Genetic population structure and demographic history of an endangered frog, Babina holsti

Babina holsti is a ranid frog that occurs on northern Okinawa (Yanbaru) and Tokashiki Islands of southwest Japan. Because of its narrow distribution and recent habitat destruction, its population size is believed to have decreased, and the species has been listed as an endangered species on the IUCN Red List. To promote effective conservation management, we examined the population structure, gene flow, and demographic history of B. holsti using a mitochondrial gene and 12 microsatellite loci. The population structure analyses first distinguished the Tokashiki Island population from the Yanbaru ones. The Yanbaru populations were further divided into main and southernmost populations. Large genetic differences were detected between the Tokashiki and Yanbaru populations, and their divergence time was estimated as 0.38 Mya. Based on demographic analyses on Yanbaru, population expansion generally occurred after the last glacial period and then decreased rapidly. Specifically, only the southern Yanbaru populations have experienced a population decline within the past 5000 years. These results suggested that prehistoric geographic events may have affected the historical population decline on Yanbaru. On Tokashiki, the lowest genetic diversity and a significant population bottleneck were detected, both probably caused by scarcer environmental resources. These results are beneficial to sustainable conservation management of B. holsti, especially the conservation priority of the populations in Tokashiki and southern Yanbaru.