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We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of Central American cichlid fishes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanning the geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade, with a relatively diverged subclade corresponding to A. kanna samples from eastern Costa Rica and Panama. Gene trees and networks revealed marked incongruences between phylogeographic structure and morpho-species taxonomy as a result of species-level polyphyly. Bayes factor comparisons of species delimitation models accounting for incomplete lineage sorting under the multispecies coalescent decisively supported the recognition of two distinct species within Amatitlania corresponding to Amatitlania nigrofasciata and A. kanna lineages. The only clearly genetically and morphologically diagnosable species was A. kanna. These results strongly suggest that incomplete lineage sorting provides the best explanation for the polyphyly of A. kanna, whereas the polyphyly of A. siquia is likely a result of an imperfect taxonomy. Additional insights from coalescent-dating, network, and historical demographic analyses suggested that the two species of Amatitlania diversified only since the early Pleistocene, and that A. nigrofasciata experienced population expansions from approximately 200 000 years ago in the mid-late Pleistocene onward. We discuss implications of our results for the taxonomy and evolutionary history of Amatitlania and, more broadly, of Central American freshwater fishes.

For groups of animals with limited or unstable taxonomic resolution, congeneric phylogeographical sampling represents a way to potentially increase resolution of species limits and internal branches during phylogenetic inference. We investigated species limits and whether there was better support for hypothesized relationships among Micropterus (black basses) using wide geographical sampling. Bayesian and maximum likelihood estimates of Micropterus phylogeny including 205 mitochondrial DNA cytochrome b (1140 bp) sequences (150 haplotypes) representing eight extant species and one subspecies recovered eight well-supported clades. Haplotypes from fish identified as Micropterus coosae, Micropterus henshalli, Micropterus punctulatus, Micropterus salmoides, and Micropterus treculii created eight forms of broad-sense polyphyly in the tree, which we hypothesized were the result of incomplete lineage sorting and hybridization-mediated introgression (natural and anthropogenic, i.e. associated with stocking). Our findings mostly agree with hypothesized relationships. However, they provide a more complex view of Micropterus biodiversity, highlighting population-level processes. Our data also provide a useful guide for expanding character sampling (nuclear loci and morphology) to evaluate the history, distinctiveness, and geographical distributions of genetic lineages within and among black basses. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 346–363.