@article {pmid35951485, year = {2022}, 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 = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13696}, pmid = {35951485}, issn = {1755-0998}, 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 non-reliance 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}, 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 4th-5th 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 = {}, number = {}, pages = {}, doi = {10.1111/mec.16642}, pmid = {35943423}, issn = {1365-294X}, abstract = {Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage 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 - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA 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 {pmid35931723, year = {2022}, author = {Silva, NM and Kreutzer, S and Souleles, A and Triantaphyllou, S and Kotsakis, K and Urem-Kotsou, D and Halstead, P and Efstratiou, N and Kotsos, S and Karamitrou-Mentessidi, G and Adaktylou, F and Chondroyianni-Metoki, A and Pappa, M and Ziota, C and Sampson, A and Papathanasiou, A and Vitelli, K and Cullen, T and Kyparissi-Apostolika, N and Lanz, AZ and Peters, J and Rio, J and Wegmann, D and Burger, J and Currat, M and Papageorgopoulou, C}, title = {Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13474}, pmid = {35931723}, issn = {2045-2322}, support = {31003A_156853/SNSF_/Swiss National Science Foundation/Switzerland ; BU 1403/6-1//German Science Foundation/ ; BIOMUSE-0195//Greek-German bilateral cooperation program 2017, European Union (EU Social Fund and European Regional Development Fund), General Secreteriat for Research and Innovation, Ministry of Development and Investments, Greece, Federal Ministry of Education and Research- BMBF, Germany./ ; }, mesh = {Bayes Theorem ; DNA, Ancient ; *DNA, Mitochondrial/genetics ; Europe ; Genetics, Population ; Greece ; History, Ancient ; Humans ; *Mitochondria/genetics ; Population Dynamics ; }, abstract = {The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.}, }
@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}, support = {Award No. NA14OAR4170078, project No. R/HCE-3//Washington Sea Grant, University of Washington/ ; Award No. NA14OAR4170078, project No. R/HCE-3//Washington Sea Grant, University of Washington/ ; Award No. NA14OAR4170078, project No. R/HCE-3//Washington Sea Grant, University of Washington/ ; Award No. NA14OAR4170078, project No. R/HCE-3//Washington Sea Grant, University of Washington/ ; Award No. NA14OAR4170078, project No. R/HCE-3//Washington Sea Grant, University of Washington/ ; Award No. NA14OAR4170078, project No. R/HCE-3//Washington Sea Grant, University of Washington/ ; Arctic Social Sciences Award No. 1203868//National Science Foundation, United States/ ; }, 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 = {2022}, 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 = {}, number = {}, pages = {}, pmid = {35922549}, issn = {1740-634X}, support = {ZIAMH002942//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; ZIAMH002717//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; ZIAMH002942//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; }, }
@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 = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2022.07.005}, pmid = {35921988}, issn = {1673-8527}, }
@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}, 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 {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-yr-old Citrullus seeds reveals use of a bitter-fleshed species prior to watermelon domestication.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msac168}, pmid = {35907246}, issn = {1537-1719}, 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-yr-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. Phylogenomic and population-genomic analyses reveal that (i) much of the nuclear genome of both ancient seeds is traceable to West African seed-use 'egusi-type' watermelon (C. mucosospermus) rather than domesticated pulp-use watermelon (C. lanatus subsp. vulgaris); (ii) the 6,000-yr-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 (iii) both ancient genomes showed admixture from C. mucosospermus, C. lanatus subsp. cordophanus, C. lanatus subsp. vulgaris, and even South African C. amarus, and evident introgression between the Libyan seed (UMB-6), 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 {pmid35896571, year = {2022}, author = {Krajcarz, M and Van Neer, W and Krajcarz, MT and Popović, D and Baca, M and De Cupere, B and Goffette, Q and Küchelmann, HC and Gręzak, A and Iwaszczuk, U and Ottoni, C and Van de Vijver, K and Wilczyński, J and Mulczyk, A and Wiejacki, J and Makowiecki, D and Bocherens, H}, title = {Stable isotopes unveil one millennium of domestic cat paleoecology in Europe.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {12775}, pmid = {35896571}, issn = {2045-2322}, support = {2017/27/B/ NZ8/00728//Narodowe Centrum Nauki/ ; 2019/35/B/HS3/02923//Narodowe Centrum Nauki/ ; 101002811 FELIX//European Research Council, European Union Horizon 2020/ ; }, mesh = {Animals ; Carbon Isotopes/analysis ; Cats ; Diet ; Ecology ; *Ecosystem ; Europe ; *Isotopes ; Nitrogen Isotopes/analysis ; }, abstract = {The domestic cat is the world's most popular pet and one of the most detrimental predators in terrestrial ecosystems. Effective protection of wildlife biodiversity demands detailed tracking of cat trophic ecology, and stable isotopes serve as a powerful proxy in dietary studies. However, a variable diet can make an isotopic pattern unreadable in opportunistic predators. To evaluate the usefulness of the isotopic method in cat ecology, we measured C and N isotope ratios in hundreds of archaeological cat bones. We determined trends in cat trophic paleoecology in northern Europe by exploiting population-scale patterns in animals from diverse locations. Our dataset shows a high variability of isotopic signals related to the socio-economic and/or geomorphological context. This points toward regularities in isotopic patterns across past cat populations. We provide a generalized guide to interpret the isotopic ecology of cats, emphasizing that regional isotopic baselines have a major impact on the isotopic signal.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2022.06.094}, pmid = {35882233}, issn = {1879-0445}, abstract = {During the late 3rd 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 3rd 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 & histology ; Biological Evolution ; Cats ; Evolution, Molecular ; *Finches/anatomy & 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}, doi = {10.1126/science.abm6536}, 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 = {Asians/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 = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btac425}, pmid = {35771611}, issn = {1367-4811}, abstract = {SUMMARY: Ancient DNA datasets are increasingly difficult to visualise 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 assists the assessment and reporting of spatio-temporal patterns of genetic changes.<br><br>AVAILABILITY: mapDATAge is a Shiny R application designed for exploring spatiotemporal patterns in ancient DNA data through a graphical user interface (GUI). 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 {pmid35768506, year = {2022}, author = {Bergström, A and Stanton, DWG and Taron, UH and Frantz, L and Sinding, MS and Ersmark, E and Pfrengle, S and Cassatt-Johnstone, M and Lebrasseur, O and Girdland-Flink, L and Fernandes, DM and Ollivier, M and Speidel, L and Gopalakrishnan, S and Westbury, MV and Ramos-Madrigal, J and Feuerborn, TR and Reiter, E and Gretzinger, J and Münzel, SC and Swali, P and Conard, NJ and Carøe, C and Haile, J and Linderholm, A and Androsov, S and Barnes, I and Baumann, C and Benecke, N and Bocherens, H and Brace, S and Carden, RF and Drucker, DG and Fedorov, S and Gasparik, M and Germonpré, M and Grigoriev, S and Groves, P and Hertwig, ST and Ivanova, VV and Janssens, L and Jennings, RP and Kasparov, AK and Kirillova, IV and Kurmaniyazov, I and Kuzmin, YV and Kosintsev, PA and Lázničková-Galetová, M and Leduc, C and Nikolskiy, P and Nussbaumer, M and O'Drisceoil, C and Orlando, L and Outram, A and Pavlova, EY and Perri, AR and Pilot, M and Pitulko, VV and Plotnikov, VV and Protopopov, AV and Rehazek, A and Sablin, M and Seguin-Orlando, A and Storå, J and Verjux, C and Zaibert, VF and Zazula, G and Crombé, P and Hansen, AJ and Willerslev, E and Leonard, JA and Götherström, A and Pinhasi, R and Schuenemann, VJ and Hofreiter, M and Gilbert, MTP and Shapiro, B and Larson, G and Krause, J and Dalén, L and Skoglund, P}, title = {Grey wolf genomic history reveals a dual ancestry of dogs.}, journal = {Nature}, volume = {607}, number = {7918}, pages = {313-320}, pmid = {35768506}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; 852558/ERC_/European Research Council/International ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 681396/ERC_/European Research Council/International ; 310763/ERC_/European Research Council/International ; ERC-2013-STG-337574-UNDEAD/ERC_/European Research Council/International ; ERC-2019-STG-853272-PALAEOFARM/ERC_/European Research Council/International ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Africa ; Animals ; DNA, Ancient/analysis ; *Dogs/genetics ; Domestication ; Europe ; *Genome/genetics ; *Genomics ; History, Ancient ; Middle East ; Mutation ; North America ; *Phylogeny ; Selection, Genetic ; Siberia ; Tumor Suppressor Proteins/genetics ; *Wolves/classification/genetics ; }, abstract = {The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.}, }
@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, BÇ 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 = {ANAGRAMS-IP-2018-01-8708//Croatian Science Foundation/ ; QLK5-CT2001-02461//European Union/ ; ANR-10-INBS-09-08//France Génomique/ ; BBS/OS/GC/000012F//the BBSRC Global Challenges Research Fund Data and Resources/ ; }, 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 {pmid35743173, year = {2022}, author = {Bodner, M and Amory, C and Olivieri, A and Gandini, F and Cardinali, I and Lancioni, H and Huber, G and Xavier, C and Pala, M and Fichera, A and Schnaller, L and Gysi, M and Sarno, S and Pettener, D and Luiselli, D and Richards, MB and Semino, O and Achilli, A and Torroni, A and Parson, W}, title = {Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample.}, journal = {International journal of molecular sciences}, volume = {23}, number = {12}, pages = {}, pmid = {35743173}, issn = {1422-0067}, support = {PRIN2017 2017CWHLHY//Italian Ministry of Education, University and Research (MIUR)/ ; Dipartimenti di Eccellenza Program (2018-2022)//Department of Biology and Biotechnology "L. Spallanzani" University of Pavia/ ; 2013042025//Intramural funding program of the Medical University of Innsbruck for young scientists MUISTART/ ; //Theodor Körner-Fonds zur Förderung von Wissenschaft und Kunst/ ; DSF 2015-1-1//D. Swarovski Förderungsfonds/ ; UNI-404/1998//Tiroler Wissenschaftsfonds (TWF)/ ; //Leverhulme Trust/ ; }, mesh = {*DNA, Mitochondrial/genetics ; Genetics, Population ; *Genome, Mitochondrial ; Haplotypes/genetics ; Nuclear Family ; Pilot Projects ; Sequence Analysis, DNA ; }, abstract = {The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.}, }
@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, 14C 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 = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2022.06.004}, pmid = {35732180}, issn = {1879-0445}, 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 16th 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 16th 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 consequences1,2. 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 Kyrgyzstan1,3-9. 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 individuals9. 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 {pmid35702131, year = {2022}, author = {Mohit,  and Sharma, I and Sharma, V and Kumar, S and Rastogi, G and Dutt, P and Shrivastava, A and Rai, N and Chand, P}, title = {Empirical assessment of allele frequencies of genome wide association study variants associated with obstructive sleep apnea.}, journal = {American journal of translational research}, volume = {14}, number = {5}, pages = {3464-3471}, pmid = {35702131}, issn = {1943-8141}, abstract = {OBJECTIVE: Obstructive Sleep Apnea (OSA) is a heterogeneous disorder with a complex interplay of genetic and environmental factors. Over the years, with advancement in genotyping and sequencing techniques, various loci have shown an association with OSA. It is pertinent to understand the status of these associated variants in different ethnic groups. The aim of the study was to assess the genetic affinity among different population groups by evaluating the risk allele frequencies of variants associated with OSA.<br><br>METHOD: The variants associated with OSA were obtained from the GWAS catalog with a significant p value of <5 × 10-7; 95 variants were obtained (www.ebi.ac.uk/gwas). Further, the variants were narrowed down on the basis of risk allele frequencies (>5%). The fst was calculated to assess the genetic affinity between super population groups and among the sub-population groups present in the 1000 genome project.<br><br>RESULT: The fst values observed indicated all super populations were genetically related (SAS, AMR, EAS and EUR) except in the African (AFR) population group. Further, the closely related super population i.e., SAS, AMR, EAS and EUR when bifurcated on the basis of sub-population groups shows population stratification and SAS population groups form separate clusters on the MDS plot.<br><br>CONCLUSION: The study highlights genetic heterogeneity among different population groups that gets diluted and results are biased when the samples are pooled irrespective of their endogamous groups. Our results provide insight to researchers to target specific endogamous groups for future studies on OSA.}, }
@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 för Vetenskaplig Forskning/ ; 19:257//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; 796877//H2020 Marie Skłodowska-Curie Actions/ ; 2017-04647//Vetenskapsrådet/ ; 2018-05973//Vetenskapsrådet/ ; 2015-676//Svenska Forskningsrådet 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 = {}, number = {}, pages = {}, pmid = {35695771}, issn = {1367-4811}, 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 (<1x average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1x 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 modelled 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 0.1x for SNP capture data (1240k) and 0.02x for whole genome sequencing data (WGS), 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 ∼45,000 and various global ancestries.<br><br>AVAILABILITY: 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}, support = {772852//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, 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 = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13658}, pmid = {35652762}, issn = {1755-0998}, support = {I3808//Austrian Science Fund/ ; 864740//Österreichische Forschungsförderungsgesellschaft/ ; //Austrian Science Fund(FWF)/ ; //Project no. P32964; Project title: Assessing food web dynamics to improve biocontrol of pest/ ; }, 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 {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 ; Sloan Research Fellowship//Alfred P. Sloan Foundation/ ; Career Award at the Scientific Interface//Burroughs Wellcome Fund/ ; R35GM142978/NH/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 = {Asians ; *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 5th and 9th 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 = {}, number = {}, pages = {e2109326119}, doi = {10.1073/pnas.2109326119}, pmid = {35609205}, issn = {1091-6490}, abstract = {SignificanceThe controversy over the taxonomic identity of the eggs exploited by Australia's first people around 50,000 y ago is resolved. The birds that laid these eggs are extinct, and distinguishing between two main candidates, a giant flightless "mihirung" Genyornis and a large megapode Progura, had proven impossible using morphological and geochemical methods. Ancient DNA sequencing remains inconclusive because of the age and burial temperature of the eggshell. In contrast, ancient protein sequences recovered from the eggshell enabled estimation of the evolutionary affinity between the egg and a range of extant taxa. The eggs are those of a Galloanseres (a group that includes extinct Dromornithidae, as well as extant landfowl and waterfowl), Genyornis, and not of the megapode (Megapodiidae, crown Galliformes).}, }
@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 ; }, 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 {pmid35580179, year = {2022}, author = {Slavin, P and Sebbane, F}, title = {Emergence and spread of ancestral Yersinia pestis in Late-Neolithic and Bronze-Age Eurasia, ca. 5,000 to 1,500 y B.P.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {21}, pages = {e2204044119}, pmid = {35580179}, issn = {1091-6490}, mesh = {Asia ; DNA, Ancient ; Europe ; Humans ; *Plague/epidemiology ; *Yersinia pestis/genetics ; *Yersinia pseudotuberculosis/genetics ; }, }
@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 (δ18O 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 (δ18O 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}, 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 ; Whites ; }, 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 = {}, number = {}, pages = {}, doi = {10.1146/annurev-genom-120621-090239}, pmid = {35537469}, issn = {1545-293X}, 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. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@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 {pmid35508651, year = {2022}, author = {Gelabert, P and Schmidt, RW and Fernandes, DM and Karsten, JK and Harper, TK and Madden, GD and Ledogar, SH and Sokhatsky, M and Oota, H and Kennett, DJ and Pinhasi, R}, title = {Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7242}, pmid = {35508651}, issn = {2045-2322}, support = {PACE #70245/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Agriculture ; *DNA, Ancient ; Europe ; Genome, Human ; History, Ancient ; *Human Migration ; Humans ; Ukraine ; }, abstract = {The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the Cucuteni-Trypillia cultural complex (CTCC, ~ 5000-3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935-825 cal BCE). Results reveal that the CTCC individuals' ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980-825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE.}, }
@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, 14C 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 {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}, support = {2020-00712//Formas/ ; //Knut and Alice Wallenberg foundation/ ; }, 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 ; Whites ; }, 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 = {}, number = {}, pages = {}, doi = {10.1146/annurev-genom-111521-121903}, pmid = {35440148}, issn = {1545-293X}, 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. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid35422088, year = {2022}, author = {Guiry, EJ and James, M and Cheung, C and Royle, TCA}, title = {Four millennia of long-term individual foraging site fidelity in a highly migratory marine predator.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {368}, pmid = {35422088}, issn = {2399-3642}, mesh = {Animals ; *Birds ; Geography ; }, abstract = {Theory and field studies suggest that long-term individual foraging site fidelity (IFSF) may be an important adaptation to competition from increasing population. However, the driving mechanisms and extent of long-term IFSF in wild populations of long-lived, migratory animals has been logistically difficult to study, with only a few confirmed instances. Temporal isotopic datasets can reveal long-term patterns in geographical foraging behaviour. We investigate the isotopic compositions of endangered short-tailed albatross (Phoebastria albatrus) over four millennia leading up to their near-extinction. Although not exhibited by short-tailed albatross today, we show past sub-populations displayed a high-degree of long-term IFSF, focusing on the same locations for hundreds of generations. This is the first large-scale evidence for the deep antiquity of long-term IFSF and suggests that it's density-driven. Globally, as populations of species like short-tailed albatross continue to recover from overexploitation, potential for resurgence of geographic specialization may increase exposure to localized hazards, requiring closer conservation monitoring.}, }
@article {pmid35421701, year = {2022}, author = {Bonsu, DOM and Afoakwah, CB and Abedi, M and Higgins, D and Austin, JJ}, title = {Ethics reporting in forensic science research publications - A review.}, journal = {Forensic science international}, volume = {335}, number = {}, pages = {111290}, doi = {10.1016/j.forsciint.2022.111290}, pmid = {35421701}, issn = {1872-6283}, mesh = {*Forensic Sciences ; Humans ; *Informed Consent ; }, abstract = {An essential element of compliance with ethical standards in scientific research is the reporting of a verifiable declaration of ethical approval and, when human subjects are involved - informed consent, in published works. The level of reporting of ethical permission for research published in forensic and investigative sciences journals has not been explored to date. Hence, we examined the reporting of ethical approval and informed consent in original research utilising human or animal subjects published in six forensic science journals from 2010 to 2019. We identified 10,192 articles and retained 3010 that satisfied the inclusion criteria of utilising human (91.2%), or animal (7.0%) or both (1.8%) subjects or tissues in experiments. Just over a third (1079/3010) of all studies declared obtaining ethical approval, with 927 (85.9%) of those indicating the name of the ethical committee, but only 392 (36%) provided an approval code. Furthermore, while consent was said to have been sought in 527 (17.5%) of studies, only 155 of those reported that written informed consent was obtained, eleven stated oral (verbal) consent, while the remaining 357 studies (67.7%) did not report the process used to gain consent. Ethical approval reporting rates differed between different research types, availability of financial support and whether authors were affiliated to academia or industry. The results demonstrate a low level of declaration of ethical approval and informed consent in forensic science research and publication, requiring urgent rectification. We support the adoption of the model proposed by Forensic Science International: Genetics as baseline recommendations to facilitate consistent nomenclature, transparency, and standard of ethical reporting in forensic science.}, }
