Strong Signatures of Selection on Candidate Genes Underlying Core Speciation Mechanisms in Desert Tortoises

Genomic incompatibilities and differential ecological adaptation are thought to be fundamental mechanisms of speciation. In this study, we generated a chromosome-scale reference genome and annotation for Gopherus morafkai , the Sonoran Desert tortoise, and conducted a detailed analysis of genes under positive selection with its sister species, the Mojave Desert tortoise. They occupy desert habitats with differing seasonal rainfall patterns and have considerable behavioural and reproductive differences, yet maintain a narrow hybrid zone. We find high conservation of synteny with other chelonian species. Results show extensive positive selection (422 candidate genes) relating to eye development and function that may reflect differences in UV exposure, as well as core reproductive isolation mechanisms of sperm-egg recognition, spindle assembly checkpoint and sister chromatid pairing. Together, our results offer strong genomic support and speciation genomic resources for processes shaping reproductive isolation in chelonians.