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

A new analysis of whole-mitogenome sequences from Jomon individuals reveals that the demographic history of these prehistoric hunter-gatherers was marked by a significant population increase during the Incipient–Initial phase, a pattern not observed in present-day Japanese populations. This finding suggests regional demographic dynamics and limited gene flow between eastern and western Jomon populations, challenging traditional assumptions about their population structure. The study also demonstrates that east-west frequency differences in haplogroups N9b and M7a could result from genetic drift under conditions of small initial population size and extreme population split, supporting a monophyletic origin scenario for the Jomon people. These insights were derived from simulation-based population genetic analysis of 40 mitogenomes, including previously unpublished data.

Yoshida, K., Wakiyama, Y., Nakamura, Y., Valverde, G., Tanino, A., Waku, D., Katsumura, T., Ogawa, M., Nagaoka, T., Hirata, K., Koganebuchi, K., Watanabe, Y., Ohashi, J., Yoneda, M., Takahashi, R., & Oota, H. (2026). Demographic history of the Jomon people: insights from whole-mitogenome analysis. Anthropological Science, 134(1), 15–28. https://doi.org/10.1537/ase.251024