Deletions are enriched within QTL for cavefish traits and genes with evidence of selection. (A) Overlap between deletions and QTLs from previous studies of the Pachón cavefish population (see Supplemental Table S8B). The histogram illustrates the number of deletions fixed in Pachón (F_ST = 1 between Pachón and Río Choy, n = 155 deletions) that were found within Pachón QTL regions in each run of a permutation test that produces a simulated VCF with deletions placed into the genome at random. The dotted line indicates the true number of deletions within QTL regions (98 deletions). (B) Proportion of genes that contain deletions and selective sweeps in three unique gene sets: (PG) Genes containing deletions that are present in the pangenome but did not have a statistical association with cave-morph fish (n = 16,617), (FOCAL) genes containing focal deletions that have a significant association with the cave-morph and are not present in surface fish (n = 1260), and (REUSE) genes that contain a unique focal deletion in each cavefish lineage (n = 67). Genes must have a selective sweep and a deletion in the same cave population. Genes are placed into a category based on their highest level of association (e.g., a gene containing both a PG deletion and a FOCAL deletion is put in the FOCAL category). (C) Proportion of control genes (i.e., genes that contain no insertion or deletion SVs, n = 5265) that contain one or more selective sweeps in each cave population.