PONE-D-24-20479Survival probabilities of thornback and spotted rays discarded by tickler chain beam trawl, pulse beam trawl and flyshoot fisheriesPLOS ONE

Dear Dr.  Schram,

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.

It is an interesting research dealing with an important field for the conservation of the entire marine ecosystem. Indeed, elasmobranchs are fundamental species for the well-being of marine ecosystems and the maintenance of ecological dynamics. The impact of the commercial fishery is one of the major concerns which heavily affect elasmobranch populations worldwide, also allowing the regional extinction of several species, as in the case of the Mediterranean Sea. ​

Please submit your revised manuscript by Jul 29 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,

Claudio D'Iglio, 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. To comply with PLOS ONE submissions requirements, in your Methods section, please provide additional information regarding the experiments involving animals and ensure you have included details on (1) methods of sacrifice, (2) methods of anesthesia and/or analgesia, and (3) efforts to alleviate suffering.

3. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. 

When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.

4. Thank you for stating the following financial disclosure: 

  "European Union, European Maritime and Fisheries Fund (EMFF)"

Please state what role the funders took in the study.  If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." 

If this statement is not correct you must amend it as needed. 

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

5. Please provide a complete Data Availability Statement in the submission form, ensuring you include all necessary access information or a reason for why you are unable to make your data freely accessible. If your research concerns only data provided within your submission, please write "All data are in the manuscript and/or supporting information files" as your Data Availability Statement.

6. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 

Additional Editor Comments:

Dear Doctor Schram,

The present Manuscript is well written, with a clear and reliable methodology and interesting results which strongly support the author's conclusion. There are some concerns to be fixed regarding the clarity of some parts of the Materials and Methods section, and some improvements which should be applied to the Discussion and Introduction sections to enhance their clarity and exhaustiveness.

Here are the reviewers' reports, please be careful to improve the Manuscript according to their suggestions.

All the bests,

Claudio D'Iglio, PhD

PLOS ONE

Accademic editor

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

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: N/A

Reviewer #3: 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

Reviewer #3: 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: No

Reviewer #2: Yes

Reviewer #3: 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: Dear Authors,

Thank you for your submission on the discard survival probabilities of thornback (Raja clavata) and spotted ray (Raja montagui). Your study provides valuable insights into this critical area of fisheries management. However, there are several areas where the manuscript would benefit from substantial revisions to improve its clarity and impact. Here are my detailed comments:

Introduction and Background:

Your introduction needs to provide a broader context for the study. The concept of discard survival should be framed within the larger scope of fisheries management and conservation. Additionally, it is crucial to cite foundational works that enhance the understanding of discard survival and the factors influencing it. In particular, the studies by Tiralongo et al. (2018) and Tiralongo et al. (2020) are fundamental for comprehending biological discards and survival, emphasizing that survival can sometimes be species-specific, as seen with Dasyatis pastinaca. Integrating these references will significantly strengthen your background section. See the attached pdf for further details.

Discussion:

The discussion needs to integrate your findings with existing literature more robustly. Again, referencing Tiralongo et al. (2018, 2020) will provide a deeper understanding of how species-specific traits influence discard survival. Discuss the implications of gear type on survival probabilities in greater detail and compare your findings with other studies on different species or in different regions. Provide a more comprehensive analysis of the interaction between water temperature, wave height, and survival probabilities. Explore why these factors might influence survival and how they interact. This analysis will add depth to your discussion and provide valuable insights.

Conclusion:

Your conclusion should be strengthened by explicitly stating the practical applications of your findings for fisheries management. How can these results be used to improve sustainability practices? Additionally, suggest areas for future research, particularly those that could address any limitations identified in your study or expand on the interaction effects observed.

Reviewer #2: The work "Survival probabilities of thornback and spotted rays discarded by tickler chain beam

trawl, pulse beam trawl and flyshoot fisheries" is well written and structured, easy to understand and deserves to be published after small corrections in the text

Reviewer #3: The manuscript titled Survival probabilities of thornback and spotted rays discarded by tickler chain beam trawl, pulse beam trawl and flyshoot fisheries reports on the discard survival of two ray species in 3 trawl fisheries in the North Sea. The methods and well-laid out and appropriate. The research was well-designed, although there was some variability in methods (number of control fish, number of rays per haul, timing in a haul that rays were collected), but not outside of what is to be expected for a field study. A really neat and tidy manuscript. The discussion covers a broad array of topics that are logical from their results.

The only think I’m not clear on is how discard mortality was recorded (see line 115 comment). Was each skate that came through the catch categorized as dead or alive, or just the ones sampled for the survival study? If the latter is the case, the dead rays were included in the tank study, but not actually placed in a tank?

Line-specific comments

Line 52: What measurement for minimum size? Total length? Disc width?

Line 60: Has any of these ray species been a choke species in a year? It’s good if they haven’t yet, but it would be good context to know how close these species have been to closing the fishery.

Line 69: What was the survival rate of Van Bogaert et al?

Line 115: Was data recorded (alive or dead) for all rays that came onboard? I think it’s also worth a statement in this section that condition of the ray was not a factor in choosing it as a test-fish, except if the ray was already dead (no spiracle movement for 15 seconds).

Line 127: Why did you focus on the big ones? Isn’t the minimum size 45-55 cm? Why 65 cm?

Line 130: I recommend moving this sentence to Line 126.

Line 266: Wasn’t the maximum time in a tank 21 days? I’m hesitant to put too much value in a leveling out of mortality at 20 days of a 21 day experiment. Looking at Fig 1a and 1c, I wouldn’t say the mortality rate has leveled off. This doesn’t change your results, just what you say about them.

Line 268: I’m not sure how direct mortality was recorded. Was every ray examined for direct mortality before discard? Or was this only of sampled rays? If the latter was the case, did you sample another ray from that haul to get to target numbers? See Line 115 comment also.

**********

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

Reviewer #3: Yes: Kelsey C James

**********

[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: PONE-D-24-20479_reviewer_User.pdf

Attachment

Submitted filename: PONE-D-24-20479_reviewer_REV.pdf

PONE-D-24-20479R1

Survival probabilities of thornback skate (Raja clavata) and spotted skate (Raja montagui) discarded by tickler chain beam trawl, pulse trawl and flyshoot fisheries

PLOS ONE

Dear Dr. Schram,

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 Ms has been strongly improved accotding to the reviewers suggestion. There are only some minor refuses and modifications that should be improved and adjusted, as stated by reviewers in their comments.

Please submit your revised manuscript by Nov 30 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,

Claudio D'Iglio, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #2: (No Response)

Reviewer #3: All comments have been addressed

**********

2. 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: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

4. 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

Reviewer #3: Yes

**********

5. 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

Reviewer #3: Yes

**********

6. 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: The manuscript presents interesting and well-structured findings on the discard survival probabilities of Raja clavata and Raja montagui in different fishing activities. However, some major revisions are necessary to fully implement the work before potential publication. In particular, attention should be given to the methodology used for survival probability analysis, the presentation of results, and certain aspects of data interpretation. The bibliography and conclusions also require particular attention to ensure they accurately reflect the current state of research and draw stronger connections between the findings and broader implications for fisheries management. Specific comments are provided in the attached PDF for a thorough revision of the manuscript.

Reviewer #2: The MS in question is well structured and easy to read. However, the authors must explain in detail what is meant by "ray". The species considered are skates, so it is suggested to check the entire text and verify when it is necessary to use skates instead of rays.

Reviewer #3: The manuscript addressed all of the reviewer comments and is generally improved. The Introduction has a broader context that appeals to a wider audience. The methods and results are clearer. The discussion does a good job of contextualizing the results with other work. I only have a few line-specific comments to address below.

Line-specific Comments:

Line 49-51: You state that starry and common skates are discarded. Is this still true after the landing obligation came into effect in 2019. Do these two species have exemptions for the landing obligation? This is not clear in this paragraph. I recommend adding the species that currently have exemptions from the landing obligation at the end of the paragraph (Line 57) or the next paragraph (Line 64).

Line 78: In the abstract you include that survival probabilities are “affected by gear, catch processing time, wave height, and the interaction between water temperature and wave height.” I think it’s worth including the that you investigated predictors of survival as an objective.

Line 120: remove the third ‘belt’ in this line since I think you mean “manually collected by crew members.”

Line 128: Why do you use a cutoff of 65 cm rather than 55 cm. I understand why you want large individuals, but why the 10 cm difference?

Line 138-140: Please rewrite this sentence to enhance clarity. I think the point of this sentence is that you were able to sample more skates when skates died while at sea and sometimes you were also able to put two skates in one tank.

**********

7. 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: Fabrizio Serena

Reviewer #3: 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.

Attachments

Attachment

Submitted filename: PONE-D-24-20479_reviewer_User.pdf

Attachment

Submitted filename: PONE-D-24-20479_reviewer_REV1.pdf

Survival probabilities of thornback skate (Raja clavata) and spotted skate (Raja montagui) discarded by tickler chain beam trawl, pulse trawl and flyshoot fisheries

PONE-D-24-20479R2

Dear Dr.Schram,

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,

Claudio D'Iglio, Ph.D.

Academic Editor

PLOS ONE

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #3: All comments have been addressed

**********

2. 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: Yes

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #3: Yes

**********

4. 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 #3: Yes

**********

5. 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 #3: Yes

**********

6. 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: Dear Authors,

the manuscript can be now accepted in its current form. Well done and congratulations for this interesting work.

Reviewer #3: (No Response)

**********

7. 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: Yes: Francesco Tiralongo

Reviewer #3: No

**********