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      The Beaker Phenomenon and the Genomic Transformation of Northwest Europe

      research-article
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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

          Bell Beaker pottery spread across western and central Europe beginning around 2750 BCE before disappearing between 2200–1800 BCE. The forces propelling its expansion are a matter of long-standing debate, with support for both cultural diffusion and migration. We present new genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 Beaker-associated individuals. We detected limited genetic affinity between Iberian and central European Beaker-associated individuals, and thus exclude migration as a significant mechanism of spread between these two regions. However, migration played a key role in the further dissemination of the Beaker Complex, a phenomenon we document most clearly in Britain, where the spread of the Beaker Complex introduced high levels of Steppe-related ancestry and was associated with a replacement of ~90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought Steppe-related ancestry into central and northern Europe 400 years earlier.

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          Most cited references47

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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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            Is Open Access

            Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

            Due to the increasing throughput of current DNA sequencing instruments, sample multiplexing is necessary for making economical use of available sequencing capacities. A widely used multiplexing strategy for the Illumina Genome Analyzer utilizes sample-specific indexes, which are embedded in one of the library adapters. However, this and similar multiplex approaches come with a risk of sample misidentification. By introducing indexes into both library adapters (double indexing), we have developed a method that reveals the rate of sample misidentification within current multiplex sequencing experiments. With ~0.3% these rates are orders of magnitude higher than expected and may severely confound applications in cancer genomics and other fields requiring accurate detection of rare variants. We identified the occurrence of mixed clusters on the flow as the predominant source of error. The accuracy of sample identification is further impaired if indexed oligonucleotides are cross-contaminated or if indexed libraries are amplified in bulk. Double-indexing eliminates these problems and increases both the scope and accuracy of multiplex sequencing on the Illumina platform.
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              Genomic insights into the origin of farming in the ancient Near East

              We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                11 January 2018
                21 February 2018
                08 March 2018
                21 August 2018
                : 555
                : 7695
                : 190-196
                Affiliations
                [1 ]Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
                [2 ]Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
                [3 ]Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen 1350, Denmark
                [4 ]School of Archaeological Sciences, University of Bradford, Bradford BD7 1DP, UK
                [5 ]University of Gothenburg, Gothenburg 405 30, Sweden
                [6 ]Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
                [7 ]Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
                [8 ]Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
                [9 ]Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
                [10 ]Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
                [11 ]Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
                [12 ]Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
                [13 ]Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
                [14 ]Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
                [15 ]Department of Anthropology, University of Vienna, Vienna 1090, Austria
                [16 ]Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
                [17 ]Wessex Archaeology, Salisbury SP4 6EB, UK
                [18 ]Center of Natural and Cultural History of Man, Danube Private University, Krems 3500, Austria
                [19 ]Department of Biomedical Engineering, Basel University, Basel 4123, Switzerland
                [20 ]Integrative Prehistory and Archaeological Science, Basel University, Switzerland
                [21 ]Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid 28049, Spain
                [22 ]ARGEA S.L., Madrid 28011, Spain
                [23 ]Área de Prehistoria, Universidad de Murcia, Murcia 30001, Spain
                [24 ]Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
                [25 ]Romano-Germanic Commission, German Archaeological Institute, Frankfurt/Main 60325, Germany
                [26 ]Museo Archeologico Nazionale di Parma, Parma 43100, Italy
                [27 ]INRAP, Institut National de Recherches Archeéologiques Preéventives, Buffard 25440, France
                [28 ]School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
                [29 ]Independent Researcher, 10 Merchiston Gardens, Edinburgh EH10 5DD, UK
                [30 ]Oxford Archaeology, Oxford, OX2 0ES, UK
                [31 ]Department of Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
                [32 ]BioArCh, Department of Archaeology, University of York, York YO10 5DD, UK
                [33 ]Scottish Universities Environmental Research Centre East Kilbride G75 0QF, UK
                [34 ]Institute of Archaeology, University of Oxford, Oxford OX1 2PG, UK
                [35 ]University of Burgundy, Dijon 21000, France
                [36 ]Oxford Archaeology East, Cambridge CB23 8SQ, UK
                [37 ]Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic
                [38 ]Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge CB3 0DT, UK
                [39 ]Labrys o.p.s., Prague 198 00, Czech Republic
                [40 ]Museu i Poblat Ibèric de Ca n’Oliver, Cerdanyola del Vallès 08290, Spain
                [41 ]School of History, Classics & Archaeology, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
                [42 ]INRAP, Institut National de Recherches Archéologiques Préventives, Nice 06300, France
                [43 ]Institute of Zoology and Biomedical Research, Jagiellonian University, Cracow 31-007, Poland
                [44 ]Great Orme Mines, Great Orme, Llandudno LL30 2XG, UK
                [45 ]Bristol Radiocarbon Accelerator Mass Spectrometry Facility, University of Bristol, Bristol BS8 1UU, UK
                [46 ]Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Munich 80539, Germany
                [47 ]INRAP, Institut National de Recherches Archéologiques Préventives, Strasbourg 67100, France
                [48 ]Université Paul-Valéry - Montpellier 3, UMR 5140 ASM, Montpellier 34199, France
                [49 ]INRAP, Institut National de Recherches Archeéologiques Preéventives, Metz 57063, France
                [50 ]UMR 5199, Pacea, équipe A3P, Université de Bordeaux, Talence 33400, France
                [51 ]TRÉBEDE, Patrimonio y Cultura SL, Torres de la Alameda 28813, Spain
                [52 ]Departamento de Ciencias de la Vida, Universidad de Alcalá, Alcalá de Henares 28801, Spain
                [53 ]Instituto Universitario de Investigación en Ciencias Policiales (IUICP), Alcalá de Henares 28801, Spain
                [54 ]Archaeom. Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
                [55 ]Department of Biology, University of Florence, Florence 50121, Italy
                [56 ]Salisbury Ltd., Budaörs 2040, Hungary
                [57 ]Ferenczy Museum Center, Szentendre 2100, Hungary
                [58 ]Budapest History Museum, Budapest 1014, Hungary
                [59 ]Department of Biological Anthropology, Eötvös Loránd University, Budapest 1117, Hungary
                [60 ]Hungarian Natural History Museum, Budapest 1083, Hungary
                [61 ]Déri Museum, Debrecen 4026, Hungary
                [62 ]Historic Environment Scotland, Edinburgh EH9 1SH, UK
                [63 ]Humanities Institute, University College Dublin, Dublin 4, Ireland
                [64 ]Department of Anthropology, National Museum, Prague 115 79, Czech Republic
                [65 ]Soprintendenza Archeologia belle arti e paesaggio per la città metropolitana di Cagliari e per le province di Oristano e Sud Sardegna, Cagliari 9124, Italy
                [66 ]Physical Anthropology Section, University of Philadelphia Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
                [67 ]Department of Environmental Biology, Sapienza University of Rome, Rome 00185, Italy
                [68 ]Professional archaeologist
                [69 ]Departamento de Prehistoria, Universidad Complutense de Madrid, Madrid 28040, Spain
                [70 ]Soprintendenza del Mare, Palermo 90133, Italia
                [71 ]Facoltà di Lettere e Filosofia, Università di Palermo, Palermo 90133, Italy
                [72 ]Soprintendenza per i beni culturali e ambientali di Trapani, Trapani 91100, Italy
                [73 ]Prima Archeologia del Mediterraneo, Partanna 91028, Italy
                [74 ]Università degli Studi di Palermo, Agrigento 92100, Italy
                [75 ]Archaeological Research Services Ltd, Bakewell DE45 1HB, UK
                [76 ]Departamento de Prehistoria, Facultad de Filosofía y Letras, Universidad de Valladolid, Valladolid 47011, Spain
                [77 ]Albion Archaeology, Bedford MK42 0AS, UK
                [78 ]Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for environmental and aquatic sciences, University of Geneva, Geneva 4, Switzerland
                [79 ]General Department of Cultural Heritage Rhineland Palatinate, Department of Archaeology, Mainz 55116, Germany
                [80 ]Institute of Archaeology, University of Wroclaw, Wrocław 50-137, Poland
                [81 ]Institute of Archaeology, Silesian University in Opava, Opava 746 01, Czech Republic
                [82 ]Department of Archaeology, University of Exeter, Exeter EX4 4QE, UK
                [83 ]Departament de Prehistòria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
                [84 ]Department of Anthropology, University of Iowa, Iowa City, Iowa 52240, USA
                [85 ]Centro de Arqueologia, Universidade de Lisboa, Lisboa 1600-214, Portugal
                [86 ]Universidade Aberta, Lisboa 1269-001, Portugal
                [87 ]Institute of Archaeology, University College London, London WC1H 0PY, UK
                [88 ]Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków 31-016, Poland
                [89 ]Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
                [90 ]University of Santiago de Compostela, Santiago de Compostela 15782, Spain
                [91 ]UMR 5204 Laboratoire Edytem, Universiteé Savoie Mont Blanc, Chambéry 73376, France
                [92 ]Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Valladolid University, Valladolid 47011, Spain
                [93 ]UMR 7268 ADES, CNRS, Aix-Marseille Univ, EFS, Faculté de médecine Nord, Marseille 13015, France
                [94 ]Service archeéologique, Conseil Geéneéral de la Haute-Savoie, Annecy 74000, France
                [95 ]Laboratory of Prehistory, Research Center for Anthropology and Health, Department of Life Science, University of Coimbra, Coimbra 3000-456, Portugal
                [96 ]Institute for History of Medicine and Foreign Languages, First Faculty of Medicine, Charles University, Prague 121 08, Czech Republic
                [97 ]ANTEA Bureau d’eétude en Archeéologie, Habsheim 68440, France
                [98 ]Institucioé Catalana de Recerca i Estudis Avançats, Barcelona 08010, Spain
                [99 ]Departament d’Història i Arqueologia, Universitat de Barcelona, Barcelona 08001, Spain
                [100 ]Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford OX1 3QY, UK
                [101 ]Department of Anthropology & Institute for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
                [102 ]Faculty of Archaeology, Leiden University, 2333 CC Leiden, The Netherlands
                [103 ]Department of Philosophy, History, Culture and Art Studies, Section of Archaeology, University of Helsinki, Helsinki 00014, Finland
                [104 ]National Museums Scotland, Edinburgh EH1 1JF, UK
                [105 ]Max Planck Institute for the Science of Human History, Jena 07745, Germany
                [106 ]Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
                [107 ]Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain
                Author notes
                To whom correspondence should be addressed: I.O. ( inigo_olalde@ 123456hms.harvard.edu ) or D.R. ( reich@ 123456genetics.med.harvard.edu )
                [*]

                Principal investigators who contributed centrally to this study

                Correspondence and requests for materials should be addressed to I.O. ( inigo_olalde@ 123456hms.harvard.edu ) or D.R. ( reich@ 123456genetics.med.harvard.edu ).

                Article
                NIHMS934070
                10.1038/nature25738
                5973796
                29466337
                6bd71cb6-cafe-4942-9244-097ae5f1b686

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