Quercus is attractive for evolutionary studies, primarily for developing the concepts of the species, speciation and adaptation; however, remarkably little is known about levels of nucleotide polymorphism in the nuclear functional genes of this genus. This article provides the first characterization of levels of nucleotide polymorphism in 11 gene fragments in natural populations of a Quercus species, Quercus crispula Blume. Results show that the level of nucleotide variation in this oak is generally higher than that in conifers, as high as that in a European oak, but lower than that in an aspen. The level of population recombination is relatively high. Withinpopulation inbreeding is negligible and between-population differentiation is modest. The decay of linkage disequilibrium is significantly faster in the species-wide samples and the three northernmost populations than in the other populations. Statistical tests support the hypothesis of a recent bottleneck for several populations in the southern part of Japan. The amounts and patterns of nucleotide variation, recombination and linkage disequilibrium, and genetic differentiation observed among populations of this species are contradictory to our expectations, given the recent colonization history of the northern Japan populations.

Genetic variation of the mangrove genus Kandelia (Rhizophoraceae) in the South China Sea region, in four populations in Vietnam and in one population each in Iriomote, Japan, and Bako, Borneo, was evaluated using microsatellite markers. A total of 54 alleles in the six populations were detected by using four microsatellite loci. The two northern Vietnamese populations (Don Rui and Xuan Thuy) showed a high allelic diversity (40 alleles in total) and a high level of gene diversity (H E = 0.773 on average). In contrast, the two southern Vietnamese populations (Can Gio and Ngoc Hien) showed low allelic diversity (11 alleles in total) and a low level of gene diversity (H E = 0.244 on average). There was only one allele common to the two regions. The Iriomote population was genetically related to the northern Vietnamese populations, while the Bako population was related to the southern populations. The findings and the morphological observations indicate that these two genetically differentiated vicariant lineages represent two different species groups, Kandelia obovata Sheue, Liu, and Yong for northern Vietnam and Japan and Kandelia candel (L.) Druce for southern Vietnam and Borneo. The difference in the amount of genetic variation shows that these two species experienced a different adaptive process during the past glacial ages.

Genetic variation is usually high within populations, and differentiation is usually low among populations of wind-pollinated outcrossing trees. As a result, population contraction causes little change in the degree of genetic diversity and differentiation among populations. The aim of this work was to determine whether or not a recent population decline has influenced the allele frequency spectrum and association among variants of different sites on the nuclear housekeeping locus methionine synthase (1376-1418 bp in length) in the oak species Quercus mongolica var. crispula. A total of 122 sequences from 18 populations were randomly sampled and analyzed in this study. Results showed that nucleotide variation was generally high within populations, and differentiation was very low among populations. Genetic diversity was slightly reduced in samples taken from the area with a recent strong reduction in population size. Nevertheless, the allele frequency spectrum was skewed toward rare variants, and the association among variants of different sites was significantly more nonrandom within these samples compared with those from the area without such a population size reduction. This pattern was robustly supported by coalescent simulations.