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. 2016 Jan;202(1):261-72.
doi: 10.1534/genetics.115.178673. Epub 2015 Oct 23.

Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu

Choongwon Jeong  1 , Shigeki Nakagome  2 , Anna Di Rienzo  3
Affiliations

Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu

Choongwon Jeong et al. Genetics. 2016 Jan.

Abstract

Despite recent advances in population genomics, much remains to be elucidated with regard to East Asian population history. The Ainu, a hunter-gatherer population of northern Japan and Sakhalin island of Russia, are thought to be key to elucidating the prehistory of Japan and the peopling of East Asia. Here, we study the genetic relationship of the Ainu with other East Asian and Siberian populations outside the Japanese archipelago using genome-wide genotyping data. We find that the Ainu represent a deep branch of East Asian diversity more basal than all present-day East Asian farmers. However, we did not find a genetic connection between the Ainu and populations of the Tibetan plateau, rejecting their long-held hypothetical connection based on Y chromosome data. Unlike all other East Asian populations investigated, the Ainu have a closer genetic relationship with northeast Siberians than with central Siberians, suggesting ancient connections among populations around the Sea of Okhotsk. We also detect a recent genetic contribution of the Ainu to nearby populations, but no evidence for reciprocal recent gene flow is observed. Whole genome sequencing of contemporary and ancient Ainu individuals will be helpful to understand the details of the deep history of East Asians.

Keywords: Jomon; Tibet; demography; migration.

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Figures

Figure 1
Figure 1
Geographic location of East Asian and Siberian population samples used in this study. The zoom-in plot highlights the region around the Japanese archipelago and the Sea of Okhotsk.
Figure 2
Figure 2
ADMIXTURE analysis of East Asian and Siberian populations with K = 8. Ainu individuals are assigned to a distinct ancestry component (dark gray), which is present also in Japanese and Ulchi individuals. Siberian ancestry is divided into two major components, one for northeast Siberians (skyblue in Chukchi, Eskimo, Itelmen, and Koryak) and the other for central Siberians (orange in Nganasan and other Siberian and northeast Asian populations). Four Yukagir individuals harboring a large proportion of European ancestry were labeled as “Yukagir2.”
Figure 3
Figure 3
A consensus tree of 15 worldwide populations inferred from 500 bootstrap replicates of maximum likelihood trees using TreeMix. Numbers show the bootstrap support on the corresponding nodes. Nodes with no number were supported in 100% of the bootstrap replicates.
Figure 4
Figure 4
The genetic affinity of East Asian and Siberian populations to the Nganasan and the Itelmen, respectively, measured by Patterson’s D(Yoruba, X; Nganasan, Itelmen). Horizontal bars around the value represent ±3 SD.
Figure 5
Figure 5
A summary of competing scenarios for the observed excess affinity of the Ainu with northeast Siberians. (A) “Scenario 1” proposes a shared ancestry between the Ainu and northeast Siberians. (B) “Scenario 2” proposes a later gene flow between the Ainu and northeast Siberians.
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