PONE-D-19-33906

Pre-colonial Amerindian legacies in forest composition of southern Brazil

PLOS ONE

Dear Dr. Pereira Cruz,

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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André Jasper, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

Dear Dr. Pereira-Cruz,

After carefully read you manuscript and both reviews opinion, I’m sending it back to you with some comments to be considered and included, if it seems relevant to you.

Both reviewers agree that this is a very interesting and original manuscript that should ultimately be published in Plos One.

Although the reviews are not conflicting, I agree with Rev #1 that a few issues must be attended before the manuscript can be accepted.

So, I kindly ask that you consider the suggestions made by Rev. #1 and do some effort to attend it.

If you do not agree with any of the suggestions made, you must justify it in accordance to Plos One editorial managing policies.

I’m looking forward to getting your revised version as soon as possible so that we can proceed with the evaluation process.

With kind regards,

André

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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: I Don't Know

Reviewer #2: N/A

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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 is a very interesting and original research on historical ecology carried out in Santa Catarina State in Brazil. The paper is fairly well organised, the topic is very important and deserves to be published. The Introduction is well-written and interesting.

However, in other part the text is sometimes not so clear and there are paragraphs that should be read again to become easy understandable.

As a general advice, I suggest to consider some aspects to be incorporated in the paper:

a) The chronological framework and diachronical succession of events seems to me not discussed; please, consider that the international audience can be not informed about what means ‘pre-colonial’ – and when the change from the hunter-gatherer to Neolithic culture (transitions or migrations?) had occurred in Brazilian regions.

b) The demography datum is missed. One should consider that the number of people changed during the different chrono-cultural phases, and therefore when you mention 11,500 BP hunter-gatherers, were they fewer or had a similar impact than the more recent human groups?

c) Are there known differences in the cultural choices (environmental-dependent?) of the human groups involved in the research? (probably they are evident from the Fig. 6 ) Or the differences are also linked to the changes of one culture along the changing millennia?

Line 36 = Araucaria can be added to the keywords

Lines 68-69 = how long is this ‘long-term’ history? It emerges from the next paragraph that it is about 11,500 years long. Therefore, a more precise chronology can be added, such as changing “identifying many archaeological sites” to “identifying many Holocene archaeological sites”, or something similar.

Line 103 = “humans are cultural niche constructors” = this statement is absolutely sharable and there is a general consensus on this vision, as well as “different cultural groups also leave differing floristic composition legacies” = please note, the presence of archaeological sites and archaeological/archaeobotanical findings is mandatory to infer the type of land use. Further information can be obtained from the ethnobotanical review, as in the discussion of this paper.

Line 244 = the first part of the discussion is well centred on geographical and geomorphological characteristics that can explain the observed results and trends. However, the timeline variable – chronology of archaeological sites/events is not reported in the following paragraphs.

Line 253 = ‘Alternatively, the species could’ = Alternatively, the plant species could

Line 255 = as an example on the need of chronological details, in the sentence “Amerindians intentionally cleared the land and used fire to produce crops,”, you should add the culture and/or Holocene period or millennia BP.

Line 264 = “may have involved selective extraction of species for fuel” = is this a speculative argument or can you make an example from a case study?

Lines 279-310 = This is an interesting ethnobotanical part of the text but it is not clear in which order the plants/uses are discussed, and why they are listed.

Line 285 = phytolits in pottery could suggest consumption or, preferably, are they evidence of plant processing?

Line 385 = practical

Citations 31. 32, 33, 77 = put ‘Aracauria’ in italics

Citation 37, 55 = check the format

Fig. 6 = it is an interesting figure (please, quote it in the text) but I am not sure that it is sufficiently clear the sense and aim of this ‘separation of plant species’ – Cultural? Phytogeographical? Current or past different exploitation? The full name of species should be preferred to the abbreviation of the genus, if possible.

