PONE-D-22-26701Understanding the genetic structure of two epiphytic orchids Pleurothallis lilijae and Masdevallia rosea in the montane forest, in southern EcuadorPLOS ONE

Dear Dr. Riofrío Guamán,

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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: Partly

Reviewer #2: Yes

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

Reviewer #1: No

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: No

Reviewer #2: No

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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: • In general, there are a lot of typographical and grammatical errors. Moreover authors should apply the right punctuation where necessary to enhance the understanding of the results.

• There are a lot of typographical and grammatical errors. Moreover authors should apply the right punctuation where necessary to enhance the understanding of the results.

• The analysis is not clear and robust enough

• The results and discussion are not extensive enough to reveal their genetic structure.

• Authors should provide the AMOVA results/table showing the % of variation among and within the populations

• Presenting the variance of the first 2 components under the PCoA analysis alone is not enough to discriminate the populations. The other components maybe significant as well.

Reviewer #2: This is an important study understanding the genetic diversity of orchids species Pleurothallis lilijae and Masdevallia rosea distributed in Andes of southern Ecuador. Author have not described the use and importance of these two orchids due to which these were illegally trade. Author have not described that why these two species of orchids are ecologically important to these mountains.

I have some queries regarding this manuscript as

Why there is much difference in the sample size taken for analysis in both two species?

In discussion portion, Seed dispersal method should be explained properly to understand the distribution of genetic groups of the population.

There are some sequential gaps in this manuscript which stops the reader to understand the manuscript properly. Improvement should be made in writing and filling the story gaps with valid interpretation with results to make this paper more interesting. I hope the Authors will take the above suggestion seriously and improve the manuscript.

Some of the mistakes and queries which should be taken care of are

1. Line 68 annual mean temperature is not provided for this site

2. Line 78 Species spelling mistake

3. Line 99 Not clear from the topic how many samples for each species taken for AFLP

4. Line 186 lilijae in italics

5. In Bidimensional plot of PCoA for Masdevallia rosea POP 4 Population seems to be different from POP1 and POP2

6. What are the anthropogenic factors due to which these species are threatened and should be conserved in-situ and ex-situ

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Reviewer #1: No

Reviewer #2: Yes: Dr. Vikrant Jaryan

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Attachments

Attachment

Submitted filename: PONE-D-22-26701reviewed.pdf

Genetic diversity and structure in two epiphytic orchids from the montane forests of southern Ecuador: the role of overcollection on Masdevallia rosea in comparison with the widespread Pleurothallis lilijae

PONE-D-22-26701R1

Dear Dr. Riofrío Guamán,

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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Kind regards,

Mehdi Rahimi, 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 #1: All comments have been addressed

Reviewer #2: 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: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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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

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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 #1: Yes

Reviewer #2: Yes

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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: Authors have adequately addressed all my comments raised in the previous review. I therefore recommend the manuscript acceptable for publication

Reviewer #2: The manuscript is highly improved and author has gone through all the queries raised by the reviewer. I have found that the English in the manuscript is improved and now the manuscript has come in the sequence of order to understand the study. But author has not described the type of pollination occurred in these orchids? Author is advised to write the conclusion separately so that reader can understand the outcome of the study. The plant species should be identified properly and should have authenticated from some recognized herbarium. Despite these, I found there are some mistakes which should be taken care of by the author are as following

Line no. 61-63.

For its size, Ecuador has the highest rate of deforestation in South America [15,16], as a consequence of land clearing for agricultural lands, mining, and new infrastructures [17].

Reframe this sentence.. As per its size, Ecuador has the highest rate of deforestation in South America due to regular anthropogenic activities like land clearing for agriculture lands, mining, and development of new infrastructure.

Line 63

These activities have caused the habitat destruction and fragmentation of the tropical forest

Line 93-94

P. lilijae in italics, M. rosea in italics

Line 130-131.

AFLP reactions were performed following the procedure of [23] with the following minor modifications

Sentence is incomplete. Procedure of what

Line 170-171.

Following the suggestions of [25], a simple matching coefficient was used to calculate the distance matrix.

Sentence is incomplete

Line 192-193

The spatial genetic structure of each species was assessed using the spatial autocorrelation method proposed by [31]

The sentence is incomplete

Line 199-200

Genetic distances between individuals were calculated using the method of [32]

Sentence is incomplete

Line 205

100 m

Line 205-209

The sentence is not clear. Reframe the sentence. You can split the sentence into two.

Line 320-322

Likewise, the threatened Cypripedium japonicum [37], Laelia rubescens [38], Laelia speciosa [39], Brassavola nodosa [40] or Neofinetia falcata [41] species also showed low genetic diversity values [42]

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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: Yes: Dr. Vikrant Jaryan, Associate Professor, Sant Baba Bhag Singh University, Jalandhar

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