Characterizing the adaptive potential of north-western Pacific reef corals to empower conservation strategies: a role for seascape genomics

Abstract

Coral reefs are suffering a major decline due to the environmental constraints imposed by climate change. Over the last 20 years, three major coral bleaching events occurred in concomitance of anomalous heat waves, provoking a severe loss of coral cover worldwide. The conservation strategies for preserving reefs, as they are implemented now, cannot cope with global climatic shifts. Consequently, researchers are advocating the set-up of preservation frameworks to reinforce coral adaptive potential. However, the main obstacle to this implementation is that studies on coral adaption are usually hard to generalize at the scale of a reef system. Here, we study the relationships between frequencies of genetic markers with that of environmental characteristics of the sea (seascape genomics), in combination with connectivity analysis, to investigate the adaptive potential of a flagship coral species of the Ryukyu Archipelago (Japan). By associating genotype frequencies with descriptors of historical environmental conditions, we discovered six genomic regions hosting polymorphisms that might promote resistance against thermal stress. Remarkably, annotations of genes in these regions were consistent with molecular roles associated with heat responses. Furthermore, we combined information on genetic and spatial distances between reefs to predict connectivity at a regional scale. The combination between the results of these analyses portrayed the adaptive potential of this population: we were able to identify reefs carrying potential adaptive genotypes and to understand how they disperse to neighbouring reefs. This information was summarized by objective, quantifiable, and mappable indices covering the whole region, which can be extremely useful for future prioritization of reefs in conservation planning. This framework is transferable to any coral species on any reef system, and therefore represents a valuable tool for empowering preservation efforts dedicated to the protection of coral reef in warming oceans.