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Dear Lara, I am pleased to inform you that your paper has been accepted for publication since your revised version of the manuscript follows well with the peer reviewers` comments. Congratulations.
[# PeerJ Staff Note - this decision was reviewed and approved by Xavier Pochon, a PeerJ Section Editor covering this Section #]
All reviewers have requested minor corrections to your revised manuscript, so I request you make the revisions and resubmit it.
I had only very minor questions and suggestions about the previous version of this manuscript, but it doesn't seem like they were addressed in this latest version. I think the paper will be ready for publication with these clarifications:
Line 218: There is a reference to a "RI" with no definition or description of it elsewhere in the Methods or Results. This seems to be in reference to the percent of the monitoring period the shark was present, but that should be clarified here to avoid confusion for the reader.
Figures 6 and 7: I still think it would be helpful and interesting to know how many of the tagged sharks demonstrated each of these occurrence probability patterns.
I have no further suggested edits or questions.
I have no further suggested edits or questions.
I have no further suggested edits or questions.
The structure of the introduction still needs improvement, while it was better that the initial version
No comment
No comment compared to the initial manuscript
The manuscript has clearly improved compared to the initial submission. The authors considered the recommendations of the reviewers. The major problems were the structure of the introduction and the discussion. Although they have been rewritten, I consider that the introduction still needs improvements. As the tittle of the manuscript and the objectives of the study are focused on the behavior of the bull shark, I suggest beginning the introduction with some theorical considerations about animal and shark behavior. The interest, limits and difficulties of studying behavior and to link the different behavior to individuals and to the environmental conditions. Then, you can highlight the interest of tagging animals. In the two first paragraph of the introduction, the focus on the methods and the direct description of what was done in the study is not relevant.
- Lines 52-53: Avoid self-citation in the first sentence of the introduction and add other more relevant references.
- Lines 53-55: need to add a reference.
- Line 159-160: Delete the sentence as this information was already provided earlier in the section
- Line 164: Briefly explain why you choose the Bernoulli distribution
- Line 167: What is an important area for the species? Change to more appropriate term
- Line 210: Change the two sentences, as it is not English
- Lines 212-213: Rewrite the sentences. A point is missing after ‘array’. What are the 21 remained attached to the sharks… I assume this is tags. But the previous sentence is about shark, not tags…
- Line 343: Delete ‘by’ and this is Matich et al. 2011, not Matichet et al. 2011)
- Legend of figure 6: Change 1S and 0s to 1 and 0
- Legend of figure 7: Add as for figure 6: 1 and 0
Most of my concerns have been addressed. I just have two minor comments:
1) Line 70 introduces bull sharks, but the scientific name is not given until line 74. It should be used the first time the common name is given.
2)Line 443: None of the citations given explore sexual segregation in sharks, they just describe that there was sexual segregation. To back up this statement why not cite a study that specifically discusses the drivers of sexual segregation in sharks (e.g. Wearmouth and Sims, see my first review).
no
no comment
The manuscript has been improved but still, both reviewers advised for one more revision. Both reviewers pointed out English usage, which needs to be focused in your revision. Reviewer # 4 suggested focusing your introduction from broader to specific. Further, advised you to write the discussion with more clarity. Hence, I request authors to do major revision by carefully following the reviewers' suggestions, especially Reviewer #4.
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
**Language Note:** The Academic Editor has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title). Alternatively, you should make your own arrangements to improve the language quality and provide details in your response letter. – PeerJ Staff
Overall the language has been tightened up considerably from the previous manuscript version, and questions regarding the methodology have been addressed. The improved clarity on the acoustic telemetry methods, definitions of the variables, and statistical analyses are a very positive change.
I have two suggested further changes:
- Line 229 - The rest of the paragraph refers to the percentage of days detected as degree of occurrence, but it is referred to as RI here (presumably a holdover from when the "residency index" terminology was being used in the previous version).
- Results and Figures 6 and 7 - The different occurrence patterns are interesting and it would be helpful to know how many sharks demonstrated each pattern.
The new manuscript version benefits greatly from the increased detail about the methods. I have no further suggestions for this section.
The improved detail and clarity on the methodology go a long way in supporting the interesting findings in this paper.
This manuscript has been greatly improved by the changes made in response to the reviewers and in my opinion only needs some minor clarifications and perhaps one more pass on language at this point. I look forward to referring to the final published version.
There are lots of grammatical errors throughout the manuscript. In some places, the most appropriate references are not being used. The structure of the introduction and results could do with better organization (for details see 'additional comments below)
The intro could do a better job in refining what the questions are and why. For example, MPAs are very briefly mentioned but given no context. Behavioral variability is mentioned but this is avague and broad term.
The analysis is very strong but organization of results could be improved.
I do have questions about the accuracy of the size estimates as sharks are not caught and measured
no comment
The authors use a Bayesian model to determine the drivers of presence of bull sharks within the Cabo Pulmo marine reserve. The authors have a nice dataset and I like the application of the Bayesian model. The results seem quite convincing in terms of showing 1) differences between the sexes, 2) seasonal residency and 3) some individual variability.
However, I see issues with the writing framework and there are still many grammatical errors throughout the manuscript. Specific points below:
Introduction: I did not review the first version of this paper, but I notice the reviewers criticized the format of the introduction. I believe some of those criticisms still remain as the format goes from being very specific (bull sharks) to being broader (value of Bayesian models for analyzing telemetry), when the introduction should go the other way round (broad to specific).
Line 103: No definition for MPA is given and no context for how this relates to the study is given.
Line 105: Define CPNP. Also, ‘behavioral variability’ is a very vague term. What does this mean. The introduction would have been better off with some background on individual variability in residency or movements (e.g., partial migration) which barely gets mentioned in the text. Behavioral variability can mean many things but here they are referring to residency and how it changes seasonally. This is never mentioned in the text.
Methods:
Line 143: One big issue I see is that the authors have a low accuracy method for measuring shark size. They determine life stage based on shark size relative to tagger size. While this may be ok, in their model they include size and seem to report it to 10 cm accuracy (e.g., ln 224). Underwater estimates from a tagger without lasers are not going to be accurate. That is probably fine for recording to 50 cm accuracy but seems very problematic for 10 cm accuracy. What are the errors and how did they estimate total length?
Where did environmental data (temperature, chlorophyll) come from?
Results:
Line 226: how do they calculate occurrence? Is this number of days detected divided by duration of detections for that tag or recording duration of the project. The authors then switch to the term RI (I assume residency index) but none of this has been defined in the methods.
I don’t have a problem with any of the results themselves, but the organization of the results is very confusing. For example, the authors repeat results about seasonal declines in presence two to three times, and it’s not clear why. From what I understand they are considering population level and individual level. If so, then sub-headings may be useful. Also, there are too many figures. We have 7 figures to show mostly seasonal differences (e.g. I don’t think fig 5 AND 6 are needed).
Discussion:
A lot of the discussion is either speculative or not particularly relevant. There are also many grammatical errors.
Line 342-344: I would remove. This reads like a figure caption.
Line 355-356; this sentence doesn’t make sense. I would then remove 356-357 which does not provide any useful information (why ontogenetic shifts in diet evolved).
Line 358: I believe the authors mean ‘residency’ not site fidelity. Residency is when an animal spends more time at a location than away from it. Site fidelity is when an animal leaves an area and is gone for a longer period than present, but returns. So an animal moving large distances can still show strong site fidelity. See Chapman et al. 2015. There and back again: a review of residency and return migrations in sharks. Annual Rev. Mar. Sci.
Line 362: values of what?
Line 383-386 repeats what is said in the first line of this paragraph and is fairly speculative anyway.
Line 399 really it is to reduce harassment from males. However, this is an odd reference to use for a broad concept like this. There have been several papers that are dedicated to this topic. E.g. Wearmouth and Sims. 2008. Sexual segregation in marine fishes, reptiles, birds, and mammals: behaviour patterns, mechanisms and conservation implications. Advances in Marine Biology
Line 400-403: The search patterns of males is not relevant to the discussion as there is no data to support it either way. Rather its what drives patterns of partial migration. See Papastamatiou et al. 2013. Telemetry and random walk models reveal complex patterns of partial migration in a marine predator. Ecology, and Espinoza et al. 2016. Evidence of partial migration in a large coastal predator: opportunistic foraging and reproduction as key drivers? PLoS One
Line 414-416 A better published citation for this would be Lubitz et al. 2023. Context drives movement patterns in a mobile marine predator. Move. Ecol.
Line 427-432: Is this true? Based on figure 8, the shortest residency periods occur when chlorophyll is lowest
Line 434-436: Why is this sentence relevant to the discussion?
Thank you for submitting your manuscript entitled "Seasonal occurrence and individual variability of bull sharks, Carcharhinus leucas, in a marine reserve of the southwestern Gulf of California". We appreciate the opportunity to review your work, and we believe that your research has the potential to make a valuable contribution to the field of shark ecology. However, after careful review, we have identified several issues that require significant revisions before we can consider your manuscript for publication. Specifically, we ask that you address the following major concerns: Reviewer #2 advised for major revision throughout the manuscript especially the introduction and discussion. Please follow all reviewers comments and suggestions. English needs to be improved.
