PONE-D-21-08410

Importance of natural land cover for plant species’ conservation: a nationwide study in The Netherlands

PLOS ONE

Dear Dr. Pan,

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 August 10 2021. 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. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Daniel de Paiva Silva, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

Dear Pan et al.

After three independent reviews, I believe you manuscript may be published in PLoS One should the issues raised by the three reviewers are taken care of in the next version of your MS. All three reviewers raised important issues to improve your MS, especially reviewer #1. Review all of your data, your analyses, and your supplmentary materials.

Considering the pandemic, please resubmit a new version of your text, along with a detailed rebuttal letter informing to the reviewers the performed changes by August 10 2021. If more time is needed, please let me know. If you are able to resubmit before the established due date, do not hesitate to do it so.

Sincerely,

Daniel Silva

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For more information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions.

In your revised cover letter, please address the following prompts:

a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially sensitive information, data are owned by a third-party organization, etc.) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent.

b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories.

We will update your Data Availability statement on your behalf to reflect the information you provide.

3. We note that Figure 1 in your submission contain map images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission:

1. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license. 

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

1. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

4. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.

[Note: HTML markup is below. Please do not edit.]

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

Reviewer #3: Yes

**********

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

Reviewer #1: I Don't Know

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

**********

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

**********

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: In this manuscript Pan et al use biodiversity data, species distribution modelling and natural land cover data to explore the relationship between natural land cover and species occurrence diversity for spermatophyte plants in the Netherlands.

At line 23 the acronym ‘NLC’ is used without first being defined. Whilst the acronym is defined later-on in the introduction (lines 42-43), I wonder if the acronym could either be defined in the abstract OR simply not used in the abstract?

With these methods can they really attempt to test sub-question (4) “how much NLC is necessary to protect conservation-relevant species?” -- surely to some extent this depends on the exact species of plant. Different species are not exactly comparable units. A large tree species will definitely need more NLC area than an endangered buttercup (Ranunculus) that does not strictly require NLC habitat -- these can grow in urban environments e.g. as roadside vegetation. There can be a lot of roadside verge habitat within 1x1km grid cells that are categorized as not natural land cover. Until additional factors are taken into consideration e.g. how large each plant is and how it lives, you will not get a good unstanding of the role of NLC (as just one factor among many).

Taxonomic precision

An examination of supplementary table 2 demonstrates that _only_ the binomial name is given for each species. There is no taxonomic authority supplied with each of these binomial names. In most cases this won’t matter but there are a few where it might be ambiguous. Best practice would be to provide the binomial name AND the taxonomic authority for each to be as precise as possible e.g. Ocimum canescens A.J. Paton

I took the liberty of running checks against all 1563 binomial names provided in supp. table 2 with the help of Taxonstand, matching to The Plant List v1.1 At least eleven of the binomial names given have more than one valid synonym, and thus greater taxonomic precision (via the provision of authority detail) is necessary to resolve what exact species concept the authors intend to use. Those eleven are: Juncus ambiguus, Potamogeton mucronatus, Arenaria leptoclados, Festuca arenaria, Orobanche picridis, Bryonia dioica, Carex oederi, Carex ovalis, Rubus fruticosus, Tilia x vulgaris, and Centaurea montana. Full .csv output from these basic data checks are available as a gist on github here: https://gist.github.com/rossmounce/e5a4c5b2b4642496ee716cf3fb9d2e20

The species scope of the study is also inadequately described - there are no bryophytes or mosses or fern species included in this study thus it is not a study covering ‘land plants’ (Embryophytes) but instead it covers terrestrial seed plants (spermatophytes) inclusive of some gymnosperms e.g. pine species but it is mostly composed of angiosperm species. They should also be more explicit that aquatic plant species such as duckweed (e.g. Wolffia) are strangely included in this study. Surely all the strictly-aquatic plant species should be removed from this analysis if the central theses to be tested are about the type of _land cover_ ? Water is not land.

Why does the manuscript talk about 1563 plant species (line 122) whilst the supplementary materials explain that supplementary figure 2 is “Response curves of 1544 plant species”. Please explain or correct this discrepancy.

