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MADRID (Euronews) – A DNA study has identified a third group of Japanese ancestors with potential links to Northeast Asia, the Ezo people who lived in the northeast of the island of Honshu.
The findings, published in Science Advances by researchers at the RIKEN Center for Integrative Medical Sciences, challenge the long-held belief that Japan had two main ancestral groups: indigenous Jomon hunter-gatherer fishermen and immigrant rice farmers from East Asia.
Chikashi Terao of RIKEN, who led the study, said the Japanese population is not as genetically homogeneous as everyone thought. He added in a statement: “Our analysis revealed a subpopulation structure in Japan at a fine scale that is well classified according to the country’s geographical location.”
Terao’s team reached those conclusions after sequencing the DNA of more than 3,200 people from seven regions of Japan, from Hokkaido in the north to Okinawa in the south. It is one of the largest genetic analyses of non-European peoples ever conducted.
The researchers used a technique called whole genome sequencing, which reveals an individual’s entire genetic makeup (all 3 billion DNA base pairs). It provides about 3,000 times more information than the DNA microarray method that has been more widely used to date. “Whole genome sequencing gives us the opportunity to look at more data, which helps us discover more interesting things,” Terao said.
To further improve the usefulness of the data and examine possible links between genes and certain diseases, he and his collaborators combined the DNA information they obtained with relevant clinical data, including disease diagnoses, test results, and medical history and family information. They compiled all of this into a database called the Japanese Encyclopedia of Whole Genome/Exome Sequencing Libraries (JEWEL).
A topic of particular interest to Terao is the study of rare genetic variants. “We believe that rare variants can sometimes be traced back to specific ancestral groups and could be informative in revealing small-scale migration patterns within Japan,” he explains.
His intuition proved to be correct, helping to reveal the geographic distribution of Japanese ancestries: Jomon ancestry, for example, was dominant along the subtropical coast of southern Okinawa (28.5% of the sample) and lowest in the west (just 13.4% of the sample).
In contrast, people living in western Japan have more genetic kinship with Han Chinese, which Terao’s team thinks may be related to the influx of East Asian immigrants between A.D. 250 and A.D. 794. The region’s legislation, language, and education system were influenced by the region’s style.
On the other hand, the Ezo ancestry is most common in northeastern Japan and gradually decreases towards the west of the country.
The researchers also examined whether JEWEL had genes inherited from Neanderthals and Denisovans, two ancient human groups that interbred with Homo sapiens. “We are interested in understanding why ancient genomes are integrated and retained in modern human DNA sequences,” Terao said, explaining that these genes are sometimes associated with certain traits or conditions.
For example, other researchers have shown that Tibetans contain DNA from Denisovans in their EPAS1 gene, which is thought to have aided their colonization of high-altitude environments. More recently, scientists have found that a set of genes inherited from Neanderthals on chromosome 3—a trait shared by about half of South Asians—is associated with an increased risk of respiratory failure and other severe COVID-19 symptoms19.
Terao’s team’s analysis revealed 44 ancient DNA regions present in modern Japanese, most of which are unique to East Asians. Among them is a denisovan derivative located within the NKX6-1 gene, known to be associated with type 2 diabetes, which the researchers say could affect a person’s sensitivity to semaglutide, an oral drug used to treat the disease. They also identified 11 segments of Neanderthal origin that have been linked to coronary artery disease, prostate cancer, rheumatoid arthritis and four other diseases.
The RIKEN-led team also used data on rare gene variants to discover possible causes of these diseases. For example, they found that a gene variant called PTPRD could be “very harmful” because it could be associated with high blood pressure, kidney failure and heart disease, said Xiaoxi Liu, a senior scientist in Terao’s lab and first author of the study.
Additionally, the team noted that there are significant variants (also called loss-of-function variants) in the GJB2 and ABCC2 genes, which are associated with hearing loss and chronic liver disease, respectively.
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