Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae)

Neotropical cichlid fishes comprise approximately 60 genera and at least 600 species, but despite this diversity, their phylogeny is only partially understood, which limits taxonomic, ecological and evolutionary research. We report the largest molecular phylogeny of Neotropical cichlids produced to date, combining data from three mitochondrial and two nuclear markers for 57 named genera and 154 species from South and Central America. Neotropical cichlids (subfamily Cichlinae) were strongly monophyletic and were grouped into two main clades in which the genera Retroculus (Tribe Retroculini) and Cichla (Cichlini) were sister to a monophyletic group containing all other lineages. This group included the tribes Chaetobranchini, Astronotini, Geophagini, Cichlasomatini and Heroini. Topological comparisons with previously published hypotheses indicated that our results are congruent with recent analyses of the tribe Cichlasomatini, but significantly more likely than published hypotheses for Geophagini, Heroini and the entire Cichlinae. Improved resolution and support are attributed to increased taxon sampling and to the addition of taxa never before included in phylogenetic analyses. Geophagini included two major subclades congruent with our own previous findings but more strongly supported; we also found a new and strongly supported sister-group relationship between Guianacara and Mazarunia. Cichlasomatini relationships were similar to recently proposed topologies, but contrastingly, we found a monophyletic Cichlasoma and support for a monophyletic grouping of the Aequidens diadema and A. tetramerus groups. Three basal South American Heroini lineages were recovered: (Hypselecara+Hoplarchus), Pterophyllum, and a grouping we refer to as mesonautines. Three other South American clades, caquetaines, Australoheros and the 'Cichlasoma'festae group, were nested within Central American clades. Most Heroini diversity was divided into two relatively well-supported large groups: the Southern Central American Clade, including clades herein referred to as nandopsines, caquetaines and amphilophines, and the Northern Central American Clade, including astatheroines, tomocichlines and herichthyines. Some of these groups have been previously identified, but often with different taxonomic compositions. Further resolution of Neotropical cichlid relationships, especially within the large amphilophine clade of Heroini, will require additional phylogenetic analysis. Nevertheless, the topology from this study provides a robust phylogenetic framework for studying evolutionary diversification in Neotropical cichlids. Significantly-short branches at the base of Geophagini and Heroini are compatible with early bursts of divergence that are characteristic of adaptive radiations. This pattern suggests diversification of Neotropical cichlid genera occurred rapidly, with subsequent convergent, adaptive ecomorphological diversification among and within South and Central American clades.