Coral populations across the Great Barrier Reef (GBR) could rapidly adapt to the warming climate if they have standing genetic variation for thermal adaptation. Here, we describe a locus likely involved in acclimatization and adaptation of Acropora millepora to cooler temperatures at higher latitudes. This locus shows a strong signal of selection in the A. millepora genome, with a steep latitudinal gradient of derived allele frequency, and harbors a cluster of eight tandemly repeated Δ9-desaturase genes adjacent to a region where a hard sweep likely occurred. In colonies reciprocally transplanted across 4.5 degrees of latitude, the expression of Δ9-desaturase was upregulated at the cooler high-latitude reef. Furthermore, corals from the warmer low-latitude reef with one or two copies of the “cold-adapted” Δ9-desaturase allele expressed the gene more and grew faster than their peers when transplanted to the cooler reef. In other organisms ranging from bacteria to fish, Δ9-desaturase is upregulated under cold conditions to adjust membrane fluidity by introducing double bonds into fatty acid chains of membrane lipids. While all these lines of evidence are suggestive rather than conclusive, they collectively make Δ9-desaturase a strong candidate marker gene for coral thermal acclimatization and adaptation.

Effective biodiversity conservation requires knowledge of species’ distributions across large areas, yet prevalence data for marine sessile species is scarce. As marine organism distributions generally depend on terrain heterogeneity, topographic variables derived from digital elevation models (DEMs) can be useful proxies in distribution modelling. However, the suitability of such variables depends on spatial resolution. Here, we (1) assess three high-resolution bathymetry DEMs for accuracy, (2) harness DEM-derived topographic variables for regional coral species distribution models (SDMs), and (3) develop a transferable framework to produce, select and integrate multi-resolution topographic variables into marine spatial modelling. We use a case study from three reef-building Acropora coral species sampled across 23 reefs of the Great Barrier Reef, Australia. Obtaining three open-source bathymetric DEMs (15m Allen Coral Atlas (ACA), 30m DeepReef, 100m DeepReef), we produce eight derived topographic variables generalised to multiple nested spatial resolutions (15m to 120m) to assess SDM sensitivity to bathymetry source and resolution. We found that the ACA and DeepReef DEMs had similar vertical accuracies, each producing topographic variables relevant to marine SDMs. Slope and vector ruggedness measure (VRM) explained most of the variance for all three species. Coral prevalence increased with slope to a moderate steepness before quickly decreasing with increasing steepness for two species, while the third species plateaued. The prevalence of all species was negatively associated with VRM. Topographic variables for coral SDMs were most relevant at 15–60m resolutions, where the optimal resolution depended on the variable type and species. Overall, we show that the finest resolution was unnecessary to achieve high-performing SDMs. Running SDMs with multi-resolution topographic variables provided insights into the importance of terrain attributes for distribution modelling of different species. We provide a transferrable framework to facilitate the adoption of multiscale SDMs for better-informed conservation and management planning.

Summer heat waves are the principal global driver of mortality in reef-building corals. Resilience-based genetic management may increase coral heat tolerance, but it is unclear how temperature responses are regulated at a genomic level and thus how corals may adapt to warming naturally or through selective breeding. Here we combine phenotypic, pedigree, and genomic marker data from colonies sourced from a warm reef on the Great Barrier Reef reproductively crossed with conspecific colonies from a cooler reef to produce combinations of warm and cool purebred and hybrid larvae and juveniles. Intra-population breeding created significantly greater genetic diversity across the coral genome and maintained diversity in key regions associated with heat tolerance and fitness. High-density genome-wide scans of single nucleotide polymorphisms (SNPs) identified alleles significantly associated with offspring reared at 27.5°C (87 – 2,224 loci), including loci putatively associated with proteins involved in responses to heat stress (cell membrane formation, metabolism, and immune responses). Underlying genetics explained 43% of PCoA variation in juvenile survival, growth, and bleaching responses at 27.5°C and 31°C between the multilocus genotypes. Genetic marker contribution to total variation in fitness traits (narrow-sense heritability) were high for survival but not for growth and bleaching in juveniles, with heritability of these traits influenced more at 31°C relative to 27.5°C. Using only a limited number of crosses, the mechanistic understanding presented here demonstrates that allele frequencies are affected by one generation of selective breeding, key information for the assessments of genetic intervention feasibility and modelling of reef futures.