Abstract

We generated genome-wide data from 69 Europeans who lived between 8,000–3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies1,2,3,4,5,6,7,8 and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000–5,000 years ago. At the beginning of the Neolithic period in Europe, 8,000–7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a 24,000-year-old Siberian6. By 6,000–5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact 4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced 75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least 3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin9 of at least some of the Indo-European languages of Europe.

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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 PRJEB8448. The Human Origins genotype dataset including ancient individuals can be found at (http://genetics.med.harvard.edu/reichlab/Reich_Lab/Datasets.html).

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Acknowledgements

We thank P. Bellwood, J. Burger, P. Heggarty, M. Lipson, C. Renfrew, J. Diamond, S.Pääbo, R. Pinhasi and P. Skoglund for critical comments, and the Initiative for the Science of the Human Past at Harvard for organizing a workshop around the issues touched on by this paper. We thank S. Pääbo for support for establishing the ancient DNA facilities in Boston, and P. Skoglund for detecting the presence of two related individuals in our data set. We thank L. Orlando, T. S. Korneliussen, and C. Gamba for help in obtaining data. We thank Agilent Technologies and G. Frommer for help in developing the capture reagents. We thank C. Der Sarkissian, G. Valverde, L. Papac and B. Nickel for wet laboratory support. We thank archaeologists V. Dresely, R. Ganslmeier, O. Balanvosky, J. Ignacio Royo Guillén, A. Osztás, V. Majerik, T. Paluch, K. Somogyi and V.Voicsek for sharing samples and discussion about archaeological context. This research was supported by an Australian Research Council grant to W.H. and B.L. (DP130102158), and German Research Foundation grants to K.W.A. (Al 287/7-1 and 7-3, Al 287/10-1 and Al 287/14-1) and to H.M. (Me 3245/1-1 and 1-3). D.R. was supported by US National Science Foundation HOMINID grant BCS-1032255, US National Institutes of Health grant GM100233, and the Howard Hughes Medical Institute.

Author information

Author notes

    • Wolfgang Haak
    •  & Iosif Lazaridis

    These authors contributed equally to this work.

Affiliations

  1. Australian Centre for Ancient DNA, School of Earth and Environmental Sciences & Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia

    • Wolfgang Haak
    • , Bastien Llamas
    •  & Alan Cooper
  2. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Iosif Lazaridis
    • , Nadin Rohland
    • , Swapan Mallick
    • , Susanne Nordenfelt
    • , Eadaoin Harney
    • , Kristin Stewardson
    • , Qiaomei Fu
    •  & David Reich
  3. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA

    • Iosif Lazaridis
    • , Nick Patterson
    • , Nadin Rohland
    • , Swapan Mallick
    • , Susanne Nordenfelt
    • , Eadaoin Harney
    • , Kristin Stewardson
    • , Qiaomei Fu
    •  & David Reich
  4. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Swapan Mallick
    • , Eadaoin Harney
    • , Kristin Stewardson
    •  & David Reich
  5. Institute of Anthropology, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany

    • Guido Brandt
    • , Nicole Nicklisch
    • , Christina Roth
    • , Anna Szécsényi-Nagy
    •  & Kurt Werner Alt
  6. Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany

    • Qiaomei Fu
    •  & Matthias Meyer
  7. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100049, China

    • Qiaomei Fu
  8. Institute for Archaeological Sciences, University of Tübingen, D-72070 Tübingen, Germany

    • Alissa Mittnik
    •  & Johannes Krause
  9. Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Science, H-1014 Budapest, Hungary

    • Eszter Bánffy
    •  & Anna Szécsényi-Nagy
  10. Römisch Germanische Kommission (RGK) Frankfurt, D-60325 Frankfurt, Germany

    • Eszter Bánffy
  11. Archaeological Research Laboratory, Stockholm University, 114 18 Stockholm, Sweden

    • Christos Economou
  12. Departments of Paleoanthropology and Archaeogenetics, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, D-72070 Tübingen, Germany

    • Michael Francken
    •  & Johannes Krause
  13. State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany

    • Susanne Friederich
    • , Harald Meller
    • , Nicole Nicklisch
    •  & Kurt Werner Alt
  14. Departamento de Prehistoria y Arqueología, Facultad de Filosofía y Letras, Universidad Autónoma de Madrid, E-28049 Madrid, Spain

    • Rafael Garrido Pena
  15. The Cultural Heritage Foundation, Västerås 722 12, Sweden

    • Fredrik Hallgren
  16. Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg 199034, Russia

    • Valery Khartanovich
    •  & Vayacheslav Moiseyev
  17. Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia

    • Aleksandr Khokhlov
    • , Pavel Kuznetsov
    •  & Oleg Mochalov
  18. Deutsches Archaeologisches Institut, Abteilung Madrid, E-28002 Madrid, Spain

    • Michael Kunst
  19. Danube Private University, A-3500 Krems, Austria

    • Nicole Nicklisch
    •  & Kurt Werner Alt
  20. Institute for Prehistory and Archaeological Science, University of Basel, CH-4003 Basel, Switzerland

    • Sandra L. Pichler
    •  & Kurt Werner Alt
  21. Departamento de Prehistòria, Universitat Autònoma de Barcelona, E-08193 Barcelona, Spain

    • Roberto Risch
  22. Departamento de Prehistòria y Arqueolgia, Universidad de Valladolid, E-47002 Valladolid, Spain

    • Manuel A. Rojo Guerra
  23. State Office for Cultural Heritage Management Baden-Württemberg, Osteology, D-78467 Konstanz, Germany

    • Joachim Wahl
  24. Max Planck Institute for the Science of Human History, D-07745 Jena, Germany

    • Johannes Krause
  25. Anthropology Department, Hartwick College, Oneonta, New York 13820, USA

    • Dorcas Brown
    •  & David Anthony

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Contributions

W.H., N.P., N.R., J.K., K.W.A. and D.R. supervised the study. W.H., E.B., C.E., M.F., S.F., R.G.P., F.H., V.K., A.K., M.K., P.K., H.M., O.M., V.M., N.N., S.L.P., R.R., M.A.R.G., C.R., A.S.-N., J.W., J.K., D.B., D.A., A.C., K.W.A. and D.R. assembled archaeological material, W.H., I.L., N.P., N.R., S.M., A.M. and D.R. analysed genetic data. I.L., N.P. and D.R. developed methods using f statistics for inferring admixture proportions. W.H., N.R., B.L., G.B., S.N., E.H., K.S. and A.M. performed wet laboratory ancient DNA work. I.L., N.R., S.M., B.L., Q.F., M.M. and D.R. developed the 390k capture reagent. W.H., I.L. and D.R. wrote the manuscript with help from all co-authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to David Reich.

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