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      The genetic history of Ice Age Europe

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      1 , 2 , 3 , 4 , 5 , 3 , 3 , 2 , 6 , 7 , 8 , 9 , 4 , 5 , 10 , 3 , 4 , 5 , 3 , 4 , 2 , 3 , 11 , 2 , 2 , 2 , 5 , 2 , 12 , 13 , 12 , 12 , 12 , 14 , 15 , 16 , 17 , 18 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 11 , 25 , 26 , 27 , 28 , 29 , 30 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 11 , 39 , 40 , 41 , 42 , 43 , 43 , 44 , 43 , 45 , 46 , 42 , 47 , 48 , 11 , 49 , 29 , 8 ,   3 , 6 , 4 , 5 , 43 , 3 , 2 , 6 , 7
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          Abstract

          Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. We analyze genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas the earliest modern humans in Europe did not contribute substantially to present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. A ~35,000 year old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe during the Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a new genetic component related to present-day Near Easterners appears in Europe. These results document how population turnover and migration have been recurring themes of European pre-history.

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          Most cited references52

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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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            A high-coverage genome sequence from an archaic Denisovan individual.

            We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from 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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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                22 April 2016
                02 May 2016
                9 June 2016
                02 November 2016
                : 534
                : 7606
                : 200-205
                Affiliations
                [1 ]Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
                [2 ]Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
                [3 ]Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
                [4 ]Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
                [5 ]Max Planck Institute for the Science of Human History, 07745 Jena, Germany
                [6 ]Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142, USA
                [7 ]Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
                [8 ]School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
                [9 ]CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
                [10 ]Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA-5005 Adelaide, Australia
                [11 ]Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
                [12 ]Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 17 Novosibirsk, RU-630090, Russia
                [13 ]Altai State University, Barnaul, RU-656049, Russia
                [14 ]Dipartimento di Civiltà e Forme del Sapere, Università di Pisa, 56126 Pisa, Italy
                [15 ]Department of Biology, University of Pisa 56126 Pisa, Italy
                [16 ]Direction régionale des affaires culturelles Rhône-Alpes, 69283 Lyon cedex 01, France
                [17 ]Dipartimento di Biologia, Università degli Studi di Bari ‘Aldo Moro’, 70125 Bari, Italy
                [18 ]Instituto Internacional de Investigaciones Prehistoricas, Universidad de Cantabria, 39005 Santander, Spain
                [19 ]Department of Anthropology MSC01 1040, University of New Mexico, Albuquerque, NM 87131-0001, USA
                [20 ]Quaternary Archaeology, Institute for Institute for Oriental and European Archaeology, Austrian Academy of Sciences, 1010 Vienna, Austria
                [21 ]Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
                [22 ]Department of Anthropology, University of Vienna, 1090 Vienna, Austria
                [23 ]“Emil Racovita” Institute of Speleology, 010986 Bucharest 12, Romania
                [24 ]“Emil Racovita” Institute of Speleology, Cluj Branch, 400006 Cluj, Romania
                [25 ]Department of Cultural Heritage, University of Bologna, Ravenna, 48121, Italy
                [26 ]Sezione di Scienze Preistoriche e Antropologiche, Dipartimento di Studi Umanistici, Università di Ferrara, 44100 Ferrara, Italy
                [27 ]Università degli Studi di Bari ‘Aldo Moro’, 70125 Bari, Italy
                [28 ]Museo di “Civiltà preclassiche della Murgia meridionale”, 72017 Ostuni, Italy
                [29 ]Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
                [30 ]Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, U.R. Preistoria e Antropologia, Università degli Studi di Siena, 53100 Siena, Italy
                [31 ]CNRS/ UMR 7041 ArScAn MAE, 92023 Nanterre, France
                [32 ]INRAP/ UMR 8215 Trajectoires 21, 92023 Nanterre, France
                [33 ]Ulmer Museum, 89073 Ulm, Germany
                [34 ]University of Bucharest, Faculty of Geology and Geophysics, Department of Geology, 01041 Bucharest, Romania
                [35 ]Department of Anthropology, California State University Northridge, Northridge, CA 91330-8244, USA
                [36 ]Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France
                [37 ]TRACES – UMR 5608, Université Toulouse Jean Jaurès, Maison de la Recherche, 31058 Toulouse Cedex 9, France
                [38 ]Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
                [39 ]Department of Archaeology, School of Culture and Society, Aarhus University, 8270 Højbjerg, Denmark
                [40 ]Service Régional d’Archéologie de Franche-Comté, 25043 Besançon Cedex, France
                [41 ]Laboratoire de Chrono-Environnement, UMR 6249 du CNRS, UFR des Sciences et Techniques, 25030 Besançon Cedex, France
                [42 ]Department of Geosciences, Biogeology, University of Tübingen, 72074 Tübingen, Germany
                [43 ]Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72072 Tübingen, Germany
                [44 ]Department of Early Prehistory and Quaternary Ecology, University of Tübingen, 72070 Tübingen, Germany
                [45 ]Institute for Archaeological Sciences, Paleoanthropology, University of Tübingen, 72070 Tübingen, Germany
                [46 ]Museum of Anthropology and Ethnography, Saint Petersburg 34, Russia
                [47 ]Department of Anthropology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
                [48 ]Institute of Archaeology at Brno, Academy of Science of the Czech Republic, 69129 Dolní Věstonice, Czech Republic
                [49 ]Department of Anthropology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
                Author notes
                Correspondence and requests for materials should be addressed to David Reich ( reich@ 123456genetics.med.harvard.edu )
                [*]

                These authors contributed equally

                [+]

                These authors co-supervised the study

                Article
                NIHMS777742
                10.1038/nature17993
                4943878
                27135931
                d9d42e93-15f8-4bf5-92bd-aa59b7a99da0

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