Depth and benthic habitat influence shallow and mesophotic predatory fishes on a remote, high-latitude coral reef

Kristy Brown; Jacquomo Monk; Joel Williams; Andrew Carroll; David Harasti; Neville Barrett

doi:10.1371/journal.pone.0265067

Peer Review History

Original SubmissionAugust 27, 2021
26 Oct 2021 Decision Letter - Fraser Andrew Januchowski-Hartley, Editor PONE-D-21-27786Depth and benthic habitat influence shallow and mesophotic predatory fishes on a remote, high-latitude coral reefPLOS ONE Dear Dr. Monk, 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. Both reviewers believe that this manuscript is a valuable addition to the literature, and helps fill a gap in our knowledge about fish in mesophotic environments. However, they also both comment that the methods require some improvement, with a focus on clarifying the classification of fishes (e.g., between top-predator and mesopredator, and standardisation of names - particularly reviewer 2), more information on how depth zones were sampled including the gap in sampling shallow zones and how this may influence conclusions, potentially using zone rather than depth in the analysis in order to strengthen the argument concerning community changes across a depth gradient, and a little more polish generally within the methods section to bring it up to the standards of the rest of the manuscript. While all comments should be addressed in the response to reviewers, please pay particular attention to reviewer one's critique of the interpretation of the community patterns shown in Figure 2. Please submit your revised manuscript by Dec 10 2021 11:59PM. 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Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). 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 ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE 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 ****** 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: This is one of the few studies that documented patterns in the abundance and biomass of predatory fish assemblages in remote atoll seamount MPAs. The study used baited cameras to efficiently sample large areas of the lagoon and reef slope of the atoll, extending to the mid-mesophotic zone. The data presented are a valuable contribution to the coral reef ecological literature as previous studies of reef fish assemblages on remote atolls are mostly limited to euphotic depths. The ms is relatively well written but there is room for some improvement. I hope the general comments below will help improve the paper. Also listed below are minor comments, suggestions and corrections. General comments 1. The work highlighted the important roles of predatory fishes in the trophic ecology of reefs, the concerns about their dwindling numbers due to overfishing, and the importance of establishing baseline reference points for their spatial distribution (L39-49). However, it was difficult to appreciate the data presented in light of these points without showing some data on the overall fish assemblage. What proportion of the species richness, abundance and biomass of the overall fish assemblage in the atoll can be accounted for by predatory fishes? How do these proportions change with location and depth within the atoll? Do these proportions differ with other remote atolls in other regions that are open or closed to fishing? Addressing these questions may enhance the value of the ms. This seems fairly easy to do because the patterns presented here were simply extracted from the pooled fish assemblage data (L151-152). 2. Distinguishing patterns in the top predators from those of mesopredators seems useful and important to this ms. In many sections (e.g. L39, L58, L353-358, L399-405), the text seems to suggest a desire to highlight patterns in the abundance and biomass of top predators like sharks, large carangids and large groupers. There was also a desire to highlight the mesopredators (L376, L406). However, the ms did not explicitly identify which ones are top predators or mesopredators, for instance in Tables 1, 3, 5, and S1. 3. The study highlighted significant differences in the structure of predatory fish assemblages between the upper- and mid-mesophotic zones and the lagoon (L333-334). However, the results did not really support this because partitioning into upper (30-60 m) and mid (60-90) mesophotic zones (L54) was not explicitly considered in the sampling design and data analysis (i.e. depth was treated as a continuous variable). 