Ancient DNA Rewrites Early Japanese History—Modern Day Populations Have Tripartite Genetic Origin


An ancient DNA recovered from human bones rewrote early Japanese history by emphasising the tripartite genetic origins of current Japanese populations – a result that refines previously recognised perspectives on double genomic ancestry.

The genetic imprint of early indigenous Jomon-hunter-gatherer-fishermen Jomon and Yayoi-fisher immigrant peasants does indicate that 12 newly-sequenced old Japanese genomes — but also a threat genetic component connected to Kofun, whose cultures expanded in Japan from the third- to seventh centuries.

Rapid cultural transformations

The Japanese archipelago has occupied people for at least 38,000 years, but only in the last 3,000 years, Japan underwent significant transitions from foraging to wet-rice and finally to technical imperial development.


The previous longstanding hypothesis has shown that continental Japanese populations come from the Indian Jomon hunting-collecting-fishers from around 16,000 to 3,000 years ago and then farmers of Yayoi from the Asian continent, who lived in Japan from approximately 900 BC to AD 300. In Japan, they had been migrated from the Asiatic continent and they lived.

The 12 newly sequenced Japanese genomes — from the pre-farming and post-farming peoples’ bodies — also indicate a later infusion of East Asian ancestry during the imperial Kofun era, which rose in Japan from 300 to 700 A.D.

Shigeki Nakagome, Assistant Professor of Psychiatry at the Dublin School of Medicine Trinity College, was responsible for leading the research that brought together an interdisciplinary team of Japanese and Ireland academics. Nakagome Professor said:

“The Jomon, Yayoi and Kofun civilizations were more and more learnt as more and more old artefacts appeared but we understood very little about the genesis and impact of the agrarian shift and the subsequent state-building era before our research.”


“We know now that its ancestors have made an important contribution to the creation of Japanese peoples in every step of the foraging, agricultural and state formation. In short, we have a completely new tripartite model with Japanese genetic roots – not an important dual model.”

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Genomic insights into key Japanese transformations

In addition to the overall find, analyses have also shown that Jomon has maintained a small effective population size of around 1,000 over several thousand years, with a large discrepancy between continental populations from 20,000 to 15,000 years ago—a period in which Japan became geographically more insular by increasing sea levels.

Jomon pottery from the Hirajo shell midden (Late Jomon) and a skull from which ancient DNA was extracted [Credit: Shigeki Nakagome, Trinity College Dublin]
“Thousands of years before rice cultivation took place in the following Yayoi period, the indigenous Jomon people had a unique lifestyle and culture in Japan. Our analysis clearly shows that they are a genetically distinct population with a remarkably close relationship between all the sampled people — even those who are thousands of years old and excavated on different sights. “Such results clearly imply that the remainder of the continent is isolated for an extended period.”

As shown in the Neolithic transition in much of Europe, agricultural spreads are frequently defined by population replacement, with little inputs from hunter-gatherer populations seen in many places. However, genetic evidence was established indicating, during the agricultural transition in prehistoric Japan, the assimilation process was not a replacement, and the indigenous Jomon and new migrants participating in wet rice-growing had almost the same genetic contribution.

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 [Credit: Shigeki Nakagome, Trinity College Dublin]
A series of archaeological findings suggest the establishment of new major towns in Japan during the Yayoi-Kofun transition, most probably from the southern Korean peninsula. The results indicate strongly the genetic interchange that takes place in this stage of state development involves the creation of new social, cultural and political characteristics.

“In view of its remarkable pre-history of long-standing continuity and fast cultural alterations, the Japanese archipelago is particularly fascinating in the globe for studying with a period of ancient samples. Again, our insights into the complexity of modern Japanese origins reveal the strength of old genomics to reveal new information that could not otherwise be seen about prehistory “The Professor of Population Genetics, Dan Bradley, added who co-led the project to the Trinity School of Genetics and Microbiology.

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