Living with the pathogenic chytrid fungus: Exploring mechanisms of coexistence in the harlequin toad Atelopus cruciger

Onil Ballestas; Margarita Lampo; Diego Rodríguez

doi:10.1371/journal.pone.0254439

Peer Review History

Original SubmissionFebruary 13, 2021
13 Apr 2021 Decision Letter - Stefan Lötters, Editor PONE-D-21-04928 Living with the pathogenic chytrid fungus: exploring mechanisms of coexistence in the harlequin toad Atelopus cruciger. PLOS ONE Dear Dr. Lampo, 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. There was one referee who was positive about the paper, as I am. It makes a valuable contribution. Ciritiques by the referee include that other studies in the field are not thoroughly considered (introduction, discussion). Including them will certainly improve the value of this contribution. Suggestions for references to be considered are made by the referee. Please submit your revised manuscript by May 28 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'. 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Kind regards, Stefan Lötters 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 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 (if provided): [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know ****** 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 ****** 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 ****** 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: This is an interesting and important paper that uses modeling to explore Bd dynamics in the Atelopus cruciger system. The authors make important contributions to the field. They find evidence that the population of free Bd zoospores in environmental reservoirs are more likely to push populations from endemic coexistence to extinction than changes in the vulnerability of adults to chytridiomycosis. Their models are informed by a wealth of field-collected demographic and ecological data in this system. I found their study to be well written and presented. My only major critique is that I believe a substantial number of important and relevant studies in this system are not discussed or cited in this paper. Their omission is notable given the immediate relevance of these papers and their prominence in this field. I think the authors should more thoroughly consider how their findings are situated in relation to previous modeling efforts of Bd, especially when it comes to modeling zoospore pools, lethal infection intensities, and comparing how changes in these affect extinction dynamics. Below I point out some minor errors in the paper and list some important citations I believe were erroneously omitted. Line 3 – This figure “500 amphibian species, including 90 presumed extinctions [1].” is not actually supported by sound evidence. See Lambert et al. 2020 response to the citation listed (DOI: 10.1126/science.aay1838). I recommend modifying this citation to omit these specific, inflated numbers or also cite the response as “[1], but see [Lambert et al. 2020]”. Line 17 – The citation for A. palmatus should be [13] not [12]. Line 25 – Should be consistent in either using the abbreviated Bd or the longer B. dendrobatidis throughout the paper. Figure 3 – It would be helpful to include in the figure legend what the colors correspond to. Line 183 – The opening statement of the discussion should have citations for the facts it is listing. Line 195 – Typo “estimated in” should be “estimated to be” Line 218 – The sentence “Harlequin toads tend to be short-lived.” needs some qualifiers. For example, harlequin toads in captivity can live up to 10 years. The citations used imply that the authors mean to say that “Harlequin toads coexisting with Bd in the wild tend to be short-lived.” Line 222 – The sentence “In the presence of a highly pathogenic Bd, only uninfected toads are likely to reproduce.” Is there data to support this assertion? If so, you should cite here and perhaps explain in a bit more detail. Line 224 – There is a typo here. “when adults” should be “when individuals are adults.” Line 238 – The citation here is a review and should be cited as such (i.e., [reviewed in 36]). Some seminal papers exploring Bd dynamics are not discussed or cited here are would add important context to this study. For example Wilbur et al. 2017 (https://doi.org/10.1111/ele.12814) used a modelling approach to find that including an environmental zoospore pool increased R0 for R. muscosa‐Bd systems. They also found that Bd‐induced extinction risk was more sensitive to host resistance and tolerance than to the transmission dynamics of Bd. The similarities/differences between this study and that should be explored in the discussion. Additionally, the paper Vredenburg et al. 2010 (https://doi.org/10.1073/pnas.0914111107) is an important citation for estimating the lethal dose of Bd on an amphibian and should at least be mentioned or cited within given the estimation of lethal dose in this paper. Further, the findings of Briggs et al. 2010 (https://doi.org/10.1073/pnas.0912886107 ) should be discussed in this paper. I think these papers should be included in the introduction and further explored in the discussion. ****** 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 [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. 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Revision 1
6 May 2021 Author Response Response to Reviewers: Line 3 – This figure “500 amphibian species, including 90 presumed extinctions [1].” is not actually supported by sound evidence. See Lambert et al. 2020 response to the citation listed (DOI: 10.1126/science.aay1838). I recommend modifying this citation to omit these specific, inflated numbers or also cite the response as “[1], but see [Lambert et al. 2020]”. We omitted figures and changed the first sentence to the more general statement: “Chytridiomycosis………has been linked to the local extirpation and extinction of amphibian populations worldwide, although the exact number of species affected remains controversial (Scheele et al 2019; Lambert et al.2020)”. We directed the reader to the suggested references to enquire further about the estimated number of species affected. Line 17 – The citation for A. palmatus should be [13] not [12]. Done Line 25 – Should be consistent in either using the abbreviated Bd or the longer B. dendrobatidis throughout the paper. We used Bd throughout the paper. Figure 3 – It would be helpful to include in the figure legend what the colors correspond to. I am not sure what the reviewer means. The figure legend reads: “Blue pixels represent combinations of parameters for which coexistence is the most likely outcome, green denotes pairs for which Bd is most likely to fail in establishing and red denotes pairs for which Bd is more likely to extirpate the toad population. Please let me know if you think we need to add more information. Line 183 – The opening statement of the discussion should have citations for the facts it is listing. We added seven references to the opening statement: “The high impact of chytridiomycosis at high elevations (Catenazzi et al. 2014; Kriger & Hero 2008; Scheele et al. 2019; Woodhams & Alford 2005) and the recent discovery of recovering populations in lowlands (Grogan et al. 2016; Phillott et al. 2013; Rodríguez-Contreras et al. 2008) suggest that warm temperatures may promote the coexistence of some amphibian species with the pathogenic fungus Bd (Puschendorf et al. 2011; Zumbado-Ulate et al. 2014). Line 195 – Typo “estimated in” should be “estimated to be”. Done Line 218 – The sentence “Harlequin toads tend to be short-lived.” needs some qualifiers. For example, harlequin toads in captivity can live up to 10 years. The citations used imply that the authors mean to say that “Harlequin toads coexisting with Bd in the wild tend to be short-lived.” We modified this sentence as follows: “Harlequin toads tend to be short-lived in the wild” Although in captivity harlequin toads can live in up to 10 years, mark-recapture studies suggest that in the wild uninfected adults of A. cruciger and A. zeteki have average life expectancy of less than one year. Thus, even in the absence of Bd, harlequin toads tend to be short-lived. In general amphibians in captivity can last many years more than in the wild. I think that there are records of R. marina of about 40 years, but I doubt that they can live that long in the wild. Line 222 – The sentence “In the presence of a highly pathogenic Bd, only uninfected toads are likely to reproduce.” Is there data to support this assertion? If so, you should cite here and perhaps explain in a bit more detail. There is no data demonstrating that infected toads cannot reproduce. However, given that they die within weeks after infection and amplexus in these toads can last months it seems unlikely that they can get infected and reproduce. I elaborated on this idea in the new version. Line 224 – There is a typo here. “when adults” should be “when individuals are adults.” Done. Line 238 – The citation here is a review and should be cited as such (i.e., [reviewed in 36]). Done Some seminal papers exploring Bd dynamics are not discussed or cited here and would add important context to this study. For example Wilbur et al. 2017 (https://doi.org/10.1111/ele.12814) used a modelling approach to find that including an environmental zoospore pool increased R0 for R. muscosa‐Bd systems. They also found that Bd‐induced extinction risk was more sensitive to host resistance and tolerance than to the transmission dynamics of Bd. The similarities/differences between this study and that should be explored in the discussion. Thanks for pointing out Wilbert et al.’s paper; it was enlightening. We mentioned their findings on the