Modelling the acclimation capacity of coral reefs to a warming ocean

The symbiotic relationship between corals and photosynthetic algae is the foundation of coral reef ecosystems. This relationship breaks down, leading to coral death, when sea temperature exceeds the thermal tolerance of the coral-algae complex. While acclimation via phenotypic plasticity at the organismal level is an important mechanism for corals to cope with global warming, community-based shifts in response to acclimating capacities may give valuable indications about the future of corals at a regional scale. Reliable regional-scale predictions, however, are hampered by uncertainties on the speed with which coral communities will be able to acclimate. Here we present a trait-based, acclimation dynamics model, which we use in combination with observational data, to provide a first, crude estimate of the speed of coral acclimation at the community level and to investigate the effects of different global warming scenarios on three iconic reef ecosystems of the tropics: Great Barrier Reef, South East Asia, and Caribbean. The model predicts that coral acclimation may confer some level of protection by delaying the decline of some reefs such as the Great Barrier Reef. However, the current rates of acclimation will not be sufficient to rescue corals from global warming. Based on our estimates of coral acclimation capacities, the model results suggest substantial declines in coral abundances in all three regions, ranging from 12% to 55%, depending on the region and on the climate change scenario considered. Our results highlight the importance and urgency of precise assessments and quantitative estimates, for example through laboratory experiments, of the natural acclimation capacity of corals and of the speed with which corals may be able to acclimate to global warming.

The reviewers have mostly addressed my previous comments, especially with the added simulations without plasticity as a baseline for comparison, as well as the added figure S6 to illustrate the benefit and cost dynamics. However, some lingering issues remain from the new changes and unresolved previous comments (all line numbers refer to the revised manuscript without tracked changes): 1. While I agree with Reviewer #1's point about shifts in community composition, I disagree with the changes made in response: with the model setup, a shift in community composition would change parameters related to coral type, such as Topt and Gmax (as mentioned on line 452-453), perhaps with some changes in N too if different coral species had different plasticity levels, but I expect that this is swamped by the other differences. Therefore, instead of adding the claim that the model captures changes in community composition (lines 345 and 403-404), I support the original reviewer feedback of adding this as a caveat, i.e. recognizing that the acclimatization rates might be over-estimated because the model doesn't capture the effects community shifts on coral cover dynamics.
Agreed. We corrected these aspects by implementing revisions in the Abstract, in the Author summary, in the Introduction (48, 56 -57, and 60 -62), in the Models and Methods (lines 232 -237), and in the and Discussion (lines 424).
I also support Reviewer #1's suggesting to include sensitivity to a couple of different values for the percent of each coral type present among the sensitivity analyses, which the authors had declined to do.
The proportion of the two most common coral morphologies was used to estimate the carrying capacities " in the different regions. Therefore, we explored the model sensitivity with respect to changes in " . These sensitivity analyses were already presented in the original submission and are now shown in Figures S3 and S4 in S5 Appendix: Sensitivity analysis. These analyses show that " is among those parameters which changes (within ± 25%) have little impact on the model results.

With moving some of the sensitivity analysis results to the main text in Figs. 5-6 as I had suggested, the authors also need to add Results text about these figures in the main text, which is currently missing.
Thank you for spotting this out. We added text describing the results of these sensitivity analyses (lines 407 -414).

While the authors indicate their agreement with my previous point about acclimation and genetic adaptation both playing
a role in coral dynamics, and the false dichotomy inherent to presenting these as an either/or, the changes to the text do not reflect this: the framing language of "however", "alternately", and "although", as well as the continued mention of generation times (which, as I mentioned before, do not necessarily mean evolution is slow given the capacity for selective sweeps) and ecological vs. evolutionary time scales (which applies to macroevolutionary processes of speciation, not microevolutionary process of changes in gene frequency), on lines 29-31, 424-426, and in the abstract third sentence still imply that these are alternate, not co-occurring dynamics, and discounts the potential role of evolution. Please rephrase to recognize that both have the potential to occur, which can still motivate this study, as some studies have explored the role of genetic adaptation, but a mechanistic investigation into the role of acclimation is less well understood (with an eventual goal, hopefully, of including both to understanding their interaction, but understanding each in turn is a reasonable starting point and important to establishing their potential relative contributions before such integration).
Corrected. We rephrased the relevant text in the Abstract, and removed the mentioned text from the Introduction (lines 27 -31) and from the Discussion (lines 446 -448).
Also, in lines 36-38, note that the rolling-window approach to approximating adaptive and acclimation potential in these papers does not have an assumed-in bleaching threshold as implied here, but rather derives the threshold from the climatology, in particular the most recent mean of maximal monthly temperatures.

4.
The added text about stress-hardening on lines 465-468, a point that I had raised in my previous review, is too vague to be useful. Please either (a) be specific about stress hardening (using that term and defining what it involves) as a potential management application, including citations on this approach, and how this model might inform that approach, or (b) delete this addition. For option (a), note that the addition is out of place: it is a sentence about management implications in the midst of a paragraph about model assumptions. Therefore, if included, it should be moved to a more appropriate place in the discussion.
Agreed. We followed your suggestion of removing the text (lines 488 -491).

For the data-based bleaching simulations: even if the parameters were estimated empirically, those parameters were somehow used in a mathematical expression (represented by code) to translate into their effect on coral dynamics. Please provide this information for full methods clarity.
Agreed. We improved and completed the description of bleaching in the Methods section (lines 198 -218 and Table 2).

To clarify my earlier comment about adaptive plasticity: what this text (lines 225-236) needs clarity on is the idea that
plasticity is always perfectly adaptive, as represented in the model, is an assumption and does not always occur in reality, as, in reality, plasticity can sometimes decrease fitness, such as in the case of evolutionary traps. The current text could be misinterpreted to mean that the idea that plasticity is always adaptive is a biological truth.
Agreed. We specified that although in our model acclimation moves the trait in the direction of increasing fitness, plastic responses in nature can actually decrease fitness and thus be maladaptive (lines 244 -245).

7.
For the addition about nutrient runoff and pollution effects on coral growth stemming from my previous feedback (lines 449), "controlling" doesn't make sense here; something like "buffering", "protecting", or (my preference) "mitigating anthropogenic impacts on" would work better (and why is this in quotes?).