Considering the geographical setting of the Japanese archipelago at the periphery of the Asian continent, regional variation in Jomon phenotypes can be interpreted as an outcome of population history. In this paper, we focused on regional variation in the Jomon craniofacial morphology and assumed that the observed regional differences were a reflection of the formation process of the Jomon population, which is a mixture of intrinsic expansion of an initial population with extrinsic influence of hypothetical gene flow. Compiled craniometric data from archeological site reports indicate that Jomon skulls, especially in the neurocranium, exhibit a discernible level of northeast-to-southwest geographical cline across the Japanese archipelago, placing the Hokkaido and Okinawa samples at both extreme ends. A quantitative genetic approach using an R-matrix method indicates that the cranial parts of the neurocranium and mandible exhibit a proportionately larger regional variation, the former of which confirms a trend of geographical cline and reveals the respective region presumably having different population histories with their respective local backgrounds. The following scenarios can be hypothesized with caution: (a) the formation of Jomon population seemed to proceed in eastern or central Japan, not western Japan (Okinawa or Kyushu regions); (b) the Kyushu Jomon could have a small-sized and isolated population history; and (c) the population history of Hokkaido Jomon could have been deeply rooted and/or affected by long-term extrinsic gene flows.

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