Peer Review History
| Original SubmissionOctober 29, 2025 |
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-->PONE-D-25-58468-->-->Dynamics analysis of disturbance propagation in ecosystem with proportional migration based on epidemic model-->-->PLOS ONE Dear Dr. Qian, 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 Jan 15 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 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:-->
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Please update your submission to use the PLOS LaTeX template. The template and more information on our requirements for LaTeX submissions can be found at http://journals.plos.org/plosone/s/latex. 6. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. [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 Reviewer #3: Yes ********** -->2. Has the statistical analysis been performed appropriately and rigorously? --> Reviewer #1: No Reviewer #2: N/A Reviewer #3: 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: No Reviewer #3: 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 Reviewer #3: 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 manuscript presents a novel and mathematically rigorous approach to modeling disturbance propagation in ecosystems using epidemic models. The theoretical results are well-supported, and the application to a real food web adds practical relevance. However, further clarification on ecological realism, parameter choices, and practical implementation of immunization strategies would strengthen the paper. Please see the attached file. Reviewer #2: Please see the attached PDF report for details. Review Report Manuscript ID: PONE-D-25-58468 This paper develops a novel mathematical framework to model the propagation of ecological disturbances by adapting a SIRS epidemic model to complex networks. The authors abstract species as nodes and predator-prey relationships as edges in a food web, where disturbances can spread from initially affected species to their neighbors. They derive a key epidemiological threshold, the basic reproduction number (R₀), proving that the disturbance will die out if R₀ < 1 and become endemic if R₀ > 1, with rigorous global stability analysis for both equilibria. Using real data from a New Zealand pine forest food web, they validate the model numerically and further analyze species conservation strategies, concluding that proactively protecting the highly connected neighbors of disturbed species is the most effective intervention to suppress disturbance spread. The following observations must be cleared up before it is considered for publication. 1. The introduction should make a compelling case for why the study is useful along with a clear statement of its novelty or originality by providing relevant information and providing answers to basic questions such as: (a). What is already known in the literature? (b). What was done and how was it done? 2. The model assumes disturbance propagates with a probability \(\rho\) along food web edges. Given that ecological interactions vary in strength and type (e.g., strong/weak predation, competition), how does the assumption of a uniform propagation probability \(\beta\) impact the model's biological realism? Could the model be extended to include weighted edges based on interaction strength. 3. The expression for \(\rho\) (Eq. 2.2.12) is crucial. Clarify the step-by-step derivation from the next-generation matrix method or the local stability analysis of the disease-free equilibrium. The current derivation in Lemma 3 seems to appear from a self-consistency condition; a more standard epidemiological derivation would strengthen the manuscript. 4. The proofs for the global stability of both the disease-free (Theorem 2) and endemic (Theorem 5) equilibria are highly technical and rely on constructing complex Lyapunov functions and sequences. For the sake of reproducibility and clarity, provide more detailed intermediate steps or intuition behind the construction of these functions, particularly in Theorem 5. 5. The degree distribution for the Otago food web is fitted to a power-law \(P(k) = 0.26/k\) (Page 28). What statistical tests were performed to justify this specific functional form over alternatives (e.g., exponential, log-normal)? Furthermore, how were the key parameters \((\beta, \sigma, \delta, \mu, \gamma, b)\) assigned specific numerical values for the simulations, and were these values informed by empirical data or chosen arbitrarily for illustration. 6. In Figures 5-9, the results are presented for a node of degree \(k=5\). How were the initial conditions \(S_k(0), I_k(0), R_k(0)\) set for these simulations, especially for the endemic case (\(\rho > 1\))? Specify if the results are for a single node, an average over all nodes of degree \(k=5\), or a density across the network. 7. Figures 7-9 show the system's state evolving over time for different parameters. To assess the robustness of the conclusions, have the authors performed a sensitivity analysis on the initial conditions or the network structure itself? For instance, how do the stability results change if the network is randomized while preserving the degree distribution. 8. In Section 3, three immunization strategies are compared based on their resulting \(R_0\) (\(\rho_3 < \rho_2 < \rho_1\)). The claim that active immunization is "most effective" relies on this inequality. However, the comparison assumes the same "cost" (i.e., the same number of protected species, \(\bar{\varphi}\)). Provide a more explicit comparison, perhaps with a simulation, showing the final outbreak size \(I(t)\) for each strategy when the same total number of species is protected. 