Species inhabiting extreme desert environments have undergone intense selective pressures, resulting in the evolution of striking adaptions. While extensive research has focused on phenotypic characteristics associated with desert adaptation, the genetic basis underlying these adaptations remains elusive, particularly in a monophyletic avian group. Here we investigate this within a remarkable lineage Podoces, comprising four ground jays that are exclusively found in desert habitats. We constructed genome assemblies for these species, which included two representative chromosomal-level genomes, and identified the evolutionary mechanisms driving desert adaptations through comparative genomics. Our findings revealed distinctive and widespread accelerated selection in ground jays across protein-coding genes, gene families, and conserved nonexonic elements linked to energy metabolism and the maintenance of water balance. Notably, gene families and noncoding regions with high evolutionary flexibility may be involved in morphological adaptations, such as the morphogenesis of the ureteric bud branching structure in ground jays. Furthermore, we found that structural variations also contribute to the important evolutionary forces driving desert adaptation in ground jays. Collectively, our study suggests that desert adaptation patterns are shaped by the co-evolution of genetic variation at multiple scales. Our results have implications for comprehending the historical processes of desertification and shed light on the intricate genetic mechanisms underlying adaptations to extreme desert environments. Key words: adaptive evolution; deserts; positive selection; accelerated evolution; Podoces
Comparative genomics reveals the genetic basis of adaptation in ground jays endemic to deserts