For decades, scientists thought the Japanese population came from two main groups. These were the Jomon hunter-gatherers and later migrants from East Asia. These migrants brought rice farming and new tools.
However, new research from RIKEN's Center for Integrative Medical Sciences shows a more complex story. A large genetic study found evidence for a third ancestral group. This group is linked to northeastern Asia and possibly the ancient Emishi people.
The findings were published in Science Advances. They support the idea that Japanese ancestry has three main sources. The study also showed that Japan's population is more genetically diverse than many believed.
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Start Your News DetoxChikashi Terao, who led the study, noted that the Japanese population is not as uniform as people think. The analysis revealed clear genetic differences based on geography.
Mapping Japan's DNA
Researchers looked at DNA from over 3,200 people across seven regions of Japan. This was one of the largest whole-genome studies on a non-European group.
The team used whole-genome sequencing. This method reads almost all three billion DNA base pairs in a person's genome. This gives about 3,000 times more information than older methods.
Terao explained that more data helps them find more interesting things.
The scientists then combined this genetic data with medical histories and other health information. This created a large database called the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL).
They focused on rare genetic changes. These changes can offer clues about ancient migration patterns and lost ancestral groups.
A Hidden Third Ancestor
The study found clear regional differences in Japan's DNA.
Jomon ancestry was strongest in Okinawa, found in 28.5% of samples. In western Japan, it was much lower at 13.4%. People in western Japan had stronger genetic links to Han Chinese populations. This likely comes from major migrations from East Asia between 250 and 794 CE. These migrations also brought Chinese-style government and education.
The newly found Emishi-related ancestry was mostly in northeastern Japan. It became less common further west.
These findings support earlier studies from 2021. Those studies first suggested that modern Japanese people came from three main ancestral sources, not two. They proposed that a third migration during the Kofun period was important.
Recent studies have continued to back this idea. Researchers looking at ancient DNA and bones have found more evidence of multiple migration waves into Japan over centuries. This created a more layered population history.
Ancient DNA Still Affects Health
The study also looked at DNA from Neanderthals and Denisovans. These ancient human groups mixed with Homo sapiens long ago.
Scientists are curious why some of this ancient DNA remains in modern humans. Often, these inherited genes are linked to health, adaptation, or disease risk.
For example, Tibetans inherited a Denisovan-related gene that may help them live in high altitudes. Also, Neanderthal DNA has been linked to severe COVID-19 in some people.
The Japanese study found 44 ancient DNA regions still present in modern Japanese people. Many of these are unique to East Asians. One Denisovan-derived region was linked to type 2 diabetes. It might affect how some patients respond to certain treatments.
Researchers also found 11 Neanderthal-derived genetic segments. These were connected to conditions like coronary artery disease, prostate cancer, and rheumatoid arthritis.
Moving Towards Personalized Medicine
Beyond tracing ancestry, this research could improve healthcare.
The team found potentially harmful variants in the PTPRD gene. These may be linked to high blood pressure, kidney failure, and heart attacks. They also found common variants in the GJB2 and ABCC2 genes. These are associated with hearing loss and chronic liver disease.
Terao explained they are trying to find and list gene variants specific to Japanese people. They want to understand why these people are more likely to have certain traits and diseases.
This study is part of a bigger change in genetics research. For years, most large genetic databases focused on people of European ancestry. This limited understanding of disease risk in other populations.
Terao hopes expanding JEWEL with more Asian genetic data will help change this. He believes it is important to expand this research to Asian populations so the results can benefit them too.
Deep Dive & References
- Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing - Science Advances, 2024
- Ancient genomics reveals tripartite origins of Japanese populations - Science Advances, 2021
- Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA - Nature, 2014
- The major genetic risk factor for severe COVID-19 is inherited from Neanderthals - Nature, 2020