@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, É 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 Skłodowska-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, Ž and Jankauskas, R and Moiseyev, V and Köhler, K and Király, Á 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//HHS | National Institutes of Health (NIH)/ ; }, 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, TÁ 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 7th 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 = {*Asians/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}, 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}, 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 = {2022}, 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 = {}, number = {}, pages = {}, doi = {10.1111/mec.16434}, pmid = {35306727}, issn = {1365-294X}, support = {//University of Otago/ ; 16-UOO-096//Royal Society Te Apārangi/ ; }, 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 {pmid35273713, year = {2022}, author = {Singh, H and Shipra,  and Sharma, V and Sharma, I and Sharma, A and Modeel, S and Gupta, N and Gupta, G and Pandita, AK and Butt, MF and Sharma, R and Pandita, S and Singh, V and Rai, E and Ikegawa, S and Sharma, S}, title = {The first study of epidemiology of adolescent idiopathic scoliosis shows lower prevalence in females of Jammu and Kashmir, India.}, journal = {American journal of translational research}, volume = {14}, number = {2}, pages = {1100-1106}, pmid = {35273713}, issn = {1943-8141}, abstract = {AIS is a heterogeneous 3D spinal deformity with Cobb angle ≥10°. It affects children in the age group of 10-16 years globally with 2-3% prevalence and significant female predominance. The exact etiology of AIS is not known however, it is supposed to be associated with factors such as anthropometric, metabolic, neuromuscular abnormalities and genetics.<br><br>OBJECTIVES: To determine the prevalence of AIS and association of anthropometric factors with AIS in the studied population group.<br><br>METHODOLOGY: Scoliosis screening of 9,500 individuals was carried out at different educational institutions of Jammu region in Jammu and Kashmir, India using a scoliosis-meter. The subjects were later examined radiologically.<br><br>RESULTS: In population of the region, AIS was most prevalent among all types of scoliosis with overall prevalence of 0.61%. The prevalence was observed to be lower in females (0.31%) than males (0.88%). Based on angle of trunk rotation (ATR), lumbar curves were more prevalent than thoracic curves. Average Cobb angle in males and females were 24.9° and 22.6°, respectively. BMI showed significant association with AIS in the age group of 12-16 years (P value =0.028). Furthermore, height was significantly associated with AIS in the overall screened population (P-value =0.029).<br><br>CONCLUSIONS: The AIS patients in the Jammu region of India have unique clinical features. In contrast to the global prevalence data, the prevalence of AIS in females in the region was less in comparison to males. Based on epidemiological literature and our findings, we hypothesized that genetic factors might be a major contributor in the AIS pathogenesis along with other confounding factors such as height, BMI, ethnicity, etc.}, }
@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, ÅJ 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}, support = {//Agencia Nacional de Promoción Científica y Tecnológica/ ; //Consejo Nacional de Investigaciones Científicas y Técnicas/ ; //Ministerio de Ciencia y Tecnología, Gobierno de la Provincia de Córdoba/ ; //Secretaria de Ciencia y Tecnología - Universidad Nacional de Córdoba/ ; }, 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 Córdoba. 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 Córdoba 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 {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 = {}, number = {}, pages = {102181}, doi = {10.1016/j.tube.2022.102181}, pmid = {35210171}, issn = {1873-281X}, 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 {pmid35205259, year = {2022}, author = {Messelodi, D and Giuliani, C and Cipriani, F and Armuzzi, S and di Palmo, E and Garagnani, P and Bertelli, L and Astolfi, A and Luiselli, D and Ricci, G and Pession, A}, title = {C5 and SRGAP3 Polymorphisms Are Linked to Paediatric Allergic Asthma in the Italian Population.}, journal = {Genes}, volume = {13}, number = {2}, pages = {}, pmid = {35205259}, issn = {2073-4425}, mesh = {*Asthma/epidemiology/genetics ; Child ; *Complement C5/genetics ; *GTPase-Activating Proteins/genetics ; Gene Frequency ; *Genetic Predisposition to Disease ; Genotype ; Humans ; Italy ; Polymorphism, Single Nucleotide ; }, abstract = {Asthma is a complex and heterogeneous disease, caused by the interaction between genetic and environmental factors with a predominant allergic background in children. The role of specific genes in asthmatic bronchial reactivity is still not clear, probably because of the many common pathways shared with other allergic disorders. This study is focused on 11 SNPs possibly related to asthma that were previously identified in a GWAS study. The genetic variability of these SNPs has been analysed in a population of 773 Italian healthy controls, and the presence of an association between the polymorphisms and the asthma onset was evaluated performing genotyping analysis on 108 children affected with asthma compared with the controls. Moreover, a pool of 171 patients with only allergic rhinoconjunctivitis has been included in the case-control analysis. The comparison of allele frequencies in asthmatic patients versus healthy controls identified two SNPs-rs1162394 (p = 0.019) and rs25681 (p = 0.044)-associated with the asthmatic condition, which were not differentially distributed in the rhinoconjunctivitis group. The rs25681 SNP, together with three other SNPs, also resulted in not being homogenously distributed in the Italian population. The significantly higher frequency of the rs25681 and rs1162394 SNPs (located, respectively, in the C5 and SRGAP3 genes) in the asthmatic population suggests an involvement of these genes in the asthmatic context, playing a role in increasing the inflammatory condition that may influence asthma onset and clinical course.}, }
@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 {pmid35201891, year = {2022}, author = {Wohns, AW and Wong, Y and Jeffery, B and Akbari, A and Mallick, S and Pinhasi, R and Patterson, N and Reich, D and Kelleher, J and McVean, G}, title = {A unified genealogy of modern and ancient genomes.}, journal = {Science (New York, N.Y.)}, volume = {375}, number = {6583}, pages = {eabi8264}, doi = {10.1126/science.abi8264}, pmid = {35201891}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa ; Chromosomes, Human, Pair 20/genetics ; Computer Simulation ; *DNA, Ancient ; Databases, Nucleic Acid ; Datasets as Topic ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; *Genome, Human ; *Genomics ; Geography ; Haplotypes ; Human Migration ; Humans ; Mutation ; *Pedigree ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; Statistics, Nonparametric ; }, abstract = {The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.}, }
@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 ; *Blacks/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 Africa1-4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. 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 - større 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 ; *Hunting ; Sequence Analysis, DNA/methods ; }, 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 {pmid35175801, year = {2022}, author = {Stone, AC}, title = {Genomes in motionOrigin: A Genetic History of the Americas Jennifer Raff Twelve, 2022. 368 pp.}, journal = {Science (New York, N.Y.)}, volume = {375}, number = {6582}, pages = {727}, doi = {10.1126/science.abn7262}, pmid = {35175801}, issn = {1095-9203}, abstract = {Ancient DNA sheds light on the peopling of the Americas.}, }
@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 {pmid35165121, year = {2022}, author = {Li, J and Zhao, B and Huang, T and Qin, Z and Wang, SM}, title = {Human BRCA pathogenic variants were originated during recent human history.}, journal = {Life science alliance}, volume = {5}, number = {5}, pages = {}, pmid = {35165121}, issn = {2575-1077}, mesh = {Animals ; BRCA1 Protein/*genetics ; BRCA2 Protein/*genetics ; Biological Evolution ; DNA, Ancient/analysis ; Databases, Genetic ; Evolution, Molecular ; Female ; Genetic Predisposition to Disease/genetics ; Germ-Line Mutation/genetics ; Haplotypes/genetics ; Humans ; Mutation ; }, abstract = {BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. BRCA germline pathogenic variants increase cancer risk. However, the evolutionary origin of human BRCA pathogenic variants remains largely elusive. We tested the 2,972 human BRCA1 and 3,652 human BRCA2 pathogenic variants from ClinVar database in 100 vertebrates across eight clades, but failed to find evidence to show cross-species evolution conservation as the origin; we searched the variants in 2,792 ancient human genome data, and identified 28 BRCA1 and 22 BRCA2 pathogenic variants in 44 cases dated from 45,000 to 300 yr ago; we analyzed the haplotype-dated human BRCA pathogenic founder variants, and observed that they were mostly arisen within the past 3,000 yr; we traced ethnic distribution of human BRCA pathogenic variants, and found that the majority were present in single or a few ethnic populations. Based on the data, we propose that human BRCA pathogenic variants were highly likely arisen in recent human history after the latest out-of-Africa migration, and the expansion of modern human population could largely increase the variation spectrum.}, }
@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 {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 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 Gowe, G and Vieira, FG and de Manuel, M and Hansen, AJ and Yamaguch, 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 [version 2; peer review: 2 approved].}, journal = {Open research Europe}, volume = {1}, number = {}, pages = {25}, pmid = {35098251}, issn = {2732-5121}, support = {681396/ERC_/European Research Council/International ; }, 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.<br><br>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.<br><br>RESULTS: We confirm a deep divergence (~20.65 Ma) within sabretoothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae.<br><br>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 ; WT220023/WT_/Wellcome Trust/United Kingdom ; WT207492/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 {pmid35052700, year = {2021}, author = {Abondio, P and Sarno, S and Giuliani, C and Laganà, V and Maletta, R and Bernardi, L and Bruno, F and Colao, R and Puccio, G and Frangipane, F and Borroni, B and Van Broeckhoven, C and Luiselli, D and Bruni, A}, title = {Amyloid Precursor Protein A713T Mutation in Calabrian Patients with Alzheimer's Disease: A Population Genomics Approach to Estimate Inheritance from a Common Ancestor.}, journal = {Biomedicines}, volume = {10}, number = {1}, pages = {}, pmid = {35052700}, issn = {2227-9059}, support = {PRIN 20177PJ9XF//Ministry of Education, Universities and Research/ ; }, abstract = {Mutation A713T in the amyloid precursor protein (APP) has been linked to cases of Alzheimer's disease (AD), cerebral amyloid angiopathy (CAA) and cerebrovascular disease. Despite its rarity, it has been observed in several families from the same geographical area, in the Calabria region in Southern Italy. Genotyping of 720,000 genome-wide SNPs with the HumanOmniExpress BeadChip was performed for six patients that were representative of apparently unrelated Calabrian families, as well as a Belgian subject of Italian descent (all with the same A713T mutation and disease). Their genomic structure and genetic relationships were analyzed. Demographic reconstruction and coalescent theory were applied to estimate the time of the most recent common ancestor (tMRCA) among patients. Results show that all A713T carriers fell into the genetic variability of Southern Italy and were not more closely related to each other than to any other healthy Calabrian individual. However, five out of seven patients shared a 1.7 Mbp-long DNA segment centered on the A713T mutation, making it possible to estimate a tMRCA for its common origin in the Calabrian region dating back over 1000 years. The analysis of affected individuals with methodologies based on human population genomics thus provides informative insights in support of clinical observations and biomedical research.}, }
@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 {pmid35047996, year = {2021}, author = {Handsley-Davis, M and Skelly, E and Johnson, NW and Kapellas, K and Lalloo, R and Kroon, J and Weyrich, LS}, title = {Biocultural Drivers of Salivary Microbiota in Australian Aboriginal and Torres Strait Islander Children.}, journal = {Frontiers in oral health}, volume = {2}, number = {}, pages = {641328}, pmid = {35047996}, issn = {2673-4842}, abstract = {Australian Aboriginal and Torres Strait Islander children experience unacceptably high rates of dental caries compared to their non-Indigenous Australian counterparts. Dental caries significantly impacts the quality of life of children and their families, particularly in remote communities. While many socioeconomic and lifestyle factors impact caries risk, the central role of the oral microbiota in mediating dental caries has not been extensively investigated in these communities. Here, we examine factors that shape diversity and composition of the salivary microbiota in Aboriginal and Torres Strait Islander children and adolescents living in the remote Northern Peninsula Area (NPA) of Far North Queensland. We employed 16S ribosomal RNA amplicon sequencing to profile bacteria present in saliva collected from 205 individuals aged 4-17 years from the NPA. Higher average microbial diversity was generally linked to increased age and salivary pH, less frequent toothbrushing, and proxies for lower socioeconomic status (SES). Differences in microbial composition were significantly related to age, salivary pH, SES proxies, and active dental caries. Notably, a feature classified as Streptococcus sobrinus increased in abundance in children who reported less frequent tooth brushing. A specific Veillonella feature was associated with caries presence, while features classified as Actinobacillus/Haemophilus and Leptotrichia were associated with absence of caries; a Lactobacillus gasseri feature increased in abundance in severe caries. Finally, we statistically assessed the interplay between dental caries and caries risk factors in shaping the oral microbiota. These data provide a detailed understanding of biological, behavioral, and socioeconomic factors that shape the oral microbiota and may underpin caries development in this group. This information can be used in the future to improve tailored caries prevention and management options for Australian Aboriginal and Torres Strait Islander children and communities.}, }
@article {pmid35038768, year = {2022}, author = {Stuart, KC and Sherwin, WB and Austin, JJ and Bateson, M and Eens, M and Brandley, MC and Rollins, LA}, title = {Historical museum samples enable the examination of divergent and parallel evolution during invasion.}, journal = {Molecular ecology}, volume = {31}, number = {6}, pages = {1836-1852}, pmid = {35038768}, issn = {1365-294X}, mesh = {Australia ; Climate Change ; Ecosystem ; *Introduced Species ; *Museums ; }, abstract = {During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline and global climate change. Concurrently, greater globalization is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in northwestern Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19th century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.}, }
@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 Beringia3-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 {pmid34953252, year = {2022}, author = {Thomas, ZA and Mooney, S and Cadd, H and Baker, A and Turney, C and Schneider, L and Hogg, A and Haberle, S and Green, K and Weyrich, LS and Perez, V and Moore, NE and Zawadzki, A and Kelloway, SJ and Khan, SJ}, title = {Corrigendum to "Late Holocene climate anomaly concurrent with fire activity and ecosystem shifts in the eastern Australian Highlands" [Sci. Total Environ. 802 (2021)149542].}, journal = {The Science of the total environment}, volume = {811}, number = {}, pages = {152367}, doi = {10.1016/j.scitotenv.2021.152367}, pmid = {34953252}, issn = {1879-1026}, }
@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 {pmid34949860, year = {2022}, author = {Carlin, N}, title = {A grave matter of ancient kinship in Neolithic Britain.}, journal = {Nature}, volume = {601}, number = {7894}, pages = {510-512}, pmid = {34949860}, issn = {1476-4687}, mesh = {*Archaeology ; *DNA, Ancient ; United Kingdom ; }, }
@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 {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 cairn1. 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 {pmid34937885, year = {2022}, author = {Bradley, DG}, title = {Bronze Age genomes reveal migration to Britain.}, journal = {Nature}, volume = {601}, number = {7894}, pages = {512-513}, pmid = {34937885}, issn = {1476-4687}, mesh = {*DNA, Ancient ; *Human Migration ; United Kingdom ; }, }
@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, ÅJ 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 HMGA2,2LCORL/NCAPG,3ZFAT, 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 {pmid34850680, year = {2021}, author = {Cristiani, E and Radini, A and Zupancich, A and Gismondi, A and D'Agostino, A and Ottoni, C and Carra, M and Vukojičić, S and Constantinescu, M and Antonović, D and Price, TD and Borić, D}, title = {Wild cereal grain consumption among Early Holocene foragers of the Balkans predates the arrival of agriculture.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34850680}, issn = {2050-084X}, support = {/WT_/Wellcome Trust/United Kingdom ; 209869/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Agriculture/*history ; Balkan Peninsula ; Domestication ; *Edible Grain ; Farmers/*history ; *Feeding Behavior ; History, Ancient ; Humans ; Tooth/anatomy &amp; histology ; }, abstract = {Forager focus on wild cereal plants has been documented in the core zone of domestication in southwestern Asia, while evidence for forager use of wild grass grains remains sporadic elsewhere. In this paper, we present starch grain and phytolith analyses of dental calculus from 60 Mesolithic and Early Neolithic individuals from five sites in the Danube Gorges of the central Balkans. This zone was inhabited by likely complex Holocene foragers for several millennia before the appearance of the first farmers ~6200 cal BC. We also analyzed forager ground stone tools (GSTs) for evidence of plant processing. Our results based on the study of dental calculus show that certain species of Poaceae (species of the genus Aegilops) were used since the Early Mesolithic, while GSTs exhibit traces of a developed grass grain processing technology. The adoption of domesticated plants in this region after ~6500 cal BC might have been eased by the existing familiarity with wild cereals.}, }
@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 {pmid34843568, year = {2021}, author = {Nath, S and Zilm, P and Jamieson, L and Kapellas, K and Goswami, N and Ketagoda, K and Weyrich, LS}, title = {Development and characterization of an oral microbiome transplant among Australians for the treatment of dental caries and periodontal disease: A study protocol.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0260433}, pmid = {34843568}, issn = {1932-6203}, mesh = {Animals ; Australia ; Dental Caries/microbiology/*therapy ; Dysbiosis/microbiology/*therapy ; Humans ; Mice, Inbred BALB C ; Microbiota ; Mouth/*microbiology ; Periodontal Diseases/microbiology/*therapy ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND: Oral microbiome transplantation (OMT) is a novel concept of introducing health-associated oral microbiota into the oral cavity of a diseased patient. The premise is to reverse the state of oral dysbiosis, and restore the ecological balance to maintain a stable homeostasis with the host immune system. This study will assess the effectiveness, feasibility, and safety of OMT using an interdisciplinary approach.<br><br>METHODS/DESIGN: To find donors suitable for microbial transplantation, supragingival plaque samples will be collected from 600 healthy participants. Each sample (200μL) will subsequently be examined in two ways: 1) 100μL of the sample will undergo high-throughput 16S rRNA gene amplicon sequencing and shotgun sequencing to identify the composition and characterisation of a healthy supragingival microbiome, 2) the remaining 100μL of the plaque sample will be mixed with 25% artificial saliva medium and inoculated into a specialised in-vitro flow cell model containing a hydroxyapatite disk. To obtain sufficient donor plaque, the samples would be grown for 14 days and further analysed microscopically and sequenced to examine and confirm the growth and survival of the microbiota. Samples with the healthiest microbiota would then be incorporated in a hydrogel delivery vehicle to enable transplantation of the donor oral microbiota. The third step would be to test the effectiveness of OMT in caries and periodontitis animal models for efficacy and safety for the treatment of oral diseases.<br><br>DISCUSSION: If OMTs are found to be successful, it can form a new treatment method for common oral diseases such as dental caries and periodontitis. OMTs may have the potential to modulate the oral microbiota and shift the ecological imbalances to a healthier state.}, }
