A tripartite structure for the genetic origin of Japanese populations states that present-day populations are descended from three main ancestors: (1) the indigenous Jomon hunter–gatherers; (2) a Northeast Asian component that arrived during the agrarian Yayoi period; and (3) a major influx of East Asian ancestry in the imperial Kofun period. However, the genetic heterogeneity observed in different regions of the Japanese archipelago highlights the need to assess the applicability and suitability of this model. Here, we analyse historic genomes from the southern Ryukyu Islands, which have unique cultural and historical backgrounds compared with other parts of Japan. Our analysis supports the tripartite structure as the best fit in this region, with significantly higher estimated proportions of Jomon ancestry than mainland Japanese. Unlike the main islands, where each continental ancestor was directly brought by immigrants from the continent, those who already possessed the tripartite ancestor migrated to the southern Ryukyu Islands and admixed with the prehistoric people around the eleventh century AD, coinciding with the emergence of the Gusuku period. These results reaffirm the tripartite model in the southernmost extremes of the Japanese archipelago and show variability in how the structure emerged in diverse geographic regions.

The Palaeolithic–Neolithic transition in East Asia is characterised by the transformation of mobile hunter-gatherer groups into sedentary communities. The existence of ‘ice-age’ pottery in the Japanese archipelago, however, is inconsistent with claims that directly link climatic warming with sedentism and the development of ceramics. Here, the authors reconsider the chronology and palaeoenvironment of the Maedakochi site in Tokyo. New AMS dating and environmental data suggest that intensified inland fishing in cold environments, immediately prior to the Late Glacial warm period, created conditions conducive to sedentism and the development of subsistence-related pottery.