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Inter-site distance analysis based on craniometric data shows that the prehistoric population of Japan in the Jomon period were morphologically homogeneous to nearly the same extent as the present-day Japanese population. But the Jomon population differ widely, with many distinctive osteological features, from the modern Japanese, and are generally close to the Ainu in Hokkaido and the Upper Paleolithic population of Eurasia. On the other hand, the contemporaneous population in Neolithic North China are morphologically distant from the Jomon population and much closer to the modern Japanese. This suggests that the archaic morphology of the Upper Paleolithic Eurasian population were maintained by the food-gathering population in the isolated islands of Japan until the end of the Jomon period. The situation in Kyushu, Shikoku, and Honshu changed rapidly in the Yayoi and Kofun periods by cultural and genetic impacts from the mainland. But, basically Jomon-like morphology survived in the traditional food-gathering population of the Ainu in Hokkaido till recently.

A Review of the Osteological Characteristics of the Jomon Population in Prehistoric Japan