Data from: Untangling the evolutionary history of a highly polymorphic species: introgressive hybridization and high genetic structure in the desert cichlid fish Herichthys minckleyi

Understanding the origin of biodiversity requires knowledge on the evolutionary processes that drive divergence and speciation, and also on the ones constraining it. Intraspecific polymorphisms can provide insights into the mechanisms that generate and maintain phenotypic, behavioural, and life-history diversification, and can help us understand not only the processes that lead to speciation but also the ones that prevent the local fixation of morphs. The “desert cichlid” Herichthys minckleyi is an example of a highly polymorphic species endemic to a biodiversity hotspot in northern Mexico, the Cuatro Ciénegas valley. This species is polymorphic in body shape and trophic apparatus, and eco-morphotypes coexist in small spring-fed lagoons across the valley. We investigated the genetic structure of these polymorphisms, and their phylogeographic history by analysing the entire control region of the mitochondrial DNA and 10 nuclear microsatellite markers in several populations from different sites and morphs. We found two very divergent mitochondrial lineages that most likely pre-date the closing of the valley and are not associated with morphotypes or sites. One of these lineages is also found in the sister species H. cyanoguttatus. Data from neutral microsatellite markers suggest that most lagoons or drainages constitute their own genetic cluster with sympatric eco-morphotypes forming panmictic populations. Alternative mechanisms such as phenotypic plasticity, single gene controlled traits or counteracting multifarious selection might be likely explanations for the sympatric coexistence of discrete non-overlapping eco-morphotypes with apparent lack of barriers to gene flow within multiple lagoons and drainages.