TL;DR: The resulting strict consensus tree topology generally agreed with the previous molecular hypothesis, and recovers a monophyletic Pomacentridae and subfamily Amphiprioninae and the two other subfamilies included, Chrominee and Pomacentrinae, were found to be polyphyletic.
TL;DR: The present study will serve the dual purpose of establishing a current species list for Malaysia and Singapore, and to update and clarify the local taxonomy of the Pomacentridae to aid studies on reefs.
Abstract: Damselfishes (Pomacentridae) are among the most common of reef fishes in tropical seas, comprising 320 species in all, with 268 species alone in the Indo-West Pacific regions. 15 genera (Abudefduf Amblyglyphidodon, Amphiprion, Chelioprion, Chromis, Chrysiptera, Dascyllus, Pristotis, Dischistodus, Hemig-lyphidodon, Neoglyphidodon, Neopomacentrus, Plectroglyphidodon, Pomacentrus, Stegastes) and at least 39 species inhabit the waters of Peninsular Malaysia and Singapore. They are important ecologically because many species are extremely abundant in reefs, and also economically, as several are collected in large numbers for the lucrative aquarium trade. This demand has led to some fishermen using destructive methods in obtaining the fishes, to the point that original standing populations may not be recoverable. This threat poses a need for conservation of the reefs. The present study based primarily on fishes collected from the waters of Singapore and specimens from the Zoological Reference Collection at the National University of Singapore, will serve the dual purpose of establishing a current species list for Malaysia and Singapore, and to update and clarify the local taxonomy of the group. An annotated list (with localities) is provided of the known or reported species to aid studies on reefs.
TL;DR: The Bayesian method of phylogenetic reconstruction was applied to the data, because even with a large number of sequences it is an efficient means of analysis that provides intuitive measures of support for tree topologies and for the parameters of the nucleotide substitution model.