Y chromosomes reveal population boom and bust in ancient Japan

Researchers have conducted a census of the Japanese population around 2,500 years ago using the Y chromosomes of men living on the main islands of modern-day Japan. This is the first time analysis of modern genomes has estimated the size of an ancient human population before they were met by a separate ancient population.

"Evidence at archaeological dig sites has been used to estimate the size of ancient human populations, but the difficulty and unpredictability of finding those sites is a big limitation. Now we have a method that uses a large amount of modern data," said Associate Professor Jun Ohashi, an expert in human evolutionary genetics and leader of the research team that performed the analysis.

Yusuke Watanabe, Izumi Naka, Seik-Soon Khor, Hiromi Sawai, Yuki Hitomi, Katsushi Tokunaga, Jun Ohashi. Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period. Scientific Reports, 2019; 9 (1)

DOI: 10.1038/s41598-019-44473-z

The Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500–2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.

 
Figure 5
Figure 5 - Phylogenetic tree and Bayesian skyline plot (BSP) of Y chromosomes of mainland Japanese in clade 1. (A) Phylogenetic tree of clade 1 estimated by BEAST 2.4.4. (B) BSP of 122 Y chromosomes of mainland Japanese in clade 1. BEAST 2.4.4 was used to obtain the plot. The red dashed lines represent 14,500 YBP (years before present; the beginning of the Jomon period) and 2,300 YBP (the beginning of the Yayoi period).