Demographic history of the Jomon people: insights from whole-mitogenome analysis

The Jomon culture that spread across the Japanese archipelago began about 16000 years ago and lasted for over 10000 years. The population history of the Jomon people, prehistoric hunter-gatherers bearing the Jomon culture, is of great interest in understanding prehistoric East Eurasians. Traditionally, population size and its fluctuations, i.e. Jomon demography, have been estimated in the archaeological context, but over the past 20 years, statistical methods using genome sequence data have been sufficiently developed. To investigate their demography, we determined the complete whole-mitochondrial genome (mitogenome) sequences from 13 Jomon individuals and conducted population genetic analysis on 40 Jomon mitogenomes, including previously published data. By simulation, we showed that east–west frequency differences between two haplogroups typical of the Jomon people, N9b and M7a, could be caused by a genetic drift under conditions of a small initial effective population size, an extreme population split, and limited migration between the eastern and western populations, suggesting that the regionally unbalanced haplogroup distribution does not necessarily contradict the monophyletic origin scenario of the Jomon people implied by recent nuclear genome analyses. We found an effective population size (Ne) increase during the Incipient–Initial phase of the Jomon period, which had not been observed in analyses of mitogenome sequences from present-day Japanese populations. This endemic demographic pattern is pronounced in the eastern part of the archipelago, under the assumption of no gene flow between the Eastern and Western Jomon. This study sheds light on the demography of the Jomon people and shows an alternative scenario of the Jomon peopling history estimated based on whole-mitogenome data.