Shared deletions between and within cavefish lineages. Heatmap depicting results of SV deletion calling from linked-read sequencing. Cells on the diagonal represent the number of deletions (50 bp–100 kb) called in each individual relative to the Río Choy reference after filtering for variants passing all Long Ranger quality filters. Darker cells on the diagonal represent a greater number of deletion calls. Cells within the triangle matrix represent the number of shared deletions between individuals from each pair of populations. Deletions were considered shared if they had 90% reciprocal overlap between populations. This cutoff increases the confidence that the variants originate from a shared SV-generating event, rather than repeated origins in a similar location. Darker cells in the triangle matrix represent a greater number of shared deletions between two populations. More deletions are shared within lineages than between lineages, in accordance with the best supported phylogenetic history of these populations.