The genomic history of southeastern Europe (original) (raw)

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References

1. Tringham, R. E. in The Transition to Agriculture in Prehistoric Europe (ed. Price, D. ) 19–56 (Cambridge Univ. Press, 2000)
2. Bellwood, P. First Farmers: The Origins of Agricultural Societies 2nd edn (Wiley–Blackwell, 2004)
3. Golitko, M. in Ancient Europe, 8000 b.c. to a.d. 1000: An Encyclopedia of the Barbarian World (eds Bogucki, P. & Crabtree, P. J. ) 259–266 (Charles Scribners & Sons, 2003)
4. VanderLinden, M. in Investigating Archaeological Cultures: Material Culture, Variability, and Transmission (eds Roberts, B. W. & VanderLinden, M. ) 289–319 (Springer, 2012)
5. Bramanti, B. et al. Genetic discontinuity between local hunter-gatherers and central Europe’s first farmers. Science 326, 137–140 (2009)
   Article ADS CAS PubMed Google Scholar
6. Skoglund, P. et al. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336, 466–469 (2012)
   Article ADS CAS PubMed Google Scholar
7. Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015)
   Article ADS CAS PubMed PubMed Central Google Scholar
8. Cassidy, L. M. et al. Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. Proc. Natl Acad. Sci. USA 113, 368–373 (2016)
   Article ADS CAS PubMed Google Scholar
9. Hofmanová, Z. et al. Early farmers from across Europe directly descended from Neolithic Aegeans. Proc. Natl Acad. Sci. USA 113, 6886–6891 (2016)
   Article CAS PubMed PubMed Central Google Scholar
10. Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015)
    Article ADS CAS PubMed PubMed Central Google Scholar
11. Omrak, A. et al. Genomic evidence establishes Anatolia as the source of the European Neolithic gene pool. Curr. Biol. 26, 270–275 (2016)
    Article CAS PubMed Google Scholar
12. Müller, J., Rassmann, K. & Videiko, M. Trypillia Mega-Sites and European Prehistory: 4100–3400 bce (Routledge, 2016)
13. Anthony, D. W. The Horse, the Wheel and Language (Princeton Univ. Press, 2007)
14. Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015)
    Article ADS CAS PubMed PubMed Central Google Scholar
15. Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015)
    Article ADS CAS PubMed Google Scholar
16. Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014)
    Article ADS CAS PubMed PubMed Central Google Scholar
17. Fu, Q. et al. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016)
    Article ADS CAS PubMed PubMed Central Google Scholar
18. Gallego Llorente, M. et al. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350, 820–822 (2015)
    Article ADS CAS PubMed Google Scholar
19. Jones, E. R. et al. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat. Commun. 6, 8912 (2015)
    Article ADS CAS PubMed Google Scholar
20. Keller, A. et al. New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. Nat. Commun. 3, 698 (2012)
    Article ADS CAS PubMed Google Scholar
21. Kılınç, G. M. et al. The demographic development of the first farmers in Anatolia. Curr. Biol. 26, 2659–2666 (2016)
    Article CAS PubMed PubMed Central Google Scholar
22. Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419–424 (2016)
    Article ADS CAS PubMed PubMed Central Google Scholar
23. Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014)
    Article ADS CAS PubMed PubMed Central Google Scholar
24. Olalde, I. et al. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507, 225–228 (2014)
    Article ADS CAS PubMed PubMed Central Google Scholar
25. Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014)
    Article ADS CAS PubMed Google Scholar
26. Lazaridis, I. et al. Genetic origins of the Minoans and Mycenaeans. Nature 548, 214–218 (2017)
    Article ADS CAS PubMed PubMed Central Google Scholar
27. Lipson, M. et al. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551, 368–372 (2017)
    Article ADS CAS PubMed PubMed Central Google Scholar
28. Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016)
    Article ADS CAS PubMed PubMed Central Google Scholar
29. Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009)
    Article CAS PubMed PubMed Central Google Scholar
30. Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012)
    Article PubMed PubMed Central Google Scholar
31. Gronenborn, D. & Dolukhanov, P. in The Oxford Handbook of Neolithic Europe (eds Fowler, C., Harding, J. & Hofmann, D. ) 195–214 (Oxford Univ. Press, 2015)
32. Telegin, D. Y. Neolithic cultures of Ukraine and adjacent areas and their chronology. J. World Prehist. 1, 307–331 (1987)
    Article Google Scholar
33. Telegin, D. Y. & Potekhina, I. D. Neolithic Cemeteries and Populations in the Dnieper Basin (British Archaeological Reports, 1987)
34. Jones, E. R. et al. The Neolithic transition in the Baltic was not driven by admixture with early European farmers. Curr. Biol. 27, 576–582 (2017)
    Article CAS PubMed PubMed Central Google Scholar
35. Mittnik, A. et al. The genetic prehistory of the Baltic Sea region. Nat. Commun. 9, 443 (2018)
    Article ADS CAS Google Scholar
36. Saag, L. et al. Extensive farming in Estonia started through a sex-biased migration from the Steppe. Curr. Biol. 27, 2185–2193.e6 (2017)
    Article CAS PubMed Google Scholar
37. Maier, A. The Central European Magdalenian: Regional Diversity and Internal Variability (Springer, 2015)
38. Boric´, D. & Price, T. D. Strontium isotopes document greater human mobility at the start of the Balkan Neolithic. Proc. Natl Acad. Sci. USA 110, 3298–3303 (2013)
    Article ADS PubMed PubMed Central Google Scholar
39. Krauß, R., Marinova, E., De Brue, H. & Weninger, B. The rapid spread of early farming from the Aegean into the Balkans via the Sub-Mediterranean–Aegean vegetation Zone. Quat. Int. https://doi.org/10.1016/j.quaint.2017.01.019 (2017)
40. Bacvarov, K. in Moments in Time: Papers Presented to Pál Raczky on his 60th Birthday (eds Anders, A. & Kulcsár, G. ) 29–34 (L’Harmattan, 2013)
41. Gurova, M. & Bonsall, C. ‘Pre-Neolithic’ in Southeast Europe: a Bulgarian perspective. Documenta Praehistorica 41, 95–109 (2014)
    Article Google Scholar
42. Brandt, G. et al. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. Science 342, 257–261 (2013)
    Article ADS CAS PubMed PubMed Central Google Scholar
43. Borić, D. in The Oxford Handbook of Neolithic Europe (eds Fowler C., Harding, J. & Hofmann, D. ) 927–957 (Oxford Univ. Press, 2015)
44. Szmyt, M. in Transition to the Bronze Age (Archaeolingua 30) (eds Heyd, V., Kulcsár, G. & Szeverényi, V. ) 93–111 (Archaeolingua, 2013)
45. Olalde, I. et al. A common genetic origin for early farmers from Mediterranean Cardial and central European LBK cultures. Mol. Biol. Evol. 32, 3132–3142 (2015)
    CAS PubMed PubMed Central Google Scholar
46. Posth, C. et al. Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a Late Glacial population turnover in Europe. Curr. Biol. 26, 827–833 (2016)
    Article CAS PubMed Google Scholar
