Exploring the radiation of a diverse reef fish family: Phylogenetics of the damselfishes (Pomacentridae), with new classifications based on molecular analyses of all genera W. James Cooper a,b, * , Lydia L. Smith b,c , Mark W. Westneat a,b a Department of Organismal Biology & Anatomy, University of Chicago, Chicago, IL 60637, USA b Department of Zoology, Field Museum of Natural History, Chicago, IL 60605, USA c Evolutionary Genetics Laboratory, The Museum of Vertebrate Zoology, The University of California, Berkeley, CA 94720-3160, USA article info Article history: Received 11 June 2008 Revised 27 November 2008 Accepted 10 December 2008 Available online 24 December 2008 Keywords: Pomacentridae Damselfish Perciformes Coral reef Reef fish Mitochondrial DNA Nuclear DNA Bayesian abstract The damselfishes (Perciformes, Pomacentridae) are an important family of marine reef fishes that occupy a range of ecological positions in the world’s oceans. In order to determine the evolutionary pattern of their radiation, we used multiple methods to examine molecular data from 104 species representing all extant genera. The analysis of 4291 DNA nucleotides (1281 bp were parsimony informative) from three nuclear genes (rag-1, rag-2 and bmp-4) and three mitochondrial genes (12s, 16s and nd3), produced well-resolved phylogenies with strong evidence for a monophyletic Pomacentridae, and support for five major damselfish clades. We found that the monotypic subfamily Lepidozyginae evolved early in the pomacentrid radiation. The placement of the genus Altrichthys indicates that brood care has evolved at least twice among the damselfishes. The subfamilies Chrominae and Pomacentrinae, and the genera Abu- defduf, Chromis, Chrysiptera, Plectroglyphidodon, and Stegastes, were always found to be polyphyletic, and monophyly was rejected for the genus Amphiprion by almost every analysis. All phylogenetic studies of the Pomacentridae have indicated that their taxonomy is in need of revision at multiple levels. We pro- vide a new classification scheme wherein each subfamily is now monophyletic, and this reorganization is consistent with all previous molecular studies of the damselfishes. The Chrominae are restricted to the genera Chromis and Dascyllus; the Pomacentrinae now represent a lineage of 16 genera that constitute a major, and relatively recent, radiation of coral reef fishes throughout the Indo-West Pacific; we erect the new subfamlies Abudefdufinae and Stegastinae; we relegate the anemonefishes (the Amphiprioninae sensu Allen) to the tribe Amphiprionini within the Pomacentrinae, and synonomize the genus Azurina with Chromis. Ó 2008 Elsevier Inc. All rights reserved. 1. Introduction The damselfishes are a species-rich, widely distributed family of reef fishes that inhabit tropical and temperate near-shore waters around the world, with their greatest diversity residing on coral reefs (Allen, 1991; Alwany et al., 2005; Bellwood and Hughes, 2001; Ceccarelli et al., 2001; Eagle and Jones, 2004; Jones, 1992; McCormick, 2003). In order to understand how these marine communities have acquired their current patterns of liv- ing diversity, it is necessary to understand the evolution and radi- ation of their component groups. Whereas the pomacentrids currently comprise an important part of these ecological patterns, and are known to have been inhabitants of coral reefs for the past 50 million years (Bellwood, 1996; Bellwood and Sorbini, 1996), it is probable that their role in the evolution of coral reef commu- nity structure has been significant. Describing this role requires detailed knowledge of pomacentrid relationships. The aim of this project was to provide a better understanding of damselfish phy- logenetics in order to more clearly describe the manner in which this lineage has come to occupy its current place in modern reef communities. The primary significance of this study is that it examines molecular data for all damselfish genera, and includes a greater number of informative characters than has been previ- ously analyzed for a dataset containing this many pomacentrid species. Damselfishes are relatively small acanthopterygian fishes (no larger than 30.0 cm) that are distinguished by possessing, among other characters, a single nostril on each side of the head, two anal spines, an incomplete lateral line, a single dorsal fin that is well-developed, small teeth and scales, and a smooth palate (Al- len, 1991; Bellwood and Sorbini, 1996; Bleeker, 1877; Günther, 1055-7903/$ - see front matter Ó 2008 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2008.12.010 * Corresponding author. Present address: Department of Biology, Syracuse University, 130 College PL, Syracuse, NY 13244, USA. Fax: +1 315 443 2012. E-mail address: wjcooper@syr.edu (W. James Cooper). Molecular Phylogenetics and Evolution 52 (2009) 1–16 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev