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Habitat fragmentation is one of the major threats to amphibian species. In a previous study, population genetic analyses of the Japanese brown frog Rana japonica were conducted using a mitochondrial DNA (mtDNA) marker in a typical Japanese agricultural landscape (known as satoyama) in Chiba, Japan. This previous study revealed that gene flow was restricted by the roads and cement-walled urban river that divide this site. In the present study, we reanalyzed the genetic structure of the same meta-population using microsatellite markers in comparison with the mtDNA results and elucidated fine-scale gene flow. The genetic structure derived from the microsatellite clustering analysis was almost identical to that of the mtDNA results, although some important details differed. We recognized boundaries of genetic structure are consistent with the major roads and cement-walled river, however, we also detected gene flow across those artificial barriers. We concluded that the current genetic structure was formed in the past when gene flow was strongly restricted. Gene flow among breeding populations is now being restored by the maintenance of breeding sites, although it is not sufficient to erase the signature of historical isolation.

Revegetation using native species requires the development of seed transfer zones that capture genetic distinctiveness and adaptive potentials while avoiding potential maladaptation and genetic contamination by exotic genotypes. Delineation based on phylogeographic information has recently been used to establish seed transfer zones; however, only a few herbaceous species that are suitable for revegetation have been investigated in the temperate regions of Japan. We investigated the phylogeography of non-coding regions of chloroplast DNA of ten native species in the temperate regions of Japan. Although no species showed clear-cut geographical distributions of the 2–14 haplotypes identified, spatially constrained Bayesian clustering showed two clusters in five species (Calamagrostis epigejos, Eragrostis ferruginea, Imperata cylindrica, Microstegium japonicum, and Microstegium vimineum) but not for others. Posterior modes of clusters for I. cylindrica and M. vimineum showed delineations at Chubu (the middle of Honshu Island), which divide the study region into northeastern and southwestern regions, indicating that these species had recovered from glacial refugia. Posterior mode of cluster for E. ferruginea showed that one consists of a coastal zone along the Pacific Ocean side of western Japan, while the other consists of the remaining area, indicating range expansion from south coast to north. Delineation of C. epigejos and M. japonicum were unclear. The mixed results indicated that establishing seed transfer zones for herbaceous species in Japan will require phylogeographical studies on a wide range of species that may be suitable for revegetation.

The effect of local pollen donor density (conspecific) and local total tree density (all species) on pollen pool diversity, outcrossing rate, and filled seed ratio were examined in a natural stand of the sub-boreal conifer Picea jezoensis Carr. Seed cones were collected from 17 mother trees, and the percentage of filled seed were calculated for five cones per tree. In addition, local stand density of pollen donors and total trees were investigated within r 30 m from the focal mother trees. Using four polymorphic microsatellite markers, the average pairwise kinship coefficient F S and multilocus outcrossing rate t m were estimated on germinated seedlings sampled from 14 mother trees. F S showed significant positive correlation to local total tree density ( r = 0.541 , p = 0.046 ). Since F S is inversely proportional to the effective number of pollen donors N ep , genetic diversity of pollen pool was decreased in mother trees with higher local total tree density. Applying a generalized linear mixed model to filled seed ratio and local stand density of pollen donors and total trees, a negative impact of local pollen donors on filled seed ratio was found. We conclude that both local stand density as well as global stand density are important in the management of a natural stand of P. jezoensis.