@article {pmid34833105, year = {2021}, author = {Sharma, M and Chopra, C and Mehta, M and Sharma, V and Mallubhotla, S and Sistla, S and Sistla, JC and Bhushan, I}, title = {An Insight into Vaginal Microbiome Techniques.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {34833105}, issn = {2075-1729}, abstract = {There is a unique microbial community in the female lower genital tract known as the vaginal microbiota, which varies in composition and density and provides significant benefits during pregnancy, reproductive cyclicity, healthy newborn delivery, protection from preterm birth, infections such as UTIs, bacterial vaginosis, and so on, and improves the efficacy of treatments for vaginal cancers. Methods: It is necessary to know how the vaginal microbiome is composed in order to make an accurate diagnosis of the diseases listed above. A microbiome's members are difficult to classify, and the way microbial communities function and influence host-pathogen interactions are difficult to understand. More and more metagenomic studies are able to unravel such complexities due to advances in high-throughput sequencing and bioinformatics. When it comes to vaginal microbiota research, we'll be looking at the use of modern techniques and strategies that can be used to investigate variations in vaginal microbiota in order to detect diseases earlier, better treat vaginal disorders, and boost women's health. Discussion: The discussed techniques and strategies may improve the treatment of vaginal disorders and may be beneficial for women's overall health.}, }
@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 {pmid34793228, year = {2021}, author = {Cooper, A and Turney, CSM and Palmer, J and Hogg, A and McGlone, M and Wilmshurst, J and Lorrey, AM and Heaton, TJ and Russell, JM and McCracken, K and Anet, JG and Rozanov, E and Friedel, M and Suter, I and Peter, T and Muscheler, R and Adolphi, F and Dosseto, A and Faith, JT and Fenwick, P and Fogwill, CJ and Hughen, K and Lipson, M and Liu, J and Nowaczyk, N and Rainsley, E and Ramsey, CB and Sebastianelli, P and Souilmi, Y and Stevenson, J and Thomas, Z and Tobler, R and Zech, R}, title = {Response to Comment on "A global environmental crisis 42,000 years ago".}, journal = {Science (New York, N.Y.)}, volume = {374}, number = {6570}, pages = {eabh3655}, doi = {10.1126/science.abh3655}, pmid = {34793228}, issn = {1095-9203}, abstract = {Our paper about the impacts of the Laschamps Geomagnetic Excursion 42,000 years ago has provoked considerable scientific and public interest, particularly in the so-called Adams Event associated with the initial transition of the magnetic poles. Although we welcome the opportunity to discuss our new ideas, Hawks’ assertions of misrepresentation are especially disappointing given his limited examination of the material.}, }
@article {pmid34793203, year = {2021}, author = {Cooper, A and Turney, CSM and Palmer, J and Hogg, A and McGlone, M and Wilmshurst, J and Lorrey, AM and Heaton, TJ and Russell, JM and McCracken, K and Anet, JG and Rozanov, E and Friedel, M and Suter, I and Peter, T and Muscheler, R and Adolphi, F and Dosseto, A and Faith, JT and Fenwick, P and Fogwill, CJ and Hughen, K and Lipson, M and Liu, J and Nowaczyk, N and Rainsley, E and Bronk Ramsey, C and Sebastianelli, P and Souilmi, Y and Stevenson, J and Thomas, Z and Tobler, R and Zech, R}, title = {Response to Comment on "A global environmental crisis 42,000 years ago".}, journal = {Science (New York, N.Y.)}, volume = {374}, number = {6570}, pages = {eabi9756}, doi = {10.1126/science.abi9756}, pmid = {34793203}, issn = {1095-9203}, abstract = {Our study on the exact timing and the potential climatic, environmental, and evolutionary consequences of the Laschamps Geomagnetic Excursion has generated the hypothesis that geomagnetism represents an unrecognized driver in environmental and evolutionary change. It is important for this hypothesis to be tested with new data, and encouragingly, none of the studies presented by Picin et al. undermine our model.}, }
@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 = {}, doi = {10.1093/g3journal/jkab357}, 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 {pmid34782694, year = {2021}, author = {Guellil, M and Rinaldo, N and Zedda, N and Kersten, O and Gonzalez Muro, X and Stenseth, NC and Gualdi-Russo, E and Bramanti, B}, title = {Bioarchaeological insights into the last plague of Imola (1630-1632).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22253}, pmid = {34782694}, issn = {2045-2322}, support = {324249//FP7 Ideas: European Research Council/ ; 324249//FP7 Ideas: European Research Council/ ; 324249//FP7 Ideas: European Research Council/ ; }, mesh = {Adult ; *Archaeology/history ; Child ; Child, Preschool ; DNA, Ancient ; DNA, Bacterial ; *Disease Outbreaks/history ; Female ; Geography, Medical ; History, 17th Century ; Humans ; Italy/epidemiology ; Male ; Metagenome ; Metagenomics ; Plague/*epidemiology/history/*microbiology ; Yersinia pestis/genetics ; }, abstract = {The plague of 1630-1632 was one of the deadliest plague epidemics to ever hit Northern Italy, and for many of the affected regions, it was also the last. While accounts on plague during the early 1630s in Florence and Milan are frequent, much less is known about the city of Imola. We analyzed the full skeletal assemblage of four mass graves (n = 133 individuals) at the Lazaretto dell'Osservanza, which date back to the outbreak of 1630-1632 in Imola and evaluated our results by integrating new archival sources. The skeletons showed little evidence of physical trauma and were covered by multiple layers of lime, which is characteristic for epidemic mass mortality sites. We screened 15 teeth for Yersinia pestis aDNA and were able to confirm the presence of plague in Imola via metagenomic analysis. Additionally, we studied a contemporaneous register, in which a friar recorded patient outcomes at the lazaretto during the last year of the epidemic. Our multidisciplinary approach combining historical, osteological and genomic data provided a unique opportunity to reconstruct an in-depth picture of the last plague of Imola through the city's main lazaretto.}, }
@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 Skłodowska-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 {pmid34773064, year = {2021}, author = {Yurtman, E and Özer, O and Yüncü, E and Dağtaş, ND and Koptekin, D and Çakan, YG and Özkan, M and Akbaba, A and Kaptan, D and Atağ, G and Vural, KB and Gündem, CY and Martin, L and Kılınç, GM and Ghalichi, A and Açan, SC and Yaka, R and Sağlıcan, E and Lagerholm, VK and Krzewińska, M and Günther, T and Morell Miranda, P and Pişkin, E and Şevketoğlu, M and Bilgin, CC and Atakuman, Ç and Erdal, YS and Sürer, E and Altınışık, NE and Lenstra, JA and Yorulmaz, S and Abazari, MF and Hoseinzadeh, J and Baird, D and Bıçakçı, E and Çevik, Ö and Gerritsen, F and Özbal, R and Götherström, A and Somel, M and Togan, İ and Özer, F}, title = {Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {1279}, pmid = {34773064}, issn = {2399-3642}, mesh = {Animals ; Archaeology ; Cell Nucleus ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Demography ; *Domestication ; *Polymorphism, Genetic ; Sheep, Domestic/*genetics ; Turkey ; }, abstract = {Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic.}, }
@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 {pmid34759290, year = {2021}, author = {Morin, J and Royle, TCA and Zhang, H and Speller, C and Alcaide, M and Morin, R and Ritchie, M and Cannon, A and George, M and George, M and Yang, D}, title = {Indigenous sex-selective salmon harvesting demonstrates pre-contact marine resource management in Burrard Inlet, British Columbia, Canada.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21160}, pmid = {34759290}, issn = {2045-2322}, mesh = {Animals ; British Columbia ; Hunting ; Male ; *Oncorhynchus keta ; Rivers ; *Seafood ; }, abstract = {To gain insight into pre-contact Coast Salish fishing practices, we used new palaeogenetic analytical techniques to assign sex identifications to salmonid bones from four archaeological sites in Burrard Inlet (Tsleil-Waut), British Columbia, Canada, dating between about 2300-1000 BP (ca. 400 BCE-CE 1200). Our results indicate that male chum salmon (Oncorhynchus keta) were preferentially targeted at two of the four sampled archaeological sites. Because a single male salmon can mate with several females, selectively harvesting male salmon can increase a fishery's maximum sustainable harvest. We suggest such selective harvesting of visually distinctive male spawning chum salmon was a common practice, most effectively undertaken at wooden weirs spanning small salmon rivers and streams. We argue that this selective harvesting of males is indicative of an ancient and probably geographically widespread practice for ensuring sustainable salmon populations. The archaeological data presented here confirms earlier ethnographic accounts describing the selective harvest of male salmon.}, }
@article {pmid34748674, year = {2021}, 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 = {}, number = {}, pages = {}, doi = {10.1111/mec.16267}, pmid = {34748674}, issn = {1365-294X}, support = {410-2005-0778//Social Sciences and Humanities Research Council of Canada/ ; EAR/SGP# 1425059//National Science Foundation/ ; FL140100260//Australian Research Council/ ; }, 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 {pmid34743803, year = {2021}, author = {Zilberman, U and Abramov, J and Smith, P}, title = {Supernumerary roots in maxillary deciduous canines: A rare anomaly with a long history.}, journal = {Archives of oral biology}, volume = {132}, number = {}, pages = {105292}, doi = {10.1016/j.archoralbio.2021.105292}, pmid = {34743803}, issn = {1879-1506}, mesh = {*Cuspid/diagnostic imaging ; Maxilla/diagnostic imaging ; Odontogenesis ; Tooth Crown ; *Tooth Root/diagnostic imaging ; Tooth, Deciduous ; }, abstract = {OBJECTIVE: To describe two maxillary deciduous bi-rooted canines, one archeological and one modern, and examine the possible etiology of this condition.<br><br>DESIGN: Two cases of bi-rooted canines were described and compared to published examples. Both specimens were radiographed and measured and compared to one-rooted samples. The archeological specimen was scanned using CBCT to facilitate detailed examination of the deciduous teeth. The extracted modern tooth was embedded in epoxy resin and two coronal sections were cut, one through the crown and one through the roots and examined with a light microscope.<br><br>RESULTS: The bi-rooted canines were larger than the control samples. They showed none of the features commonly associated with gemination. The radiographs and scans showed that the canine roots in the archeological case diverged mesio-distally like the buccal roots in the adjacent first deciduous molar. In the clinical case, the root trunk was elongated mesio-distally and the furcation was located very close to the apex with a C-shaped root canal.<br><br>CONCLUSIONS: Both variants of the condition described above are rare in deciduous canines. They do not seem to be associated with fusion or gemination. However, as the teeth are relatively flattened bucco-lingually and we tentatively propose that this form results from spatial constraints during the early stages of crown development that have contributed to the development of additional roots. The megadont dimension of the recent bi-rooted deciduous canine may affect root development and the necessity of two mesio-distally located roots for anchorage in the maxilla.}, }
@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, J 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 {pmid34718543, year = {2021}, author = {Colbran, LL and Johnson, MR and Mathieson, I and Capra, JA}, title = {Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment.}, journal = {Genome biology and evolution}, volume = {13}, number = {11}, pages = {}, pmid = {34718543}, issn = {1759-6653}, support = {T32 GM080178/GM/NIGMS NIH HHS/United States ; R35 GM133708/GM/NIGMS NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; R01 GM115836/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Biological/genetics ; Adaptation, Physiological ; Biological Evolution ; DNA, Ancient ; *Genome, Human ; Humans ; Multifactorial Inheritance ; Selection, Genetic ; }, abstract = {As humans populated the world, they adapted to many varying environmental factors, including climate, diet, and pathogens. Because many of these adaptations were mediated by multiple noncoding variants with small effects on gene regulation, it has been difficult to link genomic signals of selection to specific genes, and to describe the regulatory response to selection. To overcome this challenge, we adapted PrediXcan, a machine learning method for imputing gene regulation from genotype data, to analyze low-coverage ancient human DNA (aDNA). First, we used simulated genomes to benchmark strategies for adapting PrediXcan to increase robustness to incomplete data. Applying the resulting models to 490 ancient Eurasians, we found that genes with the strongest divergent regulation among ancient populations with hunter-gatherer, pastoralist, and agricultural lifestyles are enriched for metabolic and immune functions. Next, we explored the contribution of divergent gene regulation to two traits with strong evidence of recent adaptation: dietary metabolism and skin pigmentation. We found enrichment for divergent regulation among genes proposed to be involved in diet-related local adaptation, and the predicted effects on regulation often suggest explanations for known signals of selection, for example, at FADS1, GPX1, and LEPR. In contrast, skin pigmentation genes show little regulatory change over a 38,000-year time series of 2,999 ancient Europeans, suggesting that adaptation mainly involved large-effect coding variants. This work demonstrates that combining aDNA with present-day genomes is informative about the biological differences among ancient populations, the role of gene regulation in adaptation, and the relationship between genetic diversity and complex traits.}, }
@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 ; *Whole 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 {pmid34679854, year = {2021}, author = {Passamonti, MM and Somenzi, E and Barbato, M and Chillemi, G and Colli, L and Joost, S and Milanesi, M and Negrini, R and Santini, M and Vajana, E and Williams, JL and Ajmone-Marsan, P}, title = {The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {10}, pages = {}, pmid = {34679854}, issn = {2076-2615}, support = {INEA/CEF/ICT/A2018/1815462//Connecting European Facility (CEF) Telecommunications/ ; INEA/CEF/ICT/A2020/2373580//Connecting European Facility (CEF) Telecommunications/ ; 677353//European Union's Horizon 2020 Research and Innovation Programme/ ; 2012//European Union's Horizon 2020 Partnership for Research and Innovation in the Mediterranean Area Programme (PRIMA/ ; Project "Landscape 4.0 - food, wellbeing and environment"//Italian Ministry of Education, University and Research/ ; Livestock Environment Opendata, 16.2 - PSRN 2014-2020//Fondo Europeo Agricolo per lo Sviluppo Rurale (FEASR)./ ; }, abstract = {Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.}, }
@article {pmid34674113, year = {2021}, author = {Bonsu, DOM and Rodie, M and Higgins, D and Henry, J and Austin, JJ}, title = {Comparison of Isohelix™ and Rayon swabbing systems for touch DNA recovery from metal surfaces.}, journal = {Forensic science, medicine, and pathology}, volume = {17}, number = {4}, pages = {577-584}, pmid = {34674113}, issn = {1556-2891}, mesh = {Cellulose ; DNA ; *DNA Fingerprinting ; Humans ; Specimen Handling ; *Touch ; }, abstract = {A previous study evaluating two swabbing systems found that DNA was best recovered from sterile metal substrates using an Isohelix™ swab wetted with isopropyl alcohol rather than a Rayon swab with water as the wetting agent. We tested the same swabbing systems on metal (aluminum, brass, and stainless steel) and plastic substrates in a regularly touched environment to simulate the non-deliberate transfer of touch evidence likely seen in a casework scenario, to ascertain the performance of these swabs in an uncontrolled situation. Higher amounts of touch DNA were recovered with Isohelix™ swabs (0.5 - 3.3 ng) compared to Rayon swabs (0.13 - 1.2 ng). The Isohelix™ swabbing system was found to significantly recover more touch DNA (p = 0.04) from the metal substrates than the Rayon swabbing system, consistent with the findings of our previous work. The results contribute to our understanding of the impact of sample collection techniques on touch DNA recovery from problematic metal surfaces and suggest that supplemental cleaning of substrates as a precautionary step against the spread of infections may affect touch DNA persistence and the recovery efficiency of swabs.}, }
@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 Skłodowska-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 {pmid34671162, year = {2021}, author = {Librado, P and Khan, N and Fages, A and Kusliy, MA and Suchan, T and Tonasso-Calvière, L and Schiavinato, S and Alioglu, D and Fromentier, A and Perdereau, A and Aury, JM and Gaunitz, C and Chauvey, L and Seguin-Orlando, A and Der Sarkissian, C and Southon, J and Shapiro, B and Tishkin, AA and Kovalev, AA and Alquraishi, S and Alfarhan, AH and Al-Rasheid, KAS and Seregély, T and Klassen, L and Iversen, R and Bignon-Lau, O and Bodu, P and Olive, M and Castel, JC and Boudadi-Maligne, M and Alvarez, N and Germonpré, M and Moskal-Del Hoyo, M and Wilczyński, J and Pospuła, S and Lasota-Kuś, A and Tunia, K and Nowak, M and Rannamäe, E and Saarma, U and Boeskorov, G and Lōugas, L and Kyselý, R and Peške, L and Bălășescu, A and Dumitrașcu, V and Dobrescu, R and Gerber, D and Kiss, V and Szécsényi-Nagy, A and Mende, BG and Gallina, Z and Somogyi, K and Kulcsár, G and Gál, E and Bendrey, R and Allentoft, ME and Sirbu, G and Dergachev, V and Shephard, H and Tomadini, N and Grouard, S and Kasparov, A and Basilyan, AE and Anisimov, MA and Nikolskiy, PA and Pavlova, EY and Pitulko, V and Brem, G and Wallner, B and Schwall, C and Keller, M and Kitagawa, K and Bessudnov, AN and Bessudnov, A and Taylor, W and Magail, J and Gantulga, JO and Bayarsaikhan, J and Erdenebaatar, D and Tabaldiev, K and Mijiddorj, E and Boldgiv, B and Tsagaan, T and Pruvost, M and Olsen, S and Makarewicz, CA and Valenzuela Lamas, S and Albizuri Canadell, S and Nieto Espinet, A and Iborra, MP and Lira Garrido, J and Rodríguez González, E and Celestino, S and Olària, C and Arsuaga, JL and Kotova, N and Pryor, A and Crabtree, P and Zhumatayev, R and Toleubaev, A and Morgunova, NL and Kuznetsova, T and Lordkipanize, D and Marzullo, M and Prato, O and Bagnasco Gianni, G and Tecchiati, U and Clavel, B and Lepetz, S and Davoudi, H and Mashkour, M and Berezina, NY and Stockhammer, PW and Krause, J and Haak, W and Morales-Muñiz, A and Benecke, N and Hofreiter, M and Ludwig, A and Graphodatsky, AS and Peters, J and Kiryushin, KY and Iderkhangai, TO and Bokovenko, NA and Vasiliev, SK and Seregin, NN and Chugunov, KV and Plasteeva, NA and Baryshnikov, GF and Petrova, E and Sablin, M and Ananyevskaya, E and Logvin, A and Shevnina, I and Logvin, V and Kalieva, S and Loman, V and Kukushkin, I and Merz, I and Merz, V and Sakenov, S and Varfolomeyev, V and Usmanova, E and Zaibert, V and Arbuckle, B and Belinskiy, AB and Kalmykov, A and Reinhold, S and Hansen, S and Yudin, AI and Vybornov, AA and Epimakhov, A and Berezina, NS and Roslyakova, N and Kosintsev, PA and Kuznetsov, PF and Anthony, D and Kroonen, GJ and Kristiansen, K and Wincker, P and Outram, A and Orlando, L}, title = {The origins and spread of domestic horses from the Western Eurasian steppes.}, journal = {Nature}, volume = {598}, number = {7882}, pages = {634-640}, pmid = {34671162}, issn = {1476-4687}, mesh = {Animals ; Archaeology ; Asia ; DNA, Ancient ; *Domestication ; Europe ; *Genetics, Population ; Genome ; Grassland ; *Horses/genetics ; Phylogeny ; }, abstract = {Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2-4 at Botai, Central Asia around 3500 BC3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture11,12.}, }
@article {pmid34671161, year = {2021}, author = {Wang, Y and Pedersen, MW and Alsos, IG and De Sanctis, B and Racimo, F and Prohaska, A and Coissac, E and Owens, HL and Merkel, MKF and Fernandez-Guerra, A and Rouillard, A and Lammers, Y and Alberti, A and Denoeud, F and Money, D and Ruter, AH and McColl, H and Larsen, NK and Cherezova, AA and Edwards, ME and Fedorov, GB and Haile, J and Orlando, L and Vinner, L and Korneliussen, TS and Beilman, DW and Bjørk, AA and Cao, J and Dockter, C and Esdale, J and Gusarova, G and Kjeldsen, KK and Mangerud, J and Rasic, JT and Skadhauge, B and Svendsen, JI and Tikhonov, A and Wincker, P and Xing, Y and Zhang, Y and Froese, DG and Rahbek, C and Bravo, DN and Holden, PB and Edwards, NR and Durbin, R and Meltzer, DJ and Kjær, KH and Möller, P and Willerslev, E}, title = {Late Quaternary dynamics of Arctic biota from ancient environmental genomics.}, journal = {Nature}, volume = {600}, number = {7887}, pages = {86-92}, pmid = {34671161}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; 207492/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 069906/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Arctic Regions ; *Biota ; Climate Change/history ; DNA, Ancient/*analysis ; DNA, Environmental/*analysis ; Databases, Genetic ; Datasets as Topic ; Extinction, Biological ; Geologic Sediments ; Grassland ; Greenland ; Haplotypes/genetics ; Herbivory/genetics ; History, Ancient ; Humans ; Lakes ; Mammoths ; *Metagenomics ; Mitochondria/genetics ; Perissodactyla ; Permafrost ; Phylogeny ; Plants/genetics ; Population Dynamics ; Rain ; Siberia ; Spatio-Temporal Analysis ; Wetlands ; }, abstract = {During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.}, }
