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. Here we analyse 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 there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of 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. An ~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 at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.

Altai State University Barnaul RU 656049 Russia

Australian Centre for Ancient DNA School of Biological Sciences The University of Adelaide SA 5005 Adelaide Australia

Broad Institute of MIT and Harvard Cambridge Massachusetts 02142 USA

CIAS Department of Life Sciences University of Coimbra 3000 456 Coimbra Portugal

CNRS UMR 7041 ArScAn MAE 92023 Nanterre France

Department of Anthropology California State University Northridge Northridge California 91330 8244 USA

Department of Anthropology Faculty of Science Masaryk University 611 37 Brno Czech Republic

Department of Anthropology MSC01 1040 University of New Mexico Albuquerque New Mexico 87131 0001 USA

Department of Anthropology Natural History Museum Vienna 1010 Vienna Austria

Department of Anthropology University of Vienna 1090 Vienna Austria

Department of Archaeogenetics Max Planck Institute for the Science of Human History 07745 Jena Germany

Department of Archaeology School of Culture and Society Aarhus University 8270 Højbjerg Denmark

Department of Archaeology Simon Fraser University Burnaby British Columbia V5A 1S6 Canada

Department of Biology University of Pisa 56126 Pisa Italy

Department of Cultural Heritage University of Bologna 48121 Ravenna Italy

Department of Early Prehistory and Quaternary Ecology University of Tübingen 72070 Tübingen Germany

Department of Evolutionary Genetics Max Planck Institute for Evolutionary Anthropology 04103 Leipzig Germany

Department of Genetics Harvard Medical School Boston Massachusetts 02115 USA

Department of Geosciences Biogeology University of Tübingen 72074 Tübingen Germany

Department of Human Evolution Max Planck Institute for Evolutionary Anthropology 04103 Leipzig Germany

Dipartimento di Biologia Università degli Studi di Bari 'Aldo Moro' 70125 Bari Italy

Dipartimento di Biologia Università di Firenze 50122 Florence Italy

Dipartimento di Civiltà e Forme del Sapere Università di Pisa 56126 Pisa Italy

Dipartimento di Scienze Fisiche della Terra e dell'Ambiente U R Preistoria e Antropologia Università degli Studi di Siena 53100 Siena Italy

Direction régionale des affaires culturelles Rhône Alpes 69283 Lyon Cedex 01 France

Emil Racoviţă Institute of Speleology 010986 Bucharest 12 Romania

Emil Racoviţă Institute of Speleology Cluj Branch 400006 Cluj Romania

Howard Hughes Medical Institute Harvard Medical School Boston Massachusetts 02115 USA

INRAP UMR 8215 Trajectoires 21 92023 Nanterre France

Institute for Archaeological Sciences Archaeo and Palaeogenetics University of Tübingen 72070 Tübingen Germany

Institute for Archaeological Sciences Paleoanthropology University of Tübingen 72070 Tübingen Germany

Institute of Archaeology and Ethnography Russian Academy of Sciences Siberian Branch 17 Novosibirsk RU 630090 Russia

Institute of Archaeology at Brno Academy of Science of the Czech Republic 69129 Dolní Vĕstonice Czech Republic

Instituto Internacional de Investigaciones Prehistóricas Universidad de Cantabria 39005 Santander Spain

Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences IVPP CAS Beijing 100044 China

Laboratoire Chronoenvironnement UMR 6249 du CNRS UFR des Sciences et Techniques 25030 Besançon Cedex France

Museo di Civiltà preclassiche della Murgia meridionale 72017 Ostuni Italy

Museum of Anthropology and Ethnography Saint Petersburg 34 Russia

Quaternary Archaeology Institute for Oriental and European Archaeology Austrian Academy of Sciences 1010 Vienna Austria

Royal Belgian Institute of Natural Sciences 1000 Brussels Belgium

School of Archaeology and Earth Institute University College Dublin Belfield Dublin 4 Ireland

Senckenberg Centre for Human Evolution and Palaeoenvironment University of Tübingen 72072 Tübingen Germany

Service Régional d'Archéologie de Franche Comté 25043 Besançon Cedex France

Sezione di Scienze Preistoriche e Antropologiche Dipartimento di Studi Umanistici Università di Ferrara 44100 Ferrara Italy

TRACES UMR 5608 Université Toulouse Jean Jaurès Maison de la Recherche 31058 Toulouse Cedex 9 France

Ulmer Museum 89073 Ulm Germany

Università degli Studi di Bari 'Aldo Moro' 70125 Bari Italy

Université de Bordeaux CNRS UMR 5199 PACEA 33615 Pessac Cedex France

University of Bucharest Faculty of Geology and Geophysics Department of Geology 01041 Bucharest Romania

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