4. The depth range between about 11 to 29 m was not sampled in the south part of the atoll (Table 1). Was this a consequence of spatially balanced sampling that was weighted towards more complex habitat (L118)? Or was this simply a consequence of difficulties sampling that depth range in the south part of the atoll due to wave exposure? In any case, this gap in sampling should be clarified in the methods. More importantly, its potential implications for the conclusions must be discussed. Minor comments, suggestions and corrections L18-20 – Sentence about Middleton Reef seems out of place here. It can be moved further down, around L24 where the authors described where the study was conducted. L28 – 90% of the total fish biomass or just the total biomass of large predators? Needs clarification. L47 – Knowledge may be a better word to use here than understandings. L81 – key predatory species? L85 – Sentence needs improvement. Suggestion: “Bait was used to attract fish following methods that were approved by the Animal Ethics Committee…” L104 – Specify that you are referring to habitats and faunal communities of Middleton Reef L125 – austral (as opposed to boreal), not Astral L126 – Odd to read numbers here instead of the authors L131 – Must be camera lens, not field (and field of view is another matter) L133 – higher order predators and mesopredators L135 – were instead of was L147 – Needs correction and further explanation. Parameters a and b of length-weight models for each species are what can be sourced from Fishbase, not biomass calculations. Were length-weight models (in FL) available for all species? If not (or only available for TL), what was the procedure? L148 – spell out QA/QC (quality control and assurance?) L151 – by dividing abundance AND biomass? L154 – Suggest providing an idea of the number of times double-counting was suspected for these mobile predators, and the procedure taken to omit suspected repeats counts L161 – of THE predatory fish assemblage… L164-165 – Clarify that you are referring to abundance of the selected predatory fishes only. L168 – Suggest modifying to “abundance and biomass structures of the predator assemblage across area (north, south and lagoon) as a fixed factor” L200 – Check value for average abundance across all deployments stated in text against Table 1 L202-203 – Figure 2 does not convincingly show that sampling in the north and south areas adequately captured predator diversity. I tend to disagree that predatory species accumulation curves “largely reached asymptotes” in these regions. Instead, what Fig. 2 suggests is that the north and south areas have a higher species richness of predatory fish and that these areas were not as well-sampled as the lagoon. I think the original statement should be toned down and the higher species richness outside of the lagoon of Middleton Reef should be highlighted. L223-226 – This sentence was a little confusing because it shifts its reference from total biomass to average biomass per deployment. Also, it should refer to Table 1 not S1. L242, 246 – fish not fishes L251-255 – Check sentence construction. This is a very long sentence that is hard to read. L302 – GAMs not GAM’s L304 – bohar not Bohar L306-310 – Again, a very long sentence that is difficult to understand. Suggest reconstructing or splitting. L330 – five species THAT contributed to… L353 – remove semicolon L354 – Odd to read a number here instead of the authors L374 – Remove open parenthesis L402-403 – E. daemelii is listed as near threatened (NT) which is NOT threatened, at least not yet. L404-405 – I didn’t fully understand the latter part of this sentence. It seems to say that C. galapagensis are likely to be vulnerable even if adult distributions of the species are unknown. But the species is listed as least concern (LC) – Table S1 Fig. 3 caption – Were the outliers removed from this plot all records in that one BRUV deployment that was removed from the analysis as stated in L164-165? Reviewer #2: Well done and interesting manuscript. The figures and tables are tidy and well-presented. The information in the manuscript is pretty complete and easy to understand. I have made suggestions in the attached document that I hope improve the readability and clarity. In particular the Methods need some added information as it does not seem as polished as the other sections. ****** 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. 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: No Reviewer #2: Yes:** Dr Tiffany Sih [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. Attachments Attachment Submitted filename: ReviewPlosOne_Brown_BRUVS.docx https://doi.org/10.1371/journal.pone.0265067.r001
Revision 1
