Genomic analyses inform on migration events during the peopling of Eurasia.

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.Support was provided by: Estonian Research Infrastructure Roadmap grant no 3.2.0304.11-0312; Australian Research Council Discovery grants (DP110102635 and DP140101405) (D.M.L., M.W. and E.W.); Danish National Research Foundation; the Lundbeck Foundation and KU2016 (E.W.); ERC Starting Investigator grant (FP7 - 261213) (T.K.); Estonian Research Council grant PUT766 (G.C. and M.K.); EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (R.V.; M.Me. and A.Me.), and Centre of Excellence for Genomics and Translational Medicine Project No. 2014-2020.4.01.15-0012 to EGC of UT (A.Me.) and EBC (M.Me.); Estonian Institutional Research grant IUT24-1 (L.S., M.J., A.K., B.Y., K.T., C.B.M., Le.S., H.Sa., S.L., D.M.B., E.M., R.V., G.H., M.K., G.C., T.K. and M.Me.) and IUT20-60 (A.Me.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Gates Cambridge Trust Funding (E.J.); ICG SB RAS (No. VI.58.1.1) (D.V.L.); Leverhulme Programme grant no. RP2011-R-045 (A.B.M., P.G. and M.G.T.); Ministry of Education and Science of Russia; Project 6.656.2014/K (S.A.F.); NEFREX grant funded by the European Union (People Marie Curie Actions; International Research Staff Exchange Scheme; call FP7-PEOPLE-2012-IRSES-number 318979) (M.Me., G.H. and M.K.); NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01 (S.Tis.); Russian Foundation for Basic Research (grant N 14-06-00180a) (M.G.); Russian Foundation for Basic Research; grant 16-04-00890 (O.B. and E.B); Russian Science Foundation grant 14-14-00827 (O.B.); The Russian Foundation for Basic Research (14-04-00725-a), The Russian Humanitarian Scientific Foundation (13-11-02014) and the Program of the Basic Research of the RAS Presidium “Biological diversity” (E.K.K.); Wellcome Trust and Royal Society grant WT104125AIA & the Bristol Advanced Computing Research Centre (http://www.bris.ac.uk/acrc/) (D.J.L.); Wellcome Trust grant 098051 (Q.A.; C.T.-S. and Y.X.); Wellcome Trust Senior Research Fellowship grant 100719/Z/12/Z (M.G.T.); Young Explorers Grant from the National Geographic Society (8900-11) (C.A.E.); ERC Consolidator Grant 647787 ‘LocalAdaptatio’ (A.Ma.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.); Russian Foundation for Basic Research grant 16-06-00303 (E.B.); a Rutherford Fellowship (RDF-10-MAU-001) from the Royal Society of New Zealand (M.P.C.)

Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe

Abstract Background The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia. Results We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region. We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the “Finno-Ugric” origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main “core”, being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the “Great Siberian Vortex” directing genetic exchanges in populations across the Siberian part of Asia. Slavic speakers of Eastern Europe are, in general, very similar in their genetic composition. Ukrainians, Belarusians and Russians have almost identical proportions of Caucasus and Northern European components and have virtually no Asian influence. We capitalized on wide geographic span of our sampling to address intriguing question about the place of origin of Russian Starovers, an enigmatic Eastern Orthodox Old Believers religious group relocated to Siberia in seventeenth century. A comparative reAdmix analysis, complemented by IBD sharing, placed their roots in the region of the Northern European Plain, occupied by North Russians and Finno-Ugric Komi and Karelian people. Russians from Novosibirsk and Russian Starover exhibit ancestral proportions close to that of European Eastern Slavs, however, they also include between five to 10 % of Central Siberian ancestry, not present at this level in their European counterparts. Conclusions Our project has patched the hole in the genetic map of Eurasia: we demonstrated complexity of genetic structure of Northern Eurasians, existence of East-West and North-South genetic gradients, and assessed different inputs of ancient populations into modern populations

Additional file 1: Figure S1. of Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe

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Additional file 3: Table S1a. of Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe

List of samples included in “Extended” dataset. Table S1b List of samples included in “Core” dataset. Table S1c List of samples included in “Ancient” dataset. Table S2 Results of ADMIXTURE for K = 9. Table S3 Results of ADMIXTURE for K = 6, 7, 8. Table S4 Results of f3 test. Table S5 Results of IBD sharing analysis in 1–3 cM and 4–10 cM bins. Table S6 Total amount of shared IBD between populations. Table S7 Standard residue of linear regression analysis of distance-IBD sharing. Table S8 Distance and shared IBD between pairs of populations. Table S9: Results of f3 outgroup test with ancient samples. (XLSX 482 kb

The Genetic Legacy of the Expansion of Turkic-Speaking Nomads across Eurasia

<div><p>The Turkic peoples represent a diverse collection of ethnic groups defined by the Turkic languages. These groups have dispersed across a vast area, including Siberia, Northwest China, Central Asia, East Europe, the Caucasus, Anatolia, the Middle East, and Afghanistan. The origin and early dispersal history of the Turkic peoples is disputed, with candidates for their ancient homeland ranging from the Transcaspian steppe to Manchuria in Northeast Asia. Previous genetic studies have not identified a clear-cut unifying genetic signal for the Turkic peoples, which lends support for language replacement rather than demic diffusion as the model for the Turkic language’s expansion. We addressed the genetic origin of 373 individuals from 22 Turkic-speaking populations, representing their current geographic range, by analyzing genome-wide high-density genotype data. In agreement with the elite dominance model of language expansion most of the Turkic peoples studied genetically resemble their geographic neighbors. However, western Turkic peoples sampled across West Eurasia shared an excess of long chromosomal tracts that are identical by descent (IBD) with populations from present-day South Siberia and Mongolia (SSM), an area where historians center a series of early Turkic and non-Turkic steppe polities. While SSM matching IBD tracts (> 1cM) are also observed in non-Turkic populations, Turkic peoples demonstrate a higher percentage of such tracts (<i>p</i>-values ≤ 0.01) compared to their non-Turkic neighbors. Finally, we used the ALDER method and inferred admixture dates (~9th–17th centuries) that overlap with the Turkic migrations of the 5th–16th centuries. Thus, our results indicate historical admixture among Turkic peoples, and the recent shared ancestry with modern populations in SSM supports one of the hypothesized homelands for their nomadic Turkic and related Mongolic ancestors.</p></div

Populations with high and correlated signals of IBD sharing with western Turkic peoples.

<p>Circle positions correspond to population locations. Circle color indicates the amount of excess IBD sharing (shown in Legend) that a population shares with all 12 western Turkic populations. Populations with IBD sharing exceeding the 0.90 quantile are shown with a “plus symbol”. Panel A) IBD sharing signal based on IBD tracts of 1–2 cM. Panel B) IBD sharing signal based on IBD tracts of 2–3 cM. Panel C) IBD sharing signal based on IBD tracts of 3–4 cM</p

Pairwise IBD sharing based on 1–2 cM long segments.

<p>For each population ordered along the x–axis, IBD sharing is computed with three SSM populations (Tuvans, Buryats, Mongols) and Evenkis. Each Turkic-speaking population (shown in red) is grouped with its respective geographic neighbors using parentheses. The grouped geographic neighbors were pooled and used to perform a permutation test as described in the M&M section. Red numbers under the Turkic population name indicate how many SSM populations demonstrate a statistically significant excess of IBD sharing with a given Turkic population. Note that, for example, Bashkirs, Tatars, and Chuvashes share their geographic neighbors.</p

Admixture dates for simulated populations.

<p>Simulated populations were generated by mixing two ancestral populations G generations ago as described in the M&M section. We repeated each admixture scenario 120 times and analyzed with two admixture dating methods: ALDER and SPCO. Circles represent admixture dates for one simulated population and circle color indicates the method of admixture inference as shown in the legend. Red “plus symbols” show the true admixture date.</p

Admixture dates for Turkic-speaking populations on an absolute date scale.

<p>Blue circles show ALDER-inferred point estimates and error bars indicate 95% confidence intervals. Gray circles show SPCO-inferred point estimates and error bars in gray indicate 95% confidence intervals. The red bar shows the point estimate range (inferred using ALDER) across all the analyzed samples and the orange bar shows the same for SPCO-inferred dates. Admixture dates before Common Era (CE) are shown with a negative sign.</p

Geographic map of samples included in this study and linguistic tree of Turkic languages.

<p>Panel A) Non-Turkic-speaking populations are shown with light blue, light green, dark green, light brown, and yellow circles, depending on the region. Turkic-speaking populations are shown with red circles regardless of the region of sampling. Full population names are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005068#pgen.1005068.s009" target="_blank">S1 Table</a> Panel B) The linguistic tree of Turkic languages is adapted from Dybo 2004 and includes only those languages spoken by the Turkic peoples analyzed in this study. The x-axis shows the time scale in kilo-years (kya). Internal branches are shown with different colors.</p