PONE-D-20-00793

RapidRat: development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management

PLOS ONE

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Daniel de Paiva Silva, Ph.D.

Academic Editor

PLOS ONE

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1. Thank you for including the following ethics statement:

'All sample collection was performed under Parks Canada Agency Animal Care Committee protocol GHNPR11-5. Parks Canada is the regulatory agency that permits

field research in the study area and were the sole participants involved in sample collection.'

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4.

Additional Editor Comments (if provided):

Dear Mr. Russello,

after carefull reviews by two independent researchers, they found that your manuscript is nearly to be accepted. Nonetheless, they suggested that minor reviews are performed before it is formally accepted in the journal, especially reviewer #2, who provided some suggetions in an attached file. Therefore, considering the whole COVID-19 pandemic, I hope you are able to provide a reviewed version of the manuscript by June 30th 2020.

Best regards,

Daniel Silva

[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

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

Reviewer #1: Yes

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: Yes

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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: The paper presents novelty and describes the way the authors obtained genomic data to evalute invasive species. The authors developed, validated and deployed an effective and efficient genotyping tool (RapidRat) for informing invasive rat management in Haida Gwaii.

To improve the paper I recomend:

a) Make the results clear in the abstract section

b) Introduction and material and methods: are Ok.

c) Results: ok

d) Discussion and conclusions: Improve them to clarify the novelty, importance and the limitations of such research

Reviewer #2: The manuscript entitled “RapidRat: development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management” describes the development of a rat specific panel for genomic data to access information about invasive species of rats in an archipelago in British Columbia, Canada. The authors proposed a novel and cheaper way to genotype individuals of brown and black rats using the detection of SNPs polymorphisms to track novel and old rat invasions in the islands. I recommend this manuscript to be accepted for publication in PlosOne after the review of the suggestions pointed out in the attached file.

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: Review.docx

RapidRat: development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management

PONE-D-20-00793R1

Dear Dr. Russello,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

Daniel de Paiva Silva, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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: All comments have been addressed

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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

**********

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

Reviewer #2: Yes

Reviewer #3: Yes

**********

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: Yes

Reviewer #3: No

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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

**********

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: (No Response)

Reviewer #3: This article deals with the development of a panel of SNPs in a genotyping-by-sequencing strategy (GT-seq) and its possible application in the management of invasive species of rats in Canada. A review round has already been carried out. Although the authors have made a substantial improvement in the manuscript, I recommend some minor adjustments before being accepted for publication in PlosOne.

Introduction: ok

Material and Methods:

1) Information about the ddRAD-seq sequencing data is missing. Which sequencing platform was used to generate this data? How many RAD-tags were generated? What type of sequencing read was generated? Is this data deposited in a database? What is the mean read length? The RAD-tags represent which portion of the total size of the genome used as a reference?

2) I believe that "Study design" is not a good topic name for methods (line 131). Something like "origin of SNPs" or "SNP loci information from ddRAD-Seq" is perhaps more appropriate. After all, the other topics of the methodology are also part of the "study design".

Results: Ok

Discussion: Ok

Conclusion: Ok

Figures and tables:

As mentioned by reviewer # 2 in the previous review, the figures are still in low resolution.

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7. 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 #2: No

Reviewer #3: Yes: Rhewter Nunes