Genomes from 117 vertebrate species reveal rapidly evolving segmental duplication landscapes

Segmental duplications are major drivers of evolutionary innovation, yet their dynamics across vertebrates remain poorly understood. Here, we identify segmental duplications from long-read sequenced genomes of 117 vertebrates and the starfish, generating the largest multi-species dataset of its kind. We find that vertebrate genomes show a higher propensity for tandem duplications than for interspersed duplications. However, when focusing only on subtelomeric regions, avian and mammalian genomes show the opposite propensity toward interspersed duplications. We also observe that, across vertebrates, tandem duplications tend to be larger than interspersed duplications. Next, we construct a segmental duplication network for each species, and use network-derived properties to quantify the duplication landscape for that species. Functional enrichment analysis of hyper-duplicated genes reveals a strong enrichment in platypus for pheromone response, driven by the expansion of the vomeronasal pheromone receptor V1R gene family. Overall, our results uncover the general properties of vertebrate segmental duplication, demonstrate the rapid evolution of segmental duplication landscapes, and highlight the utility of network-based approaches for studying genome evolution. Significance Gene and regulatory region duplications are a fundamental source of evolutionary raw material. Here we generate segmental duplication calls from 117 vertebrate species. We find that vertebrate genomes have a bias towards tandem duplications relative to interspersed duplications. However, in the subtelomeric regions, birds and mammals exhibit an opposite bias toward interspersed duplications. Our analysis of segmental duplication networks demonstrate that duplication landscapes evolve rapidly, following species-specific rather than phylogenetic patterns. These findings indicate that the genomic architecture underlying segmental duplications is highly dynamic, uniquely shaping each lineage’s potential to adapt. Our study provides the most comprehensive view of vertebrate segmental duplications to date and establishes a network-based framework for studying genomic structural evolution.