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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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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.

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=).

References

  1. 1.

    Li, J. Z. et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319, 1100–1104 (2008).

    CAS  Article  Google Scholar 

  2. 2.

    Wang, C., Zöllner, S. & Rosenberg, N. A. A quantitative comparison of the similarity between genes and geography in worldwide human populations. PLoS Genet. 8, e1002886 (2012).

    CAS  Article  Google Scholar 

  3. 3.

    Jeong, C. et al. Long-term genetic stability and a high altitude East Asian origin for the peoples of the high valleys of the Himalayan arc. Proc. Natl Acad. Sci. USA 113, 7485–7490 (2016).

    CAS  Article  Google Scholar 

  4. 4.

    Yunusbayev, B. et al The Caucasus as an asymmetric semipermeable barrier to ancient human migrations. Mol. Biol. Evol. 29, 359–365 (2012).

    CAS  Article  Google Scholar 

  5. 5.

    Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).

    CAS  Article  Google Scholar 

  6. 6.

    Haber, M. et al. Genome-wide diversity in the Levant reveals recent structuring by culture. PLoS Genet. 9, e1003316 (2013).

    CAS  Article  Google Scholar 

  7. 7.

    Martiniano, R. et al. The population genomics of archaeological transition in west Iberia: investigation of ancient substructure using imputation and haplotype-based methods. PLoS Genet. 13, e1006852 (2017).

    Article  Google Scholar 

  8. 8.

    Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015).

    CAS  Article  Google Scholar 

  9. 9.

    Barfield, T. J. The Nomadic Alternative (Prentice Hall, 1993).

  10. 10.

    Frachetti, M. D. Pastoralist Landscapes and Social Interaction in Bronze Age Eurasia (Univ. California Press, 2009).

  11. 11.

    Burch, E. S. The caribou/wild reindeer as a human resource. Am. Antiq. 37, 339–368 (1972).

    Article  Google Scholar 

  12. 12.

    Sherratt, A. The secondary exploitation of animals in the Old World. World Archaeol. 15, 90–104 (1983).

    Article  Google Scholar 

  13. 13.

    Yunusbayev, B. et al. The genetic legacy of the expansion of Turkic-speaking nomads across Eurasia. PLoS Genet. 11, e1005068 (2015).

    Article  Google Scholar 

  14. 14.

    Hellenthal, G. et al. A genetic atlas of human admixture history. Science 343, 747–751 (2014).

    CAS  Article  Google Scholar 

  15. 15.

    Flegontov, P. et al. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Sci. Rep. 6, 20768 (2016).

    CAS  Article  Google Scholar 

  16. 16.

    Pugach, I. et al. The complex admixture history and recent southern origins of Siberian populations. Mol. Biol. Evol. 33, 1777–1795 (2016).

    CAS  Article  Google Scholar 

  17. 17.

    Triska, P. et al. Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe. BMC Genet. 18, 110 (2017).

    Article  Google Scholar 

  18. 18.

    Tambets, K. et al. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol. 19, 139 (2018).

    Article  Google Scholar 

  19. 19.

    Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014).

    Article  Google Scholar 

  20. 20.

    Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419–424 (2016).

    CAS  Article  Google Scholar 

  21. 21.

    Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015).

    CAS  Article  Google Scholar 

  22. 22.

    Damgaard, Pd. B. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374 (2018).

    CAS  Article  Google Scholar 

  23. 23.

    Damgaard, Pd. B. et al. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science 360, eaar7711 (2018).

    Article  Google Scholar 

  24. 24.

    Levine, M. & Kislenko, A. New Eneolithic and early Bronze Age radiocarbon dates for north Kazakhstan and south Siberia. Camb. Archaeol. 7, 297–300 (1997).

    Article  Google Scholar 

  25. 25.

    Flegontov, P. et al. Paleo-Eskimo genetic legacy across North America. Preprint at https://www.biorxiv.org/content/10.1101/203018v1 (2017).

  26. 26.

    Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).

    CAS  Article  Google Scholar 

  27. 27.

    Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014).

    CAS  Article  Google Scholar 

  28. 28.

    Fu, Q. et al. The genetic history of Ice Age Europe. Nature 534, 200–205 (2016).

    CAS  Article  Google Scholar 

  29. 29.

    Haber, M. et al. Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences. Am. J. Hum. Genet. 101, 274–282 (2017).

    CAS  Article  Google Scholar 

  30. 30.

    Jones, E. R. et al. Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat. Commun. 6, 8912 (2015).

    CAS  Article  Google Scholar 

  31. 31.

    Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014).

    CAS  Article  Google Scholar 

  32. 32.

    Lazaridis, I. et al. Genetic origins of the Minoans and Mycenaeans. Nature 548, 214–218 (2017).

    CAS  Article  Google Scholar 

  33. 33.

    Raghavan, M. et al. The genetic prehistory of the New World Arctic. Science 345, 1255832 (2014).

    Article  Google Scholar 

  34. 34.

    Rasmussen, M. et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (2014).

    CAS  Article  Google Scholar 

  35. 35.

    Rasmussen, M. et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757–762 (2010).

    CAS  Article  Google Scholar 

  36. 36.

    Rasmussen, M. et al. The ancestry and affiliations of Kennewick Man. Nature 523, 455–458 (2015).

