Who are the Japanese people? DNA study results upend previous beliefs

Population genetics can reveal surprising insights about the ancestry of any group, often challenging assumptions that have persisted for centuries. Japan is a prime example, with many believing its people descend from only two main lines of ancestry.

New evidence now indicates that there may be a third strand woven into the country’s genetic heritage. Researchers are examining DNA clues and clinical data to piece together a bigger story, and the results are shaking up conventional wisdom on what it really means to be Japanese.

A paper published in the journal Science Advances presented findings that suggest a far more intricate genetic tapestry is involved in the ultimate ancestry of people in Japan than previously thought.

The project behind this discovery is led by experts who investigated thousands of samples to paint a detailed picture of ancestry.

After sifting through these clues, RIKEN’s Chikashi Terao and colleagues propose that a third group, the so-called Emishi people, is part of this fascinating blend.

Terao, who headed the study at RIKEN’s Center for Integrative Medical Sciences, explains, “Our analysis revealed Japan’s subpopulation structure on a fine scale, which is very beautifully classified according to geographical locations in the country.”

Fresh perspective on Japanese ancestry

Researchers used whole-genome sequencing to analyze genetic information from more than 3,200 people across seven regions of Japan.

This approach zooms in on all three billion DNA base-pairs, offering a much more comprehensive view compared to previous methods.

Terao says, “Whole-genome sequencing gives us the chance to look at more data, which helps us find more interesting things.”

By examining the data, the team pinpointed differences that track with older population groups. Traditional narratives described only two main ancestral lines: the Jomon and the rice-farming migrants from east Asia.

The latest results identify a third source in the mix – people with connections to northeast Asia known as the Emishi.

One key aspect of this research is the focus on subtle markers that illuminate how these historical groups spread out across the islands.

Japan’s ancestry gets clues from JEWEL

The Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL) combines genetic material with related medical and family information.

The researchers gathered this data to explore health links and ancestry, creating a resource that also sheds light on how certain diseases appear in distinct areas.

Terao remarks, “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.”

According to the analysis, Jomon ancestry remains most prominent in Okinawa, appearing in 28.5% of the samples studied there, while it is lowest in western Japan at just 13.4%.

Meanwhile, the study found that individuals in western regions have closer connections to Han Chinese people.

The influx of migrants from east Asia between the year 250 and year 794 correlates with that finding. Emishi-related lineage appears strongest in the northeast, gradually dwindling as one moves westward.

Rare variants and their role

The study did more than trace broad patterns of ancestry. It also drilled down into uncommon gene variations to discover their potential involvement in various conditions.

One particular variant of a gene called PTPRD has the potential to be highly damaging because it could be linked with hypertension, kidney failure, and myocardial infarction, according to Xiaoxi Liu, a senior scientist in Terao’s lab and the first author of the research.

Additionally, significant incidences of variants in the GJB2 and ABCC2 genes were documented, tying them to hearing loss and chronic liver disease.

These clues demonstrate the practical potential of such extensive DNA surveys. By mapping rare changes, the researchers gain a sharper understanding of health outcomes, which may eventually guide new approaches to diagnosis or treatment.

The JEWEL database thus provides a framework for aligning genetic signals with real-world health profiles.

Clues from Neanderthals and Denisovans

The project also examined segments inherited from Neanderthals and Denisovans, two archaic human groups that intermixed with Homo sapiens millennia ago.

Terao states, “We are interested in why ancient genomes are integrated and kept in modern human DNA sequences.”

The team identified 44 ancient DNA regions present in Japanese people, many unique to East Asians.

Among these was a Denisovan-derived segment within the NKX6-1 gene, which may influence how individuals respond to semaglutide, a drug used to treat type 2 diabetes.

They also located 11 Neanderthal-derived segments possibly tied to several conditions, including coronary artery disease, prostate cancer, and rheumatoid arthritis.

Researchers in other parts of the world have shown that archaic DNA occasionally grants advantages in extreme environments or impacts susceptibility to illness.

This new study adds fresh details to the ongoing search for connections between ancient genes and modern-day health.

Japan, ancestry, and human health

Scientists point out that large-scale genetic investigations have mostly centered on European samples. Terao is keen to expand the reach of JEWEL by including more DNA profiles from Asia and beyond.

This broader approach could highlight unique markers and conditions that are otherwise overlooked. “We’d like to connect population differences with differences in genetics,” he observes.

Population research of this magnitude promises to clarify how certain traits, disorders, and susceptibilities arise.

It may also help fine-tune healthcare for specific communities by showing which variants are most influential. At the same time, it shows that no population is as uniform as once believed.

The new evidence highlights how three ancestral groups contributed to the current mosaic in Japan, blending the histories of the Jomon, east Asian migrants, and the Emishi people into a more complete picture of Japan’s past.

The full study was published in the journal Science Advances.

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