PONE-D-20-39886

Experimental warming influences species abundances in a Drosophila host community through direct effects on species performance rather than altered competition and parasitism

PLOS ONE

Dear Dr. THIERRY,

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.

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Dear authors, I have received the reviewers' revision of the manuscript, and overall they considered it an essential and novel experimental contribution to the subject species interaction and climate warming. Further, the results shed light on the mechanism describing direct and indirect effects on communities' structure and function under climate variance. Reviewers' primary concern, and mine, point out difficulties to follow the Methods section raising many questions to be clarified by the authors. Besides, provide details - i.e., which institution approved and protocol number if it was the case -  about species entrance in the country.

Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process by 27th February.

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Please submit your revised manuscript by Feb 28 2021 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,

Lucas D. B. Faria

Academic Editor

PLOS ONE

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Additional Editor Comments:

Despite some issues in the Methods section, the manuscript can be accepted under minor revision by the authors.

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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: 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: This manuscript details the results of a laboratory experiment testing whether climate warming, species interactions (intraspecific competition, interspecific competition, and parasitism), or their interaction affect 3-species tropical Drosophila communities. The manuscript is mostly well-written (aside from parts of the Methods) and is skillfully couched in terms of pertinent larger questions and the literature. The experiment appears to have been carried out using sound methods, and analyzed and presented appropriately. The results should be interesting and useful to a broad audience interested in effects of climate warming on ecological communities. My main concern is that the methods – especially relating to the experimental design – are not explained as clearly as they could be. However, this should require a relatively minor revision. I have several other concerns below, all of which are minor as well. I feel confident that upon revision, this manuscript should represent a very useful contribution to understanding of ecology and global change.

Introduction:

• Lines 56-57: clarify: evidence for what exactly is lacking?

• In the part of the paragraph following that sentence, as well as in lines 77-82, it is a little difficult to follow the flow. Transitions may help.

• Last paragraph is a confusing. Clarify what is measured and why. First sentence makes it seem like you just focus on relative abundance, but the next sentence mentions body mass without fully explaining how it fits in. Clarify predictions – that sentence is confusing. Should also be more clear about what was done, i.e. overview of the experimental design.

• Lines 95-97: seems out of place at the end of the introduction.

Methods:

• Line 103: cultures were established in both 2017 and 2018? clarify.

• Lines 105-106: clarify “together accounting for ~48% of the host communities as the study sites.” Those species comprised 48% of fly individuals across the sites? Or some other meaning?

• Lines 110-112: remember to remove this note

• Why was care taken to ensure genetic diversity in the Drosophila but not in the parasitoids?

• Line 131: 15 cm diameter holes would take up half the box – should read 15 mm?

• Line 136: I take it that the adult flies were then removed after 48 hours and before the parasitoids were added – but this should be stated to clarify.

• Lines 148-149: sentence seems out of place – could be moved to earlier in the paragraph

• Figure 1 should be altered to more accurately represent experimental design. E.g. if adult flies and parasitoids were not present at the same time, don’t show them together. Also, no larvae are shown. Perhaps just show larvae instead of adult flies.

• Lines 151-152: what does this mean – that the experiment was ended when both flies and parasitoids emerged? How long was this? But next sentence (last sentence of paragraph) seems to imply the experiment was only one day – do you mean that each block was started a day apart but then ran for many days?

• First Experimental design paragraph is confusing as methods are presented out of order. It is not easy to understand what was done. Also there is at least one important hole in the methods: how long after introducing the adult flies were the parasitoids introduced?

• Lines 163-166: clarify how this projected temperature falls among climate warming scenarios, e.g. mid-range for 2100?

• What was the experimental design of the temperature treatments, i.e. were two of the time blocks warm and two normal?

• Lines 183-185: Move this justification for looking at body mass to the introduction.

• Line 188: Since D. sulfu. represented all the “failures,” and there were many, this should be pointed out in the text, not just in the supplemental info. Relatedly, might this impact the conclusions? Maybe address this in the discussion.

• Lines 198: remove “ANOVA.” Likelihood ratio tests and the “anova()” command in R have nothing to do with ANOVA (confusingly).