Reviewer #2: The article PONE-D-19-33906 “Pre-colonial Amerindian legacies in forest composition of southern Brazil” presents the analyzes on patterns of occupations and settlements of ancient societies in Brazilian lands. The evidence left by Amerindian societies (especially Southern-Jê and Guarani) is persistent in forests around the world. This research presents some important results about how these societies have affected and managed over time the forest structure in southern Brazil. The investigation allows to evaluate the tree composition of forest fragments and the corresponding environmental variables in the state of Santa Catarina. Archaeological data were used to understand ecological niche models thinking of prediction models. The amount of inventory studied is quite significant. The methodology used is correct and can be an excellent tool for further studies. It is noteworthy that the settlements and sites of these follow the pattern already studied since the 1960s by American and Brazilian archaeologists. Which serves as confirmation of some procedural models. As for the results and analyzes on the floristic composition of forest remnants and the relationship of the distribution of ancient Amerindian groups and the species associated with each group, the sites demonstrate the patterns of occupation at altitudes and reliefs already highlighted in other classical studies of Brazilian archaeology. Structurally the manuscript is in accordance with a scientific text following the ethical and methodological rigors. The bibliography is up to date and of excellent quality. The manuscript deserves to be published and will bring important contributions to current studies on ecological and environmental history in southern Brazil, still ephemeral in archaeological studies.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-19-33906R1

Pre-colonial Amerindian legacies in forest composition of southern Brazil

PLOS ONE

Dear Dr. Pereira-Cruz,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it only a few changes are necessary that your manuscript can be accepted for publication in PLOS ONE. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

We would appreciate receiving your revised manuscript by Jun 22 2020 11:59PM. When you are 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.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

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

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

André Jasper, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (if provided):

Dear Dr. Pereira-Cruz and colleagues,

After carefully revising your resubmission, we are quite reaching a final decision that is now conditioned to a few details to be changed in your manuscript.

Both reviewers and I agreed that your manuscript is an interesting contribution for PlosOne and, for final acceptance, we kindly ask for the following (as pointed out by Dr. Mercuri):

Line 80 = instead of “Zea Mays, Manihot Esculenta, and Dioscorea sp,” = “Zea mays, Manihot esculenta, and Dioscorea sp.”

Line 123 = delete comma after ‘ (SC) ‘

Lines 157-158 = “We do not consider the temporal information of archaeological sites, as this would considerably reduce the sample size.” This sentence was added now to reply to comments by the reviewer, however it may introduce other criticisms: the chronology is a must in archaeology. Probably, it may be better changing the sentence by reporting only the information on the range of chronology of the sites studied, that is: “ the archaeological sites have been occupied during the last XX millennia”

Line 269 = “unintentionally favored certain plants and/or crops by…” = ‘certain’ is vague and, if correct, ‘synanthropic’ (or the name of the species) should be preferred

Line 359 = check “and we need”

Fig. 4 = check the green colors as it seems that the color of Brazil and the of S. America are inverted, especially in the part ‘ c ‘ of the figure.

Looking forward for you return,

André

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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

**********

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

Reviewer #1: I Don't Know

**********

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

**********

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: The clarity of the paper was notably improved, Fig. 1 is very useful and well done; also the Fig. 7 is now more useful. This research is a very good contribution to the field and I support its publication on PLOSone.

Few remarks are reported below.

Line 80 = “Zea Mays, Manihot Esculenta, and Dioscorea sp,” = “Zea mays, Manihot esculenta, and Dioscorea sp.”

Line 123 = delete comma after ‘ (SC) ‘

Lines 157-158 = “We do not consider the temporal information of archaeological sites, as this would considerably reduce the sample size.” This sentence was added now to reply to comments by the reviewer, however it may introduce other criticisms: the chronology is a must in archaeology. Probably, it may be better changing the sentence by reporting only the information on the range of chronology of the sites studied, that is: “ the archaeological sites have been occupied during the last XX millennia”

Line 269 = “unintentionally favored certain plants and/or crops by…” = ‘certain’ is vague and, if correct, ‘synanthropic’ (or the name of the species) should be preferred

Line 359 = check “and we need”

Fig. 4 = check the green colours a sit seems that the colour of Brazil and ithe S. America are inverted, especially in the part ‘ c ‘ of the figure.

**********

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: Yes: Anna Maria Mercuri

[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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Pre-colonial Amerindian legacies in forest composition of southern Brazil

PONE-D-19-33906R2

Dear Dr. Cruz and Colleagues,

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.

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Kind regards,

André Jasper, Ph.D.

Academic Editor

PLOS ONE