PCOMPBIOL-D-25-02324

How Competition can Drive Allochronic Divergence: A Case Study in the Marine Midge, Clunio marinus

PLOS Computational Biology

Dear Dr. Jacobsen,

Thank you for submitting your manuscript to PLOS Computational Biology. After careful consideration, we feel that it has merit but does not fully meet PLOS Computational Biology'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 Mar 31 2026 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 ploscompbiol@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pcompbiol/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

* A 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 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,

Tyler Cassidy

Academic Editor

PLOS Computational Biology

Natalia Komarova

Section Editor

PLOS Computational Biology

Additional Editor Comments:

In general, the reviewers appreciated this study and noted only a few areas of potential confusion. In particular, Reviewers 2 and 3 both made relatively minor comments on the clarity of the presentation. Reviewer 3 mentioned the structure of the first section of the results, which captures the biological background and a brief discussion of the model. Here, the authors may want to consider placing the methods before the results, as the model structure/parameterization is important for the results that follow. Similarly, the authors might consider including Tables S1 and S2 (the model parameters) in the Methods, as these parameter values are important aspects of the model. Finally, Reviewer 1 raises important questions on the model structure and justification for some modelling choices in points 2, 4, and 5. I think it is important to further explain these modelling choices before publication.

Journal Requirements:

1) 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.

2) Please upload all main figures as separate Figure files in .tif or .eps format. For more information about how to convert and format your figure files please see our guidelines:

https://journals.plos.org/ploscompbiol/s/figures

3) We notice that your supplementary Figures, and Tables are included in the manuscript file. Please remove them and upload them with the file type 'Supporting Information'. Please ensure that each Supporting Information file has a legend listed in the manuscript after the references list.

4) Some material included in your submission may be copyrighted. According to PLOSu2019s copyright policy, authors who use figures or other material (e.g., graphics, clipart, maps) from another author or copyright holder must demonstrate or obtain permission to publish this material under the Creative Commons Attribution 4.0 International (CC BY 4.0) License used by PLOS journals. Please closely review the details of PLOSu2019s copyright requirements here: PLOS Licenses and Copyright. If you need to request permissions from a copyright holder, you may use PLOS's Copyright Content Permission form.

Please respond directly to this email and provide any known details concerning your material's license terms and permissions required for reuse, even if you have not yet obtained copyright permissions or are unsure of your material's copyright compatibility. Once you have responded and addressed all other outstanding technical requirements, you may resubmit your manuscript within Editorial Manager.

Potential Copyright Issues:

- Figure 1. 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) a link to the source of the images or icons and their license / terms of use; or (b) 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

- https://openclipart.org/.

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: the peer review is uploaded as an attachment titled Jacobsen_et_al_PLOS-compbio_mating_types_2025_PEERREVIEW.docx.

Reviewer #2: Based on the biology of a marine midge, the authors investigate via modelling the role of competition in allochronic divergence. While their conclusions suggest that divergence should be largely promoted under multiple ecological and genetic conditions, the rarity of chronotypes really found in natural population is honestly discussed.

Although being not expert in modelling, I had a great interest in reading this manuscript and recommended it for publication.

Just, as far I understand the ecology of the studied chronotypes, is “global” sympatry describing fully their spatial distribution, or could it refer to micro-parapatry?

Also, the results are really convincing to favor allochronic divergence. However, the term speciation is sometime used in the text (for instance line 359), without clear explanation about when the authors consider that divergence lead to speciation. In other term, do they consider speciation as an ineluctable final step of the modelled divergence?

Following, few minor comments…

L16 The use of the adverb “However” sounds strange, as the second sentence introduces a concept not simply and directly in opposition or restriction to the first sentence of the abstract.

The paragraphs are easy to follow in this order, but the first paragraph of the “Results” (l 136-167) corresponds to the description of the biological case, which could be in the Introduction. In the same way, the following paragraph (l 168-213) corresponds more to an overview of Material and Methods than to Results.

