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The genetic history of admixture across inner Eurasia

Nature Ecology & Evolution volume 3, pages 966–976 (2019)Cite this article

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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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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.

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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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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

Author notes

  1. Choongwon Jeong

    Present address: School of Biological Sciences, Seoul National University, Seoul, Republic of Korea

  2. These authors contributed equally: Choongwon Jeong, Oleg Balanovsky.

Authors and Affiliations

  1. Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany

    Choongwon Jeong, Alexander Immel, Chuan-Chao Wang, Stephan Schiffels, Wolfgang Haak & Johannes Krause

  2. Eurasia3angle Research Group, Max Planck Institute for the Science of Human History, Jena, Germany

    Choongwon Jeong & Martine Robbeets

  3. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia

    Oleg Balanovsky, Elena Lukianova, Valery Zaporozhchenko, Anastasiya Agdzhoyan, Yuri Bogunov & Khadizhat Dibirova

  4. Federal State Budgetary Institution ‘Research Centre for Medical Genetics’, Moscow, Russia

    Oleg Balanovsky, Valery Zaporozhchenko, Anastasiya Agdzhoyan, Roza Skhalyakho, Denis Daragan, Yuri Bogunov, Anna Bogunova, Alexandr Shtrunov, Khadizhat Dibirova, Evgeniya Kamenshchikova & Elena Balanovska

  5. Department of Population Genetics, Institute of General Genetics and Cytology, Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Almaty, Kazakhstan

    Nurzhibek Kahbatkyzy, Olzhas Ixan, Elmira Khussainova, Bakhytzhan Bekmanov & Leyla Djansugurova

  6. Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan

    Nurzhibek Kahbatkyzy, Bakhytzhan Bekmanov & Leyla Djansugurova

  7. Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic

    Pavel Flegontov

  8. Faculty of Science, University of South Bohemia and Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic

    Pavel Flegontov

  9. Department of Anthropology and Ethnology, Xiamen University, Xiamen, China

    Chuan-Chao Wang

  10. Institute of Archeology and Steppe Civilization, Al-Farabi Kazakh National University, Almaty, Kazakhstan

    Victor Zaibert

  11. Kemerovo State Medical University, Kemerovo, Russia

    Maria Lavryashina

  12. Kuban State Medical University, Krasnodar, Russia

    Elvira Pocheshkhova

  13. Institute of Strategic Research of the Republic of Bashkortostan, Ufa, Russia

    Yuldash Yusupov

  14. Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia

    Sergey Koshel

  15. Transbaikal State University, Chita, Russia

    Andrei Bukin

  16. Mongolian Academy of Medical Sciences, Ulaanbaatar, Mongolia

    Pagbajabyn Nymadawa

  17. Center for Advanced Technologies, Ministry of Innovational Development, Tashkent, Uzbekistan

    Shahlo Turdikulova & Dilbar Dalimova

  18. Belgorod State University, Belgorod, Russia

    Mikhail Churnosov

  19. Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia

    Nadezhda Dubova

  20. National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan

    Maxat Zhabagin

  21. National Center for Biotechnology, Astana, Kazakhstan

    Maxat Zhabagin

  22. Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia

    Levon Yepiskoposyan

  23. Udmurt Institute of History, Language and Literature, Udmurt Federal Research Center, Ural Branch, Russian Academy of Sciences, Izhevsk, Russia

    Vladimir Churakov & Nikolay Pislegin

  24. Research Institute of Medical and Social Problems and Control, Healthcare Department of Tuva Republic, Kyzyl, Russia

    Larissa Damba

  25. Leprosy Research Institute, Astrakhan, Russia

    Ludmila Saroyants

  26. V. N. Karazin Kharkiv National University, Kharkiv, Ukraine

    Lubov Atramentova & Olga Utevska

  27. Astrakhan Branch, Russian Presidential Academy of National Economy and Public Administration under the President of the Russian Federation, Astrakhan, Russia

    Eldar Idrisov

  28. Northern State Medical University, Arkhangelsk, Russia

    Irina Evseeva

  29. Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia

    Mait Metspalu

  30. Department of Archaeology, University of Exeter, Exeter, UK

    Alan K. Outram

  31. Department of Genetics, Harvard Medical School, Boston, MA, USA

    David Reich

  32. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA

    David Reich

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  1. Choongwon Jeong
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  2. Oleg Balanovsky
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  49. Johannes Krause
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Contributions

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.

Corresponding authors

Correspondence to Choongwon Jeong or Johannes Krause.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

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

Reporting Summary

Supplementary Table 1

Metadata of 763 individuals newly genotyped in this study.

Supplementary Table 2

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

Supplementary Table 3

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

Supplementary Table 4

A summary of GLOBETROTTER analysis results for 73 recipient populations.

Supplementary Table 12

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

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Jeong, C., Balanovsky, O., Lukianova, E. et al. The genetic history of admixture across inner Eurasia. Nat Ecol Evol 3, 966–976 (2019). https://doi.org/10.1038/s41559-019-0878-2

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