Abstract
Background Fish of the genus Astyanax are known to be able to adapt to a wide range of ecological conditions and are especially known for repeated colorizations of cave systems. In lakes they often occur in species pairs. In the case we study here, they show major morphological differences, such that they were originally classified in different genera. Previous studies have shown that these morphological differences correlate with occupation of different trophic niches. Hence, this could be an example of ecological speciation under sympatric conditions, which predicts that differential ecological adaptation becomes coupled to assortative mating and to the formation of genetically distinct groups that may be called species. We have tested this prediction by typing a set of microsatellites for the two morphs in the lake in comparison to an allopatric population.Results While we find the expected differentiation with respect to the allopatric population, there is a complete lack of genetic differentiation between the two morphs within the lake. Hence, the two morphs in the lake are either in an extremely early phase of speciation or represent two extreme morphotypes derived from a single gene pool.Conclusions Even when we failed to recover the two morphs as reproductively isolated, this model provides a unique opportunity to characterize those factors that would promote the ecological divergence, thus, our lacustrine morphs system gives a unique opportunity to understand the genetic basis of how morphological divergence in the presence of gene flow.