Evaluation of counting methods for monitoring populations of a cryptic alpine passerine, the rock wren (Passeriformes, Acanthisittidae, Xenicus gilviventris)

Joanne M. Monks; Colin F. J. O’Donnell; Terry C. Greene; Kerry A. Weston

doi:10.1371/journal.pone.0247873

Peer Review History

Original SubmissionDecember 3, 2020
4 Jan 2021 Decision Letter - Bi-Song Yue, Editor PONE-D-20-38105 Evaluation of counting methods for monitoring populations of a cryptic alpine passerine, the rock wren (Xenicus gilviventris) PLOS ONE Dear Dr. Monks, 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 Feb 18 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. 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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: This is a well-done study that evaluates different monitoring methods and their appropriateness for a particular species of wren in New Zealand. The authors have done an excellent job conveying what they did and its importance for species conservation. I have a few remaining questions and suggestions. - I (not an ornithologist) struggled to understand why the numbers in the simple count method were given as abundance indices, and not converted to a number that would be directly comparable to the territory mapping. Would doing so have altered the statistical results in a meaningful way? - Line 84: I’d like a lot more detail about this literature review, particularly since it is called a lit review. Are these methods that are usually used in alpine bird species? Was anything in particular discarded, and if so, why? - In table 1, please add a column with a short description of each method. This information is in the body of the text but not the first time these terms are used. - Why have the methods been ordered this way in the table? As a reader, it seems to make more logical sense that territory mapping would be described first or last (as the standard to which all other methods are compared) The line numbers disappeared after Table 1. - In the Distance Sampling methods paragraph (page 10), please explain what conventional methods are in a short sentence or two. - Page 11 – NOREMARK is a different spelling than in Table 1. I think this spelling is correct and the table is wrong, but please check. - In the results, page 14, you mention that territory mapping is only reliable through the fledgling period. There is a bit of discussion of this issue on page 19, but I’d like more – is this expected to be true of all of these methods? Might one method be better for surveys in the post-fledgling period? - Fig 4 – I don’t’ see an explanation of panel a vs b (they are clearly the two study sites but it’s not clear which is which). Reviewer #2: Please include in the title the Order and the Family of the bird species. This study departs from a relevant perspective and searching for cost-effective and cost-less methods is valid if your output is equally valid, replicable, and renders strong data to be used in long-term monitoring and conservation. Comparison between different methods is also relevant, and this study is particularly important in bringing some light on this neglected subject. One of the authors' concerns is about the cost of each method x quality of the results, and this statement appears along with the manuscript. However, this topic is not explored with the details requirable in the discussion, and according to the authors, in a situation where the results must be "achievable within budget constraints" I hope to see this topic explored with the necessary details. As the authors have the raw data & costs to obtain these data in each methodology I strongly suggest that they can cover this topic more accurately. I agree that banding birds is the most expensive method and potentially harmful specially for delicate and threatened species. Although I agree that pointing counts is an effective tool, I believe the authors must provide stronger evidence in the discussion (maybe the last paragraph should be subjected to a more lengthy explanation). ****** 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: No Reviewer #2: No [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. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0247873.r001
Revision 1
14 Feb 2021 Author Response Bi-Song Yue Academic Editor PLOS ONE Dear Dr Bi-Song Yue Thank you very much for the constructive feedback on our manuscript. We have thoroughly addressed all points raised during review. Our detailed responses to reviewers’ comments are in italics below. We hope that our revised manuscript is now suitable for publication in PLOS One and look forward to hearing from you again. With best wishes, Jo Monks (on behalf of all authors) Journal requirements: 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. > Done. 2. We note that Figure 1 in your submission contain map images which may be copyrighted. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission. > On reflection, Figure 1 (a map showing location of the two study sites) is not essential to this manuscript, so we have decided to remove it rather than seeking copyright permission. Further, we now refer to another paper which includes a map showing site locations. 3. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. > Done. Reviewer #1: This is a well-done study that evaluates different monitoring methods and their appropriateness for a particular species of wren in New Zealand. The authors have done an excellent job conveying what they did and its importance for species conservation. I have a few remaining questions and suggestions. - I (not an ornithologist) struggled to understand why the numbers in the simple count method were given as abundance indices, and not converted to a number that would be directly comparable to the territory mapping. Would doing so have altered the statistical results in a meaningful way? > Simple counts are presented as abundance indices because the number of transects surveyed at each site differed according to availability of suitable habitat for rock wrens and, due to weather and logistical constraints, it was not always possible to survey all transects an equal number of times per sampling period. Furthermore, attempting to present simple counts as a number to be directly compared with estimates from territory mapping would be misleading, because they do not sample the full area and because they do not account for detectability. - Line 84: I’d like a lot more detail about this literature review, particularly