PONE-D-24-31667Functional safeguards for conservation: identifying climate change refugia for frugivorous and nectarivorous birds in a degraded area of ColombiaPLOS ONE

Dear Dr. González-Maya,

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. Your submission has been reviewed by two external reviewers. I also made my review.

Reviewer 1 suggested Major Revision and provided some compliments.

His/her major concerns are relative to the need of citation of more studies in the Introduction and Discussion, and the need of more clarity in the Methods. Also, there are numerous corrections and suggestions regarding all parts of the manuscript.

Reviewer 2 suggested Minor Revision and provided some compliments.

He/she is mainly concerned with the need of more clarity in the Methods, and some improvement in the Discussion. Also, there is a large set of minor suggestions regarding mainly the use of specific terms and writting.

My own review also provided some suggestions and corrections. Please find it below.

With this, I believe that, after corrections, this manuscript can be published in PLOS ONE.

Thus, I suggest that it keeps in the evaluation process for publication, after Major Revision.

Please let me know if you have any doubts regarding this submission.

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Dárius Pukenis Tubelis, Ph.D.

Academic Editor

PLOS ONE

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Additional Editor Comments:

Review by the editor (Dárius Tubelis):

Title page. Please check again the instructions regarding the authorship and affiliations.

Affiliation: start with the Department, and then the University, to the country (see the wrong item 1).

Abstract. Line 22. Is "poorly" really correct here ? Maybe a too strong term.

About line 25 and ahead. Could you provide 1-2 sentences regarding the methods of your study ?

Introduction

You can indent the first line of the paragraphs, except the first one. (also check this for other sections of the manuscript).

The Introduction is of good lenght and quality but the number of cited studies is considerably low.

You tended to cite only one study per sentence, but you can easily

increase it to 2-3 citations per brackets by making a new search in Scopus.

This would increase the probability of citing the main relevant papers on this topic. Consider the PLOS ONE international audience.

With this improvement, the numbers of different studies would change here and in the References Section. Please check carefully later, if you change them.

You can make this improvement easily, by making little or no changes in your current text.

Line 85. Add "Colombia".

Methods

Study Area

Well done; well written.

Species Data

Line 142. You can add a reference that you used to classify these species as frugivores and nectarivores.

Line 150-154. But are the aspects of these trais in the objectives ?

Distribution Models

Line 185. Add the valley/province and Colombia to the Table title.

Table 1. Column "Variable". Should "tres" be "trees" ?

Results

Lines 262-263. "reduction of between" sounds worng. Maybe you can write "reduction of "1-75%".

Line 269. Fix the "and" in italics. The same for line 278.

Figures 2, 3 and 4. Their captions. Add the valley/province and Colombia in the end of the first sentence. Check this for all figures and tables.

Line 314. You have to bring the captions of figures 5 and 6 here, after this paragraph where you firstly cited them.

Discussion

Within brackets, you are adding a space between consecutive numbers. It should not occur. Please check throughout the manuscript. It should be, e.g., [2,3].

You have to divide the Discussion in sub-sections with subtitles. Preferably, if you follow those of the Results, and one more regarding Conservation Issues.

Keep your mind always with an international readership.

References

Journal titles should be abbreviated.

When citing the pages of articles, you have to use a long dash, not hyphen between numbers.

Please check again if everything is in agreement with the Instructions before sending the corrected version.

Supporting Information

Please make sure that the captions and titles inform that you studied birds, in the Magdalena valley/province, in Colombia.

Figures

It is difficult to read what is written there. Maybe only a problem due download. It will be checked during the next stages.

Figures 3 and 4. I did not understand why you used letters here, instead of the numbers of each group.

Figures 5 and 6. These two black circles are useless as they are. Eliminate them or add the names of cities. Explain in the captions the meaning of "F. G. richness".

Figures 7 and 8. Add Venezuela and move Colombia to the right (gray area). Put them in bold and bigger than the names of the two cities.

Figures 7 and 8. I did not understand why you have two color legends in each figure.

Dárius

[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: No

Reviewer #2: Yes

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

Reviewer #1: No

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: Dear Editors,

Thank you for the opportunity to review the manuscript titled " Functional safeguards for conservation: identifying climate change refugia for frugivorous and nectarivorous birds in a degraded area of Colombia" submitted to Plos One.

In this manuscript, the authors group frugivorous and nectarivorous bird species occurring in a province in Colombia into functional subgroups to evaluate the impacts of climate change on species distributions. While assessing the effects of climate change on functional groups of birds is relevant for biodiversity conservation in biodiversity hotspots, the study lacks novelty. Numerous articles have already been published on the impacts of climate change on bird distributions. Although the authors claim there are very few studies exploring the effects of climate change on functional groups of birds, this assertion is questionable; I found several articles on this topic with a quick Google search (see specific comments below).

The authors mention that they also evaluated the impacts of deforestation on species occurrences, but their methodology lacks clarity. They state they used a footprint layer for this analysis, yet they do not explain essential characteristics of this layer (e.g., whether it allows for species occurrence in non-forested areas, its resolution, etc.).

Similarly, the authors omit crucial information regarding the methods they used to project species' potential distributions. I also believe that their models could be significantly improved (please see specific comments below).

The discussion is weak. Although it is natural for the study to focus on the implications of the results within the study area, the authors have done so excessively. Given that the manuscript was submitted to an international journal, it should include more comparisons with studies conducted in other tropical regions. In this regard, I have suggested some relevant studies in the comments below.

The authors also fail to discuss the implications of their results for the potential movement of species under future scenarios. For instance, is the establishment of ecological corridors relevant for species movement within the landscape? Where could these potential corridors be implemented?

Specific Comments:

Title: I suggest removing "in a degraded area of Colombia." Including regional characteristics in the title might not appeal to an international audience, although this information should be included in the abstract.

Figures: The text in the figures, especially in Figures 1, 2, 3, and 4, is difficult to read. This might be due to the low-resolution images required by the submission system, but I couldn't properly review them. Additionally, is there a reason why the figure legends are spread throughout the manuscript? This arrangement makes them hard to find. Please consider adding a small inset map of Colombia showing the location of the study area. For readers unfamiliar with Colombia's geography (like myself), the location of Magdalena Province might not be immediately clear.

Lines 34-35: I suggest excluding "for other wildlife."

Line 35: Consider removing "highly," as it sounds a bit vague.

Line 35: Replace "value" with "importance."

Keywords: Unless it is a journal requirement, I suggest using lowercase for all keywords and omitting the full stop.

Lines 59-60: "and rarely consider their effect from a functional point of view"—but see the following studies:

https://doi.org/10.1016/j.pecon.2023.12.002

https://doi.org/10.1111/ele.13830

https://doi.org/10.1111/gcb.16723

https://doi.org/10.1038/s41598-019-53409-6

Lines 114-117: Instead of providing biome names, it might be more informative to describe the vegetation types (e.g., forests, savannas, shrublands, etc.).

Lines 140-142: From where did you obtain the species list of 494 species that may occur in the region? Which classification system did you follow to categorize them as frugivorous or nectarivorous? Please clarify, even if it was based on personal knowledge.

Line 143: Why did you choose a 30-year timeframe?

Lines 145-146: Does this mean you retained species records that are more than 1 km apart? If so, could this result in occurrence points being, for example, 1.5 km apart or slightly more? This could lead to high spatial correlation of your occurrence points, potentially causing model overfitting and biasing the results toward regions with more species occurrence data.

Lines 150-154: Please clarify why you selected those particular measures as proxies for functional traits.

Lines 176-178: Please explain why you chose these bioclimatic variables. How did you handle correlation among variables?

Line 181: Is your land cover class variable categorical? It's generally not advisable to use categorical variables in species distribution modeling (SDM) studies.

Line 187: Why did you choose Maxent? Why not include other algorithms and perform an ensemble approach?

Lines 189-190: "five regularization values, and five feature combinations"—I don't understand what this means; please clarify.

Line 191: I'm not sure if AUC is the best evaluation metric. Why didn't you use TSS? https://doi.org/10.1016/j.ecolind.2022.109830

Lines 201-206: How did you perform the ensemble of your global circulation models?

Lines 211-212: Was the convex hull created for each species individually? If so, I agree. Please clarify.

Lines 215-219: I didn't understand how you considered the "effect of landscape transformation." Please provide more information about the variable you used and your analysis.

Lines 245-248: The number of species in each group, as I summed from Table S1 and Figure 1, was 58 for frugivores and 53 for nectarivores. In line 140, you mention that you estimated the distribution of 494 species. Please clarify.

Line 264: I suggest moving Figure 2 to the Supplementary Material.

Lines 267-275: Since species in each group can be seen in Figure 1 and Table S1, I suggest removing species names from the text.

Reviewer #2: This is a robust analysis in an important biodiversity hotspot that deserves more attention. The SDM methodology is traditional but sound. The focus on functional groups is a nice novel addition to this deep area of research/analysis.

I have some medium-sized comments and then a lot of minor wording suggestions below.

1. In general the manuscript is really well written but there are some sections that could be clearer. This could be accomplished by doing a close read and trying to get rid of extra words. I've noted some below. Here's another example: Line 316: "Analysis of projected climate change scenarios identified potential refugia for frugivorous birds. We categorized these refuges based on human footprint and protected area status" could be more directly reworded as "Extensive potential climate refugia were identified for frugivorous birds: Type 1 refugia:...

2. The commonly used terms in the (English) literature now are climate refugia and climate change

refugia. Best to pick one and use throughout.

3. The Methods are not detailed enough and too conceptual. I gave some examples below.

4. Discussion could use some more caveats. For example, related to Line 221: how does the 'assumption was used that this human footprint index would remain constant in future scenarios.' affect the results? Also (~272-274), need to note that SSP585 is increasingly considered unlikely (this is new science) so these results are low probability, worst case scenario. On that point, the SSP 126 results should be showcased a bit more in the text to show the range of possibilities. Also, Lines 321-322 in the Results belong in the Discussion.

Minor suggestions:

Line 21: Suggest 'drivers of the biodiversity crisis' to avoid saying loss again

Line 29: Use altitude or elevation consistently throughout (apparently elevation is the more appropriate term)

Keywords: I suggest simply 'functional group' since 'Avian functional groups' is likely too specific to be a useful keyword term

Line 44: Insert comma before since

Line 45: reword - can delete 'the population sizes of' or reword as 'there has been a 68% reduction in the populations of all (known) mammals..." nearly is not needed unless you want to say 70%

Line 48: wording makes it clear that the previous paragraph was supposed to be about habitat loss, but besides for the opening sentence, the paragraph just seems to be about the biodiversity crisis in general.

Line 57: change comma after however to semi-colon

Line 58: delete 'relative approaches to'

Line 64: change mitigate to reduce - avoid using the term mitigate in the climate change context when not referring to greenhouse gases to avoid confusion

Line 71: replace semi-colon with period

Line 127: delete commas after plantation and tributaries. And consider breaking up this very complex sentence.

Line 135-136: elevational

Line 175: delete the before Worldclim

Line 224: delete 'were used to' and change to 'identified'

Line 225-227: suggest using areas or regions when defining type 1 and type 2, not mixing

Line 230: remain remnants has complex meaning that isn't needed here. I suggest just 'areas retained between the current...'. Then on line 232, could say retained and new areas (although better just to say type 1 and type 2)

Line 232-234: this is confusing - was this done additionally? if not, it should be said earlier. this is the methods, and definitions have already been given, so this whole section should be streamlined to focus on what was done methodologically, not conceptually.

Line 235-236: refuge means something else. use refugia or refugium (singular). and no need to add 'areas'

Line 239: how were low and high footprint defined? and again, this and the following sentences are focusing on explanations and concepts and should be focused on details and methodology

Results: It would be good to list the mean. Maybe after 'scenarios,' state 'the average range loss across all species was X (range: x-x). Then you can talk about the 8 of the 12...

Also, with "(Fig 2)" list some stats about the footprint results

Figure 3 & 4: add "(m)" to y axis

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Reviewer #1: No

Reviewer #2: Yes:  Toni Lyn Morelli

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Functional safeguards for conservation: identifying climate change refugia for frugivorous and nectarivorous birds in a degraded area of Colombia

PONE-D-24-31667R1

Dear Dr. José González-Maya,

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. If you have any questions relating to publication charges, 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,

Dárius Pukenis Tubelis, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

Dear Dr José F. González-Maya,

I received the corrected version of your submission PONE-D-24-31667 by Dr Fausto Sáenz-Jiménez et al about refugia for Colombian birds.

Sorry for taking 11 days to send my decision, but my University had no internet for 8 days this month.

Thus, I could not handle the corrected manuscript immediately.

I carefully read the corrected version (R1) and noted that you followed most of the numerous suggestions, comments and corrections

provided by both reviewers and me. Also, I appreciated most of your responses to all points presented by us.

With this, I now consider that your study reached the expected standard for publication in PLOS ONE.

Your article is in agreement with the PLOS ONE Publication Criteria.

Thus, my decision is to Accept your submission.

During my last reading of your corrected version, I found a range of minor mistakes that have to be fixed prior to publication.

You can fix then along the next days and final stages of the evaluation process.

You will find my final corrections below.

Thank you for considering PLOS ONE as home of your research.

Dárius P. Tubelis

PLOS ONE Editor

UFERSA

Mossoró-RN Brazil

Last corrections to be done by authors prior to publication:

First page, authors. Replace "&" by a comma prior to the last author.

Abstract

Line 22. "remain understood" has to be fixed. Maybe you can use "have to be better understood". Or other option to replace the former "poorly".

Introduction

Line 61. This "; however," is a bit strange. Can you delete it ? Please check.

Line 76. Add a space before "Furthermore".

Line 90. I think it should be "Colombian". Add "n".

Methods

Line 166. Delete "." after "interactions".

Table 1. Line 200+, fix "tres" for Evergreen broadleaf, second column.

Results

Lines 273-278. Please fix the formatting of this paragraph. It is to the left.

Line 280. Replace "Figure 1." by "Fig 1." Please do this for all figure captions.

Line 292. Delete the dot after "Figs".

Line 303. The same.

Line 307. "and" should not be in italics.

Line 313. Delete the dot after "Figs".

Lines 315 and 318. Use "Fig" instead of "Figure". The dot comes only after the number.

Lines 325-327. Delete the dot after "Fig".

Lines 329 and 332. Use "Fig" instead of "Figure".

Line 240. Replace "Fig." by "Figs".

Lines 343 and 347. Use "Fig" instead of "Figure".

Line 356. Use "Fig 8".

Line 362. Use "Fig 9".

Lines 366 and 372. Use "Fig" instead of "Figure".

Discussion

Line 395. I think there is no need to start a new (short) paragraph. Consider merging that of "Beyond" with the previous paragraph.

Lines 404 to 407. Other too short paragraph. Merge it with the previous or next one.

Line 426. Maybe you can use "Cracids" as you use "are" ahead.

Lines 431 to 434. Other short paragraph. Consider merging with the previous one.

Line 455. Delete the dot after "m". And add a space.

Line 456. Delete the dot after "Fig". Use "Figs 4 and 5".

Line 502. Use "(Figs 8 and 9)".

Line 516. You can add another study besides 123 or change to "a study in Brazil [123] has...." . Similar to lines 530-531.

Line 526. Use a long dash between numbers.

References

I noted that the formatting was substantially improved. I found not mistakes, but please make a final checking before sending the final version.

Supporting information

There is some GREAT problem here.

You do not provide the titles for S1 Table, S2 Table and S3 Table. They were cited on the text but their titles should be here in this list. Also, their files are not in the ZIP FILE ARCHIVE.

S4 Table. It was not cited on the text and its title is not in this list of titles.

S5 Table, S6 Table, S7 Table and S8 Table. Their titles are here but they were not cited on the text.

Please fix these major problems carefully.

FIGURES

Where is Fig 1 ? Your figures start with Figure 2.

Please check the numbers of all figures again. Mistakes should not occur here. I´m confused with it.

Figures 8 and 9. The word "Colombia" is partially covered. You have to fix it maybe by reducing the size of the box with elevation data.