https://orcid.org/0000-0003-4464-1486
Peer Review History
| Original SubmissionAugust 4, 2020 |
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PONE-D-20-21262 The response of culturally important plants to experimental warming and grazing in Pakistan Himalayas PLOS ONE Dear Dr. Ali, 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. Both of the reviewers highlighted that your interesting study covers an important but understudied topic, and they appreciated the combination of experimental-ecological and ethnobotanical approaches. However, the manuscript needs more detail and clarity, as well as some improvement of statistical analyses, and has to be extensively revised. At this place, I would like to refer to two major issues only: First, the description of methods has to be improved. It remains unclear how the experiment was designed, thus more details of the experimental design have to be added. For instance, were all the (sub-)plots located within exclosures but clipped to simulate grazing? Was it a two-factorial experiment, with the factors warming and clipping crossed? Clarifying these details is essential to evaluate the appropriateness of statistical methods and the interpretation of results as well as to understand the discussion and the conclusion drawn. Second, assuming that it was a two-factorial experiment with replicates along an environmental gradient, the statistical analyses (just comparing species within each treatment) would be inadequate. An appropriate analysis will be a two-factorial ANOVA including the main effects of warming and of clipping as well as the interaction between these two factors. This model would then, for instance, allow assessing if the effect of warming depends on whether vegetation was clipped or not (reflected by the interaction term), which is an important scientific question itself. Accordingly, results of the warming x grazing treatment have to be reported and discussed as well. Furthermore, if you consider the site effect to reflect some random variation, you should use a mixed model and include site as random effect. On the other hand, if you are interested in differences between sites, i.e. if you have a specific hypothesis how sites should differ or how the effects of clipping and warming should change along your environmental gradient, you may even include site and its interactions as fixed effects! If you conducted repeated measurements on the same plots, you could either average your data across census dates or should apply a repeated measure ANOVA. The two reviews provide many helpful suggestions how to improve your statistical analyses. In general, the writing is a bit confusing and vague. The text has to be restructured in parts based on the comments by the two reviewers, and has to be carefully edited for grammar. The two reviewers provided many additional comments and detailed suggestions that have to be considered in a revised version of your manuscript. Please submit your revised manuscript by Oct 26 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. In your Methods section, please provide additional location information of the study sites, including geographic coordinates for the data set if available. 3. Please include additional information regarding the survey or questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, if you developed a questionnaire as part of this study and it is not under a copyright more restrictive than CC-BY, please include a copy, in both the original language and English, as Supporting Information. 4. In your Methods section, please provide additional information about the participant recruitment method and the demographic details of your participants. Please ensure you have provided sufficient details to replicate the analyses such as: a) the recruitment date range (month and year), b) a description of any inclusion/exclusion criteria that were applied to participant recruitment, c) a table of relevant demographic details, d) a statement as to whether your sample can be considered representative of a larger population, e) a description of how participants were recruited, and f) descriptions of where participants were recruited and where the research took place. [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: No 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: No Reviewer #2: No ********** 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: No ********** 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: Note to the editor and authors: Our evaluation of the ms is from the perspectives of plant community ecologists, as such, we are not qualified to speak to the ethnobotany survey approach and hope another reviewer will cover that aspect. Overall, this paper has potential to be an interesting study and a good contribution to the field of climate change responses, especially with the work in an important area for both biodiversity and human cultural, livestock, and medicinal use. Also importantly, the work covers a region of alpine tundra which is underrepresented in plant community climate change responses, which tend to be overly dominated by N. American and European datasets. As such, we see substantial value in the data the authors have collected. However, lack of clarity on the experimental design and potential issues with the statistical approaches make it hard to interpret the results. We have focused our suggestions on areas in the methods where the experimental design can be clarified, and some suggestions on how better to approach the statistical analyses given the study design. We recognize that these may seem like intensive changes, but encourage the authors to tackle it because we see the great intent of their project. Major comments: 1. The experimental design is really unclear. A diagram to include in or replace Figure 1 would help clarify this immensely. It was unclear whether all the measured plots were inside the grazing exclosures, or if any data was collected outside of the exclosures. It was also unclear whether there were four subplots in a factorial design (clipped, warmed, warmed + clipped, control) or some other nested design. Clarifying this is vital for readers to evaluate the statistical methods, interpret the results, and understand the discussion. 2. The statistical methods don't seem to be appropriate. It's hard to suggest an exact method that would be appropriate since the experimental design is unclear. However, a two-way model with grazing and warming as separate factors (and potentially an interaction term as well, depending on design) would be a good start. Additionally, we suggest using a mixed-effects model with a random effect for site. The authors repeatedly note that site effects were stronger than the treatment effects, and using a random effect for site will help separate these factors. Good packages in R for these types of simple mixed-effects models are 'lme4' using the lmer() function and 'nlme' using the nlme() function. For example, if there is no data collected outside the fences, and the experimental design is fully crossed warming and clipping (clipped, warmed, warmed + clipped, control), a good simple model specification (using lmer syntax) would be: biomass ~ warming * clipping + (1|site.id) (which is the same as) biomass ~ warming + clipping + warming:clipping + (1|site.id) This would then give you an output for the effect of warming, the effect of clipping, the interaction between warming and clipping, and with a random effect (intercept) for site idenity (ie: site A, site B, ...) and you could run this model for each species individually. And similar separate models for cover. There are more complex ways to approach this as well, including having all the species together in the model with either another random effect (intercept) for each species. However, if you think species respond differently to the different treatments, you would want a random slope, not just intercept. If you choose to go this route, or if there are also data collected outside the exclosure fences and you have a nested design, we would recommend consulting a statistician to help with the model design. Again, clarifying the experimental design would really help with this. An alternate approach if you think the differences between site are based on the altitude gradient, with predictable effects at high sites versus low sites, would be to use ANOVA with interaction terms (using the aov() function), and site altitude as a fixed predictor rather than site id as a random effect. The model specification could be: biomass~ warming + clipping + site.alt + warming:clipping + warming:site.alt although you might also choose to incorporate an interaction between clipping and site altitude, or even a three-way interaction if you think that's appropriate. 3. There are findings referred to in the discussion that are not included in the methods or results. These need to either be clearly incorporated as main parts of the paper, or removed from the discussion. For example, flower production, analyses of community composition, and differences in response based on site location--see more detailed comments in the "discussion" section below. The discussion in general is not clearly organized. It would help a lot if you identified your 3-4 main results, and then gave each of these a paragraph in the discussion (then connecting it to existing literature as you have done). 4. Please put the figure captions with the figures, it's very hard to evaluate it this way. 5. The data summaries are included but none of the underlying data (the actually collected data points for each plot etc) is available in the supplements or stored in repositories (ex Dryad, Figshare, etc) online. Minor Comments: Abstract - No information about any interaction between grazing and warming. Unclear if the experiment is set up to test this and they didn't find it, or if there were just the two treatments compared to one control. Introduction line 47 – 48 can you state a reference for this? line 56 this reference is not specifically about grazing, can you find more suitable ones? line 56 unclear what is meant with “selective palatability issues” line 64 you could start a new paragraph after “plant cover reduction”, this would facilitate reading the introduction and adds a clearer structure line 69-71 meaning unclear line 75 has previous research actually dealt with overgrazing or simply with the impact of grazing? line 75 -76 add references to the first part of the sentence and specify that diversity in plants in general may be well covered by studies but not so information about medicinal plants. The way the sentence is phrased now does not convey the important message that studies on medicinal plants are still underrepresented line 80 -81 sentence unclear, explain “benefit-relevant indicators” line 83 – 84 you could delete this sentence, since it does not add important information line 85 specify “resource” of what?, f.ex. income, remedies, etc. line 86 "Second," line 91--would be useful to give a rough metric of historical livestock vs current, instead of just saying it's increasing line 94--these two objectives seem pretty distinct, can you make the connection between them more clear? I think in general the introduction could be improved by adding more structure and clarity by defining open questions/research gaps for each paragraph. I also feel that references are partly missing or are not used in an accurate way Materials and Methods line 104 "July. " line 105 warmest year? warm years? line 106 only few °C below zero or much colder? line 104-107 would be good to know temp and precipitation in the specific study years line 110 "macrophylla, " line 112 "cattle and yaks" (although I recognize that cattles is also used in many countries, but it's the less common form) line 114 should be “Plantago lanceolata” line 115 should be “Poa alpina” line 117 greater than 5026 compared to what? And in what time frame and what is the unit (number of herbivores?)? Also 5026 is a very specific number, maybe just greater than 5000? Line 118 “immense burden” in what respect? line 119 varied rather than "the most versatile" line 119 - 120 need language edits in general line 128 "useful medicinal plant species are" line 128 are these questionnaires accessible in the SI? If so, please refer to them. line 119-126 this could be part of the introduction and would nicely support the aim of your study line 129 could you add information on how these valleys were different? Given you study the impact of warming and grazing on specific medicinal plants it would be interesting to know the general species abundance of those plants in these valleys. We assume you chose these valleys because they combined people with medicinal plant knowledge and abundance of your studied species? line 141 expression “collection of data the observations” unclear line 142--would be good to refer back to the altitudinal zones mentioned earlier--seems like this falls primarily into the middle zone (Alpine meadows)? If so, it may not be necessary to give such detail on the other two zones in the study site description. line 143 please also provide more details about the fence material you used i.e. height, mesh size, since this will inform the reader about the dimensions of the potential grazers in your system line 148 your experimental set up seems to focus on summer warming only. Does this align with predications for your study area? Given that your fences allow smaller rodents to pass, how did the OTCs affect those and their impact on the vegetation? line 149 does your observed temperature increase correspond with observations from other studies? Add references. FIGURE 1 -- the photos are good but (a) should ideally show the grazing exclosures (if you have it) and it would be very useful to have a basic plot layout diagram to clarify the set up. It's unclear what photos d-g are supposed to show. line 151 -- are the clipped subplots nested within the grazing exclosures? or within the open top chambers? Did you actually compare un-fenced areas, or is the clipping the only grazing treatment? That seems surprising since you have potential to do fenced and unfenced comparisons... would want better rationale for this decision. Herbivores can have many affects other than just clipping (dirt impaction, dung, nutrient cycling...) line 152-- no clipping, or no warming? So there were 2 warmed, 1 clipped, and 1 control? Or 2 warmed (1 clipped, 1 unclipped) and 2 unwarmed (1 clipped, 1 unclipped)? line 153 vegetative height? line 154-156 unclear what this means, also how often did you clip the plants, does the clipping treatment mimic the natural grazing impact, did you mark the grazing level on individual plants? Please clarify what you have measured and if your measurements were done before or after the clipping and whether they were repeated during the peak season or several years. line 169 the reference you state does not seem to focus on vegetation but on ground dwelling insects line 171 what are the selected plant