https://orcid.org/0000-0002-3687-4020
Peer Review History
| Original SubmissionNovember 4, 2024 |
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PPATHOGENS-D-24-02401 Abundant genetic variation is retained in many laboratory schistosome populations PLOS Pathogens Dear Dr. Anderson, Thank you for submitting your manuscript to PLOS Pathogens. After careful consideration, we feel that it has merit but does not fully meet PLOS Pathogens'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 within 30 days Feb 11 2025 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 plospathogens@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/ppathogens/ 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 editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. This file does not need to include responses to any formatting updates and technical items listed in the 'Journal Requirements' section below. * 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, competing interests statement, or data availability statement, please make these updates within the submission form at the time of resubmission. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. We look forward to receiving your revised manuscript. Kind regards, Erik C. Andersen, Ph.D. Guest Editor PLOS Pathogens James Collins III Section Editor PLOS Pathogens Sumita Bhaduri-McIntosh Editor-in-Chief PLOS Pathogens orcid.org/0000-0003-2946-9497 Michael Malim Editor-in-Chief PLOS Pathogens orcid.org/0000-0002-7699-2064 Journal Requirements: 1) Please ensure that the CRediT author contributions listed for every co-author are completed accurately and in full. At this stage, the following Authors/Authors require contributions: Kathrin S. Jutzeler, Roy N Platt, Robbie Diaz, Madison Morales, Winka Le Clec'h, Frédéric Chevalier, and Timothy JC Anderson. Please ensure that the full contributions of each author are acknowledged in the "Add/Edit/Remove Authors" section of our submission form. The list of CRediT author contributions may be found here: https://journals.plos.org/plospathogens/s/authorship#loc-author-contributions 2) We ask that a manuscript source file is provided at Revision. Please upload your manuscript file as a .doc, .docx, .rtf or .tex. If you are providing a .tex file, please upload it under the item type u2018LaTeX Source Fileu2019 and leave your .pdf version as the item type u2018Manuscriptu2019. 3) We do not publish any copyright or trademark symbols that usually accompany proprietary names, eg ©, ®, or TM (e.g. next to drug or reagent names). Therefore please remove all instances of trademark/copyright symbols throughout the text, including: - ® on Line: 374. 4) We have noticed that you have uploaded Supporting Information files, but you have not included a list of legends. Please add a full list of legends for your Supporting Information files after the references list. 5) Some material included in your submission may be copyrighted. 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Potential Copyright Issues: - Figures 1 and 2; Please confirm whether you drew the images / clip-art within the figure panels by hand. If you did not draw the images, please provide a link to the source of the images or icons and their license / terms of use; or written permission from the copyright holder to publish the images or icons under our CC BY 4.0 license. Alternatively, you may replace the images with open source alternatives. See these open source resources you may use to replace images / clip-art: - https://commons.wikimedia.org 6) Please ensure that the funders and grant numbers match between the Financial Disclosure field and the Funding Information tab in your submission form. Note that the funders must be provided in the same order in both places as well. State what role the funders took in the study. If the funders had no role in your study, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.". If you did not receive any funding for this study, please simply state: u201cThe authors received no specific funding for this work.u201d Reviewers' Comments: Reviewer's Responses to Questions Part I - Summary Please use this section to discuss strengths/weaknesses of study, novelty/significance, general execution and scholarship. Reviewer #1: See attached Reviewer #2: See attachment Reviewer #3: The manuscript by Jutzeler and colleagues describes their discovery of high levels of genetic diversity in schistosome populations maintained in the laboratory. This is an important and relevant finding, with bearing on the use of laboratory helminth populations to study the genetic basis of traits such as drug resistance. The experimental design seems robust, the genomic analyses and simulations seem appropriate, and the data support the claims. The paper is clearly written and was enjoyable to read, although I felt in a couple of places there was an expectation that the reader was already familiar with the papers cited; please always state the key point briefly rather than simply providing a reference for the reader to look up. I have no major corrections but have several minor edits or comments/queries. ********** Part II – Major Issues: Key Experiments Required for Acceptance Please use this section to detail the key new experiments or modifications of existing experiments that should be absolutely required to validate study conclusions. Generally, there should be no more than 3 such required experiments or major modifications for a "Major Revision" recommendation. If more than 3 experiments are necessary to validate the study conclusions, then you are encouraged to recommend "Reject". Reviewer #1: See attached Reviewer #2: (No Response) Reviewer #3: None ********** Part III – Minor Issues: Editorial and Data Presentation Modifications Please use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. Reviewer #1: See attached Reviewer #2: (No Response) Reviewer #3: 72. Please state the country the SmNMRI population was isolated from. Fig 1. Panel on RHS would be improved by showing males and females within each pair in different colours. Fig 3. Did you also generate a PCA with the exonic data only to allow inclusion of field samples? 