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Thank you for addressing all the comments raised in review. I am happy to accept your revised manuscript and move it forward into production. Congratulations on a great study.
[# PeerJ Staff Note - this decision was reviewed and approved by James Reimer, a PeerJ Section Editor covering this Section #]
Once again, I apologize for the delay in getting your manuscript back to you. The referee was not immediately available and we only now got their review back. As you can see the referee is satisfied with your revisions and I agree that your manuscript is acceptable at this point. The referee makes a couple of suggestions for possible improvement including an expanded discussion of species turnover. I see the merit in this suggestion, and believe it would make for a stronger paper in the end, but I also feel that the paper is up to the standards of the field at this point. Thus, I am returning the manuscript one last time, and leave it to the authors as to how they wish to respond to the referee feedback and what to include in the final publication.
I look forward to seeing your finalized manuscript.
In this paper a great integration of ecological and geological processes determining reef formation is used as an apporach to evaluate the benthic coral community structure along trhe Mesoamerican reef system. Authors take into account intrinsic and extrinisc factors controlling the structure of these communities. The paper is orginal and represents a great contribution because trend analyses that are guiding decision are based on regional analysis which often ignore the role of extrinsic factors, particularly geological ones, which are highly important.
Literature review is consistent and robust for the scope and goals of the paper. The article is well written, provides a good background and it is easy to follow with figures and table being selfexplainatory and easy to understand. There is transparency as the data is shared.
Results are clear and allows to answer the major questions and hypotheses being tested, likely because experimental design is appropiate for the questions presented. I really enjoyed reading this paper, the multivariate analysis apporach used is robust and the apporach presented is very interesting.
The questions of the paper are presented, they make sense and are clearly presented. The incosporation of geological and ecological processes to understand patterns is a very meaningful apporach.
The experinetal design is clear and well presented in a figure that clearly portrays the structure of the design, type of factors (Fixed and Random) and how thet related to each other (nested) are shown in the figure. The investigation is performed following high technical standards and good knowledge of experimental design and data analysis using semi parametric analysis, ordintation techniques and distance/based linear models that are extremely useful for data with lack of normality and heterogenous dispersions.
Methods are well explained and for me was very easy to follow up results after reading the section of methods, particularly statistical analyses.
The findings are meaningful and the approach presented in this paper should be used by managers that are only guided by regional assessments and reports. The replication is extensive, providing strong validity for the results.
Statistical analysis is solid and robust as I mentioned before. However, I would encourage the authors to explore more the beta diversity analysis by incorporating in the discussion more insights about the interpretation of species turnoever or nestedness to explaing changes is species among geomorphological zones across different spatial scales.
Conclussions are adjusted to the rationale of the paper and the hypotheses and questions being addressed.
This is a good paper, I really congratulate the authors. I would apporave the publication of the paper aftern minor changes are included. Particularly, I make two suggestions.
1. Include in the introduction a paragraph to say how global reports are currently being used to inform needs for coral restoration, and how coral restoration ignores the importance of geological processes.
2. Expand in the discussion the partition of beta diversity and what inferences can be made about the relative importance of different proccesses afecting the distribution and abundance of corals across the study sites. Beta diversity is currently thought as the most robust indicator of community change and only a few number of paper have used this community property (see Miyazawa et al. 2020).
I am sorry for the delay in responding to your manuscript, but we were waiting on a final review that never arrived, and now I have had to take over managing this manuscript because the AE is no longer available. As you will see, we have 2 quite divergent opinions on your submission, although both are positive about the value of the work overall. I have read both your manuscript and the reviews and find myself in agreement with the second referee that the statistical issues raised need to be addressed prior to the manuscript being considered further. The referee has provided specific concerns about inconsistencies in reporting and conceptual errors that may impact the outcome and interpretation of the analyses. Thus, I request that you undertake a major revision of your submission that will be subjected to an additional round of review before we make a final decision on your submission.
I would note here that it is PeerJ policy that additional references suggested during the peer-review process need only be included if the authors are in agreement that they are relevant and useful.
If you decide to undertake the suggested revisions, please ensure that all review comments (including those on the annotated manuscript) are addressed in a rebuttal letter that outlines how you have addressed each comment. Any edits or clarifications mentioned in the rebuttal letter should also be inserted into the revised manuscript where appropriate. It is a common mistake to address reviewer questions in the rebuttal letter but not in the revised manuscript. If a reviewer raised a question, then your readers will probably have the same question so you should ensure that the manuscript can stand alone without the rebuttal letter. Directions on how to prepare a rebuttal letter can be found at: https://peerj.com/benefits/academic-rebuttal-letters/ if you need additional guidance.
