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, 3 (6), 966-976

The Genetic History of Admixture Across Inner Eurasia

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The Genetic History of Admixture Across Inner Eurasia

Choongwon Jeong et al. Nat Ecol Evol.

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.

Conflict of interest statement

Competing Interests

The authors declare no competing interests.

Figures

Fig. 1.
Fig. 1.. Geographic locations of the Eneolithic Botai site (red triangle), 65 groups including newly sampled individuals (filled diamonds) and nearby groups with published data (filled squares).
Mean latitude and longitude values across all individuals under each group label were used. Two zoom-in plots for the Caucasus (blue) and the Altai-Sayan (magenta) regions are presented in the lower left corner. A list of new groups, their three-letter codes, and the number of new individuals (in parenthesis) are provided at the bottom. Present-day populations are color-coded based on the language family for Figs. 1–3, following key codes listed in Fig. 2. Corresponding information for the previously published groups is provided in Supplementary Table 2. The map is overlayed with ecoregional information, divided into 14 biomes, downloaded from https://ecoregions2017.appspot.com/ (credited to Ecoregions 2017 © Resolve). The main inner Eurasian map is on the Albers equal area projection and was produced using the spTransform function in the R package rgdal v1.2–5.
Fig. 2.
Fig. 2.. The genetic structure of inner Eurasian populations.
(a) The first two PCs of 2,077 Eurasian individuals separate western and eastern Eurasians (PC1) and Northeast and Southeast Asians (PC2). Most inner Eurasians are located between western and eastern Eurasians on PC1. Ancient individuals (color-filled shapes) are projected onto PCs calculated based on contemporary individuals. Present-day individuals are marked by grey dots, with their per-group mean coordinates marked by three-letter codes listed in Supplementary Table 2. Individuals are colored by their language family. (b) ADMIXTURE results for a chosen set of ancient and present-day groups (K = 14). The top row shows ancient inner Eurasians and representative present-day eastern Eurasians. The following three rows show forest-tundra, steppe-forest and southern steppe cline populations. Most inner Eurasians are modeled as a mixture of components primarily found in eastern or western Eurasians. Results for the full set of individuals are provided in Supplementary Fig. 3.
Fig. 3.
Fig. 3.. Correlation of longitude and ancestry proportion across inner Eurasian populations.
Across inner Eurasian populations, mean longitudinal coordinates (x-axis) and mean eastern Eurasian ancestry proportions (y-axis) are strongly correlated. Eastern Eurasian ancestry proportions are estimated from ADMIXTURE results with K=14 by summing up six components maximized in Surui, Chipewyan, Itelmen, Nganasan, Atayal and early Neolithic Russian Far East individuals (“Devil’s Gate”), respectively (Supplementary Fig. 3). The yellow curve shows a probit regression fit following the model in Sedghifar et al.. Three groups (Kalmyks, Dungans, Nogai2) are marked with grey square due to their substantial deviation from the curve as well as their historically known migration history.
Fig. 4.
Fig. 4.. Characterization of the western and eastern Eurasian source ancestries in inner Eurasian populations.
(a) Admixture f3 values are compared for different eastern Eurasian references (Mixe, Nganasan, Ulchi; left) or western Eurasian ones (Srubnaya, Iran_ChL; right). For each target group, darker shades mark more negative f3 values. (b) Weights of donor populations in two sources characterizing the main admixture signal (“date 1 PC 1”) in the GLOBETROTTER analysis. We merged 167 donor populations into 12 groups, as listed on the top right side. Target populations are split into five groups: Aleuts, the forest-tundra cline populations, the steppe-forest cline populations, the southern steppe cline populations and the rest of four populations (“others”), from the top to bottom.
Fig. 5.
Fig. 5.. qpAdm-based admixture models for the forest-tundra and steppe-forest cline populations.
For the forest-tundra population to the west of the Urals, Nganasan+Srubnaya+WHG+LBK_EN or its submodel provides a good fit, while additional ANE-related contribution (AG3) is required for those to the east of the Urals (Enets, Selkups, Kets, and Mansi). For the steppe-forest populations, Srubnaya+Ulchi, Srubnaya+Ulchi+AG3, or Srubnaya+Nganasan provides a good fit. 5 cM jackknifing standard errors are marked by the horizontal bar. Models with p-value between 0.01 and 0.05 are marked by grey color and those with p-value < 0.01 are marked by grey color and italic font. Details of the model information are presented in Supplementary Tables 5 and 8.

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