The evolution of structural variation across 500 million years of vertebrate evolution

Structural variants (SVs) contribute substantially to genetic variation and play vital roles in adaptation and disease^1,2. Nonetheless, SVs are poorly captured by short reads and thus remain understudied, especially in non-model organisms^3,4. Here, using haplotype-resolved genome assemblies from >600 vertebrate species, we comprehensively survey the landscape of SVs across >500 million years of evolution. We identify 35.3 million SVs and 3.12 billion single nucleotide variants (SNVs) segregating between two representative haplotypes across species, with SVs impacting ~12-fold more base pairs. SV and SNV heterozygosity are correlated across species, with endangered and threatened species exhibiting reduced genetic diversity. However, the contribution of SVs relative to SNVs fundamentally differs across major vertebrate clades: given the same number of SNVs, fishes, amphibians, and reptiles have 4.3-to-9.1 times the number of SVs than birds, and 1.7-to-3.6 times more than mammals. This reduction in the relative contribution of SVs in mammals and birds is linked to fewer non-repeat-associated SVs as well as lower transposable element (TE) abundance and diversity. We identify features underlying genomic instability across vertebrates, finding that SVs frequently occur in repetitive and SNV-rich regions and are mediated by both homology and non-canonical DNA structures. Notably, G-quadruplex structures are enriched 11.5-fold around SV breakpoints in birds, while Z-DNA structures are enriched 2.2-fold in cartilaginous fishes. TEs uniquely contribute to SVs both directly through transposition and indirectly by mediating ectopic recombination, with the proportion of TE-mediated SVs influenced by both genomic TE density and diversity. We identify >10,000 instances of recent TE turnover including extinction of LINE-2 in therian mammals and slowing of CR1 activity in passerine birds. Finally, we show that SVs have an outsized role in functional genetic variation and are >70 times more likely to strongly impact protein-coding sequences than SNVs. While SVs are on average deleterious, we identify extensive recurrent structural variation across multiple taxa in genes involved in sensory, immune, and metabolic systems. Together, this study highlights extraordinary variation in the abundance, composition, mechanism, and functional impact of SVs across vertebrates.