@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 Native Continental Ancestry Group ; 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 analyses3,6,8-12 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, ÍG 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 = {American Indians or Alaska Natives ; Americas ; Asia ; Asians ; 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 ; Whites ; }, 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 = {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 {pmid34584164, year = {2021}, author = {Wang, CC and Posth, C and Furtwängler, A and Sümegi, K and Bánfai, Z and Kásler, M and Krause, J and Melegh, B}, title = {Genome-wide autosomal, mtDNA, and Y chromosome analysis of King Bela III of the Hungarian Arpad dynasty.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19210}, pmid = {34584164}, issn = {2045-2322}, mesh = {Asians/genetics ; Chromosomes, Human, Y/genetics ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Female ; *Genetics, Population ; *Haplotypes ; Humans ; Hungary ; Male ; Pedigree ; }, abstract = {The ancient Hungarians, "Madzsars", established their control of the Carpathian Basin in the late ninth century and founded the Hungarian Kingdom around 1000AD. The origin of the Magyars as a tribal federation has been much debated in the past. From the time of the conquest to the early fourteenth century they were ruled by descendants of the Arpad family. In order to learn more about the genetic origin of this family, we here analyzed the genome of Bela III one of the most prominent members of the early Hungarian dynasty that ruled the Hungarian Kingdom from 1172 to 1196. The Y-Chromosome of Bela III belongs to haplogroup R1a-Z2123 that is today found in highest frequency in Central Asia, supporting a Central Asian origin for the ruling lineage of the Hungarian kingdom. The autosomal DNA profile of Bela III, however, falls within the genetic variation of present-day east European populations. This is further supported through his mtDNA genome that belongs to haplogroup H, the most common European maternal lineage, but also found in Central Asia. However, we didn't find an exact haplotype match for Bela III. The typical autosomal and maternal Central Eastern European ancestry among Bela III autosomes might be best explained by consecutive intermarriage with local European ruling families.}, }
@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 Skłodowska-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 {pmid34521829, year = {2021}, author = {Klein, CG and Pisani, D and Field, DJ and Lakin, R and Wills, MA and Longrich, NR}, title = {Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5335}, pmid = {34521829}, issn = {2041-1723}, support = {MR/S032177/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amphibians ; Animal Distribution/*physiology ; Animals ; Biodiversity ; Birds ; DNA, Ancient/analysis ; *Extinction, Biological ; Fishes ; Fossils/history ; *Genetic Speciation ; History, Ancient ; Mammals ; *Phylogeny ; Phylogeography ; Snakes/anatomy &amp; histology/*classification/genetics ; }, abstract = {Mass extinctions have repeatedly shaped global biodiversity. The Cretaceous-Paleogene (K-Pg) mass extinction caused the demise of numerous vertebrate groups, and its aftermath saw the rapid diversification of surviving mammals, birds, frogs, and teleost fishes. However, the effects of the K-Pg extinction on the evolution of snakes-a major clade of predators comprising over 3,700 living species-remains poorly understood. Here, we combine an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes. We reveal a potential diversification among crown snakes associated with the K-Pg mass extinction, led by the successful colonisation of Asia by the major extant clade Afrophidia. Vertebral morphometrics suggest increasing morphological specialisation among marine snakes through the Paleogene. The dispersal patterns of snakes following the K-Pg underscore the importance of this mass extinction event in shaping Earth's extant vertebrate faunas.}, }
@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 {pmid34516814, year = {2021}, author = {Gibbons, A}, title = {How farming shaped Europeans' immunity.}, journal = {Science (New York, N.Y.)}, volume = {373}, number = {6560}, pages = {1186}, doi = {10.1126/science.acx9047}, pmid = {34516814}, issn = {1095-9203}, mesh = {Agriculture/*history ; Animals ; Communicable Diseases/*history/immunology/mortality ; DNA, Ancient ; Europe ; Genetic Variation ; History, Ancient ; Humans ; *Immune System ; Immunity/genetics ; Zoonoses/history/immunology ; }, }
@article {pmid34493715, year = {2021}, author = {Coll Macià, M and Skov, L and Peter, BM and Schierup, MH}, title = {Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5317}, pmid = {34493715}, issn = {2041-1723}, mesh = {Animals ; Asia ; Crosses, Genetic ; DNA, Ancient/*analysis ; Europe ; Female ; *Gene Flow ; *Genome, Human ; History, 21st Century ; History, Ancient ; Humans ; Male ; *Mutation ; Neanderthals/*genetics ; Polymorphism, Restriction Fragment Length ; }, abstract = {After the main Out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments in all non-African genomes today. Here we investigate what can be learned about human demographic processes from the size distribution of these fragments. We observe differences in fragment length across Eurasia with 12% longer fragments in East Asians than West Eurasians. Comparisons between extant populations with ancient samples show that these differences are caused by different rates of decay in length by recombination since the Neanderthal admixture. In concordance, we observe a strong correlation between the average fragment length and the mutation accumulation, similar to what is expected by changing the ages at reproduction as estimated from trio studies. Altogether, our results suggest differences in the generation interval across Eurasia, by up 10-20%, over the past 40,000 years. We use sex-specific mutation signatures to infer whether these changes were driven by shifts in either male or female age at reproduction, or both. We also find that previously reported variation in the mutational spectrum may be largely explained by changes to the generation interval. We conclude that Neanderthal fragment lengths provide unique insight into differences among human populations over recent history.}, }
@article {pmid34483440, year = {2021}, author = {Sedig, JW and Olade, I and Patterson, N and Harney, É 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 {pmid34480555, year = {2021}, author = {Ferreira, JC and Alshamali, F and Montinaro, F and Cavadas, B and Torroni, A and Pereira, L and Raveane, A and Fernandes, V}, title = {Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations.}, journal = {Genome biology and evolution}, volume = {13}, number = {9}, pages = {}, pmid = {34480555}, issn = {1759-6653}, mesh = {Animals ; DNA, Ancient ; Genetics, Population ; Genome, Human ; Human Migration ; Humans ; Indian Ocean ; Iran ; *Neanderthals/genetics ; }, abstract = {The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.}, }
@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 {pmid34459346, year = {2021}, author = {Caramelli, D and Posth, C and Rickards, O}, title = {Reconstruction of the human peopling of Europe: a genetic insight.}, journal = {Annals of human biology}, volume = {48}, number = {3}, pages = {175-178}, doi = {10.1080/03014460.2021.1955472}, pmid = {34459346}, issn = {1464-5033}, mesh = {Europe ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; Humans ; }, }
@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 {pmid34459341, year = {2021}, author = {Scorrano, G and Yediay, FE and Pinotti, T and Feizabadifarahani, M and Kristiansen, K}, title = {The genetic and cultural impact of the Steppe migration into Europe.}, journal = {Annals of human biology}, volume = {48}, number = {3}, pages = {223-233}, doi = {10.1080/03014460.2021.1942984}, pmid = {34459341}, issn = {1464-5033}, mesh = {Archaeology ; DNA, Ancient/*analysis ; Europe ; Female ; *Genome, Human ; *Genome, Mitochondrial ; *Human Migration ; Humans ; Male ; }, abstract = {BACKGROUND: During the early 3rd millennium BCE migration from Pontic Steppe, mainly related to Yamnaya culture, has affected European populations both culturally and genetically, however, it has long been debated to what extent this migration was male-driven, and how this replacement process took place which eliminated partially/largely Neolithic male lines over time.<br><br>AIM: This paper aims to evaluate the influence of the Steppe migration on European Bronze Age populations by calculating both male and female genetic contributions of the Steppe-related ancestry to the European Bronze Age populations. With this approach, we will be able to clarify the hypotheses on whether it was male-biased migration or not.<br><br>SUBJECTS AND METHODS: To evaluate the genetic impact and the proportion of the Steppe-related ancestry to the European Bronze Age populations, we performed PCA and qpAdm analyses by using published genome-wide data. In addition, we quantified male and female genetic contribution into Europe by using the analysis of uniparental markers and the X-chromosome.<br><br>RESULTS: The Steppe migration had a considerable impact on the genetic makeup of the Bronze Age European populations. The data suggest that the Steppe-related ancestry arriving into Central Europe was male-driven, dominantly in the Corded Ware culture populations and lesser in the Bell Beaker populations. In fact, there is no evidence that this migration had a significant input on the mitochondrial genetic pool of all European Bronze Age populations.<br><br>CONCLUSIONS: Our analyses suggest that the Steppe-related ancestry had genetic impact on mainly Central-Eastern Europe. Moreover, this migration was male-driven for most of the Central European populations belonging to the Corded Ware groups, and to a lesser extent for the Bell Beaker groups.}, }
@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 Belvì (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 Belvì 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 {pmid34459339, year = {2021}, author = {Calò, CM and Vona, G and Robledo, R and Francalacci, P}, title = {From old markers to next generation: reconstructing the history of the peopling of Sardinia.}, journal = {Annals of human biology}, volume = {48}, number = {3}, pages = {203-212}, doi = {10.1080/03014460.2021.1944312}, pmid = {34459339}, issn = {1464-5033}, mesh = {DNA, Ancient/*analysis ; *Gene Flow ; *Genetic Markers ; *Genome, Human ; Genomics ; *Human Migration ; Humans ; Italy ; }, abstract = {CONTEXT: For many years the Sardinian population has been the object of numerous studies because of its unique genetic structure. Despite the extreme abundance of papers, various aspects of the peopling and genetic structure of Sardinia still remain uncertain and sometimes controversial.<br><br>OBJECTIVE: We reviewed what has emerged from different studies, focussing on some still open questions, such as the origin of Sardinians, their relationship with the Corsican population, and the intra-regional genetic heterogeneity.<br><br>METHODS: The various issues have been addressed through the analysis of classical markers, molecular markers and, finally, genomic data through next generation sequencing.<br><br>RESULTS AND CONCLUSIONS: Although the most ancient human remains date back to the end of the Palaeolithic, Mesolithic populations brought founding lineages that left evident traces in the modern population. Then, with the Neolithic, the island underwent an important demographic expansion. Subsequently, isolation and genetic drift contributed to maintain a significant genetic heterogeneity, but preserving the overall homogeneity on a regional scale. At the same time, isolation and genetic drift contributed to differentiate Sardinia from Corsica, which saw an important gene flow from the mainland. However, the isolation did not prevent gene flow from the neighbouring populations whose contribution are still recognisable in the genome of Sardinians.}, }
@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 (1st-3rd 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 {pmid34454138, year = {2022}, author = {Thomas, ZA and Mooney, S and Cadd, H and Baker, A and Turney, C and Schneider, L and Hogg, A and Haberle, S and Green, K and Weyrich, LS and Pérez, V and Moore, NE and Zawadzki, A and Kelloway, SJ and Khan, SJ}, title = {Late Holocene climate anomaly concurrent with fire activity and ecosystem shifts in the eastern Australian Highlands.}, journal = {The Science of the total environment}, volume = {802}, number = {}, pages = {149542}, doi = {10.1016/j.scitotenv.2021.149542}, pmid = {34454138}, issn = {1879-1026}, mesh = {Australia ; Climate Change ; *Ecosystem ; *Fires ; Forests ; }, abstract = {The alpine area of the Australian mainland is highly sensitive to climate and environmental change, and potentially vulnerable to ecosystem tipping points. Over the next two decades the Australian alpine region is predicted to experience temperature increases of at least 1 °C, coupled with a substantial decrease in snow cover. Extending the short instrumental record in these regions is imperative to put future change into context, and potentially provide analogues of warming. We reconstructed past temperatures, using a lipid biomarker palaeothermometer technique and mercury flux changes for the past 3500 years from the sediments of Club Lake, a high-altitude alpine tarn in the Snowy Mountains, southeastern Australia. Using a multi-proxy framework, including pollen and charcoal analyses, high-resolution geochemistry, and ancient microbial community composition, supported by high-resolution 210Pb and AMS 14C dating, we investigated local and regional ecological and environmental changes occurring in response to changes in temperature. We find the region experienced a general warming trend over the last 3500 years, with a pronounced climate anomaly occurring between 1000 and 1600 cal yrs. BP. Shifts in vegetation took place during this warm period, characterised by a decline in alpine species and an increase in open woodland taxa which co-occurred with an increase in regional fire activity. Given the narrow altitudinal band of Australian alpine vegetation, any future warming has the potential to result in the extinction of alpine species, including several endemic to the area, as treelines are driven to higher elevations. These findings suggest ongoing conservation efforts will be needed to protect the vulnerable alpine environments from the combined threats of climate changes, fire and invasive species.}, }
@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 {pmid34433944, year = {2021}, author = {Carlhoff, S and Duli, A and Nägele, K and Nur, M and Skov, L and Sumantri, I and Oktaviana, AA and Hakim, B and Burhan, B and Syahdar, FA and McGahan, DP and Bulbeck, D and Perston, YL and Newman, K and Saiful, AM and Ririmasse, M and Chia, S and Hasanuddin,  and Pulubuhu, DAT and Suryatman,  and Supriadi,  and Jeong, C and Peter, BM and Prüfer, K and Powell, A and Krause, J and Posth, C and Brumm, A}, title = {Genome of a middle Holocene hunter-gatherer from Wallacea.}, journal = {Nature}, volume = {596}, number = {7873}, pages = {543-547}, pmid = {34433944}, issn = {1476-4687}, mesh = {Asia, Southeastern ; Australia ; Bone and Bones/metabolism ; Caves ; DNA, Ancient/*analysis ; Female ; *Fossils ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/history ; Humans ; Indonesia/ethnology ; Islands/*ethnology ; New Guinea ; *Phylogeny ; }, abstract = {Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.}, }
@article {pmid34433011, year = {2021}, author = {Liu, S and Westbury, MV and Dussex, N and Mitchell, KJ and Sinding, MS and Heintzman, PD and Duchêne, DA and Kapp, JD and von Seth, J and Heiniger, H and Sánchez-Barreiro, F and Margaryan, A and André-Olsen, R and De Cahsan, B and Meng, G and Yang, C and Chen, L and van der Valk, T and Moodley, Y and Rookmaaker, K and Bruford, MW and Ryder, O and Steiner, C and Bruins-van Sonsbeek, LGR and Vartanyan, S and Guo, C and Cooper, A and Kosintsev, P and Kirillova, I and Lister, AM and Marques-Bonet, T and Gopalakrishnan, S and Dunn, RR and Lorenzen, ED and Shapiro, B and Zhang, G and Antoine, PO and Dalén, L and Gilbert, MTP}, title = {Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.}, journal = {Cell}, volume = {184}, number = {19}, pages = {4874-4885.e16}, doi = {10.1016/j.cell.2021.07.032}, pmid = {34433011}, issn = {1097-4172}, support = {681396/ERC_/European Research Council/International ; }, mesh = {Animals ; Demography ; *Evolution, Molecular ; Gene Flow ; Genetic Variation ; *Genome ; Geography ; Heterozygote ; Homozygote ; Host Specificity ; Markov Chains ; Mutation/genetics ; Perissodactyla/*genetics ; Phylogeny ; Species Specificity ; Time Factors ; }, abstract = {Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.}, }
@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, Š 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 {pmid34425243, year = {2021}, author = {Ma, P and Yang, X and Yan, S and Li, C and Gao, S and Han, B and Hou, K and Robbeets, M and Wei, LH and Cui, Y}, title = {Ancient Y-DNA with reconstructed phylogeny provides insights into the demographic history of paternal haplogroup N1a2-F1360.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {48}, number = {12}, pages = {1130-1133}, doi = {10.1016/j.jgg.2021.07.018}, pmid = {34425243}, issn = {1673-8527}, mesh = {Chromosomes, Human, Y ; *DNA, Ancient ; *Ethnicity ; Genetics, Population ; Haplotypes/genetics ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide ; }, }
@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 = {Biodiversity ; Formaldehyde ; *Metagenomics ; Phylogeny ; }, 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 = {*Genetics, Population ; }, 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 1st 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 8th-10th 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 {pmid34410492, year = {2021}, author = {Aneli, S and Caldon, M and Saupe, T and Montinaro, F and Pagani, L}, title = {Through 40,000 years of human presence in Southern Europe: the Italian case study.}, journal = {Human genetics}, volume = {140}, number = {10}, pages = {1417-1431}, pmid = {34410492}, issn = {1432-1203}, mesh = {DNA, Ancient/*analysis ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Human ; Genomics/*history ; History, Ancient ; History, Medieval ; Humans ; Italy ; Whites/*genetics/*history ; }, abstract = {The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.}, }
@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 {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 {pmid34357024, year = {2021}, author = {Onley, IR and Moseby, KE and Austin, JJ}, title = {Genomic Approaches for Conservation Management in Australia under Climate Change.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {34357024}, issn = {2075-1729}, support = {NA//Australian Government Research Training Program Scholarship/ ; 2019-07//Nature Foundation South Australia Grand Start Grant/ ; NA//Biological Society South Australia/Nature Conservation Society of South Australia Conservation Biology Grant/ ; NA//Field Naturalists Society of South Australia Lirabenda Endowment Fund Research Grant/ ; }, abstract = {Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.}, }
@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 = {Blacks/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 {pmid34349118, year = {2021}, author = {Maisano Delser, P and Jones, ER and Hovhannisyan, A and Cassidy, L and Pinhasi, R and Manica, A}, title = {A curated dataset of modern and ancient high-coverage shotgun human genomes.}, journal = {Scientific data}, volume = {8}, number = {1}, pages = {202}, pmid = {34349118}, issn = {2052-4463}, support = {649307//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 263441//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 647797//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; 647797//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; }, mesh = {Computational Biology ; DNA, Ancient ; *Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, DNA ; *Whole Genome Sequencing ; }, abstract = {Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10-18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.}, }
@article {pmid34343942, year = {2021}, author = {Rahmat, RA and Humphries, MA and Linacre, AMT and Malik, A and Saedon, NA and Austin, JJ}, title = {Freeze-drying improves DNA yield from teeth.}, journal = {Forensic science international}, volume = {326}, number = {}, pages = {110938}, doi = {10.1016/j.forsciint.2021.110938}, pmid = {34343942}, issn = {1872-6283}, abstract = {The common method of preparing teeth prior to DNA extraction involves cleaning, decontamination, drying and pulverisation. Moisture in post-mortem teeth can promote bacterial growth and hydrolytic damage that could contribute to DNA degradation, whilst also possibly reducing the efficiency of sample pulverisation and DNA release. Here we compared DNA extraction from pig teeth, with- and without freeze-drying, to examine the impact of removing moisture on DNA yield. Quantitative real-time polymerase chain reaction (qPCR) was used to quantify an 83 bp mitochondrial DNA fragment and two nuclear DNA fragments of 82 bp and 150 bp. The comparative results showed that sample preparation with freeze-drying resulted in a higher DNA yield without compromising the DNA quality. This study highlights the advantage of incorporating a freeze-drying to improve the DNA yield and minimising the loss of DNA during sample preparation of teeth.}, }
