Reconciling molecules and morphology: Molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria)

Neotropical reef fish communities are species-poor compared to those of the Indo-West Pacific. An exception to that pattern is the blenny clade Chaenopsidae, one of only three rocky and coral reef fish families largely endemic to the Neotropics. Within the chaenopsids, the genus Acanthemblemaria is the most species-rich and is characterized by elaborate spinous processes on the skull. Here we construct a species tree using five nuclear markers and compare the results to those from Bayesian and parsimony phylogenetic analyses of 60 morphological characters. The sequence-based species tree conflicted with the morphological phylogenies for Acanthemblemaria, primarily due to the convergence of a suite of characters describing the distribution of spines on the head. However, we were able to resolve some of these conflicts by performing phylogenetic analyses on suites of characters not associated with head spines. By using the species tree as a guide, we used a quantitative method to identify suites of correlated morphological characters that, together, produce the distinctive skull phenotypes found in these fishes. A time calibrated phylogeny with nearly complete taxon sampling provided divergence time estimates that recovered a mid-Miocene origin for the genus, with a temporally and geographically complex pattern of speciation both before and after the closure of the Isthmus of Panama. Some sister taxa are broadly sympatric, but many occur in allopatry. The ability to infer the geography of speciation in Acanthemblemaria is complicated by extinctions, incomplete knowledge of their present geographic ranges and by wide-spread taxa that likely represent cryptic species complexes.