Strong genetic structure and limited connectivity among populations of Clark’s Anemonefish ( Amphiprion clarkii ) in the centre of marine biodiversity

Populations of anemonefish species often show signs of local isolation due to limited dispersal potential and oceanographic conditions. Additionally, anthropogenic pressure, such as overharvesting and coral reef exploitation causes reduced population size, eventually leading to local extinction. The understanding of the genetic population structure, as well as the influence of both historical and current connectivity, is required to design effective marine protected area (MPA) networks. In this study, the genetic structure of Clark’s Anemonefish (Amphiprion clarkii ) based on 209 individuals from 16 samples sites in the Indo-Malay Archipelago (IMA) is assessed through mitochondrial control region (mtCR) sequences and eight nuclear microsatellite loci. Results provided evidence of a significant genetic structure (mtCR: Φ st = 0.42, Φ ct = 0.64; microsatellites: F st = 0.01, F ct = 0.05). Genetic breaks were identified among Western (Padang Karimunjawa), Central (Sulawesi, Borneo, Bali, Komodo, Timor) and Eastern (Biak) IMA populations, with almost no gene flow. This matches with patterns obtained for congeneric and other coral reef taxa. Due to the restricted connectivity among these three regions, it is suggested to consider them as separate management areas in the design of MPA networks.