolution}, volume = {21}, number = {5}, pages = {957-964}, doi = {10.1093/molbev/msh107}, pmid = {15014140}, issn = {0737-4038}, mesh = {Base Sequence ; Biological Evolution ; Cloning, Molecular ; DNA/genetics ; DNA Mutational Analysis/*methods ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genome, Human ; Humans ; Molecular Sequence Data ; *Mutation ; Plasmids/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Proof of authenticity is the greatest challenge in palaeogenetic research, and many safeguards have become standard routine in laboratories specialized on ancient DNA research. Here we describe an as-yet unknown source of artifacts that will require special attention in the future. We show that ancient DNA extracts on their own can have an inhibitory and mutagenic effect under PCR. We have spiked PCR reactions including known human test DNA with 14 selected ancient DNA extracts from human and nonhuman sources. We find that the ancient DNA extracts inhibit the amplification of large fragments to different degrees, suggesting that the usual control against contaminations, i.e., the absence of long amplifiable fragments, is not sufficient. But even more important, we find that the extracts induce mutations in a nonrandom fashion. We have amplified a 148-bp stretch of the mitochondrial HVRI from contemporary human template DNA in spiked PCR reactions. Subsequent analysis of 547 sequences from cloned amplicons revealed that the vast majority (76.97%) differed from the correct sequence by single nucleotide substitutions and/or indels. In total, 34 positions of a 103-bp alignment are affected, and most mutations occur repeatedly in independent PCR amplifications. Several of the induced mutations occur at positions that have previously been detected in studies of ancient hominid sequences, including the Neandertal sequences. Our data imply that PCR-induced mutations are likely to be an intrinsic and general problem of PCR amplifications of ancient templates. Therefore, ancient DNA sequences should be considered with caution, at least as long as the molecular basis for the extract-induced mutations is not understood.}, }
@article {pmid15008401, year = {2003}, author = {Orlando, L and Eisenmann, V and Reynier, F and Sondaar, P and Hänni, C}, title = {Morphological convergence in Hippidion and Equus (Amerhippus) South American equids elucidated by ancient DNA analysis.}, journal = {Journal of molecular evolution}, volume = {57 Suppl 1}, number = {}, pages = {S29-40}, pmid = {15008401}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Cytochromes b ; DNA, Mitochondrial ; Equidae/*genetics/physiology ; Fossils ; Molecular Sequence Data ; *Phylogeny ; South America ; Species Specificity ; }, abstract = {Unusual equids named hippidions inhabited South America for more than 2 MY (million years). Like many other animals they succumbed to the worldwide climatic change that occurred 10 KY (thousand years) ago and completely disappeared during the great late Pleistocene megafaunal extinction. According to fossil records and numerous dental, cranial, and postcranial characters, Hippidion and Equus lineages are known to have diverged prior to 10 MY. Some equid bones from Rio Verde and Ultima Esperanza (Patagonia, Chile) dating back to the late Pleistocene period (8-13 KY) have been identified as Hippidion saldiasi, while a few teeth have been assigned to Equus. Six samples of those remains have been obtained from the Zoological Museum of Amsterdam for ancient DNA analysis to try to place Hippidion in the evolutive tree of Perissodactyla. Two samples of Hippidion and one sample of Equus yielded 241-394 bp of the mtDNA control region and 172-296 bp of the cytochrome b gene. Unexpectedly, all the sequences clustered deep inside the Equus genus, casting doubt on the initial identification of the bones. For paleontologists, one of the striking and classical diagnostic characters of Hippidion is their extremely short and massive metapodials, a probable locomotory adaptation to the Andine steep slopes. However, our DNA analysis reveals that a very Hippidion-like metapod might also have been possessed by another South American equid, i.e., Equus (Amerhippus), an interpretation supported by complementary anatomical observations. This adaptive convergence between members of the two South American equid genera may lead paleontologists to limb bone misidentification.}, }
@article {pmid15004568, year = {2004}, author = {Kellis, M and Birren, BW and Lander, ES}, title = {Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.}, journal = {Nature}, volume = {428}, number = {6983}, pages = {617-624}, doi = {10.1038/nature02424}, pmid = {15004568}, issn = {1476-4687}, mesh = {Codon/genetics ; *Evolution, Molecular ; Gene Conversion ; *Gene Duplication ; Genes, Fungal/genetics ; *Genome, Fungal ; Models, Genetic ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Synteny/genetics ; }, abstract = {Whole-genome duplication followed by massive gene loss and specialization has long been postulated as a powerful mechanism of evolutionary innovation. Recently, it has become possible to test this notion by searching complete genome sequence for signs of ancient duplication. Here, we show that the yeast Saccharomyces cerevisiae arose from ancient whole-genome duplication, by sequencing and analysing Kluyveromyces waltii, a related yeast species that diverged before the duplication. The two genomes are related by a 1:2 mapping, with each region of K. waltii corresponding to two regions of S. cerevisiae, as expected for whole-genome duplication. This resolves the long-standing controversy on the ancestry of the yeast genome, and makes it possible to study the fate of duplicated genes directly. Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions.}, }
@article {pmid14985856, year = {2004}, author = {Krokan, HE and Kavli, B and Slupphaug, G}, title = {Novel aspects of macromolecular repair and relationship to human disease.}, journal = {Journal of molecular medicine (Berlin, Germany)}, volume = {82}, number = {5}, pages = {280-297}, pmid = {14985856}, issn = {0946-2716}, mesh = {AlkB Homolog 1, Histone H2a Dioxygenase ; Amino Acids/metabolism ; *DNA Damage ; *DNA Repair ; DNA Repair Enzymes ; Disease/*etiology ; Escherichia coli Proteins/metabolism ; Humans ; Immunity, Active/*physiology ; Mixed Function Oxygenases/metabolism ; Molecular Structure ; RNA/metabolism ; }, abstract = {Cellular and humoral defence mechanisms are essential for the survival of individuals and species. Thus, DNA repair prevents mutations and cytotoxicity from DNA damage, thereby reducing the risks of inappropriate cell death, developmental defects, premature ageing and cancer. Similarly, antigen-dependent acquired immune responses prevent infections and also have a role in cancer prevention. DNA repair is highly complex and functions in an intricate network that also involves transcription, replication, cell cycle regulation, and the immune system. DNA damage is repaired by at least four major mechanisms, each requiring many different proteins. In addition there are "subpathways", and back-up mechanisms both within and between pathways. Various defects in DNA repair result in different forms of cancer, e.g. the rare syndrome Xeroderma pigmentosum and the more common diseases early-onset breast cancer and hereditary non-polyposis colon cancer. Surprisingly, recent research has revealed molecular interactions between the ancient DNA repair mechanisms and the much younger acquired immune system. Thus, the classical base excision enzyme uracil-DNA glycosylase encoded by the UNG gene is also involved in somatic hypermutation and class switch recombination, e.g. from IgM antibodies to IgG, yielding secreted high affinity antibodies. Mutations in both alleles of UNG result in a hyper-IgM syndrome with life-threatening infections. Furthermore, it has recently become clear that not only DNA, but also RNA and proteins are repaired. Thus, certain aberrant methylations in RNA are repaired by oxidative demethylation in one step restoring the normal base, and at least in a bacterial model system this increases survival several-fold after exposure to methylating agents. Proteins are repaired both at the peptide amino acid level and at the structural level. RNA and protein repair are likely to be important to prevent the formation of cytotoxic protein aggregates of the types known to cause neurodegenerative diseases e.g. Alzheimer's, Parkinson's and Huntington's diseases, and other diseases as well. In conclusion, recent research has demonstrated an unexpected complexity of cellular defence mechanisms that function in intricate networks, rather than as independent mechanisms. The new knowledge opens for interventions that are based on a deeper understanding of the mechanisms of defence.}, }
@article {pmid14766912, year = {2004}, author = {Gilbert, MTP and Cuccui, J and White, W and Lynnerup, N and Titball, RW and Cooper, A and Prentice, MB}, title = {Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims.}, journal = {Microbiology (Reading, England)}, volume = {150}, number = {Pt 2}, pages = {341-354}, doi = {10.1099/mic.0.26594-0}, pmid = {14766912}, issn = {1350-0872}, mesh = {Base Sequence ; DNA Primers ; DNA, Bacterial/genetics/*isolation &amp; purification ; Europe/epidemiology ; Funeral Rites/history ; History, Medieval ; Humans ; Plague/history/*microbiology ; Polymerase Chain Reaction/methods ; Tooth/*microbiology ; Yersinia pestis/genetics/*isolation &amp; purification ; }, abstract = {This study reports the results of a collaborative study undertaken by two independent research groups to (a) confirm recent PCR-based detection of Yersinia pestis DNA in human teeth from medieval plague victims in France, and (b) to extend these observations over five different European burial sites believed to contain plague victims dating from the late 13th to 17th centuries. Several different sets of primers were used, including those previously documented to yield positive results on ancient DNA extracts. No Y. pestis DNA could be amplified from DNA extracted from 108 teeth belonging to 61 individuals, despite the amplification of numerous other bacterial DNA sequences. Several methods of extracting dentine prior to the DNA extraction were also compared. PCR for bacterial 16S rDNA indicated the presence of multiple bacterial species in 23 out of 27 teeth DNA extracts where dentine was extracted using previously described methods. In comparison, positive results were obtained from only five out of 44 teeth DNA extracts for which a novel contamination-minimizing embedding technique was used. Therefore, high levels of environmental bacterial DNA are present in DNA extracts where previously described methods of tooth manipulation are used. To conclude, the absence of Y. pestis-specific DNA in an exhaustive search using specimens from multiple putative European plague burial sites does not allow us to confirm the identification of Y. pestis as the aetiological agent of the Black Death and subsequent plagues. In addition, the utility of the published tooth-based ancient DNA technique used to diagnose fatal bacteraemias in historical epidemics still awaits independent corroboration.}, }
@article {pmid14726015, year = {2003}, author = {Costa, RM and Chiganças, V and Galhardo, Rda S and Carvalho, H and Menck, CF}, title = {The eukaryotic nucleotide excision repair pathway.}, journal = {Biochimie}, volume = {85}, number = {11}, pages = {1083-1099}, doi = {10.1016/j.biochi.2003.10.017}, pmid = {14726015}, issn = {0300-9084}, mesh = {Animals ; Apoptosis ; Cell Cycle ; DNA Damage ; DNA Repair/genetics/*physiology ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Humans ; }, abstract = {Nucleotide excision repair (NER) is the most versatile mechanism of DNA repair, recognizing and dealing with a variety of helix-distorting lesions, such as the UV-induced photoproducts cyclobutane pyrimidine dimers (CPDs) and pyrimidine 6-4 pyrimidone photoproducts (6-4 PPs). In this review, we describe the main protein players and the different sequential steps of the eukaryotic NER mechanism in human cells, from lesion recognition to damage removal and DNA synthesis. Studies on the dynamics of protein access to the damaged site, and the kinetics of lesion removal contribute to the knowledge of how the cells respond to genetic insult. DNA lesions as well as NER factors themselves are also implicated in changes in cell metabolism, influencing cell cycle progression or arrest, apoptosis and genetic instability. These changes are related to increased mutagenesis and carcinogenesis. Finally, the recent collection of genomic data allows one to recognize the high conservation and the evolution of eukaryotic NER. The distribution of NER orthologues in different organisms, from archaea to the metazoa, displays challenging observations. Some of NER proteins are widespread in nature, probably representing ancient DNA repair proteins, which are candidates to participate in a primitive NER mechanism.}, }
@article {pmid14708953, year = {2004}, author = {O'Keefe, JH and Cordain, L}, title = {Cardiovascular disease resulting from a diet and lifestyle at odds with our Paleolithic genome: how to become a 21st-century hunter-gatherer.}, journal = {Mayo Clinic proceedings}, volume = {79}, number = {1}, pages = {101-108}, doi = {10.4065/79.1.101}, pmid = {14708953}, issn = {0025-6196}, mesh = {Beverages ; Cardiovascular Diseases/history/*prevention &amp; control ; Diet/*history ; Energy Intake ; Exercise ; Fatty Acids, Monounsaturated/administration &amp; dosage ; Fatty Acids, Omega-3/administration &amp; dosage ; Genome, Human ; History, Ancient ; Humans ; *Life Style ; Meat ; Trans Fatty Acids/adverse effects ; }, abstract = {Our genetic make-up, shaped through millions of years of evolution, determines our nutritional and activity needs. Although the human genome has remained primarily unchanged since the agricultural revolution 10,000 years ago, our diet and lifestyle have become progressively more divergent from those of our ancient ancestors. Accumulating evidence suggests that this mismatch between our modern diet and lifestyle and our Paleolithic genome is playing a substantial role in the ongoing epidemics of obesity, hypertension, diabetes, and atherosclerotic cardiovascular disease. Until 500 generations ago, all humans consumed only wild and unprocessed food foraged and hunted from their environment. These circumstances provided a diet high in lean protein, polyunsaturated fats (especially omega-3 [omega-3] fatty acids), monounsaturated fats, fiber, vitamins, minerals, antioxidants, and other beneficial phytochemicals. Historical and anthropological studies show hunter-gatherers generally to be healthy, fit, and largely free of the degenerative cardiovascular diseases common in modern societies. This review outlines the essence of our hunter-gatherer genetic legacy and suggests practical steps to re-align our modern milieu with our ancient genome in an effort to improve cardiovascular health.}, }
@article {pmid14660491, year = {2004}, author = {Chakravarthy, MV and Booth, FW}, title = {Eating, exercise, and "thrifty" genotypes: connecting the dots toward an evolutionary understanding of modern chronic diseases.}, journal = {Journal of applied physiology (Bethesda, Md. : 1985)}, volume = {96}, number = {1}, pages = {3-10}, doi = {10.1152/japplphysiol.00757.2003}, pmid = {14660491}, issn = {8750-7587}, support = {AR-19393/AR/NIAMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Chronic Disease ; Energy Metabolism/genetics ; Feeding Behavior/*physiology ; Genotype ; Humans ; Physical Exertion/*physiology ; Starvation/*genetics/metabolism ; }, abstract = {Survival of Homo sapiens during evolution was dependent on the procurement of food, which in turn was dependent on physical activity. However, food supply was never consistent. Thus it is contended that the ancient hunter-gatherer had cycles of feast and famine, punctuated with obligate periods of physical activity and rest. Hence, gene selection in the Late-Paleolithic era was probably influenced by physical activity and rest. To ensure survival during periods of famine, certain genes evolved to regulate efficient intake and utilization of fuel stores. Such genes were termed "thrifty genes" in 1962. Furthermore, convincing evidence shows that this ancient genome has remained essentially unchanged over the past 10,000 years and certainly not changed in the past 40-100 years. Although the absolute caloric intake of modern-day humans is likely lower compared with our hunter-gatherer ancestors, it is nevertheless in positive caloric balance in the majority of the US adult population mainly due to the increased sedentary lifestyle in present society. We contend that the combination of continuous food abundance and physical inactivity eliminates the evolutionarily programmed biochemical cycles emanating from feast-famine and physical activity-rest cycles, which in turn abrogates the cycling of certain metabolic processes, ultimately resulting in metabolic derangements such as obesity and Type 2 diabetes. In this context, we postulate that perhaps a crucial mechanism to break the stall of the metabolic processes would be via exercise through the regulation of "physical activity genes," some of which may also be potential candidates for the "thrifty genes" of our hunter-gatherer ancestors. Therefore, the identification of such "thrifty gene" candidates would help provide insight into the pathogenetic processes of the numerous physical inactivity-mediated disorders.}, }
@article {pmid14659702, year = {2003}, author = {Coutinho, PM and Stam, M and Blanc, E and Henrissat, B}, title = {Why are there so many carbohydrate-active enzyme-related genes in plants?.}, journal = {Trends in plant science}, volume = {8}, number = {12}, pages = {563-565}, doi = {10.1016/j.tplants.2003.10.002}, pmid = {14659702}, issn = {1360-1385}, mesh = {*Carbohydrate Metabolism ; Cell Wall/enzymology ; Genome, Plant ; Glycoside Hydrolases/classification/*genetics/metabolism ; Glycosyltransferases/classification/*genetics/metabolism ; Plants/enzymology/*genetics ; }, abstract = {Plants contain far more carbohydrate-active enzyme-encoding genes than any other organism sequenced to date. The extremely large number of glycosidase and glycosyltransferase-related genes in plant genomes can be explained by the complex structure of the plant cell wall, by ancient genome duplication and by recent local duplications, but also by the recent emergence of novel and unrelated protein functions based on widely available pre-existing scaffolds.}, }
@article {pmid14640271, year = {2003}, author = {Andréasson, H and Allen, M}, title = {Rapid quantification and sex determination of forensic evidence materials.}, journal = {Journal of forensic sciences}, volume = {48}, number = {6}, pages = {1280-1287}, pmid = {14640271}, issn = {0022-1198}, mesh = {Amelogenin ; Case-Control Studies ; DNA/blood ; DNA Primers ; Dental Enamel Proteins/*genetics ; Female ; Forensic Medicine/*methods ; Gene Deletion ; Genetic Markers ; Hair/metabolism ; Humans ; Male ; Polymerase Chain Reaction/*methods ; *Sex Determination Processes ; Skin/metabolism ; Tooth Germ ; }, abstract = {DNA quantification of forensic evidence is very valuable for an optimal use of the available biological material. Moreover, sex determination is of great importance as additional information in criminal investigations as well as in identification of missing persons, no suspect cases, and ancient DNA studies. While routine forensic DNA analysis based on short tandem repeat markers includes a marker for sex determination, analysis of samples containing scarce amounts of DNA is often based on mitochondrial DNA, and sex determination is not performed. In order to allow quantification and simultaneous sex determination on minute amounts of DNA, an assay based on real-time PCR analysis of a marker within the human amelogenin gene has been developed. The sex determination is based on melting curve analysis, while an externally standardized kinetic analysis allows quantification of the nuclear DNA copy number in the sample. This real-time DNA quantification assay has proven to be highly sensitive, enabling quantification of single DNA copies. Although certain limitations were apparent, the system is a rapid, cost-effective, and flexible assay for analysis of forensic casework samples.}, }
@article {pmid14638327, year = {2003}, author = {Seoighe, C}, title = {Turning the clock back on ancient genome duplication.}, journal = {Current opinion in genetics &amp; development}, volume = {13}, number = {6}, pages = {636-643}, doi = {10.1016/j.gde.2003.10.005}, pmid = {14638327}, issn = {0959-437X}, mesh = {Animals ; Arabidopsis/genetics ; *Evolution, Molecular ; Fishes/genetics ; *Gene Duplication ; *Genome ; *Models, Genetic ; Polyploidy ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; Vertebrates/*genetics ; }, abstract = {Complete genome sequence data led rapidly to the conclusion that ancient genome duplications had shaped the genomes of the model organisms Saccharomyces cerevisiae and Arabidopsis thaliana. Recent contributions have gone on to refine date estimates for these duplications and, in the case of Arabidopsis, to infer additional, more ancient, rounds of duplication by reconstructing gene order before the most recent duplication event. It is becoming widely accepted that an ancient duplication occurred before the radiation of the ray-finned fish. However, despite methodological advances and the availability of complete genome sequence data the debate over whether very ancient genome duplications have occurred early in the vertebrate lineage has not yet been fully resolved.}, }
@article {pmid14615538, year = {2003}, author = {Jaenicke-Després, V and Buckler, ES and Smith, BD and Gilbert, MT and Cooper, A and Doebley, J and Pääbo, S}, title = {Early allelic selection in maize as revealed by ancient DNA.}, journal = {Science (New York, N.Y.)}, volume = {302}, number = {5648}, pages = {1206-1208}, doi = {10.1126/science.1089056}, pmid = {14615538}, issn = {1095-9203}, mesh = {*Alleles ; Archaeology ; *Biological Evolution ; Crops, Agricultural/*genetics ; DNA, Plant/*genetics ; DNA-Binding Proteins/genetics/physiology ; Gene Frequency ; Genes, Plant ; Genetic Variation ; Mass Spectrometry ; Mexico ; Plant Proteins/genetics/physiology ; *Selection, Genetic ; Southwestern United States ; Time Factors ; Transcription Factors/genetics/physiology ; Zea mays/*genetics ; }, abstract = {Maize was domesticated from teosinte, a wild grass, by approximately 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete.}, }
@article {pmid14608462, year = {2004}, author = {Ricaut, FX and Kolodesnikov, S and Keyser-Tracqui, C and Alekseev, AN and Crubézy, E and Ludes, B}, title = {Genetic analysis of human remains found in two eighteenth century Yakut graves at At-Dabaan.}, journal = {International journal of legal medicine}, volume = {118}, number = {1}, pages = {24-31}, pmid = {14608462}, issn = {0937-9827}, mesh = {Anthropology, Physical ; Base Sequence ; DNA, Mitochondrial/*genetics ; Ethnicity/*genetics ; Genetics, Population ; History, 18th Century ; Humans ; Molecular Sequence Data ; Siberia ; Tandem Repeat Sequences/*genetics ; }, abstract = {We extracted DNA from three skeletons belonging to the Yakut population, which were excavated from the At-Dabaan site (dating back 300 years) in the Sakha Republic (Russia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these three skeletons were not close relatives but probably linked to the same clan structure. Comparison of their haplotypes with the haplotypes of 8,774 Eurasian individuals suggested a relative specificity and continuity of part of the Yakut mitochondrial gene pool during the last 3 centuries.}, }
@article {pmid14595092, year = {2004}, author = {Ritchie, PA and Millar, CD and Gibb, GC and Baroni, C and Lambert, DM}, title = {Ancient DNA enables timing of the pleistocene origin and holocene expansion of two adélie penguin lineages in antarctica.}, journal = {Molecular biology and evolution}, volume = {21}, number = {2}, pages = {240-248}, doi = {10.1093/molbev/msh012}, pmid = {14595092}, issn = {0737-4038}, mesh = {Animals ; Antarctic Regions ; Birds/*genetics ; DNA/*genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The timing of divergent events in history is one of the central goals of contemporary evolutionary biology. Such studies are however dependent on accurate evolutionary rates. Recent developments in ancient DNA analysis enable the estimation of more accurate evolutionary rates and therefore more accurate timing of divergence events. Consequently, this leads to a better understanding of changes in populations through time. We use an evolutionary rate calculated from ancient DNA of Adélie penguins (Pygoscelis adeliae) to time divergent events in their history. We report the presence of two distinct and highly variable mitochondrial DNA lineages and track changes in these lineages through space and time. When the ancient DNA and the phylogenetic rates are used to estimate the time of origin of the lineages, two very different estimates resulted. In addition, these same rates provide very different estimates of the time of expansion of these lineages. We suggest that the rate calculated from ancient DNA is more consistent with the glacial history of Antarctica and requires fewer assumptions than does a narrative based on the phylogenetic rate. Finally, we suggest that our study indicates an important new role for ancient DNA studies in the timing of divergent events in history.}, }
@article {pmid14580590, year = {2003}, author = {Smith, CI and Chamberlain, AT and Riley, MS and Stringer, C and Collins, MJ}, title = {The thermal history of human fossils and the likelihood of successful DNA amplification.}, journal = {Journal of human evolution}, volume = {45}, number = {3}, pages = {203-217}, doi = {10.1016/s0047-2484(03)00106-4}, pmid = {14580590}, issn = {0047-2484}, mesh = {Animals ; Australia ; *Climate ; Europe ; *Fossils ; Hominidae/*genetics ; Humans ; *Nucleic Acid Amplification Techniques ; Survival ; Time Factors ; }, abstract = {Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site.}, }
@article {pmid14564076, year = {2000}, author = {Zeller, M and Mirghomizadeh, F and Wehner, HD and Blin, N}, title = {Frequent D-loop polymorphism in mtDNA enables genotyping of 1400-year-old human remains from Merowingian graves.}, journal = {Journal of applied genetics}, volume = {41}, number = {4}, pages = {285-292}, pmid = {14564076}, issn = {1234-1983}, abstract = {Improvements of DNA extraction and amplification techniques presently enable DNA analysis of ancient DNA (aDNA) from samples which range from several hundred years of age up to possibly 5000 years. Taking advantage of the abundance of mitochondrial DNA and its polymorphic D-loop sequence, ten individuals from multiple burial sites of the Merowingian culture (South Germany), estimated to be about 1400 years old, were genotyped to determine possible kinship. Moreover, gonosomal DNA markers from the X- and Y-chromosome were applied for sex determination of the remains. In all individuals investigated, deviations from the Anderson mtDNA consensus sequence were observed, all representing substitutions (7 transitions and 3 transversions). Although such mutations have been reported from recent populations, our study constitutes the first description of these mtDNA mutations from numerous aDNA samples recovered from multiple burial sites. The results obtained by molecular anthropology can aid in describing kinship relations and burial customs of ancient remains.}, }
@article {pmid14527199, year = {2003}, author = {Yang, DY and Eng, B and Saunders, SR}, title = {Hypersensitive PCR, ancient human mtDNA, and contamination.}, journal = {Human biology}, volume = {75}, number = {3}, pages = {355-364}, doi = {10.1353/hub.2003.0050}, pmid = {14527199}, issn = {0018-7143}, mesh = {Archaeology/*methods ; Bone and Bones/chemistry ; DNA, Mitochondrial/*analysis ; Humans ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; }, abstract = {When highly efficient polymerase was used with high cycle numbers (50-60), strong amplifications were observed, but negative controls were also unexpectedly amplified in a study of ancient human mtDNA from 2000-year-old skeletons. The results of a series of tests revealed that the hypersensitive polymerase chain reaction (PCR) generated by higher cycles and the presence of contaminant DNA (though at extremely low levels) should be responsible for the amplification of negative controls. We suggest that PCR sensitivity be optimized to take advantage of highly efficient polymerase and at the same time prevent "background DNA" from becoming "contaminant DNA" and obscuring the analysis of authentic ancient DNA. We propose the use of multiple positive controls when amplifying ancient human mtDNA samples to indicate the sensitivity of individual PCR amplifications and to monitor the contamination levels of modern human DNA. This study provides some suggestions as to how to amplify and analyze ancient human mtDNA when unavoidable and extremely tiny amounts of modern human DNA exist.}, }
@article {pmid14510002, year = {2002}, author = {Verginelli, F and Ottini, L and Esposito, D and Cama, A and Battista, P and Ciranni, R and Zavaglia, K and Mariani-Costantini, R and Fornaciari, G}, title = {[Ancient DNA studies: from paleopathology to population genetics].}, journal = {Medicina nei secoli}, volume = {14}, number = {2}, pages = {587-607}, pmid = {14510002}, issn = {0394-9001}, mesh = {DNA/*history ; Genetics, Population/*history/*methods ; History, 21st Century ; History, Ancient ; History, Early Modern 1451-1600 ; History, Medieval ; History, Modern 1601- ; Italy ; Paleopathology/*history/*methods ; }, abstract = {We discuss the relevance of ancient DNA studies for novel approaches to a variety of fields of scientific inquiry, including population and evolutionary genetics, prehistoric archaeology, paleopathology and history of human diseases. To exemplify the potential of ancient DNA research, we provide accounts of studies currently conducted at our laboratories in four different areas: 1) origins of the dog and phylogeny of prehistoric Italian canids; 2) paleogenetics of ancient Roma; 3) antiquity for variant alleles implicated in disease predisposition; 4) molecular investigation of pathologic lesions in Italian mummies of Renaissance age. The implications of the results obtained are briefly outlined.}, }
@article {pmid12968179, year = {2003}, author = {Huynen, L and Millar, CD and Scofield, RP and Lambert, DM}, title = {Nuclear DNA sequences detect species limits in ancient moa.}, journal = {Nature}, volume = {425}, number = {6954}, pages = {175-178}, doi = {10.1038/nature01838}, pmid = {12968179}, issn = {1476-4687}, mesh = {Animals ; Body Constitution ; Cell Nucleus/*genetics ; DNA/*analysis/genetics/isolation &amp; purification ; Ecosystem ; Female ; Femur/anatomy &amp; histology ; *Fossils ; Male ; Palaeognathae/anatomy &amp; histology/*classification/*genetics ; Phylogeny ; *Sex Characteristics ; Sex Determination Analysis ; Species Specificity ; }, abstract = {Ancient DNA studies have typically used multi-copy mitochondrial DNA sequences. This is largely because single-locus nuclear genes have been difficult to recover from sub-fossil material, restricting the scope of ancient DNA research. Here, we have isolated single-locus nuclear DNA markers to assign the sex of 115 extinct moa and, in combination with a mitochondrial DNA phylogeny, tested competing hypotheses about the specific status of moa taxa. Moa were large ratite birds that showed extreme size variation both within and among species. For some taxa, this large variation was hypothesized to represent sexual dimorphism, while for others it was argued to reflect the existence of different species. Our results show that moa were characterized by extreme reverse sexual dimorphism and as a result we have been able to clarify the number of moa species. For example, we show that the three recognized 'species' of Dinornis comprised only two monophyletic groups and that two of these 'species' comprised individuals of one sex only. This study also illustrates that single-locus nuclear DNA sequences can be consistently recovered from ancient material.}, }
@article {pmid12958513, year = {2003}, author = {Schmerer, WM}, title = {Reduction of shadow band synthesis during PCR amplification of repetitive sequences from modern and ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {226}, number = {}, pages = {309-314}, doi = {10.1385/1-59259-384-4:309}, pmid = {12958513}, issn = {1064-3745}, mesh = {Buffers ; DNA/*genetics ; Indicators and Reagents ; Polymerase Chain Reaction/*methods ; Protein Denaturation ; *Repetitive Sequences, Nucleic Acid ; }, }
@article {pmid12958484, year = {2003}, author = {Schmerer, WM}, title = {Extraction of ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {226}, number = {}, pages = {57-62}, doi = {10.1385/1-59259-384-4:57}, pmid = {12958484}, issn = {1064-3745}, mesh = {Biodegradation, Environmental ; DNA/*isolation &amp; purification ; Indicators and Reagents ; Polymerase Chain Reaction ; Solvents ; }, }
@article {pmid12927133, year = {2003}, author = {Orlando, L and Leonard, JA and Thenot, A and Laudet, V and Guerin, C and Hänni, C}, title = {Ancient DNA analysis reveals woolly rhino evolutionary relationships.}, journal = {Molecular phylogenetics and evolution}, volume = {28}, number = {3}, pages = {485-499}, doi = {10.1016/s1055-7903(03)00023-x}, pmid = {12927133}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; Cytochromes b/genetics ; DNA Primers ; Databases, Nucleic Acid ; *Evolution, Molecular ; *Fossils ; *Models, Biological ; Molecular Sequence Data ; Perissodactyla/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Tooth/chemistry ; }, abstract = {With ancient DNA technology, DNA sequences have been added to the list of characters available to infer the phyletic position of extinct species in evolutionary trees. We have sequenced the entire 12S rRNA and partial cytochrome b (cyt b) genes of one 60-70,000-year-old sample, and partial 12S rRNA and cyt b sequences of two 40-45,000-year-old samples of the extinct woolly rhinoceros (Coelodonta antiquitatis). Based on these two mitochondrial markers, phylogenetic analyses show that C. antiquitatis is most closely related to one of the three extant Asian rhinoceros species, Dicerorhinus sumatrensis. Calculations based on a molecular clock suggest that the lineage leading to C. antiquitatis and D. sumatrensis diverged in the Oligocene, 21-26 MYA. Both results agree with morphological models deduced from palaeontological data. Nuclear inserts of mitochondrial DNA were identified in the ancient specimens. These data should encourage the use of nuclear DNA in future ancient DNA studies. It also further establishes that the degraded nature of ancient DNA does not completely protect ancient DNA studies based on mitochondrial data from the problems associated with nuclear inserts.}, }
@article {pmid12923304, year = {2003}, author = {Pusch, CM and Broghammer, M and Blin, N}, title = {Molecular phylogenetics employing modern and ancient DNA.}, journal = {Journal of applied genetics}, volume = {44}, number = {3}, pages = {269-290}, pmid = {12923304}, issn = {1234-1983}, mesh = {Amino Acid Motifs ; Animals ; DNA/analysis ; *Evolution, Molecular ; *Fossils ; Humans ; Microscopy, Electron ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; }, abstract = {Comparative studies of DNA in recent populations and characterisation of ancient hereditary material have contributed very interesting facts to our understanding of evolution of modern mankind. Analysis of DNA homology in related species, assessment of mutations and polymorphisms in various populations and new DNA sequence data from prehistoric finds allowed - via sophisticated DNA extraction techniques, PCR, sequencing and digitalised processing of genetic information - insights into possible roots of Homo sapiens and related species, migration patterns and ancient cultural habits, thus enrhing the palaeoanthropological discipline. However, a presentation of this development would not be complete without pointing towards the methodological limitations and manifold presentations burdened with artifacts, data misinterpretation and unjustified conclusions. Presently, this modern field of research is in its consolidation phase and new parameters for quality control and authentication are being implemented to avoid spectacular but unfounded reports. It is expected that most of the problems connected to old biomolecules may be closely related to fossilisation parameters. The future challenge will be the full understanding of the complex and multi-faceted processes underlying diagenesis, including the elucidation of nucleic acid postmortem damage".}, }
@article {pmid12836686, year = {2003}, author = {Van de Peer, Y and Taylor, JS and Meyer, A}, title = {Are all fishes ancient polyploids?.}, journal = {Journal of structural and functional genomics}, volume = {3}, number = {1-4}, pages = {65-73}, pmid = {12836686}, issn = {1345-711X}, mesh = {Animals ; *Biological Evolution ; Fishes/*genetics ; Gene Duplication ; Genome ; Phylogeny ; *Polyploidy ; }, abstract = {Euteleost fishes seem to have more copies of many genes than their tetrapod relatives. Three different mechanisms could explain the origin of these 'extra' fish genes. The duplicates may have been produced during a fish-specific genome duplication event. A second explanation is an increased rate of independent gene duplications in fish. A third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. These three hypotheses have been tested by phylogenetic tree reconstruction. Phylogenetic analyses of sequences from human, mouse, chicken, frog (Xenopus laevis), zebrafish (Danio rerio) and pufferfish (Takifugu rubripes) suggest that ray-finned fishes are likely to have undergone a whole genome duplication event between 200 and 450 million years ago. We also comment here on the evolutionary consequences of this ancient genome duplication.}, }
