• intraregional variation;
  • population structure;
  • R-matrix method;
  • peopling of Northeast Asia


The people associated with the Jomon culture, the Neolithic inhabitants of Japan, are one of the key groups in the population history of East Asia, because they retain many archaic characters that may be traced back to Eurasian Upper Palaeolithic hunter–gatherers. In this study, the regional diversity of the Jomon skeletal series was estimated by applying the R-matrix method to 34 craniofacial measurements. The patterns of intraregional variation indicate little effect on the genetic structure of the Jomon from long-term gene flow stemming from an outside source. The regional diversities were further estimated by pooling all individuals into regional aggregates, and by computing the mean variance within local groups in each region. Although the pattern of phenotypic variation differs depending on the unit of analysis, the gradient of the diversity retains its identity. The Hokkaido region, the northernmost part of the Japanese archipelago, has the highest variance, followed by the regions of eastern Japan, while the southwestern regions have the lowest variance. These findings suggest that the Jomon ancestors of the northern part of Japan might have expanded southward to Honshu Island. Global analyses including samples from Eurasia, Africa, and Australia dating roughly to the same chronological periods as those of the Jomon samples, indicate that the Jomon cranial series share part of their ancestral gene pool with early northeastern Asians. The present findings support the archeologically suggested population growth and expansion in the northern half of the Eurasian continent during the late Pleistocene and early Holocene periods. Am J Phys Anthropol, 2009. © 2008 Wiley-Liss, Inc.