Unveiling hidden rocky reefs of the Mexican Atlantic coast: Topographic characterization and benthic community dynamics along the North Coast of the Yucatan Peninsula, Mexico

Ileana Ortegón-Aznar; Johnny Omar Valdez-Iuit; Armin N. Tuz-Sulub; Alain Duran

doi:10.1371/journal.pone.0341611

Peer Review History

Original SubmissionMay 14, 2025
14 Aug 2025 Decision Letter - Satheesh Sathianeson, Editor Dear Dr. Valdez Iuit, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’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 Sep 28 2025 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 plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. 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Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: No ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: No Reviewer #2: Yes ****** Reviewer #1: Dear Editor and Authors, This manuscript presents a descriptive study reporting, for the first time, the presence of rocky reefs along the Yucatan and Mexican Atlantic coast. The principal findings indicate a strong negative correlation between macroalgal abundance and Long Sediment-Laden Algal Turf (LSAT), suggesting competitive interactions influenced by environmental variables such as depth, sediment type, and topographic complexity. However, these ecological dynamics are already well-documented in existing literature (e.g., https://www.sciencedirect.com/science/article/abs/pii/S2352485521002917). A significant gap remains regarding the characterization of rock composition and formation processes, which warrants further elucidation. I strongly recommend the authors enhance the discussion section by incorporating comparisons with other rocky reefs and coral reef systems. Additionally, the conservation context should be broadened to address the vulnerability and threats these habitats face, thereby strengthening the manuscript’s claim that these reefs serve as critical hubs of biodiversity and ecosystem function. The manuscript’s organization requires improvement. Specifically, all figures and tables should be revised to remove redundant lines and markings for clarity. Furthermore, a thorough grammatical and punctuation review is necessary, as basic errors (e.g., in line 95) detract from the overall quality. In its current form, I do not consider this manuscript suitable for publication in PLOS ONE. Reviewer #2: In this manuscript, the authors characterise the bathymetric variance and benthic biodiversity of four rocky reef systems along the Yucatan Peninsula, Mexico – a habitat type that has received little research attention in this part of the world. Investigating these rocky reefs is important especially given their biological value which the author’s highlight and the growing anthropogenic pressures on these systems. Therefore, baseline data sets, such as presented in this manuscript, are vital for their management. Despite the need for these types of studies I cannot recommend publication of this manuscript in its current form. I hope that the authors can address these concerns without much difficulty, but I think it requires a major revision. Main comments 1) Overall the statistical analyses are limited and currently a little weak. This is leading to a Discussion filled with speculation and content not directly related to what was found in the study. For example, the paragraph starting on line 222 is very descriptive and some text does not reflect the study results - “SMR’s shallower slabs may boost light for macroalgae” – examining Fig7, SMR macroalgae cover was among the lowest of all reefs. The ANOVA results are not presented and unclear. I suggest the authors run a 2 way ANOVA examining a reef by season interaction for univariate response measures (e.g. macroalgae, sessile invertebrates, etc). That way differences in macroalgae etc among sites and between seasons will be quantified. This will also answer whether seasonal differences are consistent across reefs. Figure 7 should be presented as averages with standard errors. Further analysis could then look at associations between macroalgae and environmental predictors. Currently, simple linear models are looking at the effect of one predictor on the response independent of others which may be important. Multiple regressions would be more appropriate. For macroalgae a model including topographic complexity and LSAT would be more appropriate – then partial effects of each predictor can be examined. Also why is depth not included as a possible predictor? The text “SMR’s shallower slabs may boost light for macroalgae” indicates that depth may vary and be an important driver. With stronger analyses I think the Discussion will be improved as the authors will be able to relate their findings to those in the literature. 2) The measure of topographic complexity - Rugosity Index (R.I.) does not seem very sensitive with values looking quite similar. The 3d reef models, however, show quite considerable differences in rugosity within and among reefs. Is it possible to use rugosity metrics derived from the 3d model rather than the chain and tape method? Here, a range of rugosity metrics could be calculated at different spatial scales which may be more informative. 3) Line 63: Paragraphs should ideally be at least four sentences. I think this paragraph should include more information on threats to rocky reef biodiversity. For example, climate change stressors, pollution, fishing, mining, anchoring. 4) More detail in the methods would be helpful. How many sites were surveyed per reef? How many R.I. measures were taken per reef? Were water quality parameters taken on the surface or at depth? Overall I think the topic is important but stronger analyses are required to develop more robust findings and conclusions. Finally I could not find the raw data in the supplementary material. ****** what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. 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Revision 1
