- Coral reefs have become vulnerable to climate change, with mass bleaching events, the loss of symbiotic algae (Symbiodiniaceae), increasing in both frequency and severity. As climate change continues to threaten the persistence and existence of coral reefs around the world, the biggest question posed for coral reefs is “can they adapt to ongoing climate change threats?” A growing number of studies have recently shown the importance of host transcriptomic responses, evidence of genetic diversity in bleaching susceptibility, and potential adaptive responses in these traits, but there are still gaps in our understanding of these mechanisms and their distribution across corals. Therefore, the research presented in this dissertation addresses 1) the genes and genomic regions associated with genetic variation in bleaching responses, 2) heritability of thermal tolerance traits in natural populations, and 3) the roles of gene expression and symbiont communities in thermal acclimation.
In Chapter 2, I used quantitative genetic and genomic approaches to investigate heritable variation in thermal tolerance in the coral species Orbicella faveolata, as well as the genomic basis for this variation. I estimated narrow-sense heritability (h²) and used a genome-wide association study to identify loci significantly associated with thermal tolerance, indicating capacity for adaptation in this natural population of corals. In addition, profiling gene expression in corals with contrasting bleaching phenotypes uncovered substantial differences in transcriptional stress responses between heat-tolerant and heat-susceptible corals. In Chapter 3, I quantified variation in thermal tolerance and investigated its genomic basis using Anthopleura elegantissima, a model system for corals. Using SNP genotypes to compare anemone aggregations, I estimated clonal repeatability (a proxy for broad sense heritability, H²) and narrow-sense heritability, revealing substantial heritable variation. Additionally, I conducted a genome-wide association study and found significant genetic markers and genes associated with thermal tolerance. Heterozygote advantage was evident across these markers, indicating a potential role in Cnidarian thermal tolerance. In Chapter 4, I conducted a comparative study across eight coral taxa to explore variation in thermal acclimation capacity at high and low temperatures. I profiled gene expression following acclimation to investigate the functional basis for variation in thermal acclimation and pinpointed genes playing more of a mechanistic role. Additionally, I surveyed changes in algal symbiont communities to investigate changes in symbiont communities during acclimation that may contribute to subsequent changes in thermal tolerance of the holobiont. This study revealed considerable variation across coral taxa and documents potential mechanisms that might explain this variation, information important for modeling biological responses to ocean warming. Together, the work presented here provides insights into the potential for adaptation and acclimation in corals threatened by climate change, and identifies potential genomic regions and genes that may become targets of selection as ocean temperatures continue to rise.