    Article  Google Scholar 

  37. 37.

    Saag, L. et al. Extensive farming in Estonia started through a sex-biased migration from the Steppe. Curr. Biol. 27, 2185–2193 (2017).

    CAS  Article  Google Scholar 

  38. 38.

    Siska, V. et al. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. Sci. Adv. 3, e1601877 (2017).

    Article  Google Scholar 

  39. 39.

    Unterländer, M. et al. Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe. Nat. Commun. 8, 14615 (2017).

    Article  Google Scholar 

  40. 40.

    Yang, M. A. et al. 40,000-year-old individual from Asia provides insight into early population structure in Eurasia. Curr. Biol. 27, 3202–3208 (2017).

    CAS  Article  Google Scholar 

  41. 41.

    Kılınç, G. M. et al. The demographic development of the first farmers in Anatolia. Curr. Biol. 26, 2659–2666 (2016).

    Article  Google Scholar 

  42. 42.

    McColl, H. et al. The prehistoric peopling of Southeast Asia. Science 361, 88–92 (2018).

    CAS  Article  Google Scholar 

  43. 43.

    Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).

    Article  Google Scholar 

  44. 44.

    Petkova, D., Novembre, J. & Stephens, M. Visualizing spatial population structure with estimated effective migration surfaces. Nat. Genet. 48, 94–100 (2016).

    CAS  Article  Google Scholar 

  45. 45.

    Fenner, J. N. Cross‐cultural estimation of the human generation interval for use in genetics‐based population divergence studies. Am. J. Phys. Anthropol. 128, 415–423 (2005).

    Article  Google Scholar 

  46. 46.

    Narasimhan, V. M. et al. The genomic formation of South and Central Asia. Preprint at https://www.biorxiv.org/content/10.1101/292581v1 (2018).

  47. 47.

    Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).

    CAS  Article  Google Scholar 

  48. 48.

    Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. B 370, 20130624 (2015).

    Article  Google Scholar 

  49. 49.

    Kircher, M. in Ancient DNA: Methods and Protocols (eds Shapiro, B. & Hofreiter, M.) 197–228 (Humana Press, 2012).

  50. 50.

    Peltzer, A. et al. EAGER: efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).

    Article  Google Scholar 

  51. 51.

    Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).

    Article  Google Scholar 

  52. 52.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS  Article  Google Scholar 

  53. 53.

    Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  Google Scholar 

  54. 54.

    Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).

    Article  Google Scholar 

  55. 55.

    Renaud, G., Slon, V., Duggan, A. T. & Kelso, J. Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biol. 16, 224 (2015).

    Article  Google Scholar 

  56. 56.

    Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014).

    Article  Google Scholar 

  57. 57.

    Jun, G., Wing, M. K., Abecasis, G. R. & Kang, H. M. An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Res. 25, 918–925 (2015).

    CAS  Article  Google Scholar 

  58. 58.

    Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).

    CAS  Article  Google Scholar 

  59. 59.

    Poznik, G. D. Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men. Preprint at https://www.biorxiv.org/content/10.1101/088716v1 (2016).

  60. 60.

    Balanovsky, O. et al. Parallel evolution of genes and languages in the Caucasus region. Mol. Biol. Evol. 28, 2905–2920 (2011).

    CAS  Article  Google Scholar 

  61. 61.

    Koshel, S. in Sovremennaya Geograficheskaya Kartografiya (Modern Geographic Cartography) (eds Lourie, I. & Kravtsova, V.) 158–166 (Data+, 2012).

  62. 62.

    Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).

    Article  Google Scholar 

  63. 63.

    Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).

    CAS  Article  Google Scholar 

  64. 64.

    Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).

    Article  Google Scholar 

  65. 65.

    Reich, D. et al. Reconstructing native American population history. Nature 488, 370–374 (2012).

    CAS  Article  Google Scholar 

  66. 66.

    Delaneau, O., Zagury, J.-F. & Marchini, J. Improved whole-chromosome phasing for disease and population genetic studies. Nat. Methods 10, 5–6 (2013).

    CAS  Article  Google Scholar 

  67. 67.

    Lawson, D. J., Hellenthal, G., Myers, S. & Falush, D. Inference of population structure using dense haplotype data. PLoS Genet. 8, e1002453 (2012).

    CAS  Article  Google Scholar 

  68. 68.

    Loh, P.-R. et al. Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193, 1233–1254 (2013).

    Article  Google Scholar 

  69. 69.

    Sedghifar, A., Brandvain, Y., Ralph, P. & Coop, G. The spatial mixing of genomes in secondary contact zones. Genetics 201, 243–261 (2015).

    CAS  Article  Google Scholar 

  70. 70.

    Levine, M. Botai and the origins of horse domestication. J. Anthropol. Archaeol. 18, 29–78 (1999).

    Article  Google Scholar 

  71. 71.

    Bronk Ramsey, C. Bayesian analysis of radiocarbon dates. Radiocarbon 51, 337–360 (2009).

    Article  Google Scholar 

  72. 72.

    Reimer, P. J. et al. IntCal13 and Marine13 radiocarbon age calibration curves 0–50,000 years cal BP. Radiocarbon 55, 1869–1887 (2016).

    Article  Google Scholar 

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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).

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Authors

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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