PONE-D-24-56728Combining acoustic survey and citizen science data yields enhanced species distribution models for tropical rainforest birdsPLOS ONE

Dear Dr. Rumelt,

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 reviewers have multiple questions about the methods and results that require clarification, and they also have multiple suggestions for improvements in the writing of the manuscript. Please ensure that in your response to reviewer comments, you clearly address each comment from each reviewer. 

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Reviewers' comments:

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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

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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: No

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: Authors state data will be made available after review otherwise my comments are included in the attached pdf. This is a very interesting study that I feel will be relevant for the ecoacoustic community.

Reviewer #2: Overall: This paper presents unique work on integrating structured and unstructured sources of avian occurrence data in the Neotropics. The authors find that supplementing acoustic data-based distribution models with citizen science eBird data increases their flexibility with only minor predictive penalties. These conclusions seem well supported by the data and analysis. The methods section is well-detailed (almost too much so), but the results and discussion sections don’t reflect the same level of thoroughness. Careful thought should be given to making the manuscript more targeted and concise; I believe the issue here, for me at least, is less of scientific quality (the work is quite rigorous, novel, and provides a first step in a hopeful direction for neotropical ornithology), and more of clear communication of ideas and acknowledgement of assumptions. Additionally, because this is one of the first times eBird data has been integrated with any type of data resulting from structure surveys in the neotropics, I would suggest the authors improve their discussion of the limitations of neotropical eBird data, which is influenced by different sources of bias than that from north temperate regions. I would be interested in seeing future iterations of this very interesting first draft.

Introduction: This section presents clear background information on the methodologies, identifies a deficiency of this type of work in the neotropics, and states the intentions of the study. The narrative flow is generally good and easy to follow, but I suggest several considerations below.

Lines 59-64: This paragraph seems out of place to me. It interrupts the flow from the identification of increasing data availability and innovation of new tools in the first paragraph to the introduction of ARUs as tool to be used in the tropics. It would make sense to include this type of study region information at the beginning of the last paragraph in the Introduction as a way to further justify your efforts.

Line 67: You say that ARUs are more effective than humans at detecting birds in dense understory conditions but later contradict this idea in the Discussion by acknowledging the benefits of human observers.

Lines 68-71: This is fine information to include (e.g. justification of ARU usage in the tropics), but throughout the remainder of the paper conservation/survey urgency in relation to this work is not mentioned again so I wonder how beneficial it is here.

Lines 76-81: These two sentences duplicate ideas. I’d suggest condensing them into one consistent idea.

Line 92: spell out MODIS

Line 100: “data pooling has been increased the…” change to “data pooling has increased…”

Lines 119-120: While curiosity is an important component of this research, I think rephrasing this thought to something more direct and objective-like would be better for this section.

Lines 123-125: To what extent and where is this done in the manuscript? Maybe I am missing it in the discussion.

Methods: Very detailed and highly repeatable although I feel that some structure is needed for readers to understand the justification and objectives of each successive step in your modeling process. At times, it is overly dense, and the overarching methodology is sometimes muddied with small side details. Some of the finer details may be best suited for the Supplemental Material section. It is also overdeveloped in comparison to other sections, especially the results and discussion. See line-by-line comments below:

Lines 184-186: I suggest the latter half of this sentence to be changed to “… for the three seasons are available in *citation 14* and in S1 File”

Lines 188-196: This paragraph might fit better at the end of the methods section.

Lines 200-204: Add brief description of study area in relation to a larger geographic area as referenced in the figure.

Lines 216-219: I feel this and the following methodological explanation could be more clearly justified in at least one preceding sentences; some readers may be confused by the need for modeling and model selection here.

Lines 239-242: This information should be stated earlier so readers are aware of this sooner.

Lines 243-250: Not major, but this entire paragraph seems like something that could easily be reduced to one sentence. Some information here does not seem critical.

Lines 249-250: “zero-filled” is not referenced again in the manuscript.

