Population genomics of Bronze Age Eurasia

Journal name:
Nature
Volume:
522,
Pages:
167–172
Date published:
DOI:
doi:10.1038/nature14507
Received
Accepted
Published online

Abstract

The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

At a glance

Figures

  1. Distribution maps of ancient samples.
    Figure 1: Distribution maps of ancient samples.

    Localities, cultural associations, and approximate timeline of 101 sampled ancient individuals from Europe and Central Asia (left). Distribution of Early Bronze Age cultures Yamnaya, Corded Ware, and Afanasievo with arrows showing the Yamnaya expansions (top right). Middle and Late Bronze Age cultures Sintashta, Andronovo, Okunevo, and Karasuk with the eastward migration indicated (bottom right). Black markers represent chariot burials (2000–1800 bc) with similar horse cheek pieces, as evidence of expanding cultures. Tocharian is the second-oldest branch of Indo-European languages, preserved in Western China. CA, Copper Age; MN, Middle Neolithic; LN, Late Neolithic; EBA, Early Bronze Age; MBA, Middle Bronze Age; LBA, Late Bronze Age; IA, Iron Age; BAC, Battle Axe culture; CWC, Corded Ware culture.

  2. Genetic structure of ancient Europe and the Pontic-Caspian steppe.
    Figure 2: Genetic structure of ancient Europe and the Pontic-Caspian steppe.

    a, Principal component analysis (PCA) of ancient individuals (n = 93) from different periods projected onto contemporary individuals from Europe, West Asia, and Caucasus. Grey labels represent population codes showing coordinates for individuals (small) and population median (large). Coloured circles indicate ancient individuals b, ADMIXTURE ancestry components (K = 16) for ancient (n = 93) and selected contemporary individuals. The width of the bars representing ancient individuals is increased to aid visualization. Individuals with less than 20,000 SNPs have lighter colours. Coloured circles indicate corresponding group in the PCA. Probable Yamnaya-related admixture is indicated by the dashed arrow.

  3. Genetic structure of Bronze Age Asia.
    Figure 3: Genetic structure of Bronze Age Asia.

    a, Principal component analysis (PCA) of ancient individuals (n = 40) from different periods projected onto contemporary non-Africans. Grey labels represent population codes showing coordinates for individuals (small) and population median (large). Coloured circles indicate ancient individuals. b, ADMIXTURE ancestry components (K = 16) for ancient (n = 40) and selected contemporary individuals. The width of the bars representing ancient individuals is increased to aid visualization. Individuals with less than 20,000 SNPs have lighter colours. Coloured circles indicate corresponding group in the PCA. Shared ancestry of Mal’ta with Yamnaya (green component) and Okunevo (grey component) is indicated by dashed arrows.

  4. Allele frequencies for putatively positively selected SNPs.
    Figure 4: Allele frequencies for putatively positively selected SNPs.

    a, Coloured circles indicate the observed frequency of the respective SNP in ancient and modern groups (1000 Genomes panel). The size of the circle is proportional to the number of samples for each SNP and population. b, Allele frequency of rs4988235 in the LCT (lactase) gene inferred from imputation of ancient individuals. Numbers indicate the total number of chromosomes for each group. BA, Bronze Age; IA, Iron Age.

  5. Principal component analysis of ancient genomes.
    Extended Data Fig. 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.

  6. Pairwise outgroup f3 statistics.
    Extended Data Fig. 2: Pairwise outgroup f3 statistics.

    Panels depict pairwise plots of outgroup f3 statistics of the form f3(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.

  7. Yamnaya ancestry mirrors Mal/'ta ancestry in present-day Europeans and Caucasians.
    Extended Data Fig. 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.

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

    Panels show FST 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).

  9. Genetic differentiation between ancient and modern groups in 1000 Genomes data set.
    Extended Data Fig. 5: Genetic differentiation between ancient and modern groups in 1000 Genomes data set.

    Matrix of pairwise FST values between modern and ancient groups in the 1000 Genomes data set (panel B).

  10. Distribution of uniparental lineages in Bronze Age Eurasians.
    Extended Data Fig. 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.

  11. Derived allele frequencies for lactase persistence in modern and ancient groups.
    Extended Data Fig. 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.

Tables

  1. Selected D-test results from 1000 Genomes data set (panel B)
    Extended Data Table 1: Selected D-test results from 1000 Genomes data set (panel B)
  2. f3 statistic results for ancient groups
    Extended Data Table 2: f3 statistic results for ancient groups

Accession codes

Primary accessions

European Nucleotide Archive

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Author information

  1. These authors contributed equally to this work.

    • Morten E. Allentoft &
    • Martin Sikora

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, 405 30 Gothenburg, Sweden

    • Karl-Göran Sjögren,
    • Dalia Pokutta &
    • Kristian Kristiansen
  3. Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs Lyngby, Denmark

    • Simon Rasmussen,
    • Thomas Sicheritz-Pontén &
    • Søren Brunak
  4. Faculty of Archaeology, Leiden University, 2300 Leiden, The Netherlands

    • Hannes Schroeder
  5. Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden

    • Torbjörn Ahlström
  6. Oxford Radiocarbon Accelerator Unit, University of Oxford, Oxford OX1 3QY, UK

    • Tom Higham &
    • David Chivall
  7. Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, 2100 Copenhagen, Denmark

    • Niels Lynnerup &
    • Lise Harvig
  8. Institute of Archaeology, University of Wrocław, 50-139 Wrocław, Poland

    • Justyna Baron,
    • Mirosław Furmanek,
    • Tomasz Gralak &
    • Irena Lasak
  9. Archaeological Institute, University of Zurich, CH-8006, Zurich, Switzerland

    • Philippe Della Casa
  10. Department of Anatomy, Wrocław Medical University, 50-368 Wrocław, 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, 649000 Gorno-Altaisk, Russia

    • Alexander V. Ebel
  13. Institute of History and Archaeology RAS (South Ural Department), South Ural State University, 454080 Chelyabinsk, Russia

    • Andrey Epimakhov
  14. Environmental Research and Material Science and Centre for Textile Research, The National Museum of Denmark, 1471 Copenhagen K, Denmark

    • Karin Frei
  15. Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St Petersburg, Russia

    • Andrey Gromov,
    • Valeri Khartanovich &
    • Vyacheslav Moiseyev
  16. Department of Anthropology, Polish Academy of Sciences, 50–449 Wrocław, Poland

    • Stanisław Gronkiewicz
  17. Biocentre of the Ludwig-Maximilian-University München, 82152 Munich, Germany

    • Gisela Grupe &
    • George McGlynn
  18. Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, H-1117 Budapest, Hungary

    • Tamás Hajdu
  19. Department of Anthropology, Hungarian Natural History Museum, H-1083 Budapest, Hungary

    • Tamás Hajdu
  20. The Archaeological Museum of Wrocław, 50-077 Wrocław, Poland

    • Radosław Jarysz
  21. Samara State Academy of Social Science and Humanities, 443099 Samara, Russia

    • Alexandr Khokhlov
  22. Institute of Archaeology of the Hungarian Academy of Sciences, Research Center for the Humanities, H-1250 Budapest, Hungary

    • Viktória Kiss &
    • Vajk Szeverényi
  23. Institute of Archaeology and Museology, Faculty of Arts, Masaryk University, CZ-602 00 Brno, Czech Republic

    • Jan Kolář
  24. Department of Vegetation Ecology, Institute of Botany of the Czech Academy of Sciences, CZ-602 00 Brno, Czech Republic

    • Jan Kolář
  25. Department of Archaeology, University of Tartu, 51003 Tartu, Estonia

    • Aivar Kriiska &
    • Liivi Varul
  26. Archaeological Superintendence of Lombardy, 20123 Milano, Italy

    • Cristina Longhi
  27. Department of Archaeology, University of Vilnius, LT-01513 Vilnius, Lithuania

    • Algimantas Merkevicius
  28. The SAXO Institute, University of Copenhagen, 2300 Copenhagen S, Denmark

    • Inga Merkyte
  29. Department of Evolutionary Biology, Estonian Biocentre and University of Tartu, 51010 Tartu, Estonia

