DNA Analysis Rewrites Ancient History of Japan

A new study suggests the island’s modern populations trace their ancestry to three distinct groups, not two as previously proposed

Approximately 71 percent of modern Japanese people's ancestry comes from the newly identified Kofun period population. Shigeki Nakagome

The ancestors of modern Japanese populations hailed from three distinct groups that arrived on the island during three different periods, a new DNA analysis finds.

Previous research had identified two ancestor groups: hunter-gatherers who lived in Japan 15,000 years ago (and possibly much earlier) and farmers who migrated from East Asia starting around 900 B.C.E., reports Harry Baker for Live Science. The new findings, published in the journal Science Advances, show that a third group arrived during the Kofun period (around 300 to 700 C.E.), confirming a theory that some researchers had already raised.

“Archaeological evidence has long suggested three stages of migration, but the last one has largely been ignored,” Mikael Adolphson, a historian at the University of Cambridge who was not involved with the study, tells Live Science. “This new finding confirms what many of us knew, but it is good that we now get evidence also from the medical field.”

Evidence suggests that humans lived in Japan as early as 38,000 years ago. While little is known about these individuals, they may have been the ancestors of hunter-gatherers who created pottery during the Jōmon period, which spanned 13,000 to 300 B.C.E. A second group known as the Yayoi brought farming, including the cultivation of rice in wet areas, to Japan during the tail end of that period. As Reuters’ Will Dunham reports, modern Japanese people possess 13 and 16 percent of Jōmon and Yayoi genetic ancestry, respectively.

The researchers sequenced DNA from 12 people who lived in Japan during different time periods. Shigeki Nakagome

The new research sequenced genomes from the bones of 12 Japanese people who lived across a range of time periods. The team found that a new ancestral source arrived during the imperial Kofun period, in the first millennium C.E. Approximately 71 percent of modern Japanese people’s ancestry comes from this third population, notes Reuters.

“Researchers have been learning more and more about the cultures of the Jōmon, Yayoi and Kofun periods as more and more ancient artifacts show up, but before our research we knew relatively little about the genetic origins and impact of the agricultural transition and later state-formation phase,” says lead author Shigeki Nakagome, a genomic medicine researcher at Trinity College Dublin’s School of Medicine, in a statement.

“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,” Nakagome adds. “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 humans who arrived in Japan during the Kofun period came from East Asia and were probably related to the Han, who are the majority ethnic group in China today. This new population’s arrival coincided with the Kofun period, when Japan emerged as an imperial state that conducted military incursions into Korea and imported aspects of Chinese and Korean cultures. It’s unclear if the new migrants contributed to this transformation. 

“The Kofun individuals sequenced were not buried in keyhole-shaped mounds [reserved for high-ranking individuals], which implies that they were lower-ranking people,” Nakagome tells Live Science. “To see if this East Asian ancestry played a key role in the transition, we need to sequence people with a higher rank.”

In addition to shedding light on later migration to Japan, the genomic analysis revealed information about the lives of the Jōmon people in a much earlier era, writes Ian Randall for the Daily Mail. Between 20,000 and 15,000 years ago, rising sea levels cut off the connection between Japan and the Korean Peninsula, separating the Jōmon from other people in Asia. Around that same time, the Jōmon began creating a unique style of pottery.

Jomon pottery
Jōmon pottery Shigeki Nakagome

The new study shows that the size of the Jōmon population remained fairly steady, at just 1,000 or so people, for millennia. 

“The Indigenous Jōmon people had their own unique lifestyle and culture within Japan for thousands of years prior to the adoption of rice farming during the subsequent Yayoi period,” says study co-author Niall Cooke, a genomic researcher at Trinity, in the statement. “Our analysis clearly finds them to be a genetically distinct population with an unusually high affinity between all sampled individuals—even those differing by thousands of years in age and excavated from sites on different islands. These results strongly suggest a prolonged period of isolation from the rest of the continent.”

In contrast to much of Europe, where incoming farming peoples replaced Indigenous hunter-gatherers, the Yayoi rice farmers seem to have integrated with the Jōmon, with each contributing almost equally to the genetics of later Japanese populations.

“We are very excited about our findings on the tripartite structure of Japanese populations,” Nakagome tells Reuters. “This finding is significant in terms of rewriting the origins of modern Japanese by taking advantage of the power of ancient genomics.”

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