PONE-D-20-23252

High diversity of highland papayas (Caricaceae, Vasconcellea) from northern Peru revealed by an integrative approach includes five new species

PLOS ONE

Dear Dr. Bustamante,

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 Nov 13 2020 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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We look forward to receiving your revised manuscript.

Kind regards,

Himanshu Sharma

Academic Editor

PLOS ONE

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Additional Editor Comments (if provided):

Dear authors,

I have read through your work in detail and after getting reviewer's comments and I consider the current manuscript a valuable addition which enrich the existing genetic resources in Highland Papayas. The work is good and worth publishable and I am more than sure that if authors answer all the queries raised by reviewers it will be valuable addition in Papaya reserach. I have found a some major flaws in the manuscript that needs to be readdressed and MS should be majorly revised . In it's current form the paper cannot be considered for publication in Plos one.

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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: Partly

Reviewer #3: Yes

Reviewer #4: Partly

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: 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: No

Reviewer #3: Yes

Reviewer #4: 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

Reviewer #3: Yes

Reviewer #4: 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 looks sound. Provide a better title. Few queries that needs to be addressed are:

It does not reveal much about the integrated approach. Modify the review and discussion portion giving some background of 6 molecular markers, their application in phylogeny of other plants. For diversity analysis more number of individuals using other markers such as RAPD, ISSR, SSR, AFLP etc. are more suitable. Its rather a phylogeny study rather than diversity.

Reviewer #2: The present manuscript reports the molecular diversity in Papayas from northern Peru and concluded that high molecular diversity is prevailing in the analyzed germplasm. Language and overall structure of manuscript is good. They also proposed five new species based on their molecular data analyses/ works. As far as diversity is concerned paper contain good information on papayas, however, taxonomically I have many doubts which need to be clarified before the publication of this article my major issues are:

1. You are proposing five new species in this article, my question is: have you authenticated your data from any institutions/organization of your country which deals with the data related to taxonomic entities like any Botanical Garden or Botanical surveys Institutes or any other international organization like Kew Botanical Garden?

2. Comments or reports of these type of organizations are required to assign/ publish these new species as different species?

Other minor issues:

1. Title is not clear please revise it.

2. Abstract should contain clear cut statements about the work done, so please revise abstract.

3. The dendrogram/ phylogenetic tree given in figure is not clear/ words are not readable so please replace this figure by clear one.

4. You have mentioned morphological traits in your integrative approach but you did not show any analysis derived from morphological traits such as dendrogram etc.

Reviewer #3: Reviewers' comments:

The manuscript entitled " High diversity of highland papayas (Caricaceae, Vasconcellea) from northern Peru revealed by an integrative approach includes five new species" is an worthy effort, and it could be a very useful resource in area of plant science. However, it need to be address few comments before acceptance.

Major comments

Comment#1: Authors should rewrite the abstract; first six line of abstract should be 3-4 line, remaining authors should write his major findings.

Comment#2: Few place the sentences are too long, which are not clear for example line 44 to 48; 54 to 57, and 73 to 76; authors should split these to get reader easily understand.

Comment#3: The Figures 2 quality is not clear; however, I appreciate for remaining figures. It is really nice.

Comment#4: Reference section is not uniform, kindly flow uniformity, For example 43, 44, and 45 (In few doi is missing).

Reviewer #4: In the manuscript entitled as “High diversity of highland papayas (Caricaceae, Vasconcellea) from northern Peru revealed by an integrative approach includes five new species” authors have utilized integrated approaches to classify known species of papayas and ascertain new ones.

The overall quality of the manuscript is acceptable for publication in this journal. However, the identification of new species in the manuscript is mainly determined on the bases different molecular methods using different markers (ITS, matK, psbA-trnH, rbcL, rpl20-prs12, trnL-trnF) whereas morphological data remains orphan.

The markers used in this study are not the representative of the entire genome and have shown discordant patterns (authors also agrees line no. 219-222, 230-233 and 242) that raises the questions on the correct identification of new species. Further, new identified species are not cryptic species; hence, it is essential to establish relationship between morphological and molecular data present in this study or go for chloroplast genome sequencing to support the outcome of the study.

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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: Abhishek Bhandawat

Reviewer #2: No

Reviewer #3: No

Reviewer #4: 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.

PONE-D-20-23252R1

An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru

PLOS ONE

Dear Dr. Danilo Bustamante 

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 Dec 07 2020 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:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Himanshu Sharma

Academic Editor

PLOS ONE

Additional Editor Comments (if provided):

The manuscript entitled PONE-D-20-23252R1 An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru has been extensively reviewed by all the reviewers and they agreed for the acceptance, but one reviewer has raised query that they have not provided the relationship of studied species on the basis of morphology in the form of deprogram which can provide additional evidence for the study and also some grammatical errors which needs to be corrected before the final approval.

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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 #1: All comments have been addressed

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

Reviewer #4: 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 #1: Yes

Reviewer #2: Partly

Reviewer #3: Yes

Reviewer #4: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: 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 #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

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 #1: Yes

Reviewer #2: No

Reviewer #3: Yes

Reviewer #4: 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 #1: (No Response)

Reviewer #2: Although, authors have addressed all the raised issues but still they have not provided the relationship of studied species on the basis of morphology in the form of deprogram which can provide additional evidence for the study. I also advise authors to revise and thoroughly examine the language of manuscript to avoid ambiguity and to make your story more specific and objective oriented. For example in conclusion : starting of conclusion is not relevant neither it contain concrete information of your work. in line 678 what do you mean by others? please also check entire manuscript for such type of use of words and be specific. After fixing these issues manuscript can be accepted.

Reviewer #3: The manuscript entitled "An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru" is now suitable for publication.

Reviewer #4: (No Response)

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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 #1: No

Reviewer #2: No

Reviewer #3: No

Reviewer #4: Yes: Pradeep Singh

[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.

An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru

PONE-D-20-23252R2

Dear Dr. Bustamante,

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,

Himanshu Sharma

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

After second revision of the manuscript "An integrative approach reveals five new species of highland papayas (Caricaceae, Vasconcellea) from northern Peru" the reviewer is agreed to accept the manuscript. The authors have satisfactory answered the all queries. So the manuscript will be accepted for publication after correcting any mistakes which can be corrected at the time of proofreads.

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

**********

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

**********

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

Reviewer #2: 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

**********

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

**********

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: The authors have revised the manuscript as per suggestions and have incorporated the changes where ever needed. It can be accepted in its present form.

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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