Original Article

Journal of Human Genetics (2012) 57, 787–795; doi:10.1038/jhg.2012.114; published online 8 November 2012

The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations

Japanese Archipelago Human Population Genetics Consortium: Timothy Jinam18, Nao Nishida19, Momoki Hirai19, Shoji Kawamura19, Hiroki Oota19, Kazuo Umetsu19, Ryosuke Kimura19, Jun Ohashi19, Atsushi Tajima19, Toshimichi Yamamoto19, Hideyuki Tanabe19, Shuhei Mano19, Yumiko Suto19, Tadashi Kaname, Kenji Naritomi, Kumiko Yanagi, Norio Niikawa, Keiichi Omoto19, Katsushi Tokunaga19 and Naruya Saitou19 

  1. 1Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
  2. 2Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
  3. 3Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
  4. 4Laboratory of Anatomy and Physical Anthropology, Kitasato University School of Medicine, Sagamihara, Japan
  5. 5Department of Forensic Medicine, Yamagata University School of Medicine, Yamagata, Japan
  6. 6Transdisciplinary Research Organization for Subtropical and Island Studies (TRO-SIS), University of the Ryukyus, Nishihara, Japan
  7. 7Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
  8. 8Department of Human Genetics, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
  9. 9Department of Legal Medicine and Bioethics, Nagoya University School of Medicine, Nagoya, Japan
  10. 10Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, Graduate University for Advanced Studies (SOKENDAI), Hayama, Japan
  11. 11Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, Tachikawa, Tokyo, Japan
  12. 12Research Center for Radiation Emergency Medicine, National Institute of Radiological Sciences, Chiba, Japan
  13. 13Department of Medical Genetics, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
  14. 14Health Sciences University of Hokkaido, Tobetsu, Japan
  15. 15Department of Anthropology, Faculty of Science, The University of Tokyo, Tokyo, Japan
  16. 16Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
  17. 17Division of Population Genetics, National Institute of Genetics, Mishima, Japan

Correspondence: Dr N Saitou, Division of Population Genetics, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japan. E-mail: saitounr@lab.nig.ac.jp; Dr K Tokunaga, Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan. E-mail: tokunaga@m.u-tokyo.ac.jp; Dr K Omoto, Faculty of Science, Department of Anthropology, The University of Tokyo, Tokyo 113-0033, Japan. E-mail: kocolias@msg.biglobe.ne.jp

18Current address: Division of Human Genetics, National Institute of Genetics, Mishima, Japan.

19Members of the ‘Asian Archival DNA Repository Consortium’.

Received 17 March 2012; Revised 27 August 2012; Accepted 30 August 2012
Advance online publication 8 November 2012

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Abstract

The Japanese Archipelago stretches over 4000km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.

Keywords:

admixture; Ainu; Japanese Archipelago; population; Ryukyuan; SNP