Showing papers by "Pontus Skoglund published in 2020"
TL;DR: The authors' study adds data about African, Oceanian, and Amerindian populations and indicates that diversity tends to result from differences at the single-nucleotide level rather than copy number variation.
Abstract: Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.
415 citations
TL;DR: The genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, is sequenced to 27-fold genomic coverage and it is found that genes highly expressed in the Striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in NeandERTals.
Abstract: We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prufer et al., Science 358, 655-658 (2017); Hajdinjak et al., Nature 555, 652-656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Prufer et al., Nature 505, 43-49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.
156 citations
Francis Crick Institute1, Ludwig Maximilian University of Munich2, Queen Mary University of London3, University of Porto4, University College Dublin5, Swedish Museum of Natural History6, University of Liverpool7, University of Oxford8, Liverpool John Moores University9, University of Aberdeen10, National Museum of Natural History11, Stockholm University12, University of Gothenburg13, Harvard University14, Hartwick College15, Russian Academy of Sciences16, University of Tehran17, University of Haifa18, Irkutsk State University19, University of Belgrade20, North-Eastern Federal University21, Sapienza University of Rome22, Baylor University23, Royal Belgian Institute of Natural Sciences24, University of Copenhagen25, Lundbeck26, Leiden University27, Hebrew University of Jerusalem28, Tomsk State University29, University of Alberta30, Centre national de la recherche scientifique31, Istanbul University32, University of York33, University College London34, Durham University35, Hellenic Ministry of Culture and Sports36, University of Thessaly37, University of the Basque Country38, Pennsylvania State University39, Texas A&M University40, University of Vienna41
TL;DR: It is found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow.
Abstract: Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.
116 citations
Massachusetts Institute of Technology1, Harvard University2, Max Planck Society3, University of Zurich4, Francis Crick Institute5, Broad Institute6, Howard Hughes Medical Institute7, University of California, Santa Cruz8, Pennsylvania State University9, Kansas State University10, McDonald Institute for Archaeological Research11, Yale University12, University of Cambridge13, Universidad de San Martín de Porres14, University of East Anglia15, Higher University of San Andrés16, University of Reading17, National University of Central Buenos Aires18, Michigan State University19, Deutsches Archäologisches Institut20, University of Magallanes21, University of Tarapacá22, Pontifical Catholic University of Peru23, University of Adelaide24, University of California, Santa Barbara25
TL;DR: In this paper, a 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 was assembled.
59 citations
University of Copenhagen1, Spanish National Research Council2, Russian Academy of Sciences3, University of Oxford4, Queen Mary University of London5, University of York6, University of Greenland7, University of Groningen8, Arctic and Antarctic Research Institute9, Francis Crick Institute10, Harvard University11, Aarhus University12, Henan Agricultural University13, Swedish Museum of Natural History14, American Museum of Natural History15, Norwegian University of Science and Technology16
TL;DR: This analysis indicates that sled dogs represent an ancient lineage going back at least 9500 years and that wolves bred with the ancestors of sled dogs and precontact American dogs, however, gene flow between sled Dogs and wolves likely stopped before ∼9500 years ago.
Abstract: Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf We found noteworthy genetic similarity between the ancient dog and modern sled dogs We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago
50 citations
TL;DR: The genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, is sequenced to 27-fold genomic coverage and it is found that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that thestriatum may have evolved unique functions in NeandERTals.
Abstract: We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We estimate that this individual lived ~80,000 years ago and was more closely related to Neandertals in western Eurasia (1,2) than to Neandertals who lived earlier in Denisova Cave (3), which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a first view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.
17 citations
23 Oct 2020
TL;DR: In this article, the authors present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing, revealing an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions.
Abstract: Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.
15 citations
TL;DR: The results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.
Abstract: The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52- 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.
12 citations
TL;DR: 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, which may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.
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.
12 citations