I look forward to seeing your revised manuscript.
I found the paper to be very clearly written and well organised. The figures and tables are useful and clear.
I am not an expert on statistical analysis but from my understanding the methods used are relevant and correctly applied. The research question of the role of geomorphology in controlling coral cover is clear and the formulated hypothesis is testable using the data collected.
The fundamental conclusion is that "an accurate analysis of spatial ecological trends in coral reefs requires a detailed geomorphic framework in order to identify subtle changes in communities at large spatial scales". This seems reasonable to me based on the data presented.
There have been very few studies of coral reef geomorphology and this paper fills an important gap in reef research. Note also some comparable work has been done in the Great Barrier Reef:
Harris, P. T., T. C. L. Bridge, R. Beaman, J. Webster, S. Nichol and B. Brooke (2013). "Submerged banks in the Great Barrier Reef, Australia, greatly increase available coral reef habitat." ICES Journal of Marine Science 70(2): 284-293.
The paper is very interesting, it acknowledges the importance of using geomorphologic and ecological processes to understand species distribution on coral reefs across large spatial scales. I also celebrate the idea of testing the role of extrinsic factors that works at large spatial scales to explain why coral assemblages change over and space and time. Therefore, the rationale of the papers is based on solid ecological theory. Another important aspect that authors depicted is the undeniable fact that coral cover alone is a metric that lead us to flunk conclusions when trying to understand trajectories of coral communities. The literature review is good, and the hypothesis is well constructed.
The data is extensive and robust, and therefore is worth to publish. However, there are specific details in the experimental design that need clarification which I explain below. I see errors in the way the factors were declared (fixed, orthogonal, random, or nested) that may hamper the validity of the results. The paper therefore, requires substantial revision before is acceptable for publication.
The experimental design is good in the field, but I think there are conceptual mistakes in the analysis of the data that must be revised. This errors will have an impact on: (1) the outcome of the analysis, (2) the way the pesudo F in the permanova will be constructed and (3) the interpretation of the statistic test for every source of variation.
For example:
Authors declared the factor geomorphologic zone as fixed and nested in wave exposure. By definition a nested factor is random cannot be fixed as declared in the analysis. Is this a typo error or the data was actually analyzed in that way? I would like to see a table with the sources of variation to better undertand the design. Also, for random factors, authors compared between levels of these factors. This is a mistake too. Authors say that Factor A (wave exposure) and B
See below from the manuscript.
The experimental design consisted of 3 factors (Figure 2.C): Factor A: wave exposure (fixed with a = 2 levels: sheltered and exposed), Factor B: Geomorphic zones (fixed, nested in wave exposure with 3 levels nested in sheltered, and 4 levels nested in exposed), and Factor C: Site (random, nested in geomorphic zones, wave exposure) with 95 levels.
Also, authors compared between levels of these 3 factors. This is a mistake too. Authors say that Factor A (wave exposure) and B (Geomorphologic zones) and C (Site) are orthogonal. If one factor is nested to the another, then they cannot be orthogonal.
See below in the manuscript.
The estimates 237 of components of variation (S) for the three orthogonal factors were wave exposure: 178.52; Geo zone nested in wave exposure: 214.98; and site nested in Geo zone nested in wave exposure: 239 875.33.
In any case, I see a lot of contractions along the text, both were the design is explain and the outcomes from these design when results are described.
I have to have a better understanding about the design and how the data was analysed. I see inconsistency in the way the design is declared, and therefore, the sources of variation derived from the design might not be the proper ones.
For example, the use of pairwise tests to look at statistical differences between levels of a random factor is incorrect. If there is orthogonality, I see no interactions analysed. If a factor is nested, there cannot be orthogonality.
Another important factor to be included here is beta diversity. This is a measure that is better to discriminate communities across gradients and different habitat types. In this case study, beta diversity would be much more informative than alpha diversity. Beta Part is an R package that can be use for the partition of beta diversity estimated from Sorensen index or any presence-absence index. The Perm disp test is currently interpreted as a prove of statistical changes in beta diversity if the Sorensen index is used.
I think this paper is extremely interesting and the data definitely worth to publish. However, I believe there are errors in the way the experimental design was declared. Please review my comments and if necessary, run the analyses again. I would endorse this paper after substantial review of the current version.
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