Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations

Abstract

Background: Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied.

Results: We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed that Han Chinese, Japanese and Korean populations have distinct genetic makeup and can be well distinguished based on either the genome wide data or a panel of ancestry informative markers (AIMs). Their genetic structure corresponds well to their geographical distributions, indicating geographical isolation played a critical role in driving population differentiation in East Asia. The most recent common ancestor of the three populations was dated back to 3000 ~ 3600 years ago. Our analyses also revealed substantial admixture within the three populations which occurred subsequent to initial splits, and distinct gene introgression from surrounding populations, of which northern ancestral component is dominant.

Conclusions: These estimations and findings facilitate to understanding population history and mechanism of human genetic diversity in East Asia, and have implications for both evolutionary and medical studies.

Keywords: Admixture; Genetic ancestry; Han Chinese; Japanese; Korean; Population divergence; Population structure; SNP.

Fig. 1

Asian samples location and population relatedness. (a) Geographic location of the sampled populations (generated by R 2.15.2 and Microsoft PowerPoint 2010); (b) Principal component analysis (PCA) of all the 10 Asian sample populations

Fig. 2

Population level phylogenetic Tree and Principal component analysis (PCA). (A) The maximum likelihood tree was constructed based on pair-wise F_ST matrix. And the marked number are bootstrap value; (B) The top two PCs of individuals representing six East Asian populations, mapped to their corresponding geographic locations (generated by R 2.15.2 and Microsoft Excel 2010)

Fig. 3

Effective population size varied along time. Effective population size (N_e) was calculated from LD observations in 2500 distance classes (from 0.001 cM to 2.5 cM with the window size set as 0.001 cM) for each population. Results from 2000 generations ago (GA) to 200 GA are shown (generated by Microsoft Office 365)

Fig. 4

Admixture analysis of East Asian populations together with world-wide non-Asian populations. Result of K = 5 was shown and each vertical bar represents genome makeup of an sample individual (calculated by ADMIXTURE 1.23 [1] and R 2.15.2)