DATE2026.01.14 #News

Genetic Diversity of Yayoi Populations Revealed by Ancient Genome Analysis

― Genomic Evidence for Shared Ancestry between Jomon-Related and Migrant-Related Populations in Northwestern Kyushu Yayoi Individuals ―

Summary

From the Yayoi period onward, people carrying wet-rice farming techniques migrated from continental East Asia to the Japanese archipelago. Through admixture with the indigenous Jomon people, they formed the ancestral population of present-day Japanese. Understanding how this population emerged requires genomic studies of Yayoi-period individuals, especially those from northern Kyushu, which has long been considered a major gateway for migrants from the continent. Previous morphological studies have shown that Yayoi individuals from Fukuoka Prefecture in northern Kyushu (hereafter referred to as the “Northern Kyushu Yayoi”) and from Yamaguchi Prefecture exhibit tall stature and high, elongated facial morphology, whereas Yayoi individuals from Nagasaki Prefecture in northern Kyushu (hereafter referred to as the “Northwestern Kyushu Yayoi”) are characterized by shorter stature and lower facial height and are morphologically similar to the Jomon people. However, the reasons for this morphological similarity between the Northwestern Kyushu Yayoi and the Jomon have not been fully resolved. Specifically, it remains unclear whether this similarity reflects a closer genetic affinity to the Jomon population, implying that admixture was limited in northwestern Kyushu, or whether the Northwestern Kyushu Yayoi are descendants of migrants with Jomon-like morphology whose ancestral origins differed from those of the Northern Kyushu Yayoi and the Yayoi individuals from Yamaguchi Prefecture.

A research team led by Jonghyun Kim, a doctoral student (second year) at the Department of Biological Sciences, Graduate School of Science, the University of Tokyo, together with Professor Jun Ohashi and Lecturer Fuzuki Mizuno of Toho University School of Medicine, conducted nuclear genome sequence analyses of four Northwestern Kyushu Yayoi individuals dating to approximately 2,300–2,500 years ago, excavated from the Shomura and Neshiko sites in Nagasaki Prefecture. The analyses revealed that two of the four individuals retained genomic components nearly identical to those of Jomon individuals, while the remaining two individuals possessed genomic components derived from both Jomon-related and migrant-related populations.

These results indicate that the morphological similarity between the Northwestern Kyushu Yayoi individuals and the Jomon people can be explained by their genetic affinity to the Jomon population. Furthermore, our findings suggest that the migrant populations entering Nagasaki Prefecture were likely of Korean Peninsula origin, similar to the Yayoi individuals from Yamaguchi Prefecture, and that genetic interactions between Jomon-related and migrant-related populations in this region had already begun by at least approximately 2,500–2,600 years ago. In addition, the Northwestern Kyushu Yayoi individuals were found to be genetically close to individuals dating to approximately 2,800 years ago excavated from the Nagabaka site on Miyako Island, Okinawa Prefecture. Taken together, these findings provide important insights into regional variation in the timing of migration during the Yayoi period, as well as the subsequent dynamics of genetic interactions within the Japanese archipelago.

This work was published online in Scientific Reports at 11:00 (UK time) on January 7, 2026.

This study was conducted in collaboration with Project Assistant Professor Izumi Naka of the Graduate School of Science, The University of Tokyo, Professor Emeritus Shintaroh Ueda, Director Takayuki Matsushita and Curator Masami Matsushita of the Doigahama Site Anthropological Museum, Professor Kunihiko Kurosaki of Toho University School of Medicine and Professor Fuyuki Tokanai of Center for Accelerator Mass Spectrometry, Yamagata University.

Figure：Proportions of Jomon-related and migrant-related ancestry estimated from genomic data Nuclear genome data were analyzed using an admixture-based population model to estimate the proportions of genetic components derived from Jomon-related and migrant-related populations. Because ancient genomic data corresponding to a “pure” migrant population are not available, the present analysis used genomic data from present-day Koreans as a representative proxy (reference population) for migrant-related ancestry. Note that this figure does not include two Northwestern Kyushu Yayoi individuals who possess genomic components nearly identical to those of Jomon individuals.

関連リンク

Toho University School of Medicine 、Doigahama Site Anthropological Museum、Center for Accelerator Mass Spectrometry, Yamagata University

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