A large-scale genetic study using whole-genome sequencing on over 3,200 individuals across Japan has revealed new insights into the ancestry and genetic diversity of the Japanese population.
Key Findings
- The analysis supports the 'tripartite origins' theory, suggesting three major ancestral sources for modern Japanese: Jomon hunter-gatherers, later migrants from East Asia, and a third group linked to northeastern Asia (possibly the ancient Emishi) concentrated in northeastern Japan.
- Jomon ancestry was highest in Okinawa (28.5%) and lower in western Japan (13.4%). Western Japanese showed stronger genetic connections to Han Chinese, reflecting migration waves between 250-794 CE.
- The study identified 44 archaic DNA regions from Neanderthals and Denisovans in modern Japanese genomes. One Denisovan-related variant in the NKX6-1 gene is associated with type 2 diabetes; 11 Neanderthal-derived segments are linked to conditions like coronary artery disease and rheumatoid arthritis.
- Potentially harmful variants in the PTPRD gene associated with hypertension and kidney failure, and common loss-of-function variants in GJB2 (hearing loss) and ABCC2 (liver disease) were found.
Methodology and Significance
The research, published in Science Advances, used whole-genome sequencing to analyze samples from seven regions (Hokkaido to Okinawa), creating the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL). This method provides roughly 3,000 times more data than traditional DNA microarrays. The study highlights that the Japanese population is more genetically diverse than previously assumed.
According to Chikashi Terao, who led the study at RIKEN, rare genetic variants helped trace migration patterns. The findings aim to improve personalized medicine by connecting population differences with genetics.