PONE-D-19-21921

Niche-processes induced differences in plant growth, carbon balance, stress resistance, and regeneration affect community assembly over succession

PLOS ONE

Dear Mr Zhang,

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.

The review process took longer than expected because a third review was sought to resolve the conflict between the first two reviewers.  As the third review was positive, the decision was made not to reject the manuscript for publication, rather to return it for revision. Please pay careful attention to the suggestions and criticism from all three reviews.

We would appreciate receiving your revised manuscript by Feb 16 2020 11:59PM. When you are ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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

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

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

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

We look forward to receiving your revised manuscript.

Kind regards,

Craig Eliot Coleman, PhD

Academic Editor

PLOS ONE

Journal Requirements:

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

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

http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why.

3. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide.

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: No

Reviewer #2: No

Reviewer #3: Yes

**********

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

Reviewer #1: No

Reviewer #2: No

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: No

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: No

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: Understanding rules of community assembly is a central goal of community ecology, and trait-based models are useful tools to reach this goal. Therefore, the topic of this paper is interesting. Its further strength that the authors measured hard traits. Unfortunately, I have found so many problems in the manuscript that overwhelm the above mentioned advantages.

The logic of the Introduction and aims of the paper should be re-think. The coexistence of totally neutral species is stable, but not robust, because nearly neutral species cannot coexist. For more details on this topic see e.g. (Meszéna et al. 2006; Barabás et al. 2018). Thus, studying role of neutrality is meaningless, however some traits may prove to be neutral. Possibly, the authors mixed neutrality and stochasticity (it often occurs in the literature). Of course, exploring the relative role of stochastic and deterministic processes could be a valid aim. However, it would need different methodology, e.g. CATS developed by Shipley (Shipley et al. 2012; Shipley 2014). The applied methods allow quantifying importance of habitat filtering and limiting similarity, and its change during succession. Either the aims should be reformulated or different methods should be chosen.

I am missing the mentioning studies of community assembly along successional series from the Introduction. Moreover, in some references I think that the cited paper did not support well the statement (sometimes it did not say it at all, other cases it is not the main message of that paper and better citation could be found). For example, Ref3 in line 41; Ref8 in line 54; in line 55 paper that study changing trade-off along gradients also should be cited; Ref9 in line 61; Ref13 in line 74; Ref14 in line 78.

In the Methods, it remains unclear for me exactly how many plots were sampled and how they were arranged. It only mentioned later that two chronosequences were sampled.

I think the assumptions of ANCOVA (independence and normality of errors) were not satisfied. I suggest consulting with (Warton et al. 2015) and references therein. If abundance were measured by number of ramets, Poisson or negative binomial distribution would be suitable. Note, that in ANCOVA residuals should follow normal distribution, not the covariates.

To support your selection of randomization constrains please see (Götzenberger et al. 2016), and also see my paper (Botta-Dukát 2018) on possible problems of Gotelli & Grave’s SES.

Because correcting the above mentioned problems will lead to considerable changes in Results and Discussion, I stopped reviewing the manuscript at the end of Methods section.

Cited references:

Barabás G, D’Andrea R, Stump SM (2018) Chesson’s coexistence theory. Ecol Monogr 88:277–303. doi: 10.1002/ecm.1302

Botta-Dukát Z (2018) Cautionary note on calculating standardized effect size (SES) in randomization test. Community Ecol 19:77–83. doi: 10.1556/168.2018.19.1.8

Götzenberger L, Botta-Dukát Z, Lepš J, et al (2016) Which randomizations detect convergence and divergence in trait-based community assembly? A test of commonly used null models. J Veg Sci 27:1275–1287. doi: 10.1111/jvs.12452

Meszéna G, Gyllenberg M, Pásztor L, Metz JAJ (2006) Competitive exclusion and limiting similarity: A unified theory. Theor Popul Biol 69:68–87. doi: 10.1016/j.tpb.2005.07.001

Shipley B (2014) Measuring and interpreting trait-based selection versus meta-community effects during local community assembly. J Veg Sci 25:55–65

Shipley B, Paine CET, Baraloto C (2012) Quantifying the importance of local niche-based and stochastic processes to tropical tree community assembly. Ecology 93:760–769. doi: 10.1890/11-0944.1

Warton DI, Shipley B, Hastie T (2015) CATS regression – a model‐based approach to studying trait‐based community assembly. Methods Ecol Evol 6:389–398. doi: 10.1111/2041-210X.12280

Reviewer #2: The authors examined the trait-abundance relationships and trait diversity patterns among successional stages in two meadow communities. The dataset of both traits and communities gives good opportunities to explore the ecological processes. However, there are some very important issues must be clarified.

First, for the analyses of trait-abundance relationship, the authors used the model: trait = abundance+age +abundance:age. I am very confused why abundance can predict the functional traits. Also, most parts of Introduction describe how traits can influence species abundance (I agree and this is reasonable). If the true model the authors wanted to use is abundance = trait + age + trait:age, then all relevant results needed to be revised. Also, the results are not consistent with your methods (Lines 140-142).

Second, they did not give any discussion on the section of trait diversity patterns (Line 256).

Third, what is the main question want to solve? To examine the relative importance of niche and neutral processes? If so, the authors said trait-abundance relationship was difficult to infer these processes? Then why the authors perform these analyses? I think to clarify the relationship between section 1 and section 2 is important.

