Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations

Yusuke Watanabe; Jun Ohashi

doi:10.1016/j.isci.2023.106130

Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations

iScience. 2023 Feb 3;26(3):106130. doi: 10.1016/j.isci.2023.106130. eCollection 2023 Mar 17.

Authors

Yusuke Watanabe^{1

2}, Jun Ohashi¹

Affiliations

¹ Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
² Genome Medical Science Project Toyama Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan.

Abstract

Modern Japanese people have two major ancestral populations: indigenous Jomon hunter-gatherers and continental East Asian farmers. To determine the formation process of the current Japanese population, we developed a detection method for variants derived from ancestral populations using a summary statistic, the ancestry marker index (AMI). We applied AMI to modern Japanese population samples and identified 208,648 single nucleotide polymorphisms (SNPs) that were likely derived from the Jomon people (Jomon-derived variants). Analysis of Jomon-derived variants in 10,842 modern Japanese individuals recruited from all over Japan revealed that the admixture proportions of the Jomon people varied between prefectures, probably owing to the prehistoric population size difference. The estimated allele frequencies of genome-wide SNPs in the ancestral populations of the modern Japanese suggested their adaptive phenotypic characteristics to their respective livelihoods. Based on our findings, we propose a formation model for the genotypic and phenotypic gradations of the current Japanese archipelago populations.

Keywords: Biological sciences; Genetics; Genomics; Human Genetics.