New genetic study unveils complex ancestral origins of Japanese people

A groundbreaking study examining the genomes of roughly 3,200 individuals across Japan has provided fresh insights into the country's complex genetic background.

This new research, conducted by scientists at RIKEN's Center for Integrative Medical Sciences, challenges the long-held belief that Japan's ancestry derived primarily from two groups: the Jomon, indigenous hunter-gatherers, and rice-farming migrants from East Asia. Instead, the study has identified a third ancestral group with roots in northeast Asia, specifically linked to the Emishi people.

This discovery supports the "tripartite origins" theory first proposed in 2021.

"Our analysis uncovered Japan's subpopulation structure at an unprecedented level of detail, aligning beautifully with the country's geographic regions," said Chikashi Terao, the study's lead researcher.

The team conducted one of the most comprehensive genetic studies of a non-European population to date, using whole-genome sequencing to assemble the complete genomes of individuals from seven regions across Japan, ranging from Hokkaido in the north to Okinawa in the south. This method provided approximately 3,000 times more genetic data than previous approaches, offering deeper insights into the nation's ancestry.

The study revealed how various ancestral groups contribute differently to the genetic makeup of Japan's regions. For instance, Jomon ancestry is most prominent in Okinawa, while western Japan shows a closer genetic relationship to Han Chinese populations, likely due to historical migration. In northeastern Japan, the Emishi influence is more pronounced, highlighting regional variations in genetic heritage.

By examining rare genetic variants, the researchers traced specific ancestral lineages and migration patterns within Japan. This approach also helped uncover genes inherited from archaic human species such as Denisovans and Neanderthals. The team was particularly interested in how these ancient genomes have persisted in modern Japanese DNA and how they may affect health traits today.

The findings have significant implications for personalized medicine.

By cataloging genetic variants unique to the Japanese population, the researchers hope to connect certain gene markers to health conditions like chronic liver disease, hypertension, and hearing loss. "Our goal is to identify loss-of-function gene variants that are specific to the Japanese people," Terao explained, paving the way for more targeted diagnosis and treatment options in the future.