Two ancient skeletons unearthed in Japan are giving scientists a rare, detailed look at how prehistoric population shifts shaped the genetic makeup of modern Japan.
A new study, led by Koji Ishiya of Kanazawa University’s Institute for the Study of Ancient Civilizations and Cultural Resources, sequenced two of the highest quality ancient genomes ever recovered from the Japanese mainland, offering fresh evidence of how two very different ancient groups contributed to the people who live there today.
The genomes came from an individual known as IY1, who lived during the Initial Jomon period roughly 8,200 to 8,300 years ago, and an individual known as DO, who lived during the Middle Yayoi period about 2,300 years ago. Both sets of remains were pulled from petrous bones, the dense part of the skull that tends to preserve DNA well.
Researchers said the sequencing reached unusually high coverage levels, nearly 68-fold for IY1 and almost 47-fold for DO, allowing for a level of genetic detail that older, lower-quality samples could not provide.
Prehistoric population divides trace two distinct paths in Japan
The results showed the two individuals came from strikingly different genetic backgrounds. IY1, representing the indigenous hunter-gatherer Jomon culture, showed little genetic connection to mainland Asia, aside from a link to an ancient individual found on the Korean Peninsula.
DO, by contrast, carried genetic markers tying him closely to populations from Northeast Asia, including groups from the Mongolian plateau and the Shandong region of China, reflecting the wave of continental migration associated with the rise of rice farming during the Yayoi period.
The two groups also appear to have followed very different population paths after the last Ice Age. According to the study, Jomon ancestors remained relatively small and stable in number for thousands of years, while the ancestors of the Yayoi population grew steadily larger over time, a pattern researchers linked to differences in lifestyle and food gathering.
Ancient gene copies point to early starch-rich diets
One of the more unexpected findings involved a gene tied to starch digestion. The Jomon individual carried about nine copies of the AMY1 gene, which helps the body break down starchy foods, while the Yayoi individual carried about ten.
Ishiya said this suggests that a genetic adaptation for eating starch-rich foods, such as walnuts and chestnuts, was already present in Japan before rice farming became widespread, challenging the idea that this trait developed mainly because of agriculture.
The findings, published in the journal Anthropology, add rare high-resolution evidence to a period of Japanese history that has remained difficult to study because of poor DNA preservation on the mainland.
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