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Population genomics of Bronze Age Eurasia

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.

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Figure 1: Distribution maps of ancient samples.
Figure 2: Genetic structure of ancient Europe and the Pontic-Caspian steppe.
Figure 3: Genetic structure of Bronze Age Asia.
Figure 4: Allele frequencies for putatively positively selected SNPs.

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

Authors and Affiliations

Authors

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 to Eske 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 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.

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 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).

Extended Data Figure 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).

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)
Extended Data Table 2 f3 statistic results for ancient groups

Related audio

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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