Predicting species assemblages at wildlife crossing structures using multivariate regression of principal coordinates

Thomas J. Yamashita; Daniel G. Scognamillo; Kevin W. Ryer; Richard J. Kline; Michael E. Tewes; John H. Young Jr; Jason V. Lombardi

doi:10.1371/journal.pone.0335193

Peer Review History

Original SubmissionDecember 6, 2024
26 Jun 2025 Decision Letter - Julio Souza, Editor Dear Dr. Yamashita, 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. ============================== Dear authors, considering that the reviewers issued a favorable opinion, with some suggestions. Please ask them to make the adjustments and return the paper (with the adjustments highlighted) so that we can continue the process. Kind regards. ============================== Please submit your revised manuscript by Aug 10 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 . 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Thank you for stating the following in the Acknowledgments Section of your manuscript: We thank the Texas Department of Transportation for providing project funding and access to wildlife crossings. We appreciate the many graduate and undergraduate students and research technicians who provided essential help with collection of camera data and processing of photographs. We thank E. Brookover, P. Glover-Kapfer, M. Cherry, S. Riley, D. Wester, and two anonymous reviewers for their many helpful comments that improved the manuscript. This is manuscript #24-136 of the Caesar Kleberg Wildlife Research Institute. We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. 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If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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: Dear authors, considering that the reviewers issued a favorable opinion, with some suggestions. Please ask them to make the adjustments and return the paper (with the adjustments highlighted) so that we can continue the process. Kind regards. [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? Reviewer #1: Partly Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: I Don't Know Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: No Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: Article is a bit not clear when you do not explain body size of mammals and their adaptive ecology. I suggest you re-write with addition of body size and nature of structures? I wonder have you mentioned about bio-engineering structures. It may some time attract or repel movement? Also elaborating drop-onsite method clearly would be good for readers. Reviewer #2: 1. Line 35. Add a comma before "so" to properly separate the independent clauses. 2. The structure of Table 1 is excessively complex. There is too much information in this table. This table could be further broken down into two or more; e.g., information such as “timeline for WCS construction” could be a distinct table. 3. Generally, predictive modeling should include both a training dataset and a testing dataset. This study did not adhere to this rule. Was a technique such as cross-validation, transfer learning, and leveraging a pretrained model used? A model without a separate test set could be difficult to assess for its true generalization ability and be misleading. 4. Why do you not detrend the spatial and temporal autocorrelation in this study? 5. Line 503 “Our model performed relatively well for total detections but performed much worse for successful crossings and failed crossings.” A further explanation is needed regarding the poorer performance in both successful and failed crossings. This is a limitation that needs to be worked upon in the future study. ****** what does this mean? ). 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Revision 1
24 Sep 2025 Author Response Journal and Editor Comments We have made all editorial changes required by the journal and updated our funding, acknowledgements, and data availability statements. We have moved our data repository to FigShare and provided DOIs for it and the R package used for data processing. Figure 1 used imagery from the national agriculture imagery program and is in the public domain. The authorship issue was due to a missing “Jr.” in John Young’s name in the submission portal. Reviewer #1: Article is a bit not clear when you do not explain body size of mammals and their adaptive ecology. I suggest you re-write with addition of body size and nature of structures? I wonder have you mentioned about bio-engineering structures. It may some time attract or repel movement? Also elaborating drop-onsite method clearly would be good for readers. We do mention that most of the WCSs were too small for large mammals such as deer or nilgai; however, both species used WCSs when they were large enough for them so we included them in the analyses. We believe that generally body size is not relevant for the purposes of this study where we were interested in the community composition of wildlife crossings, not in examining allometric relationships with crossing use. While this could be an interesting future avenue of study, in our study system, not all crossings in our system are large enough for all species, so it would be difficult to examine body size effects on crossing rates. As such, we have added the range of body size to our description of the species captured and added some additional discussion of deer and nilgai WCS use. We are unclear what the reviewer means about bio-engineered wildlife crossings. While WCSs are often designed for particular species, this is often done based on assumptions about their behavior and preferences. Our study could help improve future WCS design by providing a method to test the potential efficacy of a WCS for a suite of species of interest and we explicitly state this in our discussion. We have clarified that our drop-one-site method is similar to the leave-one-out-cross-validation technique for assessing model validity. In our case, the unit of observation is the WCS itself so our unit of observation for cross validation was all months in a WCS rather than a single sample (one month in one WCS). See below for further explanation of the method. Reviewer #2: 1. Line 35. Add a comma before "so" to properly separate the independent clauses. We have added the requested comma. 