L 152 the sentence refers to Fig 1 top left (not bottom left).

Reviewer #3: Please note that this manuscript review was prepared in conjunction with a graduate student.

In their manuscript, “How Competition Can Drive Allochronic Divergence: A Case Study in the Marine Midge, Clunio marinus,” Jacobsen et al. describe their computational investigation of allochronic isolation using the marine midge as a model organism. When simulating reproductive ecology of the marine midge in space-limited scenarios, the authors repeatedly found allochronic divergence. This differentiation occurred with a variety of ecological and genetic parameters, suggesting that, with sufficient heritability, allochronic divergence readily occurs in the marine midge. Further, the authors argue that their findings may generalize to many organisms with time-based reproductive strategies.

The authors present a well-supported computational investigation of allochronic isolation in a marine organism, as they carefully describe model assumptions and test many simulations with variable ecological and genetic parameters. As the manuscript uses computational methods to investigate an understudied ecological divergence mechanism, allochronic isolation, and presents a novel, generalizable finding, the study is a strong fit for PLOS Computational Biology. Therefore, we recommend to accept with minor revisions.

Though a strong investigation of allochronic isolation, we note minor opportunities to improve clarity of analyses. First, the authors provide strong justifications for most of their assumptions, but they do not explain the biological relevance of their emergence time assumption (line 154), beyond model simplicity. To strengthen the article, we recommend providing additional context. Second, we recommend stating explicitly the type of simulations being used, in order to make the article more broadly informative to other researchers. Third, to strengthen the literature review of allochronic isolation, we suggest noting the role of allochrony in the ecological divergence of both Rhagoletis fruit flies and their parasitoid wasps. In particular, we note the recent publication by Yee et al. (2025), “Concordance of eclosion life history timing across trophic levels in communities of host plants, fruit flies, and parasitoid wasps in the Pacific Northwest, USA."

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.requires authors to make all data and code 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 and code 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 or code —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

**********

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 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 For information about this choice, including consent withdrawal, please see our Privacy Policy..

Reviewer #1: Yes: Xiaoyuan LiuXiaoyuan Liu

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.]

Figure resubmission:

-->While revising your submission, we strongly recommend that you use PLOS’s NAAS tool (https://ngplosjournals.pagemajik.ai/artanalysis) to test your figure files. NAAS can convert your figure files to the TIFF file type and meet basic requirements (such as print size, resolution), or provide you with a report on issues that do not meet our requirements and that NAAS cannot fix.-->-->

After uploading your figures to PLOS’s NAAS tool - https://ngplosjournals.pagemajik.ai/artanalysis, NAAS will process the files provided and display the results in the "Uploaded Files" section of the page as the processing is complete. If the uploaded figures meet our requirements (or NAAS is able to fix the files to meet our requirements), the figure will be marked as "fixed" above. If NAAS is unable to fix the files, a red "failed" label will appear above. When NAAS has confirmed that the figure files meet our requirements, please download the file via the download option, and include these NAAS processed figure files when submitting your revised manuscript.-->

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

Attachments

Attachment

Submitted filename: Jacobsen_et_al_PLOS-compbio_mating_types_2025_PEERREVIEW.docx

Dear Dr Jacobsen,

We are pleased to inform you that your manuscript 'How Competition can Drive Allochronic Divergence: A Case Study in the Marine Midge, Clunio marinus' has been provisionally accepted for publication in PLOS Computational Biology.

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 Computational Biology.

Best regards,

Tyler Cassidy

Academic Editor

PLOS Computational Biology

Natalia Komarova

Section Editor

PLOS Computational Biology

***********************************************************

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The revisions the authors have made in light of the reviewer comments has significantly improved the clarity of the manuscript.

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

**********

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 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 For information about this choice, including consent withdrawal, please see our Privacy Policy..

Reviewer #1: Yes: Xiaoyuan LiuXiaoyuan Liu