H. cyanoguttasH. minckleyi Raw sequence reads

Resource polymorphism in vertebrates has the potential to be a diversifying force leading to population divergence and speciation. In several diverse taxa, discrete intraspecific morphs show differential resource use and varying degrees of reproductive isolation. Alternatively, resource polymorphism may phenotypically characterize hybridizing lineages that are in the process of collapsing into one species. We used high through-put DNA sequencing to investigate the evolutionary factors involved in the maintenance of alternate morphotypes in a highly variable species of cichlid, Hericthys minckleyi. H. minckleyi is endemic to the Cuatro Cie´negas valley, in northern Mexico. Pharyngeal tooth size divides the species into two discrete phenotypes, with associated feeding differences. Within the valley, both pharyngeal morphotypes are found together in a series of spring- fed pools. We found evidence of genetic differentiation between allopatric populations of H. minckleyi in the Cuatro Cie´negas valley but found little genetic differentiation between the sympatric alternate morphotypes. We were not able to detect nuclear introgression between H. minckleyi and a closely related species, H. cyanoguttatus and thus did not find support for the hypothesis that alternate morphotypes may represent collapsing hybridizing lineages. These results may indicate either parallel evolution of the two morphotypes in allopatric populations or no reproductive isolation between morphotypes, despite morphological and behavioral differentiation. Further work is required to delineate the complex evolutionary relationships and the factors involved in the maintenance of alternate morphotypes in this system.