47. Anthony, D. W. & Ringe, D. The Indo-European homeland from linguistic and archaeological perspectives. Annu. Rev. Linguist. 1, 199–219 (2015)
    Article Google Scholar
48. Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013)
    Article ADS PubMed PubMed Central Google Scholar
49. Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. https://doi.org/10.1101/pdb.prot5448 (2010)
50. Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. Lond. B 370, 20130624 (2015)
    Article CAS Google Scholar
51. Korlević, P. et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques 59, 87–93 (2015)
    Article CAS PubMed Google Scholar
52. Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010)
    Article CAS PubMed Google Scholar
53. DeAngelis, M. M., Wang, D. G. & Hawkins, T. L. Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res. 23, 4742–4743 (1995)
    Article CAS PubMed PubMed Central Google Scholar
54. Rohland, N. & Reich, D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22, 939–946 (2012)
    Article CAS PubMed PubMed Central Google Scholar
55. Maricic, T., Whitten, M. & Pääbo, S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS ONE 5, e14004 (2010)
    Article ADS CAS PubMed PubMed Central Google Scholar
56. Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012)
    Article CAS PubMed Google Scholar
57. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010)
    Article CAS PubMed PubMed Central Google Scholar
58. Fu, Q. et al. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553–559 (2013)
    Article CAS PubMed PubMed Central Google Scholar
59. Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229–2234 (2014)
    Article ADS CAS PubMed PubMed Central Google Scholar
60. Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014)
    Article PubMed PubMed Central Google Scholar
61. Price, A. L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006)
    Article CAS PubMed Google Scholar
62. Petkova, D., Novembre, J. & Stephens, M. Visualizing spatial population structure with estimated effective migration surfaces. Nat. Genet. 48, 94–100 (2016)
    Article CAS PubMed Google Scholar
63. Brown, L. D., Cai, T. T. & DasGupta, A. Interval estimation for a binomial proportion. Stat. Sci. 16, 101–133 (2001)
    MathSciNet MATH Google Scholar
64. Agresti, A. & Coull, B. A. Approximate is better than ‘exact’ for interval estimation of binomial proportions. Am. Stat. 52, 119–126 (1998)
    MathSciNet Google Scholar
65. Longin, R. New method of collagen extraction for radiocarbon dating. Nature 230, 241–242 (1971)
    Article ADS CAS PubMed Google Scholar
66. Brown, T. A., Nelson, D. E., Vogel, J. S. & Southon, J. R. Improved collagen extraction by modified Longin method. Radiocarbon 30, 171–177 (1988)
    Article CAS Google Scholar
67. Kennett, D. J. et al. Archaeogenomic evidence reveals prehistoric matrilineal dynasty. Nat. Commun. 8, 14115 (2017)
    Article ADS CAS PubMed PubMed Central Google Scholar
68. van Klinken, G. J. Bone collagen quality indicators for palaeodietary and radiocarbon measurements. J. Archaeol. Sci. 26, 687–695 (1999)
    Article Google Scholar
69. Stuiver, M. & Polach, H. A. Discussion: reporting of 14C data. Radiocarbon 19, 355–363 (1977)
    Article Google Scholar
70. Bronk Ramsey, C. OxCal 4.23 Online Manualhttps://c14.arch.ox.ac.uk/oxcalhelp/hlp_contents.html (2013)
71. Cook, G. T. et al. A freshwater diet-derived 14C reservoir effect at the Stone Age sites in the Iron Gates gorge. Radiocarbon 43, 453–460 (2001)
    Article Google Scholar

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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

1. Iain Mathieson
   Present address: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
2. Ron Pinhasi and David Reich: These authors contributed equally to this work.

Authors and Affiliations

1. Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, 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, Jena, 07745, 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, Budapest, H-1097, Hungary
   Anna Szécsényi-Nagy & Mende Balázs Gusztáv
5. Howard Hughes Medical Institute, Harvard Medical School, Boston, 02115, Massachusetts, USA
   Swapan Mallick, Nasreen Broomandkhoshbacht, Matthew Ferry, Eadaoin Harney, Megan Michel, Jonas Oppenheimer, Kristin Stewardson & David Reich
6. Earth Institute, University College Dublin, Belfield, 4, Dublin, 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, Vienna, 1090, Austria
   Olivia Cheronet, Maria Teschler-Nicola & Ron Pinhasi
8. Department of Life Sciences, CIAS, University of Coimbra, Coimbra, 3000-456, 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, Adelaide, SA-5005, 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, Zagreb, 10000, 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, 30322, Georgia, USA
    Kendra Sirak
16. Dipartimento di Biologia, Università di Firenze, Florence, 50122, Italy
    Stefania Vai, Martina Lari & David Caramelli
17. National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, Sofia, BG-1000, Bulgaria
    Stefan Alexandrov, Krum Bacvarov & Yavor Boyadzhiev
18. Danube Private University, Krems, A-3500, Austria
    Kurt W. Alt
19. Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, Basel-Allschwil, CH-4123, Switzerland
    Kurt W. Alt
20. State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, 06114, Germany
    Kurt W. Alt & Harald Meller
21. National History Museum of Romania, Bucharest, 030026, 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, Tübingen, 72074, Germany
    Hervé Bocherens
25. Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, 72076, Germany
    Hervé Bocherens, Nicholas J. Conard, Dorothée G. Drucker & Katerina Harvati
26. ROCEEH Research Center, Heidelberg Academy of Sciences and Humanities, University of Tübingen, Tübingen, 72070, Germany
    Michael Bolus & Maria Malina
27. Vasile Pârvan Institute of Archaeology, Romanian Academy, Bucharest, 010667, Romania
    Adina Boroneanţ
28. Human Biology Department, Cardinal Stefan Wyszyński University, 01-938, Warsaw, Poland
    Alicja Budnik
29. KADUCEJ d.o.o.,, Split, 21000, 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, Tübingen, 72070, Germany
    Nicholas J. Conard
32. INRAP/UMR 8215 Trajectoires, Nanterre, 92023, France
    Richard Cottiaux
33. Archaeological Museum of Istria, Pula, 52100, Croatia
    Maja Čuka & Darko Komšo
34. Service Régional de l'Archéologie de Bourgogne-Franche-Comté, Besançon, 25043, Cedex, France
    Christophe Cupillard
35. Laboratoire Chronoenvironnement, UMR 6249 du CNRS, UFR des Sciences et Techniques, Besançon, 25030, 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, Tübingen, 72070, Germany
    Michael Francken & Katerina Harvati
38. Laboratory for Human Bioarchaeology, Sofia, 1202, 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. Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, Institute of Biology, H-1117, Budapest, Hungary
    Tamás Hajdu & Tamás Szeniczey
42. Department of Archaeology, Sofia University St. Kliment, 1504 Sofia, Ohridski, 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, 82071, Wyoming, USA
    Ivor Janković & Ivor Karavanić
46. Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, 10000, 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. Pediatric Department, CHU Sainte-Justine Research Center, 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, Bucharest, 50107, Romania
    Catalin Lazar
51. Institute for Pre- and Protohistoric Archaeology and the Archaeology of the Roman Provinces, Ludwig-Maximilians-University, Munich, 80799, Germany
    Maleen Leppek & Philipp W. Stockhammer
52. Dipartimento SAGAS - Sezione di Archeologia e Antico Oriente, Università degli Studi di Firenze, Florence, 50122, Italy
    Domenico Lo Vetro & Fabio Martini
53. Museo e Istituto fiorentino di Preistoria, Florence, 50122, 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, Šibenik, 22000, Croatia
    Marko Menđušić
56. Teleorman County Museum, Alexandria, 140033, 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, Iaşi, 700481, 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, Zagreb, 10000, Croatia
    Mario Šlaus
62. Regional Historical Museum Varna, Varna, BG-9000, Bulgaria
    Vladimir Slavchev
63. National Museum in Belgrade, Belgrade, Serbia
    Andrej Starović
64. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
    Sahra Talamo
65. Department of Anthropology, Natural History Museum Vienna, Vienna, 1010, Austria
    Maria Teschler-Nicola
66. INRAP/UMR 8215 Trajectoires, Nanterre, 92023, France
    Corinne Thevenet
67. CNRS/UMR 7041 ArScAn MAE, Nanterre, 92023, 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, M5S 2S2, Ontario, 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, Drniš, 22320, Croatia
    Joško Zaninović
75. anthropol - Anthropologieservice, Hechingen, 72379, 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, 10027, New York, USA
    Dušan Borić

Authors

1. Iain Mathieson
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2. Songül Alpaslan-Roodenberg
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3. Cosimo Posth
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4. Anna Szécsényi-Nagy
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5. Nadin Rohland
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6. Swapan Mallick
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7. Iñigo Olalde
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8. Nasreen Broomandkhoshbacht
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9. Francesca Candilio
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10. Olivia Cheronet
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11. Daniel Fernandes
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12. Matthew Ferry
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13. Beatriz Gamarra
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14. Gloria González Fortes
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15. Wolfgang Haak
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16. Eadaoin Harney
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17. Eppie Jones
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18. Denise Keating
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19. Ben Krause-Kyora
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20. Isil Kucukkalipci
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21. Megan Michel
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22. Alissa Mittnik
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23. Kathrin Nägele
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24. Mario Novak
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25. Jonas Oppenheimer
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26. Nick Patterson
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27. Saskia Pfrengle
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28. Kendra Sirak
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29. Kristin Stewardson
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30. Stefania Vai
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31. Stefan Alexandrov
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32. Kurt W. Alt
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33. Radian Andreescu
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34. Dragana Antonović
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35. Abigail Ash
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36. Nadezhda Atanassova
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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.

Corresponding authors

Correspondence toIain Mathieson, Ron Pinhasi or David Reich.

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Competing interests

The authors declare no competing financial interests.

Additional information

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 figures and tables

Extended Data Figure 1 Principal components analysis of ancient individuals.

Points for 486 ancient individuals are projected onto principal components defined by 777 present-day west Eurasian individuals (grey points). This differs from Fig. 1b in that the plot is not cropped and the present-day individuals are shown.

Extended Data Figure 2 Supervised ADMIXTURE analysis.

Supervised ADMIXTURE analysis modelling each ancient individual (one per row), as a mixture of populations represented by clusters that are constrained to contain northwestern-Anatolian Neolithic (grey), Yamnaya from Samara (yellow), EHG (pink) and WHG (green) populations. Dates in parentheses indicate approximate range of individuals in each population. This differs from Fig. 1d in that it contains some previously published samples7,9,10,19,23,26 and includes sample identification numbers.

Extended Data Figure 3 Unsupervised ADMIXTURE analysis.

Unsupervised ADMIXTURE plot from k = 4 to 12 on a dataset consisting of 1,099 present-day individuals and 476 ancient individuals. We show newly reported ancient individuals and some previously published individuals7,10,19,22,23,26 for comparison.

Extended Data Figure 4 Genetic spatial structure in hunter-gatherers.

We infer the estimated effective migration surface62, a model of genetic relatedness in which individuals move in a random direction from generation to generation on an underlying grid, such that genetic relatedness is determined by distance. The migration parameter, m, defining the local rate of migration, varies on the grid and is inferred. This plot shows log10(m), scaled relative to the average migration rate, which is arbitrary. Thus log10(m) = 2, for example, implies that the rate of migration at this point on the grid is 100 times higher than average. To restrict the model as much as possible to hunter-gatherer populations, the migration surface is inferred using data from 116 individuals that date to earlier than approximately 5000 bc and have no northwestern-Anatolian-Neolithic-related ancestry. Although the migration surface is sensitive to sampling and fine-scale features may not be interpretable, the migration ‘barrier’ (region of low migration) running north-to-south and separating populations with primarily WHG ancestry from those with primarily EHG ancestry seems to be robust, and consistent with inferred admixture proportions. This analysis suggests that Mesolithic hunter-gatherer population structure was clustered and not smoothly clinal (that is, genetic differentiation did not vary consistently with distance). Superimposed on this background, pie charts show the WHG, EHG and CHG ancestry proportions inferred for populations used to construct the migration surface. This represents another way of visualizing the data in Fig. 2, Supplementary Table 3.1.3; we use two population models if they fit with P > 0.01, and three population models otherwise. Pie charts with only a single colour are those that were fixed to be the source populations.

Extended Data Figure 5 Sex bias in hunter-gatherer admixture.

The log-likelihood surfaces for the proportion of female (x axis) and male (y axis) ancestors that are hunter-gatherer-related for the combined populations analysed in Fig. 3c, and the two populations with the strongest evidence for sex bias. Numbers in parentheses, number of individuals in each group. The log-likelihood scale ranges from 0 to −10, in which 0 is the feasible point with the highest likelihood.

Supplementary information

Life Sciences Reporting Summary (PDF 72 kb)

Supplementary Information

This file contains Supplementary Notes 1-3. (PDF 11029 kb)

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. (XLSX 268 kb)

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Mathieson, I., Alpaslan-Roodenberg, S., Posth, C. et al. The genomic history of southeastern Europe.Nature 555, 197–203 (2018). https://doi.org/10.1038/nature25778

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• Received: 06 May 2017
• Accepted: 16 January 2018
• Published: 21 February 2018
• Issue Date: 08 March 2018
• DOI: https://doi.org/10.1038/nature25778