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Mol Biol Evol. 2014 Nov;31(11):2929-40. doi: 10.1093/molbev/msu230. Epub 2014 Aug 1.

Genome-wide SNP analysis reveals population structure and demographic history of the ryukyu islanders in the southern part of the Japanese archipelago.

Author information

1
Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
2
Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, Tokyo, Japan.
3
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan Department of Human Anatomy, Kitasato University Graduate School of Medical Sciences, Kanagawa, Japan.
4
Haneji Oral Surgery Clinic, Medical Corporation Hayamakai, Okinawa, Japan.
5
Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan.
6
Department of Anatomy, Kitasato University School of Medicine, Kanagawa, Japan.
7
Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan Department of Medical Chemistry, Kurume University School of Medicine, Fukuoka, Japan.
8
Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan rkimura@med.u-ryukyu.ac.jp hiroki_oota@med.kitasato-u.ac.jp.
9
Department of Anatomy, Kitasato University School of Medicine, Kanagawa, Japan rkimura@med.u-ryukyu.ac.jp hiroki_oota@med.kitasato-u.ac.jp.

Abstract

The Ryukyu Islands are located to the southwest of the Japanese archipelago. Archaeological evidence has revealed the existence of prehistoric cultural differentiation between the northern Ryukyu islands of Amami and Okinawa, and the southern Ryukyu islands of Miyako and Yaeyama. To examine a genetic subdivision in the Ryukyu Islands, we conducted genome-wide single nucleotide polymorphism typing of inhabitants from the Okinawa Islands, the Miyako Islands, and the Yaeyama Islands. Principal component and cluster analyses revealed genetic differentiation among the island groups, especially between Okinawa and Miyako. No genetic affinity was observed between aboriginal Taiwanese and any of the Ryukyu populations. The genetic differentiation observed between the inhabitants of the Okinawa Islands and the Miyako Islands is likely to have arisen due to genetic drift rather than admixture with people from neighboring regions. Based on the observed genetic differences, the divergence time between the inhabitants of Okinawa and Miyako islands was dated to the Holocene. These findings suggest that the Pleistocene inhabitants, whose bones have been found on the southern Ryukyu Islands, did not make a major genetic contribution, if any, to the present-day inhabitants of the southern Ryukyu Islands.

KEYWORDS:

Japanese archipelago; Ryukyu Islanders; demographic history; genome-wide SNPs; population structure

PMID:
25086001
DOI:
10.1093/molbev/msu230
[Indexed for MEDLINE]

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