PONE-D-21-11736

Olive fruit fly and its obligate symbiont Candidatus Erwinia dacicola: two new symbiont haplotypes in the Mediterranean basin

PLOS ONE

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Nikos T Papadopoulos

Academic Editor

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: Yes

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

Reviewer #1: Yes

Reviewer #2: I Don't Know

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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

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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 author followed a holistic approach combining data from both the host and the endosymbiont. Interestingly two new 16S haplotypes regarding the Candidatus Erwnia dacicola were detected for the Tunisian olive fly populations, which is the major finding of the manuscript, adding valuable data in the existing findings regarding the endosymbiont genetic variability.

There is also an interesting overall commentary regarding the olive fly population diversity and coevolution with the symbiont.

Generally, the manuscript is well written and structured employing a wide list of genomic tools and approaches. There is a main disadvantage regarding the microsatellites part with a restricted number of flies used for the analysis in order to have a reliable estimation. Author has explained the reason behind this and therefore assumptions based on microsatellites throughout the text are minimum.

There is a short list of minor issues that I would like to be addressed through a revised version of the manuscript:

A supplemental list with the primers/probes used would be beneficial for the reader.

Please do not use “e.g.” for citing references within the text.

Line 87-88: “These changes will lead to species specific dynamics with impact on the interaction of the olive and its obligate olive fruit fly”. This is a strong statement and it should be followed by a list of relevant references.

Line 249: “following the parsimony” please explain the meaning here and if necessary add references to support it.

Line 270: correct “this bacteria was found”

Line 287: “uniquely exploit this resource” where do you refer by “resource”?

Line 287: please correct “all data suggests” to “all data suggest”.

Reviewer #2: PONE-D-21-11736: Olive fruit fly and its obligate symbiont Candidatus Erwinia dacicola: two new symbiont haplotypes in the Mediterranean basin

This paper identifies two new haplotypes of the olive fly symbiont, Ca. Erwinia dacicola, found to be uniquely associated with flies from Tunisia, and significantly different from previously described haplotypes associated with samples from Europe. These findings contrast analyses based on genomic and mitochondrial markers suggesting that the populations sampled from Africa and Europe cluster with no clear association to their geographic location. The main conclusion is that since the symbiont is vertically transmitted and essential to its host the new bacterial linages may contribute to understanding the dispersion patterns and population diversity of the fly.

The paper is well written but please note that there are many remaining typos, syntax and parsing issues which need to be attended. From the perspective of my field of expertise I have only a few comments, mostly concerning topics addressed in the results and discussion.

Please make sure that the sequencing data underlying the findings will be made publically available (I couldn’t find a note on this in the manuscript).

Introduction:

Page 4, Lines 83-84 and 222-224 (discussion): please state the hypotheses of this study in the introduction as well.

Results:

1. Figure 1 depicts the median-joining network of haplotypes derived from mitochondrial DNA analysis. In addition to the populations sampled in this study (9 locations), other flies seem to have been included in the analysis (e.g. H, GU, orange coded), which do not seem to be mentioned in the text. Please include a description of these samples. Mont = MON?

2. In Figure 2 the color codes for Montpelier and Bouficha seem to have been mixed (they do not match those in figure 1). Should there be a representation of the orange-coded cluster as well (as in figure 1)?

3. The STRUCTURE analysis and figure 3: this is a bit confusing. Should the microsatellite-based dendogram depict two clusters (as currently presented) or only one cluster? Please include a short clarification for readers which are unfamiliar with the technicalities of this specific test.

Discussion:

The discussion addresses several issues but is currently presented as one continuous mass of text. I suggest to divide the text into clear sections complying with the addressed subjects.

Lines 245 – 248: according to file S3, flies sampled from Tunisia (and other locations as well) can be associated with either one of the 4 identified symbiont haplotypes. Two points which might be considered to be included in the discussion: (1) Can the above be congruent with these two hypotheses?, and (2) can certain fly genotypes (e.g. mitochondrial haplotypes) be more prone to be associated with a certain bacterial haplotype?

Line 268: I would separate the evolution of Erwinia into an obligate symbiont from the domestication of the olive. The transition into an obligate symbiont probably occurred far into the evolutionary history of the fly, and is not associated with recent human activity.

Lines 269 – 273: another possible explanation contributing to retention of genome size of the Erwinia symbiont: it is a gut bacterium, and as such it remains exposed to transient bacteria which are ingested with the diet (probably mainly at the adult stage), and thus, to horizontal gene transfer. The composition of the gut microbiome of this fly suggest that bacteria other than the Erwinia symbiont (e.g. free living Enterobacter spp.) are intermittently associated with the fly and may contribute to DNA exchange.

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: PONE-D-21-11736.pdf

Olive fruit fly and its obligate symbiont Candidatus Erwinia dacicola: two new symbiont haplotypes in the Mediterranean basin

PONE-D-21-11736R1

Dear Dr. Nobre,

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,

Nikos T Papadopoulos

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

There is need for careful editing especially in references cited. Italics should be used for all scientific names provided

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: (No Response)

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

Reviewer #1: Yes

Reviewer #2: (No Response)

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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: (No Response)

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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: (No Response)

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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: The author addressed all my comments therefore I fully support the publication of the current manuscript.

Reviewer #2: (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

Attachments

Attachment

Submitted filename: PONE-D-21-11736_R1.pdf