PONE-D-23-16972Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera)PLOS ONE

Dear Dr. Lavrov,

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 comprehensively addresses the points raised during the review process.

Please submit your revised manuscript by Oct 22 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,

Michael Schubert

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. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, all author-generated code must be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse.

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. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

5. 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. 

[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

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

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: Yes

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: I congratulate the authors on getting this huge dataset together and writing it up! I'd also like to thank them for submitting such a polished version for review, as it makes my job easy. The discussion, especially, was very nice. I love the authors honest discussions about doubt and uncertainty regarding fossil calibration. Great work!

The dataset presented here, and its analysis, are undoubtedly valuable to the sponge community. The raw data will be used by many, and the tree will be thought provoking for a wide swath of evolutionary biologists. This value is also increased by the recent papers by Schuster et al. and Plese et al. that require correction, as pointed out (fairly) by the authors in the discussion. I would suggest the manuscript be accepted with only minor revisions required. My comments are very minor.

One point that struck me, however, was the omission of the recent paper by Pankey et al. 2022: https://www.nature.com/articles/s41559-022-01712-3 (and for the record: I'm not an author on that paper). The Pankey paper has time-calibrated phylogenies based on multiple loci, and is thus the most up-to-date and large-scale phylogeny available. The authors need to cite the work, and compare their results to Pankey. I think, for the most part, the results are very congruent -- even in terms of estimate divergence times, amazingly! -- and the papers will support each other very well (and add support to Lavrov et al.'s claims that the Plese & Schuster results are erroneous). The one possible exception might be that the established orders appear to be more problematic with the larger species sampling of Pankey -- though it is hard to tell how much data is available for any given species in their analysis, and they discuss their phylogenetic results in much less detail than Lavrov (indeed, barely at all!).

Additional, exceedingly minor points:

I believe one of the author's names is misspelled

Intro: line 52: you mean former not latter, right?

You list voucher numbers in table 1, but it is unclear if these are actually archived in a permanent collection (and I really hope they are, since morphological data supporting the species IDs is not provided here, and some could be misidentified!). The authors need to explain what museum collections each of these numbers refers to, as no one can find " 28-V-91-2-001", for example, without knowing where to look. If some of these are vouchered in the author's labs instead of museums, I highly encourage the authors to voucher them in a more stable place.

The Plenaster species name is misspelled in the time-calibrated tree, I think

Fig 4 caption mentions superorders...? Maybe proposed superorders? I don't know about any designated superorders.

Is fig S1 referenced in the paper? If it is, I missed where.

Reviewer #2: I congratulate the authors on this long awaited fine piece of work. I found no conceptual issues to remark upon, but I confess I am not proficient on the details of the analyses undertaken. I can feel the underlying anxiety of wanting to turn big pieces of the current classification upside down, but authors were correctly conservative in this respect, which is expected as long as the Linnean typological classification rules our relation with the diversity of life. Said all this, please check the attached revised MS carfully for a series of typos highlighted. Also, I see a need for a carefull review of the references too, as many are abbreviated, while others are not.

Reviewer #3: The manuscript by Lavrov and collaborators presents very interesting information regarding the systematic position of major demosponge orders recovered by the use of mitochondrial genomes, which is fundamental for understanding Porifera evolution. The authors have done a fantastic job sampling rare species and orders, and assembling a great number of new mitochondrial genomes, which are fundamental to understand sponge phylogeny. I think the manuscript deserves publication after major revision though, especially because there are some omissions of important results that should be discussed in depth. Also, figure readability is crucial to make science accessible, and I would suggest improving the quality of the figures presented here.

Introduction

There seems to be an incongruence in the number of datasets sequenced and assembled: 64 sequenced and 6 assembled from existing data in the introduction, while it says 59 sequenced and 5 assembled from existing datasets. Please ensure these numbers are correct in the manuscript.

Methods

I am afraid that the Table 1 provided is not sufficient to comply with the current standard metadata details necessary for reproducibility and open science. Please provide accurate location details, with longitude and latitude at least.

In addition, there is one species coded as Unknown sp. Although I understand the importance of sequencing, the inclusion of completely undetermined species in phylogenetic trees with such relevance for sponge systematics should be avoided. Please provide some better taxonomic identification of the sponge, which I believe would not be extremely difficult given that among the authors are some of the best sponge taxonomists of the field.

Please provide details for MAFFT alignment parameters.

Mitochondrial genes are highly conserved across demosponges in general, so it seems unnecessary to use Gblocks to produce alignments. What was the rationale behind this? Did the authors try a non-gblocked alignment to compare the convergence?

Results

The finding of multi-chromosomic mitochondrial genomes in demo sponges is highly important and novel, and deserved more attention. There is not sufficient information to understand the specific features of the mt genome of Mycale escalatei. I understand this would be in line with other preliminary data, but since that is not provided I suggest discussing here other possibilities for the lack of circularity (incompleteness, repetitive sequences, etc).

No information is provided for the position of the introns in the mt genes because it says they are being analysed in a separate study. Perhaps the phylogenetic affinities of such introns can be left for this separate study, but if the presence of introns is reported here, I would strongly encourage the authors to provide details somewhere for their positions.

Discussion

Lines 395-399: The recovery of a clade formed by Vetulina and Spongillida was also previously found by Plese et al. 2021. These lack of discussion with Plese et al. 2021 seems to be pervasive along the discussion, where it is only cited to discuss the unconventional relationships found there, which the authors claim that are likely to be found because unfortunate selection of outgroups. Although I don’t particularly agree with the view of the authors regarding these unfortunate outgroups, this could very well have been the case. However, that does not invalidate the entire results of Schuster et al. and Plese et al., which in turn found many of the same relationships found in the present study. One may wonder if there was a deliberate intention of not discussing the similar results found by these studies. For instance, the authors highlight the “unexpected” phylogenetic position of Axinella damicornis, although that was already placed within Agelasida by Plese et al. 2021. I would suggest discussing fairly and honestly the results of other researchers, giving credit where it is deserved, because it does not diminish the enormous relevance and importance of the present study.

The main figure of the paper (Figure 2) is extremely difficult to follow and in my opinion, the quality is not sufficient for publication. Same for Figure 3. I suggest editing the figure to make the tree more readable and provide a summary tree with the relationships of the orders.

Other minor comments:

The name of the last author is not spelled correctly.

**********

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: 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-23-16972_reviewer.pdf

PONE-D-23-16972R1Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera)PLOS ONE

Dear Dr. Lavrov,

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. More specifically, please address the quality issue of the figures raised by reviewer #3 and please remove the paragraph as suggested by reviewer #3, as it does not pertain to the discussion of the results obtained in this study.

Please submit your revised manuscript by Dec 15 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,

Michael Schubert

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.

[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 #3: (No Response)

**********

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: (No Response)

Reviewer #3: I believe the authors have accommodate almost all changes suggested to improve their manuscript. However, I still believe there are 2 figures without the quality necessary to fully grasp their results (2 and 3). Also, I don't fully understand their last paragraph about the results of other researchers "degrading confidence in phylomitogenomics and the field of molecular phylogenetics in general". Conflicting phylogenies are everywhere, and their inherent to the field, given the nature of the field, relying on parameter, taxa, and approach choices. There is no need to be aggressive or "nasty" to other researchers just because your results and approach disagree with them. I suggest removing the paragraph, and other than that I have no more comments.

**********

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 #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.

Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera)

PONE-D-23-16972R2

Dear Dr. Lavrov,

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,

Michael Schubert

Academic Editor

PLOS ONE