Traces of ancient immigration patterns to Japan found in 2,000-year-old genome

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A joint research group led by Jonghyun Kim and Jun Ohashi of the University of Tokyo has demonstrated that the majority of immigration to the Japanese Archipelago in the Yayoi and Kofun periods (between 3000 BCE and 538 CE) came from the Korean Peninsula.

The researchers analyzed the complete genome of a "Yayoi" individual and found that, among the non-Japanese populations, the results bore the most similarity to Korean populations. Although it is widely accepted that modern Japanese populations have a dual ancestry, the discovery provides insight into the details of immigration patterns to the archipelago that have eluded scientists thus far.

The findings were published in the Journal of Human Genetics.

Today, Japan is an international hub for both business and pleasure. However, this was not always the case. The Japanese Archipelago was relatively isolated during the Jomon period until around 3000 BCE. Then, during the Yayoi and Kofun periods, immigration to the islands from continental Asia began.

"East Asian-related and Northeast Asian-related ancestries account for over 80% of nuclear genomes of the modern Japanese population," explains Ohashi, the principal investigator of the study. "However, how the Japanese population acquired these genetic ancestries—that is, the origins of the immigration—is not fully understood."

Various theories have been proposed to explain the genetic variety in the modern population. Currently, the two contenders are the two-way and three-way admixture models. According to the two-way model, the main source of immigration was the same during the Yayoi and Kofun periods, while the three-way model assumes two different sources.

To investigate which model was the better fit, the researchers analyzed the complete nuclear genome of an individual from the Doigahama Site, the archaeological site of a Yayoi period cemetery in Yamaguchi prefecture, Japan.

The researchers compared the genome of this Yayoi-period individual with the genome of ancient and modern populations in East Asia and Northeast Asia.

The comparison showed close similarity to Kofun period individuals with distinct Jomon-related, East Asian-related, and Northeast Asian-related ancestries. However, a comparison with modern genomes also revealed that the Yayoi individual, except for modern Japanese populations, was the closest to modern Korean populations, which also have both East Asian-related and Northeast Asian-related ancestries.

"Our results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula," says Ohashi. "The results also mean the three-way admixture model, which posits that a Northeast Asian group migrated to the Japanese Archipelago during the Yayoi period and an East Asian group during the Kofun period, is incorrect."

Despite the significance of these findings, Ohashi is already looking ahead.

"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."

More information: 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 (2024). DOI: 10.1038/s10038-024-01295-w

Provided by University of Tokyo