Original Article | Published:

Unique characteristics of the Ainu population in Northern Japan

Journal of Human Genetics volume 60, pages 565571 (2015) | Download Citation

Abstract

Various genetic data (classic markers, mitochondrial DNAs, Y chromosomes and genome-wide single-nucleotide polymorphisms (SNPs)) have confirmed the coexistence of three major human populations on the Japanese Archipelago: Ainu in Hokkaido, Ryukyuans in the Southern Islands and Mainland Japanese. We compared genome-wide SNP data of the Ainu, Ryukyuans and Mainland Japanese, and found the following results: (1) the Ainu are genetically different from Mainland Japanese living in Tohoku, the northern part of Honshu Island; (2) using Ainu as descendants of the Jomon people and continental Asians (Han Chinese, Koreans) as descendants of Yayoi people, the proportion of Jomon genetic component in Mainland Japanese was ~18% and ~28% in Ryukyuans; (3) the time since admixture for Mainland Japanese ranged from 55 to 58 generations ago, and 43 to 44 generations ago for the Ryukyuans, depending on the number of Ainu individuals with varying rates of recent admixture with Mainland Japanese; (4) estimated haplotypes of some Ainu individuals suggested relatively long-term admixture with Mainland Japanese; and (5) highly differentiated genomic regions between Ainu and Mainland Japanese included EDAR and COL7A1 gene regions, which were shown to influence macroscopic phenotypes. These results clearly demonstrate the unique status of the Ainu and Ryukyuan people within East Asia.

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Acknowledgements

We thank Japanese Archipelago Human Population Genetics Consortium and Asian DNA Repository Consortium for permission of access to SNP data. This study was supported by a SOKENDAI Grant on modern human dispersal. Finally, we appreciate people on the Japanese Archipelago (Ainu, Ryukyuan and Mainland Japanese) who kindly donated their DNA to this and past anthropological studies.

Author information

Affiliations

  1. Division of Population Genetics, National Institute of Genetics, Mishima, Japan

    • Timothy A Jinam
    •  & Naruya Saitou
  2. Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan

    • Timothy A Jinam
    • , Hideaki Kanzawa-Kiriyama
    • , Ituro Inoue
    •  & Naruya Saitou
  3. Division of Human Genetics, National Institute of Genetics, Mishima, Japan

    • Timothy A Jinam
    •  & Ituro Inoue
  4. Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan

    • Hideaki Kanzawa-Kiriyama
  5. Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan

    • Katsushi Tokunaga
  6. Department of Anthropology, Faculty of Science, The University of Tokyo, Tokyo, Japan

    • Keiichi Omoto
  7. Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan

    • Naruya Saitou

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Competing interests

The authors declare no conflict of interest.

Corresponding author

Correspondence to Naruya Saitou.

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DOI

https://doi.org/10.1038/jhg.2015.79

Supplementary Information accompanies the paper on Journal of Human Genetics website (http://www.nature.com/jhg)

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