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
[# PeerJ Staff Note: The Academic Editor has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title) #]
This paper is adequately organized and well-cited, but language and presentation need work. There are some inconsistencies in terminology that make it confusing to interpret the study methods and results.
In particular, the authors do not make the distinction between presence and residency clear in the methods, and seem to imply that both are defined in the exact same way based on multiple detections in less than a 15-minute interval. Making this distinction clear, or making it clear that residency is derived from presence data (which is implied in the methods section) would help improve the clarity of the whole paper.
I also have some further suggested edits and questions, though this should not be considered an exhaustive list. They are organized by section below:
Abstract
- Line 38 – “thrifty-two” should be thirty-two or 32.
- A bit more detail about the statistical methods would be helpful. For example, what were the variables?
- A quick description of the tracking methodology should be included.
Introduction
- Line 64 – “Based on reproductive studies” isn’t necessary and can be dropped.
- In general papers can just be cited when referred to.
- Line 69 – Are you referring to the aggregations being driven by biotic factors here?
- Line 78 – Specifically state that you’re referring to Cabo Pumo National Park here.
Methods
- Lines 104-117 – This information should be included in the Introduction.
- Lines 158-161 – When defining residency, would this mean that a shark that was only present for 15 minutes would be considered resident? Or is this referring to presence instead (the next paragraph seems to suggest that)?
Results
- The distinction between "presence” and “residency” is unclear in the Methods section, which creates some confusion here.
- It would be helpful to know how many sharks exhibited each of the movement behaviors.
Discussion
- Line 350 – “thrifty-two” should be thirty-two or 32.
Tables/Figures
- Figure 3 seems a bit redundant with some of the other figures related to residence probability. It may be more interesting to see the responses to each variable.
- Figure 9 is a little overwhelming and could probably be put into the supplemental material and replaced with a figure showing typical marginal posterior distributions for each behavior type.
Overall the methodology is straightforward and appropriate to the study, and a good amount of detail is provided about the statistical methods in particular. However, the paper could benefit from including more details relevant to the methodology. My suggestions are organized by section below:
Introduction
- Line 79 – Would bull sharks truly be considered reef sharks? They also show site fidelity to a wide variety of non-reef habitats.
Methods
- Some further detail on transmitter and receiver deployments would be helpful, including the timing of transmitter and receiver deployment and a brief description of the mooring system used for the acoustic receivers.
- Line 147 – Does “in the body cavity” refer to shark mortalities or some other type of fish used for testing?
Results
- See comments in section 1 regarding the distinction between "presence" and "residency."
The findings are a real strength of this paper. The authors have made some found some very interesting patterns and relationships and do a good job directly connecting them to the effectiveness of the Cabo Pumo National Park in providing protection to juvenile bull sharks. The classification of different movement behavior types among the sharks is also fascinating. Once concerns about language and method details are addressed, I think this will be a very strong manuscript that will be of use to researchers interested in highly migratory species movements and measuring the effectiveness of marine protected areas.
English should be improved (see attachment) and the structure of the manuscript (introduction and discussion especially) should be revised
The citation of the references is problematic in many parts of the manuscript. Some references are missing in the discussion (Blaison et al. 2015, African Journal of Marine Sciences, Trystram et al. 2016, Canadian Journal of Fisheries and Aquatic Sciences, Daly et al. 2014a and b in Plos One. Several times, references are missing (see general comments)
The objective of the study should be revised and more in relation with the discussion
The research is in the scope of the journal.
Research questions could be more defined and the knowledge gaps are not well identified. The whole structure of the introduction should be revised
The period of the study and the number of tagged bull sharks are not clear. There are some differences in the methods and results (See general comments)
The data analyses is robust, but the data set is not clearly defined (number of samples)
The beginning of the discussion should underlined more the advantages of the model used to investigate the habitat use of the bull sharks
Conclusion are not well linked to the original research question
This manuscript investigated the seasonal occurrence of the bull shark (Carcharhinus leucas) in the Marine Protected Area of the National Park of Cabo Pumo in Mexico. Analyses are based on acoustic data collected in an array of listening stations deployed mostly in shallow waters along the shore of the MPA, to detect the presence of 32 tagged sharks. The residency patterns and the individual variability among studied sharks were investigated with a hierarchical logistic regression model, with inference conducted in a Baysian framework. Although this study presents scientific interests and the data analysis is robust, this manuscript cannot be published in its present format, as it suffers many weaknesses and a general lack of structure. The English should be improved.
Abstract:
- Change thrifty-two with thirty-two (32). This should be done in the whole manuscript
- In the results it is indicated that ‘the Baysian framework is used to study passive acoustic telemetry’. The used of acoustic telemetry should be indicated in the background or the methods.