31 Jan 2022 Author Response Response to reviewers’ comments Reviewer #1 This is one of the few studies that documented patterns in the abundance and biomass of predatory fish assemblages in remote atoll seamount MPAs. The study used baited cameras to efficiently sample large areas of the lagoon and reef slope of the atoll, extending to the mid-mesophotic zone. The data presented are a valuable contribution to the coral reef ecological literature as previous studies of reef fish assemblages on remote atolls are mostly limited to euphotic depths. The ms is relatively well written but there is room for some improvement. I hope the general comments below will help improve the paper. Also listed below are minor comments, suggestions and corrections. Reply: Thankyou. We have addressed your comments below that have greatly improved the manuscript. General comments 1. The work highlighted the important roles of predatory fishes in the trophic ecology of reefs, the concerns about their dwindling numbers due to overfishing, and the importance of establishing baseline reference points for their spatial distribution (L39-49). However, it was difficult to appreciate the data presented in light of these points without showing some data on the overall fish assemblage. What proportion of the species richness, abundance and biomass of the overall fish assemblage in the atoll can be accounted for by predatory fishes? How do these proportions change with location and depth within the atoll? Do these proportions differ with other remote atolls in other regions that are open or closed to fishing? Addressing these questions may enhance the value of the ms. This seems fairly easy to do because the patterns presented here were simply extracted from the pooled fish assemblage data (L151-152). Reply: We have provided an additional figure (Fig 2) along with the accompanying text to lines 271-276 to highlight the dominance of predatory fish abundance and biomass within the overall assemblage, and how this changes proportionally over depth and between locations. The entirety of Middleton Reef is protected in an IUCN II zone, so no legal fishing occurs on this reef. This is outlined on line 122. 2. Distinguishing patterns in the top predators from those of mesopredators seems useful and important to this ms. In many sections (e.g. L39, L58, L353-358, L399-405), the text seems to suggest a desire to highlight patterns in the abundance and biomass of top predators like sharks, large carangids and large groupers. There was also a desire to highlight the mesopredators (L376, L406). However, the ms did not explicitly identify which ones are top predators or mesopredators, for instance in Tables 1, 3, 5, and S1. Reply: We have added trophic classifications to Table S1 to highlight which species we have considered apex from meso. This now clarifies the various existing and new mentions throughout the text. Where apex or meso is used in the text we have attempted to qualify which species we are specifically talking about (e.g. line 303-308). 3. The study highlighted significant differences in the structure of predatory fish assemblages between the upper- and mid-mesophotic zones and the lagoon (L333-334). However, the results did not really support this because partitioning into upper (30-60 m) and mid (60-90) mesophotic zones (L54) was not explicitly considered in the sampling design and data analysis (i.e. depth was treated as a continuous variable). Reply: The spatially-balanced design did take into account the range of depths that cover these depth zones. However, as the reviewer highlights, we did not specifically classify depth into these zones for any analysis. Accordingly, we have removed reference to this depth partitioning to reduce any confusion. For example, the sentence on line 459 now reads “…across lagoonal to mesophotic shelf habitats.” 4. The depth range between about 11 to 29 m was not sampled in the south part of the atoll (Table 1). Was this a consequence of spatially balanced sampling that was weighted towards more complex habitat (L118)? Or was this simply a consequence of difficulties sampling that depth range in the south part of the atoll due to wave exposure? In any case, this gap in sampling should be clarified in the methods. More importantly, its potential implications for the conclusions must be discussed. Reply: We have added further details on the sampling design and issues we faced during survey to lines 158-165 to clarify why we could not sample areas of the reef including the shallow reef margins in the south. We have also inserted a short sentence in the results on lines 292-294 to justify that this is unlikely to impact results due to similarities in accumulation curves. Minor comments, suggestions and corrections L18-20 – Sentence about Middleton Reef seems out of place here. It can be moved further down, around L24 where the authors described where the study was conducted. Reply: Moved to lines 23-24 L28 – 90% of the total fish biomass or just the total biomass of large predators? Needs