Islam, S.; Aqil, A.; Hach, F.; Numanagic, I.; Masuda, N.; Gokcumen, O.

Evolvability, the capacity of populations to respond to selection, is influenced by genomic structural properties such as segmental duplications. These duplications establish redundancy, creating adaptive potential by co-opting duplicated elements for new functions. Here, we identify segmental duplications in 117 vertebrate species and the starfish outgroup using long-read genome assemblies. We constructed independent segmental duplication networks for each species to represent the landscape of segmental duplications therein. We quantified the duplication landscapes across species using 13 network properties and tested three hypotheses for their evolution: 1) selective constraint, 2) phylogenetic drift, and 3) species-specific dynamics. Our results show that segmental duplication profiles across vertebrates are shaped by fast-evolving, species-specific dynamics, driving unique adaptive potentials. One notable exception of lineage-specific evolution is observed within mammals, where monotremes (platypus and echidna) exhibit distinct genomic structural features, characterized by elevated insertion and deletion rates compared to therian mammals. Analysis of genome size variation in vertebrates revealed no significant correlation with segmental duplication metrics. However, in ray-finned fish, lineage-specific events such as whole-genome duplications in some species (e.g., sterlet sturgeon and brown trout) influence genome size. These findings highlight the role of segmental duplications in species-specific adaptive potential and demonstrate the utility of network-based methods in genomic research. Our dataset and framework provide a valuable resource for understanding genomic evolvability, underscoring the integration of evolutionary biology and network analysis in studying genome evolution.