title: Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data.
abstract: Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-gatherers known as Jomon, who are assumed to have originated in southeast Asia and lived in the Japanese archipelago greater than 10,000 years ago, admixed with an agricultural people known as Yayoi, whom were migrants from the East Asian continent 2,000-3,000 years ago. Meanwhile, some anthropologists propose that rather, morphological differences between the Jomon and Yayoi people can be explained by microevolution following the lifestyle change. To resolve this controversy, we compared three demographic models by approximate Bayesian computation using genome-wide single nucleotide polymorphism (gwSNP) data from the Ainu people who are thought to be direct descendants of indigenous Jomon. If we assume Chinese people sampled in Beijing from HapMap have the same ancestry as Yayoi, then the hybridization model is predicted to be between 29 and 63 times more likely than the replacement and transformation models, respectively. Furthermore, our data provide strong support for a model in which the Jomon lineages had population structure diversified in local areas before the admixture event. Initial divergence between the Jomon and Yayoi ancestries was dated to late Pleistocene, followed by the divergence of Jomon lineages at early Holocene. These results suggest gwSNP data provides a detailed picture of the complex hybridization model for Japanese population history.
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: Takehiro
authors.initials: T
authors.lastname: Sato
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 Anatomy, Kitasato University School of Medicine, Kanagawa, Japan.
authors.forename: Tsunehiko
authors.initials: T
authors.lastname: Hanihara
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 Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan.
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Kimura
authors.affiliation: Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, Tokyo, Japan smano@ism.ac.jp hiroki_oota@med.kitasato-u.ac.jp.
authors.forename: Shuhei
authors.initials: S
authors.lastname: Mano
authors.affiliation: Department of Anatomy, Kitasato University School of Medicine, Kanagawa, Japan smano@ism.ac.jp hiroki_oota@med.kitasato-u.ac.jp.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Oota
mesh_terms: D044466:Asian People / Q000235:genetics*; D001499:Bayes Theorem; D003710:Demography; D056726:Genetic Association Studies; D005828:Genetics, Population; D006801:Humans; D006824:Hybridization, Genetic; D007564:Japan; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide
keywords: Bayesian inference; genome-wide SNP data; origin of modern Japanese