@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 = {}, number = {}, pages = {}, doi = {10.1002/ajpa.24231}, pmid = {33475153}, issn = {1096-8644}, support = {//Department of Archaeology, Durham University/ ; }, 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 {pmid33474257, year = {2018}, author = {Kornienko, IV and Faleeva, TG and Oreshkova, NV and Grigoriev, SE and Grigoreva, LV and Simonov, EP and Kolesnikova, AI and Putintseva, YA and Krutovsky, KV}, title = {Complete mitochondrial genome of a woolly mammoth (Mammuthus primigenius) from Maly Lyakhovsky Island (New Siberian Islands, Russia) and its phylogenetic assessment.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {3}, number = {2}, pages = {596-598}, doi = {10.1080/23802359.2018.1473721}, pmid = {33474257}, issn = {2380-2359}, abstract = {We present a complete sequence and an annotation of the mitochondrial genome of the woolly mammoth (Mammuthus primigenius) found in 2012 on Maly Lyakhovsky Island (North-Eastern Siberia, Russia). The genome was 16,851 bp long and contained 13 protein-coding, 22 tRNA, and 2 rRNA genes. It was AT reach (61.3%) with A = 32.9%, T = 28.4%, C = 25.3%, and G = 13.4%.}, }
@article {pmid33474186, year = {2018}, author = {de Flamingh, A and Mallott, EK and Roca, AL and Boraas, AS and Malhi, RS}, title = {Species identification and mitochondrial genomes of ancient fish bones from the Riverine Kachemak tradition of the Kenai Peninsula, Alaska.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {3}, number = {1}, pages = {409-411}, doi = {10.1080/23802359.2018.1456371}, pmid = {33474186}, issn = {2380-2359}, abstract = {Seven fish vertebrae were chosen for analysis from the 49-KEN-147 archaeological site in the Kenai Peninsula, Alaska. Mitochondrial DNA analysis of the ancient fish bones revealed that they were from sockeye and coho salmon. Here, we report the ancient mitochondrial genomes for three sockeye salmon and one coho salmon fish bone.}, }
@article {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 Tange Olsen, M}, title = {Predicting sample success for large-scale ancient DNA studies on marine mammals.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13331}, pmid = {33463014}, issn = {1755-0998}, abstract = {In recent years, non-human 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 the feasibility of 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. 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 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, the 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 = {2020}, author = {Mitchell, KJ and Rawlence, NJ}, title = {Examining Natural History through the Lens of Palaeogenomics.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2020.10.005}, pmid = {33455740}, issn = {1872-8383}, 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 {pmid31975168, year = {2020}, author = {Cheng, JY and Mailund, T}, title = {Ancestral Population Genomics with Jocx, a Coalescent Hidden Markov Model.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2090}, number = {}, pages = {167-189}, doi = {10.1007/978-1-0716-0199-0_8}, pmid = {31975168}, issn = {1940-6029}, mesh = {Algorithms ; DNA, Ancient/*analysis ; Evolution, Molecular ; Genetic Variation ; Genetics, Population/*methods ; Genomics/*methods ; Humans ; Markov Chains ; Models, Genetic ; Sequence Alignment ; }, abstract = {Coalescence theory lets us probe the past demographics of present-day genetic samples and much information about the past can be gleaned from variation in rates of coalescence event as we trace genetic lineages back in time. Fewer and fewer lineages will remain, however, so there is a limit to how far back we can explore. Without recombination, we would not be able to explore ancient speciation events because of this-any meaningful species concept would require that individuals of one species are closer related than they are to individuals of another species, once speciation is complete. Recombination, however, opens a window to the deeper past. By scanning along a genomic alignment, we get a sequential variant of the coalescence process as it looked at the time of the speciation. This pattern of coalescence times is fixed at speciation time and does not erode with time; although accumulated mutations and genomic rearrangements will eventually hide the signal, it enables us to glance at events in the past that would not be observable without recombination. So-called coalescence hidden Markov models allow us to exploit this, and in this chapter, we present the tool Jocx that uses a framework of these models to infer demographic parameters in ancient speciation events.}, }
@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}, abstract = {OBJECTIVE: Detecting traces of ancient DNA of Vibrio cholerae to provide genetic information associated with the fifth cholera pandemic.<br><br>MATERIALS: Sediment samples from the sacral foramina of four individuals were analyzed, recovered from a mass grave near an institution dedicated exclusively to the isolation and treatment of citizens infected with cholera in the late 19th century in the city of Cordoba, Argentina.<br><br>METHODS: Paleogenetic techniques (ancient DNA extraction, PCR amplification, and Sanger sequencing) were applied. Specific primers for Vibrio cholerae (VCR, ctxA, ctxB, and tcpA) were designed.<br><br>RESULTS: By amplifying and sequencing the Vibrio cholerae repeats fragment, the infection in at least one individual was confirmed.<br><br>CONCLUSIONS: The synthesis of the paleogenetic results with the archaeological and historical evidence strongly supports that at least one individual from the mass grave in Cordoba, Argentina, was a victim of the fifth cholera pandemic.<br><br>SIGNIFICANCE: Confirming the presence of the disease through multiple lines of evidence, including genetic, archaeological, and historical analyses, strengthens and affirms our understanding of the presence, effects, and potential evolutionary paths of the disease in the past.<br><br>LIMITATIONS: Vibrio cholerae repeats were sequenced in one individual, while the remaining genes could not be amplified, which is likely related to gene copy number.<br><br>Paleogenetic examination of ancient samples from different locations will broaden our understanding of the origin, evolution, and past dissemination of Vibrio cholerae epidemic strains.}, }
@article {pmid33443182, year = {2021}, author = {Ju, D and Mathieson, I}, title = {The evolution of skin pigmentation-associated variation in West Eurasia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {1}, pages = {}, doi = {10.1073/pnas.2009227118}, pmid = {33443182}, issn = {1091-6490}, 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 = {}, doi = {10.1073/pnas.2022112118}, pmid = {33443177}, issn = {1091-6490}, 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 = {}, number = {}, pages = {}, pmid = {33442059}, issn = {1476-4687}, 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}, doi = {10.1002/ece3.7056}, 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 = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2020.12.015}, pmid = {33434506}, issn = {1879-0445}, 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 {pmid32438927, year = {2020}, author = {Sazzini, M and Abondio, P and Sarno, S and Gnecchi-Ruscone, GA and Ragno, M and Giuliani, C and De Fanti, S and Ojeda-Granados, C and Boattini, A and Marquis, J and Valsesia, A and Carayol, J and Raymond, F and Pirazzini, C and Marasco, E and Ferrarini, A and Xumerle, L and Collino, S and Mari, D and Arosio, B and Monti, D and Passarino, G and D'Aquila, P and Pettener, D and Luiselli, D and Castellani, G and Delledonne, M and Descombes, P and Franceschi, C and Garagnani, P}, title = {Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {51}, pmid = {32438927}, issn = {1741-7007}, support = {602757//Seventh Framework Programme/International ; 634821//Horizon 2020 Framework Programme/International ; ADAGE//JPco-fuND/International ; 074-02-2018-330//Ministry of Education and Science of the Russian Federation/International ; FFABR2017//Italian Ministry of Education and Research/International ; }, mesh = {Archaeology ; DNA, Ancient/analysis ; European Continental Ancestry Group ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Human ; Humans ; Italy ; }, abstract = {BACKGROUND: The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. However, previous SNP array-based studies failed to investigate the full spectrum of Italian variation, generally neglecting low-frequency genetic variants and examining a limited set of small effect size alleles, which may represent important determinants of population structure and complex adaptive traits. To overcome these issues, we analyzed 38 high-coverage whole-genome sequences representative of population clusters at the opposite ends of the cline of Italian variation, along with a large panel of modern and ancient Euro-Mediterranean genomes.<br><br>RESULTS: We provided evidence for the early divergence of Italian groups dating back to the Late Glacial and for Neolithic and distinct Bronze Age migrations having further differentiated their gene pools. We inferred adaptive evolution at insulin-related loci in people from Italian regions with a temperate climate, while possible adaptations to pathogens and ultraviolet radiation were observed in Mediterranean Italians. Some of these adaptive events may also have secondarily modulated population disease or longevity predisposition.<br><br>CONCLUSIONS: We disentangled the contribution of multiple migratory and adaptive events in shaping the heterogeneous Italian genomic background, which exemplify population dynamics and gene-environment interactions that played significant roles also in the formation of the Continental and Southern European genomic landscapes.}, }
@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. AD Florence highlighted by microscopy and paleogenetics.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {104713}, doi = {10.1016/j.meegid.2021.104713}, pmid = {33429070}, issn = {1567-7257}, 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}, }
@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 = {}, number = {}, pages = {}, doi = {10.1093/humrep/deaa347}, pmid = {33417716}, issn = {1460-2350}, 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 {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 {pmid33373911, year = {2020}, 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}, abstract = {Recovering DNA from modern incinerated bones can be challenging and may require alteration of routine DNA extraction protocols. It has been postulated that incinerated bones share some similarities with ancient bones, including fragmented DNA, surface contamination and highly mineralised structure, all of which can inhibit the successful recovery of genetic material. For this reason, ancient DNA extraction protocols are often used for incinerated modern samples; however, their effectiveness is still somewhat unclear. Much of this uncertainty exists around the demineralisation step of extraction, specifically the length of incubation and retention or removal of supernatant. As obtaining human samples for forensic research can be challenging, porcine models (Sus scrofa domesticus) are often used as substitutes. This study developed real time PCR assays for porcine nuclear DNA in order to investigate the effects of modified demineralisation protocols on DNA yield from femurs exposed to either short (60 min) or prolonged (120 min) burning. Gradient PCR results indicated 56 °C was the ideal amplification temperature for targeted amplicons, with melt curve analysis showing short and long amplicons corresponded to 80.3 °C and 83 °C peaks respectively. Results of altered extraction protocol showed a trend towards higher DNA yields from longer demineralisation periods however this was not significant. By comparison, retaining supernatant post-demineralisation resulted in significantly greater DNA yields compared to discarding it (P < 0.009). Although DNA content yield decreased with burn duration, the demineralisation treatment variations appeared to have the same effect for all burn lengths. These results suggest that for incinerated modern bone retaining the supernatant following demineralisation can dramatically increase DNA yield.}, }
@article {pmid33366505, year = {2019}, author = {Nedoluzhko, AV and Sharko, FS and Boulygina, ES and Tsygankova, SV and Slobodova, NV and Gruzdeva, NM and Rastorguev, SM and Spasskaya, NN and Maschenko, EN}, title = {The complete mitochondrial genome of the extinct Pleistocene horse (Equus cf. lenensis) from Kotelny Island (New Siberian Islands, Russia) and its phylogenetic assessment.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {5}, number = {1}, pages = {243-245}, pmid = {33366505}, issn = {2380-2359}, abstract = {The complete mitochondrial genome from the Pleistocene stallion horse (Equus cf. lenensis) which complete skull was found in 1901 on Kotelny Island (New Siberian Archipelago, Sakha Republic, Russia) is published in this paper. The mitochondrial DNA (mtDNA) is 16,584 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. The overall base composition of the genome in descending order was 32.3% - A, 28.5% - C, 13.4% - G, 25.8% - T without a significant AT bias of 58.2%.}, }
@article {pmid33366359, year = {2019}, author = {Grond, J and Płecha, M and Hahn, C and Wiig, 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}, 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}, 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 = {2020}, 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}, 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 = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13311}, pmid = {33319428}, issn = {1755-0998}, 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 to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborate 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}, doi = {10.1073/pnas.2015560117}, pmid = {33318213}, issn = {1091-6490}, 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}, 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}, 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. &quot;Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States&quot;.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {287}, pmid = {33272282}, issn = {1474-760X}, support = {430-21018-00662//Social Sciences and Humanities Research Council of Canada/ ; OGI-170//Ontario Genomics Institute/ ; }, 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/ ; }, 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}, 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/ ; }, 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}, support = {RFO 2017//Università di Bologna/ ; }, 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}, 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 = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1002/ajpa.24173}, pmid = {33241578}, issn = {1096-8644}, support = {20720191047//Fundamental Research Funds for the Central Universities/ ; 2020YFE0201600//Key Projects of Strategic International Scientific and Technological Innovation Cooperation of the Chinese Ministry of Science and Technology/ ; 31900406//National Natural Science Foundation of China/ ; 19VJX074//National Social Science Foundation of China/ ; 18490750300//Scientific and Technology Committee of Shanghai Municipality/ ; }, 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 &quot;Beringian standstill&quot; (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the &quot;Long-term Beringian standstill model,&quot; the &quot;Short-term Beringian standstill model,&quot; and the &quot;Multiple waves of migration model.&quot; Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of &quot;Ancient Northern Siberians&quot; 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}, 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 = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1089/brain.2020.0809}, pmid = {33218283}, issn = {2158-0022}, 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}, support = {DP190103705//Australian Research Council/ ; IN180100017//Australian Research Council/ ; FT170100448//Australian Research Council/ ; }, 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 = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1111/plb.13218}, pmid = {33202099}, issn = {1438-8677}, 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) signaling and plant responses to abiotic stresses in Arabidopsis. However, the composition and evolution history of AITRs and their roles in cotton genus are largely unknown. Here, a total of 12 putative AITR genes were identified in cultivated tetraploid cotton Gossypium hirsutum. Phylogenetic analysis of GhAITRs in these cottons and their closely related species implicate the ancient genome-wide duplication occurring after speciation of Gossypium and Theobroma could generate the duplicates of GhAITRs. Duplicated GhAITRs were stably inherited in 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 could be affected in transgenic Arabidopsis plants expressing GhAITR-A1. Together, our findings reveal that duplicates in GhAITR gene family were achieved by whole genome duplication rather than three individual duplication events, and GhAITRs function as transcription repressors and are involved in the regulation of plant responses to ABA and drought stress. These results may provide insights towards the improvement of abiotic stress tolerance in cotton by using GhAITRs.}, }
@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}, 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 {pmid33180274, year = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1007/s12024-020-00329-x}, pmid = {33180274}, issn = {1556-2891}, 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}, 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&amp;#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}, 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}, 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}, doi = {10.1016/j.cell.2020.10.015}, pmid = {33157037}, issn = {1097-4172}, 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}, 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 = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1038/s41431-020-00747-z}, pmid = {33139852}, issn = {1476-5438}, support = {087576//Wellcome Trust (Wellcome)/ ; 057559//Wellcome Trust (Wellcome)/ ; 084060//Wellcome Trust (Wellcome)/ ; 072974//Wellcome Trust (Wellcome)/ ; 088262//Wellcome Trust (Wellcome)/ ; 098051//Wellcome Trust (Wellcome)/ ; PG/16/49/32176//British Heart Foundation (BHF)/ ; F/00 212/AM//Leverhulme Trust/ ; }, 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 &quot;Evolution in Action: From Genomes to Ecosystems&quot;/ ; }, 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 = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2020.10.002}, pmid = {33125870}, issn = {1879-0445}, 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}, doi = {10.1038/d41586-020-03053-2}, 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 ; 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, 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}, mesh = {Animals ; Asian Continental Ancestry Group/*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}, 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 {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}, doi = {10.1073/pnas.2004904117}, 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 (&quot;accelerated&quot;). 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}, pmid = {33065008}, issn = {1879-0445}, 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 ; }, 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 &quot;First Remote Oceanian&quot; 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 = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1093/hmg/ddaa223}, pmid = {33059357}, issn = {1460-2083}, 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, archaeologists, 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 co-evolution 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}, 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}, 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}, doi = {10.1093/molbev/msaa189}, pmid = {33035304}, issn = {1537-1719}, 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 &quot;ancestral-type&quot; 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}, doi = {10.1016/j.cub.2020.08.081}, pmid = {33022266}, issn = {1879-0445}, 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 = {2020}, 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 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 = {}, number = {}, pages = {}, doi = {10.1002/ajpa.24149}, pmid = {33022107}, issn = {1096-8644}, support = {//The City of Charleston/ ; NGS-52378R-18//National Geographic Society/ ; NGS-54324E-18//National Geographic Society/ ; //The Gullah Society, Inc./ ; //University of Pennsylvania/ ; //University of Tennessee/ ; }, 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}, 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 ; }, abstract = {Enteric helminths are common parasites in many parts of the world and in the past were much more widespread both geographically and socially. Many enteric helminths are relatively long-lived in the human host, often benign or of low pathogenicity while producing large numbers of environmentally resistant eggs voided in the faeces or found associated with individual remains (skeletons and mummies). The combination of helminth characters offers opportunities to the field of historical pathogen research that are quite different to that of some of the more intensively studied high impact pathogens. Historically, a wealth of studies has employed microscopic techniques to diagnose infection using the morphology of the helminth eggs. More recently, various ancient DNA (aDNA) approaches have been applied in the archaeoparasitological context and these are revolutionizing the field, allowing much more specific diagnosis as well as interrogating the epidemiology of helminths. These advances have enhanced the potential for the field to provide unique information on past populations including using diseases to consider many aspects of life (e.g. sanitation, hygiene, diet, culinary practices and other aspects of society). Here, we consider the impact of helminth archaeoparasitology and more specifically the impact and potential for application of aDNA technologies as a part of the archaeologists' toolkit. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, }
@article {pmid33012228, year = {2020}, author = {Achtman, M and Zhou, Z}, title = {Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190573}, pmid = {33012228}, issn = {1471-2970}, support = {202792/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; BB/L020319/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, 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}, abstract = {Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. Mycobacterium leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.}, }
@article {pmid33012225, year = {2020}, author = {Morozova, I and Kasianov, A and Bruskin, S and Neukamm, J and Molak, M and Batieva, E and Pudło, A and Rühli, FJ and Schuenemann, VJ}, title = {New ancient Eastern European Yersinia pestis genomes illuminate the dispersal of plague in Europe.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1812}, pages = {20190569}, pmid = {33012225}, issn = {1471-2970}, 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}, 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)/ ; }, 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 = {2020}, 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 = {}, number = {}, pages = {1-11}, doi = {10.1139/gen-2019-0194}, pmid = {33002384}, issn = {1480-3321}, 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 = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1038/s10038-020-00841-6}, pmid = {32994538}, issn = {1435-232X}, 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 = {/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 &quot;confirmed pathogenic&quot; 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}, 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}, 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 ; }, 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}, doi = {10.1038/s41576-020-00285-w}, pmid = {32939074}, issn = {1471-0064}, }
@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 corrected for the effect of allele frequency drift over time. We obtained exact solutions for the estimates of corrected factors, and we provided a fast algorithm for their computation. Using computer simulations and ancient European samples, we compared geometric representations obtained from FA with PCA and with ancestry estimation programs. In admixture analyses, FA estimates agreed with tree-based statistics, and they were more accurate than those obtained from PCA projections and from ancestry estimation programs. A great advantage of FA over existing approaches is to improve descriptive analyses of ancient DNA samples without requiring inclusion of outgroup or present-day samples.}, }
@article {pmid32938680, year = {2020}, author = {Guimaraes, S and Arbuckle, BS and Peters, J and Adcock, SE and Buitenhuis, H and Chazin, H and Manaseryan, N and Uerpmann, HP and Grange, T and Geigl, EM}, title = {Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age.}, journal = {Science advances}, volume = {6}, number = {38}, pages = {}, pmid = {32938680}, issn = {2375-2548}, abstract = {Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic studies. Anatolia is a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. Our paleogenetic study of pre- and protohistoric horses in Anatolia and the Caucasus, based on a diachronic sample from the early Neolithic to the Iron Age (~8000 to ~1000 BCE) that encompasses the presumed transition from wild to domestic horses (4000 to 3000 BCE), shows the rapid and large-scale introduction of domestic horses at the end of the third millennium BCE. Thus, our results argue strongly against autochthonous independent domestication of horses in Anatolia.}, }
@article {pmid32934321, year = {2020}, author = {Pawłowska, J and Wollenburg, JE and Zajączkowski, M and Pawlowski, J}, title = {Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15102}, pmid = {32934321}, issn = {2045-2322}, support = {31003A_179125/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Arctic Regions ; *Biodiversity ; DNA, Ancient/*analysis ; Evolution, Molecular ; Foraminifera/classification/*genetics/*growth &amp; development ; Fossils ; *Genetic Variation ; Genomics/*methods ; Geologic Sediments/*analysis ; Paleography ; Phylogeny ; }, abstract = {Deciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the high-throughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies.}, }
@article {pmid32933569, year = {2020}, author = {Peyrégne, S and Peter, BM}, title = {AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {246}, pmid = {32933569}, issn = {1474-760X}, abstract = {Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.}, }
@article {pmid32915387, year = {2020}, author = {Nores, R and Rena, V and Angeletti, SC and Demarchi, DA and Modesti, N and Fabra, M}, title = {Biological kinship in 750 year old human remains from Central Argentina with signs of interpersonal violence.}, journal = {Forensic science, medicine, and pathology}, volume = {16}, number = {4}, pages = {649-658}, doi = {10.1007/s12024-020-00296-3}, pmid = {32915387}, issn = {1556-2891}, support = {FONCyT, PICT 2015-3155//Agencia Nacional de Promoción Científica y Tecnológica/International ; PID 2018-79//Ministerio de Ciencia y Tecnología de la Provincia de Córdoba/International ; }, abstract = {Human skeletal remains of an adult male (20-24 years old) and a juvenile (4-8 years old), dated to 750 ± 85 14C years BP, were found on the southern margin of Mar Chiquita Lagoon (Córdoba, Argentina). Both individuals show signs of being victims of interpersonal violence, with arrowheads associated with the remains and perimortem lesions on the juvenile, as well as an unusual form of burial, with the juvenile partially overlapped with the adult. The aim of this work is to study a possible kin relationship between these two individuals through ancient DNA analysis. Biological kinship was evaluated by autosomal and Y-chromosome STR (short tandem repeat) typing, PCR-APLP for SNP determination and hypervariable region I sequencing of the mitochondrial DNA. Genetic analyses indicated that these individuals shared the same Y-chromosomal haplotype but different mitochondrial lineages. The likelihood ratio based on autosomal loci indicates that the genetic profiles of the human remains would be more likely to be that indicating a father-son bond. The paleogenetic approach combined with forensic genetic methods applied to this study allowed us to confirm a hypothesis that originated in bioarchaeological evidence. This study constitutes a unique case in Argentina of kinship determination based on DNA profiles of human remains in an archaeological context of interpersonal violence. It is important to highlight the contribution made by these studies to address topics usually hidden in bioarchaeological studies, such as community organization, cultural customs and mortuary practices.}, }
@article {pmid32913324, year = {2020}, author = {Ermakova, GV and Kucheryavyy, AV and Zaraisky, AG and Bayramov, AV}, title = {Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {501}, pmid = {32913324}, issn = {2399-3642}, support = {20-04-00675A//Russian Foundation for Basic Research (RFBR)/ ; 18-29-07014 MK//Russian Foundation for Basic Research (RFBR)/ ; 18-04-00015//Russian Foundation for Basic Research (RFBR)/ ; 19-14-00098//Russian Science Foundation (RSF)/ ; }, abstract = {The secreted protein Noggin1 was the first discovered natural embryonic inducer produced by cells of the Spemann organizer. Thereafter, it was shown that vertebrates have a whole family of Noggin genes with different expression patterns and functional properties. For example, Noggin1 and Noggin2 inhibit the activity of BMP, Nodal/Activin and Wnt-beta-catenin signalling, while Noggin4 cannot suppress BMP but specifically modulates Wnt signalling. In this work, we described and investigated phylogeny and expression patterns of four Noggin genes in lampreys, which represent the most basally divergent group of extant vertebrates, the cyclostomes, belonging to the superclass Agnatha. Assuming that lampreys have Noggin homologues in all representatives of another superclass of vertebrates, the Gnathostomata, we propose a model for Noggin family evolution in vertebrates. This model is in agreement with the hypotheses suggesting two rounds of genome duplication in the ancestor of vertebrates before the divergence of Agnatha and Gnathostomata.}, }
@article {pmid32901061, year = {2020}, author = {Picin, A and Hajdinjak, M and Nowaczewska, W and Benazzi, S and Urbanowski, M and Marciszak, A and Fewlass, H and Socha, P and Stefaniak, K and Żarski, M and Wiśniewski, A and Hublin, JJ and Nadachowski, A and Talamo, S}, title = {New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14778}, pmid = {32901061}, issn = {2045-2322}, abstract = {The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.}, }
@article {pmid32898493, year = {2020}, author = {Ringbauer, H and Steinrücken, M and Fehren-Schmitz, L and Reich, D}, title = {Increased rate of close-kin unions in the central Andes in the half millennium before European contact.}, journal = {Current biology : CB}, volume = {30}, number = {17}, pages = {R980-R981}, doi = {10.1016/j.cub.2020.07.072}, pmid = {32898493}, issn = {1879-0445}, abstract = {Analyzing ancient DNA of the central Andes, Ringbauer and colleagues identify a markedly elevated rate of unions of closely related parents after ca. 1000 CE. This change of mating preferences sheds new light on a unique system of social organization based on ancestry (&quot;ayllu&quot;) whereby within-group unions were preferred to facilitate sharing of resources.}, }
@article {pmid32895707, year = {2020}, author = {Duchene, S and Lemey, P and Stadler, T and Ho, SYW and Duchene, DA and Dhanasekaran, V and Baele, G}, title = {Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations.}, journal = {Molecular biology and evolution}, volume = {37}, number = {11}, pages = {3363-3379}, doi = {10.1093/molbev/msaa163}, pmid = {32895707}, issn = {1537-1719}, support = {HHSN272201400006C/AI/NIAID NIH HHS/United States ; }, abstract = {Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here, we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) sampling times, and a model in which the samples are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behavior of this classification in analyses of five empirical data sets: modern samples of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus, and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.}, }
@article {pmid32894086, year = {2020}, author = {Bakshi, D and Nagpal, A and Sharma, V and Sharma, I and Shah, R and Sharma, B and Bhat, A and Verma, S and Bhat, GR and Abrol, D and Sharma, R and Vaishnavi, S and Kumar, R}, title = {MassARRAY-based single nucleotide polymorphism analysis in breast cancer of north Indian population.}, journal = {BMC cancer}, volume = {20}, number = {1}, pages = {861}, pmid = {32894086}, issn = {1471-2407}, abstract = {BACKGROUND: Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis.<br><br>METHODS: SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study.<br><br>RESULTS: The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08-2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136-5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123-0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46-0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings.<br><br>CONCLUSION: It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.}, }
@article {pmid32888333, year = {2020}, author = {Eerkens, JW and Ryder, A and Evoy, A and Hull, B}, title = {Hydrogen isotopes in serial hair samples record season of death in a mummified child from 19th century San Francisco, CA.}, journal = {American journal of physical anthropology}, volume = {173}, number = {3}, pages = {606-614}, doi = {10.1002/ajpa.24137}, pmid = {32888333}, issn = {1096-8644}, abstract = {BACKGROUND: The mummified body of a small child was found in a sealed Barstow cast iron casket during construction activity in San Francisco in 2016. Using historical records and ancient DNA the child was determined to be Edith H. Cook. She was born 28 November, 1873 in the city of San Francisco, and died of &quot;marasmus&quot; on 13 October, 1876 also in San Francisco.<br><br>AIMS: Currently, there are few techniques for estimating human season of death in archaeological cases. Hydrogen isotope ratios (δ2H) in hair keratin is known to strongly correlate with drinking water. We explore δ2H in serial hair samples as a potential technique to estimate season of death by comparing the δ2H record from hair to the known date of death.<br><br>MATERIALS &amp; METHODS: Approximately 50 hairs were removed from the scalp, aligned from the root, and cut into 5cm serial sections, each representing approximately 2 weeks of growth, and the total sequence a total of 1 year of growth. δ2H was measured on each 5cm segment and compared to previously-reported δ13C, δ15N, and δ34S values.<br><br>RESULTS: δ2H in the serial hair samples ranged between -56‰ and -48‰, consistent with her water values recorded in surface waters from San Francisco, and follow a sinusoidal pattern. Decreasing δ2H in terminal samples before death suggest Fall as the season of death, consistent with the known date of death.<br><br>DISCUSSION: This test case shows that archaeological hair preserves a seasonal signature in the form of changing keratin δ2H values that correlate to changing δ2H in surface drinking water. Terminal values in root record water ingested during the final week(s) before death.<br><br>CONCLUSIONS: We argue that this technique can be used to estimate season of death in future archaeological or forensic cases where hair has been preserved but date of death is unknown.}, }
@article {pmid32879432, year = {2020}, author = {Lord, E and Collins, C and deFrance, S and LeFebvre, MJ and Pigière, F and Eeckhout, P and Erauw, C and Fitzpatrick, SM and Healy, PF and Martínez-Polanco, MF and Garcia, JL and Ramos Roca, E and Delgado, M and Sánchez Urriago, A and Peña Léon, GA and Toyne, JM and Dahlstedt, A and Moore, KM and Laguer Diaz, C and Zori, C and Matisoo-Smith, E}, title = {Author Correction: Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14783}, doi = {10.1038/s41598-020-71841-x}, pmid = {32879432}, issn = {2045-2322}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32873779, year = {2020}, author = {Karpinski, E and Hackenberger, D and Zazula, G and Widga, C and Duggan, AT and Golding, GB and Kuch, M and Klunk, J and Jass, CN and Groves, P and Druckenmiller, P and Schubert, BW and Arroyo-Cabrales, J and Simpson, WF and Hoganson, JW and Fisher, DC and Ho, SYW and MacPhee, RDE and Poinar, HN}, title = {American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4048}, pmid = {32873779}, issn = {2041-1723}, mesh = {Animals ; *Climate Change ; DNA, Ancient/analysis/isolation &amp; purification ; DNA, Mitochondrial/genetics/isolation &amp; purification ; Female ; Fossils ; *Genetic Speciation ; *Genome, Mitochondrial ; Male ; Mastodons/*genetics ; Phylogeography ; }, abstract = {Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures.}, }
@article {pmid32859198, year = {2020}, author = {Neukamm, J and Pfrengle, S and Molak, M and Seitz, A and Francken, M and Eppenberger, P and Avanzi, C and Reiter, E and Urban, C and Welte, B and Stockhammer, PW and Teßmann, B and Herbig, A and Harvati, K and Nieselt, K and Krause, J and Schuenemann, VJ}, title = {2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {108}, pmid = {32859198}, issn = {1741-7007}, support = {845479//the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie/International ; ALTF 1086-2018//European Molecular Biology Organization (EMBO) long-term fellowship/International ; }, abstract = {BACKGROUND: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging.<br><br>RESULTS: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed.<br><br>CONCLUSIONS: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.}, }
@article {pmid32828254, year = {2020}, author = {Hofreiter, M and Hartmann, S}, title = {Reconstructing protein-coding sequences from ancient DNA.}, journal = {Methods in enzymology}, volume = {642}, number = {}, pages = {21-33}, doi = {10.1016/bs.mie.2020.05.008}, pmid = {32828254}, issn = {1557-7988}, abstract = {Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including miscoding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.}, }
@article {pmid32826299, year = {2020}, author = {He, Z and Dai, X and Beaumont, M and Yu, F}, title = {Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations.}, journal = {Genetics}, volume = {216}, number = {2}, pages = {521-541}, pmid = {32826299}, issn = {1943-2631}, abstract = {Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modeling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses.}, }
@article {pmid32815536, year = {2020}, author = {Pratas, D and Toppinen, M and Pyöriä, L and Hedman, K and Sajantila, A and Perdomo, MF}, title = {A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level.}, journal = {GigaScience}, volume = {9}, number = {8}, pages = {}, pmid = {32815536}, issn = {2047-217X}, abstract = {BACKGROUND: Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data.<br><br>FINDINGS: TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs.<br><br>CONCLUSIONS: TRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.}, }
@article {pmid32811443, year = {2020}, author = {Woods, R and Turvey, ST and Brace, S and McCabe, CV and Dalén, L and Rayfield, EJ and Brown, MJF and Barnes, I}, title = {Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean &quot;island-shrews&quot;.}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {106}, pmid = {32811443}, issn = {1471-2148}, support = {NE/L501803/1//Natural Environment Research Council/International ; BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Body Size ; DNA, Ancient/analysis ; *Fossils ; Phylogeny ; Shrews/*classification ; West Indies ; }, abstract = {BACKGROUND: The Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region's Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae (&quot;island-shrews&quot;) became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history of Nesophontes species from Hispaniola, the second-largest Caribbean island.<br><br>RESULTS: Principal component analysis of 65 Nesophontes mandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated Hispaniolan Nesophontes species. We were also able to extract and sequence ancient DNA from a ~ 750-year-old specimen of Nesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes. Nesophontes paramicrus (39-47 g) and N. zamicrus (~ 10 g) diverged recently during the Middle Pleistocene (mean estimated divergence = 0.699 Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values for N. paramicrus and N. zamicrus based on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs.<br><br>CONCLUSIONS: Our combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in Hispaniolan Nesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola's extant non-volant land mammals. Different components of Hispaniola's mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution in Nesophontes is also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.}, }
@article {pmid32795443, year = {2020}, author = {Majander, K and Pfrengle, S and Kocher, A and Neukamm, J and du Plessis, L and Pla-Díaz, M and Arora, N and Akgül, G and Salo, K and Schats, R and Inskip, S and Oinonen, M and Valk, H and Malve, M and Kriiska, A and Onkamo, P and González-Candelas, F and Kühnert, D and Krause, J and Schuenemann, VJ}, title = {Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {3788-3803.e10}, doi = {10.1016/j.cub.2020.07.058}, pmid = {32795443}, issn = {1879-0445}, abstract = {Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15th century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.}, }
@article {pmid32795436, year = {2020}, author = {Lord, E and Dussex, N and Kierczak, M and Díez-Del-Molino, D and Ryder, OA and Stanton, DWG and Gilbert, MTP and Sánchez-Barreiro, F and Zhang, G and Sinding, MS and Lorenzen, ED and Willerslev, E and Protopopov, A and Shidlovskiy, F and Fedorov, S and Bocherens, H and Nathan, SKSS and Goossens, B and van der Plicht, J and Chan, YL and Prost, S and Potapova, O and Kirillova, I and Lister, AM and Heintzman, PD and Kapp, JD and Shapiro, B and Vartanyan, S and Götherström, A and Dalén, L}, title = {Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.}, journal = {Current biology : CB}, volume = {30}, number = {19}, pages = {3871-3879.e7}, doi = {10.1016/j.cub.2020.07.046}, pmid = {32795436}, issn = {1879-0445}, abstract = {Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.}, }
@article {pmid32788984, year = {2020}, author = {Ford, BM and Cornellas, A and Leonard, JA and Weir, RD and Russello, MA}, title = {Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation.}, journal = {Ecology and evolution}, volume = {10}, number = {15}, pages = {8345-8357}, pmid = {32788984}, issn = {2045-7758}, abstract = {Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The &quot;southerly refugia model&quot; has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star-like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice-free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range-wide patterns and identifies unique genetic units that can likely be used to inform conservation of at-risk populations at the northern periphery.}, }
@article {pmid32778142, year = {2020}, author = {Nakatsuka, N and Harney, É and Mallick, S and Mah, M and Patterson, N and Reich, D}, title = {ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {199}, pmid = {32778142}, issn = {1474-760X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; HG006399/NH/NIH HHS/United States ; GM007753/GM/NIGMS NIH HHS/United States ; GM100233/NH/NIH HHS/United States ; }, abstract = {We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000 sequences covering SNPs. This method is optimized for application to aDNA, taking advantage of characteristic aDNA damage patterns to provide calibrated contamination estimates, and is available at https://github.com/nathan-nakatsuka/ContamLD .}, }
@article {pmid32778135, year = {2020}, author = {Sabin, S and Herbig, A and Vågene, ÅJ and Ahlström, T and Bozovic, G and Arcini, C and Kühnert, D and Bos, KI}, title = {A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {201}, pmid = {32778135}, issn = {1474-760X}, abstract = {BACKGROUND: Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679).<br><br>RESULTS: A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent.<br><br>CONCLUSIONS: The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.}, }
@article {pmid32770100, year = {2020}, author = {Boschin, F and Bernardini, F and Pilli, E and Vai, S and Zanolli, C and Tagliacozzo, A and Fico, R and Fedi, M and Corny, J and Dreossi, D and Lari, M and Modi, A and Vergata, C and Tuniz, C and Moroni, A and Boscato, P and Caramelli, D and Ronchitelli, A}, title = {The first evidence for Late Pleistocene dogs in Italy.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13313}, pmid = {32770100}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/*analysis ; Dogs/*genetics ; *Domestication ; *Fossils ; History, Ancient ; Humans ; Italy ; }, abstract = {The identification of the earliest dogs is challenging because of the absence and/or mosaic pattern of morphological diagnostic features in the initial phases of the domestication process. Furthermore, the natural occurrence of some of these characters in Late Pleistocene wolf populations and the time it took from the onset of traits related to domestication to their prevalence remain indefinite. For these reasons, the spatiotemporal context of the early domestication of dogs is hotly debated. Our combined molecular and morphological analyses of fossil canid remains from the sites of Grotta Paglicci and Grotta Romanelli, in southern Italy, attest of the presence of dogs at least 14,000 calibrated years before present. This unambiguously documents one of the earliest occurrence of domesticates in the Upper Palaeolithic of Europe and in the Mediterranean. The genetic affinity between the Palaeolithic dogs from southern Italy and contemporaneous ones found in Germany also suggest that these animals were an important common adjunct during the Late Glacial, when strong cultural diversification occurred between the Mediterranean world and European areas north of the Alps. Additionally, aDNA analyses indicate that this Upper Palaeolithic dog lineage from Italy may have contributed to the genetic diversity of living dogs.}, }
@article {pmid32769100, year = {2020}, author = {He, Z and Dai, X and Beaumont, M and Yu, F}, title = {Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach.}, journal = {Genetics}, volume = {216}, number = {2}, pages = {463-480}, pmid = {32769100}, issn = {1943-2631}, abstract = {Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process is a Wright-Fisher diffusion conditioned to survive until the time of the most recent sample. This formulation circumvents the assumption required in existing methods that the allele is created by mutation at a certain low frequency. We calculate the likelihood by numerically solving the resulting Kolmogorov backward equation backward in time while reweighting the solution with the emission probabilities of the observation at each sampling time point. This procedure reduces the two-dimensional numerical search for the maximum of the likelihood surface, for both the selection coefficient and the allele age, to a one-dimensional search over the selection coefficient only. We illustrate through extensive simulations that our method can produce accurate estimates of the selection coefficient and the allele age under both constant and nonconstant demographic histories. We apply our approach to reanalyze ancient DNA data associated with horse base coat colors. We find that ignoring demographic histories or grouping raw samples can significantly bias the inference results.}, }
@article {pmid32767894, year = {2020}, author = {Parolin, ML and Cortés, LI and Basso, N and Scattolin, MC}, title = {New Evidence of Ancient Mitochondrial DNA of the Southern Andes (Calchaquí Valleys, Northwest Argentina, 3,600-1,900 Years before Present).}, journal = {Human biology}, volume = {91}, number = {4}, pages = {225-247}, doi = {10.13110/humanbiology.91.4.02}, pmid = {32767894}, issn = {1534-6617}, mesh = {Adult ; Archaeology ; Argentina/epidemiology ; Child ; Child, Preschool ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics/history ; Female ; Genetic Variation ; Haplotypes/*genetics ; History, Ancient ; Humans ; Indians, South American/genetics ; Male ; Middle Aged ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Genetic studies on pre-Hispanic populations of the Southern Andes have been increasing steadily in the last decade. Nevertheless, ancient DNA characterization of Formative Period archaeological human remains is particularly scant, especially for Northwest Argentina. To expand current information on genetic characterization of the first agricultural communities of the southern Calchaquí Valleys, we present and discuss the first mitochondrial ancient DNA information obtained on samples dated to ca. 3,600-1,900 years before present from the Cajón Valley, Catamarca Province. Reproducible mtDNA hypervariable region 1 (HVR-1) sequences were obtained in seven individuals. Mitochondrial HVR-1 haplotypes were assigned to three of the four founding haplogroups, D1 (57.1%), C1 (28.5%), and B2 (14.2%), with absence of A2. Our results show that the Cajón Valley sample, with predominance of D1 and C1, differs from that commonly observed in ancient and modern Andean populations, which usually show a high prevalence of haplogroup B2. The fact that the Cajón Valley and Pampa Grande (Salta Province, Argentina) share a prevalence of haplogroup D1 could provide additional evidence to support possible genetic affinities between the valleys and the eastern sub-Andean region during the Formative Period in Northwest Argentina, expanding the archaeological evidence of contact between both populations. Future complete mitogenomic analysis will provide substantial information to formulate new hypotheses about the origins and phylogenetic relationships between the individuals of the Cajón Valley and other groups from the Andes, Gran Chaco, and the Amazon.}, }
@article {pmid32763189, year = {2020}, author = {Wagner, JK and Colwell, C and Claw, KG and Stone, AC and Bolnick, DA and Hawks, J and Brothers, KB and Garrison, NA}, title = {Fostering Responsible Research on Ancient DNA.}, journal = {American journal of human genetics}, volume = {107}, number = {2}, pages = {183-195}, doi = {10.1016/j.ajhg.2020.06.017}, pmid = {32763189}, issn = {1537-6605}, support = {K01 HG008818/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient/*analysis ; Foster Home Care ; Humans ; }, abstract = {Anticipating and addressing the social implications of scientific work is a fundamental responsibility of all scientists. However, expectations for ethically sound practices can evolve over time as the implications of science come to be better understood. Contemporary researchers who work with ancient human remains, including those who conduct ancient DNA research, face precisely this challenge as it becomes clear that practices such as community engagement are needed to address the important social implications of this work. To foster and promote ethical engagement between researchers and communities, we offer five practical recommendations for ancient DNA researchers: (1) formally consult with communities; (2) address cultural and ethical considerations; (3) engage communities and support capacity building; (4) develop plans to report results and manage data; and (5) develop plans for long-term responsibility and stewardship. Ultimately, every member of a research team has an important role in fostering ethical research on ancient DNA.}, }
@article {pmid32760427, year = {2020}, author = {Barrera-Redondo, J and Piñero, D and Eguiarte, LE}, title = {Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {742}, pmid = {32760427}, issn = {1664-8021}, abstract = {In the last decade, genomics and the related fields of transcriptomics and epigenomics have revolutionized the study of the domestication process in plants and animals, leading to new discoveries and new unresolved questions. Given that some domesticated taxa have been more studied than others, the extent of genomic data can range from vast to nonexistent, depending on the domesticated taxon of interest. This review is meant as a rough guide for students and academics that want to start a domestication research project using modern genomic tools, as well as for researchers already conducting domestication studies that are interested in following a genomic approach and looking for alternate strategies (cheaper or more efficient) and future directions. We summarize the theoretical and technical background needed to carry out domestication genomics, starting from the acquisition of a reference genome and genome assembly, to the sampling design for population genomics, paleogenomics, transcriptomics, epigenomics and experimental validation of domestication-related genes. We also describe some examples of the aforementioned approaches and the relevant discoveries they made to understand the domestication of the studied taxa.}, }
@article {pmid32747648, year = {2020}, author = {Nakatsuka, N and Luisi, P and Motti, JMB and Salemme, M and Santiago, F and D'Angelo Del Campo, MD and Vecchi, RJ and Espinosa-Parrilla, Y and Prieto, A and Adamski, N and Lawson, AM and Harper, TK and Culleton, BJ and Kennett, DJ and Lalueza-Fox, C and Mallick, S and Rohland, N and Guichón, RA and Cabana, GS and Nores, R and Reich, D}, title = {Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3868}, pmid = {32747648}, issn = {2041-1723}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Archaeology/methods ; Argentina ; Bone and Bones/metabolism ; Chile ; DNA, Ancient/*analysis ; DNA, Mitochondrial/classification/genetics ; *Fossils ; *Gene Flow ; Genetic Variation ; Genome, Human/*genetics ; Geography ; *Human Migration ; Humans ; Phylogeny ; Radiometric Dating/methods ; Sequence Analysis, DNA/methods ; Tooth/metabolism ; }, abstract = {Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.}, }
@article {pmid32745952, year = {2020}, author = {Mathieson, I}, title = {Human adaptation over the past 40,000 years.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {97-104}, pmid = {32745952}, issn = {1879-0380}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; }, abstract = {Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits.}, }
@article {pmid32743069, year = {2020}, author = {Shillito, LM and Whelton, HL and Blong, JC and Jenkins, DL and Connolly, TJ and Bull, ID}, title = {Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon.}, journal = {Science advances}, volume = {6}, number = {29}, pages = {eaba6404}, pmid = {32743069}, issn = {2375-2548}, abstract = {When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.}, }
@article {pmid32728085, year = {2020}, author = {Chessa, D and Murgia, M and Sias, E and Deligios, M and Mazzarello, V and Fiamma, M and Rovina, D and Carenti, G and Ganau, G and Pintore, E and Fiori, M and Kay, GL and Ponzeletti, A and Cappuccinelli, P and Kelvin, DJ and Wain, J and Rubino, S}, title = {Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12656}, pmid = {32728085}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/*isolation &amp; purification ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/parasitology ; High-Throughput Nucleotide Sequencing ; History, 19th Century ; Host Specificity ; Humans ; Intestinal Diseases, Parasitic/*history ; Italy ; Metagenomics/*methods ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Trichuriasis/history ; Trichuris/*classification/genetics/isolation &amp; purification ; }, abstract = {This study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.}, }
@article {pmid32722461, year = {2020}, author = {Del Corvo, M and Bongiorni, S and Stefanon, B and Sgorlon, S and Valentini, A and Ajmone Marsan, P and Chillemi, G}, title = {Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk.}, journal = {Genes}, volume = {11}, number = {8}, pages = {}, pmid = {32722461}, issn = {2073-4425}, abstract = {Dairy cattle health, wellbeing and productivity are deeply affected by stress. Its influence on metabolism and immune response is well known, but the underlying epigenetic mechanisms require further investigation. In this study, we compared DNA methylation and gene expression signatures between two dairy cattle populations falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine marker of stress in dairy cows. Reduced Representation Bisulfite Sequencing was used to obtain a methylation map from blood samples of these animals. The high and low groups exhibited similar amounts of methylated CpGs, while we found differences among non-CpG sites. Significant methylation changes were detected in 248 genes. We also identified significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) analysis showed that genes of both groups act together in several pathways, such as nervous system activity, immune regulatory functions and glucocorticoid metabolism. These preliminary results suggest that, in livestock, cortisol secretion could act as a trigger for epigenetic regulation and that peripheral changes in methylation can provide an insight into central nervous system functions.}, }
@article {pmid32704107, year = {2020}, author = {Spinney, L}, title = {Smallpox and other viruses plagued humans much earlier than suspected.}, journal = {Nature}, volume = {584}, number = {7819}, pages = {30-32}, doi = {10.1038/d41586-020-02083-0}, pmid = {32704107}, issn = {1476-4687}, mesh = {Bone and Bones/microbiology/virology ; DNA, Ancient/*analysis ; Disease Eradication/history ; Hepatitis B/epidemiology/history ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Mummies/microbiology/virology ; Plague/enzymology/history ; Smallpox/*epidemiology/*history/virology ; Time Factors ; Variola virus/classification/genetics/*isolation &amp; purification ; }, }
@article {pmid32699412, year = {2020}, author = {Ardelean, CF and Becerra-Valdivia, L and Pedersen, MW and Schwenninger, JL and Oviatt, CG and Macías-Quintero, JI and Arroyo-Cabrales, J and Sikora, M and Ocampo-Díaz, YZE and Rubio-Cisneros, II and Watling, JG and de Medeiros, VB and De Oliveira, PE and Barba-Pingarón, L and Ortiz-Butrón, A and Blancas-Vázquez, J and Rivera-González, I and Solís-Rosales, C and Rodríguez-Ceja, M and Gandy, DA and Navarro-Gutierrez, Z and De La Rosa-Díaz, JJ and Huerta-Arellano, V and Marroquín-Fernández, MB and Martínez-Riojas, LM and López-Jiménez, A and Higham, T and Willerslev, E}, title = {Evidence of human occupation in Mexico around the Last Glacial Maximum.}, journal = {Nature}, volume = {584}, number = {7819}, pages = {87-92}, doi = {10.1038/s41586-020-2509-0}, pmid = {32699412}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Altitude ; Archaeology ; Bayes Theorem ; Caves ; Cultural Diversity ; DNA, Ancient/analysis ; History, Ancient ; Human Migration/*history ; Humans ; *Ice Cover ; Mexico ; }, abstract = {The initial colonization of the Americas remains a highly debated topic1, and the exact timing of the first arrivals is unknown. The earliest archaeological record of Mexico-which holds a key geographical position in the Americas-is poorly known and understudied. Historically, the region has remained on the periphery of research focused on the first American populations2. However, recent investigations provide reliable evidence of a human presence in the northwest region of Mexico3,4, the Chiapas Highlands5, Central Mexico6 and the Caribbean coast7-9 during the Late Pleistocene and Early Holocene epochs. Here we present results of recent excavations at Chiquihuite Cave-a high-altitude site in central-northern Mexico-that corroborate previous findings in the Americas10-17of cultural evidence that dates to the Last Glacial Maximum (26,500-19,000 years ago)18, and which push back dates for human dispersal to the region possibly as early as 33,000-31,000 years ago. The site yielded about 1,900 stone artefacts within a 3-m-deep stratified sequence, revealing a previously unknown lithic industry that underwent only minor changes over millennia. More than 50 radiocarbon and luminescence dates provide chronological control, and genetic, palaeoenvironmental and chemical data document the changing environments in which the occupants lived. Our results provide new evidence for the antiquity of humans in the Americas, illustrate the cultural diversity of the earliest dispersal groups (which predate those of the Clovis culture) and open new directions of research.}, }
@article {pmid32693300, year = {2020}, author = {Cao, X and Xu, X and Bian, R and Wang, Y and Yu, H and Xu, Y and Duan, G and Bi, L and Chen, P and Gao, S and Wang, J and Peng, J and Qu, J}, title = {Sedimentary ancient DNA metabarcoding delineates the contrastingly temporal change of lake cyanobacterial communities.}, journal = {Water research}, volume = {183}, number = {}, pages = {116077}, doi = {10.1016/j.watres.2020.116077}, pmid = {32693300}, issn = {1879-2448}, mesh = {Cyanobacteria/*genetics ; DNA Barcoding, Taxonomic ; DNA, Ancient ; Ecosystem ; *Lakes ; }, abstract = {Harmful cyanobacterial blooms consisting of toxic taxa can produce a wide variety of toxins to threaten water quality, ecosystem functions and services. Of greater concern was the changing patterns of cyanobacterial assemblage were not well understood due to the lack of long-term monitoring data over the temporal scale. Biodiversity change in cyanobacterial community and paleoenvironmental variables over the past 170 years in Lake Chenghai were investigated based on sedimentary ancient DNA metabarcoding and traditional paleolimnological analysis. The results showed species richness and homogenization of cyanobacterial assemblage increased in the most recent decades, which were synchronized with the growth of artificial fertilization and decline in precipitation. Cyanobacterial co-occurrence network analysis revealed more complex interactions and weak community stability after the change point of ∼1987, while the rare cyanobacterial genera such as Anabaena, Planktothrix, Oscillatoria and Microcystis were identified to be keystone taxa affecting cyanobacterial assemblage. Furthermore, an increase of toxin-producing cyanobacterial taxa was significantly and positively associated with TN and TP, as well as TN/IP and TN/TP, which was verified by quantitative real-time PCR of mcyA and rpoC1 genes. Threshold in total nitrogen (TN) concentration should be targeted no more than 0.60 mg/L to alleviate nuisance cyanobacterial blooms in Lake Chenghai. These findings reinforce the comprehensive understanding for the long-term dynamics of cyanobacterial assemblage responding to environmental change, which could contribute to proactively regulate environmental conditions for avoiding undesirable ecological consequences.}, }
@article {pmid32688244, year = {2020}, author = {Zhang, M and Fu, Q}, title = {Human evolutionary history in Eastern Eurasia using insights from ancient DNA.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {78-84}, doi = {10.1016/j.gde.2020.06.009}, pmid = {32688244}, issn = {1879-0380}, abstract = {Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia-some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia.}, }
@article {pmid32684155, year = {2020}, author = {Duggan, AT and Klunk, J and Porter, AF and Dhody, AN and Hicks, R and Smith, GL and Humphreys, M and McCollum, AM and Davidson, WB and Wilkins, K and Li, Y and Burke, A and Polasky, H and Flanders, L and Poinar, D and Raphenya, AR and Lau, TTY and Alcock, B and McArthur, AG and Golding, GB and Holmes, EC and Poinar, HN}, title = {The origins and genomic diversity of American Civil War Era smallpox vaccine strains.}, journal = {Genome biology}, volume = {21}, number = {1}, pages = {175}, pmid = {32684155}, issn = {1474-760X}, support = {PJT-156214//CIHR/Canada ; /WT_/Wellcome Trust/United Kingdom ; }, abstract = {Vaccination has transformed public health, most notably including the eradication of smallpox. Despite its profound historical importance, little is known of the origins and diversity of the viruses used in smallpox vaccination. Prior to the twentieth century, the method, source and origin of smallpox vaccinations remained unstandardised and opaque. We reconstruct and analyse viral vaccine genomes associated with smallpox vaccination from historical artefacts. Significantly, we recover viral molecules through non-destructive sampling of historical materials lacking signs of biological residues. We use the authenticated ancient genomes to reveal the evolutionary relationships of smallpox vaccination viruses within the poxviruses as a whole.}, }
@article {pmid32682389, year = {2020}, author = {Sheng, G and Hu, J and Tong, H and Llamas, B and Yuan, J and Hou, X and Chen, S and Xiao, B and Lai, X}, title = {Ancient DNA of northern China Hystricidae sub-fossils reveals the evolutionary history of old world porcupines in the Late Pleistocene.}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {88}, pmid = {32682389}, issn = {1471-2148}, support = {41672017//National Natural Science Foundation of China/International ; }, mesh = {Animals ; *Biological Evolution ; China ; *DNA, Ancient ; *Fossils ; Geography ; Likelihood Functions ; Phylogeny ; Porcupines/*anatomy &amp; histology/*genetics ; RNA, Ribosomal/genetics ; Species Specificity ; Time Factors ; }, abstract = {BACKGROUND: Old World porcupines (Family: Hystricidae) are the third-largest rodents and inhabit southern Europe, Asia, and most regions of Africa. They are a typical indicator of warm climate and their distribution is restricted to tropical and subtropical zones. In China, porcupines are widely distributed in southern areas of the Yangtze River. However, fossil remains have been identified in a few sites in northern China, among which Tianyuan Cave-near Zhoukoudian site-represents the latest known porcupine fossil record. So far, studies have focused mainly on porcupines' husbandry and domestication but little is known about their intrafamilial phylogenetic relationships and evolutionary history.<br><br>RESULTS: In this study, we sequence partial mitochondrial 12S rRNA and cyt b genes for seven Late Pleistocene porcupine individuals from Northern, Southern and Central China. Phylogenetic analyses show that the Tianyuan Cave porcupines, which had been morphologically identified as Hystrix subcristata, have a closer relationship to Hystrix brachyura.<br><br>CONCLUSION: Together with morphological adaptation characteristics, associated fauna, and climate change evidence, the molecular results reveal that a Late Quaternary extirpation has occurred during the evolutionary history of porcupines.}, }
@article {pmid32678112, year = {2020}, author = {Li, J and Zarzar, TG and White, JD and Indencleef, K and Hoskens, H and Matthews, H and Nauwelaers, N and Zaidi, A and Eller, RJ and Herrick, N and Günther, T and Svensson, EM and Jakobsson, M and Walsh, S and Van Steen, K and Shriver, MD and Claes, P}, title = {Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11850}, pmid = {32678112}, issn = {2045-2322}, support = {R01 DE027023/DE/NIDCR NIH HHS/United States ; }, mesh = {Biometric Identification/*methods ; Continental Population Groups/history ; Datasets as Topic ; Face/*anatomy &amp; histology ; Facial Recognition/physiology ; Female ; Genetics, Population/methods ; *Genome, Human ; Genome-Wide Association Study ; History, 21st Century ; History, Ancient ; Human Genetics/*methods ; Humans ; Image Processing, Computer-Assisted ; *Inheritance Patterns ; Male ; *Models, Statistical ; }, abstract = {Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case-control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively.}, }
@article {pmid32674620, year = {2020}, author = {Mizuno, F and Taniguchi, Y and Kondo, O and Hayashi, M and Kurosaki, K and Ueda, S}, title = {A study of 8,300-year-old Jomon human remains in Japan using complete mitogenome sequences obtained by next-generation sequencing.}, journal = {Annals of human biology}, volume = {47}, number = {6}, pages = {555-559}, doi = {10.1080/03014460.2020.1797164}, pmid = {32674620}, issn = {1464-5033}, abstract = {Ancient human remains have been assigned to their mitochondrial DNA (mtDNA) haplogroups. To obtain efficiently deep and reliable nucleotide sequences of ancient DNA of interest, we achieved target enrichment followed by next-generation sequencing (NGS). Complete mitochondrial genome (mitogenome) sequences were obtained for three human remains from the Iyai rock-shelter site of the Initial Jomon Period in Japan. All the Jomon mitogenomes belong to haplogroup N9b, but no sequences among them were identical. High genetic diversity was clarified even among the Jomon human remains belonging to haplogroup N9b, which has been described as a haplogroup representing the Jomon people.}, }
@article {pmid32666166, year = {2020}, author = {Hallast, P and Agdzhoyan, A and Balanovsky, O and Xue, Y and Tyler-Smith, C}, title = {A Southeast Asian origin for present-day non-African human Y chromosomes.}, journal = {Human genetics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00439-020-02204-9}, pmid = {32666166}, issn = {1432-1203}, support = {PUT1036//Eesti Teadusagentuur/ ; 098051/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000-70,000 years ago, followed by mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. Here, we show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 50,000-55,000 years ago of all known surviving non-African male lineages (apart from recent migrants). This observation contrasts with the expectation of a West Eurasian origin predicted by a simple model of expansion from a source near Africa, and can be interpreted as resulting from extensive genetic drift in the initial population or replacement of early western Y lineages from the east, thus informing and constraining models of the initial expansion.}, }
@article {pmid32664326, year = {2020}, author = {Iwasaki, RL and Ishiya, K and Kanzawa-Kiriyama, H and Kawai, Y and Gojobori, J and Satta, Y}, title = {Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population.}, journal = {Genes}, volume = {11}, number = {7}, pages = {}, pmid = {32664326}, issn = {2073-4425}, abstract = {A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese.}, }
@article {pmid32661160, year = {2020}, author = {Bongers, JL and Nakatsuka, N and O'Shea, C and Harper, TK and Tantaleán, H and Stanish, C and Fehren-Schmitz, L}, title = {Integration of ancient DNA with transdisciplinary dataset finds strong support for Inca resettlement in the south Peruvian coast.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {31}, pages = {18359-18368}, pmid = {32661160}, issn = {1091-6490}, support = {T32 GM007753/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaeology ; DNA, Ancient/*chemistry ; Hispanic Americans ; History, Ancient ; *Human Migration ; Humans ; Indians, South American/*genetics/*history ; Peru ; }, abstract = {Ancient DNA (aDNA) analysis provides a powerful means of investigating human migration, social organization, and a plethora of other crucial questions about humanity's past. Recently, specialists have suggested that the ideal research design involving aDNA would include multiple independent lines of evidence. In this paper, we adopt a transdisciplinary approach integrating aDNA with archaeological, biogeochemical, and historical data to investigate six individuals found in two cemeteries that date to the Late Horizon (1400 to 1532 CE) and Colonial (1532 to 1825 CE) periods in the Chincha Valley of southern Peru. Genomic analyses indicate that these individuals are genetically most similar to ancient and present-day populations from the north Peruvian coast located several hundred kilometers away. These genomic data are consistent with 16th century written records as well as ceramic, textile, and isotopic data. These results provide some of the strongest evidence yet of state-sponsored resettlement in the pre-Colonial Andes. This study highlights the power of transdisciplinary research designs when using aDNA data and sets a methodological standard for investigating ancient mobility in complex societies.}, }
@article {pmid32659643, year = {2020}, author = {Mendes, M and Alvim, I and Borda, V and Tarazona-Santos, E}, title = {The history behind the mosaic of the Americas.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {72-77}, doi = {10.1016/j.gde.2020.06.007}, pmid = {32659643}, issn = {1879-0380}, abstract = {Focusing on literature published in 2018-2020, we review inferences about: (i) how ancient DNA is contributing to clarify the peopling of the Americas and the dispersal of its first inhabitants, (ii) how the interplay between environmental diversity and culture has influenced the genetic structure and adaptation of Andean and Amazon populations, (iii) how genetics has contributed to our understanding of the Pre-Columbian Tupi expansion in Eastern South America, (iv) the subcontinental origins and dynamics of Post-Columbian admixture in the Americas, and finally, (v) episodes of adaptive natural selection in the American continent, particularly in the high altitudes of the Andes.}, }
@article {pmid32653893, year = {2020}, author = {Bai, F and Zhang, X and Ji, X and Cao, P and Feng, X and Yang, R and Peng, M and Pei, S and Fu, Q}, title = {Paleolithic genetic link between Southern China and Mainland Southeast Asia revealed by ancient mitochondrial genomes.}, journal = {Journal of human genetics}, volume = {65}, number = {12}, pages = {1125-1128}, doi = {10.1038/s10038-020-0796-9}, pmid = {32653893}, issn = {1435-232X}, support = {91731303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41925009//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41630102//National Natural Science Foundation of China (National Science Foundation of China)/ ; XDB26000000//Chinese Academy of Sciences (CAS)/ ; }, abstract = {The genetic history of Southern East Asians is not well-known, especially prior to the Neolithic period. To address this, we successfully sequenced two complete mitochondrial genomes of 11,000-year-old human individuals from Southern China, thus generating the oldest ancient DNA sequences from this area. Integrating published mitochondrial genomes, we characterized M71d, a new subhaplogroup of haplogroup M71. Our results suggest a possible early migration between Southern China and mainland Southeast Asia by at least 22,000 BP.}, }
@article {pmid32650941, year = {2020}, author = {Morrison, J and McColl, S and Louhelainen, J and Sheppard, K and May, A and Girdland-Flink, L and Watts, G and Dawnay, N}, title = {Assessing the performance of quantity and quality metrics using the QIAGEN Investigator® Quantiplex® pro RGQ kit.}, journal = {Science &amp; justice : journal of the Forensic Science Society}, volume = {60}, number = {4}, pages = {388-397}, doi = {10.1016/j.scijus.2020.03.002}, pmid = {32650941}, issn = {1876-4452}, abstract = {The Quantiplex® Pro RGQ kit quantifies DNA in a sample, supports the detection of mixtures and assesses the extent of DNA degradation based on relative ratios of amplified autosomal and male markers. Data show no significant difference in the accuracy and sensitivity of quantification between this and the Promega PowerQuant® System, both detecting the lowest amount of DNA tested, 4 pg. Laboratory controlled mixed male:female DNA samples together with mock sexual assault samples were quantified across a range of mixture ratios. Analysis software detected mixed DNA samples across all ratios for both quantification kits. Subsequent STR analysis using the Investigator® 24Plex QS Kit was able to corroborate mixture detection down to 1:25 male:female DNA ratios, past which point mixtures appeared identical to single-source female samples. Analysis software also detected laboratory degraded DNA samples, with data showing a positive trend between the Degradation Index (DI) and length of time of sonication. When used on ancient remains the assay was able to triage samples for further analysis, and STR profiles were concordant with DNA quantification results in all instances. STR analyses of laboratory-controlled sensitivity, mixture, and degradation studies supports the quality metric obtained from quantification. These data support the use of the Quantiplex® Pro RGQ kit for sample screening and quantification in forensic casework and ancient DNA studies.}, }
@article {pmid32648350, year = {2020}, author = {Peyrégne, S and Prüfer, K}, title = {Present-Day DNA Contamination in Ancient DNA Datasets.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {9}, pages = {e2000081}, doi = {10.1002/bies.202000081}, pmid = {32648350}, issn = {1521-1878}, support = {//Max-Planck-Gesellschaft/International ; 694707/ERC_/European Research Council/International ; }, abstract = {Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.}, }
@article {pmid32647890, year = {2020}, author = {Giuliani, C and Franceschi, C and Luiselli, D and Garagnani, P and Ulijaszek, S}, title = {Ecological Sensing Through Taste and Chemosensation Mediates Inflammation: A Biological Anthropological Approach.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {11}, number = {6}, pages = {1671-1685}, pmid = {32647890}, issn = {2156-5376}, abstract = {Ecological sensing and inflammation have evolved to ensure optima between organism survival and reproductive success in different and changing environments. At the molecular level, ecological sensing consists of many types of receptors located in different tissues that orchestrate integrated responses (immune, neuroendocrine systems) to external and internal stimuli. This review describes emerging data on taste and chemosensory receptors, proposing them as broad ecological sensors and providing evidence that taste perception is shaped not only according to sense epitopes from nutrients but also in response to highly diverse external and internal stimuli. We apply a biological anthropological approach to examine how ecological sensing has been shaped by these stimuli through human evolution for complex interkingdom communication between a host and pathological and symbiotic bacteria, focusing on population-specific genetic diversity. We then focus on how these sensory receptors play a major role in inflammatory processes that form the basis of many modern common metabolic diseases such as obesity, type 2 diabetes, and aging. The impacts of human niche construction and cultural evolution in shaping environments are described with emphasis on consequent biological responsiveness.}, }
@article {pmid32642779, year = {2020}, author = {Santiago, E and Novo, I and Pardiñas, AF and Saura, M and Wang, J and Caballero, A}, title = {Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium.}, journal = {Molecular biology and evolution}, volume = {37}, number = {12}, pages = {3642-3653}, doi = {10.1093/molbev/msaa169}, pmid = {32642779}, issn = {1537-1719}, abstract = {Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.}, }
@article {pmid32632332, year = {2020}, author = {Betti, L and Beyer, RM and Jones, ER and Eriksson, A and Tassi, F and Siska, V and Leonardi, M and Maisano Delser, P and Bentley, LK and Nigst, PR and Stock, JT and Pinhasi, R and Manica, A}, title = {Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE.}, journal = {Nature human behaviour}, volume = {4}, number = {10}, pages = {1004-1010}, doi = {10.1038/s41562-020-0897-7}, pmid = {32632332}, issn = {2397-3374}, mesh = {Agriculture/*history ; *Climate ; *DNA, Ancient ; Europe ; History, Ancient ; Humans ; Middle East ; *Paleontology ; Population Dynamics/*history ; }, abstract = {The Neolithic transition in Europe was driven by the rapid dispersal of Near Eastern farmers who, over a period of 3,500 years, brought food production to the furthest corners of the continent. However, this wave of expansion was far from homogeneous, and climatic factors may have driven a marked slowdown observed at higher latitudes. Here, we test this hypothesis by assembling a large database of archaeological dates of first arrival of farming to quantify the expansion dynamics. We identify four axes of expansion and observe a slowdown along three axes when crossing the same climatic threshold. This threshold reflects the quality of the growing season, suggesting that Near Eastern crops might have struggled under more challenging climatic conditions. This same threshold also predicts the mixing of farmers and hunter-gatherers as estimated from ancient DNA, suggesting that unreliable yields in these regions might have favoured the contact between the two groups.}, }
@article {pmid32621020, year = {2020}, author = {Navarro-Romero, MT and Muñoz, ML and Alcala-Castañeda, E and Terreros-Espinosa, E and Domínguez-de-la-Cruz, E and García-Hernández, N and Moreno-Galeana, MÁ}, title = {A novel method of male sex identification of human ancient skeletal remains.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {28}, number = {3-4}, pages = {277-291}, pmid = {32621020}, issn = {1573-6849}, abstract = {Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in subadult, or fragmented, incomplete skeletons or when the DNA is highly degraded. Most of the methods include the identification of the male and female sexes, but the absence of a specific marker for the males does not mean that the sample obtained was from a female. This study aims (1) to identify new male-specific regions that allow male identification; (2) to contrast the effectiveness of these markers against AMELX/AMELY and anthropometric measurement procedures; and (3) to test the efficacy of these markers in archaeological samples. For the first two aims, we used known sex samples, and for the third aim, we used samples from different archaeological sites. A novel molecular technique to identify male-specific regions by amplification of TTTY7, TSPY3, TTTY2, and TTTY22 genes of the human Y chromosome was developed. The results showed amplification of the specific DNA regions of Y chromosome in male individuals, with no amplification being observed in any of the female samples, confirming their specificity for male individuals. This approach complements the current procedures, such as the AMELX/AMELY test and anthropometric principle.}, }
@article {pmid32619963, year = {2020}, author = {Traversari, M and Da Via, S and Petrella, E and Feeney, RNM and Benazzi, S}, title = {A case of dwarfism in 6th century Italy: Bioarchaeological assessment of a hereditary disorder.}, journal = {International journal of paleopathology}, volume = {30}, number = {}, pages = {110-117}, doi = {10.1016/j.ijpp.2020.03.003}, pmid = {32619963}, issn = {1879-9825}, abstract = {OBJECTIVE: The skeletal remains of a short-statured individual (T17) are described and a differential diagnosis performed to determine the etiology of the condition.<br><br>MATERIALS: An individual considered pathologically short in stature was discovered in the burial site of Piazza XX Settembre, Modena (northern Italy).<br><br>METHODS: Morphological and morphometric analyses were performed, and T17 was compared to dwarfs from other localities and periods and to the adult female population from the same site. A paleopathological survey was undertaken to assess the degree of the skeletal elements of T17 were affected.<br><br>RESULTS: T17 was a female, 20-30 years of age at death, with a stature of 128 cm and disproportionate dwarfism associated with congenital skeletal dysplasia.<br><br>CONCLUSIONS: T17 likely affected by a form of hypochondroplasia.<br><br>SIGNIFICANCE: Anatomical consequences of hypochondroplasia are presented, and the timeframe and associated burial goods suggest a 6th-century Lombard short stature belonging to one of the earliest Lombard settlements in Italy.<br><br>Future genetic analysis would resolve if the mutation in the type 3 fibroblast growth factor receptor (FGFR3) is present in the remains of T17; however, it is not exclusivly linked to hypochondroplasia.}, }
@article {pmid32612278, year = {2020}, author = {Gansauge, MT and Aximu-Petri, A and Nagel, S and Meyer, M}, title = {Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA.}, journal = {Nature protocols}, volume = {15}, number = {8}, pages = {2279-2300}, doi = {10.1038/s41596-020-0338-0}, pmid = {32612278}, issn = {1750-2799}, mesh = {Automation ; Base Sequence ; *DNA, Ancient ; DNA, Single-Stranded/*genetics ; *Gene Library ; Sequence Analysis, DNA/*methods ; }, abstract = {It has been shown that highly fragmented DNA is most efficiently converted into DNA libraries for sequencing if both strands of the DNA fragments are processed independently. We present an updated protocol for library preparation from single-stranded DNA, which is based on the splinted ligation of an adapter oligonucleotide to the 3' ends of single DNA strands, the synthesis of a complementary strand using a DNA polymerase and the addition of a 5' adapter via blunt-end ligation. The efficiency of library preparation is determined individually for each sample using a spike-in oligonucleotide. The whole workflow, including library preparation, quantification and amplification, requires two work days for up to 16 libraries. Alternatively, we provide documentation and electronic protocols enabling automated library preparation of 96 samples in parallel on a Bravo NGS Workstation (Agilent Technologies). After library preparation, molecules with uninformative short inserts (shorter than ~30-35 base pairs) can be removed by polyacrylamide gel electrophoresis if desired.}, }
@article {pmid32610222, year = {2020}, author = {Olalde, I and Posth, C}, title = {Latest trends in archaeogenetic research of west Eurasians.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {36-43}, doi = {10.1016/j.gde.2020.05.021}, pmid = {32610222}, issn = {1879-0380}, abstract = {During the past ten years, archaeogenetic research has exponentially grown to study the genetic history of human populations, using genome-wide data from large numbers of ancient individuals. Of the entire globe, Europe and the Near East are the regions where ancient DNA data is by far most abundant with over 2500 genomes published at present. In this review, we focus on archaeological contexts that have received less attention in the literature, specifically those associated with west Eurasian hunter-gatherers as well as populations from the Iron Age and later historical periods. In addition, we emphasize a recent shift from continent-wide to regional and even site-specific studies, which is starting to provide novel insights into sociocultural aspects of past societies.}, }
@article {pmid32603999, year = {2020}, author = {Barquera, R and Krause, J}, title = {An ancient view on host pathogen interaction across time and space.}, journal = {Current opinion in immunology}, volume = {65}, number = {}, pages = {65-69}, doi = {10.1016/j.coi.2020.05.004}, pmid = {32603999}, issn = {1879-0372}, abstract = {The ancient DNA revolution provided diverse fields with an unprecedented opportunity to look back into the past and shed light on research aspects that were until now subject to speculation and inference from modern data. In particular enrichment methods that allow the targeted retrieval of millions of SNP positions from ancient human genomes, or even complete bacterial and viral genomes have the potential to revolutionize our understanding of host pathogen interactions. Ancient DNA combined with new bioinformatic tools now even allows actual allele calling for immunogenetic systems such as Human Leukocyte Antigen (HLA) across time and space. The coming years will provide us with frequency data of human immunity genes, such as HLA, as well as genome wide data of ancient pathogens from many time periods of human history, and will therefore provide us with a dynamic view on historical human adaptation to pathogen exposure on a population wide scale.}, }
@article {pmid32598277, year = {2020}, author = {Arning, N and Wilson, DJ}, title = {The past, present and future of ancient bacterial DNA.}, journal = {Microbial genomics}, volume = {6}, number = {7}, pages = {}, pmid = {32598277}, issn = {2057-5858}, support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101237/Z/13/B/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.}, }
@article {pmid32586278, year = {2020}, author = {Weiß, CL and Gansauge, MT and Aximu-Petri, A and Meyer, M and Burbano, HA}, title = {Mining ancient microbiomes using selective enrichment of damaged DNA molecules.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {432}, pmid = {32586278}, issn = {1471-2164}, support = {Presidential Innovation Fund//Max-Planck-Gesellschaft/ ; }, abstract = {BACKGROUND: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains.<br><br>RESULTS: We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach.<br><br>CONCLUSIONS: Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.}, }
@article {pmid32584871, year = {2020}, author = {Kontopoulos, I and Penkman, K and Mullin, VE and Winkelbach, L and Unterländer, M and Scheu, A and Kreutzer, S and Hansen, HB and Margaryan, A and Teasdale, MD and Gehlen, B and Street, M and Lynnerup, N and Liritzis, I and Sampson, A and Papageorgopoulou, C and Allentoft, ME and Burger, J and Bradley, DG and Collins, MJ}, title = {Screening archaeological bone for palaeogenetic and palaeoproteomic studies.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0235146}, pmid = {32584871}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; Bone and Bones/*chemistry/metabolism ; DNA, Ancient/*analysis/chemistry ; *Fossils ; Humans ; *Proteomics ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals' size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.}, }
@article {pmid32582847, year = {2020}, author = {Wang, K and Goldstein, S and Bleasdale, M and Clist, B and Bostoen, K and Bakwa-Lufu, P and Buck, LT and Crowther, A and Dème, A and McIntosh, RJ and Mercader, J and Ogola, C and Power, RC and Sawchuk, E and Robertshaw, P and Wilmsen, EN and Petraglia, M and Ndiema, E and Manthi, FK and Krause, J and Roberts, P and Boivin, N and Schiffels, S}, title = {Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa.}, journal = {Science advances}, volume = {6}, number = {24}, pages = {eaaz0183}, pmid = {32582847}, issn = {2375-2548}, abstract = {Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.}, }
@article {pmid32574964, year = {2020}, author = {Mathov, Y and Batyrev, D and Meshorer, E and Carmel, L}, title = {Harnessing epigenetics to study human evolution.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {23-29}, doi = {10.1016/j.gde.2020.05.023}, pmid = {32574964}, issn = {1879-0380}, abstract = {Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates.}, }
@article {pmid32572090, year = {2020}, author = {Debortoli, G and Abbatangelo, C and Ceballos, F and Fortes-Lima, C and Norton, HL and Ozarkar, S and Parra, EJ and Jonnalagadda, M}, title = {Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10075}, doi = {10.1038/s41598-020-66953-3}, pmid = {32572090}, issn = {2045-2322}, mesh = {Ethnic Groups/*genetics ; Genetic Drift ; Genotyping Techniques ; Humans ; India/ethnology ; Population Density ; Social Class ; Whole Genome Sequencing/*methods ; }, abstract = {The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.}, }
@article {pmid32563853, year = {2020}, author = {Vicente, M and Schlebusch, CM}, title = {African population history: an ancient DNA perspective.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {8-15}, doi = {10.1016/j.gde.2020.05.008}, pmid = {32563853}, issn = {1879-0380}, abstract = {The history of human populations in Africa is complex and includes various demographic events that influenced patterns of genetic variation across the continent. Through genetic studies of modern-day, and most recently, ancient African genetic variation, it became evident that deep African history is captured by the relationships among hunter-gatherers. Furthermore, it was shown that agriculture had a large influence on the distribution of current-day Africans. These later population movements changed the demographic face of the continent and descendants of farming groups today form the majority populations across Africa. Ancient DNA methods are continually evolving, and we see evidence of this in how research has advanced in the last decade. With the increased availability of full genomic data from diverse sets of modern-day and prehistoric Africans we now have more power to infer human demography. Future ancient DNA research promises to reveal more detailed stories of human prehistory in Africa.}, }
@article {pmid32557548, year = {2020}, author = {Goude, G and Salazar-García, DC and Power, RC and Rivollat, M and Gourichon, L and Deguilloux, MF and Pemonge, MH and Bouby, L and Binder, D}, title = {New insights on Neolithic food and mobility patterns in Mediterranean coastal populations.}, journal = {American journal of physical anthropology}, volume = {173}, number = {2}, pages = {218-235}, doi = {10.1002/ajpa.24089}, pmid = {32557548}, issn = {1096-8644}, abstract = {OBJECTIVES: The aims of this research are to explore the diet, mobility, social organization, and environmental exploitation patterns of early Mediterranean farmers, particularly the role of marine and plant resources in these foodways. In addition, this work strives to document possible gendered patterns of behavior linked to the neolithization of this ecologically rich area. To achieve this, a set of multiproxy analyses (isotopic analyses, dental calculus, microremains analysis, ancient DNA) were performed on an exceptional deposit (n = 61) of human remains from the Les Bréguières site (France), dating to the transition of the sixth to the fifth millennium BCE.<br><br>MATERIALS AND METHODS: The samples used in this study were excavated from the Les Bréguières site (Mougins, Alpes-Maritimes, France), located along the southeastern Mediterranean coastline of France. Stable isotope analyses (C, N) on bone collagen (17 coxal bones, 35 craniofacial elements) were performed as a means to infer protein intake during tissue development. Sulfur isotope ratios were used as indicators of geographical and environmental points of origin. The study of ancient dental calculus helped document the consumption of plants. Strontium isotope analysis on tooth enamel (n = 56) was conducted to infer human provenance and territorial mobility. Finally, ancient DNA analysis was performed to study maternal versus paternal diversity within this Neolithic group (n = 30).<br><br>RESULTS: Stable isotope ratios for human bones range from -20.3 to -18.1‰ for C, from 8.9 to 11.1‰ for N and from 6.4 to 15‰ for S. Domestic animal data range from -22.0 to -20.2‰ for C, from 4.1 to 6.9‰ for N, and from 10.2 to 12.5‰ for S. Human enamel 87 Sr/86 Sr range from 0.7081 to 0.7102, slightly wider than the animal range (between 0.7087 and 0.7096). Starch and phytolith microremains were recovered as well as other types of remains (e.g., hairs, diatoms, fungal spores). Starch grains include Triticeae type and phytolith includes dicotyledons and monocot types as panicoid grasses. Mitochondrial DNA characterized eight different maternal lineages: H1, H3, HV (5.26%), J (10.53%), J1, K, T (5.2%), and U5 (10.53%) but no sample yielded reproducible Y chromosome SNPs, preventing paternal lineage characterization.<br><br>DISCUSSION: Carbon and nitrogen stable isotope ratios indicate a consumption of protein by humans mainly focused on terrestrial animals and possible exploitation of marine resources for one male and one undetermined adult. Sulfur stable isotope ratios allowed distinguishing groups with different geographical origins, including two females possibly more exposed to the sea spray effect. While strontium isotope data do not indicate different origins for the individuals, mitochondrial lineage diversity from petrous bone DNA suggests the burial includes genetically differentiated groups or a group practicing patrilocality. Moreover, the diversity of plant microremains recorded in dental calculus provide the first evidence that the groups of Les Bréguières consumed a wide breadth of plant foods (as cereals and wild taxa) that required access to diverse environments. This transdisciplinary research paves the way for new perspectives and highlights the relevance for novel research of contexts (whether recently discovered or in museum collections) excavated near shorelines, due to the richness of the biodiversity and the wide range of edible resources available.}, }
@article {pmid32555485, year = {2020}, author = {Cassidy, LM and Maoldúin, RÓ and Kador, T and Lynch, A and Jones, C and Woodman, PC and Murphy, E and Ramsey, G and Dowd, M and Noonan, A and Campbell, C and Jones, ER and Mattiangeli, V and Bradley, DG}, title = {A dynastic elite in monumental Neolithic society.}, journal = {Nature}, volume = {582}, number = {7812}, pages = {384-388}, doi = {10.1038/s41586-020-2378-6}, pmid = {32555485}, issn = {1476-4687}, support = {205072/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adult ; Burial/history ; *Consanguinity ; DNA, Ancient/analysis ; Family/history ; Female ; Genome, Human/genetics ; Haplotypes/genetics ; Hierarchy, Social/*history ; History, Ancient ; Humans ; Incest/*history ; Ireland ; Male ; Societies/*history ; }, abstract = {The nature and distribution of political power in Europe during the Neolithic era remains poorly understood1. During this period, many societies began to invest heavily in building monuments, which suggests an increase in social organization. The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the great passage tomb complexes, is particularly impressive2. Although co-operative ideology has often been emphasised as a driver of megalith construction1, the human expenditure required to erect the largest monuments has led some researchers to emphasize hierarchy3-of which the most extreme case is a small elite marshalling the labour of the masses. Here we present evidence that a social stratum of this type was established during the Neolithic period in Ireland. We sampled 44 whole genomes, among which we identify the adult son of a first-degree incestuous union from remains that were discovered within the most elaborate recess of the Newgrange passage tomb. Socially sanctioned matings of this nature are very rare, and are documented almost exclusively among politico-religious elites4-specifically within polygynous and patrilineal royal families that are headed by god-kings5,6. We identify relatives of this individual within two other major complexes of passage tombs 150 km to the west of Newgrange, as well as dietary differences and fine-scale haplotypic structure (which is unprecedented in resolution for a prehistoric population) between passage tomb samples and the larger dataset, which together imply hierarchy. This elite emerged against a backdrop of rapid maritime colonization that displaced a unique Mesolithic isolate population, although we also detected rare Irish hunter-gatherer introgression within the Neolithic population.}, }
@article {pmid32554575, year = {2020}, author = {Curry, A}, title = {Incest in ancient Ireland suggests an elite ruled early farmers.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6497}, pages = {1299}, doi = {10.1126/science.368.6497.1299}, pmid = {32554575}, issn = {1095-9203}, mesh = {Archaeology ; DNA, Ancient ; Farmers/*history ; History, Ancient ; Humans ; Incest/*history ; Ireland ; Middle Aged ; }, }
@article {pmid32545993, year = {2020}, author = {Vera-Villalobos, H and Pérez, V and Contreras, F and Alcayaga, V and Avalos, V and Riquelme, C and Silva-Aciares, F}, title = {Characterization and removal of biofouling from reverse osmosis membranes (ROMs) from a desalination plant in Northern Chile, using Alteromonas sp. Ni1-LEM supernatant.}, journal = {Biofouling}, volume = {36}, number = {5}, pages = {505-515}, doi = {10.1080/08927014.2020.1776268}, pmid = {32545993}, issn = {1029-2454}, mesh = {*Alteromonas ; Biofilms ; *Biofouling ; Chile ; Humans ; Membranes ; Membranes, Artificial ; Osmosis ; Plants ; *Water Purification ; }, abstract = {Biofouling control in reverse osmosis membranes (ROMs) is challenging due to the high cost of treatments, and reduction in the life of ROMs. This study characterizes the biofouling in the ROMs from a desalination plant and reports its effective removal using the supernatant obtained from Alteromonas sp. strain Ni1-LEM. The characterization of the bacterial community revealed that the most abundant taxa in ROMs were the genera Fulvivirga and Pseudoalteromonas, and unclassified species of the families Flavobacteriaceae and Sphingomonadaceae. This bacterial community significantly decreased upon treatment with the supernatant from Alteromonas sp. Ni1-LEM, resulting in the prevalence of the genus Pseudoalteromonas. Furthermore, this bacterial supernatant significantly inhibited cell adhesion of seven benthic microalgae isolated from ROMs as well as promoting cell detachment of the existing microbial biofilms. The study showed that the extracellular supernatant modified the conformation of extracellular polymeric substances (EPS) in the biofouling of ROMs without any biocidal effects.}, }
@article {pmid32539695, year = {2020}, author = {Philips, A and Stolarek, I and Handschuh, L and Nowis, K and Juras, A and Trzciński, D and Nowaczewska, W and Wrzesińska, A and Potempa, J and Figlerowicz, M}, title = {Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {402}, pmid = {32539695}, issn = {1471-2164}, support = {2014/12/W/NZ2/00466//Narodowe Centrum Nauki/ ; 2016/21/B/NZ1/00292//Narodowe Centrum Nauki/ ; R21DE026280/DE/NIDCR NIH HHS/United States ; }, abstract = {BACKGROUND: Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death.<br><br>RESULTS: In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. forsythia-containing samples were obtained revealed the pathogenic alveolar bone loss in tooth areas characteristic for advanced periodontitis. Finally, we analyzed the genetic material of ancient T. forsythia strains. As a result, we assembled four ancient T. forsythia genomes - one 2000- and three 1000- year-old. Their comparison with contemporary T. forsythia genomes revealed a lower genetic diversity within the four ancient strains than within contemporary strains. We also investigated the genes of T. forsythia virulence factors and found that several of them (KLIKK protease and bspA genes) differ significantly between ancient and modern bacteria.<br><br>CONCLUSIONS: In summary, we showed that NGS screening of the ancient human microbiome is a valid approach for the identification of disease-associated microbes. Following this protocol, we provided a new set of information on the emergence, evolution and virulence factors of T. forsythia, the member of the oral dysbiotic microbiome.}, }
@article {pmid32523989, year = {2020}, author = {Rivollat, M and Jeong, C and Schiffels, S and Küçükkalıpçı, İ and Pemonge, MH and Rohrlach, AB and Alt, KW and Binder, D and Friederich, S and Ghesquière, E and Gronenborn, D and Laporte, L and Lefranc, P and Meller, H and Réveillas, H and Rosenstock, E and Rottier, S and Scarre, C and Soler, L and Wahl, J and Krause, J and Deguilloux, MF and Haak, W}, title = {Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers.}, journal = {Science advances}, volume = {6}, number = {22}, pages = {eaaz5344}, pmid = {32523989}, issn = {2375-2548}, abstract = {Starting from 12,000 years ago in the Middle East, the Neolithic lifestyle spread across Europe via separate continental and Mediterranean routes. Genomes from early European farmers have shown a clear Near Eastern/Anatolian genetic affinity with limited contribution from hunter-gatherers. However, no genomic data are available from modern-day France, where both routes converged, as evidenced by a mosaic cultural pattern. Here, we present genome-wide data from 101 individuals from 12 sites covering today's France and Germany from the Mesolithic (N = 3) to the Neolithic (N = 98) (7000-3000 BCE). Using the genetic substructure observed in European hunter-gatherers, we characterize diverse patterns of admixture in different regions, consistent with both routes of expansion. Early western European farmers show a higher proportion of distinctly western hunter-gatherer ancestry compared to central/southeastern farmers. Our data highlight the complexity of the biological interactions during the Neolithic expansion by revealing major regional variations.}, }
@article {pmid32511234, year = {2020}, author = {Segurel, L and Guarino-Vignon, P and Marchi, N and Lafosse, S and Laurent, R and Bon, C and Fabre, A and Hegay, T and Heyer, E}, title = {Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA.}, journal = {PLoS biology}, volume = {18}, number = {6}, pages = {e3000742}, pmid = {32511234}, issn = {1545-7885}, mesh = {Animals ; Asia ; *DNA, Ancient ; Ethnic Groups/genetics ; Europe ; Fermentation ; Gene Frequency/genetics ; Genotype ; Humans ; Lactase/*genetics ; Milk ; *Selection, Genetic ; Time Factors ; }, abstract = {The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?}, }
@article {pmid32497501, year = {2020}, author = {Díez-Del-Molino, D and Dalén, L}, title = {Unroll Please: Deciphering the Genetic Code in Scrolls and Other Ancient Materials.}, journal = {Cell}, volume = {181}, number = {6}, pages = {1200-1201}, doi = {10.1016/j.cell.2020.05.031}, pmid = {32497501}, issn = {1097-4172}, mesh = {*DNA, Ancient ; Genetic Code ; }, abstract = {The unrelenting development of ancient DNA methods now allows researchers to obtain archaeogenetic data from increasingly diverse sources. In a new study in this issue of Cell, researchers apply the latest DNA technologies to unravel the mysteries of the Dead Sea Scrolls, one of the world's most famous and influential sets of ancient parchments.}, }
@article {pmid32497286, year = {2020}, author = {Coutinho, A and Günther, T and Munters, AR and Svensson, EM and Götherström, A and Storå, J and Malmström, H and Jakobsson, M}, title = {The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.}, journal = {American journal of physical anthropology}, volume = {172}, number = {4}, pages = {638-649}, doi = {10.1002/ajpa.24079}, pmid = {32497286}, issn = {1096-8644}, abstract = {OBJECTIVES: In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences.<br><br>METHODS: We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools.<br><br>RESULTS: The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style.<br><br>CONCLUSION: We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.}, }
@article {pmid32497204, year = {2020}, author = {Buckley, M and Harvey, VL and Orihuela, J and Mychajliw, AM and Keating, JN and Milan, JNA and Lawless, C and Chamberlain, AT and Egerton, VM and Manning, PL}, title = {Collagen Sequence Analysis Reveals Evolutionary History of Extinct West Indies Nesophontes (Island-Shrews).}, journal = {Molecular biology and evolution}, volume = {37}, number = {10}, pages = {2931-2943}, pmid = {32497204}, issn = {1537-1719}, abstract = {Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to assist species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba toward Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to N. major rather than N. micrus as previously speculated. This proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to the approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.}, }
@article {pmid32492404, year = {2020}, author = {Anava, S and Neuhof, M and Gingold, H and Sagy, O and Munters, A and Svensson, EM and Afshinnekoo, E and Danko, D and Foox, J and Shor, P and Riestra, B and Huchon, D and Mason, CE and Mizrahi, N and Jakobsson, M and Rechavi, O}, title = {Illuminating Genetic Mysteries of the Dead Sea Scrolls.}, journal = {Cell}, volume = {181}, number = {6}, pages = {1218-1231.e27}, doi = {10.1016/j.cell.2020.04.046}, pmid = {32492404}, issn = {1097-4172}, mesh = {Animals ; Base Sequence/*genetics ; Christianity/history ; Genetics/*history ; History, Ancient ; Humans ; Israel ; Judaism/history ; Skin/*metabolism ; }, abstract = {The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. &quot;Piecing together&quot; scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to &quot;fingerprint&quot; pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.}, }
@article {pmid32488006, year = {2020}, author = {Seersholm, FV and Werndly, DJ and Grealy, A and Johnson, T and Keenan Early, EM and Lundelius, EL and Winsborough, B and Farr, GE and Toomey, R and Hansen, AJ and Shapiro, B and Waters, MR and McDonald, G and Linderholm, A and Stafford, TW and Bunce, M}, title = {Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2770}, doi = {10.1038/s41467-020-16502-3}, pmid = {32488006}, issn = {2041-1723}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Biodiversity ; *Climate Change ; *Ecosystem ; *Extinction, Biological ; Fossils ; High-Throughput Nucleotide Sequencing ; Paleontology ; Plants/genetics ; Sequence Analysis ; Texas ; }, abstract = {Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall's Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.}, }
@article {pmid32483316, year = {2020}, author = {Lord, E and Collins, C and deFrance, S and LeFebvre, MJ and Pigière, F and Eeckhout, P and Erauw, C and Fitzpatrick, SM and Healy, PF and Martínez-Polanco, MF and Garcia, JL and Ramos Roca, E and Delgado, M and Sánchez Urriago, A and Peña Léon, GA and Toyne, JM and Dahlstedt, A and Moore, KM and Laguer Diaz, C and Zori, C and Matisoo-Smith, E}, title = {Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8901}, doi = {10.1038/s41598-020-65784-6}, pmid = {32483316}, issn = {2045-2322}, mesh = {Animals ; Belgium ; Bolivia ; Colombia ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Domestication ; Evolution, Molecular ; Guinea Pigs/*classification/genetics ; Mitochondria/*genetics ; Peru ; Phylogeny ; Phylogeography ; Population Dynamics ; Puerto Rico ; Sequence Analysis, DNA/*veterinary ; United States ; }, abstract = {Guinea pigs (Cavia spp.) have a long association with humans. From as early as 10,000 years ago they were a wild food source. Later, domesticated Cavia porcellus were dispersed well beyond their native range through pre-Columbian exchange networks and, more recently, widely across the globe. Here we present 46 complete mitogenomes of archaeological guinea pigs from sites in Peru, Bolivia, Colombia, the Caribbean, Belgium and the United States to elucidate their evolutionary history, origins and paths of dispersal. Our results indicate an independent centre of domestication of Cavia in the eastern Colombian Highlands. We identify a Peruvian origin for the initial introduction of domesticated guinea pigs (Cavia porcellus) beyond South America into the Caribbean. We also demonstrate that Peru was the probable source of the earliest known guinea pigs transported, as part of the exotic pet trade, to both Europe and the southeastern United States. Finally, we identify a modern reintroduction of guinea pigs to Puerto Rico, where local inhabitants use them for food. This research demonstrates that the natural and cultural history of guinea pigs is more complex than previously known and has implications for other studies regarding regional to global-scale studies of mammal domestication, translocation, and distribution.}, }
@article {pmid32483115, year = {2020}, author = {Ning, C and Li, T and Wang, K and Zhang, F and Li, T and Wu, X and Gao, S and Zhang, Q and Zhang, H and Hudson, MJ and Dong, G and Wu, S and Fang, Y and Liu, C and Feng, C and Li, W and Han, T and Li, R and Wei, J and Zhu, Y and Zhou, Y and Wang, CC and Fan, S and Xiong, Z and Sun, Z and Ye, M and Sun, L and Wu, X and Liang, F and Cao, Y and Wei, X and Zhu, H and Zhou, H and Krause, J and Robbeets, M and Jeong, C and Cui, Y}, title = {Ancient genomes from northern China suggest links between subsistence changes and human migration.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2700}, doi = {10.1038/s41467-020-16557-2}, pmid = {32483115}, issn = {2041-1723}, mesh = {Agriculture/*methods ; Archaeology/methods ; Asian Continental Ancestry Group/genetics/statistics &amp; numerical data ; China ; Crops, Agricultural/*growth &amp; development ; DNA, Ancient/analysis ; Edible Grain/*growth &amp; development ; Genetics, Population/methods ; *Genome, Human ; Geography ; *Human Migration ; Humans ; Population Dynamics ; Rivers ; Sequence Analysis, DNA/methods ; Time Factors ; }, abstract = {Northern China harbored the world's earliest complex societies based on millet farming, in two major centers in the Yellow (YR) and West Liao (WLR) River basins. Until now, their genetic histories have remained largely unknown. Here we present 55 ancient genomes dating to 7500-1700 BP from the YR, WLR, and Amur River (AR) regions. Contrary to the genetic stability in the AR, the YR and WLR genetic profiles substantially changed over time. The YR populations show a monotonic increase over time in their genetic affinity with present-day southern Chinese and Southeast Asians. In the WLR, intensification of farming in the Late Neolithic is correlated with increased YR affinity while the inclusion of a pastoral economy in the Bronze Age was correlated with increased AR affinity. Our results suggest a link between changes in subsistence strategy and human migration, and fuel the debate about archaeolinguistic signatures of past human migration.}, }
@article {pmid32475052, year = {2020}, author = {Barquera, R and Collen, E and Di, D and Buhler, S and Teixeira, J and Llamas, B and Nunes, JM and Sanchez-Mazas, A}, title = {Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide.}, journal = {HLA}, volume = {96}, number = {3}, pages = {277-298}, pmid = {32475052}, issn = {2059-2310}, support = {//Australian Government Research Training Program Stipend (RTPS)/International ; IN180100017//Australian Research Council Discovery Indigenous Project/International ; FT170100448//Australian Research Council Future Fellowship/International ; BM0803//European Cooperation in Science and Technology/International ; //Max-Planck-Gesellschaft/International ; 310030_188820//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/International ; 31003A_144180//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/International ; }, mesh = {Africa/epidemiology ; Americas/epidemiology ; Amino Acid Sequence ; Asia/epidemiology ; Australia/epidemiology ; Betacoronavirus/genetics/immunology ; COVID-19 ; Computational Biology ; Coronavirus Infections/*epidemiology/immunology/virology ; Europe/epidemiology ; HIV Infections/*epidemiology/immunology/virology ; HIV-1/genetics/immunology ; HLA Antigens/*chemistry/classification/genetics/immunology ; Humans ; Influenza A Virus, H1N1 Subtype/genetics/immunology ; Influenza A Virus, H3N2 Subtype/genetics/immunology ; Influenza A Virus, H7N9 Subtype/genetics/immunology ; Influenza, Human/*epidemiology/immunology/virology ; Kinetics ; Middle East Respiratory Syndrome Coronavirus/genetics/immunology ; *Pandemics ; Peptides/*chemistry/genetics/immunology ; Pneumonia, Viral/*epidemiology/immunology/virology ; Protein Binding ; SARS Virus/genetics/immunology ; SARS-CoV-2 ; Severe Acute Respiratory Syndrome/*epidemiology/immunology/virology ; Viral Proteins/*chemistry/genetics/immunology ; }, abstract = {We report detailed peptide-binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV-1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide-binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV-1. Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA-A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV-1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions. In particular, Indigenous peoples of America show both higher frequencies of strongest and lower frequencies of weakest HLA binders. As many HLA proteins are found to be strong binders of peptides derived from distinct viral families, and are hence promiscuous (or generalist), we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to past pathogenic infections. Our findings are highly relevant for both evolutionary genetics and the development of vaccine therapies. However they should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables.}, }
@article {pmid32470401, year = {2020}, author = {Skourtanioti, E and Erdal, YS and Frangipane, M and Balossi Restelli, F and Yener, KA and Pinnock, F and Matthiae, P and Özbal, R and Schoop, UD and Guliyev, F and Akhundov, T and Lyonnet, B and Hammer, EL and Nugent, SE and Burri, M and Neumann, GU and Penske, S and Ingman, T and Akar, M and Shafiq, R and Palumbi, G and Eisenmann, S and D'Andrea, M and Rohrlach, AB and Warinner, C and Jeong, C and Stockhammer, PW and Haak, W and Krause, J}, title = {Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus.}, journal = {Cell}, volume = {181}, number = {5}, pages = {1158-1175.e28}, doi = {10.1016/j.cell.2020.04.044}, pmid = {32470401}, issn = {1097-4172}, mesh = {Archaeology/methods ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Ethnic Groups/*genetics/history ; Gene Flow/*genetics/physiology ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Human/genetics ; Genomics/methods ; Haplotypes ; History, Ancient ; Human Migration/history ; Humans ; Mediterranean Region ; Middle East ; Sequence Analysis, DNA ; }, abstract = {Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6th millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today's Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age. VIDEO ABSTRACT.}, }
@article {pmid32470400, year = {2020}, author = {Agranat-Tamir, L and Waldman, S and Martin, MAS and Gokhman, D and Mishol, N and Eshel, T and Cheronet, O and Rohland, N and Mallick, S and Adamski, N and Lawson, AM and Mah, M and Michel, M and Oppenheimer, J and Stewardson, K and Candilio, F and Keating, D and Gamarra, B and Tzur, S and Novak, M and Kalisher, R and Bechar, S and Eshed, V and Kennett, DJ and Faerman, M and Yahalom-Mack, N and Monge, JM and Govrin, Y and Erel, Y and Yakir, B and Pinhasi, R and Carmi, S and Finkelstein, I and Carmel, L and Reich, D}, title = {The Genomic History of the Bronze Age Southern Levant.}, journal = {Cell}, volume = {181}, number = {5}, pages = {1146-1157.e11}, doi = {10.1016/j.cell.2020.04.024}, pmid = {32470400}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Archaeology/methods ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Ethnic Groups/*genetics/history ; Gene Flow/*genetics/physiology ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Human/genetics ; Genomics/methods ; Haplotypes ; History, Ancient ; Human Migration/history ; Humans ; Mediterranean Region ; Middle East ; Sequence Analysis, DNA ; }, abstract = {We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the &quot;Canaanite&quot; material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different &quot;Canaanite&quot; groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze-Age migrations into the region over the past 3,000 years.}, }
@article {pmid32467975, year = {2020}, author = {Brealey, JC and Leitão, HG and van der Valk, T and Xu, W and Bougiouri, K and Dalén, L and Guschanski, K}, title = {Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome.}, journal = {Molecular biology and evolution}, volume = {37}, number = {10}, pages = {3003-3022}, pmid = {32467975}, issn = {1537-1719}, abstract = {Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.}, }
@article {pmid32457149, year = {2020}, author = {Brunel, S and Bennett, EA and Cardin, L and Garraud, D and Barrand Emam, H and Beylier, A and Boulestin, B and Chenal, F and Ciesielski, E and Convertini, F and Dedet, B and Desbrosse-Degobertiere, S and Desenne, S and Dubouloz, J and Duday, H and Escalon, G and Fabre, V and Gailledrat, E and Gandelin, M and Gleize, Y and Goepfert, S and Guilaine, J and Hachem, L and Ilett, M and Lambach, F and Maziere, F and Perrin, B and Plouin, S and Pinard, E and Praud, I and Richard, I and Riquier, V and Roure, R and Sendra, B and Thevenet, C and Thiol, S and Vauquelin, E and Vergnaud, L and Grange, T and Geigl, EM and Pruvost, M}, title = {Ancient genomes from present-day France unveil 7,000 years of its demographic history.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {23}, pages = {12791-12798}, pmid = {32457149}, issn = {1091-6490}, mesh = {Chromosomes, Human, Y/genetics ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Female ; France ; Gene Flow ; *Genome, Human ; *Human Migration ; Humans ; Male ; Polymorphism, Genetic ; Population/*genetics ; }, abstract = {Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotypes of a number of nuclear loci of interest of 243 individuals sampled across present-day France over a period spanning 7,000 y, complemented with a partially overlapping dataset of 58 low-coverage genomes. This panel provides a high-resolution transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Parental lineages and genomic data both revealed demographic patterns in France for the Neolithic and Bronze Age transitions consistent with neighboring regions, first with a migration wave of Anatolian farmers followed by varying degrees of admixture with autochthonous hunter-gatherers, and then substantial gene flow from individuals deriving part of their ancestry from the Pontic steppe at the onset of the Bronze Age. Our data have also highlighted the persistence of Magdalenian-associated ancestry in hunter-gatherer populations outside of Spain and thus provide arguments for an expansion of these populations at the end of the Paleolithic Period more northerly than what has been described so far. Finally, no major demographic changes were detected during the transition between the Bronze and Iron Ages.}, }
@article {pmid32446165, year = {2020}, author = {Gonzalez, A and Cannet, C and Zvénigorosky, V and Geraut, A and Koch, G and Delabarde, T and Ludes, B and Raul, JS and Keyser, C}, title = {The petrous bone: Ideal substrate in legal medicine?.}, journal = {Forensic science international. Genetics}, volume = {47}, number = {}, pages = {102305}, doi = {10.1016/j.fsigen.2020.102305}, pmid = {32446165}, issn = {1878-0326}, abstract = {Over the last few years, palaeogenomic studies of the petrous bone (the densest part of the temporal bone) have shown that it is a source of DNA in both larger quantities and of better quality than other bones. This dense bone around the otic capsule has therefore been called the choice substrate in palaeogenomics. Because the practice of forensic genetics responds to different imperatives, we implemented a study aimed at (i) understanding how and why the petrous bone is an advantageous substrate in ancient DNA studies and (ii) establishing whether it is advantageous in forensic STR typing. We selected 50 individual skeletal remains and extracted DNA from one tooth and one petrous bone from each. We then amplified 24 STR markers commonly used in forensic identification and compared the quality of that amplification using the RFU intensities of the signal as read on the STR profiles. We also performed histological analyses to compare (i) the microscopic structure of a petrous bone and of a tooth and (ii) the microscopic structure of fresh petrous bone and of an archaeological or forensic sample. We show that the RFU intensities read on STR profiles are systematically higher in experiments using DNA extracted from petrous bones rather than teeth. For this reason, we were more likely to obtain a complete STR profile from petrous bone material, increasing the chance of identification in a forensic setting. Histological analyses revealed peculiar microstructural characteristics (tissue organization), unique to the petrous bone, that might explain the good preservation of DNA in that substrate. Therefore, it appears that despite the necessity of analysing longer fragments in forensic STR typing compared to NGS palaeogenomics, the use of petrous bones in forensic genetics could prove valuable, especially in cases involving infants, toothless individuals or very degraded skeletal remains.}, }
@article {pmid32437661, year = {2020}, author = {Yu, H and Spyrou, MA and Karapetian, M and Shnaider, S and Radzevičiūtė, R and Nägele, K and Neumann, GU and Penske, S and Zech, J and Lucas, M and LeRoux, P and Roberts, P and Pavlenok, G and Buzhilova, A and Posth, C and Jeong, C and Krause, J}, title = {Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia.}, journal = {Cell}, volume = {181}, number = {6}, pages = {1232-1245.e20}, doi = {10.1016/j.cell.2020.04.037}, pmid = {32437661}, issn = {1097-4172}, mesh = {Asia ; Continental Population Groups/*genetics/*history ; DNA, Ancient ; Europe ; Genome, Human/*genetics ; History, Ancient ; Human Migration/*history ; Humans ; Siberia ; }, abstract = {Modern humans have inhabited the Lake Baikal region since the Upper Paleolithic, though the precise history of its peoples over this long time span is still largely unknown. Here, we report genome-wide data from 19 Upper Paleolithic to Early Bronze Age individuals from this Siberian region. An Upper Paleolithic genome shows a direct link with the First Americans by sharing the admixed ancestry that gave rise to all non-Arctic Native Americans. We also demonstrate the formation of Early Neolithic and Bronze Age Baikal populations as the result of prolonged admixture throughout the eighth to sixth millennium BP. Moreover, we detect genetic interactions with western Eurasian steppe populations and reconstruct Yersinia pestis genomes from two Early Bronze Age individuals without western Eurasian ancestry. Overall, our study demonstrates the most deeply divergent connection between Upper Paleolithic Siberians and the First Americans and reveals human and pathogen mobility across Eurasia during the Bronze Age.}, }
@article {pmid32433609, year = {2020}, author = {Hublin, JJ and Sirakov, N and Aldeias, V and Bailey, S and Bard, E and Delvigne, V and Endarova, E and Fagault, Y and Fewlass, H and Hajdinjak, M and Kromer, B and Krumov, I and Marreiros, J and Martisius, NL and Paskulin, L and Sinet-Mathiot, V and Meyer, M and Pääbo, S and Popov, V and Rezek, Z and Sirakova, S and Skinner, MM and Smith, GM and Spasov, R and Talamo, S and Tuna, T and Wacker, L and Welker, F and Wilcke, A and Zahariev, N and McPherron, SP and Tsanova, T}, title = {Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria.}, journal = {Nature}, volume = {581}, number = {7808}, pages = {299-302}, doi = {10.1038/s41586-020-2259-z}, pmid = {32433609}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, mesh = {Animals ; Asia ; Bone and Bones/metabolism ; Bulgaria ; Caves ; DNA, Ancient/isolation &amp; purification ; DNA, Mitochondrial/genetics/isolation &amp; purification ; Europe ; *Fossils ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; Phylogeny ; Tool Use Behavior ; Tooth/anatomy &amp; histology/metabolism ; }, abstract = {The Middle to Upper Palaeolithic transition in Europe witnessed the replacement and partial absorption of local Neanderthal populations by Homo sapiens populations of African origin1. However, this process probably varied across regions and its details remain largely unknown. In particular, the duration of chronological overlap between the two groups is much debated, as are the implications of this overlap for the nature of the biological and cultural interactions between Neanderthals and H. sapiens. Here we report the discovery and direct dating of human remains found in association with Initial Upper Palaeolithic artefacts2, from excavations at Bacho Kiro Cave (Bulgaria). Morphological analysis of a tooth and mitochondrial DNA from several hominin bone fragments, identified through proteomic screening, assign these finds to H. sapiens and link the expansion of Initial Upper Palaeolithic technologies with the spread of H. sapiens into the mid-latitudes of Eurasia before 45 thousand years ago3. The excavations yielded a wealth of bone artefacts, including pendants manufactured from cave bear teeth that are reminiscent of those later produced by the last Neanderthals of western Europe4-6. These finds are consistent with models based on the arrival of multiple waves of H. sapiens into Europe coming into contact with declining Neanderthal populations7,8.}, }
@article {pmid32430331, year = {2020}, author = {Gryseels, S and Watts, TD and Kabongo Mpolesha, JM and Larsen, BB and Lemey, P and Muyembe-Tamfum, JJ and Teuwen, DE and Worobey, M}, title = {A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {22}, pages = {12222-12229}, pmid = {32430331}, issn = {1091-6490}, support = {R01 AI084691/AI/NIAID NIH HHS/United States ; }, mesh = {Adult ; Cell Lineage/*genetics ; Democratic Republic of the Congo ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Viral ; HIV Infections/*genetics/virology ; HIV-1/*genetics ; Humans ; Male ; Paraffin Embedding/*methods ; Phylogeny ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {With very little direct biological data of HIV-1 from before the 1980s, far-reaching evolutionary and epidemiological inferences regarding the long prediscovery phase of this pandemic are based on extrapolations by phylodynamic models of HIV-1 genomic sequences gathered mostly over recent decades. Here, using a very sensitive multiplex RT-PCR assay, we screened 1,645 formalin-fixed paraffin-embedded tissue specimens collected for pathology diagnostics in Central Africa between 1958 and 1966. We report the near-complete viral genome in one HIV-1 positive specimen from Kinshasa, Democratic Republic of Congo (DRC), from 1966 (&quot;DRC66&quot;)-a nonrecombinant sister lineage to subtype C that constitutes the oldest HIV-1 near full-length genome recovered to date. Root-to-tip plots showed the DRC66 sequence is not an outlier as would be expected if dating estimates from more recent genomes were systematically biased; and inclusion of the DRC66 sequence in tip-dated BEAST analyses did not significantly alter root and internal node age estimates based on post-1978 HIV-1 sequences. There was larger variation in divergence time estimates among datasets that were subsamples of the available HIV-1 genomes from 1978 to 2014, showing the inherent phylogenetic stochasticity across subsets of the real HIV-1 diversity. Our phylogenetic analyses date the origin of the pandemic lineage of HIV-1 to a time period around the turn of the 20th century (1881 to 1918). In conclusion, this unique archival HIV-1 sequence provides direct genomic insight into HIV-1 in 1960s DRC, and, as an ancient-DNA calibrator, it validates our understanding of HIV-1 evolutionary history.}, }
@article {pmid32428013, year = {2020}, author = {Aoki, K}, title = {A three-population wave-of-advance model for the European early Neolithic.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0233184}, pmid = {32428013}, issn = {1932-6203}, mesh = {Agriculture/*history ; *DNA, Ancient ; History, Ancient ; Human Migration/*history ; Humans ; *Models, Biological ; }, abstract = {Ancient DNA studies have shown that early farming spread through most of Europe by the range expansion of farmers of Anatolian origin rather than by the conversion to farming of the local hunter-gatherers, and have confirmed that these hunter-gatherers continued to coexist with the incoming farmers. In this short report, I extend a previous three-population wave-of-advance model to accommodate these new findings, and derive the conditions supportive of such a scenario in terms of the relative magnitudes of the parameters. The revised model predicts that the conversion rate must, not surprisingly, be low, but also that the hunter-gatherers must compete more strongly with the converted farmers than with the alien farmers. Moreover, competition with the hunter-gatherers diminishes the speed of the wave-of advance of the farmers. In addition, I briefly consider how the wave-of-advance approach may contribute to interpreting the results of archaeological studies using the summed probability distribution of radiocarbon dates.}, }
@article {pmid32421727, year = {2020}, author = {Peña-Ahumada, B and Saldarriaga-Córdoba, M and Kardailsky, O and Moncada, X and Moraga, M and Matisoo-Smith, E and Seelenfreund, D and Seelenfreund, A}, title = {A tale of textiles: Genetic characterization of historical paper mulberry barkcloth from Oceania.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0233113}, pmid = {32421727}, issn = {1932-6203}, mesh = {Broussonetia/*genetics ; Genotyping Techniques ; Humans ; Microsatellite Repeats/genetics ; Pacific Islands ; Taiwan ; *Textiles ; }, abstract = {Humans introduced paper mulberry (Broussonetia papyrifera) from Taiwan into the Pacific over 5000 years ago as a fiber source to make barkcloth textiles that were, and still are, important cultural artifacts throughout the Pacific. We have used B. papyrifera, a species closely associated to humans, as a proxy to understand the human settlement of the Pacific Islands. We report the first genetic analysis of paper mulberry textiles from historical and archaeological contexts (200 to 50 years before present) and compare our results with genetic data obtained from contemporary and herbarium paper mulberry samples. Following stringent ancient DNA protocols, we extracted DNA from 13 barkcloth textiles. We confirmed that the fiber source is paper mulberry in nine of the 13 textiles studied using the nuclear ITS-1 marker and by statistical estimates. We detected high genetic diversity in historical Pacific paper mulberry barkcloth with a set of ten microsatellites, showing new alleles and specific genetic patterns. These genetic signatures allow tracing connections to plants from the Asian homeland, Near and Remote Oceania, establishing links not observed previously (using the same genetic tools) in extant plants or herbaria samples. These results show that historic barkcloth textiles are cultural materials amenable to genetic analysis to reveal human history and that these artifacts may harbor evidence of greater genetic diversity in Pacific B. papyrifera in the past.}, }
@article {pmid32411968, year = {2019}, author = {Amankwaa, AO and Nsiah Amoako, E and Mensah Bonsu, DO and Banyeh, M}, title = {Forensic science in Ghana: A review.}, journal = {Forensic science international. Synergy}, volume = {1}, number = {}, pages = {151-160}, pmid = {32411968}, issn = {2589-871X}, abstract = {The use of forensic science continues to grow across the world. In Ghana, major advancements took off in 2011, including the introduction of modern DNA profiling and the establishment of an automated fingerprint identification system. These developments have led to some positive impacts on the delivery of justice, including the exoneration of a wrongly incarcerated individual. However, a review of the policy-related aspects of forensic science shows gaps in legislation, governance, service provision, quality assurance and accreditation, education and research. An important recommendation to improve forensic science in Ghana is the creation of a &quot;national policy strategy&quot;, a blueprint informed by relevant stakeholders, best practice from other countries and the status of the field. Resolutions to the policy issues identified in this review will ensure a more robust application of forensic science in delivering safe justice and enhancing public security.}, }
@article {pmid32409524, year = {2020}, author = {Yang, MA and Fan, X and Sun, B and Chen, C and Lang, J and Ko, YC and Tsang, CH and Chiu, H and Wang, T and Bao, Q and Wu, X and Hajdinjak, M and Ko, AM and Ding, M and Cao, P and Yang, R and Liu, F and Nickel, B and Dai, Q and Feng, X and Zhang, L and Sun, C and Ning, C and Zeng, W and Zhao, Y and Zhang, M and Gao, X and Cui, Y and Reich, D and Stoneking, M and Fu, Q}, title = {Ancient DNA indicates human population shifts and admixture in northern and southern China.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6501}, pages = {282-288}, doi = {10.1126/science.aba0909}, pmid = {32409524}, issn = {1095-9203}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Asia, Southeastern ; Asian Continental Ancestry Group/genetics ; China ; *DNA, Ancient ; Gene Flow ; *Genetics, Population ; Genome, Human ; *Human Migration ; Humans ; Siberia ; Vietnam ; }, abstract = {Human genetic history in East Asia is poorly understood. To clarify population relationships, we obtained genome-wide data from 26 ancient individuals from northern and southern East Asia spanning 9500 to 300 years ago. Genetic differentiation in this region was higher in the past than the present, which reflects a major episode of admixture involving northern East Asian ancestry spreading across southern East Asia after the Neolithic, thereby transforming the genetic ancestry of southern China. Mainland southern East Asian and Taiwan Strait island samples from the Neolithic show clear connections with modern and ancient individuals with Austronesian-related ancestry, which supports an origin in southern China for proto-Austronesians. Connections among Neolithic coastal groups from Siberia and Japan to Vietnam indicate that migration and gene flow played an important role in the prehistory of coastal Asia.}, }
@article {pmid32406954, year = {2020}, author = {Li, J and Cai, D and Zhang, Y and Zhu, H and Zhou, H}, title = {Ancient DNA reveals two paternal lineages C2a1a1b1a/F3830 and C2b1b/F845 in past nomadic peoples distributed on the Mongolian Plateau.}, journal = {American journal of physical anthropology}, volume = {172}, number = {3}, pages = {402-411}, doi = {10.1002/ajpa.24076}, pmid = {32406954}, issn = {1096-8644}, abstract = {OBJECTIVES: Since the third century CE, a series of nomadic tribes have been active on the eastern part of the Mongolian Plateau. Characterizing the genetic compositions of past nomadic people is significant for research on the nomadic cultures of the Eurasian Steppe region. Ancient DNA analysis facilitates a deeper understanding of the relationship between historical and modern nomadic populations.<br><br>MATERIALS AND METHODS: Whole-genome shotgun sequencing and capture sequencing of the nonrecombining region of the Y chromosome were performed for six ancient Hg C2/M217 individuals. The individuals were interred at six separate sites on the Mongolian Plateau and represent dates spanning the late Neolithic to Yuan Dynasty (~3,500-700 BP).<br><br>RESULTS: After NRY capture sequencing, three of the six ancient samples were attributed to C2b1b/F845 and the other three ancient samples belonged to C2a1a1b1a/F3830. Analysis of whole-genome shotgun sequencing data shows that the ancient C2b1b/F845 individuals are closely related to She, Han and other East Asian populations, while the ancient C2a1a1b1a/F3830 individuals are more similar to modern Northeast Asian peoples, such as the Ulchi and Yakut.<br><br>DISCUSSION: Hg C2/M217, widely distributed in the eastern part of the Eurasian continent, was discovered in the ancient Central Steppe and Baikal region. This study shows that there were two important subclades of Hg C2/M217 among the ancient nomadic peoples: C2a1a1b1a/F3830, which has made important genetic contributions to modern Mongolic- and Manchu-speaking populations, and C2b1b/F845, which probably originated in the farming populations of southern East Asia and made certain genetic contributions to past nomadic peoples on the Mongolian Plateau.}, }
@article {pmid32405770, year = {2020}, author = {Samida, S}, title = {[About Media Presence and Prominence of DNA-Supported Research of the Past].}, journal = {NTM}, volume = {28}, number = {2}, pages = {181-192}, doi = {10.1007/s00048-020-00249-5}, pmid = {32405770}, issn = {1420-9144}, abstract = {In recent years molecular genetics has provided a completely new approach/access to the human past. The still new and quite dynamic research field of archaeogenetics (also known as palaeogenetics or genetic history) claims to be able to write history using ancient DNA. Through numerous remarkable publications it has generated and received much interest not only in scientific discourse but also in the media. So far, however, scientists have not paid much attention to this coverage-a research desideratum this paper cannot resolve. But by looking at selected press clippings it seeks to capture first trends according to the following three theses: telling success stories, drawing boundaries, and writing in a conformist manner.}, }
@article {pmid32405262, year = {2019}, author = {Charlton, S and Booth, T and Barnes, I}, title = {The problem with petrous? A consideration of the potential biases in the utilization of pars petrosa for ancient DNA analysis.}, journal = {World archaeology}, volume = {51}, number = {4}, pages = {574-585}, pmid = {32405262}, issn = {0043-8243}, abstract = {Advances in NGS sequencing technologies, improved laboratory protocols and new bioinformatic workflows have seen huge increases in ancient DNA (aDNA) research on archaeological materials. A large proportion of aDNA work now utilizes the petrous portion of the temporal bone (pars petrosa), which is recognized as an excellent skeletal element for long-term ancient endogenous (host) DNA survival. This has been significant due to the often low endogenous content of other skeletal elements, meaning that large amounts of sequencing are frequently required to obtain sufficient genetic coverage. However, exclusive sampling of the petrous for aDNA analysis introduces a new set of potential biases into our scientific studies - and these issues are yet to be considered by ancient DNA researchers. This paper aims to outline the possible biases of utilizing petrous bones to undertake aDNA analyses and highlight how these complications may potentially be overcome in future research.}, }
@article {pmid32396835, year = {2020}, author = {Rees, JS and Castellano, S and Andrés, AM}, title = {The Genomics of Human Local Adaptation.}, journal = {Trends in genetics : TIG}, volume = {36}, number = {6}, pages = {415-428}, doi = {10.1016/j.tig.2020.03.006}, pmid = {32396835}, issn = {0168-9525}, abstract = {Modern humans inhabit a variety of environments and are exposed to a plethora of selective pressures, leading to multiple genetic adaptations to local environmental conditions. These include adaptations to climate, UV exposure, disease, diet, altitude, or cultural practice and have generated important genetic and phenotypic differences amongst populations. In recent years, new methods to identify the genomic signatures of natural selection underlying these adaptations, combined with novel types of genetic data (e.g., ancient DNA), have provided unprecedented insights into the origin of adaptive alleles and the modes of adaptation. As a result, numerous instances of local adaptation have been identified in humans. Here, we review the most exciting recent developments and discuss, in our view, the future of this field.}, }
@article {pmid32393839, year = {2020}, author = {Fewlass, H and Mitchell, PJ and Casanova, E and Cramp, LJE}, title = {Chemical evidence of dairying by hunter-gatherers in highland Lesotho in the late first millennium AD.}, journal = {Nature human behaviour}, volume = {4}, number = {8}, pages = {791-799}, doi = {10.1038/s41562-020-0859-0}, pmid = {32393839}, issn = {2397-3374}, mesh = {Animals ; CD36 Antigens/analysis ; Cattle ; Ceramics/history ; Dairying/*history ; History, Ancient ; Humans ; Lesotho ; Lipids/analysis ; Radiometric Dating ; Sheep ; }, abstract = {The recovery of Early Iron Age artefacts and domestic animal remains from hunter-gatherer contexts at Likoaeng, Lesotho, has been argued to indicate contact between highland hunter-gatherers and Early Iron Age agropastoralist communities settled in lowland areas of southeastern Africa during the second half of the first millennium AD. However, disagreement between archaeozoological studies and ancient DNA means that the possibility that those hunter-gatherers kept livestock themselves remains controversial. Here we report analyses of pottery-absorbed organic residues from two hunter-gatherer sites and one agriculturalist site in highland Lesotho to reconstruct prehistoric subsistence practices. Our results demonstrate the exploitation of secondary products from domestic livestock by hunter-gatherers in Lesotho, directly dated to the seventh century AD at Likoaeng and the tenth century AD at the nearby site of Sehonghong. The data provide compelling evidence for the keeping of livestock by hunter-gatherer groups and their probable incorporation as ancillary resources into their subsistence strategies.}, }
@article {pmid32382696, year = {2018}, author = {Ahmed, AE and Mpangase, PT and Panji, S and Baichoo, S and Souilmi, Y and Fadlelmola, FM and Alghali, M and Aron, S and Bendou, H and De Beste, E and Mbiyavanga, M and Souiai, O and Yi, L and Zermeno, J and Armstrong, D and O'Connor, BD and Mainzer, LS and Crusoe, MR and Meintjes, A and Van Heusden, P and Botha, G and Joubert, F and Jongeneel, CV and Hazelhurst, S and Mulder, N}, title = {Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience.}, journal = {AAS open research}, volume = {1}, number = {}, pages = {9}, pmid = {32382696}, issn = {2515-9321}, abstract = {The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network's Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on Quay.io.}, }
@article {pmid32386546, year = {2020}, author = {Nakatsuka, N and Lazaridis, I and Barbieri, C and Skoglund, P and Rohland, N and Mallick, S and Posth, C and Harkins-Kinkaid, K and Ferry, M and Harney, É and Michel, M and Stewardson, K and Novak-Forst, J and Capriles, JM and Durruty, MA and Álvarez, KA and Beresford-Jones, D and Burger, R and Cadwallader, L and Fujita, R and Isla, J and Lau, G and Aguirre, CL and LeBlanc, S and Maldonado, SC and Meddens, F and Messineo, PG and Culleton, BJ and Harper, TK and Quilter, J and Politis, G and Rademaker, K and Reindel, M and Rivera, M and Salazar, L and Sandoval, JR and Santoro, CM and Scheifler, N and Standen, V and Barreto, MI and Espinoza, IF and Tomasto-Cagigao, E and Valverde, G and Kennett, DJ and Cooper, A and Krause, J and Haak, W and Llamas, B and Reich, D and Fehren-Schmitz, L}, title = {A Paleogenomic Reconstruction of the Deep Population History of the Andes.}, journal = {Cell}, volume = {181}, number = {5}, pages = {1131-1145.e21}, pmid = {32386546}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM100233/GM/NIGMS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; /CRUK_/Cancer Research UK/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anthropology/*methods ; Central America ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Gene Flow/*genetics/physiology ; Genetics, Population/methods ; Haplotypes ; Humans ; Sequence Analysis, DNA ; South America ; }, abstract = {There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.}, }
@article {pmid32381237, year = {2020}, author = {Bonsu, DOM and Higgins, D and Austin, JJ}, title = {Forensic touch DNA recovery from metal surfaces - A review.}, journal = {Science &amp; justice : journal of the Forensic Science Society}, volume = {60}, number = {3}, pages = {206-215}, doi = {10.1016/j.scijus.2020.01.002}, pmid = {32381237}, issn = {1876-4452}, abstract = {Trace evidence such as touch (also known as contact) DNA has probative value as a vital forensic investigative tool that can lead to the identification and apprehension of a criminal. While the volume of touch DNA evidence items submitted to forensic laboratories has significantly increased, recovery and amplification of DNA from these items, especially from metal surfaces, remains challenging. Currently little is understood with regards to the underlying mechanisms of metal-DNA interactions in the context of forensic science and how this may impact on DNA recovery. An increased understanding of these mechanisms would allow optimisation of methods to improve outcomes when sampling these materials. This paper reviews the basis of DNA binding to metal substrates, the merits and limitations of current methods and future perspectives of improving recovery and amplification of touch DNA from metal surfaces of forensic interest.}, }
@article {pmid32375874, year = {2020}, author = {Rifkin, RF and Vikram, S and Ramond, JB and Rey-Iglesia, A and Brand, TB and Porraz, G and Val, A and Hall, G and Woodborne, S and Le Bailly, M and Potgieter, M and Underdown, SJ and Koopman, JE and Cowan, DA and Van de Peer, Y and Willerslev, E and Hansen, AJ}, title = {Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {62}, pmid = {32375874}, issn = {2049-2618}, abstract = {BACKGROUND: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.<br><br>METHODS: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM.<br><br>RESULTS: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.<br><br>CONCLUSIONS: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.}, }
@article {pmid32369585, year = {2020}, author = {Liu, X}, title = {Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions.}, journal = {Molecular biology and evolution}, volume = {37}, number = {9}, pages = {2691-2698}, doi = {10.1093/molbev/msaa112}, pmid = {32369585}, issn = {1537-1719}, support = {R01 HG009524/HG/NHGRI NIH HHS/United States ; }, abstract = {The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.}, }
@article {pmid32359431, year = {2020}, author = {Barquera, R and Lamnidis, TC and Lankapalli, AK and Kocher, A and Hernández-Zaragoza, DI and Nelson, EA and Zamora-Herrera, AC and Ramallo, P and Bernal-Felipe, N and Immel, A and Bos, K and Acuña-Alonzo, V and Barbieri, C and Roberts, P and Herbig, A and Kühnert, D and Márquez-Morfín, L and Krause, J}, title = {Origin and Health Status of First-Generation Africans from Early Colonial Mexico.}, journal = {Current biology : CB}, volume = {30}, number = {11}, pages = {2078-2091.e11}, doi = {10.1016/j.cub.2020.04.002}, pmid = {32359431}, issn = {1879-0445}, abstract = {The forced relocation of several thousand Africans during Mexico's historic period has so far been documented mostly through archival sources, which provide only sparse detail on their origins and lived experience. Here, we employ a bioarchaeological approach to explore the life history of three 16th century Africans from a mass burial at the San José de los Naturales Royal Hospital in Mexico City. Our approach draws together ancient genomic data, osteological analysis, strontium isotope data from tooth enamel, δ13C and δ15N isotope data from dentine, and ethnohistorical information to reveal unprecedented detail on their origins and health. Analyses of skeletal features, radiogenic isotopes, and genetic data from uniparental, genome-wide, and human leukocyte antigen (HLA) markers are consistent with a Sub-Saharan African origin for all three individuals. Complete genomes of Treponema pallidum sub. pertenue (causative agent of yaws) and hepatitis B virus (HBV) recovered from these individuals provide insight into their health as related to infectious disease. Phylogenetic analysis of both pathogens reveals their close relationship to strains circulating in current West African populations, lending support to their origins in this region. The further relationship between the treponemal genome retrieved and a treponemal genome previously typed in an individual from Colonial Mexico highlights the role of the transatlantic slave trade in the introduction and dissemination of pathogens into the New World. Putting together all lines of evidence, we were able to create a biological portrait of three individuals whose life stories have long been silenced by disreputable historical events.}, }
@article {pmid32355290, year = {2020}, author = {Pierini, F and Nutsua, M and Böhme, L and Özer, O and Bonczarowska, J and Susat, J and Franke, A and Nebel, A and Krause-Kyora, B and Lenz, TL}, title = {Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {7339}, pmid = {32355290}, issn = {2045-2322}, abstract = {The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.}, }
@article {pmid32343728, year = {2020}, author = {Guiry, E and Royle, TCA and Matson, RG and Ward, H and Weir, T and Waber, N and Brown, TJ and Hunt, BPV and Price, MHH and Finney, BP and Kaeriyama, M and Qin, Y and Yang, DY and Szpak, P}, title = {Differentiating salmonid migratory ecotypes through stable isotope analysis of collagen: Archaeological and ecological applications.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0232180}, pmid = {32343728}, issn = {1932-6203}, mesh = {Animal Migration ; Animal Scales/chemistry ; Animals ; Archaeology ; Biodiversity ; Bone and Bones/chemistry ; Carbon Isotopes/analysis ; Collagen/*chemistry ; Conservation of Natural Resources ; DNA, Ancient/analysis ; Ecotype ; Female ; Fish Proteins/*chemistry ; Lakes ; Male ; Pacific Ocean ; Salmon/classification/genetics/*physiology ; Salmonidae/classification/genetics/*physiology ; }, abstract = {The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ13C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare.}, }
@article {pmid32324877, year = {2020}, author = {Cai, Y and Fu, W and Cai, D and Heller, R and Zheng, Z and Wen, J and Li, H and Wang, X and Alshawi, A and Sun, Z and Zhu, S and Wang, J and Yang, M and Hu, S and Li, Y and Yang, Z and Gong, M and Hou, Y and Lan, T and Wu, K and Chen, Y and Jiang, Y and Wang, X}, title = {Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China.}, journal = {Molecular biology and evolution}, volume = {37}, number = {7}, pages = {2099-2109}, pmid = {32324877}, issn = {1537-1719}, abstract = {Goats are one of the most widespread farmed animals across the world; however, their migration route to East Asia and local evolutionary history remain poorly understood. Here, we sequenced 27 ancient Chinese goat genomes dating from the Late Neolithic period to the Iron Age. We found close genetic affinities between ancient and modern Chinese goats, demonstrating their genetic continuity. We found that Chinese goats originated from the eastern regions around the Fertile Crescent, and we estimated that the ancestors of Chinese goats diverged from this population in the Chalcolithic period. Modern Chinese goats were divided into a northern and a southern group, coinciding with the most prominent climatic division in China, and two genes related to hair follicle development, FGF5 and EDA2R, were highly divergent between these populations. We identified a likely causal de novo deletion near FGF5 in northern Chinese goats that increased to high frequency over time, whereas EDA2R harbored standing variation dating to the Neolithic. Our findings add to our understanding of the genetic composition and local evolutionary process of Chinese goats.}, }
@article {pmid32321996, year = {2020}, author = {Ferrando-Bernal, M and Morcillo-Suarez, C and de-Dios, T and Gelabert, P and Civit, S and Díaz-Carvajal, A and Ollich-Castanyer, I and Allentoft, ME and Valverde, S and Lalueza-Fox, C}, title = {Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {6843}, pmid = {32321996}, issn = {2045-2322}, mesh = {*DNA, Ancient ; Ethnic Groups/*genetics ; Europe ; European Continental Ancestry Group/*genetics/history ; Female ; *Genetic Variation ; History, Medieval ; Humans ; Male ; *Polymorphism, Single Nucleotide ; }, abstract = {Historical genetic links among similar populations can be difficult to establish. Identity by descent (IBD) analyses find genomic blocks that represent direct genealogical relationships among individuals. However, this method has rarely been applied to ancient genomes because IBD stretches are progressively fragmented by recombination and thus not recognizable after few tens of generations. To explore such genealogical relationships, we estimated long IBD blocks among modern Europeans, generating networks to uncover the genetic structures. We found that Basques, Sardinians, Icelanders and Orcadians form, each of them, highly intraconnected sub-clusters in a European network, indicating dense genealogical links within small, isolated populations. We also exposed individual genealogical links -such as the connection between one Basque and one Icelandic individual- that cannot be uncovered with other, widely used population genetics methods such as PCA or ADMIXTURE. Moreover, using ancient DNA technology we sequenced a Late Medieval individual (Barcelona, Spain) to high genomic coverage and identified IBD blocks shared between her and modern Europeans. The Medieval IBD blocks are statistically overrepresented only in modern Spaniards, which is the geographically closest population. This approach can be used to produce a fine-scale reflection of shared ancestry across different populations of the world, offering a direct genetic link from the past to the present.}, }
@article {pmid32318826, year = {2020}, author = {Zvénigorosky, V and Sabbagh, A and Gonzalez, A and Fausser, JL and Palstra, F and Romanov, G and Solovyev, A and Barashkov, N and Fedorova, S and Crubézy, É and Ludes, B and Keyser, C}, title = {The limitations of kinship determinations using STR data in ill-defined populations.}, journal = {International journal of legal medicine}, volume = {134}, number = {6}, pages = {1981-1990}, doi = {10.1007/s00414-020-02298-w}, pmid = {32318826}, issn = {1437-1596}, support = {Travel Grant//Université Toulouse III - Paul Sabatier/ ; }, abstract = {The likelihood ratio (LR) method is commonly used to determine kinship in civil, criminal, or forensic cases. For the past 15 years, our research group has also applied LR to ancient STR data and obtained kinship results for collections of graves or necropolises. Although we were able to reconstruct large genealogies, some pairs of individuals showed ambiguous results. Second-degree relationships, half-sibling pairs for example, were often inconsistent with detected first-degree relationships, such as parent/child or brother/sister pairs. We therefore set about providing empirical estimations of the error rates for the LR method in living populations with STR allelic diversities comparable to that of the ancient populations we had previously studied. We collected biological samples in the field in North-Eastern Siberia and West Africa and studied more than 800 pairs of STR profiles from individuals with known relationships. Because commercial STR panels were constructed for specific regions (namely Europe and North America), their allelic makeup showed a significant deficit in diversity when compared to European populations, replicating a situation often faced in ancient DNA studies. We assessed the capacity of the LR method to confirm known relationships (effectiveness) and its capacity to detect those relationships (reliability). Concerns over the effectiveness of LR determinations are mostly an issue in forensic studies, while the reliability of the detection of kinship is an issue for the study of necropolises or other large gatherings of unidentified individuals, such as disaster victims or mass graves. We show that the application of LR to both test populations highlights specific issues (both false positives and false negatives) that prevent the confirmation of second-degree kinship or even full siblingship in small populations. Up to 29% of detected full sibling relationships were either overestimated half-sibling relationships or underestimated parent-offspring relationships. The error rate for detected half-sibling relationships was even higher, reaching 41%. Only parent-offspring pairs were reliably detected or confirmed. This implies that, in populations that are small, ill-defined, or for which the STR loci analyzed are inappropriate, an examiner might not be able to distinguish a pair of full siblings from a pair of half-siblings. Furthermore, half-sibling pairs might be overlooked altogether, an issue that is exacerbated by the common confusion, in many languages and cultures, between half-siblings and full siblings. Consequently, in the study of ancient populations, human remains of unknown origins, or poorly surveyed modern populations, we recommend a conservative approach to kinship determined by LR. Next-generation sequencing data should be used when possible, but the costs and technology involved might be prohibitive. Therefore, in potentially contentious situations or cases lacking sufficient external information, uniparental markers should be analyzed: ideally, complete mitochondrial genomes and Y-chromosome haplotypes (STR, SNP, and/or sequencing).}, }
@article {pmid32313686, year = {2020}, author = {Dehasque, M and Ávila-Arcos, MC and Díez-Del-Molino, D and Fumagalli, M and Guschanski, K and Lorenzen, ED and Malaspinas, AS and Marques-Bonet, T and Martin, MD and Murray, GGR and Papadopulos, AST and Therkildsen, NO and Wegmann, D and Dalén, L and Foote, AD}, title = {Inference of natural selection from ancient DNA.}, journal = {Evolution letters}, volume = {4}, number = {2}, pages = {94-108}, pmid = {32313686}, issn = {2056-3744}, abstract = {Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods.}, }
@article {pmid32313080, year = {2020}, author = {Furtwängler, A and Rohrlach, AB and Lamnidis, TC and Papac, L and Neumann, GU and Siebke, I and Reiter, E and Steuri, N and Hald, J and Denaire, A and Schnitzler, B and Wahl, J and Ramstein, M and Schuenemann, VJ and Stockhammer, PW and Hafner, A and Lösch, S and Haak, W and Schiffels, S and Krause, J}, title = {Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1915}, doi = {10.1038/s41467-020-15560-x}, pmid = {32313080}, issn = {2041-1723}, mesh = {Archaeology ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Europe ; European Continental Ancestry Group/genetics ; *Evolution, Molecular ; France ; Genetics, Population/*history ; Genome, Human/*genetics ; Germany ; History, Ancient ; Humans ; Switzerland ; }, abstract = {Genetic studies of Neolithic and Bronze Age skeletons from Europe have provided evidence for strong population genetic changes at the beginning and the end of the Neolithic period. To further understand the implications of these in Southern Central Europe, we analyze 96 ancient genomes from Switzerland, Southern Germany, and the Alsace region in France, covering the Middle/Late Neolithic to Early Bronze Age. Similar to previously described genetic changes in other parts of Europe from the early 3rd millennium BCE, we detect an arrival of ancestry related to Late Neolithic pastoralists from the Pontic-Caspian steppe in Switzerland as early as 2860-2460 calBCE. Our analyses suggest that this genetic turnover was a complex process lasting almost 1000 years and involved highly genetically structured populations in this region.}, }
@article {pmid32306514, year = {2020}, author = {Lang, PLM and Weiß, CL and Kersten, S and Latorre, SM and Nagel, S and Nickel, B and Meyer, M and Burbano, HA}, title = {Hybridization ddRAD-sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA.}, journal = {Molecular ecology resources}, volume = {20}, number = {5}, pages = {1228-1247}, doi = {10.1111/1755-0998.13168}, pmid = {32306514}, issn = {1755-0998}, support = {Project 324876998 of SPP1374//Deutsche Forschungsgemeinschaft/ ; Presidential Innovation Fund//Max-Planck-Gesellschaft/ ; 324876998//German Research Foundation/ ; SPP1374//German Research Foundation/ ; //Max Planck Society/ ; }, abstract = {Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species-with small or large genomes-diversity is traditionally assessed using restriction-enzyme-based sequencing. However, age-related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced-representation sequencing and hybridization-capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced-representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference-free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost-efficient, large-scale integration of contemporary and historical specimens for assessment of genome-wide genetic trends over time, independent of genome size and presence of a reference genome.}, }
@article {pmid32304863, year = {2020}, author = {Zhang, X and Li, C and Zhou, Y and Huang, J and Yu, T and Liu, X and Shi, H and Liu, H and Chia, S and Huang, S and Guo, Y and Shoocongdej, R and Ji, X and Su, B}, title = {A Matrilineal Genetic Perspective of Hanging Coffin Custom in Southern China and Northern Thailand.}, journal = {iScience}, volume = {23}, number = {4}, pages = {101032}, doi = {10.1016/j.isci.2020.101032}, pmid = {32304863}, issn = {2589-0042}, abstract = {Hanging Coffin is a unique and ancient burial custom that has been practiced in southern China, Southeast Asia, and near Oceania regions for more than 3,000 years. Here, we conducted mitochondrial whole-genome analyses of 41 human remains sampled from 13 Hanging Coffin sites in southern China and northern Thailand, which were dated between ∼2,500 and 660 years before present. We found that there were genetic connections between the Hanging Coffin people living in different geographic regions. Notably, the matrilineal genetic diversity of the Hanging Coffin people from southern China is much higher than those from northern Thailand, consistent with the hypothesized single origin of the Hanging Coffin custom in southern China about 3,600 years ago, followed by its dispersal in southern China through demic diffusion, whereas the major dispersal pattern in Southeast Asia is cultural assimilation in the past 2,000 years.}, }
@article {pmid32303690, year = {2020}, author = {Linderholm, A and Kılınç, GM and Szczepanek, A and Włodarczak, P and Jarosz, P and Belka, Z and Dopieralska, J and Werens, K and Górski, J and Mazurek, M and Hozer, M and Rybicka, M and Ostrowski, M and Bagińska, J and Koman, W and Rodríguez-Varela, R and Storå, J and Götherström, A and Krzewińska, M}, title = {Corded Ware cultural complexity uncovered using genomic and isotopic analysis from south-eastern Poland.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {6885}, pmid = {32303690}, issn = {2045-2322}, mesh = {Burial/history ; Carbon Isotopes/*analysis/history ; Culture ; DNA, Ancient/analysis ; Europe ; Female ; *Genome, Human ; Genomics ; History, Ancient ; Human Migration/history ; Humans ; Male ; Nitrogen Isotopes/*analysis/history ; Poland ; }, abstract = {During the Final Eneolithic the Corded Ware Complex (CWC) emerges, chiefly identified by its specific burial rites. This complex spanned most of central Europe and exhibits demographic and cultural associations to the Yamnaya culture. To study the genetic structure and kin relations in CWC communities, we sequenced the genomes of 19 individuals located in the heartland of the CWC complex region, south-eastern Poland. Whole genome sequence and strontium isotope data allowed us to investigate genetic ancestry, admixture, kinship and mobility. The analysis showed a unique pattern, not detected in other parts of Poland; maternally the individuals are linked to earlier Neolithic lineages, whereas on the paternal side a Steppe ancestry is clearly visible. We identified three cases of kinship. Of these two were between individuals buried in double graves. Interestingly, we identified kinship between a local and a non-local individual thus discovering a novel, previously unknown burial custom.}, }
@article {pmid32297957, year = {2020}, author = {Sanchez-Mazas, A}, title = {A review of HLA allele and SNP associations with highly prevalent infectious diseases in human populations.}, journal = {Swiss medical weekly}, volume = {150}, number = {}, pages = {w20214}, doi = {10.4414/smw.2020.20214}, pmid = {32297957}, issn = {1424-3997}, abstract = {Human leucocyte antigen (HLA) alleles and single nucleotide polymorphisms (SNPs) lying in the HLA region are known to be associated with several infectious diseases among which acquired immunodeficiency syndrome, hepatitis B, hepatitis C, tuberculosis, leprosy and malaria are highly prevalent in many human populations worldwide. Distinct approaches such as case-control comparisons, immunogenetic analyses, bioinformatic peptide-binding predictions, ancient DNA and genome-wide association studies (GWAS) have contributed to improving this knowledge during the last decade, although many results still need stronger statistical and/or functional support. The present review updates the information regarding the main HLA allele and SNP associations observed to date for six of the most widespread and some other infectious diseases, and provides a synthetic illustration of these findings on a schematic HLA genomic map. It then discusses these results by stressing the importance of integrating information on HLA population diversity in disease-association studies.}, }
@article {pmid32297323, year = {2020}, author = {Juras, A and Makarowicz, P and Chyleński, M and Ehler, E and Malmström, H and Krzewińska, M and Pospieszny, Ł and Górski, J and Taras, H and Szczepanek, A and Polańska, M and Włodarczak, P and Szyca, A and Lasota-Kuś, A and Wójcik, I and Jakobsson, M and Dabert, M}, title = {Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations.}, journal = {American journal of physical anthropology}, volume = {172}, number = {2}, pages = {176-188}, doi = {10.1002/ajpa.24057}, pmid = {32297323}, issn = {1096-8644}, abstract = {OBJECTIVE: In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes.<br><br>MATERIALS AND METHODS: We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzyżow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS 14 C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples.<br><br>RESULTS: Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzyżów people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study.<br><br>DISCUSSION: Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzyżów-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.}, }
@article {pmid32286714, year = {2020}, author = {Schweizer, RM and Wayne, RK}, title = {Illuminating the mysteries of wolf history.}, journal = {Molecular ecology}, volume = {29}, number = {9}, pages = {1589-1591}, doi = {10.1111/mec.15438}, pmid = {32286714}, issn = {1365-294X}, mesh = {Animals ; Climate Change ; DNA, Ancient ; DNA, Mitochondrial ; Fossils ; Humans ; Wolves/*genetics ; }, abstract = {One of the most enduring surprises about the genetic history of Late Pleistocene populations is that continuity is often disturbed by upheaval. In fact, studies that support population continuity are increasingly rare in humans, a variety of vertebrate taxa, and vascular plants (Hofreiter &amp; Stewart 2009; Burbrink et al. 2016). Perhaps such continuity should not be expected as the Pleistocene is marked by episodes of climate change, glaciation and the invasions of humans into previously isolated areas. Although fossils are one of the primary sources for inferring population continuity, a problem with fossil material is that, even if similar morphological forms might exist in a place over time, they may not be from the same genetic lineage. There are now readily available methods to assess genetic continuity solely from DNA found in fossil material, provided the record is fairly continuous. In a From the Cover article in this issue of Molecular Ecology, Loog et al. (2020) apply some of these readily available methods to analyse mitochondrial genomes and model the demography of wolves over the last 50,000 years.}, }
@article {pmid32283039, year = {2020}, author = {Carr, SM}, title = {Evidence for the persistence of ancient Beothuk and Maritime Archaic mitochondrial DNA genome lineages among modern Native American peoples.}, journal = {Genome}, volume = {63}, number = {7}, pages = {349-355}, doi = {10.1139/gen-2019-0149}, pmid = {32283039}, issn = {1480-3321}, abstract = {The Beothuk were a Native American people who formerly occupied the island of Newfoundland, and who are generally accepted to have become culturally extinct in 1829. The Beothuk succeeded the Maritime Archaic people on the island after a hiatus of ca. 1.4 ka, and were themselves succeeded by the extant Mi'kmaq within historic times. Genetic continuity between ancient and modern Native Americans remains of interest. Complete aDNA mitogenomes from ancient Beothuk and Maritime Archaic were compared with the most closely related modern mitogenomes as obtained by BLAST search of GenBank. Beothuk mitogenomes in five clades are in one case identical to and otherwise differ by minima of three to eight SNPs from the most closely related modern mitogenomes. Maritime Archaic mitogenomes in 12 clades are in one case identical to and otherwise differ by minima of one to nine SNPs from the most similar modern mitogenomes. The single available modern Mi'kmaq mitogenome differs from the most similar Beothuk and Maritime Archaic mitogenomes by 12 and 22 SNPs, respectively. Phylogenetic analysis and sequence similarities imply lineage extinction of most ancient clades, as well as continuity of two Beothuk and at least one Maritime Archaic lineages in modern Native Americans and their descendants.}, }
@article {pmid32277584, year = {2020}, author = {Armbrecht, L and Herrando-Pérez, S and Eisenhofer, R and Hallegraeff, GM and Bolch, CJS and Cooper, A}, title = {An optimized method for the extraction of ancient eukaryote DNA from marine sediments.}, journal = {Molecular ecology resources}, volume = {20}, number = {4}, pages = {906-919}, doi = {10.1111/1755-0998.13162}, pmid = {32277584}, issn = {1755-0998}, support = {CE170100015//Australian Research Council/ ; DP170102261//Australian Research Council/ ; DP170104665//Australian Research Council/ ; FL140100260//Australian Research Council/ ; }, abstract = {Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.}, }
@article {pmid32271816, year = {2020}, author = {Barbato, M and Reichel, MP and Passamonti, M and Low, WY and Colli, L and Tearle, R and Williams, JL and Ajmone Marsan, P}, title = {A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231162}, pmid = {32271816}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/*genetics ; Cattle/*genetics ; Female ; Genetic Variation ; Hong Kong ; Male ; *Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Principal Component Analysis ; }, abstract = {In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.}, }
@article {pmid32269345, year = {2020}, author = {Welker, F and Ramos-Madrigal, J and Gutenbrunner, P and Mackie, M and Tiwary, S and Rakownikow Jersie-Christensen, R and Chiva, C and Dickinson, MR and Kuhlwilm, M and de Manuel, M and Gelabert, P and Martinón-Torres, M and Margvelashvili, A and Arsuaga, JL and Carbonell, E and Marques-Bonet, T and Penkman, K and Sabidó, E and Cox, J and Olsen, JV and Lordkipanidze, D and Racimo, F and Lalueza-Fox, C and Bermúdez de Castro, JM and Willerslev, E and Cappellini, E}, title = {The dental proteome of Homo antecessor.}, journal = {Nature}, volume = {580}, number = {7802}, pages = {235-238}, pmid = {32269345}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Dental Enamel/*chemistry/*metabolism ; *Fossils ; Georgia (Republic) ; *Hominidae ; Humans ; Male ; Molar/chemistry/metabolism ; Neanderthals ; Phosphoproteins/analysis/chemistry/metabolism ; Phosphorylation ; Phylogeny ; Proteome/*analysis/chemistry/*metabolism ; Spain ; }, abstract = {The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1-5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6-8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor-that is, similar to that of modern humans-may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.}, }
@article {pmid32265525, year = {2020}, author = {Frantz, LAF and Bradley, DG and Larson, G and Orlando, L}, title = {Animal domestication in the era of ancient genomics.}, journal = {Nature reviews. Genetics}, volume = {21}, number = {8}, pages = {449-460}, doi = {10.1038/s41576-020-0225-0}, pmid = {32265525}, issn = {1471-0064}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animal Husbandry ; Animals ; *Animals, Wild ; DNA, Ancient ; DNA, Mitochondrial ; *Domestication ; Founder Effect ; *Genomics/history/methods ; History, Ancient ; Models, Theoretical ; Selection, Genetic ; Spatio-Temporal Analysis ; }, abstract = {The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.}, }
@article {pmid32257320, year = {2020}, author = {Herrera, MB and Kraitsek, S and Alcalde, JA and Quiroz, D and Revelo, H and Alvarez, LA and Rosario, MF and Thomson, V and Jianlin, H and Austin, JJ and Gongora, J}, title = {European and Asian contribution to the genetic diversity of mainland South American chickens.}, journal = {Royal Society open science}, volume = {7}, number = {2}, pages = {191558}, pmid = {32257320}, issn = {2054-5703}, abstract = {Chickens (Gallus gallus domesticus) from the Americas have long been recognized as descendants of European chickens, transported by early Europeans since the fifteenth century. However, in recent years, a possible pre-Columbian introduction of chickens to South America by Polynesian seafarers has also been suggested. Here, we characterize the mitochondrial control region genetic diversity of modern chicken populations from South America and compare this to a worldwide dataset in order to investigate the potential maternal genetic origin of modern-day chicken populations in South America. The genetic analysis of newly generated chicken mitochondrial control region sequences from South America showed that the majority of chickens from the continent belong to mitochondrial haplogroup E. The rest belongs to haplogroups A, B and C, albeit at very low levels. Haplogroup D, a ubiquitous mitochondrial lineage in Island Southeast Asia and on Pacific Islands is not observed in continental South America. Modern-day mainland South American chickens are, therefore, closely allied with European and Asian chickens. Furthermore, we find high levels of genetic contributions from South Asian chickens to those in Europe and South America. Our findings demonstrate that modern-day genetic diversity of mainland South American chickens appear to have clear European and Asian contributions, and less so from Island Southeast Asia and the Pacific Islands. Furthermore, there is also some indication that South Asia has more genetic contribution to European chickens than any other Asian chicken populations.}, }
@article {pmid32238559, year = {2020}, author = {Racimo, F and Woodbridge, J and Fyfe, RM and Sikora, M and Sjögren, KG and Kristiansen, K and Vander Linden, M}, title = {The spatiotemporal spread of human migrations during the European Holocene.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {16}, pages = {8989-9000}, pmid = {32238559}, issn = {1091-6490}, mesh = {Agriculture/history ; Animal Distribution ; Archaeology/*methods ; DNA, Ancient/analysis ; Datasets as Topic ; Europe ; Farmers ; Feasibility Studies ; Forests ; *Genome, Human ; Geography ; Grassland ; History, Ancient ; Human Migration/*history ; Humans ; *Models, Genetic ; Plant Dispersal ; Radiometric Dating ; *Spatio-Temporal Analysis ; }, abstract = {The European continent was subject to two major migrations of peoples during the Holocene: the northwestward movement of Anatolian farmer populations during the Neolithic and the westward movement of Yamnaya steppe peoples during the Bronze Age. These movements changed the genetic composition of the continent's inhabitants. The Holocene was also characterized by major changes in vegetation composition, which altered the environment occupied by the original hunter-gatherer populations. We aim to test to what extent vegetation change through time is associated with changes in population composition as a consequence of these migrations, or with changes in climate. Using ancient DNA in combination with geostatistical techniques, we produce detailed maps of ancient population movements, which allow us to visualize how these migrations unfolded through time and space. We find that the spread of Neolithic farmer ancestry had a two-pronged wavefront, in agreement with similar findings on the cultural spread of farming from radiocarbon-dated archaeological sites. This movement, however, did not have a strong association with changes in the vegetational landscape. In contrast, the Yamnaya migration speed was at least twice as fast and coincided with a reduction in the amount of broad-leaf forest and an increase in the amount of pasture and natural grasslands in the continent. We demonstrate the utility of integrating ancient genomes with archaeometric datasets in a spatiotemporal statistical framework, which we foresee will enable future studies of ancient populations' movements, and their putative effects on local fauna and flora.}, }
@article {pmid32233019, year = {2020}, author = {Mai, BHA and Drancourt, M and Aboudharam, G}, title = {Ancient dental pulp: Masterpiece tissue for paleomicrobiology.}, journal = {Molecular genetics &amp; genomic medicine}, volume = {8}, number = {6}, pages = {e1202}, pmid = {32233019}, issn = {2324-9269}, abstract = {INTRODUCTION: Dental pulp with special structure has become a good reference sample in paleomicrobiology-related blood-borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins.<br><br>OBJECTIVES: This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe.<br><br>METHODS: The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: &quot;ancient,&quot; &quot;dental pulp,&quot; &quot;teeth,&quot; &quot;anatomy,&quot; &quot;structure,&quot; &quot;collection,&quot; &quot;preservation,&quot; &quot;selection,&quot; &quot;photography,&quot; &quot;radiography,&quot; &quot;contamination,&quot; &quot;decontamination,&quot; &quot;DNA,&quot; &quot;protein,&quot; &quot;extraction,&quot; &quot;bone,&quot; &quot;paleomicrobiology,&quot; &quot;bacteria,&quot; &quot;virus,&quot; &quot;pathogen,&quot; &quot;molecular biology,&quot; &quot;proteomics,&quot; &quot;PCR,&quot; &quot;MALDI-TOF,&quot; &quot;LC/MS,&quot; &quot;ELISA,&quot; &quot;immunology,&quot; &quot;immunochromatography,&quot; &quot;genome,&quot; &quot;microbiome,&quot; &quot;metagenomics.&quot;<br><br>RESULTS: The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty-seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species.<br><br>CONCLUSIONS: Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics.}, }
@article {pmid32228443, year = {2020}, author = {Cortázar-Chinarro, M and Meyer-Lucht, Y and Van der Valk, T and Richter-Boix, A and Laurila, A and Höglund, J}, title = {Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans.}, journal = {BMC genetics}, volume = {21}, number = {1}, pages = {38}, pmid = {32228443}, issn = {1471-2156}, abstract = {BACKGROUND: While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns.<br><br>RESULTS: We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values.<br><br>CONCLUSION: Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.}, }
@article {pmid32224189, year = {2019}, author = {Zhang, L and Liu, M and Long, H and Dong, W and Pasha, A and Esteban, E and Li, W and Yang, X and Li, Z and Song, A and Ran, D and Zhao, G and Zeng, Y and Chen, H and Zou, M and Li, J and Liang, F and Xie, M and Hu, J and Wang, D and Cao, H and Provart, NJ and Zhang, L and Tan, X}, title = {Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {17}, number = {6}, pages = {558-575}, pmid = {32224189}, issn = {2210-3244}, mesh = {Aleurites/*genetics/*metabolism ; Base Sequence ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Genome, Plant/genetics ; *Genomics ; Plant Oils/*metabolism ; }, abstract = {Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further whole-genome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites; 17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.}, }
@article {pmid32187203, year = {2020}, author = {Utge, J and Sévêque, N and Lartigot-Campin, AS and Testu, A and Moigne, AM and Vézian, R and Maksud, F and Begouën, R and Verna, C and Soriano, S and Elalouf, JM}, title = {A mobile laboratory for ancient DNA analysis.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0230496}, pmid = {32187203}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Bison ; DNA, Ancient/*analysis ; DNA, Mitochondrial/analysis ; Fossils ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {Mobile devices for on-field DNA analysis have been used for medical diagnostics at the point-of-care, forensic investigations and environmental surveys, but still have to be validated for ancient DNA studies. We report here on a mobile laboratory that we setup using commercially available devices, including a compact real-time PCR machine, and describe procedures to perform DNA extraction and analysis from a variety of archeological samples within 4 hours. The process is carried out on 50 mg samples that are identified at the species level using custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated the potential of this approach in museums lacking facilities for DNA studies by analyzing samples from the Enlène (MIS 2 layer) and the Portel-Ouest cave (MIS 3 deposits), and also performed experiments during an excavation campaign at the Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples only yielded DNA for the extinct steppe bison (Bison priscus), whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta crocuta spelaea) DNA together, for some of them, with DNA for the European bison sister species/subspecies (Bison schoetensacki/Bb1-X), thus highlighting the cave hyena diet. Roc-en-Pail Bovinae bone and tooth samples also contained DNA for the Bison schoetensacki/Bb1-X clade, and Cervidae bone samples only yielded reindeer (Rangifer tarandus) DNA. Subsequent DNA sequencing analyses confirmed that correct species identification had been achieved using our TaqMan assays, hence validating these assays for future studies. We conclude that our approach enables the rapid genetic characterization of tens of millennia-old archeological samples and is expected to be useful for the on-site screening of museums and freshly excavated samples for DNA content. Because our mobile laboratory is made up of commercially available instruments, this approach is easily accessible to other investigators.}, }
@article {pmid32184999, year = {2020}, author = {Moore, G and Tessler, M and Cunningham, SW and Betancourt, J and Harbert, R}, title = {Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.}, journal = {Ecology and evolution}, volume = {10}, number = {5}, pages = {2530-2544}, pmid = {32184999}, issn = {2045-7758}, abstract = {Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI &quot;nt&quot; database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.}, }
@article {pmid32183622, year = {2020}, author = {Ding, M and Wang, T and Ko, AM and Chen, H and Wang, H and Dong, G and Lu, H and He, W and Wangdue, S and Yuan, H and He, Y and Cai, L and Chen, Z and Hou, G and Zhang, D and Zhang, Z and Cao, P and Dai, Q and Feng, X and Zhang, M and Wang, H and Yang, MA and Fu, Q}, title = {Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1923}, pages = {20192968}, pmid = {32183622}, issn = {1471-2954}, support = {55008731/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Altitude ; Asian Continental Ancestry Group/*genetics ; Genetic Variation ; *Genome, Mitochondrial ; Humans ; Tibet ; }, abstract = {The clarification of the genetic origins of present-day Tibetans requires an understanding of their past relationships with the ancient populations of the Tibetan Plateau. Here we successfully sequenced 67 complete mitochondrial DNA genomes of 5200 to 300-year-old humans from the plateau. Apart from identifying two ancient plateau lineages (haplogroups D4j1b and M9a1a1c1b1a) that suggest some ancestors of Tibetans came from low-altitude areas 4750 to 2775 years ago and that some were involved in an expansion of people moving between high-altitude areas 2125 to 1100 years ago, we found limited evidence of recent matrilineal continuity on the plateau. Furthermore, deep learning of the ancient data incorporated into simulation models with an accuracy of 97% supports that present-day Tibetan matrilineal ancestry received partial contribution rather than complete continuity from the plateau populations of the last 5200 years.}, }
@article {pmid32172220, year = {2020}, author = {Emery, MV and Bolhofner, K and Winingear, S and Oldt, R and Montes, M and Kanthaswamy, S and Buikstra, JE and Fulginiti, LC and Stone, AC}, title = {Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques.}, journal = {Forensic science international. Genetics}, volume = {46}, number = {}, pages = {102272}, doi = {10.1016/j.fsigen.2020.102272}, pmid = {32172220}, issn = {1878-0326}, abstract = {Thermal degeneration of the DNA molecule presents a special challenge to medico-legal investigations since low DNA yields, fragmented DNA molecules, and damaged nucleotide bases hinder accurate STR genotyping. As a consequence, fragments of severely burned human remains are often not amenable to standard DNA recovery. However, current ancient DNA (aDNA) extraction methods have proven highly effective at obtaining ultrashort DNA fragments (∼50 bp) from degraded palaeontological and archaeological specimens. In this study, we compare DNA yields and STR results obtained from two established aDNA and forensic DNA extraction protocols by sampling multiple skeletal elements recovered from victims (n = 23) involved in fire-related incidents. DNA yields and STR results suggest an inverse correlation between DNA yield and STR quality and increasing temperature. Despite the rapid thermal destruction of DNA at high temperatures, we generated higher quality full and partial STR profiles using the aDNA extraction protocol across all burn categories than the forensic total bone demineralization extraction method. Our analysis suggests adopting aDNA extraction methods as an alternative to current forensic practices to improve DNA yields from challenging human remains.}, }
@article {pmid32172179, year = {2020}, author = {Rahmat, RA and Humphries, MA and Austin, JJ and Linacre, AMT and Raven, M and Self, P}, title = {Integrating spectrophotometric and XRD analyses in the investigation of burned dental remains.}, journal = {Forensic science international}, volume = {310}, number = {}, pages = {110236}, doi = {10.1016/j.forsciint.2020.110236}, pmid = {32172179}, issn = {1872-6283}, mesh = {*Fires ; Forensic Dentistry ; Humans ; Spectrophotometry ; Tooth/*pathology ; X-Ray Diffraction ; }, abstract = {Heat alters colour and crystallinity of teeth by destruction of the organic content and inducing hydroxyapatite crystal growth. The colour and crystallite changes can be quantified using spectrophotometric and x-ray diffraction analyses, however these analyses are not commonly used in combination to evaluate burned dental remains. In this study, thirty-nine teeth were incinerated at 300-1000 °C for 15 and 30 min and then measured using a spectrophotometer and an x-ray diffractometer. Response variables used were lightness, L*, and chromaticity a* and b* and luminance (whiteness and yellowness) for colour, and crystal size for crystallinity. Statistical analysis to determine the attribution of these variables revealed yellowness and crystal size were significantly affected by temperature (p < 0.05), whilst duration of heat-exposure showed no significant effect. This study suggests the inclusion of both spectrophotometric and x-ray diffraction in investigating thermal-heated teeth is useful to accurately estimate the temperature teeth are exposed to.}, }
@article {pmid32163678, year = {2020}, author = {Li, L and Zou, X and Zhang, G and Wang, H and Su, Y and Wang, M and He, G}, title = {Population genetic analysis of Shaanxi male Han Chinese population reveals genetic differentiation and homogenization of East Asians.}, journal = {Molecular genetics &amp; genomic medicine}, volume = {8}, number = {5}, pages = {e1209}, pmid = {32163678}, issn = {2324-9269}, abstract = {BACKGROUND: Shaanxi province, located in the upper Yellow River, has been evidenced as the geographic origin of Chinese civilization, Sino-Tibetan-speaking language, and foxtail or broomcorn millet farmers via the linguistic phylogenetic spectrum, archeological documents, and genetic evidence. Nowadays, Han Chinese is the dominant population in this area. The formation process of modern Shaanxi Han population reconstructed via the ancient DNA is on the way, however, the patterns of genetic relationships of modern Shaanxi Han, allele frequency distributions of high mutated short tandem repeats (STRs) and corresponding forensic parameters are remained to be explored.<br><br>METHODS: Here, we successfully genotyped 23 autosomal STRs in 630 unrelated Shaanxi male Han individuals using the recently updated Huaxia Platinum PCR amplification system. Forensic allele frequency and parameters of all autosomal STRs were assessed. And comprehensive population genetic structure was explored via various typical statistical technologies.<br><br>RESULTS: Population genetic analysis based on the raw-genotype dataset among 15,803 Eurasian individuals and frequency datasets among 56 populations generally illustrated that linguistic stratification is significantly associated with the genetic substructure of the East Asian population. Principal component analysis, multidimensional scaling plots and phylogenetic tree further demonstrated that Shaanxi Han has a close genetic relationship with geographically close Shanxi Han, and showed that Han Chinese is a homogeneous population during the historic and recent admixture from the STR variations. Except for Sinitic-speaking populations, Shaanxi Han harbored more alleles sharing with Tibeto-Burman-speaking populations than with other reference populations. Focused on the allele frequency correlation and forensic parameters, all loci are in accordance with the minimum requirements of HWE and LD. The observed combined probability of discrimination of 8.2201E-28 and the cumulative power of exclusion of 0.9999999995 in Shaanxi Han demonstrated that the studied STR loci are informative and polymorphic, and this system can be used as a powerful routine forensic tool in personal identification and parentage testing.<br><br>CONCLUSION: Both the geographical and linguistic divisions have shaped the genetic structure of modern East Asian. And more forensic reference data should be obtained for ethnically, culturally, geographically and linguistically different populations for better routine forensic practice and population genetic studies.}, }
@article {pmid32145389, year = {2020}, author = {Thang, TN and Vázquez-Prieto, S and Vilas, R and Paniagua, E and Ubeira, FM and Ichikawa-Seki, M}, title = {Genetic diversity of Fasciola hepatica in Spain and Peru.}, journal = {Parasitology international}, volume = {76}, number = {}, pages = {102100}, doi = {10.1016/j.parint.2020.102100}, pmid = {32145389}, issn = {1873-0329}, mesh = {Animals ; Carboxy-Lyases/analysis ; Cattle ; Cattle Diseases/*parasitology ; DNA Polymerase III/analysis ; Fasciola hepatica/*genetics ; Fascioliasis/parasitology/*veterinary ; Fungal Proteins/analysis ; *Genetic Variation ; Peru ; Phylogeny ; Sequence Analysis, DNA ; Sheep ; Sheep Diseases/*parasitology ; Spain ; }, abstract = {In the present study, molecular characterization of Fasciola flukes from Spain was performed to reveal the relation with the previously reported Peruvian F. hepatica population. The nuclear DNA markers, phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold), were used for species identification of Fasciola flukes. A total of 196 Fasciola flukes were identified as F. hepatica by pepck and pold, and 26 haplotypes were detected in mitochondrial NADH dehydrogenase subunit 1 (nad1). Only one of them was previously found in Spanish samples; which indicates the existence of high genetic diversity and population structure in F. hepatica from Spain. Three haplotypes were identical to those from Peruvian F. hepatica. The pairwise fixation index value confirmed a relatively close relationship between the Spanish and Peruvian F. hepatica samples. The Spanish samples showed clearly higher genetic variability than the Peruvian population. These results are discussed in relation with the hypothesis of the introduction of the parasite in America from Europe and recent evidence of pre-Hispanic F. hepatica from Argentina revealed by ancient DNA.}, }
@article {pmid32145021, year = {2020}, author = {Mathieson, I}, title = {Limited Evidence for Selection at the FADS Locus in Native American Populations.}, journal = {Molecular biology and evolution}, volume = {37}, number = {7}, pages = {2029-2033}, pmid = {32145021}, issn = {1537-1719}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; }, abstract = {The FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids. This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of long-chain polyunsaturated fatty acids varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals are confounded by independent selection-postdating the split from Native Americans-in the European and, possibly, the East Asian populations used in the population branch statistic test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. An explanation for the present-day distribution of the haplotype that is more consistent with the data is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown.}, }
@article {pmid32145015, year = {2020}, author = {Popitsch, N and Huber, CD and Buchumenski, I and Eisenberg, E and Jantsch, M and von Haeseler, A and Gallach, M}, title = {A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals.}, journal = {Genome biology and evolution}, volume = {12}, number = {4}, pages = {345-357}, pmid = {32145015}, issn = {1759-6653}, abstract = {In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.}, }
@article {pmid32142382, year = {2020}, author = {Zhang, J and Lees, DC and Shen, J and Cong, Q and Huertas, B and Martin, G and Grishin, NV}, title = {The mitogenome of a Malagasy butterfly Malaza fastuosus (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (Lepidoptera).}, journal = {Genome}, volume = {63}, number = {4}, pages = {195-202}, doi = {10.1139/gen-2019-0189}, pmid = {32142382}, issn = {1480-3321}, mesh = {Animals ; Butterflies/*genetics ; Female ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; Lepidoptera/*genetics ; Male ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Malaza fastuosus is a lavishly patterned skipper butterfly from a genus that has three described species, all endemic to the mainland of Madagascar. To our knowledge, M. fastuosus has not been collected for nearly 50 years. To evaluate the power of our techniques to recover DNA, we used a single foreleg of an at least 140-year-old holotype specimen from the collection of the Natural History Museum London with no destruction of external morphology to extract DNA and assemble a complete mitogenome from next generation sequencing reads. The resulting 15 540 bp mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A+T rich region, similarly to other Lepidoptera mitogenomes. Here we provide the first mitogenome also for Trapezitinae (Rachelia extrusus). Phylogenetic analysis of available skipper mitogenomes places Malaza outside of Trapezitinae and Barcinae + Hesperiinae, with a possible sister relationship to Heteropterinae. Of these, at least Heteropterinae, Trapezitinae, and almost all Hesperiinae have monocot-feeding caterpillars. Malaza appears to be an evolutionarily highly distinct ancient lineage, morphologically with several unusual hesperiid features. The monotypic subfamily Malazinae Lees &amp; Grishin subfam. nov. (type genus Malaza) is proposed to reflect this morphological and molecular evidence.}, }
@article {pmid32132541, year = {2020}, author = {Gokhman, D and Nissim-Rafinia, M and Agranat-Tamir, L and Housman, G and García-Pérez, R and Lizano, E and Cheronet, O and Mallick, S and Nieves-Colón, MA and Li, H and Alpaslan-Roodenberg, S and Novak, M and Gu, H and Osinski, JM and Ferrando-Bernal, M and Gelabert, P and Lipende, I and Mjungu, D and Kondova, I and Bontrop, R and Kullmer, O and Weber, G and Shahar, T and Dvir-Ginzberg, M and Faerman, M and Quillen, EE and Meissner, A and Lahav, Y and Kandel, L and Liebergall, M and Prada, ME and Vidal, JM and Gronostajski, RM and Stone, AC and Yakir, B and Lalueza-Fox, C and Pinhasi, R and Reich, D and Marques-Bonet, T and Meshorer, E and Carmel, L}, title = {Differential DNA methylation of vocal and facial anatomy genes in modern humans.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1189}, pmid = {32132541}, issn = {2041-1723}, support = {U01 MH106874/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adult ; Aged ; Animals ; Cells, Cultured ; Child ; Chondrocytes ; *DNA Methylation ; *DNA, Ancient ; Evolution, Molecular ; Face/*anatomy &amp; histology ; Female ; Gene Regulatory Networks ; Genetic Speciation ; Humans ; Larynx/anatomy &amp; histology ; Male ; Middle Aged ; Neanderthals/genetics ; Pan troglodytes/genetics ; *Phenotype ; Phonation/*genetics ; Primary Cell Culture ; Tongue/anatomy &amp; histology ; Vocal Cords/anatomy &amp; histology ; Vocalization, Animal ; }, abstract = {Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.}, }
@article {pmid32130218, year = {2020}, author = {Sawafuji, R and Saso, A and Suda, W and Hattori, M and Ueda, S}, title = {Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0226654}, pmid = {32130218}, issn = {1932-6203}, mesh = {Archaeology/*methods ; Body Remains ; DNA Barcoding, Taxonomic ; DNA, Ancient/*isolation &amp; purification ; DNA, Fungal/isolation &amp; purification ; DNA, Plant/isolation &amp; purification ; Dental Calculus/*chemistry ; *Feeding Behavior ; Female ; Fungi/genetics ; History, 18th Century ; History, 19th Century ; Humans ; Japan ; Male ; Oryza/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th-19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.}, }
@article {pmid32127690, year = {2020}, author = {Racimo, F and Sikora, M and Vander Linden, M and Schroeder, H and Lalueza-Fox, C}, title = {Beyond broad strokes: sociocultural insights from the study of ancient genomes.}, journal = {Nature reviews. Genetics}, volume = {21}, number = {6}, pages = {355-366}, doi = {10.1038/s41576-020-0218-z}, pmid = {32127690}, issn = {1471-0064}, mesh = {Archaeology/methods ; DNA, Ancient/*analysis ; Emigration and Immigration/statistics &amp; numerical data ; Genetics, Population/*methods ; History, Ancient ; Humans ; Metagenomics/*methods ; Socioeconomic Factors ; }, abstract = {In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from mostly large-scale supraregional studies to a more local perspective, shedding light on socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies showcasing these types of insights, focusing on methods used to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines - such as anthropology, archaeology, linguistics and genetics - that have until recently evolved in separation. Multidisciplinary dialogue is important for an integrated reconstruction of human history, which can yield extraordinary insights about past societies, reproductive behaviours and even lifestyle habits that would not be possible to obtain otherwise.}, }
@article {pmid32119793, year = {2020}, author = {Kistler, L and Bieker, VC and Martin, MD and Pedersen, MW and Ramos Madrigal, J and Wales, N}, title = {Ancient Plant Genomics in Archaeology, Herbaria, and the Environment.}, journal = {Annual review of plant biology}, volume = {71}, number = {}, pages = {605-629}, doi = {10.1146/annurev-arplant-081519-035837}, pmid = {32119793}, issn = {1545-2123}, mesh = {*Archaeology ; *DNA, Ancient ; Environment ; Genomics ; Plants/genetics ; }, abstract = {The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.}, }
@article {pmid32098773, year = {2020}, author = {Sirak, K and Fernandes, D and Cheronet, O and Harney, E and Mah, M and Mallick, S and Rohland, N and Adamski, N and Broomandkhoshbacht, N and Callan, K and Candilio, F and Lawson, AM and Mandl, K and Oppenheimer, J and Stewardson, K and Zalzala, F and Anders, A and Bartík, J and Coppa, A and Dashtseveg, T and Évinger, S and Farkaš, Z and Hajdu, T and Bayarsaikhan, J and McIntyre, L and Moiseyev, V and Okumura, M and Pap, I and Pietrusewsky, M and Raczky, P and Šefčáková, A and Soficaru, A and Szeniczey, T and Szőke, BM and Van Gerven, D and Vasilyev, S and Bell, L and Reich, D and Pinhasi, R}, title = {Human auditory ossicles as an alternative optimal source of ancient DNA.}, journal = {Genome research}, volume = {30}, number = {3}, pages = {427-436}, pmid = {32098773}, issn = {1549-5469}, abstract = {DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.}, }
@article {pmid32094539, year = {2020}, author = {Fernandes, DM and Mittnik, A and Olalde, I and Lazaridis, I and Cheronet, O and Rohland, N and Mallick, S and Bernardos, R and Broomandkhoshbacht, N and Carlsson, J and Culleton, BJ and Ferry, M and Gamarra, B and Lari, M and Mah, M and Michel, M and Modi, A and Novak, M and Oppenheimer, J and Sirak, KA and Stewardson, K and Mandl, K and Schattke, C and Özdoğan, KT and Lucci, M and Gasperetti, G and Candilio, F and Salis, G and Vai, S and Camarós, E and Calò, C and Catalano, G and Cueto, M and Forgia, V and Lozano, M and Marini, E and Micheletti, M and Miccichè, RM and Palombo, MR and Ramis, D and Schimmenti, V and Sureda, P and Teira, L and Teschler-Nicola, M and Kennett, DJ and Lalueza-Fox, C and Patterson, N and Sineo, L and Coppa, A and Caramelli, D and Pinhasi, R and Reich, D}, title = {The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {3}, pages = {334-345}, doi = {10.1038/s41559-020-1102-0}, pmid = {32094539}, issn = {2397-334X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa ; *Agriculture ; Anthropology ; *DNA, Ancient ; Emigration and Immigration ; Europe ; *Genome-Wide Association Study ; Humans ; Iran ; Islands ; Sicily ; Spain ; }, abstract = {Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.}, }
@article {pmid32094358, year = {2020}, author = {Marcus, JH and Posth, C and Ringbauer, H and Lai, L and Skeates, R and Sidore, C and Beckett, J and Furtwängler, A and Olivieri, A and Chiang, CWK and Al-Asadi, H and Dey, K and Joseph, TA and Liu, CC and Der Sarkissian, C and Radzevičiūtė, R and Michel, M and Gradoli, MG and Marongiu, P and Rubino, S and Mazzarello, V and Rovina, D and La Fragola, A and Serra, RM and Bandiera, P and Bianucci, R and Pompianu, E and Murgia, C and Guirguis, M and Orquin, RP and Tuross, N and van Dommelen, P and Haak, W and Reich, D and Schlessinger, D and Cucca, F and Krause, J and Novembre, J}, title = {Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {939}, pmid = {32094358}, issn = {2041-1723}, support = {R01 GM132383/GM/NIGMS NIH HHS/United States ; R01 HG007089/HG/NHGRI NIH HHS/United States ; HHSN271201100005C/DA/NIDA NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; }, mesh = {Archaeology/methods ; Body Remains ; Chromosomes, Human, X/genetics ; Chromosomes, Human, Y/genetics ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Datasets as Topic ; Female ; Genetics, Population/*history ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; *Human Migration ; Humans ; Italy ; Male ; *Models, Genetic ; Sequence Analysis, DNA ; }, abstract = {The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.}, }
@article {pmid32081659, year = {2020}, author = {Guedes, L and Borba, VH and Camacho, M and Neto, J and Dias, O and Iñiguez, AM}, title = {African helminth infection out of Africa: Paleoparasitological and paleogenetic investigations in Pretos Novos cemetery, Rio de Janeiro, Brazil (1769-1830).}, journal = {Acta tropica}, volume = {205}, number = {}, pages = {105399}, doi = {10.1016/j.actatropica.2020.105399}, pmid = {32081659}, issn = {1873-6254}, mesh = {Africa/epidemiology ; Animals ; Brazil/epidemiology ; *Cemeteries ; Enslavement ; Environment ; Helminthiasis/*epidemiology/*parasitology ; Helminths/*isolation &amp; purification ; Humans ; }, abstract = {Pretos Novos cemetery (PNC), Rio de Janeiro, Brazil (1769-1830) was created exclusively to bury enslaved Africans who died upon arrival at the city or before being sold in the slave market. The PNC site may be unique in the Americas in allowing the study of African parasite infections acquired in Africa. We aimed to identify parasites infecting PNC individuals through paleoparasitological and paleogenetic analyses. The bodies had been dismembered, placed in mass graves, and burned, and most human remains collected from the site are highly fragmented and show extensive degradation. Sacrum and pelvic sediments were collected from five individuals along with seven samples of sediment from other areas of the body, as controls. Samples were submitted to three parasitological techniques and, in paleogenetic analysis, to four molecular targets. Larvae, mites, pollen grains, and structure suggestive of plants and fungus were observed, but we found no evidence of helminth infection. Ascaris sp. cytb sequence was recovered in one individual. We emphasize that, even with the extensive degradation of PNC human remains and the process of curation of samples, it was possible to recover helminth aDNA. The origin of PNC individuals confirms that these infections were brought to Brazil from western and central Africa during the colonial era.}, }
@article {pmid32079752, year = {2020}, author = {Gibbons, A}, title = {Strange bedfellows for human ancestors.}, journal = {Science (New York, N.Y.)}, volume = {367}, number = {6480}, pages = {838-839}, doi = {10.1126/science.367.6480.838}, pmid = {32079752}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; DNA, Ancient ; Extinction, Biological ; Fossils ; *Hominidae/anatomy &amp; histology/genetics ; Humans ; Inbreeding ; *Mating Preference, Animal ; }, }
@article {pmid32073242, year = {2019}, author = {Wu, X and Ning, C and Bao, Q and Gao, S and Zhang, F and Wu, S and Li, T and Fan, L and Li, T and Yang, X and Cai, D and Cui, Y}, title = {Mitochondrial Genome of an 8,400-Year-Old Individual from Northern China Reveals a Novel Subclade Under C5d.}, journal = {Human biology}, volume = {91}, number = {1}, pages = {21-30}, doi = {10.13110/humanbiology.91.1.04}, pmid = {32073242}, issn = {1534-6617}, mesh = {DNA, Ancient ; DNA, Mitochondrial ; Genome, Mitochondrial/*genetics ; Genotyping Techniques ; Haplotypes/*genetics ; History, Ancient ; Humans ; Mongolia/epidemiology ; Phylogeny ; }, abstract = {Ancient DNA studies have always refreshed our understanding of the human past that cannot be tracked by modern DNA alone. Until recently, ancient mitochondrial genomic studies in East Asia were still very limited. Here, we retrieved the whole mitochondrial genome of an 8,400-year-old individual from Inner Mongolia, China. Phylogenetic analyses show that the individual belongs to a previously undescribed clade under haplogroup C5d that most probably originated in northern Asia and may have a very low frequency in extant populations that have not yet been sampled. We further characterized the demographic history of mitochondrial haplogroups C5 and C5d and found that C5 experienced a sharp increase in population size starting around 4,000 years before present, the time when intensive millet farming was developed by populations who are associated with the Lower Xiajiadian culture and was widely adopted in northern China. We caution that people related to haplogroup C5 may have added this farming technology to their original way of life and that the various forms of subsistence may have provided abundant food sources and further contributed to the increase in population size.}, }
@article {pmid32064591, year = {2020}, author = {Harding, T and Milot, E and Moreau, C and Lefebvre, JF and Bournival, JS and Vézina, H and Laprise, C and Lalueza-Fox, C and Anglada, R and Loewen, B and Casals, F and Ribot, I and Labuda, D}, title = {Historical human remains identification through maternal and paternal genetic signatures in a founder population with extensive genealogical record.}, journal = {American journal of physical anthropology}, volume = {171}, number = {4}, pages = {645-658}, doi = {10.1002/ajpa.24024}, pmid = {32064591}, issn = {1096-8644}, mesh = {Adult ; Anthropology, Physical/*methods ; Body Remains ; *Genetic Markers ; Humans ; Male ; *Maternal Inheritance ; Middle Aged ; *Paternal Inheritance ; Quebec ; Young Adult ; }, abstract = {OBJECTIVES: We describe a method to identify human remains excavated from unmarked graves in historical Québec cemeteries by combining parental-lineage genetic markers with the whole-population genealogy of Québec contained in the BALSAC database.<br><br>MATERIALS AND METHODS: The remains of six men were exhumed from four historical cemeteries in the province of Québec, Canada. DNA was extracted from the remains and genotyped to reveal their mitochondrial and Y-chromosome haplotypes, which were compared to a collection of haplotypes of genealogically-anchored modern volunteers. Maternal and paternal genealogies were searched in the BALSAC genealogical record for parental couples matching the mitochondrial and the Y-chromosome haplotypic signatures, to identify candidate sons from whom the remains could have originated.<br><br>RESULTS: Analysis of the matching genealogies identified the parents of one man inhumed in the cemetery of the investigated parish during its operating time. The candidate individual died in 1833 at the age of 58, a plausible age at death in light of osteological analysis of the remains.<br><br>DISCUSSION: This study demonstrates the promising potential of coupling genetic information from living individuals to genealogical data in BALSAC to identify historical human remains. If genetic coverage is increased, the genealogical information in BALSAC could enable the identification of 87% of the men (n = 178,435) married in Québec before 1850, with high discriminatory power in most cases since >75% of the parental couples have unique biparental signatures in most regions. Genotyping and identifying Québec's historical human remains are a key to reconstructing the genomes of the founders of Québec and reinhuming archeological remains with a marked grave.}, }
@article {pmid32047039, year = {2020}, author = {Turney, CSM and Fogwill, CJ and Golledge, NR and McKay, NP and van Sebille, E and Jones, RT and Etheridge, D and Rubino, M and Thornton, DP and Davies, SM and Ramsey, CB and Thomas, ZA and Bird, MI and Munksgaard, NC and Kohno, M and Woodward, J and Winter, K and Weyrich, LS and Rootes, CM and Millman, H and Albert, PG and Rivera, A and van Ommen, T and Curran, M and Moy, A and Rahmstorf, S and Kawamura, K and Hillenbrand, CD and Weber, ME and Manning, CJ and Young, J and Cooper, A}, title = {Early Last Interglacial ocean warming drove substantial ice mass loss from Antarctica.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {8}, pages = {3996-4006}, pmid = {32047039}, issn = {1091-6490}, abstract = {The future response of the Antarctic ice sheet to rising temperatures remains highly uncertain. A useful period for assessing the sensitivity of Antarctica to warming is the Last Interglacial (LIG) (129 to 116 ky), which experienced warmer polar temperatures and higher global mean sea level (GMSL) (+6 to 9 m) relative to present day. LIG sea level cannot be fully explained by Greenland Ice Sheet melt (∼2 m), ocean thermal expansion, and melting mountain glaciers (∼1 m), suggesting substantial Antarctic mass loss was initiated by warming of Southern Ocean waters, resulting from a weakening Atlantic meridional overturning circulation in response to North Atlantic surface freshening. Here, we report a blue-ice record of ice sheet and environmental change from the Weddell Sea Embayment at the periphery of the marine-based West Antarctic Ice Sheet (WAIS), which is underlain by major methane hydrate reserves. Constrained by a widespread volcanic horizon and supported by ancient microbial DNA analyses, we provide evidence for substantial mass loss across the Weddell Sea Embayment during the LIG, most likely driven by ocean warming and associated with destabilization of subglacial hydrates. Ice sheet modeling supports this interpretation and suggests that millennial-scale warming of the Southern Ocean could have triggered a multimeter rise in global sea levels. Our data indicate that Antarctica is highly vulnerable to projected increases in ocean temperatures and may drive ice-climate feedbacks that further amplify warming.}, }
@article {pmid32028722, year = {2020}, author = {Pérez, V and Cortés, J and Marchant, F and Dorador, C and Molina, V and Cornejo-D'Ottone, M and Hernández, K and Jeffrey, W and Barahona, S and Hengst, MB}, title = {Aquatic Thermal Reservoirs of Microbial Life in a Remote and Extreme High Andean Hydrothermal System.}, journal = {Microorganisms}, volume = {8}, number = {2}, pages = {}, pmid = {32028722}, issn = {2076-2607}, support = {1100953//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 1140356//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 1181773//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; FB0001//Centro de Biotecnología y Bioingeniería/ ; }, abstract = {Hydrothermal systems are ideal to understand how microbial communities cope with challenging conditions. Lirima, our study site, is a polyextreme, high-altitude, hydrothermal ecosystem located in the Chilean Andean highlands. Herein, we analyze the benthic communities of three nearby springs in a gradient of temperature (42-72 °C represented by stations P42, P53, and P72) and pH, and we characterize their microbial diversity by using bacteria 16S rRNA (V4) gene metabarcoding and 16S rRNA gene clone libraries (bacteria and archaea). Bacterial clone libraries of P42 and P53 springs showed that the community composition was mainly represented by phototrophic bacteria (Chlorobia, 3%, Cyanobacteria 3%, at P42; Chlorobia 5%, and Chloroflexi 5% at P53), Firmicutes (32% at P42 and 43% at P53) and Gammaproteobacteria (13% at P42 and 29% at P53). Furthermore, bacterial communities that were analyzed by 16S rRNA gene metabarcoding were characterized by an overall predominance of Chloroflexi in springs with lower temperatures (33% at P42), followed by Firmicutes in hotter springs (50% at P72). The archaeal diversity of P42 and P53 were represented by taxa belonging to Crenarchaeota, Diapherotrites, Nanoarchaeota, Hadesarchaeota, Thaumarchaeota, and Euryarchaeota. The microbial diversity of the Lirima hydrothermal system is represented by groups from deep branches of the tree of life, suggesting this ecosystem as a reservoir of primitive life and a key system to study the processes that shaped the evolution of the biosphere.}, }
@article {pmid32022848, year = {2020}, author = {Mathieson, I and Abascal, F and Vinner, L and Skoglund, P and Pomilla, C and Mitchell, P and Arthur, C and Gurdasani, D and Willerslev, E and Sandhu, MS and Dewar, G}, title = {An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa.}, journal = {Genome biology and evolution}, volume = {12}, number = {4}, pages = {407-412}, pmid = {32022848}, issn = {1759-6653}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/S003711/1/MRC_/Medical Research Council/United Kingdom ; MR/S003711/2/MRC_/Medical Research Council/United Kingdom ; R35 GM133708/GM/NIGMS NIH HHS/United States ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; WT098051/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Baboons are one of the most abundant large nonhuman primates and are widely studied in biomedical, behavioral, and anthropological research. Despite this, our knowledge of their evolutionary and demographic history remains incomplete. Here, we report a 0.9-fold coverage genome sequence from a 5800-year-old baboon from the site of Ha Makotoko in Lesotho. The ancient baboon is closely related to present-day Papio ursinus individuals from southern Africa-indicating a high degree of continuity in the southern African baboon population. This level of population continuity is rare in recent human populations but may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.}, }
@article {pmid32019465, year = {2020}, author = {Macleod, R and Sinding, MS and Olsen, MT and Collins, MJ and Rowland, SJ}, title = {DNA preserved in jetsam whale ambergris.}, journal = {Biology letters}, volume = {16}, number = {2}, pages = {20190819}, pmid = {32019465}, issn = {1744-957X}, mesh = {*Ambergris ; Animals ; DNA ; Netherlands ; New Zealand ; Whales/genetics ; }, abstract = {Jetsam ambergris, found on beaches worldwide, has always been assumed to originate as a natural product of sperm whales (Physeteroidea). However, only indirect evidence has ever been produced for this, such as the presence of whale prey remains in ambergris. Here, we extracted and analysed DNA sequences from jetsam ambergris from beaches in New Zealand and Sri Lanka, and sequences from ambergris of a sperm whale beached in The Netherlands. The lipid-rich composition of ambergris facilitated high preservation-quality of endogenous DNA, upon which we performed shotgun Illumina sequencing. Alignment of mitochondrial and nuclear genome sequences with open-access reference data for multiple whale species confirms that all three jetsam samples derived originally from sperm whales (Physeter macrocephalus). Shotgun sequencing here also provides implications for metagenomic insights into ambergris-preserved DNA. These results demonstrate significant implications for elucidating the origins of jetsam ambergris as a prized natural product, and also for the understanding of sperm whale metabolism and diet, and the ecological mechanisms underlying these coproliths.}, }
@article {pmid32017876, year = {2020}, author = {Xenikoudakis, G and Ahmed, M and Harris, JC and Wadleigh, R and Paijmans, JLA and Hartmann, S and Barlow, A and Lerner, H and Hofreiter, M}, title = {Ancient DNA reveals twenty million years of aquatic life in beavers.}, journal = {Current biology : CB}, volume = {30}, number = {3}, pages = {R110-R111}, doi = {10.1016/j.cub.2019.12.041}, pmid = {32017876}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Genome, Mitochondrial ; Life History Traits ; Rodentia/genetics/*physiology ; }, abstract = {Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.}, }
@article {pmid32015858, year = {2020}, author = {Tabares, X and Zimmermann, H and Dietze, E and Ratzmann, G and Belz, L and Vieth-Hillebrand, A and Dupont, L and Wilkes, H and Mapani, B and Herzschuh, U}, title = {Vegetation state changes in the course of shrub encroachment in an African savanna since about 1850 CE and their potential drivers.}, journal = {Ecology and evolution}, volume = {10}, number = {2}, pages = {962-979}, pmid = {32015858}, issn = {2045-7758}, abstract = {Shrub encroachment has far-reaching ecological and economic consequences in many ecosystems worldwide. Yet, compositional changes associated with shrub encroachment are often overlooked despite having important effects on ecosystem functioning.We document the compositional change and potential drivers for a northern Namibian Combretum woodland transitioning into a Terminalia shrubland. We use a multiproxy record (pollen, sedimentary ancient DNA, biomarkers, compound-specific carbon (δ13C) and deuterium (δD) isotopes, bulk carbon isotopes (δ13Corg), grain size, geochemical properties) from Lake Otjikoto at high taxonomical and temporal resolution.We provide evidence that state changes in semiarid environments may occur on a scale of one century and that transitions between stable states can span around 80 years and are characterized by a unique vegetation composition. We demonstrate that the current grass/woody ratio is exceptional for the last 170 years, as supported by n-alkane distributions and the δ13C and δ13Corg records. Comparing vegetation records to environmental proxy data and census data, we infer a complex network of global and local drivers of vegetation change. While our δD record suggests physiological adaptations of woody species to higher atmospheric pCO2 concentration and drought, our vegetation records reflect the impact of broad-scale logging for the mining industry, and the macrocharcoal record suggests a decrease in fire activity associated with the intensification of farming. Impact of selective grazing is reflected by changes in abundance and taxonomical composition of grasses and by an increase of nonpalatable and trampling-resistant taxa. In addition, grain-size and spore records suggest changes in the erodibility of soils because of reduced grass cover. Synthesis. We conclude that transitions to an encroached savanna state are supported by gradual environmental changes induced by management strategies, which affected the resilience of savanna ecosystems. In addition, feedback mechanisms that reflect the interplay between management legacies and climate change maintain the encroached state.}, }
@article {pmid32004756, year = {2020}, author = {de-Dios, T and van Dorp, L and Charlier, P and Morfopoulou, S and Lizano, E and Bon, C and Le Bitouzé, C and Alvarez-Estape, M and Marquès-Bonet, T and Balloux, F and Lalueza-Fox, C}, title = {Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793).}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {80}, number = {}, pages = {104209}, doi = {10.1016/j.meegid.2020.104209}, pmid = {32004756}, issn = {1567-7257}, support = {U01 MH106874/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; 206478/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; BB/R01356X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The French revolutionary Jean-Paul Marat (1743-1793) was assassinated in 1793 in his bathtub, where he was trying to find relief from the debilitating skin disease he was suffering from. At the time of his death, Marat was annotating newspapers, which got stained with his blood and were subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain and also from another section of the newspaper, which we used for comparison. Results from the human DNA sequence analyses were compatible with a heterogeneous ancestry of Marat, with his mother being of French origin and his father born in Sardinia. Metagenomic analyses of the non-human reads uncovered the presence of fungal, bacterial and low levels of viral DNA. Relying on the presence/absence of microbial species in the samples, we could cast doubt on several putative infectious agents that have been previously hypothesised as the cause of his condition but for which we detect not a single sequencing read. Conversely, some of the species we detect are uncommon as environmental contaminants and may represent plausible infective agents. Based on all the available evidence, we hypothesize that Marat may have suffered from a fungal infection (seborrheic dermatitis), possibly superinfected with bacterial opportunistic pathogens.}, }
@article {pmid31992804, year = {2020}, author = {Oswald, JA and Allen, JM and LeFebvre, MJ and Stucky, BJ and Folk, RA and Albury, NA and Morgan, GS and Guralnick, RP and Steadman, DW}, title = {Ancient DNA and high-resolution chronometry reveal a long-term human role in the historical diversity and biogeography of the Bahamian hutia.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1373}, pmid = {31992804}, issn = {2045-2322}, mesh = {Animals ; Bahamas ; *DNA, Ancient ; *Fossils ; Humans ; *Phylogeny ; Phylogeography ; *Rodentia/classification/genetics ; }, abstract = {Quaternary paleontological and archaeological evidence often is crucial for uncovering the historical mechanisms shaping modern diversity and distributions. We take an interdisciplinary approach using multiple lines of evidence to understand how past human activity has shaped long-term animal diversity in an island system. Islands afford unique opportunities for such studies given their robust fossil and archaeological records. Herein, we examine the only non-volant terrestrial mammal endemic to the Bahamian Archipelago, the hutia Geocapromys ingrahami. This capromyine rodent once inhabited many islands but is now restricted to several small cays. Radiocarbon dated fossils indicate that hutias were present on the Great Bahama Bank islands before humans arrived at AD ~800-1000; all dates from other islands post-date human arrival. Using ancient DNA from a subset of these fossils, along with modern representatives of Bahamian hutia and related taxa, we develop a fossil-calibrated phylogeny. We found little genetic divergence among individuals from within either the northern or southern Bahamas but discovered a relatively deep North-South divergence (~750 ka). This result, combined with radiocarbon dating and archaeological evidence, reveals a pre-human biogeographic divergence, and an unexpected human role in shaping Bahamian hutia diversity and biogeography across islands.}, }
@article {pmid31992729, year = {2020}, author = {Barbato, M and Hailer, F and Upadhyay, M and Del Corvo, M and Colli, L and Negrini, R and Kim, ES and Crooijmans, RPMA and Sonstegard, T and Ajmone-Marsan, P}, title = {Adaptive introgression from indicine cattle into white cattle breeds from Central Italy.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1279}, pmid = {31992729}, issn = {2045-2322}, mesh = {Animals ; Cattle/*genetics ; *Domestication ; Genome-Wide Association Study ; Italy ; *Polymorphism, Single Nucleotide ; *Selection, Genetic ; }, abstract = {Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.}, }
@article {pmid31990948, year = {2020}, author = {Gismondi, A and Baldoni, M and Gnes, M and Scorrano, G and D'Agostino, A and Di Marco, G and Calabria, G and Petrucci, M and Müldner, G and Von Tersch, M and Nardi, A and Enei, F and Canini, A and Rickards, O and Alexander, M and Martínez-Labarga, C}, title = {A multidisciplinary approach for investigating dietary and medicinal habits of the Medieval population of Santa Severa (7th-15th centuries, Rome, Italy).}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227433}, pmid = {31990948}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; Bone and Bones/*chemistry/metabolism ; *Cemeteries ; DNA, Ancient/*analysis ; Diet/*history ; History, Medieval ; Humans ; Rome ; }, abstract = {A multidisciplinary approach, combining stable isotope analysis from bone proteins and investigations on dental calculus using DNA analysis, light microscopy, and gas chromatography coupled with mass spectrometry, was applied to reconstruct dietary and medicinal habits of the individuals recovered in the cemetery of the Castle of Santa Severa (7th-15th centuries CE; Rome, Italy). Stable isotope analysis was performed on 120 humans, 41 faunal specimens and 8 charred seeds. Dental calculus analyses were carried out on 94 samples. Overall, isotope data indicated an omnivorous diet based on C3-terrestrial protein, although some individuals possessed carbon values indicative of C4 plant consumption. In terms of animal protein, the diet was probably based on cattle, sheep, pig and chicken products, as witnessed by the archaeozoological findings. Evidence from calculus suggested the consumption of C3 cereals, Fabaceae, Fagaceae, milk and dairy products. Secondary metabolites of herbs and wine were also detected. The detection of marine fish ancient DNA, as well as of ω3 fatty acids in calculus, hypothesized the consumption of marine foodstuffs for this coastal population, despite the lack of a clear marine isotopic signal and the presence of polyunsaturated fatty acids in plant tissues. Moreover, the knowledge of ethnopharmacological tradition and the application of medicinal plants (e.g. Punica granatum L., Ephedra sp. L.) were also identified. The detection of artemisinin, known to have antimalarial properties, led to hypothesize the presence of malaria in the area. Altogether, the combined application of microscopy and biomolecular techniques provided an innovative reconstruction of Medieval lifeways in Central Italy.}, }
@article {pmid31984637, year = {2020}, author = {Segawa, T and Yonezawa, T}, title = {Evaluation of reported sediment samples from 20 Ma using a molecular phylogenetic approach: comment on Liu et al. (2017).}, journal = {Environmental microbiology}, volume = {22}, number = {3}, pages = {813-818}, doi = {10.1111/1462-2920.14923}, pmid = {31984637}, issn = {1462-2920}, support = {JP17H01854//KAKENHI/International ; JP18H04139//KAKENHI/International ; }, mesh = {*Ascomycota/genetics ; Coal ; Fungi/genetics ; *Mycobiome ; Oceans and Seas ; Phylogeny ; }, abstract = {Liu et al. reported the cultivation and DNA sequencing of 69 fungal isolates (Ascomycota and Basidiomycota) from ancient subseafloor sediments, suggesting that they represent living fungal populations that have persisted for over 20 million years. Because these findings could bring about a paradigm shift in our understanding of the spatial breadth of the deep subsurface biosphere as well as the longevity of ancient DNA, it is extremely important to verify that their samples represent pure ancient fungi from 20 million years ago without contamination by modern species. For this purpose, we estimated the divergence times of Dikarya (Ascomycota + Basidiomycota) and Mucoromycota fungi assuming that the fungal isolates were actually sampled from 20 Ma (mega-annum) sediments and evaluated the validity of the sample ages. Using this approach, we estimate that the age of the last common ancestor of Dikarya and Mucoromycota fungi greatly exceeds the age of the Earth. Our finding emphasizes the importance of using reliable approaches to confirm the dating of ancient samples.}, }
@article {pmid31969706, year = {2020}, author = {Lipson, M and Ribot, I and Mallick, S and Rohland, N and Olalde, I and Adamski, N and Broomandkhoshbacht, N and Lawson, AM and López, S and Oppenheimer, J and Stewardson, K and Asombang, RN and Bocherens, H and Bradman, N and Culleton, BJ and Cornelissen, E and Crevecoeur, I and de Maret, P and Fomine, FLM and Lavachery, P and Mindzie, CM and Orban, R and Sawchuk, E and Semal, P and Thomas, MG and Van Neer, W and Veeramah, KR and Kennett, DJ and Patterson, N and Hellenthal, G and Lalueza-Fox, C and MacEachern, S and Prendergast, ME and Reich, D}, title = {Ancient West African foragers in the context of African population history.}, journal = {Nature}, volume = {577}, number = {7792}, pages = {665-670}, pmid = {31969706}, issn = {1476-4687}, support = {GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; 100719/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {African Continental Ancestry Group/*genetics/*history ; Alleles ; Animals ; Archaeology ; Burial ; Cameroon ; Child ; Child, Preschool ; Chromosomes, Human, Y/genetics ; DNA, Ancient/analysis ; Feeding Behavior/*ethnology ; Female ; Genetic Markers/genetics ; Genetics, Population ; Genome, Human/genetics ; Haplotypes/genetics ; History, Ancient ; Human Migration/*history ; Humans ; Language/history ; Male ; Pan troglodytes/genetics ; *Phylogeny ; Principal Component Analysis ; }, abstract = {Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1-11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.}, }
@article {pmid31969593, year = {2020}, author = {Taylor, WTT and Clark, J and Bayarsaikhan, J and Tuvshinjargal, T and Jobe, JT and Fitzhugh, W and Kortum, R and Spengler, RN and Shnaider, S and Seersholm, FV and Hart, I and Case, N and Wilkin, S and Hendy, J and Thuering, U and Miller, B and Miller, ARV and Picin, A and Vanwezer, N and Irmer, F and Brown, S and Abdykanova, A and Shultz, DR and Pham, V and Bunce, M and Douka, K and Jones, EL and Boivin, N}, title = {Early Pastoral Economies and Herding Transitions in Eastern Eurasia.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1001}, pmid = {31969593}, issn = {2045-2322}, abstract = {While classic models for the emergence of pastoral groups in Inner Asia describe mounted, horse-borne herders sweeping across the Eurasian Steppes during the Early or Middle Bronze Age (ca. 3000-1500 BCE), the actual economic basis of many early pastoral societies in the region is poorly characterized. In this paper, we use collagen mass fingerprinting and ancient DNA analysis of some of the first stratified and directly dated archaeofaunal assemblages from Mongolia's early pastoral cultures to undertake species identifications of this rare and highly fragmented material. Our results provide evidence for livestock-based, herding subsistence in Mongolia during the late 3rd and early 2nd millennia BCE. We observe no evidence for dietary exploitation of horses prior to the late Bronze Age, ca. 1200 BCE - at which point horses come to dominate ritual assemblages, play a key role in pastoral diets, and greatly influence pastoral mobility. In combination with the broader archaeofaunal record of Inner Asia, our analysis supports models for widespread changes in herding ecology linked to the innovation of horseback riding in Central Asia in the final 2nd millennium BCE. Such a framework can explain key broad-scale patterns in the movement of people, ideas, and material culture in Eurasian prehistory.}, }
@article {pmid31964606, year = {2020}, author = {Nelson, EA and Buikstra, JE and Herbig, A and Tung, TA and Bos, KI}, title = {Advances in the molecular detection of tuberculosis in pre-contact Andean South America.}, journal = {International journal of paleopathology}, volume = {29}, number = {}, pages = {128-140}, doi = {10.1016/j.ijpp.2019.12.006}, pmid = {31964606}, issn = {1879-9825}, abstract = {Andean paleopathological research has significantly enhanced knowledge about the geographical distribution and evolution of tuberculosis (TB) in pre-Columbian South America. In this paper, we review the history and progress of research on ancient tuberculosis (TB) in the Andean region, focusing on the strengths and limitations of current approaches for the molecular detection of ancient pathogens, with special attention to TB. As a case study, we describe a molecular screening approach for the detection of ancient Mycobacterium tuberculosis in individuals from Late Intermediate Period (1000-1400 CE) contexts at the site of Huari, Peru. We evaluate 34 commingled human vertebrae and combine morphological assessments of pathology with high throughput sequencing and a non-selective approach to ancient pathogen DNA screening. Our method enabled the simultaneous detection of ancient M. tuberculosis DNA and an evaluation of the environmental microbial composition of each sample. Our results show that despite the dominance of environmental DNA, molecular signatures of M. tuberculosis were identified in eight vertebrae, six of which had no observable skeletal pathology classically associated tuberculosis infection. This screening approach will assist in the identification of candidate samples for downstream genomic analyses. The method permits higher resolution disease identification in cases where pathology may be absent, or where the archaeological context may necessitate a broad differential diagnosis based on morphology alone.}, }
@article {pmid31959418, year = {2020}, author = {Napier, JD and de Lafontaine, G and Chipman, ML}, title = {The Evolution of Paleoecology.}, journal = {Trends in ecology &amp; evolution}, volume = {35}, number = {4}, pages = {293-295}, doi = {10.1016/j.tree.2019.12.006}, pmid = {31959418}, issn = {1872-8383}, mesh = {Acclimatization ; *Adaptation, Physiological/genetics ; *Climate Change ; DNA, Ancient ; }, abstract = {While the interplay between migration and adaptation dictates species response to climate change, technological limitations have obfuscated explicit tests on past adaptive responses. However, a surge in technology-driven advances in paleoecological methods coincides with breakthroughs in processing ancient DNA, providing the first opportunity to assess adaptation to past climate shifts.}, }
@article {pmid31957867, year = {2020}, author = {Schmidt, N and Schücker, K and Krause, I and Dörk, T and Klintschar, M and Hummel, S}, title = {Genome-wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains.}, journal = {American journal of physical anthropology}, volume = {172}, number = {1}, pages = {99-109}, doi = {10.1002/ajpa.23996}, pmid = {31957867}, issn = {1096-8644}, abstract = {OBJECTIVE: A genome-wide high-throughput single nucleotide polymorphism (SNP) typing method was tested with respect of the applicability to ancient and degraded DNA. The results were compared to mini-sequencing data achieved through single base extension (SBE) typing. The SNPs chosen for the study allow to determine the hair colors and eye colors of humans.<br><br>MATERIAL AND METHODS: The DNA samples were extracted from the skeletal remains of 59 human individuals dating back to the Late Bronze Age. The 3,000 years old bones had been discovered in the Lichtenstein Cave in Lower Saxony, Germany. The simultaneous typing of 24 SNPs for each of the ancient DNA samples was carried out using the 192.24 Dynamic Array™ by Fluidigm®.<br><br>RESULTS: Thirty-eight of the ancient samples (=64%) revealed full and reproducible SNP genotypes allowing hair and eye color phenotyping. In 10 samples (=17%) at least half of the SNPs were unambiguously determined, in 11 samples (=19%) the SNP typing failed. For 23 of the 59 individuals, a comparison of the SNP typing results with genotypes from an earlier performed SBE typing approach was possible. The comparison confirmed the full concordance of the results for 90% of the SNP typings. In the remaining 10% allelic dropouts were identified.<br><br>DISCUSSION: The high genotyping success rate could be achieved by introducing modifications to the preamplification protocol mainly by increasing the DNA input and the amplification cycle number. The occurrence of allelic dropouts indicates that a further increase of DNA input to the preamplification step is desirable.}, }
@article {pmid31944633, year = {2020}, author = {Selway, CA and Eisenhofer, R and Weyrich, LS}, title = {Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing.}, journal = {The journal of pathology. Clinical research}, volume = {6}, number = {2}, pages = {97-106}, pmid = {31944633}, issn = {2056-4538}, abstract = {The human microbiome can play key roles in disease, and diagnostic testing will soon have the ability to examine these roles in the context of clinical applications. Currently, most diagnostic testing in pathology applications focuses on a small number of disease-causing microbes and dismisses the whole microbial community that causes or is modulated by disease. Microbiome modifications have already provided clinically relevant insights in gut and oral diseases, such as irritable bowel disease, but there are currently limitations when clinically examining microbiomes outside of these body sites. This is critical, as the majority of microbial samples used in pathology originate from body sites that contain low concentrations of microbial DNA, including skin, tissue, blood, and urine. These samples, also known as low microbial biomass samples, are difficult to examine without careful consideration and precautions to mitigate contamination and biases. Here, we present the limitations when analysing low microbial biomass samples using current protocols and techniques and highlight the advantages that microbiome testing can offer diagnostics in the future, if the proper precautions are implemented. Specifically, we discuss the sources of contamination and biases that may result in false assessments for these sample types. Finally, we provide recommendations to mitigate contamination and biases from low microbial biomass samples during diagnostic testing, which will be especially important to effectively diagnose and treat patients using microbiome analyses.}, }
@article {pmid31943391, year = {2020}, author = {Öhrström, L and Tekin, A and Biedermann, P and Morozova, I and Habicht, M and Gascho, D and Bode-Lesniewska, B and Imhof, A and Rühli, F and Eppenberger, P}, title = {Experimental mummification-In the tracks of the ancient Egyptians.}, journal = {Clinical anatomy (New York, N.Y.)}, volume = {33}, number = {6}, pages = {860-871}, doi = {10.1002/ca.23568}, pmid = {31943391}, issn = {1098-2353}, support = {//Mäxi Stiftung, Zürich/ ; The Canopic Jar Project 162803//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, abstract = {Understanding natural and artificial postmortem alterations in different tissues of the human body is essential for bioarchaeology, paleogenetics, physical anthropology, forensic medicine, and many related disciplines. With this study, we tried to gain a better understanding of tissue alterations associated with the artificial mummification techniques of ancient Egypt, in particular for mummified visceral organs. We used several entire porcine organs and organ sections (liver, lung, stomach, ileum, and colon), which provided a close approximation to human organs. First, we dehydrated the specimens in artificial natron, before applying natural ointments, according to the ancient literary sources and recent publications. We periodically monitored the temperature, pH value, and weight of the specimens, in addition to radiodensity and volumetric measurements by clinical computed tomography and sampling for histological, bacteriological, and molecular analyses. After seven weeks, mummification was seen completed in all specimens. We observed a considerable loss of weight and volume, as well as similar courses in the decay of tissue architecture but varying levels of DNA degradation. Bacteriologically we did not detect any of the initially identified taxa in the samples by the end of the mummification process, nor any fungi. This feasibility study established an experimental protocol for future experiments modeling ancient Egyptian mummification of visceral organs using human specimens. Understanding desiccation and mummification processes in non-pathological tissues of specific visceral organs may help to identify and interpret disease-specific alterations in mummified tissues in ancient Egyptian canopic jars and organ packages contained in whole mummies.}, }
@article {pmid31940807, year = {2020}, author = {Gabbianelli, F and Alhaique, F and Romagnoli, G and Brancazi, L and Piermartini, L and Ottoni, C and Valentini, A and Chillemi, G}, title = {Was the Cinta Senese Pig Already a Luxury Food in the Late Middle Ages? Ancient DNA and Archaeozoological Evidence from Central Italy.}, journal = {Genes}, volume = {11}, number = {1}, pages = {}, pmid = {31940807}, issn = {2073-4425}, mesh = {Animals ; *DNA, Ancient ; History, Medieval ; Italy ; *Polymorphism, Single Nucleotide ; Proto-Oncogene Proteins c-kit/*genetics ; Swine/*genetics ; }, abstract = {The Cinta senese is a pig breed, highly esteemed for its meat and derived products, characterized by a black coat with a typical white &quot;belt&quot; and documented by scant iconography, since the 13th-14th century in Italy. A piece of pottery showing a Cinta pig was found in the Graffignano castle (Northern Latium, Italy) dated 15th-16th centuries, spurring us to investigate the diet of the inhabitants. Ancient DNA analysis was carried out on 21 pig specimens on three nuclear SNPs: (1) g.43597545C>T, on the KIT gene, informative for the identification of the Cinta senese breed; (2) rs81460129, on an intergenic region in chr. 16, which discriminates between domestic pigs and wild boars, and; (3) a SNP on the ZFY/ZFX homologous genes, to determine the sex of the individuals. Our results indicate that the Cinta senese was present in Northern Latium in Late Medieval time, although it was not the only breed, and that pigs, including Cinta, interbred with wild boars, suggesting free-range breeding for all types of pigs. Moreover, the unexpected high proportion of young females may be considered as evidence for the wealth of the family inhabiting the castle.}, }
@article {pmid31939994, year = {2020}, author = {Płoszaj, T and Jędrychowska-Dańska, K and Zamerska, A and Lewandowska, M and Bojarski, J and Chudziak, W and Drozd-Lipińska, A and Robaszkiewicz, A and Witas, HW}, title = {Analysis of maternal lineage structure of individuals from chamber graves placed in medieval cemetery in Kałdus, Central Poland.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {71}, number = {1}, pages = {43-50}, doi = {10.1127/homo/2020/1008}, pmid = {31939994}, issn = {1618-1301}, mesh = {Adult ; Anthropology, Physical ; Cemeteries/*history ; Child ; DNA, Mitochondrial/*genetics ; European Continental Ancestry Group/*genetics ; Female ; Haplotypes/*genetics ; History, Medieval ; Humans ; Male ; Poland ; }, abstract = {The beginning of the early Middle Ages period in Poland (10th-14th century) has been widely debated in the context of an active demographic inflow from other countries and its contribution to the creation of the new country. Finding chamber graves which are considered typical for the Scandinavian ethnic group in a few cemeteries in Poland has become the basis for the anthropological inference on the potential participation of North European people in forming the social elite of medieval Poland. However, the question of whether this fact was the result of presence of people from other countries lacks an unambiguous answer. We attempted to isolate ancient DNA from the medieval necropolis in Kałdus where several chamber graves have been found and analysed the genetic diversity of maternal lineage of this population. We analysed the HVR I fragment and coding regions to assess the mitochondrial DNA haplogroup. We have identified a few relatively rare haplogroups (A2, T2b4a, HV, K1a11, J2b1a, and X2) which were previously found in early medieval sites in Norway and Denmark. Obtained results might suggest genetic relation between the people of Kałdus and past northern Europe populations. Present and further research can undoubtedly shed new light on the aspect of the formation of the early medieval Polish population.}, }
@article {pmid31913480, year = {2020}, author = {Zhang, M and Sun, G and Ren, L and Yuan, H and Dong, G and Zhang, L and Liu, F and Cao, P and Ko, AM and Yang, MA and Hu, S and Wang, GD and Fu, Q}, title = {Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs.}, journal = {Molecular biology and evolution}, volume = {37}, number = {5}, pages = {1462-1469}, pmid = {31913480}, issn = {1537-1719}, support = {55008731/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wolf and 26 domestic dogs) from the Yellow River and Yangtze River basins (YYRB). These are the first complete ancient mtDNA of Chinese dogs from the cradle of early Chinese civilization. We found that most ancient dogs (18/26) belong to the haplogroup A1b lineage that is found in high frequency in present-day Australian dingoes and precolonial Pacific Island dogs but low frequency in present-day China. Particularly, a 7,000-year-old dog from the Tianluoshan site in Zhejiang province possesses a haplotype basal to the entire haplogroup A1b lineage. We propose that A1b lineage dogs were once widely distributed in the YYRB area. Following their dispersal to South China, and then into Southeast Asia, New Guinea and remote Oceania, they were largely replaced by dogs belonging to other lineages in the last 2,000 years in present-day China, especially North China.}, }
@article {pmid31906474, year = {2020}, author = {Barlow, A and Hartmann, S and Gonzalez, J and Hofreiter, M and Paijmans, JLA}, title = {Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates.}, journal = {Genes}, volume = {11}, number = {1}, pages = {}, pmid = {31906474}, issn = {2073-4425}, mesh = {Algorithms ; Base Sequence/genetics ; Chromosome Mapping/methods ; Cluster Analysis ; DNA, Ancient/*analysis ; Genome/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.}, }
@article {pmid31892727, year = {2019}, author = {Laza, IM and Hervella, M and Neira Zubieta, M and de-la-Rúa, C}, title = {Environmental factors modulated ancient mitochondrial DNA variability and the prevalence of rheumatic diseases in the Basque Country.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {20380}, pmid = {31892727}, issn = {2045-2322}, mesh = {*DNA, Ancient ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Predisposition to Disease ; Humans ; Prevalence ; Rheumatic Diseases/epidemiology/*genetics ; Spain ; }, abstract = {Among the factors that would explain the distribution of mitochondrial lineages in Europe, climate and diseases may have played an important role. A possible explanation lies in the nature of the mitochondrion, in which the energy generation process produces reactive oxygen species that may influence the development of different diseases. The present study is focused on the medieval necropolis of San Miguel de Ereñozar (13th-16th centuries, Basque Country), whose inhabitants presented a high prevalence of rheumatic diseases and lived during the Little Ice Age (LIA). Our results indicate a close relationship between rheumatic diseases and mitochondrial haplogroup H, and specifically between spondyloarthropathies and sub-haplogroup H2. One possible explanation may be the climate change that took place in the LIA that favoured those haplogroups that were more energy-efficient, such as haplogroup H, to endure lower temperatures and food shortage. However, it had a biological trade-off: the increased risk of developing rheumatic diseases.}, }
@article {pmid31888476, year = {2019}, author = {Silva-Pereira, TT and Ikuta, CY and Zimpel, CK and Camargo, NCS and de Souza Filho, AF and Ferreira Neto, JS and Heinemann, MB and Guimarães, AMS}, title = {Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens).}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {1030}, pmid = {31888476}, issn = {1471-2164}, support = {134266/2017-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 140003/2019-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 2017/04617-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/20147-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 1539669//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 1841/2016//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; D17ZO-307//Morris Animal Foundation/ ; }, mesh = {Animals ; Computational Biology/methods ; Genetic Markers ; *Genome, Bacterial ; *Genomics/methods ; Mycobacterium/classification/*genetics/metabolism ; Phylogeny ; Proteome ; Proteomics/methods ; Sea Lions/*microbiology ; Sequence Deletion ; *Superinfection ; Tuberculosis/*veterinary ; }, abstract = {BACKGROUND: Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization.<br><br>RESULTS: We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC.<br><br>CONCLUSION: The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.}, }
@article {pmid31881841, year = {2019}, author = {Troll, CJ and Kapp, J and Rao, V and Harkins, KM and Cole, C and Naughton, C and Morgan, JM and Shapiro, B and Green, RE}, title = {A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {1023}, pmid = {31881841}, issn = {1471-2164}, support = {R43 CA239933/CA/NCI NIH HHS/United States ; }, mesh = {*Cell-Free Nucleic Acids ; *DNA, Single-Stranded ; *Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Oligonucleotides/chemical synthesis/*chemistry ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming.<br><br>RESULTS: Here we present an efficient ligation-based single-stranded library preparation method that is engineered to produce complex libraries in under 2.5 h from as little as 1 nanogram of input DNA without alteration to the native ends of template molecules. Our method, called Single Reaction Single-stranded LibrarY or SRSLY, ligates uniquely designed Next-Generation Sequencing (NGS) adapters in a one-step combined phosphorylation/ligation reaction that foregoes end-polishing. Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation patterns to deduce nucleosome positioning and transcription factor binding.<br><br>CONCLUSIONS: SRSLY is a versatile tool for converting short and fragmented DNA molecules, like cfDNA fragments, into sequencing libraries while retaining native lengths and ends.}, }
@article {pmid31878147, year = {2019}, author = {Batyrev, D and Lapid, E and Carmel, L and Meshorer, E}, title = {Predicted Archaic 3D Genome Organization Reveals Genes Related to Head and Spinal Cord Separating Modern from Archaic Humans.}, journal = {Cells}, volume = {9}, number = {1}, pages = {}, pmid = {31878147}, issn = {2073-4409}, support = {1140/17//Israel Science Foundation/International ; }, mesh = {Animals ; DNA Methylation/genetics ; DNA, Ancient/analysis ; Databases, Genetic ; Epigenesis, Genetic/genetics ; Genome/genetics ; Genomics/methods ; Head/*anatomy &amp; histology ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; Promoter Regions, Genetic/genetics ; Spinal Cord/*anatomy &amp; histology ; }, abstract = {High coverage sequences of archaic humans enabled the reconstruction of their DNA methylation patterns. This allowed comparing gene regulation between human groups, and linking such regulatory changes to phenotypic differences. In a previous work, a detailed comparison of DNA methylation in modern humans, archaic humans, and chimpanzees revealed 873 modern human-derived differentially methylated regions (DMRs). To understand the regulatory implications of these DMRs, we defined differentially methylated genes (DMGs) as genes that harbor DMRs in their promoter or gene body. While most of the modern human-derived DMRs could be linked to DMGs, many others remained unassigned. Here, we used information on 3D genome organization to link ~70 out of the remaining 288 unassigned DMRs to genes. Combined with the previously identified DMGs, we reinforce the enrichment of these genes with vocal and facial anatomy, and additionally find significant enrichment with the spinal column, chin, hair, and scalp. These results reveal the importance of 3D genomic organization in understanding gene regulation by DNA methylation.}, }
@article {pmid31873124, year = {2019}, author = {Ottoni, C and Guellil, M and Ozga, AT and Stone, AC and Kersten, O and Bramanti, B and Porcier, S and Van Neer, W}, title = {Metagenomic analysis of dental calculus in ancient Egyptian baboons.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19637}, pmid = {31873124}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/*analysis ; Dental Calculus/*microbiology ; Egypt ; Humans ; *Metagenome ; Microbiota/*genetics ; Neanderthals ; Pan troglodytes ; Papio ; }, abstract = {Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th-6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.}, }
@article {pmid31873100, year = {2019}, author = {Clarke, CL and Edwards, ME and Gielly, L and Ehrich, D and Hughes, PDM and Morozova, LM and Haflidason, H and Mangerud, J and Svendsen, JI and Alsos, IG}, title = {Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19613}, pmid = {31873100}, issn = {2045-2322}, mesh = {Arctic Regions ; *Climate Change ; *Ecosystem ; *Plant Development ; Plants/*classification ; }, abstract = {Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could &quot;run out of space&quot; as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical evidence is fragmentary. Here we present a 24,000-year record of species persistence based on sedimentary ancient DNA (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust evidence of long-term persistence of arctic-alpine plants through large-magnitude climate changes but document a decline in their diversity during a past expansion of woody vegetation. Nevertheless, most of the plants that were present during the last glacial interval, including all of the arctic-alpines, are still found in the region today. This underlines the conservation significance of mountain landscapes via their provision of a range of habitats that confer resilience to climate change, particularly for arctic-alpine taxa.}, }
@article {pmid31872482, year = {2020}, author = {Lavretsky, P and McInerney, NR and Mohl, JE and Brown, JI and James, HF and McCracken, KG and Fleischer, RC}, title = {Assessing changes in genomic divergence following a century of human-mediated secondary contact among wild and captive-bred ducks.}, journal = {Molecular ecology}, volume = {29}, number = {3}, pages = {578-595}, doi = {10.1111/mec.15343}, pmid = {31872482}, issn = {1365-294X}, support = {G12 MD007592/MD/NIMHD NIH HHS/United States ; }, mesh = {Animals ; Animals, Wild/*genetics ; Ducks/*genetics ; Gene Flow/genetics ; Genome/*genetics ; Genomics/methods ; Humans ; Hybridization, Genetic/genetics ; North America ; }, abstract = {Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game-farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game-farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.}, }
@article {pmid31869520, year = {2020}, author = {Vershinina, AO and Kapp, JD and Baryshnikov, GF and Shapiro, B}, title = {The case of an arctic wild ass highlights the utility of ancient DNA for validating problematic identifications in museum collections.}, journal = {Molecular ecology resources}, volume = {20}, number = {5}, pages = {1182-1190}, doi = {10.1111/1755-0998.13130}, pmid = {31869520}, issn = {1755-0998}, support = {&quot;Evolution of the organic world&quot;//Russian Academy of Sciences Presidium and the Russian Ministry of Education and Science/ ; 1417036//National Science Foundation/ ; MG-30-17-0045-17//Institute of Museum and Library Services/ ; }, abstract = {Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccurate identification can lead to false biogeographic reconstructions with cascading impacts on paleontological and paleoecological research. Here, we analyzed an unusual Equid mandible found in the Far North of the Taymyr peninsula that was identified morphologically as Equus hemionus, an ancestor of present-day Asiatic wild asses. If correct, this identification represents the only finding of a putative Late Pleistocene hemione in the Arctic region, and is therefore critical to understanding wild ass evolution and paleoecology. To confirm the accuracy of this specimen's taxonomic assignment, we used ancient DNA and mitochondrial hybridization capture to identify and place this specimen in the larger equid phylogeny. We find that the specimen is actually a member of E. caballus, the ancestor of domestic horses. Our study demonstrates the utility of ancient DNA to validate morphological identification, in particular of incomplete, otherwise problematic, or taxonomically unusual museum specimens.}, }
@article {pmid31869003, year = {2020}, author = {De Simone, G and Pasquadibisceglie, A and Proietto, R and Polticelli, F and Aime, S and J M Op den Camp, H and Ascenzi, P}, title = {Contaminations in (meta)genome data: An open issue for the scientific community.}, journal = {IUBMB life}, volume = {72}, number = {4}, pages = {698-705}, doi = {10.1002/iub.2216}, pmid = {31869003}, issn = {1521-6551}, abstract = {In recent years, the high throughput and the low cost of next-generation sequencing (NGS) technologies have led to an increase of the amount of (meta)genomic data, revolutionizing genomic research studies. However, the quality of sequencing data could be affected by experimental errors derived from defective methods and protocols. This represents a serious problem for the scientific community with a negative impact on the correctness of studies that involve genomic sequence analysis. As a countermeasure, several alignment and taxonomic classification tools have been developed to uncover and correct errors. In this critical review some of these integrated software tools and pipelines used to detect contaminations in reference genome databases and sequenced samples are reported. In particular, case studies of bacterial contaminations, contaminations of human origin, mitochondrial contaminations of ancient DNA, and cross contaminations are examined.}, }
@article {pmid31861931, year = {2019}, author = {Henao, E and Rzymski, P and Waters, MN}, title = {A Review on the Study of Cyanotoxins in Paleolimnological Research: Current Knowledge and Future Needs.}, journal = {Toxins}, volume = {12}, number = {1}, pages = {}, pmid = {31861931}, issn = {2072-6651}, mesh = {Bacterial Toxins/*toxicity ; Cyanobacteria/*metabolism ; Geologic Sediments ; Lakes/microbiology ; Limnology/*methods ; Marine Toxins/*toxicity ; Microcystins/*toxicity ; Paleontology/*methods ; }, abstract = {Cyanobacterial metabolites are increasingly studied, in regards to their biosynthesis, ecological role, toxicity, and potential biomedical applications. However, the history of cyanotoxins prior to the last few decades is virtually unknown. Only a few paleolimnological studies have been undertaken to date, and these have focused exclusively on microcystins and cylindrospermopsins, both successfully identified in lake sediments up to 200 and 4700 years old, respectively. In this paper, we review direct extraction, quantification, and application of cyanotoxins in sediment cores, and put forward future research prospects in this field. Cyanobacterial toxin research is also compared to other paleo-cyanobacteria tools, such as sedimentary pigments, akinetes, and ancient DNA isolation, to identify the role of each tool in reproducing the history of cyanobacteria. Such investigations may also be beneficial for further elucidation of the biological role of cyanotoxins, particularly if coupled with analyses of other abiotic and biotic sedimentary features. In addition, we identify current limitations as well as future directions for applications in the field of paleolimnological studies on cyanotoxins.}, }
@article {pmid31848342, year = {2019}, author = {Jensen, TZT and Niemann, J and Iversen, KH and Fotakis, AK and Gopalakrishnan, S and Vågene, ÅJ and Pedersen, MW and Sinding, MS and Ellegaard, MR and Allentoft, ME and Lanigan, LT and Taurozzi, AJ and Nielsen, SH and Dee, MW and Mortensen, MN and Christensen, MC and Sørensen, SA and Collins, MJ and Gilbert, MTP and Sikora, M and Rasmussen, S and Schroeder, H}, title = {A 5700 year-old human genome and oral microbiome from chewed birch pitch.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5520}, pmid = {31848342}, issn = {2041-1723}, mesh = {Animals ; Betula/*physiology ; DNA, Ancient/*analysis ; DNA, Bacterial/analysis ; Denmark ; *Genome, Human ; Geography ; Humans ; Microbiota/*genetics ; Mouth/*microbiology ; Phenotype ; Radiometric Dating ; Sex Determination Analysis ; Time Factors ; }, abstract = {The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.}, }
@article {pmid31844110, year = {2019}, author = {Mastrantonio, V and Urbanelli, S and Porretta, D}, title = {Ancient hybridization and mtDNA introgression behind current paternal leakage and heteroplasmy in hybrid zones.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19177}, pmid = {31844110}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; Coleoptera/*genetics ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; *Hybridization, Genetic ; Phylogeny ; }, abstract = {Hybridization between heterospecific individuals has been documented as playing a direct role in promoting paternal leakage and mitochondrial heteroplasmy in both natural populations and laboratory conditions, by relaxing the egg-sperm recognition mechanisms. Here, we tested the hypothesis that hybridization can lead to mtDNA heteroplasmy also indirectly via mtDNA introgression. By using a phylogenetic approach, we showed in two reproductively isolated beetle species, Ochthebius quadricollis and O. urbanelliae, that past mtDNA introgression occurred between them in sympatric populations. Then, by developing a multiplex allele-specific PCR assay, we showed the presence of heteroplasmic individuals and argue that their origin was through paternal leakage following mating between mtDNA-introgressed and pure conspecific individuals. Our results highlight that mtDNA introgression can contribute to promote paternal leakage, generating genetic novelty in a way that has been overlooked to date. Furthermore, they highlight that the frequency and distribution of mtDNA heteroplasmy can be deeply underestimated in natural populations, as i) the commonly used PCR-Sanger sequencing approach can fail to detect mitochondrial heteroplasmy, and ii) specific studies aimed at searching for it in populations where mtDNA-introgressed and pure individuals co-occur remain scarce, despite the fact that mtDNA introgression has been widely documented in several taxa and populations.}, }
@article {pmid31842945, year = {2019}, author = {Hübler, R and Key, FM and Warinner, C and Bos, KI and Krause, J and Herbig, A}, title = {HOPS: automated detection and authentication of pathogen DNA in archaeological remains.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {280}, pmid = {31842945}, issn = {1474-760X}, mesh = {Archaeology/*methods ; DNA, Bacterial/*analysis ; *Genetic Techniques ; Metagenomics/*methods ; Software ; }, abstract = {High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.}, }
@article {pmid31841129, year = {2020}, author = {O'Neill, MB and Laval, G and Teixeira, JC and Palmenberg, AC and Pepperell, CS}, title = {Genetic susceptibility to severe childhood asthma and rhinovirus-C maintained by balancing selection in humans for 150 000 years.}, journal = {Human molecular genetics}, volume = {29}, number = {5}, pages = {736-744}, pmid = {31841129}, issn = {1460-2083}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; U19 AI104317/AI/NIAID NIH HHS/United States ; }, abstract = {Selective pressures imposed by pathogens have varied among human populations throughout their evolution, leading to marked inter-population differences at some genes mediating susceptibility to infectious and immune-related diseases. Here, we investigated the evolutionary history of a common polymorphism resulting in a Y529 versus C529 change in the cadherin related family member 3 (CDHR3) receptor which underlies variable susceptibility to rhinovirus-C infection and is associated with severe childhood asthma. The protective variant is the derived allele and is found at high frequency worldwide (69-95%). We detected genome-wide significant signatures of natural selection consistent with a rapid increase of the haplotypes carrying the allele, suggesting that non-neutral processes have acted on this locus across all human populations. However, the allele has not fixed in any population despite multiple lines of evidence suggesting that the mutation predates human migrations out of Africa. Using an approximate Bayesian computation method, we estimate the age of the mutation while explicitly accounting for past demography and positive or frequency-dependent balancing selection. Our analyses indicate a single emergence of the mutation in anatomically modern humans ~150 000 years ago and indicate that balancing selection has maintained the beneficial allele at high equilibrium frequencies worldwide. Apart from the well-known cases of the MHC and ABO genes, this study provides the first evidence that negative frequency-dependent selection plausibly acted on a human disease susceptibility locus, a form of balancing selection compatible with typical transmission dynamics of communicable respiratory viruses that might exploit CDHR3.}, }
@article {pmid31840921, year = {2020}, author = {Loog, L and Thalmann, O and Sinding, MS and Schuenemann, VJ and Perri, A and Germonpré, M and Bocherens, H and Witt, KE and Samaniego Castruita, JA and Velasco, MS and Lundstrøm, IKC and Wales, N and Sonet, G and Frantz, L and Schroeder, H and Budd, J and Jimenez, EL and Fedorov, S and Gasparyan, B and Kandel, AW and Lázničková-Galetová, M and Napierala, H and Uerpmann, HP and Nikolskiy, PA and Pavlova, EY and Pitulko, VV and Herzig, KH and Malhi, RS and Willerslev, E and Hansen, AJ and Dobney, K and Gilbert, MTP and Krause, J and Larson, G and Eriksson, A and Manica, A}, title = {Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia.}, journal = {Molecular ecology}, volume = {29}, number = {9}, pages = {1596-1610}, pmid = {31840921}, issn = {1365-294X}, abstract = {Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.}, }
@article {pmid31840056, year = {2019}, author = {Zanella, M and Vitriolo, A and Andirko, A and Martins, PT and Sturm, S and O'Rourke, T and Laugsch, M and Malerba, N and Skaros, A and Trattaro, S and Germain, PL and Mihailovic, M and Merla, G and Rada-Iglesias, A and Boeckx, C and Testa, G}, title = {Dosage analysis of the 7q11.23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication.}, journal = {Science advances}, volume = {5}, number = {12}, pages = {eaaw7908}, pmid = {31840056}, issn = {2375-2548}, support = {/ERC_/European Research Council/International ; }, mesh = {Cell Line ; Cell Movement ; Chromosomes, Human, Pair 7/*genetics ; Databases, Genetic ; *Domestication ; Epigenome ; Evolution, Molecular ; Face ; *Gene Dosage ; Gene Regulatory Networks ; Histone Code ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Neural Stem Cells/metabolism ; Transcription Factors/*genetics ; Williams Syndrome/*genetics ; }, abstract = {We undertook a functional dissection of chromatin remodeler BAZ1B in neural crest (NC) stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients harboring 7q11.23 copy number variants. Our results reveal a key contribution of BAZ1B to NCSC in vitro induction and migration, coupled with a crucial involvement in NC-specific transcriptional circuits and distal regulation. By intersecting our experimental data with new paleogenetic analyses comparing modern and archaic humans, we found a modern-specific enrichment for regulatory changes both in BAZ1B and its experimentally defined downstream targets, thereby providing the first empirical validation of the human self-domestication hypothesis and positioning BAZ1B as a master regulator of the modern human face. In so doing, we provide experimental evidence that the craniofacial and cognitive/behavioral phenotypes caused by alterations of the Williams-Beuren syndrome critical region can serve as a powerful entry point into the evolution of the modern human face and prosociality.}, }
@article {pmid31831648, year = {2019}, author = {Voosen, P}, title = {DNA from Arctic lakes traces past climate impacts.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6471}, pages = {1296-1297}, doi = {10.1126/science.366.6471.1296}, pmid = {31831648}, issn = {1095-9203}, mesh = {Animals ; Arctic Regions ; Canada ; Climate Change/*history ; DNA, Ancient/*analysis ; History, Ancient ; Lakes/*chemistry ; Plants ; }, }
@article {pmid31824712, year = {2019}, author = {Pálsdóttir, AH and Bläuer, A and Rannamäe, E and Boessenkool, S and Hallsson, JH}, title = {Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains.}, journal = {Royal Society open science}, volume = {6}, number = {10}, pages = {191059}, pmid = {31824712}, issn = {2054-5703}, abstract = {With the advent of ancient DNA, as well as other methods such as isotope analysis, destructive sampling of archaeofaunal remains has increased much faster than the effort to collect and curate them. While there has been considerable discussion regarding the ethics of destructive sampling and analysis of human remains, this dialogue has not extended to archaeofaunal material. Here we address this gap and discuss the ethical challenges surrounding destructive sampling of materials from archaeofaunal collections. We suggest ways of mitigating the negative aspects of destructive sampling and present step-by-step guidelines aimed at relevant stakeholders, including scientists, holding institutions and scientific journals. Our suggestions are in most cases easily implemented without significant increases in project costs, but with clear long-term benefits in the preservation and use of zooarchaeological material.}, }
@article {pmid31808562, year = {2020}, author = {Orlando, L}, title = {Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {1}, pages = {e1900164}, doi = {10.1002/bies.201900164}, pmid = {31808562}, issn = {1521-1878}, abstract = {The horse was essential to past human societies but became a recreational animal during the twentieth century as the world became increasingly mechanized. As the author reviews here, recent studies of ancient genomes have revisited the understanding of horse domestication, from the very early stages to the most modern developments. They have uncovered several extinct lineages roaming the far ends of Eurasia some 4000 years ago. They have shown that the domestic horse has been significantly reshaped during the last millennium and experienced a sharp decline in genetic diversity within the last two centuries. At a time when no truly wild horses exist any longer, this calls for enhanced conservation in all endangered populations. These include the Przewalski's horse native to Mongolia, and the many local breeds side-lined by the modern agenda, but yet representing the living heritage of over five millennia of horse breeding.}, }
@article {pmid31805075, year = {2019}, author = {Nazari, V and Tarmann, GM and Efetov, KA}, title = {Phylogenetic position of the 'extinct' Fijian coconut moth, Levuana iridescens (Lepidoptera: Zygaenidae).}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225590}, pmid = {31805075}, issn = {1932-6203}, mesh = {Animals ; Australia ; *Extinction, Biological ; Female ; Male ; Moths/*anatomy &amp; histology/*classification ; Phylogeny ; }, abstract = {Levuana iridescens Bethune-Baker, 1906, a day-flying moth purported to be endemic to the Fijian Island of Viti Levu and a former pest of its coconut palm trees, was last observed in 1956 and has been officially declared extinct by IUCN since 1996. The controversial classical biological control method that resulted in the (presumed) demise of this moth has given this species an iconic status in biological control studies. We investigated the sister-group relationships and phylogenetic placement of this moth using NGS-obtained ancient DNA sequences from museum specimens of L. iridescens collected in the 1920s, combined with 31 morphological characters used in earlier studies and 2 new characters. Our findings show that Levuana is most closely related to the Australian genus Myrtartona. The significance of these findings is discussed.}, }
@article {pmid31792176, year = {2019}, author = {Mordechai, L and Eisenberg, M and Newfield, TP and Izdebski, A and Kay, JE and Poinar, H}, title = {The Justinianic Plague: An inconsequential pandemic?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {51}, pages = {25546-25554}, pmid = {31792176}, issn = {1091-6490}, mesh = {Byzantium ; History, Medieval ; Humans ; Pandemics/*history ; Plague/*history ; Population Dynamics/*history ; Yersinia pestis ; }, abstract = {Existing mortality estimates assert that the Justinianic Plague (circa 541 to 750 CE) caused tens of millions of deaths throughout the Mediterranean world and Europe, helping to end antiquity and start the Middle Ages. In this article, we argue that this paradigm does not fit the evidence. We examine a series of independent quantitative and qualitative datasets that are directly or indirectly linked to demographic and economic trends during this two-century period: Written sources, legislation, coinage, papyri, inscriptions, pollen, ancient DNA, and mortuary archaeology. Individually or together, they fail to support the maximalist paradigm: None has a clear independent link to plague outbreaks and none supports maximalist reconstructions of late antique plague. Instead of large-scale, disruptive mortality, when contextualized and examined together, the datasets suggest continuity across the plague period. Although demographic, economic, and political changes continued between the 6th and 8th centuries, the evidence does not support the now commonplace claim that the Justinianic Plague was a primary causal factor of them.}, }
@article {pmid31791340, year = {2019}, author = {McHugo, GP and Dover, MJ and MacHugh, DE}, title = {Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {98}, pmid = {31791340}, issn = {1741-7007}, mesh = {Animals ; Animals, Domestic/*genetics ; *Biological Evolution ; *Breeding ; DNA, Ancient/*analysis ; *Domestication ; Genomics ; }, abstract = {Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.}, }
@article {pmid31789141, year = {2020}, author = {Beltrame, MO and Pruzzo, C and Sanabria, R and Pérez, A and Mora, MS}, title = {First report of pre-Hispanic Fasciola hepatica from South America revealed by ancient DNA.}, journal = {Parasitology}, volume = {147}, number = {3}, pages = {371-375}, doi = {10.1017/S0031182019001719}, pmid = {31789141}, issn = {1469-8161}, mesh = {*Animal Distribution ; Animals ; Argentina ; DNA, Ancient/analysis ; DNA, Helminth/analysis ; Deer/*parasitology ; Fasciola hepatica/genetics/growth &amp; development/*isolation &amp; purification ; Feces/*parasitology ; Ovum/physiology ; Phylogeny ; }, abstract = {It is generally assumed that the digenean human liver fluke, Fasciola hepatica, gained entry to South America during the 15th century upon arrival of Europeans and their livestock. Nonetheless in Patagonia, Argentina, digenean eggs similar to F. hepatica have been observed in deer coprolites dating back to 2300 years B.P. The main objective of our present study was to identify and characterize these eggs using an ancient DNA (aDNA) study. Eggs were isolated and used for aDNA extraction, amplification and sequencing of partial regions from the cytochrome c oxidase subunit 1 and the nicotinamide adenine dinucleotide dehydrogenase subunit 1 mitochondrial genes. Also, phylogenetic trees were constructed using Bayesian and maximum likelihood. Our results confirm the presence of F. hepatica in South America from at least 2300 years B.P. This is the first report and the first aDNA study of this trematode in South America prior to the arrival of the European cattle in the 15th century. The present work contributes to the study of phylogenetic and palaeobiogeographical aspects of F. hepatica and its settlement across America.}, }
@article {pmid31785113, year = {2020}, author = {Hagan, RW and Hofman, CA and Hübner, A and Reinhard, K and Schnorr, S and Lewis, CM and Sankaranarayanan, K and Warinner, CG}, title = {Comparison of extraction methods for recovering ancient microbial DNA from paleofeces.}, journal = {American journal of physical anthropology}, volume = {171}, number = {2}, pages = {275-284}, doi = {10.1002/ajpa.23978}, pmid = {31785113}, issn = {1096-8644}, support = {EXC 2051 #390713860//Deutsche Forschungsgemeinschaft/International ; //Max-Planck-Gesellschaft/International ; R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical/*methods ; Archaeology/methods ; DNA, Ancient/*analysis/*isolation &amp; purification ; Dogs ; Feces/*chemistry ; Gastrointestinal Microbiome ; Metagenomics ; Sequence Analysis, DNA/*methods/veterinary ; }, abstract = {OBJECTIVES: Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases.<br><br>METHODS: In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP).<br><br>RESULTS: Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA.<br><br>CONCLUSIONS: These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies.}, }
@article {pmid31771471, year = {2019}, author = {Ameen, C and Feuerborn, TR and Brown, SK and Linderholm, A and Hulme-Beaman, A and Lebrasseur, O and Sinding, MS and Lounsberry, ZT and Lin, AT and Appelt, M and Bachmann, L and Betts, M and Britton, K and Darwent, J and Dietz, R and Fredholm, M and Gopalakrishnan, S and Goriunova, OI and Grønnow, B and Haile, J and Hallsson, JH and Harrison, R and Heide-Jørgensen, MP and Knecht, R and Losey, RJ and Masson-MacLean, E and McGovern, TH and McManus-Fry, E and Meldgaard, M and Midtdal, Å and Moss, ML and Nikitin, IG and Nomokonova, T and Pálsdóttir, AH and Perri, A and Popov, AN and Rankin, L and Reuther, JD and Sablin, M and Schmidt, AL and Shirar, S and Smiarowski, K and Sonne, C and Stiner, MC and Vasyukov, M and West, CF and Ween, GB and Wennerberg, SE and Wiig, Ø and Woollett, J and Dalén, L and Hansen, AJ and P Gilbert, MT and Sacks, BN and Frantz, L and Larson, G and Dobney, K and Darwent, CM and Evin, A}, title = {Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1916}, pages = {20191929}, pmid = {31771471}, issn = {1471-2954}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Alaska ; *Animal Distribution ; Animals ; Archaeology ; Arctic Regions ; Canada ; DNA, Ancient/analysis ; DNA, Mitochondrial/analysis ; Dogs/*anatomy &amp; histology/*genetics ; *Genome, Mitochondrial ; Greenland ; Human Migration ; *Phenotype ; }, abstract = {Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.}, }
@article {pmid31767056, year = {2019}, author = {Thomas, JE and Carvalho, GR and Haile, J and Rawlence, NJ and Martin, MD and Ho, SY and Sigfússon, AÞ and Jósefsson, VA and Frederiksen, M and Linnebjerg, JF and Samaniego Castruita, JA and Niemann, J and Sinding, MS and Sandoval-Velasco, M and Soares, AE and Lacy, R and Barilaro, C and Best, J and Brandis, D and Cavallo, C and Elorza, M and Garrett, KL and Groot, M and Johansson, F and Lifjeld, JT and Nilson, G and Serjeanston, D and Sweet, P and Fuller, E and Hufthammer, AK and Meldgaard, M and Fjeldså, J and Shapiro, B and Hofreiter, M and Stewart, JR and Gilbert, MTP and Knapp, M}, title = {Demographic reconstruction from ancient DNA supports rapid extinction of the great auk.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31767056}, issn = {2050-084X}, support = {NE/L501694/1//NERC Environmental Bioinformatics Centre/International ; 681396-Extinction Genomics/ERC_/European Research Council/International ; Heredity Fieldwork Grant//Genetics Society/International ; Godfrey Hewitt Mobility Award//European Society for Evolutionary Biology/International ; Rutherford Discovery Fellowship//Royal Society of New Zealand/International ; }, mesh = {Animals ; Charadriiformes/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial ; *Extinction, Biological ; Genetic Variation ; Genome, Mitochondrial/genetics ; Humans ; Phylogeny ; *Population Dynamics ; }, abstract = {The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.}, }
@article {pmid31758601, year = {2020}, author = {Fenderson, LE and Kovach, AI and Llamas, B}, title = {Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time.}, journal = {Molecular ecology}, volume = {29}, number = {2}, pages = {218-246}, doi = {10.1111/mec.15315}, pmid = {31758601}, issn = {1365-294X}, mesh = {*Climate Change ; Ecology ; Genetics, Population ; Phylogeography ; Population Dynamics ; }, abstract = {Genetic time-series data from historical samples greatly facilitate inference of past population dynamics and species evolution. Yet, although climate and landscape change are often touted as post-hoc explanations of biological change, our understanding of past climate and landscape change influences on evolutionary processes is severely hindered by the limited application of methods that directly relate environmental change to species dynamics through time. Increased integration of spatiotemporal environmental and genetic data will revolutionize the interpretation of environmental influences on past population processes and the quantification of recent anthropogenic impacts on species, and vastly improve prediction of species responses under future climate change scenarios, yielding widespread revelations across evolutionary biology, landscape ecology and conservation genetics. This review encourages greater use of spatiotemporal landscape genetic analyses that explicitly link landscape, climate and genetic data through time by providing an overview of analytical approaches for integrating historical genetic and environmental data in five key research areas: population genetic structure, demography, phylogeography, metapopulation connectivity and adaptation. We also include a tabular summary of key methodological information, suggest approaches for mitigating the particular difficulties in applying these techniques to ancient DNA and palaeoclimate data, and highlight areas for future methodological development.}, }
@article {pmid31758037, year = {2019}, author = {Ozga, AT and Gilby, I and Nockerts, RS and Wilson, ML and Pusey, A and Stone, AC}, title = {Oral microbiome diversity in chimpanzees from Gombe National Park.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17354}, doi = {10.1038/s41598-019-53802-1}, pmid = {31758037}, issn = {2045-2322}, mesh = {Animals ; Cluster Analysis ; DNA, Ancient/analysis ; DNA, Bacterial/analysis/genetics ; Dental Plaque/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota/genetics ; Mouth/*microbiology ; Pan troglodytes/*microbiology ; Parks, Recreational ; Phylogeny ; RNA, Ribosomal, 16S/analysis/genetics ; Tanzania ; }, abstract = {Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.}, }
@article {pmid31754290, year = {2019}, author = {Maixner, F and Thorell, K and Granehäll, L and Linz, B and Moodley, Y and Rattei, T and Engstrand, L and Zink, A}, title = {Helicobacter pylori in ancient human remains.}, journal = {World journal of gastroenterology}, volume = {25}, number = {42}, pages = {6289-6298}, pmid = {31754290}, issn = {2219-2840}, mesh = {Body Remains/*microbiology ; DNA, Ancient/*analysis ; DNA, Bacterial/analysis ; Genome, Bacterial ; Helicobacter Infections/*microbiology ; Helicobacter pylori/isolation &amp; purification ; Humans ; *Mummies ; Stomach/microbiology ; Virulence ; }, abstract = {The bacterium Helicobacter pylori (H. pylori) infects the stomachs of approximately 50% of all humans. With its universal occurrence, high infectivity and virulence properties it is considered as one of the most severe global burdens of modern humankind. It has accompanied humans for many thousands of years, and due to its high genetic variability and vertical transmission, its population genetics reflects the history of human migrations. However, especially complex demographic events such as the colonisation of Europe cannot be resolved with population genetic analysis of modern H. pylori strains alone. This is best exemplified with the reconstruction of the 5300-year-old H. pylori genome of the Iceman, a European Copper Age mummy. Our analysis provided precious insights into the ancestry and evolution of the pathogen and underlined the high complexity of ancient European population history. In this review we will provide an overview on the molecular analysis of H. pylori in mummified human remains that were done so far and we will outline methodological advancements in the field of ancient DNA research that support the reconstruction and authentication of ancient H. pylori genome sequences.}, }
@article {pmid31745634, year = {2020}, author = {Müller, P and Sell, C and Hadrys, T and Hedman, J and Bredemeyer, S and Laurent, FX and Roewer, L and Achtruth, S and Sidstedt, M and Sijen, T and Trimborn, M and Weiler, N and Willuweit, S and Bastisch, I and Parson, W and , }, title = {Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA.}, journal = {International journal of legal medicine}, volume = {134}, number = {1}, pages = {185-198}, doi = {10.1007/s00414-019-02201-2}, pmid = {31745634}, issn = {1437-1596}, support = {IZ25-5793-2015-30 2017-2020//Horizon 2020 Framework Programme/ ; HOME/2014/ISFP/AG/LAWX/4000007135//Horizon 2020/ ; }, mesh = {Alleles ; Austria ; DNA Fingerprinting/*methods ; Electrophoresis, Capillary ; Female ; France ; *Gene Library ; Germany ; *High-Throughput Nucleotide Sequencing ; Humans ; Laboratories ; Male ; *Microsatellite Repeats ; Netherlands ; Polymerase Chain Reaction ; *Polymorphism, Single Nucleotide ; Sensitivity and Specificity ; *Sequence Analysis, DNA ; Sweden ; }, abstract = {We present results from an inter-laboratory massively parallel sequencing (MPS) study in the framework of the SeqForSTRs project to evaluate forensically relevant parameters, such as performance, concordance, and sensitivity, using a standardized sequencing library including reference material, mixtures, and ancient DNA samples. The standardized library was prepared using the ForenSeq DNA Signature Prep Kit (primer mix A). The library was shared between eight European laboratories located in Austria, France, Germany, The Netherlands, and Sweden to perform MPS on their particular MiSeq FGx sequencers. Despite variation in performance between sequencing runs, all laboratories obtained quality metrics that fell within the manufacturer's recommended ranges. Furthermore, differences in locus coverage did not inevitably adversely affect heterozygous balance. Inter-laboratory concordance showed 100% concordant genotypes for the included autosomal and Y-STRs, and still, X-STR concordance exceeded 83%. The exclusive reasons for X-STR discordances were drop-outs at DXS10103. Sensitivity experiments demonstrated that correct allele calling varied between sequencing instruments in particular for lower DNA amounts (≤ 125 pg). The analysis of compromised DNA samples showed the drop-out of one sample (FA10013B01A) while for the remaining three degraded DNA samples MPS was able to successfully type ≥ 87% of all aSTRs, ≥ 78% of all Y-STRs, ≥ 68% of all X-STRs, and ≥ 92% of all iSNPs demonstrating that MPS is a promising tool for human identity testing, which in return, has to undergo rigorous in-house validation before it can be implemented into forensic routine casework.}, }
@article {pmid31744094, year = {2019}, author = {Grugni, V and Raveane, A and Colombo, G and Nici, C and Crobu, F and Ongaro, L and Battaglia, V and Sanna, D and Al-Zahery, N and Fiorani, O and Lisa, A and Ferretti, L and Achilli, A and Olivieri, A and Francalacci, P and Piazza, A and Torroni, A and Semino, O}, title = {Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case.}, journal = {International journal of molecular sciences}, volume = {20}, number = {22}, pages = {}, pmid = {31744094}, issn = {1422-0067}, support = {2006.194//Compagnia di San Paolo/ ; }, mesh = {Chromosomes, Human, Y/classification/*genetics ; DNA, Ancient/analysis ; European Continental Ancestry Group/genetics ; Gene Frequency ; Genetic Linkage ; *Genetics, Population ; Haplotypes ; Humans ; Islands ; Italy ; Male ; Phylogeny ; Principal Component Analysis ; }, abstract = {Many anthropological, linguistic, genetic and genomic analyses have been carried out to evaluate the potential impact that evolutionary forces had in shaping the present-day Sardinian gene pool, the main outlier in the genetic landscape of Europe. However, due to the homogenizing effect of internal movements, which have intensified over the past fifty years, only partial information has been obtained about the main demographic events. To overcome this limitation, we analyzed the male-specific region of the Y chromosome in three population samples obtained by reallocating a large number of Sardinian subjects to the place of origin of their monophyletic surnames, which are paternally transmitted through generations in most of the populations, much like the Y chromosome. Three Y-chromosome founding lineages, G2-L91, I2-M26 and R1b-V88, were identified as strongly contributing to the definition of the outlying position of Sardinians in the European genetic context and marking a significant differentiation within the island. The present distribution of these lineages does not always mirror that detected in ancient DNAs. Our results show that the analysis of the Y-chromosome gene pool coupled with a sampling method based on the origin of the family name, is an efficient approach to unravelling past heterogeneity, often hidden by recent movements, in the gene pool of modern populations. Furthermore, the reconstruction and comparison of past genetic isolates represent a starting point to better assess the genetic information deriving from the increasing number of available ancient DNA samples.}, }
@article {pmid31737039, year = {2019}, author = {Chen, P and Wu, J and Luo, L and Gao, H and Wang, M and Zou, X and Li, Y and Chen, G and Luo, H and Yu, L and Han, Y and Jia, F and He, G}, title = {Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {1045}, pmid = {31737039}, issn = {1664-8021}, abstract = {Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.}, }
@article {pmid31729399, year = {2019}, author = {Översti, S and Majander, K and Salmela, E and Salo, K and Arppe, L and Belskiy, S and Etu-Sihvola, H and Laakso, V and Mikkola, E and Pfrengle, S and Putkonen, M and Taavitsainen, JP and Vuoristo, K and Wessman, A and Sajantila, A and Oinonen, M and Haak, W and Schuenemann, VJ and Krause, J and Palo, JU and Onkamo, P}, title = {Human mitochondrial DNA lineages in Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16883}, doi = {10.1038/s41598-019-51045-8}, pmid = {31729399}, issn = {2045-2322}, mesh = {Agriculture ; *Crosses, Genetic ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis/genetics ; Europe ; European Continental Ancestry Group/*genetics ; Farmers/statistics &amp; numerical data ; Farms ; Finland ; Genome, Mitochondrial/genetics ; History, Ancient ; *Human Migration/history ; Humans ; Iron ; Maternal Inheritance/*genetics ; Oceans and Seas ; }, abstract = {Human ancient DNA studies have revealed high mobility in Europe's past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300-1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns.}, }
@article {pmid31721774, year = {2019}, author = {Wasef, S and Subramanian, S and O'Rorke, R and Huynen, L and El-Marghani, S and Curtis, C and Popinga, A and Holland, B and Ikram, S and Millar, C and Willerslev, E and Lambert, D}, title = {Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0223964}, pmid = {31721774}, issn = {1932-6203}, mesh = {Africa ; Animal Husbandry/history ; Animals ; Birds/classification/*genetics ; DNA, Ancient ; DNA, Mitochondrial/blood/genetics/history ; Egypt, Ancient ; Genetic Variation ; *Genome, Mitochondrial ; History, Ancient ; *Mummies ; Phylogeny ; Religion/history ; }, abstract = {The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these 'votive' mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild migratory Sacred Ibis for the ritual yearly demand.}, }
@article {pmid31719710, year = {2019}, author = {Swift, JA and Bunce, M and Dortch, J and Douglass, K and Faith, JT and Fellows Yates, JA and Field, J and Haberle, SG and Jacob, E and Johnson, CN and Lindsey, E and Lorenzen, ED and Louys, J and Miller, G and Mychajliw, AM and Slon, V and Villavicencio, NA and Waters, MR and Welker, F and Wood, R and Petraglia, M and Boivin, N and Roberts, P}, title = {Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene.}, journal = {Bioscience}, volume = {69}, number = {11}, pages = {877-887}, pmid = {31719710}, issn = {0006-3568}, abstract = {Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today.}, }
@article {pmid31714695, year = {2018}, author = {González-Oliver, A and Pineda-Vázquez, D and Garfias-Morales, E and La Cruz-Laina, I and Medrano-González, L and Márquez-Morfín, L and Ortega-Muñoz, A}, title = {Genetic Overview of the Maya Populations: Mitochondrial DNA Haplogroups.}, journal = {Human biology}, volume = {90}, number = {4}, pages = {281-300}, doi = {10.13110/humanbiology.90.4.03}, pmid = {31714695}, issn = {1534-6617}, mesh = {Adolescent ; Adult ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; *Gene Flow ; Genetic Variation/genetics ; Genetics, Population/*statistics &amp; numerical data ; Haplotypes/*genetics ; Humans ; Indians, North American/*genetics ; Male ; Mexico/ethnology ; Phylogeny ; Young Adult ; }, abstract = {We identified mitochondrial DNA haplogroups A, B, C, and D in 75 present-day Maya individuals, 24 Maya individuals of the colonial period, and 1 pre-Columbian Maya individual from Quintana Roo, Mexico. We examined these data together with those of 21 Maya populations reported in the literature, comprising 647 present-day Maya individuals and 71 ancient Maya individuals. A demographic study based on analysis of fertility and endogamy was carried out in two modern Maya populations to identify cultural factors that influence the mitochondrial haplogroup genetic diversity. Most present-day and ancient Maya populations show a distribution pattern of mitochondrial haplogroup frequencies A, C, B, and D in decreasing order, with haplogroup D absent in several populations. Considering only modern Maya populations with at least 50 individuals analyzed, the present-day Tzotzil and Lacandon populations from Chiapas show the highest and lowest genetic diversity, 0.706 and 0.025, respectively. Our results show small genetic differences between the Maya populations, with the exception of the present-day Tojolabal and Lacandon populations from Chiapas. The present-day Lacandon population from Chiapas differs from other Maya populations in showing almost only haplogroup A. This result suggests a long history of isolation and endogamy as well as a possible founder effect inside the Lacandonian rain forest. The contemporary Tojolabal population is the only one with an unusual mitochondrial haplogroup pattern, exhibiting a frequency of haplogroup B higher than A and the absence of haplogroup C. With a small sample size, the pre-Columbian Copán Maya show a high content of haplogroup C and a low frequency of haplogroup D. The genetic homogeneity of the Maya populations is indicative of a common origin and nearly continuous gene flow in the long term within a general isolation of the whole group, in contrast to the Nahua populations that had different origins. Our demographic study showed high fertility rates and high levels of endogamy in the present-day Maya populations from Quintana Roo that are consistent with their general low genetic diversity. We propose that the genetic similarity among ancient and present-day Maya populations persists due to a strong sense of social cohesion and identity that impacts their marriage practices, keeping this cultural group isolated. These factors have constrained gene flow inside the Maya region and have impeded the differentiation among the Maya. Discernment of genetic differentiation within the peninsula is constrained by the lack of sampling documentation in the literature.}, }
@article {pmid31710665, year = {2020}, author = {Nieves-Colón, MA and Pestle, WJ and Reynolds, AW and Llamas, B and de la Fuente, C and Fowler, K and Skerry, KM and Crespo-Torres, E and Bustamante, CD and Stone, AC}, title = {Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {611-626}, doi = {10.1093/molbev/msz267}, pmid = {31710665}, issn = {1537-1719}, mesh = {Bone and Bones ; Chromosomes, Human/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Dental Calculus/*genetics ; Fossils ; Genetics, Population ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Human Migration ; Humans ; Indigenous Peoples/*genetics ; Puerto Rico/ethnology ; Tooth ; }, abstract = {Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.}, }
@article {pmid31704402, year = {2020}, author = {Liddicoat, C and Sydnor, H and Cando-Dumancela, C and Dresken, R and Liu, J and Gellie, NJC and Mills, JG and Young, JM and Weyrich, LS and Hutchinson, MR and Weinstein, P and Breed, MF}, title = {Naturally-diverse airborne environmental microbial exposures modulate the gut microbiome and may provide anxiolytic benefits in mice.}, journal = {The Science of the total environment}, volume = {701}, number = {}, pages = {134684}, doi = {10.1016/j.scitotenv.2019.134684}, pmid = {31704402}, issn = {1879-1026}, mesh = {*Air Microbiology ; Animals ; *Biodiversity ; *Environmental Exposure ; Female ; *Gastrointestinal Microbiome ; Male ; Mice ; }, abstract = {Growing epidemiological evidence links natural green space exposure with a range of health benefits, including for mental health. Conversely, greater urbanisation associates with increased risk of mental health disorders. Microbiomes are proposed as an important but understudied link that may help explain many green space-human health associations. However, there remains a lack of controlled experimental evidence testing possible beneficial effects from passive exposure to natural biodiversity via airborne microbiota. Previous mouse model studies have used unrealistic environmental microbial exposures-including excessive soil and organic matter contact, feed supplements and injections-to demonstrate host microbiota, immune biomarker, and behavioural changes. Here, in a randomised controlled experiment, we demonstrate that realistic exposures to trace-level dust from a high biodiversity soil can change mouse gut microbiota, in comparison to dust from low biodiversity soil or no soil (control) (n = 54 total mice, comprising 3 treatments × 18 mice, with 9 females + 9 males per group). Furthermore, we found a nominal soil-derived anaerobic spore-forming butyrate-producer, Kineothrix alysoides, was supplemented to a greater extent in the gut microbiomes of high biodiversity treatment mice. Also, increasing relative abundance of this rare organism correlated with reduced anxiety-like behaviour in the most anxious mice. Our results point to an intriguing new hypothesis: that biodiverse soils may represent an important supplementary source of butyrate-producing bacteria capable of resupplying the mammalian gut microbiome, with potential for gut health and mental health benefits. Our findings have potential to inform cost-effective population health interventions through microbiome-conscious green space design and, ultimately, the mainstreaming of biodiversity into health care.}, }
@article {pmid31697387, year = {2020}, author = {van Dorp, L and Gelabert, P and Rieux, A and de Manuel, M and de-Dios, T and Gopalakrishnan, S and Carøe, C and Sandoval-Velasco, M and Fregel, R and Olalde, I and Escosa, R and Aranda, C and Huijben, S and Mueller, I and Marquès-Bonet, T and Balloux, F and Gilbert, MTP and Lalueza-Fox, C}, title = {Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {773-785}, pmid = {31697387}, issn = {1537-1719}, support = {BB/R01356X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Americas ; Asia ; Evolution, Molecular ; Genetics, Population ; Genome, Protozoan ; High-Throughput Nucleotide Sequencing ; Humans ; Malaria, Vivax/*parasitology ; Oceania ; Phylogeny ; Phylogeography ; Plasmodium vivax/*classification/*genetics ; Spain ; Whole Genome Sequencing/*methods ; }, abstract = {The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.}, }
@article {pmid31697016, year = {2019}, author = {Wolinsky, H}, title = {Ancient DNA and contemporary politics: The analysis of ancient DNA challenges long-held beliefs about identity and history with potential for political abuse.}, journal = {EMBO reports}, volume = {20}, number = {12}, pages = {e49507}, pmid = {31697016}, issn = {1469-3178}, mesh = {Americas ; *DNA, Ancient ; Emigration and Immigration/history ; Europe ; Genetics, Population/history ; History, Ancient ; Human Genetics ; Human Migration/*history ; Humans ; *Politics ; Racism ; }, abstract = {The sequencing and analysis of ancient human DNA has helped to rewrite human history. But it is also tempting politicians, nationalists and supremacists to abuse this research for their agendas.}, }
@article {pmid31679935, year = {2019}, author = {Serra-Vidal, G and Lucas-Sanchez, M and Fadhlaoui-Zid, K and Bekada, A and Zalloua, P and Comas, D}, title = {Heterogeneity in Palaeolithic Population Continuity and Neolithic Expansion in North Africa.}, journal = {Current biology : CB}, volume = {29}, number = {22}, pages = {3953-3959.e4}, doi = {10.1016/j.cub.2019.09.050}, pmid = {31679935}, issn = {1879-0445}, mesh = {Africa South of the Sahara ; Africa, Northern ; African Continental Ancestry Group/*genetics ; European Continental Ancestry Group/genetics ; Fossils ; Gene Flow/*genetics ; Gene Pool ; Genetic Variation ; Genetics, Population/methods ; Genome/genetics ; Haplotypes ; History, Ancient ; Human Migration/history ; Humans ; Polymorphism, Single Nucleotide ; }, abstract = {North Africa is located at the crossroads of the Mediterranean Sea, the Middle East, and the Sahara Desert. Extensive migrations and gene flow in the region have shaped many different cultures and ancestral genetic components through time [1-6]. DNA data from ancient Moroccan sites [7, 8] has recently shed some light to the population continuity-versus-replacement debate, i.e., the question of whether current North African populations descend from Palaeolithic groups or, on the contrary, subsequent migrations swept away all pre-existing genetic signal in the region. In the present study, we analyze 21 complete North African genomes and compare them with extant and ancient genome data in order to address the demographic continuity-versus-replacement debate, to assess whether these demographic events were homogeneous (including Berber and Arabic-speaking groups), and to explore the effect of Neolithization and posterior migration waves. The North African genetic pool is defined as a melting pot of genetic components, including an endemic North African Epipalaeolithic component at low frequency that forms a declining gradient from Western to Eastern North Africa. This scenario is consistent with Neolithization having shaped most of the current genetic variation in the region when compared to posterior back-to-North-Africa migration waves such as the Arabization. A common and distinct genetic history of the region is shown, with internal different proportions of genetic components owing to differential admixture with surrounding groups as well as to genetic drift due to isolation and endogamy in certain populations.}, }
@article {pmid31679495, year = {2019}, author = {Larsson, P and von Seth, J and Hagen, IJ and Götherström, A and Androsov, S and Germonpré, M and Bergfeldt, N and Fedorov, S and Eide, NE and Sokolova, N and Berteaux, D and Angerbjörn, A and Flagstad, Ø and Plotnikov, V and Norén, K and Díez-Del-Molino, D and Dussex, N and Stanton, DWG and Dalén, L}, title = {Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1788}, pages = {20190212}, pmid = {31679495}, issn = {1471-2970}, mesh = {*Animal Distribution ; Animals ; *Climate Change ; DNA, Ancient/analysis ; Fossils ; Foxes/genetics/*physiology ; *Genetic Variation ; Genome, Mitochondrial ; *Human Activities ; Population Dynamics ; Scandinavian and Nordic Countries ; }, abstract = {Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'}, }
@article {pmid31675609, year = {2020}, author = {Gaget, V and Hobson, P and Keulen, A and Newton, K and Monis, P and Humpage, AR and Weyrich, LS and Brookes, JD}, title = {Toolbox for the sampling and monitoring of benthic cyanobacteria.}, journal = {Water research}, volume = {169}, number = {}, pages = {115222}, doi = {10.1016/j.watres.2019.115222}, pmid = {31675609}, issn = {1879-2448}, mesh = {Australia ; *Cyanobacteria ; Fresh Water ; Odorants ; Taste ; }, abstract = {Benthic cyanobacteria are a nuisance because they produce highly potent toxins and taste and odour compounds. Despite this, benthic cyanobacteria remain far less studied than their planktonic counterparts. For example, little is known about their growth or the seasonality of their secondary metabolite production. Moreover, sampling and monitoring techniques commonly used for the survey of planktonic species are not necessarily applicable to benthic forms. This study aimed to develop and validate a new sampling device for the routine monitoring of benthic mats. Molecular monitoring techniques were established and validated on environmental samples collected in a South Australian reservoir (SA-L2). A total of eight qPCR assays were applied to samples in order to track seasonal variations in cyanobacteria concentrations and associated secondary metabolite production. Next Generation Sequencing was utilised to conduct a microbial community composition analysis and to select the most appropriate substrate material for the sampling of benthic cyanobacteria. The concentration of the secondary metabolites geosmin and 2-methyl-isoborneol were quantified using High-Performance Liquid Chromatography, and concentrations of key nutrients (N, P) were quantified in water samples. The sampling device designed proved efficient and easy to use in the field. The qPCR assay designed for the amplification of the cyanobacterial MIB synthase had a high efficiency with a minimum limit of quantification of 4 cell-equivalents per reaction and identified a potential source of MIB in SA-L2 Reservoir. The peak season for benthic growth and secondary metabolite production was observed in spring. Proportionally, 35% of the variability in water geosmin concentrations can be explained by benthic actinobacterial and cyanobacterial activity, showing that freshwater benthic mats represent a significant source of taste and odour compounds.}, }
@article {pmid31646208, year = {2019}, author = {Poma, A and Cesare, P and Bonfigli, A and Vecchiotti, G and Colafarina, S and Savini, F and Redi, F and Zarivi, O}, title = {Analysis of ancient mtDNA from the medieval archeological site of Amiternum (L'Aquila), central Italy.}, journal = {Heliyon}, volume = {5}, number = {10}, pages = {e02586}, pmid = {31646208}, issn = {2405-8440}, abstract = {Study of ancient DNA makes it possible to analyze genetic relationships between individuals and populations of past and present. In this paper we have analyzed remains of human bones, dating back to the 8th-10th century AD, from the burials found in the Cathedral of Santa Maria in Civitate, archaeological site of Amiternum, L'Aquila, Italy. As a genetic marker, the hypervariable region 1 of mitochondrial DNA (HVR1) was selected. To obtain reliable sequences from the hypervariable region 1 of mtDNA (HVR1) were performed: multiple extractions, template quantification and cloning of PCR products. The sequences obtained were compared with Anderson's sequence for the identification of polymorphisms (SNP) and haplogroups. The data obtained were analyzed with various software and phylogenetic methods. For the comparison between populations, ancient and modern sequences found in databases and literature have been used. This work provides preliminary information on the correlation between the population of Amiternum, the migrant populations transited and/or established in the territory of Amiternum such as Byzantines, Longobards (Lombards), which dominated the Italian peninsula between 568 and 774 AD, and the current populations of Italy. The study of haplogroups, the analysis of genetic variability and phylogenesis studies on the sequences considered show a genetic closeness between the individuals of Amiternum, the current population of central-northern Italy and the Germanic tribe of Longobards, however, also highlights genetic traits of Byzantines in some samples of Amiternum. Using the analysis of amelogenin gene fragments, we successfully determined the sex of the bone remains on all samples.}, }
@article {pmid31638147, year = {2020}, author = {Liu, Y and Weyrich, LS and Llamas, B}, title = {More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment.}, journal = {Molecular biology and evolution}, volume = {37}, number = {2}, pages = {307-319}, doi = {10.1093/molbev/msz231}, pmid = {31638147}, issn = {1537-1719}, mesh = {*Adaptation, Physiological ; Animals ; Confounding Factors, Epidemiologic ; DNA Methylation ; DNA, Ancient/*analysis ; Epigenesis, Genetic ; Epigenomics/*methods ; Evolution, Molecular ; Mammals/*genetics/*microbiology/physiology ; Microbiota ; Paleontology ; }, abstract = {Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.}, }
@article {pmid31626767, year = {2019}, author = {Raghavan, M and Schroeder, H and Malaspinas, AS}, title = {An Ancient Genome from the Indus Valley Civilization.}, journal = {Cell}, volume = {179}, number = {3}, pages = {586-588}, doi = {10.1016/j.cell.2019.09.027}, pmid = {31626767}, issn = {1097-4172}, mesh = {Archaeology ; Asia ; *Cemeteries ; *Civilization ; Humans ; India ; }, abstract = {Shinde et al. report the first genome-wide data from an ancient individual from the Indus Valley Civilization in South Asia. Their findings have implications for the origins and spread of farming and Indo-European languages in the region and the makings of the South Asian gene pool.}, }
@article {pmid31611588, year = {2019}, author = {Shamoon-Pour, M and Li, M and Merriwether, DA}, title = {Rare human mitochondrial HV lineages spread from the Near East and Caucasus during post-LGM and Neolithic expansions.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14751}, doi = {10.1038/s41598-019-48596-1}, pmid = {31611588}, issn = {2045-2322}, mesh = {Armenia ; Asia ; Asian Continental Ancestry Group/genetics ; DNA, Mitochondrial/*genetics ; Europe ; European Continental Ancestry Group/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Middle East ; Mitochondria/genetics ; Phylogeography ; }, abstract = {Of particular significance to human population history in Eurasia are the migratory events that connected the Near East to Europe after the Last Glacial Maximum (LGM). Utilizing 315 HV*(xH,V) mitogenomes, including 27 contemporary lineages first reported here, we found the genetic signatures for distinctive movements out of the Near East and South Caucasus both westward into Europe and eastward into South Asia. The parallel phylogeographies of rare, yet widely distributed HV*(xH,V) subclades reveal a connection between the Italian Peninsula and South Caucasus, resulting from at least two (post-LGM, Neolithic) waves of migration. Many of these subclades originated in a population ancestral to contemporary Armenians and Assyrians. One such subclade, HV1b-152, supports a postexilic, northern Mesopotamian origin for the Ashkenazi HV1b2 lineages. In agreement with ancient DNA findings, our phylogenetic analysis of HV12 and HV14, the two exclusively Asian subclades of HV*(xH,V), point to the migration of lineages originating in Iran to South Asia before and during the Neolithic period. With HV12 being one of the oldest HV subclades, our results support an origin of HV haplogroup in the region defined by Western Iran, Mesopotamia, and the South Caucasus, where the highest prevalence of HV has been found.}, }
