Although most molecular ecology studies examining genetic variation have focused on natural forests, for some major tree species, natural forests are nearly extinct, and the remaining genetic resources are mainly planted forests. In order to manage the genetic variability and develop a conservation strategy for such species, it is important to examine genetic variation resulting from historical processes during repeated artificial population development through plantations. The geographic pattern of genetic diversity and structure of 49 old planted Pinus thunbergii populations (2755 trees) distributed across Japan was examined using seven nuclear microsatellite markers. We found that allelic diversity was generally lower in both northern and eastern populations; however, locally, some populations in other regions also exhibited low allelic diversity. The overall value of the standardized measure of population differentiation (G′ST = 0.206) was higher than that of both other widespread Japanese conifers and continental Pinus species. STRUCTURE software revealed a general gradual cline in genetic structure from southwestern to northeastern populations; however, some populations on the Japan Sea side showed quite a different local proportion of cluster memberships from nearby populations. These observations indicated that most of the preserved, planted populations of P. thunbergii possess regional genetic variation, but some populations were developed from seed pools derived from other regions, possibly through distribution by ship along the Japan Sea. Information on this specific genetic variation as a result of historical seed use and transfer should assist the design of several conservation units and breeding zones, while also taking care of a deep-seated need for conservation of pine forests by local people.
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