Basin isolation and oceanographic features influencing lineage divergence in the humbug damselfish (Dascyllus aruanus) in the Coral Triangle

The Coral Triangle is a hotspot for marine species diversity as well as for intraspecific genetic diversity. Here, we used nuclear RAG2 and mitochondrial D-Loop genes to identify deep genetic divergence among Dascyllus aruanus (Linnaeus, 1758) populations across relatively short scales within the Coral Triangle. Mitochondrial clades different by >20 mutational steps were completely isolated from one another across the distance between Java and the Lesser Sunda Islands, and also showed frequency differences in the eastern and western Philippines. Evidence for population structure in the Sulu Sea and at the Lesser Sunda Islands was also identified. Our results suggest that the Sulu Sea Throughflow, Bohol Sea Throughflow, Indonesian Throughflow, signatures of extinction events from Pleistocene land barriers, and other past and present forces may be potential factors leading to lineage divergence of D. aruanus, and that these hypotheses should be tested in further studies.