PONE-D-24-09865Biotic and abiotic factors affecting Atlantic ghost crab ( Ocypode quadrata ) spatiotemporal activity at an important shorebird nesting site in VirginiaPLOS ONE

Dear Dr. Call,

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.

The major issues with your submission are in your analytical approach and interpretation of results. Publications in PLOS ONE are expected to present analyses that are conducted to a high technical standard and with enough detail to be reproducible. Two reviewers have provided detailed comments below to help you with your analyses and revisions to the manuscript.

Please submit your revised manuscript by Jul 13 2024 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.

Please include the following items when submitting your revised manuscript:

• 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'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Stephanie S. Romanach, Ph.D.

Academic Editor

PLOS ONE

Journal requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process.

3. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well.

4. We note that Figure 1 in your submission contain [map/satellite] images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission:

a. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license. 

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

b. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: No

**********

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: No

**********

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: "I would appreciate a revision of the map in Fig. 1, which could display less of the USA but should provide much higher detail of Metompkin Island. Indeed, readers of the paper may be interested in better visualizing the study area. Therefore, I suggest zooming in much more on that island. It's not even necessary to show the entire island, but the position of the surveyed area should be identifiable on the map. If this proves to be practically impossible, at least the coordinates of the limits of the 3 km-long stretch of the island used for the survey should be added to ensure the research can be fully replicated in the future by other researchers.

In the Abstract, it is stated, "We observed burrows at all nest sites in our study area but found fewer burrows at nest sites than random sites." This was an unexpected result for the authors. Consequently, they suggested that "Ghost crabs may avoid shorebird nest sites due to aggressive defensive behaviors from incubating adults or differences in microhabitat characteristics selected by shorebirds versus ghost crabs." This point is intriguing for readers because the study was not solely motivated by interest in ghost crab behavior and ecology but primarily due to the threat posed by the crabs to the reproductive success of endangered birds. Therefore, it's expected that the available data would be utilized, if possible, to test which of the two suggested causes was involved. While the behavior of the nesting birds wasn't studied, as far as I'm aware, the microhabitat was examined. Microhabitat is significant because other studies have demonstrated that piping plovers prefer to nest in areas with above-average shell cover, while crabs prefer to dig in areas with a low amount of shells, where digging is easier for them. However, the interaction between the presence of shorebird nests and the amount of shell cover wasn't tested.

I speculate that this issue could be investigated by incorporating, in the glmm model, a dependent variable: the interaction term between substrate type and the presence of bird nests. If there was a reason not to test this interaction, authors should explain why. As a reader, I'd also like to understand the extent to which the increase in the number of burrows depends on the likely interaction of date and temperature. Therefore, I suggest adding this interaction term to the glmm model as well. I understand that the authors obviously didn't include all possible interaction terms between predictor variables and that they chose to test only a set of 17 models based on a priori hypotheses about the effect of each predictor variable, but the suggested two interactions seem ecologically sound.

Additionally, as a reader, I'm curious to know whether the diameter of the burrows was measured, in addition to the number of burrows. I presume that the size of crabs would be significant in their interaction with birds. Large ghost crabs pose more danger to eggs and chicks, while tiny crabs with a carapace length of 1 cm should not be dangerous or could even be considered as food for birds. Therefore, was the size of the burrows measured? If not, I expect the authors to add a brief note in the Methods section explaining why it wasn't done despite its potential significance.

Not much information is provided on the glmm used for the analysis. For example, which response distribution and error distribution were used? Please add all relevant information that can be useful for the reader.

As I'm not an expert in statistics, I would appreciate it if the authors could provide a key in the Methods section on how to evaluate when an effect size is considered significant. For example, how significant are the apparently very low beta values of 0.05 and 0.08 for temperature and date (line 189)? Again, I'm not an expert in statistics, but I wonder why the beta effect sizes of dune and back dune flat habitat reported in the Results (0.05+-0.01 and 0.05+-0.01) (line 191) do not correspond to what can be seen in Fig. 2. Please correct or explain. Is the SE of the effect size of piping plover nest really 0.01 as stated in the results (line 214)? It appears to be different in Fig. 2. Please verify.

Regarding the Acknowledgments, I find it peculiar that "In addition to the authors listed for this study, we thank staff at the University of Virginia Coastal Research Station." Does this mean that the authors are thanking themselves? Later, D. Fraser is thanked. Is he the same D. Fraser who is one of the co-authors?"

Reviewer #2: Overall impression:

This study on Atlantic ghost crabs and their potential impact on beach-nesting shorebirds is well-written and addresses an important, yet under-appreciated topic of conservation interest. I have some concerns regarding the analytical methods, however, which could be addressed with the addition of significant clarification and justification in the manuscript. Specifically, while the abstract outlines the methodology and key findings regarding ghost crab activity and habitat selection, a more thorough account of hypothesis testing and statistical significance would enhance the manuscript's rigor. Overall, the study contributes valuable insights into ghost crab ecology and its implications for shorebird conservation, but further refinement of the analysis and interpretation is needed to strengthen the manuscript.

