Structural variation identified between Mexican tetra reference genome assemblies. (A) Comparison of pangenome SV deletion alleles (left) and SV insertion alleles (right) by presence in each cave population (lineage 1 = Molino, lineage 2 = Pachón and Tinaja). Overlapping sections represent shared variant alleles between populations within the pangenome. Variants called relative to the Río Choy reference genome. (B) Total number of base pairs affected by pangenome SV insertions (positive values) and SV deletions (negative values) in each cave population. (C) Pairwise comparison of duplications (lower triangle matrix) and translocations (upper triangle matrix) in each of the four A. mexicanus reference assemblies. Variants called from pairwise whole-genome alignments between the two assemblies indicated by each cell (row × column). Values in each cell represent the total number of structural differences detected between the specific pair of assemblies. Duplication counts include both tandem and interspersed duplications but do not include tandem repeats. Darker cells indicate fewer variants identified between two assemblies and, therefore, more structurally similar genomes.