since it is called a lit review. Are these methods that are usually used in alpine bird species? Was anything in particular discarded, and if so, why? > Reviewer 1 makes a good point that we didn’t conduct a formal literature review in creating this table, rather researched the applicability of established bird counting techniques to rock wrens and this is what we present in Table 1. We have removed reference to the term ‘literature review’. > Based on our understanding from the literature, there is no ‘usual’ method for alpine bird species. Some of these techniques are applied elsewhere in the world in alpine, or more usually open, habitats, but we didn’t find strong evidence of consistency. This was part of our motivation for the present study, which we hope will contribute to the literature on methods for alpine birds. > Site occupancy was discarded because detectability can vary with rock wren behaviour in relation to the nesting season and because it is difficult to compare with other methods. See lines 93 to 95 of the Methods for this explanation. - In table 1, please add a column with a short description of each method. This information is in the body of the text but not the first time these terms are used. > We attempted to do this, but it is impossible to describe these techniques briefly in a way amenable to inclusion in a table; the detail is important! We have instead referred the reader to the Methods text and references included within the table in the footnotes of the table for these descriptions. - Why have the methods been ordered this way in the table? As a reader, it seems to make more logical sense that territory mapping would be described first or last (as the standard to which all other methods are compared) > This is a good point. We have reordered the table to begin with territory mapping (as the gold standard), followed by the other techniques in decreasing order of cost. The line numbers disappeared after Table 1. > Good point! Now fixed. - In the Distance Sampling methods paragraph (page 10), please explain what conventional methods are in a short sentence or two. > Done. We’ve added a description of distance sampling and rewritten the paragraph for clarity. - Page 11 – NOREMARK is a different spelling than in Table 1. I think this spelling is correct and the table is wrong, but please check. > Thanks – we’ve corrected the spelling error in Table 1. - In the results, page 14, you mention that territory mapping is only reliable through the fledgling period. There is a bit of discussion of this issue on page 19, but I’d like more – is this expected to be true of all of these methods? Might one method be better for surveys in the post-fledgling period? > We have added the following two sentences to the paragraph Reviewer 1 refers to in order to address this point: “We were unable to obtain sufficient data for all methods trialled to undertake a statistical comparison of methods during the post-fledging period. However, based on the limited data we were able to collect during this period, we suggest that results from all methods are more variable and less reliable in the post-fledging period than earlier in the breeding season.” - Fig 4 – I don’t’ see an explanation of panel a vs b (they are clearly the two study sites but it’s not clear which is which). > Good point! We’ve added this information into the figure title. Reviewer #2: Please include in the title the Order and the Family of the bird species. > Done. This study departs from a relevant perspective and searching for cost-effective and cost-less methods is valid if your output is equally valid, replicable, and renders strong data to be used in long-term monitoring and conservation. Comparison between different methods is also relevant, and this study is particularly important in bringing some light on this neglected subject. One of the authors' concerns is about the cost of each method x quality of the results, and this statement appears along with the manuscript. However, this topic is not explored with the details requirable in the discussion, and according to the authors, in a situation where the results must be "achievable within budget constraints" I hope to see this topic explored with the necessary details. As the authors have the raw data & costs to obtain these data in each methodology I strongly suggest that they can cover this topic more accurately. I agree that banding birds is the most expensive method and potentially harmful specially for delicate and threatened species. > This is a very good point. In response we collated information on set-up, annual maintenance and annual monitoring costs for all four field methods. This information is now presented in a new table (Table 5), described in the methods and results section, and referred to in the discussion. Although I agree that pointing counts is an effective tool, I believe the authors must provide stronger evidence in the discussion (maybe the last paragraph should be subjected to a more lengthy explanation). > We have expanded this paragraph of the discussion to strengthen the evidence for utility of repeated counts on line transects as a suitable technique for trend monitoring in rock wrens and potentially other passerines in open habitat. In doing so, we made it explicit that in our study indices of abundance from line transects were strongly correlated with estimates from territory mapping at both study sites over a 6-year period. We also added a case study in which the technique was successfully applied to a forest-dwelling passerine and resulted in strong management recommendations. Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0247873.r002
16 Feb 2021 Decision Letter - Bi-Song Yue, Editor Evaluation of counting methods for monitoring populations of a cryptic alpine passerine, the rock wren (Passeriformes, Acanthisittidae, Xenicus gilviventris) PONE-D-20-38105R1 Dear Dr. Monks, 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, Bi-Song Yue, Ph.D Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0247873.r003
Formally Accepted
23 Feb 2021 Acceptance Letter - Bi-Song Yue, Editor PONE-D-20-38105R1 Evaluation of counting methods for monitoring populations of a cryptic alpine passerine, the rock wren (Passeriformes, Acanthisittidae, Xenicus gilviventris) Dear Dr. Monks: 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. Bi-Song Yue Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0247873.r004

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