Population genomics unravel structural variation of venom-encoding genes across the desert viper genus Cerastes

Understanding the molecular mechanisms underlying phenotypic differentiation is central to evolutionary biology. Yet most traits are shaped by complex, polygenic architectures, making links between genomic change and phenotype difficult to resolve. Venom provides an advantageous model for genotype–phenotype research because it is produced in a specialized secretory tissue, governed by a modular regulatory system, and largely composed of proteins from a limited set of recurrent toxin gene families. In parallel, genomics enables reconstruction of species evolutionary histories and detection of structural variation within and between species. Here we used whole genome sequencing data from 27 individuals to investigate the evolutionary history of the three species of the desert viper genus Cerastes ( C. cerastes , C. gasperettii and C. vipera ), a group of arid-adapted Palearctic snakes. Whole genome produced broadly concordant inferences of population structure, phylogenomic relationships, and introgression, with previous studies based on genome-wide datasets, although whole genomes provided finer resolution. Conservation genomic analyses further revealed pronounced genomic consequences of long-term isolation in relict Arabian populations of C. cerastes . We also detected extensive interspecific and intraspecific structural variation across major toxin gene regions, suggesting that genomic structural changes may contribute to variation in venom composition. These findings indicate that structural variation is consistent with previously reported differences in venom composition among Cerastes . Overall, our study underscores the value of integrative genomic approaches for disentangling the multiple evolutionary processes shaping complex adaptive traits such as venom.