The Japanese archipelago, which has been occupied by humans for at least 38,000 years, underwent rapid transformations in the past 3,000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis suggested that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers, who inhabited the Japanese archipelago from around 16,000 to 3,000 years ago, and succeeding Yayoi farmers, who migrated from the Asian continent and lived in Japan from around 900 BCE to 300 CE. In new research, scientists from Japan and Ireland identified a later influx of East Asian ancestry during the imperial Kofun period, which lasted from around 300 to 700 CE and which saw the emergence of political centralization in Japan.
Japanese samurai in armor, print by Kusakabe Kimbei, 1870s. Image credit: Getty’s Open Content Program.
“Researchers have been learning more and more about the cultures of the Jomon, 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,” said Professor Shigeki Nakagome, a researcher in the School of Medicine at Trinity College Dublin.
“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.”
In their new research, the authors sequenced 12 ancient Japanese genomes spanning 8,000 years of the Japanese archipelago’s pre- and protohistory.
“To our knowledge, this is the largest set of time-stamped genomes from the archipelago, including the oldest Jomon individual and the first genomic data from the imperial Kofun period,” they said.
“We also included five published prehistoric Japanese genomes in our analysis: three Jomon individuals as well as two 2,000-year-old individuals associated with the Yayoi culture from the northwestern part of Kyushu Island.”
In addition to the overarching discovery, the researchers found that the Jomon maintained a small effective population size of around 1,000 over several millennia, with a deep divergence from continental populations dated to 20,000-15,000 years ago — a period which saw Japan become more geographically insular through rising sea-levels.
The Japanese archipelago had become accessible through the Korean Peninsula at the beginning of the Last Glacial Maximum, some 28,000 years ago, enabling movement between.
And the widening of the Korea Strait 16,000 to 17,000 years ago due to rising sea-levels may have led to the subsequent isolation of the Jomon lineage from the rest of the continent.
These time frames also coincide with the oldest evidence of Jomon pottery production.
“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,” said first author Dr. Niall Cooke, also from the School of Medicine 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.”
The spread of agriculture is often marked by population replacement, as documented in the Neolithic transition throughout most of Europe, with only minimal contributions from hunter-gatherer populations observed in many regions.
However, the scientists found genetic evidence that the agricultural transition in prehistoric Japan involved the process of assimilation, rather than replacement, with almost equal genetic contributions from the indigenous Jomon and new immigrants associated with wet-rice farming.
Several lines of archaeological evidence support the introduction of new large settlements to Japan, most likely from the southern Korean Peninsula, during the Yayoi-Kofun transition.
And the analyses provide strong support for the genetic exchange involved in the appearance of new social, cultural, and political traits in this state-formation phase.
“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,” said co-author Professor Dan Bradley, a researcher in the School of Genetics and Microbiology at Trinity College Dublin.
“Our insights into the complex origins of modern-day Japanese once again shows the power of ancient genomics to uncover new information about human prehistory that could not be seen otherwise.”
The team’s results were published in the journal Science Advances.
_____
Niall P. Cooke et al. 2021. Ancient genomics reveals tripartite origins of Japanese populations. Science Advances 7 (38); doi: 10.1126/sciadv.abh2419