144. The 51% reduction presumably reflects the very high diversity of the Tanzanian field population (and the low diversity of SmBRE), but as far as is stated in the paper, none of the lab isolates originated from Tanzania. What is the reduction if you do the most relevant pairwise comparisons e.g. each Brazilian lab isolate with the Brazilian field sample? 148. Did you look at which genes were encoded in regions of high nucleotide diversity across the different isolates? In Discussion, suggest that balancing selection due to host immune response could maintain genetic variation as per Stevens et al 2023, so might expect to see enrichment for gene families that interact with the host immune response in these loci? 169. I don’t think ‘nearly significantly’ is appropriate description. 193. ‘The reasons for this are explained elsewhere [19].’ Please state the reasons briefly. 199. Are overlapping generations relevant for laboratory maintenance of schistosome populations? 256. Worth also commenting on the distinct allele frequency spectra here (Fig S1). Table 4. Could be interesting to include data from lab and field isolates of other well studied outbreeding helminth populations (e.g. C. remanei and H. contortus) if available for comparison. 349. Please add ‘or PacBio’ 373. Individual males and female heads were sequenced for SmBRE only, but previously stated (line 363) the avoidance of sampling adults in case derived from clonal cercariae from a single snail – is there a risk this did happen for SmBRE and relates to the very low genetic variation measured in this isolate? Good to highlight any technical differences in the discussion. 375 and 384. Do you expect any bias from the WGA step that could affect the results? 414. Unclear why lifted merged vcf to different genome assembly? ********** 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: Stephen R. Doyle 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.] Figure resubmission: 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. If there are other versions of figure files still present in your submission file inventory at resubmission, please replace them with the PACE-processed versions. Reproducibility: To enhance the reproducibility of your results, we recommend that authors of applicable studies deposit laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols
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| Revision 1 |
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Dear Dr. Anderson, We are pleased to inform you that your manuscript 'Abundant genetic variation is retained in many laboratory schistosome populations' has been provisionally accepted for publication in PLOS Pathogens. Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests. Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated. IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript. Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS. Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Erik C. Andersen, Ph.D. Guest Editor PLOS Pathogens James Collins III Section Editor PLOS Pathogens Sumita Bhaduri-McIntosh Editor-in-Chief PLOS Pathogens orcid.org/0000-0003-2946-9497 Michael Malim Editor-in-Chief PLOS Pathogens orcid.org/0000-0002-7699-2064 *********************************************************** Reviewer Comments (if any, and for reference): Reviewer's Responses to Questions Part I - Summary Please use this section to discuss strengths/weaknesses of study, novelty/significance, general execution and scholarship. Reviewer #2: Thanks to the authors for their efforts and responses. All looks good to me. I look forward to seeing it in print. Many kind regards, Stephen Doyle Reviewer #3: I am satisfied that the authors have addressed all my concerns in their revised submission. ********** Part II – Major Issues: Key Experiments Required for Acceptance Please use this section to detail the key new experiments or modifications of existing experiments that should be absolutely required to validate study conclusions. Generally, there should be no more than 3 such required experiments or major modifications for a "Major Revision" recommendation. If more than 3 experiments are necessary to validate the study conclusions, then you are encouraged to recommend "Reject". Reviewer #2: (No Response) Reviewer #3: (No Response) ********** Part III – Minor Issues: Editorial and Data Presentation Modifications Please use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. Reviewer #2: (No Response) Reviewer #3: (No Response) ********** 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: Stephen R. Doyle Reviewer #3: No |
| Formally Accepted |
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Dear Dr. Anderson, We are delighted to inform you that your manuscript, "Abundant genetic variation is retained in many laboratory schistosome populations," has been formally accepted for publication in PLOS Pathogens. We have now passed your article onto the PLOS Production Department who will complete the rest of the pre-publication process. All authors will receive a confirmation email upon publication. The corresponding author will soon be receiving a typeset proof for review, to ensure errors have not been introduced during production. Please review the PDF proof of your manuscript carefully, as this is the last chance to correct any scientific or type-setting errors. Please note that major changes, or those which affect the scientific understanding of the work, will likely cause delays to the publication date of your manuscript. Note: Proofs for Front Matter articles (Pearls, Reviews, Opinions, etc...) are generated on a different schedule and may not be made available as quickly. Soon after your final files are uploaded, the early version of your manuscript, if you opted to have an early version of your article, will be published online. The date of the early version will be your article's publication date. The final article will be published to the same URL, and all versions of the paper will be accessible to readers. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. Thank you again for supporting open-access publishing; we are looking forward to publishing your work in PLOS Pathogens. Best regards, Sumita Bhaduri-McIntosh Editor-in-Chief PLOS Pathogens orcid.org/0000-0003-2946-9497 Michael Malim Editor-in-Chief PLOS Pathogens orcid.org/0000-0002-7699-2064 |
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