@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 ; Whites/*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 14th 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, Ł 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 ; Whites/*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 Złota, 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 Złota-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 Złota 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 (Złota, 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 Złota 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 {pmid34303876, year = {2021}, author = {Gerussi, A and Carbone, M and Corpechot, C and Schramm, C and Asselta, R and Invernizzi, P}, title = {The genetic architecture of primary biliary cholangitis.}, journal = {European journal of medical genetics}, volume = {64}, number = {9}, pages = {104292}, doi = {10.1016/j.ejmg.2021.104292}, pmid = {34303876}, issn = {1878-0849}, mesh = {Animals ; *Genetic Predisposition to Disease ; Humans ; Liver Cirrhosis, Biliary/*genetics/pathology ; Multifactorial Inheritance ; }, abstract = {Primary biliary cholangitis (PBC) is a rare autoimmune disease of the liver affecting the small bile ducts. From a genetic point of view, PBC is a complex trait and several genetic and environmental factors have been called in action to explain its etiopathogenesis. Similarly to other complex traits, PBC has benefited from the introduction of genome-wide association studies (GWAS), which identified many variants predisposing or protecting toward the development of the disease. While a progressive endeavour toward the characterization of candidate loci and downstream pathways is currently ongoing, there is still a relatively large portion of heritability of PBC to be revealed. In addition, genetic variation behind progression of the disease and therapeutic response are mostly to be investigated yet. This review outlines the state-of-the-art regarding the genetic architecture of PBC and provides some hints for future investigations, focusing on the study of gene-gene interactions, the application of whole-genome sequencing techniques, and the investigation of X chromosome that can be helpful to cover the missing heritability gap in PBC.}, }
@article {pmid34302465, year = {2021}, author = {Wang, W and Han, GZ}, title = {Ancient Adaptative Evolution of ACE2 in East Asians.}, journal = {Genome biology and evolution}, volume = {13}, number = {8}, pages = {}, doi = {10.1093/gbe/evab173}, pmid = {34302465}, issn = {1759-6653}, mesh = {Adaptation, Physiological ; Angiotensin-Converting Enzyme 2/*genetics ; Asians/*genetics ; DNA, Ancient ; *Evolution, Molecular ; Haplotypes ; Humans ; Selection, Genetic ; }, abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been posing an unprecedented challenge to global public health. SARS-CoV-2 and several other coronaviruses utilize angiotensin-converting enzyme 2 (ACE2) as their entry receptors. The ACE2 gene has been found to experience episodic positive selection across mammals. However, much remains unknown about how the ACE2 gene evolved in human populations. Here, we use population genetics approaches to investigate the evolution of the ACE2 gene in 26 human populations sampled globally. We find the ACE2 gene exhibits an extremely low nucleotide diversity in the East Asian populations. Strong signals of selective sweep are detected in the East Asian populations, but not in the other human populations. The selective sweep in ACE2 is estimated to begin in East Asian populations ∼23,600 years ago. Our study provides novel insights into the evolution of the ACE2 gene within human populations.}, }
@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 {pmid34202821, year = {2021}, author = {Purnomo, GA and Mitchell, KJ and O'Connor, S and Kealy, S and Taufik, L and Schiller, S and Rohrlach, A and Cooper, A and Llamas, B and Sudoyo, H and Teixeira, JC and Tobler, R}, title = {Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact.}, journal = {Genes}, volume = {12}, number = {7}, pages = {}, pmid = {34202821}, issn = {2073-4425}, mesh = {Animals ; Archaeology/history ; Asia ; Australia ; Coleoptera/genetics ; Female ; *Genetics, Population ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; History, Ancient ; Humans ; Male ; New Guinea ; Oceania ; *Phylogeny ; *Phylogeography ; }, abstract = {The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul-i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level-by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000-4000 years ago (3-4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.}, }
@article {pmid34202264, year = {2021}, author = {Baldoni, M and Nardi, A and De Angelis, F and Rickards, O and Martínez-Labarga, C}, title = {How Does Diet Influence Our Lives? Evaluating the Relationship between Isotopic Signatures and Mortality Patterns in Italian Roman Imperial and Medieval Periods.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {13}, pages = {}, pmid = {34202264}, issn = {1420-3049}, mesh = {Carbon Isotopes/analysis ; Diet/*history ; History, Ancient ; History, Medieval ; Humans ; Italy ; Mortality/*history ; Nitrogen Isotopes/analysis ; }, abstract = {The present research investigates the relationship between dietary habits and mortality patterns in the Roman Imperial and Medieval periods. The reconstructions of population dynamics and subsistence strategies provide a fascinating source of information for understanding our history. This is particularly true given that the changes in social, economic, political, and religious aspects related to the transition from the Roman period to the Middle Ages have been widely discussed. We analyzed the isotopic and mortality patterns of 616 individuals from 18 archeological sites (the Medieval Latium sites of Colonna, Santa Severa, Allumiere, Cencelle, and 14 Medieval and Imperial funerary contexts from Rome) to compile a survivorship analysis. A semi-parametric approach was applied, suggesting variations in mortality patterns between sexes in the Roman period. Nitrogen isotopic signatures influenced mortality in both periods, showing a quadratic and a linear effect for Roman Imperial and Medieval populations, respectively. No influence of carbon isotopic signatures has been detected for Roman Imperial populations. Conversely, increased mortality risk for rising carbon isotopic values was observed in Medieval samples.}, }
@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 = {Archaeology ; *Genomics ; History, Ancient ; *Human Migration ; Humans ; *Isotopes ; Turkey ; }, 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 = {*American Indians or Alaska Natives ; *Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Female ; Genetic Markers/genetics ; Genetic Variation/genetics ; Genetics, Population ; Haplotypes ; Humans ; Male ; }, 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 {pmid34181791, year = {2021}, author = {Sacks, BN and Mitchell, KJ and Quinn, CB and Hennelly, LM and Sinding, MS and Statham, MJ and Preckler-Quisquater, S and Fain, SR and Kistler, L and Vanderzwan, SL and Meachen, JA and Ostrander, EA and Frantz, LAF}, title = {Pleistocene origins, western ghost lineages, and the emerging phylogeographic history of the red wolf and coyote.}, journal = {Molecular ecology}, volume = {30}, number = {17}, pages = {4292-4304}, doi = {10.1111/mec.16048}, pmid = {34181791}, issn = {1365-294X}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Coyotes/genetics ; Ecosystem ; Hybridization, Genetic ; Phylogeography ; *Wolves/genetics ; }, abstract = {The red wolf (Canis rufus) of the eastern US was driven to near-extinction by colonial-era persecution and habitat conversion, which facilitated coyote (C. latrans) range expansion and widespread hybridization with red wolves. The observation of some grey wolf (C. lupus) ancestry within red wolves sparked controversy over whether it was historically a subspecies of grey wolf with its predominant "coyote-like" ancestry obtained from post-colonial coyote hybridization (2-species hypothesis) versus a distinct species closely related to the coyote that hybridized with grey wolf (3-species hypothesis). We analysed mitogenomes sourced from before the 20th century bottleneck and coyote invasion, along with hundreds of modern amplicons, which led us to reject the 2-species model and to investigate a broader phylogeographic 3-species model suggested by the fossil record. Our findings broadly support this model, in which red wolves ranged the width of the American continent prior to arrival of the grey wolf to the mid-continent 60-80 ka; red wolves subsequently disappeared from the mid-continent, relegated to California and the eastern forests, which ushered in emergence of the coyote in their place (50-30 ka); by the early Holocene (12-10 ka), coyotes had expanded into California, where they admixed with and phenotypically replaced western red wolves in a process analogous to the 20th century coyote invasion of the eastern forests. Findings indicate that the red wolf pre-dated not only European colonization but human, and possibly coyote, presence in North America. These findings highlight the urgency of expanding conservation efforts for the red wolf.}, }
@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 ; Far East ; *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 {pmid34171302, year = {2021}, author = {Souilmi, Y and Lauterbur, ME and Tobler, R and Huber, CD and Johar, AS and Moradi, SV and Johnston, WA and Krogan, NJ and Alexandrov, K and Enard, D}, title = {An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.}, journal = {Current biology : CB}, volume = {31}, number = {16}, pages = {3504-3514.e9}, doi = {10.1016/j.cub.2021.05.067}, pmid = {34171302}, issn = {1879-0445}, support = {R01 AI120694/AI/NIAID NIH HHS/United States ; U19 AI135990/AI/NIAID NIH HHS/United States ; R01 AI122747/AI/NIAID NIH HHS/United States ; U19 AI135972/AI/NIAID NIH HHS/United States ; P01 AI063302/AI/NIAID NIH HHS/United States ; P50 AI150476/AI/NIAID NIH HHS/United States ; R01 AI143292/AI/NIAID NIH HHS/United States ; }, mesh = {Coronavirus/*genetics ; Coronavirus Infections/*history/virology ; Datasets as Topic ; Evolution, Molecular ; Far East/epidemiology ; Gene Frequency ; Genetic Predisposition to Disease ; Genome, Human/*genetics ; Genome, Viral/genetics ; Genome-Wide Association Study ; History, Ancient ; Host Microbial Interactions/*genetics ; Human Genome Project ; Humans ; Mutation ; Pandemics/*history ; Phylogeny ; Selection, Genetic ; }, abstract = {The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors-pointing to which viruses have future pandemic potential. Here, we apply evolutionary analyses to human genomic datasets to recover selection events involving tens of human genes that interact with coronaviruses, including SARS-CoV-2, that likely started more than 20,000 years ago. These adaptive events were limited to the population ancestral to East Asian populations. Multiple lines of functional evidence support an ancient viral selective pressure, and East Asia is the geographical origin of several modern coronavirus epidemics. An arms race with an ancient coronavirus, or with a different virus that happened to use similar interactions as coronaviruses with human hosts, may thus have taken place in ancestral East Asian populations. By learning more about our ancient viral foes, our study highlights the promise of evolutionary information to better predict the pandemics of the future. Importantly, adaptation to ancient viral epidemics in specific human populations does not necessarily imply any difference in genetic susceptibility between different human populations, and the current evidence points toward an overwhelming impact of socioeconomic factors in the case of coronavirus disease 2019 (COVID-19).}, }
@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 {pmid34163072, year = {2021}, author = {Zavala, EI and Jacobs, Z and Vernot, B and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Essel, E and de Fillipo, C and Nagel, S and Richter, J and Romagné, F and Schmidt, A and Li, B and O'Gorman, K and Slon, V and Kelso, J and Pääbo, S and Roberts, RG and Meyer, M}, title = {Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave.}, journal = {Nature}, volume = {595}, number = {7867}, pages = {399-403}, pmid = {34163072}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaeology ; *Caves ; DNA, Ancient/*analysis ; DNA, Mitochondrial/analysis/genetics ; Fossils ; Geologic Sediments/*chemistry ; History, Ancient ; Hominidae/*genetics ; Neanderthals/genetics ; Siberia ; }, abstract = {Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1-4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8-11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly-possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.}, }
@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 lived3 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 {pmid34140364, year = {2021}, author = {Gibbons, A}, title = {Genomes offer rare glimpse of Neanderthal family groups.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6548}, pages = {1251-1252}, doi = {10.1126/science.372.6548.1251}, pmid = {34140364}, issn = {1095-9203}, mesh = {Animals ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Family ; Female ; *Genome ; Male ; Neanderthals/*genetics ; Sociological Factors ; Y Chromosome ; }, }
@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 {pmid34135357, year = {2021}, author = {Lentz, DL and Hamilton, TL and Dunning, NP and Tepe, EJ and Scarborough, VL and Meyers, SA and Grazioso, L and Weiss, AA}, title = {Environmental DNA reveals arboreal cityscapes at the Ancient Maya Center of Tikal.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12725}, pmid = {34135357}, issn = {2045-2322}, mesh = {Archaeology ; Cities/history ; DNA, Ancient/*analysis ; DNA, Environmental/*analysis ; DNA, Plant/*analysis ; Forests ; Geologic Sediments/chemistry ; Guatemala ; History, Ancient ; *Plants ; *Trees ; Water Supply/*history ; }, abstract = {Tikal, a major city of the ancient Maya world, has been the focus of archaeological research for over a century, yet the interactions between the Maya and the surrounding Neotropical forests remain largely enigmatic. This study aimed to help fill that void by using a powerful new technology, environmental DNA analysis, that enabled us to characterize the site core vegetation growing in association with the artificial reservoirs that provided the city water supply. Because the area has no permanent water sources, such as lakes or rivers, these reservoirs were key to the survival of the city, especially during the population expansion of the Classic period (250-850 CE). In the absence of specific evidence, the nature of the vegetation surrounding the reservoirs has been the subject of scientific hypotheses and artistic renderings for decades. To address these hypotheses we captured homologous sequences of vascular plant DNA extracted from reservoir sediments by using a targeted enrichment approach involving 120-bp genetic probes. Our samples encompassed the time before, during and after the occupation of Tikal (1000 BCE-900 CE). Results indicate that the banks of the ancient reservoirs were primarily fringed with native tropical forest vegetation rather than domesticated species during the Maya occupation.}, }
@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 ; }, }
@article {pmid34122501, year = {2021}, author = {Del Corvo, M and Lazzari, B and Capra, E and Zavarez, L and Milanesi, M and Utsunomiya, YT and Utsunomiya, ATH and Stella, A and de Paula Nogueira, G and Garcia, JF and Ajmone-Marsan, P}, title = {Methylome Patterns of Cattle Adaptation to Heat Stress.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {633132}, pmid = {34122501}, issn = {1664-8021}, abstract = {Heat stress has a detrimental impact on cattle health, welfare and productivity by affecting gene expression, metabolism and immune response, but little is known on the epigenetic mechanisms mediating the effect of temperature at the cellular and organism level. In this study, we investigated genome-wide DNA methylation in blood samples collected from 5 bulls of the heat stress resilient Nellore breed and 5 bulls of the Angus that are more heat stress susceptible, exposed to the sun and high temperature-high humidity during the summer season of the Brazilian South-East region. The methylomes were analyzed during and after the exposure by Reduced Representation Bisulfite Sequencing, which provided genome-wide single-base resolution methylation profiles. Significant methylation changes between stressful and recovery periods were observed in 819 genes. Among these, 351 were only seen in Angus, 366 were specific to Nellore, and 102 showed significant changes in methylation patterns in both breeds. KEGG and Gene Ontology (GO) enrichment analyses showed that responses were breed-specific. Interestingly, in Nellore significant genes and pathways were mainly involved in stress responses and cellular defense and were under methylated during heat stress, whereas in Angus the response was less focused. These preliminary results suggest that heat challenge induces changes in methylation patterns in specific loci, which should be further scrutinized to assess their role in heat tolerance.}, }
@article {pmid34113375, year = {2021}, author = {Fareed, M and Sharma, V and Singh, I and Rehman, SU and Singh, G and Afzal, M}, title = {Whole-Exome Sequencing Reveals a Rare Variant of OTOF Gene Causing Congenital Non-syndromic Hearing Loss Among Large Muslim Families Favoring Consanguinity.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {641925}, pmid = {34113375}, issn = {1664-8021}, abstract = {Non-syndromic hearing loss (NSHL) is one of the most frequent auditory deficits in humans characterized by high clinical and genetic heterogeneity. Very few studies have reported the relationship between OTOF (Locus: DFNB9) and hereditary hearing loss in India. We aimed to decipher the genetic cause of prelingual NSHL in a large affected Muslim consanguineous families using whole-exome sequencing (WES). The study was performed following the guidelines and regulations of the Indian Council of Medical Research (ICMR), New Delhi. The population was identified from Jammu and Kashmir, the Northernmost part of India. Near about 100 individuals were born deaf-mute in the village of 3,000 inhabitants. A total of 103 individuals (with 52 cases and 51 controls) agreed to participate in this study. Our study revealed a rare non-sense homozygous mutation NC_000002.11:g.2:26702224G>A; NM_001287489.2:c.2122C>T; NP_001274418.1:p.(Arg708∗) in the 18th exon of the OTOF gene. Our study provides the first insight into this homozygous condition, which has not been previously reported in ExAC, 1,000 Genome and genomAD databases. Furthermore, the variant was confirmed in the population cohort (n = 103) using Sanger sequencing. In addition to the pathogenic OTOF variant, the WES data also revealed novel and recurrent mutations in CDH23, GJB2, MYO15A, OTOG, and SLC26A4 genes. The rare pathogenic and the novel variants observed in this study have been submitted to the ClinVar database and are publicly available online with the accessions SCV001448680.1, SCV001448682.1 and SCV001448681.1. We conclude that OTOF-related NSHL hearing loss is prevalent in the region due to successive inbreeding in its generations. We recommend premarital genetic testing and genetic counseling strategies to minimize and control the disease risk in future generations.}, }
@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 {pmid34095864, year = {2021}, author = {Zhou, Y and Browning, SR}, title = {Protocol for detecting introgressed archaic variants with SPrime.}, journal = {STAR protocols}, volume = {2}, number = {2}, pages = {100550}, pmid = {34095864}, issn = {2666-1667}, support = {R01 HG010869/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient/analysis ; Genetic Introgression/*genetics ; Genomics/*methods ; Hominidae/genetics ; Humans ; Neanderthals/*genetics ; }, abstract = {The SPrime program detects the variants in current-day populations that were introgressed from an archaic source in the past. It is optimized for detecting introgression from Neanderthals and Denisovans in modern humans. We provide a protocol for detecting Neanderthal and Denisovan introgression in 1000 Genomes Project data, specifically focusing on the CHB (Han Chinese in Beijing) population. For complete details on the use and execution of this protocol, please refer to Browning et al. (2018).}, }
@article {pmid34084657, year = {2021}, author = {Redjala, O and Sari-Ahmed, M and Cherifi, M and Smati, L and Benhassine, F and Baghriche, M and Chibane, A and Lopez-Sublet, M and Monsuez, JJ and Benkhedda, S}, title = {Children hypertension in Northern Africa.}, journal = {American journal of cardiovascular disease}, volume = {11}, number = {2}, pages = {222-230}, pmid = {34084657}, issn = {2160-200X}, abstract = {OBJECTIVES: To assess factors associated with prehypertension and hypertension among children in North Africa.<br><br>METHODS: An epidemiological observational, school- and college-based study among 3562 healthy children and adolescents to assess factors associated with blood pressure categories (normal, prehypertensive, hypertensive), including perinatal (gestational age, birth weight, breastfeeding) and current lifestyle characteristics (body mass index, time spent watching a screen and time spent exercising).<br><br>RESULTS: Prevalence of hypertension increased with age from 8.7% between 6-10 years to 14.7% between 11-15 years, and 15.6% above 15 years. Prevalence of prehypertension and hypertension increased with body mass index from 9.9% and 11.5% among children not overweight to 15.6% (RR 1.58, 95% CI 1.24-2.02, P<0.001) and 17.2% (RR 1.50, 95% CI 1.22-1.85, P<0.001) among those overweight and to 26.8% (RR 2.72, 95% CI 2.04-3.64, P<0.01) and 32.3% (RR 2.82, 95% CI 2.27-3.50, P<0.01) among obese children. There was a trend of association of prehypertension with the time spent watching Television, internet and electronic games. Children whose mother or father had a history of hypertension had a trend to be prehypertensive or hypertensive. A parental hypertension was found in 33.6% of normotensive, 38.2% of prehypertensive, and 42.6% of hypertensive children (P=0.05). Children with prehypertension or hypertension were more likely to have a diabetic father or mother (22.8% and 22.6% vs 15.8%, respectively, P=0.01). Also, prehypertension and hypertension were associated with shorter gestational age, early birth, reduced birth weight, and shorter breastfeeding.<br><br>CONCLUSION: Prehypertension and hypertension have a high prevalence among children in North Africa. They are associated with overweight, obesity, diabetes, a shorter gestational age, a lower birth weight and a shorter breastfeeding.}, }
