Systematic revision of Gatesona (Crassiclitellata, Lumbricidae), an endemic earthworm genus from the Massif Central (France)

Daniel F. Marchán; Sergio Jiménez; Thibaud Decaëns; Jorge Domínguez

doi:10.1371/journal.pone.0255978

Peer Review History

Original SubmissionMarch 6, 2021
15 Apr 2021 Decision Letter - Michael Schubert, Editor PONE-D-21-07434 Systematic revision of Gatesona (Crassiclitellata, Lumbricidae), an endemic earthworm genus from the Massif Central (France) PLOS ONE Dear Dr. Marchán, 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 May 30 2021 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. 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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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. 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. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 ****** 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: No ****** 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: Authors present a very interesting paper about the identity of several Lumbricidae species and subspecies that are placed in a new genus. These new arrangements are due to the use of an integrative approach (molecular genetics, phylogenetic analysis and morphological revisions). English is ok, as well as molecular and phylogenetic methods and results. There are, however, some modifications that should be done (mainly in regard to classical nomenclatural arrangements) before the paper could be accepted. The paper, thus, is ACCEPTED WITH MINOR CHANGES. I directly wrote several comments and suggestions over the main text; following are some of my main points: 1) In the title it is mentioned the word Crassiclitellata; in the classification of the new genus Gatesona, however, this word is not included. Thus, include in the supraorder classification this word with its hierarchical associated level. 2) There are several mistakes in regard of the “types” of the two re-described species. Please attend comments of the text. 3) As authors do not reviewed types of these species, maybe the name (from an already described species) in fact does not correspond to the collected and molecular sequenced material. I strongly suggest contact Dr. Bouché in order to obtain in loan the types (or paratypes) to confirm that the morphology of Gatesona chaetophora rutena and Gatesona chaetophora lablacherensis really correspond to the species you collected. Even more because there is some variation that could be an indication of different morphological species (e.g. the number of spermathecae). 4) In benefit of readers, please explain in the discussion why the genus was named as Gatesona and not Acystodrilus. Reviewer #2: There are a few small corrections of grammar and content in the MS that I uploaded with this review. The revision of the taxonomy has to be modified to make it clear that G. chaetophora is the type species, and in particular, that G. chaetophora chaetophora is the type species. The subspecies G. c. argentatus could be tentatively excluded. The remaining species are "other species" under a heading. ****** 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. Attachments Attachment Submitted filename: PONE-D-21-07434_reviewer 1.pdf Attachment Submitted filename: PONE-D-21-07434_reviewerSJ.pdf https://doi.org/10.1371/journal.pone.0255978.r001
Revision 1
20 Jun 2021 Author Response Reviewer #1: Authors present a very interesting paper about the identity of several Lumbricidae species and subspecies that are placed in a new genus. These new arrangements are due to the use of an integrative approach (molecular genetics, phylogenetic analysis and morphological revisions). English is ok, as well as molecular and phylogenetic methods and results. We want to thank the reviewer for his/her interest on our manuscript and his/her constructive suggestions in order to improve it. All of them have been considered and included. There are, however, some modifications that should be done (mainly in regard to classical nomenclatural arrangements) before the paper could be accepted. The paper, thus, is ACCEPTED WITH MINOR CHANGES. I directly wrote several comments and suggestions over the main text; following are some of my main points: 1) In the title it is mentioned the word Crassiclitellata; in the classification of the new genus Gatesona, however, this word is not included. Thus, include in the supraorder classification this word with its hierarchical associated level. We have included Crassiclitellata in the taxonomy section. 2) There are several mistakes in regard of the “types” of the two re-described species. Please attend comments of the text. We have corrected the taxonomic errors regarding the types. 3) As authors do not reviewed types of these species, maybe the name (from an already described species) in fact does not correspond to the collected and molecular sequenced material. I strongly suggest contact Dr. Bouché in order to obtain in loan the types (or paratypes) to confirm that the morphology of Gatesona chaetophora rutena and Gatesona chaetophora lablacherensis really correspond to the species you collected. Even more because there is some variation that could be an indication of different morphological species (e.g. the number of spermathecae). We have contacted Marcel Bouché and revised the holotypes for lablacherensis, rutena but also serninensis and chaetophora. Thanks to that, we can state with certainty that the (morpho-molecularly) studied material is morphologically compatible with the types of the original taxa. The morphological differences initially detected could be actually due to faulty/incomplete descriptions (in the end, it was done through tables and not through an orthodox text); when comparing with the types, the differences were non-existant or comprised within intra-individual variation (Gatesona rutena holotype possessed three spermathecae on one side but only two on the other). 4) In benefit of readers, please explain in the discussion why the genus was named as Gatesona and not Acystodrilus. We have included a sentence explaining that point in the “Remarks” section of the Systematic changes to the genus Gatesona. Reviewer #2: There are a few small corrections of grammar and content in the MS that I uploaded with this review. The revision of the taxonomy has to be modified to make it clear that G. chaetophora is the type species, and in particular, that G. chaetophora chaetophora is the type species. The subspecies G. c. argentatus could be tentatively excluded. The remaining species are "other species" under a heading. We are thankful for the constructive revision and suggestions for improvement of our manuscript. As seen in the document with tracked changes, we have aknowledged and included all the suggested changes. Most importantly, we contacted Marcel Bouché and revised the holotypes for lablacherensis, rutena but also serninensis and chaetophora. This allowed to check for morphological differences, actually ruling out most of them (holotypes were more consistent with our material tan suggested in the incomplete, informal descriptions provided in Bouché 1972). In addition, we sampled additional material of Gatesona serninensis, which allowed us to provide a formal redescription. We have decided to mantain argentatensis within Gatesona chaetophora as it clearly belongs to the genus but we lack enough information to robustly elevate it to its own species. Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0255978.r002
26 Jul 2021 Decision Letter - Michael Schubert, Editor PONE-D-21-07434R1 Systematic revision of Gatesona (Crassiclitellata, Lumbricidae), an endemic earthworm genus from the Massif Central (France) PLOS ONE Dear Dr. Marchán, 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 Sep 09 2021 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: http://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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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 paper is now ready for its publication. I'm, however, sending in the 2nd round reviewed paper very few suggestions and changes (mainly of style) to improve the paper. These suggestions include change of a word, italics, improve of figure 3 legend, a doubt about the identity of a personal communication and (and this is up to the author to include or not) the addition of a nomenclatural comment. ****** 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 [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-21-07434_R1_reviewer 1 2nd round.pdf https://doi.org/10.1371/journal.pone.0255978.r003
Revision 2
26 Jul 2021 Author Response We have accepted all the proposed changes Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0255978.r004
28 Jul 2021 Decision Letter - Michael Schubert, Editor Systematic revision of Gatesona (Crassiclitellata, Lumbricidae), an endemic earthworm genus from the Massif Central (France) PONE-D-21-07434R2 Dear Dr. Marchán, 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 https://doi.org/10.1371/journal.pone.0255978.r005
Formally Accepted
25 Aug 2021 Acceptance Letter - Michael Schubert, Editor PONE-D-21-07434R2 Systematic revision of Gatesona (Crassiclitellata, Lumbricidae), an endemic earthworm genus from the Massif Central (France) Dear Dr. Marchán: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Michael Schubert Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0255978.r006

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