Taxonomic name cleaning

Taxonomic name cleaning was apparently absent from this study. Which is a big flaw that should be corrected before publication. Many of the species binomials included in this study are not valid names according to The Plant List v1.1 . In total 108 of the 1563 are synonyms according to TPL v1.1 . For instance “Ranunculus ficaria” is either Ficaria verna Huds. according to TPL v1.1 or Caltha palustris L. according to Plants of the World Online (POWO). Please clean all taxonomic names to either TPL v1.1 or POWO or the Leipzig Catalogue of Vascular Plants (LCVP) and reanalyse the data. This is very important - some of those species aren’t recognized as full species anymore, it undermines the thesis of some of these analyses to not be using _only_ taxonomically accepted/robust species.

Neither POWO nor TPL v1.1 recognize “Rosa henkeri-schulzei” as an accepted species.

Similarly Salix ‘Sekka’ is not taxonomically valid or precise binomial name.

Line 213, states that data was obtained on (1) threatened status, (2) rarity, and (3) species origin from the Red List of Vascular Plants of Netherlands (2012). I can see that threatened status (column U) and species origin (column T) data are given in supplementary table 2 but where is the rarity data they used - it does not seem to be contained within supplementary table 2? Can the authors please make sure that the rarity assertion data they used is provided within supplementary table 2.

I’m surprised to see no information given about higher level taxonomy for each of the 1563 species in supplementary table 2, nor any real discussion of it in the manuscript. Surely it would be interesting to know which are gymnosperms, which are angiosperms, are there patterns to be observed within and between species at the family level (or lower). Surely ‘grass’ (Poaceae) species might have a different set of results relative to ‘pine’ (Pinaceae) species?

Although this journal does not strictly require the authors to provide the code underlying the analyses presented, I think it would certainly put this reviewer more at ease if some of underlying code used in this analysis was provided, so that we could better see what has been done computationally on this data. Please consider sharing some or all of the underlying code.

I hereby knowingly waive my right to anonymity and intentionally sign my peer review report,

Ross Mounce

Reviewer #2: The manuscript analyzed the importance of natural land cover to the occurrence of plant species in the Netherlands through species distribution models. The paper is well organized. The methods and analyses in the manuscript are robust. This is a potentially useful case study, but it is of uneven quality at present. Below are some of my suggestions.

1. I think if Fig. 1a was a map of plant species richness, it could provide more information. I’d also like to see pictures of species richness of different plant groups. Besides, could the authors please demonstrate grid cells with different proportions of natural land cover with different colors in Fig. 1b?

2. There are 1,563 species in Supplementary Table 2 while 1,544 species in Supplementary Fig. 2. Please clarify why the numbers don't tally.

3. In line 257-259, the authors wrote “b-d, Response curves 258 of species with increasing (each magenta line indicates one species) (b), unimodal (each blue line indicates one 259 species) (c) and decreasing (each green line indicates one species) (d) relations with NLC”. However, I think Fig. 2b showed the decreasing and Fig. 2d showed the increasing relationship with increasing NLC.

4. Please add a horizontal line to signify the line of “Representiveness = 0.0” in Fig. 3.

5. Most contents of the discussion were about the preferences of species of different groups for natural landscapes, but the relevant figures were placed mostly in Supporting Information. Meanwhile the authors classified species with unimodal response curves into four classes and showed several figures in the result section though with little discussion later. I think it’s better to reduce this part of the result charts and exchange with some figures regarding to preferences of different species groups.

6. In line 351-352, the authors wrote “Contingency Analysis revealed that threatened and rare species were more likely to occur in 352 landscapes with NLC, NLC-F and NLC-O more than 75%”. However, Fig. 5b and 5e showed that threatened and rare species were more likely to occur in landscapes with NLC-F less than 75%. The conclusions drawn from Fig. 5 were not convincing and rigorous.

7. The authors must have their supporting information carefully edited. There are some errors such as “rariy” in Supplementary Figure 9 and several whitespace problems.

8. I suggest the authors put Supplementary Table 5 in the manuscript, not in the Supplementary information.

9. Discussion 4.1 and 4.2 seems a little repetitive, the authors need to reorganize these two parts.

Reviewer #3: Based on the detailed and comprehensive data, this study carried out a comprehensive study on the relationship between natural land cover types and species distribution in the Netherlands. The topics concerned by the authors have certain guiding significance for the formulation of plant diversity protection strategies and decision-making at the regional scale. However, I think the authors combined different subjects in the article, which may greatly weaken the value and significance of this study. I suggest that the author divide this research at least two papers. One is to discuss the distribution status and laws of natural land cover types from different classification perspectives. The second is the relationship between different types of gradient coverage and the distribution of species diversity of different groups. At present, because the author combines the two topics together, it is difficult to get the Internal connection between them. It is suggested that the authors should revise the paper. Other minor issues are listed below:

1. Line 23: The full name of NLC should be provided. Otherwise, readers don’t know what NLC is if they don't read the text.

2. Line 30: The word ‘informs’ should be ‘inform’.

3. Lines 81-82: the words ‘natural land cover (NLC)’ should be ‘NLC’. The authors should standardize the use of abbreviations. For the words NLC, NLC –F and NLC-O, authors always used their abbreviations, or their full names, even both of them in through article. This is not in line with writing the general norms of writing.

**********

6. 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: Ross Mounce

Reviewer #2: No

Reviewer #3: No

[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.

PONE-D-21-08410R1Importance of natural land cover for plant species’ conservation: a nationwide study in The NetherlandsPLOS ONE

Dear Dr. Pan,

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 October 28th, 2021. 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Daniel de Paiva Silva, 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 (if provided):

Dear Pan et al.,

Congratulations, we are almost there! Please find attached the reviews from three independent reviewers. Two of them decided for the acceptance of the manuscript. The third one still raised some minor issues. In general, I think those may be corrected in the proofreading phase. Nonetheless, considering what has been raised by the reviewer, I believe we still need one final review round to solve the issues. Please be patient, because I really believe these issues will be solved very rapidly. I will grant you a one-month period. In case you need more, please let me know. DO not hesitate to submit earlier if you can.

Best regards,

Daniel Silva, PhD

[Note: HTML markup is below. Please do not edit.]

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 #2: All comments have been addressed

Reviewer #3: All comments have been addressed

**********

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 #2: Yes

Reviewer #3: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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

Reviewer #2: (No Response)

Reviewer #3: 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

Reviewer #2: Yes

Reviewer #3: 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: 1.) I am pleased the authors have removed the acronym NLC from the abstract. Issue resolved.

2.) I am pleased the authors have reworded their hypothesis to better match their methods. Issue resolved.

3.) I infer that PLOS ONE is an international journal aiming to adhere to global standards, for a global audience. I don’t perceive that informal names like “ Salix ‘Sekka’ “ are good enough by international standards regardless of whether they are accepted by the Dutch government or not. Nonetheless, now that the authors have matched the Dutch names to World Flora Online names, authorities, and species concepts – I think this does partially resolve the issue for me. Although it does open a new can of worms… So let’s look at the changes…

a) “ Salix ‘Sekka’ “ is revealed as “ Salix udensis Trautv. & C.A.Mey. “

Good. I am happy.

b) “ Arenaria leptoclados “ is revealed as “ Arenaria serpyllifolia subsp. leptoclados (Rchb.) Nyman “

It is problematic to include this taxon in this analysis as World Flora Online recognises it only as a mere subspecies of Arenaria serpyllifolia L. which itself is included in the analysis already. I would recommend that the authors remove all taxa which World Flora Online only recognises as a subspecies, to ensure methodological ‘purity’ in only performing analyses on robust species-level taxa and not ‘species-level + subspecies-level taxa’. Needlessly including taxa that are considered to be only subspecies-level by some authorities (even if not necessarily Dutch authorities), weakens the robustness of the overall analysis. If there are only a few such taxa that are questionably subspecies-only, why not simply remove them, or perform additional/complementary analyses with them removed, to demonstrate the robustness of the results?

The data that the authors themselves present in column B (“Species name World Flora Online”) of Table S2, reveals that there are eleven taxa in their dataset, including Arenaria serpyllifolia subsp. leptoclados (Rchb.) Nyman that World Flora Online recognises as subspecies only. I understand the desire to perform analyses relative to Dutch accepted species-level taxa given the Dutch geographical context, but please also (or only) perform analyses in the global/international context – that is using full, robust species-level taxa only.

Those 11 subspecies taxa are:

Arenaria serpyllifolia subsp. leptoclados (Rchb.) Nyman

Clinopodium nepeta subsp. glandulosum (Req.) Govaerts

Ranunculus peltatus subsp. baudotii (Godr.) Meikle ex C.D.K.Cook

Raphanus raphanistrum subsp. sativus (L.) Domin

Salsola kali subsp. tragus (L.) Celak.

