Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations

Yamamoto, Kenichi; Namba, Shinichi; Sonehara, Kyuto; Suzuki, Ken; Sakaue, Saori; Cooke, P. Niall; Higashiue, Shinichi; Kobayashi, Shuzo; Afuso, Hisaaki; Matsuura, Kosho; Mitsumoto, Yojiro; Fujita, Yasuhiko; Tokuda, Torao; the Biobank Japan Project; Matsuda, Koichi; Gakuhari, Takashi; Yamauchi, Toshimasa; Kadowaki, Takashi; Nakagome, Shigeki; Okada, Yukinori

doi:https://doi.org/10.1038/s41467-024-54052-0

Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations

Yamamoto, Kenichi; Namba, Shinichi; Sonehara, Kyuto et al.

Nature Communications, 2024, 15, 9780

Number of Access:1,889（2025-07-29 17:32 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/99695

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Title	Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations
Creator	NRID 1000090875585 1000090875585 researchmap permalink KenichiYamamotoPed KenichiYamamotoPed Scopus Author ID 57204724143 57204724143 ORCID 0000-0001-9594-7050 0000-0001-9594-7050 CreatorName Yamamoto, Kenichi
	CreatorName Namba, Shinichi
	NRID 1000060975358 1000060975358 CreatorName Sonehara, Kyuto
	NRID 1000090838806 1000090838806 researchmap permalink kensuzuki kensuzuki CreatorName Suzuki, Ken
	ORCID 0000-0003-3618-9717 0000-0003-3618-9717 researchmap permalink saorisakaue saorisakaue CreatorName Sakaue, Saori
	CreatorName Cooke, P. Niall
	CreatorName Higashiue, Shinichi
	NRID 1000060195782 1000060195782 CreatorName Kobayashi, Shuzo
	CreatorName Afuso, Hisaaki
	NRID 1000090401257 1000090401257 CreatorName Matsuura, Kosho
	CreatorName Mitsumoto, Yojiro
	CreatorName Fujita, Yasuhiko
	CreatorName Tokuda, Torao
	CreatorName the Biobank Japan Project
	CreatorName Matsuda, Koichi
	NRID 1000070749530 1000070749530 CreatorName Gakuhari, Takashi
	NRID 1000040372370 1000040372370 CreatorName Yamauchi, Toshimasa
	NRID 1000030185889 1000030185889 CreatorName Kadowaki, Takashi
	NRID 1000040625208 1000040625208 CreatorName Nakagome, Shigeki
	NRID 1000070727411 1000070727411 ORCID 0000-0002-0311-8472 0000-0002-0311-8472 researchmap permalink yokada yokada Scopus Author ID 7005443464 7005443464 CreatorName Okada, Yukinori
Description	Yamamoto K., Namba S., Sonehara K., et al. Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations. Nature Communications 15, 9780 (2024); https://doi.org/10.1038/s41467-024-54052-0.
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.
Publisher	Nature Research
Source Title	Nature Communications
Volume (Issue)	15
Page	9780
Date of Issued	2024-11-12
Language	English
Handle URL	https://hdl.handle.net/11094/99695
eISSN	20411723
Relation.isIdenticalTo	DOI (Publisher Version) https://doi.org/10.1038/s41467-024-54052-0
Access Rights	open access
CopyRight	This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
oaire:version	Version of Record
Category	学術雑誌論文 Journal Article

Resource Type	journal article
Local Type	Journal Article
DCTERMS.bibliographicCitation	Nature Communications. 2024, 15, p. 9780
DC.title	Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations
DC.creator	Yamamoto, Kenichi
	Namba, Shinichi
	Sonehara, Kyuto
	Suzuki, Ken
	Sakaue, Saori
	Cooke, P. Niall
	Higashiue, Shinichi
	Kobayashi, Shuzo
	Afuso, Hisaaki
	Matsuura, Kosho
	Mitsumoto, Yojiro
	Fujita, Yasuhiko
	Tokuda, Torao
	the Biobank Japan Project
	Matsuda, Koichi
	Gakuhari, Takashi
	Yamauchi, Toshimasa
	Kadowaki, Takashi
	Nakagome, Shigeki
	Okada, Yukinori
DC.publisher	Nature Research
DC.language' scheme='DCTERMS.RFC1766	English
DCTERMS.issued' scheme='DCTERMS.W3CDTF	2024-11-12
DC.identifier	https://doi.org/10.1038/s41467-024-54052-0
DC.description	Yamamoto K., Namba S., Sonehara K., et al. Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations. Nature Communications 15, 9780 (2024); https://doi.org/10.1038/s41467-024-54052-0.
DCTERMS.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.
DC.rights	This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
DC.format	99695
citation_title	Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations
citation_author	Yamamoto, Kenichi
	Namba, Shinichi
	Sonehara, Kyuto
	Suzuki, Ken
	Sakaue, Saori
	Cooke, P. Niall
	Higashiue, Shinichi
	Kobayashi, Shuzo
	Afuso, Hisaaki
	Matsuura, Kosho
	Mitsumoto, Yojiro
	Fujita, Yasuhiko
	Tokuda, Torao
	the Biobank Japan Project
	Matsuda, Koichi
	Gakuhari, Takashi
	Yamauchi, Toshimasa
	Kadowaki, Takashi
	Nakagome, Shigeki
	Okada, Yukinori
citation_publisher	Nature Research
citation_language	English
citation_date	2024-11-12
citation_journal_title	Nature Communications
citation_volume	15
citation_firstpage	9780
citation_doi	https://doi.org/10.1038/s41467-024-54052-0
citation_public_url	https://hdl.handle.net/11094/99695

Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations

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