Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found that phenotypic convergence is due to parallel genetic changes. This suggests a substantial role for constraint and determinism in evolution and indicates that certain mutations are more likely to contribute to phenotypic evolution. Here we use whole-genome resequencing in the Mexican tetra, Astyanax mexicanus, to investigate how selection has shaped the repeated evolution of both trait loss and enhancement across independent cavefish lineages. We show that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Our findings provide empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the cave environment may impact the rate at which mutations occur.

The data is comprised of summary statisitcs and annotations for each gene in the assembly Astyanax_mexicanus-2.0 GCF_000372685.2. These data were generated using whole genome sequences from a total of 248 Astyanax mexicanus individuals across 18 cave and eight surface populations throughout the range of A. mexicanus in northeastern and central Mexico. We conducted scans for selection within populations and generated population genetic statistics. We also used Ensembl's biomart tool to retrieve phenotype annotations and GO terms associated with each gene in the genome.