Detecting inter- and intra-island genetic diversity: population structure of the endangered crocodile newt, Echinotriton andersoni, in the Ryukyus

The endangered crocodile newt, Echinotriton andersoni, is a relatively large species of the family Salamandridae and is distributed on six islands in the central part of the Ryukyu Archipelago, Japan. Because of an originally small distribution range and recent habitat loss, this species has been steadily declining in number. To elucidate fine-scale population structure, which is essential for effective conservation management, we analyzed genetic diversity and gene flow based on nine microsatellite loci. Our results identified three different island groups (Amamioshima, Tokunoshima, and Okinawajima) and multiple genetic assemblages within the Amami and Okinawa island groups. The gross genetic variation within each island was positively correlated with island size. Population structure followed a latitudinal cline and isolation by distance, even among geographically isolated islands. In northern Okinawajima, relatively complex genetic structure was observed. This unexpected population structure seems to reflect historical migration and distribution expansion through the formation of land bridges and shifted coastlines in the Pleistocene. We also found that small islands showed little genetic variation (Ukeshima, Sesokojima, and Tokashikijima). In particular, our findings revealed that the Tokashikijima population is at greater risk for extinction than the other populations because it has the smallest effective population size.