species? line 174 briefly explain this method in a short sub sentence line 176 did you sample all occurring species or only those that you previously selecting. If the latter, why were they sampled for classification? line 178-179 Was this done in each year or just at the end of the study? Was it only done in the open top chambers or also the unwarmed controls? Was it for the whole 1 m x 1 m plot or just a portion of it? Was biomass sorted to species or just total biomass? line 179 What was the timing of the clipping relative to the plot surveys? Did you survey before or after clipping? line 180 why not a two-way ANOVA? are these treatments not interacting with each other? line 181 If the treatments are interacting, it should be a two-way ANOVA. If they're not interacting, a Tukey test still doesn't seem like the best fit, since it's generally for different levels of the same type of treatments (ex-low intensity vs high intensity grazing). We have suggested a mixed-effects model as the best option (see major comment #2 above). Given that you talk about “plant species” did you run separate models for each species? line 188 "The 'vegan' R package" Table 1 The inputs on what people have observed as climate change effects are really interesting! I think you could maybe highlight this more in your abstract/methods as a key component of the study. It would also be really interesting to directly compare the measured cover/biomass responses of species in the three categories: 1. observed by locals to have increased 2. observed by locals to have not changed in abundance 3. observed by locals to have decreased. Even if this is too small a sample to be statistically tested, it would be a great way to bridge the two components of the study. Also looking at the last two where the locals have observed range shifts--does this fit with the study's findings? Is “no effect” and “not observed” the same? What does “forage availability” mean, i.e. due to climate change this species is now available for forage? Just out of curiousity: all species occur at quite high elevations, presumably with snow cover during winter, still some of them are available all year round (f. ex. flowers and leaves of Primula macrophylla) is there simply no snow cover or do these species prevail under the snow? line 227 Saxifraga -- particular species? Fig 2. not really neccessary, can just go into the table Fig 3. Looks like the warming and grazing treatments were crossed? line 237 All the more important to include site as a random factor in the model, also did you expect to see differences among warming treatments? Line 240 is the grazing treatment the actual grazing treatment or the clipping treatment? line 259 This is where a two-way ANOVA with the interaction term would really show these results, not just having to visualize them graphically. line 259-260 this is interesting and novel and should be emphasized more throughout the ms line 264 are these results from a model across species? line 265 -269 what are the statistics for these results? Are they mentioned in the data analysis part? If not, please add! Figure 4 Are these the averages across sites? How do you define "susceptibility zones"? Please add more detail to the methods about this approach S2 Fig are the different colored points the three years? I think this would be clearer without the lines. Are the non-warmed plots here to compare to? Discussion In general, try to line the discussion sections up with your main results, which will help with the organization of it. In the very beginning you can have a summary of your most important findings, which should not only focus on the ethnobotanical survey, but also on the warming/grazing results. line 294 – 296 have you tested this relationship? line 297-299 this is repeated line 307 Did you analyze community composition overall? Or just visually with the NMDS? There is a function for this in the 'vegan' package, adonis() for PERMANOVA analysis that would be useful to support this part of your manuscript especially if it is one of your key findings. line 309 You haven't mentioned flower production as part of your methods or results--either remove this from the discussion or include it as part of your paper (i.e. in Methods and Results). line 311 Where in your results section do you discuss differences between species responses to warming at different elevations? This would be really interesting, but it isn't clear. line 313-314 “new opportunities” this is quite a bold statement, maybe you can put it in context with medicinal plant use line 314 to improve the structure of your discussion you could start a new paragraph after ending with “… for people living under cold conditions”. Remove “while” from the beginning of the sentence, otherwise the sentence does not make sense line 318-319 as mentioned earlier it is unclear whether your data are from inside fences only or also from outside the fences. If you did not collect data from outside the fences than it does not make sense to argue with different cattle density. Please clarify this already in the Methods and adapt this sentence accordingly. line 321 Here you mention cover collected outside cattle exclusion plots, but it's not clear from your methods or results that this data was collected and how it was collected/analyzed. Please either incorporate it fully or remove it from the discussion. Conclusion line 329 “grasslands” is mentioned here for the first time, so it feels a bit out of place, maybe you can add “alpine”? line 330 this sentence is nice, though we think an evaluation of ethnobotanical survey methods is not the focus of your study. As plant ecologist we suggest to highlight here plant responses to your experimental treatments and put that into context with the medicinal plants. Reviewer #2: This study addressed how culturally important alpine plants will respond to climate warming and increased grazing pressure. This is a relevant and understudied topic, and I appreciate the integration of experimental manipulations with data collected from interviews of local people. However, I was confused by the study design- were the grazing treatments simulated grazing (clipping) as stated in the methods (lines 151-152), or grazed by animals, as suggested in the discussion (lines 318-319)? There was mention of grazing exclosures, but it was not clear whether plots were established both within and outside of them. Also, how many plots were established at each site? A diagram of the different sites, plots, and subplots would be helpful in clarifying the study design. Also, were species responses averaged over all 5 sites? The authors state that there are large differences between the 5 sites along the elevational gradient, so it doesn’t seem appropriate to completely ignore this gradient. It seems that the 5 sites were treated as experimental replicates, but they are inherently different. Were there replicate plots at each site, as well? In general, the methods and results could use much more detail (see line edits below). For instance, wasn’t there a warming x grazing treatment? I don’t see those results reported anywhere- just the separate effects of warming and grazing. Also, the discussion section could provide more synthesis about how the survey data and experimental results complement each other. Overall, this is an interesting study (great work!), but the manuscript needs more detail and clarity. It also needs to be revised for grammar. Line edits: Lines 25-26: The description of the treatments is confusing, and lists 2 separate “controls” Lines 30-31: Is the percentage cover or biomass reported here? Lines 67-68: how do nutrients “counteract” the harsh environment- need more explanation Lines 70-71: This is worded awkwardly Line 80: Please explain what “benefit-relevant indicators” are Lines 128-137: Need much more detail about the surveys. What types of questions were asked? Were they oral or written? How were people selected for the survey? Lines 143-144: How do 2 plots fit inside a 5x5 m fenced area, when a single plot is 5x5 m (containing four 2.5x2.5 m subplots)? Lines 151-152: The un-closed parentheses make this sentence confusing. What is considered a “control” in this experiment? It would be helpful to assign unique names to all your treatments so that you can remain consistent when referring to them. Line 154: Does clipping (simulated grazing) one time each year effectively simulate the continuous season-long grazing this region usually experiences? Line 169: I know you cite a source for this, but it would be helpful to briefly describe the “quadrat sampling method.” Line 172: Size of the quadrat grids? Also, I thought the subplots were 2.5 x 2.5 m (not 1 x 1 m)? Lines 174-175: Plant height is measured, but not reported in the results. Line 177: What does it mean that plants were “sampled”? Weren’t they just identified to species? Lines 178-179: Were the entire plots clipped? And does repeated clipping of the same location for multiple years affect results? Are plant species mostly annuals or perennials? Were the control and grazing plots also clipped (only the OTC plots are mentioned). Lines 180-181: It looks like the ANOVAs were just done to find differences between species within a single treatment (warming or grazing). However, you might want to compare the responses across the different treatments to determine if there are differences between plant growth in the control, grazing, warming, and grazing x warming plots. I find that a much more compelling question than differences between individual plant species. Also, it looks like you compared relative increases of the treatment plots compared to control plots (% increase/decrease), but this is not stated anywhere in your methods. Finally, are responses averaged over all 3 treatments years? Since you sampled the same plots multiple years in a row, you probably need to use a repeated measures ANOVA. Lines 190-192: This sentence is not needed. Lines 192-197: This should be included in the “Ethnobotanical Surveys” section of the Methods. It is out of place here. Lines 201-207: Need more details about the results of the surveys Line 213: I think a part was omitted since it starts in the middle of a sentence. Line 234: Since you calculated % increase in the treatment plots compared to the control plots, how did you account for pre-existing variation in plant cover of the different species between the 2 plots? Lines 259-269: What data is used here? It looks like you are using separate plant responses to just the warming and just grazing plots. Where are the results for the warming x grazing plots? Line 295-296: How does the RFC value influence plant availability in the warming treatments? I thought RFC was just an indicator of how often people mentioned the species in the interviews. Lines 297-299: These sentences are repeated. Lines 309-310: This is the first mention of flower production- it is not reported in the methods or results. You can’t introduce new results in the discussion section. Lines 323-324: “A constant increase in species cover through time can occur under moderate grazing conditions” --- Are there sources to back up this claim? Your results do not necessarily support this. Lines 334-338: Citations for this? Also, this would be good to mention earlier, maybe in the introduction. Tables & Figures: Table 1: You should specify which information is from the surveys and which is from another source (which should be cited). Also, how are the “most preferable” forage species determined? Fig 1: These pictures are lovely, but I think they are mostly unnecessary. Maybe just panel b showing the OTC. A better figure would be a diagram (or annotated picture) of your plots and study design. Fig 2: It might be nice to color the bars by plant functional group (shrub, forb, grass), so someone unfamiliar with the species can at least know the growth form. Fig 3: The figures are very fuzzy, so it is hard to read, but I don’t see any letters showing statistical significance as stated in the legend. Also, what do the geometric shapes around each error bar show? You need units for the y-axis: Biomass (% change). Fig 4: What does each point represent? A different site? A different year? Also, similar to my comment above, what data is shown? I don’t see how you can report these 4 zones if just showing the response to the combined warming x grazing treatment. Fig S1: The colors in the pie chart (panel b) are impossible to distinguish- there are way too many categories. Consider an alternative format. Also, I’m unclear as to what is shown in that chart- is the “study area” across all 5 sites? And before or after the treatments? Doesn’t plant species coverage change significantly between the sites? Could be good to show separated by site. Fig S2: Isn’t one of the OTC “grazed” for each site? I would be helpful to specify which one is grazed for each site. Also, I assume each color is a different year of the study? If so, you need to add a legend. Table S1: In order to visualize which species are present across multiple sites, it would be better to list all possible species in a column on the left, and then put an “X” next to a species when it is present at a site. That way, a common species will have five “X’s” all the way across to indicate it’s present at all the sites. Table S3: You don’t need both columns- just include the mean ± SE column. Also, what values are reported? It looks like relative differences between the treatment and control plots (and not actual biomass (g/m2)). If so, this needs to be stated in the table legend. Is there also a table for the warming x grazing treatment? ********** 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. 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PONE-D-20-21262R1 The Response of Culturally Important Plants to Experimental Warming and Clipping in Pakistan Himalayas PLOS ONE Dear Dr. Ali, 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. First of all, we acknowledge the substantial improvements of the manuscript in response to previous reviewers' comments, however there are still various issues that have to be considered in a thoroughly revised version. For instance, you applied a variety of different statistical approaches for the same research questions, which makes the interpretation of results difficult and confusing. You may wish to focus on the approach that is most appropriate for a respective research question or hypothesis, and show only tables and figures related to that particular approach. The reviewers provide various further recommendations how to improve the clarity of figures and tables. In addition, the storyline, or direction, of your manuscript is still a bit unclear. For instance, you could have stronger focus on how your experimental results provide information about the future abundance of culturally important plants in your region. Furthermore, I recommend considering the detailed recommendations and suggestions by the reviewers how to improve the introduction, the methods section, the results and also