For sixty years, scientists told the same story about Japanese ancestry. The population originated from two ancient groups: Jōmon hunter-gatherers, who arrived thousands of years ago, and later East Asian migrants, who brought rice cultivation.
Research from the RIKEN Center for Integrative Medical Sciences, published in Science Advances, completely refutes that statement. The researchers discovered a third major ancestral population through their genomic sequencing study, including more than 3200 Japanese participants that had previously been overlooked by scientists.
The team used whole-genome sequencing instead of previously available DNA microarray technology. This involves determining virtually all three billion base pairs that make up an individual’s genome, which is 3,000 times more data than previous approaches.
Their data were then plotted from Hokkaido in the far north to Okinawa in the south, resulting in the largest study of its kind for a non-European population at the time.
What surprised scientists was the strong Jomon ancestry in the genome, which was found in 28.5% of the people tested in Okinawa and only 13.4% in western Japan. Additionally, the western Japanese islands showed stronger genetic similarity with Han Chinese people due to extensive migration between 250 and 794 AD. The new Emishi-related lineage was found mostly in the northeastern islands.
“Japan’s population is not as genetically homogeneous as everyone thinks,” said study leader Chikashi Terao. This research revealed 44 genetic loci of Neanderthals and Denisovans that are still functional in the genome of today’s Japanese population, some of which are unique. The variant of a Denisovan gene associated with type 2 diabetes may affect drug sensitivity.