@article {pmid12808718, year = {2003}, author = {Alonso, A and Martin, P and Albarrán, C and García, P and Primorac, D and García, O and Fernández de Simón, L and García-Hirschfeld, J and Sancho, M and Fernández-Piqueras, J}, title = {Specific quantification of human genomes from low copy number DNA samples in forensic and ancient DNA studies.}, journal = {Croatian medical journal}, volume = {44}, number = {3}, pages = {273-280}, pmid = {12808718}, issn = {0353-9504}, mesh = {Amelogenin ; Complementarity Determining Regions ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/genetics ; Dental Enamel Proteins/genetics ; Forensic Anthropology/*methods ; Humans ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Sex Determination Analysis/methods ; Tandem Repeat Sequences ; }, abstract = {We reviewed the current methodologies used for human DNA quantitation in forensic and ancient DNA studies, including sensitive hybridization methods based on the detection of nuclear alpha-satellite repetitive DNA regions or more recently developed fluorogenic real-time polymerase chain reaction (PCR) designs for the detection of both nuclear and mitochondrial DNA regions. Special emphasis has been put on the applicability of recently described different real-time PCR designs targeting different fragments of the HV1 mtDNA control region, and a segment of the X-Y homologous amelogenin gene. The importance of these quantitative assays is to ensure the consistency of low copy number DNA typing (STR profiling and mtDNA sequencing).}, }
@article {pmid12782040, year = {2003}, author = {Culjković, B and Savić, D and Stojković, O and Romac, S}, title = {Poly(A) tailing of ancient DNA: a method for reproducible microsatellite genotyping.}, journal = {Analytical biochemistry}, volume = {318}, number = {1}, pages = {124-131}, doi = {10.1016/s0003-2697(03)00160-x}, pmid = {12782040}, issn = {0003-2697}, mesh = {Animals ; Archaeology/history ; DNA/analysis/*chemistry/genetics/history ; DNA Fragmentation ; Dinucleotide Repeats/genetics ; Genotype ; History, Ancient ; Humans ; Microsatellite Repeats/*genetics ; Poly A/analysis/*chemistry/genetics ; Polymerase Chain Reaction/methods ; Trinucleotide Repeats/genetics ; Yugoslavia ; }, abstract = {Microsatellites could be of great potential use in the analysis of ancient remains, but so far such analyses have failed to be reproducible mainly because of the high degree of ancient DNA (aDNA) degradation. During PCR, annealing of the primers to the complementary sequences of microsatellites occurs together with cross-annealing of partially degraded repeated sequences. This could create chimeric alleles that do not correspond to the authentic ones. Here we report a simple method for processing aDNA fragments prior to PCR that greatly reduces the production of chimeric alleles. This approach eliminates aDNA molecules broken within the repeats as targets for Taq polymerase by adding poly(A) tails at the 3(') ends of the DNA fragments, which disrupts the homology in the region and thus prevents annealing out of register. We have analyzed one dinucleotide- (D6S337) and two trinucleotide-containing loci (IT15 and SCA1) using poly(A)-tailed and the same untreated aDNA as template. aDNAs were isolated from 28 human remains, 600 and 7000 years of age. In repeated experiments with untreated aDNAs we obtained three to five times more alleles compared to poly(A)-tailed aDNAs. According to our results, modification of aDNA by poly(A) tailing is an efficient pretreatment for accurate genotyping.}, }
@article {pmid12743370, year = {2003}, author = {Caramelli, D and Lalueza-Fox, C and Vernesi, C and Lari, M and Casoli, A and Mallegni, F and Chiarelli, B and Dupanloup, I and Bertranpetit, J and Barbujani, G and Bertorelle, G}, title = {Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {11}, pages = {6593-6597}, pmid = {12743370}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA Primers ; DNA, Mitochondrial/genetics ; Europe ; Hominidae/*genetics ; Humans ; Molecular Sequence Data ; }, abstract = {During the late Pleistocene, early anatomically modern humans coexisted in Europe with the anatomically archaic Neandertals for some thousand years. Under the recent variants of the multiregional model of human evolution, modern and archaic forms were different but related populations within a single evolving species, and both have contributed to the gene pool of current humans. Conversely, the Out-of-Africa model considers the transition between Neandertals and anatomically modern humans as the result of a demographic replacement, and hence it predicts a genetic discontinuity between them. Following the most stringent current standards for validation of ancient DNA sequences, we typed the mtDNA hypervariable region I of two anatomically modern Homo sapiens sapiens individuals of the Cro-Magnon type dated at about 23 and 25 thousand years ago. Here we show that the mtDNAs of these individuals fall well within the range of variation of today's humans, but differ sharply from the available sequences of the chronologically closer Neandertals. This discontinuity is difficult to reconcile with the hypothesis that both Neandertals and early anatomically modern humans contributed to the current European gene pool.}, }
@article {pmid12742759, year = {2003}, author = {Olson, LE and Hassanin, A}, title = {Contamination and chimerism are perpetuating the legend of the snake-eating cow with twisted horns (Pseudonovibos spiralis). A case study of the pitfalls of ancient DNA.}, journal = {Molecular phylogenetics and evolution}, volume = {27}, number = {3}, pages = {545-548}, doi = {10.1016/s1055-7903(03)00022-8}, pmid = {12742759}, issn = {1055-7903}, mesh = {Animals ; Chimera/*genetics ; RNA, Ribosomal/genetics ; Research Design ; Ruminants/classification/*genetics ; }, }
@article {pmid12740954, year = {2003}, author = {Reed, FA and Kontanis, EJ and Kennedy, KA and Aquadro, CF}, title = {Brief communication: ancient DNA prospects from Sri Lankan highland dry caves support an emerging global pattern.}, journal = {American journal of physical anthropology}, volume = {121}, number = {2}, pages = {112-116}, doi = {10.1002/ajpa.10211}, pmid = {12740954}, issn = {0002-9483}, support = {R01 GM036431/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acids/analysis ; Archaeology/*methods ; DNA/*analysis/*history ; History, Ancient ; Humans ; *Microclimate ; *Preservation, Biological ; Sri Lanka ; Tropical Climate ; }, abstract = {Recovery of ancient DNA has become an increasingly important tool in elucidating the origins of past populations and their relationships. Unfortunately, many human skeletal remains do not contain original DNA amplifiable by polymerase chain reaction (PCR). Amino-acid racemization has proven to be a useful predictor of ancient DNA results. We analyzed the relative levels of amino-acid preservation and racemization of human samples from two highland dry-cave sites in Sri Lanka, and found that amino-acid enantiomer ratios were inconsistent with successful authentic DNA recovery. A review of the literature reveals that these results are consistent with a global pattern of poor DNA preservation in the tropics.}, }
@article {pmid12740952, year = {2003}, author = {Lalueza-Fox, C and Gilbert, MT and Martínez-Fuentes, AJ and Calafell, F and Bertranpetit, J}, title = {Mitochondrial DNA from pre-Columbian Ciboneys from Cuba and the prehistoric colonization of the Caribbean.}, journal = {American journal of physical anthropology}, volume = {121}, number = {2}, pages = {97-108}, doi = {10.1002/ajpa.10236}, pmid = {12740952}, issn = {0002-9483}, mesh = {Bone and Bones/chemistry ; Caribbean Region ; Cuba ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Emigration and Immigration/*history ; Genetic Variation/genetics ; Genetic Vectors ; Haplotypes/genetics ; History, Ancient ; Humans ; Indians, North American/*genetics/history ; Sequence Analysis, DNA ; Tooth/chemistry ; }, abstract = {To assess the genetic affinities of extinct Ciboneys (also called Guanajuatabeys) from Cuba, 47 pre-Columbian skeletal samples belonging to this group were analyzed using ancient DNA techniques. At the time of European contact, the center and east of Cuba were occupied by agriculturalist Taino groups, while the west was mainly inhabited by Ciboneys, hunter-gatherers who have traditionally been considered a relic population descending from the initial colonization of the Caribbean. The mtDNA hypervariable region I (HVR-I) and haplogroup-specific markers were amplified and sequenced in 15 specimens using overlapping fragments; amplification from second extractions from the same sample, independent replication in different laboratories, and cloning of some PCR products support the authenticity of the sequences. Three of the five major mtDNA Amerindian lineages (A, C, and D) are present in the sample analyzed, in frequencies of 0.07, 0.60, and 0.33, respectively. Different phylogenetic analyses seem to suggest that the Caribbean most likely was populated from South America, although the data are still inconclusive, and Central American influences cannot be discarded. Our hypothesis is that the colonization of the Caribbean mainly took place in successive migration movements that emanated from the same area in South America, around the Lower Orinoco Valley: the first wave consisted of hunter-gatherer groups (ancestors of the Ciboneys), a subsequent wave of agriculturalists (ancestors of the Tainos), and a latter one of nomadic Carib warriors. However, further genetic studies are needed to confirm this scenario.}, }
@article {pmid12729192, year = {2003}, author = {Zink, AR and Grabner, W and Reischl, U and Wolf, H and Nerlich, AG}, title = {Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt.}, journal = {Epidemiology and infection}, volume = {130}, number = {2}, pages = {239-249}, doi = {10.1017/s0950268802008257}, pmid = {12729192}, issn = {0950-2688}, mesh = {Bone and Bones/pathology ; DNA, Bacterial/*analysis/history ; Egypt, Ancient ; Gene Amplification ; History, Ancient ; Mycobacterium tuberculosis/*genetics ; Paleopathology ; Tuberculosis/genetics/*history/pathology ; }, abstract = {We describe the molecular identification of human tuberculosis (TB) from vertebral bone tissue samples from three different populations of ancient Egypt. The specimens were obtained from the predynastic to early dynastic necropolis of Abydos (7 individuals, c. 3500-2650 B.C.), from a Middle Kingdom to Second Intermediate Period tomb of the necropolis of Thebes-West (37. c. 2100-1550 B.C.) and from five further Theban tombs used in the New Kingdom and the Late Period (39, c. 1450-500 B.C.). A total of 18 cases tested positive for the presence of ancient DNA (aDNA) of the M. tuberculosis complex. Out of the 9 cases with typical macromorphological signs of tuberculous spondylitis, 6 were positive for mycobacterial aDNA (66.7%). Of 24 cases with non-specific pathological alterations, 5 provided a positive result (20.8%). In 50 cases of normally appearing vertebral bones 7 tested positive (14.0%). There were only minor differences in the frequencies between the three populations. These data strongly support the notion that tuberculosis was present and prevalent in ancient Egypt since very early periods of this civilization. The unexpectedly high rate of mycobacterial aDNA in normal bone samples is presumably due to a pre- to perimortal systemic spread of the bacteria and indicates a generalized infection by M. tuberculosis.}, }
@article {pmid12713151, year = {2003}, author = {Bramanti, B and Hummel, S and Chiarelli, B and Herrmann, B}, title = {Ancient DNA analysis of the delta F508 mutation.}, journal = {Human biology}, volume = {75}, number = {1}, pages = {105-115}, doi = {10.1353/hub.2003.0017}, pmid = {12713151}, issn = {0018-7143}, mesh = {Cystic Fibrosis/*genetics ; DNA/genetics/isolation &amp; purification ; *DNA Mutational Analysis ; DNA Primers ; Humans ; Sicily ; }, abstract = {When working with highly degraded DNA, validating the results of a slightly polymorphic system always complicates the analysis because of the difficulties in recognizing contamination and artifacts. Recognition can be greatly simplified by employing a multiplex reaction that coamplifies the fragments together with several highly polymorphic markers, for instance, short tandem repeats. In this work, we successfully included newly designed oligonucleotide primers for the detection of delta F508, the most frequent mutation causing cystic fibrosis, in the commercial AmpFlSTR Profiler Plus PCR Amplification Kit (PE Applied Biosystems). This coamplification enabled us to test the hypothesis of a heterozygote advantage associated with cystic fibrosis-specifically, higher resistance to toxin-mediated diarrheas--in a Sicilian skeletal sample of individuals who died in a cholera epidemic in 1837. The proposed method should also be suitable for the genetic characterization of other slightly polymorphic loci tested on human and animal ancient DNA; it should permit simple authentication of results by comparing the fingerprints obtained from independent amplifications repeated several times.}, }
@article {pmid12702849, year = {2003}, author = {Stokstad, E}, title = {Paleontology. Ancient DNA pulled from soil.}, journal = {Science (New York, N.Y.)}, volume = {300}, number = {5618}, pages = {407}, doi = {10.1126/science.300.5618.407a}, pmid = {12702849}, issn = {1095-9203}, mesh = {Animals ; Climate ; DNA/history/*isolation &amp; purification ; DNA, Chloroplast/history/*isolation &amp; purification ; Fossils ; *Geologic Sediments ; History, Ancient ; New Zealand ; Paleontology/*methods ; Plant Development ; Siberia ; *Soil ; }, }
@article {pmid12702808, year = {2003}, author = {Willerslev, E and Hansen, AJ and Binladen, J and Brand, TB and Gilbert, MT and Shapiro, B and Bunce, M and Wiuf, C and Gilichinsky, DA and Cooper, A}, title = {Diverse plant and animal genetic records from Holocene and Pleistocene sediments.}, journal = {Science (New York, N.Y.)}, volume = {300}, number = {5620}, pages = {791-795}, doi = {10.1126/science.1084114}, pmid = {12702808}, issn = {1095-9203}, mesh = {Animals ; Base Sequence ; Bryopsida/classification/genetics ; Cloning, Molecular ; Cycadopsida/classification/genetics ; DNA/*analysis/genetics ; DNA, Chloroplast/analysis ; DNA, Mitochondrial/analysis/genetics ; DNA, Plant/*analysis/genetics ; Ecosystem ; Fossils ; *Geologic Sediments ; History, Ancient ; Magnoliopsida/classification/genetics ; Mammals/classification/genetics ; New Zealand ; Phylogeny ; *Plants/classification ; Polymerase Chain Reaction ; Siberia ; *Soil ; *Vertebrates/classification/genetics ; }, abstract = {Genetic analyses of permafrost and temperate sediments reveal that plant and animal DNA may be preserved for long periods, even in the absence of obvious macrofossils. In Siberia, five permafrost cores ranging from 400,000 to 10,000 years old contained at least 19 different plant taxa, including the oldest authenticated ancient DNA sequences known, and megafaunal sequences including mammoth, bison, and horse. The genetic data record a number of dramatic changes in the taxonomic diversity and composition of Beringian vegetation and fauna. Temperate cave sediments in New Zealand also yielded DNA sequences of extinct biota, including two species of ratite moa, and 29 plant taxa characteristic of the prehuman environment. Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments.}, }
@article {pmid12687766, year = {2003}, author = {Iñiguez, AM and Reinhard, KJ and Araújo, A and Ferreira, LF and Vicente, AC}, title = {Enterobius vermicularis: ancient DNA from North and South American human coprolites.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {98 Suppl 1}, number = {}, pages = {67-69}, doi = {10.1590/s0074-02762003000900013}, pmid = {12687766}, issn = {0074-0276}, mesh = {Animals ; Chile ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Enterobius/*genetics ; Feces/*parasitology ; *Fossils ; Humans ; RNA, Helminth/genetics ; RNA, Ribosomal, 5S/*genetics ; United States ; }, abstract = {A molecular paleoparasitological diagnostic approach was developed for Enterobius vermicularis. Ancient DNA was extracted from 27 coprolites from archaeological sites in Chile and USA. Enzymatic amplification of human mtDNA sequences confirmed the human origin. We designed primers specific to the E. vermicularis 5S ribosomal RNA spacer region and they allowed reproducible polymerase chain reaction identification of ancient material. We suggested that the paleoparasitological microscopic identification could accompany molecular diagnosis, which also opens the possibility of sequence analysis to understand parasite-host evolution.}, }
@article {pmid12687765, year = {2003}, author = {Iñiguez, AM and Araújo, A and Ferreira, LF and Vicente, AC}, title = {Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {98 Suppl 1}, number = {}, pages = {63-65}, doi = {10.1590/s0074-02762003000900012}, pmid = {12687765}, issn = {0074-0276}, mesh = {Animals ; DNA, Helminth/genetics/*isolation &amp; purification ; Electrophoresis, Agar Gel ; Feces/*parasitology ; *Fossils ; Humans ; Paleopathology/methods ; *Random Amplified Polymorphic DNA Technique ; }, abstract = {The aim of this work was to determine approaches that would improve the quality of ancient DNA (aDNA) present in coprolites to enhance the possibility of success in retrieving specific sequence targets. We worked with coprolites from South American archaeological sites in Brazil and Chile dating up to 7,000 years ago. Using established protocols for aDNA extraction we obtained samples showing high degradation as usually happens with this kind of material. The reconstructive polymerization pretreatment was essential to overcome the DNA degradation and the serial dilutions helped with to prevent polymerase chain reaction (PCR) inhibitors. Moreover, the random amplified polymorphic DNA-PCR has been shown to be a reliable technique for further experiments to recover specific aDNA sequences.}, }
@article {pmid12687761, year = {2003}, author = {Loreille, O and Bouchet, F}, title = {Evolution of ascariasis in humans and pigs: a multi-disciplinary approach.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {98 Suppl 1}, number = {}, pages = {39-46}, doi = {10.1590/s0074-02762003000900008}, pmid = {12687761}, issn = {0074-0276}, mesh = {Animals ; Ascariasis/*history/*veterinary ; Ascaris lumbricoides/*genetics ; Ascaris suum/*genetics ; *Biological Evolution ; DNA Primers ; DNA, Mitochondrial/*genetics ; Genes, Helminth ; Genetic Markers ; Haplotypes ; History, Ancient ; Host-Parasite Interactions ; Humans ; Polymorphism, Genetic ; Swine ; Swine Diseases/*history/parasitology ; }, abstract = {The nematode parasite Ascaris lumbricoides infects the digestive tracts of over 1.4 billion people worldwide, and its sister species, Ascaris suum, has infected a countless number of domesticated and feral pigs. It is generally thought that the putative ancestor to these worms infected either humans or pigs, but with the advent of domestication, they had ample opportunity to jump to a new host and subsequently specialize and evolve into a new species. While nuclear DNA makers decisively separate the two populations, mitochondrial sequences reveal that three major haplotypes are found in A. suum and in A. lumbricoides, indicating either occasional hybridization, causing introgression of gene trees, or retention of polymorphism dating back to the original ancestral species. This article provides an illustration of the combined contribution of parasitology, archaeoparasitology, genetics and paleogenetics to the history of ascariasis. We specifically investigate the molecular history of ascariasis in humans by sequencing DNA from the eggs of Ascaris found among ancient archeological remains. The findings of this paleogenetic survey will explain whether the three mitochondrial haplotypes result from recent hybridization and introgression, due to intensive human-pig interaction, or whether their co-occurrence predates pig husbandry, perhaps dating back to the common ancestor. We hope to show how human-pig interaction has shaped the recent evolutionary history of this disease, perhaps revealing the identify of the ancestral host.}, }
@article {pmid12679076, year = {2003}, author = {Orlando, L and Mauffrey, JF and Cuisin, J and Patton, JL and Hänni, C and Catzeflis, F}, title = {Napoleon Bonaparte and the fate of an Amazonian rat: new data on the taxonomy of Mesomys hispidus (Rodentia: Echimyidae).}, journal = {Molecular phylogenetics and evolution}, volume = {27}, number = {1}, pages = {113-120}, doi = {10.1016/s1055-7903(02)00372-x}, pmid = {12679076}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Biometry ; Cluster Analysis ; Cytochrome b Group/genetics ; Geography ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; Rodentia/anatomy &amp; histology/*classification/genetics ; South America ; }, abstract = {The spiny rat Mesomys hispidus is one of many South American rodents that lack adequate taxonomic definition. The few sampled populations of this broadly distributed trans-Amazonian arboreal rat have come from widely separated regions and are typically highly divergent. The holotype was described in 1817 by A.-G. Desmarest, after Napoleon's army brought it to Paris following the plunder of Lisbon in 1808; however, the locality of origin has remained unknown. Here we examine the taxonomic status of this species by direct comparison of 50 extant individuals with the holotype at the morphometric and genetic levels, the latter based on 331 bp of the mitochondrial cytochrome b gene retrieved from a small skin fragment of the holotype with ancient DNA technology. Extensive sequence divergence is present among samples of M. hispidus collected from throughout its range, from French Guiana across Amazonia to Bolivia and Peru, with at least seven mitochondrial clades recognized (average divergence of 7.7% Kimura 2-parameter distance). Sequence from the holotype is, however, only weakly divergent from those of recent samples from French Guiana. Moreover, the holotype clusters with greater that 99% posterior probability with samples from this part of Amazonia in a discriminant analysis based on 22 cranial and dental measurements. Thus, we suggest that the holotype was originally obtained in eastern Amazonia north of the Amazon River, most likely in the Brazilian state of Amapá. Despite the high level of sequence diversity and marked morphological differences in size across the range of M. hispidus, we continue to regard this assemblage as a single species until additional samples and analyses suggest otherwise.}, }
@article {pmid12653310, year = {2002}, author = {Kaestle, FA and Horsburgh, KA}, title = {Ancient DNA in anthropology: methods, applications, and ethics.}, journal = {American journal of physical anthropology}, volume = {Suppl 35}, number = {}, pages = {92-130}, doi = {10.1002/ajpa.10179}, pmid = {12653310}, issn = {0002-9483}, mesh = {Animals ; Anthropology, Cultural/methods ; Anthropology, Physical/ethics/*methods ; DNA/*analysis ; *Evolution, Molecular ; Female ; Genetics, Population/ethics/*methods ; Genotype ; Humans ; Male ; Pedigree ; Phylogeny ; Species Specificity ; }, abstract = {Anthropologists were quick to recognize the potential of new techniques in molecular biology to provide additional lines of evidence on questions long investigated in anthropology, as well as those questions that, while always of interest, could not have been addressed by more traditional techniques. The earliest ancient DNA studies, both within anthropology and in other fields, lacked rigorous hypothesis testing. However, more recently the true value of ancient DNA studies is being realized, and methods are being applied to a wide variety of anthropological questions. We review the most common methods and applications to date, and describe promising avenues of future research. We find that ancient DNA analyses have a valuable place in the array of anthropological techniques, but argue that such studies must not be undertaken merely to demonstrate that surviving DNA is present in organic remains, and that no such work should be performed before a careful consideration of the possible ethical ramifications of the research is undertaken.}, }
@article {pmid12644401, year = {2003}, author = {Debruyne, R and Barriel, V and Tassy, P}, title = {Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): new data and phylogenetic analyses of Elephantidae.}, journal = {Molecular phylogenetics and evolution}, volume = {26}, number = {3}, pages = {421-434}, doi = {10.1016/s1055-7903(02)00292-0}, pmid = {12644401}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; *Elephants/*classification/genetics ; Evolution, Molecular ; Fossils ; Likelihood Functions ; Molecular Sequence Data ; Siberia ; }, abstract = {The phylogenetic relationships between recent Elephantidae (Proboscidea, Mammalia), that is to say extant elephants (Asian and African) and extinct woolly mammoth, have remained unclear to date. The prevailing morphological scheme (mammoth grouped with Asian elephant) is either supported or questioned by the molecular results. Recently, the monophyly of woolly mammoths on mitochondrial grounds has been demonstrated (Thomas, et al., 2000), but it conflicts with previous studies (Barriel et al., 1999; Derenko et al., 1997). Here, we report the partial sequencing of two mitochondrial genes: 128 bp of 12S rDNA and 561 bp of cytochrome b for the Lyakhov mammoth, a 49,000-year-old Siberian individual. We use the most comprehensive sample of mammoth (11 sequences) to determine whether the sequences achieved by former studies were congruent or not. The monophyly of a major subset of mammoths sequences (including ours) is recovered. Such a result is assumed to be a good criterion for ascertaining the origin of ancient DNA. Our sequence is incongruent with that of Yang et al. (1996), though obtained for the same individual. As far as the latter sequence is concerned, a contamination by non-identified exogenous DNA is suspected. The robustness and reliability of the sister group relation between Mammuthus primigenius and Loxodonta africana are examined: down-weighting saturated substitutions has no impact on the topology; analyzing data partitions proves that the support of this clade can be assigned to the most conservative phylogenetic signal; insufficient taxonomic and/or characters sampling contributed to former discordant conclusions. We therefore assume the monophyly of "real mammoth sequences" and the (Mammuthus, Loxodonta) clade.}, }
@article {pmid12598688, year = {2003}, author = {Yao, YG and Kong, QP and Man, XY and Bandelt, HJ and Zhang, YP}, title = {Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA.}, journal = {Molecular biology and evolution}, volume = {20}, number = {2}, pages = {214-219}, doi = {10.1093/molbev/msg026}, pmid = {12598688}, issn = {0737-4038}, mesh = {Asian People ; China ; DNA, Mitochondrial/*analysis ; Evolution, Molecular ; Gene Frequency ; Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Paleontology ; Polymorphism, Genetic ; Principal Component Analysis ; Sequence Analysis, DNA/*methods ; }, abstract = {The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modern data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (approximately 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modern populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.}, }
@article {pmid12505472, year = {2003}, author = {Capelli, C and Tschentscher, F and Pascali, VL}, title = {"Ancient" protocols for the crime scene? Similarities and differences between forensic genetics and ancient DNA analysis.}, journal = {Forensic science international}, volume = {131}, number = {1}, pages = {59-64}, doi = {10.1016/s0379-0738(02)00396-1}, pmid = {12505472}, issn = {0379-0738}, mesh = {DNA/*analysis ; Forensic Medicine/*methods/*trends ; Humans ; Reproducibility of Results ; }, abstract = {We provide a short overview on some current issues in the fields of forensic genetics and ancient DNA (aDNA) analysis. We discuss about the existence of the possible points of contact between the two disciplines, in terms of open problems and the inherent approach to their solution. We mainly focus on the problem of results authentication, its theoretical and technical aspects.}, }
@article {pmid12489338, year = {2002}, author = {Tönnies, H and Klunker, R and Saar, K and Göbbel, L and Musil, A and Schultka, R}, title = {[Molecular-cytogenetic analysis of ancient DNA (aDNA) from preparations from the Meckel collection in Halle (Saale)].}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {184}, number = {6}, pages = {541-545}, doi = {10.1016/s0940-9602(02)80094-2}, pmid = {12489338}, issn = {0940-9602}, mesh = {Chromosomes, Human/genetics ; DNA/*genetics ; Germany ; Humans ; Karyotyping ; Nucleic Acid Hybridization/methods ; Umbilical Cord/chemistry ; }, }
@article {pmid12461639, year = {2002}, author = {Hummel, S and Schmidt, D and Kahle, M and Herrmann, B}, title = {AB0 blood group genotyping of ancient DNA by PCR-RFLP.}, journal = {International journal of legal medicine}, volume = {116}, number = {6}, pages = {327-333}, doi = {10.1007/s00414-002-0315-x}, pmid = {12461639}, issn = {0937-9827}, mesh = {*ABO Blood-Group System ; Alleles ; Archaeology ; Bone and Bones/chemistry ; DNA/analysis/*blood/*genetics ; Forensic Anthropology ; Forensic Dentistry ; Gene Amplification ; Genotype ; Humans ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Reproducibility of Results ; Sequence Analysis ; }, abstract = {The paper presents an PCR-RFLP-based method to determine AB0 blood groups at the genotype level. In order to ensure the applicability of the method to severely degraded DNA, new sets of primers were designed that amplify 103/104 bp and 64 bp sequences on exon 6 and exon 7 of chromosome 9, respectively. The amplification of the two PCR products and the subsequent RFLP analysis with four endonucleases was revealed to be an effective and reliable way to determine AB0 bloodgroups at the genotype level, distinguishing the alleles A, B, 0(1), 0(1v), and 0(2). PCR analysis of severely degraded sample material may possibly require higher cycle numbers. Therefore, the experiments presented here including those on positive control samples, were carried out employing 45 amplification cycles in order to ensure the validity of the amplification and RFLP analysis. As positive controls, small amounts of modern intact DNA extracted from saliva samples of 12 individuals with known AB0 phenotypes were used. The protocols for the AB0 typing were then applied to ancient degraded DNA extracted from 15 archaeological bones and teeth about 250 and 3,000 years old, respectively. The results presented for the archaeological sample material are based on repeated analysis derived from two independently processed DNA extracts of each sample. Moreover, the authentification process for the results derived from the archaeological samples included repeated multiplex STR genotyping of the extracts, showing the genetic uniqueness of the extracts which is the strongest possible indicator for the authenticity of an unknown DNA sample. Additionally, it was possible to compare the STR typing results to those from previous studies using the same material. Both the AB0 typing and the STR typing revealed fully reproducible results in all cases.}, }
@article {pmid12446908, year = {2002}, author = {Leonard, JA and Wayne, RK and Wheeler, J and Valadez, R and Guillén, S and Vilà, C}, title = {Ancient DNA evidence for Old World origin of New World dogs.}, journal = {Science (New York, N.Y.)}, volume = {298}, number = {5598}, pages = {1613-1616}, doi = {10.1126/science.1076980}, pmid = {12446908}, issn = {1095-9203}, mesh = {Alaska ; Animals ; Animals, Domestic/classification/*genetics ; Bolivia ; Breeding ; DNA, Mitochondrial/*genetics ; Dogs/classification/*genetics ; Europe ; Haplotypes ; Humans ; Mexico ; North America ; Peru ; Phylogeny ; Time ; Wolves/genetics ; }, abstract = {Mitochondrial DNA sequences isolated from ancient dog remains from Latin America and Alaska showed that native American dogs originated from multiple Old World lineages of dogs that accompanied late Pleistocene humans across the Bering Strait. One clade of dog sequences was unique to the New World, which is consistent with a period of geographic isolation. This unique clade was absent from a large sample of modern dogs, which implies that European colonists systematically discouraged the breeding of native American dogs.}, }
@article {pmid12411601, year = {2002}, author = {Orlando, L and Bonjean, D and Bocherens, H and Thenot, A and Argant, A and Otte, M and Hänni, C}, title = {Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time.}, journal = {Molecular biology and evolution}, volume = {19}, number = {11}, pages = {1920-1933}, doi = {10.1093/oxfordjournals.molbev.a004016}, pmid = {12411601}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Europe ; *Evolution, Molecular ; *Fossils ; Haplotypes/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Time Factors ; Ursidae/*genetics ; }, abstract = {The cave bear spread from Western Europe to the Near East during the Riss glaciation (250 KYA) before becoming extinct approximately 12 KYA. During that period, the climatic conditions were highly dynamic, oscillating between glacial and temperate episodes. Such events have constrained the geographic repartition of species, the movements of populations and shaped their genetic diversity. We retrieved and analyzed ancient DNA from 21 samples from five European caves ranging from 40 to 130 KYA. Combined with available data, our data set accounts for a total of 41 sequences of cave bear, coming from 18 European caves. We distinguish four haplogroups at the level of the mitochondrial DNA control region. The large population size of cave bear could account for the maintenance of such polymorphism. Extensive gene flow seems to have connected European populations because two haplogroups cover wide geographic areas. Furthermore, the extensive sampling of the deposits of the Scladina cave located in Belgium allowed us to correlate changes in climatic conditions with the intrapopulational genetic diversity over 90 KY.}, }
@article {pmid12209571, year = {2002}, author = {Mays, S and Fysh, E and Taylor, GM}, title = {Investigation of the link between visceral surface rib lesions and tuberculosis in a Medieval skeletal series from England using ancient DNA.}, journal = {American journal of physical anthropology}, volume = {119}, number = {1}, pages = {27-36}, doi = {10.1002/ajpa.10099}, pmid = {12209571}, issn = {0002-9483}, mesh = {Adolescent ; Adult ; Child ; DNA, Bacterial/*genetics ; England ; Female ; History, Medieval ; Humans ; Male ; Middle Aged ; Mycobacterium tuberculosis/*genetics ; Paleopathology ; Polymerase Chain Reaction ; Ribs/*pathology ; Tuberculosis, Pulmonary/*history/microbiology ; }, abstract = {Seven human skeletons from a large assemblage from a rural English Medieval burial site show lesions, predominantly proliferative in nature, on the visceral surfaces of the ribs. In order to investigate whether these rib lesions were regularly associated with tuberculous infection, these individuals, together with a group of age- and sex-matched control skeletons without bony signs of infection, were subjected to polymerase chain reaction (PCR) assays aimed at detecting traces of DNA from infecting microorganisms of the Mycobacterium tuberculosis complex. The results provided no evidence for any regular association between visceral surface rib lesions and the presence of M. tuberculosis complex DNA in the study group. The significance of these findings for the paleopathological interpretation of visceral surface rib lesions is discussed.}, }
@article {pmid12177525, year = {2002}, author = {Pusch, CM and Kayademir, T and Prangenberg, K and Conard, NJ and Czarnetzki, A and Blin, N}, title = {Documenting ancient DNA quality via alpha satellite amplification and assessment of clone sequence diversity.}, journal = {Journal of applied genetics}, volume = {43}, number = {3}, pages = {351-364}, pmid = {12177525}, issn = {1234-1983}, mesh = {Base Sequence ; Bone and Bones/*chemistry ; DNA, Satellite/*analysis ; Gene Amplification ; Genetic Variation ; Genotype ; Humans ; Molecular Sequence Data ; Paleopathology ; Polymerase Chain Reaction/*methods ; Repetitive Sequences, Nucleic Acid ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Homology, Nucleic Acid ; }, abstract = {C/G-->T/A nucleotide alterations have been shown to hamper the straightforward interpretation of mitochondrial DNA sequence data derived from ancient tissues. Attempting to characterise this finding with respect to nuclear DNA, we contrasted two established protocols: (i) an enzymatic repair of damaged DNA, thereby translating and closing nicks in the DNA, and (ii) the application of N-phenacylthiazolium bromide, which cleaves glucose-derived protein crosslinks, presumably derived from Maillard reactions. We used medieval human bones that were refractory to standard PCR procedures. Due to negligible presence of short tandem repeat loci and also mitochondrial sequences, the extracted ancient DNA needed a higher copy PCR system to yield amplification products. The chosen PCR target was specific alphoid repetitive DNA with an experimentally determined minimum of 1000 copies per haploid genome. Alphoid repeat segments were generated from both contemporary DNA and DNA extracts of two human skeletons dating from 450-600 AD (omitting uracil N-glycosylase pre-treatment of the extracted samples), and were subsequently cloned and sequenced. The sequences were evaluated for the number and type of nucleotide alterations noted after the different pre-treatments, and were compared to our alphoid consensus sequence generated from modern DNA. Both methods failed to reflect the expected 32% variability among single alphoid repeats (accounting for locus-specific differences and polymerase errors) as well as to display the actual 2.88 ratio of transitions to transversions. Our data obtained from high-copy-number nuclear DNA mirror the phenomenon of sequence deviations observed in mitochondrial DNA extracted from old specimens.}, }
@article {pmid12167530, year = {2002}, author = {Zink, AR and Reischl, U and Wolf, H and Nerlich, AG}, title = {Molecular analysis of ancient microbial infections.}, journal = {FEMS microbiology letters}, volume = {213}, number = {2}, pages = {141-147}, doi = {10.1111/j.1574-6968.2002.tb11298.x}, pmid = {12167530}, issn = {0378-1097}, mesh = {Animals ; Biological Evolution ; Communicable Diseases/*history ; DNA, Bacterial/analysis/genetics ; History, Ancient ; Humans ; Mummies ; Paleopathology ; Tuberculosis/epidemiology/*history/microbiology ; }, abstract = {The detection of ancient microbial DNA offers a new approach for the study of infectious diseases, their occurrence, frequency and host-pathogen interaction in historic times and populations. Moreover, data obtained from skeletal and mummified tissue may represent an important completion of contemporary phylogenetic analyses of pathogens. In the last few years, a variety of bacterial, protozoal and viral infections have been detected in ancient tissue samples by amplification and characterization of specific DNA fragments. This holds particularly true for the identification of the Mycobacterium tuberculosis complex, which seems to be more robust than other microbes due to its waxy, hydrophobic and lipid-rich cell wall. These observations provided useful information about the occurrence, but also the frequency of tuberculosis in former populations. Moreover, these studies suggest new evolutionary models and indicate the route of transmission between human and animals. Until now, other pathogens, such as Mycobacterium leprae, Yersinia pestis, Plasmodium falciparum and others, have occasionally been identified - mostly in single case studies or small sample sizes - as well, although much less information is available on these pathogens in ancient settings. The main reason therefore seems to be the degradation and modification of ancient DNA by progressive oxidative damage. Furthermore, the constant risk of contamination by recent DNA forces to take time and cost effective measures and renders the analysis of ancient microbes difficult. Nevertheless, the study of microbial ancient DNA significantly contributes to the understanding of transmission and spread of infectious diseases, and potentially to the evolution and phylogenetic pathways of pathogens.}, }
