Kamikuroiwa Rock Shelter: This site is located in Kumakogen District, Kamiukena District of Ehime Prefecture, Shikoku. It is where the oldest Jomon individual was sequenced. Credit: Shigeki Nagaome, lead researcher and assistant professor in psychiatry at Trinity College Dublin.
The ancient DNA taken from bones of human beings has changed the history of Japan. It revealed that Japan's modern-day populations have a tripartite genetic heritage. This confirms previous views that there was a dual genealogical ancestry.
Twelve newly sequenced ancient Japanese genomes show that modern day populations do indeed show the genetic signatures of early indigenous Jomon hunter-gatherer-fishers and immigrant Yayoi farmersbut also add a third genetic component that is linked to the Kofun peoples, whose culture spread in Japan between the 3rd and 7th centuries.
Rapid cultural changes
Although the Japanese archipelago is occupied by humans since at least 38,000 years ago, Japan has undergone rapid transformations in the last 3,000 year. First, it went from being foraged to wet-rice agriculture, then to an technologically advanced imperial nation.
The previous, long-standing hypothesis suggested that mainland Japanese populations derive dual-ancestry from the indigenous Jomon hunter-gatherer-fishers, who inhabited the Japanese archipelago from around 16,000 to 3,000 years ago, and later Yayoi farmers, who migrated from the Asian continent and lived in Japan from around 900 BC to 300 AD.
The 12 newly-sequenced Japanese genomes, which were derived from bones from people who lived in pre- and/or post-farming times, also identify an earlier influx of East Asian ancestry in the imperial Kofun period. This period lasted approximately 300-700 AD and saw the rise of political centralisation in Japan.
Excavated from the Odake Shell Midden (Early Jomon) were Jomon potteries. This site contained a skeleton that was buried. It had a unique burial method in which the body was placed in an upright position with bent legs. Credit: Shigeki Nagome, lead researcher and assistant professor in psychiatry at Trinity College Dublin.
Shigeki Nakagome (Assistant Professor in Psychiatry at Trinity College Dublin's School of Medicine), led the research that brought together a multidisciplinary team of researchers from Japan, Ireland, and other countries. Professor Nakagome stated:
"Researchers are learning more about the cultures and times of the Jomon, Yayoi and Kofun periods as more ancient artifacts appear. But before our research, we knew very little about the genetic origins of the agricultural transition, and the impact on the later state-formation phases.
We now know that each of the state-formation, foraging and agrarian phases contributed significantly to the creation of Japanese populations. We now have a new tripartite model of Japanese genetic origins, replacing the long-standing dual-ancestry model.
Key Japanese transformations: Genomic insights
The Jomon had a relatively small population of about 1,000 over several millennia. This was in addition to the overall discovery. It also revealed a deep divergence with continental populations that dates back to between 20,000 and 15,000 years ago. This period saw Japan become more isolated geographically due to rising sea-levels.
At the beginning of The Last Glacial Maximum (28,000 years ago), the Japanese archipelago was accessible via the Korean Peninsula, which allowed movement between. The Korea Strait's widening 16,000-17,000 years ago may have caused the isolation of the Jomon lineage. These dates also correspond with the oldest evidence for Jomon pottery production.
Jomon pottery made from Hirajo shell middens (Late Jomon), and a skull containing ancient DNA. Credit: Shigeki Nagome, Assistant Professor in Psychology, School of Medicine at Trinity College Dublin.
"The Japanese indigenous Jomon people lived a unique lifestyle and culture for thousands of years before rice farming was introduced during the Yayoi period. Their analysis clearly shows that they are a distinct genetic population, with an uncanny affinity among all samples. This is despite the fact that some of them differ by thousands of years and were excavated from different locations on islands." Niall Cooke, Ph.D. Trinity Researcher. These results strongly suggest that the continent has been isolated for a long time."
As evidenced by the Neolithic transition in most of Europe, which saw a significant increase in agriculture, there is often a process of population replacement. In many cases, however, hunter-gatherer populations made very little contribution to agricultural spread. Researchers found genetic evidence that prehistoric Japan's agricultural transition was a process of assimilation rather than replacement. They also observed almost equal genetic contributions from the native Jomon and new wet-rice farmers.
Numerous archaeological evidence supports the idea of large new settlements in Japan. These were most likely to have originated from the south Korean peninsula during the Yayoi–Kofun transition. The analyses support the strong genetic exchange that was involved in the appearance new social, political, and cultural traits during this phase of state-formation.
The Japanese archipelago is a fascinating part of the world that can be investigated using time series of ancient samples. This is due to its extraordinary prehistory of continuity and rapid cultural changes. The complex origins of the modern-day Japanese show once more the power of ancient genomes to reveal new information about human prehistory," said Dan Bradley, Professor of Population Genetics at Trinity's School of Genetics and Microbiology. He also co-led this project.
Science Advances has published the eye-opening research.
Continue reading New genetic evidence reveals the origins of modern Japanese culture
Information: Science Advances (2021): "Ancient genomes reveals tripartite roots of Japanese populations" Information from Science Advances: "Ancient genomes reveals tripartite roots of Japanese populations" (2021). www.science.org/doi/10.1126/sciadv.abh2419