clarification. Reply: Total biomass of predatory fish. Has been updated on line 30. L47 – Knowledge may be a better word to use here than understandings. Reply: Changed to “knowledge” on line 49 L81 – key predatory species? Reply: Changed to “key predatory fish species” on line 105-106 L85 – Sentence needs improvement. Suggestion: “Bait was used to attract fish following methods that were approved by the Animal Ethics Committee…” Reply: Changed to “Bait was used to attract fish following methods that were approved by the University of Tasmania Animal Ethics Committee” on line 114-116 L104 – Specify that you are referring to habitats and faunal communities of Middleton Reef Reply: Have inserted “…of Middleton Reef…” to line 137 L125 – austral (as opposed to boreal), not Astral Reply: Changed on line 169 L126 – Odd to read numbers here instead of the authors Reply: Have added “Langlois et al.” before numbers line 171. Happy to alter as per Editor advice L131 – Must be camera lens, not field (and field of view is another matter) Reply: Yes, have altered text to “an estimated 8 m of the stereo BRUV to…” on line 185 L133 – higher order predators and mesopredators Reply: Have added “predators” to line 177 L135 – were instead of was Reply: Replaced with “were” on line 180 L147 – Needs correction and further explanation. Parameters a and b of length-weight models for each species are what can be sourced from Fishbase, not biomass calculations. Were length-weight models (in FL) available for all species? If not (or only available for TL), what was the procedure? Reply: We have altered text on Lines 189-202 to correct this and provide further explanation around process. All fish (unless ray) were measured using FL. L148 – spell out QA/QC (quality control and assurance?) Reply: Changed to “Quality control and assurance” on line 202-203 L151 – by dividing abundance AND biomass? Reply: Changed to “or” as it is exclusive from each other on line 206 L154 – Suggest providing an idea of the number of times double-counting was suspected for these mobile predators, and the procedure taken to omit suspected repeats counts. Reply: The following text has been added to lines 210-212 to clarify this point: “Where double counting was suspected the individual was excluded from the dataset, which only occurred in the large tiger shark individuals recorded in the lagoon.” L161 – of THE predatory fish assemblage… Reply: Changed on line 223 L164-165 – Clarify that you are referring to abundance of the selected predatory fishes only. Reply: Inserted “predator” to indicate we are only talking about predatory fishes and not entire assemblage on line 236 L168 – Suggest modifying to “abundance and biomass structures of the predator assemblage across area (north, south and lagoon) as a fixed factor” Reply: changed on line 231-233 L200 – Check value for average abundance across all deployments stated in text against Table 1 Reply: Thankyou for picking up this typo. Have updated SD text on line 280 to match table 1 values L202-203 – Figure 2 does not convincingly show that sampling in the north and south areas adequately captured predator diversity. I tend to disagree that predatory species accumulation curves “largely reached asymptotes” in these regions. Instead, what Fig. 2 suggests is that the north and south areas have a higher species richness of predatory fish and that these areas were not as well-sampled as the lagoon. I think the original statement should be toned down and the higher species richness outside of the lagoon of Middleton Reef should be highlighted. Reply: We have toned down this statement in line with the above comment. Lines 310-318 now reads: “The species accumulation curve for the predator fishes in the lagoon reached asymptote, indicating that sampling effort adequately captured diversity (Fig 3). However, the species accumulation curve for the predator fishes in the north and south areas suggest that although outside reef areas were not as well sampled, there was a higher predator richness outside of Middleton Reef lagoon (Fig 3). Importantly, both north and south areas exhibited similar accumulation patterns suggesting that, although there were issues accessing the shallow reef margins (i.e. 10-20 m) in the south, it is unlikely to overly impact results.” L223-226 – This sentence was a little confusing because it shifts its reference from total biomass to average biomass per deployment. Also, it should refer to Table 1 not S1. Reply: We have changed text to be all average for abundance and biomass. We have restructured these sentences on lines 314-321. Also updated to S1 to Table 1 on lines 324 and 325. L242, 246 – fish not fishes Reply: Changed to fish on lines 345 and 350 L251-255 – Check sentence construction. This