Are 150 km of open sea enough? Gene flow and population differentiation in a bat-pollinated columnar cactus

Sebastián Arenas; Alberto Búrquez; Enriquena Bustamante; Enrique Scheinvar; Luis E. Eguiarte

doi:10.1371/journal.pone.0282932

Peer Review History

Original SubmissionFebruary 25, 2023
23 Mar 2023 Decision Letter - Janice L. Bossart, Editor PONE-D-23-05594Are 150 km of open sea enough? Gene flow and population differentiation in a bat-pollinated columnar cactusPLOS ONE Dear Dr. Búrquez, 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. Both reviewers had a favorable response to your manuscript and noted only minor revisions were necessary. Some rewriting and reworking of the Intro and Discussion is needed to improve clarity, flow, and to add missing details, but shouldn't be too time consuming to accomplish. Please submit your revised manuscript by May 07 2023 11:59PM. 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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: 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: An excellent, well done and interesting study. I suggest streamlining the introduction and background and explanding the discussion. In the discussion, the significance of several results seems to not be covered in enough detail. The discussion would be improved by using subheadings that are in the same order as the presentation of results. Reviewer #2: The Gulf of California is an extremely interesting oceanic barrier that dramatically divides the Sonoran Desert in two: the mainland deserts and the Baja California Peninsula. Both subdivisions are biologically very distinct, possibly due the 6-5 million years of isolation imposed by the geologic rift, and by the complex interplay of spatial isolation and gene flow across the Gulf. This uses the distribution and genetic traits of the organ-pipe cactus (Stenocereus thurberi) to infer the evolution of the species during the late Pleistocene, the role of the species’ pollinators and seed dispersers in gene flow across the Gulf, and to understand the current status of the species’ overall genetic diversity and genetic differentiation into local populations. The driving hypothesis of the paper is extremely interest and scientifically relevant, the methods are robust and carefully developed, and the results add a very important piece of knowledge to our current understanding on the evolution of the unique biota of the Baja California Peninsula. Minor edits and corrections are attached in the edited comments to the pdf of the original manuscript. ****** 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: Yes: Exequiel Ezcurra ******** [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: Review comments.pdf Attachment Submitted filename: PONE-D-23-05594.pdf https://doi.org/10.1371/journal.pone.0282932.r001
Revision 1
3 May 2023 Author Response Response to reviewers We appreciate the comments and queries made by the reviewers. These significantly improved the manuscript. We attended to all suggestions. Two citations were removed and several paragraphs deemed unnecessary were deleted. As a consequence, the reference section was updated. We added text to clarify some sections as requested by the reviewers. In total, the reduction of unnecessary text and additions asked by reviewers left the manuscript almost the same size. All figures are original and do not need copyright permission for publication. Figure 6 is redrawn from public data and the authors are acknowledged. We confirm this work has not been published elsewhere, nor is it currently under consideration for publication, nor do we have conflicts of interest to disclose. Abstract: Corrected species name in italics. Introduction: Line 46, We described explicitly the query by the reviewer on founder effects Following the suggested abridging and focusing of the introduction led us to reduce the content by deleting the following paragraphs: Lines 49-52. The repetitive paragraph was deleted, including citation number 5. Lines 60-64. Unnecessary information. The paragraph and citation 13 were deleted. In line 64 we deleted "In" line 88 deleted citation 23 (Karig), deleted ", and reduced gene flow" line 115. added "]." Line 114: Myrtillocactus cochal authorities are correct as originally stated in the ms. The basionym was described by C.R. Orcutt in 1889 and later assigned to Myrtillocactus by Britton & Rose. https://tropicos.org/name/5100588 Lines 115-116. Deleted "Their presence is likely the result of vicariant events." Lines 119-123. Rearrangement of the sentence. Deleted as suggested "that has a highly specialized pollinator mutualism by moths [32]," Line 123. Made clear that Pachycereus pringlei does not have an extensive distribution on the mainland. Line 128. Added suggested comments on the narrow endemics at the tip of the peninsula (from line 114 onward). Material and Methods: Line 138. Added a brief description of the distribution range. Line 167. Answered to the reviewer's question "Did you find you