@article {pmid12140236, year = {2002}, author = {Hofreiter, M and Capelli, C and Krings, M and Waits, L and Conard, N and Münzel, S and Rabeder, G and Nagel, D and Paunovic, M and Jambrĕsić, G and Meyer, S and Weiss, G and Pääbo, S}, title = {Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of late pleistocene cave bears.}, journal = {Molecular biology and evolution}, volume = {19}, number = {8}, pages = {1244-1250}, doi = {10.1093/oxfordjournals.molbev.a004185}, pmid = {12140236}, issn = {0737-4038}, mesh = {Animals ; DNA, Mitochondrial/*analysis/genetics ; *Evolution, Molecular ; Fossils ; *Genetic Variation ; Genetics, Population ; Phylogeny ; Ursidae/classification/*genetics ; }, abstract = {Cave bears (Ursus spelaeus) existed in Europe and western Asia until the end of the last glaciation some 10,000 years ago. To investigate the genetic diversity, population history, and relationship among different cave bear populations, we have determined mitochondrial DNA sequences from 12 cave bears that range in age from about 26,500 to at least 49,000 years and originate from nine caves. The samples include one individual from the type specimen population, as well as two small-sized high-Alpine bears. The results show that about 49,000 years ago, the mtDNA diversity among cave bears was about 1.8-fold lower than the current species-wide diversity of brown bears (Ursus arctos). However, the current brown bear mtDNA gene pool consists of three clades, and cave bear mtDNA diversity is similar to the diversity observed within each of these clades. The results also show that geographically separated populations of the high-Alpine cave bear form were polyphyletic with respect to their mtDNA. This suggests that small size may have been an ancestral trait in cave bears and that large size evolved at least twice independently.}, }
@article {pmid12098752, year = {2002}, author = {Salzano, FM}, title = {Molecular variability in Amerindians: widespread but uneven information.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {74}, number = {2}, pages = {223-263}, doi = {10.1590/s0001-37652002000200005}, pmid = {12098752}, issn = {0001-3765}, mesh = {DNA, Mitochondrial/genetics ; Genetic Markers ; *Genetic Variation ; Humans ; Indians, Central American/*genetics ; Indians, North American/*genetics ; Indians, South American/*genetics ; Polymorphism, Genetic ; }, abstract = {A review was made in relation to the molecular variability present in North, Central, and South American Indian populations. It involved results from ancient DNA, mitochondrial DNA in extant populations, HLA and other autosomal markers, X and Y chromosome variation, as well as data from parasitic viruses which could show coevolutionary changes. The questions considered were their origin, ways in which the early colonization of the continent took place, types and levels of the variability which developed, peculiarities of the Amerindian evolutionary processes, and eventual genetic heterogeneity which evolved in different geographical areas. Although much information is already available, it is highly heterogeneous in relation to populations and types of genetic systems investigated. Unfortunately, the present trend of favoring essentially applied research suggest that the situation will not basically improve in the future.}, }
@article {pmid12064866, year = {2002}, author = {Christensen, LS and Scholler, S and Schierup, MH and Vestergaard, BF and Mordhorst, CH}, title = {Sequence analysis of measles virus strains collected during the pre- and early-vaccination era in Denmark reveals a considerable diversity of ancient strains.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {110}, number = {2}, pages = {113-122}, doi = {10.1034/j.1600-0463.2002.100201.x}, pmid = {12064866}, issn = {0903-4641}, mesh = {Child ; Denmark/epidemiology ; *Evolution, Molecular ; Hemagglutinins, Viral/genetics ; Humans ; Measles/epidemiology/prevention &amp; control/*virology ; Measles Vaccine/administration &amp; dosage ; Measles virus/classification/*genetics/immunology ; Molecular Epidemiology ; Phylogeny ; RNA, Viral/genetics ; Vaccination ; }, abstract = {A total of 199 serum samples from patients with measles collected in Denmark, Greenland and the Faroe Islands from 1964 to 1983 were analysed by PCR. Measles virus (MV) RNA could be detected in 38 (19%) of the samples and a total of 18 strains were subjected to partial sequence analysis of the hemagglutinin gene. The strains exhibited a considerable genomic diversity, which is at odds with the assumption that one genome type prevailed among globally circulating MV strains prior to the advent of live-attenuated vaccines. Our data indicate that the similarity of the various vaccine strains is attributed to their having originated from the same primary isolate. Consequently, it is implied that a small number of clinical manifestations of MV worldwide from which strains similar to the vaccine strain were identified were vaccine related rather than being caused by members of a persistently circulating ancient genome type. The Danish pre- and early-vaccination era MV strains seem to change the evolutionary spectrum of genome types A, C2 and E into one coherent group, suggesting that the genome types of MV strains circulating in the world at present do not represent far ranging evolutionary lineages but merely members of an evolutionary continuum of pre-vaccination era MV strains which by chance or due to an improved capability survived the worldwide partial herd immunity accomplished through vaccination.}, }
@article {pmid12032567, year = {2002}, author = {McLysaght, A and Hokamp, K and Wolfe, KH}, title = {Extensive genomic duplication during early chordate evolution.}, journal = {Nature genetics}, volume = {31}, number = {2}, pages = {200-204}, doi = {10.1038/ng884}, pmid = {12032567}, issn = {1061-4036}, mesh = {Animals ; Caenorhabditis elegans/genetics ; Chordata, Nonvertebrate/genetics ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; *Gene Duplication ; Genome ; *Genome, Human ; Humans ; Polyploidy ; }, abstract = {Opinions on the hypothesis that ancient genome duplications contributed to the vertebrate genome range from strong skepticism to strong credence. Previous studies concentrated on small numbers of gene families or chromosomal regions that might not have been representative of the whole genome, or used subjective methods to identify paralogous genes and regions. Here we report a systematic and objective analysis of the draft human genome sequence to identify paralogous chromosomal regions (paralogons) formed during chordate evolution and to estimate the ages of duplicate genes. We found that the human genome contains many more paralogons than would be expected by chance. Molecular clock analysis of all protein families in humans that have orthologs in the fly and nematode indicated that a burst of gene duplication activity took place in the period 350 650 Myr ago and that many of the duplicate genes formed at this time are located within paralogons. Our results support the contention that many of the gene families in vertebrates were formed or expanded by large-scale DNA duplications in an early chordate. Considering the incompleteness of the sequence data and the antiquity of the event, the results are compatible with at least one round of polyploidy.}, }
@article {pmid12024211, year = {2002}, author = {Fish, SA and Shepherd, TJ and McGenity, TJ and Grant, WD}, title = {Recovery of 16S ribosomal RNA gene fragments from ancient halite.}, journal = {Nature}, volume = {417}, number = {6887}, pages = {432-436}, doi = {10.1038/417432a}, pmid = {12024211}, issn = {0028-0836}, mesh = {Brazil ; DNA, Archaeal/genetics/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics/*isolation &amp; purification ; *Fossils ; Geologic Sediments/*microbiology ; Michigan ; Molecular Sequence Data ; Phylogeny ; Poland ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics/*isolation &amp; purification ; *Sodium Chloride ; Thailand ; Time Factors ; }, abstract = {During the last decade, sensitive techniques for detecting DNA have been successfully applied to archaeological and other samples that were a few hundred to a few thousand years old. Nevertheless, there is still controversy and doubt over claims of exceptionally ancient DNA. Additional accounts stretching back nearly a century suggest that microorganisms may survive over geological time in evaporite deposits. There is, however, often doubt over the age relationship between evaporite formation and the incorporation of microorganisms. Here, we have used petrographic and geochemical techniques (laser ablation microprobe inductively coupled plasma mass spectrometry) to verify the estimated geological age of halite (NaCl) evaporite samples. Fragments of 16S ribosomal RNA genes were detected by polymerase chain reaction amplification of DNA extracted from halite samples ranging in age from 11 to 425 Myr (millions of years). Haloarchaeal 16S rDNA amplicons were present in one sample (11 16 Myr), whereas other samples (65 425 Myr) yielded only bacterial 16S rDNA amplicons. Terminal restriction fragment length polymorphism analyses indicate complex and different populations of microorganisms or their free DNA in ancient halites of different ages.}, }
@article {pmid12012364, year = {2002}, author = {Nicholson, GJ and Tomiuk, J and Czarnetzki, A and Bachmann, L and Pusch, CM}, title = {Detection of bone glue treatment as a major source of contamination in ancient DNA analyses.}, journal = {American journal of physical anthropology}, volume = {118}, number = {2}, pages = {117-120}, doi = {10.1002/ajpa.10061}, pmid = {12012364}, issn = {0002-9483}, mesh = {Animals ; Artifacts ; Bone Cements/*chemistry ; Bone and Bones ; DNA/*isolation &amp; purification ; *Fossils ; Humans ; Polymerase Chain Reaction ; Reproducibility of Results ; Serine ; Specimen Handling ; }, abstract = {Paleogenetic investigations of ancient DNA extracted from fossil material is for many reasons susceptible to falsification by the presence of more recent contamination from several sources. Gelatine-based bone glue that has been used extensively for nearly two centuries by curators to preserve hard tissues contributes nonauthentic DNA to paleontological material. This fact has been frequently neglected and is barely mentioned in the literature. Now paleogeneticists, curators, and conservators are faced with the problem that treatment of samples with adhesives and consolidants for conservatory purposes has seldom been recorded. Here, we show that racemization of amino acids, and in particular serine, is an excellent indicator for the treatment of paleontological samples with glue.}, }
@article {pmid11991725, year = {2002}, author = {Irwin, DM}, title = {Ancient duplications of the human proglucagon gene.}, journal = {Genomics}, volume = {79}, number = {5}, pages = {741-746}, doi = {10.1006/geno.2002.6762}, pmid = {11991725}, issn = {0888-7543}, mesh = {Animals ; Calcium-Binding Proteins/genetics ; Chromosomes, Human, Pair 17/genetics ; Chromosomes, Human, Pair 2/genetics ; Dipeptidyl Peptidase 4/genetics ; Endopeptidases ; Evolution, Molecular ; *Gelatinases ; *Gene Duplication ; Gene Order ; Glucagon/*genetics ; Humans ; Membrane Proteins/genetics ; Mice ; Mitochondrial ADP, ATP Translocases/genetics ; Phylogeny ; Proglucagon ; Protein Precursors/*genetics ; Pseudogenes/genetics ; Serine Endopeptidases/genetics ; Vertebrates/genetics ; }, abstract = {The human proglucagon gene (GCG) is encoded within a finished 576-kb DNA sequence generated by the Human Genome Project. GCG is flanked by 18 kb and 65 kb of DNA, 5' and 3', respectively, that do not encode genes. The genomic sequence that includes GCG was found to have a long history of gene duplication events. Some members of the glucagon-like family of genes, GCG on chromosome 2 and GIP on chromosome 17, may be products of ancient genome duplications on the early vertebrate lineage. A large genomic tandem duplication event that included DPP4-like and GCG genes occurred before the amphibian-mammal divergence, but one of the duplicated copies of GCG has been lost on the human lineage. Recently, a processed pseudogene of the X-chromosome-linked gene TIMM8A was inserted downstream of GCG. Some ancient duplicates of GCG may retain physiological functions in other vertebrates.}, }
@article {pmid11964504, year = {2001}, author = {Yoder, AD}, title = {Ancient DNA from Megaladapis edwardsi.}, journal = {Folia primatologica; international journal of primatology}, volume = {72}, number = {6}, pages = {342-3; author reply 343-4}, doi = {10.1159/000052752}, pmid = {11964504}, issn = {0015-5713}, mesh = {Animals ; Cheirogaleidae/*classification/*genetics ; Cytochrome b Group/genetics ; DNA/genetics/*isolation &amp; purification ; Ecosystem ; Equipment Contamination ; *Fossils ; Phylogeny ; Reproducibility of Results ; Species Specificity ; }, }
@article {pmid11938969, year = {1998}, author = {Wu, P and Zhou, K and Zhang, Z and Xu, L}, title = {[Molecular genetic marker identification of traditional Chinese drug hippocampus].}, journal = {Yao xue xue bao = Acta pharmaceutica Sinica}, volume = {33}, number = {3}, pages = {226-233}, pmid = {11938969}, issn = {0513-4870}, mesh = {Cytochrome b Group/*genetics ; DNA/isolation &amp; purification ; Drug Contamination ; Genetic Markers ; *Materia Medica ; Molecular Biology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/*genetics ; Smegmamorpha/*genetics ; }, abstract = {Ancient DNA technique was used to extract DNA from 5 species of Chinese traditional drugs Hippocampus. The 12S rRNA gene fragment and cytochrome b gene fragment were amplified from DNA extract using Polymerase Chain Reaction (PCR) method. Restriction Fragment Length Polymorphism (RFLP) analysis and DNA sequence analysis were performed. The RFLP analysis method can identify 2 species of Hippocampus. The molecular genetic markers produced by DNA sequence method can identify all 5 species of Hippocampus. This method will be valuable for the identification of other animal drugs.}, }
@article {pmid11910113, year = {2002}, author = {Lambert, DM and Ritchie, PA and Millar, CD and Holland, B and Drummond, AJ and Baroni, C}, title = {Rates of evolution in ancient DNA from Adélie penguins.}, journal = {Science (New York, N.Y.)}, volume = {295}, number = {5563}, pages = {2270-2273}, doi = {10.1126/science.1068105}, pmid = {11910113}, issn = {1095-9203}, mesh = {Animals ; Antarctic Regions ; Birds/*genetics ; Bone and Bones/metabolism ; Calibration ; Carbon Radioisotopes ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Ecosystem ; *Evolution, Molecular ; Fossils ; Haplotypes/genetics ; Least-Squares Analysis ; Markov Chains ; Monte Carlo Method ; Phylogeny ; Polymerase Chain Reaction ; Time Factors ; }, abstract = {Well-preserved subfossil bones of Adélie penguins, Pygoscelis adeliae, underlie existing and abandoned nesting colonies in Antarctica. These bones, dating back to more than 7000 years before the present, harbor some of the best-preserved ancient DNA yet discovered. From 96 radiocarbon-aged bones, we report large numbers of mitochondrial haplotypes, some of which appear to be extinct, given the 380 living birds sampled. We demonstrate DNA sequence evolution through time and estimate the rate of evolution of the hypervariable region I using a Markov chain Monte Carlo integration and a least-squares regression analysis. Our calculated rates of evolution are approximately two to seven times higher than previous indirect phylogenetic estimates.}, }
@article {pmid11910085, year = {2002}, author = {Pennisi, E}, title = {Evolutionary biology. Ancient DNA untangles evolutionary paths.}, journal = {Science (New York, N.Y.)}, volume = {295}, number = {5563}, pages = {2197}, doi = {10.1126/science.295.5563.2197}, pmid = {11910085}, issn = {1095-9203}, mesh = {Animals ; Antarctic Regions ; Birds/blood/*genetics ; Bone and Bones/metabolism ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Emigration and Immigration ; *Evolution, Molecular ; *Fossils ; Genetic Variation/genetics ; *Ice ; Mutagenesis/genetics ; Phylogeny ; Siberia ; Time Factors ; Ursidae/*genetics ; }, }
@article {pmid11846037, year = {2002}, author = {Marota, I and Rollo, F}, title = {Molecular paleontology.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {59}, number = {1}, pages = {97-111}, doi = {10.1007/s00018-002-8408-8}, pmid = {11846037}, issn = {1420-682X}, mesh = {Animals ; DNA/*analysis/chemistry/*isolation &amp; purification/metabolism ; *Evolution, Molecular ; Freezing ; Hominidae/*genetics ; Humans ; Ice ; Mammals/*genetics ; Mummies ; Paleontology/*methods ; Reproducibility of Results ; }, abstract = {Molecular paleontology, i.e., the recovery of DNA from ancient human, animal, and plant remains is an innovative research field that has received progressively more attention from the scientific community since the 1980s. In the last decade, the field was punctuated by claims which aroused great interest but eventually turned out to be fakes--the most famous being the sequence of dinosaur DNA later shown to be of human origin. At present, the discipline is characterized by some certainties and many doubts. We know, for example, that we have reasonable chances to recover authentic DNA from a mammoth carcass, while our chances are negligible (or nonexistent) in the case of a dynastic mummy from Egypt. On the other hand, though we are developing convincing models of DNA decay in bone, we are not yet able to predict whether a certain paleontological or archeological site will yield material amenable to DNA analysis. This article reviews some of the most important and promising investigations using molecular paleontology approaches, such as studies on the conservation of DNA in human bone, the quest for ancient DNA in permafrost-frozen fauna, the Tyrolean iceman, and the Neandertals.}, }
@article {pmid11842404, year = {2002}, author = {Williams, SR and Chagnon, NA and Spielman, RS}, title = {Nuclear and mitochondrial genetic variation in the Yanomamö: a test case for ancient DNA studies of prehistoric populations.}, journal = {American journal of physical anthropology}, volume = {117}, number = {3}, pages = {246-259}, doi = {10.1002/ajpa.10035}, pmid = {11842404}, issn = {0002-9483}, mesh = {Adult ; Cultural Characteristics ; *DNA ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Female ; Genetic Markers ; *Genetic Variation ; Humans ; Indians, North American/*genetics ; Male ; Polymerase Chain Reaction ; Population Dynamics ; }, abstract = {Ancient DNA provides a potentially revolutionary way to study biological relationships in prehistoric populations, but genetic patterns are complex and require careful interpretation based on robust, well-tested models. In this study, nuclear and mitochondrial markers were compared in the Yanomamö, to assess how well each data set could differentiate among closely related groups. The villages selected for the study share a recent fission history and are closely related to each other, as would likely be the case among prehistoric peoples living in the same valley or region. The Yanomamö generally practice village-level endogamy, but some migration and gene flow are known to occur between villages. Nuclear and mitochondrial DNA data were compared using F-statistics and genetic distance analyses. The nuclear data performed as expected, males and females from the same village were similar, and the villages were genetically distinct, with the magnitude of genetic differences correlated with historical relationship. However, mtDNA analyses did not yield the expected results. The genetic distances between villages did not correlate with historical relationship, and the sexes were significantly different from each other in two villages. Both the Lane and Sublett and the Spence methods, used to test for archaeological residence patterns, were consistent with endogamy. Hence, ancient DNA can, in principle, provide us with a unique opportunity to study genetic structure and gene flow in archaeological populations. However, interpretations, particularly those based on single loci such as mitochondrial DNA, should be cautious because sex-specific migration and sampling issues may have dramatic effects.}, }
@article {pmid11842122, year = {2002}, author = {Di Bernardo, G and Del Gaudio, S and Cammarota, M and Galderisi, U and Cascino, A and Cipollaro, M}, title = {Enzymatic repair of selected cross-linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains.}, journal = {Nucleic acids research}, volume = {30}, number = {4}, pages = {e16}, pmid = {11842122}, issn = {1362-4962}, mesh = {Animals ; Base Sequence ; Bone and Bones/chemistry ; Cell Nucleus/genetics ; DNA/*analysis ; DNA Damage ; DNA Ligases/chemistry ; DNA Polymerase I/chemistry ; *DNA Repair ; Equidae/genetics ; History, Ancient ; Italy ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Paleontology ; Polymerase Chain Reaction/*methods ; Sequence Alignment ; }, abstract = {Ancient DNA (aDNA) samples extracted from the bone remains of six equids buried by the Vesuvius eruption in 79 AD were investigated to test pre-amplification and enzymatic repair procedures designed to enhance the rescue of nuclear genes. The extracts, which proved all positive for Equidae mtDNA amplification, proved positive only four times out of 18 when tested for single-copy Equidae nuclear genes (epsilon globin, p53 and gamma interferon). Pre-amplification did not change the number of retrieved aDNA sequences but 10 times out of 14 enzymatic repair restored the amplifiability of the genes analysed, proving that repair increases the rate of successful rescue from 22 to alpha(lambda)mu(omicron)sigma(tau) 80%. These findings support the hypothesis that some of these cross-linked aDNA molecules, which are not completely separated when DNA is extracted under denaturing conditions, become homoduplex substrates for Pol I and/or T4 ligase action upon renaturation. aDNA authenticity is proved by the homology of the nucleotide sequences of loci tested to the corresponding modern Equidae sequences. Data also indicate that cross-linked homoduplex molecules selected by denaturation of the extract are repaired without any chimera formation. The general features of aDNA amplification with and without denaturation and enzymatic repair are discussed.}, }
@article {pmid11839197, year = {2002}, author = {Limburg, PA and Weider, LJ}, title = {'Ancient' DNA in the resting egg bank of a microcrustacean can serve as a palaeolimnological database.}, journal = {Proceedings. Biological sciences}, volume = {269}, number = {1488}, pages = {281-287}, pmid = {11839197}, issn = {0962-8452}, mesh = {Alleles ; Animals ; Crustacea/*cytology/*genetics ; DNA/genetics/*isolation &amp; purification ; Databases, Nucleic Acid ; Ecosystem ; *Fossils ; Fresh Water/parasitology ; *Genetics, Population ; Germany ; Microsatellite Repeats/genetics ; Mutation/genetics ; Ovum/*metabolism ; Time Factors ; Zooplankton/*cytology/*genetics ; }, abstract = {Recent work on the diapausing egg banks of zooplankton, such as Daphnia (Crustacea: Anomopoda), indicates that these eggs can remain viable for decades while, theoretically, DNA can remain intact for even longer periods (i.e. centuries or millennia). We isolated diapausing eggs of Daphnia from a 30 m long sediment core taken from a hypereutrophic, northern German lake (Belauer See), with some eggs found in dated core material as old as 4500 years. Using microsatellite markers, we analysed the genetic structure of the resting eggs dated as old as ca. 200 years, and found that, although levels of heterozygosity remained remarkably stable, significant genetic differentiation (Nei's D = 0.36; F(ST) = 0.15) between recent and 'ancient' resting eggs (including allele frequency shifts and private alleles) was detected. These shifts represent either species-level changes in this complex (i.e. species-specific characters of ephippia are not always robust), or intraspecific shifts in genetic variation, or a combination of both. This study demonstrates that the egg banks of aquatic zooplankton can serve as repositories of both genetic (intrapopulational) and ecological (interspecific) information. The use of molecular markers, such as microsatellites, on diapausing egg/seed banks may open new avenues of enquiry related to tracking the long-term genetic (and/or species) shifts that are associated with long-term environmental changes.}, }
@article {pmid11824596, year = {2001}, author = {Eshleman, J and Smith, DG}, title = {Use of DNase to eliminate contamination in ancient DNA analysis.}, journal = {Electrophoresis}, volume = {22}, number = {20}, pages = {4316-4319}, doi = {10.1002/1522-2683(200112)22:20&lt;4316::AID-ELPS4316&gt;3.0.CO;2-V}, pmid = {11824596}, issn = {0173-0835}, support = {RR00169/RR/NCRR NIH HHS/United States ; RR05090/RR/NCRR NIH HHS/United States ; }, mesh = {Deoxyribonucleases/*metabolism ; Polymerase Chain Reaction ; Temperature ; }, abstract = {Using polymerase chain reaction (PCR) amplification, it is possible to analyze DNA from limited source template. This method has proved especially valuable in studies of ancient DNA and in forensic investigations. However, PCR reactions containing minimal or damaged source template are prone to contamination by DNA from a number of other sources. While standard protocols to prevent and/or detect contamination do exist, methods of eliminating contamination are needed to ensure the validity of results obtained. We present a method to eliminate sources of contamination in reagents and labware through the use of a DNase prior to PCR amplification without damaging even the minimal amounts of template present in ancient DNA samples. This method, suggested previously for forensics applications, appears to be effective in eliminating contamination without interfering with the amplification of ancient template.}, }
@article {pmid11808678, year = {2001}, author = {Holm, S}, title = {The privacy of Tutankhamen--utilising the genetic information in stored tissue samples.}, journal = {Theoretical medicine and bioethics}, volume = {22}, number = {5}, pages = {437-449}, pmid = {11808678}, issn = {1386-7415}, mesh = {Austria ; Cadaver ; *Cultural Characteristics ; Decision Making ; Egypt ; Famous Persons ; Genetic Privacy/*standards ; *Genetic Research ; Humans ; Indians, North American ; *Mummies ; Ownership ; *Third-Party Consent ; Tissue Banks/standards ; Tissue Preservation ; Tissue and Organ Harvesting ; United States ; }, abstract = {Recent technical developments in genetic testing has led to a situation where the DNA in previously stored tissue samples can be extracted and used for genetic analysis. This raises the question of how to decide whether a specific use of such samples should be allowed. Using the genetic testing of ancient DNA in general, and the DNA of the pharaoh Tutankhamen in particular as examples this paper analyses the question. It investigates whether ethical frameworks based on proxy consent, cultural affiliation, ownership, or the privacy rights of the dead are appropriate and justifiable in this context. The conclusion is that frameworks based on proxy consent, cultural affiliation, and ownership are not very useful.}, }
@article {pmid11782109, year = {2001}, author = {King, SJ and Godfrey, LR and Simons, EL}, title = {Adaptive and phylogenetic significance of ontogenetic sequences in Archaeolemur, subfossil lemur from Madagascar.}, journal = {Journal of human evolution}, volume = {41}, number = {6}, pages = {545-576}, doi = {10.1006/jhev.2001.0509}, pmid = {11782109}, issn = {0047-2484}, mesh = {*Adaptation, Physiological ; Animals ; Face/anatomy &amp; histology ; Female ; Fossils ; Lemur/*anatomy &amp; histology/growth &amp; development ; *Phylogeny ; Skull/anatomy &amp; histology ; Tooth Eruption ; }, abstract = {Among the best known of recently extinct Malagasy lemurs is Archaeolemur, which is represented by many hundreds of specimens. The phylogenetic affinities of this taxon are unclear, especially in light of recent preliminary analysis of ancient DNA which does not support its previously accepted close relationship with the living Indridae. We examined the nearly complete skeletons of two adults and one juvenile and other less complete specimens to reconstruct aspects of the ontogeny of Archaeolemur. To compare the development of Archaeolemur to that of living strepsirrhines we collected data on Propithecus verreauxi, Eulemur fulvus, and Lemur catta. Additionally, because Archaeolemur exhibits some morphological convergences with distantly related papionins, we tested for convergence in the developmental patterns of Archaeolemur and Macaca fascicularis. Data include the status of tooth eruption, craniofacial sutural closure, and postcranial epiphyseal fusion, as well as linear measurements. We used discriminant function analysis and other tools to explore ontogenetic similarities and differences. The adaptive and phylogenetic significance of ontogenetic information is discussed. Our analysis shows that Archaeolemur displays a clear strepsirrhine pattern of development with only minor macaque convergences. Among the Strepsirrhini, Archaeolemur is slightly more similar developmentally to E. fulvus and L. catta than to P. verreauxi. Some of the distinctive features of the ontogeny of Archaeolemur may be related to diet, while others bear apparent testimony to a relatively rapid absolute pace of growth and development.}, }
@article {pmid11758690, year = {2001}, author = {Montiel, R and Malgosa, A and Francalacci, P}, title = {Authenticating ancient human mitochondrial DNA.}, journal = {Human biology}, volume = {73}, number = {5}, pages = {689-713}, doi = {10.1353/hub.2001.0069}, pmid = {11758690}, issn = {0018-7143}, mesh = {Adult ; Amino Acid Substitution/genetics ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/genetics/*history ; Female ; Forensic Anthropology/*methods/standards ; Haplotypes ; History, 15th Century ; History, 16th Century ; Humans ; Male ; Peptides, Cyclic/*genetics/*history ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Restriction Mapping ; Sequence Analysis, DNA/*methods/standards ; Spain ; Specimen Handling/standards ; Tooth ; }, abstract = {The use of ancient DNA techniques in human studies has been hampered by problems of contamination with modern human DNA. The main problem has been that the object of study belongs to the same species as the observer, and the complete elimination of the contamination risk is seemingly unlikely. Contamination has even been detected in the most specialized laboratories in this field. In these kinds of studies it is therefore very important to detect contamination and to distinguish contaminants from authentic results. Here, we report the use of a strategy to authenticate the identity of ancient mitochondrial DNA (mtDNA), based on the previously established relationship between D-loop sequence substitutions and haplogroup-specific restriction site changes. Forty-four individuals from a 16th-century necropolis were analyzed, from which 28 control region sequences were obtained. These sequences were preclassified into haplogroups, according to the observed motifs. Subsequently, the DNA extracts from which the sequences were obtained, along with independent extracts of subsets of the same individuals, were subjected to restriction fragment length polymorphism (RFLP) analysis to compare and corroborate the results. Using this approach, 24 sequences were authenticated, while two were discarded because of result mismatches. The final distribution of the haplogroups in the sample, and the differences in the sequences, are two additional criteria of authentication.}, }
@article {pmid11756672, year = {2002}, author = {Greally, JM}, title = {Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {1}, pages = {327-332}, pmid = {11756672}, issn = {0027-8424}, support = {DK02467/DK/NIDDK NIH HHS/United States ; DK56786/DK/NIDDK NIH HHS/United States ; }, mesh = {CpG Islands ; Cytosine ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; *Genome, Human ; *Genomic Imprinting ; Guanine ; Humans ; Models, Genetic ; Open Reading Frames ; Retroelements/genetics ; Sequence Analysis, DNA ; Short Interspersed Nucleotide Elements/*genetics ; Time Factors ; }, abstract = {To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival.}, }
@article {pmid11752268, year = {2002}, author = {Van de Peer, Y and Taylor, JS and Joseph, J and Meyer, A}, title = {Wanda: a database of duplicated fish genes.}, journal = {Nucleic acids research}, volume = {30}, number = {1}, pages = {109-112}, pmid = {11752268}, issn = {1362-4962}, mesh = {Animals ; Chickens ; Chromosome Mapping ; *Databases, Genetic ; Evolution, Molecular ; Fishes/*genetics/growth &amp; development/physiology ; *Gene Duplication ; Genetic Variation ; Humans ; Information Storage and Retrieval ; Internet ; Mice ; Phylogeny ; Sequence Alignment ; Xenopus ; Zebrafish/genetics ; }, abstract = {Comparative genomics has shown that ray-finned fish (Actinopterygii) contain more copies of many genes than other vertebrates. A large number of these additional genes appear to have been produced during a genome duplication event that occurred early during the evolution of Actinopterygii (i.e. before the teleost radiation). In addition to this ancient genome duplication event, many lineages within Actinopterygii have experienced more recent genome duplications. Here we introduce a curated database named Wanda that lists groups of orthologous genes with one copy from man, mouse and chicken, one or two from tetraploid Xenopus and two or more ancient copies (i.e. paralogs) from ray-finned fish. The database also contains the sequence alignments and phylogenetic trees that were necessary for determining the correct orthologous and paralogous relationships among genes. Where available, map positions and functional data are also reported. The Wanda database should be of particular use to evolutionary and developmental biologists who are interested in the evolutionary and functional divergence of genes after duplication. Wanda is available at http://www.evolutionsbiologie.uni-konstanz.de/Wanda/.}, }
@article {pmid11734907, year = {2002}, author = {Nickle, DC and Learn, GH and Rain, MW and Mullins, JI and Mittler, JE}, title = {Curiously modern DNA for a "250 million-year-old" bacterium.}, journal = {Journal of molecular evolution}, volume = {54}, number = {1}, pages = {134-137}, doi = {10.1007/s00239-001-0025-x}, pmid = {11734907}, issn = {0022-2844}, support = {AI27757/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; Crystallization ; *DNA, Bacterial ; *Evolution, Molecular ; Fossils ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the approximately 59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies.}, }
@article {pmid11726688, year = {2001}, author = {Hofreiter, M and Jaenicke, V and Serre, D and von Haeseler, A and Pääbo, S}, title = {DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA.}, journal = {Nucleic acids research}, volume = {29}, number = {23}, pages = {4793-4799}, pmid = {11726688}, issn = {1362-4962}, mesh = {Animals ; *Artifacts ; Base Sequence ; Bone and Bones ; Cloning, Molecular ; Cytosine/*metabolism ; DNA/genetics/*metabolism ; *DNA Glycosylases ; Deamination ; History, Ancient ; Models, Genetic ; Molecular Sequence Data ; Mutagenesis ; N-Glycosyl Hydrolases/chemistry ; Paleontology/*methods ; Polymerase Chain Reaction/*methods ; Sequence Analysis, DNA ; Uracil-DNA Glycosidase ; }, abstract = {We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C-->T and G-->A substitutions. These substitutions can reach high proportions among the molecules amplified and are due to the occurrence of modified deoxycytidine residues in the template DNA. If the template DNA is treated with uracil N-glycosylase, these substitutions are dramatically reduced. They are thus likely to result from deamination of deoxycytidine residues. In addition, 'jumping PCR', i.e. the occurrence of template switching during PCR, may contribute to these substitutions. When DNA sequences are amplified from ancient DNA extracts where few template molecules initiate the PCR, precautions such as DNA sequence determination of multiple clones derived from more than one independent amplification are necessary in order to reduce the risk of determination of incorrect DNA sequences. When such precautionary measures are taken, errors induced by damage to the DNA template are unlikely to be more frequent than approximately 0.1% even under the unlikely scenario where each amplification starts from a single template molecule.}, }
@article {pmid11604130, year = {2001}, author = {Taylor, JS and Van de Peer, Y and Braasch, I and Meyer, A}, title = {Comparative genomics provides evidence for an ancient genome duplication event in fish.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {356}, number = {1414}, pages = {1661-1679}, pmid = {11604130}, issn = {0962-8436}, mesh = {Animals ; Chromosome Mapping ; Fishes/*genetics ; Gene Dosage ; *Gene Duplication ; Genome ; Genomics/*methods ; Humans ; *Phylogeny ; Sequence Alignment ; Zebrafish Proteins/*genetics ; }, abstract = {There are approximately 25 000 species in the division Teleostei and most are believed to have arisen during a relatively short period of time ca. 200 Myr ago. The discovery of 'extra' Hox gene clusters in zebrafish (Danio rerio), medaka (Oryzias latipes), and pufferfish (Fugu rubripes), has led to the hypothesis that genome duplication provided the genetic raw material necessary for the teleost radiation. We identified 27 groups of orthologous genes which included one gene from man, mouse and chicken, one or two genes from tetraploid Xenopus and two genes from zebrafish. A genome duplication in the ancestor of teleost fishes is the most parsimonious explanation for the observations that for 15 of these genes, the two zebrafish orthologues are sister sequences in phylogenies that otherwise match the expected organismal tree, the zebrafish gene pairs appear to have been formed at approximately the same time, and are unlinked. Phylogenies of nine genes differ a little from the tree predicted by the fish-specific genome duplication hypothesis: one tree shows a sister sequence relationship for the zebrafish genes but differs slightly from the expected organismal tree and in eight trees, one zebrafish gene is the sister sequence to a clade which includes the second zebrafish gene and orthologues from Xenopus, chicken, mouse and man. For these nine gene trees, deviations from the predictions of the fish-specific genome duplication hypothesis are poorly supported. The two zebrafish orthologues for each of the three remaining genes are tightly linked and are, therefore, unlikely to have been formed during a genome duplication event. We estimated that the unlinked duplicated zebrafish genes are between 300 and 450 Myr. Thus, genome duplication could have provided the genetic raw material for teleost radiation. Alternatively, the loss of different duplicates in different populations (i.e. 'divergent resolution') may have promoted speciation in ancient teleost populations.}, }
