-->PONE-D-25-39513-->-->Integrated approach to model distribution and assess habitat suitability of killifish species in Oman’s local streams (wadis) under current and future climate conditions-->-->PLOS ONE

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Academic Editor

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Additional Editor Comments (if provided):

Dear Dr. Al Adhoobi,

After this first review round, the reviewers indicated positive features of your manuscript that may allow it to be accepted for publication in PLoS One. Still, there are major issues that need to be considered before your study is accepted for publication in this journal. Please consider the suggestions made by the reviewers and prepare a newe version fo the text, along with a rebuttal letter explaining which of the suggestions were included or excluded from the new version of the study.

Sincerely,

Daniel Silva

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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: Partly

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-->2. Has the statistical analysis been performed appropriately and rigorously? -->

Reviewer #1: Yes

Reviewer #2: Yes

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-->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: Yes

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-->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

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-->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: The manuscript addresses an important and timely topic by forecasting habitat suitability for two arid-land killifishes (Aphaniops kruppi and A. stoliczkanus) and linking these results to conservation planning for Omani wadis. The integration of SDMs, habitat suitability indices, community data, and protected-area overlays is promising and highlights the potential for valuable contributions to conservation science. To further strengthen the study, I suggest the following points of improvement:

Model calibration – Provide more detail on how the accessible area (M) was defined, how background points were selected, and whether any bias correction or model tuning procedures were applied.

Performance and thresholds – In addition to discrimination metrics (AUC, TSS), consider reporting calibration metrics (e.g., Boyce, CBI) and briefly discuss limitations related to prevalence mismatches. Clarify the rationale for using equal suitability classes and how thresholding decisions affect interpretation.

Predictor variables – Clarify how predictors were screened for collinearity (e.g., correlation thresholds, VIF), and provide more detail about the source and processing of the elevation data.

Sample size and spatial structure – Acknowledge the relatively small sample size for A. kruppi and specify whether spatial blocking or other methods were used to reduce spatial autocorrelation during model evaluation.

Future projections – Indicate which climate models (ensemble or single GCMs) were used for future scenarios, and include uncertainty and extrapolation maps to strengthen interpretation.

HSI and diversity analyses – Present measures of uncertainty (e.g., confidence intervals) for the HSI and diversity analyses to provide a clearer picture of variability.

Conservation guidance – Strengthen the conservation section by quantifying representation within protected areas and suggesting clear targets (e.g., percentage of suitable habitat to be protected).

Figures – Improve figure readability by adding scale bars, north arrows, clear units, and consistent palettes. Label SSPs and time periods directly on the figures, and consider including response curves with confidence intervals.

Overall, this is a valuable study with strong potential to inform conservation planning in arid ecosystems. Addressing these points will enhance the clarity, transparency, and applicability of the results.

Reviewer #2: The study addresses interesting and important questions about spatial distribution patterns of species at broader scales across integrated climate change scenarios and site-based habitat assessments, raising concerns for conservation planning. I would like to congratulate the authors on developing this research, which I consider highly relevant. However, I also have a few comments.

There are some points in the text that need refinement because I got lost with the number of figures presented and some long paragraphs (mainly in the discussion). There are also points where the discussion mixes with the results, making the text repetitive. The results are robust, and I believe the text would benefit from a complete and substantial revision; please see my additional comments below.

Fig 1. Systematic methodology framework: I did not find it cited in the text.

Fig 2; 5; 6 e 9: My suggestion is to include them as Supporting Information. The environmental variable and model performance plots are interesting but, in my opinion, highlight information that is not the main result.

Tables 2–3: Is it essential to have two separate tables? I would suggest just one table for both species. However, this is at the authors' discretion.

Line 202: It is necessary to state what the acronym UAE means. Intuitively, we can conclude it is "United Arab Emirates," but it's best to avoid confusion.

Lines 237: The GBIF search must be referenced. When performing a search, GBIF creates a citation; thus, I suggest you include it in the text.

Lines 282: This section does not clearly state the use of training data (used to calibrate the distribution models) and test data (used to evaluate predictive ability), nor the proportion of each relative to the total occurrences of the two species. I believe this is relevant information for fully understanding the modeling process and for the experiment's replicability.

Line 308: The authors state that they used the MaxSS from the training data. Evaluating the model on the training data is similar to taking a test with the answer key, as it measures the model's fit to the data it has already seen. Generally, this leads to an overestimation of performance. The model can become overly complex, capturing not only the ecological effect but also noise and specific errors from the training set, which can lead to overfitting, making the model validation biased. Therefore, it is imperative to review the model evaluation metrics, as performance should be assessed using a test dataset. In the case of small datasets (few occurrences), cross-validation is the most recommended technique. Always prioritize evaluation with test data (or via cross-validation) to make decisions about the quality and usefulness of your species distribution model. Evaluation on training data is useful for diagnosing problems like overfitting but should not be used as the final performance measure.

If possible, this procedure could also be adopted for the "Habitat Suitability Index (HSI) model for Aphaniops spp."

These were just a few considerations so that the study can soon be published and available to the community as a product that can serve as a warning (climate change) while offering ways to mitigate negative impacts on Oman's local aquatic communities and killifish species populations.

Congratulations on the manuscript.

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-->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: Yes: Luciano Montag

Reviewer #2: No

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Integrated approach to model distribution and assess habitat suitability of killifish species in Oman's local streams (wadis) under current and future climate conditions

PONE-D-25-39513R1

Dear Dr. Al Adhoobi,

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.

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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,

Daniel de Paiva Silva, 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 #2: All comments have been addressed

Reviewer #3: All comments have been addressed

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-->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 #2: Yes

Reviewer #3: Yes

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-->3. Has the statistical analysis been performed appropriately and rigorously? -->

Reviewer #2: Yes

Reviewer #3: Yes

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-->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 #2: Yes

Reviewer #3: Yes

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-->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 #2: Yes

Reviewer #3: Yes

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-->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 #2: I thank the authors for their dedicated attention and for the careful and comprehensive implementation of the suggestions presented in the previous round of review; the changes made have fully addressed the issues raised, substantially enhancing the clarity, methodological rigor, and overall impact of the manuscript.

Reviewer #3: I would like to congratulate the authors on their excellent revision of the manuscript, as the detailed analysis of the updated version and the response letter to the reviewers demonstrates that all previous concerns have been addressed with due scientific rigor. The study presents an integrated and innovative approach by combining species distribution modeling with the field habitat suitability index, resulting in a robust tool for conservation in arid ecosystems. The inclusion of additional validation metrics, such as the Continuous Boyce Index and uncertainty analysis, significantly strengthened the credibility of the climate projections for the year 2100, while the application of the Jackknife method was a technically appropriate response to address the limited sampling of the species Aphaniops kruppi. Furthermore, linking the results to the goals of Oman Vision 2040 and global biodiversity commitments elevates the manuscript from a theoretical study to a practical and timely high-impact contribution. The text now features a cohesive narrative, a balanced discussion of its limitations, and grammatically correct flow, with no outstanding ethical concerns. Given the methodological maturity achieved and the relevance of the findings for water resource management and biodiversity conservation, I recommend accepting this manuscript for publication.

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-->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 #2: No

Reviewer #3: Yes: Emilly Layne Martins do Nascimento

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