Journal of Human Genetics

, Volume 49, Issue 4, pp 187–193 | Cite as

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

  • Atsushi Tajima
  • Masanori Hayami
  • Katsushi Tokunaga
  • Takeo Juji
  • Masafumi Matsuo
  • Sangkot Marzuki
  • Keiichi Omoto
  • Satoshi HoraiEmail author
Original Article


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 



We thank Dr. P.A. Underhill for helpful comments on our newly discovered Y-markers. This work was supported in part by Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology of Japan to S. Horai.


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Copyright information

© The Japan Society of Human Genetics and Springer-Verlag 2004

Authors and Affiliations

  • Atsushi Tajima
    • 1
  • Masanori Hayami
    • 2
  • Katsushi Tokunaga
    • 3
  • Takeo Juji
    • 4
  • Masafumi Matsuo
    • 5
  • Sangkot Marzuki
    • 6
  • Keiichi Omoto
    • 7
  • Satoshi Horai
    • 1
    Email author
  1. 1.Department of Biosystems ScienceThe Graduate University for Advanced Studies (Sokendai)HayamaJapan
  2. 2.Laboratory of Viral PathogenesisInstitute for Virus Research, Kyoto UniversityKyotoJapan
  3. 3.Department of Human GeneticsGraduate School of Medicine, University of TokyoTokyoJapan
  4. 4.Japanese Red Cross Central Blood CenterTokyoJapan
  5. 5.Division of Pediatrics, Department of Development and AgingKobe University Graduate School of MedicineKobeJapan
  6. 6.Eijkman Institute for Molecular BiologyJakartaIndonesia
  7. 7.St. Andrew’s UniversityOsakaJapan

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