PONE-D-24-16245Genetic drift, historic migration, and limited gene flow contributing to the subpopulation divergence in wild sea beet (Beta vulgaris ssp. maritima)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

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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: Yes

Reviewer #3: 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

Reviewer #3: 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: First, I extend my gratitude to the authors for their outstanding work and well-constructed text. In this study, authors investigated 599 sea beet (Beta maritima) accessions collected from the north Atlantic Ocean and Mediterranean Sea coasts. It is a comprehensive study about the distribution and origin of sea beet and cultivated beet. The title explains the research properly, and the results are described well in details. I think the manuscript contains a good research question and explains the migration route of wild beet along the north Atlantic Ocean and Mediterranean Sea coasts. In the future, the findings will be useful to identify novel genomic regions related to resistance against abiotic/biotic stress factors in Beta vulgaris. However, I have some comments as follows. I recommend minor revisions.

Here are my comments:

-In Materials and Methods, authors did not describe the growth conditions of beet accessions. Authors should mention how many accessions they used from each of the following: Africa, Asia, northern Europe, southern Europe, western Europe, eastern Europe, and North America.

-In Figures 4 and S3, why did not authors show the location of Cluster 6? That map does not show the locations correctly unless I have missed something. For example, I do not see Greece and Italy in Cluster 2 (please see discussion, line 306). Why do you think the Cluster 2 is the center of origin for sea beet and cultivated beet? You may highlight the experimental results for clearer explanation. In addition, each cluster (1-8) must be briefly described in the legend of figure S3.

Reviewer #2: Correct name: Beta vulgaris subsp. maritima (L.) Arcang.

Adding to the title and in the first citation of the text the authorship of the species -> Verify: www.tropicos.org

I suggest adding the botanical family name to the title or in the keywords.

I suggest adding the scientific name of the causal agents of the diseases mentioned in paragraph 3 of the Introduction.

I congratulate the authors on this present work, of fundamental importance for the establishment or better management of genetic improvement programs, as well as for the conservation of wild species.

Reviewer #3: The origin of cultivated plants and the identification of the most closely related native populations, as well as their crop wild relatives, is a highly topical subject, given its potential for the genetic improvement of crops. Following on from other work that has been carried out on sugar beet, the submitted manuscript analyses more than six hundred samples of Beta maritima from various regions of the world. The results presented are interesting and improve the knowledge of the phylogenetic relationships of the populations, particularly those occurring in the Mediterranean region.

In general, the manuscript is well-written, well-structured, and easy to understand.

Apart from a few minor suggestions/comments (listed below), there is one aspect that I would like to highlight because I think it should be corrected: some of the samples used are from areas where Beta maritima is not native, but naturalised (this is the case with the samples from North America). I think this should be mentioned/analysed throughout the text (material and methods, results and discussion, tables, etc.). This aspect can even add value to the discussion, as hypotheses can be put forward for the origin of the populations in the regions where Beta maritima is naturalised.

Other comments:

Ln. 54 – ‘Sea beet (Beta vulgaris L. ssp. maritima Arcang., referred to as B. maritima hereafter)’ – Currently, some of the world's most important taxonomic databases (e.g. Plants of the World Online - POWO; and World Flora Online - WFO) only accept Beta vulgaris subsp. vulgaris and consider Beta vulgaris subsp. maritima as a synonym. This does not invalidate the work developed, but it can be mentioned in the text that the work carried out used the classification adopted by the US National Plant Germplasm System (NPGS).

ln. 59 – ‘Wild B. maritima populations extend along the Mediterranean basin and the Atlantic coast.’ – This description should be more detailed (see POWO) and the regions where the species is introduced should be indicated.

Ln. 76 – ‘Tehseen et al’ - Tehseen et al. The full stop is missing.

Ln. 108 to 111 – Detail the distribution (native or non-native) in the mentioned regions. In Table 1, mark (e.g. with a *) the accessions collected in regions where the taxa is not native (e.g. North America). Check the values in this table: the total is 601 and not 599 as it should be.

Check the legend of Fig. 1 (ln 524) - references to A and B are missing.

In Results section, I think Fig. 3 (Ln. 208) could be made supplementary and Fig. S3 (ln. 231) be included in the main text. The latter is quite enlightening. However, its graphic presentation could be improved.

ln. 273 – ‘… is influenced by a combination of landscape characteristics.’ - I suggest replacing 'landscape' (which has aesthetic connotations) with environment.

Ln. 300 – In the discussion, this manuscript could also consider the results of the paper Veloso et al. 2021 (Genetic Diversity and Population Structure of Wild Beets (Beta spp.) from the Western Iberian Peninsula and the Azores and Madeira Islands) which also highlights the importance of ocean currents in species dispersal.

Finally, I suggest complementing the discussion by including some conservation proposals, namely the prioritisation of certain populations / regions taking into account their phylogenetic affinities and genetic diversity.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Genetic drift, historic migration, and limited gene flow contributing to the subpopulation divergence in wild sea beet (Beta vulgaris ssp. maritima (L.) Arcang)

PONE-D-24-16245R1

Dear Dr. Chenggen Chu,

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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Awatif Abid Al-Judaibi, PhD

Academic Editor

PLOS ONE

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: (No Response)

Reviewer #3: 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 #3: (No Response)

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

Reviewer #1: Yes

Reviewer #3: (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 #3: (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 #3: (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 authors have improved the manuscript based on the reviewers' comments, I congratulate them for this comprehensive study. I recommend acceptance.

Reviewer #3: (No Response)

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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: Seher Yolcu

Reviewer #3: No

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