Data from: Multispecies pangenomes reveal a pervasive influence of population size on structural variation

Structural variants (SVs) are widespread in vertebrate genomes, yet their
evolutionary dynamics remain poorly understood. Using 45 long-read de novo
genome assemblies and pangenome tools, we analyze SVs within three closely
related species of North American jays (Aphelocoma, scrub-jays) displaying
a 60-fold range in effective population size. We find rapid evolution of
genome architecture, including ~100 Mb variation in genome size driven by
dynamic satellite landscapes with unexpectedly long (> 10 kb)
repeat units and widespread variation in gene content, influencing gene
expression. SVs exhibit slightly deleterious dynamics modulated by variant
length and population size, with strong evidence of adaptive fixation only
in large populations. Our results demonstrate how population size shapes
the distribution of SVs and the importance of pangenomes to characterizing
genomic diversity.