PONE-D-21-00412

The critical role of natural forest as refugium for generalist species in oil palm-dominated landscapes.

PLOS ONE

Dear Dr. Guerrero-Sanchez,

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.

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We look forward to receiving your revised manuscript.

Kind regards,

Deborah Faria, PhD

Academic Editor

PLOS ONE

Additional Editor Comments:

Dear Dr. Guerrero-Sanchez,

I have received the reports from the advisors on your manuscript entitled " The critical role of natural forest as refugium for generalist species in oil palm-dominated landscapes ", which you submitted to the PlosOne.

Based on the reviews received, your manuscript could be considered for publication pending the incorporation of major revisions. For this reason, you are asked to carefully consider the comments of both reviewers. Both reviewers made an exceptional work, bringing sound suggestions while raised questions and concerns that should be tackled accordingly. I share the concerns of reviewer #2, regarding the possible river effect due to the spatial segregation of forests and plantations, and the statistical analysis in which you are using AIC values to compare models built from distinct data sets (different sampling sizes). These points need to be fully addressed in your review.

I am looking forward to receiving your revised manuscript within 30 days. Should you need more time to accomplish the revision please do not hesitate to inform me promptly.

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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: No

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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 authors,

this is an interesting piece of work on the effects of oil palm plantations and forests on the populations of a large monitor lizard. I understand that most theoretical ecologists would start criticizing your study areas: too few replicates and too heterogeneous environments (as one plantation is full of refuges due to the presence of limestone and one natural forest is susceptible to flooding, which may not represent a big problem for large monitors but maybe for offspring and eggs). However, I am a field biologist myself, and thus know how difficult it is sometimes to chose ideal areas in heavily altered environments. Sometimes forest fragments are so small that the whole fragment may "behave" as a forest edge. However, that should not impede the study of these areas because that could simply lead to nobody never studying them because they do not fit into an ideal sampling design.

As a whole I liked your study. It reads well and is far from being too wordy. Most parts have just the right size. However some issues need to be addressed before this manuscript could move to the next stage. Before I start I would like to mention that I am a frog specialist and thus maybe some of my observations do not perfectly fit for large lizards. So please feel free to refute those comments.

Lines 43-48: While your text dealing with conservation concerns including extraction quota sounds interesting it is irrelevant for your article as your aim is not to discuss these quotas or other threats that may be affecting this species. In fact it is enough to quote that it is highly abundant and linked to human-dominated habitats as you already do.

Lines 76-78: Your hypotheses need to be better explained and contextualized. If you write that you expect the presence of larger animals in anthropogenic habitats than in protected forests it would be nice to have some examples in the intro of species where something like that has already been observed.

Line 81-88: Something I am missing in the characterization of your study region is if the LKWS is achieving its mission, in other words, if it is really an effective conservation unit. Some conservation units may exist on paper but that is often no guarantee that they also exist in-situ as several studies have shown that conservation units, if not properly administered, suffer with logging, hunting and even with conversion to farmland. It would be good if you could explain a bit how effective this conservation unit is.

Line 92: You mention the limestone hills and how they turn the plantation more uneven. It would be interesting if you could write a bit more about these limestone hills: are they also covered by oil palms or are these tiny islands of other types of vegetation?

Line 101-106: Before reading your manuscript, just after reading the abstract I thought: Why did they only use mark recapture when tracking them with telemetry would have revealed so much additional and interesting data to answer their main questions? Tracking would allow to check if animals living on the borders (and in fact all your natural forest sites can be viewed as borders as the few hundred meters are no real obstacle for so large and fast moving monitors) use the plantation for feeding and the forests for shelter and kernels would also show how all this mosaic is used by them. Then I saw that at least you have data on tagged individuals. It is a pity that these data on tagged individuals has not already been published. It would have helped a lot to better understand this study here. Further, as the home range data has not been published it is impossible to check if they have been calculated accurately and using the best statistical approaches as this issue has been subject to very interesting discussions recently (see Fleming & Calabrese 2016 (https://doi.org/10.1111/2041-210X.12673). We have no other option than to trust that the unpublished manuscript has been done with the same accuracy and quality as the study we are reviewing here.

Line 110-115: I have some issues regarding your traps measuring 90x40x40 cm: Is this the standard device used to capture large monitors? If yes please cite some other studies where this traps were successfully used. Do these traps allow capture of small and large individuals with the same efficiency or are they more efficient for smaller individuals? I have trouble imagining a large monitor, e.g. of 107.80 cm (the largest from your own study) getting stuck in a 90x40x40 trap, but maybe it's a quite common event.

Line 189: While you state in your text that birth/immigration estimates are larger in forest areas your table 2 clearly shows that this is not valid for all studied areas as your southern forest area and your southern oil palm area show values that are very similar (44.39 vs 41.63). Your data only seems to be statistically significant when you roll all two forest areas and both oil palm areas into two areas.

Line 256-259: If I get you right natural forests may be playing a fundamental role as source areas of new monitors and oil palm plantations could be so called sinks. Maybe you could widen your discussion here including some literature on sources and sinks in populational biology (e. g. Dias 1996 (https://doi.org/10.1016/0169-5347(96)10037-9) or Kawecki 2004 (https://doi.org/10.1016/B978-012323448-3/50018-0) or Gravel et al. 2010 (https://doi.org/10.1890/09-0843.1) among others).

Line 260-267: That is exactly what is missing in your area description (see comment concerning line 92 above). Maybe what influences monitor densities is less related to an intact forest or not and more related to the presence of micro-niches and shelters. Kuril estate offers a lot of these refuges and thus functionally may be working as an old grown forest.

Line 286: "It" should not be capitalized.

Reviewer #2: Does the manuscript adhere to the PLOS Data Policy?

(Answer options: Yes, No) YES, IF THEY MAKE THEIR DATA AVAILABLE

This is an interesting and generally well-constructed and implemented study. However, I have two main concerns. The first is with the study design as the plots in forest appear to be mostly located along the river while the sites in oil palm are not. Therefore, the result you found could be nothing to do with forest versus oil palm but rather a river effect. I think you need to better describe the sampling design and how you paired forest and palm oil sites to avoid these types of confounding effects. And if there are potential confounding effects they need to, at the very least, be controlled for in the statistical analysis. The second issue is that you appear to compare the AIC from models fitted to different data sets. You cannot do this as the comparison is confounded by the effect of sample size and data on the likelihood. I expand on these comments below and also include a number of other comments.

Lines 41-43: The species is highly abundant but you also state it is threatened – these seem to be contradictory.

Lines 48-54: Distance sampling and mark-recapture actually provide different types of information so I think it is less about accuracy and more about the purpose of the survey.

Sampling design. Need more information about the sampling design and how you matched plantation and forest plots to control for confounding variables (for example, why are all the forest plots along the river? This is likely to bias your results).

Statistical analysis. What is the spatial unit for which you estimated population size? Is it the transect? This should be made clear.

Lines 149-157. What do you mean by “suitable area” and how did you measure it?

Lines 161-162. How many recaptures where there in total? I presume here you mean that an individual trapped at one site was never recaptured at another site rather than there were no recaptures at all?

I suggest avoid using acronyms as the manuscript is difficult to read with the use of acronyms so often (I had to keep reminding myself what each acronym meant).

Lines 200-204. You cannot compare the AIC of models fitted to different data sets (which seems to be what you are doing here unless I am mistaken).

Lines 205-207. I wonder whether this is because you measured the size of habitat differently between the two habitat types. It is hard to tell since you don’t describe how you measured the size of habitat.

Table 3. See my comments above about not comparing AIC among models with different data sets. The AIC for the full data set will have a larger AIC since it has more data points so the likelihood is larger (hence cannot be compared to the models fitted to the other data sets).

Line 230. less accurate that what other methods?

Line 275. Do you mean “density dependent”?

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Reviewer #1: Yes: Mirco Solé

Reviewer #2: Yes: JONATHAN RHODES

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PONE-D-21-00412R1

The critical role of natural forest as refugium for generalist species in oil palm-dominated landscapes.

PLOS ONE

Dear Dr. Guerrero-Sanchez,

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 Sep 03 2021 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: http://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,

Bilal Habib

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 (if provided):

I am happy with the revision, but one of the reviewers have still some issues with resect to methodology. If you are unable to answer the questions with resect to concerns raised by reviewer, i suggest adding paragraph about the limitations of the study and highlighting this particular issue for further research. I hope this is helpful.

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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: All comments have been addressed

Reviewer #2: (No Response)

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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: Yes

Reviewer #2: No

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

Reviewer #1: Yes

Reviewer #2: No

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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 #1: Yes

Reviewer #2: No

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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: Yes

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: Dear authors

I am glad that the comments made by both reviewers have helped to turn your manuscript even better than it already was. You have addressed all comments in a very positive and constructive way and thus I feel that your study is now ready for the next stage.

Reviewer #2: Although you have partially addressed my previous concerns, I feel some still remain unaddressed in your responses. My remaining concerns are as follows:

"R2-C2. Lines 48-54: Distance sampling and mark-recapture actually provide different types of

information so I think it is less about accuracy and more about the purpose of the survey."

In your response you state that Distance Sampling cannot account for variation in detectability between the two habitats, but this is strictly untrue. This is exactly what Distance Sampling is designed to do and I suggest you modify this statement.

"R2-C3. Sampling design. Need more information about the sampling design and how you

matched plantation and forest plots to control for confounding variables (for example, why are all the forest plots along the river? This is likely to bias your results)."

In your response you seem to explain how you achieved independence among sampling sites not how you dealt with confounding factors. I understand that accounting for confounding factors may be difficulty, but at the very least it needs to be discussed as a major limitation (if they can’t be dealt with) and provide an explanation that, if there are unaccounted for confounding factors, the ability to generalise your results to other systems will be limited (i.e., making general statements about the differences between oil palm and natural forest will not be possible).

"R2-C4. Statistical analysis. What is the spatial unit for which you estimated population size? Is it the transect? This should be made clear."

In your modified paragraph what does “higher probability of occurrence” really mean? I think you need to be much more specific here. I assume you set a threshold that defined suitable habitat and if this is what you did then that threshold needs to be defined.

"R2-C8. Lines 200-204. You cannot compare the AIC of models fitted to different data sets (which seems to be what you are doing here unless I am mistaken)."

In your response you never answer my question about whether you compare AIC values for models fitted to different data sets. It still sounds like you did, which would be incorrect if so.

Overall I feel that the questions I raised still need some more careful thinking about and more complete and targeted responses.

Jonathan Rhodes

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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: Yes: Mirco Solé

Reviewer #2: Yes: Jonathan Rhodes

[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.]

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The critical role of natural forest as refugium for generalist species in oil palm-dominated landscapes.

PONE-D-21-00412R2

Dear Dr. Guerrero-Sanchez,

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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

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Kind regards,

Bilal Habib

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

The responses to the comments are satisfactory, the paper shall be accepted for publications.

Reviewers' comments: