Peer Review History
| Original SubmissionMay 2, 2022 |
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PONE-D-22-12898Coexistence or conflict: black bear habitat use along an urban-wildland gradientPLOS ONE Dear Dr. Klees van Bommel, 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 Aug 18 2022 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:
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Reviewer #1: Yes Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ********** 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 ********** 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 ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors analyze camera detection rates of black bears in and around a conflict hotspot. Urban-wildlife interfaces are expanding rapidly and understanding habitat use of key species in human environments is critical for their management. The manuscript is well-written, the objectives are clearly defined and addressed, and the findings are discussed within a relevant context. I have few comments: The authors acknowledge complexities with individual bear identification and discuss future directions of research that include density estimates and individual movements. Is there however any indication that multiple and enough individuals have been captured during your study to be representative for the broader population. In particular because generalist species typically display a great amount of behavioral plasticity, and the extent of the study area is rather small (~80km2). Related to above comment and a potential avenue for future research, would there be any (expected) differences in habitat use between adult males, adult females, and females with cubs? And how would this influence conflict or coexistence? How did you deal with the fact that not detecting a bear at a camera trap location may be a false absence? And consequently the zero’s in the zero inflated model may not all be true absences, which may induce bias in inferences on habitat use? L388-393: It is not clear to me on what base you make these inferences. You report, for example, a negative association between bear habitat use and human density, but no effects of trail density are reported. From looking at Fig3, it seems however that both variables have similar coefficient estimates, standard errors (not overlapping zero) and confidence intervals (overlapping zero). The same applies for the quadratic term of human density and elevation. I would therefore think that only ‘Active Days’ and ‘EVI’ are informative predictors of bear habitat use. L414-418: Please be consistent in reporting p-values and could you include these in the previous results section? L416: maybe add ‘compared to spring’. L460-463 & L469-471: Is there any previous research in natural systems that shows seasonal shifts in habitat use as a consequence of hyperphagia? Reviewer #2: # Review for: *Coexistence or conflict: black bear habitat use along an urban-wildland gradient* Note: This was written in markdown format. I've also included a PDF if that is easier for you to read. In this paper the authors look at spatio-temporal variation in the distribution of black bears in an area where conflict between black bears and humans is high. Additionally, they also look at the correlation between black bear detections and the probability of black-bear conflict that was estimated from previous research. In general, I think this is an interesting and well written piece of research. I often found myself in agreement with the logical flow of the research, the modeling choices made, and the interpretation of said models. Great work! Perhaps my biggest concern is the secondary modeling approach, which treats the estimated conflict probability as known, when in fact it is something that is estimated with error. In my review below I have a number of hopefully helpful citations about this specific issue for the authors. I also suggest the authors look at a recent article of mine (Fidino et al. 2022), which shows how integrated models could be use to combine human-wildlife conflict data with camera trap data. I'm not on the hunt for a citation here, but since it is relevant to this piece of research I am sharing in case you were interested in how to do this in the future. ``` Fidino, M., Lehrer, E. W., Kay, C. A., Yarmey, N. T., Murray, M. H., Fake, K., ... & Magle, S. B. (2022). Integrated species distribution models reveal spatiotemporal patterns of human–wildlife conflict. Ecological Applications, e2647. ``` If you have any specific questions about any of my comments, feel free to email me at mfidino@lpzoo.org. Again, great work on this! - Mason Fidino ## Abstract --- ### Line by line comments Line 46: The 'such as' breaks up this sentence in a weird way. I think you can remove it and the examples become a little more clear. ## Introduction --- ### Top-level thoughts 1. Well written introduction, I only have some minor comments on some of the wording / sentence structure. ### Line by line comments Line 64: Is sustainable the correct word here? I think it could be, but also it tends to have a bit of a positive connotation to it, so it reads a little off to say sustainable risks of death. Maybe 'acceptable' could be used instead? Just a minor point, feel free to ignore if you disagree. Line 69: This sentence is a little circular. Changes to avoid direct conflict can increase direct conflict when risk of direct conflict is lower. I think it's the second use of direct conflict, which makes it feel a little redundant. Could that bit right after the first (e.g.,) just get removed? I think the point still comes across. Line 76-77: Is 'year round' needed when you already state they are available consistently? "...as they are predictable, consistent, and spatially aggregated sources of..." Line 82-84: Does it help here to remind the reader that the urban-wildlife interface is increases, and therefore increased risk of ecological traps for such species? Line 88: ...to signal wildlife mortality risks... Line 98: ...and can alter their foraging patterns to... Line 103: ..., and can result in seasonal... Line 103-105: Sentence starting with "If such attractants" reads a little weird. Maybe it's the 'attractants can attract animals' part or that the '...and food-conditioning' bit at the end feels like a different thought tacked on. Line 105 - 108: This sentence could be made more active (and therefore a little more succinct). "In Nevada, urban black bears are less active each day (as they satisfied their caloric needs faster), more nocturnal, and hibernate less." Line 116-120: Conflict probability of what? Do you mean human-wildlife conflict probability in general? Human-bear conflict in particular? Line 123-125: Great point, and the introduction sets a really strong foundation for the need to study this. ## Methods --- ### Top-level thoughts 1. I would imagine that the distance between camera trapping locations would be species specific to maintain spatial independence. For black bear, multiple camera traps can be contained within the home range of a single bear, and therefore I would assume that spatial independence is not met. This citation is also a pre-print, though it's been around for 12 years. Maybe just soften the language here (e.g,. say to increase spatial independence rather than maintain spatial independence). 2. Was the sampling effort term included as an offset to the model or did you just include it as a covariate? If the latter was done, I would encourage adding a log offset term instead, as that is a more standard approach when there is variation in sampling effort. If I had to guess, you used a log-offset, so just be specific about that here in the methods. 3. I could see some readers get their hackles up about not using an occupancy model here. I leave it to the authors, but it may help to just get ahead of it here (by using a zero-inflated model you may be estimating habitat use conditional on presence anyways, depending on the class of zero-inflated model you fit). Likewise, occupancy models are literally just zero-inflated logistic regression, so your approach has substantial overlap. For example, the old MacKenzie et al. occupancy modeling book talks about these similarities on about page 135 (i.e., the use of the zero-inflated binomial to model occupancy). ``` MacKenzie, D. I., Nichols, J. D., Royle, J. A., Pollock, K. H., Bailey, L. L., & Hines, J. E. (2017). Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Elsevier. ``` 4. There are a few different kinds of zero-inflated glmms, can you be a little more specific? For example, what is the error distribution that was used (negative binomial, Poisson, etc.). Is this a two part model and therefore the conditional model cannot include zeroes or is it a mixture model and therefore the conditional models can include zero? A little more explanation here would be helpful. note: I see now that the distributional information is shared much lower, around line 297. I'd move that little bit of info upwards so it's not separated from when you introduce the modeling framework. 5. Thank you for using a set of candidate models to assess your different hypotheses. Solid approach. Given the two set hypotheses brought up in the introduction, in may help to add a little more connection between those hypotheses and the set of candidate models given that there are two hypotheses but four candidate models. You should also fit a fifth null model as well (just the active days term plus the site random effect). Given the results I suspect the null will provide the worst fit (highest delta AIC), but it's nice to demonstrate this. 6. Based on the introduction (lines 133-134) I thought that modeled conflict probabilities would be incorporated into your glmms, but instead it looks like counts of conflict are included instead. I suspect other readers will also be confused about this. What makes this more confusing, is that there is a second batch of models done that uses the estimated conflict probabilities. 7. Why conflicts over the year instead of conflicts per month? 8. Using the output from one model as a predictor in another is okay, but the uncertainty of those estimates should also be propagated into the secondary model. From my reading of this secondary model set, I'm guessing that these spatially explicit probabilities are treated as known (i.e., measured without error). If this is the case, using such predictions in secondary analysis leads to anticonservative tests because this error is excluded from further tests (i.e., estimates are too precise). Some papers about this topic that the authors may find useful include: ``` Hadfield, J. D., Wilson, A. J., Garant, D., Sheldon, B. C., & Kruuk, L. E. (2010). The misuse of BLUP in ecology and evolution. The American Naturalist, 175(1), 116-125. Houslay, T. M., & Wilson, A. J. (2017). Avoiding the misuse of BLUP in behavioural ecology. Behavioral Ecology, 28(4), 948-952. Link, W. A. (1999). Modeling pattern in collections of parameters. The Journal of wildlife management, 1017-1027. ``` The Houslay & Wilson paper is open access, so that is where I'd start. I've personally found this easiest to account for in a Bayesian framework (e.g., if you have the mean and SE of each prediction you can set a prior for each data point to propagate that uncertainty), but there are likely ways to deal with this in a frequentist framework as well (e.g., bootstrapping, but resampling the predicted covariate instead of the response variable). 9. What is a reported conflict in these data? Do they vary in severity? ## Results --- ### Top-level thoughts 1. Failing to detect an effect does not mean that there was no effect (e.g., line 391 - 392). I'd just reword to "We failed to detect an effect of road density" so that you avoid confirming the null (which these tests do not do). Other than that, great breakdown of the results. ## Discussion --- ### Top-level thoughts 1. Given the conflicting hypotheses, do the authors feel that one hypothesis was supported more than the other? 2. Any caveats worth bringing up here? For example, there was the assumption that EVI indicates forage availability. Is it possible for there to be human-bear conflicts that go unreported and so the conflicts / year metric used may have some error? ### Line by line comments Line 530: You used ecological trap earlier. ## Tables & figures --- ### Top-level thoughts 1. The axis text on many of the figures is a very light gray, I'd suggest replacing with black to make it easier to read. 2. You could increase the line width for the 95% CI's on figure 3&4, plus the mean estimate on figure 5. ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: Yes: Stijn Verschueren Reviewer #2: Yes: Mason Fidino ********** [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. 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Coexistence or conflict: black bear habitat use along an urban-wildland gradient PONE-D-22-12898R1 Dear Dr. Klees van Bommel, 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. 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, Bogdan Cristescu Academic Editor PLOS ONE Additional Editor Comments: The revisions helped improve clarity and strengthened the manuscript. Congratulations on your paper. |
| Formally Accepted |
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PONE-D-22-12898R1 Coexistence or conflict: black bear habitat use along an urban-wildland gradient Dear Dr. Klees van Bommel: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Bogdan Cristescu Academic Editor PLOS ONE |
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