Heat tolerance varies considerably within a reef-building coral species on the Great Barrier Reef

Climate change and marine heatwaves pose significant threats to reef-building corals, causing widespread bleaching and mortality. However, significant intraspecific variation in heat tolerance exists, offering potential for adaptation and persistence. Understanding this variation is crucial for predicting future reef dynamics and informing conservation strategies. This study focuses on the *Acropora hyacinthus* complex, a group of Indo-Pacific corals of high ecological value but with high vulnerability to climate warming. While intraspecific variation in heat tolerance has been observed among reef populations, the distribution and underlying drivers of this variation at individual and ecosystem scales remain poorly understood. This study aims to quantify intraspecific variation in heat tolerance of *A. hyacinthus* across the GBR, identifying the spatial distribution of heat-tolerant individuals and populations. It also explores the relative influence of environmental factors, Symbiodiniaceae community composition, and host genomic identity on heat tolerance traits. This comprehensive understanding is critical for improving coral projection models, informing selective breeding programs, and guiding conservation planning.

Previous research has demonstrated intraspecific variation in coral heat tolerance among reef populations, attributing this to factors such as thermal history (adaptation and acclimatization). Studies have shown positive associations between heat tolerance and historical thermal anomalies or temperature variability. However, a detailed understanding of the distribution and drivers of this variation at fine spatial scales is lacking. The *Acropora hyacinthus* complex, the focus of this study, presents unique challenges due to cryptic species diversity, making it difficult to distinguish species without genetic data. These cryptic lineages may differ in traits like growth rate, microhabitat distribution, and heat tolerance. Additionally, the community composition of algal endosymbionts (Symbiodiniaceae) significantly influences coral heat tolerance, although host-specific effects and the influence of Symbiodiniaceae at the intrageneric level require further investigation.

Researchers collected 583 *Acropora hyacinthus* colonies from 17 reefs across the GBR, targeting the "neat" morphotype but inadvertently including some non-target morphotypes. Colonies were subjected to a standardized acute heat stress assay, measuring photochemical efficiency (Fv/Fm) and chlorophyll content (NDVI) as indicators of heat tolerance. Two heat tolerance metrics were calculated for each trait: an absolute thermal threshold (ED50) and retained performance at 9°C above the local climatology. Genomic DNA was extracted from a subset of colonies to identify distinct genomic clusters, potentially representing cryptic species. Symbiodiniaceae communities were quantified using the ITS2 rDNA marker. Environmental variables (temperature, thermal history, nutrient availability) were compiled from various sources. Boosted regression trees (BRTs) were used to model the relationship between heat tolerance traits and environmental, Symbiodiniaceae, and genomic predictors.

Significant variation in heat tolerance was observed across the GBR. Mean ED50 thermal thresholds were 36.4°C (Fv/Fm) and 35.6°C (NDVI), but these varied by as much as 3.5°C and 7.3°C, respectively, among individual colonies. For absolute thermal thresholds (ED50), the most heat-tolerant individuals were predominantly found on northern reefs. However, for retained performance, the most heat-tolerant individuals were generally found on southern reefs. Variance in heat tolerance was higher among sites than within sites for Fv/Fm metrics, but higher within sites than among sites for NDVI metrics. Genomic analysis revealed four distinct genomic clusters, likely representing cryptic species within the *A. hyacinthus* complex. These clusters varied spatially, with one cluster (A. hyacinthus "neat") dominant in the central and northern GBR. Symbiodiniaceae communities were overwhelmingly composed of *Cladocopium* variants, with spatial variation primarily along the inshore-offshore gradient. BRT models revealed that temperature variables were the most important predictors of heat tolerance variation. Maximum monthly mean (MMM) temperature positively correlated with ED50 but negatively with retained performance. Degree Heating Weeks (DHW) at the time of collection positively influenced Fv/Fm ED50 and retained NDVI, indicating acclimatization to recent heat stress. Symbiodiniaceae variables were important predictors for NDVI metrics, but host genomic cluster was not a major predictor.

The findings highlight substantial intraspecific variation in heat tolerance within the *A. hyacinthus* complex, with thermal history being a major driver. Northern populations exhibited higher absolute thermal thresholds but were closer to their upper thermal limits, while southern populations showed lower thresholds but greater capacity to withstand future warming. Recent heat stress (DHW) influenced heat tolerance, suggesting acclimatization plays a role. While Symbiodiniaceae communities and host genomic clusters showed spatial variation, their impact on heat tolerance was relatively minor. The high within-reef variation suggests the importance of other factors, likely including functional genomic variation within the host or Symbiodiniaceae, which warrants further investigation. The study supports the use of multiple traits to capture a comprehensive picture of heat tolerance.

This study demonstrates considerable intraspecific variation in coral heat tolerance across the GBR, with variation sometimes being greater within reefs than among reefs. Thermal history is a key driver of this variation, with both adaptation and acclimatization playing a role. While symbiont community and host genomic identity show spatial variation, their influence on heat tolerance is minor. The substantial unexplained within-reef variation highlights the potential importance of unmeasured factors, particularly genomic variation. Future research should focus on identifying and characterizing these factors to enhance conservation and restoration efforts.

The study acknowledges several limitations. The sample size for non-target morphotypes was relatively low, potentially affecting the analysis of interspecific differences in heat tolerance. Acclimatization to recent heat stress may complicate the interpretation of heritable phenotypic variation. The ITS2 marker may not fully capture the functional diversity of Symbiodiniaceae. Finally, unmeasured microhabitat factors could also influence within-reef heat tolerance variation.