At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterizing the mechanisms of coral resilience to climate change. To explore these mechanisms in the reef coral Acropora tenuis , we collected samples from lagoon and reef slope habitats and combined whole-genome sequencing, ITS2 metabarcoding, experimental heat stress, and transcriptomics. Despite high gene flow across the atoll, we identified clear shifts in allele frequencies between habitats at relatively small linked genomic islands. Common garden heat stress assays showed corals from the lagoon to be more resistant to bleaching, and RNA sequencing revealed marked differences in baseline levels of gene expression between habitats. Our results provide new insight into the complex mechanisms of coral resilience to climate change and highlight the potential for spatially varying selection across complex coral reef seascapes to drive pronounced ecological divergence in climate-related traits.

This study uses numerical modeling to study hydrodynamic drivers of fine-scale connectivity within a coral reef atoll off the North West Shelf of Australia.

Waves and tides are often the two primary forcing mechanisms responsible for driving hydrodynamic processes within coral reefs worldwide. Although wave‐ and tide‐driven flows are individually well understood, there remain considerable gaps in our understanding of how their interactions control the reef circulation, and consequently how they shape a range of ecological processes. During 11 months of hydrodynamic measurements across Mermaid Reef, a coral reef atoll off northwestern Australia, the atoll was regularly exposed to a range of wave and tidal conditions. Using a validated wave‐flow numerical model, we showed that wave‐ and tidally driven processes interacted to drive the reef's circulation through several mechanisms including wave‐current interactions and tidal water level modulation of wave‐driven flows. The atoll morphology, particularly the higher elevation of the western reef flat, was found to be a key factor controlling the relative importance of waves and tides. Wave‐driven processes dominated for tidal ranges smaller than required to expose the shallower western reef flat. In contrast, tidal processes dominated for larger tidal ranges, when the western reef flat temporarily acted as a physical barrier to incoming and outgoing flows. The residual (tidally averaged) circulation was consistently directed eastward across the atoll. Over time scales of several months to years, Mermaid Reef can be classified as a tide‐dominated reef. However, due to the incident wave energy and spring‐neap tidal range variability, the relative importance of the dominant hydrodynamic drivers can vary on time scales of hours to days allowing wave processes to episodically dominate the reef circulation.