Dataset Information

Mitochondrial genome variation in eastern Asia and the peopling of Japan.

ABSTRACT: 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.

SUBMITTER: Tanaka M

PROVIDER: S-EPMC524407 | biostudies-literature | 2004 Oct

REPOSITORIES: biostudies-literature

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Publications

Mitochondrial genome variation in eastern Asia and the peopling of Japan.

Tanaka Masashi M Cabrera Vicente M VM González Ana M AM Larruga José M JM Takeyasu Takeshi T Fuku Noriyuki N Guo Li-Jun LJ Hirose Raita R Fujita Yasunori Y Kurata Miyuki M Shinoda Ken-ichi K Umetsu Kazuo K Yamada Yoshiji Y Oshida Yoshiharu Y Sato Yuzo Y Hattori Nobutaka N Mizuno Yoshikuni Y Arai Yasumichi Y Hirose Nobuyoshi N Ohta Shigeo S Ogawa Osamu O Tanaka Yasushi Y Kawamori Ryuzo R Shamoto-Nagai Masayo M Maruyama Wakako W Shimokata Hiroshi H Suzuki Ryota R Shimodaira Hidetoshi H

Genome research 20041001 10A

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, ...[more]

PMID: 15466285

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Project description:There is considerable ethno-linguistic and genetic variation among human populations in Asia, although tracing the origins of this diversity is complicated by migration events. Thailand is at the center of Mainland Southeast Asia (MSEA), a region within Asia that has not been extensively studied. Genetic substructure may exist in the Thai population, since waves of migration from southern China throughout its recent history may have contributed to substantial gene flow. Autosomal SNP data were collated for 438,503 markers from 992 Thai individuals. Using the available self-reported regional origin, four Thai subpopulations genetically distinct from each other and from other Asian populations were resolved by Neighbor-Joining analysis using a 41,569 marker subset. Using an independent Principal Components-based unsupervised clustering approach, four major MSEA subpopulations were resolved in which regional bias was apparent. A major ancestry component was common to these MSEA subpopulations and distinguishes them from other Asian subpopulations. On the other hand, these MSEA subpopulations were admixed with other ancestries, in particular one shared with Chinese. Subpopulation clustering using only Thai individuals and the complete marker set resolved four subpopulations, which are distributed differently across Thailand. A Sino-Thai subpopulation was concentrated in the Central region of Thailand, although this constituted a minority in an otherwise diverse region. Among the most highly differentiated markers which distinguish the Thai subpopulations, several map to regions known to affect phenotypic traits such as skin pigmentation and susceptibility to common diseases. The subpopulation patterns elucidated have important implications for evolutionary and medical genetics. The subpopulation structure within Thailand may reflect the contributions of different migrants throughout the history of MSEA. The information will also be important for genetic association studies to account for population-structure confounding effects.

Dataset Information

Mitochondrial genome variation in eastern Asia and the peopling of Japan.

Publications

Mitochondrial genome variation in eastern Asia and the peopling of Japan.

Similar Datasets

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