importance of resistance and tolerance on risk extinction in the Introduction section (lines X) Also, we included a whole paragraph explaining differences between these two models as I believe the comparison is highlight the need for context-specific modeling. Additionally, the paper Vredenburg et al. 2010 (https://doi.org/10.1073/pnas.0914111107) is an important citation for estimating the lethal dose of Bd on an amphibian and should at least be mentioned or cited within given the estimation of lethal dose in this paper. Vredenburg et al., 2010 was added to the list of sources of lethal doses used on Table 1 in the Appendix. Further, the findings of Briggs et al. 2010 (https://doi.org/10.1073/pnas.0912886107 ) should be discussed in this paper. I think these papers should be included in the introduction and further explored in the discussion. Briggs et al.’s paper was added to the list of papers supporting the importance of biotic or abiotic reservoirs in the extinction risk of host populations in the introduction and discussion sections. Attachments Attachment Submitted filename: ResponseToReviewers.pdf https://doi.org/10.1371/journal.pone.0254439.r002
23 Jun 2021 Decision Letter - Stefan Lötters, Editor PONE-D-21-04928R1 Living with the pathogenic chytrid fungus: exploring mechanisms of coexistence in the harlequin toad Atelopus cruciger. PLOS ONE Dear Dr. Lampo, 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 authors have done a proper job in revising their paper. It satisfied the referee and myself. So, the paper can be accepted, but there are a few minor thigs that need some attention why this is a technical "minor revision". Please submit your revised manuscript by Aug 07 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, Stefan Lötters 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: I am satisfied with the changes made by the authors and feel that all comments have been adequately addressed. I especially like the new discussion paragraph discussing how the model describing this system compares to that built to describe the mountain yellow-legged frog system. I did notice a few typos/grammatical errors (mostly in the new text additions) that I will note below. Nice work! In the abstract: - replace "a disease produced by" with "a disease caused by" - "most of the others are in high risk of extinction" should be "most of the others are at high risk of extinction" Line 267: "have proved to be" should be "has proved to be" Line 271 (and throughout this paragraph): The common name for Rana muscosa is "Mountain Yellow-legged Frog" not "yellow-legged frog" Line 276: The sentence that reads: "That is, not only recruiting health juveniles contribute to the susceptible population but also infected adults that have cleared infection." should be "That is, not only does the recruitment of healthy juveniles contribute to the susceptible population, but also the presence of infected adults that have cleared infection." ****** 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. https://doi.org/10.1371/journal.pone.0254439.r003
Revision 2
23 Jun 2021 Author Response In the abstract: - replace "a disease produced by" with "a disease caused by" Replaced as suggested. - "most of the others are in high risk of extinction" should be "most of the others are at high risk of extinction" Replaced as suggested. Line 267: "have proved to be" should be "has proved to be" Replaced as suggested. Line 271 (and throughout this paragraph): The common name for Rana muscosa is "Mountain Yellow-legged Frog" not "yellow-legged frog" Replaced as suggested. Line 276: The sentence that reads: "That is, not only recruiting health juveniles contribute to the susceptible population but also infected adults that have cleared infection." should be "That is, not only does the recruitment of healthy juveniles contribute to the susceptible population, but also the presence of infected adults that have cleared infection." Replaced as suggested. Attachments Attachment Submitted filename: ResponseToReviewers2.docx https://doi.org/10.1371/journal.pone.0254439.r004
28 Jun 2021 Decision Letter - Stefan Lötters, Editor Living with the pathogenic chytrid fungus: exploring mechanisms of coexistence in the harlequin toad Atelopus cruciger. PONE-D-21-04928R2 Dear Dr. Lampo, 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, listo el pollo! Stefan Lötters Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0254439.r005
Formally Accepted
5 Jul 2021 Acceptance Letter - Stefan Lötters, Editor PONE-D-21-04928R2 Living with the pathogenic chytrid fungus: exploring mechanisms of coexistence in the harlequin toad Atelopus cruciger. Dear Dr. Lampo: 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 Prof. Dr. Stefan Lötters Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0254439.r006

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