PONE-D-24-15741Predicting the Habitat Suitability of Ilex verticillata in China with Field-Test ValidationsPLOS ONE

Dear Dr. yin,

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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I have received two expert assessments of your paper, and although I agree with the reviewers' opinions and suggestions, I understand that the paper still needs to adjust the methodology used. Note that this was one of the main points raised by the reviewers. Below I present the main criticisms regarding the methodology.

General comments after my reading:

-The use of MaxEnt is widely accepted; however, modeling algorithms are very diverse and can produce different predictions. This becomes particularly important for non-native species and for estimates considering future climate change scenarios. There is a vast scientific literature recommending the use of different algorithms (e.g., MaxEnt, BIOCLIM, RandomForest among others). Therefore, I recommend that the authors use various modeling techniques and produce a consensus map

-The species “Ilex verticillata” originates from the Northeast of the United States and has already been introduced in various parts of the world. This was briefly mentioned by the authors. The critical point is which points were used for modeling? Note that this was also not clear to reviewer 1. According to the text and figure 1, the authors used points from the native region (USA) and China. By doing this, the authors are assuming that the species' niche is in equilibrium. Another option is to use only the points from the native area and project the species' distribution in the invaded area. This approach assumes that the niche is conserved. There is a vast literature discussing the transferability of niche models for the case of invasive species, and the authors need to justify the methodology used.

-Please note that it is necessary to use the International Code of Nomenclature for algae, fungi, and plants when citing a plant species. For example, is necessary inform the taxonomic group (e.g. family) and author of the species.

Therefore, I invite the authors to review the manuscript and respond to the comments/suggestions presented.

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Please submit your revised manuscript by Jul 31 2024 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.

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We look forward to receiving your revised manuscript.

Kind regards,

João Carlos Nabout

Academic Editor

PLOS ONE

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Grant No. JATS[2022]396"

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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: Yes

Reviewer #2: 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

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: No

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 study by Yin et al. used a fashioned and improved method to evaluate the suitability of Ilex verticillata in China using MaxEnt, plus a nice evaluation in field using fitness related traits of fruits. My general impression is that the methodological section sounds logical but the overall manuscript will benefit from a better streamlining (specially a workflow figure at the beginning of the methods), and a consistency of terms. I have a major suggestion of how to improve part of the methods, specially the selection of suitability types, by using a comparison of an introduced model (China) vs a global one. However, I will understand if these changes are not totally feasible as you authors have already selected the 12 sites to test with field data. Other revisions are needed in typos, format, and discussion of soil variables. All in all, I had a great time reviewing the article so I will be glad of reviewing it again after the revisions.

Please see more detailed comments ahead:

Abstract

-line 22: MaxEntropy is also the software or type of algorithm, to be more consistent just says habitat suitability model as in line 26.

So, something like “In this study we evaluated the habitat suitability of the species using MaxEnt, combined with climate and…”

-line 26: “excellently” looks arbitrary and not too scientific. I would rewrite the sentence.

-line 30-31: I think you do not need to repeat “pathway”

Introduction

-line 37: include the letters for the scientific name author

-line 37: “originally thrived”-> native?

-line 40: gardens( -> gardens (

-line 41: you already said “holly genus”, so better say “Aquifoliaceae family”

-line 44-45: check citation style

-line 46: evolving into -> would be better “emerging as”

-line 47-48: the sentence of greenhouse effect, climate change factors and climate change, could be rewritten for smoothness. Also, is quite long, so do this change:

“regions. Drought, flooding, overheating, and extreme cold, may negatively impact the yield and quality of I. verticillata, thereby affecting the economic benefits of related industries, affecting the economic traits of its cut flowers (Parrotta et al., 2023)”

-line 52: “hence” without captions

-line 53-56: seems that this sentence needs a missing reference

-line 60: citation format

-line 61: I find difficult to understand this sentence “exhibits remarkable…its negative effects” What are those small-scale migrations within plantations? Please explain

-line 71: points = occurrences

-line 72: species(Elith et al., 2011).For -> species (Elith et al., 2011). For

-line 72-74: These examples are in China I guess, so mention that. If not, better to use only examples in China to by more robust with the statement.

-line 76: delete “model”

-line 77: “MaxEnt, in comparison to other models..”

-line 82: why here you mention climate-ecological models? That should be explained before in bioclimatic models, otherwise readers can start to confusing with different terms (even though they are the same)

-line 85-87: the sentence “its worth noting that…” needs more background. A quick search in Google Scholar shows that several articles have indeed validated MaxEnt predicitons. Maybe to improve the sentence you can say that few have done it using additional fieldwork data, or only few in Asia/China. So, in that way you are more precise.

-line 87-89: the first sentence you specify for “tree”, but then you comeback to be broader using “plants”. Also, your species is a shrub, so use that word, and change the order from macro to micro.

-line 90-91: “important indicator” of what? Seems that you have missing words.

-line 91-92: “different climate soil…” this sentence seems to not be in the correct part, as you first started with fruit traits, then soil, and then you comeback to fruits.

