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Ancient DNA Analysis Highlights Three Ancestral Populations in Japan

NEW YORK – An ancient DNA analysis reaching back thousands of years has provided a more detailed view of the ancestral groups contributing to present-day populations in Japan, uncovering genetic signals from three historical populations spanning pre- and post-agricultural periods.

"[O]ur study provides a detailed look into the changing genomic profile of the people who lived in the Japanese archipelago, both before and after agricultural and technologically driven population movements ended thousands of years of isolation from the rest of the continent," the study's authors, from research centers in Ireland and Japan, wrote.

For their analysis, published in Science Advances on Friday, the investigators sequenced the genomes of a dozen ancient samples from Japan, stretching back some 8,000 years, including representatives from pre-farming populations and populations present after agriculture was introduced.

When they analyzed the sequences in combination with five published genomes representing ancient individuals from an Indigenous Jomon hunter-gatherer-fisher population and a Yayoi farming population, they saw not only Jomon and Yayoi ancestry but also additional East Asian ancestry that arrived in the so-called Kofun period within the past 1,700 years.

The genetic features appeared to coincide with significant cultural changes in the region, the team pointed out. While pottery artifacts linked to the Jomon period have been detected as far back as 16,500 years ago, for example, wet rice paddy-based agriculture has been traced back some 3,000 years to the start of the Yayoi period. On the other hand, the Kofun period has been linked to an imperial state, with additional technological advances and a central political system.

"We now know that the ancestors derived from each of the foraging, agrarian, and state-formation phases made a significant contribution to the formation of Japanese populations today," co-senior author Shigeki Nakagome, a researcher at Trinity College Dublin, said in a statement. "In short, we have an entirely new tripartite model of Japanese genomic origins — instead of the dual-ancestry model that has been held for a significant time."

The investigators started by screening 14 ancient bone or tooth samples at six archeological sites in western and central regions of Japan, ultimately subjecting 12 samples to shotgun sequencing, including nine samples from the initial, early, middle, and late Jomon period and three Kofun period samples. The genomes were analyzed alongside published genomes for two Yayoi representatives dated at 2,000 years old and three individuals from late stages of the Jomon period.

The team's nuclear genome and mitochondrial haplogroup analyses highlighted the three ancestral groups contributing to the populations in Japan, while offering clues to the origins of groups migrating into the area. In particular, the Yayoi population that introduced wet rice agriculture showed genetic ties to Korea and other parts of northeast Asia, whereas the Kofun period was marked by new East Asian ancestry.

Based on admixture patterns, the authors found that agricultural populations in the Yayoi period carried both Jomon ancestry and ancestry from northeast Asia, whereas all three ancestry groups were represented in the genomes of the Kofun individuals and in today's Japanese.

"Our data provide evidence of a tri-ancestry structure for present-day Japanese populations, refining the established dual-structure model of admixed Jomon and Yayoi origins," the authors reported, adding that "ancestors characterizing each of the Jomon, Yayoi, and Kofun cultures made a significant contribution to the formation of Japanese populations today."