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. 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.

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Accessions

Primary accessions

European Nucleotide Archive

Data deposits

The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB13123.

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Acknowledgements

We thank B. Alex, D. Meltzer, P. Moorjani, I. Olalde, S. Sankararaman and B. Viola for comments, K. Stewardson and E. Harney for sample screening, and F. Hallgren for sharing a radiocarbon date for Motala12. The Fig. 1 map is plotted using data available under the Open Database License © OpenStreetMap (http://www.openstreetmap.org/copyright). The Goyet project led by H.R. was funded by the Wenner-Gren Foundation (Gr. 7837), the College of Social and Behavioral Sciences of CSUN, the CSUN Competition for Research, Scholarship and Creative Activity Awards, and the RBINS. The excavation of the El Mirón Cave burial, led by L.G.S. and M.R.G.M., was supported by the Gobierno de Cantabria, the L.S.B. Leakey Foundation, the University of New Mexico, the Stone Age Research Fund (J. and R. Auel, principal donors), the town of Ramales de la Victoria and the Universidad de Cantabria. Excavations at Grotta Paglicci were performed by A. Palma di Cesnola in collaboration with the Soprintendenza Archeologia della Puglia (founded by MIUR and local Institutions). Research at Riparo Villabruna was supported by MIBACT and the Veneto Region. Q.F. was funded by the Special Foundation of the President of the Chinese Academy of Sciences (2015–2016), the Bureau of International Cooperation of the Chinese Academy of Sciences, the Chinese Academy of Sciences (XDA05130202), the National Natural Science Foundation of China (L1524016) and the Chinese Academy of Sciences Discipline Development Strategy Project (2015-DX-C-03). D.Fe was supported by an Irish Research Council grant (GOIPG/2013/36). I.M. was supported by a long-term fellowship from the Human Frontier Science Program LT001095/2014-L. P.Sk was supported by the Swedish Research Council (VR 2014-453). S.T., and M.P.R. were funded by the Max Planck Society. C.N.-M. was funded by FWF P-17258, P-19347, P-21660 and P-23612. S.C. and O.T.M. were funded by a ‘Karsthives’ Grant PCCE 31/2010 (CNCS-UEFISCDI, Romania). A.P.D., N.D., V.Sla and N.D. were funded by the Russian Science Foundation (project No.14-50-00036). M.A.M. was funded by a Marie Curie Intra-European Fellowship within the 7th European Community Framework Programme (grant number PIEF-GA-2008-219965). M.La and D.C. were funded by grants PRIN 2010-11 and 2010EL8TXP_003. C.C. and the research about the French Jura sites of Rochedane, Rigney and Ranchot was funded by the Collective Research Program (PCR) (2005-2008). K.H. was supported by the European Research Council (ERC StG 283503) and the Deutsche Forschungsgemeinschaft (DFG INST37/706-1FUGG, DFG FOR2237). D.G.D. was funded by the European Social Fund and Ministry of Science, Research and Arts of Baden-Württemberg. R.P. was funded by ERC starting grant ADNABIOARC (263441). J.Ke was funded by a grant from the Deutsche Forschungsgemeinschaft (SFB1052, project A02). J.Kr was funded by DFG grant KR 4015/1-1, the Baden Württemberg Foundation, and the Max Planck Society. S.P. were funded by the Max Planck Society and the Krekeler Foundation. D.R. was funded by NSF HOMINID grant BCS-1032255, NIH (NIGMS) grant GM100233, and the Howard Hughes Medical Institute.

Author information

Author notes

    • Cosimo Posth
    •  & Mateja Hajdinjak

    These authors contributed equally to this work.

    • Johannes Krause
    • , Svante Pääbo
    •  & David Reich

    These authors jointly supervised this work.

Affiliations

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

    • Qiaomei Fu
  2. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Qiaomei Fu
    • , Swapan Mallick
    • , Nadin Rohland
    • , Iosif Lazaridis
    • , Mark Lipson
    • , Iain Mathieson
    • , Pontus Skoglund
    •  & David Reich
  3. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany

    • Qiaomei Fu
    • , Mateja Hajdinjak
    • , Martin Petr
    • , Matthias Meyer
    • , Birgit Nickel
    • , Viviane Slon
    • , Janet Kelso
    •  & Svante Pääbo
  4. Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany

    • Cosimo Posth
    • , Anja Furtwängler
    • , Alissa Mittnik
    • , Alexander Peltzer
    •  & Johannes Krause
  5. Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany

    • Cosimo Posth
    • , Wolfgang Haak
    • , Alissa Mittnik
    • , Stephan Schiffels
    •  & Johannes Krause
  6. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • Swapan Mallick
    • , Nick Patterson
    •  & David Reich
  7. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Swapan Mallick
    •  & David Reich
  8. School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland

    • Daniel Fernandes
    •  & Ron Pinhasi
  9. CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal

    • Daniel Fernandes
  10. Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA-5005 Adelaide, Australia

    • Wolfgang Haak
  11. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany

    • Sahra Talamo
    • , Stefano Benazzi
    • , Marcello A. Mannino
    •  & Michael P. Richards
  12. Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 17 Novosibirsk, RU-630090, Russia

    • Anatoly P. Derevianko
    • , Nikolai Drozdov
    • , Vyacheslav Slavinsky
    •  & Alexander Tsybankov
  13. Altai State University, Barnaul, RU-656049, Russia

    • Anatoly P. Derevianko
  14. Dipartimento di Civiltà e Forme del Sapere, Università di Pisa, 56126 Pisa, Italy

    • Renata Grifoni Cremonesi
  15. Department of Biology, University of Pisa, 56126 Pisa, Italy

    • Francesco Mallegni
  16. Direction régionale des affaires culturelles Rhône-Alpes, 69283 Lyon, Cedex 01, France

