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, 3 (2), e1601877
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Genome-wide Data From Two Early Neolithic East Asian Individuals Dating to 7700 Years Ago

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Genome-wide Data From Two Early Neolithic East Asian Individuals Dating to 7700 Years Ago

Veronika Siska et al. Sci Adv.

Abstract

Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.

Keywords: East Asia; Russian Far East; ancient genetics; human population genetics; neolithic.

Figures

Fig. 1
Fig. 1. Regional reference panel, PCA, and ADMIXTURE analysis.
(A) Map of Asia showing the location of Devil’s Gate (black triangle) and of modern populations forming the regional panel of our analysis. (B) Plot of the first two principal components as defined by our regional panel of modern populations from East Asia and central Asia shown on (A), with the two samples from Devil’s Gate (black triangles) projected upon them (18). (C) ADMIXTURE analysis (19) performed on Devil’s Gate and our regional panel, for K = 5 (lowest cross-validation error) and K = 8 (appearance of Devil’s Gate–specific cluster).
Fig. 2
Fig. 2. Outgroup f3 statistics.
Outgroup f3 measuring shared drift between Devil’s Gate (black triangle shows sampling location) and modern populations with respect to an African outgroup (Khomani). (A) Map of the whole world. (B) Fifteen populations with the highest shared drift with Devil’s Gate, color-coded by regions as in Fig. 1. Error bars represent 1 SE.
Fig. 3
Fig. 3. Spatial pattern of outgroup f3 statistics.
Relationship between outgroup f3(X, Devil’s Gate; Khomani) and distance on land from Devil’s Gate using DevilsGate1 and all single-nucleotide polymorphisms (SNPs). Populations up to 9000 km away from Devil’s Gate were considered when computing correlation. The highest distance considered was chosen to acquire the highest Pearson correlation in steps of 500 km. Best linear fit (r2 = 0.772, F1,108 = 368.4, P < 0.001) is shown as blue line, with 95% CI indicated by the shaded area.
Fig. 4
Fig. 4. Admixture f3 statistics.
Admixture f3 representing modern Koreans and Japanese as a mixture of two populations, X and Y, color-coded by regions as in Fig. 1. (A) Thirty pairs with the lowest f3 score for the Koreans as the target, out of those giving a significant (z < −2) value. (B) All four pairs giving a significantly (z < −2) negative score for the Japanese as the target. Error bars represent 1 SE.

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