Neotropical rivers are home to the largest assemblage of freshwater fishes, but little is known about the phylogeny of these fishes at the species level using multi-locus molecular markers. Here, we present a phylogeny for all known species of the genus Satanoperca, a widespread group of Neotropical cichlid fishes, based on analysis of six unlinked genetic loci. To test nominal and proposed species limits for this group, we surveyed mtDNA sequence variation among 320 individuals representing all know species. Most nominal species were supported by this approach but we determined that populations in the Xingu, Tapajós, and Araguaia+Paraná Rivers are likely undescribed species, while S. jurupari and S. mapiritensis did not show clear genetic distinction. To infer a phylogeny of these putative species, we conducted maximum likelihood and Bayesian non-clock and relaxed clock analyses of concatenated data from three genes (one mitochondrial, two nuclear). We also used a multi-species coalescent model to estimate a species tree from six unlinked loci (one mitochondrial, five nuclear). The topologies obtained were congruent with other results, but showed only minimal to moderate support for some nodes, suggesting that more loci will be needed to satisfactorily estimate the distribution of coalescent histories within Satanoperca. We determined that this variation results from topological discordance among separate gene trees, likely due to differential sorting of ancestral polymorphisms.
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