Original Article

Journal of Human Genetics (2004) 49, 187–193; doi:10.1007/s10038-004-0131-x

Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages

Atsushi Tajima1, Masanori Hayami2, Katsushi Tokunaga3, Takeo Juji4, Masafumi Matsuo5, Sangkot Marzuki6, Keiichi Omoto7 and Satoshi Horai1

  1. 1Department of Biosystems Science, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan
  2. 2Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Japan
  3. 3Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
  4. 4Japanese Red Cross Central Blood Center, Tokyo, Japan
  5. 5Division of Pediatrics, Department of Development and Aging, Kobe University Graduate School of Medicine, Kobe, Japan
  6. 6Eijkman Institute for Molecular Biology, Jakarta, Indonesia
  7. 7St. Andrew's University, Osaka, Japan

Correspondence: Satoshi Horai, Department of Biosystems Science, The Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan. Fax: +81-46-8581544. E-mail: horai@soken.ac.jp

Received 10 November 2003; Accepted 13 January 2004; Published online 2 March 2004.



The Ainu, a minority ethnic group from the northernmost island of Japan, was investigated for DNA polymorphisms both from maternal (mitochondrial DNA) and paternal (Y chromosome) lineages extensively. Other Asian populations inhabiting North, East, and Southeast Asia were also examined for detailed phylogeographic analyses at the mtDNA sequence type as well as Y-haplogroup levels. The maternal and paternal gene pools of the Ainu contained 25 mtDNA sequence types and three Y-haplogroups, respectively. Eleven of the 25 mtDNA sequence types were unique to the Ainu and accounted for over 50% of the population, whereas 14 were widely distributed among other Asian populations. Of the 14 shared types, the most frequently shared type was found in common among the Ainu, Nivkhi in northern Sakhalin, and Koryaks in the Kamchatka Peninsula. Moreover, analysis of genetic distances calculated from the mtDNA data revealed that the Ainu seemed to be related to both the Nivkhi and other Japanese populations (such as mainland Japanese and Okinawans) at the population level. On the paternal side, the vast majority (87.5%) of the Ainu exhibited the Asian-specific YAP+ lineages (Y-haplogroups D-M55* and D-M125), which were distributed only in the Japanese Archipelago in this analysis. On the other hand, the Ainu exhibited no other Y-haplogroups (C-M8, O-M175*, and O-M122*) common in mainland Japanese and Okinawans. It is noteworthy that the rest of the Ainu gene pool was occupied by the paternal lineage (Y-haplogroup C-M217*) from North Asia including Sakhalin. Thus, the present findings suggest that the Ainu retain a certain degree of their own genetic uniqueness, while having higher genetic affinities with other regional populations in Japan and the Nivkhi among Asian populations.


Ainu, Genetic origins, Mitochondrial DNA, Y chromosome, DNA polymorphisms


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