Montia fontana subsp. chondrosperma (Fenzl) Walters

Ononis spinosa subsp. procurrens (Wallr.) Briq.

Pilosella piloselloides subsp. praealta (Gochnat) S.Bräut. & Greuter

Tripolium pannonicum subsp. tripolium (L.) Greuter

Viola tricolor subsp. curtisii (E.Forst.) Syme

Amaranthus powellii subsp. bouchonii (Thell.) Costea & Carretero

c) “ Juncus ambiguus “ is revealed as “ Juncus hybridus Brot. “

Okay.

d) “ Potamogeton mucronatus “ is revealed as “ Potamogeton friesii Rupr. “

Okay.

e) “ Festuca arenaria “ is revealed as “ Poa robusta Steud. “

Okay.

f) “ Orobanche picridis “ is revealed as “ Orobanche artemisiae-campestris Gaudin “

Okay.

g) “ Bryonia dioica “ is revealed as “ Bryonia cretica (Jacq.) Tutin “

Okay.

h) “ Carex oederi “ is revealed as “ Carex viridula Michx. “

Okay.

i) “ Carex ovalis “ is revealed as “ Carex leporina L. “

Okay.

j) “ Rubus fruticosus “ is revealed as “ Rubus vestitus Weihe “

Okay.

k) “ Tilia x vulgaris “ is revealed as “ Tilia × europaea L. “

Okay.

l) “ Centaurea montana “ is revealed as “ Cyanus montanus (L.) Hill “

Okay.

With the addition of mappings to World Flora Online names and authorities, the data now becomes less cryptic, and more reproducible. Thank you.

4a) I apologise to authors for mistakenly alleging they did not include fern & clubmoss species in this analysis in my first-round review, I can see now they indeed do have some fern and clubmoss species. It would be nice to include a Class-level indication for each taxon in Table S2 e.g. “Lycopodiopsida” , “Polypodiopsida” , “Pinopsida” , “Magnoliopsida” to better illustrate the diversity of the data. If not Class-level then relative to the Order-level of the APG III system?

b) with respect to _land cover_ and entirely aquatic plant species such as the duckweed species included in this work

I think I may have also made a mistake here in assuming that water could not be a type of ‘land cover’. I now see that by normal parlance water is an accepted type of land cover.

Nevertheless, I can’t help but feel that strictly aquatic-only species might have considerably different properties to strictly terrestrial-only species. Does aquatic non-natural land cover even exist? Isn’t all aquatic land cover ‘natural’ or ‘semi-natural’, and thus aren’t aquatic-only species a possible source of bias in this analysis (assuming non-natural aquatic land cover does not exist).

Relatedly how do aquatic-only species fit into testing the sub-hypothesis of “forests” versus “open habitats”. “Forests” and “open habitats” seem to me to be defined on the basis of terrestriality – I think the aquatic-only species should be excluded from this sub-hypothesis analysis, as I wouldn’t expect to find duckweed in areas of predominantly “forest” land-cover. I also note (~line 108) that cells containing >10% of open water were excluded from the analysis – isn’t that excluding the cells where duckweed and other aquatic-only species are quite likely to be found? Does this really not bias this sub-hypothesis analysis to be including aquatic-only vascular plant species in it?

5.) I am satisfied with the explanation given in the reply to reviewers, but please explain this in the manuscript too.

6.) I am pleased that the authors have matched Dutch names to World Flora Online names. As I mention in 3b) this reveals some further issues.

7.) Thank you for including this extra data

8.) Hmmm… I guess it’s not strictly necessary to add this information but it would certainly be helpful

9.) Why not just upload the code to Zenodo? Zenodo just not charge, it is also a not for profit organisation. Whilst I understand the data has some proprietary protections on it imposed by NDFF, your code has no such encumberment.

Thank you.

Reviewer #2: (No Response)

Reviewer #3: (No Response)

**********

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: Ross Mounce

Reviewer #2: Yes: Yue Xu

Reviewer #3: No

[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.

Importance of natural land cover for plant species’ conservation: a nationwide study in The Netherlands

PONE-D-21-08410R2

Dear Dr. Pan,

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.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Daniel de Paiva Silva, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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

**********

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: 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

**********

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: Thank you for patiently explaining it to me. I have nothing more to say.

**********

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: Ross Mounce