-line 94: What is an “excellent ecological value”?. Maybe sounds better “high ecological value” or “important ecological value”

-line 95-97: rewrite because sounds as a circular argument: like “because of scattered distribution, we studied its distribution, and we found was scattered”

-line 97-111: All these sentences are really related to the methods, so improve the streamlining or just move it to the methods section to move quicker to the aim of the study. Considering all the step that you have in the methods, a suggestion would be to have a workflow as a initial figure, so you can easily show to readers all the steps that you did.

Material and methods:

-line 116: why manifestation data? Why not just occurrences?

-line 117: dispersion -> distribution

-line 126: the reference for ENMTools is missing

-line 128: 2.5 x 2.5 arcmin

-line 131-134: why you needed the map of China? That was not clear. I guess it is for subtracting environmental data for the background envelope. Please explain

-Figure 1: “Specices” -> Specimens or species distribution

-general comment: so far is not clear for me is you pretend to do only one SDM at the global scale, or two, comparing native versus introduced area. If the first is the selecting, you need to explain why a comparison between the native and introduce area were not included

-line 137: most probably the high-quality image will still have too low resolution to see the triangles given their size. So, consider to change them to “dots”

-line 140: consider change it to “Climatic variables have shown to have important ecological significance for plants, affecting their distribution at broader scales”

-line 142: weather data -> “climatic data”. You used the biovariables so by the definition is climate (averages for 30 years period).

-line 142: Worldclim 2.1 or 1.4? (I guess is the first). Please include the version and the corresponding timeframe (1970-2000). You also need to discuss if the temporal frame of the biovariables correspond to most of your occurrence data. I guess that many I. verticilata in China have been introduced after the 2000’s, so they may not match properly the environmental data. That selection needs justification. For example, in this research says it was introduced since 2006 https://apsjournals.apsnet.org/doi/10.1094/PDIS-07-22-1688-PDN

-line 144: 2.5 arcmin

-line 144: you still do not know the potential future distribution, just selected the future climate scenarios, then should be “…of 2.5 arcmin. Future climate scenarios were selected…”

-line 146-150: improve the writing to avoid the overuse socioeconomic.

-general comment: I saw in the methods that you used R for correlations, for kuenm, and I guess that also for ENMTools, but you also used several other software such as ArcGis, SPSS 26 and Origin 95. I wonder why not do directly all in R to simplify and to be more replicable?

-Figure 2: is not cited in the manuscript

-line 162: which DEM resolution?

-line 181: check citation format

-line 207: is a bit awkward as it says that you collected fruits in sites without fruits. Rewrite the idea.

-line 208: tree or shrub?

-line 209: citation format

-line 212-213: seems to be a repeated idea

-line 228: after reading the whole document, I did not see any result about leaf traits, so better to exclude this sentence

-line 233: now you mention the reference period. This should be the first time that you talk about WorldClim

-line 238-243: the breaks still seem a bit arbitrary without explanation. Why these have different magnitude of interval? Here, I think that would be better for you to compare the global model vs and introduced model. The introduced model that will be more local, could behave quite differently, so would be wise to compare them. I suggest to review the methods of Gallien et al., 2012 https://onlinelibrary.wiley.com/doi/full/10.1111/j.1466-8238.2012.00768.x (specifically figure 3)

There you can have 4 different habitat suitability comparing both model with a threshold of 0.5, and more importantly for your study, with clear ecological – dispersion significance. For other examples, see fig 5a. of this research https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.5295

Results:

-line 263: a good level of what?

-line 271: what do you mean with “covering the entire expanse in China”? As fig 3 shows that large part of the country is unsuitable

-line 294: I just wonder, these differences would all continue to express with a Tukey test (that is most robust). Would be nice to check.

-line 304: “varieties” -> “types”

-line 315-319: I had difficulties following the idea. Its look all the same to me, but the “In contrast” makes me feels that should not. Can you rewrite for clarity?

Line 320-330: I do not see the value of expressing all the results and all these percentages. It makes it really hard to follow. Try to streamline the idea with the most important results and interpretation. Readers should be able to read this in a figure/table. By the way, I do not know which figure I should read to follow all these percentages.

-Figure 7 & 8: I do not see them cited in the text. Fig. 8 seems to be important

-line 341: shrub or tree? Decide and keep constant

-line 346-348: improve writing. Avoid using three times “prediction”

-line 348-349: what are those “true species growth indicators”? Here the tricky word is “true” as is a difficult word to use in science.

-line 351-352: What do you mean with “high consistency”? It was not clear for me. Maybe you were you trying to say something like the field data (traits) was a novel way of validate the SDM?

-line 355: climate.The -> climate, the

Discussion:

-lines 360-381: you have a long discussion about soil variables, but these had a really low contribution in your model. Why you decide to give them such big importance?

