One Crossing or Many? Whole-Mitogenome Analysis Reframes the Jomon Peopling of Japan

Did Japan’s Jomon people arrive in multiple waves by different sea routes, or settle once and then diverge within the islands? A long-running debate has been reframed by a whole-mitogenome study led by Hiroki Oota at the University of Tokyo.

Scholars had interpreted the mitochondrial-DNA difference between eastern and western Jomon as evidence that people reached the archipelago along separate routes at different times. Pooling whole mitogenomes from 17 sites, the new study argues the difference more likely arose after a single ancestral arrival, through isolation, random drift, and cultural divergence under contrasting eastern and western ecologies.

Ecology is the key: eastern Japan offered rich forests and salmon-trout resources, while western Japan was relatively poorer in food productivity—differences enough to drive genetic divergence over the long Jomon period. Bayesian skyline analysis also shows the eastern Jomon population expanded markedly between 13,000 and 8,000 years ago.

The conclusion recasts the question from “which migration routes were taken” to “how environment and culture drove divergence within the islands,” offering a simpler framework for understanding the formation of early island populations.

Source: Koki Yoshida et al.; corresponding Hiroki Oota. The University of Tokyo / Anthropological Science, 2026-02-17.