Recent distribution changes affect geographic clines in genetic diversity and structure of Pinus densiflora natural populations in Japan

Abstract

Geographic patterns of genetic diversity of widespread tree species with a disturbance-dependent distribution can be influenced by not only past climate change but also disturbance by human activities. This is especially true for species that are dominant mainly in semi-mountainous areas and near human habitation, and also available for forestry. Pinus densiflora is both an economically and ecologically important conifer in semi-mountainous forest landscapes of Japan, and information on its genetic variation is essential for designing programs to manage its natural genetic resources and breeding zones. The geographic pattern of genetic diversity and structure of 62 P. densiflora populations (a total of 1883 trees) across their natural distribution in Japan was examined using eight nuclear microsatellite markers. We found that the allelic richness was somewhat, but significantly, lower in both northern and eastern marginal populations. Analysis of recent bottlenecks detected a significant heterozygosity excess more frequently in the northern and eastern populations. The overall value of the standardized measure of population differentiation was moderate (GST′=0.122) and similar both to other widespread Japanese tree species and to continental Pinus species. STRUCTURE software analysis revealed a gradual cline in the genetic structure, with three main clusters corresponding to the western, central and northeastern populations; the northeastern cluster showed the highest F value. These results indicated strong genetic drift in the past through rapid population expansion of P. densiflora in northeastern Japan, related to progress in agriculture suggested by anthropological and paleoecological studies. Results obtained on this neutral genetic variation in the nuclear genome should provide fundamental information for designing conservation units and breeding zones and in light of evaluation of its adaptive genetic variation in future studies.