For sixty years, scientists told the same story about Japanese origins. The population was descended from two ancient groups: Jomon hunter-gatherers, who arrived thousands of years ago, and later East Asian migrants, who brought rice cultivation.
Research from RIKEN’s Center for Integrative Medical Sciences, published in Science Advances, has completely refuted this story. The researchers discovered a third major ancestral population through their genomic sequencing study, which involved more than 3,200 Japanese participants who had previously been overlooked by scientists.
The team used whole-genome sequencing instead of the previously available DNA microarray technology. This involves sequencing virtually all three billion base pairs that make up a person’s genome, 3,000 times more data than previous approaches.
Their data was 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.
To the scientists’ surprise, the genome had strong Jomon ancestry: 28.5% of people tested in Okinawa and only 13.4% in western Japan. At the same time, the western Japanese islands showed much closer genetic similarity to Han Chinese peoples as a result of extensive migrations between 250 and 794 AD. The new Emishi-related ancestry was mainly found in the northeastern islands.
“The Japanese population is not as genetically homogeneous as everyone thinks,” says study leader Chikashi Terao. This research revealed 44 genetic locations of Neanderthals and Denisovans that are still functional in the genome of the current Japanese population, some of which are unique. The variant of one Denisovan gene associated with type 2 diabetes may influence drug sensitivity.