also had to manually adjust the alignment?" is yes. Added at the beginning of paragraph "After removing some nucleotides in the initial and final portion of the sequences (~15 nucleotides), multiple..." Line 222, 223, 239. changed values to scientific notation Line 248 Query by reviewer "What spatial relationship did the occurrences have? Was it necessary to do any thinning or adjustment to match the climate scale?" Yes. We tried to attain a homogeneous cover of the distribution range and bioclimatic envelope. Results: Line 398. Query by reviewer "This seems like perhaps the model was overfit somewhat. Maybe because .70 is a pretty high cutoff for correlation? The use of 9 climate variables is a lot of predictors. A pretty complex model." Added a note of caution highlighting the value of the three top bioclimatic variables. Line 411. As suggested by the reviewer, the explanation of refuges was moved to the discussion. Line 428. Reduced and moved to discussion Discussion: Line 434. Added subheadings to the discussion: 1) The role of vicariance and long-distance dispersal, 2) Ecological niche modeling and evolution, 3) The role of bats in shaping the genetic structure, and 4) Genetic structure suggests gene flow across the Gulf of California Line 472. We rearranged the paragraph and included the niche modeling discussion suggested by reviewers in line 411. Line 515. The query by the reviewer is relevant. "I guess it doesn't seem necessary to state the direction of dispersal? It seems highly unlikely that thurberi would have originated on the peninsula. But I could be wrong." We added a sentence explaining the possible evolutionary forces acting upon these populations. Line 517. Made clear that Baja Californian populations are likely vicariant after the extensive separation of the peninsula. Line 547. Made clear the lack of data on bat flight and seed dispersal. Line 559. Agree. We might attempt it for the cardón sahueso (Pachycereus pringlei), widespread species of the islands. Line 569. As suggested by the reviewer, we added a short paragraph summarizing the main findings Attachments Attachment Submitted filename: response to reviewers.docx https://doi.org/10.1371/journal.pone.0282932.r002
15 May 2023 Decision Letter - Janice L. Bossart, Editor PONE-D-23-05594R1Are 150 km of open sea enough? Gene flow and population differentiation in a bat-pollinated columnar cactusPLOS ONE Dear Dr. Búrquez, 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. Both reviewers had very favorable responses to your manuscript and noted it was interesting and an important study. Congratulations! Reviewer 1 has identified multiple areas where text needs to be modified/rewritten to improve clarity and flow, and to ensure key results are discussed. Thoughtful rewriting will take a bit of time but shouldn't be too onerous. Please submit your revised manuscript by Jun 29 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, Dr. Janice L. Bossart 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: [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.0282932.r003
Revision 2
18 May 2023 Author Response We attended all of the queries and included all corrections made by reviewers. In particular, in the response letter we detail how we included in the manuscript Reviewer 1 research questions and how we improved, with the aid of a copy editor, these areas where reviewer 1 found our text needed to be modified or rewritten to improve it. Reviewer's comments were valuable in ensuring that our key results were discussed. Thanks to their effort, we ended with a more concise and clear article. Attachments Attachment Submitted filename: response to reviewers.docx https://doi.org/10.1371/journal.pone.0282932.r004
29 May 2023 Decision Letter - Janice L. Bossart, Editor Are 150 km of open sea enough? Gene flow and population differentiation in a bat-pollinated columnar cactus PONE-D-23-05594R2 Dear Dr. Búrquez, 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. Congratulations! It's a very interesting study. The modifications you've made to increase flow and clarity are much appreciated. Please note that PLOS ONE has specific requirements for Supporting Information, e.g. a list of captions at the end of the manuscript, and strongly recommends that each caption has a title (https://journals.plos.org/plosone/s/supporting-information). I know I personally prefer titles when I'm reading an article and accessing any supporting files. 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, Dr. Janice L. Bossart Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0282932.r005
Formally Accepted
19 Jun 2023 Acceptance Letter - Janice L. Bossart, Editor PONE-D-23-05594R2 Are 150 km of open sea enough? Gene flow and population differentiation in a bat-pollinated columnar cactus Dear Dr. Búrquez: 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. Janice L. Bossart Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0282932.r006

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