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      A genomic history of Aboriginal Australia.

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          Abstract

          The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

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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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              Inferring human population size and separation history from multiple genome sequences

              The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The Multiple Sequentially Markovian Coalescent (MSMC) analyses the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago, and give information about human population history as recently as 2,000 years ago, including the bottleneck in the peopling of the Americas, and separations within Africa, East Asia and Europe.
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                Author and article information

                Journal
                Nature
                Nature
                Springer Nature
                1476-4687
                0028-0836
                Oct 13 2016
                : 538
                : 7624
                Affiliations
                [1 ] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
                [2 ] Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland.
                [3 ] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
                [4 ] Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia.
                [5 ] CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
                [6 ] Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
                [7 ] Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal.
                [8 ] Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
                [9 ] Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.
                [10 ] Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
                [11 ] Verily Life Sciences, 2425 Garcia Ave, Mountain View, California 94043, USA.
                [12 ] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
                [13 ] Interfaculty Bioinformatics Unit University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland.
                [14 ] Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, 2800 Kongens Lyngby, Denmark.
                [15 ] Department for Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.
                [16 ] The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
                [17 ] Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.
                [18 ] Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
                [19 ] Integrative Systems Biology Laboratory, Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia.
                [20 ] Institute for Theoretical Physics, ETH Zürich, Wolfgang-Pauli-Str. 27, 8093 Zürich, Switzerland.
                [21 ] Jeffrey Cheah School of Medicine &Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, 46150 Selangor, Malaysia.
                [22 ] Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, 31073 Toulouse, France.
                [23 ] Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
                [24 ] CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
                [25 ] National Parks and Wildlife, Sturt Highway, Buronga, New South Wales 2739, Australia.
                [26 ] Explico Foundation, Vågavegen 16, 6900 Florø, Norway.
                [27 ] Giriwandi, Gimuy Yidinji Country, Queensland 4868, Australia.
                [28 ] Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
                [29 ] UCL Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK.
                [30 ] Yinhawangka elder, Perth, Western Australia 6062, Australia.
                [31 ] Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Papua New Guinea.
                [32 ] Archaeology, School of Humanities &Social Sciences, University PO Box 320, University of Papua New Guinea &College of Arts, Society &Education, James Cook University, Cairns, Queensland 4811, Australia.
                [33 ] Ngadju elder, Coolgardie, Western Australia 6429, Australia.
                [34 ] Wongatha elder, Kurrawang, Western Australia 6430, Australia.
                [35 ] Department of Anatomy, University of Otago, Dunedin 9054, New Zealand.
                [36 ] 2209 Springbrook Road, Springbrook, Queensland 4213, Australia.
                [37 ] Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
                [38 ] Estonian Biocentre, Riia 23b, Tartu 51010, Estonia.
                [39 ] 86 Workshop Road, Yarrabah, Queensland 4871, Australia.
                [40 ] Esperance Nyungar elder, Esperance, Western Australia 6450, Australia.
                [41 ] Atakani Street, Napranum, Queensland 4874, Australia.
                [42 ] 2 Wynnum North Road, Wynnum, Queensland 4178, Australia.
                [43 ] School of Anthropology and Museum Ethnography, Oxford University, Oxford OX2 6PE, UK.
                [44 ] Centre for Rock Art Research and Management, M257, University of Western Australia, Perth, Western Australia 6009, Australia.
                [45 ] Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK.
                [46 ] Department of Linguistics, Yale University, 370 Temple Street, New Haven, Connecticut 06520, USA.
                [47 ] Institute for Human Genetics, University of California, San Francisco, California 94143, USA.
                [48 ] Departments of Integrative Biology and Statistics, University of California, Berkeley, California 94720, USA.
                Article
                nature18299
                10.1038/nature18299
                27654914
                2a63114b-89c6-461e-bd71-249bd2c3f442
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