Lines 253-260: Why did you filter eBird data using these criteria? Are you basing this off previous work? You discuss this briefly in the Discussion, but more justification here is desired. eBird data from the tropics is notoriously biased by checklists submitted by birders from other regions who are less experienced with the local avifauna, or guides who inflate their lists in an effort to make their services more appealing. How much quality control was done on the eBird data? I think these ideas are worth addressing, if not in the Methods, then with more detail in the Discussion than is currently present. The following paper provides some structure on this process in a north temperate study: Hallman, T.A., Robinson, W.D. Supplemental structured surveys and pre-existing detection models improve fine-scale density and population estimation with opportunistic community science data. Sci Rep 14, 11070 (2024). https://doi.org/10.1038/s41598-024-61582-6

Lines 260-263: What are you defining as present on a checklist? What about checklists with “Xs”?

Lines 264-267: True, this is the case in north temperate eBirding communities where the majority of checklists are submitted by those very familiar with the local species, but can the same assumption be made for the neotropics?

Lines 273-277: This sentence could be condensed.

Line 275: Is “short” the right word choice here?

Line 278: terra firme is italicized here but not consistently elsewhere is the manuscript.

Lines 316-317: Provide a citation for this sentence.

Line 317: “proportional” seems like not the correct word here, maybe “synonymous”?

Lines 345-346: If you are including traveling checklists with < 1km distance, this buffer needs to be expanded to 1 km. When using data from eBird hotspots you should also consider the implications of extracting habitat predictor data at the coordinates of the checklist. This should be reflected here or in more detail in the discussion.

Lines 376-387: this paragraph is out of place in the Methods section. Either cut it or condense these ideas into a sentence or to two to preface the following ideas.

Line 377: maybe spell out percent here.

Line 379: change colon to semi-colon

Lines 399-402: This is not valid justification for your choice. Rather than acknowledging a lack of literature, explain why you selected 90 days and not shorter or longer.

Lines 414-416: I’m uncertain why you made this choice. Could you perhaps provide some clarification here?

Lines 425-431: This information belongs in either the results or Supplemental Material.

Lines 458-460: Do song rates change in the wet and dry seasons? This likely impacts detectability, no?

Results: Mostly well written and clear. It is comparatively sparse given the detail in the methods section. Are the results from all methods reported or at least referenced as Supplemental Material? There also seems to be a significant amount of interpretation which should be limited to the discussion.

Line 481: “respectively” is not needed.

Line 492: the idea in parentheses should be explored in the Discussion and excluded here.

Lines 510-520: This entire paragraph seems better suited for the Discussion.

Lines 510-513: State this idea more directly; “Importance values of predictors indicates that…”

Line 562: Maybe spell out percent here

Line 571: Quantify “good job” here. This is an example of where the results section verges on the side of too much interpretation.

Discussion: This section touches on key ideas mentioned throughout the paper, but I feel the writing and ideas could be improved and tightened. Like the Results, it feels under-developed in comparison to the Methods with assumptions made in that section unexplored and not fully acknowledged.

Lines 599-600: This sentence could be stronger and more concise; “tropical species as a whole” is clunky.

Lines 612-616: This point is not clearly communicated and I am confused by this sentence.

Lines 616-618: This sentence should include a citation.

Line 624: Is “Tropics” intended to indicate Neotropics? If so, please correct.

Lines 599-625: This entire paragraph could be tighter. I get lost in smaller details and lengthy sentences. The focus here should be on punchy, big take-aways.

Lines 632-638: This sentence is much too long.

Line 644: Change “This be evidence…” to “This is evidence…”

Lines 653-661: Again, this sentence is much too long.

Line 664: Spell out TNC, also add mention of USGS Breeding Bird Survey, and other regional highly structured surveys (such as in the cited paper above).

Lines 687-689: Are any of these species known to lek, if so identify them? What about variation in vocalization rates throughout wet-dry seasons? In other parts of the neotropics, the wet season dawn choruses are characteristically reduced in length and intensity.

Lines 692-695: This is interesting but not necessarily useful here.

Lines 696-711: This paragraph introduces too much new information. Yes, it puts this study in the broader conservation context, but this can be done more concisely while also restating the major findings.

