New Genetic Study Redefines Origins On Japan's Ancestry
New Genetic Study Redefines Origins On Japan's Ancestry
Challenging the Traditional Dual-Origin Theory of Japanese Ancestry
A groundbreaking genetic study conducted by researchers at the RIKEN Center for Integrative Medical Sciences has uncovered new evidence that challenges the longstanding belief in a dual-origin model of Japanese ancestry. The research, published in Science Advances1 in April 2024, reveals that the people of Japan descend from three distinct ancestral groups rather than two, as previously believed. This discovery lends further support to the emerging "tripartite origins" theory, suggesting that the genetic heritage of the Japanese population is far more complex than earlier models suggested.
Revisiting Japan's Genetic Past
For decades, anthropologists and geneticists have attributed Japan's ancestry to two primary groups: the Jomon hunter-gatherer-fishers, who inhabited the Japanese archipelago for thousands of years, and rice-farming migrants from East Asia who began arriving around 3,000 years ago. However, the new study introduces a third ancestral group with possible ties to Northeast Asia, often referred to as the Emishi people, which significantly reshapes the understanding of Japan’s genetic history.
Chikashi Terao, who led the study, noted that,
“Japan’s subpopulation structure is far more nuanced than previously thought,” and that their analysis reveals “beautifully classified genetic variations according to geographical locations in the country.”
DNA Analysis: Tracing Ancestry Across Japan
Terao’s team analyzed the DNA of over 3,200 individuals from seven regions across Japan, ranging from Hokkaido in the north to Okinawa in the south. By employing whole-genome sequencing, which provides a comprehensive overview of an individual’s complete genetic makeup, the researchers were able to gather 3,000 times more information than previous techniques that relied on DNA microarray methods. This allowed them to identify rare genetic variants and trace back migration patterns within Japan with greater accuracy.
The results of their analysis showed that Jomon ancestry is most pronounced in the southern subtropical region of Okinawa, comprising 28.5% of the genetic makeup there, while it decreases to just 13.4% in western Japan. In contrast, western Japan displayed stronger genetic ties to Han Chinese populations, likely reflecting the historical influx of East Asian migrants during the Yayoi period (250 to 794 CE). This migration wave was also accompanied by the adoption of Chinese-style laws, language, and cultural practices.
Discovering the Emishi Legacy
The presence of the Emishi ancestral group adds a fascinating layer to Japan’s genetic history. Found primarily in northeastern Japan, the Emishi people were believed to have been a significant population before their gradual assimilation by other groups in later centuries. This study shows that their genetic legacy persists, with their ancestry decreasing as one moves westward across Japan.
These findings suggest that early Japanese populations were shaped by distinct waves of migration from different regions of Asia, resulting in a rich and diverse genetic landscape.
Echoes of Ancient DNA
In addition to uncovering Japan's ancestral groups, the researchers explored how ancient human DNA persists in modern populations. They identified 44 regions of ancient DNA, inherited from archaic humans like Neanderthals and Denisovans, that are still present in Japanese genomes today. Most of these segments are unique to East Asians, and some are linked to modern traits and conditions.
One such Denisovan-derived gene within the NKX6-1 gene is associated with type 2 diabetes and could impact sensitivity to the diabetes drug semaglutide. Meanwhile, Neanderthal-derived genes have been connected to various conditions, including coronary artery disease, prostate cancer, and rheumatoid arthritis.
Toward Personalized Medicine in Japan
Beyond tracing ancestry, the research team examined rare genetic variants for their potential links to diseases, hoping to advance the field of personalized medicine. Xiaoxi Liu, the study’s first author, highlighted a gene variant in PTPRD that could be highly damaging, as it is potentially linked to hypertension, kidney failure, and heart attacks.
The team also discovered variants in genes associated with hearing loss and chronic liver disease that are more prevalent in Japanese populations. These findings provide a critical first step in understanding how certain populations may be predisposed to specific diseases based on their genetic heritage. As Terao notes,
“Connecting population differences with differences in genetics will pave the way for future advances in personalized medicine.”
Expanding Genetic Research to Benefit All Populations
The RIKEN-led study marks a major milestone in expanding large-scale genomic research beyond populations of European descent. Historically, the majority of genetic studies have been Eurocentric, limiting their applicability to other regions. However, Terao emphasized the importance of expanding research to Asian populations, stating,
“In the long run, this will benefit not just Japan, but the world at large.”
By building on the JEWEL (Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library) database and continuing to collect DNA samples from across Japan, researchers hope to uncover even more insights into the complex tapestry of human ancestry, and how ancient genetic variants influence modern health outcomes.
This study is a crucial reminder that the story of human evolution is far from complete. With each new discovery, scientists are uncovering deeper layers of our shared history, revealing that our ancestors were much more interconnected than previously believed.
Liu, X., Koyama, S., Tomizuka, K., Takata, S., Ishikawa, Y., Ito, S., Kosugi, S., Suzuki, K., Hikino, K., Koido, M., Koike, Y., Horikoshi, M., Gakuhari, T., Ikegawa, S., Matsuda, K., Momozawa, Y., Ito, K., Kamatani, Y., & Terao, C. (2024). Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing. Science Advances, 10(16). https://doi.org/10.1126/sciadv.adi8419