@article {pmid11596002, year = {2001}, author = {González-Oliver, A and Márquez-Morfín, L and Jiménez, JC and Torre-Blanco, A}, title = {Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo.}, journal = {American journal of physical anthropology}, volume = {116}, number = {3}, pages = {230-235}, doi = {10.1002/ajpa.1118}, pmid = {11596002}, issn = {0002-9483}, mesh = {Anthropology, Physical ; Bone and Bones ; DNA Primers ; DNA, Mitochondrial/*genetics ; Fossils ; *Genetics, Population ; Humans ; Indians, North American/*genetics ; Mexico ; Pedigree ; Polymerase Chain Reaction ; }, abstract = {Ancient DNA from the bone remains of 25 out of 28 pre-Columbian individuals from the Late Classic-Postclassic Maya site of Xcaret, Quintana Roo, was recovered, and mitochondrial DNA (mtDNA) was amplified by using the polymerase chain reaction. The presence of the four founding Amerindian mtDNA lineages was investigated by restriction analysis and by direct sequencing in selected individuals. The mtDNA lineages A, B, and C were found in this population. Eighty-four percent of the individuals were lineage A, whereas lineages B and C were present at low frequencies, 4% and 8%, respectively. Lineage D was absent from our sample. One individual did not possess any of the four lineages. Six skeletons out of 7 dated from the Late Classic period were haplotype A, whereas 11 skeletons out of 16 dated from the Postclassic period were also haplotype A. The distribution of mtDNA lineages in the Xcaret population contrasts sharply with that found in ancient Maya from Copán, which lack lineages A and B. On the other hand, our results resemble more closely the frequencies of mtDNA lineages found in contemporary Maya from the Yucatán Peninsula and in other Native American contemporary populations of Mesoamerican origin.}, }
@article {pmid11590044, year = {2001}, author = {Willmann, MR}, title = {Studying the historic migrations of the Irish potato famine pathogen using ancient DNA.}, journal = {Trends in plant science}, volume = {6}, number = {10}, pages = {450}, doi = {10.1016/s1360-1385(01)02147-1}, pmid = {11590044}, issn = {1360-1385}, mesh = {Biological Specimen Banks ; DNA, Mitochondrial ; DNA, Plant ; History, 19th Century ; History, 20th Century ; Ireland ; Mexico ; Phytophthora/*genetics ; Plant Diseases/history/*microbiology ; Solanum tuberosum/*microbiology ; United States ; }, }
@article {pmid11584593, year = {2001}, author = {Gernaey, AM and Minnikin, DE and Copley, MS and Dixon, RA and Middleton, JC and Roberts, CA}, title = {Mycolic acids and ancient DNA confirm an osteological diagnosis of tuberculosis.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {81}, number = {4}, pages = {259-265}, doi = {10.1054/tube.2001.0295}, pmid = {11584593}, issn = {1472-9792}, mesh = {Adult ; Biomarkers/analysis ; Chromatography, High Pressure Liquid ; DNA, Bacterial/*analysis ; History, Medieval ; Humans ; Male ; Mycobacterium tuberculosis/*chemistry ; Mycolic Acids/*analysis ; Paleopathology ; Polymerase Chain Reaction/methods ; Ribs/microbiology ; Tuberculosis, Osteoarticular/*diagnosis/history ; Tuberculosis, Spinal/diagnosis/history ; }, abstract = {SETTING: The underlying trends in the past epidemiology of tuberculosis (TB) are obscure, requiring recourse to the archaeological record. It would therefore be of value to develop methods for reliable TB diagnosis in ancient populations.<br><br>OBJECTIVE: To test the capability of two biomarkers, Mycobacterium tuberculosis complex mycolic acids and a DNA target (IS6110), for confirming an osteological diagnosis of TB in medieval individuals, based on the presence of Pott's disease and/or rib lesions.<br><br>DESIGN: Osteological examination of three archaeological individuals (Medieval: approximately 1000 years old) revealed a Pott's disease case, one with no changes consistent with TB and one with rib lesions. Rib samples from these individuals were examined for the presence of Mycobacterium tuberculosis complex mycolic acids and mycobacterial DNA.<br><br>RESULTS: Mycobacterium tuberculosis complex mycolic acids and the DNA target were detected in the Pott's disease case, whilst mycolic acids (insufficient for confirmation) alone were detected in the rib lesion case.<br><br>CONCLUSIONS: Biomarkers provide a sensitive tool to detect ancient TB. Mycobacterium tuberculosis DNA is not distributed homogeneously, making multiple sampling essential. Mycolic acids seem more reliable for ancient TB diagnosis than IS6110. The demonstrated stability of mycolic acids show that they may be of value in tracing the palaeoepidemiology of tuberculosis back into antiquity.}, }
@article {pmid11441456, year = {2001}, author = {Schutkowski, H}, title = {5th International Ancient DNA Conference, 12-14 July 2000.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {59}, number = {2}, pages = {179-181}, pmid = {11441456}, issn = {0003-5548}, mesh = {DNA/*history ; Europe ; Genetics, Population/*history ; History, Ancient ; History, Medieval ; Humans ; Transients and Migrants/*history ; }, }
@article {pmid11429174, year = {2001}, author = {Loreille, O and Roumat, E and Verneau, O and Bouchet, F and Hänni, C}, title = {Ancient DNA from Ascaris: extraction amplification and sequences from eggs collected in coprolites.}, journal = {International journal for parasitology}, volume = {31}, number = {10}, pages = {1101-1106}, doi = {10.1016/s0020-7519(01)00214-4}, pmid = {11429174}, issn = {0020-7519}, mesh = {Animals ; Ascaris/*genetics ; Base Sequence ; Belgium ; Cytochrome b Group/chemistry/genetics ; DNA, Helminth/chemistry/genetics/*isolation &amp; purification ; Feces/parasitology ; *Fossils ; Molecular Sequence Data ; Paleopathology/methods ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/chemistry/genetics/isolation &amp; purification ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {On the Middle-Age site of Namur (Belgium) the analysis of coprolites revealed the presence of many well-preserved Ascaris eggs. Following rehydratation of the coprolite samples, 104 eggs were collected and extracted with an ultrasonication and phenol-chloroform based method. Three overlapping fragments of the 18S rRNA gene and one fragment of the cytochrome b gene have been reproducibly amplified, cloned and sequenced. The analysis of these sequences confirms the identification of the eggs as coming from Ascaris. Our study reveals that coprolites can be an interesting source of parasites that can be readily identified using molecular approaches. The study of ancient DNA from helminth parasites is of interest as it may answer long-standing questions in the history of infectious diseases and gives a possibility to compare these ancient sequences with those of modern populations.}, }
@article {pmid11428465, year = {2001}, author = {Watanobe, T and Ishiguro, N and Okumura, N and Nakano, M and Matsui, A and Hongo, H and Ushiro, H}, title = {Ancient mitochondrial DNA reveals the origin of Sus scrofa from Rebun Island, Japan.}, journal = {Journal of molecular evolution}, volume = {52}, number = {3}, pages = {281-289}, doi = {10.1007/s002390010156}, pmid = {11428465}, issn = {0022-2844}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Haplotypes/*genetics ; Japan ; *Phylogeny ; Polymerase Chain Reaction ; Swine/*genetics ; }, abstract = {The Kabukai A site (5 to 8C A.D.) of the Okhotsk cultural area is on Rebun Island, a small island near the coast, north-northwest of Hokkaido, Japan. Specimens of Sus scrofa, called the Sakhalin pig, were discovered in five cultural layers at the Kabukai A site. Ancient DNA was extracted from the remains of 42 Sakhalin pig bones. Thirty-nine nucleotide sequences of the 574-bp mitochondrial DNA control region, estimated to have originated from at least 21 individuals, were amplified and analyzed phylogenetically. Nine distinct haplotypes (A1, A2, A3, B1, B2, C1, C2, D1, and D2) from this site were classified into four haplotype groups (A, B, C, and D) by parsimonious network analysis. Phylogenetic analysis of 9 ancient and 55 modern haplotypes indicated that the population of Sakhalin pigs at the Kabukai A site belonged to two distinct clusters; haplotype groups A and B formed a cluster comprised only of themselves, and haplotype groups C and D belonged to the cluster of one of the two genetic groups of Japanese wild boars uniquely distributed in the western part of Japan, including one northeast Mongolian wild boar. Analysis of the haplotype distribution among three archaeological sites and their historical transitions among the five layers reflecting the cultural periods at the Kabukai A site suggests that the Sakhalin pig populations were introduced from Sakhalin island and the Amur River basin in the northeastern Eurasian continent together with some cultural influences.}, }
@article {pmid11387643, year = {2001}, author = {Melton, T and Nelson, K}, title = {Forensic mitochondrial DNA analysis: two years of commercial casework experience in the United States.}, journal = {Croatian medical journal}, volume = {42}, number = {3}, pages = {298-303}, pmid = {11387643}, issn = {0353-9504}, mesh = {Blood Chemical Analysis/statistics &amp; numerical data ; Bone and Bones/chemistry ; DNA Fingerprinting/methods/standards/*statistics &amp; numerical data ; DNA, Mitochondrial/*analysis ; Equipment Contamination/statistics &amp; numerical data ; Female ; Forensic Medicine/*methods/*statistics &amp; numerical data ; Hair/chemistry ; Humans ; Male ; Nucleic Acid Amplification Techniques/standards/statistics &amp; numerical data ; Sensitivity and Specificity ; United States ; }, abstract = {AIM: To describe mitochondrial DNA (mtDNA) forensic casework experience in a commercial laboratory in the United States.<br><br>METHODS: Frequency statistics were kept for two years on all aspects of mtDNA forensic cases, including types of clientele, types of samples, levels of sample success and failure, site heteroplasmy, length heteroplasmy, contamination, rates of failures to exclude, and match statistics using a mtDNA sequence database.<br><br>RESULTS: Low sample failure rate was observed, especially since an "ancient DNA" approach was used for samples with degraded DNA. Levels of contamination were low, and the observed site and length heteroplasmy did not confound the interpretation of results. The data collected from mtDNA haplotypes developed in casework showed extremely high diversity of haplotypes consistent with other formally developed databases.<br><br>CONCLUSIONS: MtDNA forensic analysis in the private sector was successfully applied to many different types of samples overall, with minimal rates of complication due to sample handling challenges (degraded DNA, minimal samples, contamination) and sequence-specific phenomena (site and length heteroplasmy).}, }
@article {pmid11337473, year = {2001}, author = {Hughes, AL and da Silva, J and Friedman, R}, title = {Ancient genome duplications did not structure the human Hox-bearing chromosomes.}, journal = {Genome research}, volume = {11}, number = {5}, pages = {771-780}, pmid = {11337473}, issn = {1088-9051}, support = {GM34940/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromosomes, Human/*genetics ; *Evolution, Molecular ; *Gene Duplication ; Genes, Homeobox/*genetics ; *Genome ; Humans ; Multigene Family/genetics ; Phylogeny ; Time ; }, abstract = {The fact that there are four homeobox (Hox) clusters in most vertebrates but only one in invertebrates is often cited as evidence for the hypothesis that two rounds of genome duplication by polyploidization occurred early in vertebrate history. In addition, it has been observed in humans and other mammals that numerous gene families include paralogs on two or more of the four Hox-bearing chromosomes (the chromosomes bearing the Hox clusters; i.e., human chromosomes 2, 7, 12, and 17), and the existence of these paralogs has been taken as evidence that these genes were duplicated along with the Hox clusters by polyploidization. We tested this hypothesis by phylogenetic analysis of 42 gene families including members on two or more of the human Hox-bearing chromosomes. In 32 of these families there was evidence against the hypothesis that gene duplication occurred simultaneously with duplication of the Hox clusters. Phylogenies of 14 families supported the occurrence of one or more gene duplications before the origin of vertebrates, and of 15 gene duplication times estimated for gene families evolving in a clock-like manner, only six were dated to the same time period early in vertebrate history during which the Hox clusters duplicated. Furthermore, of gene families duplicated around the same time as the Hox clusters, the majority showed topologies inconsistent with their having duplicated simultaneously with the Hox clusters. The results thus indicate that ancient events of genome duplication, if they occurred at all, did not play an important role in structuring the mammalian Hox-bearing chromosomes.}, }
@article {pmid11331901, year = {2001}, author = {Hofreiter, M and Serre, D and Poinar, HN and Kuch, M and Pääbo, S}, title = {Ancient DNA.}, journal = {Nature reviews. Genetics}, volume = {2}, number = {5}, pages = {353-359}, doi = {10.1038/35072071}, pmid = {11331901}, issn = {1471-0056}, mesh = {Animals ; *Biological Evolution ; DNA/*genetics ; Humans ; *Paleontology ; *Phylogeny ; }, abstract = {DNA that has been recovered from archaeological and palaeontological remains makes it possible to go back in time and study the genetic relationships of extinct organisms to their contemporary relatives. This provides a new perspective on the evolution of organisms and DNA sequences. However, the field is fraught with technical pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human remains are studied.}, }
@article {pmid11319267, year = {2001}, author = {Greenwood, AD and Lee, F and Capelli, C and DeSalle, R and Tikhonov, A and Marx, PA and MacPhee, RD}, title = {Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives.}, journal = {Molecular biology and evolution}, volume = {18}, number = {5}, pages = {840-847}, doi = {10.1093/oxfordjournals.molbev.a003865}, pmid = {11319267}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Bone and Bones/chemistry ; Cloning, Molecular ; Consensus Sequence ; Cytochrome b Group/*genetics ; Cytosine/chemistry ; DNA/blood/genetics/*isolation &amp; purification ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; DNA, Viral/analysis ; Elephants/blood/classification/*genetics ; *Endogenous Retroviruses/*genetics ; *Evolution, Molecular ; *Fossils ; Genes, Viral ; Genes, pol ; Genomic Library ; Guanosine/chemistry ; Hyraxes/*genetics ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; Muscles/chemistry ; Nucleic Acid Amplification Techniques ; Phylogeny ; Polymerase Chain Reaction ; Proviruses/*genetics/*isolation &amp; purification ; Retroviridae/*genetics/*isolation &amp; purification ; Sequence Homology, Amino Acid ; Species Specificity ; Tooth/chemistry ; Trichechus manatus/blood/*genetics ; }, abstract = {Endogenous retrovirus-like elements characterizable by a leucine tRNA primer (ERV-Ls) are reiterated genomic sequences known to be widespread in mammals, including humans. They may have arisen from an ancestral foamy virus-like element by successful germ line infection followed by copy number expansion. However, among mammals, only primates and rodents have thus far exhibited high copy number amplification and sequence diversification. Conventionally, empirical studies of proviral amplification and diversification have been limited to extant species, but taxa having good Quaternary fossil records could potentially be investigated using the techniques of "ancient" DNA research. To examine evolutionary parameters of ERV-Ls across both time and taxa, we characterized this proviral class in the extinct woolly mammoth (Mammuthus primigenius) and living elephants, as well as extant members of the larger clade to which they belong (Uranotheria, a group containing proboscideans, sirenians, hyraxes, and their extinct relatives). Ungulates and carnivores previously analyzed demonstrated low copy numbers of ERV-L sequences, and thus it was expected that uranotheres should as well. Here, we show that all uranothere taxa exhibit unexpectedly numerous and diverse ERV-L sequence complements, indicating active expansion within this group of lineages. Selection is the most parsimonious explanation for observed differences in ERV-L distribution and frequency, with relative success being reflected in the persistence of certain elements over a variety of sampled time depths (as can be observed by comparing sequences from fossil and extant elephantid samples).}, }
@article {pmid11309754, year = {2001}, author = {Relethford, JH}, title = {Absence of regional affinities of Neandertal DNA with living humans does not reject multiregional evolution.}, journal = {American journal of physical anthropology}, volume = {115}, number = {1}, pages = {95-98}, doi = {10.1002/ajpa.1060}, pmid = {11309754}, issn = {0002-9483}, mesh = {Africa ; Animals ; Anthropology, Physical ; *Biological Evolution ; DNA Fingerprinting ; DNA, Mitochondrial/*genetics ; *Emigration and Immigration ; Europe ; *Gene Frequency ; Hominidae/*genetics ; Humans ; Models, Theoretical ; }, abstract = {The recent extraction of mitochondrial DNA sequences from three European Neandertal fossils has led many to the conclusion that ancient DNA analysis supports the African replacement model of modern human origins and rejects models of multiregional evolution that propose some Neandertal ancestry in living humans. This conclusion is based, in part, on the lack of regional affinity of Neandertal DNA to that from living Europeans. Consideration of migration matrix models shows that this conclusion is premature, since under a model of interregional gene flow we expect to see similar levels of Neandertal ancestry in all contemporary regions, and living Europeans should not necessarily show closer affinity. The absence of regional affinity in Neandertal DNA does not distinguish between replacement and multiregional models.}, }
@article {pmid11305426, year = {2001}, author = {Gabriel, MN and Huffine, EF and Ryan, JH and Holland, MM and Parsons, TJ}, title = {Improved MtDNA sequence analysis of forensic remains using a "mini-primer set" amplification strategy.}, journal = {Journal of forensic sciences}, volume = {46}, number = {2}, pages = {247-253}, pmid = {11305426}, issn = {0022-1198}, mesh = {Bone and Bones ; DNA Primers ; DNA, Mitochondrial/*genetics ; Forensic Anthropology/*methods ; Humans ; *Nucleic Acid Amplification Techniques ; Polymerase Chain Reaction ; Reference Values ; Specimen Handling ; Time Factors ; }, abstract = {Mitochondrial DNA (mtDNA) analysis of highly degraded skeletal remains is often used for forensic identification due largely to the high genome copy number per cell. Literature from the "ancient DNA" field has shown that highly degraded samples contain populations of intact DNA molecules that are severely restricted in size (1-4). Hand et al. have demonstrated the targeting and preferential amplification of authentic human DNA sequences with small amplicon products of 150 bp or less (1,2). Given this understanding of ancient DNA preservation and amplification, we report an improved approach to forensic mtDNA analysis of hypervariable regions 1 and 2 (HV1/HV2) in highly degraded specimens. This "mini-primer set" (MPS) amplification strategy consists of four overlapping products that span each of the HV regions and range from 126 to 170 bp, with an average size of 141 bp. For this study, 11 extracts representing a range of sample quality were prepared from nonprobative forensic specimens. We demonstrate a significant increase in MPS amplification success when compared to testing methods using approximately 250 bp amplicons. Further, 16 of 17 independent amplifications previously "unreported" due to mixed sequences provided potentially reportable sequence data from a single, authentic template with MPS testing.}, }
@article {pmid11296282, year = {2001}, author = {Poinar, HN and Kuch, M and Sobolik, KD and Barnes, I and Stankiewicz, AB and Kuder, T and Spaulding, WG and Bryant, VM and Cooper, A and Pääbo, S}, title = {A molecular analysis of dietary diversity for three archaic Native Americans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {8}, pages = {4317-4322}, pmid = {11296282}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial ; *Diet ; Feces ; *Fossils ; Gas Chromatography-Mass Spectrometry ; Humans ; *Indians, North American ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; Texas ; }, abstract = {DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2-4 different animal species and 4-8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.}, }
@article {pmid11289521, year = {2001}, author = {Zink, A and Haas, CJ and Reischl, U and Szeimies, U and Nerlich, AG}, title = {Molecular analysis of skeletal tuberculosis in an ancient Egyptian population.}, journal = {Journal of medical microbiology}, volume = {50}, number = {4}, pages = {355-366}, doi = {10.1099/0022-1317-50-4-355}, pmid = {11289521}, issn = {0022-2615}, mesh = {Amelogenin ; Bone and Bones/*microbiology ; DNA Transposable Elements ; DNA, Bacterial/*analysis/isolation &amp; purification ; DNA-Binding Proteins/genetics ; Dental Enamel Proteins/genetics ; Egypt, Ancient/epidemiology ; Female ; History, Ancient ; Humans ; Male ; Mycobacterium tuberculosis/classification/genetics/*isolation &amp; purification ; *Nuclear Proteins ; *Paleopathology ; Polymerase Chain Reaction ; Sex Determination Analysis/methods ; Sex-Determining Region Y Protein ; *Transcription Factors ; Tuberculosis, Osteoarticular/epidemiology/*history/microbiology/pathology ; }, abstract = {A paleomicrobiological study was performed on 37 skeletal tissue specimens from cadavers in the necropolis of Thebes-West, Upper Egypt, (2120-500 BC) and four from the necropolis of Abydos (3000 BC). The subjects had typical macromorphological evidence of osseous tuberculosis (n = 3), morphological alterations that were not specific, but probably resulted from tuberculosis (n = 17), or were without morphological osseous changes (n = 21). DNA was extracted from these bone samples and amplified by PCR with a primer pair that recognised the Mycobacterium tuberculosis complex insertion sequence IS6110. To confirm specificity of the analysis, the amplification products of several samples were subjected to restriction enzyme digestion, or direct sequencing, or both. In 30 of the 41 cases analysed, ancient DNA was demonstrated by amplification by the presence of the human beta-actin or the amelogenin gene and nine of these cases were positive for M. tuberculosis DNA. The results were confirmed by restriction endonuclease digestion and sequencing. A positive result for M. tuberculosis DNA was seen in two of the three cases with typical morphological signs of tuberculosis and amplifiable DNA, in five of 13 non-specific, but probable cases (including two cases from c. 3000 BC), but also in two of 14 cases without pathological bone changes. These observations confirm that tuberculosis may be diagnosed unequivocally in skeletal material from ancient Egypt, even dating back to c. 3000 BC. As a positive molecular reaction was observed in most of the typical cases of skeletal tuberculosis, in about one-third of non-specific, but probable tuberculous osseous changes and, surprisingly, in about one-seventh of unremarkable samples, this suggests that infection with M. tuberculosis was relatively frequent in ancient Egypt.}, }
@article {pmid11275746, year = {2001}, author = {Montagnon, D and Ravaoarimanana, B and Rakotosamimanana, B and Rumpler, Y}, title = {Ancient DNA from Megaladapis edwardsi (Malagasy Subfossil): preliminary results using partial cytochrome b sequence.}, journal = {Folia primatologica; international journal of primatology}, volume = {72}, number = {1}, pages = {30-32}, doi = {10.1159/000049916}, pmid = {11275746}, issn = {0015-5713}, mesh = {Animals ; Base Sequence ; Bone and Bones/chemistry/enzymology ; Cytochrome b Group/*genetics ; DNA/*chemistry ; Databases, Factual ; *Fossils ; Lemur/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; }, }
@article {pmid11231157, year = {2001}, author = {Loreille, O and Orlando, L and Patou-Mathis, M and Philippe, M and Taberlet, P and Hänni, C}, title = {Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages.}, journal = {Current biology : CB}, volume = {11}, number = {3}, pages = {200-203}, doi = {10.1016/s0960-9822(01)00046-x}, pmid = {11231157}, issn = {0960-9822}, mesh = {Animals ; Carnivora/*genetics ; Fossils ; Phylogeny ; Polymerase Chain Reaction ; *Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The cave bear, Ursus spelaeus, represents one of the most frequently found paleontological remains from the Pleistocene in Europe. The species has always been confined to Europe and was contemporary with the brown bear, Ursus arctos. Relationships between the cave bear and the two lineages of brown bears defined in Europe, as well as the origins of the two species, remain controversial, mainly due to the wide morphological diversity of the fossil remains, which makes interpretation difficult [1, 2]. Sequence analysis of ancient DNA is a useful tool for resolving such problems because it provides an independent source of data [3]. We previously amplified a short DNA fragment of the mitochondrial DNA control region (mt control region) of a 40,000-year-old Ursus spelaeus sample [4]. In this paper, we describe the DNA analysis of two mtDNA regions, the control region and the cytochrome b gene. Control region sequences were obtained from ten samples of cave bears ranging from 130,000 to 20,000 years BP, and one particularly well-conserved sample gave a complete cyt b sequence. Our data demonstrate that cave bears split largely before the lineages of brown bears around 1.2 million years ago. Given its abundance, its wide distribution in space and time, and its large morphological diversity, the cave bear is a promising model for direct observation of the evolution of sequences throughout time, extinction periods, and the differentiation of populations shaped by climatic fluctuations during the Pleistocene.}, }
@article {pmid11209041, year = {2001}, author = {Relethford, JH}, title = {Ancient DNA and the origin of modern humans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {2}, pages = {390-391}, pmid = {11209041}, issn = {0027-8424}, mesh = {Africa, Eastern ; Animals ; Archaeology ; Australia ; *Biological Evolution ; Chromosomes, Human, Pair 11/genetics ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Evolution, Molecular ; Fossils ; Hominidae/classification/*genetics ; Humans ; Species Specificity ; }, }
@article {pmid11204924, year = {2000}, author = {Sola, C and Filliol, I and Legrand, E and Rastogi, N}, title = {[Recent developments of spoligotyping as applied to the study of epidemiology, biodiversity and molecular phylogeny of the Mycobacterium tuberculosis complex].}, journal = {Pathologie-biologie}, volume = {48}, number = {10}, pages = {921-932}, pmid = {11204924}, issn = {0369-8114}, mesh = {Animals ; Cattle ; DNA, Intergenic ; *Ecosystem ; *Evolution, Molecular ; Genotype ; Humans ; Mycobacterium tuberculosis/classification/*genetics ; Nucleic Acid Hybridization ; Oligonucleotides ; *Phylogeny ; Repetitive Sequences, Nucleic Acid ; Tuberculosis/*epidemiology/microbiology ; }, abstract = {Spoligotyping (for 'spacer-oligonucleotide-typing'), a rapid method for genotyping of Mycobacterium tuberculosis complex using the principle of reverse hybridization, is based on the structure of the direct repeat (DR) locus. The DR locus is made up of a variable number of 36 bp DR repeats that are separated by unique inter-DR sequences of 35 to 41 bp. Fast and highly discriminatory, spoligotyping is an useful alternative to the IS6110-RFLP reference method for molecular typing of M. tuberculosis, in particular for isolates possessing five or few copies of IS6110. In this paper, we review the state of the art of spoligotyping through its main current applications. After a brief introduction to the principle of the technique and its description, we successively review recently published results concerning the molecular epidemiology of tuberculosis in humans and cattle, and discuss the main genotyping strategies currently in use to fingerprint the M. tuberculosis complex organisms. We also describe the recent applications of spoligotyping to study ancient DNA and report on recent developments of this technique to study the biodiversity of the M. tuberculosis complex, its contribution towards improved taxonomy and phylogenetics of the M. tuberculosis complex. Last but not least, potential applications of spoligotyping to study DNA recombination mechanisms are also discussed.}, }
@article {pmid11196299, year = {2001}, author = {Madden, M and Salo, WL and Streitz, J and Aufderheide, AC and Fornaciari, G and Jaramillo, C and Vallejo, GA and Yockteng, R and Arriaza, B and Cárdenas-Arroyo, F and Guhl, F}, title = {Hybridization screening of very short PCR products for paleoepidemiological studies of Chagas' disease.}, journal = {BioTechniques}, volume = {30}, number = {1}, pages = {102-4, 106, 108-9}, doi = {10.2144/01301st07}, pmid = {11196299}, issn = {0736-6205}, mesh = {Animals ; Base Sequence ; Chagas Disease/*genetics/parasitology ; DNA, Kinetoplast/*genetics ; Humans ; Molecular Sequence Data ; Mummies/parasitology ; Nucleic Acid Hybridization ; Paleopathology ; Polymerase Chain Reaction ; RNA Probes ; Sequence Homology, Nucleic Acid ; Trypanosoma cruzi/*genetics ; }, abstract = {Single strands of very short PCR products can be covalently immobilized to a slide and then easily detected by probe hybridization. In this work, the PCR product was a 70-nucleotide segment of ancient DNA, representing a portion of repeat mini-circle DNA from the kinetoplast of Trypanosoma cruzi, the infectious agent of Chagas' disease (American Trypanosomiasis). The target segment was initially established to be present in soft tissue samples taken from four "naturally" mummified Andean bodies using PCR followed by cloning and sequencing. Hybridization screening of the covalently immobilized PCR products positively identified products from 25 of 27 specimens of different tissues from these four mummies. The method appears to be ideal for the purpose of screening a large number of specimens when the target PCR product is very short.}, }
@article {pmid11185910, year = {2000}, author = {Ueda, S}, title = {[Human dispersal across the earth disclosed by ancient DNA analysis].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {45}, number = {16}, pages = {2572-2578}, pmid = {11185910}, issn = {0039-9450}, mesh = {Animals ; Asia ; DNA/*genetics ; Europe ; *Fossils ; Genetic Variation ; Hominidae/*genetics ; Humans ; *Phylogeny ; *Sequence Analysis, DNA ; }, }
@article {pmid11179647, year = {2001}, author = {Möhlenhoff, P and Müller, L and Gorbushina, AA and Petersen, K}, title = {Molecular approach to the characterisation of fungal communities: methods for DNA extraction, PCR amplification and DGGE analysis of painted art objects.}, journal = {FEMS microbiology letters}, volume = {195}, number = {2}, pages = {169-173}, doi = {10.1111/j.1574-6968.2001.tb10516.x}, pmid = {11179647}, issn = {0378-1097}, mesh = {Biofilms ; DNA, Fungal/*analysis ; DNA, Ribosomal/*analysis ; Electrophoresis/*methods ; Fungi/growth &amp; development/*isolation &amp; purification/ultrastructure ; Microscopy, Electron, Scanning ; *Paintings ; Polymerase Chain Reaction ; RNA, Ribosomal, 28S/genetics ; }, abstract = {A protocol for efficient extraction of fungal DNA from micromycetes colonising painted art objects was developed. Polymerase chain reaction (PCR) inhibitors were successfully removed by a combined application of a Chelex-100 adsorption resin and a Geneclean Kit for Ancient DNA. Universal fungal primers for PCR amplification of 28S rDNA (U1 and U2) were tested for their applicability in denaturing gradient gel electrophoresis (DGGE) analysis of fungal communities. Artificially produced mortar samples inoculated with fungal pure cultures isolated from mural paintings were used as model objects for DNA extractions and DGGE analysis. Good resolution in DGGE was achieved using 260-bp rDNA fragments amplified with U1/DGGE and U2 primers directly from model communities.}, }
@article {pmid11158385, year = {2001}, author = {Hansen, A and Willerslev, E and Wiuf, C and Mourier, T and Arctander, P}, title = {Statistical evidence for miscoding lesions in ancient DNA templates.}, journal = {Molecular biology and evolution}, volume = {18}, number = {2}, pages = {262-265}, doi = {10.1093/oxfordjournals.molbev.a003800}, pmid = {11158385}, issn = {0737-4038}, mesh = {Animals ; Artifacts ; DNA/*analysis ; *Fossils ; *Genetic Variation ; Mutation ; Plants/genetics ; Polymerase Chain Reaction ; Taq Polymerase/metabolism ; }, }
@article {pmid11148985, year = {1999}, author = {Marin, A and Cerutti, N and Massa, ER}, title = {Use of the amplification refractory mutation system (ARMS) in the study of HbS in predynastic Egyptian remains.}, journal = {Bollettino della Societa italiana di biologia sperimentale}, volume = {75}, number = {5-6}, pages = {27-30}, pmid = {11148985}, issn = {0037-8771}, mesh = {Anemia, Sickle Cell/ethnology/*genetics/pathology ; DNA/*analysis/isolation &amp; purification ; Egypt/ethnology ; Hemoglobin, Sickle/*genetics ; Humans ; *Mummies/pathology ; Mutation ; Polymerase Chain Reaction/*methods ; Tooth/chemistry ; }, abstract = {We conducted a molecular investigation of the presence of sicklemia in six predynastic Egyptian mummies (about 3200 BC) from the Anthropological and Ethnographic Museum of Turin. Previous studies of these remains showed the presence of severe anemia, while histological preparations of mummified tissues revealed hemolytic disorders. DNA was extracted from dental samples with a silica-gel method specific for ancient DNA. A modification of the polymerase chain reaction (PCR), called amplification refractory mutation system (ARMS) was then applied. ARMS is based on specific priming of the PCR and it permits diagnosis of single nucleotide mutations. In this method, amplification can occur only in the presence of the specific mutation being studied. The amplified DNA was analyzed by electrophoresis. In samples of three individuals, there was a band at the level of the HbS mutated fragment, indicating that they were affected by sicklemia. On the basis of our results, we discuss the possible uses of new molecular investigation systems in paleopathological diagnoses of genetic diseases and viral, bacterial and fungal infections.}, }
@article {pmid11110896, year = {2000}, author = {Drummond, A and Rodrigo, AG}, title = {Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA.}, journal = {Molecular biology and evolution}, volume = {17}, number = {12}, pages = {1807-1815}, doi = {10.1093/oxfordjournals.molbev.a026281}, pmid = {11110896}, issn = {0737-4038}, support = {59174//PHS HHS/United States ; }, mesh = {DNA, Viral/genetics ; *Evolution, Molecular ; HIV/genetics ; *Models, Statistical ; Mutation ; *Phylogeny ; }, abstract = {Reconstruction of evolutionary relationships from noncontemporaneous molecular samples provides a new challenge for phylogenetic reconstruction methods. With recent biotechnological advances there has been an increase in molecular sequencing throughput, and the potential to obtain serial samples of sequences from populations, including rapidly evolving pathogens, is fast being realized. A new method called the serial-sample unweighted pair grouping method with arithmetic means (sUPGMA) is presented that reconstructs a genealogy or phylogeny of sequences sampled serially in time using a matrix of pairwise distances. The resulting tree depicts the terminal lineages of each sample ending at a different level consistent with the sample's temporal order. Since sUPGMA is a variant of UPGMA, it will perform best when sequences have evolved at a constant rate (i.e., according to a molecular clock). On simulated data, this new method performs better than standard cluster analysis under a variety of longitudinal sampling strategies. Serial-sample UPGMA is particularly useful for analysis of longitudinal samples of viruses and bacteria, as well as ancient DNA samples, with the minimal requirement that samples of sequences be ordered in time.}, }
@article {pmid11082781, year = {2000}, author = {Pusch, CM and Broghammer, M and Scholz, M}, title = {Cremation practices and the survival of ancient DNA: burnt bone analyses via RAPD-mediated PCR.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {3}, pages = {237-251}, pmid = {11082781}, issn = {0003-5548}, mesh = {Age Determination by Skeleton ; Animals ; Bone and Bones/*chemistry ; DNA Damage/*genetics ; DNA, Mitochondrial/*genetics ; Humans ; *Mortuary Practice ; *Paleontology ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Sequence Analysis, DNA ; }, abstract = {Numerous burial rites have been developed in different time periods of human cultural evolution. One of the most interesting burial practices was the ritual cremation of human bodies. Due to the respective cultural and religious background, brand graves are known where human remains had been buried together with burnt bones of animal origin. To date, burnt bone samples have been refractory to PCR-mediated amplification. D/L values of aspartic acid far greater than 80 x 10(-3) were measured in the samples thus indicating the presence of severely nicked and fragmented nucleic acids. In order to differentiate between burial gift of animal origin and burnt human specimens we established a highly sensitive protocol that addresses all the shortcomings connected to degraded ancient DNA. With the novel procedure it was possible to classify 4 specimens ranging from 2,000-5,000 BP on the basis of mitochondrial DNA sequences.}, }
