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Letter

Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan

¹ Department of Gene Therapy, Gifu International Institute of Biotechnology, Kakamigahara, Gifu 504-0838, Japan ² Department of Genetics, Faculty of Biology, University of La Laguna, Tenerife 38271, Spain ³ Department of Sports Medicine, Graduate School of Medicine, Nagoya University, Nagoya 464-8601, Japan ⁴ Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan ⁵ Department of Anthropology, National Science Museum, Tokyo 169-0073, Japan ⁶ Department of Forensic Medicine, Yamagata University School of Medicine, Yamagata 990-9585, Japan ⁷ Department of Human Functional Genomics, Life Science Research Center, Mie University, Tu-shi, Mie 514-8507, Japan ⁸ Department of Neurology, Metabolism and Endocrinology, Juntendo University School of Medicine, Tokyo 113-8421, Japan ⁹ Department of Medicine, Metabolism and Endocrinology, Juntendo University School of Medicine, Tokyo 113-8421, Japan ¹⁰ Department of Geriatric Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan ¹¹ Department of Biochemistry and Cell Biology, Institute of Gerontology, Nihon Medical School, Kawasaki 211-8533, Japan ¹² Laboratory of Biochemistry and Metabolism, Department of Basic Gerontology, National Institute for Longevity Sciences, Obu 474-8522, Japan ¹³ Department of Epidemiology, National Institute for Longevity Sciences, Obu 474-8522, Japan ¹⁴ Department of Mathematical and Computing Sciences, Tokyo Institute of Technology, Tokyo 152-8552, Japan

To construct an East Asia mitochondrial DNA (mtDNA) phylogeny, we sequenced the complete mitochondrial genomes of 672 Japanese individuals (http://www.giib.or.jp/mtsnp/index_e.html). This allowed us to perform a phylogenetic analysis with a pool of 942 Asiatic sequences. New clades and subclades emerged from the Japanese data. On the basis of this unequivocal phylogeny, we classified 4713 Asian partial mitochondrial sequences, with <10% ambiguity. Applying population and phylogeographic methods, we used these sequences to shed light on the controversial issue of the peopling of Japan. Population-based comparisons confirmed that present-day Japanese have their closest genetic affinity to northern Asian populations, especially to Koreans, which finding is congruent with the proposed Continental gene flow to Japan after the Yayoi period. This phylogeographic approach unraveled a high degree of differentiation in Paleolithic Japanese. Ancient southern and northern migrations were detected based on the existence of basic M and N lineages in Ryukyuans and Ainu. Direct connections with Tibet, parallel to those found for the Y-chromosome, were also apparent. Furthermore, the highest diversity found in Japan for some derived clades suggests that Japan could be included in an area of migratory expansion to Continental Asia. All the theories that have been proposed up to now to explain the peopling of Japan seem insufficient to accommodate fully this complex picture.

[Supplemental material is available online at www.genome.org.]

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2286304.

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