2. The structure of Table 1 is excessively complex. There is too much information in this table. This table could be further broken down into two or more; e.g., information such as “timeline for WCS construction” could be a distinct table. We have split Table 1 into two tables, one for the characteristics of the WCSs on the study roads and the other for the timeline of construction and monitoring of the WCSs. 3. Generally, predictive modeling should include both a training dataset and a testing dataset. This study did not adhere to this rule. Was a technique such as cross-validation, transfer learning, and leveraging a pretrained model used? A model without a separate test set could be difficult to assess for its true generalization ability and be misleading. We agree that for predictive modeling, ideally we should have both a training dataset and a testing dataset and we acknowledge this in the methods, line 359. Because our sample size of WCSs was small (n = 18) and highly variable, we opted against leaving out a set of WCSs as a testing dataset. Instead we used a technique similar to LOOCV where we excluded all months from one WCS, reran the model, then predicted the dropped WCS using the fitted model. We originally described this in the paragraph starting on Line 363 and have clarified how our drop-one-site approach is similar to LOOCV. 4. Why do you not detrend the spatial and temporal autocorrelation in this study? We detrended the spatial and temporal autocorrelation using a dbMEM when we ran our variation partitioning. However, for our predictive modeling, we wanted to create a model that could be used to predict future use of other (unbuilt) wildlife crossings in the system and be generalizable to other systems. The issue with using dbMEM to detrend autocorrelation is that the dbMEM axes that get included are model specific and you cannot add new values of dbMEM axes for additional testing data without changing the whole model. This makes the model useless for prediction purposes. We did, however, test the differences in model fit between a model fitted with raw coordinates and months and a detrended model and found little to no difference in the model fits, indicating that, for our purposes at least, detrending the autocorrelation was likely not necessary and results in a less useful predictive model. We have added some clarification to Lines 334-340. 5. Line 503 “Our model performed relatively well for total detections but performed much worse for successful crossings and failed crossings.” A further explanation is needed regarding the poorer performance in both successful and failed crossings. This is a limitation that needs to be worked upon in the future study. We believe that the poor performance of the successful crossings and failed crossings models was due to the additional factors that influence actual crossing rates, such as the presence of vehicles, noise or light levels, or the individual’s behavior/reason for being at the WCS itself. Another study in the same study area showed that opossums avoid crossing through WCSs when there is more vehicle noise [1]. Additionally, based on observation and videos in the study system, many species forage around WCSs and they may approach the WCS, appearing to interact with the structure on still image camera traps, as used in this study, but not actually have intentions of crossing. References 1. Yamashita TJ, Tanner AM, Tanner EP, Scognamillo DG, Tewes ME, Young Jr JH, et al. The importance of soundscapes in monitoring wildlife crossing structures. Ecological Applications. In Review. Attachments Attachment Submitted filename: PlosOne_ResponseToReviewers_Rnd1_v2.docx https://doi.org/10.1371/journal.pone.0335193.r002
7 Oct 2025 Decision Letter - Julio Souza, Editor Predicting species assemblages at wildlife crossing structures using multivariate regression of principal coordinates PONE-D-24-56498R1 Dear Dr. Yamashita, 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. For questions related to billing, please contact billing support . 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, Julio Cesar de Souza, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Considering that the reviewers considered a Minor Revision and that the authors accepted the suggestions and made changes to the text, I am in favor of publishing this paper. Best regards Julio Souza Reviewers' comments: https://doi.org/10.1371/journal.pone.0335193.r003
Formally Accepted
Acceptance Letter - Julio Souza, Editor PONE-D-24-56498R1 PLOS ONE Dear Dr. Yamashita, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@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. Julio Cesar de Souza Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0335193.r004

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