Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations

Kenichi Yamamoto, Shinichi Namba, Kyuto Sonehara, Ken Suzuki, Saori Sakaue, Niall P. Cooke, Shinichi Higashiue, Shuzo Kobayashi, Hisaaki Afuso, Kosho Matsuura, Yojiro Mitsumoto, Yasuhiko Fujita, Torao Tokuda, Koichi Matsuda, Takashi Gakuhari, Toshimasa Yamauchi, Takashi Kadowaki, Shigeki Nakagome () and Yukinori Okada ()
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Kenichi Yamamoto: Osaka University Graduate School of Medicine
Shinichi Namba: Osaka University Graduate School of Medicine
Kyuto Sonehara: Osaka University Graduate School of Medicine
Ken Suzuki: Osaka University Graduate School of Medicine
Saori Sakaue: Osaka University Graduate School of Medicine
Niall P. Cooke: Trinity College Dublin
Shinichi Higashiue: Tokushukai Group
Shuzo Kobayashi: Tokushukai Group
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
Takashi Gakuhari: Kanazawa University
Toshimasa Yamauchi: The University of Tokyo
Takashi Kadowaki: Toranomon Hospital
Shigeki Nakagome: Trinity College Dublin
Yukinori Okada: Osaka University Graduate School of Medicine

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-54052-0

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