Abstract: Thermally induced coral bleaching is a major cause of reef decline, though it could be offset by coral adaptation. In this study, we used three complementary approaches to identify which environmental gradients drive local adaptation in two common Florida corals, Porites astreoides and Agaricia agaricites. We hypothesized that corals exhibit fine-scale population structure associated with certain abiotic differences, particularly depth and summer temperature. Using 2bRAD sequencing, we developed a large genomic dataset for two ubiquitous coral species- P. astreoides and A. agaricites - across all reef habitats in the Florida Keys. We compared genetic structure and loci under selection to 226 environmental variables from public remote-sensing and water quality datasets. Both species revealed three sympatric cryptic genetic lineages, specialized to different depth ranges. Additionally, each lineage harbors genetic variation aligning with other environmental gradients, though elevated temperature is typically not one of them. In A. agaricites, nitrogen variation predicts genetic divergence in the deep and mid-depth lineages, while cold temperature is the most important driver within the shallow lineage. Nitrogen and cold are also associated with genetic variation in P. astreoides, and high temperature was highlighted only once in the deep lineage of P. astreoides. In both species, lineages don’t share environment-associated groups of SNPs, indicating that lineages adapt independently. Overall, the locally available genetic variation in our two corals species seems unlikely to provide thermally adaptive genetic variants for future warming. Our results map the environmental gradients that create the strongest genetic barriers for corals, which could serve as a guide for reef restoration.
