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

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

Author information

1
Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan.
2
Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan.
3
Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan.
4
Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan.
5
Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan.
6
Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
7
Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan.
8
Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan.
9
Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
10
NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.
11
Life Sciences Institute, National University of Singapore, Singapore, Singapore.
12
College of the Life Sciences and Technology, Xinjiang University, Urumqi, China.
13
Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, Yinchuan, Ningxia, China.
14
Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China.
15
School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.
16
Collaborative Innovation Center of Genetics and Development, Shanghai, China.
17
Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.
18
Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore.

Abstract

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.

PMID:
29091727
PMCID:
PMC5665431
DOI:
10.1371/journal.pone.0185487
[Indexed for MEDLINE]
Free PMC Article

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