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

  • ️Tue Jan 01 2019

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

Yusuke Watanabe et al. Sci Rep. 2019.

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.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1

Overview of the currently accepted demographic model of the mainland Japanese population.

Figure 2
Figure 2

Neighbor-joining tree of mainland Japanese Y chromosomes. The neighbor-joining tree of 345 mainland Japanese Y chromosomes was constructed using MEGA7 based on 28,254 SNPs.

Figure 3
Figure 3

Frequencies of seven Y-chromosomal clades in East Asian populations. Y chromosomes in clade 1 were observed only in the Japanese among the East Asian populations. Frequencies of five East Asian populations were obtained from the 1000 Genomes Project phase 3 data. JPT: Japanese in Tokyo, Japan; CHB: Han Chinese in Beijing, China; CHS: Southern Han Chinese; CDX: Chinese Dai in Xishuangbanna, China; and KHV: Kinh in Ho Chi Minh City, Vietnam.

Figure 4
Figure 4

Estimated frequency of each clade in the Jomon people by Monte-Carlo simulation. Twenty sets of clade frequencies were selected from 108 simulated data sets in ascending order of Similarity Index (SI). The mean frequency of 20 sets in each clade is shown above the box.

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).

Figure 6
Figure 6

Bayesian skyline plots of major clades of simulated genealogies by Fastsimcoal2. BEAST 2.4.4 was used to obtain the BSPs for 200 simulated chromosomes only in a major clade produced by fastsimcoal2. The solid lines represent BSPs that detected the recent changes in population size (decrease of 3,000 YBP and increase of 2,000 YBP). The dashed lines represent BSPs that could not detect the population change assumed.

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