@article {pmid11082780, year = {2000}, author = {Scholz, M and Pusch, CM}, title = {[Contamination through preparation: risk of molecular genetic studies by using biological preservatives for museum collections].}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {3}, pages = {225-235}, pmid = {11082780}, issn = {0003-5548}, mesh = {Artifacts ; *Bone Cements ; Bone and Bones/*chemistry ; Humans ; *Molecular Biology ; *Museums ; *Paleontology ; *Preservation, Biological ; Risk Factors ; Sequence Analysis, DNA ; Specimen Handling ; }, abstract = {In paleogenetic science, artifacts (i.e. non-authentic DNA sequences) are mainly produced by cryptic contamination with (i) edaphon DNA sequences and/or (ii) human biomolecules derived from the involved researchers and the laboratory equipment. A third, and yet underestimated source of contamination with exogenous nucleic acids is provided by (iii) conservation practices applied to old material. Bone glue has been successfully used from the beginning of the 19th century up to the middle of this century, and comprises a rich source of non-authentic nucleic acids. An unequivocal identification of treated samples remains difficult since bone and the glue used for conservatory purposes bear similar chemical properties. Since the majority of agents used for the preservation of museum collections are of biological origin, the differentiation between contaminated and non-treated samples is required.}, }
@article {pmid11069110, year = {2000}, author = {Weber, DS and Stewart, BS and Garza, JC and Lehman, N}, title = {An empirical genetic assessment of the severity of the northern elephant seal population bottleneck.}, journal = {Current biology : CB}, volume = {10}, number = {20}, pages = {1287-1290}, doi = {10.1016/s0960-9822(00)00759-4}, pmid = {11069110}, issn = {0960-9822}, mesh = {Animals ; California ; DNA, Mitochondrial/blood/*genetics ; Demography ; Documentation ; *Genetic Variation ; Genotype ; Haplotypes ; Pacific Ocean ; Population Growth ; Seals, Earless/*genetics ; }, abstract = {A bottleneck in population size of a species is often correlated with a sharp reduction in genetic variation. The northern elephant seal (Mirounga angustirostris) has undergone at least one extreme bottleneck, having rebounded from 20-100 individuals a century ago to over 175,000 individuals today. The relative lack of molecular-genetic variation in contemporary populations has been documented, but the extent of variation before the late 19th century remains unknown. We have determined the nucleotide sequence of a 179 base-pair segment of the mitochondrial DNA (mtDNA) control region from seals that lived before, during and after a bottleneck low in 1892. A 'primerless' PCR was used to improve the recovery of information from older samples. Only two mtDNA genotypes were present in all 150+ seals from the 1892 bottleneck on, but we discovered four genotypes in five pre-bottleneck seals. This suggests a much greater amount of mtDNA genotypic variation before this bottleneck, and that the persistence of two genotypes today is a consequence of random lineage sampling. We cannot correlate the loss of mtDNA genotypes with a lowered mean fitness of individuals in the species today. However, we show that the species historically possessed additional genotypes to those present now, and that sampling of ancient DNA could elucidate the genetic consequences of severe reductions in population size.}, }
@article {pmid10989644, year = {2000}, author = {Haas, CJ and Zink, A and Pálfi, G and Szeimies, U and Nerlich, AG}, title = {Detection of leprosy in ancient human skeletal remains by molecular identification of Mycobacterium leprae.}, journal = {American journal of clinical pathology}, volume = {114}, number = {3}, pages = {428-436}, doi = {10.1093/ajcp/114.3.428}, pmid = {10989644}, issn = {0002-9173}, mesh = {Base Sequence ; Bone and Bones/*microbiology ; DNA, Bacterial/*analysis ; Female ; History, Medieval ; History, Modern 1601- ; Humans ; Leprosy/*diagnosis/history/microbiology ; Male ; Middle Aged ; Molecular Sequence Data ; Mycobacterium leprae/genetics/*isolation &amp; purification ; Paleopathology/*methods ; Peptides, Cyclic ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {We isolated ancient DNA from skeletal remains obtained from a South German ossuary (approximately 1400-1800 AD) and from a 10th century Hungarian cemetery partially indicating macromorphologic evidence of leprosy. In samples taken of 2 skulls from Germany and of 1 hard palate from Hungary, Mycobacterium leprae-specific fragments of RLEP1 and RLEP3 were amplified using polymerase chain reaction (PCR), thereby confirming their specificity by sequencing. In another case, PCR with primers targeting IS6110 of Mycobacterium tuberculosis gave positive results only for a mandibular specimen. No signal for any mycobacterial DNA was observed in samples from 2 Hungarian foot bones. In ancient material, osseous involvement of M leprae may be detected and distinguished from other mycobacterial infections by specific PCR. In the small bones of leprous hands and feet, not enough M leprae DNA seems to be present for detection. This supports the view that rhinomaxillary leprous alterations result from direct bacterial involvement, while osseous mutilations of hands and feet result from a nervous involvement and/or secondary infections due to small lacerations of the overlying soft tissues.}, }
@article {pmid10970224, year = {2000}, author = {Cooper, A and Poinar, HN}, title = {Ancient DNA: do it right or not at all.}, journal = {Science (New York, N.Y.)}, volume = {289}, number = {5482}, pages = {1139}, doi = {10.1126/science.289.5482.1139b}, pmid = {10970224}, issn = {0036-8075}, mesh = {Cloning, Molecular ; *DNA ; DNA Primers ; *Fossils ; Humans ; Polymerase Chain Reaction/*standards ; Publishing ; Reproducibility of Results ; Research/*standards ; }, }
@article {pmid10962710, year = {2000}, author = {Scholz, M and Pusch, CM}, title = {[Molecular genetic analysis for taxonomic determination of fossil skull fragments of Warendorf-Neuwarendorf].}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {2}, pages = {129-135}, pmid = {10962710}, issn = {0003-5548}, mesh = {Anthropology, Physical ; DNA/*genetics ; DNA Probes ; *Fossils ; Germany ; Humans ; In Situ Hybridization ; *Paleopathology ; Polymerase Chain Reaction ; Skull/*anatomy &amp; histology ; }, abstract = {The isolation and examination DNA segments from prehistoric and fossil bone samples has become one of the biggest challenges in anthropology within the past years. By using specially developed and/or adapted genetic methods, it is possible under laboratory conditions to amplify portions of DNA from bone remains in states of good preservation by the polymerase chain reaction (PCR). DNA sequence data can provide far more specific answers to palaeanthropological questions than one would expect solely by morphologic comparison. Here we introduce an alternative approach for the classification of total ancient DNA by means of Southern hybridisation techniques.}, }
@article {pmid10954626, year = {2000}, author = {Kumar, SS and Nasidze, I and Walimbe, SR and Stoneking, M}, title = {Brief communication: discouraging prospects for ancient DNA from India.}, journal = {American journal of physical anthropology}, volume = {113}, number = {1}, pages = {129-133}, doi = {10.1002/1096-8644(200009)113:1&lt;129::AID-AJPA12&gt;3.0.CO;2-2}, pmid = {10954626}, issn = {0002-9483}, mesh = {Amino Acids/analysis ; Bone and Bones/chemistry ; Chromatography, High Pressure Liquid ; DNA/*chemistry ; Humans ; India ; Isomerism ; *Paleopathology ; Polymerase Chain Reaction ; }, }
@article {pmid10954622, year = {2000}, author = {Carlyle, SW and Parr, RL and Hayes, MG and O'Rourke, DH}, title = {Context of maternal lineages in the Greater Southwest.}, journal = {American journal of physical anthropology}, volume = {113}, number = {1}, pages = {85-101}, doi = {10.1002/1096-8644(200009)113:1&lt;85::AID-AJPA8&gt;3.0.CO;2-1}, pmid = {10954622}, issn = {0002-9483}, mesh = {DNA, Mitochondrial/*chemistry ; Female ; Genetic Variation ; Haplotypes ; Humans ; Indians, North American/*genetics ; Southwestern United States ; }, abstract = {We present mitochondrial haplogroup characterizations of the prehistoric Anasazi of the United States (US) Southwest. These data are part of a long-term project to characterize ancient Great Basin and US Southwest samples for mitochondrial DNA (mtDNA) diversity. Three restriction site polymorphisms (RSPs) and one length polymorphism identify four common Native American matrilines (A, B, C, and D). The Anasazi (n = 27) are shown to have a moderate frequency of haplogroup A (22%), a high frequency of haplogroup B (56%), and a low frequency of C (15%). Haplogroup D has not yet been detected among the Anasazi. In comparison to modern Native American groups from the US Southwest, the Anasazi are shown to have a distribution of haplogroups similar to the frequency pattern exhibited by modern Pueblo groups. A principal component analysis also clusters the Anasazi with some modern (Pueblo) Southwestern populations, and away from other modern (Athapaskan speaking) Southwestern populations. The Anasazi are also shown to have a significantly different distribution of the four haplogroups as compared to the eastern Great Basin Great Salt Lake Fremont (n = 32), although both groups cluster together in a principal component analysis. The context of our data suggests substantial stability within the US Southwest, even in the face of the serious cultural and biological disruption caused by colonization of the region by European settlers. We conclude that although sample numbers are fairly low, ancient DNA (aDNA) data are useful for assessing long-term populational affinities and for discerning regional population structure.}, }
@article {pmid10939960, year = {2000}, author = {Stokstad, E}, title = {5TH International Ancient DNA Conference. Divining diet and disease from DNA.}, journal = {Science (New York, N.Y.)}, volume = {289}, number = {5479}, pages = {530-531}, doi = {10.1126/science.289.5479.530}, pmid = {10939960}, issn = {0036-8075}, mesh = {Animals ; Bone and Bones/virology ; DNA/*analysis/history ; DNA, Viral/analysis/*history ; Diet/*history ; Elephants/*genetics/virology ; Feces/*chemistry ; Female ; Fossils ; History, Ancient ; Humans ; Male ; Texas ; }, abstract = {Some 110 scientists from a range of disciplines gathered in the overcast British midlands for the 5th International Ancient DNA Conference, held here from 12 to 14 July. Among the attractions were new insights into the diets of early Americans gleaned from ancient human coprolites and intriguing reports of nuclear DNA and ancient viral sequences extracted from mammoth bones.}, }
@article {pmid10871390, year = {2000}, author = {Kalmár, T and Bachrati, CZ and Marcsik, A and Raskó, I}, title = {A simple and efficient method for PCR amplifiable DNA extraction from ancient bones.}, journal = {Nucleic acids research}, volume = {28}, number = {12}, pages = {E67}, pmid = {10871390}, issn = {1362-4962}, mesh = {Adolescent ; Adult ; Aged ; Bone and Bones/*chemistry ; DNA/history/*isolation &amp; purification ; Female ; History, 15th Century ; History, Medieval ; Humans ; Hungary ; Male ; Middle Aged ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; }, abstract = {A simple and effective modified ethanol precipitation-based protocol is described for the preparation of DNA from ancient human bones. This method is fast and requires neither hazardous chemicals nor special devices. After the powdering and incubating of the bone samples Dextran Blue was added as a carrier for removing the PCR inhibitors with selective ethanol precipitation. This method could eliminate the time-consuming separate decalcification step, dialysis, application of centrifugation-driven microconcentrators and the second consecutive PCR amplification. The efficiency of this procedure was demonstrated on ten 500-1200-year-old human bones from four different Hungarian burial sites. A mitochondrial specific primer pair was used to obtain sequence information from the purified ancient DNA. The PCR amplification, after our DNA extraction protocol, was successful from each of the 10 bone samples investigated. The results demonstrate that extraction of DNA from ancient bone samples with this new approach increases the success rate of PCR amplification.}, }
@article {pmid10871343, year = {2000}, author = {Grishin, NV}, title = {Two tricks in one bundle: helix-turn-helix gains enzymatic activity.}, journal = {Nucleic acids research}, volume = {28}, number = {11}, pages = {2229-2233}, pmid = {10871343}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Bacteriophages ; Binding Sites ; DNA Nucleotidyltransferases/chemistry/genetics ; DNA Topoisomerases, Type I/chemistry/genetics ; DNA-Binding Proteins/chemistry/*genetics ; Escherichia coli ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics ; Helix-Turn-Helix Motifs/*genetics ; Integrases/chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Recombinases ; Trans-Activators/chemistry/genetics ; Tyrosine/genetics ; Viral Proteins/chemistry/genetics ; }, abstract = {Many examples of enzymes that have lost their catalytic activity and perform other biological functions are known. The opposite situation is rare. A previously unnoticed structural similarity between the lambda integrase family (Int) proteins and the AraC family of transcriptional activators implies that the Int family evolved by duplication of an ancient DNA-binding homeodomain-like module, which acquired enzymatic activity. The two helix-turn-helix (HTH) motifs in Int proteins incorporate catalytic residues and participate in DNA binding. The active site of Int proteins, which include the type IB topoisomerases, is formed at the domain interface and the catalytic tyrosine residue is located in the second helix of the C-terminal HTH motif. Structural analysis of other 'tyrosine' DNA-breaking/rejoining enzymes with similar enzyme mechanisms, namely prokaryotic topoisomerase I, topoisomerase II and archaeal topoisomerase VI, reveals that the catalytic tyrosine is placed in a HTH domain as well. Surprisingly, the location of this tyrosine residue in the structure is not conserved, suggesting independent, parallel evolution leading to the same catalytic function by homologous HTH domains. The 'tyrosine' recombinases give a rare example of enzymes that evolved from ancient DNA-binding modules and present a unique case for homologous enzymatic domains with similar catalytic mechanisms but different locations of catalytic residues, which are placed at non-homologous sites.}, }
@article {pmid10832878, year = {2000}, author = {Bachmann, L and Scholz, M and Broghammer, M and Giddings, I and Pusch, CM}, title = {Voltage-induced release of nucleic acids from palaeontological samples.}, journal = {Electrophoresis}, volume = {21}, number = {8}, pages = {1488-1492}, doi = {10.1002/(SICI)1522-2683(20000501)21:8&lt;1488::AID-ELPS1488&gt;3.0.CO;2-N}, pmid = {10832878}, issn = {0173-0835}, mesh = {DNA/*isolation &amp; purification ; Electric Conductivity ; *Fossils ; Humans ; Polymerase Chain Reaction/methods ; }, abstract = {Most of the protocols for the recovery of ancient DNA from palaeontological specimens are time-consuming and tend to yield inconsistent polymerase chain reaction (PCR) results. "Voltage-induced release" is a novel and rapid approach for the extraction of ancient DNA. Nucleic acids are directly electrophoresed out of powder derived from hard and soft tissues. This technique is much faster than other methods in which pulverized tissue conventionally undergoes time-consuming crude lysis steps. The total preparation time is 5-6 h. The reliability of the voltage-induced release method was validated by (i) measuring the ratio of D-to L-enantiomers of the amino acids aspartic acid, alanine, and leucine, and (ii) by specific PCR amplification of four single-copy markers of human chromosome 17 and 18. We compare voltage-induced release to a frequently used silica-based protocol. DNA extracted employing voltage-induced release was more effective in PCR amplifications, which may be attributed to the effective removal of PCR inhibitors.}, }
@article {pmid10816792, year = {2000}, author = {Wiechmann, I}, title = {Molecular genetic analysis of the polymorphic apolipoprotein E in modern and ancient human DNA samples.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {1}, pages = {93-98}, pmid = {10816792}, issn = {0003-5548}, mesh = {Apolipoproteins E/*history ; DNA/history ; *Genetics, Population ; History, Ancient ; Humans ; Paleodontology ; Peru ; *Polymerase Chain Reaction ; Polymorphism, Genetic/*genetics ; }, abstract = {In this report, methodical bases for the molecular genetic analysis of the three common apolipoprotein E alleles APOE*2, APOE*3 and APOE*4 in DNA isolated from ancient human skeletal remains are described. Considering that ancient DNA target regions for amplification are generally quite small, the detection method is based on short amplification products in the range from 71 bp to 75 bp. The applicability of the modified method for APOE genotyping was examined in modern human DNA samples.}, }
@article {pmid10816789, year = {2000}, author = {Burger, J and Hummel, S and Pfeiffer, I and Herrmann, B}, title = {Palaeogenetic analysis of (pre)historic artifacts and its significance for anthropology.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {1}, pages = {69-76}, pmid = {10816789}, issn = {0003-5548}, mesh = {*Archaeology ; Female ; *Forensic Anthropology ; Genetics, Population ; Germany ; History, Ancient ; Humans ; Life Style ; Male ; *Paleopathology ; Polymerase Chain Reaction ; }, abstract = {The possibility of isolating ancient DNA (aDNA) from all kinds of (pre)historic anthropogenetic artifacts opens new perspectives. This study applies palaeogenetic techniques to three anthropological issues: 1. Palaeodiet. DNA sequences from organic residues in vessels identify Precolumbian Aztec diet. 2. (Pre)historic husbandry and economic structures. aDNA data can reveal the species and the genetic evolutionary stage of animals and plants and show the manner and the extent of their growth, cultivation, or domestication. 3. Production techniques, use, and functionality. Identification of the plant or animal source of an archaeological find can reveal the use or the function of the find. Examples from a Celtic "sausage-end" and an Aztec "eye salve" are given.}, }
@article {pmid10816787, year = {2000}, author = {Faerman, M and Jankauskas, R}, title = {Paleopathological and molecular evidence of human bone tuberculosis in Iron Age Lithuania.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {1}, pages = {57-62}, pmid = {10816787}, issn = {0003-5548}, mesh = {Adult ; Female ; *Forensic Anthropology ; History, Ancient ; Humans ; Lithuania ; Male ; Mycobacterium tuberculosis/*genetics ; *Paleopathology ; *Polymerase Chain Reaction ; Sex Determination Processes ; Tuberculosis, Osteoarticular/*history ; }, abstract = {Skeletal remains of two individuals, showing lesions suggestive of bone tuberculosis, from the archaeological sites of Marvele and Sukioniai in Lithuania were analyzed at the DNA level. The diagnosis of bone tuberculosis was confirmed in the remains from Marvele by amplifiying a 245-bp fragment of a repetitive insertion element-like sequence (IS 6110) of Mycobacterium tuberculosis DNA. This is direct evidence for the presence of tuberculosis in Lithuania at the beginning of the first millennium AD. The individual from Sukioniai was found to be tuberculosis-negative. No PCR product was obtained for the 245-bp target sequence or for a smaller 123-bp DNA fragment specific for Mycobacterium tuberculosis. However, amplifiable ancient DNA appeared to be present in the examined specimen as was shown by the results of the DNA-based sex identification, which indicated, consistent with the bone morphology, a male individual.}, }
@article {pmid10816786, year = {2000}, author = {Haack, K and Hummel, S and Hummel, B}, title = {Ancient DNA fragments longer than 300 bp.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {1}, pages = {51-56}, pmid = {10816786}, issn = {0003-5548}, mesh = {DNA/*genetics ; *Forensic Anthropology ; History, 18th Century ; History, Ancient ; Humans ; Paleopathology ; Peptide Fragments/*genetics ; *Polymerase Chain Reaction ; Reproducibility of Results ; Tandem Repeat Sequences/genetics ; }, abstract = {It is widely assumed that ancient DNA (aDNA) extracts contain no authentic templates longer than 300 bp. Here we present results which show that fragments of up to 800 bp in length can be reproducibly amplified from aDNA extracts. The amplification involves the short tandem repeat (STR) locus HUMVWA31A. Authentication of the amplified fragments is carried out by measures of expectancy.}, }
@article {pmid10816784, year = {2000}, author = {Schultes, T and Hummel, S and Herrmann, B}, title = {Ancient DNA-typing approaches for the determination of kinship in a disturbed collective burial site.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {1}, pages = {37-44}, pmid = {10816784}, issn = {0003-5548}, mesh = {Bone and Bones/pathology ; *DNA Fingerprinting ; DNA, Mitochondrial/genetics ; Female ; *Forensic Anthropology ; *Genetics, Population ; Germany ; History, Ancient ; Humans ; Male ; Mortuary Practice ; Paleopathology ; *Paternity ; Reproducibility of Results ; Y Chromosome ; }, abstract = {Several DNA-typing approaches are applied for identification and kinship analysis. Autosomal Short Tandem Repeat (STR) typing produces the genetic fingerprint that is unique to an individual. Y-chromosomal STR typing identifies individuals of the same paternal lineage, and sequence analysis of the hypervariable region of the mitochondrion can identify maternally related individuals. The combined approach of these DNA-typing methods allows the determination of kinship even in complex collective burial situations. In a bronze age collective site, the typing methods were tested for applicability to ancient DNA. For each approach, results were obtained, leading to the conclusion that the determination of kinship is achievable.}, }
@article {pmid10816783, year = {2000}, author = {Schmerer, WM and Hummel, S and Herrmann, B}, title = {STR-genotyping of archaeological human bone: experimental design to improve reproducibility by optimisation of DNA extraction.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {1}, pages = {29-35}, pmid = {10816783}, issn = {0003-5548}, mesh = {*Archaeology ; Artifacts ; Bone and Bones/*pathology ; DNA/*genetics ; *Forensic Anthropology ; *Genotype ; Humans ; Polymerase Chain Reaction ; Reproducibility of Results ; }, abstract = {The analysis of degraded DNA with the help of short tandem repeat loci (STRs) is an important source of information both in forensic casework and in the anthropological context. The reproducibility of STR-genotyping of highly degraded or "ancient" DNA can be reduced by the generation of artifacts during PCR amplification. The frequency and amount of these artifacts--allelic dropout and the generation of shadow bands--are related to the quality and quantity of the extracted DNA amplified in a PCR reaction. Therefore, one important strategy to increase the reproducibility of STR-genotyping of samples containing degraded DNA is the optimisation of the DNA extraction.}, }
@article {pmid10816781, year = {2000}, author = {Hummel, S and Bramanti, B and Schultes, T and Kahle, M and Haffner, S and Herrmann, B}, title = {Megaplex DNA typing can provide a strong indication of the authenticity of ancient DNA amplifications by clearly recognizing any possible type of modern contamination.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {1}, pages = {15-21}, pmid = {10816781}, issn = {0003-5548}, mesh = {Artifacts ; *DNA Fingerprinting ; Gene Amplification/*genetics ; History, Ancient ; Humans ; *Paleopathology ; *Polymerase Chain Reaction ; Sensitivity and Specificity ; Specimen Handling ; Tandem Repeat Sequences/*genetics ; }, abstract = {Recent experiments revealed the perfect applicability of megaplex typing by autosomal short tandem repeats (STRs) to degraded DNA. The advantages of megaplex approaches lie in reduced amounts of sample material that are necessary and in remarkable time saving. Furthermore, megaplex typing clearly recognizes possible contaminations and thus has a large potential for indicating authenticity in ancient DNA analysis. This is demonstrated by three examples in which various types of contaminations could clearly be identified as such and even traced back to their origin. This would have been impossible using control samples, due to the sporadic nature of these types of contaminations.}, }
@article {pmid10816779, year = {2000}, author = {Lassen, C and Hummel, S and Herrmann, B}, title = {Molecular sex identification of stillborn and neonate individuals ("Traufkinder") from the burial site Aegerten.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {58}, number = {1}, pages = {1-8}, pmid = {10816779}, issn = {0003-5548}, mesh = {Female ; Fetal Death/*history ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, Medieval ; Humans ; Infant ; Infant, Newborn ; Male ; Paleopathology ; Pregnancy ; *Sex Determination Processes ; *Sex Ratio ; Switzerland ; }, abstract = {The study reconstructs the sex ratio of 121 stillborn and neonate individuals from the early modern burial site Aegerten, Switzerland. The immature individuals, who were not baptised before death, were buried along the walls of the church. To perform a molecular sex identification, bone samples from the infants were collected from different skeletal elements. Ancient DNA (aDNA) was isolated by a combination of automated phenol/chloroform extraction and precipitation with silica powder. A combination of manuell Chelex extraction and purification kit was also used to perform an extraction. Finally, the aDNA extracts were amplified with a primer system that amplifies a part of the amelogenin gene located on the human sex chromosomes. The morphometrical sex determination of the children suggests a large disproportion of female individuals (about 60%). This finding was compared to PCR-based amplification results. In contrast, the results of the molecular sex identification were a high proportion of male individuals. Looking at these results, it should be noted that the high mortality of male individuals during the last months of pregnancy and during the first month after birth is in accordance with the natural sequence of death also found in recent populations.}, }
@article {pmid10750053, year = {2000}, author = {Lalueza-Fox, C and Bertranpetit, J and Alcover, JA and Shailer, N and Hagelberg, E}, title = {Mitochondrial DNA from Myotragus balearicus, an extinct bovid from the Balearic Islands.}, journal = {The Journal of experimental zoology}, volume = {288}, number = {1}, pages = {56-62}, doi = {10.1002/(sici)1097-010x(20000415)288:1&lt;56::aid-jez6&gt;3.0.co;2-x}, pmid = {10750053}, issn = {0022-104X}, mesh = {Animals ; Bone and Bones ; Cattle/*genetics ; *Classification ; DNA, Mitochondrial/*genetics ; Fossils ; Tooth ; }, abstract = {DNA was extracted from teeth and bones of Myotragus balearicus, a bovid that evolved in isolation on the Balearic Islands (Western Mediterranean) from the end of the Miocene, becoming extinct 4,000 years BP, after the arrival of humans in the islands. The numerous morphological apomorphies of Myotragus, most strikingly its dwarfism, frontal eyes, and ever-growing incisors, obscure its phylogenetic relationships with extant bovids. Therefore, the recovery of genetic information from Myotragus is of significant interest to help clarify the taxonomic position of this species. In this study we amplified and sequenced a 95 bp (base pair) fragment of the mtDNA cytochrome b gene from 6,000-year-old specimens of Myotragus. Several experimental controls, such as amino acid analysis, independent reproduction in two different laboratories, and cloning of the PCR product, support the authenticity of the ancient DNA sequence recovered. Phylogenetic comparison with orthologous sequences from supposedly related extant genera (serow, goral, mountain goat, chamois, takin, sheep, goat, Himalayan tahr, arctic musk ox, barbary sheep, blue sheep, and saiga) from the Caprinae subfamily suggests that Myotragus is related to some of these species. However, the real phylogenetic position of Myotragus is difficult to assess, due to the lack of resolution of the present molecular study, which can be partially attributed to the short length of the genetic fragment recovered.}, }
@article {pmid10750049, year = {2000}, author = {Birnbaum, D and Coulier, F and Pébusque, MJ and Pontarotti, P}, title = {"Paleogenomics": looking in the past to the future.}, journal = {The Journal of experimental zoology}, volume = {288}, number = {1}, pages = {21-22}, doi = {10.1002/(sici)1097-010x(20000415)288:1&lt;21::aid-jez2&gt;3.0.co;2-q}, pmid = {10750049}, issn = {0022-104X}, mesh = {Animals ; DNA/*genetics ; *Evolution, Molecular ; Fossils ; *Genome ; Humans ; Invertebrates/genetics ; Models, Theoretical ; *Paleontology ; Vertebrates/genetics ; }, abstract = {The complete sequence of the human and other vertebrate and nonvertebrate genomes provide a wealth of information on the organization, relationships and evolution of the metazoans. Soon the fine structure of our innermost biological identity will be unveiled and what has so far remained deep and secret will shine like an unearthed treasure and shape and fuel our future quests. A key treasure, for many molecular scientists interested in molecular evolution and development would be the knowledge of the genome of the ancestral precursor of all metazoans. In the absence of fossil DNA, this knowledge will forever remain a yearning for dreamy molecular biologists. And yet, will not the power of deduction and reconstitution of information gained through man's sophisticated technologies one day recreate a "virtual" metazoan ancestor?}, }
@article {pmid10677855, year = {2000}, author = {Costas, J and Naveira, H}, title = {Evolutionary history of the human endogenous retrovirus family ERV9.}, journal = {Molecular biology and evolution}, volume = {17}, number = {2}, pages = {320-330}, doi = {10.1093/oxfordjournals.molbev.a026312}, pmid = {10677855}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Consensus Sequence ; DNA Transposable Elements/genetics ; DNA, Viral/chemistry/genetics ; Endogenous Retroviruses/classification/*genetics ; *Evolution, Molecular ; Genetic Variation ; Humans ; Molecular Sequence Data ; *Phylogeny ; Primates/classification/genetics/virology ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {Several distinct families of endogenous retrovirus-like elements (ERVs) exist in the genomes of primates. Despite the important evolutionary consequences that carrying these intragenomic parasites may have for their hosts, our knowledge about their evolution is still scarce. A matter of particular interest is whether evolution of ERVs occurs via a master lineage or through several lineages coexisting over long periods of time. In this work, the paleogenomic approach has been applied to the study of the evolution of ERV9, one of the human endogenous retrovirus families mobilized during primate evolution. By searching the GenBank database with the first 676 bp of the ERV9 long terminal repeat, we identified 156 different element insertions into the human genome. These elements were grouped into 14 subfamilies based on several characteristic nucleotide differences. The age of each subfamily was roughly estimated based on the average sequence divergence of its members from the subfamily consensus sequence. Determination of the sequential order of diagnostic substitutions led to the identification of four distinct lineages, which retained their capacity of transposition over extended periods of evolution. Strong evidence for mosaic evolution of some of these lineages is presented. Taken altogether, the available data indicate that the possibility of ERV9 still being active in the human lineage can not be discarded.}, }
@article {pmid10683241, year = {2000}, author = {Pusch, CM and Nicholson, GJ and Bachmann, L and Scholz, M}, title = {Degenerate oligonucleotide-primed preamplification of ancient DNA allows the retrieval of authentic DNA sequences.}, journal = {Analytical biochemistry}, volume = {279}, number = {1}, pages = {118-122}, doi = {10.1006/abio.1999.4463}, pmid = {10683241}, issn = {0003-2697}, mesh = {Animals ; Base Sequence ; Cattle ; DNA/*genetics/isolation &amp; purification ; DNA Primers/genetics ; Evaluation Studies as Topic ; *Fossils ; Humans ; Paleontology/*methods ; Polymerase Chain Reaction/*methods ; Swine ; }, }
@article {pmid10649633, year = {1999}, author = {Sorenson, MD and Cooper, A and Paxinos, EE and Quinn, TW and James, HF and Olson, SL and Fleischer, RC}, title = {Relationships of the extinct moa-nalos, flightless Hawaiian waterfowl, based on ancient DNA.}, journal = {Proceedings. Biological sciences}, volume = {266}, number = {1434}, pages = {2187-2193}, pmid = {10649633}, issn = {0962-8452}, mesh = {Animals ; Birds/classification/*genetics ; DNA, Mitochondrial/*genetics ; Ducks/genetics ; Evolution, Molecular ; *Fossils ; Hawaii ; Locomotion ; *Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {The extinct moa-nalos were very large, flightless waterfowl from the Hawaiian islands. We extracted, amplified and sequenced mitochondrial DNA from fossil moa-nalo bones to determine their systematic relationships and lend insight into their biogeographical history. The closest living relatives of these massive, goose-like birds are the familiar dabbling ducks (tribe Anatini). Moa-nalos, however, are not closely related to any one extant species, but represent an ancient lineage that colonized the Hawaiian islands and evolved flightlessness long before the emergence of the youngest island, Hawaii, from which they are absent. Ancient DNA yields a novel hypothesis for the relationships of these bizarre birds, whereas the evidence of phylogeny in morphological characters was obscured by the evolutionary transformation of a small, volant duck into a giant, terrestrial herbivore.}, }
@article {pmid10626565, year = {1999}, author = {Poinar, HN}, title = {DNA from fossils: the past and the future.}, journal = {Acta paediatrica (Oslo, Norway : 1992). Supplement}, volume = {88}, number = {433}, pages = {133-140}, doi = {10.1111/j.1651-2227.1999.tb14423.x}, pmid = {10626565}, issn = {0803-5326}, mesh = {DNA/*analysis ; *Fossils ; History, 20th Century ; History, Medieval ; Humans ; Influenza, Human/history ; Tuberculosis/history ; }, abstract = {The recovery of DNA from archaeological and palaeontological remains has intrigued scientists for many years. The DNA molecule is a relatively weak molecule compared with other biomacromolecules in tissues, but the sequence of its bases holds insights into questions that cannot be resolved by standard palaeontological methods. Recent advances in the field, such as the recovery of DNA sequences from coprolites found in the southwestern USA, as well as from the Neanderthal-type specimen, have shed new light on populations that are now extinct. A better understanding of how DNA is preserved in fossils, as well as the use of novel agents that can release the DNA from archaeological and palaeontological materials, will likely lead to new successes in the field. The analysis of ancient DNA may provide new clues about human evolution and answer questions, for example, relating to the diversity of the Neanderthals and the mammoths.}, }
@article {pmid10618586, year = {2000}, author = {Kolman, CJ and Tuross, N}, title = {Ancient DNA analysis of human populations.}, journal = {American journal of physical anthropology}, volume = {111}, number = {1}, pages = {5-23}, doi = {10.1002/(SICI)1096-8644(200001)111:1&lt;5::AID-AJPA2&gt;3.0.CO;2-3}, pmid = {10618586}, issn = {0002-9483}, mesh = {Animals ; *Biological Evolution ; DNA/*analysis ; DNA, Mitochondrial/genetics ; Hominidae/*genetics ; Humans ; Nucleic Acid Amplification Techniques ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Specimen Handling ; }, abstract = {The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. The resultant increase in number of samples and polymorphic sites assayed and the number of studies published may give the impression that all technological hurdles associated with aDNA technology have been overcome. However, analysis of aDNA is still plagued by two issues that emerged at the advent of aDNA technology, namely the inability to amplify a significant number of samples and the contamination of samples with modern DNA. Herein, we analyze five well-preserved skeletal specimens from the western United States dating from 800-1600 A.D. These specimens yielded DNA samples with levels of contamination ranging from 0-100%, as determined by the presence or absence of New World-specific mitochondrial markers. All samples were analyzed by a variety of protocols intended to assay genetic variability and detect contamination, including amplification of variously sized DNA targets, direct DNA sequence analysis of amplification products and sequence analysis of cloned amplification products, analysis of restriction fragment length polymorphisms, quantitation of target DNA, amino acid racemization, and amino acid quantitation. Only the determination of DNA sequence from a cloned amplification product clearly revealed the presence of both ancient DNA and contaminating DNA in the same extract. Our results demonstrate that the analysis of aDNA is still an excruciatingly slow and meticulous process. All experiments, including stringent quality and contamination controls, must be performed in an environment as free as possible of potential sources of contaminating DNA, including modern DNA extracts. Careful selection of polymorphic markers capable of discriminating between ancient DNA and probable DNA contaminants is critical. Research strategies must be designed with a goal of identifying all DNA contaminants in order to differentiate convincingly between contamination and endogenous DNA.}, }
@article {pmid10563020, year = {1999}, author = {Bailey, JF and Henneberg, M and Colson, IB and Ciarallo, A and Hedges, RE and Sykes, B}, title = {Monkey business in Pompeii--unique find of a juvenile barbary macaque skeleton in Pompeii identified using osteology and ancient DNA techniques.}, journal = {Molecular biology and evolution}, volume = {16}, number = {10}, pages = {1410-1414}, doi = {10.1093/oxfordjournals.molbev.a026051}, pmid = {10563020}, issn = {0737-4038}, mesh = {Animals ; Bone and Bones/anatomy &amp; histology/metabolism ; DNA/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; Evolution, Molecular ; *Fossils ; History, Ancient ; Italy ; Macaca/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, }
@article {pmid10541662, year = {1999}, author = {Hummel, S and Herrmann, B and Rameckers, J and Müller, D and Sperling, K and Neitzel, H and Tönnies, H}, title = {Proving the authenticity of ancient DNA by comparative genomic hybridization.}, journal = {Die Naturwissenschaften}, volume = {86}, number = {10}, pages = {500-503}, doi = {10.1007/s001140050663}, pmid = {10541662}, issn = {0028-1042}, mesh = {*Chromosomes, Human ; Congenital Abnormalities/embryology/genetics ; DNA/*genetics ; Fetus ; Humans ; Karyotyping ; Nucleic Acid Hybridization/*methods ; Paleontology/methods ; Polymerase Chain Reaction/*methods ; Telomere/genetics ; }, abstract = {In PCR-supported amplification of ancient, degraded DNA, contamination with contemporary DNA can lead to false-positive results, which frequently give rise to discussions in which the mere existence of ancient DNA is doubted. Our confirmation of ancient DNA using comparative genome hybridization (CGH) eliminates these doubts. Unlike PCR methods, CGH requires no amplification of the DNA to be analyzed if adequate amounts of specimen DNA is used. Thus, false results traceable to contaminations are practically ruled out. The examples provided here prove the authenticity of ancient DNA for a 250-year-old and a 3,000-year-old sample. At the same time, the CGH of ancient DNA offers the chance to gain insight into the pattern of DNA degradation and to monitor the preservation of certain chromosomal segments.}, }
@article {pmid10508842, year = {1999}, author = {Reiter, LT and Liehr, T and Rautenstrauss, B and Robertson, HM and Lupski, JR}, title = {Localization of mariner DNA transposons in the human genome by PRINS.}, journal = {Genome research}, volume = {9}, number = {9}, pages = {839-843}, pmid = {10508842}, issn = {1088-9051}, support = {R01NS2742/NS/NINDS NIH HHS/United States ; }, mesh = {Chromosome Mapping ; Chromosomes, Human, Pair 17 ; DNA Transposable Elements/*genetics ; DNA-Binding Proteins ; Databases, Factual ; Female ; *Genome, Human ; Humans ; Lymphocytes/metabolism ; Primed In Situ Labeling/*methods ; Transposases ; X Chromosome ; }, abstract = {Homologous recombination occurring among misaligned repeated sequences is a significant source of the molecular rearrangements resulting in human genetic disease. Studies of the Charcot-Marie-Tooth disease locus on chromosome 17 have implicated the involvement of an ancient DNA transposon of the mariner family (Hsmar2) in the initiation of double-strand break events leading to homologous recombination. In this study, the genomic locations of 109 Hsmar2 elements were determined by primed in situ labeling (PRINS) using primers designed to match the right and left inverted terminal repeats (ITRs) of the transposon. Although the resolution of the PRINS technique is approximately 400 chromosomal Giemsa bands, the data presented here provide the first large-scale mapping study of these elements, which may be involved in initiation of homologous recombination events in the human genome.}, }
@article {pmid10436657, year = {1998}, author = {Araújo, A and Reinhard, K and Bastos, OM and Costa, LC and Pirmez, C and Iñiguez, A and Vicente, AC and Morel, CM and Ferreira, LF}, title = {Paleoparasitology: perspectives with new techniques.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {40}, number = {6}, pages = {371-376}, doi = {10.1590/s0036-46651998000600006}, pmid = {10436657}, issn = {0036-4665}, mesh = {Animals ; *Archaeology ; DNA/*isolation &amp; purification ; Feces/*parasitology ; Forecasting ; History, 20th Century ; Humans ; Molecular Biology/*methods ; Mummies/*parasitology ; Paleontology/history/*trends ; Parasite Egg Count ; Parasitology/history/*trends ; Polymerase Chain Reaction ; }, abstract = {Paleoparasitology is the study of parasites found in archaeological material. The development of this field of research began with histological identification of helminth eggs in mummy tissues, analysis of coprolites, and recently through molecular biology. An approach to the history of paleoparasitology is reviewed in this paper, with special reference to the studies of ancient DNA identified in archaeological material.}, }
@article {pmid10435437, year = {1999}, author = {Hummel, S and Schultes, T and Bramanti, B and Herrmann, B}, title = {Ancient DNA profiling by megaplex amplications.}, journal = {Electrophoresis}, volume = {20}, number = {8}, pages = {1717-1721}, doi = {10.1002/(SICI)1522-2683(19990101)20:8&lt;1717::AID-ELPS1717&gt;3.0.CO;2-D}, pmid = {10435437}, issn = {0173-0835}, mesh = {Amelogenin ; *Anthropology, Physical ; DNA/*genetics ; Dental Enamel Proteins/genetics ; Female ; Humans ; Male ; Tandem Repeat Sequences ; }, abstract = {Simultaneous amplification of nine human short tandem repeat (STR) DNA sequences and the amelogenin locus allows reducing to an absolute minimum the amount of sample material that is necessary for genetic identification or kinship analysis. Valuable remains can be studied this way without any visible damage, as is demonstrated by typing the DNA of a tooth root from the Saxon warrior Widukind, who died about 1200 years ago. The broad applicability of the megaplex approach is shown by typing bone and teeth specimens ranging from a few months to 3000 years of age employing AmpFISTR Profiler Plus. Additionally, megaplex STR typing is the method of choice for proving the authenticity of molecular results derived from ancient degraded DNA.}, }
@article {pmid10435436, year = {1999}, author = {Schmerer, WM and Hummel, S and Herrmann, B}, title = {Optimized DNA extraction to improve reproducibility of short tandem repeat genotyping with highly degraded DNA as target.}, journal = {Electrophoresis}, volume = {20}, number = {8}, pages = {1712-1716}, doi = {10.1002/(SICI)1522-2683(19990101)20:8&lt;1712::AID-ELPS1712&gt;3.0.CO;2-6}, pmid = {10435436}, issn = {0173-0835}, mesh = {DNA/*genetics ; Genotype ; Humans ; Reproducibility of Results ; *Tandem Repeat Sequences ; }, abstract = {The reproducibility of short tandem repeat (STR) genotyping of highly degraded DNA is often reduced due to artifacts generated during polymerase chain reaction (PCR) amplification. The frequency and amount of these artifacts are related to the quality and quantity of the DNA amplified. Consequently, the aim of this investigation was the optimization of DNA extraction to increase the reproducibility of STR genotyping of samples containing highly degraded DNA. Starting from a standard extraction protocol, systematic variation of individual parameters resulted in optimized protocols for three categories of ancient human bone material (different degrees of DNA degradation) and a consensus protocol for the extraction of a broad range of ancient DNA preservation states.}, }
@article {pmid10411967, year = {1999}, author = {Cipollaro, M and Di Bernado, G and Forte, A and Galano, G and De Masi, L and Galderisi, U and Guarino, FM and Angelini, F and Cascino, A}, title = {Histological analysis and ancient DNA amplification of human bone remains found in caius iulius polybius house in pompeii.}, journal = {Croatian medical journal}, volume = {40}, number = {3}, pages = {392-397}, pmid = {10411967}, issn = {0353-9504}, mesh = {Alleles ; Amelogenin ; Bone and Bones/*anatomy &amp; histology ; Chromosome Mapping ; Chromosomes, Human, Pair 12/genetics ; DNA/*analysis/genetics ; DNA Fragmentation ; Dental Enamel Proteins/genetics ; Enzyme Inhibitors/adverse effects ; Female ; *Flavonoids ; Gene Amplification ; History, Ancient ; Humans ; Italy ; Male ; Metals/adverse effects ; Microsatellite Repeats/genetics ; Osteocytes/metabolism ; *Paleontology ; Phenols/adverse effects ; Polymerase Chain Reaction ; Polymers/adverse effects ; Polyphenols ; Repetitive Sequences, Nucleic Acid/genetics ; Taq Polymerase/antagonists &amp; inhibitors ; X Chromosome/genetics ; Y Chromosome/genetics ; von Willebrand Factor/genetics ; }, abstract = {Thirteen skeletons found in the Caius Iulius Polybius house, which has been the object of intensive study since its discovery in Pompeii 250 years ago, have provided an opportunity to study either bone diagenesis by histological investigation or ancient DNA by polymerase chain reaction analysis. DNA analysis was done by amplifying both X- and Y-chromosomes amelogenin loci and Y-specific alphoid repeat locus. The von Willebrand factor (vWF) microsatellite locus on chromosome 12 was also analyzed for personal identification in two individuals showing alleles with 10/11 and 12/12 TCTA repeats, respectively. Technical problems were the scarcity of DNA content from osteocytes, DNA molecule fragmentation, microbial contamination which change bone structure, contaminating human DNA which results from mishandling, and frequent presence of Taq DNA polymerase inhibiting molecules like polyphenols and heavy metals. The results suggest that the remains contain endogenous human DNA that can be amplified and analyzed. The amplifiability of DNA corresponds to the bone preservation and dynamics of the burial conditions subsequent to the 79 A.D. eruption.}, }
@article {pmid10411891, year = {1999}, author = {Poinar, HN and Stankiewicz, BA}, title = {Protein preservation and DNA retrieval from ancient tissues.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {15}, pages = {8426-8431}, pmid = {10411891}, issn = {0027-8424}, mesh = {Amino Acids/analysis ; Animals ; Archaeology ; DNA/*chemistry ; *Fossils ; Humans ; Hydantoins/analysis ; Mass Spectrometry ; Paleontology ; Proteins/*chemistry ; Sequence Analysis, DNA ; *Tissue Preservation ; }, abstract = {The retrieval of DNA from fossils remains controversial. To substantiate claims of DNA recovery, one needs additional information on the preservation of other molecules within the same sample. Flash pyrolysis with GC and MS was used to assess the quality of protein preservation in 11 archaeological and paleontological remains, some of which have yielded ancient DNA sequences authenticated via a number of criteria and some of which have consistently failed to yield any meaningful DNA. Several samples, including the Neanderthal-type specimen from which DNA sequences were recently reported, yielded abundant pyrolysis products assigned to 2,5-diketopiperazines of proline-containing dipeptides. The relative amounts of these products provide a good index of the amount of peptide hydrolysis and DNA preservation. Of these samples, four stem from arctic or subarctic regions, emphasizing the importance of cooler temperatures for the preservation of macromolecules. Flash pyrolysis with GC and MS offers a rapid and effective method for assessing fossils for the possibility of DNA preservation.}, }
@article {pmid10352937, year = {1999}, author = {Gerstenberger, J and Hummel, S and Schultes, T and Häck, B and Herrmann, B}, title = {Reconstruction of a historical genealogy by means of STR analysis and Y-haplotyping of ancient DNA.}, journal = {European journal of human genetics : EJHG}, volume = {7}, number = {4}, pages = {469-477}, doi = {10.1038/sj.ejhg.5200322}, pmid = {10352937}, issn = {1018-4813}, mesh = {Burial ; DNA/*genetics ; DNA Fingerprinting ; Female ; Germany ; *Haplotypes ; History, 16th Century ; History, 17th Century ; History, 18th Century ; Humans ; Male ; Paternity ; *Pedigree ; Polymerase Chain Reaction ; Sex Determination Analysis ; Tandem Repeat Sequences/*genetics ; Y Chromosome/*genetics ; }, abstract = {Archaeological excavations in St Margaretha's church at Reichersdorf, Germany, in 1993 led to the discovery of eight skeletons, so far assumed to be of the Earls of Königsfeld, who used the church as a family sepulchre over a period of seven generations from 1546 to 1749. DNA-based sex testing and analysis of autosomal short tandem repeat systems (STR) was carried out to confirm the assumption of kinship. Since five of the individuals were determined as males, analysis of Y-specific STRs seemed feasible. A comparison of Y-haplotypes revealed that one individual could not be linked to the Königsfeld patrilineage, an observation supported by autosomal STR evidence. Two individuals typed as females posed an identification problem, since supposedly only male members of the family were buried in St Margaretha's. Nevertheless, these individuals could tentatively be identified as members of the House of Königsfeld through genetic fingerprinting.}, }
@article {pmid10331265, year = {1999}, author = {Bosma, PT and Blázquez, M and Collins, MA and Bishop, JD and Drouin, G and Priede, IG and Docherty, K and Trudeau, VL}, title = {Multiplicity of glutamic acid decarboxylases (GAD) in vertebrates: molecular phylogeny and evidence for a new GAD paralog.}, journal = {Molecular biology and evolution}, volume = {16}, number = {3}, pages = {397-404}, doi = {10.1093/oxfordjournals.molbev.a026120}, pmid = {10331265}, issn = {0737-4038}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Alternative Splicing ; Amino Acid Sequence ; Animals ; Base Sequence ; Brain/enzymology ; DNA Primers/genetics ; *Evolution, Molecular ; Gene Duplication ; Glutamate Decarboxylase/*genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Vertebrates/genetics ; }, abstract = {The evolution of chordate glutamic acid decarboxylase (GAD; EC 4.1.1.15), a key enzyme in the central nervous system synthesizing the neurotransmitter gamma-amino-butyric acid (GABA) from glutamate, was studied. Prior to this study, molecular data of GAD had been restricted to mammals, which express two distinct forms, GAD65 and GAD67. These are the products of separate genes and probably are derived from a common ancestral GAD following gene duplication at some point during vertebrate evolution. To enable a comprehensive phylogenetic analysis, molecular information of GAD forms in other vertebrate classes was essential. By reverse transcriptase-polymerase chain reaction (RT-PCR), partial nucleotide sequences of GAD were cloned from brains of zebra finch (Taeniopygia guttata), turtle (Trachemys scripta), goldfish (Carassius auratus), zebrafish (Danio rerio), and armoured grenadier (Coryphaenoides (Nematonurus) armatus, a deep-sea fish), and from the cerebral ganglion plus neural gland of Ciona intestinalis, a protochordate. Whereas GAD65 and GAD67 homologs were expressed in birds, reptiles, and fish, only a single GAD cDNA with equal similarities to both vertebrate GAD forms was found in the protochordate. This indicates that the duplication of the vertebrate GAD gene occurred between 400 and 560 million years ago. For both GAD65 and GAD67, the generated phylogenetic tree followed the general tree topology for the major vertebrate classes. In turtle, an alternative spliced form of GAD65, putatively encoding a truncated, nonactive GAD, was found. Furthermore, a third GAD form, which is equally divergent from both GAD65 and GAD67, is expressed in C. (N.) armatus. This third form might have originated from an ancient genome duplication specific to modern ray-finned fishes.}, }
@article {pmid10190328, year = {1999}, author = {Schultes, T and Hummel, S and Herrmann, B}, title = {Amplification of Y-chromosomal STRs from ancient skeletal material.}, journal = {Human genetics}, volume = {104}, number = {2}, pages = {164-166}, doi = {10.1007/s004390050930}, pmid = {10190328}, issn = {0340-6717}, mesh = {Bone and Bones/pathology ; Child ; *Gene Amplification ; Humans ; Infant ; *Tandem Repeat Sequences ; *Y Chromosome ; }, abstract = {The adaptation to ancient DNA analysis of a Y-chromosomal STR (short tandem repeat) multiplex comprising the four STR systems DYS19, DYS390, and DYS389I/II shows the suitability of Y-chromosomal STR typing on ancient human remains. A new primer site for the system, DYS389I/II, resulting in products shortened by 94 bp, was chosen to serve the special needs of amplification of ancient DNA. For the first time, it was possible to amplify STR loci of the Y chromosome from historical and prehistorical bones of up to 3000 years old.}, }
@article {pmid10091255, year = {1999}, author = {Stone, AC and Stoneking, M}, title = {Analysis of ancient DNA from a prehistoric Amerindian cemetery.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {354}, number = {1379}, pages = {153-159}, pmid = {10091255}, issn = {0962-8436}, mesh = {Amelogenin ; DNA/genetics/*history/isolation &amp; purification ; DNA, Mitochondrial/genetics/*history/isolation &amp; purification ; Dental Enamel Proteins/genetics ; Evolution, Molecular ; Female ; Genetic Variation ; Genetics, Population ; Haplotypes ; History, Medieval ; Humans ; Illinois ; Indians, North American/genetics/*history ; Male ; Paleontology ; Polymerase Chain Reaction ; Sex Determination Analysis ; }, abstract = {The Norris Farms No. 36 cemetery in central Illinois has been the subject of considerable archaeological and genetic research. Both mitochondrial DNA (mtDNA) and nuclear DNA have been examined in this 700-year-old population. DNA preservation at the site was good, with about 70% of the samples producing mtDNA results and approximately 15% yielding nuclear DNA data. All four of the major Amerindian mtDNA haplogroups were found, in addition to a fifth haplogroup. Sequences of the first hypervariable region of the mtDNA control region revealed a high level of diversity in the Norris Farms population and confirmed that the fifth haplogroup associates with Mongolian sequences and hence is probably authentic. Other than a possible reduction in the number of rare mtDNA lineages in many populations, it does not appear as if European contact significantly altered patterns of Amerindian mtDNA variation, despite the large decrease in population size that occurred. For nuclear DNA analysis, a novel method for DNA-based sex identification that uses nucleotide differences between the X and Y copies of the amelogenin gene was developed and applied successfully in approximately 20 individuals. Despite the well-known problems of poor DNA preservation and the ever-present possibility of contamination with modern DNA, genetic analysis of the Norris Farms No. 36 population demonstrates that ancient DNA can be a fruitful source of new insights into prehistoric populations.}, }
@article {pmid10091251, year = {1999}, author = {Rollo, F and Marota, I}, title = {How microbial ancient DNA, found in association with human remains, can be interpreted.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {354}, number = {1379}, pages = {111-119}, pmid = {10091251}, issn = {0962-8436}, mesh = {Animals ; Base Sequence ; Colon/microbiology ; DNA/genetics/*history/isolation &amp; purification ; DNA Primers/genetics ; DNA, Bacterial/genetics/history/isolation &amp; purification ; Evolution, Molecular ; History, Ancient ; History, Medieval ; Humans ; Microbiology ; *Mummies ; Paleontology ; Polymerase Chain Reaction ; }, abstract = {The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies.}, }
@article {pmid9914206, year = {1998}, author = {Skrabanek, L and Wolfe, KH}, title = {Eukaryote genome duplication - where's the evidence?.}, journal = {Current opinion in genetics &amp; development}, volume = {8}, number = {6}, pages = {694-700}, doi = {10.1016/s0959-437x(98)80039-7}, pmid = {9914206}, issn = {0959-437X}, mesh = {Animals ; *Genome ; Humans ; *Polyploidy ; Saccharomyces cerevisiae ; Xenopus ; Zea mays ; }, abstract = {Several eukaryotes, including maize, yeast and Xenopus, are degenerate polyploids formed by relatively recent whole-genome duplications. Ohno's conjecture that more ancient genome duplications occurred in an ancestor of vertebrates is probably at least partly true but the present shortage of gene sequence and map information from vertebrates makes it difficult to either prove or disprove this hypothesis. Candidate paralogous segments in mammalian genomes have been identified but the lack of statistical rigour means that many of the proposals in the literature are probably artefacts.}, }
@article {pmid9830142, year = {1998}, author = {Donoghue, HD and Spigelman, M and Zias, J and Gernaey-Child, AM and Minnikin, DE}, title = {Mycobacterium tuberculosis complex DNA in calcified pleura from remains 1400 years old.}, journal = {Letters in applied microbiology}, volume = {27}, number = {5}, pages = {265-269}, pmid = {9830142}, issn = {0266-8254}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Chromatography, High Pressure Liquid ; DNA, Bacterial/*isolation &amp; purification ; Electrophoresis, Agar Gel ; Humans ; Male ; Mycobacterium tuberculosis/genetics/*isolation &amp; purification ; Mycolic Acids/analysis ; Paleopathology ; Pleura/*microbiology ; Polymerase Chain Reaction ; }, abstract = {Mycobacterium tuberculosis complex DNA was isolated and identified in calcified pleura from remains 1400 years old, with the polymerase chain reaction. This is the first demonstration of tuberculosis in non-mummified archaeological tissue other than bone; the presence of mycobacterial mycolic acids in the sample supports this conclusion. The study of ancient DNA from microbial pathogens is of interest as it enables verification of traditional diagnoses, may answer long-standing questions in the history of disease, and provides ancient DNA sequences that can be compared with those of modern isolates.}, }
@article {pmid9770538, year = {1998}, author = {Drancourt, M and Aboudharam, G and Signoli, M and Dutour, O and Raoult, D}, title = {Detection of 400-year-old Yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {21}, pages = {12637-12640}, pmid = {9770538}, issn = {0027-8424}, mesh = {Base Sequence ; DNA Primers ; DNA, Bacterial/*isolation &amp; purification ; Dental Pulp/*microbiology ; Forensic Medicine ; Humans ; Yersinia pestis/*genetics ; }, abstract = {Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on which to base such research. We hypothesized that it would be a lasting refuge for Yersinia pestis, the plague agent. DNA extracts were made from the dental pulp of 12 unerupted teeth extracted from skeletons excavated from 16th and 18th century French graves of persons thought to have died of plague ("plague teeth") and from 7 ancient negative control teeth. PCRs incorporating ancient DNA extracts and primers specific for the human beta-globin gene demonstrated the absence of inhibitors in these preparations. The incorporation of primers specific for Y. pestis rpoB (the RNA polymerase beta-subunit-encoding gene) and the recognized virulence-associated pla (the plasminogen activator-encoding gene) repeatedly yielded products that had a nucleotide sequence indistinguishable from that of modern day isolates of the bacterium. The specific pla sequence was obtained from 6 of 12 plague skeleton teeth but 0 of 7 negative controls (P < 0.034, Fisher exact test). A nucleic acid-based confirmation of ancient plague was achieved for historically identified victims, and we have confirmed the presence of the disease at the end of 16th century in France. Dental pulp is an attractive target in the quest to determine the etiology of septicemic illnesses detected in ancient corpses. Molecular techniques could be applied to this material to resolve historical outbreaks.}, }
@article {pmid9759357, year = {1998}, author = {Fily, ML and Crubézy, E and Courtaud, P and Keyser, C and Ebrard, D and Ludes, B}, title = {[Paleogenetic analysis of the skeletons from the sepulchral cave of Elzarreko Karbia (Bronze Age, Basque Country)].}, journal = {Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie}, volume = {321}, number = {1}, pages = {79-85}, doi = {10.1016/s0764-4469(97)89629-1}, pmid = {9759357}, issn = {0764-4469}, mesh = {Adolescent ; Female ; France ; Genetic Markers ; Humans ; Immunoglobulin Variable Region/genetics ; Male ; *Paleontology ; Sequence Analysis, DNA ; Sex Determination Analysis ; }, abstract = {Through paleogenetic studies we have characterised the sampling of a sepulchral cave named Elzarreko Karbia, in the Basque Country (France). Four people had been buried in this cave in the Ancient Bronze Age, three men, including an adolescent, and a woman, dating from 3,700 BP. In addition to a confirmation of the anatomical sex determination through amelogenin first intron amplification, we obtained a mitochondrial second hypervariable region (HVR II) sequence for each individual, and thus, we excluded maternal relationship between some of the skeletons.}, }
@article {pmid9705702, year = {1998}, author = {Stokstad, E}, title = {A fruitful scoop for ancient DNA.}, journal = {Science (New York, N.Y.)}, volume = {281}, number = {5375}, pages = {319-320}, doi = {10.1126/science.281.5375.319b}, pmid = {9705702}, issn = {0036-8075}, mesh = {Animals ; DNA, Mitochondrial/analysis/*isolation &amp; purification ; DNA, Plant/analysis/*isolation &amp; purification ; Diet ; Feces/*chemistry ; *Fossils ; Hominidae ; Humans ; *Sloths/genetics ; Thiazoles ; }, }
@article {pmid9667992, year = {1998}, author = {Smith, AB}, title = {What does palaeontology contribute to systematics in a molecular world?.}, journal = {Molecular phylogenetics and evolution}, volume = {9}, number = {3}, pages = {437-447}, doi = {10.1006/mpev.1998.0488}, pmid = {9667992}, issn = {1055-7903}, mesh = {Animals ; DNA/chemistry/*genetics/isolation &amp; purification ; *Evolution, Molecular ; Fishes/classification/genetics ; *Fossils ; Genetic Variation ; *Paleontology ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/*methods ; Time ; Vertebrates/classification/genetics ; }, abstract = {Palaeontology provides the only direct record for morphological and genetic change through time and uniquely contributes to systematics in two ways: by providing access to denser taxon sampling than is otherwise possible and by dating divergence times. Claims that ancient DNA has survived millions of years in certain fossils suggested the possibility that palaeontology could contribute directly to molecular systematic studies. Unfortunately, none of the supposed geologically ancient DNA records stands up to detailed scrutiny and fossils therefore contribute primarily through the morphological information they preserve. Denser taxon sampling can improve the accuracy of phylogenetic estimates primarily through allowing better discrimination of homoplasy from homology. This in turn leads to more accurate hypotheses of character transformation. Denser taxon sampling also offers the opportunity for more accurate rooting, since more characters can be polarized by reference to a stem-group taxon than to an extant sister-group taxon. Missing data can be a problem for fossils, but is not crippling. Finally the temporal order of clade appearances in the fossil record can provide ancillary evidence for selecting a working phylogeny from among a number of equally most parsimonious cladograms.}, }
@article {pmid9656493, year = {1998}, author = {Gutiérrez, G and Marín, A}, title = {The most ancient DNA recovered from an amber-preserved specimen may not be as ancient as it seems.}, journal = {Molecular biology and evolution}, volume = {15}, number = {7}, pages = {926-929}, doi = {10.1093/oxfordjournals.molbev.a025998}, pmid = {9656493}, issn = {0737-4038}, mesh = {*Amber ; Animals ; Base Sequence ; Coleoptera/*genetics ; DNA, Ribosomal/*genetics ; *Fossils ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; }, }
@article {pmid9647790, year = {1998}, author = {Cipollaro, M and Di Bernardo, G and Galano, G and Galderisi, U and Guarino, F and Angelini, F and Cascino, A}, title = {Ancient DNA in human bone remains from Pompeii archaeological site.}, journal = {Biochemical and biophysical research communications}, volume = {247}, number = {3}, pages = {901-904}, doi = {10.1006/bbrc.1998.8881}, pmid = {9647790}, issn = {0006-291X}, mesh = {Amelogenin ; Ancient Lands ; Anthropometry ; Bone and Bones/*chemistry ; DNA/*chemistry ; Dental Enamel Proteins ; Female ; *Fossils ; Genetic Markers/genetics ; Humans ; Italy ; Male ; Microscopy, Polarization ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid ; Sex Determination Analysis/methods ; X Chromosome/genetics ; Y Chromosome/genetics ; }, abstract = {aDNA extraction and amplification procedures have been optimized for Pompeian human bone remains whose diagenesis has been determined by histological analysis. Single copy genes amplification (X and Y amelogenin loci and Y specific alphoid repeat sequences) have been performed and compared with anthropometric data on sexing.}, }
@article {pmid9618509, year = {1998}, author = {Hadly, EA and Kohn, MH and Leonard, JA and Wayne, RK}, title = {A genetic record of population isolation in pocket gophers during Holocene climatic change.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {12}, pages = {6893-6896}, pmid = {9618509}, issn = {0027-8424}, support = {UE1 EH001259/EH/NCEH CDC HHS/United States ; }, mesh = {*Biological Evolution ; Cytochrome b Group/genetics ; DNA/*analysis ; Genetic Variation ; *Genetics, Population ; Humans ; Paleontology ; }, abstract = {A long-standing question in Quaternary paleontology is whether climate-induced, population-level phenotypic change is a result of large-scale migration or evolution in isolation. To directly measure genetic variation through time, ancient DNA and morphologic variation was measured over 2,400 years in a Holocene sequence of pocket gophers (Thomomys talpoides) from Lamar Cave, Yellowstone National Park, Wyoming. Ancient specimens and modern samples collected near Lamar Cave share mitochondrial cytochrome b sequences that are absent from adjacent localities, suggesting that the population was isolated for the entire period. In contrast, diastemal length, a morphologic character correlated with body size and nutritional level, changed predictably in response to climatic change. Our results demonstrate that small mammal populations can experience the long-term isolation assumed by many theoretical models of microevolutionary change.}, }
@article {pmid9601629, year = {1998}, author = {Dickman, S}, title = {Svante Pääbo: pushing ancient DNA to the limit.}, journal = {Current biology : CB}, volume = {8}, number = {10}, pages = {R329-30}, doi = {10.1016/s0960-9822(98)70212-x}, pmid = {9601629}, issn = {0960-9822}, mesh = {Animals ; Archaeology/*history ; DNA/*analysis ; History, 20th Century ; Hominidae/genetics ; Humans ; Mummies ; Sweden ; }, }
@article {pmid9569974, year = {1998}, author = {Ovchinnikov, IV and Ovtchinnikova, OI and Druzina, EB and Buzhilova, AP and Makarov, NA}, title = {Molecular genetic sex determination of Medieval human remains from north Russia: comparison with archaeological and anthropological criteria.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {56}, number = {1}, pages = {7-15}, pmid = {9569974}, issn = {0003-5548}, mesh = {Adult ; Age Determination by Teeth ; Anthropology, Physical/methods ; Archaeology ; Bone and Bones/chemistry ; Child ; DNA/analysis ; Female ; History, Medieval ; Humans ; Male ; Mortuary Practice/history ; Polymerase Chain Reaction ; Russia ; *Sex Determination Processes ; Tooth/chemistry ; }, abstract = {Sex determination presents a difficult problem in archaeology and anthropology in cases of fragmentary or juvenile remains, and where grave goods are absent. Here, a molecular genetic analysis of the sex of human remain from the Early Medieval cemetery at Nefedievo, North Russia, was carried out and the results were compared with archaeological and anthropological data. Teeth without cavities (15 samples) and bones (9 samples) were used as the ancient DNA source. The repetitive sequences in DYZ1, DYZ3, DXZ3 loci, and a unique sequence in the first intron of the X-Y homologous gene amelogenin, were amplified. Sex was determined in 87.5% of the samples by archaeological criteria, in 95.8% of the samples by anthropological methods, and in 79.2% of the samples by DNA analysis. PCR allowed the sex of infant's remains to be identified in individual where the sex could not be determined by anthropological methods and in three remains where sex could not be inferred from archaeological data. Uneven preservation of nuclear DNA loci was evident.}, }
@article {pmid9503587, year = {1998}, author = {Cooper, A and Wayne, R}, title = {New uses for old DNA.}, journal = {Current opinion in biotechnology}, volume = {9}, number = {1}, pages = {49-53}, doi = {10.1016/s0958-1669(98)80083-9}, pmid = {9503587}, issn = {0958-1669}, mesh = {Animals ; DNA/analysis/*genetics ; *Fossils ; *Genome, Human ; Humans ; Paleontology/*methods ; Phylogeny ; Time Factors ; }, abstract = {Several years have elapsed since the last report of million-year-old DNA, coinciding with increased standards for experimental procedures in ancient DNA research. Whereas many earlier studies are now regarded as erroneous, the recent successful characterisation of Neanderthal DNA has set new standards for the field. Researchers continue to find new ways to exploit preserved genetic information in studies of more recent remains, widening the utility of ancient DNA.}, }
@article {pmid9443981, year = {1998}, author = {Pusch, CM and Giddings, I and Scholz, M}, title = {Repair of degraded duplex DNA from prehistoric samples using Escherichia coli DNA polymerase I and T4 DNA ligase.}, journal = {Nucleic acids research}, volume = {26}, number = {3}, pages = {857-859}, pmid = {9443981}, issn = {0305-1048}, mesh = {*Antigens, Neoplasm ; Base Sequence ; Blood Proteins/genetics ; DNA/*chemistry/history ; *DNA Damage ; *DNA Ligases ; *DNA Polymerase I ; DNA Repair ; Escherichia coli/enzymology ; Germany ; *Haptoglobins ; History, Ancient ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; }, abstract = {The most notable feature of DNA extracted from prehistoric material is that it is of poor quality. Amplification of PCR products from such DNA is consequently an exception. Here we present a simple method for the repair of degraded duplex DNA using the enzymes Escherichia coli DNA polymerase I and T4 DNA ligase. Adjacent sequences separated by nicks do not split up into intact strands during the denaturation step of PCR. Thus the target DNA is refractory to amplification. The proposed repair of nicked, fragmented ancient DNA results in an increase of amplification efficiency, such that the correct base order of the respective nuclear DNA segment can be obtained.}, }
@article {pmid9306399, year = {1997}, author = {Audic, S and Béraud-Colomb, E}, title = {Ancient DNA is thirteen years old.}, journal = {Nature biotechnology}, volume = {15}, number = {9}, pages = {855-858}, doi = {10.1038/nbt0997-855}, pmid = {9306399}, issn = {1087-0156}, mesh = {Animals ; Archaeology ; Communicable Diseases/genetics ; DNA/chemistry/*genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Plant/chemistry/genetics ; Genetic Diseases, Inborn/genetics ; Humans ; *Paleontology ; Polymerase Chain Reaction ; Templates, Genetic ; }, abstract = {The first successful recovery of ancient DNA, from quagga and human mummies inspired significant enough interest to open an entire field of research. Efforts from many research groups, often in a hunt for the oldest sequences, showed that ancient DNA was a poor substrate for the enzymes used in molecular biology; it is present in tiny amounts, hard to purify, and frequently damaged. These obstacles have been partially overcome by the use of drastic laboratory precautions and by the introduction of polymerase chain reaction and phylogenetic studies. Ancient DNA analysis now finds applications in many research domains.}, }
@article {pmid9335147, year = {1997}, author = {Walden, KK and Robertson, HM}, title = {Ancient DNA from amber fossil bees?.}, journal = {Molecular biology and evolution}, volume = {14}, number = {10}, pages = {1075-1077}, doi = {10.1093/oxfordjournals.molbev.a025713}, pmid = {9335147}, issn = {0737-4038}, mesh = {Amber ; Animals ; Base Sequence ; Bees/*genetics ; DNA, Ribosomal/chemistry/*isolation &amp; purification ; *Evolution, Molecular ; *Fossils ; Humans ; Molecular Sequence Data ; RNA, Ribosomal, 18S/*genetics ; Sequence Alignment ; }, }
@article {pmid9286706, year = {1997}, author = {Street, VA and Tempel, BL}, title = {Physical mapping of potassium channel gene clusters on mouse chromosomes three and six.}, journal = {Genomics}, volume = {44}, number = {1}, pages = {110-117}, doi = {10.1006/geno.1997.4799}, pmid = {9286706}, issn = {0888-7543}, support = {R01-NS27206/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Chromosomes, Artificial, Yeast/genetics ; Cloning, Molecular ; DNA Probes ; Drosophila/genetics ; Drosophila Proteins ; Electrophoresis, Gel, Pulsed-Field ; Evolution, Molecular ; Genetic Linkage ; Ion Channel Gating/physiology ; Mice ; Molecular Sequence Data ; *Multigene Family ; Polymerase Chain Reaction ; Potassium Channels/*genetics ; *Restriction Mapping ; Sequence Homology, Amino Acid ; Shaker Superfamily of Potassium Channels ; Transcription, Genetic ; }, abstract = {Mammalian voltage-gated K channel genes have been divided into four subfamilies (Shaker, Shab, Shal, and Shaw) based on their sequence identity and similarity to related genes in Drosophila. Genetic mapping of the voltage-gated K channel genes has shown that similar multigene clusters exist on mouse Chr 3 and 6 and suggests that the clusters may have arisen through chromosomal duplication. In this report, YAC-based physical maps of the clustered mouse Shaker-like K channel genes have been constructed using restriction endonuclease and yeast chromosome fragmentation approaches. These data define the physical spacing as 5'-Kcna3-(60 kb)-Kcna2-(90 kb)-Kcna8-3' on Chr 3, and as 5'-Kcna6-(80 kb)-Kcna1-(110 kb)-Kcna5-3' on Chr 6, with all genes oriented in a head-to-tail manner within their respective clusters. These detailed physical maps of both K channel gene clusters provide additional support for the idea of an ancient genome tetraploidization event.}, }
@article {pmid9378117, year = {1997}, author = {Matisoo-Smith, E and Allen, JS and Ladefoged, TN and Roberts, RM and Lambert, DM}, title = {Ancient DNA from Polynesian rats: extraction, amplification and sequence from single small bones.}, journal = {Electrophoresis}, volume = {18}, number = {9}, pages = {1534-1537}, doi = {10.1002/elps.1150180908}, pmid = {9378117}, issn = {0173-0835}, mesh = {Animals ; Base Sequence ; Bone and Bones/*chemistry ; DNA/*analysis/*chemistry ; DNA, Mitochondrial/analysis/chemistry ; *Fossils ; Molecular Sequence Data ; Muridae/*genetics ; Polymerase Chain Reaction ; Polynesia ; Rats ; *Sequence Analysis, DNA ; }, abstract = {The human colonisation of Polynesia was a major event in world prehistory. It represents one of the last human population migrations, and one which required crossing major water barriers. Though the subject of Pacific population origins has been approached by scholars from numerous fields for nearly a century, recent years have seen the problem addressed by human geneticists. Since the initial report describing the recovery of DNA from skeletal remains, ancient DNA studies have also focused on the Pacific region. In this paper we present the results of ancient DNA analyses of Rattus exulans, an animal that was transported by ancestral Polynesians through the Pacific to the far reaches of the Polynesian triangle. Analysis of DNA of R. exulans skeletal remains has many advantages over studies of ancient human remains, yet the one drawback has been the recovery of ancient DNA from single bones of these very small rodents. We have successfully modified standard extraction protocols for ancient DNA and have consistently extracted, amplified and sequenced mitochondrial DNA (mtDNA) from less than 0.1 g of R. exulans bone and tooth samples recovered from archaeological sites throughout the Pacific, ranging from 400 to 2000 years old.}, }
