Population genomics of Gymnogeophagus labiatus and G. lacustris reinforces the role of hydrographic isolation between evolutionary lineages (Cichlidae: Geophagini)

Gymnogeophagus labiatus and G. lacustris represent a pair of sister taxa distributed in Southern Brazil and Uruguay. G. labiatus has been traditionally assigned to the Patos Lagoon (ELP) and Tramandai-Mampituba (ETM) ecoregions, while G. lacustris was endemic to ETM. G. labiatus is distinguished from G. lacustris by its hypertrophied lips, which represent an adaptation for foraging in rocky environments, and by the variation in coloration. A recent study using mtDNA and morphological data challenged this interpretation and suggested that G. labiatus is exclusive of ELP, and that all individuals in ETM should be considered G. lacustris. In this work we generated ddRADseq genome data to evaluate the evolutionary relationships between these species. The results corroborated early findings that each ecoregion harbors an independent evolutionary lineage, and that all individuals in ETM represent G. lacustris. Our results do not support the idea that lacustrine and riverine populations in ETM represent a case of recent speciation. However, we found evidence for secondary contact between G. labiatus and the riverine population of G. lacustris, suggesting that the hypertrophied lips in both groups may have a common genetic background, and may indicate an instance of adaptive introgression.