PCLM-D-21-00006Local-scale oceanographic features are unlikely to provide future thermal refugia for coral reefsPLOS Climate

Dear Dr. Dixon,

Thank you for submitting your manuscript to PLOS Climate. After careful consideration, we feel that it has merit but does not fully meet PLOS Climate’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. After the reviewers' independent assessment and my own reading, we request you to make revisions to your manuscript. You will see in particular that the two reviewers are both positive about the quality of the manuscript and agree on the merits of your work, but ask a few additional clarifications. Additionally, both point out that the definition of the refugia should be better discussed. The fact that you will need to provide deeper discussions in the revised version of the manuscript leads to a Major revision request, although I am confident that you will promptly be able to address all the comments.

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Andrea Storto

Academic Editor

PLOS Climate

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1. Does this manuscript meet PLOS Climate’s publication criteria? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: N/A

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Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Review of

“Local-scale oceanographic features are unlikely to provide future thermal refugia for coral reefs”, submitted to PLoS Climate.

Comments:

Firstly, I would like to thank the editor and the authors for the opportunity to review this manuscript.

This work investigated, using fine-resolution thermal projections, which reef areas (across 12 regions) may be considered refugia and which may be considered susceptible to bleaching in the current and +1.5 ºC and +2.0 ºC scenarios. Reef areas were considered refugia when experiencing 0.1 or less bleaching episodes yr-1, and susceptible when experiencing 0.2 or more bleaching episodes yr-1.

This kind of assessment seems to perfectly fit the journal scope, and it is certainly relevant and timely, especially considering its global scale of analyses and the novel 1-km resolution. In addition, its findings are very important in providing additional evidence that the current form of the Paris Agreement simply will not do for coral reefs.

The writing is clear and concise, and the relevant literature seems well-covered. The Introduction is excellently written, and the M&M seem adequate although I should point out that I am not an expert in the kind of techniques used for interpreting the data. The figures are also clear and well-presented, therefore I will focus my attention more on the Discussion.

Minor points:

- Title: I would say that, based on your findings, thermal refugia will not exist in the future, regardless of it being local-scale or not. Maybe that could be a bit clearer in the title?

- I think that the authors need to make it a bit clearer somewhere in the text that their findings are relevant for shallow water coral reefs. The dynamics for mesophotic reefs would be entirely different. What is the depth threshold used in this investigation?

- Reef areas are categorized into “thermal refugia”, “intermediate” and “exposed”. The latter reads a bit odd; perhaps change to “susceptible”?

- The tropicalization effect could be more explored; its mention in lines 299-300 is too brief.

- Line 308: Remove “we hope” and state clearly that they are indeed valuable tools. It is certainly the case.

Major point:

Morelli et al. (2020), cited in the manuscript, provides a modern definition of refugium:

- “Climate-change refugia can serve as a “slow lane”, in that their relative buffering from climate change can protect native species and ecosystems from the negative effects of climate change in the short term, and provide longer-term havens from climate impacts for biodiversity and ecosystem function”

- “Climate-change refugia can be identified and managed by evaluating ecological complexity, scale, and species traits as well as climate and landscape factors”

I feel that this manuscript focused solely on the physical oceanography/temperature aspects of what a refugium may be. Based on the Morelli et al. (2020) passages above, we can state that:

(i) Refugia are areas where the impacts of climate change are less intense; not necessarily that the temperature increase was lower.

(ii) Other environmental factors, and especially biological and ecological factors, have a critical role in determining whether an area will serve as refugium or not.

My point is: the biological aspects used to define a refugium seem to have been a bit left out. I’ll use Brazil as an example, which is one of the areas investigated and also one that needs a bit more attention internationally: in Mies et al. (2020) in Front Mar Sci, we are shown that DHW values above 15 provide little to no mortality in Brazil. Therefore, although it was clearly a thermal stress episode, the impacts were minimal and thus the area is considered a refugium (“slow lane”) for the species living there. The explanations are all environmental or biological: reefs in Brazil are turbid, corals have resilient symbiotic associations, resilient morphology, among others.

Therefore, although your dataset is very relevant, you do need to discuss this refugium definition a bit more and grant that your assessment has refugium criteria that are exclusively based on physical oceanography and temperature. Your paragraph in lines 271-280 is a good place to expand on this. And, of course, as mentioned in my previous paragraph, it is important to recognize that your criteria, although very relevant and indeed the ones to use, they are not universal as there is global disparity in coral resilience to bleaching.

Therefore, I recommend a minor revision before this manuscript is accepted for publication.

Best regards

Reviewer #2: ‘Local- scale oceanographic features are unlikely to provide future thermal refugia for coral reefs’ is a well-written paper that I have been waiting for, for a long time. However, I would like to challenge the authors with a few major and minor questions. The authors, however, do not have to re-write the paper if they manage to justify what I do not agree with.

1- Line 85-88 and throughout the paper the authors refer to high variable environments as refugia. However, we know that refugia can retain environmental conditions suitable for particular species when changes cause surrounding areas to become inhospitable (Ashcroft, 2010; Stewart et al., 2010; Keppel et al., 2012). Therefore, sites with high variability, although increase the chance of species to survive via acclimation / adaptation, they should not be considered refugia (Kavoos & Keppel, 2018) and you mentioned in your paper the reason. How do you fix this, in my opinion, problem?

https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2699.2010.02300.x

https://royalsocietypublishing.org/doi/full/10.1098/rspb.2009.1272

https://onlinelibrary.wiley.com/doi/full/10.1111/j.1466-8238.2011.00686.x

https://academic.oup.com/icesjms/article/75/1/43/4080230?login=true

2- Line 102: you categorized your reef pixels as ‘intermediate’. We know, based on the aforementioned references that refugia are dynamic entities and they are defined based on their ‘refugial capacities’ (Keppel et al. 2015: https://esajournals.onlinelibrary.wiley.com/doi/10.1890/140055). Therefore, your ‘intermediate’ category may be low capacity refugia or nothing (it depends on many other factors (Kavoos & Keppel 2018). I know it does not affect your outcome, but it’s misleading. I wish you could have followed the approach by van Hooidonk et al., 2013, 2014.

https://www.nature.com/articles/nclimate1829

3- Line 108: interesting, but can you explain why?

4- Line 127-128: Is there a mistake here?

5- Line 191-193 and other places in the text (202-204; 2013-2016, etc.): you emphasize on the role of adaptive responses in combination of refugia. However, some scientists suggest refugial capacities and adaptation potential have inverse relationships (https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.14924). If that’s the case, I don’t know if it changes your results, but it should not be ignored. How do you respond to such an argument?

6- Line 361: You give a vague definition of refugia. However, refugia even for coral reefs have been defined (see papers by Keppel, Kavoos & Keppel).

7- Line 365-366: Can you explain why? (re-centring the monthly mean SST to the 1985-1990 + 1993 period [26].)

8- Line 373: can you please explain it a bit.

9- 381: ‘High variability thermal refugia’ are not refugia!

Thank you for this nice paper. :)

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Future loss of local-scale thermal refugia in coral reef ecosystems

PCLM-D-21-00006R1

Dear Dr. Dixon,

We're pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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PLOS Climate

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Does this manuscript meet PLOS Climate’s publication criteria? Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe methodologically and ethically rigorous research with conclusions that are appropriately drawn based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available (please refer to the Data Availability Statement at the start of the manuscript PDF file)?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception. The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS Climate does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: I am fully satisfied with the corrections. Therefore, I recommend publication.

Reviewer #2: Good job. Congratulations.

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Reviewer #1: No

Reviewer #2: No

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