A trailblazing investigation of the genomes of approximately 3,200 people all over Japan is redefining our insight into the country’s ancestry. This study uncovers that the genetic background of the Japanese people is way more complex than formerly thought.
New insights into ancestry
Traditionally, there was a belief that the Japanese population came down from two major groups: the rice-farming migrants from East Asia and the indigenous Jomon- – the hunter-gatherers.

However, this recent study, led by scientists at

RIKEN

’s Center for Integrative Medical Sciences, pinpoints a third ancestral group with associations to north-east Asia, particularly the

Emishi people

. This discovery backs the “tripartite origins” theory proposed in 2021.
“Our analysis revealed Japan’s subpopulation structure on a fine scale, which is very beautifully classified according to geographical locations in the country,” elaborates Chikashi Terao, the lead researcher of the study.

Comprehensive genetic analysis
The research team carried out one of the largest genetic studies of a non-European population. They assembled the entire genomes of individuals from seven regions, spanning from Hokkaido in the north to Okinawa in the south. Utilizing

whole-genome sequencing

facilitated them to access in-depth genetic information- – approximately 3,000 times more than previous methods.
“Whole-genome sequencing gives us the chance to look at more data, which helps us find more interesting things,” Terao explains.

Mapping genetic diversity
The research investigated how different ancestral groups play a role in the genetic makeup of various regions in Japan. For example- –

Jomon ancestry

is most widespread in Okinawa, whereas western Japan highlights a stronger genetic affinity with Han Chinese, probably because of historical migration patterns.
Emishi ancestry is commonly found in northeastern Japan, uncovering distinct geographic variations in genetic heritage.
Exploring rare genetic variants
The scientists also inquired into rare genetic variants, which can offer insights into ancestry and migration patterns. Terao explains, “We reasoned that rare variants can sometimes be traced back to specific ancestral populations, and could be informative in revealing fine-scale migration patterns within Japan.”
This strategy has led to a better understanding of how certain genetic traits are allocated across the country.
Ancient DNA and modern health
The research also reviewed the genes inherited from archaic human species such as Denisovans and Neanderthals. “We are interested in why ancient genomes are integrated and kept in modern human DNA sequences”, Terao elaborated.
For instance, certain genetic markers linked to health conditions were determined, which may illuminate variations in disease susceptibility among Japanese people.
Implications for personalized medicine
The researchers offer possibilities for future advancements in personalized medicine. By organizing specific gene variants that affect health, the scientists aim to connect genetic differences with disease predisposition.
“What we’ve tried to do is to find and catalog loss-of-function gene variants that are very specific to the Japanese people,” Terao stated. This work could lead to better understanding and treatment of conditions such as chronic liver disease, hypertension, and hearing loss.
This comprehensive genetic study has provided new insights into the complexity of Japan’s ancestry, revealing the influence of a third ancestral group and highlighting the diversity within the population. The findings not only deepen our understanding of Japan’s genetic history but also have significant implications for personalized medicine, potentially improving the diagnosis and treatment of various health conditions. This research marks an important step in uncovering the intricate layers of Japan’s genetic heritage.