    • Bernard Gély
  17. Dipartimento di Biologia, Università degli Studi di Bari ‘Aldo Moro’, 70125 Bari, Italy

    • Eligio Vacca
  18. Instituto Internacional de Investigaciones Prehistóricas, Universidad de Cantabria, 39005 Santander, Spain

    • Manuel R. González Morales
    •  & Lawrence G. Straus
  19. Department of Anthropology, MSC01 1040, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA

    • Lawrence G. Straus
  20. Quaternary Archaeology, Institute for Oriental and European Archaeology, Austrian Academy of Sciences, 1010 Vienna, Austria

    • Christine Neugebauer-Maresch
  21. Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria

    • Maria Teschler-Nicola
  22. Department of Anthropology, University of Vienna, 1090 Vienna, Austria

    • Maria Teschler-Nicola
  23. “Emil Racoviţă” Institute of Speleology, 010986 Bucharest 12, Romania

    • Silviu Constantin
  24. “Emil Racoviţă” Institute of Speleology, Cluj Branch, 400006 Cluj, Romania

    • Oana Teodora Moldovan
  25. Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy

    • Stefano Benazzi
  26. Sezione di Scienze Preistoriche e Antropologiche, Dipartimento di Studi Umanistici, Università di Ferrara, 44100 Ferrara, Italy

    • Marco Peresani
  27. Università degli Studi di Bari ‘Aldo Moro’, 70125 Bari, Italy

    • Donato Coppola
  28. Museo di “Civiltà preclassiche della Murgia meridionale”, 72017 Ostuni, Italy

    • Donato Coppola
  29. Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy

    • Martina Lari
    •  & David Caramelli
  30. Dipartimento di Scienze Fisiche, della Terra e dell’Ambiente, U.R. Preistoria e Antropologia, Università degli Studi di Siena, 53100 Siena, Italy

    • Stefano Ricci
    •  & Annamaria Ronchitelli
  31. CNRS/UMR 7041 ArScAn MAE, 92023 Nanterre, France

    • Frédérique Valentin
  32. INRAP/UMR 8215 Trajectoires 21, 92023 Nanterre, France

    • Corinne Thevenet
  33. Ulmer Museum, 89073 Ulm, Germany

    • Kurt Wehrberger
  34. University of Bucharest, Faculty of Geology and Geophysics, Department of Geology, 01041 Bucharest, Romania

    • Dan Grigorescu
  35. Department of Anthropology, California State University Northridge, Northridge, California 91330-8244, USA

    • Hélène Rougier
  36. Université de Bordeaux, CNRS, UMR 5199-PACEA, 33615 Pessac Cedex, France

    • Isabelle Crevecoeur
  37. TRACES – UMR 5608, Université Toulouse Jean Jaurès, Maison de la Recherche, 31058 Toulouse Cedex 9, France

    • Damien Flas
  38. Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium

    • Patrick Semal
  39. Department of Archaeology, School of Culture and Society, Aarhus University, 8270 Højbjerg, Denmark

    • Marcello A. Mannino
  40. Service Régional d’Archéologie de Franche-Comté, 25043 Besançon Cedex, France

    • Christophe Cupillard
  41. Laboratoire Chronoenvironnement, UMR 6249 du CNRS, UFR des Sciences et Techniques, 25030 Besançon Cedex, France

    • Christophe Cupillard
  42. Department of Geosciences, Biogeology, University of Tübingen, 72074 Tübingen, Germany

    • Hervé Bocherens
    •  & Dorothée G. Drucker
  43. Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72072 Tübingen, Germany

    • Hervé Bocherens
    • , Nicholas J. Conard
    • , Katerina Harvati
    •  & Johannes Krause
  44. Department of Early Prehistory and Quaternary Ecology, University of Tübingen, 72070 Tübingen, Germany

    • Nicholas J. Conard
  45. Institute for Archaeological Sciences, Paleoanthropology, University of Tübingen, 72070 Tübingen, Germany

    • Katerina Harvati
  46. Museum of Anthropology and Ethnography, Saint Petersburg 34, Russia

    • Vyacheslav Moiseyev
  47. Department of Anthropology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic

    • Jiří Svoboda
  48. Institute of Archaeology at Brno, Academy of Science of the Czech Republic, 69129 Dolní Vĕstonice, Czech Republic

    • Jiří Svoboda
  49. Department of Archaeology, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada

    • Michael P. Richards

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Contributions

J.Kr, S.P. and D.R. conceived the idea for the study. Q.F., C.P., M.H., W.H., M.Me, V.Slo, R.G.C., A.P.D., N.D., V.Sla, A.T., F.M., B.G., E.V., M.R.G.M., L.G.S., C.N.-M., M.T.-N., S.C., O.T.M., S.B., M.Per, D.Co, M.La, S.R., A.R., F.V., C.T., K.W., D.G., H.R., I.C., D.Fl, P.Se, M.A.M., C.C., H.B., N.J.C., K.H., V.M., D.G.D., J.S., D.Ca, R.P., J.Kr, S.P. and D.R. assembled archaeological material. Q.F., C.P., M.H., D.Fe, A.F., W.H., M.Me, A.M., B.N., N.R., V.Slo, S.T., H.B., D.G.D., M.P.R., R.P., J.Kr, S.P. and D.R. performed or supervised wet laboratory work. Q.F., C.P., M.H., M.Pet, S.M., A.P., I.L., M.Li, I.M., S.S., P.Sk, J.Ke, N.P. and D.R. analysed data. Q.F., C.P., M.H., M.Pet, J.Ke, S.P. and D.R. wrote the manuscript and supplements.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to David Reich.

Reviewer Information Nature thanks C. Lalueza-Fox and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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https://doi.org/10.1038/nature17993

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