Endemic demographics of the Jomon people estimated based on complete mitogenomes reveal their regional diversity

Abstract

The Jomon culture that spread across Japanese archipelago began about 16,000 years ago and lasted for over 10,000 years. The genetic diversity of the Jomon people, prehistoric hunter-gatherers bearing the Jomon culture, is of great interest in understanding prehistoric East Eurasians. Until now, their demographic history has been estimated using archaeological sites and present-day genomes, but detailed studies using Jomon genomes has not been sufficient. To investigate the Jomon demography, we determined complete mitochondrial genome (mitogenome) sequences from 13 Jomon individuals and conducted population genetic analysis on 40 Jomon genomes including previously published data. Our results revealed an effective population size increase during the Incipient - Initial phase of Jomon period, which was not observed in present-day Japanese populations. This endemic demographic pattern is pronounced in the eastern part of the archipelago, suggesting regional diversity in Jomon demographic history.