PONE-D-22-29095Untangling the systematic mystery behind the roughskin spurdog Cirrhigaleus asper (Merrett, 1973) (Chondrichthyes: Squaliformes), with phylogeny of Squalidae and a key to speciesPLOS ONE

Dear Dr. Viana,

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Kind regards,

Jürgen Kriwet

Academic Editor

PLOS ONE

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Additional Editor Comments:

Dear authors:

Thank you very much for submitting this excellent study to Plos One. Two reviewers commented on your manuscript and both agree with your results and only have some minor comments and/or suggestion, which I would like to aks to consider carefully. I agree with the second reviewer that it is unforunate that you did not provide the complete data matrix. I would suggest to include the full matrix in the manuscript and also a nexus file in the supplementary information, so that it is possible to recapitulate your analysis.

Kind regards,

Jürgen Kriwet

[Note: HTML markup is below. Please do not edit.]

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: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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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

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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

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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 editors, authors,

It was my pleasure to read and review the paper by Viana & Soares entitled ‘Untangling the systematic mystery behind the roughskin spurdog Cirrhigaleus asper (Merrett, 1973) (Chondrichthyes: Squaliformes), with phylogeny of Squalidae and a key to species’.

This topic is of taxonomic importance, and the paper itself is well organised, written and apparently prepared with much care as relatively little typo’s and mistakes in cross-references to Figs etc. occur. It is also noticeable that authors are experts in this field.

Nevertheless, please allow me to suggest the following improvements (on headlines):

- Titel: avoid the word ‘mystery’ (perhaps better: dilemma), and be more specific about

the key that is for the genus, whereas the title only mentions a single species and the

family (now confusing).

- Introduction: visualise the main hypotheses by simplified trees in an additional Fig.

- Morp. phyl. reconstruction: there is a problem in the lettering of the Clades, either

in the text of the MS, or in the Fig 13 itself (I guess in the latter). This needs special

attention and if needed correction throughout the entire MS.

- Key: in terms of presentation, I think it would be better to place this key at the final end

of the paper (i.e. after ‘Taxonoic considerations within Cirrhigaleus’), somewhat as a

conclusion.

- Figures: perhaps better to put the lettering of all panels in CAPITALS (A, B, C…) for

better contrast with abbreviations in Figs, and better contrast with Figs of external

references. Also check for scale bars.

- Smaller comments: for several smaller comments (e.g., rows vs. files, holotype info C.

barbifer, etc. etc.), please check the annotated MS carefully (see attached).

Wishing you all the best with finalising the MS,

Best regards,

Frederik

Reviewer #2: Overall a really good work with tons of information that can be put on larger context within Neoselachians. My only concern with the work is that the authors did not provide their full matrix, only the discrete features were provided. Consequently there is no way evaluate their results. Furthermore, I would suggest to the authors to provide their matrices in nexus file to facilitate the revision of their coding, as their matrix seems to present some non-informative characters (these features do not provide grouping information, but can inflate the CI and RI of the tree).

I have added some comments in a PDF of the paper (see comments with acrobat or other PDF readers, the browser one wont display them).

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Reviewer #1: No

Reviewer #2: Yes: Eduardo Villalobos Segura

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Attachments

Attachment

Submitted filename: PONE-D-22-29095_reviewer (annot FHM).pdf

Attachment

Submitted filename: Review cover letter FHM (2022-11-04).pdf

Attachment

Submitted filename: PONE-D-22-29095_reviewer (1).pdf

PONE-D-22-29095R1Untangling the systematic dilemma behind the roughskin spurdog Cirrhigaleus asper (Merrett, 1973) (Chondrichthyes: Squaliformes), with phylogeny of Squalidae and a key to Cirrhigaleus speciesPLOS ONE

Dear Dr. Viana,

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.

Please submit your revised manuscript by Mar 13 2023 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,

Jürgen Kriwet

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.

Additional Editor Comments:

Dear authors:

Thank you very much for considerng the comments by the reviewers and also for your patience. Reviewer 2 has raised an important aspect concerning character 16. Please check this comment and address it shortly in your manuscript. Please also check Figures 14 and 15 as there quality seems to be very low and improve the quality if necessary.

Please re-submit the manuscript once you have done the required improvements. I will check it (without another reviewer round) and make asap a final decision.

Kind regards,

Jürgen

[Note: HTML markup is below. Please do not edit.]

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 #2: 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: (No Response)

Reviewer #2: Yes

**********

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

Reviewer #1: (No Response)

Reviewer #2: N/A

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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: (No Response)

Reviewer #2: (No Response)

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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: (No Response)

Reviewer #2: (No Response)

**********

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: (No Response)

Reviewer #2: Char. 16. While I agree, the objective of the present work is not to address the homology of structures between batoids and sharks or in group shark relations. By naming a character, for example, Antorbital cartilages in the neurocranium, some sense of homology is implied in the name, the limitations on the generalisations on the observations need to be adequately clarified in their character description, so the reader interprets no untested homology. While I do not expect a full anatomical revision, I would hope that the authors include a short statement mentioning that while they are using the term Antorbital cartilage, no homology between this observed feature and the one present on batoids is implied by them as this need to be further tested. The same goes for characters 9 and 10. Furthermore, if they are following Shirai (1992 and 1996) in the codification of character 16 for this paper need to be cited to add context to their character description, same goes for Maisey's works (1982, 1983).

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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.

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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: Frederik H. Mollen (Elasmobranch Research, Belgium)

Reviewer #2: Yes: Eduardo Villalobos Segura

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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.

Untangling the systematic dilemma behind the roughskin spurdog Cirrhigaleus asper (Merrett, 1973) (Chondrichthyes: Squaliformes), with phylogeny of Squalidae and a key to Cirrhigaleus species

PONE-D-22-29095R2

Dear Dr. Viana,

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,

Jürgen Kriwet

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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 #2: 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 #2: Yes

**********

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

Reviewer #2: 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 #2: 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 #2: 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 #2: I would like to thank the authors for addressing the issues raised on previous revision rounds and congratulate them on their work. I consider that the manuscript is publishable.

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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 #2: Yes: Eduardo Villalobos Segura

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