• Include overview of the fly species’ thermal performances rather than just citing the papers.

Results:

• Table 1 & Table S3: Remove “ANOVA,” since you ran GLMs, not ANOVAs.

• Include line numbers in second half of ms.

• “Direct effect of warming” paragraph: also mention the third species. 4th sentence: clarify rel. abundances changed from which treatment to which treatment?

• Figures are blurry – provide high definition versions.

• Fig. 3: include the shapes/species in the legend(s), rather than in the caption.

• Last part of the final sentence in the Results sounds more like discussion.

Discussion:

• First paragraph: first sentence sounds a bit general – include study species/system. Include more in this paragraph: especially, competition.

• Towards the end of second paragraph: a bit confusing that you say D. pseudoananassae did not have the highest thermal tolerance in the paper but did in this experiment. Why mention the first part about the other study?

• The claim that climate change will affect tropical communities more severely needs to be backed up with a citation.

• Last sentence should be moved to earlier in the discussion.

References:

Need to be edited.

Reviewer #2: Thierry et al. performed a community-level experiment to understand the direct and indirect effects of warming on host species. They found that warming directly affect the abundance of host species and decrease parasitism rates for host-parasitoid pairs. Besides, the top-down control was still maintained by the presence of parasitoids decreasing host abundance regardless of the temperature. They conclude that the warming had a direct effect on host community structure through differences in host thermal performance but not via biotic interactions (competition and parasitism).

The manuscript is well written and makes novel contributions to a topic underexplored in the literature because it access the impact of warming on a community-wide system incorporating direct and indirect effects. Although the experiment was conducted over a single host generation, the results shed a light on how the direct and indirect effects could play a role in structuring a host community under warming conditions.

Detailed comments as follows:

Abstract:

line 23: Would it be more clear to use global climate change instead of global change?

line 30: it may be more clear if authors specify what metric was used when saying ‘host communities’. E.g host species abundance and frequency

Introduction: overall, really well written and provide a good context for the predictions stated at the end of this section.

Lines 88 - 91: If possible, I would rephrase the prediction for clarity. e.g We tested the predictions that the elevated temperature will affect the relative abundance of the host directly through the thermal performance of the species, and indirectly through effects on their interactions such as hosts competitive abilities and parasitoids virulence.

Throughout the manuscript, you use the terms: attack rates, parasitoid virulence, parasitism (yes or not) and parasitism rates (host-parasitoid species pair). I think the manuscript would benefit from explaining or deleting some of these terms. For example: I think it would be clearer if you could specify in the manuscript what do you consider as the parasitoid virulence metric? Is it the parasitism rates, the ‘yes or no parasitism’, both or none? In the Line 92 the word ‘parasitism’ refers to: ‘yes or no parasitism’ or to ‘parasitism rates (host-parasitoid species pair)’?. Please, could you rephrase the sentence in lines 92 – 93 (…while the effects on parasitism will be linked to effects of temperature on parasitoid attack rate and virulence.) for clarity?

Methods:

Line 116: what do you mean by revive genetic variation? Would it be to ensure or to rescue?

Lines 133 – 135: the single species and multiple species treatments were only for hosts right? The parasitoid-host species interaction was a sample from the single and multiple host species treatment, right? In these lines I would add ‘single-host species’ and ‘multiple-host species’ for clarity.

Line 160: In figure 1 legend we read ‘c)parasitism only’. However this treatment also includes host intraspecific competition according to what it is showing in Figure1, right? I would then change this label.

In Figure1: I think it would be more informative if you could add a dashed line (or indicate somehow) the intraspecific competition in letter a and c. Besides, in the mixed-species treatment do you think that intraspecific competition could also have happened together with the interspecific competition? If yes, do you think intraspecific could have been stronger than interspecific competition in these mixed-species treatments (figure 1 letter b and d)?

In Line 171 ‘the sampled pupae were identified to their corresponding host species’, how was it done? Do the Drosophila species have visually different pupal case? Was it how you link a parasitoid to a host species to calculate parasitism rates?

Line 176: I would make it more clear here that the parasitism rates was calculated for each host-parasitoid pair.

Line 182 we read ‘second generation started’, does it mean the F1 offspring? Are you counting the Parental generation as first?

