Structural Complexity of Coral Reefs in Guam, Mariana Islands

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The central aim of this research was to utilize Structure-from-Motion (SfM) for the accurate reconstruction of reef topography while quantifying structural complexity. The authors applied SfM to analyze a range of field measurements collected from eight reefs in the proximity of Guam. The paper exhibits a well-organized and well-articulated structure. The results are presented with clarity and bear a notable relevance to the study's objectives. The conclusion seamlessly aligns with the abstract and methodological framework of the work.

Comments on the Quality of English Language

Minor editing of English language required

Author Response

Please see the attachment. 

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

This study offers an examination of structural habitat complexity of shallow-water reefs in Guam using the new imagery-based Structure-from-motion tool. It also assesses the link between derived structural measures and benthic diversity and coral cover.

Overall, the manuscript is well-written and easy to follow. To increase the relevance of findings, I would suggest to better specify benthic diversity data used in the study – perhaps include species number information, what exactly was Shannon Diversity based on? An explained formula would be good here. Is it faunal diversity, morpho-types diversity? How exactly was coral cover defined? So far I think it remained rather poorly explained. Some images of seafloor (or orthomosaics) from transects with low and high cover per reef at least in the supplementary would be great.  

 

Comments/suggestions:

L17 Suggestion “However, while average structural complexity did not differ among most metrics used and sites…” (otherwise for Abstract it seems unclear - isn't complexity is a metric itself?)

L93 what were the reasons, main factors of that disturbance?

LL105-107 “.. photogrammetry … covered… factors… including wave exposure, dominant benthic groups, habitat heterogeneity, and human impact.”  I guess survey covered it, not the photogrammerty itself?

Figure 1. inlay outlined in green somehow looks like it is upside-down – should it be like that ? Another  inlet with the more global map extend would be great - not everybody know where Guam is.

Since this is an imagery-based study related to biodiversity, another figure with an exemplary underwater photo showing some typical habitats and species from each investigated site would be useful. How were water clarity and visibility conditions during the survey?

L126 why “remaining five” - not 6? if 8 in total, minus Lafac Bay and Gab Gab

L132 “ground sampling distance of 1.3 mm” - unclear how does in result in ground sampling distance 1.3 mm, and what does it mean at all?

L134 please specify what kind of plates

L147 “Coordinates and elevation were referenced to arbitrary da-147 tums.” - for what reason? why not using some common regional standard?

Please consider to provide geographical coordinates of each transect, e.g. in Table S1, it would increase transparency

L181-182 please better highlight how were benthic community diversity and coral cover estimated

L183 how exactly collinearity was tested, what were the results and thresholds used to omit metrics from analysis ?

L184 what was the size of photoquadrats, based on how many quadrants per transect …? Please provide more details

Figure 2 - perhaps it is a matter of taste but does not seem to be the best representation idea to me - i would also suggest to add classical letters - for the case of color-blindness or b/w printout

Regarding results in Table 2: how far were transects apart within each reef site - had distance any effect on similarity between features?

L215-218 – reporting correlation coefficient and not only p seems relevant

L218-219 – “effects of significant terrain metrics on benthic diversity and coral cover were not consistent across sites” - than why site was not left within the final model? seems contra-intuitive. At least to illustrate those differences in Figures 3 and 4 data points in different symbols for each site could be shown (coded by colour or shape)

Discussion

Overall, based on derived results, could authors suggest what conclusions can be made about health and condition of studied reefs? Are all good?

L248-251 “Transect slope… was also steeper than has been reported from other shallow-water reefs [14, 34]. The steepness of shallow reef slopes measured from Guam was in line with those measured for mesophotic reefs”. Isn't here some contradiction in those two sentence?

L254-257 if depth is known to influence the complexity and structure of the surveyed reefs, what was the argumentation behind the survey designed focused on such limited depth range? How deep do those reefs extend? What are the keystone species there?

L258-264 “scales as small as individual coral colonies have been shown to be sufficiently indicative of reef structure and complexity… This is also the likely explanation why site as a factor was not included in the best fit models when investigating the relationship between ecological and terrain metrics.” So based on those statements, the meaningful way to proceed in analysing the dataset in focus would be to break down each transect to smaller relevant units and repeat the analysis, and compare the results from those at finer scale?

L268 “there were contrasting effects of terrain on coral cover and diversity” - this is also very interesting- so the more healthy the corals are with higher cover, the less the diversity is? going further - higher coral cover is bad for diversity... would be great if authors could elaborate more on it, also discussing few recent findings in the field...

L304-306 “measurements of structural complexity across multiple spatial scales would provide more insight in the topographic complexity of benthic communities and habitats on Guam’s reefs.” Again, so why not doing it here? - you have all the data for it, to do relevant and more meaningful multi-scale analysis

L334-335 “this study demonstrates that fast, effective, and repeatable surveys are feasible at ecologically-relevant are feasible at ecologically-relevant scales”. I would encourage authors to elaborate more with argumentation to justify why the chosen scale in this study was ecologically-relevant. To do that, it would be particularly interesting to see more ecological and benthic data involved. Typical underwater images, species lists, even simple species richness data per reef and transect would be quite interesting.

 

Author Response

Please see the attachment. 

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

The article provides an important assessment on the Guam's coral reefs, taking some insights into the synergies among coral coverage and a wide range of terrain descriptors. Additionally they contributed to the establishment of a crucial baseline to identify possible changes in coral coverage and diversity, as well as overall structural complexity. I would like to congratulate the authors for its exhaustive work and I leave bellow a series of suggestions to the authors :

Keywords: It is always recommended to avoid repetitions of keywords in Title or Abstract to increase the findability of your article by different search strategies in search engines.

