Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period

Yusuke Watanabe,Jun Ohashi,Hiromi Sawai,Seik-Soon Khor,Yuki Hitomi,Izumi Naka,Katsushi Tokunaga

doi:10.1038/s41598-019-44473-z

Abstract

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.

Highlights

Archaeological studies have shown that the Japanese prehistory is divided into three periods: the Paleolithic period, the Jomon period (14,500-2,300 YBP), and the Yayoi period (2,300-1,700 YBP)[1]
The prevailing hypothesis on the origins of the Japanese is “the dual structure model,2” where the present-day Japanese population is formed by an admixture between indigenous Jomon people and Yayoi immigrants who migrated from continental East Asia (Fig. 1)
A recent study of ancient DNA extracted from the remains of Jomon individuals who had lived in mainland Japan (Fukushima Prefecture) 3,000 YBP suggested that (1) the Jomon people were strongly divergent from the current East Asians (Fig. 1), (2) the Ainu people are most closely related to the Jomon people among the three Japanese populations, and (3) ~12% of the genomic components of the modern mainland Japanese were derived from the Jomon people[7]

Summary

Introduction

Archaeological studies have shown that the Japanese prehistory is divided into three periods: the Paleolithic period (older than 14,500 years before present [YBP]), the Jomon period (14,500-2,300 YBP), and the Yayoi period (2,300-1,700 YBP)[1]. The prevailing hypothesis on the origins of the Japanese is “the dual structure model,2” where the present-day Japanese population is formed by an admixture between indigenous Jomon people and Yayoi immigrants who migrated from continental East Asia (Fig. 1) According to this model, modern mainland Japanese should have genomic components derived from both the Jomon people and those originating from the Yayoi immigrants. The mainland Japanese are closely related to Koreans, followed by Han Chinese, and by other Continental East Asians[3] These findings suggest that a large number of Yayoi immigrants came mainly through the Korean Peninsula to mainland Japan, and the mainland Japanese still retain genomic components from the Jomon people. Our results suggested that the Jomon people underwent a major decrease in population size at the end of the Jomon period, with a recovery occurring soon after the beginning of the Yayoi period

Methods

Results

Conclusion