Population genetic structure of the insular Ryukyu flying fox Pteropus dasymallus

Small isolated populations are vulnerable to both stochastic events and the negative consequences of genetic drift. For threatened species, the genetic management of such populations has therefore become a crucial aspect of conservation. Flying foxes (Pteropus spp, Chiroptera) are keystone species with essential roles in pollination and seed dispersal in tropical and subtropical ecosystems. However, many flying fox species are also threatened, having experienced dramatic population declines driven by habitat loss and hunting. The insular Ryukyu flying fox (Pteropus dasymallus) ranges from the Ryukyu Archipelago of Japan through Taiwan to the northern Philippines and has undergone precipitous population crashes on several islands in recent decades. To assess the population genetic structure and diversity in P. dasymallus, and its likely causes, we analyzed mitochondrial and microsatellite DNA. Both markers showed significant genetic differentiation among most island populations, with mitochondrial haplotypes showing some mixing across the region, likely reflecting historical colonization and/or dispersal events. In contrast, microsatellite markers showed an overall pattern of isolation by distance; however, this pattern appeared to be driven by the presence of deep ocean trenches between geographically distant populations. Thus the current distribution of P. dasymallus and its subspecific diversity appears to have arisen through vicariance coupled with a long history of restricted gene flow across oceanic barriers. We conclude that isolated island subgroups should be managed separately, with efforts directed at reducing further declines in genetic diversity.