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Comprehensive analysis of Japanese archipelago population history by detecting ancestry-marker polymorphisms without using ancient DNA data

Modern Japanese have two major ancestral populations: the indigenous Jomon people and immigrants from continental East Asia. To figure out the population history in Japanese archipelago, we developed a reference-free detection method of genetic components from ancestral populations using a summary statistic, the ancestry-marker index (AMI). We applied the AMI to modern Japanese samples and identified 208,648 SNPs that were likely derived from the Jomon people (Jomon-derived SNPs). The analysis of Jomon-derived SNPs in 10,842 modern Japanese individuals recruited from all the 47 prefectures of Japan showed that the genetic differences among the prefectures were mainly caused by differences in the admixture proportion of the Jomon people and the population size of immigrants varied between regions in mainland Japan. We also estimated the migration route of the ancestral Jomon population to Japanese archipelago and their phenotype frequencies based on the haplotype structures of modern Japanese composed of Jomon-derived SNPs.