12 Dec 2025 Author Response PONE-D-25-26194 "Unveiling Hidden Rocky Reefs of the Mexican Atlantic Coast: Topographic Characterization and Benthic Community Dynamics along the North Coast of the Yucatan Peninsula, Mexico," Reviewers' comments: 5. Review Comments to the Author We thank both reviewers for their thoughtful and constructive feedback. We appreciate their recognition of the importance of documenting rocky reef ecosystems along the Yucatan coast and agree that the manuscript will benefit from substantial revisions. Below, we detail our responses and the changes made to address each comment. Reviewer #1:Dear Editor and Authors, This manuscript presents a descriptive study reporting, for the first time, the presence of rocky reefs along the Yucatan and Mexican Atlantic coast. The principal findings indicate a strong negative correlation between macroalgal abundance and Long Sediment-Laden Algal Turf (LSAT), suggesting competitive interactions influenced by environmental variables such as depth, sediment type, and topographic complexity. However, these ecological dynamics are already well-documented in existing literature (e.g., https://www.sciencedirect.com/science/article/abs/pii/S2352485521002917). Response: We acknowledge that competitive interactions between macroalgae and sediment-laden turfs have been previously described. However, our study contributes novel insights by documenting these dynamics in a previously unreported habitat type—rocky reefs of the Mexican Atlantic coast. We have revised the Discussion to clarify this distinction and emphasize the geographic novelty and ecological relevance of our findings. A significant gap remains regarding the characterization of rock composition and formation processes, which warrants further elucidation. Response: We agree that further geological characterization would strengthen the manuscript. While our study focused on ecological and topographic features, we have now included a paragraph in the Discussion acknowledging this limitation and proposing future research directions, including petrographic and geochemical analyses to elucidate reef formation processes. I strongly recommend the authors enhance the discussion section by incorporating comparisons with other rocky reefs and coral reef systems. Additionally, the conservation context should be broadened to address the vulnerability and threats these habitats face, thereby strengthening the manuscript’s claim that these reefs serve as critical hubs of biodiversity and ecosystem function. We added comparative context with similar reef systems, highlighting how our findings align or diverge from established patterns. The manuscript’s organization requires improvement. Specifically, all figures and tables should be revised to remove redundant lines and markings for clarity. Furthermore, a thorough grammatical and punctuation review is necessary, as basic errors (e.g., in line 95) detract from the overall quality. All figures and tables have been revised to remove redundant lines, improve labeling, and enhance visual clarity. We also reorganized sections for better flow and readability. The manuscript has undergone a thorough language revision to correct grammatical errors, punctuation inconsistencies, and improve overall clarity. We change paragraph as the e.g.line95 Reviewer #2: In this manuscript, the authors characterize the bathymetric variance and benthic biodiversity of four rocky reef systems along the Yucatan Peninsula, Mexico – a habitat type that has received little research attention in this part of the world. Investigating these rocky reefs is important especially given their biological value which the author’s highlight and the growing anthropogenic pressures on these systems. Therefore, baseline data sets, such as presented in this manuscript, are vital for their management. Despite the need for these types of studies I cannot recommend publication of this manuscript in its current form. I hope that the authors can address these concerns without much difficulty, but I think it requires a major revision. Main comments 1) Overall the statistical analyses are limited and currently a little weak. This is leading to a Discussion filled with speculation and content not directly related to what was found in the study. For example, the paragraph starting on line 222 is very descriptive and some text does not reflect the study results - “SMR’s shallower slabs may boost light for macroalgae” – examining Fig7, SMR macroalgae cover was among the lowest of all reefs. The ANOVA results are not presented and unclear. I suggest the authors run a 2 way ANOVA examining a reef by season interaction for univariate response measures (e.g. macroalgae, sessile invertebrates, etc). That way differences in macroalgae etc among sites and between seasons will be quantified. This will also answer whether seasonal differences are consistent across reefs. Figure 7 should be presented as averages with standard errors. We agree that the statistical analysis can be strengthened. In response: • We have now conducted a two-way ANOVA to assess the interaction between reef site and season for macroalgae, LSAT, and sessile invertebrate cover. These results are now clearly presented in the revised Results section, including F-values, degrees of freedom, and P-values. • Post-hoc Tukey tests have been added to identify specific pairwise differences. • Figure 7 has been updated to present mean values ± standard error for each benthic category across sites and seasons. Further analysis could then look at associations between macroalgae and environmental predictors. Currently, simple linear models are looking at the effect of one predictor on the response independent of others which may be important. Multiple regressions would be more appropriate. For macroalgae a model including topographic complexity and LSAT would be more appropriate – then partial effects of each predictor can be examined. Also why is depth not included as a possible predictor? The text “SMR’s shallower slabs may boost light for macroalgae” indicates that depth may vary and be an important driver. With stronger analyses I think the Discussion will be improved as the authors will be able to relate their findings to those in the literature. • A multilinear regression model was added, and We also add the depth but the previous analysis showed that they were not statistically significant 2) The measure of topographic complexity - Rugosity Index (R.I.) does not seem very sensitive with values looking quite similar. The 3d reef models, however, show quite considerable differences in rugosity within and among reefs. Is it possible to use rugosity metrics derived from the 3d model rather than the chain and tape method? Here, a range of rugosity metrics could be calculated at different spatial scales which may be more informative. We appreciate the reviewer’s insightful observation regarding the limitations of the chain-and-tape method for assessing topographic complexity. While we agree that 3D-derived rugosity metrics can offer more nuanced spatial resolution, unfortunately, our current dataset does not include the necessary georeferenced point cloud or mesh data to extract quantitative rugosity metrics from the 3D models. The models were generated primarily for visual representation using bathymetric contours and do not retain sufficient spatial fidelity for metric derivation at multiple scales. Given these constraints, we relied on the chain-and-tape method as a standardized and field-validated approach to estimate rugosity across sites. We acknowledge its limitations and have now clarified this in the revised Methods and Discussion sections. We also highlight the need for future studies to incorporate high-resolution 3D mapping techniques (e.g., photogrammetry ) to improve topographic assessments and enable multi-scale rugosity analyses. 3) Line 63: Paragraphs should ideally be at least four sentences. I think this paragraph should include more information on threats to rocky reef biodiversity. For example, climate change stressors, pollution, fishing, mining, anchoring. As noted in Reviewer #1’s comments, we have expanded the Introduction to include a broader range of threats, including climate change, pollution, fishing, mining, and anchoring. 4) More detail in the methods would be helpful. How many sites were surveyed per reef? How many R.I. measures were taken per reef? Were water quality parameters taken on the surface or at depth? We have clarified the number of sites per reef, number of R.I. measurements, and specified that water quality parameters were taken Attachments Attachment Submitted filename: Response to Reviewers final.docx https://doi.org/10.1371/journal.pone.0341611.r002
25 Dec 2025 Decision Letter - Satheesh Sathianeson, Editor Dear Dr. Valdez Iuit, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’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 Feb 08 2026 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 plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. A letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. 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We look forward to receiving your revised manuscript. Kind regards, Satheesh Sathianeson, Ph.D Academic Editor PLOS One Journal Requirements: 1. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. 2. 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. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: All comments have been addressed Reviewer #2: (No Response) ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> 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??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: (No Response) Reviewer #2: I thank the authors for their thorough responses to my comments. I think the ms will be suitable for publication following a minor revision. My suggestions are below and they should not be hard for the authors to address. L27: “Rocky” should not be capitalised. L63: I think these two sentences should be combined. Strange for the topic sentence to focus only on erosive degradation. Topic sentence should be on all threats to rocky reef habitats. L234: I suggest rewording. An option – “Although not statistically significant (α = 0.05), the two-way ANOVA revealed a….”. L244: Post-hoc comparisons should not be made as p > 0.05 for the interaction term. Instead talk about the trends in the data across seasons and reefs. L252-L257: I would not say these associations are weak with these R squared values, especially in the field of ecology. Reword to ‘moderate’. L262: remove the word “drivers”. That is causal language which is inappropriate given the statistical analyses used. I suggest “To identify the environmental variables that influence the abundance of macroalgae” or “To identify the environmental variables that are associated with the abundance of macroalgae”. L337: Discussion should not have a “statistical analyses” subheading. Rather the results from the data analysis should be inform the ecological interpretation and discussion. Figure 7 has not been updated. It should be presented as averages with standard errors. I suggest bringing into the main text too. Also it should be referred to in the 2 way ANOVA results section. ****** what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy Reviewer #1:Yes: 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.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. 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Revision 2
8 Jan 2026 Author Response We did all the recommendations provided by the reviewer. Reviewer #2: I thank the authors for their thorough responses to my comments. I think the ms will be suitable for publication following a minor revision. My suggestions are below and they should not be hard for the authors to address. L27: “Rocky” should not be capitalised. Done L63: I think these two sentences should be combined. Strange for the topic sentence to focus only on erosive degradation. Topic sentence should be on all threats to rocky reef habitats. Done L234: I suggest rewording. An option – “Although not statistically significant (α = 0.05), the two-way ANOVA revealed a….”.Done L244: Post-hoc comparisons should not be made as p > 0.05 for the interaction term. Instead talk about the trends in the data across seasons and reefs. Done L252-L257: I would not say these associations are weak with these R squared values, especially in the field of ecology. Reword to ‘moderate’. Done L262: remove the word “drivers”. That is causal language which is inappropriate given the statistical analyses used. I suggest “To identify the environmental variables that influence the abundance of macroalgae” or “To identify the environmental variables that are associated with the abundance of macroalgae”. Done L337: Discussion should not have a “statistical analyses” subheading. Rather the results from the data analysis should be inform the ecological interpretation and discussion. Done Figure 7 has not been updated. It should be presented as averages with standard errors.DONE I suggest bringing into the main text too. Also it should be referred to in the 2 way ANOVA results section. Done in L242 in revised manuscript with track and in L237 in the manuscript with out track changes Attachments Attachment Submitted filename: response to reviewers.docx https://doi.org/10.1371/journal.pone.0341611.r004
11 Jan 2026 Decision Letter - Satheesh Sathianeson, Editor "Unveiling Hidden Rocky Reefs of the Mexican Atlantic Coast: Topographic Characterization and Benthic Community Dynamics along the North Coast of the Yucatan Peninsula, Mexico," PONE-D-25-26194R2 Dear Dr. Valdez Iuit, 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. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support . 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 onepress@plos.org. Kind regards, Satheesh Sathianeson, Ph.D Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0341611.r005
Formally Accepted
Acceptance Letter - Satheesh Sathianeson, Editor PONE-D-25-26194R2 PLOS One Dear Dr. Valdez Iuit, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Satheesh Sathianeson Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0341611.r006

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