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

Japanese Genome Variation Consortium

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish
Article numbere0185487
JournalPloS one
Volume12
Issue number11
DOIs
Publication statusPublished - 2017 Nov 1
Externally publishedYes

Fingerprint

Molecular Evolution
Genetic Structures
Polymorphism
Principal component analysis
Statistical methods
Nucleotides
Genes
Medical Genetics
genetic variation
Population
Genetic Drift
Geography
Population Genetics
Principal Component Analysis
ancestry
Haplotypes
Single Nucleotide Polymorphism
Japan
Genome
geography

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

The fine-scale genetic structure and evolution of the Japanese population. / Japanese Genome Variation Consortium.

In: PloS one, Vol. 12, No. 11, e0185487, 01.11.2017.

Research output: Contribution to journalArticle

Japanese Genome Variation Consortium. / The fine-scale genetic structure and evolution of the Japanese population. In: PloS one. 2017 ; Vol. 12, No. 11.
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