https://orcid.org/0000-0003-3712-6144
Peer Review History
| Original SubmissionDecember 22, 2023 |
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PCLM-D-23-00285 High coral heat tolerance at local-scale thermal refugia PLOS Climate Dear Dr. Lachs, 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. Please see the comments of one reviewer below. Please note that we have only been able to secure a single reviewer to assess your manuscript. We are issuing a decision on your manuscript at this point to prevent further delays in the evaluation of your manuscript. Please be aware that the editor who handles your revised manuscript might find it necessary to invite additional reviewers to assess this work once the revised manuscript is submitted. However, we will aim to proceed on the basis of this single review if possible. Please note that there is no requirement to cite any of the specific references suggested by the reviewer. You'll find specific journal requests on providing further information on field permits below, and how to provide a copy of our "Inclusivity in Global Research" questionnaire. Please submit your revised manuscript by Apr 08 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at climate@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pclm/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. We look forward to receiving your revised manuscript. Kind regards, Hanna Landenmark Staff Editor PLOS Climate Journal Requirements: 1. Please include a complete copy of PLOS’ questionnaire on inclusivity in global research in your revised manuscript. Our policy for research in this area aims to improve transparency in the reporting of research performed outside of researchers’ own country or community. The policy applies to researchers who have travelled to a different country to conduct research, research with Indigenous populations or their lands, and research on cultural artefacts. The questionnaire can also be requested at the journal’s discretion for any other submissions, even if these conditions are not met. Please find more information on the policy and a link to download a blank copy of the questionnaire here: https://journals.plos.org/climate/s/best-practices-in-research-reporting. Please upload a completed version of your questionnaire as Supporting Information when you resubmit your manuscript.” 2. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. Please note that PLOS CLIMATE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, all author-generated code must be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/climate/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. 4. Please amend your detailed Financial Disclosure statement. This is published with the article. It must therefore be completed in full sentences and contain the exact wording you wish to be published. a. State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” b. If any authors received a salary from any of your funders, please state which authors and which funders. If you did not receive any funding for this study, please simply state: “The authors received no specific funding for this work. 5. Please upload all main figures as separate Figure files in .tif or .eps format only. For more information about how to convert and format your figure files please see our guidelines: https://journals.plos.org/climate/s/figures 6. In the online submission form, you indicated that "All original data and code (R version 4.0.2, GNU Bash version 5.0.16(1) and CDO version 1.9.9rc1) have been deposited at 10.25405/data.ncl.22731194 (available before publication at https://figshare.com/s/faac387cb999778055cc to be completed). All datasets analysed are publicly available as of the date of publication. Any additional information required to reanalyse the data reported in this paper is available from the lead contact upon request". All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons by return email and your exemption request will be escalated to the editor for approval. Your exemption request will be handled independently and will not hold up the peer review process, but will need to be resolved should your manuscript be accepted for publication. One of the Editorial team will then be in touch if there are any issues. Additional Editor Comments (if provided): [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 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: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ********** 3. 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 ********** 4. 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 ********** 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 High coral heat tolerance at local-1 scale thermal refugia. This is an interesting, well written paper having results of likely interest to a coral reef readership. Detailed comments required to be addressed in a revised manuscript are detailed below. I have only one main concern with the data presented in this manuscript and that is the use of coral assemblage level bleaching data to examine spatial variability in assemblage wide coral bleaching but then then species specific heat tolerance data for A. digitifera. The different taxonomic resolution of the two data sets calls into question the veracity of the main results of the paper. If possible, I suggest the analyses using coral assemblage data be run with digitate Acropora or ideally A.digitifera data only. If this is not possible the authors should provide a more significant justification of the mismatched datasets in the methods and discussion to justify their results. Detailed comments Line 8. Change vary to varies. Line 77. Additional non-thermal environmental variables could be discussed here, for example turbidity (Sully and Van Woesik (2020)), water flow (Page et al (2023) High survival following bleaching underscores the resilience of a frequently disturbed region of the Great Barrier Reef) is this discussion of the effect of environmental variables on bleaching. Line 99 “From a management perspective, it is desirable if heterogeneity in recent (i.e., in the satellite record) past exposure of reefs to marine heatwave stress leads to predictable differences in coral population responses across seascapes, as this could allow managers to prioritise interventions in locations where they are likely to be most effective”. This statement would be strengthened if it also referred to those studies of winners and losers after bleaching in different regions or changes over time in bleaching winners and losers e.g. van Woesik et al. Revisiting the winners and the losers a decade after coral bleaching and McClanahan (2020) Highly variable taxa-specific coral bleaching responses to thermal stresses. Line 173. DHW is an acronym frequently used in the coral reef literature. I suggest you replace DHW with mDHW or some other variant of DHW to avoid confusion. Please change throughout the manuscript. Line 188. Please define SD before using this acronym. Line 204. Given that the heat stress experiment is performed on A.digitifera, I was surprised to see the assemblage wide coral data provided as apposed to data on A.digitifera only bleaching severity. Please justify the use of the two different data sets. Line 215. It would be more useful to here use bleaching in A.digitifera or at least digitate Acropora only colonies, rather than all hard coral taxa, given the high variability in coral taxa susceptibilities to bleaching. Please justify the use of all coral taxa here, rather than the target A.digitifera. Ideally this analysis should be replaced with the species specific or life-form specific data and analysis, otherwise justification of this exclusion should be included in the manuscript. Line 268. Please include estimate of nubbin average size. Line 284. Write MMM acronym in full and define on its first usage. Line 293. I am curious as to why no ramping in light was used in this experiment to replicate sunrise and sunset? Please include rationale in manuscript. Line 213. Change N to a lower case n throughout the manuscript. Line 727. Potential tradeoffs between heat tolerance and reproduction could also be mentioned here, with the inclusion of relevant references. 358. Please provide more explanation of the ‘flexible’ threshold parametrisation and justification of this approach. Line 360. Please provide a description of how colonies were chosen for this element of the project. Chosen at random from a set area of reef? This is needed to justify the result at line 530. Line 586. The use of life-form or species level data would have negated this speculation. Please consider the use of life-form or species level data for this analysis as suggested above. Without this level of data is it difficult to ascertain that site level differences in beaching don’t just reflect difference sin communities at these sites. The justification “given widespread temporal stability of Acropora populations (Gouezo et al., 2019).”: is insufficient and a more detailed justification should be proposed or species level data used instead. Line 631. Provide a more recent reference if possible to demonstrate higher heat tolerance of Durusdinium. ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. Do you want your identity to be public for this peer review? If you choose “no”, your identity will remain anonymous but your review may still be made public. For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. |
| Revision 1 |
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PCLM-D-23-00285R1 High coral heat tolerance at local-scale thermal refugia PLOS Climate Dear Dr. Lachs, 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. Please submit your revised manuscript by Jul 05 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at climate@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pclm/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript:
Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. We look forward to receiving your revised manuscript. Kind regards, Liqiang Xu Academic Editor PLOS Climate Journal Requirements: 1. Please include the following request in the decision letter, and ping me with follow up. “Please include a complete copy of PLOS’ questionnaire on inclusivity in global research in your revised manuscript. Our policy for research in this area aims to improve transparency in the reporting of research performed outside of researchers’ own country or community. The policy applies to researchers who have travelled to a different country to conduct research, research with Indigenous populations or their lands, and research on cultural artefacts. The questionnaire can also be requested at the journal’s discretion for any other submissions, even if these conditions are not met. Please find more information on the policy and a link to download a blank copy of the questionnaire here: https://journals.plos.org/climate/s/best-practices-in-research-reporting. Please upload a completed version of your questionnaire as Supporting Information when you resubmit your manuscript 2. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. Please note that PLOS CLIMATE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, all author-generated code must be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/climate/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments (if provided): Reviewer #1 I believe the authors have provided a very thorough response to my reviews and I now find the manuscript suitable for publication. Reviewer #2 Global warming is big challenge that human faces. The study of tolerance of corals to heat is thus of great significance. The manuscript entitled “High coral heat tolerance at local-scale thermal refugia” by Lachs et al. analyzed coral responses to 36 years of satellite-derived cumulative heat stress. It was found that corals located at local-scale hotspots are not necessarily more heat tolerant than those at nearby thermal refugia. This is a good case study, which provides key scientific basis for environmental management and decision-makers. Though I am not the original reviewer, I quite enjoy reading it. The paper is well designed, and has a clear logic. It is well written, and I suggest publication of this work. I have only several minor comments, see follows. Abstract: The Republic of Palau could be better than Palau. Author affiliations are usually provided after the name list, and before abstract. I do not think this is a big problem, but it looks strange. The unit for Degree Heating Weeks is “°C-weeks”, which is not a commonly used unit. It is well known in the community of people who studies heat stress, but researches in other areas who also concern climate change may not be very familiar with it. I suggest the authors explain it. For example, “a unit combining intensity and duration of heat stress”? Can the authors give a scale bar in Fig. 1c or 1e? A section of conclusion may not be mandatory for PLOS Climate, but it may be helpful for readers to obtain the key ideas rapidly. I suggest the authors consider this in their future research. For Data and code availability, the authors mentioned all data and code will be available at a https://figshare.com/s/faac387cb999778055cc, but the link is still unavailable. Please check it. Line 845: eLife, rather than Elife. [Note: HTML markup is below. Please do not edit.] 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 #2: All comments have been addressed ********** 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 #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? 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 #2: Yes ********** 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 #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 #2: Global warming is big challenge that human faces. The study of tolerance of corals to heat is thus of great significance. The manuscript entitled “High coral heat tolerance at local-scale thermal refugia” by Lachs et al. analyzed coral responses to 36 years of satellite-derived cumulative heat stress. It was found that corals located at local-scale hotspots are not necessarily more heat tolerant than those at nearby thermal refugia. This is a good case study, which provides key scientific basis for environmental management and decision-makers. Though I am not the original reviewer, I quite enjoy reading it. The paper is well designed, and has a clear logic. It is well written, and I suggest publication of this work. I have only several minor comments, see follows. Abstract: The Republic of Palau could be better than Palau. Author affiliations are usually provided after the name list, and before abstract. I do not think this is a big problem, but it looks strange. The unit for Degree Heating Weeks is “°C-weeks”, which is not a commonly used unit. It is well known in the community of people who studies heat stress, but researches in other areas who also concern climate change may not be very familiar with it. I suggest the authors explain it. For example, “a unit combining intensity and duration of heat stress”? Can the authors give a scale bar in Fig. 1c or 1e? A section of conclusion may not be mandatory for PLOS Climate, but it may be helpful for readers to obtain the key ideas rapidly. I suggest the authors consider this in their future research. For Data and code availability, the authors mentioned all data and code will be available at a https://figshare.com/s/faac387cb999778055cc, but the link is still unavailable. Please check it. Line 845: eLife, rather than Elife. ********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. Do you want your identity to be public for this peer review? If you choose “no”, your identity will remain anonymous but your review may still be made public. For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #2: No ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. |
| Revision 2 |
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High coral heat tolerance at local-scale thermal refugia PCLM-D-23-00285R2 Dear Mr Lachs, We are pleased to inform you that your manuscript 'High coral heat tolerance at local-scale thermal refugia' has been provisionally accepted for publication in PLOS Climate. Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow-up email from a member of our team. Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated. IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they'll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact climate@plos.org. Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Climate. Best regards, Liqiang Xu Academic Editor PLOS Climate *********************************************************** Reviewer Comments (if any, and for reference): |
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