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      Ancient human genomes suggest three ancestral populations for present-day Europeans

      1 , 2 , 2 , 3 , 4 , 1 , 2 , 5 , 6 , 7 , 4 , 8 , 2 , 8 , 9 , 5 , 1 , 4 , 10 , 3 , 1 , 2 , 1 , 2 , 4 , 4 , 4 , 3 , 11 , 12 , 12 , 1 , 2 , 13 , 14 , 15 , 13 , 16 , 17 , 18 , 19 , 20 , 21 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 20 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 35 , 41 , 42 , 43 , 44 , 40 , 45 , 46 , 47 , 46 , 47 , 48 , 49 , 7 , 50 , 51 , 52 , 46 , 47 , 51 , , 54 , 26 , 55 , 56 , 57 , 58 , 45 , 59 , 35 , 55 , 60 , 35 , 61 , 62 , 63 , 64 , 65 , 66 , 51 , 67 , 68 , 69 , 70 , 37 , 71 , 45 , 72 , 50 , 73 , 74 , 74 , 35 , 75 , 76 , 67 , 77 , 78 , 79 , 11 , 29 , 80 , 80 , 81 , 82 , 82 , 51 , 55 , 84 , 85 , 37 , 51 , 4 , 6 , 86 , 5 , 7 , 4 ,   4 , 1 , 2 , 87 ,   3 , 88 , 90

      Nature

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes 14 with 2,345 contemporary humans to show that most present 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) related to Upper Paleolithic Siberians 3 , who 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 ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages.

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          Ancient admixture in human history.

          Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean "Iceman."
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            Is Open Access

            Efficient Moment-Based Inference of Admixture Parameters and Sources of Gene Flow

            The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for complicated models involving many populations. Here, we present MixMapper, an efficient, interactive method for constructing phylogenetic trees including admixture events using single nucleotide polymorphism (SNP) genotype data. MixMapper implements a novel two-phase approach to admixture inference using moment statistics, first building an unadmixed scaffold tree and then adding admixed populations by solving systems of equations that express allele frequency divergences in terms of mixture parameters. Importantly, all features of the model, including topology, sources of gene flow, branch lengths, and mixture proportions, are optimized automatically from the data and include estimates of statistical uncertainty. MixMapper also uses a new method to express branch lengths in easily interpretable drift units. We apply MixMapper to recently published data for Human Genome Diversity Cell Line Panel individuals genotyped on a SNP array designed especially for use in population genetics studies, obtaining confident results for 30 populations, 20 of them admixed. Notably, we confirm a signal of ancient admixture in European populations—including previously undetected admixture in Sardinians and Basques—involving a proportion of 20–40% ancient northern Eurasian ancestry.
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              Author and article information

