Peer Review History

Original SubmissionAugust 31, 2021
Decision Letter - Charles R. Brown, Editor

PONE-D-21-28285Interclutch variability in egg characteristics in two species of rail: is maternal identity encoded in eggshell patterns?PLOS ONE

Dear Dr. McRae,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has considerable 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.  The reviewers' comments can be found below.  The changes required are relatively minor.

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Charles R. Brown

Academic Editor

PLOS ONE

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“This project was made possible by funding from the U.S. Fish and Wildlife Service and the Association of Field Ornithologists. V”

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Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

“This study was conducted with support from the U.S. Fish and Wildlife Service, Refuge System Inventory and Monitoring program through a Piedmont South Atlantic Coast Cooperative Ecosystems Studies Unit (http://www.cesu.psu.edu/unit_portals/PSAC_portal.htm) agreement to SBM (F19AC00629), and an E. Alexander Bergstrom Memorial Research Award from the Association of Field Ornithologists (https://afonet.org/grants-awards/bergstrom/) to EWJ. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”

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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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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. 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: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

**********

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: This paper is very well written and methodologically sound. It makes novel contributions and presents promising results regarding the use of pattern matching and statistical analyses to assess intra- vs inter-clutch variation in multi-year samples of eggs of two bird species. The discussion of results also describes how such analyses may lead to the detection of potential instances of conspecific brood parasitism, re-nests and return breeders without the need for genetic or more detailed observational studies.

Methodologically the paper is sound and generally easy to follow, although the sequence of steps described in some sections, such as "Spatial and temporal analysis of King Rail matching results", could in my opinion be more clearly, concisely and unambiguously conveyed by replacing or augmenting the prose with a diagram such as a flow chart or some pseudo-code.

Implementation decisions, such as "we used the top 8 matches", are justified in the text, but it would be good to conduct at least some rudimentary sensitivity analysis to determine whether the analyses that were performed are highly dependent on such choices. A little more analysis regarding the impact of confounding factors such as differences in photographic and image processing across the different years, as well as differences in sample sizes, would also have strengthened the assertions made in the paper.

Figures 3 and 4 are very useful in clarifying the spatial and pattern similarity linkages, but a few more detailed exemplars of matched egg images would have been helpful.

Reviewer #2: This is well-conceived research project about an interesting topic. It was cleverly and meticulously carried out, with both the methods and statistical analyses thoroughly described. The comparison between moorhens and rails added substantially to the authors arguments. My only suggestion is to explain symmetrical and non-symmetrical matching the first time it is mentioned in the text--it took me a couple of read-throughs to understand what that meant.

**********

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Reviewer #1: No

Reviewer #2: No

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Revision 1

Responses to reviews below

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

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https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

done

2. Thank you for stating the following in the Acknowledgments Section of your manuscript:

“This project was made possible by funding from the U.S. Fish and Wildlife Service and the Association of Field Ornithologists. V”

We note that you have provided funding information within the Acknowledgements Section. Please note that 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.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

“This study was conducted with support from the U.S. Fish and Wildlife Service, Refuge System Inventory and Monitoring program through a Piedmont South Atlantic Coast Cooperative Ecosystems Studies Unit (http://www.cesu.psu.edu/unit_portals/PSAC_portal.htm) agreement to SBM (F19AC00629), and an E. Alexander Bergstrom Memorial Research Award from the Association of Field Ornithologists (https://afonet.org/grants-awards/bergstrom/) to EWJ. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

We have removed the sentence in the Acknowledgments. We do not wish to amend the funding statement.

3. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide.

The full dataset can be found at https://doi.org/10.5061/dryad.6q573n60j

We have not yet received accession numbers from DataDryad because the datasets are still being reviewed by the curators. It was a challenge to get the revisions and data curation completed with my co-author over distance. It was a busy hybrid academic term for me, and we completed these revisions while Emily was translocating to a new position in the Florida Keys. We wanted to get the revisions back to you by the deadline, but I will send along the accession numbers as soon as they are available.

4. We note that you have included the phrase “unpublished data” in your manuscript. Unfortunately, this does not meet our data sharing requirements. P LOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

The reference ‘Clauser AJ, McRae SB. King Rails (Rallus elegans) vary building effort and nest height in relation to water level. Waterbirds. 2016;39(3): 268–76’ reports the nest predation rate over a 2-year period of study, which is representative of the population. We now include a reference to that paper. We have also replaced the citation of the thesis by C.L. Brackett and replaced it with other citations, because it is not available online.

5. We note that Figure 3 and 4 in your submission contain satellite images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

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:

a. You may seek permission from the original copyright holder of Figure 3 and 4 to publish the content specifically under the CC BY 4.0 license.

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

b. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

We only used open source maps. We have added language to the methods to clarify the origin of these maps. All imagery to create maps was accessed from the open access platform NOAA Data Access Viewer (https://coast.noaa.gov/dataviewer/#/) and the exact imagery file (2018 NOAA Ortho-rectified color Mosaic of Dismal Swamp and Albemarle and Chesapeake Canals, Virginia) name has been provided in the text, as well as the date the imagery file was originally downloaded by the authors (24 October 2019).

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.

N/A

[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?

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: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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

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: This paper is very well written and methodologically sound. It makes novel contributions and presents promising results regarding the use of pattern matching and statistical analyses to assess intra- vs inter-clutch variation in multi-year samples of eggs of two bird species. The discussion of results also describes how such analyses may lead to the detection of potential instances of conspecific brood parasitism, re-nests and return breeders without the need for genetic or more detailed observational studies.

Thank you!

Methodologically the paper is sound and generally easy to follow, although the sequence of steps described in some sections, such as "Spatial and temporal analysis of King Rail matching results", could in my opinion be more clearly, concisely and unambiguously conveyed by replacing or augmenting the prose with a diagram such as a flow chart or some pseudo-code.

We have added a flow chart (new Fig 2) to facilitate understanding of this section.

Implementation decisions, such as "we used the top 8 matches", are justified in the text, but it would be good to conduct at least some rudimentary sensitivity analysis to determine whether the analyses that were performed are highly dependent on such choices.

In our criteria for including nest pairs with non-symmetric matching, we examined the 8 top pattern matches for each egg due to that being the mean clutch size in the king rail population. We conducted a sensitivity analysis to determine how increasing the stringency by limiting the number of top matches further would have affected the results. When we reduced the number of top matches we included decrementally from 8 to 5, only one pair of clutches with matches that we inferred to be a returning breeder dropped out (N=65 clutches, 40 on the South side and 25 on the North side; table of results below). We have added a couple of sentences to the Results to explain this.

Number of top matches included Total (%) clutches with match % Returning breeder % CBP % Renesting

5 5 (7.7%) 1.5% 4.6% 1.5%

6 5 (7.7%) 1.5% 4.6% 1.5%

7 5 (7.7%) 1.5% 4.6% 1.5%

8 6 (9.2%) 3.1% 4.6% 1.5%

A little more analysis regarding the impact of confounding factors such as differences in photographic and image processing across the different years, as well as differences in sample sizes, would also have strengthened the assertions made in the paper.

Please see next answer.

Figures 3 and 4 are very useful in clarifying the spatial and pattern similarity linkages, but a few more detailed exemplars of matched egg images would have been helpful.

Thank you for the positive feedback. We have now also added a figure (Fig 3) illustrating three clutches of Common Moorhen eggs laid by the same female, showing multiple within-clutch best matches, as well as between-clutch matches within- and between years. This illustration and description helps to address the previous comment also in that it shows how eggs within the same photograph were more likely to have other eggs in the same clutch and photograph as their top matches. We have added an explanation of this in the text.

Reviewer #2: This is well-conceived research project about an interesting topic. It was cleverly and meticulously carried out, with both the methods and statistical analyses thoroughly described. The comparison between moorhens and rails added substantially to the authors arguments. My only suggestion is to explain symmetrical and non-symmetrical matching the first time it is mentioned in the text--it took me a couple of read-throughs to understand what that meant.

Thank you for your comments and for pointing out this omission. We have added some language earlier in the methods (lines 335 and 344) to explain symmetrical and non-symmetrical matching.

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.

Decision Letter - Charles R. Brown, Editor

Interclutch variability in egg characteristics in two species of rail: is maternal identity encoded in eggshell patterns?

PONE-D-21-28285R1

Dear Dr. McRae,

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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Sincerely,

Charles R. Brown

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Formally Accepted
Acceptance Letter - Charles R. Brown, Editor

PONE-D-21-28285R1

Interclutch variability in egg characteristics in two species of rail: Is maternal identity encoded in eggshell patterns?

Dear Dr. McRae:

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. Charles R. Brown

Academic Editor

PLOS ONE

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