Fourth, the Conclusion needs to be reframed and some conclusions of section 1 needs to be added.

Fifth, the authors used the rank of successional age as the treatment. However, the year is different for each successional age, how the authors explain these differences?

Minor comments:

Lines 68-71: the authors did not use the hydraulic conductivity traits.

Line 97: which one is easy-to-measure trait and which one is hard-to-measure trait?

Line 101: I think “the relative importance” may be more appropriate.

Line 88: add “is”.

Line 152: delete “Hence in this study”.

Lines 178-181: these might be redundant.

Tables 1 and 2: please re-organize the table (e.g., delete the line inside) and make it clear.

Line 191: only two traits significant in sites 2.

Lines 193-198: please re-write these results (e.g., which is negative and which is positive?)

Line 391: delete “-”,

Fig. 1: I think it is better to indicate the p values and significance in this figure, also to indicate the difference of these trait values.

Figs. 2 and 3: I think it is better to indicate which fitted lines in each panel were significant. What are the points in each panel?

Line 420: “The distributions of standard effect size (SES)” of what?

Reviewer #3: This paper addresses the several questions pertinent to community ecology about the relevance of species’ traits in determining species abundance. The authors have collected data on a number of traits related to carbon acquisition, stress tolerance, and reproduction on plants growing across two chronosequences following agricultural abandonment in alpine grasslands in China. A strength of the paper is the measurement of traits that are typically avoided due to their difficulty in assessing.

Overall the study was well-done. The manuscript was excellent in terms of experimental design and analysis. The study has specific goals and focused on an area which was not studied. The authors focused on interrelationships among successional age, functional traits, neutral-related traits, and species’ relative abundance. They also supported these observations by environmental characterization, intensive and prolonged UV radiation, the extremes of temperature, the short growing season in addition to the impact of these factors on some key physiological traits. These goals can help to find the differences between species relative abundance and the contribution of niche and neutral processes to species abundance during succession and abiotic stress tolerance. They collected the samples from high land 3000 m above sea level, they used different successional ages (4-, 6-, 10-, 13-years, and undisturbed for at least 40-years) and from a field. Their way of sample collection (two sites), random samples, size of the selected area and space also show data was measured in a proper way. Such things can convince us of the robustness of the statistical analysis.

The way of discussing the points was good; they discussed what their results mean in terms of ecology, stress tolerance and relationship between the species. Also, they express their opinion in all these issues and why they used the selected traits and how importantly these traits validate the hypothesis. They use most of the relevant references. Thus, I merely have some minor comments below:

Lines 32 Please change these sub-alpine meadow communities into these sub-alpine meadow communities during succession.

Lines 62-63 It is not so good to use shortcomings here. I do suggest to change to use three questions remains to be explored. Thus, please change the sentence “our current understanding of trait-abundance relationships suffers from at least two shortcomings that limit the predictable power of traits for community assembly processes” into “there are two following questions remains to be explored for current trait-abundance relationship studies”.

Line 96 Please change the sentence “Here we attempt to address the first shortcoming of trait-abundance studies by assembling data on six easy-to-measure morphological and hard-to-measure physiological traits (specific leaf area (SLA), seed mass, seed germination rate, height, leaf proline content and photosynthesis rate) to test trait-abundance relationships in a successional chronosequence of subalpine meadow plant” into “Here we attempt to utilize assembling data on six easy-to-measure morphological and hard-to-measure physiological traits (specific leaf area (SLA), seed mass, seed germination rate, height, leaf proline content and photosynthesis rate) to test trait-abundance relationships in a successional chronosequence of subalpine meadow plant communities”

Line 212 Please change “are support” into “support”

Line 235 Please change “is” into “was”

Line 237 Please change “appears” into “appeared”

Line 252 Please change “tend” into “tended”

Line 253 Please change “are” into “were”

Line 258 Please change “was” into “is”

Line 263 Please change “find” into “found”

Lines 267-275 Please check the tense of the Conclusion part, usually Conclusion should be written by past tense, as it has not published.

**********

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: Zoltán Botta-Dukát

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 to be viewed.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org. Please note that Supporting Information files do not need this step.

Niche-processes induced differences in plant growth, carbon balance, stress resistance, and regeneration affect community assembly over succession

PONE-D-19-21921R1

Dear Dr. Zhang,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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.

With kind regards,

Craig Eliot Coleman, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):  One of your reviewers suggested some additional corrections which you should consider as you prepare the final manuscript for publication but I did not feel they were enough to warrant having to revise and resubmit.

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

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 #2: Yes

Reviewer #3: Yes

**********

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

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 #2: Yes

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 #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 #2: Thanks for the careful revisions of the authors. I think there is a great improvement of this manuscript. There I have only few minor comments:

Line 165: please add an error term

Tables 1-2: I think it is better to give the information of coefficients instead of F value

Line 481: I will say each point is one species.

Figs. 2 and other: I suggest only adding the significant lines.

Fig. 1. Please added the statistical methods or in the fig legend text.

Fig. 4. Although the authors give the SES values of all traits-based FD, there are much information in individual-trait based SES.FD patterns.

Reviewer #3: The authors have done a fine job of responding to all of my comments. I congratulate the Authors for producing this paper and I look forward to reading it in print.

**********

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 #2: No

Reviewer #3: No