@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//Vetenskapsrådet/ ; 2019-05191//Vetenskapsrådet/ ; FFL15-0196//Stiftelsen för 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 > 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 {pmid34078254, year = {2021}, author = {Senczuk, G and Mastrangelo, S and Ajmone-Marsan, P and Becskei, Z and Colangelo, P and Colli, L and Ferretti, L and Karsli, T and Lancioni, H and Lasagna, E and Marletta, D and Persichilli, C and Portolano, B and Sarti, FM and Ciani, E and Pilla, F}, title = {On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data.}, journal = {Genetics, selection, evolution : GSE}, volume = {53}, number = {1}, pages = {48}, pmid = {34078254}, issn = {1297-9686}, mesh = {Animal Distribution ; Animals ; Bayes Theorem ; Cattle/*genetics ; Evolution, Molecular ; Gene Frequency ; *Models, Genetic ; *Polymorphism, Single Nucleotide ; *Selective Breeding ; }, abstract = {BACKGROUND: During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach.<br><br>RESULTS: Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools.<br><br>CONCLUSIONS: This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.}, }
@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 ; Far East ; 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 {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.<br><br>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 ; Asians/classification/ethnology/genetics ; China/ethnology ; Chromosomes, Human, Y/*genetics ; Civilization/*history ; Ethnicity/classification/genetics/*history ; Far East/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//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; #2017/2616-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; #2018/15425-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 351649567//Deutsche Forschungsgemeinschaft/ ; 431589/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 306623/2018-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, 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 {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 {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 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}, doi = {10.1016/j.coi.2021.04.006}, 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 {pmid33986160, year = {2021}, author = {Curry, A}, title = {Ancient poop reveals extinction in gut bacteria.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6543}, pages = {671}, doi = {10.1126/science.372.6543.671}, pmid = {33986160}, issn = {1095-9203}, mesh = {*Bacteria/classification/genetics ; *DNA, Ancient ; *DNA, Bacterial ; Diet ; Extinction, Biological ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Mexico ; Utah ; }, }
@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 {pmid33945536, year = {2021}, author = {Nerlich, AG and Kirchhoff, SM and Panzer, S and Lehn, C and Bachmeier, BE and Bayer, B and Anslinger, K and Röcker, P and Peschel, OK}, title = {Chronic active non-lethal human-type tuberculosis in a high royal Bavarian officer of Napoleonic times-a mummy study.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0249955}, pmid = {33945536}, issn = {1932-6203}, mesh = {DNA, Ancient/chemistry ; Humans ; Male ; Mummies/diagnostic imaging/microbiology/*pathology ; Spine/diagnostic imaging/pathology ; Tomography, X-Ray Computed ; Tuberculosis/diagnostic imaging/microbiology/*pathology ; }, abstract = {In paleopathology, morphological and molecular evidence for infection by mycobacteria of the M. tuberculosis complex (MTC) is frequently associated with early death. In the present report, we describe a multidisciplinary study of a well-preserved mummy from Napoleonic times with a long-standing tuberculous infection by M. tuberculosis senso stricto who died at the age of 88 years of focal and non-MTB related bronchopneumonia. The well-preserved natural mummy of the Royal Bavarian General, Count Heinrich LII Reuss-Köstritz (1763-1851 CE), was extensively investigated by macro- and histomorphology, whole body CT scans and organ radiography, various molecular tissue analyses, including stable isotope analysis and molecular genetic tests. We identified signs for a long-standing, but terminally inactive pulmonary tuberculosis, tuberculous destruction of the second lumbar vertebral body, and a large tuberculous abscess in the right (retroperitoneal) psoas region (a cold abscess). This cold abscess harboured an active tuberculous infection as evidenced by histological and molecular tests. Radiological and histological analysis further revealed extensive arteriosclerosis with (non-obliterating) coronary and significant carotid arteriosclerosis, healthy bone tissue without evidence of age-related osteopenia, evidence for diffuse idiopathic skeletal hyperostosis and mild osteoarthrosis of few joints. This suggests excellent living conditions correlating well with his diet indicated by stable isotope results and literary evidence. Despite the clear evidence of a tuberculous cold abscess with bacterioscopic and molecular proof for a persisting MTC infection of a human-type M. tuberculosis strain, we can exclude the chronic MTC infection as cause of death. The detection of MTC in historic individuals should therefore be interpreted with great caution and include further data, such as their nutritional status.}, }
@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 {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 = {}, number = {}, pages = {}, 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>AVAILABILITY: 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 resilience1 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 species6-8 and communities9-18 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 {pmid33878301, year = {2021}, author = {Pedersen, MW and De Sanctis, B and Saremi, NF and Sikora, M and Puckett, EE and Gu, Z and Moon, KL and Kapp, JD and Vinner, L and Vardanyan, Z and Ardelean, CF and Arroyo-Cabrales, J and Cahill, JA and Heintzman, PD and Zazula, G and MacPhee, RDE and Shapiro, B and Durbin, R and Willerslev, E}, title = {Environmental genomics of Late Pleistocene black bears and giant short-faced bears.}, journal = {Current biology : CB}, volume = {31}, number = {12}, pages = {2728-2736.e8}, doi = {10.1016/j.cub.2021.04.027}, pmid = {33878301}, issn = {1879-0445}, support = {WT220023/WT_/Wellcome Trust/United Kingdom ; WT207492/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial ; Fossils ; Humans ; Metagenomics ; Phylogeny ; *Ursidae/genetics ; }, abstract = {Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.}, }
@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 {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 {pmid33856032, year = {2021}, author = {García, A and Nores, R and Motti, JMB and Pauro, M and Luisi, P and Bravi, CM and Fabra, M and Gosling, AL and Kardailsky, O and Boocock, J and Solé-Morata, N and Matisoo-Smith, EA and Comas, D and Demarchi, DA}, title = {Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America.}, journal = {Human molecular genetics}, volume = {30}, number = {13}, pages = {1200-1217}, doi = {10.1093/hmg/ddab105}, pmid = {33856032}, issn = {1460-2083}, mesh = {Argentina ; DNA, Ancient/analysis ; DNA, Mitochondrial/analysis/classification/*genetics ; *Genetic Variation ; *Genetics, Population ; Genome, Mitochondrial/*genetics ; Geography ; Haplotypes ; *Human Migration ; Humans ; Phylogeny ; Sequence Analysis, DNA ; South America ; Time Factors ; }, abstract = {The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.}, }
@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 {pmid33833103, year = {2021}, author = {Gibbons, A}, title = {When modern humans met Neanderthals.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6538}, pages = {115-116}, doi = {10.1126/science.372.6538.115}, pmid = {33833103}, issn = {1095-9203}, mesh = {Animals ; Bulgaria ; Czech Republic ; *DNA, Ancient ; Female ; Genetics, Population ; *Genome, Human ; Hominidae/*genetics ; Humans ; Male ; Neanderthals/*genetics ; Sexual Behavior ; Sexual Behavior, Animal ; }, }
@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 {pmid33828320, year = {2021}, author = {Hajdinjak, M and Mafessoni, F and Skov, L and Vernot, B and Hübner, A and Fu, Q and Essel, E and Nagel, S and Nickel, B and Richter, J and Moldovan, OT and Constantin, S and Endarova, E and Zahariev, N and Spasov, R and Welker, F and Smith, GM and Sinet-Mathiot, V and Paskulin, L and Fewlass, H and Talamo, S and Rezek, Z and Sirakova, S and Sirakov, N and McPherron, SP and Tsanova, T and Hublin, JJ and Peter, BM and Meyer, M and Skoglund, P and Kelso, J and Pääbo, S}, title = {Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry.}, journal = {Nature}, volume = {592}, number = {7853}, pages = {253-257}, pmid = {33828320}, issn = {1476-4687}, support = {852558/ERC_/European Research Council/International ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595//Wellcome Trust/United Kingdom ; 694707/ERC_/European Research Council/International ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Alleles ; Americas/ethnology ; Animals ; Archaeology ; Bulgaria/ethnology ; Caves ; DNA, Ancient/*analysis ; Far East/ethnology ; Female ; Genome, Human/*genetics ; History, Ancient ; Humans ; Male ; Neanderthals/*genetics ; Phylogeny ; }, abstract = {Modern humans appeared in Europe by at least 45,000 years ago1-5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.}, }
@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 {pmid33808521, year = {2021}, author = {Gînguță, A and Rusu, I and Mircea, C and Ioniță, A and Banciu, HL and Kelemen, B}, title = {Mitochondrial DNA Profiles of Individuals from a 12th Century Necropolis in Feldioara (Transylvania).}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33808521}, issn = {2073-4425}, mesh = {Asia/ethnology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics/*history ; Genetics, Population ; History, Medieval ; Humans ; Mitochondria/*genetics ; Phylogeny ; Population Dynamics ; Romania/ethnology ; Whites/*genetics ; }, abstract = {The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such minute genetic cycle in a sea of genetic interactions by reconstructing part of the genetic story of the migration, settlement, interaction, and legacy of what is today the Transylvanian Saxon. The analysis of the mitochondrial DNA control region of 13 medieval individuals from Feldioara necropolis (Transylvania region, Romania) reveals a genetically heterogeneous group where all identified haplotypes are different. Most of the perceived maternal lineages are of Western Eurasian origin, except for the Central Asiatic haplogroup C seen in only one sample. Comparisons with historical and modern populations describe the contribution of the investigated Saxon settlers to the genetic history of this part of Europe.}, }
@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 {pmid33802878, year = {2021}, author = {Wang, X and Vlok, M and Flibotte, S and Jan, E}, title = {Resurrection of a Viral Internal Ribosome Entry Site from a 700 Year Old Ancient Northwest Territories Cripavirus.}, journal = {Viruses}, volume = {13}, number = {3}, pages = {}, pmid = {33802878}, issn = {1999-4915}, support = {PJT-148761//CIHR/Canada ; }, mesh = {Animals ; DNA, Ancient ; DNA, Intergenic/metabolism ; *Dicistroviridae/genetics/physiology ; Feces/virology ; *Internal Ribosome Entry Sites ; Northwest Territories ; Reindeer/*virology ; Ribosomes/metabolism ; }, abstract = {The dicistrovirus intergenic region internal ribosome entry site (IGR IRES) uses an unprecedented, streamlined mechanism whereby the IRES adopts a triple-pseudoknot (PK) structure to directly bind to the conserved core of the ribosome and drive translation from a non-AUG codon. The origin of this IRES mechanism is not known. Previously, a partial fragment of a divergent dicistrovirus RNA genome, named ancient Northwest territories cripavirus (aNCV), was extracted from 700-year-old caribou feces trapped in a subarctic ice patch. The aNCV IGR sequence adopts a secondary structure similar to contemporary IGR IRES structures, however, there are subtle differences including 105 nucleotides upstream of the IRES of unknown function. Using filter binding assays, we showed that the aNCV IRES could bind to purified ribosomes, and toeprinting analysis pinpointed the start site at a GCU alanine codon adjacent to PKI. Using a bicistronic reporter RNA, the aNCV IGR can direct translation in vitro in a PKI-dependent manner. Lastly, a chimeric infectious clone swapping in the aNCV IRES supported translation and virus infection. The characterization and resurrection of a functional IGR IRES from a divergent 700-year-old virus provides a historical framework for the importance of this viral translational mechanism.}, }
@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 {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, É 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 {pmid33769498, year = {2021}, author = {Sjödin, P and McKenna, J and Jakobsson, M}, title = {Estimating divergence times from DNA sequences.}, journal = {Genetics}, volume = {217}, number = {4}, pages = {}, pmid = {33769498}, issn = {1943-2631}, mesh = {Animals ; DNA, Ancient ; Genetic Drift ; Humans ; *Mutation Rate ; Neanderthals/genetics ; *Polymorphism, Genetic ; Population/*genetics ; Time ; }, abstract = {The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the "Two-Two (TT)" and the "Two-Two-outgroup (TTo)" methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.}, }
@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 {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 {pmid33753899, year = {2021}, author = {Teixeira, JC and Jacobs, GS and Stringer, C and Tuke, J and Hudjashov, G and Purnomo, GA and Sudoyo, H and Cox, MP and Tobler, R and Turney, CSM and Cooper, A and Helgen, KM}, title = {Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {5}, pages = {616-624}, pmid = {33753899}, issn = {2397-334X}, mesh = {Animals ; Asia, Southeastern ; Fossils ; *Hominidae/genetics ; Humans ; Islands ; *Neanderthals ; }, abstract = {The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.}, }
@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 = {}, doi = {10.1128/ecosalplus.ESP-0027-2020}, 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 Científico, Tecnológico y de Innovación Tecnológica/ ; 1020316//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; 1130917//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 1140785//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, 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., Sci Adv (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 {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 approach2 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 lakes3 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, Ž 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 {pmid33668883, year = {2021}, author = {Lanubile, A and Borrelli, VMG and Soccio, M and Giorni, P and Stagnati, L and Busconi, M and Marocco, A}, title = {Loss of ZmLIPOXYGENASE4 Decreases Fusarium verticillioides Resistance in Maize Seedlings.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33668883}, issn = {2073-4425}, mesh = {*Disease Resistance ; Fusarium/pathogenicity ; Gene Expression Regulation, Plant ; Lipoxygenases/*genetics ; Mutagenesis, Insertional ; Phenotype ; Plant Proteins/genetics ; Seedlings/genetics/microbiology ; Sequence Analysis, RNA ; Zea mays/*genetics/microbiology ; }, abstract = {Fusarium verticillioides is one of the most relevant fungal species in maize responsible for ear, stalk and seedling rot, as well as the fumonisin contamination of kernels. Plant lipoxygenases (LOX) synthesize oxylipins that play a crucial role in the regulation of defense mechanisms against pathogens and influence the outcome of pathogenesis. To better uncover the role of these signaling molecules in maize resistance against F. verticillioides, the functional characterization of the 9-LOX gene, ZmLOX4, was carried out in this study by employing mutants carrying Mu insertions in this gene (named as UFMulox4). In this regard, the genotyping of five UFMulox4 identified the mutant UFMu10924 as the only one having an insertion in the coding region of the gene. The impact of ZmLOX4 mutagenesis on kernel defense against F. verticillioides and fumonisin accumulation were investigated, resulting in an increased fungal susceptibility compared to the inbred lines W22 and Tzi18. Moreover, the expression of most of the genes involved in the LOX, jasmonic acid (JA) and green leaf volatiles (GLV) pathways, as well as LOX enzymatic activity, decreased or were unaffected by fungal inoculation in the mutant UFMu10924. These results confirm the strategic role of ZmLOX4 in controlling defense against F. verticillioides and its influence on the expression of several LOX, JA and GLV genes.}, }
@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 {pmid33658608, year = {2021}, author = {Cabrera, VM}, title = {Human molecular evolutionary rate, time dependency and transient polymorphism effects viewed through ancient and modern mitochondrial DNA genomes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5036}, pmid = {33658608}, issn = {2045-2322}, mesh = {DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics/history ; *Evolution, Molecular ; Genetics, Population/*history ; *Genome, Mitochondrial ; Haplotypes ; History, 21st Century ; History, Ancient ; Humans ; Mitochondria/genetics ; *Mutation Rate ; Population Density ; Time Factors ; }, abstract = {Human evolutionary genetics gives a chronological framework to interpret the human history. It is based on the molecular clock hypothesis that suppose a straightforward relationship between the mutation rate and the substitution rate with independence of other factors as demography dynamics. Analyzing ancient and modern human complete mitochondrial genomes we show here that, along the time, the substitution rate can be significantly slower or faster than the average germline mutation rate confirming a time dependence effect mainly attributable to changes in the effective population size of the human populations, with an exponential growth in recent times. We also detect that transient polymorphisms play a slowdown role in the evolutionary rate deduced from haplogroup intraspecific trees. Finally, we propose the use of the most divergent lineages within haplogroups as a practical approach to correct these molecular clock mismatches.}, }
@article {pmid33655354, year = {2021}, author = {Rahmat, RA and Humphries, MA and Austin, JJ and Linacre, AMT and Self, P}, title = {The development of a tool to predict temperature-exposure of incinerated teeth using colourimetric and hydroxyapatite crystal size data.}, journal = {International journal of legal medicine}, volume = {135}, number = {5}, pages = {2045-2053}, pmid = {33655354}, issn = {1437-1596}, mesh = {Animals ; Burns/*physiopathology ; Colorimetry ; Crystallization ; Durapatite/*analysis ; Fires ; *Hot Temperature ; Models, Animal ; Models, Statistical ; Sus scrofa ; Tooth/*chemistry/*physiopathology ; Tooth Discoloration/*physiopathology ; }, abstract = {This study presents a novel tool to predict temperature-exposure of incinerated pig teeth as a proxy for understanding impacts of fire on human teeth. Previous studies on the estimation of temperature-exposure of skeletal elements have been limited to that of heat-exposed bone. This predictive tool was developed using a multinomial regression model of colourimetric and hydroxyapatite crystal size variables using data obtained from unheated pig teeth and teeth incinerated at 300 °C, 600 °C, 800 °C and 1000 °C. An additional variable based on the observed appearance of the tooth was included in the tool. This enables the tooth to be classified as definitely burnt (600 °C-1000 °C) or uncertain (27 °C/300 °C). As a result, the model predicting the temperature-exposure of the incinerated teeth had an accuracy of 95%. This tool is a holistic, robust and reliable approach to estimate temperature of heat-exposed pig teeth, with high accuracy, and may act as a valuable proxy to estimate heat exposure for human teeth in forensic casework.}, }
@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 = {Asians/*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 = {Asians/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 {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 people1,2. 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 {pmid33602851, year = {2021}, author = {Cooper, A and Turney, CSM and Palmer, J and Hogg, A and McGlone, M and Wilmshurst, J and Lorrey, AM and Heaton, TJ and Russell, JM and McCracken, K and Anet, JG and Rozanov, E and Friedel, M and Suter, I and Peter, T and Muscheler, R and Adolphi, F and Dosseto, A and Faith, JT and Fenwick, P and Fogwill, CJ and Hughen, K and Lipson, M and Liu, J and Nowaczyk, N and Rainsley, E and Bronk Ramsey, C and Sebastianelli, P and Souilmi, Y and Stevenson, J and Thomas, Z and Tobler, R and Zech, R}, title = {A global environmental crisis 42,000 years ago.}, journal = {Science (New York, N.Y.)}, volume = {371}, number = {6531}, pages = {811-818}, doi = {10.1126/science.abb8677}, pmid = {33602851}, issn = {1095-9203}, abstract = {Geological archives record multiple reversals of Earth's magnetic poles, but the global impacts of these events, if any, remain unclear. Uncertain radiocarbon calibration has limited investigation of the potential effects of the last major magnetic inversion, known as the Laschamps Excursion [41 to 42 thousand years ago (ka)]. We use ancient New Zealand kauri trees (Agathis australis) to develop a detailed record of atmospheric radiocarbon levels across the Laschamps Excursion. We precisely characterize the geomagnetic reversal and perform global chemistry-climate modeling and detailed radiocarbon dating of paleoenvironmental records to investigate impacts. We find that geomagnetic field minima ~42 ka, in combination with Grand Solar Minima, caused substantial changes in atmospheric ozone concentration and circulation, driving synchronous global climate shifts that caused major environmental changes, extinction events, and transformations in the archaeological record.}, }
@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 {pmid33597750, year = {2021}, author = {van der Valk, T and Pečnerová, P and Díez-Del-Molino, D and Bergström, A and Oppenheimer, J and Hartmann, S and Xenikoudakis, G and Thomas, JA and Dehasque, M and Sağlıcan, E and Fidan, FR and Barnes, I and Liu, S and Somel, M and Heintzman, PD and Nikolskiy, P and Shapiro, B and Skoglund, P and Hofreiter, M and Lister, AM and Götherström, A and Dalén, L}, title = {Million-year-old DNA sheds light on the genomic history of mammoths.}, journal = {Nature}, volume = {591}, number = {7849}, pages = {265-269}, pmid = {33597750}, issn = {1476-4687}, support = {852558/ERC_/European Research Council/International ; T32 HG008345/HG/NHGRI NIH HHS/United States ; 310763/ERC_/European Research Council/International ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595//Wellcome Trust/United Kingdom ; //Wellcome Trust/United Kingdom ; FC001595//Arthritis Research UK/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Acclimatization/genetics ; Alleles ; Animals ; Bayes Theorem ; DNA, Ancient/*analysis/isolation &amp; purification ; Elephants/genetics ; Europe ; *Evolution, Molecular ; Female ; Fossils ; Genetic Variation/genetics ; Genome, Mitochondrial/*genetics ; *Genomics ; Mammoths/*genetics ; Markov Chains ; Molar ; North America ; *Phylogeny ; Radiometric Dating ; Siberia ; Time Factors ; }, abstract = {Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.}, }
@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/ ; //Secretaría Nacional de Ciencia y Tecnología e Innovación/ ; 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 {pmid33585897, year = {2021}, author = {Lan, D and Tobler, R and Souilmi, Y and Llamas, B}, title = {Genozip - A Universal Extensible Genomic Data Compressor.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, pmid = {33585897}, issn = {1367-4811}, abstract = {We present Genozip, a universal and fully featured compression software for genomic data. Genozip is designed to be a general-purpose software and a development framework for genomic compression by providing five core capabilities - universality (support for all common genomic file formats), high compression ratios, speed, feature-richness, and extensibility. Genozip delivers high-performance compression for widely-used genomic data formats in genomics research, namely FASTQ, SAM/BAM/CRAM, VCF, GVF, FASTA, PHYLIP, and 23andMe formats. Our test results show that Genozip is fast and achieves greatly improved compression ratios, even when the files are already compressed. Further, Genozip is architected with a separation of the Genozip Framework from file-format-specific Segmenters and data-type-specific Codecs. With this, we intend for Genozip to be a general-purpose compression platform where researchers can implement compression for additional file formats, as well as new codecs for data types or fields within files, in the future. We anticipate that this will ultimately increase the visibility and adoption of these algorithms by the user community, thereby accelerating further innovation in this space. Availability: Genozip is written in C. The code is open-source and available on GitHub (https://github.com/divonlan/genozip). The package is free for non-commercial use. It is distributed as a Docker container on DockerHub and through the conda package manager. Genozip is tested on Linux, Mac, and Windows. Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid33579752, year = {2021}, author = {Harney, É 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, Á 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 {pmid33574393, year = {2021}, author = {Porru, E and Giorgi, E and Turroni, S and Helg, R and Silani, M and Candela, M and Fiori, J and Roda, A}, title = {Bile acids and oxo-metabolites as markers of human faecal input in the ancient Pompeii ruins.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3650}, pmid = {33574393}, issn = {2045-2322}, mesh = {Archaeology ; Bile Acids and Salts/chemistry/*isolation &amp; purification ; Body Remains/*chemistry ; DNA/chemistry ; DNA, Ancient/chemistry ; Feces/*chemistry ; Humans ; Lipids/*chemistry ; Metabolome/genetics ; Proteins/chemistry ; }, abstract = {Small organic molecules, lipids, proteins, and DNA fragments can remain stable over centuries. Powerful and sensitive chemical analysis can therefore be used to characterize ancient remains for classical archaeological studies. This bio-ecological dimension of archaeology can contribute knowledge about several aspects of ancient life, including social organization, daily habits, nutrition, and food storage. Faecal remains (i.e. coprolites) are particularly interesting in this regard, with scientists seeking to identify new faecal markers. Here, we report the analysis of faecal samples from modern-day humans and faecal samples from a discharge pit on the site of the ruins of ancient Pompeii. We propose that bile acids and their gut microbiota oxo-metabolites are the most specific steroid markers for detecting faecal inputs. This is due to their extreme chemical stability and their exclusive occurrence in vertebrate faeces, compared to other ubiquitous sterols and steroids.}, }
@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 {pmid33564028, year = {2021}, author = {Kehlmaier, C and Albury, NA and Steadman, DW and Graciá, E and Franz, R and Fritz, U}, title = {Ancient mitogenomics elucidates diversity of extinct West Indian tortoises.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3224}, pmid = {33564028}, issn = {2045-2322}, mesh = {Animals ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; *Extinction, Biological ; *Genome, Mitochondrial ; *Phylogeny ; Turtles/*genetics ; West Indies ; }, abstract = {We present 10 nearly complete mitochondrial genomes of the extinct tortoise Chelonoidis alburyorum from the Bahamas. While our samples represent morphologically distinct populations from six islands, their genetic divergences were shallow and resembled those among Galápagos tortoises. Our molecular clock estimates revealed that divergence among Bahamian tortoises began ~ 1.5 mya, whereas divergence among the Galápagos tortoises (C. niger complex) began ~ 2 mya. The inter-island divergences of tortoises from within the Bahamas and within the Galápagos Islands are much younger (0.09-0.59 mya, and 0.08-1.43 mya, respectively) than the genetic differentiation between any other congeneric pair of tortoise species. The shallow mitochondrial divergences of the two radiations on the Bahamas and the Galápagos Islands suggest that each archipelago sustained only one species of tortoise, and that the taxa currently regarded as distinct species in the Galápagos should be returned to subspecies status. The extinct tortoises from the Bahamas have two well-supported clades: the first includes one sample from Great Abaco and two from Crooked Island; the second clade includes tortoises from Great Abaco, Eleuthera, Crooked Island, Mayaguana, Middle Caicos, and Grand Turk. Tortoises belonging to both clades on Great Abaco and Crooked Island suggest late Holocene inter-island transport by prehistoric humans.}, }
@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, İ 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 Doğu Teknik Üniversitesi/ ; 113Z405//Türkiye Bilimsel ve Teknolojik Araştirma 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 14C dating on human teeth from Fuyan and Yangjiapo caves showed they derive from the Holocene. OSL dating of sediments and AMS 14C 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 {pmid33542324, year = {2021}, author = {Sarno, S and Petrilli, R and Abondio, P and De Giovanni, A and Boattini, A and Sazzini, M and De Fanti, S and Cilli, E and Ciani, G and Gentilini, D and Pettener, D and Romeo, G and Giuliani, C and Luiselli, D}, title = {Genetic history of Calabrian Greeks reveals ancient events and long term isolation in the Aspromonte area of Southern Italy.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3045}, pmid = {33542324}, issn = {2045-2322}, mesh = {Chromosomes, Human, Y/*genetics ; DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; Genetic Drift ; *Genetics, Population ; Genome, Human/*genetics ; Genotype ; Greece ; Haplotypes/genetics ; History, Ancient ; Humans ; Italy ; Language ; Whites/genetics ; }, abstract = {Calabrian Greeks are an enigmatic population that have preserved and evolved a unique variety of language, Greco, survived in the isolated Aspromonte mountain area of Southern Italy. To understand their genetic ancestry and explore possible effects of geographic and cultural isolation, we genome-wide genotyped a large set of South Italian samples including both communities that still speak Greco nowadays and those that lost the use of this language earlier in time. Comparisons with modern and ancient populations highlighted ancient, long-lasting genetic links with Eastern Mediterranean and Caucasian/Near-Eastern groups as ancestral sources of Southern Italians. Our results suggest that the Aspromonte communities might be interpreted as genetically drifted remnants that departed from such ancient genetic background as a consequence of long-term isolation. Specific patterns of population structuring and higher levels of genetic drift were indeed observed in these populations, reflecting geographic isolation amplified by cultural differences in the groups that still conserve the Greco language. Isolation and drift also affected the current genetic differentiation at specific gene pathways, prompting for future genome-wide association studies aimed at exploring trait-related loci that have drifted up in frequency in these isolated groups.}, }
@article {pmid33542301, year = {2021}, author = {Witt, KE and Yarlagadda, K and Allen, JM and Bader, AC and Simon, ML and Kuehn, SR and Swanson, KS and Cross, TL and Hedman, KM and Ambrose, SH and Malhi, RS}, title = {Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3113}, pmid = {33542301}, issn = {2045-2322}, support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaeology/methods ; Birds/classification/genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Ancient/*analysis ; Diet, Paleolithic/*history ; Dogs ; *Feces/microbiology/parasitology ; Fishes/classification/genetics ; Gastrointestinal Microbiome/*genetics ; History, Medieval ; Humans ; Illinois ; Nematoda/classification/*genetics ; Plants/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Here we present an integrative analysis of dog coprolites, combining macroscopic analyses, stable isotope measurements, and DNA shotgun sequencing to examine diet and health status. Dog coprolites used in this study were recovered from the Janey B. Goode and East Saint Louis archaeological sites, both of which are located in the American Bottom, an extensive Mississippi River floodplain in Southwestern Illinois. Based on the context of recovery, coprolites are assigned to the Late Woodland and Terminal Late Woodland periods (ca. 600-1050 AD). Given the scarcity of human remains from this time period, these dog coprolites can be useful as a proxy for understanding human diet during the Late Woodland period. We find that the Late Woodland dogs consumed a variety of fish as well as bird and plant taxa, possibly including maize, and also harbored intestinal parasites and pathogenic bacteria. By sequencing the fecal microbiome of the coprolites, we find some similarities to modern dog microbiomes, as well as specific taxa that can be used to discriminate between modern and ancient microbiomes, excluding soil contaminants. As dogs are often used as a surrogate to assess human diet, humans living with these dogs likely had a similar diet and were affected by similar parasites. These analyses, when integrated, show a more comprehensive view of ancient dog and human diet and health in the region during the initial expansion of maize agriculture than any individual method could alone.}, }
@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 km2 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 {pmid33514802, year = {2021}, author = {De Angelis, F and Pellegrini, M and Martínez-Labarga, C and Anzivino, L and Scorrano, G and Brilli, M and Giustini, F and Angle, M and Calattini, M and Carboni, G and Catalano, P and Ceccaroni, E and Cosentino, S and Di Giannantonio, S and Isola, I and Martini, F and Pacciani, E and Radina, F and Rolfo, MF and Silvestrini, M and Volante, N and Zanchetta, G and Sarti, L and Rickards, O}, title = {Exploring mobility in Italian Neolithic and Copper Age communities.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2697}, pmid = {33514802}, issn = {2045-2322}, abstract = {As a means for investigating human mobility during late the Neolithic to the Copper Age in central and southern Italy, this study presents a novel dataset of enamel oxygen and carbon isotope values (δ18Oca and δ13Cca) from the carbonate fraction of biogenic apatite for one hundred and twenty-six individual teeth coming from two Neolithic and eight Copper Age communities. The measured δ18Oca values suggest a significant role of local sources in the water inputs to the body water, whereas δ13Cca values indicate food resources, principally based on C3 plants. Both δ13Cca and δ18Oca ranges vary substantially when samples are broken down into local populations. Statistically defined thresholds, accounting for intra-site variability, allow the identification of only a few outliers in the eight Copper Age communities, suggesting that sedentary lifestyle rather than extensive mobility characterized the investigated populations. This seems to be also typical of the two studied Neolithic communities. Overall, this research shows that the investigated periods in peninsular Italy differed in mobility pattern from the following Bronze Age communities from more northern areas.}, }
@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 = 6) and D (N = 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 {pmid33510007, year = {2021}, author = {Grimm, D}, title = {Siberia may be long-sought site of dog domestication.}, journal = {Science (New York, N.Y.)}, volume = {371}, number = {6528}, pages = {451-452}, doi = {10.1126/science.371.6528.451}, pmid = {33510007}, issn = {1095-9203}, mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; *Domestication ; Humans ; Phenotype ; Siberia ; Wolves/genetics ; }, }
@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 für Bildung und Forschung/ ; 01UQ1711//Bundesministerium für 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, ÅJ 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 Autónoma de México (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, Ș 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 {pmid33495542, year = {2021}, author = {Immel, A and Pierini, F and Rinne, C and Meadows, J and Barquera, R and Szolek, A and Susat, J and Böhme, L and Dose, J and Bonczarowska, J and Drummer, C and Fuchs, K and Ellinghaus, D and Kässens, JC and Furholt, M and Kohlbacher, O and Schade-Lindig, S and Franke, A and Schreiber, S and Krause, J and Müller, J and Lenz, TL and Nebel, A and Krause-Kyora, B}, title = {Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {113}, pmid = {33495542}, issn = {2399-3642}, mesh = {*Agriculture ; Animals ; Archaeology ; DNA, Ancient/analysis ; Europe ; Evolution, Molecular ; Feeding Behavior/*physiology ; Genetic Variation ; Genetics, Population ; Genome, Human ; Genome-Wide Association Study ; Germany ; HLA Antigens/*genetics ; History, Ancient ; Human Migration ; Humans ; Polymorphism, Single Nucleotide ; Predatory Behavior/*physiology ; Racial Groups/genetics ; Residence Characteristics ; }, abstract = {The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34-58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections.}, }
@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 {pmid33494619, year = {2021}, author = {Singh, G and Yellapu, S and Sandhu, HS and Sharma, I and Sharma, V and Bhanwer, AJS}, title = {Genetic characterisation of the North-West Indian populations: analysis of mitochondrial DNA control region variations.}, journal = {Annals of human biology}, volume = {48}, number = {2}, pages = {166-172}, doi = {10.1080/03014460.2021.1879933}, pmid = {33494619}, issn = {1464-5033}, mesh = {DNA, Mitochondrial/*genetics ; Ethnicity/*genetics ; *Haplotypes ; Humans ; India ; Phylogeny ; }, abstract = {BACKGROUND: Human mitochondrial DNA presents several interesting characteristics, making it a favourable tool in the field of molecular anthropology, medical genetics, population history, and forensic science.<br><br>AIM: The present study investigated the mitochondrial DNA (mtDNA) control region variations in diverse ethnic groups of North-West India for which population data is insufficient.<br><br>SUBJECTS AND METHODS: The complete mtDNA control regions of 197 unrelated (for up to three generations) healthy individuals belonging to different ethnic groups of North-West India were sequenced. The haplotype frequencies, haplogroup distribution, and pairwise FST values between the studied and other worldwide populations were generated to study patterns of variation in human mtDNA.<br><br>RESULTS: The results ascertained high gene diversity (0.998) in the studied maternal lineages, identifying 166 distinct haplotypes, of which 158 were unique and characterised by 117 variable sites. Three haplogroups: M3, M30, and U7 were observed to be the most prevalent, and phylogeographically a total of 55.86% of sequences were characterised into South Asian, followed by West Eurasian (40.18%) and East Asian (3.96%), ancestry haplogroups. Pairwise genetic differentiation comparisons revealed maternal homogeneity in the studied groups. No population substructure was detected within the North-West Indian populations.<br><br>CONCLUSION: The results of this preliminary study will contribute to an existing database of mtDNA variations of the Indian population and facilitate prospective studies investigating population genetics and human diseases.}, }
@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 São 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 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 {pmid33444387, year = {2021}, author = {Egfjord, AF and Margaryan, A and Fischer, A and Sjögren, KG and Price, TD and Johannsen, NN and Nielsen, PO and Sørensen, L and Willerslev, E and Iversen, R and Sikora, M and Kristiansen, K and Allentoft, ME}, title = {Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244872}, pmid = {33444387}, issn = {1932-6203}, mesh = {*Archaeology ; DNA, Ancient ; Denmark ; Female ; *Genomics ; Haplotypes ; History, Ancient ; Human Migration ; Humans ; Male ; Sex Determination Analysis ; Skeleton/*metabolism ; }, abstract = {The Gjerrild burial provides the largest and best-preserved assemblage of human skeletal material presently known from the Single Grave Culture (SGC) in Denmark. For generations it has been debated among archaeologists if the appearance of this archaeological complex represents a continuation of the previous Neolithic communities, or was facilitated by incoming migrants. We sampled and analysed five skeletons from the Gjerrild cist, buried over a period of c. 300 years, 2600/2500-2200 cal BCE. Despite poor DNA preservation, we managed to sequence the genome (>1X) of one individual and the partial genomes (0.007X and 0.02X) of another two individuals. Our genetic data document a female (Gjerrild 1) and two males (Gjerrild 5 + 8), harbouring typical Neolithic K2a and HV0 mtDNA haplogroups, but also a rare basal variant of the R1b1 Y-chromosomal haplogroup. Genome-wide analyses demonstrate that these people had a significant Yamnaya-derived (i.e. steppe) ancestry component and a close genetic resemblance to the Corded Ware (and related) groups that were present in large parts of Northern and Central Europe at the time. Assuming that the Gjerrild skeletons are genetically representative of the population of the SGC in broader terms, the transition from the local Neolithic Funnel Beaker Culture (TRB) to SGC is not characterized by demographic continuity. Rather, the emergence of SGC in Denmark was part of the Late Neolithic and Early Bronze Age population expansion that swept across the European continent in the 3rd millennium BCE, resulting in various degrees of genetic replacement and admixture processes with previous Neolithic populations.}, }
@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 ; Asians/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 ; Whites/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 Other 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 {pmid33442059, year = {2021}, author = {Perri, AR and Mitchell, KJ and Mouton, A and Álvarez-Carretero, S and Hulme-Beaman, A and Haile, J and Jamieson, A and Meachen, J and Lin, AT and Schubert, BW and Ameen, C and Antipina, EE and Bover, P and Brace, S and Carmagnini, A and Carøe, C and Samaniego Castruita, JA and Chatters, JC and Dobney, K and Dos Reis, M and Evin, A and Gaubert, P and Gopalakrishnan, S and Gower, G and Heiniger, H and Helgen, KM and Kapp, J and Kosintsev, PA and Linderholm, A and Ozga, AT and Presslee, S and Salis, AT and Saremi, NF and Shew, C and Skerry, K and Taranenko, DE and Thompson, M and Sablin, MV and Kuzmin, YV and Collins, MJ and Sinding, MS and Gilbert, MTP and Stone, AC and Shapiro, B and Van Valkenburgh, B and Wayne, RK and Larson, G and Cooper, A and Frantz, LAF}, title = {Dire wolves were the last of an ancient New World canid lineage.}, journal = {Nature}, volume = {591}, number = {7848}, pages = {87-91}, pmid = {33442059}, issn = {1476-4687}, support = {S10 OD018174/OD/NIH HHS/United States ; /ERC_/European Research Council/International ; 210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Extinction, Biological ; Fossils ; Gene Flow ; Genome/genetics ; Genomics ; Geographic Mapping ; North America ; Paleontology ; Phenotype ; *Phylogeny ; Wolves/*classification/genetics ; }, abstract = {Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.}, }
