Genomics of a novel ecological phase shift: the case of a ‘weedy’ Montipora coral in Ulithi, Micronesia

Abstract Local and global ecological stressors are leading to increased documentation of phase shifts in coral reefs from healthy stony corals to macrophytes. In more rare cases, phase shifts result in sponge, zoantharian or other dominant species. In Ulithi Atoll, Federated States of Micronesia, we have documented an unusual phase shift from reefs with a diverse stony coral assemblage to reefs dominated by a single species of stony coral: Montipora sp.—a coral-to-coral phase shift. This monospecific type of reef lowers fish diversity and biomass, impacting both ecological integrity, and livelihoods of reef-dependent human communities. In this study, we used a genomic approach to characterize such a reef. We assembled a de-novo reference genome and used RAD seq data with thousands of SNPs to determine if different reefs result from sexual or asexual reproduction, if weedy Montipora fragments are transported between islands by human activities, and if there is evidence of natural selection on specific genotypes, thus favoring spreading success. We found that sexual reproduction is predominant in the focal species, that there is no evidence of human-mediated spread, and that some genomic regions might be under selection. While such results eliminate a number of spreading hypotheses, more precise dispersal maps will be important to determine the tempo and mode of ‘invasion’ of Montipora in Ulithi Atoll. This study shows that selection and adaptation may be contributing to the success of a stony coral (e.g., Phase shift). While a stony coral may be successful in a disturbed environment, it does not necessarily provide the type of habitat that is conducive to high fish biomass and coral diversity. These results serve as a cautionary tale for restoration efforts that focus on single species coral resilience rather than ecosystem function.