is a very long sentence that is hard to read. Reply: We have completely rewritten this section of results to improve clarity (Lines 355-365). L302 – GAMs not GAM’s Reply: Changed to “GAMs” on line 423 L304 – bohar not Bohar Reply: Removed when modified ms to use common names throughout as per Reviewer 2 comments L306-310 – Again, a very long sentence that is difficult to understand. Suggest reconstructing or splitting. Reply: We have restructure both sections to reduce sentence length to improve clarity on lines 424-428. L330 – five species THAT contributed to… Reply: inserted “that” to line 454 L353 – remove semicolon Reply: deleted semicolon on line 503 L354 – Odd to read a number here instead of the authors [433] Reply: Have inserted authors in text to line 505 L374 – Remove open parenthesis Reply: removed parenthesis on line 527 L402-403 – E. daemelii is listed as near threatened (NT) which is NOT threatened, at least not yet. Reply: Agree, this is not formally listed internationally, but is species identified as vulnerable in NSW. We have revised to text as follows “…high abundances of vulnerable species…” on line 538 L404-405 – I didn’t fully understand the latter part of this sentence. It seems to say that C. galapagensis are likely to be vulnerable even if adult distributions of the species are unknown. But the species is listed as least concern (LC) – Table S1 Reply: We have removed the latter part of this sentence to reduce confusion from line 541 Fig. 3 caption – Were the outliers removed from this plot all records in that one BRUV deployment that was removed from the analysis as stated in L164-165? Reply: We have removed the sentence about a single outlier on line 228 to remove confusion as it was just individual values state in Fig 4 caption to were removed. We have also spelt this out in Fig 4 caption. Reviewer #2 Well done and interesting manuscript. The figures and tables are tidy and well-presented. The information in the manuscript is pretty complete and easy to understand. I have made suggestions in the attached document that I hope improve the readability and clarity. In particular the Methods need some added information as it does not seem as polished as the other sections. ________________________________________ 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. 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: No Reviewer #2: Yes: Dr Tiffany Sih [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. Review for PLOS One Depth and benthic habitat influence shallow and mesophotic predatory fishes on a remote, high-latitude coral reef Brown, Monk, Williams, Carroll, Harasti, Barrett Spatial distribution and extent of predatory fish in shallow to mesophotic shelf environments BRUVS lagoon and outer shelf habitats 0-100 m Remote location subject to varied oceanographic processes FYI, Check journal’s taxon naming specifications before publication, for Journal of Fish Biology the common name and authority/year need to be included at first mention of species. While some common names are included not all species in the text have common names mentioned, also be careful of capitalisation depending on if you are using common names or the Australian Standard Names (e.g. Fishes of Australia website for correct info). Would be helpful to include more common names as it could help internet searches to your publication and also is helpful to include in tables, etc for enhanced understanding. Reply: Thank you. We have used common names throughout based on Fishes of Australia. We have provided the scientific name at first use of common name. We have added both common and scientific names to Table S1 as well. There is no need to provide authority or year associated with PLoS guidelines. Abstract: Line 20: Add “fish” in between “predatory populations” Reply: Completed on line 20 Line 27: “…five predatory fish” makes it sound like you will list them. Not necessary here because of abstract word limits but I would suggest replacing “while” with “and” and starting a new sentence about Galapagos shark and Black cod or in some way splitting that long sentence. Reply: We have split the sentence following your suggestion on line 30 Introduction: Line 28: be consistent with capital letters and if you ae using Australian Standard Names (both capitalised) or ‘common names’ are generally not capitalised. Fishes of Australia website has the correct ASN Reply: Thank you for this insight. Names are now adjusted to common names based on Australian Standard Names. Line 47: Baseline understanding (singular?)