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.

Global environmental change is rapidly driving deterioration of many ecosystems- such as coral reefs- though the rate of decline could be offset by genetic adaptation. We aimed to identify which environmental gradients drive local adaptation in two common corals across the Florida Keys Reef Tract, Porites astreoides and Agaricia agaricites. Both species contained three genetically distinct lineages distributed across depths in a remarkably similar way. Additionally, each lineage harbored genetic variation that aligned with other environmental gradients. The most commonly highlighted driver of within-lineage genetic structure was temperature during the coldest winter month, which is warmer at offshore sites especially in the upper Keys. Other repeatedly highlighted environmental drivers were high variation in bottom temperature at nearshore sites along the main island chain, more pronounced ocean stratification west of Key West, and outlying values of several water quality parameters (such as dissolved oxygen, carbon, turbidity, and salinity) at nearshore and Florida Bay locations of the lower and middle Keys. Synthesizing these results, we provide a map of adaptive neighborhoods in the Florida Keys that are likely to harbor differentially adapted coral populations, which can be regarded as different genetic stocks from the perspective of reef conservation and restoration.