9. The model employs the "empty-lattice" theory to handle network dynamics (species migration/extinction). How does this assumption of immediate replacement by an identical, susceptible node affect the long-term dynamics, especially regarding the conservation of keystone species whose loss might fundamentally alter the network topology, not just a node's state? 10. Figure 2 is described as a topology map but is not visually present in the provided text. If included, does it provide any topological analysis (e.g., highlighting hubs, clustering coefficient, community structure)? A simple visualization of 85 nodes is often a "hairball." How was this figure rendered to provide insight into the network's structure that informs the dynamical results? 11. The simulations in Figures 5 and 6 are used to validate the theoretical threshold \(\rho_c = 1\). Do the authors observe a sharp transition in the final density of disturbed species \(I(\infty)\) as \(\beta\) crosses the critical value \(\beta_c\) predicted by Eq. (2.2.13)? A figure plotting \(I(\infty)\) against \(\beta\) (or \(\rho\)) would provide stronger numerical evidence for the existence of this epidemic threshold. 12. Authors may look for some punctuation, typos and editing issues. Reviewer #3: The manuscript ingeniously analogizes the propagation dynamics of ecological disturbances in food webs to the spread of infectious diseases on complex networks. It constructs a disturbance propagation model for ecological networks, analyzes and verifies the propagation process. The research idea is novel, the logic is clear, and the conclusions have practical reference value. The manuscript is well-written, with model derivation and empirical analysis supporting the core viewpoints, meeting the basic requirements for publication. It is recommended to be accepted after minor revisions. Major Comments: 1.In the abstract, the definition of " medium-sized and large-sized " in the phrase " the medium-sized and large-sized neighbor nodes" is somewhat ambiguous. Does this refer to the degree (number of connections) of the nodes, their centrality, betweenness centrality, or other measures related to biomass/size?. 2.The introduction provides a good overview of the application of complex network theory in ecosystems and the research foundation of infectious disease models. However, it should be supplemented with a clearer statement of the core differences and innovative aspects of this study compared to existing literature. It is recommended to explicitly highlight the unique contributions of this work in terms of model assumptions (e.g., definition of species states, disturbance propagation mechanisms), research objectives (e.g., optimization of protection strategies), or empirical context (validation using real food web data), to avoid ambiguity regarding its distinction from prior research. 3.It is advisable to briefly elaborate on why the food chain can be considered the core pathway for disturbance propagation (e.g., based on the logic of energy flow and resource dependence among species), as well as the rationale behind the "immunity" analogy (e.g., how protective measures equivalently reduce the probability of species being disturbed or enhance their recovery capacity). This would strengthen the theoretical foundation of the model construction. 4.While the manuscript outlines the research framework (model construction, strategy comparison, empirical validation), the introduction lacks sufficient context for the definition of key parameters. It is suggested to briefly mention the central role of core parameters (such as disturbance propagation probability, species recovery probability, and the basic reproduction number) either at the end of the introduction or in a preliminary section of the research methods, to ensure smoother logical transition to the model derivation in subsequent sections. 5.Standardize the literature citation format throughout the manuscript to ensure academic rigor and consistency in presentation.. ********** -->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 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.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.
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| Revision 1 |
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Dynamics analysis of disturbance propagation in ecosystem with proportional migration based on epidemic model PONE-D-25-58468R1 Dear Dr. Qian, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support. 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, Md. Kamrujjaman, Ph.D Academic Editor PLOS One Additional Editor Comments (optional): 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 Reviewer #2: (No Response) ********** -->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 Reviewer #2: (No Response) ********** -->3. Has the statistical analysis been performed appropriately and rigorously? --> Reviewer #1: N/A Reviewer #2: (No Response) ********** -->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 Reviewer #2: (No Response) ********** -->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: (No Response) Reviewer #2: (No Response) ********** -->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: (No Response) Reviewer #2: (No Response) ********** -->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 Reviewer #2: No ********** |
| Formally Accepted |
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PONE-D-25-58468R1 PLOS One Dear Dr. Qian, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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. 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. If we can help with anything else, please email us at customercare@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. Md. Kamrujjaman Academic Editor PLOS One |
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