Peer Review History
Original SubmissionMarch 14, 2020 |
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PONE-D-20-07402 Direct and indirect effects of land-use intensity on plant communities across elevation in semi-natural grasslands PLOS ONE Dear Dr. Buzhdygan, 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. We appreciate that your study shows the whole complexity of the issue rather than oversimplifying it, and that it refers to a regions largely underrepresented in scientific literature. However, the reviewers have a couple of concerns, some of them referring to data analysis: In a revised version, you may wish to describe / discuss more explicitly how spatial autocorrelation among sampling plots was handled. In addition, elevation, grazing intensity and soil potentially affect community composition, but they are correlated themselves. I think that SEM was used to disentangle their effects, but according to the reviews, this should be discussed more explicitly as well. According to one of the reviewers, it becomes not clear if information included in Table S1 and Fig. 1 might already be a result of your study. I think figure and table just underpin and detail your main hypotheses about direct and indirect effects, and are therefore rather useful for understanding the rationale and the approach of your study. I suggest, however, referring to this issue more explicitly in the Introduction, e.g. that Fig. 1 shows the conceptual graph underlying your study in general and the SEM in particular. Furthermore, it should be deduced in the Introduction which hypothesis was intended to test using NMDS. There are several further, rather minor comments provided by the reviewers, that should be carefully considered in a revised version of your manuscript. Please submit your revised manuscript by Aug 02 2020 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:
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 We look forward to receiving your revised manuscript. Kind regards, Harald Auge Academic Editor PLOS ONE 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 2. 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. 3. We note that Figure 2 and FigS1 in your submission contain map images which may be copyrighted. 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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].” 3.2. 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: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ********** 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 ********** 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 ********** 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: Paper review PONE-D-20-07402 Title: Direct and indirect effects of land-use intensity on plant communities across elevation in semi-natural grasslands General comments: This is a well-written manuscript about an interesting topic: Direct and indirect effects of land-use intensity on plant communities across an elevational gradient. The studied plant communities were semi-natural grasslands in the Eastern Carpathians in Ukraine. This region is in fact largely under-represented in the scientific literature, as the authors state in their conclusion. Further, I like the combination of vegetation data with data from other organisms, e.g. earthworms. The dataset is therefore promising, but I have some concerns about the analysis and the presentation of the data. My largest concern is about the relation between the elevation and the grazing intensity. The authors show in the results that grazing intensity is negatively related to elevation, which is quite logic. Further, they quote that grazing intensity has large direct effects on the vegetation independent from elevation. I cannot see, in the current version of the manuscript, how the applied methods can disentangle this interrelationship. This leads me to another concern: I am not sure if the data presentation is optimal. While some tables in the supporting information seem to be relevant for understanding the argumentation of the data analyses (e.g. table S5 and S6), I do not see the benefit of figure 4, which shows the relationship between elevation and grazing intensity. I think more emphasize has to be laid on how this overlay of the gradients (elevation, grazing intensity and soil types as shown by Fig. S1) was disentangled. Another question I have is concerned with the introduction: For me it is quite unusual to cite tables of the supporting information and to include a figure in the introduction. Does this fit to the journal guideline of PlosOne? Additionally, which methods were used to come up with figure 1, is it already a product of this study? Then I would handle it as such. Overall, I recommend major revisions of this article. Minor comments: Abstract: Line 24: most vulnerable compared to what? Line 26: “may depend on environmental conditions and indirect effects are rarely considered” is very vague. Could you specify what you mean? Line 29-30: The cattle grazing took place for two years? I guess you mean your sampling, you have to change the structure of the sentence. Introduction: Fig. 1: Why has the elevation no influence on the soil community? Could the soil community not influence the bare soil? When was this figure produced, was it for this paper? Maybe it is already a result of the study? Line 133: I recommend to cite your map (figure 2) in the section about the study area. Line 133-137: I would recommend formulating more specific research questions or hypotheses. Methods: Line 142: “for decades” to the end of the sentence. Line 146: “significant amount of precipitation” sounds strange, please rephrase. Line 175-176: Use the full names of the tree species. Line 186-188: Use the full names of the tree species. Line 188: Explain the term polonynas. Line 192-193: Not possible to change now, but why was the study design not balanced? Line 197-198: Order from plain to mountains, as you did in your description of the zones. Line 202: Was the handheld GPS precise enough for measuring the elevation? How large is the uncertainty with this method? Please add in the manuscript. Line 222: Why did you average across the two sampling years? Line 228: “species richness per 100 m²“ to be consistent with the other quotations of the 100 m² plots. Line 287-310: Could you explain a bit how the SEM disentangles direct and indirect effects? Results: Line 334: What does “s.e.m.” stand for? I am used to “S.E.” as abbreviation for standard error. Discussion: Overall: I think the red line of arguments could be a bit more consistent throughout the manuscript. For instance, I miss some discussion on the role of earthworms, which were mentioned in all parts of the manuscript except for the discussion. Effects of grazing generally: What about the selection effect of the grazing animals? They avoid toxic plants, which you analyzed separately, but you did not include the “selective grazing” topic in the discussion. Line 387-397: These sentences are results. Do not repeat them in the discussion. You should delete this part here and include these sentences in the results section, if they are not already in the results. Line 430: Why “Similarly”? Isn´t the following sentence an antipode to the sentence before? Line 454: Do you really have a larger site productivity in the higher elevated zone? If yes, could you explain this, because usually productivity decreases with elevation? Line 458: two points at the end of the sentence Line 458: When you use “on the other hand” you should also have “on one hand” before. Line 469: How does this fit to Fig. 4? Reviewer #2: This manuscript presents the results of a study across 31 grassland sites that represent an elevational and cattle density gradient in the eastern Carpathians. In particular, I appreciate that the authors present this complex issue in a way that is detailed and shows that complexity rather than oversimplifying it. There are three major take home messages: 1. Cattle grazing intensity both directly and indirectly decreases plant species richness and functional diversity and increases the proportion of the community that is considered undesirable weeds. 2. Elevation had a strong direct positive effect on plant species richness but also two negative indirect effects. 2. The effect of cattle grazing does not change with increasing elevation. In general, I find these results to be compelling and important and likely address some inconsistencies within the literature that are pointed out by the authors. However, I have two major concerns regarding the analyses presented. 1. Spatial autocorrelation – I could not find in the manuscript a discussion of how spatial autocorrelation was handled. This may have important implications for the results as the plots appear to be collocated in three different regions which are also associated with elevation and cattle density and how close they are to each other may also exert some control over species richness. It could be that I’ve just missed this – in which case I would ask that the authors highlight this a bit more prominently. In the event that I didn’t miss this – I don’t have a particular favorite way of addressing spatial autocorrelation but I’ve included a methods paper that discusses the pros and cons of some different methods (Dormann et al. Ecography). I would be happy with any of these methods as long as spatial autocorrelation is accounted for. 2. The community composition analysis using the NMDS is not well introduced in the introduction and the hypothesis is not as clear to me as the hypothesis for the SEM. I would suggest either removing it or providing a specific hypothesis that is introduced in the introduction along with the predictions for the SEM. Minor comments: Undesirable weeds is a tricky thing to say and I would like a description of how species were identified as undesirable. I would also maybe consider different language that isn’t so values oriented, depending on how the species were identified as undesirable maybe non-forage species would be applicable? 24 – land use should be “land use change” 26 – indirect effects should be “the indirect effects” 27 – direct should be “the direct” 34 – direct should be “the direct” 44 – I would say along an elevation gradient here instead 45 – with elevation should be “with increasing elevation”, I think throughout 58 – I would appreciate a few examples of what ecosystem functions and services you are referencing 65 – land use intensity should be “the land use intensity” 67 – I would change can to may here – or could whichever you prefer (I prefer may, � ) 70-116 – I really appreciate the complexity here and how thorough you are with the predictions. I would make sure however, that each of these paragraphs has a sentence at the beginning that signals the intention of the paragraph and gives an overarching topic that isn’t linked directly to the first prediction on the list. You do this quite well with the paragraph starting on line 70. 117- 127 – I would consider moving this paragraph up to before you start your prediction paragraphs as it outlines your argument about the novelty and importance of this paper. 292 – I would say “meet the assumptions of normality…” rather than meet Discussion – I would appreciate a paragraph that goes back to the idea introduced in the introduction about the conflicting results seen in previous studies. Do these results explain some of those conflicts? ********** 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: No Reviewer #2: 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.
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Revision 1 |
PONE-D-20-07402R1 Direct and indirect effects of land-use intensity on plant communities across elevation in semi-natural grasslands PLOS ONE Dear Dr. Buzhdygan, 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 reviewers and I appreciate the careful revisions made, and there are just two, really minor points (see also reviewer #1) that should be addressed before I can make a final decision: Lines 520 - 521: Please rephrase the sentence, e.g. "The positive effect of elevation on species number of rushes and sedges as observed in our study (S8 Table) might be attributed ..." Line 596: Please use plural: "... along elevation gradients". Please submit your revised manuscript by Nov 30 2020 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:
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 We look forward to receiving your revised manuscript. Kind regards, Harald Auge Academic Editor PLOS ONE [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 ********** 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 ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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) ********** 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: (No Response) ********** 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: General comments: I enjoyed reading this revision about the direct and indirect effects of land-use intensity on plant communities across an elevational gradient. The manuscript improved much from the first to the revised version, especially the introduction is now clearer and the discussion is more consistent with the red line of the manuscript. The authors considered all comments on an earlier version of the manuscript or responded to my suggestions. Therefore, I have no more concerns. Two minor comments: Line 520: The sentence should start with “in our study”. Line 596: along elevation gradients (plural). Reviewer #2: Many thanks to the authors for carefully addressing my comments especially as pertains to the spatial autocorrelation analysis! I'm happy to see that these results did not alter the main take home messages of this paper. I believe that this paper will make an excellent contribution to the literature and am happy with the revisions as they currently stand. ********** 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: No Reviewer #2: 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. |
Revision 2 |
Direct and indirect effects of land-use intensity on plant communities across elevation in semi-natural grasslands PONE-D-20-07402R2 Dear Dr. Buzhdygan, 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, Harald Auge Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
Formally Accepted |
PONE-D-20-07402R2 Direct and indirect effects of land-use intensity on plant communitiesacross elevation in semi-natural grasslands Dear Dr. Buzhdygan: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Harald Auge Academic Editor PLOS ONE |
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