Population genetics and systematics of a species-rich clade of Neotropical reef fishes, the tubeblenny genus Acanthemblemaria

Neotropical coral 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 coral reef fish families endemic to the Neotropics. Within the chaenopsids, the genus Acanthemblemaria is the most species-rich. To understand the origin and maintenance of genetic and species diversity in these fishes, I characterized the population genetics for two Acanthemblemaria species, reconstructed the phylogeny of the group, and identified suites of correlated morphological characters responsible for the distinctive skull morphology of these fishes. By combining nuclear and mitochondrial sequence data I was able to recover the complex demographic history of two closely related Acanthemblemaria species, A. aspera and A. spinosa. Old population expansions in both species were obscured by a rapid mitochondrial substitution rate, but the mitochondrial DNA allowed the recovery of a recent expansion in A. aspera corresponding to a period of increased habitat availability. However, the older expansions that took place in both species were only recovered using the nuclear markers. Across the genus I found that mitochondrial COI is evolving nearly 100X faster than the nuclear markers and at an absolute rate of nearly 25% pairwise sequence divergence per million years. Replicate Bayesian phylogenetic analyses failed to converge on the same posterior distributions because proposals to update the rate multiplier parameter were rarely accepted, but when the tuning parameter was adjusted, all datasets converged quickly on to the same posterior distribution. When COI was included, posterior probabilities of the species tree were lower and topological estimates were worse than those from the nuclear-only dataset. The species tree that was constructed for the genus conflicted with the morphological phylogeny for the group, primarily due to the convergence of skull bones with spines. By performing phylogenetic analyses on these characters, I resolved some of the conflicts between the morphological and molecular phylogenies. Divergence time estimates recovered a mid-Miocene origin for the genus, with speciation both before and after the closure of the Isthmus of Panama. Some sister taxa were broadly sympatric, but many occur in allopatry