Phenotypic plasticity can serve as a stepping stone towards adaptation. Recently, studies have shown that gene expression contributes to emergent stress responses such as thermal tolerance, with tolerant and susceptible populations showing distinct transcriptional profiles. However, given the dynamic nature of gene expression, interpreting transcriptomic results in a way that elucidates the functional connection between gene expression and the observed stress response is challenging. Here, we present a conceptual framework to guide interpretation of gene expression reaction norms in the context of stress tolerance. We consider the evolutionary and adaptive potential of gene expression reaction norms and discuss the influence of sampling timing, transcriptomic resilience, as well as complexities related to life history when interpreting gene expression dynamics and how these patterns relate to host tolerance. We highlight corals as a case study to demonstrate the value of this framework for non‐model systems. As species face rapidly changing environmental conditions, modulating gene expression can serve as a mechanistic link from genetic and cellular processes to the physiological responses that allow organisms to thrive under novel conditions. Interpreting how or whether a species can employ gene expression plasticity to ensure short‐term survival will be critical for understanding the global impacts of climate change across diverse taxa.

The Florida Keys Reef Tract has suffered extraordinary losses in live coral cover over the past four decades and is now battling an unprecedented coral disease outbreak. Here, colonies of Siderastrea siderea (Ellis and Solander, 1786) and Pseudodiploria strigosa (Dana, 1846) were tracked over 3 yrs (2015)(2016)(2017) across two pairs of inner and outer reef sites in the upper keys, offering a unique perspective into the distribution of disease throughout the reef tract. We found that outer reef colonies of both coral species exhibited greater disease incidence and mortality associated with this ongoing epidemic, while inner patch reef colonies remained largely unaffected. These findings suggest that ecological or biological factors that differentiate coral populations across these reef zones may play an important role in susceptibility to disease.

For most reef-building corals, the establishment of symbiosis occurs via horizontal transmission, where juvenile coral recruits acquire their algal symbionts (family Symbiodiniaceae) from their surrounding environment post-settlement. This transmission strategy allows corals to interact with a diverse array of symbionts, potentially facilitating adaptation to the newly settled environment. We exposed aposymbiotic Pseudodiploria strigosa recruits from the Flower Garden Banks to natal reef sediment (C-S+), symbiotic adult coral fragments (C+S-), sediment and coral fragments (C+S+), or seawater controls (C-S-) and quantified rates of symbiont uptake and Symbiodiniaceae community composition within each recruit using metabarcoding of the ITS2 locus. The most rapid uptake was observed in C+S+ treatments and this combination also led to the highest symbiont alpha diversity in recruits. While C-S+ treatments exhibited the next highest uptake rate, only one individual recruit successfully established symbiosis in the C+S-treatment, suggesting that sediment both serves as a direct symbiont source for coral recruits and promotes (or, potentially, mediates) transmission from adult coral colonies. In turn, presence of adult corals facilitated uptake from the sediment, perhaps via chemical signaling. Taken together, our results reinforce the key role of sediment in algal symbiont uptake by P. strigosa recruits and suggest that sediment plays a necessary, but perhaps not sufficient, role in the life cycle of the algal Symbiodinaceae symbionts.

Within microeukaryotes, genetic and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellies), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.

No abstract