The population history of northeastern Siberia since the Pleistocene

Abstract

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

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Fig. 1: Genetic structure of ancient northeast Siberians.
Fig. 2: Demographic modelling of Siberian and Native American populations.
Fig. 3: Genetic legacy of ancient Eurasians.

Data availability

Sequence data have been deposited in the European Nucleotide Archive (ENA) under accessions PRJEB29700 and PRJEB26336.

Code availability

Source code with functions for calculating f-statistics is available as an R package at GitHub (https://github.com/martinsikora/admixr)

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Acknowledgements

We thank F. Shidlovskiy (Ice Age Museum, Moscow) for providing access to the Kolyma1 sample. E.W., D.J.M. and M.S. thank St. John’s College (Cambridge University) for providing a congenial environment for scientific discussions. This work was supported by the Lundbeck Foundation, the Danish National Research Foundation, KU2016, the Novo Nordisk Foundation and the Wellcome Trust (GeoGenetics). I.D. and V.C.S. were supported by Swiss NSF grants 310030B-166605 and 31003A-143393 to L.E., and V.C.S. was further supported by Portuguese FCT (UID/BIA/00329/2013). V.V.P., E.Y.P. and P.A.N. are supported by Russian Science Foundation project N 16-18-10265-RNF. P.A.N. is supported by the Federal research program no. 0135-2016-0024. V.V.P., E.Y.P. and V.G.C thank the Rock Foundation of New York, USA for long-term support of the Yana research. D.J.M. is supported by the Quest Archaeological Research Program. P.S.G., A.I.L. and B.A.M. are funded by RFBR (19-09-00144). A.Y.F. was supported by the IAET SB RAS project no. 0329-2019-0001. R.M. was supported by an EMBO Long-Term Fellowship (ALTF 133-2017) and R.D. by Wellcome grant WT207492. M. Peyrot is supported by an ERC starting grant ERC-2017-STG 758855. S.R. was supported by the Novo Nordisk Foundation (NNF14CC0001). Q.F. was supported by NSFC (91731303, 41672021, 41630102). V.I.K. and V.M. are funded by RFBR (18-09-00349), A.S. thanks Medicinska understödsföreningen Liv och Hälsa r.f. and the Finnish Society of Sciences and Letters for financial support. M.E.A. was funded by the Villum Foundation (Young Investigator, grant no. 10120). M.M.L. was supported by an ERC advanced grant (no. 295907).

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Nature thanks Pontus Skoglund and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Authors

Contributions

E.W. initiated and led the study. V.V.P., S.V.V., E.V., M.G., E.Y.P., V.G.C., P.A.N., A.V.G., V.I.K., V.M., P.S.G., A.Y.F., A.I.L., S.B.S., B.A.M., M.M., L.A., J.U.P., T.S., K.M., M. Putkonen, N.B., K.-G.S., K.K., A.W., A.S. and E.W. excavated, curated, sampled and/or described analysed skeletons. M.E.A., L.V., A.M., P.d.B.D, C.d.l.F. and H.M. performed laboratory work. M.S., V.C.S., M.E.A., S.R., G.R., M.A.Y., Q.F., I.D., K.G., D.N.-B., G.K., M. Peyrot, R.M., V.A. and C.P. analysed or assisted in analysis of data. M.S., E.W., V.C.S., L.E., M.E.A., D.J.M. and V.V.P interpreted results with considerable input from M.M.L. and R.S.M. E.W., L.E., R.N., R.D. and C.R. supervised analysis. M.S., E.W. and D.J.M. wrote the manuscript with considerable input from V.V.P, V.C.S., L.E. and M.M.L., and contributions from all other authors. All authors contributed to the final interpretation of data.

Corresponding authors

Correspondence to Martin Sikora or Vladimir V. Pitulko or Laurent Excoffier or Eske Willerslev.

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The authors declare no competing interests.

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Extended data figures and tables

Extended Data Fig. 1 Geographical, chronological and archaeological context for the earliest human remains discovered in northern Siberia.

a, Map of known 14C-dated anatomically modern human fossils of late Pleistocene and early Holocene age (yellow dots) found in Siberia54,82,83,84,85,86,87. Yellow star, Yana RHS site; red triangle, Denisova Cave, which has yielded Neanderthal and Denisovan remains88,89; white line, reconstructed maximum ice sheet extent at about 60 ka; blue filling, ice sheet extent during the LGM, around 20 ka (refs 90,91); potentially glaciated areas are cross-hatched. b, General view of the Northern Point excavation area at the Yana RHS site4. c, Cultural layer in H29 unit in which the human tooth was found. d, Cryolithological profile for Northern Point of Yana RHS92. e, Human tooth found during the excavations in unit 2V26 shown in occlusal and lateral view (e1); human tooth found in unit X26 shown in occlusal view (e2); and human tooth found in unit H29 shown in occlusal and lateral view (e3). The samples e2 (Yana2 genome) and e3 (Yana1 with high-coverage (25.6×) genome sequence) are used in this study. In the key for d (bottom): 1, sand with small pebbles; 2, sandy silt; 3, clayey-sand silt; 4, sandy-clayey silt; 5, interbedding of clayey silt bands and sandy-clayey silt with beds and lenses of peat; 6, soil–vegetation layer; 7, cultural layer; 8, polygonal ice wedges; 9, boundary of seasonally active layer; 10, location of bones of Pleistocene animals sampled for 14С dating; 11, location of 14С samples of plant remains; 12, radiocarbon date and laboratory code.