@article {pmid31611361, year = {2019}, author = {Guitor, AK and Raphenya, AR and Klunk, J and Kuch, M and Alcock, B and Surette, MG and McArthur, AG and Poinar, HN and Wright, GD}, title = {Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes.}, journal = {Antimicrobial agents and chemotherapy}, volume = {64}, number = {1}, pages = {}, pmid = {31611361}, issn = {1098-6596}, support = {MT-14981//CIHR/Canada ; PJT-156214//CIHR/Canada ; }, mesh = {Bacteria/drug effects/genetics/isolation &amp; purification ; DNA Probes/genetics ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/genetics ; Genome, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Microbiota/drug effects/genetics ; Whole Genome Sequencing ; }, abstract = {Identification of the nucleotide sequences encoding antibiotic resistance elements and determination of their association with antibiotic resistance are critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, both of which are heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the sequences in the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2,000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probe set on DNA libraries generated from multidrug-resistant bacteria to selectively capture resistance genes reproducibly produced higher numbers of reads on target at a greater length of coverage than shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables a sensitive means of gene detection in diverse environments where genes encoding antibiotic resistance represent less than 0.1% of the metagenome.}, }
@article {pmid31607556, year = {2019}, author = {Tett, A and Huang, KD and Asnicar, F and Fehlner-Peach, H and Pasolli, E and Karcher, N and Armanini, F and Manghi, P and Bonham, K and Zolfo, M and De Filippis, F and Magnabosco, C and Bonneau, R and Lusingu, J and Amuasi, J and Reinhard, K and Rattei, T and Boulund, F and Engstrand, L and Zink, A and Collado, MC and Littman, DR and Eibach, D and Ercolini, D and Rota-Stabelli, O and Huttenhower, C and Maixner, F and Segata, N}, title = {The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {5}, pages = {666-679.e7}, doi = {10.1016/j.chom.2019.08.018}, pmid = {31607556}, issn = {1934-6069}, support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; /ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 DK103358/DK/NIDDK NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Diet ; Ethiopia ; Feces/microbiology ; Fossils/*microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Ghana ; Humans ; Prevotella/*classification/*genetics/isolation &amp; purification ; Tanzania ; }, abstract = {Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.}, }
@article {pmid31603617, year = {2019}, author = {Crump, SE and Miller, GH and Power, M and Sepúlveda, J and Dildar, N and Coghlan, M and Bunce, M}, title = {Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada.}, journal = {Global change biology}, volume = {25}, number = {12}, pages = {4244-4256}, doi = {10.1111/gcb.14836}, pmid = {31603617}, issn = {1365-2486}, support = {DGE1144083//NSF/ ; BCS1657743//NSF/ ; ARC1737712//NSF/ ; //National Geographic Society/ ; //Geological Society of America/ ; //CU Department of Geological Sciences/ ; //CU Center for the Study of Origins/ ; //INSTAAR/ ; }, mesh = {Arctic Regions ; Canada ; Climate Change ; *Lakes ; *Tundra ; }, abstract = {Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global-scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be biased by the influx of exotic pollen to tundra settings. Here, we reconstruct past plant communities using sedimentary ancient DNA (sedaDNA), which has a more local source area than pollen. We additionally reconstruct past temperature variability using bacterial cell membrane lipids (branched glycerol dialkyl glycerol tetraethers) and an aquatic productivity indicator (biogenic silica) to evaluate the relative timing of postglacial ecological and climate changes at a lake on southern Baffin Island, Arctic Canada. The sedaDNA record tightly constrains the colonization of dwarf birch (Betula, a thermophilous shrub) to 5.9 ± 0.1 ka, ~3 ka after local deglaciation as determined by cosmogenic 10 Be moraine dating and >2 ka later than Betula pollen is recorded in nearby lake sediment. We then assess the paleovegetation history within the context of summer temperature and find that paleotemperatures were highest prior to 6.3 ka, followed by cooling in the centuries preceding Betula establishment. Together, these molecular proxies reveal that Betula colonization lagged peak summer temperatures, suggesting that inefficient dispersal, rather than climate, may have limited Arctic shrub migration in this region. In addition, these data suggest that pollen-based climate reconstructions from high latitudes, which rely heavily on the presence and abundance of pollen from thermophilous taxa like Betula, can be compromised by both exotic pollen fluxes and vegetation migration lags.}, }
@article {pmid31601754, year = {2019}, author = {Vogel, G}, title = {Seeing fossils in a new light.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6462}, pages = {176-178}, doi = {10.1126/science.366.6462.176}, pmid = {31601754}, issn = {1095-9203}, mesh = {Animals ; DNA, Ancient ; *Dinosaurs ; *Fossils ; Proteins/analysis/*chemistry ; Proteolysis ; Tissue Preservation ; Tooth/chemistry ; }, }
@article {pmid31601705, year = {2019}, author = {Mittnik, A and Massy, K and Knipper, C and Wittenborn, F and Friedrich, R and Pfrengle, S and Burri, M and Carlichi-Witjes, N and Deeg, H and Furtwängler, A and Harbeck, M and von Heyking, K and Kociumaka, C and Kucukkalipci, I and Lindauer, S and Metz, S and Staskiewicz, A and Thiel, A and Wahl, J and Haak, W and Pernicka, E and Schiffels, S and Stockhammer, PW and Krause, J}, title = {Kinship-based social inequality in Bronze Age Europe.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6466}, pages = {731-734}, doi = {10.1126/science.aax6219}, pmid = {31601705}, issn = {1095-9203}, mesh = {Anthropology ; DNA, Ancient ; Family Characteristics/*history ; Female ; Germany ; History, Ancient ; Humans ; Male ; Pedigree ; Polymorphism, Single Nucleotide ; Social Class/*history ; }, abstract = {Revealing and understanding the mechanisms behind social inequality in prehistoric societies is a major challenge. By combining genome-wide data, isotopic evidence, and anthropological and archaeological data, we have gone beyond the dominating supraregional approaches in archaeogenetics to shed light on the complexity of social status, inheritance rules, and mobility during the Bronze Age. We applied a deep microregional approach and analyzed genome-wide data of 104 human individuals deriving from farmstead-related cemeteries from the Late Neolithic to the Middle Bronze Age in southern Germany. Our results reveal individual households, lasting several generations, that consisted of a high-status core family and unrelated low-status individuals; a social organization accompanied by patrilocality and female exogamy; and the stability of this system over 700 years.}, }
@article {pmid31594846, year = {2019}, author = {Cox, SL and Ruff, CB and Maier, RM and Mathieson, I}, title = {Genetic contributions to variation in human stature in prehistoric Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {43}, pages = {21484-21492}, pmid = {31594846}, issn = {1091-6490}, support = {R35 GM133708/GM/NIGMS NIH HHS/United States ; }, mesh = {*Body Height ; DNA, Ancient/*chemistry ; Europe ; European Continental Ancestry Group/*genetics/*history ; *Genetic Variation ; Genetics, Population/history ; History, Ancient ; Human Genetics/*history ; Humans ; Paleontology ; Phenotype ; Polymorphism, Single Nucleotide ; }, abstract = {The relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 y in European height predicted using DNA from 1,071 ancient individuals are consistent with changes observed in 1,159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height-consistent with genetic predictions-although genetics predicts a small post-Neolithic increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change.}, }
@article {pmid31594508, year = {2019}, author = {Malmström, H and Günther, T and Svensson, EM and Juras, A and Fraser, M and Munters, AR and Pospieszny, Ł and Tõrv, M and Lindström, J and Götherström, A and Storå, J and Jakobsson, M}, title = {The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1912}, pages = {20191528}, pmid = {31594508}, issn = {1471-2954}, mesh = {Baltic States ; Base Sequence ; *Culture ; DNA, Ancient ; Europe ; European Continental Ancestry Group ; Farmers ; Genomics ; *History, Ancient ; *Human Migration ; Humans ; Poland ; Population Dynamics ; Scandinavian and Nordic Countries ; Sweden ; }, abstract = {The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24× coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.}, }
@article {pmid31593209, year = {2019}, author = {Fiumi Sermattei, I and Traversari, M and Serventi, P and Cilli, E and Gruppioni, G and Tomassini, L and Benazzi, S and Galassi, FM}, title = {Pope Leo XII's death: the twist to a longstanding dispute by novel historical documents and paleopathographic analysis.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {70}, number = {3}, pages = {225-232}, doi = {10.1127/homo/2019/1138}, pmid = {31593209}, issn = {1618-1301}, mesh = {Aged ; Autopsy/*history ; *Bacterial Infections ; Catholicism/*history ; Diagnosis, Differential ; Hemorrhoids ; History, 19th Century ; Humans ; Male ; Paleopathology ; Sepsis ; *Superinfection ; Vatican City ; }, abstract = {Although the practice of autopsy on the Pope's corpse was performed from the 16th century, autopsy reports are only rarely analysed, and never with the aim of investigating the real causes of the death from a concomitant medical and historical point of view. Here, for the first time, we report on the discovery of new unpublished documents from the Vatican Secret Archives and their investigation by a scientific and inter-disciplinary approach. This analysis allows us to draw new conclusions on the true cause of Leo XII's mysterious death. His sudden death, that occurred on February 10th, 1829 after a short illness, particularly struck the public. Suspicions of poisoning or surgeon's guilt or inexperience and even the shadow of a venereal disease, contributed to create a &quot;black legend&quot; on his pontificate and death. On the contrary, the present paleopathographic analysis points toward a new conclusion. The regular use of catheterization with a silver syringe provided an easy access for bacterial superinfection, confirmed by the observed early emphysematous stage of the corpse. So, the most substantiated hypothesis concerning the cause of Leo XII's death indicates a severe form of sepsis, exacerbated by a weakened state due to chronic hemorrhoids.}, }
@article {pmid31589588, year = {2019}, author = {Kowal, E and Llamas, B}, title = {Race in a genome: long read sequencing, ethnicity-specific reference genomes and the shifting horizon of race.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {96}, number = {}, pages = {91-106}, doi = {10.4436/JASS.97004}, pmid = {31589588}, issn = {2037-0644}, mesh = {Anthropology, Physical ; Continental Population Groups/*genetics ; Databases, Genetic ; Genetic Variation/genetics ; Genome, Human/*genetics ; Genomics ; Humans ; Racism ; Sequence Analysis, DNA/*methods ; }, abstract = {The sequencing of the human genome at the turn of the 21st century was hailed as revealing the overwhelming genetic similarity of human groups. Scholars of genomics have critiqued the subsequent persistence of race-based genetic science, but were reassured that the wide availability of gene sequencing would end the use of race as a proxy for genetic difference. Once an individual's whole gene sequence could be read, they hoped, their ethnoracial classification would become redundant. At the same time, genome science was recognising that the differences between human genomes went beyond the genome sequence to the structure of the genome itself. 'Structural variation' between genomes, including insertions, deletions, translocations, inversions, and copy number variations, mean that the 'universal' reference genome used for genome sequencing is not so universal. As conventional, 'short-read' sequencing wrongly assumes that all genomes have the same structure, significant genetic variation can be missed. This paper examines the twin phenomena that have been posed as a solution to the biases of short-read sequencing: 'long-read' sequencing and 'ethnicity-specific reference genomes'. Long-read sequencing is a method of generating a genome sequence that can be assembled de novo rather than relying on the reference genome. In recent years, a number of countries including China, Korea, and Denmark have used long-read sequencing and de novo assembly to develop 'national' reference genomes. Our analysis of one ethnicity-specific reference genome project, the Korean Reference Genome (KOREF), finds that it unduly emphasises the importance of population structural variation, framed in nationalist terms, and discounts the importance of individual structural variation. We argue that the intellectual labour required to make a Korean reference genome a coherent concept works to extend the horizon of race, prolonging the temporality of the 'meantime' in which race remains a seemingly valid concept in genomic science.}, }
@article {pmid31565086, year = {2019}, author = {Robson, HK and Skipitytė, R and Piličiauskienė, G and Lucquin, A and Heron, C and Craig, OE and Piličiauskas, G}, title = {Diet, cuisine and consumption practices of the first farmers in the southeastern Baltic.}, journal = {Archaeological and anthropological sciences}, volume = {11}, number = {8}, pages = {4011-4024}, pmid = {31565086}, issn = {1866-9557}, abstract = {With the arrival of the Early Neolithic Globular Amphora and Corded Ware cultures into the southeastern Baltic, ca. 2900/2800-2400 cal BC, a new type of economy was introduced, animal husbandry. However, the degree to which this transformed the subsistence economy is unknown. Here, we conducted organic residue analyses of 64 ceramic vessels to identify their contents. The vessels were sampled from 10 Lithuanian archaeological sites dating across the Subneolithic-Neolithic transition to the Early Bronze Age (ca. 2900/2800-1300 cal BC). Our results demonstrate that regardless of location or vessel type, many ceramics were used to process aquatic resources. Against our expectations, this association continued even after marked economic change concurrent with the migration of pastoralists from central and southeastern Europe, as evidenced by recent ancient DNA analysis of human remains. Moreover, we observed dairy fats in pottery from all cultures of the Early Neolithic (i.e. Rzucewo, Globular Amphora and Corded Ware) but unlike other regions of Europe, it seems that these were incorporated into indigenous culinary practices. Furthermore, some vessels were used to process plant foods, and others may have been used for the production and/or storage of birch bark tar. However, evidence for domesticated plant processing, for example millet, was absent. We show that organic residue analysis of pottery provides a different picture of past consumption patterns compared to the stable isotope analysis of human remains from isolated burials where a clear dietary shift is evident.}, }
@article {pmid31563810, year = {2019}, author = {Jones, R and Velasco, MS and Harris, LG and Morgan, S and Temple, M and Ruddy, MC and Williams, R and Perry, MD and Hitchings, M and Wilkinson, TS and Humphrey, T and Gilbert, MTP and Davies, AP}, title = {Resolving a clinical tuberculosis outbreak using palaeogenomic genome reconstruction methodologies.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {119}, number = {}, pages = {101865}, doi = {10.1016/j.tube.2019.101865}, pmid = {31563810}, issn = {1873-281X}, mesh = {Child ; DNA, Bacterial/*genetics ; Disease Outbreaks ; Genome, Bacterial/*genetics ; Global Health ; Humans ; Multilocus Sequence Typing ; Mycobacterium tuberculosis/*genetics ; *Polymorphism, Single Nucleotide ; Tuberculosis/epidemiology/*microbiology ; Whole Genome Sequencing ; }, abstract = {This study describes the analysis of DNA from heat-killed (boilate) isolates of Mycobacterium tuberculosis from two UK outbreaks where DNA was of sub-optimal quality for the standard methodologies routinely used in microbial genomics. An Illumina library construction method developed for sequencing ancient DNA was successfully used to obtain whole genome sequences, allowing analysis of the outbreak by gene-by-gene MLST, SNP mapping and phylogenetic analysis. All cases were spoligotyped to the same Haarlem H1 sub-lineage. This is the first described application of ancient DNA library construction protocols to allow whole genome sequencing of a clinical tuberculosis outbreak. Using this method it is possible to obtain epidemiologically meaningful data even when DNA is of insufficient quality for standard methods.}, }
@article {pmid31561553, year = {2019}, author = {Yankova, I and Marinov, M and Neov, B and Petrova, M and Spassov, N and Hristov, P and Radoslavov, G}, title = {Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages.}, journal = {Genes}, volume = {10}, number = {10}, pages = {}, pmid = {31561553}, issn = {2073-4425}, mesh = {Animal Distribution ; Animals ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; Evolution, Molecular ; *Fossils ; Haplotypes ; *Phylogeny ; }, abstract = {The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs' populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire.}, }
@article {pmid31558742, year = {2019}, author = {Morley, MW and Goldberg, P and Uliyanov, VA and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Jacobs, Z and Roberts, RG}, title = {Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13785}, doi = {10.1038/s41598-019-49930-3}, pmid = {31558742}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; *Caves ; Cold Climate ; DNA, Ancient/isolation &amp; purification ; *Fossils ; History, Ancient ; *Hominidae/genetics ; Humans ; Neanderthals/genetics ; Paleontology ; Siberia ; }, abstract = {Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal-Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.}, }
@article {pmid31552062, year = {2019}, author = {Wang, C and Lu, H and Zhang, J and Mao, L and Ge, Y}, title = {Bulliform Phytolith Size of Rice and Its Correlation With Hydrothermal Environment: A Preliminary Morphological Study on Species in Southern China.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1037}, pmid = {31552062}, issn = {1664-462X}, abstract = {In the last decade, our understanding of rice domestication has improved by new archaeological findings using advanced analytical techniques such as morphological and morphometric analyses on rice grains, spikelet bases and phytoliths, and ancient DNA analysis on rice remains. Previous studies have considered the size of rice bulliform phytoliths as a proxy for tracking the domestication process. These phytoliths are often abundant and well preserved in sediments, and their shape is under the control of numerous genes, which may shift toward larger sizes by genetic mutation in domestication. Therefore, it has been assumed that the bulliforms of domesticated rice are usually larger than those of wild ones; however, morphometric data supporting this assumption are lacking in the literature, thereby requiring additional evidence to test its veracity. In this study, the vertical and horizonal lengths of bulliform phytoliths were measured in four rice species (domesticated Oryza sativa and wild Oryza rufipogon, Oryza officinalis, and Oryza meyeriana) from different regions of southern China. We found that the bulliform morphometric data of wild and domesticated rice overlapped and that there was no statistically significant difference between them. Therefore, bulliform size could not be used as a diagnostic indicator to distinguish domesticated rice from wild species and is a supporting rather than conclusive proxy for determining the domesticated status of rice in archaeological research. We further found that larger rice bulliform sizes likely occurred at the locations with higher temperature, precipitation, and water levels, indicating hydrothermal environment is an alternative factor influencing the size of rice bulliform phytoliths. For further archaeological use of an increasing size trend of bulliform phytoliths to reveal the process of rice domestication, we present some suggestions for controlling the influence of hydrothermal factors. Even so, the combination of bulliform phytolith size with other established criteria is strongly suggested to provide precise identification of wild and domesticated rice in future research.}, }
@article {pmid33365931, year = {2019}, author = {Stelbrink, B and Kehlmaier, C and Wilke, T and Albrecht, C}, title = {The near-complete mitogenome of the critically endangered Pseudocleopatra dartevellei (Caenogastropoda: Paludomidae) from the Congo River assembled from historical museum material.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {4}, number = {2}, pages = {3229-3231}, pmid = {33365931}, issn = {2380-2359}, abstract = {Here, we present the first near-complete mitogenome of a member of the freshwater gastropod family Paludomidae, Pseudocleopatra dartevellei. This Congo River species is of particular importance because the sister to the Lake Tanganyika radiation is supposed to be a paludomid riverine species. We used ancient DNA (aDNA) techniques including single-stranded DNA library preparation in order to assemble the mitogenome from historical museum material collected in 1937. The mitogenome was 15,368 bp long and showed typical characteristics as identified in other freshwater gastropods. The present phylogeny shows a closer relationship between Pseudocleoptra dartevellei and another non-Tanganyikan species, Cleopatra johnstoni.}, }
@article {pmid31542986, year = {2019}, author = {Chen, SG and Li, J and Zhang, F and Xiao, B and Hu, JM and Cui, YQ and Hofreiter, M and Hou, XD and Sheng, GL and Lai, XL and Yuan, JX}, title = {Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {30}, number = {7}, pages = {786-793}, doi = {10.1080/24701394.2019.1659250}, pmid = {31542986}, issn = {2470-1408}, mesh = {Animals ; Camelus/*genetics ; China ; Computational Biology ; Female ; Genome, Mitochondrial/*genetics ; Phylogeny ; *Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. years before present (yBP). Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis suggest a slow increase in female effective population size of C. bactrianus from 5000 years ago, which corresponds to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.}, }
@article {pmid31537848, year = {2019}, author = {Tamm, E and Di Cristofaro, J and Mazières, S and Pennarun, E and Kushniarevich, A and Raveane, A and Semino, O and Chiaroni, J and Pereira, L and Metspalu, M and Montinaro, F}, title = {Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13581}, doi = {10.1038/s41598-019-49901-8}, pmid = {31537848}, issn = {2045-2322}, mesh = {Africa, Northern ; European Continental Ancestry Group/ethnology/*genetics ; France/ethnology ; Gene Frequency ; Genetics, Population ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Italy/ethnology ; Phylogeny ; Population Dynamics ; Selection, Genetic ; Whole Genome Sequencing/*methods ; }, abstract = {Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians.}, }
@article {pmid31523131, year = {2019}, author = {Ishiya, K and Mizuno, F and Wang, L and Ueda, S}, title = {MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome.}, journal = {Bioinformatics and biology insights}, volume = {13}, number = {}, pages = {1177932219873884}, pmid = {31523131}, issn = {1177-9322}, abstract = {The incompleteness of partial human mitochondrial genome sequences makes it difficult to perform relevant comparisons among multiple resources. To deal with this issue, we propose a computational framework for deducing missing nucleotides in the human mitochondrial genome. We applied it to worldwide mitochondrial haplogroup lineages and assessed its performance. Our approach can deduce the missing nucleotides with a precision of 0.99 or higher in most human mitochondrial DNA lineages. Furthermore, although low-coverage mitochondrial genome sequences often lead to a blurred relationship in the multidimensional scaling analysis, our approach can correct this positional arrangement according to the corresponding mitochondrial DNA lineages. Therefore, our framework will provide a practical solution to compensate for the lack of genome coverage in partial and fragmented human mitochondrial genome sequences. In this study, we developed an open-source computer program, MitoIMP, implementing our imputation procedure. MitoIMP is freely available from https://github.com/omics-tools/mitoimp.}, }
@article {pmid31517046, year = {2019}, author = {Bennett, EA and Crevecoeur, I and Viola, B and Derevianko, AP and Shunkov, MV and Grange, T and Maureille, B and Geigl, EM}, title = {Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals.}, journal = {Science advances}, volume = {5}, number = {9}, pages = {eaaw3950}, pmid = {31517046}, issn = {2375-2548}, mesh = {Animals ; Finger Phalanges/*anatomy &amp; histology ; *Genome, Human ; Humans ; Molar/*anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology/genetics ; Species Specificity ; }, abstract = {A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.}, }
@article {pmid31517044, year = {2019}, author = {Raveane, A and Aneli, S and Montinaro, F and Athanasiadis, G and Barlera, S and Birolo, G and Boncoraglio, G and Di Blasio, AM and Di Gaetano, C and Pagani, L and Parolo, S and Paschou, P and Piazza, A and Stamatoyannopoulos, G and Angius, A and Brucato, N and Cucca, F and Hellenthal, G and Mulas, A and Peyret-Guzzon, M and Zoledziewska, M and Baali, A and Bycroft, C and Cherkaoui, M and Chiaroni, J and Di Cristofaro, J and Dina, C and Dugoujon, JM and Galan, P and Giemza, J and Kivisild, T and Mazieres, S and Melhaoui, M and Metspalu, M and Myers, S and Pereira, L and Ricaut, FX and Brisighelli, F and Cardinali, I and Grugni, V and Lancioni, H and Pascali, VL and Torroni, A and Semino, O and Matullo, G and Achilli, A and Olivieri, A and Capelli, C}, title = {Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe.}, journal = {Science advances}, volume = {5}, number = {9}, pages = {eaaw3492}, pmid = {31517044}, issn = {2375-2548}, mesh = {Animals ; *DNA, Ancient ; *Databases, Genetic ; European Continental Ancestry Group/*genetics ; *Genetic Drift ; *Genome, Human ; Genome-Wide Association Study ; History, Ancient ; Human Genetics ; Humans ; Italy ; Neanderthals/genetics ; }, abstract = {European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.}, }
@article {pmid31513651, year = {2019}, author = {Menardo, F and Duchêne, S and Brites, D and Gagneux, S}, title = {The molecular clock of Mycobacterium tuberculosis.}, journal = {PLoS pathogens}, volume = {15}, number = {9}, pages = {e1008067}, pmid = {31513651}, issn = {1553-7374}, mesh = {Bayes Theorem ; Biological Clocks/*genetics/physiology ; DNA, Bacterial/genetics ; Evolution, Molecular ; Genome, Bacterial ; Humans ; Models, Biological ; Molecular Epidemiology ; Mycobacterium bovis/genetics/physiology ; Mycobacterium tuberculosis/*genetics/pathogenicity/physiology ; Phylogeny ; Polymorphism, Single Nucleotide ; Time Factors ; Tuberculosis/epidemiology/microbiology ; }, abstract = {The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.}, }
@article {pmid31511700, year = {2019}, author = {Cappellini, E and Welker, F and Pandolfi, L and Ramos-Madrigal, J and Samodova, D and Rüther, PL and Fotakis, AK and Lyon, D and Moreno-Mayar, JV and Bukhsianidze, M and Rakownikow Jersie-Christensen, R and Mackie, M and Ginolhac, A and Ferring, R and Tappen, M and Palkopoulou, E and Dickinson, MR and Stafford, TW and Chan, YL and Götherström, A and Nathan, SKSS and Heintzman, PD and Kapp, JD and Kirillova, I and Moodley, Y and Agusti, J and Kahlke, RD and Kiladze, G and Martínez-Navarro, B and Liu, S and Sandoval Velasco, M and Sinding, MS and Kelstrup, CD and Allentoft, ME and Orlando, L and Penkman, K and Shapiro, B and Rook, L and Dalén, L and Gilbert, MTP and Olsen, JV and Lordkipanidze, D and Willerslev, E}, title = {Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.}, journal = {Nature}, volume = {574}, number = {7776}, pages = {103-107}, doi = {10.1038/s41586-019-1555-y}, pmid = {31511700}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bayes Theorem ; DNA, Ancient/*analysis ; Dental Enamel/*metabolism ; *Fossils ; History, Ancient ; Humans ; Male ; Perissodactyla/*classification/*genetics/metabolism ; Phosphorylation/genetics ; *Phylogeny ; Proteome/analysis/*genetics ; *Proteomics ; }, abstract = {The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5-although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7-9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.}, }
@article {pmid31504166, year = {2020}, author = {Moreno-Mayar, JV and Korneliussen, TS and Dalal, J and Renaud, G and Albrechtsen, A and Nielsen, R and Malaspinas, AS}, title = {A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {3}, pages = {828-841}, doi = {10.1093/bioinformatics/btz660}, pmid = {31504166}, issn = {1367-4811}, mesh = {Chromosomes ; *DNA, Ancient ; *High-Throughput Nucleotide Sequencing ; Humans ; Likelihood Functions ; Male ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: The presence of present-day human contaminating DNA fragments is one of the challenges defining ancient DNA (aDNA) research. This is especially relevant to the ancient human DNA field where it is difficult to distinguish endogenous molecules from human contaminants due to their genetic similarity. Recently, with the advent of high-throughput sequencing and new aDNA protocols, hundreds of ancient human genomes have become available. Contamination in those genomes has been measured with computational methods often developed specifically for these empirical studies. Consequently, some of these methods have not been implemented and tested for general use while few are aimed at low-depth nuclear data, a common feature in aDNA datasets.<br><br>RESULTS: We develop a new X-chromosome-based maximum likelihood method for estimating present-day human contamination in low-depth sequencing data from male individuals. We implement our method for general use, assess its performance under conditions typical of ancient human DNA research, and compare it to previous nuclear data-based methods through extensive simulations. For low-depth data, we show that existing methods can produce unusable estimates or substantially underestimate contamination. In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5× on the X-chromosome when contamination is below 25%. Moreover, our method still yields meaningful estimates in very challenging situations, i.e. when the contaminant and the target come from closely related populations or with increased error rates. With a running time below 5 min, our method is applicable to large scale aDNA genomic studies.<br><br>The method is implemented in C++ and R and is available in github.com/sapfo/contaminationX and popgen.dk/angsd.}, }
@article {pmid31495572, year = {2019}, author = {Shinde, V and Narasimhan, VM and Rohland, N and Mallick, S and Mah, M and Lipson, M and Nakatsuka, N and Adamski, N and Broomandkhoshbacht, N and Ferry, M and Lawson, AM and Michel, M and Oppenheimer, J and Stewardson, K and Jadhav, N and Kim, YJ and Chatterjee, M and Munshi, A and Panyam, A and Waghmare, P and Yadav, Y and Patel, H and Kaushik, A and Thangaraj, K and Meyer, M and Patterson, N and Rai, N and Reich, D}, title = {An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers.}, journal = {Cell}, volume = {179}, number = {3}, pages = {729-735.e10}, doi = {10.1016/j.cell.2019.08.048}, pmid = {31495572}, issn = {1097-4172}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; }, mesh = {Asian Continental Ancestry Group/genetics ; DNA, Ancient/*chemistry ; Evolution, Molecular ; *Genome, Human ; *Human Migration ; Humans ; Iran ; Pakistan ; *Pedigree ; Population/*genetics ; }, abstract = {We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.}, }
@article {pmid31495003, year = {2019}, author = {Littleford-Colquhoun, BL and Weyrich, LS and Kent, N and Frere, CH}, title = {City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii).}, journal = {Molecular ecology}, volume = {28}, number = {20}, pages = {4592-4607}, doi = {10.1111/mec.15240}, pmid = {31495003}, issn = {1365-294X}, mesh = {Animals ; Australia ; Biodiversity ; Cities ; DNA, Bacterial/genetics ; *Diet ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Iguanas ; Nitrogen Isotopes/*blood ; *Urbanization ; }, abstract = {Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non-model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non-model species - the eastern water dragon (Intellagama lesueurii) in Queensland, Australia. City dragons exhibit a more diverse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen-15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human-altered landscapes.}, }
@article {pmid31486822, year = {2019}, author = {Balázs, J and Rózsa, Z and Bereczki, Z and Marcsik, A and Tihanyi, B and Karlinger, K and Pölöskei, G and Molnár, E and Donoghue, HD and Pálfi, G}, title = {Osteoarcheological and biomolecular evidence of leprosy from an 11-13th century CE Muslim cemetery in Europe (Orosháza, Southeast Hungary).}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {70}, number = {2}, pages = {105-118}, doi = {10.1127/homo/2019/1071}, pmid = {31486822}, issn = {1618-1301}, mesh = {Adult ; Bone and Bones/microbiology/pathology ; Cemeteries/*history ; DNA, Ancient/analysis ; DNA, Bacterial/analysis/genetics ; Female ; History, Medieval ; Humans ; Hungary ; Islam/*history ; Leprosy/*history/microbiology ; Male ; Mycobacterium leprae/genetics ; Paleopathology ; Young Adult ; }, abstract = {Orosháza site no. 10 (Southeast Hungary) contains the partially excavated archaeological remains of an 11-13th century CE Muslim merchant village and its cemetery located in close proximity to Christian villages of the same era. The skeleton of a young woman (grave no. 16) from the last phase of the cemetery use was identified with rhinomaxillary lesions associated with lepromatous leprosy. The right parietal bone also exhibited signs of cranial trauma, possibly caused by symbolic trepanation, a well-known ritual practice in the 9-11th century CE Carpathian Basin. The retrospective diagnosis of the disease was supported by ancient DNA analysis, as the samples were positive for Mycobacterium leprae aDNA, shown to be of genotype 3. Contrary to the general practice of the era, the body of the young female with severe signs of leprosy was interred among the regular graves of the Muslim cemetery in Orosháza, which may reflect the unique cultural background of the community.}, }
@article {pmid31481615, year = {2019}, author = {Gilbert, E and O'Reilly, S and Merrigan, M and McGettigan, D and Vitart, V and Joshi, PK and Clark, DW and Campbell, H and Hayward, C and Ring, SM and Golding, J and Goodfellow, S and Navarro, P and Kerr, SM and Amador, C and Campbell, A and Haley, CS and Porteous, DJ and Cavalleri, GL and Wilson, JF}, title = {The genetic landscape of Scotland and the Isles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {38}, pages = {19064-19070}, pmid = {31481615}, issn = {1091-6490}, support = {MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; MR/K026992/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_U127592696/MRC_/Medical Research Council/United Kingdom ; G0700704/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; /CSO_/Chief Scientist Office/United Kingdom ; /ARC_/Arthritis Research UK/United Kingdom ; }, mesh = {DNA, Ancient/*analysis ; Ethnic Groups/*genetics ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Humans ; Ireland ; Islands ; Scotland ; }, abstract = {Britain and Ireland are known to show population genetic structure; however, large swathes of Scotland, in particular, have yet to be described. Delineating the structure and ancestry of these populations will allow variant discovery efforts to focus efficiently on areas not represented in existing cohorts. Thus, we assembled genotype data for 2,554 individuals from across the entire archipelago with geographically restricted ancestry, and performed population structure analyses and comparisons to ancient DNA. Extensive geographic structuring is revealed, from broad scales such as a NE to SW divide in mainland Scotland, through to the finest scale observed to date: across 3 km in the Northern Isles. Many genetic boundaries are consistent with Dark Age kingdoms of Gaels, Picts, Britons, and Norse. Populations in the Hebrides, the Highlands, Argyll, Donegal, and the Isle of Man show characteristics of isolation. We document a pole of Norwegian ancestry in the north of the archipelago (reaching 23 to 28% in Shetland) which complements previously described poles of Germanic ancestry in the east, and &quot;Celtic&quot; to the west. This modern genetic structure suggests a northwestern British or Irish source population for the ancient Gaels that contributed to the founding of Iceland. As rarer variants, often with larger effect sizes, become the focus of complex trait genetics, more diverse rural cohorts may be required to optimize discoveries in British and Irish populations and their considerable global diaspora.}, }
@article {pmid31481609, year = {2019}, author = {Gower, G and Fenderson, LE and Salis, AT and Helgen, KM and van Loenen, AL and Heiniger, H and Hofman-Kamińska, E and Kowalczyk, R and Mitchell, KJ and Llamas, B and Cooper, A}, title = {Widespread male sex bias in mammal fossil and museum collections.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {38}, pages = {19019-19024}, pmid = {31481609}, issn = {1091-6490}, mesh = {Animals ; Bison/genetics ; DNA, Ancient/*analysis ; Female ; *Fossils ; High-Throughput Nucleotide Sequencing ; Male ; Mammals/*genetics ; Mammoths/genetics ; *Models, Genetic ; *Museums ; Phylogeny ; Sexism/*statistics &amp; numerical data ; Ursidae/genetics ; }, abstract = {A recent study of mammoth subfossil remains has demonstrated the potential of using relatively low-coverage high-throughput DNA sequencing to genetically sex specimens, revealing a strong male-biased sex ratio [P. Pečnerová et al., Curr. Biol. 27, 3505-3510.e3 (2017)]. Similar patterns were predicted for steppe bison, based on their analogous female herd-based structure. We genetically sexed subfossil remains of 186 Holarctic bison (Bison spp.), and also 91 brown bears (Ursus arctos), which are not female herd-based, and found that ∼75% of both groups were male, very close to the ratio observed in mammoths (72%). This large deviation from a 1:1 ratio was unexpected, but we found no evidence for sex differences with respect to DNA preservation, sample age, material type, or overall spatial distribution. We further examined ratios of male and female specimens from 4 large museum mammal collections and found a strong male bias, observable in almost all mammalian orders. We suggest that, in mammals at least, 1) wider male geographic ranges can lead to considerably increased chances of detection in fossil studies, and 2) sexual dimorphic behavior or appearance can facilitate a considerable sex bias in fossil and modern collections, on a previously unacknowledged scale. This finding has major implications for a wide range of studies of fossil and museum material.}, }
@article {pmid31480978, year = {2019}, author = {Hermes, TR and Frachetti, MD and Doumani Dupuy, PN and Mar'yashev, A and Nebel, A and Makarewicz, CA}, title = {Early integration of pastoralism and millet cultivation in Bronze Age Eurasia.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1910}, pages = {20191273}, pmid = {31480978}, issn = {1471-2954}, mesh = {Agriculture/*history ; Animals ; Archaeology ; Cattle ; China ; Crops, Agricultural/*history ; Domestication ; Goats ; History, Ancient ; Humans ; Kazakhstan ; Livestock ; *Millets ; Radiometric Dating ; Sheep ; }, abstract = {Mobile pastoralists are thought to have facilitated the first trans-Eurasian dispersals of domesticated plants during the Early Bronze Age (ca 2500-2300 BC). Problematically, the earliest seeds of wheat, barley and millet in Inner Asia were recovered from human mortuary contexts and do not inform on local cultivation or subsistence use, while contemporaneous evidence for the use and management of domesticated livestock in the region remains ambiguous. We analysed mitochondrial DNA and multi-stable isotopic ratios (δ13C, δ15N and δ18O) of faunal remains from key pastoralist sites in the Dzhungar Mountains of southeastern Kazakhstan. At ca 2700 BC, Near Eastern domesticated sheep and goat were present at the settlement of Dali, which were also winter foddered with the region's earliest cultivated millet spreading from its centre of domestication in northern China. In the following centuries, millet cultivation and caprine management became increasingly intertwined at the nearby site of Begash. Cattle, on the other hand, received low levels of millet fodder at the sites for millennia. By primarily examining livestock dietary intake, this study reveals that the initial transmission of millet across the mountains of Inner Asia coincided with a substantial connection between pastoralism and plant cultivation, suggesting that pastoralist livestock herding was integral for the westward dispersal of millet from farming societies in China.}, }
@article {pmid31462911, year = {2019}, author = {Oosting, T and Star, B and Barrett, JH and Wellenreuther, M and Ritchie, PA and Rawlence, NJ}, title = {Unlocking the potential of ancient fish DNA in the genomic era.}, journal = {Evolutionary applications}, volume = {12}, number = {8}, pages = {1513-1522}, pmid = {31462911}, issn = {1752-4571}, abstract = {Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.}, }
@article {pmid31462783, year = {2019}, author = {Fox, K and Hawks, J}, title = {Use ancient remains more wisely.}, journal = {Nature}, volume = {572}, number = {7771}, pages = {581-583}, pmid = {31462783}, issn = {1476-4687}, mesh = {Animals ; Archaeology/*ethics/*methods ; DNA, Ancient/*analysis/*isolation &amp; purification ; Female ; Genomics/*ethics/*methods ; Hawaii/ethnology ; History, 18th Century ; History, Ancient ; Humans ; Male ; Neanderthals/genetics ; Stakeholder Participation ; }, }
@article {pmid31455916, year = {2019}, author = {Lewis, D}, title = {'Paralysed by anxiety': researchers speak about life in troubled ancient-DNA lab.}, journal = {Nature}, volume = {572}, number = {7771}, pages = {571-572}, pmid = {31455916}, issn = {1476-4687}, mesh = {DNA, Ancient ; *Dental Plaque ; *Diet ; Humans ; *Microbiota ; Mouth/microbiology ; }, }
@article {pmid31437436, year = {2019}, author = {Leles, D and Frías, L and Araújo, A and Brener, B and Sudré, A and Chame, M and Laurentino, V}, title = {Are immunoenzymatic tests for intestinal protozoans reliable when used on archaeological material?.}, journal = {Experimental parasitology}, volume = {205}, number = {}, pages = {107739}, doi = {10.1016/j.exppara.2019.107739}, pmid = {31437436}, issn = {1090-2449}, mesh = {Animals ; Antigens, Protozoan/analysis/genetics ; Archaeology/*methods ; Cryptosporidium/genetics/immunology/*isolation &amp; purification ; Entamoeba/genetics/immunology/*isolation &amp; purification ; Entamoeba histolytica/genetics/immunology/isolation &amp; purification ; Feces/*parasitology ; Giardia lamblia/genetics/immunology/*isolation &amp; purification ; Humans ; Immunoenzyme Techniques/*standards ; Intestinal Diseases, Parasitic/parasitology ; Rodentia ; Sensitivity and Specificity ; South America ; }, abstract = {Intestinal protozoans found in ancient human samples have been studied primarily by microscopy and immunodiagnostic assays. However, such methods are not suitable for the detection of zoonotic genotypes. The objectives of the present study were to utilize immunoenzimatic assays for coproantigen detection of Cryptosporidium sp., Giardia duodenalis, and Entamoeba histolytica/Entamoeba dispar in sixty ancient human and animal samples collected from 14 archaeological sites in South America, and to carry out a critical analysis of G. duodenalis according to results obtained from three diagnostic methodologies: microscopy, immunodiagnostic tests (immunoenzymatic and immunofluorescence), and molecular biology (PCR and sequencing). More than half (31/60) of the samples analyzed using immunoenzymatic tests were positive for at least one of the intestinal protozoans, with 46.6% (28/60) corresponding to G. duodenalis, 26.6% (16/60) to Cryptosporidium sp., and 5% (3/60) to E. histolytica/E. dispar. Cryptosporidium sp. and G. duodenalis coinfection was observed in 15% (9/60) of the samples, whereas all three protozoans were found in 5% (3/60) of samples. In the Northeast Region of Brazil, by immunoenzymatic tests there is evidence that G. duodenlais and Cryptosporidium sp. have infected humans and rodents for at least 7150 years. However, for G. duodenalis, the results from the three diagnostic tests were discordant. Specifically, despite the efficiency of the molecular biology assay in the experimental models, G. duodenalis DNA could not be amplified from the ancient samples. These results raise the following question: Are all ancient samples positive for coproantigen of G. duodenalis by immunoenzymatic tests truly positive? This scenario highlights the importance of further studies to evaluate the sensitivity and specificity of the immunoenzymatic method in the archaeological context.}, }
@article {pmid31433816, year = {2019}, author = {Fernandes, D and Sirak, K and Cheronet, O and Howcroft, R and Čavka, M and Los, D and Burmaz, J and Pinhasi, R and Novak, M}, title = {Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0216366}, pmid = {31433816}, issn = {1932-6203}, mesh = {Adolescent ; *Archaeology ; Croatia ; *Genetic Variation ; *Human Migration ; Humans ; Male ; Skull/*abnormalities/diagnostic imaging ; Tomography, X-Ray Computed ; }, abstract = {Three individuals dating to the Great Migration Period (5th century CE) were discovered in a pit at the Hermanov vinograd site in Osijek, Croatia. We were inspired to study these individuals based on their unusual burial context as well as the identification of two different types of artificial cranial deformation in two of the individuals. We combine bioarchaeological analysis with radiographic imaging, stable isotopes analysis, and ancient DNA to analyze their dietary patterns, molecular sex, and genetic affinities in the context of the archaeological data and their bioarchaeological attributes. While all three individuals were adolescent males with skeletal evidence of severe malnutrition and similar diets, the most striking observation is that they had major differences in their genetic ancestry. Results of the genetic analyses of the nuclear ancient DNA data for these individuals indicate that the individual without artificial cranial deformation shows broadly West Eurasian associated-ancestry, the individual with tabular oblique-type has East Asian ancestry and the third individual with circular erect-type has Near Eastern associated-ancestry. Based on these results, we speculate that artificial cranial deformation type may have been a visual indicator membership in a specific cultural group, and that these groups were interacting intimately on the Pannonian Plain during the Migration Period.}, }
@article {pmid31431750, year = {2019}, author = {Lewis, D}, title = {Head of prestigious ancient-DNA lab suspended amid bullying allegations.}, journal = {Nature}, volume = {572}, number = {7770}, pages = {424-425}, doi = {10.1038/d41586-019-02490-y}, pmid = {31431750}, issn = {1476-4687}, mesh = {Bullying/ethics/*prevention &amp; control ; *DNA, Ancient ; Research Personnel/*ethics/*legislation &amp; jurisprudence ; South Australia ; Universities ; }, }
@article {pmid31431628, year = {2019}, author = {Harney, É and Nayak, A and Patterson, N and Joglekar, P and Mushrif-Tripathy, V and Mallick, S and Rohland, N and Sedig, J and Adamski, N and Bernardos, R and Broomandkhoshbacht, N and Culleton, BJ and Ferry, M and Harper, TK and Michel, M and Oppenheimer, J and Stewardson, K and Zhang, Z and Harashawaradhana,  and Bartwal, MS and Kumar, S and Diyundi, SC and Roberts, P and Boivin, N and Kennett, DJ and Thangaraj, K and Reich, D and Rai, N}, title = {Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3670}, doi = {10.1038/s41467-019-11357-9}, pmid = {31431628}, issn = {2041-1723}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Body Remains/*cytology ; Continental Population Groups/*genetics ; DNA/*genetics ; Diet ; *Fossils ; Human Migration ; Humans ; India ; Mediterranean Region ; Polymorphism, Single Nucleotide/genetics ; Radiometric Dating ; }, abstract = {Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.}, }
@article {pmid31424543, year = {2019}, author = {Aris-Brosou, S}, title = {Direct Evidence of an Increasing Mutational Load in Humans.}, journal = {Molecular biology and evolution}, volume = {36}, number = {12}, pages = {2823-2829}, doi = {10.1093/molbev/msz192}, pmid = {31424543}, issn = {1537-1719}, mesh = {Alleles ; Disease/*genetics ; Gene Frequency ; *Genetic Load ; *Genome, Human ; Homozygote ; Humans ; Mutation ; }, abstract = {The extent to which selection has shaped present-day human populations has attracted intense scrutiny, and examples of local adaptations abound. However, the evolutionary trajectory of alleles that, today, are deleterious has received much less attention. To address this question, the genomes of 2,062 individuals, including 1,179 ancient humans, were reanalyzed to assess how frequencies of risk alleles and their homozygosity changed through space and time in Europe over the past 45,000 years. Although the overall deleterious homozygosity has consistently decreased, risk alleles have steadily increased in frequency over that period of time. Those that increased most are associated with diseases such as asthma, Crohn disease, diabetes, and obesity, which are highly prevalent in present-day populations. These findings may not run against the existence of local adaptations but highlight the limitations imposed by drift and population dynamics on the strength of selection in purging deleterious mutations from human populations.}, }
@article {pmid31412470, year = {2019}, author = {Legrand, B and Miras, Y and Beauger, A and Dussauze, M and Latour, D}, title = {Akinetes and ancient DNA reveal toxic cyanobacterial recurrences and their potential for resurrection in a 6700-year-old core from a eutrophic lake.}, journal = {The Science of the total environment}, volume = {687}, number = {}, pages = {1369-1380}, doi = {10.1016/j.scitotenv.2019.07.100}, pmid = {31412470}, issn = {1879-1026}, mesh = {Cyanobacteria/*genetics ; *Environmental Monitoring ; Eutrophication ; Geologic Sediments/microbiology ; Lakes/microbiology ; Microcystins ; Recurrence ; Seasons ; Tropanes ; Water Pollution/*statistics &amp; numerical data ; }, abstract = {In order to evaluate the recurrence of toxic cyanobacterial blooms and to determine the survival capabilities of the resistance cells through time, a sedimentary core spanning 6700 years was drilled in the eutrophic Lake Aydat. A multiproxy approach (density, magnetic susceptibility, XRF, pollen and non-pollen palynomorph analyses), was used initially to determine the sedimentation model and the land uses around the lake. Comparison with the akinete count revealed that Nostocales cyanobacteria have been present in Lake Aydat over a six thousand year period. This long-term cyanobacterial recurrence also highlights the past presence of both the anaC and mcyB genes, involved in anatoxin-a and microcystin biosynthesis, respectively, throughout the core. The first appearance of cyanobacteria seems to be linked to the natural damming of the river, while the large increase in akinete density around 1800 cal.yr BP can be correlated with the intensification of human activities (woodland clearance, crop planting, grazing, etc.) in the catchment area of the lake, and marks the beginning of a long period of eutrophication. This first investigation into the viability and germination potential of cyanobacteria over thousands of years reveals the ability of intact akinetes to undergo cell divisions even after 1800 years of sedimentation, which is 10 times longer than previously observed. This exceptional cellular resistance, coupled with the long-term eutrophic conditions of this lake, could partly explain the past and current recurrences of cyanobacterial proliferations.}, }
@article {pmid31405970, year = {2019}, author = {Frantz, LAF and Haile, J and Lin, AT and Scheu, A and Geörg, C and Benecke, N and Alexander, M and Linderholm, A and Mullin, VE and Daly, KG and Battista, VM and Price, M and Gron, KJ and Alexandri, P and Arbogast, RM and Arbuckle, B and Bӑlӑşescu, A and Barnett, R and Bartosiewicz, L and Baryshnikov, G and Bonsall, C and Borić, D and Boroneanţ, A and Bulatović, J and Çakirlar, C and Carretero, JM and Chapman, J and Church, M and Crooijmans, R and De Cupere, B and Detry, C and Dimitrijevic, V and Dumitraşcu, V and du Plessis, L and Edwards, CJ and Erek, CM and Erim-Özdoğan, A and Ervynck, A and Fulgione, D and Gligor, M and Götherström, A and Gourichon, L and Groenen, MAM and Helmer, D and Hongo, H and Horwitz, LK and Irving-Pease, EK and Lebrasseur, O and Lesur, J and Malone, C and Manaseryan, N and Marciniak, A and Martlew, H and Mashkour, M and Matthews, R and Matuzeviciute, GM and Maziar, S and Meijaard, E and McGovern, T and Megens, HJ and Miller, R and Mohaseb, AF and Orschiedt, J and Orton, D and Papathanasiou, A and Pearson, MP and Pinhasi, R and Radmanović, D and Ricaut, FX and Richards, M and Sabin, R and Sarti, L and Schier, W and Sheikhi, S and Stephan, E and Stewart, JR and Stoddart, S and Tagliacozzo, A and Tasić, N and Trantalidou, K and Tresset, A and Valdiosera, C and van den Hurk, Y and Van Poucke, S and Vigne, JD and Yanevich, A and Zeeb-Lanz, A and Triantafyllidis, A and Gilbert, MTP and Schibler, J and Rowley-Conwy, P and Zeder, M and Peters, J and Cucchi, T and Bradley, DG and Dobney, K and Burger, J and Evin, A and Girdland-Flink, L and Larson, G}, title = {Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {35}, pages = {17231-17238}, pmid = {31405970}, issn = {1091-6490}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *DNA, Ancient ; DNA, Mitochondrial/*genetics ; *Domestication ; Europe ; *Gene Flow ; History, Ancient ; Middle East ; *Phylogeny ; Skin Pigmentation/genetics ; Swine/*genetics ; }, abstract = {Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.}, }
@article {pmid31397436, year = {2019}, author = {Kornienko, IV and Faleeva, TG and Oreshkova, NV and Grigoriev, SE and Grigorieva, LV and Putintseva, YA and Krutovsky, KV}, title = {[Structural and Functional Organization of the Mitochondrial DNA Control Region in the Woolly Mammoth (Mammuthus primigenius)].}, journal = {Molekuliarnaia biologiia}, volume = {53}, number = {4}, pages = {627-637}, doi = {10.1134/S0026898419040062}, pmid = {31397436}, issn = {0026-8984}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Fossils ; Genome, Mitochondrial/*genetics ; Locus Control Region/*genetics ; Mammoths/*genetics ; }, abstract = {The woolly mammoth mitochondrial genome (including the Malolyakhovsky mammoth) has been previously sequenced, followed by the annotation of all its genes (MF770243). In this study, based on the Malolyakhovsky mammoth, we describe for the first time the sites of functional significance in the control region of the woolly mammoth mitogenome.}, }
@article {pmid31389364, year = {2019}, author = {Peterson, A}, title = {On Reconstruction of ancestral footfalls in South Asia using genomic data By Saikat Chakraborty and Analabha Basu.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389364}, issn = {0973-7138}, mesh = {African Continental Ancestry Group/*history ; Archaeology/methods ; Asia/ethnology ; Asian Continental Ancestry Group/*history ; Chromosomes, Human, Y/chemistry ; Culture ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; European Continental Ancestry Group/*history ; Female ; Genetics, Population/*history ; *Genome, Human ; Haplotypes ; History, Ancient ; Human Migration/*history ; Humans ; Linguistics/*history ; Male ; Sequence Analysis, DNA ; }, }
@article {pmid31389363, year = {2019}, author = {Chakraborty, S and Basu, A}, title = {Reconstruction of ancestral footfalls in South Asia using genomic data.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389363}, issn = {0973-7138}, mesh = {Anthropology/methods ; Archaeology/methods ; Asia/ethnology ; Asian Continental Ancestry Group/*history ; DNA, Ancient/*analysis ; *Ethnic Groups ; Female ; Genetic Markers ; Genetic Variation ; *Genetics, Population ; Genome, Mitochondrial ; History, Ancient ; Human Migration/*trends ; Humans ; Inheritance Patterns ; Language/*history ; Male ; Mitochondria/genetics ; }, abstract = {Due to its unique geographical position, juxtaposed in the middle of south-central Asia, east Asia and Southeast Asia, the South Asian Region (SAS) has repeatedly come into contact with people from adjacent regions throughout history and prehistory. The antiquity of the populations and the intricate history of admixture have shaped SAS as one of the most genetically diverse regions in the world. In this article we review our current understanding of the peopling and populations structure of SAS. We do not attempt to be exhaustive but summarize the salient conclusions that have been reached using genetic data and evaluate their robustness. We also identify the unanswered questions and suggest possible approaches that may lead to their answers.}, }
@article {pmid31389362, year = {2019}, author = {Pitchappan, R}, title = {On Historic migration to South Asia in the last two millennia: A case of Jewish and Parsi populations By Ajai Kumar Pathak, et al.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389362}, issn = {0973-7138}, mesh = {Archaeology/methods ; Asian Continental Ancestry Group/*history ; Culture ; DNA, Ancient/analysis ; Female ; Genetics, Population/*history ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; India/ethnology ; Jews/*history ; Linguistics/*history ; Male ; Middle East/ethnology ; Sequence Analysis, DNA ; }, }
@article {pmid31389361, year = {2019}, author = {Pathak, AK and Srivastava, A and Singh, PP and DAS, D and Bandopadhyay, A and Singh, P and Chaubey, G}, title = {Historic migration to South Asia in the last two millennia: A case of Jewish and Parsi populations.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389361}, issn = {0973-7138}, mesh = {Acculturation ; Anthropology/methods ; Asian Continental Ancestry Group/*history ; DNA, Ancient/*analysis ; Ethnic Groups ; European Continental Ancestry Group/*history ; Female ; Genetic Variation ; *Genetics, Population ; History, Ancient ; Human Migration/*trends ; Humans ; India/ethnology ; Iran/ethnology ; Jews/genetics/*history ; Male ; }, abstract = {The South Asian populations have a mosaic of ancestries likely due to the interactions of long-term populations of the landmass and those of East andWest Eurasia. Apart from prehistoric dispersals, there are some known population movements to India. In this study,we focussed on the migration of Jewish and Parsi populations on temporal and spatial scales. The existence of Jewish and Parsi communities in India are recorded since ancient times. However, due to the lack of high-resolution genetic data, their origin and affiliation with other Indian and non-Indian populations remains shrouded in legends. Earlier genetic studies on populations of Indian Jews have found evidence for a minor shared ancestry of Indian Jews with Middle Eastern (Jews) populations, whereas for Parsis, the Iranian link was proposed. Recently, in our high-resolution study, we were able to quantify the admixture dynamics of these groups, which has suggested a male-biased admixture. Here, we added the newly available ancient samples and revisited the interplay of genes and cultures. Thus, in this study we reconstructed a broad genetic profile of Indian Jews and Parsis to paint a fine-grained picture of these ethnic groups.}, }
@article {pmid31389360, year = {2019}, author = {Das, R}, title = {OnPeopling of India: Ancient DNA perspectives By K Thangaraj and Niraj Rai.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389360}, issn = {0973-7138}, mesh = {*DNA, Ancient ; India ; }, }
@article {pmid31389359, year = {2019}, author = {Thangaraj, K and Rai, N}, title = {Peopling of India: Ancient DNA perspectives.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389359}, issn = {0973-7138}, mesh = {Anthropology/methods ; Archaeology/methods ; Asian Continental Ancestry Group/*history ; Biological Evolution ; DNA, Ancient/*analysis ; Ethnic Groups ; European Continental Ancestry Group/*history ; Female ; Genetic Variation ; *Genetics, Population ; History, Ancient ; Human Migration/*trends ; Humans ; India/ethnology ; Language/*history ; Male ; Selection, Genetic ; }, abstract = {To reconstruct and explain patterns of genetic diversity of modern humans, understanding their past and present genetic profile is crucial. While genomes of contemporary people can provide information about present day population structure, analysis of ancient genomes may provide unprecedented insights about the past demographic events that have shaped the contemporary gene pool. Population genetics has recently witnessed an explosion in studies on ancient human population histories, primarily from Europe and America. South Asia has no representation in the ancient genomics literature, despite the wealth of archaeological richness in the form of human skeletal remains that exist in collections all over the country. Representing one-fifth of present day humanity calls for understanding the demographic history of south Asia not merely as a prerequisite but as an urgent need to understand its genetic variations on a global scale. Although the overall picture is taking form, new archaeological and genetic information from the region has started to reveal a more complex scenario of ancient human migrations and admixtures than was ever known before. In this article, we discuss a meaningful insight on the current status of ancient DNA (aDNA) research in India. We have also summarized a few but important aDNA studies, which have been successfully carried out in India. Furthermore, we have highlighted the potential opportunity of aDNA research in the Indian subcontinent.}, }
@article {pmid31389358, year = {2019}, author = {Silva, M and Koch, JT and Pala, M and Edwards, CJ and Soares, P and Richards, MB}, title = {On Methodological issues in the Indo-European debate By Michel Danino.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389358}, issn = {0973-7138}, mesh = {Archaeology/methods ; Asian Continental Ancestry Group/*history ; Culture ; DNA, Ancient/analysis ; Europe/ethnology ; European Continental Ancestry Group/*history ; Genetics, Population/*history ; History, Ancient ; Human Migration/*history ; Humans ; India/ethnology ; Linguistics/*history ; Sequence Analysis, DNA ; }, }
@article {pmid31389349, year = {2019}, author = {Kochhar, R}, title = {Ancient Indian history: What do we know and how?.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389349}, issn = {0973-7138}, mesh = {Agriculture/*history ; Animals ; Archaeology/*methods ; Asian Continental Ancestry Group/*history ; Ceremonial Behavior ; DNA, Ancient/analysis ; Domestication ; Droughts ; *Ethnic Groups ; European Continental Ancestry Group/*history ; Female ; Genetics, Population/methods ; History, Ancient ; Horses ; Human Migration/*trends ; Humans ; India/ethnology ; Linguistics/methods ; Male ; Plant Breeding/history ; }, abstract = {When and where was the Rigveda (Rv) composed? How are the Vedic people related to the vast Harappan archaeological tradition? These quintessential questions have no direct answers. At our current level of understanding, archaeology and sacred texts constitute two distinct streams which do not intersect. We must therefore collate evidence from different sources and try to produce a synthesis. It is particularly important to take note of archaeological evidence from Central Asia, because it has not received the attention it deserves. What is well known in science must be kept in mind in the case of history also. A theory to be valid must explain each and every fact (known at present or to be known in future) in a selfconsistent manner. Conversely, even if there is one piece of evidence that a theory is unable to explain, it should be put on hold, modified or even rejected.}, }
@article {pmid31389347, year = {2019}, author = {Witzel, M}, title = {Early 'Aryans' and their neighbors outside and inside India.}, journal = {Journal of biosciences}, volume = {44}, number = {3}, pages = {}, pmid = {31389347}, issn = {0973-7138}, mesh = {Animals ; Archaeology/*methods ; Asian Continental Ancestry Group/*history ; Ceremonial Behavior ; DNA, Ancient/*analysis ; Equidae ; *Ethnic Groups ; European Continental Ancestry Group/*history ; Female ; Genetics, Population/methods ; History, Ancient ; Horses ; Human Migration/*trends ; Humans ; India/ethnology ; Linguistics/methods ; Male ; }, abstract = {Data from archaeology, linguistics, population genetics, and from early Vedic texts, which deal with religion, mythology and rituals, have to be assembled and closely compared in order to gain a comprehensive picture of the early 'Aryans'. Such interdisciplinary dialogue is necessary in order to establish areas of overlap of data. This paper attempts to indicate a western Central Asian origin of the Indo-Aryan speakers, in the steppe belt near the Urals, from where they moved, via the Inner Asian Mountain belt and Bactria, into India. Their gradual migration entailed acculturation with previous populations, their languages and cultures.}, }
@article {pmid31386837, year = {2019}, author = {Valente, L and Etienne, RS and Garcia-R, JC}, title = {Deep Macroevolutionary Impact of Humans on New Zealand's Unique Avifauna.}, journal = {Current biology : CB}, volume = {29}, number = {15}, pages = {2563-2569.e4}, doi = {10.1016/j.cub.2019.06.058}, pmid = {31386837}, issn = {1879-0445}, mesh = {Animals ; *Biodiversity ; *Biological Evolution ; *Birds ; *Conservation of Natural Resources ; DNA, Ancient ; *Extinction, Biological ; Fossils ; New Zealand ; }, abstract = {Islands are at the frontline of the anthropogenic extinction crisis [1]. A vast number of island birds have gone extinct since human colonization [2], and an important proportion is currently threatened with extinction [3]. While the number of lost or threatened avian species has often been quantified [4], the macroevolutionary consequences of human impact on island biodiversity have rarely been measured [5]. Here, we estimate the amount of evolutionary time that has been lost or is under threat due to anthropogenic activity in a classic example, New Zealand. Half of its bird taxa have gone extinct since humans arrived [6, 7] and many are threatened [8], including lineages forming highly distinct branches in the avian tree of life [9-11]. Using paleontological and ancient DNA information, we compiled a dated phylogenetic dataset for New Zealand's terrestrial avifauna. We extend the method DAISIE developed for island biogeography [12] to allow for the fact that many of New Zealand's birds are evolutionarily isolated and use it to estimate natural rates of speciation, extinction, and colonization. Simulating under a range of human-induced extinction scenarios, we find that it would take approximately 50 million years (Ma) to recover the number of species lost since human colonization of New Zealand and up to 10 Ma to return to today's species numbers if currently threatened species go extinct. This study puts into macroevolutionary perspective the impact of humans in an isolated fauna and reveals how conservation decisions we take today will have repercussions for millions of years.}, }
@article {pmid31381968, year = {2019}, author = {Oswald, JA and Allen, JM and Witt, KE and Folk, RA and Albury, NA and Steadman, DW and Guralnick, RP}, title = {Ancient DNA from a 2,500-year-old Caribbean fossil places an extinct bird (Caracara creightoni) in a phylogenetic context.}, journal = {Molecular phylogenetics and evolution}, volume = {140}, number = {}, pages = {106576}, doi = {10.1016/j.ympev.2019.106576}, pmid = {31381968}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Birds/genetics ; Caribbean Region ; DNA, Ancient/*analysis ; *Extinction, Biological ; Falconiformes/*classification/*genetics ; *Fossils ; Genome, Mitochondrial ; Geography ; *Phylogeny ; }, abstract = {Since the late Pleistocene humans have caused the extinction of species across our planet. Placing these extinct species in the tree of life with genetic data is essential to understanding the ecological and evolutionary implications of these losses. While ancient DNA (aDNA) techniques have advanced rapidly in recent decades, aDNA from tropical species, especially birds, has been historically difficult to obtain, leaving a gap in our knowledge of the extinction processes that have influenced current distributions and biodiversity. Here we report the recovery of a nearly complete mitochondrial genome from a 2,500 year old (late Holocene) bone of an extinct species of bird, Caracara creightoni, recovered from the anoxic saltwater environment of a blue hole in the Bahamas. Our results suggest that this extinct species is sister (1.6% sequence divergence) to a clade containing the extant C. cheriway and C. plancus. Caracara creightoni shared a common ancestor with these extant species during the Pleistocene (1.2-0.4 MYA) and presumably survived on Cuba when the Bahamas was mostly underwater during Quaternary interglacial intervals (periods of high sea levels). Tropical blue holes have been collecting animals for thousands of years and will continue to improve our understanding of faunal extinctions and distributions. In particular, new aDNA techniques combined with radiocarbon dating from Holocene Bahamian fossils will allow us to place other extinct (species-level loss) and extirpated (population-level loss) vertebrate taxa in improved phylogenetic, evolutionary, biogeographic, and temporal contexts.}, }
@article {pmid31361744, year = {2019}, author = {Smith, O and Dunshea, G and Sinding, MS and Fedorov, S and Germonpre, M and Bocherens, H and Gilbert, MTP}, title = {Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival.}, journal = {PLoS biology}, volume = {17}, number = {7}, pages = {e3000166}, pmid = {31361744}, issn = {1545-7885}, mesh = {Animals ; Canidae/classification/*genetics ; Cartilage/metabolism ; *Fossils ; High-Throughput Nucleotide Sequencing/methods ; Liver/*metabolism ; Organ Specificity/*genetics ; Permafrost/chemistry ; RNA/*genetics/metabolism ; Sequence Analysis, RNA/methods ; Skin/metabolism ; Species Specificity ; Transcriptome/*genetics ; Wolves/genetics ; }, abstract = {While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data's authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology.}, }
@article {pmid31353181, year = {2019}, author = {Ning, C and Wang, CC and Gao, S and Yang, Y and Zhang, X and Wu, X and Zhang, F and Nie, Z and Tang, Y and Robbeets, M and Ma, J and Krause, J and Cui, Y}, title = {Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan.}, journal = {Current biology : CB}, volume = {29}, number = {15}, pages = {2526-2532.e4}, doi = {10.1016/j.cub.2019.06.044}, pmid = {31353181}, issn = {1879-0445}, mesh = {Archaeology ; Asian Continental Ancestry Group/genetics ; China ; DNA, Ancient/*analysis ; European Continental Ancestry Group/genetics ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Language ; }, abstract = {Recent studies of early Bronze Age human genomes revealed a massive population expansion by individuals-related to the Yamnaya culture, from the Pontic Caspian steppe into Western and Eastern Eurasia, likely accompanied by the spread of Indo-European languages [1-5]. The south eastern extent of this migration is currently not known. Modern-day human populations from the Xinjiang region in northwestern China show a complex population history, with genetic links to both Eastern and Western Eurasia [6-10]. However, due to the lack of ancient genomic data, it remains unclear which source populations contributed to the Xinjiang population and what was the timing and the number of admixture events. Here, we report the first genome-wide data of 10 ancient individuals from northeastern Xinjiang. They are dated to around 2,200 years ago and were found at the Iron Age Shirenzigou site. We find them to be already genetically admixed between Eastern and Western Eurasians. We also find that the majority of the East Eurasian ancestry in the Shirenzigou individuals is-related to northeastern Asian populations, while the West Eurasian ancestry is best presented by ∼20% to 80% Yamnaya-like ancestry. Our data thus suggest a Western Eurasian steppe origin for at least part of the ancient Xinjiang population. Our findings furthermore support a Yamnaya-related origin for the now extinct Tocharian languages in the Tarim Basin, in southern Xinjiang.}, }
@article {pmid31351222, year = {2019}, author = {Molto, JE and Kirkpatrick, CL and Keron, J}, title = {The paleoepidemiology of Sacral Spina Bifida Occulta in population samples from the Dakhleh Oasis, Egypt.}, journal = {International journal of paleopathology}, volume = {26}, number = {}, pages = {93-103}, doi = {10.1016/j.ijpp.2019.06.006}, pmid = {31351222}, issn = {1879-9825}, mesh = {Adult ; Egypt ; Female ; History, Ancient ; Humans ; Male ; *Paleopathology ; Prevalence ; Sacrococcygeal Region ; Spina Bifida Occulta/*epidemiology/*history ; Young Adult ; }, abstract = {OBJECTIVE: To document sacral spina bifida occulta (SSB0) prevalence in a population sample from the Dakhleh Oasis, Egypt, and address methodological issues in recording and quantifying SSBO variations.<br><br>MATERIALS: 442 adult sacra from two temporally disjunct samples from the same deme traversing the 3rd intermediate (TIP) and the Roman Periods.<br><br>METHODS: Sacra were scored for SSBO, excluding the sacral hiatus. Risk of SSBO was calculated with the common odds ratio and statistical significance by X2. Data were compared to other archaeological SSBO data.<br><br>RESULTS: SSBO was present in 15.6% of the sample with a slight, but not significant, temporal increase (TIP to Roman Period) in males, and a significant age-correlated increase in both sexes. Most open sacra occurred in young adults.<br><br>CONCLUSIONS: Data support that SSBO can be considered as a morphogenetic variant. Dakhleh data fall within the prevalence range for most populations, however inter-population comparisons are complicated by methodological inconsistencies.<br><br>SIGNIFICANCE: SSBO can be used in paleogenetic research.<br><br>LIMITATIONS: Methodological differences in scoring SSBO prevent effective comparative study.<br><br>SUGGESTED FUTURE RESEARCH: Future studies require more rigorous and standardized scoring methods. aDNA may be used to corroborate the morphogenetic value of SSBO and determine its clinical significance.}, }
@article {pmid31348818, year = {2019}, author = {Günther, T and Nettelblad, C}, title = {The presence and impact of reference bias on population genomic studies of prehistoric human populations.}, journal = {PLoS genetics}, volume = {15}, number = {7}, pages = {e1008302}, pmid = {31348818}, issn = {1553-7404}, mesh = {Animals ; Bias ; DNA, Ancient/*analysis ; Genome, Human ; High-Throughput Nucleotide Sequencing/methods ; Hominidae/*genetics ; Humans ; Metagenomics/*methods ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Haploid high quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele. In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp-reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudo-haploid data, i.e. they randomly sample only one sequencing read per site. We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Most genomic regions we investigated show little to no mapping bias but even a small proportion of sites with bias can impact analyses of those particular loci or slightly skew genome-wide estimates. Therefore, reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.}, }
@article {pmid31328768, year = {2019}, author = {Mas-Sandoval, A and Arauna, LR and Gouveia, MH and Barreto, ML and Horta, BL and Lima-Costa, MF and Pereira, AC and Salzano, FM and Hünemeier, T and Tarazona-Santos, E and Bortolini, MC and Comas, D}, title = {Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry.}, journal = {Genome biology and evolution}, volume = {11}, number = {9}, pages = {2593-2604}, pmid = {31328768}, issn = {1759-6653}, mesh = {Brazil ; Genetic Variation ; Genome, Human ; Geography ; Haplotypes ; Humans ; Indians, South American/*genetics ; Population Density ; }, abstract = {After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.}, }
@article {pmid31318917, year = {2019}, author = {Prufer, KM and Alsgaard, AV and Robinson, M and Meredith, CR and Culleton, BJ and Dennehy, T and Magee, S and Huckell, BB and Stemp, WJ and Awe, JJ and Capriles, JM and Kennett, DJ}, title = {Linking late Paleoindian stone tool technologies and populations in North, Central and South America.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219812}, pmid = {31318917}, issn = {1932-6203}, mesh = {Americas ; *Archaeology/methods ; Geography ; Humans ; *Technology ; }, abstract = {From the perspective of Central and South America, the peopling of the New World was a complex process lasting thousands of years and involving multiple waves of Pleistocene and early Holocene period immigrants entering into the neotropics. These Paleoindian colonists initially brought with them technologies developed for adaptation to environments and resources found in North America. As the ice age ended across the New World people adapted more generalized stone tools to exploit changing environments and resources. In the neotropics these changes would have been pronounced as patchy forests and grasslands gave way to broadleaf tropical forests. We document a late Pleistocene/early Holocene stone tool tradition from Belize, located in southern Mesoamerica. This represents the first endogenous Paleoindian stone tool technocomplex recovered from well dated stratigraphic contexts for Mesoamerica. Previously designated Lowe, these artifacts share multiple features with contemporary North and South American Paleoindian tool types. Once hafted, these bifaces appear to have served multiple functions for cutting, hooking, thrusting, or throwing. The tools were developed at a time of technological regionalization reflecting the diverse demands of a period of pronounced environmental change and population movement. Combined stratigraphic, technological, and population paleogenetic data suggests that there were strong ties between lowland neotropic regions at the onset of the Holocene.}, }
@article {pmid31310584, year = {2019}, author = {Hong, JH and Seo, M and Oh, CS and Shin, DH}, title = {Genetic Analysis of Small-Subunit Ribosomal RNA, Internal Transcribed Spacer 2, and ATP Synthase Subunit 8 of Trichuris trichiura Ancient DNA Retrieved from the 15th to 18th Century Joseon Dynasty Mummies' Coprolites from Korea.}, journal = {The Journal of parasitology}, volume = {105}, number = {4}, pages = {539-545}, pmid = {31310584}, issn = {1937-2345}, mesh = {Animals ; DNA, Helminth/analysis/genetics/history ; Feces/parasitology ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; Humans ; Korea ; Mitochondrial Proton-Translocating ATPases/analysis/genetics/history ; Mummies/*history ; Phylogeny ; RNA, Ribosomal/genetics/history ; Trichuriasis/*history ; Trichuris/classification/genetics/*isolation &amp; purification ; }, abstract = {Although parasitic infection by Trichuris trichiura is a very common intestinal helminthic disease worldwide, there is still insufficient information on the genetic characteristics of ancient T. trichiura in different spatiotemporal perspectives. Utilizing coprolite specimens obtained from 15th-18th century mummies dating to the Joseon Dynasty, we analyzed small-subunit ribosomal RNA, internal transcribed spacer 2, and ATP synthase subunit 8 of T. trichiura ancient DNA (aDNA). In BLAST and phylogenetic analyses, the T. trichiura aDNA sequences of this study belong to a separate cluster that is evidently distinct from the other genus Trichuris spp. reported in GenBank. This report characterizes T. trichiura aDNA of pre-20th century East Asia, and in so doing, it also proves the potential of aDNA analysis for differential diagnosis of T. trichiura in cases where ancient parasite eggs are morphologically indeterminate for species identification.}, }
