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      Upper Palaeolithic genomes reveal deep roots of modern Eurasians

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          Abstract

          We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

          Abstract

          Upper Palaeolithic and Mesolithic genomes from western Europe and the Caucasus reveal a previously undescribed strand of Eurasian ancestry with a deep divergence from other hunter-gatherer genomes. This had a profound impact on ancient and modern populations from the Atlantic to Central Asia.

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          Most cited references30

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          The complete genome sequence of a Neandertal from the Altai Mountains

          We present a high-quality genome sequence of a Neandertal woman from Siberia. We show that her parents were related at the level of half siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neandertal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neandertals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high quality Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans.
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            Ancient human genomes suggest three ancestral populations for present-day Europeans

            We sequenced genomes from a $\sim$7,000 year old early farmer from Stuttgart in Germany, an $\sim$8,000 year old hunter-gatherer from Luxembourg, and seven $\sim$8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great majority of present-day Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE), who were most closely related to Upper Paleolithic Siberians and contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations' deep relationships and show that EEF had $\sim$44% ancestry from a "Basal Eurasian" lineage that split prior to the diversification of all other non-African lineages.
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              Patterns of damage in genomic DNA sequences from a Neandertal.

              High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                16 November 2015
                2015
                : 6
                : 8912
                Affiliations
                [1 ]Smurfit Institute of Genetics, Trinity College Dublin , Dublin, Dublin 2, Ireland
                [2 ]Department of Mathematics and Natural Sciences, Institute of Biochemistry and Biology, University of Potsdam , Karl-Liebknecht-Straße 24–25, Potsdam 14476, Germany
                [3 ]Department of Biology and Evolution, University of Ferrara , Via L. Borsari 46, Ferrara I-44100, Italy
                [4 ]School of Archaeology and Earth Institute, University College Dublin , Belfield, Dublin 4, Ireland
                [5 ]Department of Zoology, University of Cambridge , Cambridge, CB2 3EJ, UK
                [6 ]Integrative Systems Biology Laboratory, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Kingdom of Saudi Arabia
                [7 ]Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen , Øster Voldgade 5–7, Copenhagen 1350, Denmark
                [8 ]Georgian National Museum , 3 Rustaveli Avenue, Tbilisi 0105, Georgia
                [9 ]Department of Anthropology, Peabody Museum, Harvard University , Cambridge, Massachusetts 02138, USA
                [10 ]Laboratoire d'archéozoologie, Université de Neuchâtel , Neuchâtel 2000, Switzerland
                [11 ]Office du patrimoine et de l'archéologie de Neuchâtel, Section archéologie, LATÉNIUM , Hauterive 2068, Switzerland
                [12 ]Institute of Archaeology, Hebrew University , Jerusalem 91905, Israel
                [13 ]Israel Antiquities Authority , PO Box 586, Jerusalem 91004, Israel
                [14 ]Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology & the History of Art, University of Oxford , Oxford OX1 3QY, UK
                [15 ]Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution - Anthropology Unit, University of Geneva , Geneva 1227, Switzerland
                Author notes
                [*]

                These authors contributed equally to this work.

                Author information
                http://orcid.org/0000-0003-3436-3726
                http://orcid.org/0000-0003-1895-450X
                Article
                ncomms9912
                10.1038/ncomms9912
                4660371
                26567969
                63d3e238-d2ba-4eaa-acfe-3dc0202db97d
                Copyright © 2015, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 20 July 2015
                : 15 October 2015
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