Ancient DNA Rewrites Japanese History

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Ancient DNA Rewrites Japanese History

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Genome sequencing traces Japanese ancestry to three distinct peoples.

Present-day Japanese people can track their ancestry back to three distinct genetic groups, according to a study that is rewriting our perceptions of early Japanese history.

Japan is made up of more than 6,500 individual islands that cover more than 3,000 square miles and while this vast area has been occupied for at least 38,000 years, the region underwent swift and monumental changes during the last three millennia, as its inhabitants transitioned from a hunter-gather society to wet-rice agriculture and finally to a technologically advanced state.

Historians, archaeologists and anthropologists have long believed that the ancestry of the modern Japanese people stems from two genetic groups.

The first of these two groups was the Jomon who were early indigenous hunter-gatherers inhabiting the archipelago from 16,000 to 3000 years ago.

The second was the Yayoi, farmers who migrated from the Asian continent to establish themselves on the Japanese archipelago from 900 BC to AD 300.

However, stunning research published in the leading academic journal Science Advances has now identified a third group that contributed to the genetic make-ups of modern Japanese people, exploding previous interpretations of Japanese development and forcing fresh analysis.

The people identified in the study are the Kofun, a culture that spread in Japan between the 3rd and 7th centuries AD as people migrated there from the Korean peninsula. This is around the same time as the rise of the Shinto religion in Japan and the rise to power of the Yamato Clan who eventually established the Japanese imperial throne and dynasty. 

Jomon potteries excavated from the Odake shell midden (Early Jomon). A buried skeleton in this site had a specific burial practice in which the body was placed in a flexed position with bent legs. Via Shigeki Nakagome, Lead researcher, Assistant Professor in Psychiatry, School of Medicine, Trinity College Dublin.

The links were identified through the sequencing of 12 ancient Japanese genomes from the bones of people who lived in the region before and after farming was introduced. They found that an influx of East Asian ancestry during the Kofun period contributed to the genetic makeup of Japanese people today.

“Researchers have been learning more and more about the cultures of the Jomon, Yayoi and Kofun periods as more and more ancient artefacts 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 professor of psychiatry at Trinity College Dublin’s School of Medicine.

“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. 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.”

Beyond the discovery of a three-pronged genetic origin for Japan, the team found that the Jomon hunter-gatherers sustained a small population size of around 1000 over several millennia around 20,000 to 15,000 years ago, at a time when Japan became isolated from the mainland by rising sea levels.

Kamikuroiwa rock shelter: this site is located in Kumakogen, Kamiukena District, Ehime Prefecture of Shikoku, where the oldest Jomon individual sequenced in this study was found. Credit: Shigeki

The Jomon had arrived in Japan through the Korean Peninsula at the beginning of the Last Glacial Maximum, some 28,000 years ago, but rising sea levels around 17,000 years ago isolated them from the rest of the continent. It’s from around this time that the earliest Jomon pottery is found.

“The indigenous Jomon 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,” explains Niall Cooke, a PhD researcher at Trinity College, Dublin.

“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.”

While the spread of agriculture in ancient history is often marked by wholesale population replacement, the team’s results also show that the transition to agriculture in Japan was adopted by the Jomon and that they intermingled with the newcomers – the Jomon and Yayoi peoples gave equal genetic contributions to the region’s modern-day population.

“The Japanese archipelago is an especially interesting part of the world to investigate using a time series of ancient samples given its exceptional prehistory of long-standing continuity followed by rapid cultural transformations,” says co-author Dan Bradley, a professor of population genetics in Trinity’s School of Genetics and Microbiology.

“Our insights into the complex origins of modern-day Japanese people once again shows the power of ancient genomics to uncover new information about human prehistory that could not be seen otherwise.” 

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