Molecular phylogeny reveals extensive ancient and ongoing radiations in a snapping shrimp species complex (Crustacea, Alpheidae, Alpheus armillatus).

Tropical marine habitats often harbor high biodiversity, including many cryptic taxa. Though the prevalence of cryptic marine taxa is well known, the evolutionary histories of these groups remain poorly understood. The snapping shrimp genus Alpheus is a good model for such investigations, as cryptic species complexes are very common, indicating widespread genetic diversification with little or no morphological change. Here, we present an extensive phylogeographic investigation of the diversified amphi-American Alpheus armillatus species complex, with geographic sampling in the Caribbean Sea, Gulf of Mexico, Florida, Brazil, and the tropical Eastern Pacific. Sequence data from two mitochondrial genes (16SrRNA and cytochrome oxidase I) and one nuclear gene (myosin heavy chain) provide strong evidence for division of the species complex into six major clades, with extensive substructure within each clade. Our total data set suggests that the A. armillatus complex includes no less than 19 putative divergent lineages, 11 in the Western Atlantic and 8 in the Eastern Pacific. Estimates of divergence times from Bayesian analyses indicate that the radiation of the species complex began approximately 10 MYA with the most recent divergences among subclades dating to within the last 3 MY. Furthermore, individuals from the six major clades had broadly overlapping geographic distributions, which may reflect secondary contact among previously isolated lineages, and have apparently undergone several changes in superficial coloration, which is typically the most pronounced phenotypic character distinguishing lineages. In addition, the extensive substructure within clades indicates a great deal of molecular diversification following the rise of the Isthmus of Panama. In summary, this investigation reflects substantial biodiversity concealed by morphological similarity, and suggests that both ancient and ongoing divergences have contributed to the generation of this biodiversity. It also underlines the necessity to work with the most complete data set possible, which includes comprehensive and wide-ranging sampling of taxa.