@article {pmid9378116, year = {1997}, author = {Hagelberg, E}, title = {Ancient and modern mitochondrial DNA sequences and the colonization of the Pacific.}, journal = {Electrophoresis}, volume = {18}, number = {9}, pages = {1529-1533}, doi = {10.1002/elps.1150180907}, pmid = {9378116}, issn = {0173-0835}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Asia/ethnology ; DNA, Mitochondrial/*chemistry ; Emigration and Immigration ; Fossils ; Gene Deletion ; Genetic Variation ; Humans ; Pacific Islands ; Polynesia ; }, abstract = {Mitochondrial DNA (mtDNA) is a valuable tool for the study of recent human evolution because it is easy to analyse, is inherited uniparentally and has a relatively rapid rate of evolution. mtDNA analysis has been used extensively for the elucidation of the pattern of migrations of human populations. Several studies have focused on the Pacific because Polynesia was settled by humans for the first time relatively recently and there is a wealth of archaeological and linguistic data to complement genetic data on the region. Results of mtDNA analyses on modern-day Pacific populations indicate reduced genetic variability, and suggest that the Polynesians descend from people who migrated relatively recently from island Southeast Asia and that a population bottleneck occurred during the settlement of the central Pacific. Several informative polymorphisms have been identified in the hypervariable control region of mtDNA in modern-day Pacific populations that are helpful in tracing the ancestral affinities of these people. Studies of these mtDNA polymorphisms in ancient bones of prehistoric Pacific islanders indicate that the proto-Polynesian colonizers may have descended from the early settlers of island Melanesia. Although fraught with technical difficulties, studies of ancient DNA can provide valuable evidence on the genetic affinities of past peoples.}, }
@article {pmid9230295, year = {1997}, author = {Lindahl, T}, title = {Facts and artifacts of ancient DNA.}, journal = {Cell}, volume = {90}, number = {1}, pages = {1-3}, doi = {10.1016/s0092-8674(00)80306-2}, pmid = {9230295}, issn = {0092-8674}, mesh = {Animals ; *Artifacts ; Base Sequence ; Bone and Bones/chemistry ; DNA/*chemistry ; DNA, Mitochondrial/chemistry ; *Fossils ; Germany ; Hominidae/genetics ; Humans ; }, }
@article {pmid9341088, year = {1997}, author = {Schultes, T and Hummel, S and Herrmann, B}, title = {[Classification of isolated skeletal elements using aDNA typing].}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {55}, number = {2}, pages = {207-216}, pmid = {9341088}, issn = {0003-5548}, mesh = {Bone and Bones/*metabolism ; Burial/history ; DNA/genetics/*history ; Germany ; History, Ancient ; Humans ; Paleopathology ; *Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid/*genetics ; }, abstract = {Analysis of ancient DNA of material found in the Lichtensteinhöhle, a burial site of the Younger Bronze Age has been used for the first time to assign isolated skeletal elements to corresponding individuals. The method involved DNA typing through amplification of five Short Tandem Repeat loci which are also used in forensic genetics for the determination of kinship and identification. From all of the examined bone samples DNA was successfully extracted and amplification by means of Polymerase Chain Reaction could be carried out. For the skeletal elements allelic profiles which are specific for an individual were set up. These profiles made it possible to recognize bones belonging to one individual. Elements which were not from this individual could be excluded with certainty by aDNA analysis.}, }
@article {pmid9332711, year = {1997}, author = {Yang, H and Golenberg, EM and Shoshani, J}, title = {Proboscidean DNA from museum and fossil specimens: an assessment of ancient DNA extraction and amplification techniques.}, journal = {Biochemical genetics}, volume = {35}, number = {5-6}, pages = {165-179}, doi = {10.1023/a:1021902125382}, pmid = {9332711}, issn = {0006-2928}, mesh = {Animals ; DNA/*isolation &amp; purification ; *Elephants ; *Fossils ; Humans ; Polymerase Chain Reaction/*methods ; }, abstract = {Applications of reliable DNA extraction and amplification techniques to postmortem samples are critical to ancient DNA research. Commonly used methods for isolating DNA from ancient material were tested and compared using both soft tissue and bones from fossil and contemporary museum proboscideans. DNAs isolated using three principal methods served as templates in subsequent PCR amplifications, and the PCR products were directly sequenced. Authentication of the ancient origin of obtained nucleotide sequences was established by demonstrating reproducibility under a blind testing system and by phylogenetic analysis. Our results indicate that ancient samples may respond differently to extraction buffers or purification procedures, and no single method was universally successful. A CTAB buffer method, modified from plant DNA extraction protocols, was found to have the highest success rate. Nested PCR was shown to be a reliable approach to amplify ancient DNA templates that failed in primary amplification.}, }
@article {pmid9126729, year = {1997}, author = {Sykes, B}, title = {Really ancient DNA. Lights turning red on amber.}, journal = {Nature}, volume = {386}, number = {6627}, pages = {764-765}, doi = {10.1038/386764a0}, pmid = {9126729}, issn = {0028-0836}, mesh = {*Amber ; Animals ; *DNA ; *Fossils ; Insecta/*genetics ; }, }
@article {pmid9149422, year = {1997}, author = {Austin, JJ and Ross, AJ and Smith, AB and Fortey, RA and Thomas, RH}, title = {Problems of reproducibility--does geologically ancient DNA survive in amber-preserved insects?.}, journal = {Proceedings. Biological sciences}, volume = {264}, number = {1381}, pages = {467-474}, pmid = {9149422}, issn = {0962-8452}, mesh = {Amber ; Animals ; Base Sequence ; Biological Evolution ; DNA/*analysis/genetics ; DNA Replication ; *Fossils ; Genes, Insect ; Insecta/*genetics ; Molecular Sequence Data ; }, abstract = {Apparently ancient DNA has been reported from amber-preserved insects many millions of years old. Rigorous attempts to reproduce these DNA sequences from amber- and copal-preserved bees and flies have failed to detect any authentic ancient insect DNA. Lack of reproducibility suggests that DNA does not survive over millions of years even in amber, the most promising of fossil environments.}, }
@article {pmid9126568, year = {1997}, author = {Yang, H and Golenberg, EM and Shoshani, J}, title = {A blind testing design for authenticating ancient DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {7}, number = {2}, pages = {261-265}, doi = {10.1006/mpev.1996.0398}, pmid = {9126568}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/genetics ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Elephants/genetics ; Evaluation Studies as Topic ; Evolution, Molecular ; Female ; *Fossils ; *Genetic Techniques/statistics &amp; numerical data ; Male ; Mammals/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction/statistics &amp; numerical data ; Reproducibility of Results ; }, abstract = {Reproducibility is a serious concern among researchers of ancient DNA. We designed a blind testing procedure to evaluate laboratory accuracy and authenticity of ancient DNA obtained from closely related extant and extinct species. Soft tissue and bones of fossil and contemporary museum proboscideans were collected and identified based on morphology by one researcher, and other researchers carried out DNA testing on the samples, which were assigned anonymous numbers. DNA extracted using three principal isolation methods served as template in PCR amplifications of a segment of the cytochrome b gene (mitochondrial genome), and the PCR product was directly sequenced and analyzed. The results show that such a blind testing design performed in one laboratory, when coupled with phylogenetic analysis, can nonarbitrarily test the consistency and reliability of ancient DNA results. Such reproducible results obtained from the blind testing can increase confidence in the authenticity of ancient sequences obtained from postmortem specimens and avoid bias in phylogenetic analysis. A blind testing design may be applicable as an alternative to confirm ancient DNA results in one laboratory when independent testing by two laboratories is not available.}, }
@article {pmid9106549, year = {1997}, author = {Cooper, A}, title = {Reply to Stoneking: ancient DNA--how do you really know when you have it?.}, journal = {American journal of human genetics}, volume = {60}, number = {4}, pages = {1001-1003}, pmid = {9106549}, issn = {0002-9297}, mesh = {Archaeology/standards ; Artifacts ; *Bone and Bones ; DNA/*isolation &amp; purification ; *Fossils ; Gene Amplification ; Genetics/standards ; Humans ; }, }
@article {pmid9244759, year = {1997}, author = {Tëtushkin, EIa}, title = {[Molecular paleogenetics of primates].}, journal = {Genetika}, volume = {33}, number = {3}, pages = {293-307}, pmid = {9244759}, issn = {0016-6758}, mesh = {Animals ; Antigens/genetics ; Chromosome Mapping ; Genetic Markers ; Humans ; Paleontology ; Phylogeny ; Primates/*genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {Genetic distances between the major members of the primate order obtained from data on blood serum antigens, amino-acid sequences of intracell proteins, electrophoretic gene markers, and nucleotide sequences of nuclear and mitochondrial DNA are analyzed. Conclusions regarding phylogeny and systematics of the primate order based on evidence of molecular evolutionary genetics are discussed.}, }
@article {pmid9404456, year = {1997}, author = {Loreille, O and Mounolou, JC and Monnerot, M}, title = {[History of the rabbit and ancient DNA].}, journal = {Comptes rendus des seances de la Societe de biologie et de ses filiales}, volume = {191}, number = {4}, pages = {537-544}, pmid = {9404456}, issn = {0037-9026}, mesh = {Animals ; Cell Lineage ; DNA, Mitochondrial/genetics/*history ; Evolution, Molecular ; Geography ; History, Ancient ; Humans ; Rabbits ; }, abstract = {Present populations of Rabbits (Oryctolagus cuniculus) are organized into two well defined groups A and B according to their mitochondrial DNA sequences. Group A is restricted to the South Western part of the Iberian Peninsula while group B is found everywhere else. Domestic breeds belong to the latter. As evidenced from data on ancient bones (up to 12,000 years BP) the mitochondrial type B1, predominant in domestic animals, originated from Spain. B1 animals were introduced in France by man between late Roman times and Middle Ages.}, }
@article {pmid9002668, year = {1997}, author = {Lalueza, C and Pérez-Pérez, A and Prats, E and Cornudella, L and Turbón, D}, title = {Lack of founding Amerindian mitochondrial DNA lineages in extinct aborigines from Tierra del Fuego-Patagonia.}, journal = {Human molecular genetics}, volume = {6}, number = {1}, pages = {41-46}, doi = {10.1093/hmg/6.1.41}, pmid = {9002668}, issn = {0964-6906}, mesh = {Argentina ; Base Sequence ; DNA ; *DNA, Mitochondrial ; Indians, South American/*genetics ; Molecular Sequence Data ; Polymorphism, Genetic ; Restriction Mapping ; Sequence Analysis, DNA ; }, abstract = {Ancient DNA from bones and teeth of 60 individuals from four extinct human populations from Tierra del Fuego-Patagonia (Selknam, Yamana, Kaweskar and Aonikenk) has been extracted and the mitochondrial DNA (mtDNA) amplified by using the polymerase chain reaction. High-resolution analysis of endonuclease restriction site variation in the mtDNA and sequencing of its hypervariable non-coding control region, revealed complete absence of two of the four primary mitochondrial haplotype groups present in contemporary Amerinds, namely A and B. In contrast, haplogroups C and D were found in all but one sample with frequencies of approximately 38% and 60%. These results, together with the decreasing incidence of group A in more southerly latitudes in the American continent and the absence of cluster B above 55 degrees North in America and Asia, argue that the first settlers entering America 21000-14000 years ago already lacked both mtDNA lineages.}, }
@article {pmid8952089, year = {1996}, author = {Bailey, JF and Richards, MB and Macaulay, VA and Colson, IB and James, IT and Bradley, DG and Hedges, RE and Sykes, BC}, title = {Ancient DNA suggests a recent expansion of European cattle from a diverse wild progenitor species.}, journal = {Proceedings. Biological sciences}, volume = {263}, number = {1376}, pages = {1467-1473}, doi = {10.1098/rspb.1996.0214}, pmid = {8952089}, issn = {0962-8452}, mesh = {Animals ; Animals, Domestic/genetics ; Base Sequence ; Biological Evolution ; Cattle/*genetics ; DNA, Mitochondrial/*genetics ; Europe ; History, Ancient ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {A total of 11 Bos primigenius and Bos taurus bones from archaeological sites between 500 and 12000 years old were examined for the presence of DNA. It was possible to amplify and sequence mitochondrial control region DNA extracted from seven of the 11 samples, including two Pleistocene B. primigenius samples. We compared the results with published data by constructing phylogenetic networks. The two B. primigenius samples clustered with the extant B. taurus samples in the networks. The similarity between B. primigenius and modern taurine cattle confirms that these should be considered members of a single species. The sequences obtained from the B. taurus specimens were either identical to the reference sequence for modern European cattle or closely related to it. They included two sequences not previously documented. The network analysis of the ancient data highlights the intermediary nature of the B. primigenius sequences between modern European and African B. taurus and the proximity of the ancient DNA B. taurus sequences to modern European B. taurus. Further analysis of the extant data in the light of the ancient DNA results suggests that a degree of Pleistocene diversity survives in the extant European Bos population that is mainly derived from a more recent population expansion.}, }
@article {pmid8755923, year = {1996}, author = {Handt, O and Krings, M and Ward, RH and Pääbo, S}, title = {The retrieval of ancient human DNA sequences.}, journal = {American journal of human genetics}, volume = {59}, number = {2}, pages = {368-376}, pmid = {8755923}, issn = {0002-9297}, mesh = {Archaeology/*methods ; Arizona ; Asian People/*genetics ; Base Sequence ; DNA, Mitochondrial/*isolation &amp; purification ; Humans ; *Indians, North American ; Molecular Sequence Data ; *Mummies ; Polymerase Chain Reaction/methods ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {DNA was extracted from approximately 600-year-old human remains found at an archaeological site in the southwestern United States, and mtDNA fragments were amplified by PCR. When these fragments were sequenced directly, multiple sequences seemed to be present. From three representative individuals, DNA fragments of different lengths were quantified and short overlapping amplification products cloned. When amplifications started from <40 molecules, clones contained several different sequences. In contrast, when they were initiated by a few thousand molecules, unambiguous and reproducible results were achieved. These results show that more experimental work than is often applied is necessary to ensure that DNA sequences amplified from ancient human remains are authentic. In particular, quantitation of the numbers of amplifiable molecules is a useful tool to determine the role of contaminating contemporary molecules and PCR errors in amplifications from ancient DNA.}, }
@article {pmid8632821, year = {1996}, author = {Cooper, A and Rhymer, J and James, HF and Olson, SL and McIntosh, CE and Sorenson, MD and Fleischer, RC}, title = {Ancient DNA and island endemics.}, journal = {Nature}, volume = {381}, number = {6582}, pages = {484}, doi = {10.1038/381484a0}, pmid = {8632821}, issn = {0028-0836}, mesh = {Animals ; Base Sequence ; Bone and Bones ; *DNA ; *Ducks/classification/genetics ; Geography ; Molecular Sequence Data ; *Paleontology/methods ; Sequence Homology, Nucleic Acid ; }, }
@article {pmid8629020, year = {1996}, author = {Poinar, HN and Höss, M and Bada, JL and Pääbo, S}, title = {Amino acid racemization and the preservation of ancient DNA.}, journal = {Science (New York, N.Y.)}, volume = {272}, number = {5263}, pages = {864-866}, doi = {10.1126/science.272.5263.864}, pmid = {8629020}, issn = {0036-8075}, mesh = {Alanine/chemistry ; *Amber/chemistry ; Amino Acids/*chemistry ; Animals ; Aspartic Acid/chemistry ; DNA/*analysis/chemistry ; *Fossils ; History, Ancient ; Humans ; Leucine/chemistry ; *Paleontology ; Stereoisomerism ; }, abstract = {The extent of racemization of aspartic acid, alanine, and leucine provides criteria for assessing whether ancient tissue samples contain endogenous DNA. In samples in which the D/L ratio of aspartic acid exceeds 0.08, ancient DNA sequences could not be retrieved. Paleontological finds from which DNA sequences purportedly millions of years old have been reported show extensive racemization, and the amino acids present are mainly contaminates. An exception is the amino acids in some insects preserved in amber.}, }
@article {pmid8838911, year = {1996}, author = {Zierdt, H and Hummel, S and Herrmann, B}, title = {Amplification of human short tandem repeats from medieval teeth and bone samples.}, journal = {Human biology}, volume = {68}, number = {2}, pages = {185-199}, pmid = {8838911}, issn = {0018-7143}, mesh = {Alleles ; *Anthropology ; Base Sequence ; Bone and Bones ; DNA/*analysis/genetics ; Gene Amplification ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid/*genetics ; }, abstract = {The suitability of typing hypervariable DNA loci for the genetic analysis of prehistoric populations is demonstrated for the first time. Alleles of the human short tandem repeat locus VWA31/A have been amplified from ancient teeth and bone samples derived from an early medieval burial site at Weingarten, Germany, using the polymerase chain reaction. The DNA results for 76 individuals reveal remarkable similarity of the allelic frequencies between the past and modern populations. A surplus of apparent homozygotes in the ancient population is most likely due to a stochastic problem of amplification of degraded DNA. Therefore technical obstacles for the application to ancient DNA were evaluated. The substantial perspectives of using microsatellite typing for the analysis of heritable diseases, determination of relatedness, and establishment of genealogies in prehistoric populations are outlined.}, }
@article {pmid8779335, year = {1996}, author = {Parr, RL and Carlyle, SW and O'Rourke, DH}, title = {Ancient DNA analysis of Fremont Amerindians of the Great Salt Lake Wetlands.}, journal = {American journal of physical anthropology}, volume = {99}, number = {4}, pages = {507-518}, doi = {10.1002/(SICI)1096-8644(199604)99:4&lt;507::AID-AJPA1&gt;3.0.CO;2-R}, pmid = {8779335}, issn = {0002-9483}, mesh = {Base Sequence ; Bone and Bones/*chemistry ; DNA Primers/chemistry ; DNA, Mitochondrial/*analysis/genetics ; Gene Frequency ; Haplotypes ; History, Medieval ; Humans ; Indians, North American/genetics/*history ; Molecular Sequence Data ; Utah ; }, abstract = {Skeletal remains of 47 individuals from the Great Salt Lake Wetlands, affiliated principally with Bear River (A.D. 400-1000) and Levee Phase (A.D. 1000-1350) Fremont cultural elements, were assessed for four mitochondrial DNA (mtDNA) markers that, in particular association, define four haplogroups (A, B, C, and D) widely shared among contemporary Amerindian groups. The most striking result is the absence of haplogroup A in this Fremont series, despite its predominance in contemporary Amerindian groups. Additionally, haplogroup B, defined by the presence of a 9bp deletion in region V, is present at the moderately high frequency of 60%. Haplogroups C and D are present at low frequencies. An additional haplotype, "N," observed in some modern populations and two other prehistoric samples, is also present in this Fremont skeletal collection.}, }
@article {pmid8650373, year = {1996}, author = {Ueda, S}, title = {[Ancient DNA].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {41}, number = {5}, pages = {733-737}, pmid = {8650373}, issn = {0039-9450}, mesh = {Animals ; *Archaeology ; Base Sequence ; DNA/*genetics ; Family ; Humans ; Molecular Sequence Data ; Repetitive Sequences, Nucleic Acid/genetics ; }, }
@article {pmid8614634, year = {1996}, author = {Höss, M and Jaruga, P and Zastawny, TH and Dizdaroglu, M and Pääbo, S}, title = {DNA damage and DNA sequence retrieval from ancient tissues.}, journal = {Nucleic acids research}, volume = {24}, number = {7}, pages = {1304-1307}, pmid = {8614634}, issn = {0305-1048}, mesh = {Animals ; Archaeology/*methods ; DNA/*isolation &amp; purification/metabolism ; Gas Chromatography-Mass Spectrometry ; Humans ; Oxidation-Reduction ; Polymerase Chain Reaction/*methods ; }, abstract = {Gas chromatography/mass spectrometry (GC/MS) was used to determine the amounts of eight oxidative base modifications in DNA extracted from 11 specimens of bones and soft tissues, ranging in age from 40 to >50 000 years. Among the compounds assayed hydantoin derivatives of pyrimidines were quantitatively dominant. From five of the specimens endogenous ancient DNA sequences could be amplified by PCR. The DNA from these specimens contained substantially lower amounts of hydantoins than the six specimens from which no DNA could be amplified. Other types of damage, e.g. oxidation products of purines, did not correlate with the inability to retrieve DNA sequences. Furthermore, all samples with low amounts of damage and from which DNA could be amplified stemmed from regions where low temperatures have prevailed throughout the burial period of the specimens.}, }
@article {pmid8859328, year = {1996}, author = {Kelman, Z and Moran, L}, title = {Degradation of ancient DNA.}, journal = {Current biology : CB}, volume = {6}, number = {3}, pages = {223}, doi = {10.1016/s0960-9822(02)00460-8}, pmid = {8859328}, issn = {0960-9822}, mesh = {Chromatin/metabolism ; *DNA/metabolism ; DNA Fragmentation ; Endonucleases/metabolism ; *Fossils ; Nucleosomes/metabolism ; }, }
@article {pmid9022353, year = {1996}, author = {Cano, RJ}, title = {Analysing ancient DNA.}, journal = {Endeavour}, volume = {20}, number = {4}, pages = {162-167}, doi = {10.1016/s0160-9327(96)10031-4}, pmid = {9022353}, issn = {0160-9327}, mesh = {Amber ; Base Sequence ; Conserved Sequence ; DNA/*analysis ; *Fossils ; Gene Amplification ; Phylogeny ; Polymerase Chain Reaction ; Software ; }, abstract = {Much of what we know about extinct organisms comes from traits that are not preserved in the fossil record. Until recently, morphological analysis was the only tool available for scientists to determine relationships for extinct fossil organisms. We now know that "ancient' DNA can be preserved in the remains of extinct organisms. By targeting specific gene sequences, it may be possible to deduce biochemical characteristics and through sequence comparisons, to estimate the extent of evolutionary divergence. By comparing the amount and type of these changes, one could estimate how quickly some DNA 'evolves' relative to other segments, or which genes have the most flexibility or are more conserved over time. The compilation of these data would yield greater understanding of the physiology of extinct organisms and provide a much clearer picture of genetic change over time, and the mechanics behind 'evolution'.}, }
@article {pmid8583902, year = {1996}, author = {Taylor, PG}, title = {Reproducibility of ancient DNA sequences from extinct Pleistocene fauna.}, journal = {Molecular biology and evolution}, volume = {13}, number = {1}, pages = {283-285}, doi = {10.1093/oxfordjournals.molbev.a025566}, pmid = {8583902}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; DNA/*genetics ; *Evolution, Molecular ; *Fossils ; Mammals/*genetics ; Molecular Sequence Data ; Sequence Analysis ; }, }
@article {pmid8587143, year = {1995}, author = {Pauly, M and Kayser, I and Schmitz, M and Ries, F and Hentges, F and Dicato, M}, title = {Repetitive DNA sequences located in the central region of the human mdr1 (multidrug resistance) gene may account for a gene fusion event during its evolution.}, journal = {Journal of molecular evolution}, volume = {41}, number = {6}, pages = {974-978}, pmid = {8587143}, issn = {0022-2844}, mesh = {Base Sequence ; Drug Resistance, Multiple/*genetics ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Polymorphism, Restriction Fragment Length ; *Repetitive Sequences, Nucleic Acid ; Sequence Analysis ; }, abstract = {The mdr1 gene, first member of the human multidrug-resistance gene family, is a major gene involved in cellular resistance to several drugs used in anticancer chemotherapy. Its product, the drug-excreting P-glycoprotein, shows a bipartite structure formed by two similar adjacent halves. According to one hypothesis, the fusion of two related ancestral genes during evolution could have resulted in this structure. The DNA sequence analysis of the introns located in the region connecting the two halves of the human mdr1 gene revealed a highly conserved poly(CA).poly (TG) sequence in intron 15 and repeated sequences of the Alu family in introns 14 and 17. These repeated sequences most likely represent "molecular fossils" of ancient DNA elements which were involved in such a recombination event.}, }
@article {pmid8533753, year = {1995}, author = {Stoneking, M}, title = {Ancient DNA: how do you know when you have it and what can you do with it?.}, journal = {American journal of human genetics}, volume = {57}, number = {6}, pages = {1259-1262}, pmid = {8533753}, issn = {0002-9297}, mesh = {Anthropology ; DNA/*genetics ; Genetic Techniques ; Humans ; }, }
@article {pmid7638613, year = {1995}, author = {Williams, N}, title = {Ancient DNA. The trials and tribulations of cracking the prehistoric code.}, journal = {Science (New York, N.Y.)}, volume = {269}, number = {5226}, pages = {923-924}, doi = {10.1126/science.7638613}, pmid = {7638613}, issn = {0036-8075}, mesh = {DNA/*genetics/history ; DNA, Mitochondrial/genetics ; Emigration and Immigration ; Europe ; Genetics, Population/*history ; History, Ancient ; Humans ; Indians, North American/genetics ; *Paleontology ; }, }
@article {pmid8532630, year = {1995}, author = {Restagno, G and Ferrone, M and Doriguzzi, C and Palmucci, L and Mongini, T and Carbonara, A}, title = {Carrier detection of Duchenne muscular dystrophy through analysis of DNA from deciduous teeth of a dead affected child.}, journal = {Prenatal diagnosis}, volume = {15}, number = {7}, pages = {672-674}, doi = {10.1002/pd.1970150715}, pmid = {8532630}, issn = {0197-3851}, mesh = {Child ; DNA/*analysis/genetics ; Exons ; Female ; Genetic Counseling ; Genetic Linkage ; *Heterozygote ; Humans ; Male ; Muscular Dystrophies/*diagnosis/*genetics ; Pedigree ; Tooth, Deciduous/*chemistry ; X Chromosome ; }, abstract = {The sister of a child affected by Duchenne muscular dystrophy (DMD) was referred for genetic counselling to assess the risk of her being a carrier. Her brother had died 15 years previously at the age of 8. There were no other affected males in the family. There were no methods for DNA investigation at the time of the child's death and the family had never been studied for linkage with polymorphic probes on the chromosomal region Xp21. The only tissue from which an assessment of the risk could be made by DNA linkage analysis was two of the child's deciduous teeth that the parents had kept. DNA was extracted using a protocol described for the recovery of ancient DNA from museum specimens and archaeological finds. Multiplex amplification did not reveal deletions in 19 exons spanning the hot-spot regions for deletions within the dystrophin gene in Xp21. Linkage analysis using three highly polymorphic microsatellites demonstrated that the sister had not received the X chromosome borne by her brother. These results show that DNA extracted from teeth is a reliable source for molecular diagnosis.}, }
@article {pmid7543951, year = {1995}, author = {van der Kuyl, AC and Kuiken, CL and Dekker, JT and Perizonius, WR and Goudsmit, J}, title = {Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: a problem of ancient DNA and molecular phylogenies.}, journal = {Journal of molecular evolution}, volume = {40}, number = {6}, pages = {652-657}, pmid = {7543951}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Cercocebus ; DNA/*genetics ; DNA Primers ; Humans ; Molecular Sequence Data ; Mummies ; Papio/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Primates/genetics ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Alignment ; }, abstract = {Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.}, }
@article {pmid7723050, year = {1995}, author = {Hardy, C and Callou, C and Vigne, JD and Casane, D and Dennebouy, N and Mounolou, JC and Monnerot, M}, title = {Rabbit mitochondrial DNA diversity from prehistoric to modern times.}, journal = {Journal of molecular evolution}, volume = {40}, number = {3}, pages = {227-237}, pmid = {7723050}, issn = {0022-2844}, mesh = {Africa, Northern ; Animals ; Base Sequence ; Biological Evolution ; Bone and Bones/chemistry ; Cytochrome b Group/genetics ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics ; Europe ; Genes ; Molecular Sequence Data ; Rabbits/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {The mitochondrial genetic variability in European rabbit (Oryctolagus cuniculus) populations present in Europe and North Africa from 11,000 years ago to the present day has been analyzed using ancient DNA techniques. DNA was extracted from 90 rabbit bones found in 22 archaeological sites dated between the Mesolithic and recent times. Nucleotide sequences present in a variable 233-bp domain of the cytochrome b gene were compared to those present in modern-day rabbits. The results show that the structure of ancient populations of wild rabbit exhibited remarkable stability over time until the Middle Ages. At this time, a novel type of mtDNA molecule abruptly appears into most wild populations studied from France. This mtDNA type corresponds to that currently present in the domestic breeds of rabbit examined so far. The relative rapidity by which this mtDNA type established and its absence in all sites examined before 1,700 years ago lend support to the hypothesis that between 2,000 and 1,000 years ago, man may have favored the development, into all regions of France, of animals carrying this particular mtDNA molecule. The origin of such animals has still to be found: animals previously living outside of France or within France but in very restricted areas? This event was concomitant with the documented establishment of warrens after the tenth century A.D. in Europe.}, }
@article {pmid7750909, year = {1995}, author = {Höss, M}, title = {Ancient DNA.}, journal = {Hormone research}, volume = {43}, number = {4}, pages = {118-120}, doi = {10.1159/000184253}, pmid = {7750909}, issn = {0301-0163}, mesh = {Animals ; *Biological Evolution ; DNA/*genetics ; Humans ; *Paleontology ; Phylogeny ; }, abstract = {The investigation of molecular traits for evolutionary studies is a valuable alternative to the classic morphological approach. Since the mid-1980s molecular evolution has extended its field of investigation into the past. This has become possible with development of the polymerase chain reaction, which allows amplification of, and hence the study of, DNA from individuals long since dead. Many ancient, mostly extinct, animals and plants have been studied in order to determine their phylogenetic relationships with extant species. The biochemical properties of ancient DNA are also under investigation. The modifications that this molecule undergoes over long periods of time are of great interest as attempts are made to retrieve DNA from increasingly older remains.}, }
@article {pmid7888749, year = {1994}, author = {DeSalle, R and Grimaldi, D}, title = {Very old DNA.}, journal = {Current opinion in genetics &amp; development}, volume = {4}, number = {6}, pages = {810-815}, doi = {10.1016/0959-437x(94)90064-7}, pmid = {7888749}, issn = {0959-437X}, mesh = {Amber ; Animals ; DNA/*chemistry ; DNA, Bacterial ; DNA, Plant ; *Fossils ; Insecta/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {The verification of DNA sequences obtained from very old tissue sources as indeed ancient is a major point of discussion in the ancient DNA field. Proper controls and the use of the phylogenetic approach are the general methods employed for verification of the ancient DNA. Most studies have reported the recovery of extremely small amounts of nucleic acids which are sheared into rather small fragments. In addition, problems such as 'PCR jumping' can produce spurious sequence information. These observations suggest that random amplification techniques and the development of primers for highly informative but short target regions are essential for the further development of the ancient DNA field.}, }
@article {pmid7937895, year = {1994}, author = {Tan, S and Garrett, KP and Conaway, RC and Conaway, JW}, title = {Cryptic DNA-binding domain in the C terminus of RNA polymerase II general transcription factor RAP30.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {21}, pages = {9808-9812}, pmid = {7937895}, issn = {0027-8424}, support = {GM41628/GM/NIGMS NIH HHS/United States ; }, mesh = {*ATP-Binding Cassette Transporters ; Amino Acid Sequence ; Animals ; Bacillus subtilis/metabolism ; Base Sequence ; Binding Sites ; Carrier Proteins/biosynthesis/metabolism ; Cloning, Molecular ; DNA/*metabolism ; DNA-Binding Proteins/isolation &amp; purification/*metabolism ; Escherichia coli/metabolism ; *Escherichia coli Proteins ; Maltose-Binding Proteins ; Mammals ; Molecular Sequence Data ; *Monosaccharide Transport Proteins ; Oligodeoxyribonucleotides/*metabolism ; RNA Polymerase II/*metabolism ; Recombinant Fusion Proteins/isolation &amp; purification/metabolism ; Sigma Factor/metabolism ; Transcription Factors/biosynthesis/isolation &amp; purification/*metabolism ; *Transcription Factors, TFII ; Transcription, Genetic ; }, abstract = {The C terminus of mammalian transcription factor RAP30 has been found to be a cryptic DNA-binding domain strikingly similar to the C-terminal DNA-binding domain present in conserved region 4 of members of the sigma 70 family of bacterial sigma factors. This RAP30 domain shares strongest sequence similarity with the DNA-binding domain present in region 4 of Bacillus subtilis sporulation-specific sigma K. Like the region 4 DNA-binding activity of Escherichia coli sigma 70, the RAP30 C-terminal DNA binding activity is masked in intact RAP30 but is readily detectable when the RAP30 C terminus is expressed as a fusion protein. Consistent with a role for RAP30 DNA-binding activity in transcription, mutations that abolish DNA binding also abolish transcription. Therefore, RAP30 may function at least in part through the action of an evolutionarily ancient DNA-binding domain that first appeared prior to the divergence of bacteria and eukaryotes.}, }
@article {pmid7980476, year = {1994}, author = {Brown, TA and Brown, KA}, title = {Ancient DNA: using molecular biology to explore the past.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {16}, number = {10}, pages = {719-726}, doi = {10.1002/bies.950161006}, pmid = {7980476}, issn = {0265-9247}, mesh = {Agriculture ; Alleles ; Animals ; *Archaeology ; Base Sequence ; DNA/chemistry/*genetics ; Fossils ; Genetic Markers ; Genetic Techniques ; Humans ; Insecta/genetics ; Molecular Biology/methods ; Molecular Sequence Data ; Mummies ; Plants/genetics ; Skin/chemistry ; }, abstract = {Ancient DNA has been discovered in many types of preserved biological material, including bones, mummies, museum skins, insects in amber and plant fossils, and has become an important research tool in disciplines as diverse as archaeology, conservation biology and forensic science. In archaeology, ancient DNA can contribute both to the interpretation of individual sites and to the development of hypotheses about past populations. Site interpretation is aided by DNA-based sex typing of fragmentary human bones, and by the use of genetic techniques to assess the degree of kinship between the remains of different individuals. On a broader scale, population migrations can be traced by studying genetic markers in ancient DNA, as in recent studies of the colonisation of the Pacific islands, while ancient DNA in preserved plant remains can provide information on the development of agriculture.}, }
@article {pmid7807714, year = {1994}, author = {Uchihi, R and Yamamoto, T and Kojima, T and Tamaki, K and Katsumata, Y}, title = {Efficient amplification of the HLA-DQA1 gene in single genomes using a semi-nested polymerase chain reaction.}, journal = {Nihon hoigaku zasshi = The Japanese journal of legal medicine}, volume = {48}, number = {5}, pages = {329-335}, pmid = {7807714}, issn = {0047-1887}, mesh = {Base Sequence ; *Gene Amplification ; *Genes, MHC Class II ; *Genome, Human ; HLA-DQ Antigens/*genetics ; HLA-DQ alpha-Chains ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; }, abstract = {A semi-nested polymerase chain reaction (PCR) was introduced to amplification of the HLA-DQA1 gene, which is a single-copy gene, in a single genome. The limitation of template DNA for genotyping is 1 ng of genomic DNA, or more in the case of ordinary PCR. When reamplification with the same primers was performed, primer dimer was generated and the sensitivity was not improved. We designed a semi-nested primer for the second round of PCR, using the semi-nested PCR, more than 3 pg of template DNA could be amplified and typed. Furthermore, this method was applied to amplify DQA1 gene in single human sperm having haploid DNA, and followed by typing with sequence-specific oligonucleotide (SSO) probes. The semi-nested PCR technique was found to enhance the sensitivity of the amplification reaction and allowed the successful typing of the HLA-DQA1 gene. This is helpful for genotyping from samples with extremely small amounts of DNA, such as forensic or ancient DNA samples.}, }
