PONE-D-20-05030

The role of ecological niche evolution on speciation patterns of birds  distinctly distributed between the Amazonia and Atlantic Rainforests

PLOS ONE

Dear Mr. Silva,

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.

The manuscript is very interesting. I received one review and the referee shared this opinion, but found some major aspects that require reconsideration, such foundation of hypotheses, poorly described methods and sometimes a speculative discussion. Moreover, the text sections in part need better connection and the language might need revision by a native speaker. For detailed comments please see below. I agree with the critics raised by the referee why the decision was 'major revision'.

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We look forward to receiving your revised manuscript.

Kind regards,

Stefan Lötters

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: Partly

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

Reviewer #1: 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

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

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Reviewer #1: 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: This manuscript investigates whether birds with disjunct distribution in the Amazon and Atlantic forests exhibit either niche conservatism or niche divergence. Authors gathered occurrence data of 37 bird species and built ecological niche models to infer if there is niche overlap between isolated populations in Amazon and Atlantic forests. Despite it has an interesting study question, the manuscript missed foundations of hypotheses. Methods were properly applied. However, authors should consider include Amazon and Atlantic forest in a single model (see below). Sometimes I found discussion very speculative with absence of a properly rejection or acceptance of presented hypotheses in the introduction. The text missed cohesion among subsections. The language needs work. The paper needs a major English language revision by a native speaker. Below, I outlined specific comments:

INTRODUCTION

- I missed a paragraph presenting theoretical basis of niche evolution. Authors gave much focus on Amazon and Atlantic forest disjunction.

- Line 36: you missed Pleistocene.

- Line 45: something is missing between population and species.

- Line 52: authors said “This dynamic may have had some effect on species' niche”. But “some” is vague. You should be more specific.

- Lines 56-58: who said this? Include the reference.

- The arguments presented in introduction did not allow to comprehend why authors evaluated niche overlap of disjunct populations of birds in Amazon and Atlantic forests. Why does check for niche overlap matter? I recommend authors do a better job in reviewing theoretical basis of niche evolution. Then, they will be able indicate why is important check niche overlap for these birds.

- Lines 87-91: Here authors tried to present the study hypotheses (I could not understand the second hypothesis, sentence need to be rewrite). However, it was poor explored. Authors should do a better job in presenting theories that support such hypotheses. In addition, they must present expectations of their hypotheses according to methods they area applying. Then, the readers will be able tom comprehend which hypothesis will be accepted.

MATERIAL AND METHODS

I found methods well written. Sometimes it seems that was wrote for a different person that produced the manuscript.

- Why did the authors only use temperature and precipitation data from Bioclim to infer the niche of species? Why do not include other variables, such as vegetation cover (e.g. EVI: https://www.earthenv.org/), solar radiation, wind speed, water vapor pressure (they are available at the new worldclim version https://www.worldclim.org/data/worldclim21.html), etc?

RESULTS

- why did model Amazon and Atlantic forest separately? As there is evidence of niche conservatism due to a recent divergence, it is better to build a single model for both biomes. Then they can split Amazon and Atlantic Forest after build the models and infer niche overlap. Otherwise, if they decide to maintain their original procedure a convincing justification must be presented.

- I am thinking if the niche overlap result observed in most species would not be biased by modeling Amazon and Atlantic forest separately. Ecological niche models for most species recovered the distribution in Amazon when modelling Atlantic Forest, or vice-versa (as seen in figure 2). However, if the authors aim to infer niche overlap between disjunct populations in these two forests, the niche inferred by Atlantic Forest populations must not include areas in Amazon, because species cannot disperse into that, despite similarities in temperature and precipitation. The opposite happens for Amazon populations.

- I missed a figure and/or table that summarize/combine the niche overlap of all species. I could not find the D values of each species comparison. Maybe include a graph with D values for each species. It will provide an easier way to observe a general pattern in your results.

DISCUSSION

- I found some parts of discussion quite confuse and not linked to the results. In lines 267-271, authors said that found niche overlap, but in results they said that species presented low niche overlap (Schoener's D values below 0.4) (lines 248-249). I cannot follow this, it is very confused.

- lines 280-282: how many was predicted? in how many species?

- lines 287-289: again, different from results in lines 248-249.

- lines 316-326: It is quite speculative. Authors can analyze the genetic data available for some species to check this. Otherwise, they must consider remove this from the text.

- Lines 327: it is also in Pliocene.

- Lines 349-351: I did not understand. If they have subspecies one would expect exactly no niche overlap.

- lines 395: You did not measure phylogenetic diversity.

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Reviewer #1: No

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PONE-D-20-05030R1

The role of ecological niche evolution on speciation patterns of birds  distinctly distributed between the Amazonia and Atlantic Rainforests

PLOS ONE

Dear Dr. Silva,

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.

Thanks for improving your paper. The (same) referee is satisfied, so am I. there are a few minor things left, as raised by the referee. Please consider them accordingly and submit your revised manuscript by Sep 27 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,

Stefan Lötters

Academic Editor

PLOS ONE

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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

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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

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

Reviewer #1: 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

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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

**********

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 made a very good job in reviewing the manuscript. This new version is substantially improved. I am satisfied with modifications and author’s responses. I have some minor comments:

TITLE: change the word "speciation" to "diversification" as most of isolated populations on both biomes are not ranked as distinct species.

Lines 26-28: This statement was proposed by classical papers, instead these new ones. Please correct the citation including Haffer (1969) and Brown & Ab’Saber (1979).

Lines 194-197: Why do the authors choose these thresholds? It is better use commonly used values from previous studies, than arbitrary values.

Line 233: correct is 0.05.

Lines 247-248: Actually, your results indicate both niche divergence and conservatism. You should put in evidence both scenarios, as evidenced in your results.

Lines 257-258: what do you mean with "considered evolutionary time"? We might expect recent splits for most co-distributed species in both biomes, due to lack of phenotypic divergence.

Line 259: which phylogeographic studies?

Lines 301-302: include Ledo and Coli (2017) and Batalha-Filho et al (2013) in the citations, as they properly showed this hypothesis.

References:

Batalha-Filho H, Fjeldså J, Fabre P-H, et al (2013) Connections between the Atlantic and the Amazonian forest avifaunas represent distinct historical events. J Ornithol 154:41–50.

Brown, K.S., Ab’Saber, A.N., 1979. Ice-ages forest refuges and evolution in the Neotropics: correlation of paleoclimatological, geomorphological, and pedological data with modern biological endemism. Paleoclimas 5, 1–30.

Haffer, J., 1969. Speciation in Amazonian forest birds. Science 165, 131–137.

Ledo, RMD, Colli, GR. The historical connections between the Amazon and the Atlantic Forest revisited. J Biogeogr. 2017; 44: 2551– 2563.

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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.

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Reviewer #1: No

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The role of ecological niche evolution on diversification  patterns of birds distinctly distributed between the Amazonia and Atlantic Rainforests

PONE-D-20-05030R2

Dear Dr. Silva,

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,

Stefan Lötters

Academic Editor

PLOS ONE

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