    • Mait Metspalu &
    • Lehti Saag
  30. Department of History, Yerevan State University, 0025 Yerevan, Armenia

    • Ruzan Mkrtchyan
  31. Hungarian National Museum, H-1083 Budapest, Hungary

    • László Paja
  32. Department of Biological Anthropology, University of Szeged, H-6726 Szeged, Hungary

    • László Paja &
    • György Pálfi
  33. Institute of Archaeology and Ethnology of the Polish Academy of Sciences, 61-612 Poznań, Poland

    • Łukasz Pospieszny
  34. Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA

    • T. Douglas Price
  35. Zoological Institute of the Russian Academy of Sciences, 199034 St Petersburg, Russia

    • Mikhail Sablin
  36. Department of Archaeology, State Historical Museum, 109012 Moscow, Russia

    • Natalia Shishlina
  37. Institute for History of Medicine and Foreign Languages of the First Faculty of Medicine, Charles University, 121 08 Prague, Czech Republic

    • Václav Smrčka
  38. Research Center for the History and Culture of the Turkic Peoples, Gorno-Altaisk State University, 649000 Gorno-Altaisk, Russia

    • Vasilii I. Soenov &
    • Synaru V. Trifanova
  39. Department of Pre- and Early History, Institute of Archaeological Sciences, Faculty of Humanities, Eötvös Loránd University, H-1088 Budapest, Hungary

    • Gusztáv Tóth
  40. Matrica Museum, 2440 Százhalombatta, Hungary

    • Magdolna Vicze
  41. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, 0014 Yerevan, Armenia

    • Levon Yepiskoposyan
  42. Department of Archaeology, Faculty of History, Moscow State University, 119991 Moscow, Russia

    • Vladislav Zhitenev
  43. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark

    • Søren Brunak
  44. Center for Theoretical Evolutionary Genetics, University of California, Berkeley, California 94720-3140, USA

    • Rasmus Nielsen

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.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to:

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

Author details

Extended data figures and tables

Extended Data Figures

  1. Extended Data Figure 1: Principal component analysis of ancient genomes. (110 KB)

    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.

  2. Extended Data Figure 2: Pairwise outgroup f3 statistics. (186 KB)

    Panels depict pairwise plots of outgroup f3 statistics of the form f3(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.

  3. Extended Data Figure 3: Yamnaya ancestry mirrors Mal’ta ancestry in present-day Europeans and Caucasians. (101 KB)

    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.

  4. Extended Data Figure 4: Genetic differentiation between ancient and modern groups in Human Origins data set. (410 KB)

    Panels show FST 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).

  5. Extended Data Figure 5: Genetic differentiation between ancient and modern groups in 1000 Genomes data set. (722 KB)

    Matrix of pairwise FST values between modern and ancient groups in the 1000 Genomes data set (panel B).

  6. Extended Data Figure 6: Distribution of uniparental lineages in Bronze Age Eurasians. (168 KB)

    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.

  7. Extended Data Figure 7: Derived allele frequencies for lactase persistence in modern and ancient groups. (93 KB)

    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 Tables

  1. Extended Data Table 1: Selected D-test results from 1000 Genomes data set (panel B) (167 KB)
  2. Extended Data Table 2: f3 statistic results for ancient groups (270 KB)

Supplementary information

PDF files

  1. Supplementary Information (4.2 MB)

    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).

Excel files

  1. Supplementary Table 6 (20 KB)

    This table contains sequencing summary statistics.

  2. Supplementary Table 7 (44 KB)

    This table contains an overview of aDNA damage statistics.

  3. Supplementary Table 8 (18 KB)

    This table contains results of DNA contamination tests.

  4. Supplementary Table 10 (1.8 MB)

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

  5. Supplementary Table 11 (748 KB)

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

  6. Supplementary Table 12 (3.8 MB)

    This table contains all-pair “admixture” f3-statistics; 1000 Genomes dataset.

  7. Supplementary Table 13 (63 KB)

    This table contains derived allele frequencies of 104 SNP catalogue for putative selection; 1000 Genomes dataset.

  8. Supplementary Table 14 (97 KB)

    This table contains an overview of mtDNA haplogroups and identified variants.

Additional data