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Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations

Author

Listed:
  • Kenichi Yamamoto

    (Osaka University Graduate School of Medicine
    Osaka University Graduate School of Medicine
    Osaka University Graduate School of Medicine
    Osaka University)

  • Shinichi Namba

    (Osaka University Graduate School of Medicine
    The University of Tokyo
    RIKEN Center for Integrative Medical Sciences)

  • Kyuto Sonehara

    (Osaka University Graduate School of Medicine
    The University of Tokyo
    RIKEN Center for Integrative Medical Sciences)

  • Ken Suzuki

    (Osaka University Graduate School of Medicine
    The University of Tokyo)

  • Saori Sakaue

    (Osaka University Graduate School of Medicine
    Harvard Medical School
    Harvard Medical School
    Broad Institute of MIT and Harvard)

  • Niall P. Cooke

    (Trinity College Dublin)

  • Shinichi Higashiue

    (Tokushukai Group)

  • Shuzo Kobayashi

    (Tokushukai Group
    Shonan Kamakura General Hospital)

  • Hisaaki Afuso

    (Tokushukai Group)

  • Kosho Matsuura

    (Tokushukai Group)

  • Yojiro Mitsumoto

    (Tokushukai Group)

  • Yasuhiko Fujita

    (Tokushukai Group)

  • Torao Tokuda

    (Tokushukai Group)

  • Koichi Matsuda

    (The University of Tokyo
    the University of Tokyo)

  • Takashi Gakuhari

    (Kanazawa University
    Kanazawa University)

  • Toshimasa Yamauchi

    (The University of Tokyo)

  • Takashi Kadowaki

    (Toranomon Hospital)

  • Shigeki Nakagome

    (Trinity College Dublin
    Kanazawa University
    Kanazawa University)

  • Yukinori Okada

    (Osaka University Graduate School of Medicine
    Osaka University
    The University of Tokyo
    RIKEN Center for Integrative Medical Sciences)

Abstract

The tripartite ancestral structure is a recently proposed model for the genetic origin of modern Japanese, comprising indigenous Jomon hunter-gatherers and two additional continental ancestors from Northeast Asia and East Asia. To investigate the impact of the tripartite structure on genetic and phenotypic variation today, we conducted biobank-scale analyses by merging Biobank Japan (BBJ; n = 171,287) with ancient Japanese and Eurasian genomes (n = 22). We demonstrate the applicability of the tripartite model to Japanese populations throughout the archipelago, with an extremely strong correlation between Jomon ancestry and genomic variation among individuals. We also find that the genetic legacy of Jomon ancestry underlies an elevated body mass index (BMI). Genome-wide association analysis with rigorous adjustments for geographical and ancestral substructures identifies 132 variants that are informative for predicting individual Jomon ancestry. This prediction model is validated using independent Japanese cohorts (Nagahama cohort, n = 2993; the second cohort of BBJ, n = 72,695). We further confirm the phenotypic association between Jomon ancestry and BMI using East Asian individuals from UK Biobank (n = 2286). Our extensive analysis of ancient and modern genomes, involving over 250,000 participants, provides valuable insights into the genetic legacy of ancient hunter-gatherers in contemporary populations.

Suggested Citation

  • Kenichi Yamamoto & Shinichi Namba & Kyuto Sonehara & Ken Suzuki & Saori Sakaue & Niall P. Cooke & Shinichi Higashiue & Shuzo Kobayashi & Hisaaki Afuso & Kosho Matsuura & Yojiro Mitsumoto & Yasuhiko Fu, 2024. "Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54052-0
    DOI: 10.1038/s41467-024-54052-0
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