Introduction: greatly summarize and contextualize the study at hand.

I would only suggest adding some references in line 82 and/or 85 regarding the assessment of three-dimensionality as a proxy for many ecological functions, such as the works of Prof. Urbina Bareto in Reunion Island (Urbina-Barreto, I., Chiroleu, F., Pinel, R., Fréchon, L., Mahamadaly, V., Elise, S., Kulbicki, M., Quod, J.P., Dutrieux, E., Garnier, R. and Bruggemann, J.H., 2021. Quantifying the shelter capacity of coral reefs using photogrammetric 3D modeling: From colonies to reefscapes. Ecological Indicators, 121, p.107151.) and Dr. González-Rivero (González-Rivero, M., Harborne, A.R., Herrera-Reveles, A., Bozec, Y.M., Rogers, A., Friedman, A., Ganase, A. and Hoegh-Guldberg, O., 2017. Linking fishes to multiple metrics of coral reef structural complexity using three-dimensional technology. Scientific reports, 7(1), p.13965) both addressing the shelter capacity of this habitats from different perspectives. In addition, in line 31 and/or 75, the recent review on the evolution of photogrammetry from land to underwater applications (Pulido Mantas, T., Roveta, C., Calcinai, B., di Camillo, C.G., Gambardella, C., Gregorin, C., Coppari, M., Marrocco, T., Puce, S., Riccardi, A. and Cerrano, C., 2023. Photogrammetry, from the Land to the Sea and Beyond: A Unifying Approach to Study Terrestrial and Marine Environments. Journal of Marine Science and Engineering, 11(4), p.759.) may also be an interesting complementary reference.

Material and Methods: detailed and complete.

Line 106-108: I would advise the authors to rephrase the first sentence on the Study Area section. In specific, I would recommend to split the first phrase to better explain how along the 8 different reefs surveyed, different ecological conditions and anthropic influence was covered.

Figure 1: I would consider to add a small location map inside the figure to locate Guam Island in a wider geographical context.

Line 127: Please specify if 5x50 m or 6x50 m was applied in those transects.

Line 144: as far as I know, Metashape is a Russian software with a reference similar to this one “(Agisoft LLC, St. Petersburg, Russia)”. While Autodesk is a completely different software. Please double check the reference of Agisoft Metashape.

Results

Line 189: In the Material and Methods section, line 146, it was specified that DSM were produced at a spatial resolution of 1mm, then in results is 13mm. Was is resampled to 13 mm in order standardized resolution among all DSMs since some did not arrive to 1mm? Please specify this change in spatial resolution among sections in Material and Methods.

Figure 2. I would suggest adding the unit (when applicable) of the terrain descriptors in the Y axis or figure caption. Additionally, I would consider to make the figure slightly smaller in order to make it fit in the same page together with the caption (although I assume this may be also resolved by the editing team during the proofing step).

Figure 3-4: I would strongly consider to homogenize the captions in terms of “GLM demonstrating positive/negative correlation […]” and “GLM indicating positive/negative correlation […]”. And I suggest to keep the second one.

Author Response

Please see the attachment. 

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

I greatly appreciate authors efforts and responses. I think the paper have improved, however, some of my concerns remained. My following comments from the 1st review were ignored (despite authors write in the response that they were addressed, nothing was done and no relevant response provided): "what exactly was Shannon Diversity based on? An explained formula would be good here. ... How exactly was coral cover defined?   

Included list of organisms (benthic categories) identified in this study and sites at which they were observed shows that identification was not consistent and taxonomy was not harmonized, that may have implementation on the results. E.g., before calculating diversity, Acanthastrea brevis and Acanthastrea sp. should presumably be merged to Acanthastrea sp.; Cyanobacterium green tuft and Cyanobacterium sp.  - to Cyanobacterium sp. etc.

I would suggest to follow the recommendation of Horton et al., 2021  https://doi.org/10.3389/fmars.2021.620702 and after that redo the diversity calculation and the analysis of its relationship with functional complexity. I particular I mean the following recommendation: "for reporting or analysis purposes, taxa may need to be merged where consistent identification or discrimination of those taxa was not possible across all the images annotated... For example, two morphotypes can be identified as belonging to the same taxonomic group (e.g., genus or family) based on visible characteristics, but the identifier is unable to distinguish these two morphotypes consistently in the entire set of images, because the distinguishing features are not always visible (e.g., owing to variation in image quality and altitude of the camera). In such cases it is reasonable to merge the taxa to the next higher taxonomic rank (also called taxonomic roll-up) and to label this new merged group, which obviously contains more than one taxon, Family spp. or Genus spp."

Figure 1 now provides no labels for each site - this information should be added. The figure also shifted away from were it belongs in the file with track-changes.

I have some concerns remaining regarding authors "Response 11: We elaborated on the photoquadrat surveys to explain how the data was used to calculate diversity and coral cover and included references to the two studies (both currently in review) the data was taken from"

The mentioned sources of data under review are not available in the unpublished form. Since this data is essential for the outcome of the present study, I do not this that it is sufficient and acceptable to cite those not yet accepted /not yet peer-review approved articles instead of presenting the quality-assured data here. There are no preprints, no way the data presented there can be accessed by reviewers of this manuscript here to solve the doubts that here benthic community diversity is correctly estimated.

Regarding the comment and response 24, again, I acknowledge that "the focus of this study was on the structural complexity of the reefs", not on "in-depth ecological discussion and assessment", but if the aim is "to better understand the correlation between structural complexity and biodiversity, community composition, and coral cover", as still stated at the end of revised introduction, evidence should be provided that those are correctly estimated.

I think those issues should be addressed more carefully before paper can be recommended for publication. 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf