Ancient DNA extracted from human bones has rewritten early Japanese history by highlighting the fact that modern-day Japanese populations have a tripartite genetic origin, refining previously held views of a dual genomic ancestry.
Twelve newly sequenced ancient Japanese genomes reveal that modern-day populations share the genetic signatures of early indigenous Jomon hunter-gatherer-fishers and immigrant Yayoi farmers, but also add a third genetic component linked to the Kofun peoples, whose culture spread throughout Japan between the third and seventh centuries.
Rapid cultural shifts are occurring
Humans have lived on the Japanese archipelago for at least 38,000 years, but it was only in the last 3,000 years that Japan underwent rapid transformations, first from foraging to wet-rice farming, and then to a technologically advanced imperial state.
The previous, long-held hypothesis suggested that mainland Japanese populations are descended from indigenous Jomon hunter-gatherer-fishers who lived in the Japanese archipelago from 16,000 to 3,000 years ago, and later Yayoi farmers who migrated from Asia and lived in Japan from around 900 BC to 300 AD.
However, the 12 newly sequenced ancient Japanese genomes — which came from the bones of people who lived before and after farming — also reveal a later influx of East Asian ancestry during the imperial Kofun period, which lasted from around 300 to 700 AD and saw the emergence of political centralisation in Japan.
Shigeki Nakagome, Assistant Professor of Psychiatry at Trinity College Dublin’s School of Medicine, led the study, which brought together an interdisciplinary team of Japanese and Irish researchers. Professor Nakagome expressed his thoughts as follows:
“As more ancient artifacts are discovered, researchers are learning more about the cultures of the Jomon, Yayoi, and Kofun periods, but we knew relatively little about the genetic origins and impact of the agricultural transition and later state-formation phase before our research.”
“We now know that ancestors from each of the foraging, agrarian, and state-formation stages contributed significantly to the establishment of today’s Japanese people; in short, we have an altogether new tripartite model of Japanese genomic origins — rather than the long-held dual-ancestry model.”
Insights into key Japanese transformations from a genomic perspective
In addition to the overarching finding, the analyses revealed that the Jomon maintained a small effective population size of around 1,000 for millennia, with a significant divergence from continental populations dating from 20,000-15,000 years ago — a period during which Japan became more geographically isolated due to rising sea levels.
At the start of the Last Glacial Maximum, 28,000 years ago, the Japanese archipelago became accessible through the Korean Peninsula, allowing movement between them. The isolation of the Jomon lineage from the rest of the continent may have resulted from the widening of the Korea Strait due to rising sea levels 16,000 to 17,000 years ago. These dates correspond to the earliest 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. 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,” explained Niall Cooke, PhD Researcher at Trinity. “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 researchers 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. 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,” added Dan Bradley, Professor of Population Genetics in Trinity’s School of Genetics and Microbiology, who co-led the project.