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Reviewer #1: No

Reviewer #2: Yes:  Nolan Michael Clements

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PONE-D-24-56728R1Combining acoustic survey and citizen science data yields enhanced species distribution models for tropical rainforest birdsPLOS ONE

Dear Dr. Rumelt,

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 revised version that you submitted contained additional analyses in response to reviewer comments, which generated additional minor revision suggestions.  If these can be addressed, it may not be necessary to send the manuscript out for additional review.

Please submit your revised manuscript by Jul 21 2025 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,

Julia A. Jones

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.

Additional Editor Comments:

The revised manuscript had new analyses in response to reviewer comments, which generated some minor revision suggestions. If these can be addressed, it should not be necessary to send the R2 version out for another review.

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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: (No Response)

Reviewer #2: 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 #1: Partly

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: 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

Reviewer #2: 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 #1: (No Response)

Reviewer #2: 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 #1: The authors have spent considerable time and effort on their revisions and responses to questions and I find responses thoroughly addressed my original comments. I appreciate the author’s extension of the modeling to now incorporate multiple spatial summaries of the data as the importance of different buffer sizes can vary. The addition of the 1km analysis strengthens the generalizability of the study; however, it adds significant analysis and results which require minor attention.

I have minor comments related to the new analysis/changes:

- 297: GEDI lidar: GEDI should be spelled out

- 392-423, Table S3, Fig4: Even though RF is extremely robust against multicollinearity, interpretation of variable importance using Gini impurity scores can be highly impacted by multicollinearity, where correlated predictors that are important can “share” importance among the highly correlated predictors resulting in importance dilution (e.g., doi.org/10.1186/1471-2105-11-110). This may make interpretability of the novel 1km predictors less reliable. Table S3 correlations are frequently >0.8 which is highly correlated and may impact variable importance, especially considering some of those variables are frequently important in fig S6. I do not think remodeling necessary, particularly because the discussion focuses more on the findings from the occupancy modeling, but the results section does include the encounter model findings and it is important to acknowledge that variable importance with the addition of the 1km covariates introduces possibly confounding effects on variable importance interpretations. If the authors chose to update the variable importances, the permutation importance option in ranger is more robust to multicollinearity than impurity.

- Fig4: it would be helpful to keep the facet panel titles consistent in the figure and the caption (e.g., in C “Other” in figure but “non-forest habitat predictors” in caption). Also the case in 589-599 in the results which mirrors the caption.

- Table 3: it appears the caption is below the table

Reviewer #2: This is a much-improved draft, with tighter writing and nice adjustments to the modeling. I have no additional comments on the Abstract, Introduction, or Results sections, and only a few limited notes overall.

Line 84: Please spell out MODIS here, rather than only in the Methods section. This is my oversight — I made a similar comment regarding the reference in the Methods but didn’t catch this instance.

The Methods section now feels clearer, and the progression of information is more intuitive. I wonder if a logical workflow diagram in the supplementary materials might help readers follow the many steps involved in data processing, pooling, and analysis. For a proof-of-concept paper like this, I think a visualization of the methods might help others who hope to implement similar tools in the tropics. This is by no means a requirement — just a suggestion if time permits.

Lines 778–784: This is a fantastic point that many eBird users fail to recognize.

Throughout the discussion you do a really nice job of optimistically identifying the shortcomings of using eBird data from the tropics without undercutting your own work. I think part of my first-round grouchiness surrounding the assumptions of eBird data was mostly driven by inherent differences in how citizen observers collect and submit data in temperate versus tropical systems – a process which is not fully acknowledged in the literature. Since you are one of the first to use tropical eBird data for any purpose which involves rigorous models, your thoughts really set a good precedent for what others should expect or account for.

This is really interesting work with clear and impactful results. It has been a pleasure to review this manuscript and watch it improve with each revision.

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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 #1: No

Reviewer #2: Yes:  Nolan M. Clements

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[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.

Combining acoustic survey and citizen science data yields enhanced species distribution models for tropical rainforest birds

PONE-D-24-56728R2

Dear Dr. Rumelt,

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.

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Kind regards,

Julia A. Jones

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: