Population genomics of Bronze Age Eurasia (original) (raw)

Accession codes

Primary accessions

European Nucleotide Archive

Data deposits

DNA sequence alignments are available from the European Nucleotide Archive (http://www.ebi.ac.uk/ena) under accession number PRJEB9021.

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Acknowledgements

We thank K. Magnussen, L. A. Petersen, C. D. Mortensen and A. Seguin-Orlando at the Danish National Sequencing Centre for help with the sequencing. We thank C. G. Zacho for technical assistance. The project was funded by The European Research Council (FP/2007-2013, grant no. 269442, The Rise), The University of Copenhagen (KU2016 programme), Marie Curie Actions of the European Union (FP7/2007-2013, grant no. 300554), The Villum Foundation (Young Investigator Programme, grant no. 10120), Frederik Paulsen, The Miller Institute, University of California, Berkeley, The Lundbeck Foundation, and The Danish National Research Foundation.

Author information

Author notes

1. Morten E. Allentoft and Martin Sikora: These authors contributed equally to this work.

Authors and Affiliations

1. Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
   Morten E. Allentoft, Martin Sikora, Morten Rasmussen, Jesper Stenderup, Peter B. Damgaard, Hannes Schroeder, Lasse Vinner, Anna-Sapfo Malaspinas, Ashot Margaryan, Ludovic Orlando & Eske Willerslev
2. Department of Historical Studies, University of Gothenburg, Gothenburg, 405 30, Sweden
   Karl-Göran Sjögren, Dalia Pokutta & Kristian Kristiansen
3. Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
   Simon Rasmussen, Thomas Sicheritz-Pontén & Søren Brunak
4. Faculty of Archaeology, Leiden University, Leiden, 2300, The Netherlands
   Hannes Schroeder
5. Department of Archaeology and Ancient History, Lund University, Lund, 221 00, Sweden
   Torbjörn Ahlström
6. Oxford Radiocarbon Accelerator Unit, University of Oxford, Oxford, OX1 3QY, UK
   Tom Higham & David Chivall
7. Department of Forensic Medicine, Unit of Forensic Anthropology, University of Copenhagen, Copenhagen, 2100, Denmark
   Niels Lynnerup & Lise Harvig
8. Institute of Archaeology, University of Wrocław, Wrocław, 50-139, Poland
   Justyna Baron, Mirosław Furmanek, Tomasz Gralak & Irena Lasak
9. Archaeological Institute, University of Zurich, Zurich, CH-8006, Switzerland
   Philippe Della Casa
10. Department of Anatomy, Wrocław Medical University, Wrocław, 50-368, Poland
    Paweł Dąbrowski
11. Department of Anthropology, University of Toronto, Toronto, ONM5S 2S2, Canada
    Paul R. Duffy
12. Department of Archeology and General History, Gorno-Altaisk State University, Gorno-Altaisk, 649000, Russia
    Alexander V. Ebel
13. Institute of History and Archaeology RAS (South Ural Department), South Ural State University, Chelyabinsk, 454080, Russia
    Andrey Epimakhov
14. Environmental Research and Material Science and Centre for Textile Research, The National Museum of Denmark, Copenhagen K, 1471, Denmark
    Karin Frei
15. Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg, 199034, Russia
    Andrey Gromov, Valeri Khartanovich & Vyacheslav Moiseyev
16. Department of Anthropology, Polish Academy of Sciences, Wrocław, 50–449, Poland
    Stanisław Gronkiewicz
17. Biocentre of the Ludwig-Maximilian-University München, Munich, 82152, Germany
    Gisela Grupe & George McGlynn
18. Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, H-1117, Hungary
    Tamás Hajdu
19. Department of Anthropology, Hungarian Natural History Museum, Budapest, H-1083, Hungary
    Tamás Hajdu
20. The Archaeological Museum of Wrocław, Wrocław, 50-077, Poland
    Radosław Jarysz
21. Samara State Academy of Social Science and Humanities, Samara, 443099, Russia
    Alexandr Khokhlov
22. Institute of Archaeology of the Hungarian Academy of Sciences, Research Center for the Humanities, Budapest, H-1250, Hungary
    Viktória Kiss & Vajk Szeverényi
23. Institute of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, CZ-602 00, Czech Republic
    Jan Kolář
24. Department of Vegetation Ecology, Institute of Botany of the Czech Academy of Sciences, Brno, CZ-602 00, Czech Republic
    Jan Kolář
25. Department of Archaeology, University of Tartu, Tartu, 51003, Estonia
    Aivar Kriiska & Liivi Varul
26. Archaeological Superintendence of Lombardy, Milano, 20123, Italy
    Cristina Longhi
27. Department of Archaeology, University of Vilnius, Vilnius, LT-01513, Lithuania
    Algimantas Merkevicius
28. The SAXO Institute, University of Copenhagen, Copenhagen S, 2300, Denmark
    Inga Merkyte
29. Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, Tartu, 51010, Estonia
    Mait Metspalu & Lehti Saag
30. Department of History, Yerevan State University, Yerevan, 0025, Armenia
    Ruzan Mkrtchyan
31. Hungarian National Museum, Budapest, H-1083, Hungary
    László Paja
32. Department of Biological Anthropology, University of Szeged, Szeged, H-6726, Hungary
    László Paja & György Pálfi
33. Institute of Archaeology and Ethnology of the Polish Academy of Sciences, Poznań, 61-612, Poland
    Łukasz Pospieszny
34. Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, 53706, Wisconsin, USA
    T. Douglas Price
35. Zoological Institute of the Russian Academy of Sciences, St Petersburg, 199034, Russia
    Mikhail Sablin
36. Department of Archaeology, State Historical Museum, Moscow, 109012, Russia
    Natalia Shishlina
37. Institute for History of Medicine and Foreign Languages of the First Faculty of Medicine, Charles University, Prague, 121 08, Czech Republic
    Václav Smrčka
38. Research Center for the History and Culture of the Turkic Peoples, Gorno-Altaisk State University, Gorno-Altaisk, 649000, Russia
    Vasilii I. Soenov & Synaru V. Trifanova
39. Department of Pre- and Early History, Institute of Archaeological Sciences, Faculty of Humanities, Eötvös Loránd University, Budapest, H-1088, Hungary
    Gusztáv Tóth
40. Matrica Museum, Százhalombatta, 2440, Hungary
    Magdolna Vicze
41. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, 0014, Armenia
    Levon Yepiskoposyan
42. Department of Archaeology, Faculty of History, Moscow State University, Moscow, 119991, Russia
    Vladislav Zhitenev
43. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, 2200, Denmark
    Søren Brunak
44. Center for Theoretical Evolutionary Genetics, University of California, Berkeley, 94720-3140, California, USA
    Rasmus Nielsen

Authors

1. Morten E. Allentoft
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2. Martin Sikora
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3. Karl-Göran Sjögren
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4. Simon Rasmussen
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5. Morten Rasmussen
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6. Jesper Stenderup
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7. Peter B. Damgaard
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8. Hannes Schroeder
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9. Torbjörn Ahlström
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10. Lasse Vinner
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11. Anna-Sapfo Malaspinas
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12. Ashot Margaryan
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13. Tom Higham
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14. David Chivall
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15. Niels Lynnerup
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16. Lise Harvig
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17. Justyna Baron
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18. Philippe Della Casa
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19. Paweł Dąbrowski
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20. Paul R. Duffy
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21. Alexander V. Ebel
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22. Andrey Epimakhov
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23. Karin Frei
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24. Mirosław Furmanek
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25. Tomasz Gralak
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26. Andrey Gromov
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27. Stanisław Gronkiewicz
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28. Gisela Grupe
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29. Tamás Hajdu
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30. Radosław Jarysz
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31. Valeri Khartanovich
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32. Alexandr Khokhlov
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33. Viktória Kiss
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34. Jan Kolář
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35. Aivar Kriiska
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36. Irena Lasak
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37. Cristina Longhi
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38. George McGlynn
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39. Algimantas Merkevicius
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40. Inga Merkyte
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41. Mait Metspalu
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42. Ruzan Mkrtchyan
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43. Vyacheslav Moiseyev
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44. László Paja
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45. György Pálfi
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46. Dalia Pokutta
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47. Łukasz Pospieszny
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48. T. Douglas Price
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49. Lehti Saag
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50. Mikhail Sablin
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51. Natalia Shishlina
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52. Václav Smrčka
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53. Vasilii I. Soenov
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54. Vajk Szeverényi
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55. Gusztáv Tóth
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56. Synaru V. Trifanova
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57. Liivi Varul
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58. Magdolna Vicze
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59. Levon Yepiskoposyan
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60. Vladislav Zhitenev
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61. Ludovic Orlando
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62. Thomas Sicheritz-Pontén
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63. Søren Brunak
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64. Rasmus Nielsen
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65. Kristian Kristiansen
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66. Eske Willerslev
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Contributions

E.W. and K.K. initiated and led the study. M.E.A., J.S., L.V., H.S., P.B.D., A.M., M.R., L.S. performed the DNA laboratory work. M.Si., S.R., M.E.A., A.-S.M., P.B.D., A.M. analysed the genetic data. K.-G.S., T.A., N.L., L.H., J.B., P.D.C., P.D., P.R.D., A.E., A.V.E., K.F., M.F., G.G., T.G., A.G., S.G., T.H., R.J., J.K., V.K., A.K., V.K., A.K., I.L., C.L., A.M., G.M., I.M., M.M., R.M., V.M., D.Po., G.P., L.P., D.Pr., L.P., M.Sa., N.S., V.Sm., V.Sz., V.I.S., G.T., S.V.T., L.V., M.V., L.Y., V.Z. collected the samples and/or provided input to the archaeological interpretations. T.H. and D.C. conducted radiocarbon dating. T.S.-P., L.O., S.B., R.N. provided input to the genetic analyses. E.W., K.K., M.E.A., M.Si., K.-G.S. wrote the paper with input from all co-authors.

Corresponding author

Correspondence toEske Willerslev.

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Competing interests

The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Principal component analysis of ancient genomes.

a, b, Principal component analysis of ancient individuals projected onto contemporary individuals from non-African populations (a), Europe, West Asia and the Caucasus (b). Grey labels represent population codes indicating coordinates for individuals (small) and median of the population (large). Coloured labels indicate positions for ancient individuals (small) and median for ancient groups (large). Ancient individuals within a group are connected to the respective median position by coloured lines.

Extended Data Figure 2 Pairwise outgroup _f_3 statistics.

Panels depict pairwise plots of outgroup _f_3 statistics of the form _f_3(Ju’hoan North;Population1, Population2), showing the correlation of the amount of shared genetic drift for a pair of ancient groups (Population1) with all modern populations (Population2) in the Human Origins data set (panel A). Closely related ancient groups are expected to show highly correlated statistics. a, Sintashta/Corded Ware. b, Yamnaya/Afanasievo. c, Sintashta/Andronovo. d, Okunevo/Mal’ta. Coloured circles indicate modern populations; error bars indicate ± 1 standard error from the block jackknife.

Extended Data Figure 3 Yamnaya ancestry mirrors Mal’ta ancestry in present-day Europeans and Caucasians.

Panels show pairwise plots of D-statistics D(Outgroup, Ancient)(Bedouin, Modern), contrasting Mal’ta (MA1) and Hunter-gatherers (a), and MA1 and Yamnaya (b). Coloured labels indicate modern populations, with lines corresponding to ± 1 standard error of the respective _D_-statistic from block jacknife. Text away from the diagonal line indicates an ancient group with relative increase in allele sharing with the respective modern populations.

Extended Data Figure 4 Genetic differentiation between ancient and modern groups in Human Origins data set.

Panels show F ST between pairs of modern and ancient groups (coloured lines) for subsets of ancient groups, with results for the remaining groups in the background (grey). Top, early Europeans. Middle, Bronze Age Europeans and steppe/Caucasus. Bottom, Bronze Age Asians. Results based on Human Origins data set (panel A).

Extended Data Figure 6 Distribution of uniparental lineages in Bronze Age Eurasians.

a, b, Barplots showing the relative frequency of Y chromosome (a) and mitochondrial DNA lineages (b) in different Bronze Age groups. Top row shows overall frequencies for all individuals combined.

Extended Data Figure 7 Derived allele frequencies for lactase persistence in modern and ancient groups.

Derived allele frequency of rs4988235 in the LCT gene inferred from imputation of ancient individuals. Numbers indicate the total number of chromosomes for each group.

Extended Data Table 1 Selected D-test results from 1000 Genomes data set (panel B)

Full size table

Extended Data Table 2 _f_3 statistic results for ancient groups

Full size table

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Supplementary information

Supplementary Information

This file contains Supplementary Information sections 1-6. Section 1: An introduction to the sampled cultures and their dating. Section 2: Brief description of the samples (including Supplementary Tables 1-3). Section 3: Laboratory work and sample selection (including Supplementary Tables 4-5, and Supplementary Figure 1). Section 4: Radiocarbon dating. Section 5: Bioinformatics and DNA authentication. Section 6: Population genomics (including Supplementary Table 9 and Supplementary Figures 2-6). (PDF 4331 kb)

Supplementary Table 6

This table contains sequencing summary statistics. (XLSX 20 kb)

Supplementary Table 7

This table contains an overview of aDNA damage statistics. (XLS 44 kb)

Supplementary Table 8

This table contains results of DNA contamination tests. (XLSX 18 kb)

Supplementary Table 10

This table contains D-test for all combinations D(Outgroup,Ancient1)(Ancient2)(Ancient3); 1000 Genomes dataset. (XLSX 1915 kb)

Supplementary Table 11

This table contains “Outgroup” f3-statistics for all combinations of ancient and modern groups; Human Origins dataset. (XLSX 748 kb)

Supplementary Table 12

This table contains all-pair “admixture” f3-statistics; 1000 Genomes dataset. (XLSX 3921 kb)

Supplementary Table 13

This table contains derived allele frequencies of 104 SNP catalogue for putative selection; 1000 Genomes dataset. (XLSX 63 kb)

Supplementary Table 14

This table contains an overview of mtDNA haplogroups and identified variants. (XLS 97 kb)

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Allentoft, M., Sikora, M., Sjögren, KG. et al. Population genomics of Bronze Age Eurasia.Nature 522, 167–172 (2015). https://doi.org/10.1038/nature14507

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• Received: 14 February 2015
• Accepted: 01 May 2015
• Published: 10 June 2015
• Issue Date: 11 June 2015
• DOI: https://doi.org/10.1038/nature14507