-line 395: citation format

-line 442: citation format

-line 455: I. verticillate should be in italics

Reviewer #2: In the methodology it is important to add a GBIF doi of the data used. A way to get this doi in R is: "require(rgbif) require(dplyr)". It would be good to improve the resolution of figures 5 and 8, as the legends and scale are blurred. Have you evaluated the extrapolation of models in the methodology? This can be a critical point, the exclusion of adequacy predictions in environmental conditions considered extrapolative could be interesting to incorporate. See: https://nsojournals.onlinelibrary.wiley.com/doi/10.1111/ecog.06992

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Reviewer #1: Yes: Dr. Nicolas Velasco

Reviewer #2: Yes: Emilly Layne Martins do Nascimento

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PONE-D-24-15741R1Predicting the Habitat Suitability of Ilex verticillata in China with Field-Test ValidationsPLOS ONE

Dear Dr. yin,

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.

Thank you for accepting the suggestions from both myself and the reviewers. In this new version, one reviewer has accepted the article while another has provided additional comments, necessitating a major revision. I also agree with the reviewer and indeed, some adjustments to the manuscript are still required. In addition to the reviewer’s comments, I also recommend the following:

1 - In the title, it is important to indicate the family Aquifoliaceae after the species name. This is a rule of botanical nomenclature, which I had previously commented on/suggested in the first version.

2 - A suggestion: The introduction consists of two long paragraphs. If the authors agree, it might be beneficial to divide them into smaller paragraphs. This would improve the readability of the manuscript.

3 - Reserve the last paragraph of the introduction to presented the objectives of the study.

4 - In the caption of Figure 1, remove the word "global." The figure highlights the distribution of points in China only.

5 - Line 130, merge this sentence with the previous paragraph.

6 - Line 170, it is mentioned that the models were generated for North America. Why? I believe the models were generated for China.

7 - Line 202, the authors indicated 12 sites to assess model accuracy. It would be helpful to show these 12 sites on a map. This could be done in Figure 1 along with the points used in the model. Simply indicate the 12 sites in different colors. I noticed that the coordinates were provided in Table 2, but the figure might present this information more clearly.

8 - Line 214: Were the assumptions of ANOVA tested? ANOVA is only cited in the table. It is important to include this information in the methods section of the text.

Please submit your revised manuscript by Oct 18 2024 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: 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,

João Carlos Nabout

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: (No Response)

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 #1: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

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 #1: Yes

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 #1: Yes

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 #1: Thanks for addressing most of my previous comments. Here I have some additional recommendations to polish further the manuscript

Line 112: “Global Biodiversity Information Facility”

Line 129: Figure 1. The chinese distribution points of I. verticillata.

Line 142: check the formats of the socioeconomic pathways � SSP1-2.6, SSP2-4.5, SSP5-8.5

Line 172: you should include a short explanation of this coefficients to select the models. What they tell to the reader? For example, is the first time that I see the KAPPA. Additionally, in Table 1 how the reader can discriminate between the different values? For example, RF values are very similar to MaxEnt. Is intuitive that you discriminate through higher values, but if a model has only a thousandth higher than other, that would be sufficient?

Line 256: I’m a bit confused here. I believe you need to mention earlier that you selected 15 variables, which were then used in the SDMs comparison. Some of this information should be moved to before line 242.

Line 264: This line is confusing to me for two reasons. First, when you mention “models using the first four climate variables,” are you implying that you tested models with different sets of variables? This is a common approach in optimization, but in the methods section, I didn’t catch that different sets of climate variables were tested. Second, I’m unclear about where to find the statement that these models “gave better results (AUC > 0.8)” or what they are being compared against.

Line 291: there is no legend

Line 296-299: SSP5-8.5

Line 307: Given that you have many figures, I suggest moving Figure 7 to the supplementary materials.

Fig 6: can also be a supplemental

Line 313: check SSP format from here onwards, and also in figure 6, 7, 8 and 9

Line 316: add a separation between the dot and However

Figures 6 & 9: Considering their size and resolution, these figures could benefit from removing the empty columns and rows separating the nine subgraphs.

Figure 8: Since there are significant differences between the types of suitability (making it hard to see differences in the categories with better suitability), it might be better to use a logarithmic scale for the y-axis.

Line 361: I do not understand what you mean here “two types of variables were included in the identical model”. What is the identical model?

Line 385: “sufficient” without capital

Line 451-455: is quite long. Try to separate the idea in two or three sentences

Reviewer #2: After analysing the revisions and corrections made by the authors in response to the suggestions and recommendations, I conclude that all the proposed changes have been duly implemented. The article now presents significant improvements in terms of clarity, consistency and scientific rigour for publication. The methodological and theoretical aspects have been adequately addressed, which reinforces the quality and relevance of the results presented. I therefore recommend that the article be accepted for publication, considering that it is capable of making a significant contribution to the scientific community.

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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.

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: Dr. Nicolás Velasco

Reviewer #2: Yes: Emilly Layne Martins do Nascimento

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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.

Predicting the Habitat Suitability of Ilex verticillata (Aquifoliaceae)  in China with Field-Test Validations

PONE-D-24-15741R2

Dear Dr. yin,

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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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,

João Carlos Nabout

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

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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: (No Response)

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

Reviewer #1: (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: (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: (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: (No Response)

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Reviewer #1: Yes: Dr. Nicolás Velasco

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