Molecular phylogeny of the family Pomacentridae (Actinopterygii, Perciformes) inferred from mitochondrial 16S rDNA sequences

Damselfish (Actinopterygii, Perciformes, Pomacentridae) are a diverse and widespread family consisting primarily of marine fish found throughout tropical oceans, and they are major members of coral reef communities. The phylogenetic relationships among the pomacentrids are highly controversial due to their dramatic and complicated morphological variations, and there are striking differences between the traditional phylogeny, which is based on morphologies, and the molecular phylogeny, which is based on DNA sequences. In the present study, the phylogenetic relationships among the pomacentrids were investigated using partial mitochondrial 16S rDNA sequences from 40 species, 19 genera, and 3 subfamilies. The partial 16S rDNAs from the four pomacentrid species (Pomacentrus coelestis, Pomacentrus bankaensis, Chromis fumea and Abudefduf vaigiensis) were newly sequenced in this study. Bayesian analysis based on the 16S rDNA sequences reveals that the family Pomacentridae (BPP 74%) and the subfamily Amphiprioninae (99%), Dascyllus (90%), Stegastes (100%) and Abudefduf (100%) are monophyletic groups. However, this study also shows that the subfamily Pomacentrinae may be divided into a primitive Assemblage I and an advanced Assemblage II. Pomacentrinae Assemblage II and the subfamily Amphiprioninae are grouped together (96%), and Assemblage II appears to be paraphyletic to the subfamily Amphiprioninae. Mecaenichthys immaculatus and Acanthochromis polyacanthus, which have traditionally been considered putative chromine members, appear with Chromis cyanea within Assemblage I and within Pomacentrinae Assemblage II, respectively. This study also reveals that Chromis, Amphiprion and Chrysiptera may not be monophyletic groups. These results are generally coincident with previous molecular findings. It is very likely that the traditional pomacentrid classification scheme needs to be thoroughly re-examined.