Genetic Diversity and Structure of Quercus hondae, a Rare Evergreen Oak Species in Southwestern Japan

Conservation of rare species is essential for maintaining ecosystem function. Quercus hondae is a rare evergreen oak species (Cyclobalanopsis) endemic to Japan. This species is found in several locations in Southwestern Japan; small populations remain in the tutelary forests of the Japanese shrine. To evaluate the genetic diversity and phylogeographic structure of this rare species, 11 microsatellite loci and chloroplast DNA sequences are analyzed for 12 populations of Q. hondae and 8 populations of the more widespread congeneric species, Q. glauca. It is found that heterozygosity at both the population and species level is substantially lower in Q. hondae than in Q. glauca. Genetic differentiation among populations of Q. hondae was high, in contrast to Q. glauca, in which populations exhibit largely insignificant differentiation. STRUCTURE analysis shows that at K = 7, the clusters largely corresponded to major predefined populations. This study suggests that there is little gene flow among extant Q. hondae populations and that Q. hondae is genetically differentiated due to the greater effect of genetic drift in small populations. This pattern is in sharp contrast to that of a more common congeneric species, which will be an important consideration in the conservation of Q. hondae.