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

doi:10.1371/journal.pone.0185487

	The fine-scale genetic structure and evolution of the Japanese population
	Takeuchi, Fumihiko 1; Katsuya, Tomohiro 2; Kimura, Ryosuke 3; Nabika, Toru 4; Isomura, Minoru 4; Ohkubo, Takayoshi 5; Tabara, Yasuharu 6; Yamamoto, Ken 7; Yokota, Mitsuhiro 8; Liu, Xuanyao 9,10; Saw, Woei-Yuh 9,11; Mamatyusupu, Dolikun 12; Yang, Wenjun 13; Xu, Shuhua14,15,16,17 ; Teo, Yik-Ying 1,9,10,11,18,19; Kato, Norihiro 1
	2017-11
发表期刊	PLOS ONE
ISSN	1932-6203
卷号	12 期号:11
发表状态	已发表
DOI	10.1371/journal.pone.0185487
摘要	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.
收录类别	SCI
语种	英语
资助项目	Program of Shanghai Subject Chief Scientist[16XD1404700]
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000414229700007
出版者	PUBLIC LIBRARY SCIENCE
WOS关键词	WHOLE-GENOME ASSOCIATION ; EAST-ASIAN POPULATIONS ; INTERPRETING F-ST ; POSITIVE SELECTION ; LINKAGE DISEQUILIBRIUM ; DUAL STRUCTURE ; SNP GENOTYPES ; DIVERSITY ; AINU ; INFERENCE
原始文献类型	Article
引用统计
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/10011
专题	生命科学与技术学院_特聘教授组_徐书华组
通讯作者	Takeuchi, Fumihiko; Kato, Norihiro
作者单位	1.Natl Ctr Global Hlth & Med, Dept Gene Diagnost & Therapeut, Tokyo, Japan 2.Osaka Univ, Grad Sch Med, Dept Clin Gene Therapy, Suita, Osaka, Japan 3.Univ Ryukyus, Dept Human Biol & Anat, Grad Sch Med, Nishihara, Okinawa, Japan 4.Shimane Univ, Sch Med, Dept Funct Pathol, Izumo, Shimane, Japan 5.Teikyo Univ, Sch Med, Dept Hyg & Publ Hlth, Tokyo, Japan 6.Kyoto Univ, Grad Sch Med, Ctr Genom Med, Kyoto, Japan 7.Kurume Univ, Sch Med, Dept Med Chem, Kurume, Fukuoka, Japan 8.Aichi Gakuin Univ, Sch Dent, Dept Genome Sci, Nagoya, Aichi, Japan 9.Natl Univ Singapore, Saw Swee Hock Sch Publ Hlth, Singapore, Singapore 10.Natl Univ Singapore, Grad Sch Integrat Sci & Engn, Singapore, Singapore 11.Natl Univ Singapore, Life Sci Inst, Singapore, Singapore 12.Xinjiang Univ, Coll Life Sci & Technol, Urumqi, Peoples R China 13.Ningxia Med Univ, Key Lab Reprod & Hered Ningxia Reg, Ningxia, Peoples R China 14.Chinese Acad Sci, Max Planck Independent Res Grp Populat Genom, Shanghai, Peoples R China 15.Chinese Acad Sci, Max Planck Soc Partner Inst Computat Biol, Shanghai Inst Biol Sci, Shanghai, Peoples R China 16.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China 17.Collaborat Innovat Ctr Genet & Dev, Shanghai, Peoples R China 18.Agcy Sci Technol & Res, Genome Inst Singapore, Singapore, Singapore 19.Natl Univ Singapore, Dept Stat & Appl Probabil, Singapore, Singapore
推荐引用方式 GB/T 7714	Takeuchi, Fumihiko,Katsuya, Tomohiro,Kimura, Ryosuke,et al. The fine-scale genetic structure and evolution of the Japanese population[J]. PLOS ONE,2017,12(11).
APA	Takeuchi, Fumihiko.,Katsuya, Tomohiro.,Kimura, Ryosuke.,Nabika, Toru.,Isomura, Minoru.,...&Kato, Norihiro.(2017).The fine-scale genetic structure and evolution of the Japanese population.PLOS ONE,12(11).
MLA	Takeuchi, Fumihiko,et al."The fine-scale genetic structure and evolution of the Japanese population".PLOS ONE 12.11(2017).