@article {pmid31308224, year = {2019}, author = {Bokelmann, L and Hajdinjak, M and Peyrégne, S and Brace, S and Essel, E and de Filippo, C and Glocke, I and Grote, S and Mafessoni, F and Nagel, S and Kelso, J and Prüfer, K and Vernot, B and Barnes, I and Pääbo, S and Meyer, M and Stringer, C}, title = {A genetic analysis of the Gibraltar Neanderthals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {31}, pages = {15610-15615}, pmid = {31308224}, issn = {1091-6490}, support = {100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *DNA, Ancient ; Gibraltar ; History, Ancient ; Humans ; Neanderthals/*genetics ; *Oligonucleotide Array Sequence Analysis ; }, abstract = {The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.}, }
@article {pmid31303491, year = {2019}, author = {Järve, M and Saag, L and Scheib, CL and Pathak, AK and Montinaro, F and Pagani, L and Flores, R and Guellil, M and Saag, L and Tambets, K and Kushniarevich, A and Solnik, A and Varul, L and Zadnikov, S and Petrauskas, O and Avramenko, M and Magomedov, B and Didenko, S and Toshev, G and Bruyako, I and Grechko, D and Okatenko, V and Gorbenko, K and Smyrnov, O and Heiko, A and Reida, R and Sapiehin, S and Sirotin, S and Tairov, A and Beisenov, A and Starodubtsev, M and Vasilev, V and Nechvaloda, A and Atabiev, B and Litvinov, S and Ekomasova, N and Dzhaubermezov, M and Voroniatov, S and Utevska, O and Shramko, I and Khusnutdinova, E and Metspalu, M and Savelev, N and Kriiska, A and Kivisild, T and Villems, R}, title = {Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance.}, journal = {Current biology : CB}, volume = {29}, number = {14}, pages = {2430-2441.e10}, doi = {10.1016/j.cub.2019.06.019}, pmid = {31303491}, issn = {1879-0445}, mesh = {Archaeology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Ethnic Groups/genetics ; *Genetic Drift ; Genome, Human ; History, Ancient ; *Human Migration ; Humans ; Male ; Ukraine ; }, abstract = {The Early Iron Age nomadic Scythians have been described as a confederation of tribes of different origins, based on ancient DNA evidence [1-3]. It is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome sequences of 31 ancient Western and Eastern Steppe individuals, including Scythians as well as samples pre- and postdating them, allowing us to set the Scythians in a temporal context (in the Western, i.e., Ponto-Caspian Steppe). We detect an increase of eastern (Altaian) affinity along with a decrease in eastern hunter-gatherer (EHG) ancestry in the Early Iron Age Ponto-Caspian gene pool at the start of the Scythian dominance. On the other hand, samples of the Chernyakhiv culture postdating the Scythians in Ukraine have a significantly higher proportion of Near Eastern ancestry than other samples of this study. Our results agree with the Gothic source of the Chernyakhiv culture and support the hypothesis that the Scythian dominance did involve a demic component.}, }
@article {pmid31303107, year = {2019}, author = {Houldcroft, CJ and Rifkin, RF and Underdown, SJ}, title = {Human biology and ancient DNA: exploring disease, domestication and movement.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {95-98}, doi = {10.1080/03014460.2019.1629536}, pmid = {31303107}, issn = {1464-5033}, mesh = {Archaeology ; *Biological Evolution ; DNA, Ancient/*analysis ; Domestication ; Genetic Predisposition to Disease/*etiology/history ; History, Ancient ; Human Migration/*history ; Humans ; }, }
@article {pmid31300536, year = {2019}, author = {Teixeira, JC and Cooper, A}, title = {Using hominin introgression to trace modern human dispersals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {31}, pages = {15327-15332}, pmid = {31300536}, issn = {1091-6490}, mesh = {Africa ; Animals ; Asia, Southeastern ; DNA/genetics ; Geography ; Hominidae/*physiology ; *Human Migration ; Humans ; Population Dynamics ; }, abstract = {The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace's Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.}, }
@article {pmid31297530, year = {2019}, author = {Koch, E and Schweizer, RM and Schweizer, TM and Stahler, DR and Smith, DW and Wayne, RK and Novembre, J}, title = {De novo mutation rate estimation in wolves of known pedigree.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, pmid = {31297530}, issn = {1537-1719}, support = {R01 GM108805/GM/NIGMS NIH HHS/United States ; S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; T32 GM007197/GM/NIGMS NIH HHS/United States ; }, abstract = {Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obtain an estimate of ∼4.5 x 10-9 per base pair per generation and provide conservative bounds from 2.6 x 10-9 and 7.1 x 10-9. Although our estimate is consistent with recent mutation rate estimates from ancient DNA (4.0 x 10-9 and 3.0-4.5 x 10-9), it implies a wider possible range. We also examined the consequences of our rate and the accompanying interval for dating several critical events in canid demographic history. For example, applying our full range of rates to coalescent models of dog and wolf demographic history implies a wide set of possible divergence times between the ancestral populations of dogs and extant Eurasian wolves (16,000 - 64,000 years ago) although our point estimate indicates a date between 25,000 and 33,000 years ago. Aside from one study in mice, ours provides the only direct mammalian mutation rate outside of primates, and is likely to be vital to future investigations of mutation rate evolution.}, }
@article {pmid31296442, year = {2019}, author = {Cornille, A and Antolín, F and Garcia, E and Vernesi, C and Fietta, A and Brinkkemper, O and Kirleis, W and Schlumbaum, A and Roldán-Ruiz, I}, title = {A Multifaceted Overview of Apple Tree Domestication.}, journal = {Trends in plant science}, volume = {24}, number = {8}, pages = {770-782}, doi = {10.1016/j.tplants.2019.05.007}, pmid = {31296442}, issn = {1878-4372}, mesh = {Breeding ; Crops, Agricultural ; Domestication ; Fruit ; *Malus ; }, abstract = {The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.}, }
@article {pmid31291259, year = {2019}, author = {Zimmermann, HH and Harms, L and Epp, LS and Mewes, N and Bernhardt, N and Kruse, S and Stoof-Leichsenring, KR and Pestryakova, LA and Wieczorek, M and Trense, D and Herzschuh, U}, title = {Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0216966}, pmid = {31291259}, issn = {1932-6203}, mesh = {Chromosome Mapping ; DNA, Ancient ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Genetic Variation ; Genetics, Population ; Genome, Chloroplast ; Genome, Mitochondrial ; Genome, Plant ; Haplotypes ; History, Ancient ; Larix/classification/*genetics ; Polymorphism, Single Nucleotide ; Siberia ; Taiga ; Tundra ; }, abstract = {Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.}, }
@article {pmid31284503, year = {2019}, author = {Lan, TM and Lin, Y and Njaramba-Ngatia, J and Guo, XS and Li, RG and Li, HM and Kumar-Sahu, S and Wang, X and Yang, XJ and Guo, HB and Xu, WH and Kristiansen, K and Liu, H and Xu, YC}, title = {Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data.}, journal = {Genes}, volume = {10}, number = {7}, pages = {}, pmid = {31284503}, issn = {2073-4425}, mesh = {Algorithms ; Animals ; DNA, Mitochondrial ; Genome ; Goats/*genetics ; High-Throughput Nucleotide Sequencing ; Horses/*genetics ; Humans ; Mammoths/*genetics ; Paleontology ; Ruminants/*genetics ; }, abstract = {The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.}, }
@article {pmid31283430, year = {2019}, author = {Bos, KI and Kühnert, D and Herbig, A and Esquivel-Gomez, LR and Andrades Valtueña, A and Barquera, R and Giffin, K and Kumar Lankapalli, A and Nelson, EA and Sabin, S and Spyrou, MA and Krause, J}, title = {Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens.}, journal = {Annual review of microbiology}, volume = {73}, number = {}, pages = {639-666}, doi = {10.1146/annurev-micro-090817-062436}, pmid = {31283430}, issn = {1545-3251}, mesh = {Biological Evolution ; Communicable Diseases/*history ; DNA, Ancient/*analysis ; DNA, Bacterial ; Fossils/*microbiology/parasitology ; Genome, Bacterial ; Genomics/methods ; Helicobacter pylori/genetics ; High-Throughput Nucleotide Sequencing/methods ; History, Ancient ; Humans ; Mycobacterium leprae/genetics ; Mycobacterium tuberculosis/genetics ; Paleontology/methods ; Paleopathology/*methods ; Phylogeny ; Yersinia pestis/genetics ; }, abstract = {The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.}, }
@article {pmid31281897, year = {2019}, author = {Feldman, M and Master, DM and Bianco, RA and Burri, M and Stockhammer, PW and Mittnik, A and Aja, AJ and Jeong, C and Krause, J}, title = {Ancient DNA sheds light on the genetic origins of early Iron Age Philistines.}, journal = {Science advances}, volume = {5}, number = {7}, pages = {eaax0061}, pmid = {31281897}, issn = {2375-2548}, mesh = {*DNA, Ancient ; European Continental Ancestry Group/history/*legislation &amp; jurisprudence ; *Genetics, Population ; Genome-Wide Association Study ; History, Ancient ; *Human Migration ; Humans ; }, abstract = {The ancient Mediterranean port city of Ashkelon, identified as &quot;Philistine&quot; during the Iron Age, underwent a marked cultural change between the Late Bronze and the early Iron Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called &quot;Sea Peoples.&quot; Here, we report genome-wide data of 10 Bronze and Iron Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European-related admixture. This genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze to Iron Age transition in Ashkelon but did not leave a long-lasting genetic signature.}, }
@article {pmid31279340, year = {2019}, author = {Velsko, IM and Fellows Yates, JA and Aron, F and Hagan, RW and Frantz, LAF and Loe, L and Martinez, JBR and Chaves, E and Gosden, C and Larson, G and Warinner, C}, title = {Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {102}, pmid = {31279340}, issn = {2049-2618}, mesh = {Bacteria/*classification ; *Bacterial Physiological Phenomena ; Bacterial Proteins/genetics ; Biofilms/*growth &amp; development ; Bone and Bones/microbiology ; DNA, Ancient/analysis ; DNA, Bacterial/genetics ; Dental Calculus/history/*microbiology ; Dental Plaque/*microbiology ; Female ; History, Ancient ; Humans ; Male ; Metagenomics ; Microbiota/*physiology ; Periodontal Diseases/microbiology ; Proteomics ; Tooth/*microbiology ; }, abstract = {BACKGROUND: Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.<br><br>RESULTS: Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.<br><br>CONCLUSIONS: Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.}, }
@article {pmid31273106, year = {2019}, author = {Gibbons, A}, title = {DNA reveals European roots of the ancient Philistines.}, journal = {Science (New York, N.Y.)}, volume = {365}, number = {6448}, pages = {17}, doi = {10.1126/science.365.6448.17}, pmid = {31273106}, issn = {1095-9203}, mesh = {Archaeology ; DNA, Ancient ; Europe/ethnology ; History, Ancient ; Human Migration/*history ; Israel/ethnology ; }, }
@article {pmid31270812, year = {2019}, author = {Fleskes, RE and Bruwelheide, KS and West, FL and Owsley, DW and Griffith, DR and Barca, KG and Cabana, GS and Schurr, TG}, title = {Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier.}, journal = {American journal of physical anthropology}, volume = {170}, number = {2}, pages = {232-245}, doi = {10.1002/ajpa.23887}, pmid = {31270812}, issn = {1096-8644}, support = {//The University of Pennsylvania/International ; }, mesh = {Adult ; *African Continental Ancestry Group/ethnology/genetics/history ; Archaeology ; Cemeteries/history ; Child, Preschool ; Colonialism/*history ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Delaware ; Enslavement/*history ; *European Continental Ancestry Group/ethnology/genetics/history ; Female ; History, 17th Century ; History, 18th Century ; Humans ; Infant ; Male ; Middle Aged ; }, abstract = {OBJECTIVES: Ancient DNA (aDNA) and standard osteological analyses applied to 11 skeletons at a late 17th to early 18th century farmstead site in Delaware to investigate the biological and social factors of settlement and slavery in colonial America.<br><br>MATERIALS AND METHODS: Osteological analysis and mitochondrial DNA (mtDNA) sequencing were conducted for all individuals and the resulting data contextualized with archaeological and documentary evidence.<br><br>RESULTS: Individuals of European and African descent were spatially separated in this colonial cemetery. The skeletal remains exhibited differences in osteological features and maternal genetic ancestry. A specific mtDNA haplotype appeared in a subset of the European-descended individuals suggesting they were maternally related. Individuals of African descent were not maternally related, and instead showed a diversity of haplotypes affiliated with present-day Western, Central, and Eastern regions of Africa.<br><br>DISCUSSION: Along with the bioarchaeological and documentary evidence, the aDNA findings contribute to our understanding of life on the colonial Delaware frontier. Evidence of maternal relatedness among European-descended individuals at the site demonstrates kin-based settlements in 17th century Delaware and provides preliminary identifications of individuals. The maternal genetic diversity of the individuals with African descent aligns with the routes of the trans-Atlantic slave trade but broadens our understanding of the ancestries of persons involved in it. Burial positioning, osteological pathology, and lack of maternal kinship among individuals of African descent provide tangible evidence for the emergence of racialized labor and society in Delaware during the late 17th century.}, }
@article {pmid31267777, year = {2019}, author = {Silva, M and Justeau, P and Rodrigues, S and Oteo-Garcia, G and Dulias, K and Foody, G and Fichera, A and Yau, B and Rito, T and Wilson, JF and Gandini, F and Edwards, CJ and Pala, M and Soares, PA and Richards, MB}, title = {Untangling Neolithic and Bronze Age mitochondrial lineages in South Asia.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {140-144}, doi = {10.1080/03014460.2019.1623319}, pmid = {31267777}, issn = {1464-5033}, mesh = {Archaeology ; Asia ; Asian Continental Ancestry Group/genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis/genetics ; Gene Pool ; Haplotypes ; History, Ancient ; Human Migration/*history ; Humans ; Iran ; Phylogeography ; }, abstract = {Two key moments shaped the extant South Asian gene pool within the last 10 thousand years (ka): the Neolithic period, with the advent of agriculture and the rise of the Harappan/Indus Valley Civilisation; and Late Bronze Age events that witnessed the abrupt fall of the Harappan Civilisation and the arrival of Indo-European speakers. This study focuses on the phylogeographic patterns of mitochondrial haplogroups H2 and H13 in the Indian Subcontinent and incorporates evidence from recently released ancient genomes from Central and South Asia. It found signals of Neolithic arrivals from Iran and later movements in the Bronze Age from Central Asia that derived ultimately from the Steppe. This study shows how a detailed mtDNA phylogeographic approach, combining both modern and ancient variation, can provide evidence of population movements, even in a scenario of strong male bias such as in the case of the Bronze Age Steppe dispersals.}, }
@article {pmid31256878, year = {2019}, author = {Joseph, TA and Pe'er, I}, title = {Inference of Population Structure from Time-Series Genotype Data.}, journal = {American journal of human genetics}, volume = {105}, number = {2}, pages = {317-333}, pmid = {31256878}, issn = {1537-6605}, support = {U54 CA209997/CA/NCI NIH HHS/United States ; }, mesh = {*Algorithms ; Europe ; Gene Frequency ; Genetic Predisposition to Disease ; *Genetic Variation ; *Genetics, Population ; Genome-Wide Association Study ; Genotype ; Humans ; Middle East ; *Models, Genetic ; *Models, Statistical ; Population Groups/*genetics ; Time Factors ; }, abstract = {Sequencing ancient DNA can offer direct probing of population history. Yet, such data are commonly analyzed with standard tools that assume DNA samples are all contemporary. We present DyStruct, a model and inference algorithm for inferring shared ancestry from temporally sampled genotype data. DyStruct explicitly incorporates temporal dynamics by modeling individuals as mixtures of unobserved populations whose allele frequencies drift over time. We develop an efficient inference algorithm for our model using stochastic variational inference. On simulated data, we show that DyStruct outperforms the current state of the art when individuals are sampled over time. Using a dataset of 296 modern and 80 ancient samples, we demonstrate DyStruct is able to capture a well-supported admixture event of steppe ancestry into modern Europe. We further apply DyStruct to a genome-wide dataset of 2,067 modern and 262 ancient samples used to study the origin of farming in the Near East. We show that DyStruct provides new insight into population history when compared with alternate approaches, within feasible run time.}, }
@article {pmid31251487, year = {2019}, author = {Angelici, FM and Ciucani, MM and Angelini, S and Annesi, F and Caniglia, R and Castiglia, R and Fabbri, E and Galaverni, M and Palumbo, D and Ravegnini, G and Rossi, L and Siracusa, AM and Cilli, E}, title = {The Sicilian Wolf: Genetic Identity of a Recently Extinct Insular Population.}, journal = {Zoological science}, volume = {36}, number = {3}, pages = {189-197}, doi = {10.2108/zs180180}, pmid = {31251487}, issn = {0289-0003}, mesh = {Animal Distribution ; Animals ; DNA, Mitochondrial/genetics ; Extinction, Biological ; Genotype ; Haplotypes ; Phylogeny ; Sicily ; Wolves/*genetics ; }, abstract = {Historically, many local grey wolf (Canis lupus) populations have undergone substantial reductions in size or become extinct. Among these, the wolf population once living in Sicily, the largest island in the Mediterranean Sea, was completely eradicated by human activity in the early decades of the 20th century. To gain a better understanding of the genetic identity of the Sicilian wolf, we used techniques for the study of ancient DNA to analyze the mitochondrial (mt) variability of six specimens stored in Italian museums. We were able to amplify a diagnostic mtDNA fragment of the control region (CR) in four of the samples. Two of the samples shared the same haplotype, differing by two substitutions from the currently most diffused Italian wolf haplotype (W14) and one substitution from the only other Italian haplotype (W16). The third sample showed a previously unreported wolf-like haplotype, and the fourth a haplotype commonly found in dogs. All of the wolf haplotypes analyzed in this study belonged to the mitochondrial haplogroup that includes haplotypes detected in all the known European Pleistocene wolves and in several modern southern European populations. Unfortunately, this endemic island population, which exhibited unique mtDNA variability, was definitively lost before it was possible to understand its taxonomic uniqueness and conservational value.}, }
@article {pmid31249793, year = {2019}, author = {Silva, PC and Malabarba, MC and Vari In Memoriam, R and Malabarba, LR}, title = {Comparison and optimization for DNA extraction of archived fish specimens.}, journal = {MethodsX}, volume = {6}, number = {}, pages = {1433-1442}, pmid = {31249793}, issn = {2215-0161}, abstract = {The DNA extracted from museum alcohol-fixed specimens can be a valuable source of information for solving taxonomic, phylogenetic, ecological and conservational questions. However, this type of DNA, also called ancient DNA, is routinely obtained in small portions and highly fragmented. We have tested two different extraction kits in museum type-specimens of the fish family Characidae. Aiming to increase the DNA yield, we made modifications on a Qiagen manufacturer protocol, in the elution step. Also, to overcome the issue of DNA fragmentation, we applied our efforts in Sanger sequencing, to find a highly variable and, in result, informative COI fragment. Based on our results, there is no correlation between amount of the DNA extracted and the age of the sample. The Sanger sequencing generated sequences which are useful in solving taxonomic puzzles. Here are presented the customization and guidelines that allowed us to recover DNA from the archived fish specimens. •DNA extraction from archived fish specimens is more effective when using silica columns.•Change of the elution times from minutes in room temperature to 24 h in freezer greatly improved the DNA yielded.•Short but highly variable sequences replace the need to sequence the entire gene to identify a species.}, }
@article {pmid31246567, year = {2019}, author = {Botbayev, D and Ravegnini, G and Sammarini, G and Kazymbet, P and Cilli, E and Serventi, P and Khanseitova, A and Alzhanuly, B and Belkozhaev, A and Aitkhozhina, N and Bakhtin, M and Lodi, V and Hrelia, P and Angelini, S}, title = {Absence of mutations in the human interferon alpha-2b gene in workers chronically exposed to ionising radiation.}, journal = {Arhiv za higijenu rada i toksikologiju}, volume = {70}, number = {2}, pages = {104-108}, doi = {10.2478/aiht-2019-70-3202}, pmid = {31246567}, issn = {1848-6312}, mesh = {Adult ; *Coal Mining ; Environmental Biomarkers/*genetics ; Humans ; Interferon-alpha/*genetics/*radiation effects ; Italy ; Kazakhstan ; Male ; Middle Aged ; Mutation/*radiation effects ; Occupational Diseases/*genetics ; Occupational Exposure ; Radiation Exposure/*adverse effects ; *Radiation, Ionizing ; }, abstract = {Individuals chronically exposed to low-level ionising radiation (IR) run the risk of harmful and long-term adverse health effects, including gene mutations and cancer development. The search for reliable biomarkers of IR exposure in human population is still of great interest, as they may have a great implementation potential for the surveillance of occupationally exposed individuals. In this context, and considering previous literature, this study aimed to identify mutations in the human interferon alpha-2b (hIFNα-2b) as a potential biomarker of occupational chronic low-dose IR exposure linking low-IR exposure to the effects on haematopoiesis and reduced immunity. The analysis was performed in the genomic DNA of 51 uranium miners and 38 controls from Kazakhstan, and in 21 medical radiology workers and 21 controls from Italy. hIFNα-2b gene mutations were analysed with the real-time polymerase chain reaction (PCR) or Sanger sequencing. However, none of the investigated workers had the hIFNα-2b mutation. This finding highlights the need for further research to identify biomarkers for early detection of health effects associated with chronic low-dose IR exposure.}, }
@article {pmid31243383, year = {2019}, author = {Warren, M}, title = {Move over, DNA: ancient proteins are starting to reveal humanity's history.}, journal = {Nature}, volume = {570}, number = {7762}, pages = {433-436}, doi = {10.1038/d41586-019-01986-x}, pmid = {31243383}, issn = {1476-4687}, mesh = {Animals ; Bone and Bones/chemistry ; Caves ; China ; DNA, Ancient/analysis/isolation &amp; purification ; Egg Shell/chemistry ; Evolution, Molecular ; *Fossils ; Hominidae/*classification ; Humans ; Paleontology/*methods/*trends ; Protein Stability ; Proteins/*analysis/*isolation &amp; purification ; Proteomics/trends ; Time Factors ; Tooth/chemistry ; }, }
@article {pmid31235841, year = {2019}, author = {De Schepper, S and Ray, JL and Skaar, KS and Sadatzki, H and Ijaz, UZ and Stein, R and Larsen, A}, title = {The potential of sedimentary ancient DNA for reconstructing past sea ice evolution.}, journal = {The ISME journal}, volume = {13}, number = {10}, pages = {2566-2577}, doi = {10.1038/s41396-019-0457-1}, pmid = {31235841}, issn = {1751-7370}, mesh = {Arctic Regions ; Biodiversity ; Climate ; DNA, Ancient/*analysis ; Eukaryota/*genetics/isolation &amp; purification ; Fossils ; Geologic Sediments/*chemistry ; Greenland ; Ice Cover/*chemistry ; }, abstract = {Sea ice is a crucial component of the Arctic climate system, yet the tools to document the evolution of sea ice conditions on historical and geological time scales are few and have limitations. Such records are essential for documenting and understanding the natural variations in Arctic sea ice extent. Here we explore sedimentary ancient DNA (aDNA), as a novel tool that unlocks and exploits the genetic (eukaryote) biodiversity preserved in marine sediments specifically for past sea ice reconstructions. Although use of sedimentary aDNA in paleoceanographic and paleoclimatic studies is still in its infancy, we use here metabarcoding and single-species quantitative DNA detection methods to document the sea ice conditions in a Greenland Sea marine sediment core. Metabarcoding has allowed identifying biodiversity changes in the geological record back to almost ~100,000 years ago that were related to changing sea ice conditions. Detailed bioinformatic analyses on the metabarcoding data revealed several sea-ice-associated taxa, most of which previously unknown from the fossil record. Finally, we quantitatively traced one known sea ice dinoflagellate in the sediment core. We show that aDNA can be recovered from deep-ocean sediments with generally oxic bottom waters and that past sea ice conditions can be documented beyond instrumental time scales. Our results corroborate sea ice reconstructions made by traditional tools, and thus demonstrate the potential of sedimentary aDNA, focusing primarily on microbial eukaryotes, as a new tool to better understand sea ice evolution in the climate system.}, }
@article {pmid31223116, year = {2019}, author = {Eisenhofer, R and Cooper, A}, title = {A new home for microbes.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31223116}, issn = {2050-084X}, mesh = {Animals ; Bacteria/*genetics/growth &amp; development ; DNA, Ancient/*analysis ; Dinosaurs/genetics/*microbiology ; Fossils/*microbiology ; Humans ; }, abstract = {Modern microorganisms growing in fossils provide major challenges for researchers trying to detect ancient molecules in the same fossils.}, }
@article {pmid31220249, year = {2019}, author = {Borówka, P and Pułaski, Ł and Marciniak, B and Borowska-Strugińska, B and Dziadek, J and Żądzińska, E and Lorkiewicz, W and Strapagiel, D}, title = {Screening methods for detection of ancient Mycobacterium tuberculosis complex fingerprints in next-generation sequencing data derived from skeletal samples.}, journal = {GigaScience}, volume = {8}, number = {6}, pages = {}, pmid = {31220249}, issn = {2047-217X}, mesh = {Body Remains/*microbiology ; Bone and Bones/microbiology ; DNA Barcoding, Taxonomic/*methods ; *DNA, Ancient ; DNA, Bacterial ; Female ; High-Throughput Nucleotide Sequencing/*methods ; History, Ancient ; Humans ; Male ; Mycobacterium tuberculosis/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Recent advances in ancient DNA studies, especially in increasing isolated DNA yields and quality, have opened the possibility of analysis of ancient host microbiome. However, such pitfalls as spurious identification of pathogens based on fragmentary data or environmental contamination could lead to incorrect epidaemiological conclusions. Within the Mycobacterium genus, Mycobacterium tuberculosis complex members responsible for tuberculosis share up to ∼99% genomic sequence identity, while other more distantly related Mycobacteria other than M. tuberculosis can be causative agents for pulmonary diseases or soil dwellers. Therefore, reliable determination of species complex is crucial for interpretation of sequencing results.<br><br>RESULTS: Here we present a novel bioinformatical approach, used for screening of ancient tuberculosis in sequencing data, derived from 28 individuals (dated 4400-4000 and 3100-2900 BC) from central Poland. We demonstrate that cost-effective next-generation screening sequencing data (∼20M reads per sample) could yield enough information to provide statistically supported identification of probable ancient disease cases.<br><br>CONCLUSIONS: Application of appropriate bioinformatic tools, including an unbiased selection of genomic alignment targets for species specificity, makes it possible to extract valid data from full-sample sequencing results (without subjective targeted enrichment procedures). This approach broadens the potential scope of palaeoepidaemiology both to older, suboptimally preserved samples and to pathogens with difficult intrageneric taxonomy.}, }
@article {pmid31216503, year = {2019}, author = {Xavier, C and Eduardoff, M and Strobl, C and Parson, W}, title = {SD quants-Sensitive detection tetraplex-system for nuclear and mitochondrial DNA quantification and degradation inference.}, journal = {Forensic science international. Genetics}, volume = {42}, number = {}, pages = {39-44}, doi = {10.1016/j.fsigen.2019.06.004}, pmid = {31216503}, issn = {1878-0326}, mesh = {Bone and Bones/chemistry ; Cell Nucleus/*genetics ; DNA/*analysis ; *DNA Degradation, Necrotic ; *DNA Fingerprinting ; DNA, Mitochondrial/*analysis ; Hair/chemistry ; Humans ; Real-Time Polymerase Chain Reaction/*methods ; Tooth/chemistry ; }, abstract = {Measuring the quantity of DNA present in a forensic sample is relevant in a number of ways. First, it informs the analyst about the general DNA content to adjust the volume of DNA extract used for the genotyping assay to the optimal conditions (when possible). Second, quantification values can serve as plausibility checks for the performance of the DNA extraction method used as extraction positive and negative controls demand expected values. Third and relevant to highly compromised specimens, DNA quantification can inform about the degradation state of the DNA extracted from the unknown biological sample and aid the choice of downstream genotyping assays. While there are different, commercial products for the quantification of nuclear DNA available, commercial mitochondrial DNA (mtDNA) quantification systems are rare. Even more so, the simultaneous quantification of nuclear and mtDNA that is of relevance in highly degraded forensic specimens has rarely been described. We present here a novel real-time qPCR based tetraplex system termed SD quants that targets two different-sized mtDNA and a nuclear DNA region and includes an internal positive control to monitor potential inhibition. SD quants was compared to other existing quantification systems and subjected to analysis of severely degraded DNA present in ancient DNA and aged forensic specimens. This study complies with the MIQE (Bustin et al., 2009) guidelines (when applicable).}, }
@article {pmid31216315, year = {2019}, author = {Wren, CD and Burke, A}, title = {Habitat suitability and the genetic structure of human populations during the Last Glacial Maximum (LGM) in Western Europe.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0217996}, pmid = {31216315}, issn = {1932-6203}, mesh = {Archaeology ; *Biological Evolution ; Climate ; DNA, Mitochondrial/*genetics ; Ecosystem ; Europe ; France ; *Genetics, Population ; Haplotypes ; Humans ; Italy ; Paleontology ; Phylogeny ; *Phylogeography ; Population Density ; Refugium ; Sequence Analysis, DNA ; Spain ; }, abstract = {Human populations in Western Europe during the Last Glacial Maximum were geographically constrained to glacial refugia by the severity of the climate and ecological risk factors. In this research we use an agent-based model of human mobility and interaction, based on ethnographic and archaeological data, to explore the impact of ecological risk on human population structure via a reconstructed landscape of habitat suitability. The agent-based model allows us to evaluate the size and location of glacial refugia, the size of the populations occupying them and the degree of genetic relatedness between people occupying these areas. To do this, we model the probability of an agent foraging groups' survival as a function of habitat suitability. The model's simulated &quot;genomes&quot; (composed of regionally specific genetic markers) allow us to track long-term trends of inter-regional interaction and mobility. The results agree with previous archaeological studies situating a large glacial refugium spanning southern France and northeastern Spain, but we expand on those studies by demonstrating that higher rates of population growth in this central refugium led to continuous out-migration and therefore genetic homogeneity across Western Europe, with the possible exception of the Italian peninsula. These results concur with material culture data from known archaeological sites dating to the Last Glacial Maximum and make predictions for future ancient DNA studies.}, }
@article {pmid31216119, year = {2019}, author = {Epp, LS}, title = {A global perspective for biodiversity history with ancient environmental DNA.}, journal = {Molecular ecology}, volume = {28}, number = {10}, pages = {2456-2458}, doi = {10.1111/mec.15118}, pmid = {31216119}, issn = {1365-294X}, mesh = {Animals ; Australia ; Biodiversity ; Climate Change ; Coral Reefs ; DNA, Ancient/*analysis ; *Ecosystem ; Environmental DNA/*genetics ; Geologic Sediments/analysis ; Humans ; }, abstract = {The past centuries have seen tremendous turnovers in species distributions and biodiversity due to anthropogenic impacts on a global scale. The processes are ongoing and mostly not well documented. Long-term records of biotic change can be recovered from sedimentary deposits, but traditional analyses were restricted to organisms that leave behind visible traces and molecular genetic tools were mostly employed on samples that promised good DNA preservation. In this issue of Molecular Ecology, Shaw, Weyrich, Hallegraeff and Cooper (2019) and Gomez Cabrera et al. (2019) present two studies on marine sedimentary records from warm environments, in which they successfully analyze ancient environmental DNA (aeDNA) on a decadal and centennial scale. Notably, the studies were conducted on novel samples with nonoptimal preservation conditions for ancient DNA - historical collections of ship ballast tank sediments from Australia and two coral reef cores spanning up to 750 years (Figure 1) - but yielded a high diversity of taxa. This highlights that aeDNA is a promising tool to globally study biodiversity history on scales of decades to centuries - the timeframe most relevant to human society in the context of both current climate change and direct anthropogenic modifications of the environment.}, }
@article {pmid31209287, year = {2019}, author = {Bradshaw, CJA and Ulm, S and Williams, AN and Bird, MI and Roberts, RG and Jacobs, Z and Laviano, F and Weyrich, LS and Friedrich, T and Norman, K and Saltré, F}, title = {Minimum founding populations for the first peopling of Sahul.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {7}, pages = {1057-1063}, doi = {10.1038/s41559-019-0902-6}, pmid = {31209287}, issn = {2397-334X}, mesh = {*Archaeology ; Demography ; Humans ; }, abstract = {The timing, context and nature of the first people to enter Sahul is still poorly understood owing to a fragmented archaeological record. However, quantifying the plausible demographic context of this founding population is essential to determine how and why the initial peopling of Sahul occurred. We developed a stochastic, age-structured model using demographic rates from hunter-gatherer societies, and relative carrying capacity hindcasted with LOVECLIM's net primary productivity for northern Sahul. We projected these populations to determine the resilience and minimum sizes required to avoid extinction. A census founding population of between 1,300 and 1,550 individuals was necessary to maintain a quasi-extinction threshold of ≲0.1. This minimum founding population could have arrived at a single point in time, or through multiple voyages of ≥130 people over ~700-900 years. This result shows that substantial population amalgamation in Sunda and Wallacea in Marine Isotope Stages 3-4 provided the conditions for the successful, large-scale and probably planned peopling of Sahul.}, }
@article {pmid31196226, year = {2019}, author = {Petrigh, RS and Martínez, JG and Mondini, M and Fugassa, MH}, title = {Ancient parasitic DNA reveals Toxascaris leonina presence in Final Pleistocene of South America.}, journal = {Parasitology}, volume = {146}, number = {10}, pages = {1284-1288}, doi = {10.1017/S0031182019000787}, pmid = {31196226}, issn = {1469-8161}, mesh = {Animals ; Argentina ; DNA, Ancient/*isolation &amp; purification ; DNA, Mitochondrial/genetics/isolation &amp; purification ; Feces/parasitology ; Ovum/cytology ; Puma/*parasitology ; Toxascariasis/*parasitology/*veterinary ; Toxascaris/*genetics/*isolation &amp; purification ; }, abstract = {Parasitological analysis of coprolites has allowed exploring ecological relationships in ancient times. Ancient DNA analysis contributes to the identification of coprolites and their parasites. Pleistocene mammalian carnivore coprolites were recovered from paleontological and archaeological site Peñas de las Trampas 1.1 in the southern Puna of Argentina. With the aim of exploring ancient ecological relationships, parasitological analysis was performed to one of them, dated to 16 573-17 002 calibrated years BP, with 95.4% probability. Parasite eggs attributed to Toxascaris sp. by morphological characters were isolated. DNA of coprolite and eggs was extracted to molecular identification. Ancient mitochondrial DNA analysis confirmed the zoological origin of the coprolite as Puma concolor and that of parasite eggs as Toxascaris leonina. This is the oldest molecular parasite record worldwide, and it supports the presence of this parasite since the Pleistocene in America. These findings have implications for the biogeographic history of parasites and for the natural history of the region.}, }
@article {pmid31184205, year = {2019}, author = {Scheib, CL and Hui, R and D'Atanasio, E and Wohns, AW and Inskip, SA and Rose, A and Cessford, C and O'Connell, TC and Robb, JE and Evans, C and Patten, R and Kivisild, T}, title = {East Anglian early Neolithic monument burial linked to contemporary Megaliths.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {145-149}, pmid = {31184205}, issn = {1464-5033}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; Burial/*history ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; England ; History, Ancient ; Humans ; Male ; Whole Genome Sequencing ; }, abstract = {In the fourth millennium BCE a cultural phenomenon of monumental burial structures spread along the Atlantic façade. Megalithic burials have been targeted for aDNA analyses, but a gap remains in East Anglia, where Neolithic structures were generally earthen or timber. An early Neolithic (3762-3648 cal. BCE) burial monument at the site of Trumpington Meadows, Cambridgeshire, UK, contained the partially articulated remains of at least three individuals. To determine whether this monument fits a pattern present in megalithic burials regarding sex bias, kinship, diet and relationship to modern populations, teeth and ribs were analysed for DNA and carbon and nitrogen isotopic values, respectively. Whole ancient genomes were sequenced from two individuals to a mean genomic coverage of 1.6 and 1.2X and genotypes imputed. Results show that they were brothers from a small population genetically and isotopically similar to previously published British Neolithic individuals, with a level of genome-wide homozygosity consistent with a small island population sourced from continental Europe, but bearing no signs of recent inbreeding. The first Neolithic whole genomes from a monumental burial in East Anglia confirm that this region was connected with the larger pattern of Neolithic megaliths in the British Isles and the Atlantic façade.}, }
@article {pmid31178321, year = {2019}, author = {Delsuc, F and Kuch, M and Gibb, GC and Karpinski, E and Hackenberger, D and Szpak, P and Martínez, JG and Mead, JI and McDonald, HG and MacPhee, RDE and Billet, G and Hautier, L and Poinar, HN}, title = {Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths.}, journal = {Current biology : CB}, volume = {29}, number = {12}, pages = {2031-2042.e6}, doi = {10.1016/j.cub.2019.05.043}, pmid = {31178321}, issn = {1879-0445}, mesh = {Animal Distribution ; Animals ; *Biological Evolution ; DNA, Ancient/*analysis ; *Genome, Mitochondrial ; *Phylogeny ; Sloths/*classification/genetics/physiology ; }, abstract = {Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history.}, }
@article {pmid31171860, year = {2019}, author = {Presslee, S and Slater, GJ and Pujos, F and Forasiepi, AM and Fischer, R and Molloy, K and Mackie, M and Olsen, JV and Kramarz, A and Taglioretti, M and Scaglia, F and Lezcano, M and Lanata, JL and Southon, J and Feranec, R and Bloch, J and Hajduk, A and Martin, FM and Salas Gismondi, R and Reguero, M and de Muizon, C and Greenwood, A and Chait, BT and Penkman, K and Collins, M and MacPhee, RDE}, title = {Palaeoproteomics resolves sloth relationships.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {7}, pages = {1121-1130}, doi = {10.1038/s41559-019-0909-z}, pmid = {31171860}, issn = {2397-334X}, mesh = {Animals ; DNA, Mitochondrial ; Fossils ; Phylogeny ; *Sloths ; }, abstract = {The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.}, }
@article {pmid31168093, year = {2019}, author = {Sikora, M and Pitulko, VV and Sousa, VC and Allentoft, ME and Vinner, L and Rasmussen, S and Margaryan, A and de Barros Damgaard, P and de la Fuente, C and Renaud, G and Yang, MA and Fu, Q and Dupanloup, I and Giampoudakis, K and Nogués-Bravo, D and Rahbek, C and Kroonen, G and Peyrot, M and McColl, H and Vasilyev, SV and Veselovskaya, E and Gerasimova, M and Pavlova, EY and Chasnyk, VG and Nikolskiy, PA and Gromov, AV and Khartanovich, VI and Moiseyev, V and Grebenyuk, PS and Fedorchenko, AY and Lebedintsev, AI and Slobodin, SB and Malyarchuk, BA and Martiniano, R and Meldgaard, M and Arppe, L and Palo, JU and Sundell, T and Mannermaa, K and Putkonen, M and Alexandersen, V and Primeau, C and Baimukhanov, N and Malhi, RS and Sjögren, KG and Kristiansen, K and Wessman, A and Sajantila, A and Lahr, MM and Durbin, R and Nielsen, R and Meltzer, DJ and Excoffier, L and Willerslev, E}, title = {The population history of northeastern Siberia since the Pleistocene.}, journal = {Nature}, volume = {570}, number = {7760}, pages = {182-188}, doi = {10.1038/s41586-019-1279-z}, pmid = {31168093}, issn = {1476-4687}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Asia/ethnology ; DNA, Ancient/analysis ; Europe/ethnology ; Gene Pool ; Genome, Human/*genetics ; Haplotypes ; History, 15th Century ; History, Ancient ; History, Medieval ; Human Migration/*history ; Humans ; Indians, North American ; Male ; Siberia/ethnology ; }, abstract = {Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.}, }
@article {pmid31164419, year = {2019}, author = {Keller, M and Spyrou, MA and Scheib, CL and Neumann, GU and Kröpelin, A and Haas-Gebhard, B and Päffgen, B and Haberstroh, J and Ribera I Lacomba, A and Raynaud, C and Cessford, C and Durand, R and Stadler, P and Nägele, K and Bates, JS and Trautmann, B and Inskip, SA and Peters, J and Robb, JE and Kivisild, T and Castex, D and McCormick, M and Bos, KI and Harbeck, M and Herbig, A and Krause, J}, title = {Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {25}, pages = {12363-12372}, pmid = {31164419}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; 2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Disease Outbreaks/*history ; Europe/epidemiology ; *Genome, Bacterial ; History, Medieval ; Humans ; Plague/epidemiology/history/*microbiology ; Yersinia pestis/*genetics/pathogenicity ; }, abstract = {The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.}, }
@article {pmid31163991, year = {2019}, author = {Santander, C and Montinaro, F and Capelli, C}, title = {Searching for archaic contribution in Africa.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {129-139}, doi = {10.1080/03014460.2019.1624823}, pmid = {31163991}, issn = {1464-5033}, mesh = {Africa ; African Continental Ancestry Group/*genetics ; Animals ; DNA, Ancient/*analysis ; Genome, Human ; Hominidae/*genetics ; Humans ; *Hybridization, Genetic ; }, abstract = {Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence of Homo sapiens. However, once humans dispersed beyond Africa, the history of those who stayed remains vastly under-studied, lacking the proper attention the birthplace of both modern and archaic humans deserves. The sequencing of Neanderthal and Denisovan genomes has elucidated evidence of admixture between archaic and modern humans outside of Africa, but has not aided efforts in answering whether archaic admixture happened within Africa. Objectives: This article reviews the state of research for archaic introgression in African populations and discusses recent insights into this topic. Methods: Gathering published sources and recently released preprints, this review reports on the different methods developed for detecting archaic introgression. Particularly it discusses how relevant these are when implemented on African populations and what findings these studies have shown so far. Results: Methods for detecting archaic introgression have been predominantly developed and implemented on non-African populations. Recent preprints present new methods considering African populations. While a number of studies using these methods suggest archaic introgression in Africa, without an African archaic genome to validate these results, such findings remain as putative archaic introgression. Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent.}, }
@article {pmid31161006, year = {2019}, author = {Ersmark, E and Baryshnikov, G and Higham, T and Argant, A and Castaños, P and Döppes, D and Gasparik, M and Germonpré, M and Lidén, K and Lipecki, G and Marciszak, A and Miller, R and Moreno-García, M and Pacher, M and Robu, M and Rodriguez-Varela, R and Rojo Guerra, M and Sabol, M and Spassov, N and Storå, J and Valdiosera, C and Villaluenga, A and Stewart, JR and Dalén, L}, title = {Genetic turnovers and northern survival during the last glacial maximum in European brown bears.}, journal = {Ecology and evolution}, volume = {9}, number = {10}, pages = {5891-5905}, pmid = {31161006}, issn = {2045-7758}, abstract = {The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.}, }
@article {pmid31147405, year = {2019}, author = {Prendergast, ME and Lipson, M and Sawchuk, EA and Olalde, I and Ogola, CA and Rohland, N and Sirak, KA and Adamski, N and Bernardos, R and Broomandkhoshbacht, N and Callan, K and Culleton, BJ and Eccles, L and Harper, TK and Lawson, AM and Mah, M and Oppenheimer, J and Stewardson, K and Zalzala, F and Ambrose, SH and Ayodo, G and Gates, HL and Gidna, AO and Katongo, M and Kwekason, A and Mabulla, AZP and Mudenda, GS and Ndiema, EK and Nelson, C and Robertshaw, P and Kennett, DJ and Manthi, FK and Reich, D}, title = {Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.}, journal = {Science (New York, N.Y.)}, volume = {365}, number = {6448}, pages = {}, pmid = {31147405}, issn = {1095-9203}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Agriculture/*history ; DNA, Ancient ; *Genome, Human ; History, Ancient ; Human Migration/*history ; Humans ; Kenya ; Occupations/*history ; Tanzania ; }, abstract = {How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.}, }
@article {pmid31137975, year = {2019}, author = {Donoghue, HD}, title = {Tuberculosis and leprosy associated with historical human population movements in Europe and beyond - an overview based on mycobacterial ancient DNA.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {120-128}, doi = {10.1080/03014460.2019.1624822}, pmid = {31137975}, issn = {1464-5033}, mesh = {DNA, Ancient/*analysis ; Europe ; Genotype ; History, 17th Century ; History, 18th Century ; History, Medieval ; Human Migration/*history ; Humans ; Leprosy/*history/microbiology ; Mycobacterium leprae/*genetics ; Mycobacterium tuberculosis/*genetics ; Paleopathology ; Polymerase Chain Reaction ; Tuberculosis/*history/microbiology ; Whole Genome Sequencing ; }, abstract = {Context: Tuberculosis and leprosy are readily recognised in human remains due to their typical palaeopathology. Both Mycobacterium tuberculosis (MTB) and Mycobacterium leprae (ML) are obligate pathogens and have been detected in ancient human populations. Objective: To demonstrate historical tuberculosis and leprosy cases in Europe and beyond using molecular methods, as human populations are associated with different mycobacterial genotypes. Methods: MTB and ML ancient DNA (aDNA) has been detected by DNA amplification using PCR, or by whole genome sequencing. Mycobacterial cell wall lipids also provide specific markers for identification. Results: In 18th century Hungary, the European indigenous MTB genotype 4 strains have been found. However, many individuals were co-infected with up to three MTB sub-genotypes. In 8th-14th century Europe significant differences in ML genotypes were found between northwest Europe compared with central, southern, or eastern Europe. In addition, several co-infections of MTB and ML were detected in historical samples. Conclusion: Both MTB and ML strain types differ between geographically separate populations. This is associated with ancient human migration after an evolutionary bottleneck and clonal expansion. The absence of indigenous leprosy in Europe today may be due to the greater mortality of tuberculosis in individuals who are co-infected with both organisms.}, }
@article {pmid31134682, year = {2019}, author = {Wu, X and Ding, B and Zhang, B and Feng, J and Wang, Y and Ning, C and Wu, H and Zhang, F and Zhang, Q and Li, N and Zhang, Z and Sun, X and Zhang, Q and Li, W and Liu, B and Cui, Y and Gong, L}, title = {Phylogenetic and population structural inference from genomic ancestry maintained in present-day common wheat Chinese landraces.}, journal = {The Plant journal : for cell and molecular biology}, volume = {99}, number = {2}, pages = {201-215}, doi = {10.1111/tpj.14421}, pmid = {31134682}, issn = {1365-313X}, mesh = {China ; DNA, Plant/chemistry ; Gene Frequency ; *Genome, Plant ; Phylogeny ; Seed Dispersal ; Seeds/anatomy &amp; histology/genetics ; Sequence Analysis, RNA ; Triticum/anatomy &amp; histology/*genetics ; }, abstract = {Hexaploid common wheat is one of the most important food crops worldwide. Common wheat domestication began in the Fertile Crescent of the Near East approximately 10 000 years ago and then spread west into Europe and eastward into East Asia and China. However, the possible spreading route into and within China is still unclear. In this study, we successfully extracted DNA from single ancient wheat seeds and sequenced the whole genome of seven ancient samples from Xiaohe and Gumugou cemeteries in Xinjiang, China. Genomic inference and morphological observation confirmed their identity as hexaploid common wheat grown in prehistoric China at least 3200 years before present (BP). Phylogenetic and admixture analyses with RNA-seq data of modern hexaploid wheat cultivars from both China and Western countries demonstrated a close kinship of the ancient wheat to extant common wheat landraces in southwestern China. The highly similar allelic frequencies in modern landraces of the Qinghai-Tibetan plateau with the ancient wheat support the previously suggested southwestern spreading route into highland China. A subsequent dispersal route from the Qinghai-Tibetan plateau margins to the Yangtze valley was proposed in this study. Furthermore, the common wheat populations grown in the Middle and Lower Yangtze valley wheat zones were also proposed to be established by population admixture with the wheat grown in the Upper Yangtze valley. Our study reports ancient common wheat sequences at a genome-wide scale, providing important information on the origin, dispersal, and genetic improvement under cultivation of present-day wheat landraces grown in China.}, }
@article {pmid31124326, year = {2019}, author = {Hong, JH and Oh, CS and Chai, JY and Seo, M and Shin, DH}, title = {Cytochrome C Oxidase Subunit 1, Internal Transcribed Spacer 1, Nicotinamide Adenine Dinucleotide Hydrogen Dehydrogenase Subunits 2 and 5 of Clonorchis sinensis Ancient DNA Retrieved from Joseon Dynasty Mummy Specimens.}, journal = {Journal of Korean medical science}, volume = {34}, number = {20}, pages = {e149}, pmid = {31124326}, issn = {1598-6357}, support = {NRF-2016R1A2B4015669/NRF/National Research Foundation of Korea/Korea ; }, mesh = {Animals ; Clonorchiasis/diagnosis/epidemiology ; Clonorchis sinensis/classification/*genetics ; DNA, Ancient/*chemistry/isolation &amp; purification ; Electron Transport Complex IV/chemistry/classification/*genetics ; Humans ; Mummies/parasitology ; Oxidoreductases/chemistry/classification/*genetics ; Phylogeny ; Protein Subunits/chemistry/classification/genetics ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {We analyzed Clonorchis sinensis ancient DNA (aDNA) acquired from the specimens of the Joseon mummies. The target regions were cytochrome C oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits 2 (NAD2) and 5 (NAD5). The sequences of C. sinensis aDNA was completely or almost identical to modern C. sinensis sequences in GenBank. We also found that ITS1, NAD2 and NAD5 could be good markers for molecular diagnosis between C. sinensis and the other trematode parasite species. The current result could improve our knowledge about genetic history of C. sinensis.}, }
@article {pmid31123709, year = {2019}, author = {Kashuba, N and Kırdök, E and Damlien, H and Manninen, MA and Nordqvist, B and Persson, P and Götherström, A}, title = {Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {185}, pmid = {31123709}, issn = {2399-3642}, mesh = {Anthropology, Cultural/history ; Betula/chemistry ; Chewing Gum/history ; DNA, Ancient/*isolation &amp; purification ; DNA, Mitochondrial/genetics/history ; Genetics, Population/history ; History, Ancient ; Human Migration/history ; Humans ; Mastic Resin/history ; Resins, Plant/history ; Scandinavian and Nordic Countries ; }, abstract = {Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations.}, }
@article {pmid31116227, year = {2019}, author = {Hong, JH and Oh, CS and Seo, M and Shin, DH}, title = {Analysis of COI and ITS2 regions of DNA obtained from Paragonimus westermani eggs in ancient coprolites on Joseon dynasty mummies.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {114}, number = {}, pages = {e180595}, pmid = {31116227}, issn = {1678-8060}, mesh = {Animals ; Asia ; DNA, Helminth/*genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Feces/*parasitology ; Humans ; Mummies/*parasitology ; Paleodontology ; Paragonimus westermani/genetics/*isolation &amp; purification ; Parasite Egg Count ; Phylogeny ; }, abstract = {The genetic information of ancient Paragonimus westermani, the oriental lung fluke infecting over 20 million people worldwide, has not been thoroughly investigated thus far. We analysed genetic markers (COI and ITS2) of P. westermani from coprolite specimens (n = 6) obtained from 15th to 18th century Korean mummies. Our results indicated that all P. westermani sequences were generally distinct from the other species of the genus Paragonimus. The sequences were clustered into three groups: Group I for East Asia; Group II for South and Southeast Asia; and Group III for India and Sri Lanka. In this study, we found that ancient P. westermani sequences in Korea belong to Group I, adding invaluable information to the existing knowledge of Paragonimus paleogenetics.}, }
@article {pmid31113254, year = {2019}, author = {Ham, E and Underdown, SJ and Houldcroft, CJ}, title = {The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {99-108}, doi = {10.1080/03014460.2019.1622038}, pmid = {31113254}, issn = {1464-5033}, mesh = {Alleles ; Animals ; Europe ; European Continental Ancestry Group ; Gene Frequency ; Humans ; Longevity/*genetics ; Mothers/*statistics &amp; numerical data ; Neanderthals/genetics ; P-Selectin/*genetics/metabolism ; Physical Abuse/*statistics &amp; numerical data ; Polymorphism, Single Nucleotide/*genetics ; *Selection, Genetic ; Tanzania ; Thrombophilia/genetics ; }, abstract = {Background: Simonti et al. reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious, but can also help prevent blood loss. Aim: To investigate two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth. Subjects and methods: Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture. Results: National census data indicates a positive correlation between the presence of rs3917862 and decreased maternal mortality ratios. When the maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862. Conclusion: These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.}, }
@article {pmid31109769, year = {2019}, author = {Perry, GH and Makarewicz, CA}, title = {Horse Paleogenomes and Human-Animal Interactions in Prehistory.}, journal = {Trends in genetics : TIG}, volume = {35}, number = {7}, pages = {473-475}, doi = {10.1016/j.tig.2019.04.006}, pmid = {31109769}, issn = {0168-9525}, mesh = {Animals ; *Genome ; Horses ; Humans ; }, abstract = {A new analysis of paleogenomic data from 278 ancient horses (Fages et al. Cellhttp://doi.org/10.1016/j.cell.2019.03.049) finds that this animal - crucially important to many ancient and contemporary human societies for subsistence, transportation, conflict, and more - was domesticated in at least two different regions, but with the geographic and cultural origins of the modern domestic horse lineage remaining unknown. By tracing ancient horse population movements and inferring the spatiotemporal trajectories of phenotypic adaptations, this study provides fresh perspectives on past human group interactions and activities.}, }
@article {pmid31095634, year = {2019}, author = {Yuan, JX and Hou, XD and Barlow, A and Preick, M and Taron, UH and Alberti, F and Basler, N and Deng, T and Lai, XL and Hofreiter, M and Sheng, GL}, title = {Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216883}, pmid = {31095634}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; *DNA, Ancient ; *Equidae/classification/genetics ; *Genome, Mitochondrial ; *Haplotypes ; *Phylogeny ; }, abstract = {The extant diversity of horses (family Equidae) represents a small fraction of that occurring over their evolutionary history. One such lost lineage is the subgenus Sussemionus, which is thought to have become extinct during the Middle Pleistocene. However, recent molecular studies and morphological analysis have revealed that one of their representatives, E. ovodovi, did exist in Siberia during the Late Pleistocene. Fossil materials of E. ovodovi have thus far only been found in Russia. In this study, we extracted DNA from three equid fossil specimens excavated from northeastern China dated at 12,770-12,596, 29,525-28,887 and 40,201-38,848 cal. yBP, respectively, and retrieved three near-complete mitochondrial genomes from the specimens. Phylogenetic analyses cluster the Chinese haplotypes together with previously published Russian E. ovodovi, strongly supporting the assignment of these samples to this taxon. The molecular identification of E. ovodovi in northeastern China extends the known geographical range of this fossil species by several thousand kilometers to the east. The estimated coalescence time of all E. ovodovi haplotypes is approximately 199 Kya, with the Chinese haplotypes coalescing approximately 130 Kya. With a radiocarbon age of 12,770-12,596 cal. yBP, the youngest sample in this study represents the first E. ovodovi sample dating to the terminal Pleistocene, moving the extinction date of this species forwards considerably compared to previously documented fossils. Overall, comparison of our three mitochondrial genomes with the two published ones suggests a genetic diversity similar to several extant species of the genus Equus.}, }
@article {pmid31092597, year = {2019}, author = {Bennett, RJ and Baker, KS}, title = {Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes.}, journal = {Journal of clinical microbiology}, volume = {57}, number = {8}, pages = {}, pmid = {31092597}, issn = {1098-660X}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 106690/A/14/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/pathogenicity ; DNA, Ancient/*analysis ; Drug Resistance, Multiple, Bacterial/genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Bacterial ; Humans ; Mycobacterium leprae/genetics/pathogenicity ; Mycobacterium tuberculosis/genetics/pathogenicity ; Phylogeny ; *Sequence Analysis, DNA ; Yersinia pestis/genetics/pathogenicity ; }, abstract = {Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens.}, }
@article {pmid31088861, year = {2019}, author = {Renaud, G and Hanghøj, K and Korneliussen, TS and Willerslev, E and Orlando, L}, title = {Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.}, journal = {Genetics}, volume = {212}, number = {3}, pages = {587-614}, pmid = {31088861}, issn = {1943-2631}, mesh = {Animals ; Bayes Theorem ; *DNA, Ancient ; Genotyping Techniques/*methods/standards ; *Heterozygote ; *Homozygote ; Humans ; Markov Chains ; }, abstract = {Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6× and down to 7-8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.}, }
@article {pmid31080507, year = {2019}, author = {Upadhyay, M and Bortoluzzi, C and Barbato, M and Ajmone-Marsan, P and Colli, L and Ginja, C and Sonstegard, TS and Bosse, M and Lenstra, JA and Groenen, MAM and Crooijmans, RPMA}, title = {Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs.}, journal = {Evolutionary applications}, volume = {12}, number = {5}, pages = {951-963}, pmid = {31080507}, issn = {1752-4571}, abstract = {The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non-European cattle ancestry in these cattle breeds.}, }
@article {pmid31080083, year = {2019}, author = {Saag, L and Laneman, M and Varul, L and Malve, M and Valk, H and Razzak, MA and Shirobokov, IG and Khartanovich, VI and Mikhaylova, ER and Kushniarevich, A and Scheib, CL and Solnik, A and Reisberg, T and Parik, J and Saag, L and Metspalu, E and Rootsi, S and Montinaro, F and Remm, M and Mägi, R and D'Atanasio, E and Crema, ER and Díez-Del-Molino, D and Thomas, MG and Kriiska, A and Kivisild, T and Villems, R and Lang, V and Metspalu, M and Tambets, K}, title = {The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East.}, journal = {Current biology : CB}, volume = {29}, number = {10}, pages = {1701-1711.e16}, pmid = {31080083}, issn = {1879-0445}, support = {261213/ERC_/European Research Council/International ; 100719/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaeology ; DNA, Ancient/*analysis ; Estonia ; Female ; *Gene Flow ; History, Ancient ; History, Medieval ; *Human Migration ; Humans ; Male ; *Phenotype ; }, abstract = {In this study, we compare the genetic ancestry of individuals from two as yet genetically unstudied cultural traditions in Estonia in the context of available modern and ancient datasets: 15 from the Late Bronze Age stone-cist graves (1200-400 BC) (EstBA) and 6 from the Pre-Roman Iron Age tarand cemeteries (800/500 BC-50 AD) (EstIA). We also included 5 Pre-Roman to Roman Iron Age Ingrian (500 BC-450 AD) (IngIA) and 7 Middle Age Estonian (1200-1600 AD) (EstMA) individuals to build a dataset for studying the demographic history of the northern parts of the Eastern Baltic from the earliest layer of Mesolithic to modern times. Our findings are consistent with EstBA receiving gene flow from regions with strong Western hunter-gatherer (WHG) affinities and EstIA from populations related to modern Siberians. The latter inference is in accordance with Y chromosome (chrY) distributions in present day populations of the Eastern Baltic, as well as patterns of autosomal variation in the majority of the westernmost Uralic speakers [1-5]. This ancestry reached the coasts of the Baltic Sea no later than the mid-first millennium BC; i.e., in the same time window as the diversification of west Uralic (Finnic) languages [6]. Furthermore, phenotypic traits often associated with modern Northern Europeans, like light eyes, hair, and skin, as well as lactose tolerance, can be traced back to the Bronze Age in the Eastern Baltic. VIDEO ABSTRACT.}, }
@article {pmid31080081, year = {2019}, author = {Sheng, GL and Basler, N and Ji, XP and Paijmans, JLA and Alberti, F and Preick, M and Hartmann, S and Westbury, MV and Yuan, JX and Jablonski, NG and Xenikoudakis, G and Hou, XD and Xiao, B and Liu, JH and Hofreiter, M and Lai, XL and Barlow, A}, title = {Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations.}, journal = {Current biology : CB}, volume = {29}, number = {10}, pages = {1695-1700.e6}, doi = {10.1016/j.cub.2019.04.021}, pmid = {31080081}, issn = {1879-0445}, mesh = {Animals ; China ; DNA, Ancient/*analysis ; Endangered Species ; *Genetic Variation ; *Genome ; Male ; Ursidae/*genetics ; }, abstract = {Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an ∼5,000-year-old giant panda from Jiangdongshan, Tengchong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions.}, }
@article {pmid31075917, year = {2019}, author = {Merheb, M and Matar, R and Hodeify, R and Siddiqui, SS and Vazhappilly, CG and Marton, J and Azharuddin, S and Al Zouabi, H}, title = {Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases.}, journal = {Cells}, volume = {8}, number = {5}, pages = {}, pmid = {31075917}, issn = {2073-4409}, mesh = {*Civilization ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; *Domestication ; History, 18th Century ; Homicide/*history ; Humans ; *Music ; }, abstract = {Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases-and profiling, in certain conditions-especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven's grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.}, }
@article {pmid31074010, year = {2019}, author = {Maurer-Alcalá, XX and Nowacki, M}, title = {Evolutionary origins and impacts of genome architecture in ciliates.}, journal = {Annals of the New York Academy of Sciences}, volume = {1447}, number = {1}, pages = {110-118}, pmid = {31074010}, issn = {1749-6632}, support = {//NCCR RNA &amp; Disease/International ; G-EDIT//H2020 European Research Council/International ; }, mesh = {Animals ; Ciliophora/*genetics ; Epigenesis, Genetic/*genetics ; *Evolution, Molecular ; Humans ; }, abstract = {Genome architecture is well diversified among eukaryotes in terms of size and content, with many being radically shaped by ancient and ongoing genome conflicts with transposable elements (e.g., the large transposon-rich genomes common among plants). In ciliates, a group of microbial eukaryotes with distinct somatic and germ-line genomes present in a single cell, the consequences of these genome conflicts are most apparent in their developmentally programmed genome rearrangements. This complicated developmental phenomenon has largely overshadowed and outpaced our understanding of how germ-line and somatic genome architectures have influenced the evolutionary dynamism and potential in these taxa. In our review, we highlight three central concepts: how the evolution of atypical ciliate germ-line genome architectures is linked to ancient genome conflicts; how the complex, epigenetically guided transformation of germline to soma during development can generate widespread genetic variation; and how these features, coupled with their unusual life cycle, have increased the rate of molecular evolution linked to genome architecture in these taxa.}, }
@article {pmid31061125, year = {2019}, author = {Schroeder, H and Margaryan, A and Szmyt, M and Theulot, B and Włodarczak, P and Rasmussen, S and Gopalakrishnan, S and Szczepanek, A and Konopka, T and Jensen, TZT and Witkowska, B and Wilk, S and Przybyła, MM and Pospieszny, Ł and Sjögren, KG and Belka, Z and Olsen, J and Kristiansen, K and Willerslev, E and Frei, KM and Sikora, M and Johannsen, NN and Allentoft, ME}, title = {Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {22}, pages = {10705-10710}, pmid = {31061125}, issn = {1091-6490}, mesh = {Adolescent ; Adult ; Archaeology ; Burial/*history ; Child ; Child, Preschool ; DNA, Ancient/*analysis ; Female ; History, Ancient ; Human Migration ; Humans ; Infant ; Male ; Middle Aged ; Pedigree ; Poland ; Violence/*history ; Young Adult ; }, abstract = {The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300-2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community.}, }
@article {pmid31056281, year = {2019}, author = {Fages, A and Hanghøj, K and Khan, N and Gaunitz, C and Seguin-Orlando, A and Leonardi, M and McCrory Constantz, C and Gamba, C and Al-Rasheid, KAS and Albizuri, S and Alfarhan, AH and Allentoft, M and Alquraishi, S and Anthony, D and Baimukhanov, N and Barrett, JH and Bayarsaikhan, J and Benecke, N and Bernáldez-Sánchez, E and Berrocal-Rangel, L and Biglari, F and Boessenkool, S and Boldgiv, B and Brem, G and Brown, D and Burger, J and Crubézy, E and Daugnora, L and Davoudi, H and de Barros Damgaard, P and de Los Ángeles de Chorro Y de Villa-Ceballos, M and Deschler-Erb, S and Detry, C and Dill, N and do Mar Oom, M and Dohr, A and Ellingvåg, S and Erdenebaatar, D and Fathi, H and Felkel, S and Fernández-Rodríguez, C and García-Viñas, E and Germonpré, M and Granado, JD and Hallsson, JH and Hemmer, H and Hofreiter, M and Kasparov, A and Khasanov, M and Khazaeli, R and Kosintsev, P and Kristiansen, K and Kubatbek, T and Kuderna, L and Kuznetsov, P and Laleh, H and Leonard, JA and Lhuillier, J and Liesau von Lettow-Vorbeck, C and Logvin, A and Lõugas, L and Ludwig, A and Luis, C and Arruda, AM and Marques-Bonet, T and Matoso Silva, R and Merz, V and Mijiddorj, E and Miller, BK and Monchalov, O and Mohaseb, FA and Morales, A and Nieto-Espinet, A and Nistelberger, H and Onar, V and Pálsdóttir, AH and Pitulko, V and Pitskhelauri, K and Pruvost, M and Rajic Sikanjic, P and Rapan Papeša, A and Roslyakova, N and Sardari, A and Sauer, E and Schafberg, R and Scheu, A and Schibler, J and Schlumbaum, A and Serrand, N and Serres-Armero, A and Shapiro, B and Sheikhi Seno, S and Shevnina, I and Shidrang, S and Southon, J and Star, B and Sykes, N and Taheri, K and Taylor, W and Teegen, WR and Trbojević Vukičević, T and Trixl, S and Tumen, D and Undrakhbold, S and Usmanova, E and Vahdati, A and Valenzuela-Lamas, S and Viegas, C and Wallner, B and Weinstock, J and Zaibert, V and Clavel, B and Lepetz, S and Mashkour, M and Helgason, A and Stefánsson, K and Barrey, E and Willerslev, E and Outram, AK and Librado, P and Orlando, L}, title = {Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.}, journal = {Cell}, volume = {177}, number = {6}, pages = {1419-1435.e31}, pmid = {31056281}, issn = {1097-4172}, support = {U01 MH106874/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Asia ; Biological Evolution ; Breeding/history ; DNA, Ancient/analysis ; Domestication ; Equidae/genetics ; Europe ; Female ; Genetic Variation/genetics ; Genome/genetics ; History, Ancient ; Horses/*genetics ; Male ; Phylogeny ; }, abstract = {Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN &quot;speed gene,&quot; only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.}, }
@article {pmid31040238, year = {2019}, author = {Aouizerat, T and Gutman, I and Paz, Y and Maeir, AM and Gadot, Y and Gelman, D and Szitenberg, A and Drori, E and Pinkus, A and Schoemann, M and Kaplan, R and Ben-Gedalya, T and Coppenhagen-Glazer, S and Reich, E and Saragovi, A and Lipschits, O and Klutstein, M and Hazan, R}, title = {Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, pmid = {31040238}, issn = {2150-7511}, mesh = {Archaeology/*methods ; Fossils/*microbiology ; Genotype ; Geologic Sediments/*microbiology ; Microbiological Techniques/*methods ; Yeasts/*isolation &amp; purification ; }, abstract = {Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.IMPORTANCE So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms-yeast in this case-from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products.}, }
@article {pmid31036834, year = {2019}, author = {Stahlschmidt, MC and Collin, TC and Fernandes, DM and Bar-Oz, G and Belfer-Cohen, A and Gao, Z and Jakeli, N and Matskevich, Z and Meshveliani, T and Pritchard, JK and McDermott, F and Pinhasi, R}, title = {Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6628}, doi = {10.1038/s41598-019-43147-0}, pmid = {31036834}, issn = {2045-2322}, mesh = {Animals ; *DNA, Ancient ; DNA, Plant/*genetics ; Georgia ; Mammals/*genetics ; Paleontology ; }, abstract = {Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.}, }
@article {pmid31036632, year = {2019}, author = {Shaw, B and Burrell, CL and Green, D and Navarro-Martinez, A and Scott, D and Daroszewska, A and van 't Hof, R and Smith, L and Hargrave, F and Mistry, S and Bottrill, A and Kessler, BM and Fischer, R and Singh, A and Dalmay, T and Fraser, WD and Henneberger, K and King, T and Gonzalez, S and Layfield, R}, title = {Molecular insights into an ancient form of Paget's disease of bone.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {21}, pages = {10463-10472}, pmid = {31036632}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/P020941/1/MRC_/Medical Research Council/United Kingdom ; 107720/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bone and Bones/*metabolism/pathology ; History, Medieval ; Humans ; MicroRNAs/metabolism ; Osteitis Deformans/complications/*metabolism/pathology ; Osteosarcoma/etiology/metabolism ; Paleopathology ; *Proteome ; Sequence Analysis, DNA ; Sequestosome-1 Protein/chemistry/*metabolism ; }, abstract = {Paget's disease of bone (PDB) is a chronic skeletal disorder that can affect one or several bones in individuals older than 55 y of age. PDB-like changes have been reported in archaeological remains as old as Roman, although accurate diagnosis and natural history of the disease is lacking. Six skeletons from a collection of 130 excavated at Norton Priory in the North West of England, which dates to medieval times, show atypical and extensive pathological changes resembling contemporary PDB affecting as many as 75% of individual skeletons. Disease prevalence in the remaining collection is high, at least 16% of adults, with age at death estimations as low as 35 y. Despite these atypical features, paleoproteomic analysis identified sequestosome 1 (SQSTM1) or p62, a protein central to the pathological milieu of PDB, as one of the few noncollagenous human sequences preserved in skeletal samples. Targeted proteomic analysis detected >60% of the ancient p62 primary sequence, with Western blotting indicating p62 abnormalities, including in dentition. Direct sequencing of ancient DNA excluded contemporary PDB-associated SQSTM1 mutations. Our observations indicate that the ancient p62 protein is likely modified within its C-terminal ubiquitin-associated domain. Ancient miRNAs were remarkably preserved in an osteosarcoma from a skeleton with extensive disease, with miR-16 expression consistent with that reported in contemporary PDB-associated bone tumors. Our work displays the use of proteomics to inform diagnosis of ancient diseases such as atypical PDB, which has unusual features presumably potentiated by yet-unidentified environmental or genetic factors.}, }
@article {pmid31013797, year = {2019}, author = {Santiago-Rodriguez, TM and Fornaciari, A and Fornaciari, G and Luciani, S and Marota, I and Vercellotti, G and Toranzos, GA and Giuffra, V and Cano, RJ}, title = {Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries.}, journal = {Genes}, volume = {10}, number = {4}, pages = {}, pmid = {31013797}, issn = {2073-4425}, mesh = {Adult ; Archaeology ; Bacteria/*classification/genetics/isolation &amp; purification ; Dental Calculus/history/*microbiology ; Feces/microbiology ; Female ; High-Throughput Nucleotide Sequencing/*methods ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, Medieval ; Humans ; Italy ; Male ; Microbiota ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA/methods ; Symbiosis ; Young Adult ; }, abstract = {The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), with differences in socioeconomic status, time period, burial type, and sex. Samples dating from the Middle Ages (11th century) to the Industrial Revolution era (19th century) were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Consistent with previous studies, individuals from Badia Pozzeveri possessed commensal oral bacteria that resembled modern oral microbiomes. These results suggest that members of the oral microbiome are ubiquitous despite differences in geographical regions, time period, sex, and socioeconomic status. The presence of fecal bacteria could be in agreement with poor hygiene practices, consistent with the time period. Respiratory tract, nosocomial, and other rare pathogens detected in the dental calculus samples are intriguing and could suggest subject-specific comorbidities that could be reflected in the oral microbiome.}, }
@article {pmid31006515, year = {2019}, author = {Haber, M and Doumet-Serhal, C and Scheib, CL and Xue, Y and Mikulski, R and Martiniano, R and Fischer-Genz, B and Schutkowski, H and Kivisild, T and Tyler-Smith, C}, title = {A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences.}, journal = {American journal of human genetics}, volume = {104}, number = {5}, pages = {977-984}, pmid = {31006515}, issn = {1537-6605}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/analysis/genetics ; Ethnic Groups/*genetics/*history ; European Continental Ancestry Group/*genetics ; Female ; *Gene Flow ; *Genetics, Population ; *Genome, Human ; History, Ancient ; Humans ; Lebanon/ethnology ; Male ; }, abstract = {During the medieval period, hundreds of thousands of Europeans migrated to the Near East to take part in the Crusades, and many of them settled in the newly established Christian states along the Eastern Mediterranean coast. Here, we present a genetic snapshot of these events and their aftermath by sequencing the whole genomes of 13 individuals who lived in what is today known as Lebanon between the 3rd and 13th centuries CE. These include nine individuals from the &quot;Crusaders' pit&quot; in Sidon, a mass burial in South Lebanon identified from the archaeology as the grave of Crusaders killed during a battle in the 13th century CE. We show that all of the Crusaders' pit individuals were males; some were Western Europeans from diverse origins, some were locals (genetically indistinguishable from present-day Lebanese), and two individuals were a mixture of European and Near Eastern ancestries, providing direct evidence that the Crusaders admixed with the local population. However, these mixtures appear to have had limited genetic consequences since signals of admixture with Europeans are not significant in any Lebanese group today-in particular, Lebanese Christians are today genetically similar to local people who lived during the Roman period which preceded the Crusades by more than four centuries.}, }
