For a long time scientists thought Japanese people came from just two ancient groups: the Jomon hunters and later farmers from mainland Asia.
New research from RIKEN shows the story is more tangled. By sequencing the whole genomes of over 3,200 volunteers from every corner of Japan, researchers found a third ancestor that lived in northeastern Asia, possibly linked to the old Emishi people.
A Huge DNA Map of Japan
The team collected DNA from seven regions, from Hokkaido down to Okinawa. Instead of older DNA chip methods, they read almost every one of the three billion letters in each genome. That gives about 3,000 times more detail.
They mixed this genetic data with medical records, family histories, and lab tests to create a database called JEWEL – the Japanese Encyclopedia of Whole‑Genome/Exome Sequencing Library.
Rare DNA changes were a special focus because they can keep clues about ancient migrations.
The Secret Third Ancestor
Results showed clear regional patterns. Okinawa people had the strongest Jomon signal (about 28%). Western Japan showed more DNA similar to Han Chinese, reflecting big migration waves between the 3rd and 8th centuries CE.
The newly spotted Emishi‑related ancestry was strongest in the northeast and faded toward the west. This supports the growing “tripartite origins” idea that modern Japanese descend from three main groups.
Ancient DNA Still Matters
The study also looked at DNA left over from Neanderthals and Denisovans. They found 44 ancient DNA segments still present in Japanese people, many unique to East Asians.
One Denisovan piece inside the NKX6‑1 gene is linked to type‑2 diabetes and may affect how patients respond to certain medicines. Eleven Neanderthal pieces were tied to heart disease, prostate cancer, and arthritis.
Toward Personalized Medicine
Beyond ancestry, the researchers identified harmful variants in genes such as PTPRD (linked to hypertension and heart attacks) and common loss‑of‑function changes in GJB2 and ABCC2 (related to hearing loss and liver disease).
By cataloguing these Japan‑specific gene variants, scientists hope to improve disease prediction and treatment for the Japanese population.
Most large genetic databases have focused on Europeans, leaving gaps in knowledge for other groups. Expanding JEWEL with more Asian genomes could close that gap and bring health benefits to many people.