Strong signatures of selection on genes underlying core reinforcement mechanisms in speciating desert tortoises

Genomic reinforcement and differential ecological adaptation are thought to be fundamental mechanisms of speciation. In this study we investigate the genomic basis of adaptation and reinforcement between two desert tortoise species of North America that occupy desert habitats with differing seasonal rainfall patterns and have considerable behavioral and reproductive differences yet maintain a narrow hybrid zone. We generated a chromosome-scale reference genome for Gopherus morafkai and performed analysis of synteny, genes under positive selection, and environmental niche modeling. Results show extensive positive selection (422 genes) including related to eye development and function that may relate to environmental differences, as well as prezygotic isolation mechanisms such as sperm-egg recognition, and postzygotic reinforcement mechanisms such as the spindle assembly checkpoint, and sister chromatid pairing. Together, results offer strong genetic support for the role of these classic processes in shaping reproductive isolation and lineage divergence of speciating tortoises.