… is necessary Reply: Have altered to “Understanding” on line 51 Line 60-62: split the sentence/re-write [66-68] Reply: We have thoroughly re-written this paragraph to improve clarity (lines 55-97) Materials and methods Line 92: oceanographic influences (plural?) Reply: Changed to “influences” on line 124 Line 93: replace influence with strength or magnitude? Reply: Changed to “magnitude” on line 126 Line 101: add latitudinal degree and specify typical of tropical or shallow-water corals (vs deepwater coral latitudinal limits). “what is the lat limits of coral growth” (~ lat) of tropical. Reply: Have defined this on line 133-135 Line 105: “The reef structure morphology resembles a system that is modified by both hard coral formation and rubble accretion, which reflects seasonal variation…” This sentence could be improved. Reply: Revised sentence structure to improve clarity on line 138-140 Line 119: “across depths from just below the surface to 100 m deep.” Reply: changed on line 154 Line 121: Source of existing bathymetry? Geoscience Australia or? Reply: We have added “sourced from Geoscience Australia” to line 157-158 Line 125: austral summer Reply: corrected on line 169 Paragraph beginning Line 118 or Line 123: add approx minimum space between deployments to maintain independence of replicates (on the map they look close, but that is probably just the size of the markers) Reply: We have added “…with a minimum spacing of 250m between concurrent deployments.” to line 154-155 Line 130: Sardinops sagax Reply: changed on line 175 Line 138: position of “.” Should be “GoPro .mp4”? Reply: inserted on line 183 Line 140: “within an estimated 8 m field of view” Reply: We have altered text in line with Reviewer 1 suggestion. Line 185 now reads: “All fish within an estimated 8 m of the stereo BRUV to the lowest classification possible were annotated” Line 142: “and length measurements were taken for each individual encountered” Reply: Altered on line 188 Line 143: “For teleost fishes, length was measured from the most anterior position (snout) to tail fork. Rays were measured across the widest portion of the disc. Other elasmobranchs were measured from snout to posterior tip on caudal fin.” Was this total length? Reply: We have altered the text to improve clarify this point on lines 188-202 Line 145: “When fish were in large schools…” here you are referring to a school of one species or a school with more than one species? I would re-write this sentence to specify that you measured 20 individuals of the same species. Reply: Correct, individual species, not mixed schools. We have altered the text to improve clarify this point on lines 191-194. Line 154: either a comma is needed between the common and scientific names or move the parentheses? Reply: inserted a comma as it is already within parentheses on line 209 Paragraph beginning Line 157: more information is needed like the number of habitat points per deployment or was this based on estimated percent cover? How many habitat categories and what were they? From what I can remember CATAMI just specified the naming convention/types/categories, but not specifically how to measure/quantify within a BRUVS field of view. Reply: We have provided additional information on lines 216-221 Line 163 “data did not need to be transformed”? Not sure if untransformed is a word. Also, raw data does not necessarily need to be transformed but I would clarify if you used any tests (visual or statistical) to check the distribution of data, etc? Also, if this is the first mention of Primer, please include the software details here. Reply: We have altered the text here to improve logic on line 225-226. We have also added citation for PRIMER on line 225 full details are provided on line 262-263 Line 164: One outlier… I would add more information here. Was this a replicate where no individuals were sampled? Reply: We have deleted this sentence and provided more detail in caption of Fig 4 following Reviewer 1 comments. Line 168: “across the fixed factor area”? Also this sentence is confusing how it is worded, perhaps move the clause “on the predator…and biomass structure” to the end of the sentence. Also, in this instance can “predator community assemblage abundance” be shortened to “predator relative abundance”? Reply: we have reworded this sentence on line 230-233 Line 169: I would clarify that the SIMPER function is the “percentage similarity of….” And clarify if you used presence-absence or abundance data. Reply: We have altered text on line 234 inline with this comment Line 173: missing “transformed” Reply: inserted on line 239 Line 174: “Vectors representing the most influential species/habitat variables were overlaid…”? Reply: inserted on line 239-240 Paragraph beginning Line 176 could be re-written for clarity with more details. E.g., “To understand the relationships between taxa and measured habitat variables, a number of analyses were conducted. Species influential