Anomalous heat waves are causing a major decline of hard corals around the world and threatening the persistence of coral reefs. There are, however, reefs that have been exposed to recurrent thermal stress over the years and whose corals appear to have been tolerant against heat. One of the mechanisms that could explain this phenomenon is local adaptation, but the underlying molecular mechanisms are poorly known. In this work, we applied a seascape genomics approach to study heat stress adaptation in three coral species of New Caledonia (southwestern Pacific) and to uncover the molecular actors potentially involved. We used remote sensing data to characterize the environmental trends across the reef system, and sampled corals living at the most contrasted sites. These samples underwent next generation sequencing to reveal single nucleotide polymorphisms (SNPs), frequencies of which were associated with heat stress gradients. As these SNPs might underpin an adaptive role, we characterized the functional roles of the genes located in their genomic region. In each of the studied species, we found heat stress‐associated SNPs located in proximity of genes involved in pathways well known to contribute to the cellular responses against heat, such as protein folding, oxidative stress homeostasis, inflammatory and apoptotic pathways, and DNA damage‐repair. In some cases, the same candidate molecular targets of heat stress adaptation recurred among species. Together, these results underline the relevance and the power of the seascape genomics approach for the discovery of adaptive traits that could allow corals to persist across wider thermal ranges.

We investigated the occurrence of intracolonial genetic variability (IGV) in Pocillopora corals in the southwestern Indian Ocean. Ninety‐six colonies were threefold‐sampled from three sites in Reunion Island. Nubbins were genotyped using 13 microsatellite loci, and their multilocus genotypes compared. Over 50% of the colonies presented at least two different genotypes among their three nubbins, and IGV was found abundant in all sites (from 36.7% to 58.1%). To define the threshold distinguishing mosaicism from chimerism, we developed a new method based on different evolution models by computing the number of different alleles for the infinite allele model (IAM) and the Bruvo's distance for the stepwise mutation model (SMM). Colonies were considered as chimeras if their nubbins differed from more than four alleles and if the pairwise Bruvo's distance was higher than 0.12. Thus 80% of the IGV colonies were mosaics and 20% chimeras (representing almost 10% of the total sampling). IGV seems widespread in scleractinians and beyond the disabilities of this phenomenon reported in several studies, it should also bring benefits. Next steps are to identify these benefits and to understand processes leading to IGV, as well as factors influencing them.

Accurate species delimitation and identification are prerequisites for many studies. The common reef-building coral Pocillopora has been extensively studied and used as model species to understand coral biology, physiology, and ecology, but understanding the species diversity and boundaries in this genus has been challenging. In the Arabian region, two species have been generally recognised based on macro-morphology, P. damicornis and P. verrucosa, the latter including two mitochondrial lineages that have recently been considered to represent two cryptic species. Here, using target-capture of ultra-conserved elements and exons, we demonstrate that all these morphs and lineages belong to a single species. Using an integrative approach with genomic, morphological, and geographical lines of evidence, we also show that this species is distinct from other Indo-Pacific species and restricted to the Arabian Peninsula. We resurrect P. favosa Hemprich & Ehrenberg, 1834 for this ecologically important and extensively studied Red Sea Pocillopora species. These results facilitate our understanding of the physiology, biology, and ecology of this major reef coral adapted to the extreme environmental conditions around the Arabian Peninsula.