PONE-D-24-32533Tracing the Emergence of Domesticated Grapevine in ItalyPLOS ONE

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M.U. received funding from the European Union Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement (No 101019563 –VITALY). L. Bouby and S. Ivorra were supported by the ANR MICA project (grat agreement ANR-22- CE27-0026). We are grateful to the Centre de Ressources Biologiques de la Vigne, Domaine de Vassal-Montpellier (INRAE) (https://vassal.montpellier.hub.inrae.fr) which provided pips from modern cultivated varieties used in this study. The authors thank the Soprintendenza Archeologia, Belle Arti e Paesaggio per la città metropolitana di Cagliari e le province di Oristano e Sud Sardegna for allowing us to analyse the seeds from Sa Osa and the Soprintendenza Archeologia, Belle Arti e Paesaggio per le province di Verona, Rovigo e Vicenza, and Giuseppe Zenezini for allowing us to analyse the seeds from Canar. Many thanks to, Gabriella Poggesi, Monica Salvini, and Andrea Pessina from Soprintendenza Archeologia, Belle Arti e Paesaggio per la città metropolitana di Firenze e le province di Pistoia e Prato for allowing us to analyse the seeds from S. Lorenzo a Greve and Gonfienti. Thanks to BRAIN network and database - https://brainplants.successoterra.net - are acknowledged for the archaeological sites mentioned in the paper. The authors also thank Marta Mazzanti, Rossella Rinaldi (UNIMORE) and all students who worked with us on the sites cited in this work. Special thanks to Paola Bigi (Musei di Stato, Repubblica di San Marino), Mauro Cremaschi (Università degli Studi di Milano), Chiara Guarnieri, Donato Labate, Mirella Marini Calvani (già Soprintendenze Archeologia, Belle Arti e Paesaggio della Regione Emilia-Romagna), Roberto Macellari (già Musei Civici di Reggio Emilia), Daniela Rovina (già Soprintendenza Archeologia, Belle Arti e Paesaggio per le province di Sassari e Nuoro). The research of the Marmotta site has been carried out in the collaboration agreement between the Museo delle Civiltà and the Spanish Scientific Research Council (centres in Barcelona IMF515 CSIC and Rome EEHAR-CSIC). The authors would like to thank all the staff at the Museo delle Civiltà (curators, administrative staff, technicians, etc.) This research is part of the following research projects: ‘AGER. Crescita agricola nell'Europa preistorica. Un approccio al cambio tecnologico, economico e sociale’ project (PGR18BQHM7) funded by the Italian Ministry for Education, Universities and Research within the ‘Rita Levi Montalcini’ program; and the project ‘Tools, Techniques and Specialists: the keys to understand the Mesolithic– Neolithic transition in Mediterranean Europe’ (PID2020-112513RB-I00) funded by MCIN/AEI/ 10.13039/501100011033. A.M.M., A.F. and G.B. acknowledge the NRRP, Mission 4, Component 2 Investment 1.4 -Call for tender No.3138 of 16 December 2021, rectified by Decree 363 n.3175 of 18 December 2021 of MUR funded by EU– NextGenerationEU. Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by MUR, CUP E93C22001090001, Project title “National Biodiversity Future Center– NBFC”

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Additional Editor Comments :

Dear Mariano Ucchesu,

The paper is very interesting and of high scientific value, however according to the review some more information and corrections is in needed. I also encourage you to go over the manuscripts in terms of language editing for final polishing and make sure references, figures and inferences are accurate. Please provide a detailed response letter elaborating all the corrections made.

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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: Partly

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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?

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Reviewer #1: No

Reviewer #2: No

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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 authors reported the morphometrics analysis of several waterlogged archaeological grape pips collected in Italian archaeological sites and covering 7000 years of history. Using geometric morphometrics and linear discriminant analyses, they suggested insights into the evolution of grapevine cultivation in Italy and the transition from wild to domesticated grapevines.

The manuscript reports interesting and original results and provides a potential contribution to understanding the diffusion and evolution of viticulture in Italy. These data should be supported in the future by genetic analyses that could suggest links with modern varieties cultivated in Italy and Southern Europe.

I suggest reporting the numerical results of the pips classification (wild, domesticate, non allocated) in the supplementary table SM2 next to the discovery sites. In this way the first part of the results (lines 229-260) could be lightened by many numerical data to make it less "boring" and similar to a list.

In addition, to meet the needs of open research, I would suggest that the authors report the raw data of all the measurements conducted on all the pips (in the supplementary materials or in some public repository), both the modern ones used to create the reference database and the archaeological ones.

Reviewer #2: 1. The method applied in the research, Fourier transforms, is widely used for morphometric identification of plants, and grape pips. It is important to add here in this paper a figure/ table to visualize the choice of the “six first harmonics, that were utilized here (although it is a continuation of the previously published method – Ref #20 and #30. Accordingly, the data of the measurements – the raw data for statistics, should be presented. Now, it is presented in figure 4, where individual measurements are unclear.

Next, the “48 EFT coefficients” – should be presented in the paper.

As for the results, means and covariances for the wild and domesticated types, as well, means and covariances for each period should be presented in the paper. This can be estimated from the training set. In this case, the data will help the readers to follow the authors and will allow us to evaluate the results, and to apply the results in future studies of other grape populations. Presenting the data will enlarge our understanding of the changes in the grape pip’s morphology with time and domestication.

Each method has its cautions and limitations, so it is critical to address this issue, and to discuss the pros and contra of applying the method on the results.

2. The reference list is incorrect. Page 2 [7] – Mangafa is not the source for the size and shape of wild vs cultivated pips. [13] – Dong et al. is the source for the two simultaneous domestication events 11,000 years ago in W Asia and Caucasus, which led to different routes and timing of dispersal and further introgressions of the primary cultivars. The reference [16] is dated to 2021, while [13] to 2023 – so the style of the sentence “However, the hypothesis of a second, independent, grape domestication event outside the original primary domestication center is still [sic! - reviewer] debated” - is confusing and misleading.

Page 2—Connection of the spread of viticulture with “emergence of complex societies”—please add more here for those who are not familiar with the development of societies in Italy. Add that in Italy, the first evidence of a hierarchical society was during the MB.

When citing only one single work in a sentence, such as “different research has employed pip outline analysis study grape subspecies [20] – the chosen reference should be a review, or please add “e.g.” before the single chosen work.

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: Review Tracing the Grapevine in Italy.docx

PONE-D-24-32533R1Tracing the Emergence of Domesticated Grapevine in ItalyPLOS ONE

Dear Dr. Ucchesu,

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 26 2025 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.

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We look forward to receiving your revised manuscript.

Kind regards,

Iris Groman-Yaroslavski, Ph.D

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

Please note the last remarks by reviewer 2.

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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 #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 #2: Yes

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

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 #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 #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 #2: The paper presents important data that visualizes the non-linear evolution of wine domesticates in Italy. The raw data included now in the paper helps to follow the results and conclusions. I would suggest a minor change—in my opinion, a photo of grape pips from different stages of domestication would illustrate the process even better and significantly upgrade the visual appearance of the publication.

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Reviewer #2: Yes:  Suembikya Frumin

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Attachments

Attachment

Submitted filename: review of revised manuscript.docx

Tracing the Emergence of Domesticated Grapevine in Italy

PONE-D-24-32533R2

Dear Dr. Mariano Ucchesu,

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.

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Iris Groman-Yaroslavski, Ph.D

Academic Editor

PLOS ONE

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