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The genetic history of admixture across inner Eurasia

Abstract

The indigenous populations of inner Eurasia—a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra—harbour tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine and Uzbekistan. We furthermore report additional damage-reduced genome-wide data of two previously published individuals from the Eneolithic Botai culture in Kazakhstan (~5,400 bp). We find that present-day inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries, mirroring geography. The Botai and more recent ancient genomes from Siberia show a decrease in contributions from so-called ‘ancient North Eurasian’ ancestry over time, which is detectable only in the northern-most ‘forest-tundra’ cline. The intermediate ‘steppe-forest’ cline descends from the Late Bronze Age steppe ancestries, while the ‘southern steppe’ cline further to the south shows a strong West/South Asian influence. Ancient genomes suggest a northward spread of the southern steppe cline in Central Asia during the first millennium bc. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.

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Data availability

Genome-wide sequence data of two Botai individuals (BAM format) are available at the European Nucleotide Archive under the accession number PRJEB31152 (ERP113669). Eigenstrat-format array genotype data of 763 present-day individuals and 1,240 K pulldown genotype data of two ancient Botai individuals are available at the Edmond data repository of the Max Planck Society (https://edmond.mpdl.mpg.de/imeji/collection/Aoh9c69DscnxSNjm?q=).

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

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Acknowledgements

We thank I. Mathieson and I. Lazaridis for helpful comments. The research leading to these results has received funding from the Max Planck Society, Max Planck Society Donation Award and European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 646612 to M.R.). Analysis of the Caucasus dataset was supported by RFBR grant 16-06-00364, and analysis of the Far East dataset was supported by Russian Scientific Fund project 17-14-01345. D.R. was supported by the US National Science Foundation HOMINID grant BCS-1032255, the US National Institutes of Health grant GM100233 and an Allen Discovery Center grant, and is an investigator of the Howard Hughes Medical Institute. P.F. was supported by IRP projects of the University of Ostrava, and by the Czech Ministry of Education, Youth and Sports (project OPVVV 16_019/0000759). C.-C.W. was funded by the Nanqiang Outstanding Young Talents Program of Xiamen University and the Fundamental Research Funds for the Central Universities. M.Z. has been funded by research grants from the Ministry of Education and Science of the Republic of Kazakhstan (numbers AP05134955 and 0114RK00492).

Author information

C.J., O.B., E.B., S.S., W.H., D.R. and J.K. conceived and coordinated the study. O.B., M.L., E.P., Y.Y., A.A., S.K., A.Bu., P.N., S.T., D.Dal., M.C., R.S., D.Dar., Y.B., A.Bo., A.S., N.D., M.Z., L.Y., V.C., N.P., L.Da., L.S., K.D., L.A., O.U., E.I., E.Ka., I.E., M.M. and E.B. contributed the present-day samples. N.K., O.I., E.Kh., B.B., V.Zai., L.Dj. and A.K.O. contributed the ancient Botai samples. N.K. and A.I. performed the ancient DNA laboratory works. C.J., O.B., E.L., V.Zap. and C.-C.W. conducted the population genetic analyses. C.J., O.B., S.S., W.H., P.F., M.R., L.Dj., D.R. and J.K. wrote the paper with input from all co-authors.

Competing interests

The authors declare no competing interests.

Correspondence to Choongwon Jeong or Johannes Krause.

Supplementary information

  1. Supplementary Information

    Supplementary notes, Supplementary Figs. 1–17, Supplementary Tables 5–11.

  2. Reporting Summary

  3. Supplementary Table 1

    Metadata of 763 individuals newly genotyped in this study.

  4. Supplementary Table 2

    A list of 333 groups used for the population genetic analyses in this study.

  5. Supplementary Table 3

    Admixture-f3 test results for 73 inner Eurasian target populations.

  6. Supplementary Table 4

    A summary of GLOBETROTTER analysis results for 73 recipient populations.

  7. Supplementary Table 12

    A skeleton R1b tree comprised of positions covered by the 1,240 K capture panel.

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Fig. 1: Geographic locations of the Eneolithic Botai, groups including newly sampled individuals, and nearby groups with published data.
Fig. 2: Genetic structure of inner Eurasian populations.
Fig. 3: Correlation of longitude and ancestry proportion across inner Eurasian populations.
Fig. 4: Characterization of the Western and Eastern Eurasian source ancestries in inner Eurasian populations.
Fig. 5: qpAdm-based admixture models for the forest-tundra and steppe-forest cline populations.