Extended Data Fig. 2 Y chromosome phylogeny.

Maximum likelihood tree of Y chromosome sequences for modern and ancient individuals, with major haplogroups highlighted. Numbers on internal nodes show bootstrap support values from 100 replicates for nodes with bootstrap values < 100.

Extended Data Fig. 3 Genetic affinities of Yana RHS individuals.

ac, Geographical heat maps depicting the outgroup-f3 statistics for Yana1 (a), Tianyuan (b) and Sunghir3 (c) individuals with 167 worldwide populations. d, f4-statistics contrasting allele sharing of Yana RHS individuals and other selected Upper Palaeolithic groups with early West Eurasians (represented by the Kostenki 14 individual) or East Asians (represented by the Tianyuan individual). e, f4-statistics for highlighting groups with affinities to both early West Eurasians and East Asians (joined with dashed lines). Error bars indicate ± 3 s.e., obtained using a block jackknife (Methods). f, Admixture graph models of ancient and modern populations for western Eurasia (left) and East Asia and the Americas (right). Newly reported individuals are highlighted with a coloured background. Early Upper Palaeolithic individuals were modelled allowing for a possible additional Neanderthal contribution to account for higher levels of Neanderthal ancestry (dotted lines).

Extended Data Fig. 4 Relatedness and identity-by-descent.

a, Kinship coefficient and R1 ratio (number of double-heterozygous (Aa/Aa) sites divided by the total number of discordant genotypes) for newly reported ancient groups with multiple individuals per site. b, Number and length of homozygosity-by-descent (HBD) segments in ancient and modern individuals. Grey ellipses indicate 95% confidence region obtained from simulations of 100 haploid genomes of indicated effective population size. c, Distribution of total identity-by-descent (IBD) lengths for simulations of varying effective population sizes. Observed values for pairs from the Sunghir and Yana individuals are indicated by dashed lines.

Extended Data Fig. 5 Genetic affinities of the Kolyma1 individual.

a, b, Geographical heat maps depicting genetic affinities of the Kolyma1 individual using outgroup-f3 statistics with 167 modern populations (a) and total length of haplotype chunks donated to 206 modern populations in chromosome painting (b). c, Chromosome-painting symmetry statistic contrasting the total length of haplotypes donated from ancient and modern non-American donor groups to pairs of Native American populations, for two different datasets (1240K and WGS; Supplementary Information 3). The top panels show a greater excess in donations to Athabascans from Kolyma1. The bottom panels show the same statistic for West Greenland Inuit, a population with known affinity to Palaeo-Eskimos, which is reflected in the excess donations observed from the Saqqaq individual. Error bars indicate ± 3 s.e., obtained using a block jackknife.

Extended Data Fig. 6 Palaeoclimatic niche modelling.

Maps showing regions that are climatically suitable for human occupation, across temporal and spatial dimensions. Projections are bounded from 60° E to 180° E and from 38° N to 80° N. The colour key represents suitability values; darker colours correspond to higher—and lighter colours to lower—suitability values. a, Examples of climatic suitability for human occupation for different time slices. b, Median and s.d. of climatic suitability across 23 climatic periods of millennial or bimillennial time resolution. c, Regions that are highly climatically suitable for humans are shown in red; regions of low suitability are shown in grey; and regions with periods of both high and low suitability are shown in orange.

Extended Data Fig. 7 Admixture modelling using qpAdm.

a, Maps showing locations and ancestry proportions of ancient (left) and modern (right) groups. bd, Ancestry proportions and fit for all possible two-way (b), three-way (c) and four-way (d) reference population combinations. Transparent shading indicates model fit, with lighter transparency indicating models accepted with 0.05 > P ≥ 0.01 in qpAdm. Numbers of individuals for source and target populations are given in parentheses.

Extended Data Fig. 8 Genetic diversity in northern Eurasia related to ancient genomes.

a, Principal component analysis of 93 ancient individuals projected onto a set of 587 modern Eurasian and Native American individuals. b, c, Multidimensional scaling (MDS) plots of 715 individuals from 91 modern populations, obtained from the chromosome-painting co-ancestry matrix using modern Africans and high-coverage ancient individuals as donors, based on total length of chunks (b) or total number of chunks (c).

Extended Data Table 1 Key f-statistics

Supplementary information

Supplementary Information

This file contains Supplementary Information Sections 1-9 and an Appendix

Reporting Summary

Supplementary Data

This file contains Supplementary Data Tables 1-5. Supplementary Data Table 1 contains details of the newly sequenced individuals; Supplementary Data Table 2 shows sequencing statistics; Supplementary Data Table 3 contains panels of ancient individuals used in the analyses; Supplementary Data Table 4 contains panels of modern individuals used in the analyses and Supplementary Data Table 5 shows full qpAdm results for all 2-, 3- and 4-way models

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Sikora, M., Pitulko, V.V., Sousa, V.C. et al. The population history of northeastern Siberia since the Pleistocene. Nature 570, 182–188 (2019). https://doi.org/10.1038/s41586-019-1279-z

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