in distinguishing communities among areas around Middleton Reef (north, south, lagoon) from the SIMPER analysis were then used to test the relationships between habitat variables. Only species with sufficient abundance (MaxN > xx or n � xx ) were included.” Reply: Have replaced start of paragraph you reviewers suggested text on lines 242-249 Line 182: split up sentence for clarity and include a citation for Tweedie distribution being an appropriate choice. Reply: Split sentences and added citation for Tweedie on line 255 Line 184-185: Change “3” to “three” Reply: changed on line 257 Line 192: here the use of ‘predatory’ seems like the species accumulation curve was being aggressive. Perhaps change to Predator species accumulation curve or Species accumulation curves of predatory species? Or add a ‘ after species. Line 202 and 204 same comment. Note this is just a suggestion but I think predator species sounds better than predatory species also throughout the results section. Reply: we have altered text on lines 286-294 to say “Species accumulation curves of predator…”. We have changed to predator fish/species throughout where appropriate. Line 215: This is not the correct common name for Pristipomoides filamentosus. It is easy to be confused because there are many names but most often Rosy Jobfish (ASN) or crimson jobfish are used, sometimes rosy snapper. This is to differentiate it from the other deepwater and eteline snappers (e.g. lavendar jobfish, ruby snapper, flame snapper and the half dozen species referred to as ‘red snapper’) ;-) Reply: We have altered to Rosy Jobfish throughout. Results The results section is well-written. I only have a few comments. Reply: Thankyou Line 263 I think Pearson should be capitalised. Reply: altered on line 380 Table 3: Not necessary but it might be nice to have some way of distinguishing the most similar/dissimilar, either with color, font differences (i.e. bold) or like a heat map. Reply: We have not altered table as we have highlighted the key species in the text on line 358-359 and 363. Line 302: Remove the apostrophe after GAM, should be GAMs Reply: removed on line 423 Line 317: In serranid the ‘s’ should be lowercase but for Serranidae the ‘s’ is capitalised. Reply: We have altered throughout Table 5: Great table! Reply: Thankyou Discussion Overall I found the Discussion well-written and interesting. I only have a few comments. Reply: Thankyou Paragraph beginning Line 339: This is a big paragraph and might benefit from splitting. Perhaps around “Complex habitat…” how you do it is up to you. Reply: We have split paragraph at “Previous studies…” on line 480 Line 372: change fishing to “fishing effort” Reply: inserted “effort” to line 500 Line 381: This first/topic sentence lacks a little oomph. I think it can be fixed by switching the order of words or a different word than concide. It does not match with the direction of the paragraph. Reply: We agree. We have deleted the entire first sentence on line 510-511 as we agree it didn’t fit with remaining direction of the paragraph. Line 391: I would write out East Australian Current (EAC) since it is the first mention in the Discussion. Reply: Spelt out in full on line 520-521 Conclusion Line 402-403: This sentence could be re-worded/re-structured for clarity Reply: We have worded the sentence on line 536-537 for clarity Line 407: beter segue between sentences? Or the sentence beginning with “Declines…” could be moved to the beginning of the paragraph Reply: We have moved the sentence and next that were originally on lines 543-546 to start of paragraph (lines 529-532) Attachments Attachment Submitted filename: Brown et al Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0265067.r002
23 Feb 2022 Decision Letter - Fraser Andrew Januchowski-Hartley, Editor Depth and benthic habitat influence shallow and mesophotic predatory fishes on a remote, high-latitude coral reef PONE-D-21-27786R1 Dear Dr. Monk, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. 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, Fraser Andrew Januchowski-Hartley, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0265067.r003
Formally Accepted
11 Mar 2022 Acceptance Letter - Fraser Andrew Januchowski-Hartley, Editor PONE-D-21-27786R1 Depth and benthic habitat influence shallow and mesophotic predatory fishes on a remote, high-latitude coral reef Dear Dr. Monk: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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. If we can help with anything else, please email us at plosone@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. Fraser Andrew Januchowski-Hartley Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0265067.r004

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