title: Genome-wide SNP analysis reveals population structure and demographic history of the ryukyu islanders in the southern part of the Japanese archipelago.
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.
authors.affiliation: Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
authors.forename: Takehiro
authors.initials: T
authors.lastname: Sato
authors.affiliation: Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, Tokyo, Japan.
authors.forename: Shigeki
authors.initials: S
authors.lastname: Nakagome
authors.affiliation: Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
authors.forename: Chiaki
authors.initials: C
authors.lastname: Watanabe
authors.affiliation: Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
authors.forename: Kyoko
authors.initials: K
authors.lastname: Yamaguchi
authors.affiliation: Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Kawaguchi
authors.affiliation: 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.
authors.forename: Kae
authors.initials: K
authors.lastname: Koganebuchi
authors.affiliation: Haneji Oral Surgery Clinic, Medical Corporation Hayamakai, Okinawa, Japan.
authors.forename: Kuniaki
authors.initials: K
authors.lastname: Haneji
authors.affiliation: Department of Orthodontics, School of Dentistry, Showa University, Tokyo, Japan.
authors.forename: Tetsutaro
authors.initials: T
authors.lastname: Yamaguchi
authors.affiliation: Department of Anatomy, Kitasato University School of Medicine, Kanagawa, Japan.
authors.forename: Tsunehiko
authors.initials: T
authors.lastname: Hanihara
authors.affiliation: 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.
authors.forename: Ken
authors.initials: K
authors.lastname: Yamamoto
authors.affiliation: Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
authors.forename: Hajime
authors.initials: H
authors.lastname: Ishida
authors.affiliation: Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, Tokyo, Japan.
authors.forename: Shuhei
authors.initials: S
authors.lastname: Mano
authors.affiliation: 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.
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Kimura
authors.affiliation: Department of Anatomy, Kitasato University School of Medicine, Kanagawa, Japan rkimura@med.u-ryukyu.ac.jp hiroki_oota@med.kitasato-u.ac.jp.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Oota
mesh_terms: D044466:Asian People; D016000:Cluster Analysis; D005260:Female; D040961:Genetic Drift; D005828:Genetics, Population; D015894:Genome, Human; D006801:Humans; D062312:Islands; D007564:Japan; D008297:Male; D010163:Paleontology; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D060047:Reproductive Isolation
keywords: Japanese archipelago; Ryukyu Islanders; demographic history; genome-wide SNPs; population structure