PONE-D-22-29377Structural resources and generalist avian predators: implications for tree expansion in shrubland ecosystemsPLOS ONE

Dear Dr. Young,

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.

Both reviewers acknowledge that the manuscript addresses an interesting question, although they have reasonable concerns about some aspects of the manuscript. I kindly invite the authors to try to address the methodological queries raised by reviewer 1, and to try to clarify the focus of the introduction and title of the manuscript as suggested by reviewer 2. 

Please submit your revised manuscript by Feb 23 2023 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.

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PLOS ONE

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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: No

Reviewer #2: Partly

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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: No

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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: This manuscript addresses an interesting management question and is based on a relatively large dataset. However, before it can be considered ready for publication I think it requires some work, both in its format and in some of the approaches/analyses.

I suggest that you phrase the hypotheses in a non-conditional way. E.g. “structural resources ARE the primary influence…”

The methods section requires much more detail and clarity. I would say that very few paragraphs would pass the test of successfully having a reader to replicate what you did. For instance, how many visits per year and per transect were done? Please explain. Also, during what season (or date ranges) was the field work done? What was the criterion for the inclusion of flying birds?, etc.

I do not understand the sentence “We did not adjust songbird observations for detection probability because differences in detectability among species would bias our abundance estimates…”. Precisely, adjusting for detectability tries to correct for a bias that is likely affecting your data. And in your case it could not only be related to species, sex and age of individual birds, but on habitat structure as well. Besides, simply because someone published a study without including such a correction, does not make it right. Because I assume that you did not record the distance at which individuals were detected, you may not be able to conduct this correction. So I suggest that you simply acknowledge that you did not do it, and later discuss the potential implications of this decision.

Please explain in detail how did you predict the abundance of small mammals for those transects where no trapping was conducted. I see a potential problem in this approach (i.e. using vegetation structure as a predictor of rodent abundance) since, later, you analyze both vegetation and prey abundance as, supposedly independent, predictors of predator occupancy.

The explanation for the procedure to generate the prey abundance score is very confusing, and, from what I could understand, rather arbitrary. The weights used for each attribute and value need to be better justified. Why, for instance, having presence of ground squirrels in the transect is equal to it being located at 5 km from the nearest lek? A more parsimonious way of integrating these different prey data could be using biomass per unit area. Probably you would have to make some assumptions for each case, but, at least you would have a more natural way of integrating these data.

If I understand it correctly, when you state “Multi-season occupancy models assume that occupancy of a survey location is closed during each year but may change between years.”, that means that the model considers that individuals are restricted to an area similar to that of the transect (i.e. 80 hectares) during a single season (year?). Although the home range of a hawk is likely much larger than that, I do not see a big problem if only one visit is made during the season. But if there are more than one visit during a year, then the closure assumption would be violated. As I mentioned in a previous paragraph, this information is not presented, but from my reading of the results section, it becomes evident that more that one visit was conducted in a year. I do not see a clear and easy way to address this problem, but it is certainly something that needs to be dealt with and, if possible, corrected.

I wonder to what extent the lack of patterns observed for red-tailed hawks is due to the spatial scale of the analysis. If you use a sampling area that is much smaller than the species’ territory or home range, then “occupancy” loses its meaning. First, because you likely have very few individuals to sample from, and, mostly because at some point they may leave the sampling area even for a few minutes or hours and you might miss them. You discuss this issue in lines 484-505, but I cannot understand why you conclude that in your case detection probability can be considered be equivalent to “availability”.

In order to rule out a significant effect of prey density on predator occupancy, it is important that this predictor is estimated with enough accuracy. In this particular study, different prey types (all with different methodological issues) were integrated in an index whose structure is not strongly justified. In addition, it is important to consider that in many cases, even though predators are likely to be attracted to areas with high abundance of prey, their very presence/abundance may reduce the carrying capacity for the prey, making more difficult the detection of such a relationship. You should be more cautious with your conclusions regarding this topic.

Reviewer #2: Review of Young et al.

This work assesses the relationship of habitat and prey availability with the occupancy of two generalist avian predators, common raven and red-tailed hawk. The authors analysed the habitat changes developed on an area that has suffered the elimination of conifer forest in order to compare it with areas that have not been eliminated, considering it to be an area of special interest for the conservation of the greater sage-grouse. The field work conducted, the variable selection and the methodology used are appropriate and provide great value to the manuscript. However, there are some aspects, mainly in the focus of the introduction, that could be improved for the understanding the results obtained in this study.

The authors introduce this manuscript with an focus that does not fit exactly with the context of the analyses performed and results obtained, since the introduction explains the effects of greater sage-grouse in relation to the removal of juniperus, due to the indirect effects that predators associated with juniperus forests may have. I consider that this relationship of causal effects is a more ambitious context than that which is subsequently analyzed in the models and the results obtained. I suggest focusing the introduction on what is strictly analyzed in methods, which is to address the factors that influence the occupancy of ravens and red-tailed hawks (e.g. L. 419-435). However, this can be contextualized that these results may have indirect implications for the greater sage-grouse, which has been explained in the "management implications" section.

L. 553-561. As indicated here, when more years of monitoring are available, the indirect relationship of predators on the greater sage-grouse due to juniperus management could be evaluated.

L. 105-117. Here, the authors focus this study in the sage-grouse, but the methodology is not developed in this way.

However, if the authors want to evaluate the grouse conservation problem, or the landscape management actions due to the elimination of conifers, they should specifically analyze the occupation of the grouse in relation to the % of junipers, as well as the abundance of predators, to know specifically if it is a problem of sage-grouse habitat or of predators. The juniper habitat may be removed, but the predators may still be there because they may be ecotone zones and the predators may have extensive hunting areas.

Other comments:

Title: I suggest a more concise and causal title: Implications of tree expansion in shrubland ecosystems on two generalist avian predators.

L. 33-37. I suggest to remove or summarize these sentences since I believe that it is not the main focus of this study.

L. 47. The latin name of western juniper should be previously in the abstract.

L. 53: ….”Therefor, we suggest that …” since it is not evaluated.

L.91. Please, include references about nest-trees as a resource for raptors and other predators.

L. 122-123. Rewrite this sentence if you refer to the relationship between forest expansion with predator occupancy and their indirect effects on prey, since specific effects of conifer exapansion and raptor occupancy could be for instance Jiménez-Franco et al. 2018. Plos One. Nest sites as a key resource for population persistence: A case study modelling nest occupancy under forestry practices.

L. 165: … of the study area…

L. 201-205: You shoukld justify the selected prey groups since in the introduction you only mention the sage-grouse.

L. 219: It should be the same unit that L. 197?

L. 246-253. Explain if this index is from previous work or is designed specifically for this study. Include an example of value or equation for its replication.

L. 323. Where is the results of the rest of models? Include them in Appendix.

L. 334-340. Include a table with these results.

Table 1. It should be explained if these variables are included in the same models, o different models.

L. 519: “ … generalist predators, the ravens”.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-22-29377R1Implications of tree expansion in shrubland ecosystems on two generalist avian predators .PLOS ONE

Dear Dr. Young,

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.

We are sorry to be late with your MS decision, but we were unable to contact one of the previous reviewers, so  we had to invite a new reviewer. 

Despite this, both reviewers are very positive and have only shown minor concerns that are easily addressed by you. 

Please submit your revised manuscript by Jun 12 2023 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,

Juan Manuel Pérez-García, PhD

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.

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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 #2: All comments have been addressed

Reviewer #3: (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 #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: No

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: The manuscript is clear and easy to foollow, it is now appropiate for publication. I have included only a couple of minor comments related to editing and to the replicability of this work in terms of its statistical analyses.

Line 170. Replace project by study area: "The climate of the study area is ...".

I suggest including a JAGS code in an appendix for the replicability of the work in other contexts. I believe that this information will add value to the manuscript, as it is free software that is being included in an increasing way of scientific articles and open source journals.

Reviewer #3: This is a well-written paper that uses a robust dataset to evaluate the implications of tree expansion over two generalist predator presence in a sagebrush ecosystem. Clearly a lot of work went into data collection, which includes predator species and his prey across a sagebrush steppe. The study has strong potential to be useful for management and conservation, but in my opinion there are some issues that need to be resolved before this paper is published.

The authors discuss potential implications of their study for the management and conservation of Sage-grouse but the data and results support this indirectly. Although data on the abundance of the potential prey of two generalist predators were used, there are no data on the abundance or presence of the Sage-grouse. In the same way, the authors argue that the abundance of prey does not influence the habitat use by the two species of predators, but only a part of the potential prey was studied. I suggest caution with the conclusions drawn from the results. Is it possible to predators are responding to another prey species present in the area?

Detailed comments

Introduction

Overall, the introduction is very well written and does a great job of setting the study.

L 96-97 delete space before “For”

You mentioned “For generalist predators that may utilize a wide variety of prey items, structural resources may be an important factor influencing habitat use.” But this also happens with forest-dwelling species and specialists. See Martínez-Hesterkamp S, Rebollo S, Pérez-Camacho L, García-Salgado G, Fernández-Pereira JM (2018) Assessing the ability of novel ecosystems to support animal wildlife through analysis of diurnal raptor territoriality.PLoSONE13(10):e0205799

Also, could you include a reference supporting those lines.

In the title and abstract you mentioned the term generalist predators but in the introduction only referred to avian predators, except in L. 96-97. This may be confused for readers. I suggest being consistently with one term for predators. In the objectives L. 148-155 you use avian predators not generalist predators. I suggest the use of generalist predators in the manuscript.

Methods

Please include references in the section of Raven and raptors counts.

L 198 How much time did you spend in stationary counts? This was equal in all transects? Please describe.

L 215 Please mention the ground squirrel species

L225-226 The transects for songbirds was an extension of 1.200 m, you mentioned that transects for avian predators had 800 m with 3 points counts within the transect in L 194-195. This it is not clear.

L 233-235 “Belding’s ground squirrels (Urocitellus beldingi), which occur in large semi-colonial populations, are the most common ground squirrel at our study site.” This could be used in the first paragraph of prey abundance. L. 214-216.

Discussion

L 555-560 I suggest being more cautious with these lines, the relationship between the study and the presence of the sage-grouse is not clear.

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Reviewer #2: No

Reviewer #3: No

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Implications of tree expansion in shrubland ecosystems for two generalist avian predators .

PONE-D-22-29377R2

Dear Dr. Young,

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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Kind regards,

Juan Manuel Pérez-García, PhD

Academic Editor

PLOS ONE