Comparisons of Genomic Drivers of Speciation Across Two North American Desert Genera

Speciation produces new lineages that are reinforced through reproductive isolation by prezygotic or postzygotic barriers. Lineage divergence occurs through a variety of processes, including through environmental differences across regions. Intrinsic drivers of speciation can include genomic structural changes, positive selection, and gene duplication. The Sonoran Desert houses many endemic and diverse species. Two of these desert-adapted groups are the brittlebushes, shrubs that are well-known for thriving in arid regions, and the desert tortoises, chelonians adapted to the North American deserts. In this dissertation, I investigate the genomic drivers of speciation in the shrub genus Encelia and the tortoise genus Gopherus and compare the mechanisms between these systems in order to understand how divergence has occurred in these different taxa that reside in the same regions, and assess whether there is evidence for ecological speciation in these sympatric groups. I generated the reference genome assemblies and annotations for E. farinosa, E. californica, G. morafkai, and G. berlandieri, and found conservation of synteny between E. farinosa and E. californica, as well as in the four Gopherus species. There were many genes under positive selection between each of the respective species’ pairs, both related to ecology and to core intrinsic speciation functions. The positively selected genes between E. farinosa and E. californica associated with defense responses, circadian rhythm, light responses, and stomatal associations. Between the three desert tortoise species, G. morafkai, G. agassizii, and G. evgoodei, there were positively selected genes related to reproductive isolation, reinforcement mechanisms, and eye development. Between G. berlandieri and the three desert tortoises, most of the positive selection was found in genes related to the immune system. Genome-wide segmental duplications were identified in E. farinosa and E. californica, with both uniquely and jointly retained duplicates in each species. These findings show that selection is the main genomic driver of speciation in Gopherus rather than structural changes, while in Encelia, the additive effects of selection and segmental duplications may be driving speciation. Results suggest differentiation in temperature and precipitation in the ranges of the sister lineages within each group are driving adaptive ecological divergence in both of these systems.