              Affiliations
              [1 ]Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
              [2 ]Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
              [3 ]Institute for Archaeological Sciences, University of Tübingen, Tübingen, 72074, Germany
              [4 ]Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
              [5 ]Johannes Gutenberg University Mainz, Institute of Anthropology, Mainz, D-55128, Germany
              [6 ]Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
              [7 ]Department of Integrative Biology, University of California, Berkeley, CA, 94720-3140, USA
              [8 ]Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
              [9 ]Archaeological Research Laboratory, Stockholm University, 114 18, Sweden
              [10 ]Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, 100049, China
              [11 ]Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, SA 5005, Australia
              [12 ]The Cultural Heritage Foundation, Västerås, 722 12, Sweden
              [13 ]National Museum of Natural History, L-2160, Luxembourg
              [14 ]National Center of Archaeological Research, National Museum of History and Art, L-2345, Luxembourg
              [15 ]Department of Paleoanthropology, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, D-72070, Germany
              [16 ]State Office for Cultural Heritage Management Baden-Württemberg, Osteology, Konstanz, D-78467, Germany
              [17 ]Center for Global Health and Child Development, Kisumu, 40100, Kenya
              [18 ]Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK
              [19 ]Biochemistry Department, Faculty of Medicine, Sultan Qaboos University, Alkhod, Muscat, 123, Oman
              [20 ]Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET & CICPBA, La Plata, B1906APO, Argentina
              [21 ]Research Centre for Medical Genetics, Moscow, 115478, Russia
              [22 ]Vavilov Institute for General Genetics, Moscow, 119991, Russia
              [23 ]Escuela de Biología, Universidad de Costa Rica, San José, 2060, Costa Rica
              [24 ]Institute of Biology, Research group GENMOL, Universidad de Antioquia, Medellín, Colombia
              [25 ]Rambam Health Care Campus, Haifa, 31096, Israel
              [26 ]Department of Medical Genetics and Szentagothai Research Center, University of Pécs, Pécs, H-7624 Hungary
              [27 ]Al Akhawayn University in Ifrane (AUI), School of Science and Engineering, Ifrane, 53000, Morocco
              [28 ]Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, 00168, Italy
              [29 ]Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
              [30 ]Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
              [31 ]Laboratorio di Genetica Molecolare, IRCCS Associazione Oasi Maria SS, Troina, 94018, Italy
              [32 ]Belgorod State University, Belgorod, 308015, Russia
              [33 ]Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5G 1L5, Canada
              [34 ]Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires, 1113 CABA, Argentina
              [35 ]Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
              [36 ]Institute of Linguistics, University of Bern, Bern, CH-3012, Switzerland
              [37 ]Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Russian Academy of Science, Siberian Branch, Novosibirsk, 630090, Russia
              [38 ]Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier Toulouse III, Toulouse, 31000, France
              [39 ]Yakut Research Center of Complex Medical Problems and North-Eastern Federal University, Yakutsk, 677010, Russia
              [40 ]Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
              [41 ]ARL Division of Biotechnology, University of Arizona, Tucson, AZ, 85721, USA
              [42 ]Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
              [43 ]Department of Clinical Science, University of Bergen, Bergen, 5021, Norway
              [44 ]NextBio, part of Illumina, Santa Clara, CA, USA 95050
              [45 ]Dept. of Medical Genetics, National Human Genome Center, Medical University Sofia, Sofia, 1431, Bulgaria
              [46 ]Institute of Biochemistry and Genetics, Ufa Research Centre, Russian Academy of Sciences, Ufa, 450054, Russia
              [47 ]Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450074, Russia
              [48 ]College of Medicine, University of Illinois at Chicago, Chicago, IL, 60607, USA
              [49 ]Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom CB2 1QH
              [50 ]Department of Human and Medical Genetics, Vilnius University, Vilnius, LT-08661, Lithuania
              [51 ]Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia
              [52 ]Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, France
              [54 ]Gladstone Institutes, San Francisco, CA, 94158, USA
              [55 ]Department of Evolutionary Biology, University of Tartu, Tartu, 51010, Estonia
              [56 ]Centro de Investigaciones Biomédicas de Guatemala, Ciudad de Guatemala, Guatemala
              [57 ]Research Department, 23andMe, Inc. Mountain View, CA, 94043, USA
              [58 ]Cultural Anthropology Program, University of Oulu, Oulu, 90014, Finland
              [59 ]Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
              [60 ]Research Institute of Health, North-Eastern Federal University, Yakutsk, 677000, Russia
              [61 ]Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, 90128, Italy
              [62 ]Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
              [63 ]Programa de Genética Humana ICBM Facultad de Medicina Universidad de Chile, Santiago, Chile
              [64 ]Centro de Investigaciones del Hombre en el Desierto, Arica, Chile
              [65 ]Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, Scotland, EH8 9AG, UK
              [66 ]Deceased: formerly of the Institute of Immunology, Academy of Science, Tashkent, 70000, Uzbekistan
              [67 ]Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, 0014, Armenia
              [68 ]Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki, 00014, Finland
              [69 ]Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
              [70 ]Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galcia, 15872, Spain
              [71 ]Research Fellow, Henry Stewart Group, Russell House, London WC1A 2HN, UK
              [72 ]Institute of Bioorganic Chemistry Academy of Sciences Republic of Uzbekistan, Tashkent, 100125, Uzbekistan
              [73 ]Department of Genetics and Cytology, V.N. Karazin Kharkiv National University, Kharkiv, 61077, Ukraine
              [74 ]Instituto Boliviano de Biología de la Altura, Universidad Autonoma Tomás Frías, Potosí, Bolivia
              [75 ]Inst. of Internal Medicine, Siberian Branch of Russian Acad. of Medical Sciences, Novosibirsk, 630089, Russia
              [76 ]Basic Research Laboratory, NCI, NIH, Frederick National Laboratory, Leidos Biomedical, Inc., Frederick, MD 21702, USA
              [77 ]Lebanese American University, School of Medicine, Beirut, 13-5053, Lebanon
              [78 ]Harvard School of Public Health, Boston, 02115, USA
              [79 ]Department of Medical Biology, University of Split, School of Medicine, Split, 21000, Croatia
              [80 ]Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK
              [81 ]Department of Biology and Genetics. University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
              [82 ]CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500 007, India
              [84 ]Estonian Academy of Sciences, Tallinn, 10130, Estonia
              [85 ]Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, 08003, Spain
              [86 ]Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA 98195
              [87 ]Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
              [88 ]Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070, Germany
              [90 ]Max Planck Institut für Geschichte und Naturwissenschaften, Jena, 07745, Germany
              Author notes
              []Correspondence and requests for materials should be addressed to David Reich ( reich@ 123456genetics.med.harvard.edu ) or Johannes Krause ( johannes.krause@ 123456uni-tuebingen.de )
              [53]

              Currently employed by AMGEN; 33 Kazantzaki Str, Ilioupolis 16342, Athens, Greece

              [83]

              Present address: Banaras Hindu University, Varanasi, 221 005, India

              Journal
              0410462
              6011
              Nature
              Nature
              Nature
              0028-0836
              1476-4687
              6 August 2014
              18 September 2014
              18 March 2015
              : 513
              : 7518
              : 409-413
              NIHMS613260
              10.1038/nature13673
              4170574
              25230663
              1312.6639
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