@article {pmid31004175, year = {2019}, author = {Membrebe, JV and Suchard, MA and Rambaut, A and Baele, G and Lemey, P}, title = {Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates.}, journal = {Molecular biology and evolution}, volume = {36}, number = {8}, pages = {1793-1803}, pmid = {31004175}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI107034/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; *Evolution, Molecular ; *Genetic Techniques ; Mammoths/*genetics ; Time Factors ; Viruses/*genetics ; }, abstract = {Many factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.}, }
@article {pmid31004132, year = {2019}, author = {Hanghøj, K and Renaud, G and Albrechtsen, A and Orlando, L}, title = {DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, pmid = {31004132}, issn = {2047-217X}, mesh = {Algorithms ; Autopsy ; *Computational Biology/methods ; CpG Islands ; DNA Damage ; *DNA Methylation ; Epigenomics/*methods ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing ; Humans ; *Software ; }, abstract = {BACKGROUND: Recent computational advances in ancient DNA research have opened access to the detection of ancient DNA methylation footprints at the genome-wide scale. The most commonly used approach infers the methylation state of a given genomic region on the basis of the amount of nucleotide mis-incorporations observed at CpG dinucleotide sites. However, this approach overlooks a number of confounding factors, including the presence of sequencing errors and true variants. The scale and distribution of the inferred methylation measurements are also variable across samples, precluding direct comparisons.<br><br>FINDINGS: Here, we present DamMet, an open-source software program retrieving maximum likelihood estimates of regional CpG methylation levels from ancient DNA sequencing data. It builds on a novel statistical model of post-mortem DNA damage for dinucleotides, accounting for sequencing errors, genotypes, and differential post-mortem cytosine deamination rates at both methylated and unmethylated sites. To validate DamMet, we extended gargammel, a sequence simulator for ancient DNA data, by introducing methylation-dependent features of post-mortem DNA decay. This new simulator provides direct validation of DamMet predictions. Additionally, the methylation levels inferred by DamMet were found to be correlated to those inferred by epiPALEOMIX and both on par and directly comparable to those measured from whole-genome bisulphite sequencing experiments of fresh tissues.<br><br>CONCLUSIONS: DamMet provides genuine estimates for local DNA methylation levels in ancient individual genomes. The returned estimates are directly cross-sample comparable, and the software is available as an open-source C++ program hosted at https://gitlab.com/KHanghoj/DamMet along with a manual and tutorial.}, }
@article {pmid30994442, year = {2019}, author = {Meffray, A and Perrin, M and Richier, A and Schmitt, A and Ardagna, Y and Biagini, P}, title = {Molecular detection of Treponema pallidum subspecies pallidum in 150-year-old foetal remains, southeastern France.}, journal = {Journal of medical microbiology}, volume = {68}, number = {5}, pages = {761-769}, doi = {10.1099/jmm.0.000978}, pmid = {30994442}, issn = {1473-5644}, mesh = {Archaeology ; Cemeteries ; DNA, Ancient/*isolation &amp; purification ; Fetus/microbiology ; France ; History, 19th Century ; Humans ; Infant ; Mycobacterium tuberculosis/genetics ; Plasmodium falciparum/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Syphilis, Congenital/history/*microbiology ; Treponema pallidum/classification/*isolation &amp; purification ; }, abstract = {PURPOSE: Syphilis, caused by Treponema pallidum subspecies pallidum , is considered as an old disease affecting humans; traces of such infections, including congenital syphilis, are potentially identifiable in archaeological samples. The aim of this research was to perform macroscopic and molecular investigations of T. pallidum on six infant remains, buried between 1837 and 1867, from the cemetery of 'Les Crottes' in Marseille city (southeastern France).<br><br>METHODOLOGY: Pathological analysis of bones from individuals, aged from the twenty-ninth week of amenorrhea to 4-9 months, was performed. Samples served also as a source of ancient DNA (aDNA) for PCR-based molecular investigations targeting T. pallidum DNA; all samples were also tested for Mycobacterium tuberculosis and Plasmodium falciparum DNA. Sequences characterized were cloned and sequenced, and compared to those available in databases.Results/Key findings. All samples tested displayed widespread osteoporotic lesions across the skeleton possibly related to some metabolic or infectious disorders. Subsequent molecular analysis revealed that one individual, SP332 (unborn, 29 amenorrhea weeks, inhumation date 1864-1866), exhibited positive signals for the five T. pallidum amplification systems tested; sequence analysis provided strong evidence for the effective detection of T. pallidum subspecies pallidum DNA.<br><br>CONCLUSIONS: Individual SP332 is the first PCR-confirmed palaeopathological case of syphilis identified in France, and the youngest specimen ever to be diagnosed with certainty for congenital syphilis. Future research aimed at better characterizing this 150-year-old treponeme genome and exploring new archaelogical cases of syphilis in the very young should contribute to a better comprehension of the disease's history.}, }
@article {pmid30992587, year = {2019}, author = {Guglielmi, G}, title = {Facing up to injustice in genome science.}, journal = {Nature}, volume = {568}, number = {7752}, pages = {290-293}, doi = {10.1038/d41586-019-01166-x}, pmid = {30992587}, issn = {1476-4687}, mesh = {DNA, Ancient/analysis ; Female ; Genomics/*ethics ; Humans ; Indians, North American/genetics ; Minority Groups/psychology ; Population Groups/*genetics/psychology ; Pregnancy ; *Research Design ; Research Personnel/*ethics/psychology ; *Social Marginalization/psychology ; }, }
@article {pmid30992585, year = {2019}, author = {Phillips, N}, title = {Indigenous groups look to ancient DNA to bring their ancestors home.}, journal = {Nature}, volume = {568}, number = {7752}, pages = {294-297}, doi = {10.1038/d41586-019-01167-w}, pmid = {30992585}, issn = {1476-4687}, mesh = {Archaeology ; *Body Remains ; *DNA, Ancient ; DNA, Mitochondrial ; Humans ; }, }
@article {pmid30988490, year = {2019}, author = {Brace, S and Diekmann, Y and Booth, TJ and van Dorp, L and Faltyskova, Z and Rohland, N and Mallick, S and Olalde, I and Ferry, M and Michel, M and Oppenheimer, J and Broomandkhoshbacht, N and Stewardson, K and Martiniano, R and Walsh, S and Kayser, M and Charlton, S and Hellenthal, G and Armit, I and Schulting, R and Craig, OE and Sheridan, A and Parker Pearson, M and Stringer, C and Reich, D and Thomas, MG and Barnes, I}, title = {Ancient genomes indicate population replacement in Early Neolithic Britain.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {5}, pages = {765-771}, doi = {10.1038/s41559-019-0871-9}, pmid = {30988490}, issn = {2397-334X}, support = {100713//Wellcome Trust/United Kingdom ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA, Ancient ; Europe ; *Genome ; Humans ; Population Dynamics ; United Kingdom ; }, abstract = {The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.}, }
@article {pmid30980085, year = {2019}, author = {Kutanan, W and Kampuansai, J and Srikummool, M and Brunelli, A and Ghirotto, S and Arias, L and Macholdt, E and Hübner, A and Schröder, R and Stoneking, M}, title = {Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations.}, journal = {Molecular biology and evolution}, volume = {36}, number = {7}, pages = {1490-1506}, pmid = {30980085}, issn = {1537-1719}, mesh = {Chromosomes, Human, Y/*genetics ; Demography ; *Family Characteristics ; Female ; Genetic Variation ; *Genome, Mitochondrial ; Human Migration ; Humans ; Language ; Laos ; Male ; Thailand ; }, abstract = {The human demographic history of Mainland Southeast Asia (MSEA) has not been well studied; in particular, there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major Mainland Southeast Asia families: Austroasiatic, Tai-Kadai, and Sino-Tibetan. Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* [O-M95*] and O2a* [O-M324*]) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyze complete mitochondrial DNA genome sequences published previously from the same groups and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of postmarital residence pattern on genetic diversity in patrilocal versus matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 ka), with two later major male-specific expansions during the Neolithic period (∼4-5 ka) and the Bronze/Iron Age (∼2.0-2.5 ka). These two later expansions are characteristic of the modern Austroasiatic and Tai-Kadai groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion, and cultural diffusion) of major Thai groups and find different results from mitochondrial DNA simulations, supporting contrasting male and female genetic histories.}, }
@article {pmid30977781, year = {2019}, author = {Oliva, A and Pulicani, S and Lefort, V and Bréhélin, L and Gascuel, O and Guindon, S}, title = {Accounting for ambiguity in ancestral sequence reconstruction.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {21}, pages = {4290-4297}, doi = {10.1093/bioinformatics/btz249}, pmid = {30977781}, issn = {1367-4811}, mesh = {Amino Acid Sequence ; Biometry ; Evolution, Molecular ; Likelihood Functions ; Phylogeny ; *Sequence Analysis ; }, abstract = {MOTIVATION: The reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve our understanding of molecular evolution. Various statistical criteria defined in a phylogenetic framework can be used to infer nucleotide, amino-acid or codon states at internal nodes of the tree, for every position along the sequence. These criteria generally select the state that maximizes (or minimizes) a given criterion. Although it is perfectly sensible from a statistical perspective, that strategy fails to convey useful information about the level of uncertainty associated to the inference.<br><br>RESULTS: The present study introduces a new criterion for ancestral sequence reconstruction, the minimum posterior expected error (MPEE), that selects a single state whenever the signal conveyed by the data is strong, and a combination of multiple states otherwise. We also assess the performance of a criterion based on the Brier scoring scheme which, like MPEE, does not rely on any tuning parameters. The precision and accuracy of several other criteria that involve arbitrarily set tuning parameters are also evaluated. Large scale simulations demonstrate the benefits of using the MPEE and Brier-based criteria with a substantial increase in the accuracy of the inference of past sequences compared to the standard approach and realistic compromises on the precision of the solutions returned.<br><br>The software package PhyML (https://github.com/stephaneguindon/phyml) provides an implementation of the Maximum A Posteriori (MAP) and MPEE criteria for reconstructing ancestral nucleotide and amino-acid sequences.}, }
@article {pmid30972043, year = {2019}, author = {Mills, JG and Brookes, JD and Gellie, NJC and Liddicoat, C and Lowe, AJ and Sydnor, HR and Thomas, T and Weinstein, P and Weyrich, LS and Breed, MF}, title = {Relating Urban Biodiversity to Human Health With the 'Holobiont' Concept.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {550}, pmid = {30972043}, issn = {1664-302X}, abstract = {A relatively unaccounted ecosystem service from biodiversity is the benefit to human health via symbiotic microbiota from our environment. This benefit occurs because humans evolved alongside microbes and have been constantly exposed to diverse microbiota. Plants and animals, including humans, are organised as a host with symbiotic microbiota, whose collective genome and life history form a single holobiont. As such, there are interdependencies between biodiversity, holobionts, and public health which lead us to argue that human health outcomes could be improved by increasing contact with biodiversity in an urban context. We propose that humans, like all holobionts, likely require a diverse microbial habitat to appropriate resources for living healthy, long lives. We discuss how industrial urbanisation likely disrupts the symbiosis between microbiota and their hosts, leading to negative health outcomes. The industrialised urban habitat is low in macro and microbial biodiversity and discourages contact with beneficial environmental microbiota. These habitat factors, alongside diet, antibiotics, and others, are associated with the epidemic of non-communicable diseases in these societies. We suggest that restoration of urban microbial biodiversity and micro-ecological processes through microbiome rewilding can benefit holobiont health and aid in treating the urban non-communicable disease epidemic. Further, we identify research gaps and some solutions to economic and strategic hurdles in applying microbiome rewilding into daily urban life.}, }
@article {pmid30964548, year = {2019}, author = {Klunk, J and Duggan, AT and Redfern, R and Gamble, J and Boldsen, JL and Golding, GB and Walter, BS and Eaton, K and Stangroom, J and Rouillard, JM and Devault, A and DeWitte, SN and Poinar, HN}, title = {Genetic resiliency and the Black Death: No apparent loss of mitogenomic diversity due to the Black Death in medieval London and Denmark.}, journal = {American journal of physical anthropology}, volume = {169}, number = {2}, pages = {240-252}, doi = {10.1002/ajpa.23820}, pmid = {30964548}, issn = {1096-8644}, support = {APP1065106//National Health and Medical Research Council (NHMRC)/International ; RGPIN-2015-04477//Natural Sciences and Engineering Research Council of Canada (NSERC)/International ; 430-2017-01193//Social Sciences and Humanities Research Council of Canada (SSHRC)/International ; 435-2018-0465//Social Sciences and Humanities Research Council of Canada (SSHRC)/International ; //Arbor Biosciences/International ; //McMaster University/International ; //Canada Research Chair Program/International ; //University of Toronto/International ; }, mesh = {Bone and Bones/chemistry ; DNA, Ancient/analysis ; DNA, Mitochondrial/analysis ; Denmark ; Female ; Genetic Variation/*genetics ; Genome, Mitochondrial/*genetics ; History, Medieval ; Human Migration/history ; Humans ; London ; Male ; Plague/*history ; Tooth/chemistry ; }, abstract = {OBJECTIVES: In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isotope data. This study uses ancient DNA (aDNA) isolated from skeletal remains to examine whether evidence for large-scale population movement can be gleaned from the complete mitochondrial genomes of 264 medieval individuals from England (London) and Denmark.<br><br>MATERIALS AND METHODS: Using a novel library-conserving approach to targeted capture, we recovered 264 full mitochondrial genomes from the petrous portion of the temporal bones and teeth and compared genetic diversity across the medieval period within and between English (London) and Danish populations and with contemporary populations through population pairwise ΦST analysis.<br><br>RESULTS: We find no evidence of significant differences in genetic diversity spatially or temporally in our dataset, yet there is a high degree of haplotype diversity in our medieval samples with little exact sequence sharing.<br><br>DISCUSSION: The mitochondrial genomes of both medieval Londoners and medieval Danes suggest high mitochondrial diversity before, during and after the Black Death. While our mitochondrial genomic data lack geographically correlated signals, these data could be the result of high, continual female migration before and after the Black Death or may simply indicate a large female effective population size unaffected by the upheaval of the medieval period. Either scenario suggests a genetic resiliency in areas of northwestern medieval Europe.}, }
@article {pmid30963935, year = {2019}, author = {Nakagome, S and Hudson, RR and Di Rienzo, A}, title = {Inferring the model and onset of natural selection under varying population size from the site frequency spectrum and haplotype structure.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1896}, pages = {20182541}, pmid = {30963935}, issn = {1471-2954}, support = {R01 GM101682/GM/NIGMS NIH HHS/United States ; }, mesh = {Bayes Theorem ; DNA, Ancient/*analysis ; Europe ; *Gene Frequency ; Haplotypes/*genetics ; *Human Migration ; Humans ; Models, Genetic ; Population Density ; *Selection, Genetic ; Skin Pigmentation/*genetics ; Time Factors ; }, abstract = {A fundamental question about adaptation in a population is the time of onset of the selective pressure acting on beneficial alleles. Inferring this time, in turn, depends on the selection model. We develop a framework of approximate Bayesian computation (ABC) that enables the use of the full site frequency spectrum and haplotype structure to test the goodness-of-fit of selection models and estimate the timing of selection under varying population size scenarios. We show that our method has sufficient power to distinguish natural selection from neutrality even if relatively old selection increased the frequency of a pre-existing allele from 20% to 50% or from 40% to 80%. Our ABC can accurately estimate the time of onset of selection on a new mutation. However, estimates are prone to bias under the standing variation model, possibly due to the uncertainty in the allele frequency at the onset of selection. We further extend our approach to take advantage of ancient DNA data that provides information on the allele frequency path of the beneficial allele. Applying our ABC, including both modern and ancient human DNA data, to four pigmentation alleles in Europeans, we detected selection on standing variants that occurred after the dispersal from Africa even though models of selection on a new mutation were initially supported for two of these alleles without the ancient data.}, }
@article {pmid30957607, year = {2019}, author = {Siripan, S and Wonnapinij, P and Auetrakulvit, P and Wangthongchaicharoen, N and Surat, W}, title = {Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {30}, number = {4}, pages = {609-617}, doi = {10.1080/24701394.2019.1597072}, pmid = {30957607}, issn = {2470-1408}, mesh = {Animals ; Cattle/*genetics ; DNA, Mitochondrial/genetics ; Haplotypes ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Thailand ; }, abstract = {Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B.taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.}, }
@article {pmid30954285, year = {2019}, author = {Brunson, K and Reich, D}, title = {The Promise of Paleogenomics Beyond Our Own Species.}, journal = {Trends in genetics : TIG}, volume = {35}, number = {5}, pages = {319-329}, doi = {10.1016/j.tig.2019.02.006}, pmid = {30954285}, issn = {0168-9525}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Biological Evolution ; DNA, Ancient ; Genome-Wide Association Study ; *Genomics/methods ; Geography ; Horses ; Humans ; *Paleontology/methods ; Species Specificity ; Zea mays/genetics ; }, abstract = {Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.}, }
@article {pmid30953039, year = {2019}, author = {Spyrou, MA and Bos, KI and Herbig, A and Krause, J}, title = {Ancient pathogen genomics as an emerging tool for infectious disease research.}, journal = {Nature reviews. Genetics}, volume = {20}, number = {6}, pages = {323-340}, doi = {10.1038/s41576-019-0119-1}, pmid = {30953039}, issn = {1471-0064}, mesh = {Archaea/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification ; Biological Evolution ; Communicable Diseases/*history/microbiology/parasitology/virology ; DNA, Ancient/*analysis/isolation &amp; purification ; Fossils ; *Genome ; Genomics/*methods ; Global Health/history ; High-Throughput Nucleotide Sequencing/*methods ; History, 19th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Humans ; Public Health Surveillance/methods ; Viruses/genetics/isolation &amp; purification ; }, abstract = {Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.}, }
@article {pmid30952160, year = {2019}, author = {Yelmen, B and Mondal, M and Marnetto, D and Pathak, AK and Montinaro, F and Gallego Romero, I and Kivisild, T and Metspalu, M and Pagani, L}, title = {Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations.}, journal = {Molecular biology and evolution}, volume = {36}, number = {8}, pages = {1628-1642}, pmid = {30952160}, issn = {1537-1719}, mesh = {Adaptation, Biological ; Demography ; *Genome, Human ; Genomics/*methods ; Haplotypes ; Humans ; India ; Pakistan ; Phylogeography ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Selection, Genetic ; }, abstract = {Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high-quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations and showed our approach to be robust via coalescent simulations. Our f3 and f4 statistics-based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex interpopulation relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively.}, }
@article {pmid30944772, year = {2019}, author = {Ciucani, MM and Palumbo, D and Galaverni, M and Serventi, P and Fabbri, E and Ravegnini, G and Angelini, S and Maini, E and Persico, D and Caniglia, R and Cilli, E}, title = {Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6424}, pmid = {30944772}, issn = {2167-8359}, abstract = {Background: The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated.<br><br>Methods: In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses.<br><br>Results: Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1.<br><br>Discussion: In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence in this area. Moreover, the unexpected discovery of a 24,700-year-old sample carrying a haplotype that, from the fragment here obtained, falls within the canine clade A, could represent the oldest evidence in Europe of such dog-rich clade. All these findings suggest complex population dynamics that deserve to be further investigated based on mitochondrial or whole genome sequencing.}, }
@article {pmid30942856, year = {2019}, author = {Harris, DN and Ruczinski, I and Yanek, LR and Becker, LC and Becker, DM and Guio, H and Cui, T and Chilton, FH and Mathias, RA and O'Connor, TD}, title = {Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World.}, journal = {Genome biology and evolution}, volume = {11}, number = {5}, pages = {1417-1430}, pmid = {30942856}, issn = {1759-6653}, support = {R01 AT008621/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Fatty Acid Desaturases/*genetics/metabolism ; Fatty Acids, Unsaturated/*metabolism ; Hominidae/*genetics/metabolism ; Humans ; Indians, North American/genetics ; Selection, Genetic ; Siberia ; }, abstract = {The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (>20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.}, }
@article {pmid30931994, year = {2019}, author = {Modi, A and Nesheva, D and Sarno, S and Vai, S and Karachanak-Yankova, S and Luiselli, D and Pilli, E and Lari, M and Vergata, C and Yordanov, Y and Dimitrova, D and Kalcev, P and Staneva, R and Antonova, O and Hadjidekova, S and Galabov, A and Toncheva, D and Caramelli, D}, title = {Ancient human mitochondrial genomes from Bronze Age Bulgaria: new insights into the genetic history of Thracians.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5412}, doi = {10.1038/s41598-019-41945-0}, pmid = {30931994}, issn = {2045-2322}, mesh = {Bulgaria ; DNA, Ancient/*analysis ; DNA, Mitochondrial/classification/*genetics/*history ; Genetics, Population/methods ; Genome, Human/genetics ; Genome, Mitochondrial/*genetics ; Geography ; History, Ancient ; Humans ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA ; }, abstract = {One of the best documented Indo-European civilizations that inhabited Bulgaria is the Thracians, who lasted for more than five millennia and whose origin and relationships with other past and present-day populations are debated among researchers. Here we report 25 new complete mitochondrial genomes of ancient individuals coming from three necropolises located in different regions of Bulgaria - Shekerdja mogila, Gabrova mogila and Bereketska mogila - dated to II-III millennium BC. The identified mtDNA haplogroup composition reflects the mitochondrial variability of Western Eurasia. In particular, within the ancient Eurasian genetic landscape, Thracians locate in an intermediate position between Early Neolithic farmers and Late Neolithic-Bronze Age steppe pastoralists, supporting the scenario that the Balkan region has been a link between Eastern Europe and the Mediterranean since the prehistoric time. Spatial Principal Component Analysis (sPCA) performed on Thracian and modern mtDNA sequences, confirms the pattern highlighted on ancient populations, overall indicating that the maternal gene pool of Thracians reflects their central geographical position at the gateway of Europe.}, }
@article {pmid30913508, year = {2019}, author = {Traversari, M and Serrangeli, MC and Catalano, G and Petrella, E and Piciucchi, S and Feletti, F and Oxilia, G and Cristiani, E and Vazzana, A and Sorrentino, R and De Fanti, S and Luiselli, D and Calcagnile, L and Saragoni, L and Feeney, RNM and Gruppioni, G and Cilli, E and Benazzi, S}, title = {Multi-analytic study of a probable case of fibrous dysplasia (FD) from certosa monumental cemetery (Bologna, Italy).}, journal = {International journal of paleopathology}, volume = {25}, number = {}, pages = {1-8}, doi = {10.1016/j.ijpp.2019.03.003}, pmid = {30913508}, issn = {1879-9825}, mesh = {Adult ; Amino Acid Substitution ; Cemeteries/history ; Craniofacial Fibrous Dysplasia/*diagnostic imaging/genetics/history/pathology ; Fibrous Dysplasia, Polyostotic/diagnostic imaging/history/pathology ; History, 19th Century ; History, 20th Century ; Humans ; Italy ; Male ; Mutation ; Osteitis Deformans/diagnostic imaging/pathology ; Osteosarcoma/diagnostic imaging/history/pathology ; Tomography, X-Ray Computed/history ; }, abstract = {OBJECTIVE: To evaluate, via a multidisciplinary approach, a distinctive paleopathological condition believed to be fibrous dysplasia, found on a 19th/20th century skeleton from Certosa Monumental Cemetery, Bologna, Italy.<br><br>MATERIALS: A skeletonized cranium and mandible recovered from an ossuary in 2014.<br><br>METHODS: Pathological alterations were analysed by radiological examination, dental macrowear, histopathological and genetic analyses.<br><br>RESULT: The skeleton is believed to be an adult male. Differential diagnoses include Paget's disease, McCune-Albright syndrome, osteochondroma and osteosarcoma. The radiographic findings, along with the solitary nature of the lesions, are strong evidence for the diagnosis of fibrous dysplasia (FD). Genetic analysis further revealed a frequency of ˜1% of mutant alleles with the R201C substitution, one of the post-zygotic activating mutation frequently associated with FD.<br><br>CONCLUSIONS: The multi-analytical method employed suggests a diagnosis of monostotic form of FD. The diagnostic design incorporates multiple lines of evidence, including macroscopic, histopathological, and genetic analyses.<br><br>SIGNIFICANCE: Through the use of a multi-analytic approach, robust diagnoses can be offered. This case serves as one of the oldest examples of FD from an historical context. The genetic mutation detected, associated with FD, has not been previously reported in historical/ancient samples.}, }
@article {pmid30893326, year = {2019}, author = {Di Maida, G and Mannino, MA and Krause-Kyora, B and Jensen, TZT and Talamo, S}, title = {Radiocarbon dating and isotope analysis on the purported Aurignacian skeletal remains from Fontana Nuova (Ragusa, Italy).}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213173}, pmid = {30893326}, issn = {1932-6203}, mesh = {Body Remains/chemistry ; Carbon Radioisotopes/*analysis ; Fossils/*history ; History, Ancient ; Humans ; Italy ; Radiometric Dating/*methods ; Tooth/chemistry ; }, abstract = {Proving voyaging at sea by Palaeolithic humans is a difficult archaeological task, even for short distances. In the Mediterranean, a commonly accepted sea crossing is that from the Italian Peninsula to Sicily by anatomically modern humans, purportedly of the Aurignacian culture. This claim, however, was only supported by the typological attribution to the Aurignacian of the lithic industries from the insular site of Fontana Nuova. AMS radiocarbon dating undertaken as part of our research shows that the faunal remains, previously considered Aurignacian, actually date to the Holocene. Absolute dating on dentinal collagen also attributes the human teeth from the site to the early Holocene, although we were unable to obtain ancient DNA to evaluate their ancestry. Ten radiocarbon dates on human and other taxa are comprised between 9910-9700 cal. BP and 8600-8480 cal. BP, indicating that Fontana Nuova was occupied by Mesolithic and not Aurignacian hunter-gatherers. Only a new study of the lithic assemblage could establish if the material from Fontana Nuova is a mixed collection that includes both late Upper Palaeolithic (Epigravettian) and Mesolithic artefacts, as can be suggested by taking into account both the results of our study and of the most recent reinterpretation of the lithics. Nevertheless, this research suggests that the notion that Aurignacian groups were present in Sicily should now be revised. Another outcome of our study is that we found that three specimens, attributed on grounds both of morphological and ZooMS identifications to Cervus elaphus, had δ13C values significantly higher than any available for such species in Europe.}, }
@article {pmid30890703, year = {2019}, author = {Feldman, M and Fernández-Domínguez, E and Reynolds, L and Baird, D and Pearson, J and Hershkovitz, I and May, H and Goring-Morris, N and Benz, M and Gresky, J and Bianco, RA and Fairbairn, A and Mustafaoğlu, G and Stockhammer, PW and Posth, C and Haak, W and Jeong, C and Krause, J}, title = {Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1218}, doi = {10.1038/s41467-019-09209-7}, pmid = {30890703}, issn = {2041-1723}, mesh = {Adult ; Agriculture/*history ; Archaeology ; Bone and Bones ; DNA, Ancient/*analysis/isolation &amp; purification ; Europe ; Farmers/*history ; Female ; Genome, Human/*genetics ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Human Migration/*history ; Humans ; Iran ; Male ; Radiometric Dating ; }, abstract = {Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80-90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.}, }
@article {pmid30887686, year = {2019}, author = {Weyrich, LS and Farrer, AG and Eisenhofer, R and Arriola, LA and Young, J and Selway, CA and Handsley-Davis, M and Adler, CJ and Breen, J and Cooper, A}, title = {Laboratory contamination over time during low-biomass sample analysis.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {982-996}, pmid = {30887686}, issn = {1755-0998}, support = {DECRA 150101574//Australian Research Council/ ; }, mesh = {*DNA Contamination ; *Diagnostic Errors ; Metagenomics/*methods ; Molecular Biology/*methods ; }, abstract = {Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.}, }
@article {pmid30886779, year = {2019}, author = {Eisenhofer, R and Weyrich, LS}, title = {Assessing alignment-based taxonomic classification of ancient microbial DNA.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6594}, pmid = {30886779}, issn = {2167-8359}, abstract = {The field of palaeomicrobiology-the study of ancient microorganisms-is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic divergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.}, }
@article {pmid30884759, year = {2019}, author = {Abondio, P and Sazzini, M and Garagnani, P and Boattini, A and Monti, D and Franceschi, C and Luiselli, D and Giuliani, C}, title = {The Genetic Variability of APOE in Different Human Populations and Its Implications for Longevity.}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, pmid = {30884759}, issn = {2073-4425}, mesh = {Apolipoproteins E/*genetics ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; *Longevity ; Multifactorial Inheritance ; }, abstract = {Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer's disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved.}, }
@article {pmid30880015, year = {2019}, author = {Villalba-Mouco, V and van de Loosdrecht, MS and Posth, C and Mora, R and Martínez-Moreno, J and Rojo-Guerra, M and Salazar-García, DC and Royo-Guillén, JI and Kunst, M and Rougier, H and Crevecoeur, I and Arcusa-Magallón, H and Tejedor-Rodríguez, C and García-Martínez de Lagrán, I and Garrido-Pena, R and Alt, KW and Jeong, C and Schiffels, S and Utrilla, P and Krause, J and Haak, W}, title = {Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula.}, journal = {Current biology : CB}, volume = {29}, number = {7}, pages = {1169-1177.e7}, doi = {10.1016/j.cub.2019.02.006}, pmid = {30880015}, issn = {1879-0445}, mesh = {DNA, Ancient/*analysis ; *Genome, Human ; *Human Migration ; Humans ; Spain ; }, abstract = {The Iberian Peninsula in southwestern Europe represents an important test case for the study of human population movements during prehistoric periods. During the Last Glacial Maximum (LGM), the peninsula formed a periglacial refugium [1] for hunter-gatherers (HGs) and thus served as a potential source for the re-peopling of northern latitudes [2]. The post-LGM genetic signature was previously described as a cline from Western HG (WHG) to Eastern HG (EHG), further shaped by later Holocene expansions from the Near East and the North Pontic steppes [3-9]. Western and central Europe were dominated by ancestry associated with the ∼14,000-year-old individual from Villabruna, Italy, which had largely replaced earlier genetic ancestry, represented by 19,000-15,000-year-old individuals associated with the Magdalenian culture [2]. However, little is known about the genetic diversity in southern European refugia, the presence of distinct genetic clusters, and correspondence with geography. Here, we report new genome-wide data from 11 HGs and Neolithic individuals that highlight the late survival of Paleolithic ancestry in Iberia, reported previously in Magdalenian-associated individuals. We show that all Iberian HGs, including the oldest, a ∼19,000-year-old individual from El Mirón in Spain, carry dual ancestry from both Villabruna and the Magdalenian-related individuals. Thus, our results suggest an early connection between two potential refugia, resulting in a genetic ancestry that survived in later Iberian HGs. Our new genomic data from Iberian Early and Middle Neolithic individuals show that the dual Iberian HG genomic legacy pertains in the peninsula, suggesting that expanding farmers mixed with local HGs. VIDEO ABSTRACT.}, }
@article {pmid30875055, year = {2019}, author = {Hahn, C}, title = {Assembly of Ancient Mitochondrial Genomes Without a Closely Related Reference Sequence.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {195-213}, doi = {10.1007/978-1-4939-9176-1_18}, pmid = {30875055}, issn = {1940-6029}, mesh = {DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Genomics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Reference Standards ; Sequence Analysis, DNA/methods/*standards ; Software ; }, abstract = {Recent methodological advances have transformed the field of ancient DNA (aDNA). Basic bioinformatics skills are becoming essential requirements to process and analyze the sheer amounts of data generated by current aDNA studies and in biomedical research in general. This chapter is intended as a practical guide to the assembly of ancient mitochondrial genomes, directly from genomic DNA-derived next-generation sequencing (NGS) data, specifically in the absence of closely related reference genomes. In a hands-on tutorial suitable for readers with little to no prior bioinformatics experience, we reconstruct the mitochondrial genome of a woolly mammoth deposited ~45,000 years ago. We introduce key software tools and outline general strategies for mitogenome assembly, including the critical quality assessment of assembly results without a reference genome.}, }
@article {pmid30875054, year = {2019}, author = {Renaud, G and Schubert, M and Sawyer, S and Orlando, L}, title = {Authentication and Assessment of Contamination in Ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {163-194}, doi = {10.1007/978-1-4939-9176-1_17}, pmid = {30875054}, issn = {1940-6029}, mesh = {Cell Nucleus/*genetics ; *DNA Contamination ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial ; Humans ; Sequence Analysis, DNA/*methods ; }, abstract = {Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.}, }
@article {pmid30875053, year = {2019}, author = {Nichols, RV and Curd, E and Heintzman, PD and Shapiro, B}, title = {Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {149-161}, doi = {10.1007/978-1-4939-9176-1_16}, pmid = {30875053}, issn = {1940-6029}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Ancient/*analysis ; Environmental Monitoring/*methods ; Geologic Sediments/*analysis ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleic Acid Amplification Techniques/*methods ; Polymerase Chain Reaction/*methods ; }, abstract = {All organisms release their DNA into the environment through processes such as excretion and the senescence of tissues and limbs. This DNA, often referred to as environmental DNA (eDNA) or sedimentary ancient DNA (sedaDNA), can be recovered from both present-day and ancient soils, fecal samples, bodies of water and lake cores, and even air. While eDNA is a potentially useful record of past and present biodiversity, several challenges complicate data generation and interpretation of results. Most importantly, eDNA samples tend to be highly taxonomically mixed, and the target organism or group of organisms may be present at very low abundance within this mixture. To overcome this challenge, enrichment approaches are often used to target specific taxa of interest. Here, we describe a protocol to amplify metabarcodes or short, variable loci that identify lineages within broad taxonomic groups (e.g., plants, mammals), using the polymerase chain reaction (PCR) with established generic &quot;barcode&quot; primers. We also provide a catalog of animal and plant barcode primers that, because they target relatively short fragments of DNA, are potentially suitable for use with degraded DNA.}, }
@article {pmid30875052, year = {2019}, author = {Wutke, S and Ludwig, A}, title = {Targeted PCR Amplification and Multiplex Sequencing of Ancient DNA for SNP Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {141-147}, doi = {10.1007/978-1-4939-9176-1_15}, pmid = {30875052}, issn = {1940-6029}, mesh = {DNA Fingerprinting/*methods ; DNA, Ancient/*analysis ; Forensic Genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Multiplex Polymerase Chain Reaction/*methods ; *Polymorphism, Single Nucleotide ; }, abstract = {The analysis of single-nucleotide polymorphisms (SNPs) has proven to be advantageous for addressing variation within samples of highly degraded or low-quality DNA samples. This is because only short fragments need to be amplified to analyze SNPs, and this can be achieved by multiplex PCR. Here, we present a sensitive method for the targeted sequencing of SNP loci that requires only small amounts of template DNA. The approach combines multiplex amplification of very short fragments covering SNP positions followed by sample barcoding and next-generation sequencing. This method allows generation of data from large sample sets of poorly preserved specimens, such as fossil remains, forensic samples, and museum specimens. The approach is cost-effective, rapid, and applicable to forensics, population genetics, and phylogenetic research questions.}, }
@article {pmid30875051, year = {2019}, author = {Paijmans, JLA and González Fortes, G and Förster, DW}, title = {Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {129-139}, doi = {10.1007/978-1-4939-9176-1_14}, pmid = {30875051}, issn = {1940-6029}, mesh = {DNA, Ancient/chemistry/*isolation &amp; purification ; *Gene Library ; *Genome, Mitochondrial ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleic Acid Hybridization/*methods ; RNA/*chemistry/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted &quot;contaminant&quot; DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment.}, }
@article {pmid30875050, year = {2019}, author = {Soares, AER}, title = {Hybridization Capture of Ancient DNA Using RNA Baits.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {121-128}, doi = {10.1007/978-1-4939-9176-1_13}, pmid = {30875050}, issn = {1940-6029}, mesh = {*DNA Contamination ; DNA, Ancient/chemistry/*isolation &amp; purification ; Gene Library ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Nucleic Acid Hybridization/*methods ; RNA/chemistry/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The majority of DNA recovered from ancient remains is derived from organisms that colonize the remains post-mortem, such as soil microbes, or from contaminants, such as DNA from living humans. Additionally, some ancient DNA research projects aim to target specific genomic regions, such as mitochondrial genomes or variable single nucleotide polymorphisms (SNPs). To overcome the challenge of targeting specific fragments of DNA from within a complex DNA extract, methods have been developed to enrich ancient DNA extracts for target DNA relative to nontarget DNA. This chapter describes a method for target DNA enrichment that uses hybridization to biotinylated RNA baits to capture and amplify specific ancient DNA fragments from within the pool of extracted fragments.}, }
@article {pmid30875049, year = {2019}, author = {Snyder-Mackler, N and Voyles, T and Tung, J}, title = {Generating RNA Baits for Capture-Based Enrichment.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {107-120}, doi = {10.1007/978-1-4939-9176-1_12}, pmid = {30875049}, issn = {1940-6029}, mesh = {Biotin/*chemistry ; DNA, Ancient/chemistry/*isolation &amp; purification ; *Gene Library ; *Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; RNA/*chemistry/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Capture-based enrichment techniques have revolutionized genomic analysis of species and populations for which only low-quality or contaminated DNA samples (e.g., ancient DNA, noninvasively collected DNA, environmental DNA) are available. This chapter outlines an optimized laboratory protocol for generating RNA &quot;baits&quot; for genome-wide capture of target DNA from a larger pool of DNA. This method relies on the in vitro transcription of biotinylated RNA baits, which has the dual benefit of eliminating the high cost of synthesizing custom baits and producing a bait set that targets the majority of regions genome-wide. We provide a detailed protocol for the three main steps involved in bait library construction: (1) making a DNA library from a high-quality DNA sample for the organism of interest or a closely related species; (2) using duplex-specific nuclease digestion to reduce the representation of repetitive regions in the DNA library; and (3) performing in vitro transcription of the repetitive region-depleted DNA library to generate biotinylated RNA baits. Where applicable, we include notes and recommendations based on our own experiences.}, }
@article {pmid30875048, year = {2019}, author = {González Fortes, G and Paijmans, JLA}, title = {Whole-Genome Capture of Ancient DNA Using Homemade Baits.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {93-105}, doi = {10.1007/978-1-4939-9176-1_11}, pmid = {30875048}, issn = {1940-6029}, mesh = {Biotin/*chemistry ; DNA, Ancient/chemistry/*isolation &amp; purification ; *Gene Library ; *Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Sequence Analysis, DNA/*methods ; }, abstract = {For many archaeological and paleontological samples, the relative content of endogenous compared to contaminant DNA is low. In such cases, enriching sequencing libraries for endogenous DNA, prior to sequencing can make the final research project more cost-effective. Here, we present an in-solution enrichment protocol based on homemade baits that can be applied to recover complete nuclear genomes from ancient remains. The approach is based on the preparation of DNA baits by biotinylated adapter ligation. The procedure has been developed for use with human remains but can be adapted to other species or target regions by choosing the appropriate template DNA from which to build the capture baits. By using homemade rather than commercially acquired baits, this protocol may offer increased flexibility and cost efficiency.}, }
@article {pmid30875047, year = {2019}, author = {Martins, RF and Kampmann, ML and Förster, DW}, title = {Sequencing Library Preparation from Degraded Samples for Non-illumina Sequencing Platforms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {85-92}, doi = {10.1007/978-1-4939-9176-1_10}, pmid = {30875047}, issn = {1940-6029}, mesh = {*DNA Damage ; DNA, Ancient/*analysis/chemistry/isolation &amp; purification ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Efficient methods for building genomic sequencing libraries from degraded DNA have been in place for Illumina sequencing platforms for some years now, but such methods are still lacking for other sequencing platforms. Here, we provide a protocol for building genomic libraries from degraded DNA (archival or ancient sample material) for sequencing on the Ion Torrent™ high-throughput sequencing platforms. In addition to a reduction in time and cost in comparison to commercial kits, this protocol removes purification steps prior to library amplification, an important consideration for work involving historical samples. Libraries prepared using this method are appropriate for either shotgun sequencing or enrichment-based downstream approaches.}, }
@article {pmid30875046, year = {2019}, author = {Gansauge, MT and Meyer, M}, title = {A Method for Single-Stranded Ancient DNA Library Preparation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {75-83}, doi = {10.1007/978-1-4939-9176-1_9}, pmid = {30875046}, issn = {1940-6029}, mesh = {DNA, Ancient/*analysis/chemistry/isolation &amp; purification ; DNA, Single-Stranded/*genetics ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {Genomic library preparation from highly degraded DNA is more efficient when library molecules are prepared separately from the complementary strands of DNA fragments. We describe a protocol in which libraries are constructed from single DNA strands in a three-step procedure: single-stranded ligation of the first adapter with T4 DNA ligase in the presence of a splinter oligonucleotide, copying of the DNA strand with a proofreading polymerase, and blunt-end ligation of the second double-stranded adapter with T4 DNA ligase.}, }
@article {pmid30875045, year = {2019}, author = {Henneberger, K and Barlow, A and Paijmans, JLA}, title = {Double-Stranded Library Preparation for Ancient and Other Degraded Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {65-73}, doi = {10.1007/978-1-4939-9176-1_8}, pmid = {30875045}, issn = {1940-6029}, mesh = {DNA/*genetics ; *DNA Damage ; DNA, Ancient/*analysis/chemistry/isolation &amp; purification ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {High-throughput sequencing (HTS) allows fast and cost-efficient sequencing of ancient DNA (aDNA) without prior information about what sequences should be targeted. One necessary step for HTS is the preparation of a sequencing library. Commercial kits are available for this purpose, but many of these are not suitable for aDNA or other types of damaged DNA. Here, we outline a protocol for HTS library preparation that is optimized for ancient DNA. We report the library conversion rate for a range of input template and adapter concentrations. Our results show that the protocol performs at a high efficiency.}, }
@article {pmid30875044, year = {2019}, author = {Campos, PF and Gilbert, MTP}, title = {DNA Extraction from Keratin and Chitin.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {57-63}, doi = {10.1007/978-1-4939-9176-1_7}, pmid = {30875044}, issn = {1940-6029}, mesh = {Animals ; Chitin/*chemistry ; DNA/*analysis/*isolation &amp; purification ; Endopeptidase K/metabolism ; Humans ; Keratins/*chemistry ; Silicon Dioxide/chemistry ; }, abstract = {DNA extracted from keratinous and chitinous materials can be a useful source of genetic information. To effectively liberate the DNA from these materials, buffers containing relatively high levels of DTT, proteinase K, and detergent are recommended, followed by purification using either silica column or organic methods.}, }
@article {pmid30875043, year = {2019}, author = {Wales, N and Kistler, L}, title = {Extraction of Ancient DNA from Plant Remains.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {45-55}, doi = {10.1007/978-1-4939-9176-1_6}, pmid = {30875043}, issn = {1940-6029}, mesh = {DNA, Ancient/*analysis/*isolation &amp; purification ; DNA, Plant/*analysis/*isolation &amp; purification ; Plants/classification/*genetics ; Specimen Handling/*methods ; }, abstract = {Ancient plant remains from archaeological sites, paleoenvironmental contexts, and herbaria provide excellent opportunities for interrogating plant genetics over Quaternary timescales using ancient DNA (aDNA)-based analyses. A variety of plant tissues, preserved primarily by desiccation and anaerobic waterlogging, have proven to be viable sources of aDNA. Plant tissues are anatomically and chemically diverse and therefore require optimized DNA extraction approaches. Here, we describe a plant DNA isolation protocol that performs well in most contexts. We include recommendations for optimization to retain the very short DNA fragments that are expected to be preserved in degraded tissues.}, }
@article {pmid30875042, year = {2019}, author = {Epp, LS and Zimmermann, HH and Stoof-Leichsenring, KR}, title = {Sampling and Extraction of Ancient DNA from Sediments.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {31-44}, doi = {10.1007/978-1-4939-9176-1_5}, pmid = {30875042}, issn = {1940-6029}, mesh = {DNA, Ancient/*analysis/*isolation &amp; purification ; DNA, Plant/*analysis/*isolation &amp; purification ; Ecosystem ; Geologic Sediments/*analysis ; Plants/classification/*genetics ; Specimen Handling/*methods ; }, abstract = {Environmental DNA preserved in sediments is rapidly gaining importance as a tool in paleoecology. Sampling procedures for sedimentary ancient DNA (sedaDNA) have to be well planned to ensure clean subsampling of the inside of sediment cores and avoid introducing contamination. Additionally, ancient DNA extraction protocols may need to be optimized for the recovery of DNA from sediments, which may contain inhibitors. Here we describe procedures for subsampling both nonfrozen and frozen sediment cores, and we describe an efficient method for ancient DNA extraction from such samples.}, }
@article {pmid30875041, year = {2019}, author = {Dabney, J and Meyer, M}, title = {Extraction of Highly Degraded DNA from Ancient Bones and Teeth.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {25-29}, doi = {10.1007/978-1-4939-9176-1_4}, pmid = {30875041}, issn = {1940-6029}, mesh = {Bone and Bones/*metabolism ; *DNA Degradation, Necrotic ; DNA, Ancient/*isolation &amp; purification ; Edetic Acid/*metabolism ; Endopeptidase K/*metabolism ; Humans ; Silicon Dioxide/chemistry ; Tooth/*metabolism ; }, abstract = {We provide a DNA extraction protocol optimized for the recovery of highly fragmented molecules preserved within bones and teeth. In this method, the hard tissue matrix is degraded using an EDTA/Proteinase K lysis buffer, and the DNA is purified using spin columns with silica membranes. This method efficiently recovers molecules as short as 35 base-pairs long.}, }
@article {pmid30875040, year = {2019}, author = {Schroeder, H and de Barros Damgaard, P and Allentoft, ME}, title = {Pretreatment: Improving Endogenous Ancient DNA Yields Using a Simple Enzymatic Predigestion Step.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {21-24}, doi = {10.1007/978-1-4939-9176-1_3}, pmid = {30875040}, issn = {1940-6029}, mesh = {Bone and Bones/*metabolism ; *DNA Contamination ; DNA, Ancient/*analysis/*isolation &amp; purification ; Edetic Acid/*metabolism ; Endopeptidase K/*metabolism ; Humans ; Tooth/*metabolism ; }, abstract = {Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.}, }
@article {pmid30875039, year = {2019}, author = {Korlević, P and Meyer, M}, title = {Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {15-19}, doi = {10.1007/978-1-4939-9176-1_2}, pmid = {30875039}, issn = {1940-6029}, mesh = {Animals ; Bone and Bones/*metabolism ; DNA/*analysis/chemistry/*isolation &amp; purification ; *DNA Contamination ; Decontamination ; Neanderthals ; Phosphates/*chemistry ; Polymerase Chain Reaction ; Sodium Hypochlorite/*chemistry ; Specimen Handling/methods ; Tooth/*metabolism ; }, abstract = {DNA isolated from ancient bones and teeth comprises a mixture of microbial contamination and DNA from the organism under study. In addition, analyses of ancient human remains are often complicated by contamination with present-day human DNA, which can be introduced during excavation and subsequent handling of the specimens. In most cases, the relative abundance of contaminant DNA is much greater than that of the target organism. Here we present two techniques for reducing the proportion of contaminant DNA in bones and teeth. The first and most efficient technique uses a sodium hypochlorite (bleach) pretreatment to destroy contaminant DNA that may be bound or otherwise attached to the surface of bone/tooth powder. The second, less destructive pretreatment uses a phosphate buffer to release surface-bound DNA.}, }
@article {pmid30875038, year = {2019}, author = {Fulton, TL and Shapiro, B}, title = {Setting Up an Ancient DNA Laboratory.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1963}, number = {}, pages = {1-13}, doi = {10.1007/978-1-4939-9176-1_1}, pmid = {30875038}, issn = {1940-6029}, mesh = {Animals ; *DNA Contamination ; DNA Damage ; DNA, Ancient/*analysis/chemistry/isolation &amp; purification ; Fossils ; Humans ; Laboratories/standards ; Sequence Analysis, DNA/*methods/standards ; }, abstract = {Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential is high for contamination of ancient samples, ancient DNA extracts, and genomic sequencing libraries prepared from these extracts with non-degraded DNA from the present-day environment. To minimize the risk of contamination in ancient DNA environments, experimental protocols specific to handling ancient specimens, including those that outline the design and layout of laboratory space, have been introduced. Here, we outline challenges associated with working with ancient samples, including providing guidelines for setting up a new ancient DNA laboratory. We also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination of ancient DNA experiments with exogenous sources of DNA.}, }
@article {pmid30872771, year = {2019}, author = {Rey-Iglesia, A and García-Vázquez, A and Treadaway, EC and van der Plicht, J and Baryshnikov, GF and Szpak, P and Bocherens, H and Boeskorov, GG and Lorenzen, ED}, title = {Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4462}, doi = {10.1038/s41598-019-40168-7}, pmid = {30872771}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; Body Remains ; Carbon Isotopes/analysis ; Carnivora ; *DNA, Ancient ; *DNA, Mitochondrial ; History, Ancient ; Nitrogen Isotopes/analysis ; Siberia ; Ursidae/*genetics ; }, abstract = {Over 60% of the modern distribution range of brown bears falls within Russia, yet palaeoecological data from the region remain scarce. Complete modern Russian brown bear mitogenomes are abundant in the published literature, yet examples of their ancient counterparts are absent. Similarly, there is only limited stable isotopic data of prehistoric brown bears from the region. We used ancient DNA and stable carbon (δ13C) and nitrogen (δ15N) isotopes retrieved from five Pleistocene Yakutian brown bears (one Middle Pleistocene and four Late Pleistocene), to elucidate the evolutionary history and palaeoecology of the species in the region. We were able to reconstruct the complete mitogenome of one of the Late Pleistocene specimens, but we were unable to assign it to any of the previously published brown bear mitogenome clades. A subsequent analysis of published mtDNA control region sequences, which included sequences of extinct clades from other geographic regions, assigned the ancient Yakutian bear to the extinct clade 3c; a clade previously identified from Late Quaternary specimens from Eastern Beringia and Northern Spain. Our analyses of stable isotopes showed relatively high δ15N values in the Pleistocene Yakutian brown bears, suggesting a more carnivorous diet than contemporary brown bears from Eastern Beringia.}, }
@article {pmid30862131, year = {2019}, author = {Chyleński, M and Ehler, E and Somel, M and Yaka, R and Krzewińska, M and Dabert, M and Juras, A and Marciniak, A}, title = {Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities.}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, pmid = {30862131}, issn = {2073-4425}, mesh = {*DNA, Ancient ; Evolution, Molecular ; *Genome, Mitochondrial ; Humans ; *Maternal Inheritance ; *Pedigree ; Turkey ; }, abstract = {Çatalhöyük is one of the most widely recognized and extensively researched Neolithic settlements. The site has been used to discuss a wide range of aspects associated with the spread of the Neolithic lifestyle and the social organization of Neolithic societies. Here, we address both topics using newly generated mitochondrial genomes, obtained by direct sequencing and capture-based enrichment of genomic libraries, for a group of individuals buried under a cluster of neighboring houses from the classical layer of the site's occupation. Our data suggests a lack of maternal kinship between individuals interred under the floors of Çatalhöyük buildings. The findings could potentially be explained either by a high variability of maternal lineages within a larger kin group, or alternatively, an intentional selection of individuals for burial based on factors other than biological kinship. Our population analyses shows that Neolithic Central Anatolian groups, including Çatalhöyük, share the closest affinity with the population from the Marmara Region and are, in contrast, set further apart from the Levantine populations. Our findings support the hypothesis about the emergence and the direction of spread of the Neolithic within Anatolian Peninsula and beyond, emphasizing a significant role of Central Anatolia in this process.}, }
@article {pmid30848092, year = {2020}, author = {van der Valk, T and Vezzi, F and Ormestad, M and Dalén, L and Guschanski, K}, title = {Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.}, journal = {Molecular ecology resources}, volume = {20}, number = {5}, pages = {1171-1181}, doi = {10.1111/1755-0998.13009}, pmid = {30848092}, issn = {1755-0998}, support = {//Jan Löfqvist Endowments of the Royal Physiographic Society of Lund/ ; 2015-676//Svenska Forskningsrådet Formas/ ; 2016-00835//Svenska Forskningsrådet Formas/ ; //Science for Life Laboratory/ ; //Knut and Alice Wallenberg Foundation/ ; //National Genomics Infrastructure funded by the Swedish Research Council/ ; //Uppsala Multidisciplinary Center for Advanced Computational Science/ ; }, abstract = {The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low-quantity and low-quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100-year old museum-preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample-specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.}, }
@article {pmid30842617, year = {2019}, author = {Pinhasi, R and Fernandes, DM and Sirak, K and Cheronet, O}, title = {Isolating the human cochlea to generate bone powder for ancient DNA analysis.}, journal = {Nature protocols}, volume = {14}, number = {4}, pages = {1194-1205}, doi = {10.1038/s41596-019-0137-7}, pmid = {30842617}, issn = {1750-2799}, mesh = {Cochlea/anatomy &amp; histology/*chemistry ; DNA, Ancient/*analysis/isolation &amp; purification ; Gene Library ; History, Ancient ; Humans ; Liquid-Liquid Extraction/*methods ; Petrous Bone/anatomy &amp; histology/*chemistry ; Powders ; Sequence Analysis, DNA/methods ; }, abstract = {The cortical bone that forms the structure of the cochlea, part of the osseous labyrinth of the inner ear, is now one of the most frequently used skeletal elements in analyses of human ancient DNA. However, there is currently no published, standardized method for its sampling. This protocol describes the preparation of bone powder from the cochlea of fragmented skulls in which the petrous pyramid of the temporal bone is accessible. Using a systematic process of bone removal based on distinct anatomical landmarks and the identification of relevant morphological features, a petrous pyramid is cleaned with a sandblaster, and the cochlea is located, isolated, and reduced to a homogeneous bone powder. All steps are carried out in dedicated ancient DNA facilities, thus reducing the introduction of contamination. This protocol requires an understanding of ancient DNA clean-room procedures and basic knowledge of petrous pyramid anatomy. In 50-65 min, it results in bone powder with endogenous DNA yields that can exceed those from teeth and other bones by up to two orders of magnitude. Compared with drilling methods, this method facilitates a more precise targeting of the cochlea, allows the user to visually inspect the cochlea and remove any residual sediment before the generation of bone powder, and confines the damage to the inner ear region and surface of the petrous portion of fragmentary crania.}, }
@article {pmid30828717, year = {2019}, author = {Signore, AV and Paijmans, JLA and Hofreiter, M and Fago, A and Weber, RE and Springer, MS and Campbell, KL}, title = {Emergence of a Chimeric Globin Pseudogene and Increased Hemoglobin Oxygen Affinity Underlie the Evolution of Aquatic Specializations in Sirenia.}, journal = {Molecular biology and evolution}, volume = {36}, number = {6}, pages = {1134-1147}, pmid = {30828717}, issn = {1537-1719}, mesh = {*Adaptation, Biological ; Animals ; *Evolution, Molecular ; Gene Conversion ; Globins/*genetics/metabolism ; Male ; Multigene Family ; Mutant Chimeric Proteins ; Oxygen/metabolism ; *Pseudogenes ; Selection, Genetic ; Sirenia/*genetics/metabolism ; }, abstract = {As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller's sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb-O2 affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb-O2 affinity in (sub)Arctic Steller's sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.}, }
@article {pmid30805020, year = {2019}, author = {Ballard, JWO and Wilson, LAB}, title = {The Australian dingo: untamed or feral?.}, journal = {Frontiers in zoology}, volume = {16}, number = {}, pages = {2}, pmid = {30805020}, issn = {1742-9994}, abstract = {Background: The Australian dingo continues to cause debate amongst Aboriginal people, pastoralists, scientists and the government in Australia. A lingering controversy is whether the dingo has been tamed and has now reverted to its ancestral wild state or whether its ancestors were domesticated and it now resides on the continent as a feral dog. The goal of this article is to place the discussion onto a theoretical framework, highlight what is currently known about dingo origins and taxonomy and then make a series of experimentally testable organismal, cellular and biochemical predictions that we propose can focus future research.<br><br>Discussion: We consider a canid that has been unconsciously selected as a tamed animal and the endpoint of methodical or what we now call artificial selection as a domesticated animal. We consider wild animals that were formerly tamed as untamed and those wild animals that were formerly domesticated as feralized. Untamed canids are predicted to be marked by a signature of unconscious selection whereas feral animals are hypothesized to be marked by signatures of both unconscious and artificial selection. First, we review the movement of dingo ancestors into Australia. We then discuss how differences between taming and domestication may influence the organismal traits of skull morphometrics, brain and size, seasonal breeding, and sociability. Finally, we consider cellular and molecular level traits including hypotheses concerning the phylogenetic position of dingoes, metabolic genes that appear to be under positive selection and the potential for micronutrient compensation by the gut microbiome.<br><br>Conclusions: Western Australian Government policy is currently being revised to allow the widespread killing of the Australian dingo. These policies are based on an incomplete understanding of the evolutionary history of the canid and assume the dingo is feralized. However, accumulated evidence does not definitively show that the dingo was ever domesticated and additional focused research is required. We suggest that incorporating ancient DNA data into the debate concerning dingo origins will be pivotal to understanding the evolutionary history of the canid. Further, we advocate that future morphological, behavioural and genetic studies should focus on including genetically pure Alpine and Desert dingoes and not dingo-dog hybrids. Finally, we propose that future studies critically examine genes under selection in the dingo and employ the genome from a wild canid for comparison.}, }
@article {pmid30804909, year = {2019}, author = {Dick, JM and Yu, M and Tan, J and Lu, A}, title = {Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {120}, pmid = {30804909}, issn = {1664-302X}, abstract = {There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator.}, }
@article {pmid30798090, year = {2019}, author = {Mao, Y and Satoh, N}, title = {A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora.}, journal = {iScience}, volume = {13}, number = {}, pages = {20-32}, doi = {10.1016/j.isci.2019.02.001}, pmid = {30798090}, issn = {2589-0042}, abstract = {Whole-genome duplication (WGD) has been recognized as a significant evolutionary force in the origin and diversification of multiple organisms. Acropora, a speciose reef-building coral genus, is suspected to have originated by polyploidy. Yet, there is no genetic evidence to support this hypothesis. Using comprehensive phylogenomic and comparative genomic approaches, we analyzed six Acroporid genomes and found that a WGD event likely occurred ∼31 million years ago in the most recent common ancestor of Acropora, concurrent with a worldwide coral extinction. We found that duplicated genes were highly enriched in gene regulation functions, including those of stress responses. The functional clusters of duplicated genes are related to the divergence of gene expression patterns during development. Some proteinaceous toxins were generated by WGD in Acropora compared with other cnidarian species. Collectively, this study provides evidence for an ancient WGD event in corals, which helps explain the origin and diversification of Acropora.}, }
@article {pmid30793442, year = {2019}, author = {Shaw, JLA and Weyrich, LS and Hallegraeff, G and Cooper, A}, title = {Retrospective eDNA assessment of potentially harmful algae in historical ship ballast tank and marine port sediments.}, journal = {Molecular ecology}, volume = {28}, number = {10}, pages = {2476-2485}, doi = {10.1111/mec.15055}, pmid = {30793442}, issn = {1365-294X}, mesh = {Aquaculture ; Australia ; *Climate Change ; *DNA Barcoding, Taxonomic ; *Ecosystem ; Geologic Sediments/microbiology ; *Harmful Algal Bloom ; Microalgae/*growth &amp; development/pathogenicity ; Retrospective Studies ; Ships ; }, abstract = {Microalgal bloom events can cause major ecosystem disturbances, devastate local marine economies, and endanger public health. Therefore, detecting and monitoring harmful microalgal taxa is essential to ensure effective risk management in waterways used for fisheries, aquaculture, recreational activity, and shipping. To fully understand the current status and future direction of algal bloom distributions, we need to know how populations and ecosystems have changed over time. This baseline knowledge is critical for predicting ecosystem responses to future anthropogenic change and will assist in the future management of coastal ecosystems. We explore a NGS metabarcoding approach to rapidly identify potentially harmful microalgal taxa in 63 historic and modern Australian marine port and ballast tank sediment samples. The results provide a record of past microalgal distribution and important baseline data that can be used to assess the efficacy of shipping guidelines, nutrient pollution mitigation, and predict the impact of climate change. Critically, eDNA surveys of archived sediments were able to detect harmful algal taxa that do not produce microscopic fossils, such as Chattonella, Heterosigma, Karlodinium, and Noctiluca. Our data suggest a potential increase in Australian harmful microalgal taxa over the past 30 years, and confirm ship ballast tanks as key dispersal vectors. These molecular mapping tools will assist in the creation of policies aimed at reducing the global increase and spread of harmful algal taxa and help prevent economic and public-health problems caused by harmful algal blooms.}, }
@article {pmid30773819, year = {2019}, author = {Grealy, A and Bunce, M and Holleley, CE}, title = {Avian mitochondrial genomes retrieved from museum eggshell.}, journal = {Molecular ecology resources}, volume = {19}, number = {4}, pages = {1052-1062}, doi = {10.1111/1755-0998.13007}, pmid = {30773819}, issn = {1755-0998}, support = {DP160104473//Australian Research Council/ ; DP180100021//Australian Research Council/ ; //CSIRO Strategic Investment Funds (NCRA)/ ; }, mesh = {Animals ; Australia ; *Birds ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; Egg Shell/*chemistry ; *Genome, Mitochondrial ; Museums ; Sequence Analysis, DNA ; }, abstract = {Avian eggshell is a bio-ceramic material with exceptional properties for preserving DNA within its crystalline structure, presenting an opportunity to retrieve genomic information from extinct or historical populations of birds. However, intracrystalline DNA has only been recovered from the large, thick eggshell of palaeognaths; members of their more-diverse sister group (neognaths) lay smaller, thinner eggs that may not exhibit the same propensity for DNA preservation. Here, we use three 40-60-year-old museum eggshell specimens of Australian neognath birds to determine the minimum mass of eggshell from which intracrystalline DNA can be retrieved, and to characterize the yield and quality of such DNA. In doing so, we describe the first protocol for successful extraction of intracrystalline DNA from neognath eggshells, with the view to unlocking the potential of vast museum egg collections for genetic research. We were able to retrieve DNA fragments over 200 bp in length from 10 mg of eggshell powder from all three specimens, and demonstrate that expanding the existing blow-hole can allow sufficient material to be collected for DNA extraction while minimizing damage to the appearance and structural integrity of the egg. Furthermore, we were able to reconstruct near-complete mitochondrial genomes at a coverage of 40-83X through shotgun sequencing of these extracts on three NextSeq lanes. Given the current extinction and extirpation rates of many avian species world-wide, genetic data from eggshell could provide a rapid and cost-effective approach to examining temporal changes in avian diversity, which is not only becoming crucial for conservation management, but also serve to deepen our understanding of genome-wide evolutionary processes.}, }
@article {pmid30753886, year = {2019}, author = {Knapp, M and Thomas, JE and Haile, J and Prost, S and Ho, SYW and Dussex, N and Cameron-Christie, S and Kardailsky, O and Barnett, R and Bunce, M and Gilbert, MTP and Scofield, RP}, title = {Mitogenomic evidence of close relationships between New Zealand's extinct giant raptors and small-sized Australian sister-taxa.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {122-128}, doi = {10.1016/j.ympev.2019.01.026}, pmid = {30753886}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Body Size/*genetics ; *Extinction, Biological ; *Genome, Mitochondrial ; New Zealand ; Phylogeny ; Raptors/*anatomy &amp; histology/*genetics ; }, abstract = {Prior to human arrival in the 13th century, two large birds of prey were the top predators in New Zealand. In the absence of non-volant mammals, the extinct Haast's eagle (Hieraaetus moorei), the largest eagle in the world, and the extinct Eyles' harrier (Circus teauteensis) the largest harrier in the world, had filled ecological niches that are on other landmasses occupied by animals such as large cats or canines. The evolutionary and biogeographic history of these island giants has long been a mystery. Here we reconstruct the origin and evolution of New Zealand's giant raptors using complete mitochondrial genome data. We show that both Eyles' harrier and Haast's eagle diverged from much smaller, open land adapted Australasian relatives in the late Pliocene to early Pleistocene. These events coincided with the development of open habitat in the previously densely forested islands of New Zealand. Our study provides evidence of rapid evolution of island gigantism in New Zealand's extinct birds of prey. Early Pleistocene climate and environmental changes were likely to have triggered the establishment of Australian raptors into New Zealand. Our results shed light on the evolution of two of the most impressive cases of island gigantism in the world.}, }
@article {pmid30744646, year = {2019}, author = {Pont, C and Wagner, S and Kremer, A and Orlando, L and Plomion, C and Salse, J}, title = {Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {29}, pmid = {30744646}, issn = {1474-760X}, mesh = {DNA, Ancient/*analysis ; DNA, Plant/analysis ; *Evolution, Molecular ; *Genome, Plant ; Genomics/*methods ; Paleontology ; }, abstract = {How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.}, }
@article {pmid30742038, year = {2019}, author = {Tennant, RK and Lux, TM and Sambles, CM and Kuhn, NJ and Petticrew, EL and Oldfield, R and Parker, DA and Hatton, J and Moore, KA and Lee, R and Turney, CSM and Jones, RT and Love, J}, title = {Palaeogenomics of the Hydrocarbon Producing Microalga Botryococcus braunii.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1776}, pmid = {30742038}, issn = {2045-2322}, support = {MR/M008924/1/MRC_/Medical Research Council/United Kingdom ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {DNA, Plant/genetics ; *Fossils ; *Genome, Plant ; Hydrocarbons/*metabolism ; Microalgae/*genetics/*metabolism ; }, abstract = {Botryococcus braunii is a colonial microalga that appears early in the fossil record and is a sensitive proxy of environmental and hydroclimatic conditions. Palaeozoic Botryococcus fossils which contribute up to 90% of oil shales and approximately 1% of crude oil, co-localise with diagnostic geolipids from the degradation of source-signature hydrocarbons. However more recent Holocene sediments demonstrate no such association. Consequently, Botryococcus are identified in younger sediments by morphology alone, where potential misclassifications could lead to inaccurate paleoenvironmental reconstructions. Here we show that a combination of flow cytometry and ancient DNA (aDNA) sequencing can unambiguously identify Botryococcus microfossils in Holocene sediments with hitherto unparalleled accuracy and rapidity. The application of aDNA sequencing to microfossils offers a far-reaching opportunity for understanding environmental change in the recent geological record. When allied with other high-resolution palaeoenvironmental information such as aDNA sequencing of humans and megafauna, aDNA from microfossils may allow a deeper and more precise understanding of past environments, ecologies and migrations.}, }
@article {pmid30723959, year = {2019}, author = {Del Carmen Gomez Cabrera, M and Young, JM and Roff, G and Staples, T and Ortiz, JC and Pandolfi, JM and Cooper, A}, title = {Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA.}, journal = {Molecular ecology}, volume = {28}, number = {10}, pages = {2636-2652}, doi = {10.1111/mec.15038}, pmid = {30723959}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*genetics ; *Biodiversity ; *Coral Reefs ; DNA Barcoding, Taxonomic ; DNA, Ancient/*analysis ; Ecology ; Ecosystem ; Humans ; Paleontology ; RNA, Ribosomal, 18S/genetics ; Seaweed/classification/genetics ; }, abstract = {Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high-throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft-bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft-bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales.}, }
@article {pmid30722030, year = {2019}, author = {Cole, TL and Ksepka, DT and Mitchell, KJ and Tennyson, AJD and Thomas, DB and Pan, H and Zhang, G and Rawlence, NJ and Wood, JR and Bover, P and Bouzat, JL and Cooper, A and Fiddaman, SR and Hart, T and Miller, G and Ryan, PG and Shepherd, LD and Wilmshurst, JM and Waters, JM}, title = {Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation.}, journal = {Molecular biology and evolution}, volume = {36}, number = {4}, pages = {784-797}, doi = {10.1093/molbev/msz017}, pmid = {30722030}, issn = {1537-1719}, mesh = {Animals ; Fossils ; *Genetic Speciation ; *Genome, Mitochondrial ; *Islands ; New Zealand ; Phylogeography ; Spheniscidae/*genetics ; }, abstract = {The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand's Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami diverged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the diversification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere's isolated archipelagos.}, }
@article {pmid30716066, year = {2019}, author = {Richards, SM and Hovhannisyan, N and Gilliham, M and Ingram, J and Skadhauge, B and Heiniger, H and Llamas, B and Mitchell, KJ and Meachen, J and Fincher, GB and Austin, JJ and Cooper, A}, title = {Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0209499}, pmid = {30716066}, issn = {1932-6203}, abstract = {Hybridization capture with in-solution oligonucleotide probes has quickly become the preferred method for enriching specific DNA loci from degraded or ancient samples prior to high-throughput sequencing (HTS). Several companies synthesize sets of probes for in-solution hybridization capture, but these commercial reagents are usually expensive. Methods for economical in-house probe synthesis have been described, but they do not directly address one of the major advantages of commercially synthesised probes: that probe sequences matching many species can be synthesised in parallel and pooled. The ability to make &quot;phylogenetically diverse&quot; probes increases the cost-effectiveness of commercial probe sets, as they can be used across multiple projects (or for projects involving multiple species). However, it is labour-intensive to replicate this with in-house methods, as template molecules must first be generated for each species of interest. While it has been observed that probes can be used to enrich for phylogenetically distant targets, the ability of this effect to compensate for the lack of phylogenetically diverse probes in in-house synthesised probe sets has not been tested. In this study, we present a refined protocol for in-house RNA probe synthesis and evaluated the ability of probes generated using this method from a single species to successfully enrich for the target locus in phylogenetically distant species. We demonstrated that probes synthesized using long-range PCR products from a placental mammal mitochondrion (Bison spp.) could be used to enrich for mitochondrial DNA in birds and marsupials (but not plants). Importantly, our results were obtained for approximately a third of the cost of similar commercially available reagents.}, }
