Genotypes of cave, surface and hybrid Astyanax mexicanus

Genetic divergence in the presence of gene flow has been well documented, but there is little information on the specific factors maintaining divergence. The present study investigates this in the Mexican tetra (Astyanax mexicanus), an excellent model for studying this question because surface and cave populations differ markedly in phenotype and genotype, but are interfertile.  Previous population studies documented significant gene flow among cave and surface populations but they focused on analyses of neutral markers, whose evolutionary dynamics likely differ from those of genes involved in cave adaptation. The present study advances our understanding of this question by focusing specifically on the genetics responsible for eye and pigmentation reduction, signature traits of cave populations. Direct observations of two cave populations over the course of 63 years verify that surface fish frequently move into the caves and even hybridize with the cavefish. Importantly, however, historical records show that surface alleles for pigmentation and eye size do not persist, but are rapidly eliminated from the cave gene pool. It has been argued that the regression of eyes and pigmentation was driven by drift, but the results of this study suggest that strong selection actively eliminates surface alleles from the cave populations. 

Methods
The data consist of genotypes of surface and cave fishes and their hybrids as determined by the use of an ABI automated sequencer.