The tripartite origins theory of Japanese populations from ancient genomic analysis challenges the established dual-structure model

Based on ancient genomic analysis of human remains from the Jomon, Yayoi, and Kofun Ages –from 9000 B.P. to 1300 B.P. – this research team, including Professor Naoto Tomioka, Okayama University of Science, has uncovered evidence that modern Japanese people trace their ancestry to three genomic groups from the mainland. The findings were published in “Science Advances”7(38).
This research group also included, Niall P. Cooke of the School of Medicine at Trinity College Dublin, Takashi Gakuhari, and Shigeki Nakagome of the Institute for the Study of Ancient Civilizations and Cultural Resources at Kanazawa University’s College of Human and Social Sciences. Other contributors included Daniel Bradley of Trinity College Dublin, Kenji Okazaki of Tottori University, and Kenji Kasai of the Toyama Prefectural Center for Archaeological Operations, among others.
This team analyzed genomes from 12 individuals unearthed at six Prehistoric Japanese archaeological sites: the Kamikuroiwa cave (Initial Jomon period, Kuma Kogen Town, Ehime Prefecture), Odake Shell Midden (Early Jomon period, Toyama City), Funagura Shell Midden (Early Jomon period, Kurashiki City, Okayama Prefecture), Kosaku Shell Midden (Late Jomon period, Funabashi City, Chiba Prefecture), Hirajo Shell Midden (Late Jomon period, Ainan Town, Ehime Prefecture), and the Iwade Tunnel Tomb (Final Kofun, Kanazawa-City). These were compared with genomic data from previously reported archaeological remains in Japan and mainland sites.
The results revealed that the ancestors of the Jomon people migrated from a basal continental population around 20,000 to 15,000 years ago, forming a small group of approximately 1,000 individuals. During the Yayoi period, groups of Northeast Asian origin migrated to Japan, followed by additional migrations from East Asian populations during the Kofun period. Each wave of migration involved genetic mixing with the local populations.
These findings provide robust evidence suggesting that two distinct waves of genetically different populations from the mainland migrated to Japan by the Kofun period, integrating with the indigenous Jomon people who had separated from a basal continental population. The research team proposed a new "triple-structure model" as an alternative to the long-standing "dual-structure model." This study represents a groundbreaking achievement, offering a scientifically backed perspective on the ancestry of the Japanese people and presenting a new hypothesis. However, the number of ancient human skeletal genome samples remains limited, and further analyses are required to strengthen the findings. Studies conducted by RIKEN and other institutions have supported the triple-structure model based on large-scale genomic data from modern Japanese populations.