@article {pmid7979081, year = {1994}, author = {Spigelman, M}, title = {Ancient DNA.}, journal = {Annals of the Royal College of Surgeons of England}, volume = {76}, number = {5}, pages = {351}, pmid = {7979081}, issn = {0035-8843}, mesh = {DNA, Bacterial/*isolation &amp; purification ; Humans ; *Mummies ; Polymerase Chain Reaction ; }, }
@article {pmid8020619, year = {1994}, author = {Hauswirth, WW and Dickel, CD and Rowold, DJ and Hauswirth, MA}, title = {Inter- and intrapopulation studies of ancient humans.}, journal = {Experientia}, volume = {50}, number = {6}, pages = {585-591}, pmid = {8020619}, issn = {0014-4754}, mesh = {Alleles ; Base Sequence ; Brain Chemistry ; DNA/*analysis ; DNA, Mitochondrial/analysis ; *Fossils ; Histocompatibility Antigens Class I/genetics ; Humans ; Indians, North American/*genetics ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Polymerase Chain Reaction ; }, abstract = {For a genetic analysis of ancient human populations to be useful, it must be demonstrated that the DNA samples under investigation represent a single human population. Toward that end, we have analyzed human DNA from the Windover site (7000-8000 BP). MHC-I analysis, using allele-specific oligonucleotide hybridization to PCR amplified Windover DNA, microsatellite analysis by PCR of the APO-A2 repeat and mtD-loop 3' region sequencing on multiple individuals spanning nearly the full range of estimated burial dates all confirm the hypothesis that there is a persistence of both nuclear and mitochondrial haplotypes at Windover throughout its entire period of use. Thus, Windover can be considered a single population. Neighbor-joining tree analysis of mtDNA sequences suggests that some mitochondrial types are clearly related to extant Amerind types, whereas others, more distantly related, may reflect genetically distinct origins. A more complete sequence analysis will be required to firmly resolve this issue. Calibrating genetic relationships deduced by tree analysis, radiocarbon dates and burial position, yields a human mtD-loop DNA rate of evolution of 3700 to 14,000 years per percent change. Both values are within the range of recent, independently calculated values using estimates of evolutionary divergence or theoretical population genetics. Thus we are beginning to realize the promise of ancient DNA analysis to experimentally answer heretofore unapproachable questions regarding human prehistory and genetic change.}, }
@article {pmid8020618, year = {1994}, author = {Brown, TA and Allaby, RG and Brown, KA and O'Donoghue, K and Sallares, R}, title = {DNA in wheat seeds from European archaeological sites.}, journal = {Experientia}, volume = {50}, number = {6}, pages = {571-575}, pmid = {8020618}, issn = {0014-4754}, mesh = {Base Sequence ; DNA/*analysis ; Europe ; *Fossils ; Glutens/analogs &amp; derivatives/genetics ; Molecular Sequence Data ; Seeds/*genetics ; Triticum/*genetics ; }, abstract = {We have used hybridization analysis to detect ancient DNA in wheat seeds collected from three archaeological sites in Europe and the Middle East. One of these samples, carbonized T. spelta dated to the first millennium BC, has yielded PCR products after amplification with primers directed at the leader regions of the HMW (high molecular weight) glutenin alleles. Sequences obtained from these products suggest that the DNA present in the Danebury seeds is chemically damaged, as expected for ancient DNA, and also indicate that it should be possible to study the genetic variability of archaeological wheat by ancient DNA analysis. Finally, we describe a PCR-based system that enables tetraploid and hexaploid wheats to be distinguished.}, }
@article {pmid8020617, year = {1994}, author = {Hardy, C and Casane, D and Vigne, JD and Callou, C and Dennebouy, N and Mounolou, JC and Monnerot, M}, title = {Ancient DNA from Bronze Age bones of European rabbit (Oryctolagus cuniculus).}, journal = {Experientia}, volume = {50}, number = {6}, pages = {564-570}, pmid = {8020617}, issn = {0014-4754}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/genetics ; DNA/*analysis ; DNA, Mitochondrial/analysis/chemistry ; Europe ; *Fossils ; Mediterranean Islands ; Molecular Sequence Data ; Polymerase Chain Reaction ; Rabbits/*genetics ; }, abstract = {The European rabbit (Oryctolagus cuniculus) is now widely distributed throughout the world as a result of transportation by man. The original populations, however, were confined to southern France and Spain. In order to investigate the role of human intervention in determining the genetic diversity of rabbit populations, we are studying the origin of rabbits introduced onto a small Mediterranean island (Zembra) near Tunis over 1400 years ago, by examining ancient DNA extracted from rabbit bones found both on Zembra and on the European mainland. Ancient DNA was successfully extracted from rabbit bones found at two archaeological sites dated to at least the Early Bronze Age (more than 3500 years ago) in south-central France, and compared to that found in modern mainland and island populations using a small variable region of the cytochrome b gene. The results confirm that the Zembra Island population is descended from that present over 1400 years ago. The technical aspects of DNA extraction from bones and the implications of this type of research for determining the origin of introduced rabbit populations are discussed.}, }
@article {pmid8020616, year = {1994}, author = {Cooper, A}, title = {Ancient DNA sequences reveal unsuspected phylogenetic relationships within New Zealand wrens (Acanthisittidae).}, journal = {Experientia}, volume = {50}, number = {6}, pages = {558-563}, pmid = {8020616}, issn = {0014-4754}, mesh = {Animals ; Base Sequence ; Birds/*genetics ; DNA/*analysis ; *Fossils ; Molecular Sequence Data ; New Zealand ; *Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Ancient DNA sequences from preserved specimens are increasingly being used for the investigation of Pacific Island ecosystems prior to the large scale modification and extinction of endemic biota associated with human colonization. However, many difficulties are associated with the use of ancient DNA sequences in studies of genetically close taxa. In this paper, these difficulties are discussed as they relate to a study involving extinct and extant members of an ancient New Zealand avian family, the New Zealand wrens (Acanthisittidae). Sequences of the mitochondrial small ribosomal subunit RNA gene (12S) were obtained from museum specimens of several wren taxa in order to investigate their phylogenetic relationships and the taxonomic status of a rock wren (Xenicus gilviventris) subspecies. Limitations due to sample size and 12S sequence variability as well as the difficulties in authenticating ancient DNA sequences prevent firm conclusions but the data suggest unsuspected phylogenetic relationships exist and raise the possibility that conservation management of rock wren populations is required.}, }
@article {pmid8020614, year = {1994}, author = {DeSalle, R}, title = {Implications of ancient DNA for phylogenetic studies.}, journal = {Experientia}, volume = {50}, number = {6}, pages = {543-550}, pmid = {8020614}, issn = {0014-4754}, mesh = {Animals ; Base Sequence ; DNA/*analysis/chemistry ; *Fossils ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {The utility of DNA sequence characters from fossil specimens is examined from a phylogenetic perspective. Four ways that fossil characters can alter phylogenetic hypotheses are discussed. Two empirical examples and a third hypothetical example concerning amber-preserved insects are presented to illustrate these phenomena. Fossil DNA sequences as characters will be affected by the problem of missing data and missing taxa. In general, cladogram accuracy will be more greatly affected by missing taxa and cladogram resolution will be affected more acutely by missing data. Due to these points, an examination of the importance of the phylogenetic question being addressed, the utility of the fossil DNA sequences and the rarity of the fossil should be considered before damage of a fossil is undertaken.}, }
@article {pmid8020612, year = {1994}, author = {Handt, O and Höss, M and Krings, M and Pääbo, S}, title = {Ancient DNA: methodological challenges.}, journal = {Experientia}, volume = {50}, number = {6}, pages = {524-529}, pmid = {8020612}, issn = {0014-4754}, mesh = {Base Sequence ; DNA/*analysis/chemistry ; DNA Damage ; Drug Contamination ; *Fossils ; Molecular Sequence Data ; Polymerase Chain Reaction ; Reproducibility of Results ; Sequence Alignment ; }, abstract = {The study of ancient DNA offers the possibility of following genetic change over time. However, the field is plagued by a problem which is unique in molecular biology--the difficulty of verifying results by reproduction. Some of the reasons for this are technical and derive from the low copy number and damaged state of ancient DNA molecules. Other reasons are the unique nature of many of the objects from which DNA is extracted. We describe methodological approaches with which these problems can be alleviated in order to ensure that results are scientific in the sense that they can be reproduced by others.}, }
@article {pmid8020611, year = {1994}, author = {Hauswirth, WW}, title = {Ancient DNA: an introduction.}, journal = {Experientia}, volume = {50}, number = {6}, pages = {521-523}, doi = {10.1007/BF01921719}, pmid = {8020611}, issn = {0014-4754}, mesh = {DNA/*analysis ; *Fossils ; Paleontology ; Polymerase Chain Reaction ; }, }
@article {pmid7517371, year = {1994}, author = {Tuross, N}, title = {The biochemistry of ancient DNA in bone.}, journal = {Experientia}, volume = {50}, number = {6}, pages = {530-535}, pmid = {7517371}, issn = {0014-4754}, mesh = {Benzopyrans/isolation &amp; purification ; Bone and Bones/*chemistry ; DNA/*analysis ; Decalcification Technique ; Ethidium ; *Fossils ; Humans ; Nucleic Acid Synthesis Inhibitors ; Paleontology ; Staining and Labeling ; Taq Polymerase ; }, abstract = {The amount of DNA in ancient bone was determined by ethidium bromide staining after the removal of the potent Taq inhibitor, fulvic acid. A complete decalcification and a perfusion protocol were used to recover DNA from bone. A variety of purification techniques including molecular sieve, hydroxyapatite binding and 'Magic' preparations yielded DNA that spanned from 3.4 micrograms/g of bone to below detectable limits. Fulvic acid was shown to interfere with the quantification of DNA derived from ancient human skeletal material one hundred to over seven thousand years old. Scanning UV in the 300 to 230 nm range is a simple and sensitive technique for documenting fulvic acid contamination in ancient bone extracts.}, }
@article {pmid8019234, year = {1994}, author = {Spigelman, M}, title = {Studying ancient DNA.}, journal = {BMJ (Clinical research ed.)}, volume = {308}, number = {6940}, pages = {1370}, doi = {10.1136/bmj.308.6940.1370}, pmid = {8019234}, issn = {0959-8138}, mesh = {DNA, Bacterial/*history/isolation &amp; purification ; History, Ancient ; Humans ; *Mummies ; Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Tuberculosis/history ; }, }
@article {pmid8179883, year = {1994}, author = {Goodyear, PD and MacLaughlin-Black, S and Mason, IJ}, title = {A reliable method for the removal of co-purifying PCR inhibitors from ancient DNA.}, journal = {BioTechniques}, volume = {16}, number = {2}, pages = {232-235}, pmid = {8179883}, issn = {0736-6205}, mesh = {Base Sequence ; Biotechnology ; Chromatography, Ion Exchange ; DNA/*genetics/*isolation &amp; purification ; DNA Primers/genetics ; Fossils ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; }, }
@article {pmid7702279, year = {1994}, author = {Perrin, C and Noly, V and Mourer, R and Schmitt, D}, title = {[Preservation of cutaneous structures of egyptian mummies. An ultrastructural study].}, journal = {Annales de dermatologie et de venereologie}, volume = {121}, number = {6-7}, pages = {470-475}, pmid = {7702279}, issn = {0151-9638}, mesh = {Collagen/ultrastructure ; Desmosomes/ultrastructure ; Egypt, Ancient ; Epidermis/ultrastructure ; Extracellular Matrix/ultrastructure ; Fluid Therapy ; History, Ancient ; Humans ; In Situ Hybridization ; Microscopy, Electron, Scanning Transmission ; Mummies/*pathology ; Paleopathology ; Skin/*ultrastructure ; }, abstract = {INTRODUCTION: The recent development of studies applied to ancient materials may be explained by the application of molecular biology techniques on the extracted ancient DNA mainly the polymerase chain reaction (PCR), the ultrasensitive DNA-amplification technique that hit the headlines in the late 1980s. PCR was used to amplify human immunodeficiency virus (HIV), genetic material in stored tissue specimens and to document people who died in 1976. In addition, recent discoveries of mummified bodies in ice of the Tyrolean Alps or Greenland allowed a new approach in archeological studies. Mummies are a good material for investigations of ancient tissues. The studies concern the techniques of embalming, tissue preservation and palepathological aspects. In cutaneous paleopathology, mummies from Egypt, South or North America and Europe were considered. Various skin lesions were characterized: histiocytoma, Chagas' disease, smallpox, syphilis. Recently drugs (cocaine, hashish and nicotine) were extracted from skin and head hair of Egyptian mummies. Only a few studies were concerned with the ultrastructure of the skin of such mummies.<br><br>MATERIAL AND METHODS: We had the opportunity to obtain skin samples of two Egyptian mummies. One of them was embalmed between 150 BC-90 AC. The skin was studied by transmission electron microscopy. As the mummified materials had dried out and shrunk, it was necessary to rehydrate them for ultrastructural observation. Skin samples were fragmented into small pieces before fixation with 2 p. 100 glutaraldehyde in sodium cacodylate buffer for 10 days (allowing for removal of the materials used for embalming). The samples were then washed in the same buffer for 10 days. After washing the pieces were post-fixed with 1 p. 100 osmium tetroxyde, dehydrated and embedded in Epoxy medium.<br><br>RESULTS: With this process, it was possible to observe the excellent preservation of the cutaneous structures. The epidermis was well preserved. It was possible to observe the different cell layers and mainly the upper layers. The nuclei and the desmosomes of keratinocytes were recognized. Intercellular spaces were narrow. Desmosomes showed dense thickenings of the cell membrane on both sides and an intercellular band with narrow lucent spaces adjacent to the dense cell membrane. The nuclei showed dense spots of chromatin and in the cytoplasm recognizable tonofilament bundles were identified. Langerhans cells and melanocytes were not observed. In the dermis, the collagen fibrils formed thick bundles and showed the characteristic axial periodicity. Elastic fibers were also recognized showing two main components: the amorphous substance and the fibrils. Throughout the dermis, a number of round or oval structures were found. They had the typical appearance of spores of bacteria. In the centre, they had an electron dense and granular core surrounded by an inner membrane and a spore coat.<br><br>DISCUSSION: Only a few investigations were performed on the ultrastructure of the skin of the Egyptian mummies. In the majority of cases, the epidermis was not preserved. The present work demonstrates the good preservation of epidermal structures and specially desmosomes and intercellular connections. The presence of spores of bacteria was previously reported. These spores enter a highly resistant resting phase in order to survive in a dormant state for a long period of starvation or other adverse environmental conditions. Similar investigations were performed on skin obtained from Eskimo mummies preserved by the extremely cold and dry polar weather. In these conditions, the authors reported the observation of melanocytes, vessels and nerves. Additionally, biochemical investigations demonstrated the very good preservation of collagen and glycosaminoglycans of the dermal extracellular matrix.}, }
@article {pmid8255287, year = {1993}, author = {Sykes, B}, title = {Ancient DNA. Less cause for grave concern.}, journal = {Nature}, volume = {366}, number = {6455}, pages = {513}, doi = {10.1038/366513a0}, pmid = {8255287}, issn = {0028-0836}, mesh = {Animals ; Anthropometry ; Bone and Bones/anatomy &amp; histology/chemistry ; DNA/*genetics/isolation &amp; purification ; DNA, Mitochondrial/genetics ; Escherichia coli/genetics ; Female ; Humans ; Male ; *Paleontology ; }, }
@article {pmid8296875, year = {1993}, author = {Stone, AC and Stoneking, M}, title = {Ancient DNA from a pre-Columbian Amerindian population.}, journal = {American journal of physical anthropology}, volume = {92}, number = {4}, pages = {463-471}, doi = {10.1002/ajpa.1330920405}, pmid = {8296875}, issn = {0002-9483}, mesh = {Adult ; Base Sequence ; DNA, Mitochondrial/*history ; Female ; Genetic Markers ; *Genetic Variation ; History, Medieval ; Humans ; Illinois ; Indians, North American/classification/genetics/*history ; Male ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Deletion ; }, abstract = {Ancient DNA was obtained from skeletal remains from the Norris Farms #36 cemetery, a pre-Columbian archeological site in central Illinois that dates to A.D. 1300. Four mitochondrial DNA (mtDNA) markers were analyzed that delineate the four primary mtDNA lineages found in contemporary Amerindian populations. mtDNA types were determined for 50 individuals; 49 belonged to one of these four lineages. One lineage occurred only in males, suggesting an immigration of maternally related males into this community. There was no significant spatial patterning of mtDNA lineages within the cemetery. This survey of ancient DNA variation in a pre-Columbian population supports the view that the initial colonization of the New World comprised just four primary mtDNA lineages.}, }
@article {pmid8235556, year = {1993}, author = {Pääbo, S}, title = {Ancient DNA.}, journal = {Scientific American}, volume = {269}, number = {5}, pages = {86-92}, doi = {10.1038/scientificamerican1193-86}, pmid = {8235556}, issn = {0036-8733}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Bone and Bones/chemistry ; Cloning, Molecular ; DNA/*chemistry ; *Fossils ; Horses/genetics ; Humans ; Molecular Sequence Data ; *Mummies ; Muscles/chemistry ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; Skin/chemistry ; }, }
@article {pmid7901907, year = {1993}, author = {Fischman, J}, title = {Going for the old: ancient DNA draws a crowd.}, journal = {Science (New York, N.Y.)}, volume = {262}, number = {5134}, pages = {655-656}, doi = {10.1126/science.7901907}, pmid = {7901907}, issn = {0036-8075}, mesh = {Animals ; DNA/*history ; History, Ancient ; Humans ; Paleontology ; }, abstract = {Approximately 170 researchers interested in reconstructing the past convened for the 2nd International Conference on Ancient DNA, held in Washington, D.C., from 7 to 9 October. While rejuvenated celluloid dinosaurs have grabbed headlines this year, these scientists were more concerned with topics such as tracing ancient human populations and understanding how DNA can survive the millennia.}, }
@article {pmid8224109, year = {1993}, author = {DeSalle, R and Barcia, M and Wray, C}, title = {PCR jumping in clones of 30-million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus).}, journal = {Experientia}, volume = {49}, number = {10}, pages = {906-909}, pmid = {8224109}, issn = {0014-4754}, mesh = {Animals ; Base Sequence ; Cloning, Molecular ; DNA/*chemistry ; Drosophila melanogaster/genetics ; *Fossils ; Genetic Vectors ; Insecta/*genetics ; Molecular Sequence Data ; Phylogeny ; *Polymerase Chain Reaction ; Sequence Homology ; }, abstract = {DNA from 30-million-year-old amber preserved termites (Mastotermes electrodominicus) was PCR amplified with nuclear ribosomal RNA small subunit primers and cloned into the TA vector (INVITROGEN). We obtained several classes of recombinant clones as a result. Authentic Mastotermes electrodominicus clones were identified. The source of other classes of clones was identified as contaminants of the ancient DNA template. Several of the clones appeared to be chimeric in structure with half of the clone identical to the termite sequence and the other half identical to contaminant sequences. The phenomenon of PCR jumping was identified as a possible source for the chimeric clones.}, }
@article {pmid1472835, year = {1992}, author = {Epplen, JT and Melmer, G and Schmidt, P and Roewer, L and Hundrieser, J and Epplen, C and Buitkamp, J}, title = {On the potential of simple repetitive DNA for fingerprinting in clinical, forensic, and evolutionary dynamic studies.}, journal = {The Clinical investigator}, volume = {70}, number = {11}, pages = {1043-1051}, pmid = {1472835}, issn = {0941-0198}, mesh = {Animals ; Artifacts ; Biological Evolution ; *DNA Fingerprinting ; DNA Probes ; DNA, Satellite/*analysis ; Forecasting ; Forensic Medicine/*methods ; Humans ; In Situ Hybridization ; Paternity ; Polymerase Chain Reaction ; *Repetitive Sequences, Nucleic Acid ; Sensitivity and Specificity ; }, abstract = {The purpose of this review is to discuss critically the practical meaning of a specific genome component, simple repetitive desoxyribonucleic acid (DNA) sequences as clinical and forensic and diagnostic and research tools. Previously, multilocus DNA fingerprinting was the major technology employed to visualize such simple repeat sequences. This technique enables many polymorphic loci to be simultaneously detected thus yielding vast amounts of information. With the advent of enzymatic DNA amplification via the polymerase chain reaction (PCR), individual simple repeat loci can be demonstrated, theoretically even from single DNA molecules and so a wealth of additional approaches have also become feasible. In general investigating, small, known, single copy parts of genomes have not posed truly insurmountable problems if enough material was available. There have even been a few (anecdotal) reports on the amplification of simple repeats from ancient DNA (see, e.g. [30]. Here we would like to after a solid basis for an earnest discussion of the applications of these simple repetitive sequences using various methodological approaches relevant for clinical diagnosis, setting aside the obvious unsolved mysteries of their biology.}, }
@article {pmid1415267, year = {1992}, author = {Hubert, R and Weber, JL and Schmitt, K and Zhang, L and Arnheim, N}, title = {A new source of polymorphic DNA markers for sperm typing: analysis of microsatellite repeats in single cells.}, journal = {American journal of human genetics}, volume = {51}, number = {5}, pages = {985-991}, pmid = {1415267}, issn = {0002-9297}, support = {GM36745/GM/NIGMS NIH HHS/United States ; HG00248/HG/NHGRI NIH HHS/United States ; HG00328/HG/NHGRI NIH HHS/United States ; }, mesh = {Apolipoprotein C-II ; Apolipoproteins C/genetics ; Base Sequence ; Genetic Markers/*genetics ; Heterozygote ; Humans ; Male ; Molecular Sequence Data ; Oligodeoxyribonucleotides/genetics ; Polymerase Chain Reaction ; Polymorphism, Genetic/*genetics ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid/*genetics ; *Spermatozoa ; }, abstract = {We show that dinucleotide and tetranucleotide repeat polymorphisms can be analyzed in single cells without using radioactivity or denaturing gels. This provides a rich new source of DNA polymorphisms for genetic mapping by sperm typing. The recombination fraction between two CA repeat polymorphisms was determined after whole genome amplification of single sperm, followed by typing of two different aliquots, one aliquot for each polymorphic locus. Single-cell analysis of microsatellites may also be valuable both for preimplantation genetic disease diagnosis based on single-blastomere or polar-body analysis and for the typing of forensic or ancient DNA samples containing very small amounts of nucleic acid.}, }
@article {pmid1408822, year = {1992}, author = {Walsh, PS and Varlaro, J and Reynolds, R}, title = {A rapid chemiluminescent method for quantitation of human DNA.}, journal = {Nucleic acids research}, volume = {20}, number = {19}, pages = {5061-5065}, pmid = {1408822}, issn = {0305-1048}, mesh = {Animals ; Base Sequence ; Blood Stains ; Cattle ; DNA/*analysis/blood ; DNA Probes ; Genome, Human ; Hair/chemistry ; Humans ; Luminescent Measurements ; Male ; Microchemistry/methods ; Molecular Sequence Data ; }, abstract = {A sensitive and simple method for the quantitation of human DNA is described. This method is based on probe hybridization to a human alpha satellite locus, D17Z1. The biotinylated probe is hybridized to sample DNA immobilized on nylon membrane. The subsequent binding of streptavidin-horseradish peroxidase to the bound probe allows for chemiluminescent detection using a luminol-based reagent and X-ray film. Less than 150 pg of human DNA can easily be detected with a 15 minute exposure. The entire procedure can be performed in 1.5 hours. Microgram quantities of nonhuman DNA have been tested and the results indicate very high specificity for human DNA. The data on film can be scanned into a computer and a commercially available program can be used to create a standard curve where DNA quantity is plotted against the mean density of each slot blot signal. The methods described can also be applied to the very sensitive determination of quantity and quality (size) of DNA on Southern blots. The high sensitivity of this quantitation method requires the consumption of only a fraction of sample for analysis. Determination of DNA quantity is necessary for RFLP and many PCR-based tests where optimal results are obtained only with a relatively narrow range of DNA quantities. The specificity of this quantitation method for human DNA will be useful for the analysis of samples that may also contain bacterial or other non-human DNA, for example forensic evidence samples, ancient DNA samples, or clinical samples.}, }
@article {pmid1522919, year = {1992}, author = {Hummel, S and Nordsiek, G and Herrmann, B}, title = {Improved efficiency in amplification of ancient DNA and its sequence analysis.}, journal = {Die Naturwissenschaften}, volume = {79}, number = {8}, pages = {359-360}, pmid = {1522919}, issn = {0028-1042}, mesh = {Base Sequence ; Bone and Bones/chemistry ; DNA/analysis/*genetics ; Escherichia coli/genetics ; Female ; Humans ; Male ; Molecular Sequence Data ; *Paleontology ; Polymerase Chain Reaction/*methods ; }, }
@article {pmid1631067, year = {1992}, author = {Zhang, L and Cui, X and Schmitt, K and Hubert, R and Navidi, W and Arnheim, N}, title = {Whole genome amplification from a single cell: implications for genetic analysis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {89}, number = {13}, pages = {5847-5851}, pmid = {1631067}, issn = {0027-8424}, support = {GM36745/GM/NIGMS NIH HHS/United States ; HG00328/HG/NHGRI NIH HHS/United States ; }, mesh = {Base Sequence ; Genes ; Humans ; Male ; Molecular Sequence Data ; Oligodeoxyribonucleotides/chemistry ; Polymerase Chain Reaction/*methods ; Polymorphism, Genetic ; Prenatal Diagnosis/methods ; Repetitive Sequences, Nucleic Acid ; Spermatozoa ; }, abstract = {We have developed an in vitro method for amplifying a large fraction of the DNA sequences present in a single haploid cell by repeated primer extensions using a mixture of 15-base random oligonucleotides. We studied 12 genetic loci and estimate that the probability of amplifying any sequence in the genome to a minimum of 30 copies is not less than 0.78 (95% confidence). Whole genome amplification beginning with a single cell, or other samples with very small amounts of DNA, has significant implications for multipoint mapping by sperm or oocyte typing and possibly for genetic disease diagnosis, forensics, and the analysis of ancient DNA samples.}, }
@article {pmid1642883, year = {1992}, author = {Foo, I and Salo, WL and Aufderheide, AC}, title = {PCR libraries of ancient DNA using a generalized PCR method.}, journal = {BioTechniques}, volume = {12}, number = {6}, pages = {811-4, 817}, pmid = {1642883}, issn = {0736-6205}, mesh = {Base Sequence ; DNA/*analysis ; *Genomic Library ; Humans ; Molecular Sequence Data ; *Mummies ; Polymerase Chain Reaction/*methods ; }, abstract = {We describe a generalized PCR method that will amplify fragments of DNA without any knowledge of sequence using a single primer. Although we are presently using this method to amplify DNA fragments isolated from ancient preserved tissues, in effect, producing PCR libraries, it may prove to have other applications.}, }
@article {pmid1684052, year = {1991}, author = {Golenberg, EM}, title = {Amplification and analysis of Miocene plant fossil DNA.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {333}, number = {1268}, pages = {419-26; discussion 426-7}, doi = {10.1098/rstb.1991.0092}, pmid = {1684052}, issn = {0962-8436}, mesh = {Base Sequence ; Biological Evolution ; DNA/analysis/*genetics ; *Fossils ; Gene Amplification ; Molecular Sequence Data ; Plants/*genetics ; }, abstract = {Ancient DNA has been extracted and sequenced from several animal and plant specimens. Previous considerations of the damage to ancient DNA have suggested that both the age and size of DNA fragments that can be retrieved and sequenced may be limited, the former to between several thousand and at most tens of thousands of years old, and the latter to at most a few hundred bases. A recent report of a 770 base pair (b.p.) sequence from the chloroplast gene rbcL from a Miocene Magnolia latahensis leaf indicates that both estimated limitations may be too conservative. Further work has indicated that analysis of Miocene fossil DNA can be replicated, and can, therefore, open up the prospects for future development of the field of molecular palaeontology. Successful amplification of fossil DNA is sometimes confounded by factors inherent to fossil DNA or to samples with minimal amounts of target DNA. Techniques that alter denaturation, reduce inhibitors and the problem of contaminants, and repair DNA prior to polymerase chain reaction amplification can increase the probability of success.}, }
@article {pmid1910205, year = {1991}, author = {Cherfas, J}, title = {Ancient DNA: still busy after death.}, journal = {Science (New York, N.Y.)}, volume = {253}, number = {5026}, pages = {1354-1356}, doi = {10.1126/science.1910205}, pmid = {1910205}, issn = {0036-8075}, mesh = {Animals ; Cloning, Molecular ; DNA/*genetics ; Egypt ; Florida ; *Fossils ; Haplorhini/*genetics ; Humans ; *Mummies ; Plants/genetics ; }, }
@article {pmid1861718, year = {1991}, author = {Sykes, B}, title = {Ancient DNA. The past comes alive.}, journal = {Nature}, volume = {352}, number = {6334}, pages = {381-382}, doi = {10.1038/352381a0}, pmid = {1861718}, issn = {0028-0836}, mesh = {Animals ; Cloning, Molecular ; DNA, Mitochondrial/*genetics ; *Fossils ; Gene Amplification ; Humans ; }, }
@article {pmid2325772, year = {1990}, author = {Golenberg, EM and Giannasi, DE and Clegg, MT and Smiley, CJ and Durbin, M and Henderson, D and Zurawski, G}, title = {Chloroplast DNA sequence from a miocene Magnolia species.}, journal = {Nature}, volume = {344}, number = {6267}, pages = {656-658}, doi = {10.1038/344656a0}, pmid = {2325772}, issn = {0028-0836}, mesh = {Base Sequence ; Chloroplasts/*analysis ; Codon ; DNA/*genetics ; *Fossils ; Molecular Sequence Data ; *Paleontology ; Polymerase Chain Reaction ; Ribulose-Bisphosphate Carboxylase/genetics ; Trees ; }, abstract = {DNA has been successfully extracted from several samples of preserved tissue, the oldest so far reported originating from a 13,000-year-old ground sloth. Both severe damage to the preserved DNA, primarily due to oxidation of the pyrimidines, has prevented the acquisition of sequence data from ancient samples except in a few cases. We report here the extraction of DNA from fossil leaf samples from the Miocene Clarkia deposit (17-20 Myr old), the amplification of an 820-base pair (bp) DNA fragment from the chloroplast gene rbcL from a fossil of the genus Magnolia, and its subsequent sequencing. The sequence was verified by comparison with published and unpublished rbcL sequences. These results extend our ability to analyse ancient DNA and may open new avenues into problems in palaeobotany, biogeography, and in the calibration of mutation rates.}, }
@article {pmid2656708, year = {1989}, author = {Pääbo, S and Higuchi, RG and Wilson, AC}, title = {Ancient DNA and the polymerase chain reaction. The emerging field of molecular archaeology.}, journal = {The Journal of biological chemistry}, volume = {264}, number = {17}, pages = {9709-9712}, pmid = {2656708}, issn = {0021-9258}, mesh = {Animals ; *Biological Evolution ; DNA/*genetics ; DNA-Directed DNA Polymerase ; *Gene Amplification ; Gene Frequency ; *Genes ; Proteins/genetics ; }, }
@article {pmid2928314, year = {1989}, author = {Pääbo, S}, title = {Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {86}, number = {6}, pages = {1939-1943}, pmid = {2928314}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Chromatography, High Pressure Liquid ; *Cloning, Molecular ; *DNA/genetics/isolation &amp; purification/ultrastructure ; DNA Damage ; DNA-Directed DNA Polymerase ; Electrophoresis, Agar Gel ; *Fossils ; *Gene Amplification ; Humans ; Microscopy, Electron ; Molecular Sequence Data ; *Mummies ; Oxidation-Reduction ; *Paleontology ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, including two extinct animals (the marsupial wolf and giant ground sloth). The DNA obtained was invariably of a low average molecular size and damaged by oxidative processes, which primarily manifest themselves as modifications of pyrimidines and sugar residues as well as baseless sites and intermolecular cross-links. This renders molecular cloning difficult. However, the polymerase chain reaction can be used to amplify and study short mitochondrial DNA sequences that are of anthropological and evolutionary significance. This opens up the prospect of performing diachronical studies of molecular evolutionary genetics.}, }
@article {pmid3185708, year = {1988}, author = {Rollo, F and Amici, A and Salvi, R and Garbuglia, A}, title = {Short but faithful pieces of ancient DNA.}, journal = {Nature}, volume = {335}, number = {6193}, pages = {774}, doi = {10.1038/335774a0}, pmid = {3185708}, issn = {0028-0836}, mesh = {Base Sequence ; DNA/*genetics ; Gene Amplification ; *Paleontology ; Zea mays/*genetics ; }, }
@article {pmid3186445, year = {1988}, author = {Pääbo, S and Gifford, JA and Wilson, AC}, title = {Mitochondrial DNA sequences from a 7000-year old brain.}, journal = {Nucleic acids research}, volume = {16}, number = {20}, pages = {9775-9787}, pmid = {3186445}, issn = {0305-1048}, mesh = {*Anthropology ; Base Sequence ; *Brain Chemistry ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; DNA-Directed DNA Polymerase ; Electrophoresis, Agar Gel ; Gene Amplification ; Humans ; Molecular Sequence Data ; }, abstract = {Pieces of mitochondrial DNA from a 7000-year-old human brain were amplified by the polymerase chain reaction and sequenced. Albumin and high concentrations of polymerase were required to overcome a factor in the brain extract that inhibits amplification. For this and other sources of ancient DNA, we find an extreme inverse dependence of the amplification efficiency on the length of the sequence to be amplified. This property of ancient DNA distinguishes it from modern DNA and thus provides a new criterion of authenticity for use in research on ancient DNA. The brain is from an individual recently excavated from Little Salt Spring in southwestern Florida and the anthropologically informative sequences it yielded are the first obtained from archaeologically retrieved remains. The sequences show that this ancient individual belonged to a mitochondrial lineage that is rare in the Old World and not previously known to exist among Native Americans. Our finding brings to three the number of maternal lineages known to have been involved in the prehistoric colonization of the New World.}, }
@article {pmid7205964, year = {1980}, author = {Holmquist, R and Pearl, D}, title = {Theoretical foundations for quantitative paleogenetics. Part III: The molecular divergence of nucleic acids and proteins for the case of genetic events of unequal probability.}, journal = {Journal of molecular evolution}, volume = {16}, number = {3-4}, pages = {211-267}, pmid = {7205964}, issn = {0022-2844}, mesh = {Base Composition ; Codon/metabolism ; Genes ; Hemoglobins/biosynthesis ; Mathematics ; *Models, Genetic ; Mutation ; Nucleic Acids/*genetics ; Probability ; Proteins/*genetics ; RNA, Messenger/analysis ; *Selection, Genetic ; }, }
@article {pmid1159803, year = {1975}, author = {Iizuka, M and Ishii, K and Matsuda, H}, title = {Comments of Holmquist's theory for paleogenetics: the effect of multiple hits on nucleotide differences between homologous DNA's.}, journal = {Journal of molecular evolution}, volume = {5}, number = {3}, pages = {249-254}, pmid = {1159803}, issn = {0022-2844}, mesh = {Base Sequence ; *Biological Evolution ; DNA/*metabolism ; *Models, Biological ; *Mutation ; }, abstract = {The notion of the probability of back mutation is introduced and the method of probability generating functions is used in order to simplify and unify the Holmquist's (1972) investigation of the effect of multiple hits on nucleotide differences between homologous DNAs. We obtain explicit expressions for the distribution of the number of hit nucleotide sites, the number of altered sites, and the number of differences between two homologous DNAs, as functions of the total number of hits. For the case where the hit rate is a known function of time, we derive a formula for extending these results as functions of time.}, }
@article {pmid5173652, year = {1971}, author = {Holmquist, R}, title = {Theoretical foundations for a quantitative approach to paleogenetics. Part II: proteins.}, journal = {Journal of molecular evolution}, volume = {1}, number = {1}, pages = {134-149}, pmid = {5173652}, issn = {0022-2844}, mesh = {*Amino Acid Sequence ; *Biological Evolution ; Codon ; *Models, Biological ; Mutation ; Proteins/analysis ; }, }
@article {pmid5173651, year = {1971}, author = {Holmquist, R}, title = {Theoretical foundations for a quantitative approach to paleogenetics. Part I: DNA.}, journal = {Journal of molecular evolution}, volume = {1}, number = {1}, pages = {115-133}, doi = {10.1007/BF01659159}, pmid = {5173651}, issn = {0022-2844}, mesh = {Base Sequence ; *Biological Evolution ; *DNA ; *Models, Biological ; Mutation ; }, }
@article {pmid13941849, year = {1962}, author = {PATOIR, G and LEDUC, M and SPY, E and PROYE, C}, title = {[Rare tumor of kidney. Riopelle's true hypernephroma or paleogenetic metanephroma].}, journal = {Journal d'urologie et de nephrologie}, volume = {68}, number = {}, pages = {694-701}, pmid = {13941849}, issn = {0021-8200}, mesh = {*Adenocarcinoma ; *Carcinoma, Renal Cell ; Humans ; *Kidney ; *Kidney Neoplasms ; *Neoplasms ; }, }