PTC distribution by population. a) Distribution of PTCs in cave and surface Mexican tetra populations. The number of PTCs shown for each population is the total PTCs found in the population divided by the number of individuals sampled. While both cave and surface populations have many PTCs within the population and fewer PTCs which occur at high frequency, cave populations harbor significantly more PTCs at high frequency than are present in surface populations. b) Total PTCs found in each cave broken down by presence in other cave populations (number of PTCs normalized by population sample size). PTCs unique to one cave are found only in the focal cave population. PTCs also present in caves from the same lineage are shared in one or more caves from the same lineage as the focal cave. Finally, PTCs present in caves from both lineages are found in at least one cave from each lineage. As expected, PTCs are shared more frequently among caves from the same evolutionary lineage than between lineages. c) Comparison of total and high-frequency PTCs found on chromosome 12 in surface, cave, and simulated populations. Values for Rio Choy (n = 9), Mante (n = 10), Rascón (n = 14), and Pachón (n = 19) are the observed PTC counts found in the population genomic dataset. Values for SLiM simulated cave populations (population size 1 thousand, 32 thousand, and 250 thousand individuals, respectively) are from 19 random individuals (same sample size as Pachón) output at the end of the simulation (see Materials and Methods).