Microsatellite markers can yield high-resolution genetic profiles for individual identification, and for parentage analysis, when evaluating gene dispersal in populations. Fagus crenata is an important dominant species in the cool temperate forests in Japan, and although many studies on the species have been conducted the patterns of gene dispersal via pollen and seeds are poorly understood. In order to be better informed about gene dispersal in Fagus crenata , we have developed 16 new microsatellite loci from an enriched library of genomic DNA. These 16 loci were highly variable, with 3-40 alleles per locus and an expected heterozygosity value of 0.11-0.98.

The within-population genetic structure of Fagus crenata in a 4-ha plot (200 x 200 m) of an old-growth beech forest was analysed using microsatellite markers. To assess the genetic structure, Moran's I spatial autocorrelation coefficient was calculated. Correlograms of Moran's I showed significant positive values less than 0.100 for short-distance classes, indicating weak genetic structure. The genetic structure within the population is created by limited seed dispersal, and is probably weakened by overlapping seed shadow, secondary seed dispersal, extensive pollen flow and the thinning process. Genetic structure was detected in a western subplot of 50 x 200 m with immature soils and almost no dwarf bamboos (Sasa spp.), where small and intermediate-sized individuals were distributed in aggregations with high density because of successful regeneration. By contrast, genetic structure was not found in an eastern subplot of the same size with mature soils and Sasa cover, where successful regeneration was prevented, and the density of the small and intermediate-sized individuals was low. Moreover, genetic structure of individuals in a small-size class (diameter at breast height < 12 cm) was more obvious than in a large-size class (diameter at breast height >/= 12 cm). The apparent genetic structure detected in the 4-ha plot was therefore probably the result of the structure in the western portion of the plot and in small and intermediate-sized individuals that successfully regenerated under the favourable environment. The heterogeneity in genetic structure presumably reflects variation in the density that should be affected by differences in regeneration dynamics associated with heterogeneity in environmental conditions.

Half-sib family structure of Fagus crenata saplings was examined in an old-growth beechdwarf bamboo ( Sasa spp.) forest using microsatellite genotypes in parentage analysis to identify the half-sib families in two 50 × × × × 50 m plots: one with 36 adults, 641 saplings and no Sasa cover, the other with 21 adults, 61 saplings and Sasa cover. For large proportions of the saplings (44.6% and 75.4%, respectively) both of their parents were found within the same plot, indicating that pollination events frequently involved short-range pollen dispersal, probably because of the high density of adults in the study population. Although almost all of the adults had half-sib families, the number of offspring in the families was highly variable. In the plot with no Sasa cover, the variation in the number of offspring was significantly explained by the size of parents, i.e. the reproductive success is higher for large adults than for small adults. The half-sibs were aggregately distributed around their parents and the distribution overlapped among different half-sib families, which may be due to the limited seed dispersal and overlapping seed shadows of this species. As expected, there was weak genetic structure in the plot. By contrast, in the plot with Sasa cover, the half-sibs were distributed sparsely with a low density, and the degree of genetic structure was very weak. The difference in the half-sib family structure and genetic structure among saplings presumably reflects the difference in density that should be affected by regeneration dynamics associated with environmental conditions.

Pollen-mediated gene flow was analyzed in a small, fragmented, natural population of Fagus crenata Blume by surveying five microsatellite markers in seedlings derived from open-pollinated crosses. Paternity of 162 seedlings derived from two maternal trees was assigned by the maximum-likelihood method using CERVUS 2.0, and pollen dispersal patterns within the study site were determined. Most of the trees within the site sired seeds, although we found evidence of limited pollen-mediated gene flow from outside the stand; 92% of the matings that generated the seedlings occurred between trees within the population, and 8% of the matings were mediated by pollen derived from trees located outside the study site. Although the pollen-mediated gene flow within the site was not strongly limited, mating frequencies of paternal trees were found to be weakly negatively correlated with their distance from the mother trees, positively correlated with their stem diameter at breast height, and uncorrelated with their relatedness to the mother trees.