Introduction:
The introduction has to be fully revised. The structure does not fit the standard of a peer-reviewed publication. There is a mix of general information and particular information, which should not be in the introduction for most of them.
- The first paragraph of the introduction is an example of this mix of general and specific information. More than one sentence (the first) of theoretical background is necessary
- The last sentence of the first paragraph should not be here. The second paragraph of the introduction should be in Materials and Methods section
- Sentence Lines58-59 should be improved, as 25km2 is 35% of the reserve. No need for repetition
- Sentence Lines 59-60 should be deleted, as this information is not useful for this study. It could be placed in the Materials and Methods section
- Sentence Lines 63-64 should be revised, with coastal waters first and then brackish and freshwater systems
- Lines 64-66: Why is it important to provide the size at maturity, since you do not use this information in the analyses, the results and discussion
- Lines 67-68: Not used for the discussion
- Line 69-70: Not sure that reproduction is considered a biotic factor in ecology. It is more related to life history traits
- Lines 74-76: Should specify where the studies were conducted. Are you sure that these information can be applied to the species in all locations?
- Line 79: Does reef shark included the bull shark? Lines 62-4 you mentioned brackish and freshwater rivers. You should clarify this point
- Lines 80-81: Reference citation needs some revision on the form. In several occasions for the citation of the references you should use the brackets rather than ‘by authors and al…’
- Lines 82-84: Why is CPNP an ideal site for your investigation. From the information of the introduction I am not convinced of this affirmation
- Lines 84-85: You should either revised your objective or having a discussion more structured to provide clear information in relation with this objective
Materials and methods:
- Line 94 is a repetition of the line 91 on the fact that CPNP is influenced by tropical and subtropical conditions
- Lines 106-117: ‘The movements of sharks…they leave…’. Are you talking about the sharks in general as suggested in this paragraph? If you do so, this should be revised, as this information you provided do not apply to all shark species. See Lines 107-108 as an example
- Figure 1: Please provide information about shallow and deep receivers (depth range for each type of receivers)
- Not clear what is the study period. Lines 132-133, you mentioned the deployment of receivers in CNPN from 2011-2016, but the first sentence of the results you mentioned 2015-2019. Similarly Line 134, you mention 28 bull sharks, but line 217 you mentioned 45 bull sharks in the study. This should be clarified
- Line 140 you mentioned three stages of maturity (juvenile, sub-adult, adult) with very limited information on the size range and age for these different stages. In your data analyses, did you considered the growth of your studied bull sharks, as you analysed data produced over at least 5 years?
- Lines 151-152: The tests of range for the receivers were conducted in one type of sea condition, while it is known that the sea condition can affect the range of detection especially in coastal area. If you have no opportunity to conduct more tests, you should either mention this limit in the discussion or demonstrate that the sea conditions in your study area are most of the time similar to those of the range test
- Lines 187-189: Add a reference at least to justify the 220cm, as it is not the size at maturity in all locations for the species
Results:
- Although I am not familiar with the method used in to model the data, I have the feeling that some of the analyses are redundant (timing of residence in months and days of the year). Most of the legends of the figures 3 to 7 have to be corrected, as the years, size, colour are not coherent with the graphs
- Line 314: Change ‘today’ with ‘to day’
Discussion:
- The whole discussion should be revised and restructured, as the link between paragraphs is not clear. As such, the whole message is not clear. The discussion should mirror the introduction
- Line 357: Werry et al. (2012) is in Australia, not in Florida
- Line 366: revise the sentence: individual level residency probability curves to each shark
- Line 370: Delete the coma after Simpfendorfer and Tobin (2015)
- Lines 375-376: Revise the sentence ‘upon by (Matichet et al.)…’ See Trystram et al. (2016) in Canadian Journal of Fisheries and Aquatic Sciences on ontogenetic change in foraging habitat of bull shark
- Lines 377-378: Revise ‘Other studies Karl et al. (2011), … shows’
- Line 385: Move ‘year-round’ before ‘residence probability’
- Line 386: Revise ‘Previous studies by Mendiola (2015) suggests…’
- Lines 424: The chlorophyll does not lead to the residency of the bull shark. There is a relationship or a correlation between these two factors. Rephrase
- Lines 444-445: Need references
- Paragraph starting at line 444 is awkward and needs strong revisions. The link between the sentences is not clear
- Paragraph starting at line 454 does not work on its own. This is part of the restructuration of the discussion that is needed
- Lines 459-462: Need references or addition in the results
It is an exciting piece of work. But it needs more precision in the presentation, especially the methodology part seems to be much longer.
Acceptable, but you need to be precise it
Contains novel information
Many careless typos and formatting issues were found throughout the MS.
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