Article | Published:

The genomic history of southeastern Europe

Nature volume 555, pages 197203 (08 March 2018) | Download Citation

Abstract

Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west–east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.

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Acknowledgements

We thank D. Anthony, I. Lazaridis and M. Lipson for comments on the manuscript, B. Llamas, A. Cooper and A. Furtwängler for contributions to laboratory work, R. Evershed for contributing 14C dates and F. Novotny for assistance with samples. Support for this project was provided by the Human Frontier Science Program fellowship LT001095/2014-L to I.M., by DFG grant AL 287 / 14-1 to K.W.A.; by Irish Research Council grant GOIPG/2013/36 to D.F.; by the NSF Archaeometry program BCS-1460369 to D.J.K. for AMS 14C work; by MEN-UEFISCDI grant, Partnerships in Priority Areas Program – PN II (PN-II-PT-PCCA-2013-4-2302) to C.L.; by Croatian Science Foundation grant IP-2016-06-1450 to M.N. and I.J.; by European Research Council grant ERC CoG 724703 and Deutsche Forschungsgemeinschaft DFG FOR2237 to K.H.; by ERC starting grant ADNABIOARC (263441) to R.P.; and by US National Science Foundation HOMINID grant BCS-1032255, US National Institutes of Health grant GM100233, the Howard Hughes Medical Institute and an Allen Discovery Center grant from the Paul Allen Foundation to D.R.

Author information

Author notes

    • Iain Mathieson

    Present address: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

    • Ron Pinhasi
    •  & David Reich

    These authors contributed equally to this work.

Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Iain Mathieson
    • , Songül Alpaslan-Roodenberg
    • , Nadin Rohland
    • , Swapan Mallick
    • , Iñigo Olalde
    • , Nasreen Broomandkhoshbacht
    • , Matthew Ferry
    • , Eadaoin Harney
    • , Megan Michel
    • , Jonas Oppenheimer
    • , Kristin Stewardson
    •  & David Reich
  2. Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany

    • Cosimo Posth
    • , Wolfgang Haak
    • , Ben Krause-Kyora
    • , Alissa Mittnik
    • , Kathrin Nägele
    • , Philipp W. Stockhammer
    •  & Johannes Krause
  3. Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany

    • Cosimo Posth
    • , Isil Kucukkalipci
    • , Alissa Mittnik
    • , Saskia Pfrengle
    •  & Johannes Krause
  4. Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary

    • Anna Szécsényi-Nagy
    •  & Mende Balázs Gusztáv
  5. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Swapan Mallick
    • , Nasreen Broomandkhoshbacht
    • , Matthew Ferry
    • , Eadaoin Harney
    • , Megan Michel
    • , Jonas Oppenheimer
    • , Kristin Stewardson
    •  & David Reich
  6. Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland

    • Francesca Candilio
    • , Olivia Cheronet
    • , Daniel Fernandes
    • , Beatriz Gamarra
    • , Denise Keating
    • , Mario Novak
    • , Kendra Sirak
    • , Abigail Ash
    •  & Ron Pinhasi
  7. Department of Anthropology, University of Vienna, 1090 Vienna, Austria

    • Olivia Cheronet
    • , Maria Teschler-Nicola
    •  & Ron Pinhasi
  8. CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal

    • Daniel Fernandes
  9. Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44100, Italy

    • Gloria González Fortes
  10. Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA-5005 Adelaide, South Australia, Australia

    • Wolfgang Haak
  11. Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland

    • Eppie Jones
  12. Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK

    • Eppie Jones
  13. Institute for Anthropological Research, 10000 Zagreb, Croatia

    • Mario Novak
    •  & Ivor Janković
  14. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA

    • Nick Patterson
    •  & David Reich
  15. Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA

    • Kendra Sirak
  16. Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy

    • Stefania Vai
    • , Martina Lari
    •  & David Caramelli
  17. National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria

    • Stefan Alexandrov
    • , Krum Bacvarov
    •  & Yavor Boyadzhiev
  18. Danube Private University, A-3500 Krems, Austria

    • Kurt W. Alt
  19. Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, CH-4123 Basel-Allschwil, Switzerland

    • Kurt W. Alt
  20. State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, 06114 Halle, Germany

    • Kurt W. Alt
    •  & Harald Meller
  21. National History Museum of Romania, 030026, Bucharest, Romania

    • Radian Andreescu
    •  & Catalin Lazar
  22. Institute of Archaeology, Belgrade, Serbia

    • Dragana Antonović
  23. Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria

    • Nadezhda Atanassova
  24. Department of Geosciences, Biogeology, Universität Tübingen, 72074 Tübingen, Germany

