Genetic Evidence Reveals Ancient Migration to Japan
Yayoi Genome Analysis Links Early Japanese Populations to Immigrants from the Korean Peninsula
A groundbreaking genetic study led by Jonghyun Kim and Jun Ohashi at the University of Tokyo has unveiled new insights into the immigration patterns that shaped Japan’s population during the Yayoi (3000 BCE - 300 CE) and Kofun periods (300 - 538 CE). Through the analysis of a complete genome from an individual of the Yayoi period, researchers have provided evidence linking the majority of ancient immigrants to the Japanese Archipelago directly to the Korean Peninsula. The findings offer clarity on how Japan’s dual genetic ancestry emerged, enriching the current understanding of ancient East Asian migration.
The study was published in the Journal of Human Genetics1 and offers a refined perspective on the genetic diversity and ancestral composition of modern Japanese populations, which have long been thought to derive from two primary sources: the indigenous Jomon people and continental Asian migrants.
Genetic Insights into Ancient Japanese Populations
Historically, Japan was largely isolated during the Jomon period. However, the introduction of agriculture and the onset of the Yayoi period marked significant demographic shifts. Increased contact with continental Asia, particularly the Korean Peninsula, led to waves of immigration that fundamentally transformed the region’s demographic composition. Principal investigator Jun Ohashi,
"East Asian-related and Northeast Asian-related ancestries account for over 80% of nuclear genomes of the modern Japanese population.”
Despite this, details regarding the origins and timing of these ancestral migrations have remained elusive until now.
Testing Migration Models: Two-Way vs. Three-Way Admixture
The study assessed two competing models explaining Japan's genetic composition: the two-way and three-way admixture models. The two-way model suggests a singular source of migration during both the Yayoi and Kofun periods, while the three-way model proposes two distinct sources. To resolve this, the researchers analyzed the genome of a Yayoi-period individual from the Doigahama Site in Yamaguchi Prefecture.
The genetic data showed that the Yayoi individual’s genome was closely related to both ancient and modern Korean populations. The comparison also revealed significant genetic overlap with Kofun period individuals, who displayed distinct genetic components: Jomon-related, East Asian-related, and Northeast Asian-related ancestries. However, when compared with modern genomes, the Yayoi individual's genetic markers were most similar to modern Korean populations. Ohashi says,
“Our results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula.”
This finding directly challenges the three-way admixture model, which proposed that two separate waves from Northeast and East Asia arrived at different times.
Shaping the Modern Japanese Genome
The new evidence supports the idea that the Korean Peninsula was the primary source of migration during both periods, reinforcing the two-way model of population admixture. Ohashi notes that understanding this genetic foundation is vital for interpreting how modern Japanese populations evolved.
Despite these findings, further research remains critical. Ohashi says,
“Since our study has identified the primary origins of the immigrants, our next goal is to examine the genomes of more Yayoi individuals to clarify why more than 80% of the genomic components of the modern Japanese population are derived from immigration and how the admixture between continental Asian and indigenous Jomon people progressed within the Japanese Archipelago.”
By expanding the genetic dataset, the team aims to reconstruct the intricate narrative of how different groups integrated and influenced the formation of modern Japan's genetic landscape. The work highlights how ancient migration shaped not just the genetic but also the cultural fabric of the Japanese Archipelago, offering fresh perspectives on the interconnectedness of early East Asian societies.
Kim, J., Mizuno, F., Matsushita, T., Matsushita, M., Aoto, S., Ishiya, K., Kamio, M., Naka, I., Hayashi, M., Kurosaki, K., Ueda, S., & Ohashi, J. (2024). Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago. Journal of Human Genetics, 1–11. https://doi.org/10.1038/s10038-024-01295-w