@article {pmid30712776, year = {2019}, author = {Costedoat, C and Adalian, P and Bouzaid, E and Martinet, A and Vanrell, L and von Gartzen, L and Castellano, P and Signoli, M and Tzortzis, S and Stevanovitch, A}, title = {When a lost &quot;Petit Prince&quot; meets Antoine de Saint Exupéry: An anthropological case report.}, journal = {Forensic science international}, volume = {296}, number = {}, pages = {145-152}, doi = {10.1016/j.forsciint.2019.01.015}, pmid = {30712776}, issn = {1872-6283}, mesh = {Age Determination by Skeleton/methods ; Age Determination by Teeth/methods ; Bone and Bones/*chemistry/*pathology ; DNA/isolation &amp; purification ; *DNA Fingerprinting ; DNA, Mitochondrial/genetics ; *Forensic Anthropology ; France ; History, 20th Century ; Humans ; Male ; Microsatellite Repeats ; Military Personnel ; *Pilots ; Polymerase Chain Reaction ; Radiometric Dating ; Sex Determination by Skeleton/methods ; World War II ; }, abstract = {This case study reports the anthropological analysis of bones remains discovered on Riou Island (Marseille, France) and the story of two World War II fighter pilots. The discovery of bones on &quot;The Fountain of the Greeks&quot; square on Riou Island occurred in the 1960's and a first anthropological study described a 35-year-old man, about 1.77 m tall, buried since an estimated period between the 13th and 16th centuries. The case was &quot;closed&quot; and the bones were considered as isolated archaeological remains. Few years later, near the coasts of Riou Island, parts of two planes were discovered. One was from of a German Messerschmitt Bf 109 F-4 of the Luftwaffe piloted by Prince Alexis fürst zu Bentheim und Steinfurt, and the other from a French P-38 Lightning F-5 B piloted by Antoine de Saint-Exupery. Therefore, the identification of the skeletal remains mentioned above was then thought to be perhaps one of the two World War II pilots. In this particular context we performed forensic and molecular biology analyses to resolve this identification.}, }
@article {pmid30706600, year = {2019}, author = {Díaz, FP and Latorre, C and Carrasco-Puga, G and Wood, JR and Wilmshurst, JM and Soto, DC and Cole, TL and Gutiérrez, RA}, title = {Multiscale climate change impacts on plant diversity in the Atacama Desert.}, journal = {Global change biology}, volume = {25}, number = {5}, pages = {1733-1745}, doi = {10.1111/gcb.14583}, pmid = {30706600}, issn = {1365-2486}, mesh = {*Biodiversity ; Chile ; *Climate Change ; DNA, Ancient/analysis ; *Desert Climate ; Ecosystem ; Fossils ; Plant Dispersal ; *Plants/classification/genetics ; Population Dynamics ; }, abstract = {Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows biodiversity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo-informed millennial record with contemporary observations of interannual variations in diversity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future.}, }
@article {pmid30700787, year = {2019}, author = {Rusu, I and Modi, A and Radu, C and Mircea, C and Vulpoi, A and Dobrinescu, C and Bodolică, V and Potârniche, T and Popescu, O and Caramelli, D and Kelemen, B}, title = {Mitochondrial ancestry of medieval individuals carelessly interred in a multiple burial from southeastern Romania.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {961}, pmid = {30700787}, issn = {2045-2322}, mesh = {Archaeology ; Bone and Bones/metabolism ; Burial/*history ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; Genome, Human ; Genome, Mitochondrial ; Geography ; Haplotypes/genetics ; History, Medieval ; Humans ; Male ; Mitochondria/*genetics ; *Phylogeny ; Romania ; }, abstract = {The historical province of Dobruja, located in southeastern Romania, has experienced intense human population movement, invasions, and conflictual episodes during the Middle Ages, being an important intersection point between Asia and Europe. The most informative source of maternal population histories is the complete mitochondrial genome of archaeological specimens, but currently, there is insufficient ancient DNA data available for the medieval period in this geographical region to complement the archaeological findings. In this study, we reconstructed, by using Next Generation Sequencing, the entire mitochondrial genomes (mitogenomes) of six medieval individuals neglectfully buried in a multiple burial from Capidava necropolis (Dobruja), some presenting signs of a violent death. Six distinct maternal lineages (H11a1, U4d2, J1c15, U6a1a1, T2b, and N1a3a) with different phylogenetic background were identified, pointing out the heterogeneous genetic aspect of the analyzed medieval group. Using population genetic analysis based on high-resolution mitochondrial data, we inferred the genetic affinities of the available medieval dataset from Capidava to other ancient Eurasian populations. The genetic data were integrated with the archaeological and anthropological information in order to sketch a small, local piece of the mosaic that is the image of medieval European population history.}, }
@article {pmid30693949, year = {2019}, author = {Cilli, E and Sarno, S and Gnecchi Ruscone, GA and Serventi, P and De Fanti, S and Delaini, P and Ognibene, P and Basello, GP and Ravegnini, G and Angelini, S and Ferri, G and Gentilini, D and Di Blasio, AM and Pelotti, S and Pettener, D and Sazzini, M and Panaino, A and Luiselli, D and Gruppioni, G}, title = {The genetic legacy of the Yaghnobis: A witness of an ancient Eurasian ancestry in the historically reshuffled central Asian gene pool.}, journal = {American journal of physical anthropology}, volume = {168}, number = {4}, pages = {717-728}, doi = {10.1002/ajpa.23789}, pmid = {30693949}, issn = {1096-8644}, support = {FdM/1200//Fondazione del Monte di Bologna e Ravenna/International ; ERC-2011-AdG295733//FP7 Ideas: European Research Council/International ; }, mesh = {Anthropology, Physical ; Asian Continental Ancestry Group/*genetics ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Ethnic Groups/*genetics ; European Continental Ancestry Group/*genetics ; Human Migration ; Humans ; Male ; Metagenomics ; Polymorphism, Single Nucleotide/genetics ; Tajikistan ; }, abstract = {OBJECTIVES: The Yaghnobis are an ethno-linguistic minority historically settled along the Yaghnob River in the Upper-Zarafshan Valley in Tajikistan. They speak a language of Old Sogdian origin, which is the only present-day witness of the Lingua Franca used along the Silk Road in Late Antiquity. The aim of this study was to reconstruct the genetic history of this community in order to shed light on its isolation and genetic ancestry within the Euro-Asiatic context.<br><br>MATERIALS AND METHODS: A total of 100 DNA samples were collected in the Yaghnob and Matcha Valleys during several expeditions and their mitochondrial, Y-chromosome and autosomal genome-wide variation were compared with that from a large set of modern and ancient Euro-Asiatic samples.<br><br>RESULTS: Findings from uniparental markers highlighted the long-term isolation of the Yaghnobis. Mitochondrial DNA ancestry traced an ancient link with Middle Eastern populations, whereas Y-chromosome legacy showed more tight relationships with Central Asians. Admixture, outgroup-f3, and D-statistics computed on autosomal variation corroborated Y-chromosome evidence, pointing respectively to low Anatolian Neolithic and high Steppe ancestry proportions in Yaghnobis, and to their closer affinity with Tajiks than to Iranians.<br><br>DISCUSSION: Although the Yaghnobis do not show evident signs of recent admixture, they could be considered a modern proxy for the source of gene flow for many Central Asian and Middle Eastern groups. Accordingly, they seem to retain a peculiar genomic ancestry probably ascribable to an ancient gene pool originally wide spread across a vast area and subsequently reshuffled by distinct demographic events occurred in Middle East and Central Asia.}, }
@article {pmid30682121, year = {2019}, author = {Slepchenko, SM and Gusev, AV and Svyatova, EO and Hong, JH and Oh, CS and Lim, DS and Shin, DH}, title = {Medieval mummies of Zeleny Yar burial ground in the Arctic Zone of Western Siberia.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210718}, pmid = {30682121}, issn = {1932-6203}, mesh = {Arctic Regions ; Burial ; Cemeteries ; DNA, Mitochondrial/genetics ; Haplotypes ; Humans ; *Mummies ; Siberia ; }, abstract = {Notwithstanding the pioneering achievements of studies on arctic mummies in Siberia, there are insufficient data for any comprehensive understanding of the bio-cultural details of medieval people living in the region. In the Western Siberian arctic, permafrost mummies have been found in 12th to 13th century graves located in the Zeleny Yar (Z-Y) burial ground (66°19'4.54&quot;С; 67°21'13.54&quot;В). In 2013-2016, we were fortunate to be able to excavate that cemetery, locating a total of 47 burials, including cases of mummification. Some of these mummies had been wrapped in a multi-layered birch-bark cocoon. After removal of the cocoon, we conducted interdisciplinary studies using various scientific techniques. Gross anatomical examination and CT radiography showed that the internal organs were still well preserved inside the body cavities. Under light and electron microscopy, the histological findings were very similar to those for naturally mummified specimens discovered in other countries. Ancient DNA analysis showed that the Z-Y mummies' mtDNA haplotypes belong to five different haplogroups, namely U5a (#34), H3ao (#53), D (#67-1), U4b1b1 (#67-2), and D4j8 (#68), which distinguish them for their unique combination of Western- and Eastern Siberia-specific mtDNA haplogroups. Our interdisciplinary study obtained fundamental information that will form the foundation of successful future investigations on medieval mummies found in the Western Siberian arctic.}, }
@article {pmid30664775, year = {2019}, author = {Lin, M and Kussell, E}, title = {Inferring bacterial recombination rates from large-scale sequencing datasets.}, journal = {Nature methods}, volume = {16}, number = {2}, pages = {199-204}, doi = {10.1038/s41592-018-0293-7}, pmid = {30664775}, issn = {1548-7105}, mesh = {Computational Biology/*methods ; Computer Simulation ; *DNA, Ancient ; DNA, Bacterial ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Escherichia coli/genetics ; Gastrointestinal Microbiome ; Genetic Techniques ; Genetic Variation ; Helicobacter pylori/genetics ; History, Medieval ; Humans ; Metagenomics/*methods ; Models, Genetic ; Mutation ; Plague/history/microbiology ; *Recombination, Genetic ; *Sequence Analysis, DNA ; Yersinia pestis/genetics ; }, abstract = {We present a robust, computationally efficient method (https://github.com/kussell-lab/mcorr) for inferring the parameters of homologous recombination in bacteria, which can be applied in diverse datasets, from whole-genome sequencing to metagenomic shotgun sequencing data. Using correlation profiles of synonymous substitutions, we determine recombination rates and diversity levels of the shared gene pool that has contributed to a given sample. We validated the recombination parameters using data from laboratory experiments. We determined the recombination parameters for a wide range of bacterial species, and inferred the distribution of shared gene pools for global Helicobacter pylori isolates. Using metagenomics data of the infant gut microbiome, we measured the recombination parameters of multidrug-resistant Escherichia coli ST131. Lastly, we analyzed ancient samples of bacterial DNA from the Copper Age 'Iceman' mummy and from 14th century victims of the Black Death, obtaining measurements of bacterial recombination rates and gene pool diversity of earlier eras.}, }
@article {pmid30651584, year = {2019}, author = {Vai, S and Brunelli, A and Modi, A and Tassi, F and Vergata, C and Pilli, E and Lari, M and Susca, RR and Giostra, C and Baricco, LP and Bedini, E and Koncz, I and Vida, T and Mende, BG and Winger, D and Loskotová, Z and Veeramah, K and Geary, P and Barbujani, G and Caramelli, D and Ghirotto, S}, title = {A genetic perspective on Longobard-Era migrations.}, journal = {European journal of human genetics : EJHG}, volume = {27}, number = {4}, pages = {647-656}, pmid = {30651584}, issn = {1476-5438}, mesh = {Bayes Theorem ; Cemeteries ; Czech Republic ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; History, Medieval ; Human Migration/*history ; Humans ; Hungary ; Italy ; }, abstract = {From the first century AD, Europe has been interested by population movements, commonly known as Barbarian migrations. Among these processes, the one involving the Longobard culture interested a vast region, but its dynamics and demographic impact remains largely unknown. Here we report 87 new complete mitochondrial sequences coming from nine early-medieval cemeteries located along the area interested by the Longobard migration (Czech Republic, Hungary and Italy). From the same areas, we sampled necropoleis characterized by cultural markers associated with the Longobard culture (LC) and coeval burials where no such markers were found, or with a chronology slightly preceding the presumed arrival of the Longobards in that region (NLC). Population genetics analysis and demographic modeling highlighted a similarity between LC individuals, as reflected by the sharing of quite rare haplogroups and by the degree of genetic resemblance between Hungarian and Italian LC necropoleis estimated via a Bayesian approach, ABC. The demographic model receiving the strongest statistical support also postulates a contact between LC and NLC communities, thus indicating a complex dynamics of admixture in medieval Europe.}, }
@article {pmid30633908, year = {2019}, author = {O'Connor, TD}, title = {Native American Genomic Diversity through Ancient DNA.}, journal = {Cell}, volume = {176}, number = {1-2}, pages = {405-406}, doi = {10.1016/j.cell.2018.12.033}, pmid = {30633908}, issn = {1097-4172}, }
@article {pmid30628076, year = {2019}, author = {Tackney, J and Jensen, AM and Kisielinski, C and O'Rourke, DH}, title = {Molecular analysis of an ancient Thule population at Nuvuk, Point Barrow, Alaska.}, journal = {American journal of physical anthropology}, volume = {168}, number = {2}, pages = {303-317}, doi = {10.1002/ajpa.23746}, pmid = {30628076}, issn = {1096-8644}, support = {OPP-0732846//Office of Polar Programs/International ; OPP-0732857//Office of Polar Programs/International ; OPP-0637246//Office of Polar Programs/International ; OPP-0535356//Office of Polar Programs/International ; OPP-1460387//Office of Polar Programs/International ; OPP-0820790//Office of Polar Programs/International ; OPP-0726253//Office of Polar Programs/International ; OPP-0820790//National Science Foundation (NSF)/International ; ARC-0726253//National Science Foundation (NSF)/International ; OPP-1460387//National Science Foundation (NSF)/International ; OPP-0535356//National Science Foundation (NSF)/International ; OPP-0637246//National Science Foundation (NSF)/International ; OPP-0732857//International Polar Year grant/International ; OPP-0732846//International Polar Year grant/International ; }, mesh = {Alaska ; Anthropology, Physical ; Arctic Regions ; DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics ; Haplotypes/genetics ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, Medieval ; Humans ; Inuits/*genetics/*history ; Phylogeography ; }, abstract = {OBJECTIVES: The North American archaeological record supports a Holocene origin of Arctic Indigenous peoples. Although the Paleo-Inuit were present for millennia, archaeological and genetic studies suggest that modern peoples descend from a second, more recent tradition known as the Neo-Inuit. Origins of the Neo-Inuit and their relations to the earlier and later Indigenous peoples are an area of active study. Here, we genetically analyze the maternal lineages present at Nuvuk, once the northernmost community in Alaska and located in a region identified as a possible origin point of the Neo-Inuit Thule. The cemetery at Nuvuk contains human remains representing a nearly one thousand year uninterrupted occupation from early Thule to post-contact Iñupiat.<br><br>MATERIALS AND METHODS: We selected 44 individuals from Nuvuk with calibrated dates between 981 AD and 1885 AD for molecular analysis. We amplified and sequenced the hypervariable segment I of the mitogenome. We compared the Nuvuk data with previously published sequences from 68 modern and ancient communities from across Asia and North America. Phylogeographic analyses suggest possible scenarios of Holocene Arctic and sub-Arctic population movements.<br><br>RESULTS: We successfully retrieved sequence data from 39 individuals. Haplogroup frequencies in Nuvuk were typed as 66.7% A2b1, 25.6% A2a, and 7.7% D4b1a2a1a. These results suggest that the population at Nuvuk was closest to the ancient Thule and modern Inuit of Canada, and to the Siberian Naukan people. We confirm that haplogroups A2a, A2b1, D2a, and D4b1a2a1a appear at high frequency in Arctic and sub-Arctic populations of North America and Chukotka. Sister clades D2b and D4b1a2a1b are present in Asian and Eastern European populations.<br><br>DISCUSSION: The ancient mitochondrial sequences from Nuvuk confirm the link between the North Slope and the Thule who later spread east, and the maternal discontinuity between the Neo-Inuit and Paleo-Inuit. We suggest haplogroups A2a, A2b, and D4b1a2a1a are linked to the ancestors of the Thule in eastern Beringia, whereas the D2 and D4b1a2a1 clades appear to have Asian Holocene origins. Further Siberian and Alaskan genomes are necessary to clarify these population migrations beyond a simple two-wave scenario of Neo-Inuit and Paleo-Inuit.}, }
@article {pmid30622634, year = {2019}, author = {Wales, N and Akman, M and Watson, RHB and Sánchez Barreiro, F and Smith, BD and Gremillion, KJ and Gilbert, MTP and Blackman, BK}, title = {Ancient DNA reveals the timing and persistence of organellar genetic bottlenecks over 3,000 years of sunflower domestication and improvement.}, journal = {Evolutionary applications}, volume = {12}, number = {1}, pages = {38-53}, pmid = {30622634}, issn = {1752-4571}, abstract = {Here, we report a comprehensive paleogenomic study of archaeological and ethnographic sunflower remains that provides significant new insights into the process of domestication of this important crop. DNA from both ancient and historic contexts yielded high proportions of endogenous DNA, and although archaeological DNA was found to be highly degraded, it still provided sufficient coverage to analyze genetic changes over time. Shotgun sequencing data from specimens from the Eden's Bluff archaeological site in Arkansas yielded organellar DNA sequence from specimens up to 3,100 years old. Their sequences match those of modern cultivated sunflowers and are consistent with an early domestication bottleneck in this species. Our findings also suggest that recent breeding of sunflowers has led to a loss of genetic diversity that was present only a century ago in Native American landraces. These breeding episodes also left a profound signature on the mitochondrial and plastid haplotypes in cultivars, as two types were intentionally introduced from other Helianthus species for crop improvement. These findings gained from ancient and historic sunflower specimens underscore how future in-depth gene-based analyses can advance our understanding of the pace and targets of selection during the domestication of sunflower and other crop species.}, }
@article {pmid30615665, year = {2019}, author = {Harris, AJT and Duggan, AT and Marciniak, S and Marshall, I and Fuller, BT and Southon, J and Poinar, HN and Grimes, V}, title = {Dorset Pre-Inuit and Beothuk foodways in Newfoundland, ca. AD 500-1829.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210187}, pmid = {30615665}, issn = {1932-6203}, mesh = {*Archaeology ; Bone and Bones/chemistry ; Carbon Isotopes/analysis ; Collagen/chemistry ; Diet ; *Feeding Behavior ; Fossils ; History, Ancient ; Humans ; Indians, North American/*history ; Inuits/*history ; Newfoundland and Labrador/ethnology ; Nitrogen Isotopes/analysis ; Radiometric Dating ; Rivers ; Seafood/analysis ; Taiga ; }, abstract = {Archaeological research on the Canadian island of Newfoundland increasingly demonstrates that the island's subarctic climate and paucity of terrestrial food resources did not restrict past Pre-Inuit (Dorset) and Native American (Beothuk) hunter-gatherer populations to a single subsistence pattern. This study first sought to characterize hunter-gatherer diets over the past 1500 years; and second, to assess the impact of European colonization on Beothuk lifeways by comparing the bone chemistry of Beothuk skeletal remains before and after the intensification of European settlement in the early 18th century. We employed radiocarbon dating and stable carbon and nitrogen isotope ratio analysis of bulk bone collagen from both Dorset (n = 9) and Beothuk (n = 13) cultures, including a naturally mummified 17th century Beothuk individual. Carbon and nitrogen isotope analysis of 108 faunal samples from Dorset and Beothuk archaeological sites around the island were used as a dietary baseline for the humans. We combined our results with previously published isotope data and radiocarbon dates from Dorset (n = 12) and Beothuk (n = 18) individuals and conducted a palaeodietary analysis using Bayesian modelling, cluster analysis and comparative statistical tests. Dorset diets featured more marine protein than those of the Beothuk, and the diets of Beothuk after the 18th century featured less high trophic level marine protein than those of individuals predating the 18th century. Despite inhabiting the same island, Dorset and Beothuk cultures employed markedly different dietary strategies, consistent with interpretations of other archaeological data. Significantly, European colonization had a profound effect on Beothuk lifeways, as in response to the increasing European presence on the coast, the Beothuk relied more extensively on the limited resources of the island's boreal forests and rivers.}, }
@article {pmid30586168, year = {2019}, author = {Ziesemer, KA and Ramos-Madrigal, J and Mann, AE and Brandt, BW and Sankaranarayanan, K and Ozga, AT and Hoogland, M and Hofman, CA and Salazar-García, DC and Frohlich, B and Milner, GR and Stone, AC and Aldenderfer, M and Lewis, CM and Hofman, CL and Warinner, C and Schroeder, H}, title = {The efficacy of whole human genome capture on ancient dental calculus and dentin.}, journal = {American journal of physical anthropology}, volume = {168}, number = {3}, pages = {496-509}, pmid = {30586168}, issn = {1096-8644}, support = {319209//H2020 European Research Council/International ; 649307DK-TAF 5662//Horizon 2020 Framework Programme/International ; BCS 1516633//National Science Foundation/International ; BCS‐1528698//National Science Foundation/International ; }, mesh = {Archaeology ; *DNA, Ancient/analysis/isolation &amp; purification ; Dental Calculus/*chemistry/microbiology ; Dentin/*chemistry ; Female ; Genome, Human/*genetics ; Genomics/*methods ; Humans ; Male ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.<br><br>MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing.<br><br>RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction.<br><br>DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.}, }
@article {pmid30581455, year = {2018}, author = {Aguiar, TS and Torrecilha, RBP and Milanesi, M and Utsunomiya, ATH and Trigo, BB and Tijjani, A and Musa, HH and Lopes, FL and Ajmone-Marsan, P and Carvalheiro, R and Neves, HHR and do Carmo, AS and Hanotte, O and Sonstegard, TS and Garcia, JF and Utsunomiya, YT}, title = {Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {627}, pmid = {30581455}, issn = {1664-8021}, abstract = {Navel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (Bos indicus) using data from 2,016 animals and 503,088 single nucleotide polymorphism (SNP) markers. The strongest signal (p = 1.01 × 10-9) was found on chromosome 5 spanning positions 47.9-48.2 Mbp. This region contains introns 3 and 4 and exons 4 and 5 of the high mobility group AT-hook 2 gene (HMGA2). Further inspection of the region with whole genome sequence data of 21 Nellore bulls revealed correlations between counts of the significant haplotype and copy number gains of a ∼6.2 kbp segment of intron 3 of HMGA2. Analysis of genome sequences from five African B. indicus and four European Bos taurus breeds revealed that the copy number variant (CNV) is indicine-specific. This intronic CNV was then validated through quantitative polymerase chain reaction (qPCR) using Angus animals as copy neutral controls. Importantly, the CNV was not detectable by means of conventional SNP-based GWAS or SNP probe intensity analyses. Given that HMGA2 affects the expression of the insulin-like growth factor 2 gene (IGF2) together with the pleomorphic adenoma gene 1 (PLAG1), and that the latter has been repeatedly shown to be associated with quantitative traits of economic importance in cattle, these findings highlight the emerging role of variants impacting the insulin-like growth factor pathway to cattle breeding.}, }
@article {pmid30581024, year = {2019}, author = {Pinotti, T and Bergström, A and Geppert, M and Bawn, M and Ohasi, D and Shi, W and Lacerda, DR and Solli, A and Norstedt, J and Reed, K and Dawtry, K and González-Andrade, F and Paz-Y-Miño, C and Revollo, S and Cuellar, C and Jota, MS and Santos, JE and Ayub, Q and Kivisild, T and Sandoval, JR and Fujita, R and Xue, Y and Roewer, L and Santos, FR and Tyler-Smith, C}, title = {Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders.}, journal = {Current biology : CB}, volume = {29}, number = {1}, pages = {149-157.e3}, doi = {10.1016/j.cub.2018.11.029}, pmid = {30581024}, issn = {1879-0445}, support = {098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {American Native Continental Ancestry Group/*genetics ; Archaeology ; Chromosomes, Human, Y/*genetics ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Female ; Genome, Human/genetics ; *Genotype ; *Human Migration ; Humans ; Male ; }, abstract = {The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15-25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1-4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation (&quot;Beringian Standstill&quot; [8, 9]) for 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.}, }
@article {pmid30568243, year = {2019}, author = {Rutgers, L and Ostrer, H and Prowse, T and Schroeder, H}, title = {Diaspora, migration, and the sciences: a new integrated perspective.}, journal = {European journal of human genetics : EJHG}, volume = {27}, number = {4}, pages = {509-510}, pmid = {30568243}, issn = {1476-5438}, mesh = {Animals ; DNA, Ancient/*analysis ; *Emigration and Immigration ; *Fossils ; *Human Migration ; Humans ; Plants/genetics ; }, }
@article {pmid30558455, year = {2018}, author = {Varano, S and Gaspari, L and De Angelis, F and Scano, G and Contini, I and Martínez-Labarga, C and Rickards, O}, title = {Mitochondrial characterisation of two Spanish populations from the Vera and Bejar valleys (Central Spain).}, journal = {Annals of human biology}, volume = {45}, number = {6-8}, pages = {531-539}, doi = {10.1080/03014460.2018.1559355}, pmid = {30558455}, issn = {1464-5033}, mesh = {DNA, Mitochondrial/*genetics ; Genes, Mitochondrial/*genetics ; *Genetic Variation ; Humans ; Polymorphism, Single Nucleotide ; Spain ; }, abstract = {This survey reports the mitochondrial data of two Spanish populations living in the Vera and Bejar valleys, on the opposite slopes of the Sierra de Gredos (Central Spain), which crosses Spain east to west. The aim of the study was to characterise the mitochondrial genetic pool of the Vera and Bejar populations to investigate a putative mitogenetic differentiation between them, evidence that would support the role of the Sierra de Gredos as a genetic barrier in their micro-evolutionary histories. Blood samples of 137 people (66 from Vera and 71 from Bejar) were collected and mtDNA hypervariable regions I and II (HVR-I and HVR-II) were dissected along with several mtDNA-coding region SNPs. The main European mitochondrial lineages have been found both in Vera and in Bejar, together with the typical African haplogroups L (in Vera) and U6 (in Bejar). FST value and the 95% credible regions calculated for haplogroup frequencies do not reveal genetic differentiation among the populations. Vera and Bejar contain an expected mitochondrial variability within them, but they do not seem to be genetically different from each other, leading us to conclude that the Sierra de Gredos is not a significant genetic barrier in their maternal genetic history.}, }
@article {pmid30556221, year = {2019}, author = {Afonso, C and Nociarova, D and Santos, C and Martinez-Labarga, C and Mestres, I and Duran, M and Malgosa, A}, title = {Sex selection in late Iberian infant burials: Integrating evidence from morphological and genetic data.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {31}, number = {1}, pages = {e23204}, doi = {10.1002/ajhb.23204}, pmid = {30556221}, issn = {1520-6300}, support = {//Tona City Council/International ; //Museu d'Arqueologia de Catalunya/International ; 2017SGR1630//Generalitat de Catalunya/International ; SFRH/BD/76765/2011//Fundação para a Ciência e a Tecnologia/International ; }, mesh = {Archaeology ; Burial/*history/statistics &amp; numerical data ; Female ; History, Ancient ; Humans ; Infant ; Infant, Newborn ; Infanticide/history ; Male ; Sex Preselection/*history/statistics &amp; numerical data ; Spain ; }, abstract = {OBJECTIVE: The aim of this study was to analyze the infant burials found inside Iberian homes in relation to a possible case of sex selection.<br><br>METHODS: The study included the remains of 11 infant individuals buried under the 10 houses excavated in the late Iberian village of Camp de les Lloses (Tona, Barcelona, Spain). Sex was determined using genetic analysis.<br><br>RESULTS: Our results showed that almost all the burials were females. However, the age interval of death was wide enough to weaken the premise of infanticide, and the burials probably represent cases of natural death.<br><br>DISCUSSION: Infanticide in its different forms has long been argued as an explanation for the infant remains found throughout various burial sites. Many authors thought that infanticide, mainly femicide, was the main method of population control in ancient times. However, there is no anthropological evidence (age distribution and sex analyzed genetically) to support the intentional killing of females in this or in other cases. We hypothesized that there was a positive selection for females to be buried inside the houses, probably related to their benefactor roles.}, }
@article {pmid30554877, year = {2019}, author = {Mohni, KN and Wessel, SR and Zhao, R and Wojciechowski, AC and Luzwick, JW and Layden, H and Eichman, BF and Thompson, PS and Mehta, KPM and Cortez, D}, title = {HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA.}, journal = {Cell}, volume = {176}, number = {1-2}, pages = {144-153.e13}, pmid = {30554877}, issn = {1097-4172}, support = {T32 CA009582/CA/NCI NIH HHS/United States ; F30 CA228242/CA/NCI NIH HHS/United States ; R01 GM116616/GM/NIGMS NIH HHS/United States ; P01 CA092584/CA/NCI NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; F32 GM126646/GM/NIGMS NIH HHS/United States ; }, mesh = {5-Methylcytosine/*analogs &amp; derivatives/metabolism ; Apurinic Acid/metabolism ; DNA/metabolism ; DNA Damage/physiology ; DNA Repair/*physiology ; DNA Replication/physiology ; DNA, Single-Stranded/metabolism/*physiology ; DNA-Binding Proteins/genetics/metabolism ; Endonucleases ; Escherichia coli/metabolism ; Polynucleotides/metabolism ; Proliferating Cell Nuclear Antigen/metabolism ; }, abstract = {Abasic sites are one of the most common DNA lesions. All known abasic site repair mechanisms operate only when the damage is in double-stranded DNA. Here, we report the discovery of 5-hydroxymethylcytosine (5hmC) binding, ESC-specific (HMCES) as a sensor of abasic sites in single-stranded DNA. HMCES acts at replication forks, binds PCNA and single-stranded DNA, and generates a DNA-protein crosslink to shield abasic sites from error-prone processing. This unusual HMCES DNA-protein crosslink intermediate is resolved by proteasome-mediated degradation. Acting as a suicide enzyme, HMCES prevents translesion DNA synthesis and the action of endonucleases that would otherwise generate mutations and double-strand breaks. HMCES is evolutionarily conserved in all domains of life, and its biochemical properties are shared with its E. coli ortholog. Thus, HMCES is an ancient DNA lesion recognition protein that preserves genome integrity by promoting error-free repair of abasic sites in single-stranded DNA.}, }
@article {pmid30550639, year = {2019}, author = {Winters, M and Monroe, C and Barta, JL and Kemp, BM}, title = {Evaluating the Efficiency of Primer Extension Capture as a Method to Enrich DNA Extractions.}, journal = {Journal of forensic sciences}, volume = {64}, number = {4}, pages = {1145-1151}, doi = {10.1111/1556-4029.13973}, pmid = {30550639}, issn = {1556-4029}, support = {2011-DN-BX- K549//National Institute of Justice/ ; //Office of Justice Programs/ ; //U.S. Department of Justice/ ; }, mesh = {DNA/*isolation &amp; purification ; *DNA Primers ; Forensic Genetics/methods ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; Streptavidin/chemistry ; }, abstract = {In this study, we sought to document the efficiency of primer extension capture (PEC) as a method to enrich DNA eluates of targeted DNA molecules and remove nontarget molecules from pools containing both. Efficiency of the method was estimated by comparing number of &quot;copies in&quot; to &quot;copies out&quot; by quantitative polymerase chain reaction. PEC retention of DNA targets ranging 109-288 base pairs (bps) in length was 15.88-2.14% (i.e., loss of 84.12-97.86% of target molecules). Experimental modifications of the PEC method resulted in no significant improvements. However, the benefit of PEC was revealed in its ability to remove most nontarget DNA molecules (99.99%). We also discovered that many (56.69%) of the target molecules are &quot;lost&quot; prior to their immobilization on the streptavidin-coated beads. These estimates of methodological efficiency are directly comparable to previous ones observed following &quot;fishing&quot; for DNA, an alternative method for DNA enrichment.}, }
@article {pmid30545868, year = {2018}, author = {Gibbons, A}, title = {Why modern humans have round heads.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6420}, pages = {1229}, doi = {10.1126/science.362.6420.1229-a}, pmid = {30545868}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Brain/*anatomy &amp; histology ; *DNA, Ancient ; Head/*anatomy &amp; histology ; Humans ; Neanderthals/*genetics ; }, }
@article {pmid30545160, year = {2018}, author = {Esposito, U and Das, R and Syed, S and Pirooznia, M and Elhaik, E}, title = {Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians.}, journal = {Genes}, volume = {9}, number = {12}, pages = {}, pmid = {30545160}, issn = {2073-4425}, support = {MC_PC_14115//Medical Research Council/United Kingdom ; MR/R025126/1//Medical Research Council/United Kingdom ; }, abstract = {The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, thereby, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA, provided that the high missingness rates in ancient-and oftentimes haploid-DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories.}, }
@article {pmid30538303, year = {2019}, author = {Ortega-Del Vecchyo, D and Slatkin, M}, title = {FST between archaic and present-day samples.}, journal = {Heredity}, volume = {122}, number = {6}, pages = {711-718}, pmid = {30538303}, issn = {1365-2540}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Ancient/*analysis ; Fossils/history ; Genetics, Population/*history ; *Genome ; History, Ancient ; Models, Genetic ; }, abstract = {The increasing abundance of DNA sequences obtained from fossils calls for new population genetics theory that takes account of both the temporal and spatial separation of samples. Here, we exploit the relationship between Wright's FST and average coalescence times to develop an analytic theory describing how FST depends on both the distance and time separating pairs of sampled genomes. We apply this theory to several simple models of population history. If there is a time series of samples, partial population replacement creates a discontinuity in pairwise FST values. The magnitude of the discontinuity depends on the extent of replacement. In stepping-stone models, pairwise FST values between archaic and present-day samples reflect both the spatial and temporal separation. At long distances, an isolation by distance pattern dominates. At short distances, the time separation dominates. Analytic predictions fit patterns generated by simulations. We illustrate our results with applications to archaic samples from European human populations. We compare present-day samples with a pair of archaic samples taken before and after a replacement event.}, }
@article {pmid30528431, year = {2019}, author = {Rascovan, N and Sjögren, KG and Kristiansen, K and Nielsen, R and Willerslev, E and Desnues, C and Rasmussen, S}, title = {Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline.}, journal = {Cell}, volume = {176}, number = {1-2}, pages = {295-305.e10}, doi = {10.1016/j.cell.2018.11.005}, pmid = {30528431}, issn = {1097-4172}, mesh = {Biological Evolution ; DNA, Bacterial/genetics ; Europe ; Genome, Bacterial ; History, Ancient ; Humans ; Pandemics ; Phylogeny ; Plague/*history ; Yersinia pestis/*classification/*pathogenicity ; }, abstract = {Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.}, }
@article {pmid30521562, year = {2018}, author = {Fischer, CE and Lefort, A and Pemonge, MH and Couture-Veschambre, C and Rottier, S and Deguilloux, MF}, title = {The multiple maternal legacy of the Late Iron Age group of Urville-Nacqueville (France, Normandy) documents a long-standing genetic contact zone in northwestern France.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207459}, pmid = {30521562}, issn = {1932-6203}, mesh = {Archaeology/methods ; DNA, Ancient/analysis ; DNA, Mitochondrial/analysis/*genetics ; Europe/ethnology ; European Continental Ancestry Group/*genetics ; France/ethnology ; Gene Pool ; Genetic Variation/genetics ; Genetics, Population/methods ; Genotype ; Haplotypes ; History, Ancient ; Humans ; United Kingdom ; }, abstract = {The compilation of archaeological and genetic data for ancient European human groups has provided persuasive evidence for a complex series of migrations, population replacements and admixture until the Bronze Age. If the Bronze-to-Iron Age transition has been well documented archaeologically, ancient DNA (aDNA) remains rare for the latter period and does not precisely reflect the genetic diversity of European Celtic groups. In order to document the evolution of European communities, we analysed 45 individuals from the Late Iron Age (La Tène) Urville-Nacqueville necropolis in northwestern France, a region recognized as a major cultural contact zone between groups from both sides of the Channel. The characterization of 37 HVS-I mitochondrial sequences and 40 haplogroups provided the largest maternal gene pool yet recovered for the European Iron Age. First, descriptive analyses allowed us to demonstrate the presence of substantial amounts of steppe-related mitochondrial ancestry in the community, which is consistent with the expansion of Bell Beaker groups bearing an important steppe legacy in northwestern Europe at approximately 2500 BC. Second, maternal genetic affinities highlighted with Bronze Age groups from Great Britain and the Iberian Peninsula regions tends to support the idea that the continuous cultural exchanges documented archaeologically across the Channel and along the Atlantic coast (during and after the Bronze Age period) were accompanied by significant gene flow. Lastly, our results suggest a maternal genetic continuity between Bronze Age and Iron Age groups that would argue in favour of a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. The palaeogenetic data gathered for the Urville-Nacqueville group constitute an important step in the biological characterization of European Iron age groups. Clearly, more numerous and diachronic aDNA data are needed to fully understand the complex relationship between the cultural and biological evolution of groups from the period.}, }
@article {pmid30517116, year = {2018}, author = {Winkel, T and Aguirre, MG and Arizio, CM and Aschero, CA and Babot, MDP and Benoit, L and Burgarella, C and Costa-Tártara, S and Dubois, MP and Gay, L and Hocsman, S and Jullien, M and López-Campeny, SML and Manifesto, MM and Navascués, M and Oliszewski, N and Pintar, E and Zenboudji, S and Bertero, HD and Joffre, R}, title = {Discontinuities in quinoa biodiversity in the dry Andes: An 18-century perspective based on allelic genotyping.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207519}, pmid = {30517116}, issn = {1932-6203}, mesh = {Alleles ; Argentina ; Biodiversity ; Chenopodium quinoa/*genetics ; DNA, Ancient/analysis ; Gene Pool ; Genetic Variation/genetics ; Genotype ; Genotyping Techniques/history/*methods ; History, 18th Century ; Seeds ; }, abstract = {History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries-a time of agricultural intensification well before the Inka and Spanish conquests-and then between the 13th century and today-a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories.}, }
@article {pmid30514893, year = {2018}, author = {Zalloua, P and Collins, CJ and Gosling, A and Biagini, SA and Costa, B and Kardailsky, O and Nigro, L and Khalil, W and Calafell, F and Matisoo-Smith, E}, title = {Ancient DNA of Phoenician remains indicates discontinuity in the settlement history of Ibiza.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17567}, pmid = {30514893}, issn = {2045-2322}, mesh = {African Continental Ancestry Group/genetics/*history ; Archaeology ; Body Remains ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Emigration and Immigration/*history ; European Continental Ancestry Group/genetics/*history ; Genetic Variation ; Genome, Mitochondrial/genetics ; History, Ancient ; Humans ; Male ; Phylogeography ; Spain ; }, abstract = {Ibiza was permanently settled around the 7th century BCE by founders arriving from west Phoenicia. The founding population grew significantly and reached its height during the 4th century BCE. We obtained nine complete mitochondrial genomes from skeletal remains from two Punic necropoli in Ibiza and a Bronze Age site from Formentara. We also obtained low coverage (0.47X average depth) of the genome of one individual, directly dated to 361-178 cal BCE, from the Cas Molí site on Ibiza. We analysed and compared ancient DNA results with 18 new mitochondrial genomes from modern Ibizans to determine the ancestry of the founders of Ibiza. The mitochondrial results indicate a predominantly recent European maternal ancestry for the current Ibizan population while the whole genome data suggest a significant Eastern Mediterranean component. Our mitochondrial results suggest a genetic discontinuity between the early Phoenician settlers and the island's modern inhabitants. Our data, while limited, suggest that the Eastern or North African influence in the Punic population of Ibiza was primarily male dominated.}, }
@article {pmid30514813, year = {2019}, author = {Thompson, TQ and Bellinger, MR and O'Rourke, SM and Prince, DJ and Stevenson, AE and Rodrigues, AT and Sloat, MR and Speller, CF and Yang, DY and Butler, VL and Banks, MA and Miller, MR}, title = {Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {1}, pages = {177-186}, pmid = {30514813}, issn = {1091-6490}, mesh = {*Adaptation, Physiological/genetics ; Alleles ; Animal Migration ; Animals ; *Ecosystem ; Genetic Loci/genetics ; Genetic Variation/genetics ; Oregon ; *Salmon/genetics ; }, abstract = {Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.}, }
@article {pmid30498238, year = {2018}, author = {Epp, LS and Kruse, S and Kath, NJ and Stoof-Leichsenring, KR and Tiedemann, R and Pestryakova, LA and Herzschuh, U}, title = {Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17436}, pmid = {30498238}, issn = {2045-2322}, mesh = {Biodiversity ; *DNA, Mitochondrial ; Forests ; Geography ; *Haplotypes ; Larix/*genetics ; Mitochondria/*genetics ; Siberia ; Spatio-Temporal Analysis ; }, abstract = {Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.}, }
@article {pmid30497919, year = {2019}, author = {Eisenhofer, R and Minich, JJ and Marotz, C and Cooper, A and Knight, R and Weyrich, LS}, title = {Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations.}, journal = {Trends in microbiology}, volume = {27}, number = {2}, pages = {105-117}, doi = {10.1016/j.tim.2018.11.003}, pmid = {30497919}, issn = {1878-4380}, mesh = {*Biomass ; *DNA Contamination ; DNA, Bacterial/analysis/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Microbiological Techniques/methods/standards ; Microbiota/*genetics ; Reproducibility of Results ; Specimen Handling ; }, abstract = {Next-generation sequencing approaches in microbiome research have allowed surveys of microbial communities, their genomes, and their functions with higher sensitivity than ever before. However, this sensitivity is a double-edged sword because these tools also efficiently detect contaminant DNA and cross-contamination, which can confound the interpretation of microbiome data. Therefore, there is an urgent need to integrate key controls into microbiome research to improve the integrity of microbiome studies. Here, we review how contaminant DNA and cross-contamination arise within microbiome studies and discuss their negative impacts, especially during the analysis of low microbial biomass samples. We then identify several key measures that researchers can implement to reduce the impact of contaminant DNA and cross-contamination during microbiome research. We put forward a set of minimal experimental criteria, the 'RIDE' checklist, to improve the validity of future low microbial biomass research.}, }
@article {pmid30486782, year = {2018}, author = {Baichoo, S and Souilmi, Y and Panji, S and Botha, G and Meintjes, A and Hazelhurst, S and Bendou, H and Beste, E and Mpangase, PT and Souiai, O and Alghali, M and Yi, L and O'Connor, BD and Crusoe, M and Armstrong, D and Aron, S and Joubert, F and Ahmed, AE and Mbiyavanga, M and Heusden, PV and Magosi, LE and Zermeno, J and Mainzer, LS and Fadlelmola, FM and Jongeneel, CV and Mulder, N}, title = {Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {457}, pmid = {30486782}, issn = {1471-2105}, support = {U24 HG006941/HG/NHGRI NIH HHS/United States ; U41 HG006941/HG/NHGRI NIH HHS/United States ; U41HG006941//National Human Genome Research Institute/ ; }, mesh = {Africa ; Computational Biology/*methods ; Genomics/*methods ; Humans ; Reproducibility of Results ; }, abstract = {BACKGROUND: The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research consortium funded by the US National Institutes of Health and the UK Wellcome Trust, aimed at using genomics to study and improve the health of Africans. A key role of H3ABioNet is to support H3Africa projects by building bioinformatics infrastructure such as portable and reproducible bioinformatics workflows for use on heterogeneous African computing environments. Processing and analysis of genomic data is an example of a big data application requiring complex interdependent data analysis workflows. Such bioinformatics workflows take the primary and secondary input data through several computationally-intensive processing steps using different software packages, where some of the outputs form inputs for other steps. Implementing scalable, reproducible, portable and easy-to-use workflows is particularly challenging.<br><br>RESULTS: H3ABioNet has built four workflows to support (1) the calling of variants from high-throughput sequencing data; (2) the analysis of microbial populations from 16S rDNA sequence data; (3) genotyping and genome-wide association studies; and (4) single nucleotide polymorphism imputation. A week-long hackathon was organized in August 2016 with participants from six African bioinformatics groups, and US and European collaborators. Two of the workflows are built using the Common Workflow Language framework (CWL) and two using Nextflow. All the workflows are containerized for improved portability and reproducibility using Docker, and are publicly available for use by members of the H3Africa consortium and the international research community.<br><br>CONCLUSION: The H3ABioNet workflows have been implemented in view of offering ease of use for the end user and high levels of reproducibility and portability, all while following modern state of the art bioinformatics data processing protocols. The H3ABioNet workflows will service the H3Africa consortium projects and are currently in use. All four workflows are also publicly available for research scientists worldwide to use and adapt for their respective needs. The H3ABioNet workflows will help develop bioinformatics capacity and assist genomics research within Africa and serve to increase the scientific output of H3Africa and its Pan-African Bioinformatics Network.}, }
@article {pmid30481358, year = {2019}, author = {Cascini, M and Mitchell, KJ and Cooper, A and Phillips, MJ}, title = {Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence.}, journal = {Systematic biology}, volume = {68}, number = {3}, pages = {520-537}, doi = {10.1093/sysbio/syy080}, pmid = {30481358}, issn = {1076-836X}, mesh = {Animals ; Classification ; DNA/*genetics ; DNA, Ancient ; Fossils/*anatomy &amp; histology ; Macropodidae/anatomy &amp; histology/*classification/genetics ; *Phylogeny ; }, abstract = {Combined &quot;total evidence&quot; analysis of molecular and morphological data offers the opportunity to objectively merge fossils into the tree of life, and challenges the primacy of solely DNA based phylogenetic and dating inference, even among modern taxa. To investigate the relative utility of DNA, morphology, and total evidence for evolutionary inference, we sequenced the first near-complete mitochondrial genomes from extinct Australian megafauna: a 40-50 thousand year old giant short-faced kangaroo (Simosthenurus occidentalis) and giant wallaby (Protemnodon anak). We analyzed the ancient DNA and fossil data alongside comparable data from extant species to infer phylogeny, divergence times, and ancestral body mass among macropods (kangaroos and wallabies). Our results confirm a close relationship between Protemnodon and the iconic kangaroo genus complex &quot;Macropus&quot;, and unite the giant Simothenurus with the hare-sized Lagostrophus fasciatus (banded hare-wallaby), suggesting that the latter is the closest living link to the once diverse sthenurine kangaroo radiation. We find that large body size evolved multiple times among kangaroos, coincident with expansion of open woodland habitats beginning in the Late Miocene. In addition, our results suggest that morphological data mislead macropod phylogeny reconstruction and in turn can distort total evidence estimation of divergence dates. However, a novel result with potentially broad application is that the accuracy and precision of reconstructing ancestral body mass was improved by tracing body mass on morphological branch lengths. This is likely due to positive allometric correlation between morphological and body size variation-a relationship that may be masked or even misleadingly inverted with the temporal or molecular branch lengths that typically underpin ancestral body size reconstruction. Our study supports complementary roles for DNA and morphology in evolutionary inference, and opens a new window into the evolution of Australia's unique marsupial fauna.}, }
@article {pmid30479341, year = {2018}, author = {Lamnidis, TC and Majander, K and Jeong, C and Salmela, E and Wessman, A and Moiseyev, V and Khartanovich, V and Balanovsky, O and Ongyerth, M and Weihmann, A and Sajantila, A and Kelso, J and Pääbo, S and Onkamo, P and Haak, W and Krause, J and Schiffels, S}, title = {Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5018}, pmid = {30479341}, issn = {2041-1723}, mesh = {Archaeology ; Female ; Finland ; *Genealogy and Heraldry ; Genetics, Population ; *Genome, Human ; Geography ; Humans ; Male ; Principal Component Analysis ; Siberia ; }, abstract = {European population history has been shaped by migrations of people, and their subsequent admixture. Recently, ancient DNA has brought new insights into European migration events linked to the advent of agriculture, and possibly to the spread of Indo-European languages. However, little is known about the ancient population history of north-eastern Europe, in particular about populations speaking Uralic languages, such as Finns and Saami. Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland.}, }
@article {pmid30478308, year = {2019}, author = {Kosintsev, P and Mitchell, KJ and Devièse, T and van der Plicht, J and Kuitems, M and Petrova, E and Tikhonov, A and Higham, T and Comeskey, D and Turney, C and Cooper, A and van Kolfschoten, T and Stuart, AJ and Lister, AM}, title = {Evolution and extinction of the giant rhinoceros Elasmotherium sibiricum sheds light on late Quaternary megafaunal extinctions.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {1}, pages = {31-38}, doi = {10.1038/s41559-018-0722-0}, pmid = {30478308}, issn = {2397-334X}, mesh = {Animals ; Bone and Bones/chemistry ; Carbon Isotopes/analysis ; DNA/analysis ; Evolution, Molecular ; *Extinction, Biological ; Nitrogen Isotopes/analysis ; *Perissodactyla/genetics ; Phylogeny ; }, abstract = {Understanding extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the 'Siberian unicorn', was believed to have gone extinct around 200,000 years ago-well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 individuals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000 years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had diverged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the 'Siberian unicorn' marked the extinction of this subfamily.}, }
@article {pmid30478041, year = {2018}, author = {Namouchi, A and Guellil, M and Kersten, O and Hänsch, S and Ottoni, C and Schmid, BV and Pacciani, E and Quaglia, L and Vermunt, M and Bauer, EL and Derrick, M and Jensen, AØ and Kacki, S and Cohn, SK and Stenseth, NC and Bramanti, B}, title = {Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {50}, pages = {E11790-E11797}, pmid = {30478041}, issn = {1091-6490}, mesh = {DNA, Bacterial/genetics/isolation &amp; purification ; Europe/epidemiology ; Evolution, Molecular ; Fossils/microbiology ; Genome, Bacterial ; History, Medieval ; Humans ; Pandemics/*history ; Phylogeny ; Plague/epidemiology/*history/microbiology ; Polymorphism, Single Nucleotide ; Time Factors ; Yersinia pestis/classification/*genetics ; }, abstract = {Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.}, }
@article {pmid30471018, year = {2019}, author = {Santi, R and Rizzolo, P and Pietragalla, M and Valentini, V and Zelli, V and Galassi, FM and Ottini, L and Nesi, G}, title = {The antiquity of hydrocephalus: the first full palaeo-neuropathological description.}, journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology}, volume = {40}, number = {6}, pages = {1315-1322}, pmid = {30471018}, issn = {1590-3478}, support = {no grant number//Mäxi Foundation/ ; }, mesh = {DNA, Ancient ; History, 19th Century ; Humans ; Hydrocephalus/diagnostic imaging/*genetics/history/*pathology ; Infant ; Italy ; Male ; *Models, Anatomic ; Museums ; Sculpture ; Waxes ; }, abstract = {The Pathology Museum of the University of Florence houses a rich collection of anatomical specimens and over a hundred waxworks portraying pathological conditions occurring in the nineteenth century, when the museum was established. Clinical and autopsy findings of these cases can still be retrieved from the original museum catalogue, offering a rare opportunity for retrospective palaeo-pathological diagnostics. We present a historical case of severe hydrocephalus backed by modern-day anthropological, radiological and molecular analyses conducted on the skeleton of an 18-month-old male infant deceased in 1831. Luigi Calamai (1796-1851), a wax craftsman of La Specola workshop in Florence, was commissioned to create a life-sized wax model of the child's head, neck and upper thorax. This artwork allows us to appreciate the cranial and facial alterations determined by 30 lb of cerebrospinal fluid (CSF) accumulated within the cerebral ventricular system. Based on the autopsy report, gross malformations of the neural tube, tumours and haemorrhage could be excluded. A molecular approach proved helpful in confirming sex. We present this case as the so-far most compelling case of hydrocephalus in palaeo-pathological research.}, }
@article {pmid30468917, year = {2019}, author = {Buckley, M and Lawless, C and Rybczynski, N}, title = {Collagen sequence analysis of fossil camels, Camelops and c.f. Paracamelus, from the Arctic and sub-Arctic of Plio-Pleistocene North America.}, journal = {Journal of proteomics}, volume = {194}, number = {}, pages = {218-225}, doi = {10.1016/j.jprot.2018.11.014}, pmid = {30468917}, issn = {1876-7737}, support = {BB/L002817/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Arctic Regions ; Camelids, New World/*genetics ; Collagen/*genetics ; *DNA, Ancient ; *Fossils ; North America ; *Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Proteomic analyses of ancient remains are increasing in number and offer great potential to recover phylogenetic information on extinct animals beyond the reach of ancient DNA, but limitations in proteomic techniques remain unclear. Here we carry out LC-MS/MS sequence analysis of a ~3.5 million year old giant camel specimen from Nunavut along with the younger Pleistocene remains of the Yukon giant camel (c.f. Paracamelus) and the western camel (Camelops hesternus) for comparison with complete sequences to both extant camels (Bactrian and Dromedary) and the alpaca. Although not complete (~75-80% sequence coverage), no amino acid sequence differences were confidently observed between the giant camels and the extant Dromedary, indicative of a closer relationship than that of the extant Bactrian lineage. However, multiple amino acid changes were observed for the western camel (Camelops) collagen sequence, placing it as a sister group to these members of the Camelini tribe consistent recent ancient DNA analyses. Although this supports a role for the sequencing of ancient collagen in the understanding of vertebrate evolution, these analyses highlight the limitations in phylogenetic reconstructions based on partial sequence data retrieved from proteomic analyses, particularly, the impact of omitting even only a single peptide on the resulting tree topology. The presence of other non-collagenous proteins, such as biglycan and PEDF, indicates a further resource for phylogenetic information, but none more promising than the degraded camel albumin seemingly observed in the Pliocene specimen. SIGNIFICANCE: As proteomics is becoming more frequently used in the study of ancient proteins, an emerging field known as 'palaeoproteomics' (or 'paleoproteomics'), understanding the limitations of the technique is essential. Here, through the study of the oldest undisputed collagen sequences obtained from proteomics, we confirm that some peptides following diagenetic modifications of tryptic sites are no longer matched with standard searches, but can be matched with Error Tolerant searches. We also demonstrate the ability to retrieve phylogenetic information consistent with that of ancient DNA methods, but that with the omission of only one or more key peptides, the inferred evolutionary relationships change. This is a significant finding for the field of palaeoproteomics implying a need for better understanding the particular composition of the partial sequences retrieved from proteomic analyses.}, }
@article {pmid30464240, year = {2018}, author = {Wood, JR and Díaz, FP and Latorre, C and Wilmshurst, JM and Burge, OR and Gutiérrez, RA}, title = {Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {17208}, pmid = {30464240}, issn = {2045-2322}, support = {Core funding for Crown Research Institutes//Ministry of Business, Innovation and Employment (MBIE)/International ; Core funding to Crown Research Institutes//Ministry for Business Innovation and Employment (MBIE)/International ; }, mesh = {Animals ; Chile ; *Climate Change ; DNA, Ancient/*isolation &amp; purification ; DNA, Fungal/*isolation &amp; purification ; Desert Climate ; Feces/chemistry ; *Fossils ; Fungi/*classification/*genetics ; Metagenomics/methods ; Plant Diseases/*microbiology ; RNA, Ribosomal, 18S/genetics ; Rodentia ; }, abstract = {Future climate change has the potential to alter the distribution and prevalence of plant pathogens, which may have significant implications for both agricultural crops and natural plant communities. However, there are few long-term datasets against which modelled predictions of pathogen responses to climate change can be tested. Here, we use 18S metabarcoding of 28 rodent middens (solidified deposits of rodent coprolites and nesting material) from the Central Atacama, spanning the last ca. 49 ka, to provide the first long-term late Quaternary record of change in plant pathogen communities in response to changing climate. Plant pathogen richness was significantly greater in middens deposited during the Central Andean Pluvial Event (CAPE); a period of increased precipitation between 17.5-8.5 ka. Moreover, the occurrence frequency of Pucciniaceae (rust fungi) was significantly greater during the CAPE, and the highest relative abundances for five additional potentially pathogenic taxa also occurred during this period. The results demonstrate the promising potential for ancient DNA analysis of late Quaternary samples to reveal insights into how plant pathogens responded to past climatic and environmental change, which could help predict how pathogens may responded to future change.}, }
@article {pmid30459334, year = {2018}, author = {Jersie-Christensen, RR and Lanigan, LT and Lyon, D and Mackie, M and Belstrøm, D and Kelstrup, CD and Fotakis, AK and Willerslev, E and Lynnerup, N and Jensen, LJ and Cappellini, E and Olsen, JV}, title = {Quantitative metaproteomics of medieval dental calculus reveals individual oral health status.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4744}, pmid = {30459334}, issn = {2041-1723}, mesh = {Adult ; Archaeology/methods ; Bacteria/classification ; Bacterial Proteins/analysis ; DNA, Ancient/analysis ; DNA, Bacterial/analysis ; Denmark ; Dental Calculus/*microbiology ; Dental Plaque/microbiology ; Dietary Proteins ; Female ; *Health Status ; Humans ; Male ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; *Oral Health ; Proteomics/*methods ; }, abstract = {The composition of ancient oral microbiomes has recently become accessible owing to advanced biomolecular methods such as metagenomics and metaproteomics, but the utility of metaproteomics for such analyses is less explored. Here, we use quantitative metaproteomics to characterize the dental calculus associated with the remains of 21 humans retrieved during the archeological excavation of the medieval (ca. 1100-1450 CE) cemetery of Tjærby, Denmark. We identify 3671 protein groups, covering 220 bacterial species and 81 genera across all medieval samples. The metaproteome profiles of bacterial and human proteins suggest two distinct groups of archeological remains corresponding to health-predisposed and oral disease-susceptible individuals, which is supported by comparison to the calculus metaproteomes of healthy living individuals. Notably, the groupings identified by metaproteomics are not apparent from the bioarchaeological analysis, illustrating that quantitative metaproteomics has the potential to provide additional levels of molecular information about the oral health status of individuals from archeological contexts.}, }
@article {pmid30455210, year = {2018}, author = {Andrew, C and Diez, J and James, TY and Kauserud, H}, title = {Fungarium specimens: a largely untapped source in global change biology and beyond.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1763}, pages = {}, pmid = {30455210}, issn = {1471-2970}, mesh = {*Climate Change ; *Fungi ; *Museums ; Specimen Handling ; }, abstract = {For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.}, }
@article {pmid30445034, year = {2018}, author = {O'Connor, TD}, title = {Native American Genomic Diversity through Ancient DNA.}, journal = {Cell}, volume = {175}, number = {5}, pages = {1173-1174}, doi = {10.1016/j.cell.2018.10.058}, pmid = {30445034}, issn = {1097-4172}, mesh = {*DNA, Ancient ; Genetics, Population ; Genomics ; Humans ; *Indians, North American ; South America ; }, abstract = {Ancient DNA is a powerful tool to understand the evolutionary dynamics of both current and ancestral populations. Posth et al. use ancient DNA to elucidate important questions surrounding the peopling of Central and South America, giving us greater insights into the ancestry of genetically understudied populations.}, }
@article {pmid30425363, year = {2018}, author = {Callaway, E}, title = {Ancient genomics is recasting the story of the Americas' first residents.}, journal = {Nature}, volume = {563}, number = {7731}, pages = {303-304}, doi = {10.1038/d41586-018-07374-1}, pmid = {30425363}, issn = {1476-4687}, mesh = {Archaeology ; Central America/ethnology ; DNA, Ancient/*analysis ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/*history ; Humans ; Indians, North American/genetics ; Infant ; Male ; Montana ; Oceanic Ancestry Group/genetics ; South America/ethnology ; }, }
@article {pmid30420497, year = {2018}, author = {Woods, R and Turvey, ST and Brace, S and MacPhee, RDE and Barnes, I}, title = {Ancient DNA of the extinct Jamaican monkey Xenothrix reveals extreme insular change within a morphologically conservative radiation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {50}, pages = {12769-12774}, pmid = {30420497}, issn = {1091-6490}, mesh = {Adaptation, Physiological/genetics ; Animals ; Biodiversity ; Caribbean Region ; Cell Nucleus/genetics ; DNA, Ancient/*analysis ; Fossils ; Genome, Mitochondrial/genetics ; Haplorhini/*genetics ; Phylogeny ; Water ; }, abstract = {The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5-18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations.}, }
@article {pmid30417096, year = {2018}, author = {Lindo, J and Haas, R and Hofman, C and Apata, M and Moraga, M and Verdugo, RA and Watson, JT and Viviano Llave, C and Witonsky, D and Beall, C and Warinner, C and Novembre, J and Aldenderfer, M and Di Rienzo, A}, title = {The genetic prehistory of the Andean highlands 7000 years BP though European contact.}, journal = {Science advances}, volume = {4}, number = {11}, pages = {eaau4921}, pmid = {30417096}, issn = {2375-2548}, support = {R01 HL119577/HL/NHLBI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; DNA, Ancient/*analysis ; *Genetics, Population ; *Genome, Human ; Genotype ; Humans ; Hypoxia/*genetics ; Indians, South American/*genetics ; *Polymorphism, Single Nucleotide ; Population Dynamics ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.}, }
@article {pmid30415837, year = {2018}, author = {Posth, C and Nakatsuka, N and Lazaridis, I and Skoglund, P and Mallick, S and Lamnidis, TC and Rohland, N and Nägele, K and Adamski, N and Bertolini, E and Broomandkhoshbacht, N and Cooper, A and Culleton, BJ and Ferraz, T and Ferry, M and Furtwängler, A and Haak, W and Harkins, K and Harper, TK and Hünemeier, T and Lawson, AM and Llamas, B and Michel, M and Nelson, E and Oppenheimer, J and Patterson, N and Schiffels, S and Sedig, J and Stewardson, K and Talamo, S and Wang, CC and Hublin, JJ and Hubbe, M and Harvati, K and Nuevo Delaunay, A and Beier, J and Francken, M and Kaulicke, P and Reyes-Centeno, H and Rademaker, K and Trask, WR and Robinson, M and Gutierrez, SM and Prufer, KM and Salazar-García, DC and Chim, EN and Müller Plumm Gomes, L and Alves, ML and Liryo, A and Inglez, M and Oliveira, RE and Bernardo, DV and Barioni, A and Wesolowski, V and Scheifler, NA and Rivera, MA and Plens, CR and Messineo, PG and Figuti, L and Corach, D and Scabuzzo, C and Eggers, S and DeBlasis, P and Reindel, M and Méndez, C and Politis, G and Tomasto-Cagigao, E and Kennett, DJ and Strauss, A and Fehren-Schmitz, L and Krause, J and Reich, D}, title = {Reconstructing the Deep Population History of Central and South America.}, journal = {Cell}, volume = {175}, number = {5}, pages = {1185-1197.e22}, pmid = {30415837}, issn = {1097-4172}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; FC001595/MRC_/Medical Research Council/United Kingdom ; T32 GM007753/GM/NIGMS NIH HHS/United States ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; }, mesh = {Central America ; DNA, Ancient/analysis ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetics, Population/*history ; *Genome, Human ; History, Ancient ; Humans ; Models, Theoretical ; South America ; }, abstract = {We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.}, }
@article {pmid30409866, year = {2018}, author = {Wade, L}, title = {Ancient DNA tracks migrations around Americas.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6415}, pages = {627-628}, doi = {10.1126/science.362.6415.627}, pmid = {30409866}, issn = {1095-9203}, mesh = {Americas ; DNA, Ancient/*analysis ; History, Ancient ; Human Migration/*history ; Humans ; }, }
@article {pmid30408262, year = {2018}, author = {Karafet, TM and Osipova, LP and Savina, OV and Hallmark, B and Hammer, MF}, title = {Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations.}, journal = {American journal of human biology : the official journal of the Human Biology Council}, volume = {30}, number = {6}, pages = {e23194}, doi = {10.1002/ajhb.23194}, pmid = {30408262}, issn = {1520-6300}, support = {0324-2018-0016//State Research Project/International ; PLR-1203874//National Science Foundation/International ; }, mesh = {Chromosomes, Human, Y/genetics ; DNA, Ancient/analysis ; *Genetic Variation ; Human Migration ; Humans ; *Linguistics ; *Polymorphism, Single Nucleotide ; Siberia ; }, abstract = {OBJECTIVES: We examined autosomal genome-wide SNPs and Y-chromosome data from 15 Siberian and 12 reference populations to study the affinities of Siberian populations, and to address hypotheses about the origin of the Samoyed peoples.<br><br>METHODS: Samples were genotyped for 567 096 autosomal SNPs and 147 Y-chromosome polymorphic sites. For several analyses, we used 281 093 SNPs from the intersection of our data with publicly available ancient Siberian samples. To examine genetic relatedness among populations, we applied PCA, FST , TreeMix, and ADMIXTURE analyses. To explore the potential effect of demography and evolutionary processes, the distribution of ROH and IBD sharing within population were studied.<br><br>RESULTS: Analyses of autosomal and Y-chromosome data reveal high differentiation of the Siberian groups. The Siberian populations have a large proportion of their genome in ROH and IBD segments. Several populations (ie, Nganasans, Evenks, Yukagirs, and Koryaks) do not appear to have experienced admixture with other Siberian populations (ie, producing only positive f3), while for the other tested populations the composition of mixing sources always included Nganasans or Evenks. The Nganasans from the Taymyr Peninsula demonstrate the greatest level of shared shorter ROH and IBD with nearly all other Siberian populations.<br><br>CONCLUSIONS: Autosomal SNP and Y-chromosome data demonstrate that Samoyedic populations differ significantly in their genetic composition. Genetic relationship is observed only between Forest and Tundra Nentsi. Selkups are affiliated with the Kets from the Yenisey River, while the Nganasans are separated from their linguistic neighbors, showing closer affinities with the Evenks and Yukagirs.}, }
@article {pmid30408154, year = {2019}, author = {Quillen, EE and Norton, HL and Parra, EJ and Lona-Durazo, F and Ang, KC and Illiescu, FM and Pearson, LN and Shriver, MD and Lasisi, T and Gokcumen, O and Starr, I and Lin, YL and Martin, AR and Jablonski, NG}, title = {Shades of complexity: New perspectives on the evolution and genetic architecture of human skin.}, journal = {American journal of physical anthropology}, volume = {168 Suppl 67}, number = {}, pages = {4-26}, doi = {10.1002/ajpa.23737}, pmid = {30408154}, issn = {1096-8644}, support = {K99 MH117229/MH/NIMH NIH HHS/United States ; 1714867//National Science Foundation/International ; }, mesh = {Anthropology, Physical ; Antiporters/genetics ; *Biological Evolution ; Genetics, Population ; Guanine Nucleotide Exchange Factors/genetics ; Humans ; Membrane Proteins/genetics ; Membrane Transport Proteins/genetics ; Receptor, Melanocortin, Type 1/genetics ; Skin/metabolism ; *Skin Physiological Phenomena ; *Skin Pigmentation/genetics/physiology ; Ubiquitin-Protein Ligases ; }, abstract = {Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.}, }
@article {pmid30406142, year = {2018}, author = {Guedes, L and Dias, O and Neto, J and Ribeiro da Silva, LDP and Mendonça de Souza, SMF and Iñiguez, AM}, title = {First Paleogenetic Evidence of Probable Syphilis and Treponematoses Cases in the Brazilian Colonial Period.}, journal = {BioMed research international}, volume = {2018}, number = {}, pages = {8304129}, pmid = {30406142}, issn = {2314-6141}, mesh = {Adolescent ; Adult ; Base Sequence ; Brazil ; Female ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Male ; *Paleopathology ; Syphilis/*genetics/*history/pathology ; Treponema/genetics ; Treponemal Infections/*genetics/*history/pathology ; Young Adult ; }, abstract = {Despite interest in the origins of syphilis, paleopathological analysis has not provided answers, and paleogenetic diagnosis remains a challenge. Even venereal syphilis has low infectivity which means there are few circulating bacteria for most of the individual's life. Human remains recovered from the Nossa Senhora do Carmo Church (17th to 19th centuries) and the Praça XV Cemetery (18th to 19th centuries), Rio de Janeiro, Brazil, were subjected to Treponema paleogenetic analysis. Historical data point to endemic treponemal infections in the city, including venereal syphilis. Based on the physiopathology of Treponema pallidum infection, 25 samples, mostly from skull remains of young adults, with no visible paleopathological evidence of treponematoses, were analyzed. PCR with three molecular targets, tpp47, polA, and tpp15, were applied. Ancient DNA tpp15 sequences were recovered from two young adults from each archaeological site and revealed the polymorphism that characterizes T. p. subsp. pallidum in a female up to 18 years old, suggesting a probable case of syphilis infection. The results indicated that the epidemiological context and the physiopathology of the disease should be considered in syphilis paleogenetic detection. The findings of Treponema sp. aDNA are consistent with historical documents that describe venereal syphilis and yaws as endemic diseases in Rio de Janeiro. Data on the epidemiological characteristics of the disease and its pathophysiology offer new perspectives in paleopathology.}, }
@article {pmid30399480, year = {2019}, author = {Pfeiffer, S and Harrington, L and Lombard, M}, title = {The people behind the samples: Biographical features of Past Hunter-Gatherers from KwaZulu-Natal who yielded aDNA.}, journal = {International journal of paleopathology}, volume = {24}, number = {}, pages = {158-164}, doi = {10.1016/j.ijpp.2018.10.008}, pmid = {30399480}, issn = {1879-9825}, mesh = {Adult ; Base Sequence/genetics ; Bone and Bones/*pathology ; Child ; DNA, Ancient/*analysis ; Humans ; Malaria ; Male ; Schistosomiasis/diagnosis/*pathology ; Skull/*pathology ; South Africa ; }, abstract = {PURPOSE: Skeletons sampled for ancient human DNA analysis are sometimes complete enough to provide information about the lives of the people they represent. We focus on three Later Stone Age skeletons, ca. 2000 B.P., from coastal KwaZulu-Natal, South Africa, whose ancient genomes have been sequenced (Schlebusch et al., 2017).<br><br>METHODS: Bioarchaeological approaches are integrated with aDNA information.<br><br>RESULTS: All skeletons are male. Dental development shows that the boy, with prominent cribra orbitalia, died at age 6-7 years. Two men show cranial and spinal trauma, extensive tooth wear, plus mild cribra orbitalia in one.<br><br>CONCLUSIONS: Dental wear and trauma of the adults are consistent with hunter-gatherer lives. Even partial aDNA evidence contributes to sex determination. Parasitic infection such as schistosomiasis is the best-fit cause for the child's anemia in this case.<br><br>CONTRIBUTION TO KNOWLEDGE: The convergence of genomic and bioarchaeological approaches expands our knowledge of the past lives of a boy and two men whose lives as hunter-gatherers included episodes of trauma and disease.<br><br>LIMITATIONS: The skeletons are incomplete, in variable condition, and from poorly characterized local cultural contexts.<br><br>Thorough osteobiographic analysis should accompany paleogenomic investigations. Such disciplinary collaboration enriches our understanding of the human past.}, }
@article {pmid30391623, year = {2019}, author = {Hefetz, I and Einot, N and Faerman, M and Horowitz, M and Almog, J}, title = {Touch DNA: The effect of the deposition pressure on the quality of latent fingermarks and STR profiles.}, journal = {Forensic science international. Genetics}, volume = {38}, number = {}, pages = {105-112}, doi = {10.1016/j.fsigen.2018.10.016}, pmid = {30391623}, issn = {1878-0326}, mesh = {DNA/*isolation &amp; purification ; *DNA Fingerprinting ; *Dermatoglyphics ; Glass ; Humans ; *Microsatellite Repeats ; Paper ; Polyethylene ; Porosity ; *Pressure ; *Touch ; }, abstract = {Latent fingermarks (FMs) present unique, and sometimes the only, evidence found at a crime scene. Several factors affect their quality, including deposition pressure (DP). Its effect on FM size and quality, and on STR amplification success rate, is an emerging area of interest in forensic science. This study examined 540 FM samples, each consisting of index, middle and ring fingers, deposited by 30 donors on glass, polythene (PE) and paper under a range of weights from 0.1 to 10 kg. Both length and width of FMs increased with the increasing DP. FMs deposited under lower (≤0.5 kg) DPs varied in size (p < 0.01), while those deposited at higher (≥3 kg) DPs were more consistent. FM quality on glass and PE, as determined by the AFIS minutiae count and by a fingerprint examiner on a scale from 0 to 4, improved with the increasing DP, but it deteriorated on PE at DP of 10 kg. FM quality on paper continued to improve from DP of 1 kg up to the maximum DP of 10 kg. The effect DP has on the efficacy of DNA profiling from latent FMs was significant as shown by an increase in the DNA amount recovered, the number of amplified loci per FM sample, and the number of forensica