@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 steppes2,3 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 ∼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 ∼82 000 and 43 000 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 ≥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 {pmid33367711, year = {2021}, author = {Choudhury, A and Sengupta, D and Ramsay, M and Schlebusch, C}, title = {Bantu-speaker migration and admixture in southern Africa.}, journal = {Human molecular genetics}, volume = {30}, number = {R1}, pages = {R56-R63}, pmid = {33367711}, issn = {1460-2083}, support = {U54 HG006938/HG/NHGRI NIH HHS/United States ; }, mesh = {Africa, Southern/ethnology ; Blacks/*genetics ; DNA, Ancient/*analysis ; Genetics, Population ; Haplotypes ; History, Ancient ; Human Migration/*history ; Humans ; Language ; Whole Genome Sequencing ; }, abstract = {The presence of Early and Middle Stone Age human remains and associated archeological artifacts from various sites scattered across southern Africa, suggests this geographic region to be one of the first abodes of anatomically modern humans. Although the presence of hunter-gatherer cultures in this region dates back to deep times, the peopling of southern Africa has largely been reshaped by three major sets of migrations over the last 2000 years. These migrations have led to a confluence of four distinct ancestries (San hunter-gatherer, East-African pastoralist, Bantu-speaker farmer and Eurasian) in populations from this region. In this review, we have summarized the recent insights into the refinement of timelines and routes of the migration of Bantu-speaking populations to southern Africa and their admixture with resident southern African Khoe-San populations. We highlight two recent studies providing evidence for the emergence of fine-scale population structure within some South-Eastern Bantu-speaker groups. We also accentuate whole genome sequencing studies (current and ancient) that have both enhanced our understanding of the peopling of southern Africa and demonstrated a huge potential for novel variant discovery in populations from this region. Finally, we identify some of the major gaps and inconsistencies in our understanding and emphasize the importance of more systematic studies of southern African populations from diverse ethnolinguistic groups and geographic locations.}, }
@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, Ø 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 (14C 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 Other 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 {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 = {/WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595/WT_/Wellcome Trust/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 -14C 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 14C age of 41.7-40.8 ka cal BP (95%), younger than the 14C 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 {pmid33273524, year = {2020}, author = {Verma, S and Sharma, I and Sharma, V and Bhat, A and Shah, R and Bhat, GR and Sharma, B and Bakshi, D and Nagpal, A and Wakhloo, A and Bhat, A and Kumar, R}, title = {MassArray analysis of genomic susceptibility variants in ovarian cancer.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21101}, pmid = {33273524}, issn = {2045-2322}, mesh = {Alleles ; Case-Control Studies ; Female ; Gene Frequency ; *Genetic Predisposition to Disease ; *Genetic Variation ; *Genome, Human ; Humans ; Middle Aged ; Molecular Sequence Annotation ; *Oligonucleotide Array Sequence Analysis ; Ovarian Neoplasms/*genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Ovarian cancer (OC), a multifaceted and genetically heterogeneous malignancy is one of the most common cancers among women. The aim of the study is to unravel the genetic factors associated with OC and the extent of genetic heterogeneity in the populations of Jammu and Kashmir (J&amp;K).Using the high throughput Agena MassARRAY platform, present case control study was designed which comprises 200 histopathological confirmed OC patients and 400 age and ethnicity matched healthy controls to ascertain the association of previously reported eleven single nucleotide polymorphisms (SNPs) spread over ten genes (DNMT3A, PIK3CA, FGFR2, GSTP1, ERCC5, AKT1, CASC16, CYP19A1, BCL2 and ERCC1) within the OC population of Jammu and Kashmir, India. The association of each variant was estimated using logistic regression analyses. Out of the 11 SNPs the odds ratio observed for three SNPs; rs2699887 was (1.72 at 95% CI: 1.19-2.48, p = 0.004), rs1695 was (1.87 at 95% CI: 1.28-2.71, p = 0.001), and rs2298881 was (0.66 at 95% CI: 0.46-0.96, p = 0.03) were found significantly associated with the OC after correction with confounding factors i.e. age &amp; BMI. Furthermore, the estimation of interactive analyses was performed and odds ratio observed was 2.44 (1.72-3.47), p value < 0. 001 suggests that there was a strong existence of interplay between the selected genetic variants in OC, which demonstrate that interactive analysis highlights the role of gene-gene interaction that provides an insight among multiple little effects of various polymorphisms in OC.}, }
@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//Vetenskapsrådet/ ; CTS 17:109//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; CTS 19:257//Carl Tryggers Stiftelse för 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 Forskningsrådet Formas/ ; 676154//H2020 Marie Skłodowska-Curie Actions/ ; 210119/Z/18/Z//Velux Fonden/ ; CTS17:109//Carl Tryggers Stiftelse för 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 = {*American Indians or Alaska Natives/classification/genetics/history ; Anthropology, Physical ; Asia, Northern ; *Asians/classification/genetics/history ; Chromosomes, Human, Y/*genetics ; History, Ancient ; Human Migration/*history ; Humans ; Male ; North America ; Phylogeny ; }, 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 = 43) and ancient individuals (n = 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 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}, doi = {10.1089/brain.2020.0809}, 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 {pmid33196640, year = {2020}, author = {Sjögren, KG and Olalde, I and Carver, S and Allentoft, ME and Knowles, T and Kroonen, G and Pike, AWG and Schröter, P and Brown, KA and Brown, KR and Harrison, RJ and Bertemes, F and Reich, D and Kristiansen, K and Heyd, V}, title = {Kinship and social organization in Copper Age Europe. A cross-disciplinary analysis of archaeology, DNA, isotopes, and anthropology from two Bell Beaker cemeteries.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241278}, pmid = {33196640}, issn = {1932-6203}, mesh = {*Anthropology ; *Archaeology ; *Cemeteries ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Female ; Geography ; Germany ; Haplotypes/genetics ; *Hierarchy, Social ; Humans ; *Isotope Labeling ; Male ; Models, Theoretical ; Principal Component Analysis ; Sex Determination Analysis ; Time Factors ; }, abstract = {We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0-14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups.}, }
@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 {pmid33180274, year = {2021}, author = {Bonsu, DOM and Higgins, D and Henry, J and Austin, JJ}, title = {Evaluation of the efficiency of Isohelix™ and Rayon swabs for recovery of DNA from metal surfaces.}, journal = {Forensic science, medicine, and pathology}, volume = {17}, number = {2}, pages = {199-207}, pmid = {33180274}, issn = {1556-2891}, mesh = {*Cellulose/chemistry ; DNA/analysis ; *Forensic Genetics/instrumentation/methods ; *Specimen Handling/instrumentation/standards ; }, abstract = {PURPOSE: We investigated the recovery and extraction efficiency of DNA from three metal surfaces (brass, copper, steel) relevant to forensic casework, and plastic (control) using two different swabbing systems; Rayon and Isohelix™ swabs, with sterile water and isopropyl alcohol respectively, as the wetting solutions.<br><br>METHODS: Twenty nanograms of human genomic DNA were applied directly to Isohelix™ and Rayon swabs; and to the metal and plastic substrates. All substrates were left to dry for 24 h, followed by single wet swabbing and extraction with the DNA IQ™ System. DNA extracts were quantified using real time quantitative PCR assays with SYBR green chemistry.<br><br>RESULTS: DNA was extracted from directly seeded Isohelix™ swabs with a high efficiency of 98%, indicating effective DNA-release from the swab into the extraction buffer. In contrast, only 58% of input DNA was recovered from seeded Rayon swabs, indicating higher DNA retention by these swabs. Isohelix™ swabs recovered 32 - 53% of DNA from metal surfaces, whilst the Rayon swabs recovered 11-29%. DNA recovery was lowest from copper and highest from brass. Interestingly, Rayon swabs appeared to collect more DNA from the plastic surface than Isohelix™ swabs, however, due to the lower release of DNA from Rayon swabs they returned less DNA overall following extraction than Isohelix™ swabs.<br><br>CONCLUSION: These results demonstrate that DNA samples deposited on metal surfaces can be more efficiently recovered using Isohelix™ swabs wetted with isopropyl alcohol than Rayon swabs wetted with sterile water, although recovery is affected by the substrate type.}, }
@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 {pmid33149844, year = {2020}, author = {Skelly, E and Johnson, NW and Kapellas, K and Kroon, J and Lalloo, R and Weyrich, L}, title = {Response of Salivary Microbiota to Caries Preventive Treatment in Aboriginal and Torres Strait Islander Children.}, journal = {Journal of oral microbiology}, volume = {12}, number = {1}, pages = {1830623}, pmid = {33149844}, issn = {2000-2297}, abstract = {A once-annual caries preventive (Intervention) treatment was offered to Aboriginal and Torres Strait Islander schoolchildren-a population with disproportionately poorer oral health than non-Indigenous Australian children-in the Northern Peninsula Area (NPA) of Far North Queensland (FNQ), which significantly improved their oral health. Here, we examine the salivary microbiota of these children (mean age = 10 ± 2.96 years; n = 103), reconstructing the bacterial community composition with high-throughput sequencing of the V4 region of bacterial 16S rRNA gene. Microbial communities of children who received the Intervention had lower taxonomic diversity than those who did not receive treatment (Shannon, p < 0.05). Moreover, the Intervention resulted in further decreased microbial diversity in children with active carious lesions existing at the time of saliva collection. Microbial species associated with caries were detected; Lactobacillus salivarius, Lactobacillus reuteri, Lactobacillus gasseri, Prevotella multisaccharivorax, Parascardovia denticolens, and Mitsuokella HMT 131 were significantly increased (p < 0.05) in children with severe caries, especially in children who did not receive the Intervention. These insights into microbial associations and community differences prompt future considerations to the mechanisms behind caries-preventive therapy induced change; important for understanding the long-term implications of like treatment to improve oral health disparities within Australia. Trial registration: ANZCTR, ACTRN12615000693527. Registered 3 July 2015, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=368750&amp;isReview=true.}, }
@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 ; *Whites ; }, 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, Ø 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 ; Far East ; 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 {pmid33122839, year = {2020}, author = {Callaway, E}, title = {Ancient dog DNA reveals 11,000 years of canine evolution.}, journal = {Nature}, volume = {587}, number = {7832}, pages = {20}, pmid = {33122839}, issn = {1476-4687}, mesh = {Animals ; *DNA, Ancient ; Dogs ; Evolution, Molecular ; *Heredity ; Phylogeny ; }, }
@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 {pmid33122381, year = {2020}, author = {Zhang, D and Xia, H and Chen, F and Li, B and Slon, V and Cheng, T and Yang, R and Jacobs, Z and Dai, Q and Massilani, D and Shen, X and Wang, J and Feng, X and Cao, P and Yang, MA and Yao, J and Yang, J and Madsen, DB and Han, Y and Ping, W and Liu, F and Perreault, C and Chen, X and Meyer, M and Kelso, J and Pääbo, S and Fu, Q}, title = {Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau.}, journal = {Science (New York, N.Y.)}, volume = {370}, number = {6516}, pages = {584-587}, doi = {10.1126/science.abb6320}, pmid = {33122381}, issn = {1095-9203}, mesh = {Animals ; *Caves ; DNA, Ancient/*isolation &amp; purification ; DNA, Mitochondrial/genetics ; Geologic Sediments/*chemistry ; Hominidae/*classification/*genetics ; Humans ; Phylogeny ; Tibet ; }, abstract = {A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau.}, }
@article {pmid33122380, year = {2020}, author = {Massilani, D and Skov, L and Hajdinjak, M and Gunchinsuren, B and Tseveendorj, D and Yi, S and Lee, J and Nagel, S and Nickel, B and Devièse, T and Higham, T and Meyer, M and Kelso, J and Peter, BM and Pääbo, S}, title = {Denisovan ancestry and population history of early East Asians.}, journal = {Science (New York, N.Y.)}, volume = {370}, number = {6516}, pages = {579-583}, doi = {10.1126/science.abc1166}, pmid = {33122380}, issn = {1095-9203}, support = {324139/ERC_/European Research Council/International ; 694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Asians/*genetics ; DNA, Ancient ; *Evolution, Molecular ; Female ; Hominidae/*genetics ; Humans ; Mongolia ; Population ; Skull ; }, abstract = {We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in northeastern Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians.}, }
@article {pmid33122362, year = {2020}, author = {Gibbons, A}, title = {Denisovan DNA found in cave on Tibetan Plateau.}, journal = {Science (New York, N.Y.)}, volume = {370}, number = {6516}, pages = {512-513}, doi = {10.1126/science.370.6516.512}, pmid = {33122362}, issn = {1095-9203}, mesh = {Altitude ; Animals ; Caves ; Cold Temperature ; DNA, Ancient/*isolation &amp; purification ; DNA, Mitochondrial/*isolation &amp; purification ; Geologic Sediments/*chemistry ; Hominidae/*genetics ; Humans ; Tibet ; }, }
@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 {pmid33083459, year = {2020}, author = {Bazarragchaa, M and Uuganbayar, U and Lee, KH and Kim, KY and Kim, K}, title = {Skin Pigmentation Differences between Mongolian, Korean, and Uzbekistan Ancient Human DNA Samples.}, journal = {BioMed research international}, volume = {2020}, number = {}, pages = {2585324}, pmid = {33083459}, issn = {2314-6141}, mesh = {Asians/*genetics ; DNA, Ancient/*analysis ; Genotype ; Humans ; Mongolia ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide/genetics ; Republic of Korea ; Skin Pigmentation/*genetics ; Uzbekistan ; }, abstract = {BACKGROUND: This study reports the use of real-time PCR to identify the SNP rs1545397 in the intron region on the OCA2 gene from ancient and degraded DNA isolated from ancient human bones from Mongolia, Korea, and Uzbekistan. This SNP is a marker for skin pigmentation. LightCycler-based probes (HybProbes) were designed. A LightCycler (version 2.0) system was used for the real-time PCR.<br><br>RESULTS: The results of the real-time PCRs of three different genotypes of SNP rs1545397 were compared with those of the direct sequencing. Melting curve analysis was used for genotype determination. Three genotypes were distinguished: the homozygous T (T/T) SNP type formed a distinct melting peak at 53.3 ± 0.14°C, the homozygous A (A/A) SNP type formed a distinct melting peak at 57.8 ± 0.12°C, and the heterozygous A/T SNP type formed two distinct melting peaks at 53.3 ± 0.17°C and 57.8 ± 0.15°C. Mongolian aDNA samples tested in this study carried all three types of the SNP (A/T, A/A, and T/T) with no distinctly predominant type observed. In contrast, Korean aDNA samples carried the Asian genotype (T/T), while the Uzbekistan aDNA samples carried the European genotype (A/A) more often than the Asian genotype (T/T).<br><br>CONCLUSIONS: Human Mongolian aDNA samples had A/T, A/A, and T/T SNP rs1545397 with no distinct predominant genotype. When combined with the archeological and aDNA studies of other coupling morphologies with aDNA, our results infer that Mongolia's prehistoric population had considerable heterogeneity of skin color and morphological traits and that in the Neolithic period, a Eurasian or mixed population inhabited the western part of Mongolia.}, }
@article {pmid33077604, year = {2020}, author = {Earn, DJD and Ma, J and Poinar, H and Dushoff, J and Bolker, BM}, title = {Acceleration of plague outbreaks in the second pandemic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {44}, pages = {27703-27711}, pmid = {33077604}, issn = {1091-6490}, mesh = {Animals ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, Medieval ; Humans ; London ; Pandemics/*history ; Plague/*epidemiology/*history/transmission ; Population Density ; Rats ; }, abstract = {Historical records reveal the temporal patterns of a sequence of plague epidemics in London, United Kingdom, from the 14th to 17th centuries. Analysis of these records shows that later epidemics spread significantly faster ("accelerated"). Between the Black Death of 1348 and the later epidemics that culminated with the Great Plague of 1665, we estimate that the epidemic growth rate increased fourfold. Currently available data do not provide enough information to infer the mode of plague transmission in any given epidemic; nevertheless, order-of-magnitude estimates of epidemic parameters suggest that the observed slow growth rates in the 14th century are inconsistent with direct (pneumonic) transmission. We discuss the potential roles of demographic and ecological factors, such as climate change or human or rat population density, in driving the observed acceleration.}, }
@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}, doi = {10.1016/j.cub.2020.09.051}, pmid = {33065008}, issn = {1879-0445}, 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}, doi = {10.1016/j.cub.2020.09.035}, 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 ; Native Hawaiian or Other Pacific Islander/*genetics ; *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 ; Far East ; *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 20th 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 {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 {pmid33012230, year = {2020}, author = {Jacobson, DK and Honap, TP and Monroe, C and Lund, J and Houk, BA and Novotny, AC and Robin, C and Marini, E and Lewis, CM}, title = {Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190586}, pmid = {33012230}, issn = {1471-2970}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeology ; Bacteria/*isolation &amp; purification ; Belize ; DNA, Ancient/*analysis ; DNA, Bacterial/analysis ; Dental Calculus/*history/microbiology ; Feces/*microbiology ; High-Throughput Nucleotide Sequencing ; History, Ancient ; History, Medieval ; Humans ; Italy ; Mexico ; *Microbiota ; }, abstract = {Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770-1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400-850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter-gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution. 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 = {202792/Z/16/Z//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, ÅJ}, 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 {pmid33012226, year = {2020}, author = {Stone, AC and Lewis, CM and Schuenemann, VJ}, title = {Insights into health and disease from ancient biomolecules.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190568}, pmid = {33012226}, issn = {1471-2970}, mesh = {*Bacterial Physiological Phenomena ; DNA, Ancient/*analysis ; *Evolution, Molecular ; Fungi/*physiology ; *Host-Pathogen Interactions ; Humans ; }, }
@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% = 754 CFU ml- 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD95% = 5234 CFU ml- 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 {pmid33002215, year = {2020}, author = {Vinueza-Espinosa, DC and Santos, C and Martínez-Labarga, C and Malgosa, A}, title = {Human DNA extraction from highly degraded skeletal remains: How to find a suitable method?.}, journal = {Electrophoresis}, volume = {}, number = {}, pages = {}, doi = {10.1002/elps.202000171}, pmid = {33002215}, issn = {1522-2683}, support = {//Generalitat of Cataluña/ ; }, abstract = {Retrieving DNA from highly degraded human skeletal remains is still a challenge due to low concentration and fragmentation, which makes it difficult to extract and purify. Recent works showed that silica-based methods allow better DNA recovery and this fact may be attributed to the type of bones and the quality of the preserved tissue. However, more systematic studies are needed to evaluate the efficiency of the different silica-based extraction methods considering the type of bones. The main goal of the present study is to establish the best extraction method and the type of bone that can maximize the recovery of PCR-amplifiable DNA and the subsequent retrieval of mitochondrial and nuclear genetic information. Five individuals were selected from an archaeological site located in Catalonia-Spain dating from 5th to 11th centuries AD. For each individual, five samples from different skeletal regions were collected: petrous bone, pulp cavity and cementum of tooth, and rib and limb bones. Four extraction methods were tested, three silica-based (silica in-suspension, HE column and XS plasma column) and the classical method based on phenol-chloroform. Silica in-suspension method from petrous bone and pulp cavity showed the best results. However, the remains preservation will ultimately be the key to the molecular result success.}, }
@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 ; *Asians/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 {pmid32970680, year = {2020}, author = {Toncheva, D and Serbezov, D and Karachanak-Yankova, S and Nesheva, D}, title = {Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease.}, journal = {PloS one}, volume = {15}, number = {9}, pages = {e0233666}, pmid = {32970680}, issn = {1932-6203}, mesh = {*DNA, Ancient ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Female ; *Genes, Mitochondrial ; Humans ; Male ; Mitochondria/genetics ; Mitochondrial Diseases/*genetics ; Mutation ; RNA, Transfer/genetics ; }, abstract = {Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics.}, }
@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 = {WT206194/WT_/Wellcome Trust/United Kingdom ; WT207492/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 history1,2. 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