This manuscript evaluates the effectiveness of using adult coral thermal tolerance traits—specifically photochemical efficiency thresholds—as selection criteria in a selective breeding framework aimed at enhancing larval heat tolerance. The authors tested this approach using two Acropora species from the Great Barrier Reef and found that selecting broodstock based on adult heat tolerance did not result in significantly higher larval survival under thermal stress. The study challenges assumptions about trait heritability and highlights potential mismatches between adult and larval thermal responses. Overall, this is a well-designed and clearly presented study. The following points are mostly minor and intended to improve clarity and impact prior to acceptance.
Major Comment

While the study addresses an important and timely question, the novelty is not sufficiently emphasized in the current version. I recommend revising the Abstract and Introduction to explicitly state what gap in knowledge this study addresses, and how it advances the field beyond previous work. A concise summary of recent studies on thermal tolerance in both adult and larval corals would also help clarify the manuscript’s contribution and strengthen its framing.

Introduction

Lines 23–24: While elevated seawater temperature is a primary driver of coral bleaching, it would improve clarity to acknowledge that other environmental stressors (e.g., solar irradiance, sedimentation, salinity fluctuations) can also contribute. This would offer a more accurate and nuanced perspective on coral stress.

Please consider adding a paragraph summarizing recent findings on heat tolerance in both adult colonies and larvae. This would better situate your work within the current literature and offer a clear contrast between knowns and unknowns. It also provides an ideal opportunity to highlight the novelty of your study.

Methods

Lines 104–111: Including a simple map or diagram of the sampling locations would greatly aid in visualizing the study design and environmental context.

Lines 124–129: The +6°C and +9°C temperature treatments may appear extreme relative to natural coral environments. Please clarify the rationale for using such high temperatures—perhaps emphasizing the short-term exposure or the need to induce measurable physiological responses.

Lines 164–165: The manuscript states that both Tukey’s HSD and Bonferroni correction were applied for multiple comparisons. Since Tukey’s test already controls the family-wise error rate, applying both may be overly conservative and is not standard practice. Please clarify which correction was actually used and revise the description accordingly.

Lines 208–230: The use of a Bayesian GLMM is appreciated, particularly to address convergence issues and complex random effects. However, other sections of the manuscript (e.g., ANOVA and post hoc tests) rely on frequentist approaches without including relevant random effects (e.g., tank, genet identity), which are later discussed in the manuscript as potentially important. This raises questions about consistency in the statistical framework. It would be helpful to explain the rationale for using different modeling approaches in different parts of the study.

Additionally, the Bayesian models are said to account for random variation among polyps and fragments, but the manuscript also states that the response variables (egg number and size) were averaged across multiple levels. If the models were fitted to these averaged values, it is unclear how the nested structure was retained. Please clarify whether hierarchical structure was modeled using individual-level data or averages, and how this affected the random effects structure.

Lines 262–291: The statistical approach in the larval stress testing section is sound. The use of a binomial GLMM with nested random effects is appropriate and well justified. That said, given the use of Bayesian methods in earlier sections, it would improve consistency and clarity to briefly explain why different statistical paradigms (Bayesian vs. frequentist) were chosen for different analyses.

Results

Figures 1 and 2: These figures primarily depict photochemical efficiency and chlorophyll content, but they do not clearly support the core hypothesis concerning the relationship between heat tolerance and fecundity. Please consider revising the figure legends and/or text to clearly connect these data to the study’s main aim, or supplement them with more directly relevant visualizations.

Figure 4: The color scheme could be improved for accessibility. Light yellow is difficult to distinguish, particularly for readers with color vision deficiencies. Please consider using darker, more contrasting colors.

Figure 5 / Lines 352–353: There appears to be a mismatch between the written interpretation and the data shown in the figure. The manuscript states that “the decrease in the odds of survival over time was greater for the RR and Bulk offspring than for the SS offspring,” yet Bulk and SS appear to have similar trajectories. Please revise the figure or text for consistency.

Discussion

Comparison with Sanaz et al. (2022): Sanaz et al. suggest that corals may adopt a strategy of producing more heat-tolerant larvae under stress. Your results differ from theirs. A brief comparison discussing why these differences might occur—whether due to species, methodological design, or ecological context—would be valuable.

Lines 381–383: The idea that corals occupy different ecological niches across life stages may be overstated. The example of Littorina obtusata, a mobile species, is not an appropriate comparison for mostly sessile corals. Unless you are referring to specific mobile life stages (e.g., larvae), this statement may be misleading and should be revised or removed.