Line 186: you mean fully-ecloded?

Results:

Line 213: do you mean host frequencies instead of host proportions?

In Figure 3 legend: in letter ‘b’ we read: (b) Parasitism was reduced at higher temperature. Do you mean here parasitism rates? In your manuscript I separate parasitism as ’yes or no’ and parasitism rates as ‘the host-parasitoid pair.’

In Figure 2 legend: do you refer to ‘proportion’ as the host frequency?

Discussion:

Below I apologize for not indicating the line number that I’m referring to. It happened because the number of the lines is not appearing in my pdf version.

In the third paragraph of the discussion you have: ‘However, presence of parasitoids significantly decreased... parasitoid virulence’. It would be more clear if there is a following up sentence to better explain this sentence and the decrease in virulence. For example, why parasitoids would decrease virulence with increasing temperature?

The idea that warming decreased parasitism rates, but did not impact the effect of the presence of parasitoid in decreasing host abundance, could be better explored in the discussion. For example, although parasitoid preference for host species was not quantified, Lavandero and Tylianakis et al 2013 shows that genetically similar parasitoids become more likely to attack genetically similar hosts in warmer sites. Therefore, there could be a shift in the parasitoid preference for a host species or even for a narrower subset of host species that would decrease parasitism rates (host-parasitoid pair) due to parasitoid competition under warming conditions.

In the fourth paragraph, fourth line we read: ‘…allowed us to detect their effects on host species relative abundances if they were any.’ Should the word ‘they’ be ‘there’?

In the last paragraph for the discussion we read: ‘The role of parasitoids as essential… after several generations’. What do you mean by suggesting that the indirect effects of the temperature on the host community through parasitism could be observed after several generations?

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Reviewer #1: No

Reviewer #2: No

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PONE-D-20-39886R1

Experimental warming influences species abundances in a Drosophila host community through direct effects on species performance rather than altered competition and parasitism

PLOS ONE

Dear Dr. THIERRY,

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 Mar 13 2021 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,

Lucas D. B. Faria

Academic Editor

PLOS ONE

Additional Editor Comments (if provided):

Dear THIERRY, M. and authors

I have gone through the revised manuscript. Comments raised by the reviewers were responded by the authors ok. However, I still have doubts about figures (2, 3 and S7) and statistical tests.

Line 227 points out the existence of Tukey's post hoc test, however, I could not find through the text or at the figures any reference to it. Please confirm it and add the information or remove it from the text.

Figure 2, 3 and S7 labels ascribe (The small points represent the values from each block and each host-parasitoid pair, the large points represent the grand mean, and the bars represent standard errors of the means). However, I could no find a difference between point sizes. Please confirm it and add the information or remove it from the text.

Figure 3(b) label legends species as follow (□: Asobara sp. - D. pseudoananassae, ˄: Asobara sp. - D. birchii, +: Asobara sp. - D. sulfurigaster, × Leptopilina sp. - D. pseudoananassae, ◊: Leptopilina sp. - D. birchii, ˅: Leptopilina sp. - D. sulfurigaster). However, figure did not shows it. Please add it to the figure.

Tables 2 and S5 labels are quite similar (difference consist only "...for the whole dataset". Please explain the difference between them - by means of the whole dataset - in the S5 label so readers could follow the authors' idea easily. Further and regarding to F-values legend [F-values are presented with the significance of the effect: (***) P < 0.001, (**) P < 0.01, (*) P < 0.05, (.) P < 0.1, (ns) P > 0.05"] - I understand that p-values greater than 0.05 are non-significative, so "(.) P < 0.1" does not make sense to me, and I am asking to avoid it, even though R model summary gives it. Then change it at the tables (.) to (ns).

Kind regards

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[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.

Experimental warming influences species abundances in a Drosophila host community through direct effects on species performance rather than altered competition and parasitism

PONE-D-20-39886R2

Dear Dr. THIERRY,

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,

Lucas D. B. Faria

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

I have gone through the revised manuscript (R2) and I am satisfied with the changes. So I am pleased to say that the manuscript is accepted to be published in Plos One Journal.

Congratulations and kind regards

Reviewers' comments: