Japanese People May Have Three Ancestral Lineages

Japanese people and three ancestral lineages

The genes of present-day Japanese people may preserve evidence of a long-lost ancestral lineage that once travelled to the northern reaches of the archipelago from north-eastern mainland Asia.

This finding adds weight to growing evidence that modern Japanese people descend from three, rather than two, ancestral lineages.

Until recently, the prevailing view held that Japan’s population arose from the intermingling of two ancestral groups: the Indigenous Jōmon people, who reached Japan from ancient East Asia more than 10,000 years ago, and rice-growing people from north-east Asia, who began arriving from the continental mainland around 2,300 years ago.

However, a genetic study in 2021 identified a third migration wave for the first time, creating an alternative account of Japan’s origins.

Geneticist Chikashi Terao, the senior author of the latest analysis, says that he and his colleagues have uncovered Japan’s "subpopulation structure on a fine scale". According to him, the findings are "beautifully classified" across seven regions spanning the country from end to end.

By sequencing the DNA of more than 3,200 people from these areas, Terao and his team produced what they say is among the largest genetic analyses of a non-European population undertaken so far. The work offers insights into the population’s genetic structure that may have implications for personalised medicine.

"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," explains Terao, who is based at the RIKEN Center.

Genetic ancestry across Japan

Using modern and ancient genetic data, the researchers compared both common and rare variants, identifying three principal ancestry clusters among most of Japan’s population.

Their findings indicate that Jōmon ancestry is strongest in southern Japan today. In western Japan, meanwhile, people are more closely related to Han Chinese, who continued migrating from the East Asian continental mainland until roughly 800 CE.

In north-eastern Japan, however, a different ancestry is predominant. The team says the genetic composition of this group remains less certain, although it could reflect a two-way mixture of Korean and Han Chinese ancestry.

Historical accounts indicate that the north-east was inhabited by another ancient lineage, the Emishi people, during the fifth century CE. Their name literally means "shrimp barbarians". Although their origins are not known, one proposal is that they descended from people who lived on the land that is now the Korean peninsula.

Breast cancer genes and limits of ancient DNA

The research also identified probable origins for two genes associated with inherited breast cancer in Japanese people. One example is a Japanese-specific BRCA1 mutation that occurs at a substantially higher frequency in eastern Japan. It appears to have emerged among people with north-eastern Japanese ancestry before spreading to other parts of the country.

"This comprehensive genetic dataset enables us to delve into uncharted territories concerning population and medical genetics of the Japanese population," the authors of the genetic analysis write.

Ancient genome samples are difficult to obtain, limiting comparisons between genetic features observed in people today and those from earlier populations. Up to 40 percent of the genetic variants found in the current research had not previously been registered.

Terao and his colleagues stress that uncertainty remains in the data, although their results align with the ‘tripartite’ origin hypothesis in most Japanese regions.

Even so, the developing evidence indicates that Japan’s population history is more complex than scientists had first believed. Including diverse populations in genetic studies is important for improving understanding of human history and health.

The study was published in Science Advances.