The fine-scale genetic structure and evolution of the Japanese population

PLoS One. 2017 Nov 1;12(11):e0185487. doi: 10.1371/journal.pone.0185487. eCollection 2017.


The contemporary Japanese populations largely consist of three genetically distinct groups-Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.

MeSH terms

  • Asian Continental Ancestry Group*
  • Genome-Wide Association Study
  • Humans
  • Japan
  • Multigene Family
  • Polymorphism, Single Nucleotide*

Grant support

N.K. acknowledges support from the grants (26S-111 and 26S-115) of National Center for Global Health and Medicine; a grant-in-aid from the MEXT/JSPS KAKENHI (Grant Number 26290067); and grants from SENSHIN Medical Research Foundation. W.Y.S. and Y.Y.T. acknowledge support from the Saw Swee Hock School of Public Health, and Life Sciences Institute from the National University of Singapore. Y.Y.T. also acknowledges support from the National Research Foundation Singapore (NRF-RF-2010-05). S.X. gratefully acknowledges the support of the National Natural Science Foundation of China (NSFC) grants (91331204), the National Science Fund for Distinguished Young Scholars (31525014) and Program of Shanghai Subject Chief Scientist (16XD1404700). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.