    • Hervé Bocherens
  25. Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany

    • Hervé Bocherens
    • , Nicholas J. Conard
    • , Dorothée G. Drucker
    •  & Katerina Harvati
  26. ROCEEH Research Center, Heidelberg Academy of Sciences and Humanities, University of Tübingen, 72070 Tübingen, Germany

    • Michael Bolus
    •  & Maria Malina
  27. Vasile Pârvan Institute of Archaeology, Romanian Academy, 010667 Bucharest, Romania

    • Adina Boroneanţ
  28. Human Biology Department, Cardinal Stefan Wyszyński University, 01-938 Warsaw, Poland

    • Alicja Budnik
  29. KADUCEJ d.o.o., 21000 Split, Croatia

    • Josip Burmaz
    •  & Dženi Los
  30. St. Cyril and Methodius University, 5000 Veliko Turnovo, Bulgaria

    • Stefan Chohadzhiev
  31. Department of Early Prehistory and Quaternary Ecology, University of Tübingen, 72070 Tübingen, Germany

    • Nicholas J. Conard
  32. INRAP/UMR 8215 Trajectoires, 92023 Nanterre, France

    • Richard Cottiaux
  33. Archaeological Museum of Istria, 52100 Pula, Croatia

    • Maja Čuka
    •  & Darko Komšo
  34. Service Régional de l'Archéologie de Bourgogne-Franche-Comté, 25043 Besançon Cedex, France

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

    • Christophe Cupillard
  36. Regional Museum of History Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria

    • Nedko Elenski
    •  & Petar Stanev
  37. Institute for Archaeological Sciences, Paleoanthropology, University of Tübingen, 72070 Tübingen, Germany

    • Michael Francken
    •  & Katerina Harvati
  38. Laboratory for Human Bioarchaeology, 1202 Sofia, Bulgaria

    • Borislava Galabova
  39. Regional Museum of History, 3000 Vratsa, Bulgaria

    • Georgi Ganetsovski
  40. DRAC Auvergne - Rhône Alpes, Ministère de la Culture, Lyon Cedex 01, France

    • Bernard Gély
  41. Eötvös Loránd University, Faculty of Science, Institute of Biology, Department of Biological Anthropology, H-1117 Budapest, Hungary

    • Tamás Hajdu
    •  & Tamás Szeniczey
  42. Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria

    • Veneta Handzhyiska
    • , Krassimir Leshtakov
    • , Ivaylo Lozanov
    • , Vanya Petrova
    •  & Ivan Valchev
  43. Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, Oxford OX1 3QY, UK

    • Thomas Higham
  44. Regional Museum of History, 6300 Haskovo, Bulgaria

    • Stanislav Iliev
  45. Department of Anthropology, University of Wyoming, Laramie, Wyoming 82071, USA

    • Ivor Janković
    •  & Ivor Karavanić
  46. Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia

    • Ivor Karavanić
  47. Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, Pennsylvania 16802, USA

    • Douglas J. Kennett
  48. Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210 Kiev, Ukraine

    • Alexandra Kozak
    •  & Inna Potekhina
  49. CHU Sainte-Justine Research Center, Pediatric Department, Université de Montréal, Montreal, Québec H3T 1C5, Canada

    • Damian Labuda
  50. Department of Ancient History, Archaeology and History of Art, Faculty of History, University of Bucharest, 50107 Bucharest, Romania

    • Catalin Lazar
  51. Institute for Pre- and Protohistoric Archaeology and the Archaeology of the Roman Provinces, Ludwig-Maximilians-University, 80799 Munich, Germany

    • Maleen Leppek
    •  & Philipp W. Stockhammer
  52. Dipartimento SAGAS - Sezione di Archeologia e Antico Oriente, Università degli Studi di Firenze, 50122 Florence, Italy

    • Domenico Lo Vetro
    •  & Fabio Martini
  53. Museo e Istituto fiorentino di Preistoria, 50122 Florence, Italy

    • Domenico Lo Vetro
    •  & Fabio Martini
  54. School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK

    • Kath McSweeney
    •  & Clive Bonsall
  55. Conservation Department in Šibenik, Ministry of Culture of the Republic of Croatia, 22000 Šibenik, Croatia

    • Marko Menđušić
  56. Teleorman County Museum, 140033 Alexandria, Romania

    • Pavel Mirea
  57. Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia

    • Vyacheslav Moiseyev
  58. Department of Anthropology, University of Wisconsin, Madison, Wisconsin 53706, USA

    • T. Douglas Price
  59. Olga Necrasov Centre for Anthropological Research, Romanian Academy – Iaşi Branch, 700481 Iaşi, Romania

    • Angela Simalcsik
  60. Dipartimento di Scienze e tecnologie biologiche, chimiche e farmaceutiche, Lab. of Anthropology, Università degli studi di Palermo, 90133 Palermo, Italy

    • Luca Sineo
    •  & Giulio Catalano
  61. Anthropological Center, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia

    • Mario Šlaus
  62. Regional Historical Museum Varna, BG-9000 Varna, Bulgaria

    • Vladimir Slavchev
  63. National Museum in Belgrade, Belgrade, Serbia

    • Andrej Starović
  64. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany

    • Sahra Talamo
  65. Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria

    • Maria Teschler-Nicola
  66. INRAP/UMR 8215 Trajectoires, 92023 Nanterre, France

    • Corinne Thevenet
  67. CNRS/UMR 7041 ArScAn MAE, 92023 Nanterre, France

    • Frédérique Valentin
  68. Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119991, Russia

    • Sergey Vasilyev
    •  & Elizaveta Veselovskaya
  69. Archaeological Museum of Macedonia, 1000 Skopje, the former Yugoslav Republic of Macedonia

    • Fanica Veljanovska
  70. Regional Museum of History, 9700 Shumen, Bulgaria

    • Svetlana Venelinova
  71. Department of Anthropology, University of Toronto, Toronto, Ontario, M5S 2S2, Canada

    • Bence Viola
  72. Institute of Archaeology & Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia

    • Bence Viola
  73. Satu Mare County Museum Archaeology Department, 440026 Satu Mare, Romania

    • Cristian Virag
  74. Municipal Museum Drniš, 22320 Drniš, Croatia

    • Joško Zaninović
  75. anthropol - Anthropologieservice, 72379 Hechingen, Germany

    • Steve Zäuner
  76. Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany

    • Raiko Krauß
  77. Institute of Latvian History, University of Latvia, Rı¯ga 1050, Latvia

    • Gunita Zariņa
  78. Department of Archaeology, Durham University, Durham DH1 3LE, UK

    • Bisserka Gaydarska
  79. School of Environmental Sciences, Geography, University of Hull, Hull HU6 7RX, UK

    • Malcolm Lillie
  80. Department of Biology, Grand Valley State University, Allendale, Michigan 49401, USA

    • Alexey G. Nikitin
  81. Ephorate of Paleoanthropology and Speleology, 11636 Athens, Greece

    • Anastasia Papathanasiou
  82. The Italian Academy for Advanced Studies in America, Columbia University, New York, New York 10027, USA

    • Dušan Borić

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Contributions

S.A.-R., A.S.-N., S.Vai., S.A., K.W.A., R.A., D.A., A.A., N.A., K.B., M.B.G., H.B., M.B., A.Bo., Y.B., A.Bu., J.B., S.C., N.J.C., R.C., M.C., C.C., D.G.D., N.E., M.Fr., B.Gal., G.G., B.Ge., T.Ha., V.H., K.H., T.Hi., S.I., I.J., I.Ka., D.Ko., A.K., D.La., M.La., C.L., M.Le., K.L., D.L.V., D.Lo., I.L., M.Ma., F.M., K.M., H.M., M.Me., P.M., V.M., V.P., T.D.P., A.Si., L.S., M.Š., V.S., P.S., A.St., T.S., M.T.-N., C.T., I.V., F.Va., S.Vas., F.Ve., S.Ve., E.V., B.V., C.V., J.Z., S.Z., P.W.S., G.C., R.K., D.C., G.Z., B.Gay., M.Li., A.G.N., I.P., A.P., D.B., C.B., J.K., R.P. and D.R. assembled and interpreted archaeological material. C.P., A.S.-N., N.R., N.B., F.C., O.C., D.F., M.Fe., B.Gam., G.G.F., W.H., E.H., E.J., D.Ke., B.K.-K., I.Ku., M.Mi., A.M., K.N., M.N., J.O., S.P., K.Si., K.St. and S.Vai. performed laboratory work. I.M., C.P., A.S.-N., S.M., I.O., N.P. and D.R. analysed data. D.J.K., S.T., D.B. and C.B. interpreted 14C dates. J.K., R.P. and D.R. supervised analysis or laboratory work. I.M. and D.R. wrote the paper with input from all co-authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Iain Mathieson or Ron Pinhasi or David Reich.

Reviewer Information Nature thanks C. Renfrew, A. Scally and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

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    Life Sciences Reporting Summary

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    This file contains Supplementary Notes 1-3.

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    Supplementary Data

    This file contains Supplementary Tables 1-5. Supplementary Table 1 shows the details of ancient individuals analysed in this study, Supplementary Table 2 shows the key D-statistics to support statements about population history, Supplementary Table 3 shows the qpAdm models with 7-population outgroup set, Supplementary Table 4 shows the qpAdm models with extended 14-population outgroup set, Supplementary Table 5 shows the qpAdm models for Neolithic populations for chromosome X and Supplementary Table 6 shows the additional 14C dating information.

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https://doi.org/10.1038/nature25778

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