Major comments:

1) The authors should provide further clarification on the methods used for counting burrows between the random point locations and the nest sites. If random point surveys were indeed a point, then a 2m radius around the outside of a nest would yield a greater surface area (based on basic geometric principles) for examination compared to a 2m radius around a point, correct? If nest size varies greatly, this would also cause variability in surface area for surveys. Perhaps the diameter of the nests are small enough that the difference in area would be negligible, but the authors should address this possibility and provide further clarification on the characteristics of shorebird nest size.

2) The abstract and introduction state that the authors tested whether ghost crab activity was greater at shorebird nest sites than random sites, however the results presented in the manuscript do not adequately answer this question and lack testing with any level of statistical significance. While the model procedure used for analysis seems appropriate, the text is lacking proper explanation of full analysis procedures. Additionally, it does not appear that the authors have conducted any significance tests (e.g. Wald tests or likelihood ratio tests) along with their models. Upon inspection of Figure 2, it appears that many of the model effects are not statistically significant (i.e. the confidence intervals include zero). If this is not the proper interpretation, the authors should take care to provide further details and explanation in the methods and results sections.

Minor comments:

Line 23— The first line of the abstract makes it sound like ghost crabs prey on hatched chicks and adult shorebirds, but it is clear in the other text that they are potential predators only of nests and eggs. Please clarify here to be in agreement with other sections of the text.

Line 52— causes used twice, please replace one instance

Line 60— reword to “are not often targeted.” Are the authors aware of any instances where ghost crabs are targeted, aside from the one report citation from FL?

Line 62—change to “evidence” from isolated studies

Line 70— are conditions “inhospitable” or simply outside the preferred or optimal temperature range? Consider word use here, perhaps “suboptimal” would be a better fit?

Line 72— what kind of “change” in population is being referred to here. Please be more explicit.

Line 80— change “spatiotemporal” to spatial and temporal

Methods

Line 107— Please, remove one instance of “species” to avoid repetition

Line 130— Do the shorebird nests vary in size/diameter? This would affect the total area of surveys when using a 2m radius around a nest. Similarly for the point surveys. Please see major comment #1 above.

Statistical analysis

Line 166— What type of mixed effects model? In this case, “global” is used improperly and the type of model should be explicitly stated. I assume you are referring to a generalized linear mixed-effects model (GLMM)? The distribution and function family used in the GLMM should also be clearly described. Please, define your global model with all covariates in a separate sentence, with each variable explicitly listed as a fixed or random effect along with relevant interaction terms.

From the current analysis description, it is unclear whether you tested different distributions (e.g. negative binomial, poisson, or ordinary least squares) in the process of model selection.

Line 172— what are the a priori hypotheses that were tested in the candidate models? This is unclear based on the predictions outlined in the introduction and should be explicitly stated. “Considering what is known about ghost crab ecology” is a vague rationale for the choice of candidate models and additional text is needed here to explain and justify model construction.

Results

Lines 182-183— is it not clear that the parentheticals contain the mean values, please include “mean” for each.

Lines 188-191 – Please edit the parenthethicals containing statistical results to explicitly include SE and p-values , where appropriate for fixed effects.

Line 189— when examining Fig. 2, it does not appear that these are significant terms in model (date and temperature). Can the authors please explain?

Line 190— if habitat was included as a fixed effect in the model, how are you reporting statistical results for levels within habitat? This is not clear in the analysis methods, and if post hoc tests with multiple comparisons were made then this should be explicit.

Discussion

Line 248— delete “However”

Line 271— change “may need to” to “should”

Line 274— authors should be clear what they mean by “future research” directions. For example, it seems like it would be helpful to have data that could potentially help capture phenological shifts in predation risk. The authors should also consider including a final conclusion sentence (or two) that highlights the strength of their contribution and how this study can provide a basis for these future research in this area.

Line 275—change to “spatiotemporal ghost crab activity” as the crab is the noun in this sentence.

Figures and Tables

Table 1— It is not necessary to identify all levels for each variable of the model in the caption, but the variables should be clearly listed as fixed factors. If not explicitly including the random effect on each line, the caption should read “All models included a random effect of sampling point. Additionally, the code is not available so it is not possible to check whether the random effect was coded properly.

The manuscript has minimal figures. While I think the present figures/tables are effective, I suggest that the authors consider including an image figure to show nest sites and random point sites, highlighting the burrows that were counted. This could be included in the main text given the current low figure count, or included as an appendix.

**********

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: 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.]

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.

Biotic and abiotic factors affecting Atlantic ghost crab ( Ocypode quadrata ) spatiotemporal activity at an important shorebird nesting site in Virginia

PONE-D-24-09865R1

Dear Dr. Call,

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. If you have any questions relating to publication charges, 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,

Stephanie S. Romanach, Ph.D.

Academic Editor

PLOS ONE