the discussion. Finally, the whole text would benefit from a thorough edit for grammar (including typos) as well as more clarity. Please submit your revised manuscript by Jan 24 2021 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: (No Response) ********** 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: Partly ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: No ********** 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 Reviewer #2: 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: No ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors' revisions have improved this manuscript substantially, especially with the clarification of the experimental set up and much clearer flow in the introduction and discussion. We appreciate all their work. In its current form, this manuscript still needs substantial edits to be ready for publication. Most importantly, the statistical approaches need to be focused and clarified--we suggest ways to do that. Our major suggestion is that you focus on one statistical approach, and highlight the model output and related figures from that approach. At the moment you have added the approaches suggested by the reviewers, but as a result have ended up with multiple overlapping modeling approaches. This makes the results difficult to interpret, and also an overwhelming number of supplemental tables and figures. The most appropriate one seems to us to be the linear mixed model with the random effects for site and species, which is discussed in the methods and highlighted in Figure 2 and Supplemental table S5a. Having both the ANOVA and the mixed model for the same response variables is redundant and causes confusion. In our following comments we highlight ways that you can focus on and further clarify this statistical analysis and the results, as well as other more minor areas in the manuscript that need some revision. Other general comments: Plant height is mentioned in the methods as data you collected, and again in the discussion. However, it is not included in the statistical analysis methods or in the results. You either need to clearly explain how you analyzed height and what the results were or remove it from the manuscript. Check for typos in the main manuscript (species needs the 's' at the end for both one species and many species, authors names should be capitalized, other small typos) and the supplementary information Figures Figure 1 is very helpful but is still somewhat unclear. For a start, please add the more detailed information you gave in your responses to the reviewers on the plot layout to the figure caption--the current caption is insufficient. Also, please make the various rectangles areas roughly to scale (the 1 x 1 m sampling plot inside of the 2.5 m x 2.5 m area is much bigger than it should be). Additionally, it's unclear what the smaller extra "control plot" areas adjacent to the OTC diagrams are supposed to be, or what they were used for--are those part of your study and sampling design? It would be really helpful if you could mark where one year's biomass sampling would have been conducted, since this is still somewhat unclear in the methods--for example by shading the relevant area in grey. Finally, it's not clear what the "Species composition" labels are supposed to indicate. Figure 2 seems to us to be the most useful results figure, and just needs some small edits. The subplots should be labeled A, B, C, D not A.A, A.B etc for clarity. Specify in the figure caption if the error bars show standard error, standard deviation, or something else. Also, the *** significance marks are not clear--do these show differences from the control? from each other? Figure 3 this is mostly overlapping information with the second half of figure 2, and should be removed or moved to the supplement. Figure 4 is good as it is Supplemental Figure S1 good as-is, although it would be clearer to write out "percentage" rather than "%age" Supplemental Figure S2 the order of the treatments in A and B is different, which is very confusing when looking quickly at the figure. Please change the order for S2B to match the order in Figure 2 and S2A. Please add more information to the figure caption with what tests etc were used to produce the figure. Supplemental Figure S3 is redundant with Figure 2 and can be removed Supplemental Figure S4 needs information in the figure caption as to what the different colors represent. Also, the caption says "The relative abundance of plant species (presence/absence)" Which is it? Abundance measures are generally biomass or maybe cover, while presence/absence is a binary. Tables Supplemental table S2 This would be better to have one column for each site, and mark which species occur where rather than just tallying the number of sites they occur at. "Understudy" (used here and elsewhere in the ms) is unclear--do you mean understudied, that they have not been paid attention to in the literature? Supplemental table S3 we recommend focusing on the linear mixed effects model and dropping the ANOVA approach in the methods, results, and here. For that reason, we suggest deleting these tables. Supplemental table S4 is good as it is Supplemental table S5. We suggest moving Table a to the main manuscript, and including F-values rather than just p-values. These can be gotten by using the summary() function on the model fit. Table b should be dropped -- it's better to have the interaction between the treatments than combining them in this way. Table c can be kept in the supplement. Introduction Line 56 – 61 These information are all good, but go beyond scope of the introduction. From my point of view, the essential information would be contained in a sentence like “ Repeated grazing can lead to exploitation and reduction of highly palatable species which are less resistant to severe grazing”. I still think that “selective palatability issue” is little unclear. Maybe instead of using this term you can rephrase it into the issues you are talking about. For example, do you mean that grazing leads to a change in forage species availability grazing animals can chose from? You could say “This leads to changes in plant availability that grazing animals can feed on and also to changes in nutrient availability”. Nutrient availability of what? Leaves? Line 85-86 Maybe you can add a reference to this sentence Line 88-89 Even though you nicely improved this sentence, I still don’t have any idea about what these indicators are, maybe you can provide an example of such an indicator or explicitly write what are the indicators in your study. This information is essential for readers who have not been working with these kind of indicators before. Line 94 unique richness of what? Plants? Line 108 you may mean “investigate” instead of “indicate”? Line 110 “factors” is not necessary Line 112 -114 This could be deleted since the information are already given in the objectives before. If you want to keep it, change the order so it matches the order of the objectives. Methods: Line 119 km2, lowercase k Line 120 replace “it” with “the study” Line 121 replace “it” with “summer” Line 120-121 simplify this to just "from May till August" since it's also August at higher elevations Line 126 declines of what? Line 129 "The alpine KNP region includes the following..." Line 141 space missing between “biomass” and “(“ Line 148 -151 The exact same sentences appear earlier in the introduction, you might want to delete them here to avoid unnecessary redundancy? Line 153 Needs to refer to a specific table or part of the supplementary information (currently Supplement S6?). It may also be helpful to have one supplementary document with figures and tables and another one for the questionnaires only. This you could for example name supplementary information II, so the interested reader directly knows where to find the respective information. Line 161 -163 This is phrased little awkward, I assume you mean that those species were abundant in your experimental sites? I suggest to rephrase this sentence. Line 163 This would be a good place to add more information on what main questions you asked about each plant, since most of your readers won't want to be searching through your supplement. Something like "For each species, we collected asked informants about... [climate change responses, etc]" Line 206 -209 I suggest that this entire part could be integrated into the data sampling part Line 216 Why to simulate growth, isn't the intention to simulate herbivory? Or do you mean you want to observe growth under herbivory? Line 219 -220 For consistency it would be good to move the sentence about the height measurements to the data sampling paragraph Line 257- 260 In the first part you write that you analyzed species-specific responses, but the tables show model results across species. I suggest you either adjust this in the text or refer to a table/graph with species-specific results. Furthermore, table b in S3 does report results of linear mixed effect models (according to the subscript of the table), this is confusing, because you don’t mention linear mixed effect models when you refer to the table in the supplementary information. Also related to table b in S3, it is not clear to me whether site and species were used as random or fixed factors in the model. In the text in your ms you report them as random factors, but in the table they seem to be reported as fixed factors. Also, you only report the interaction of W x CL but no main effects. It would be good to include these in the table and also specify which test you used to assess the significance of the treatments like F- or ChiSq test. You can access these tests after you have run your mixed effect model via the Anova command from the “car”-package: Anova(mymodel, test.statistic = “F”) for F-test. Instead of using the summary statistics as you now did in table S5 you can instead report F-test results. Related to table S5 do you have an explanation for why the conditional R2results in NA when percentage cover is the response variable? Line 261 Please add a reference to the R package you used. The most common packages to run linear mixed effect models are either lme4 (Bates et al. 2015) or nlme. Line 264 -267 This is a key section that needs to be clarified. First, I think your response variables were the same as in your ANOVA models e.g. biomass and percentage cover, so these should not be termed as fixed factors but as response variables. Second, neither biomass nor percentage cover are metrics of diversity! It can be helpful to actually include the model formulation here, which I think what you're trying to say is: cover ~ warming * clipping + (1|site) + (1|species). The best way to describe this model would be something like "Response variables of percentage cover and biomass were modeled using [xx package] with fixed effect predictors of the warming treatment, the clipping treatment, and their two-way interaction, and random effects for site and species (Table xx). We separately ran models with species as fixed effect to check the effect of treatment for each species (Table xx)" Line 267 I suggest starting a new paragraph for each different analysis you conducted--one for the linear mixed model, one for the susceptibility zones, one for the NMDS. I think you also need more information about this "susceptibility zones" figure 4--why did you do it, how did you do it, what is it intended to show? Line 275 You should also report which version of R or RStudio you used (latest version in R is 4.0.3). You can f.ex. write: We used R (RStudio) to run all analyses (R Core Team 2020 version XXX). For the vegan package you have to cite (Oksanen et al. 2017). There is a neat function in R called citation() which shows you how to cite the packages you used Results Line 321 - 328 This section with the ANOVA can be removed if you focus on the results from the linear mixed effect model. Also the numbers reported here don't match the p-values in S3 Table B, shouldn't they be consistent with that? Line 331 - 343 The language here makes it sound like you are testing the effect of the site "impact" rather than just variation. Also words like "increased" and "changes" make it sound like you're looking at the change through time, but your methods indicate you're just looking at the differences between treatments. Instead you should use statements like "has higher cover than the control" to match the analyses you're doing. Line 337 It is advisable to avoid “seem” if you have statistical evidence for something having an effect. Line 340 Negative? I thought it was positive--higher in the warmed plots? Line 341 How can you state this, if you have pooled the data across years? Did you run separate models for separate years or did you include year as a fixed factor in your mixed effect model? You would need to either explain these models in your statistical analysis section and include them as ex supplemental tables, or remove this part. Line 344 You should have 1-2 more sentences here on the species-specific results that are presented in Figure 2B Line 347-351 This sentence is not clear to me. Do you intent to say that sites did not significantly increase the variation in your data? Assuming you had site as a random effect in your model. Line 355 You can compare the responses in your treatments plots to the control, but usually control is not considered a treatment. It would thus sound better if you wrote something like "...in above ground biomass of each species in response to warming, clipping and warming x clipping compared to control. Line 378 Should there be a new paragraph here from the NMDS results? Line 380 Isn't this supplemental figure S4? Line 382 This supports the choice to incorporate site as a random effect in your mixed effects model Line 403 Delete “for” Discussion In your discussion it would be really nice if you could further emphasize the connection between your experimental findings and the ethnobotanical survey. Also, instead of AGB just say biomass, it doesn't take much more space and is much easier to read. Line 418 You did not really measure community data, but rather species-specific warming and clipping responses. Line 419 - 420 The commas before and after "was" should be removed, and there should be a comma added after "sites" Line 425-427 In your methods section (the statistical analysis) you don't report that you have used height as a response variable, nor do you report it in any of your results. If you did, you should add it, otherwise you cannot discuss it here. Line 429 I think you are combining two plausible mechanisms here: competition for resources and limitation in space. You might want to elaborate on both of them. Check ex. Borer et al. 2014 in Nature Line 463 "Other studies on alpine meadows [where?] also suggested..." Line 469 Since intensity and frequency of clipping should have been the same for all of your studied species I think it is rather something else that drives this species-specific response. You could think about whether this species has specific traits allowing it to regrow fast after clipping/grazing which the other species might not have. Line 473 "clipping" not grazing Line 478 "stronger" not "sturdy"? Line 490-492 This sentence is not clear to me. Do you want to state that the species you studied are more susceptible to warming than to grazing? Line 493 Wang et al. add the year Line 494-499 The first part of this part is about the impact of clipping, but you then refer to results of your survey in relation to warming. Please, clarify this. Also, can you state references for the loss of biodiversity. There are plenty of good ones available! Line 501 You haven't reported any measures of diversity related variables like species richness, so speaking about biodiversity isn't appropriate here. Reviewer #2: The authors have made substantial improvements, especially with describing the experimental design and survey methods. However, while there have been clear attempts to improve the statistical methods and results, I’m unclear about which approaches were used and why. It seems the authors used several different models (one-way ANOVA, two-way ANOVA, mixed models with different random factors), but I don’t think they are all necessary. The model interpretations in the results section are confusing, and do not clearly align with specific experimental questions. Instead, the authors should decide which questions are most interesting and choose 1-2 statistical methods based on that. Also, I’m unclear on how the % increase/decrease values were calculated (lines 250-252) and whether they represent the entire 3-year experimental duration. I still think it could be best to use repeated measures with year as a variable in the statistical model to see how the warming and clipping effects built up (or not) over multiple treatment years. Also, there is some discussion about differences between elevational plots (i.e., lines 333-335, 500-505) but it’s unclear how that was formally assessed. The survey and experimental data are better integrated in this revision, but the paper still lacks a clear storyline. There needs to be more discussion around how the experimental results provide information about the future survival/abundance of culturally important plants in the region. The figures also need refinement (see comments below), and the entire manuscript needs to be edited for grammar and clarity. Lastly, this might be the journal format, but I found it extremely difficult to review the figures and supplemental figures when they were all separated from their legends (figure legends embedded in text, figures at end, supplementary legends at end, supplemental figures had to be individually downloaded). Again, I believe this is an interesting study, but the manuscript still needs improvement. Lines edits: Lines 44-46: This is unclear. Land and water degradation does not “cause” climate change. Line 49: Not “global” mean surface temperature if just referring to the Himalayan region. Lines 85-86: I appreciate that “ecosystem change assessment” is defined, but the definition is still unclear. Also, the rest of the paragraph doesn’t mention these “ecosystem change assessments,” so why is it brought up here? Line 106: “primarily runs the financial circle” is unclear Lines 112-114: This last sentence is unnecessary Line 123: Incomplete sentence Line 133: Is “yoks” supposed to be “yaks”? Lines 144-151: This was all stated in introduction already, so is not needed here. Lines 156-160: Put this description of the valleys into the previous section (Study Area). Lines 161-162: Put this sentence into the next section (Warming and Grazing Experiments) Lines 167-170: The RFC description should be included in the “statistical analyses” section instead. Lines 171: What does “we involved plant material” mean? Lines 182-183: What does “which lies in alpine meadow of the vegetation zones” mean? Line 184: Since there was only 1 replicate for each elevation, the entire experiment is an RBD, but not each site. Lines 186-188: Were the data collected outside of this fenced area used for any analyses? I don’t see it used. Line 191: Where was this reported earlier? Or do you mean it was reported by another prior study? Line 197: How can a hexagonal shape have the dimensions of 1.5 x 1.5 m or 1 x 1 m? This reporting style is reserved for squares/rectangles. Do each of the six sides have that length? If so, that needs to be stated. Line 198: Since your fences prevented grazing, they should be called “exclosures” instead of enclosures throughout the paper. Lines 212-214: This is confusing. Line 214: Define the abbreviation “W x CL” the first time it’s used. Line 216: Simulate “grazing” (instead of “growth”)? Lines 218-219: What is described here? I don’t understand the 2 grazing comparisons. The analyses only discuss the manually clipped plots. Line 220-221: This is confusing. Line 224-225: Remove this sentence. Line 132: How large were the quadrats and the quadrat grids? Line 234: How were the “selected plant species” determined? Lines 236-241: Put all the species into a table and reference it instead. Lines 243-244: What does “vertical projections of vegetation” mean? Line 248: How large were the clipping areas? Were the same areas clipped multiple years in a row? Line 250-252: I’m unclear about what you used to calculate % increase/decrease for the data. If the values were averaged over all 3 years, how was % increase/decrease calculated as the “difference between control and last year data points”? Lines 155-156: This sentence not needed here. Line 290: Missing % for Asteraceae Lines 291-293: Unclear Lines 301-302: This sentence not needed. Lines 306-308: Save for discussion section Lines 308-309: This is confusing. Lines 313-315: This sentence not needed here. Line 321: What does “across all three growing seasons” mean in this context? Average over 3 years? The value at the end of year 3? Each year assessed independently (then year would need to be included in the statistical model)? Line 425: Plant height was not statistically analyzed or discussed in results section, so should not be mentioned here. Lines 425-428: Unclear Line 456: State author’s names (instead of reference number) if specifically referring to a study. Lines 490-494: Unclear Lines 496-497: How does the data support this assumption? Lines 500-505: I like the biodiversity discussion. Expand on this more. Figures: Figure 1: The figure legend needs to include much more detail – it needs to fully describe each component of the plot design. For example, why are there control plots in the warming and warming x clipping larger plots? What do the letters on the OTC mean? Unclear what the 1 m and 1.5 m arrow are pointing to. Figure 2A: First, these should be bar charts or box and whisker plots instead of line graphs. Line graphs are usually used to represent changes through time. What do the stars signify? Panel A needs a better y-axis label (no shortened words, underscores). Legend line 348-349: Is there statistical evidence for this claim? Line 349-351: This is not needed here. Figure 2B: First, why is this labeled “2B”? It appears to be an entirely separate figure, so should be “Fig 3.” What do the stars and dots represent? The axis labels should be written without underscores. Also, why does it appear that most of the control plots increased? How is it that none happened to decrease over the 3-yr period? Figure 3: You explain in your review response what the “beans” represent, but this description needs to be included in the figure legend. It would be helpful to label each panel as “warming” or “clipping” depending on what it shows. It might also be nice to identify (maybe by color) which species are the most culturally important- it ties this data to the survey responses that way. Again, there are still no letters indicating statistical significance (as stated in the legend). The stars show statistical significance of each bar compared to what- each other? Figure 4: What do the stars mean? Figure S1: Improve y-axis label Figure S2: Similar to figure 2A, these should all be bar chars or box plots. Improve axis labels. For the right panels, re-order species to group by cultural importance or functional group. Much more detailed legend needed. Figure S3: Omit or re-structure this figure- it’s unreadable. Figure S4: What do the different colored dots represent? It’s hard to tell which labels go with which points. I’m not familiar with these types of plots, but this is confusing to me. Maybe put more description in the legend? Table S2: Thanks for editing this table. One suggestion – make separate columns for each elevation, and then put an X in each column where a species is present at that elevation. Right now, you can’t tell which species are present at which elevation. Table S3 & S5: Include the full ANOVA tables/statistical output. More than just the p-values should be included. Data points: Need metadata- full description of what each dataset it and the meaning of each abbreviation. ********** 7. 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| Revision 2 |
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PONE-D-20-21262R2 The Response of Culturally Important Plants to Experimental Warming and Clipping in Pakistan Himalayas PLOS ONE Dear Dr. Ali, 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 manuscript has improved significantly after tow rounds of revisions. However, there are still some minor issues, particularly related to statistical tests and language, which need further attention. Please submit your revised manuscript by Apr 19 2021 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, Abid Hussain 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 Authors, There are still some minor issues in statistical testing and language. Please address reviewer's all comment adequately and resubmit. [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) ********** 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: Partly ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No ********** 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 ********** 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 ********** 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 comment The manuscript has hugely improved and is much easier to read and understand. There are still some issues of confusion with the statistics, including the "Factor x species" model on line 240, use of t-test to assess the significances of the treatments, and understanding/reporting/interpretation of the interactive effect. Furthermore, the authors present results for the different sites for which the description of the analysis and model output tables are missing. Specific comments marked with * are particularly important. There is still some language that is confusing or unclear in wording, especially in the results and discussion. Also, please check for upper- and lower-case letters throughout your figures and tables and chose a consistent style. Consistency is also needed concerning the terminology of the clipping/grazing treatment and aboveground biomass. The authors state that "Yes - all data are fully available without restriction" and "All relevant data are within the manuscript and its Supporting Information files." but we see NO raw data in the supporting information file, just the supplemental tables with output. We hope this is an accidental error but it needs to be corrected to meet the journal data requirements. Running title and abstract Line 13: Lowercase “H” in herbivory Line 22-23: This sentence may be easier to understand and read if you wrote: “Experimental warming increased biomass and percent cover throughout the experiment”. It is not necessary to report the p-value or that you used sites as a random factor. The abstract should highlight your main findings in a concise form, so avoid any unnecessary detail. Line 27: Unclear what “due to it’s abundance at the site” means. Line 28: Had instead of “has”. Line 29: For consistency it would be good to give the same names to your treatments. Clipping and simulated grazing are the same, right? Can you change this? Line 31: Stronger effects, what does this mean? Please, report whether this refers to an increase or decrease. Introduction Line 58-59: Sentence unclear, maybe the “to” needs to be replaced with “for”? Line 60: Delete the “s” at the end of “causes”. Line 83: underrepresented? Line 84-85: Sentence unclear. Line 101: This is the first time your mention KNP, please provide an explanation of the abbreviation. Methods: Line 117: No brackets needed when you mention the altitude. Line 126: Parking area?? Line 132: Comma missing between lanceolata and Saxifraga. Line 139: I think you mean individuals instead of species here. Line 190: Here you write that your clipping plot inside the fence is 2.5 m2, but from Figure 1 it looks like it is 1m2. Please clarify this. Line 193: Could you add the clipped area inside the OTC to Figure 1? Line 209: Lowercase “a” in “all”. Line 212: As pointed out in an earlier review, this reference seems not appropriate for plant metrics, but focusses on ground dwelling insects in riverbeds. You could cite for example Shaver and Chapin 1991: Production: biomass relationships and element cycling in contrasting arctic vegetation types, Ecological Monographs. Line 223-224: What do you mean with “We clipped the vegetation from OTC”? This sentence needs clarification. * Line 240: The model formulation for this second, species-specific model isn't clear. What is "Factor" in this model? I think what you're intending to write is Factor * species + (1|site)? Line 241 -244: Sentence unclear. *Line 244: “polygons- based susceptibility zones” unclear. If this is an established method you should provide references. * Line 246: You should add here which kind if test you used to assess the significances of the treatments, and what function or package you used for that test. Line 250: Point missing between “groups” and “the”. Results Line 267: Percentage for Asteraceae is missing. Line 295: You state that clipping is not significant, but in Figure 2a there are three asterisks to indicate high significance. Same for the interaction which is not significant according to Table2. Also based on Table 2 there should be two asterisks for the interaction the Figure 2b and only one for the clipping treatment. Line 307: Why two models? What you show in the table can be derived from one model which contains both the main effects and the interaction. Line 314 – 316: Species is missing an “s”, the sentence is unclear. Line 318 -320: This sentence could be moved to the results, but is not needed to describe the figure. You already do that in a) and b). Line 319: Write the full name of the treatment, not just “warm” and “clip”. It is always good to be consistent in the use of treatment names/terminology! Line 319 – 320: If clipping had a consistent negative effect you would see this as a main effect. Here you need to think about why the combination of warming and clipping decreases percentage cover. Line 322: See the above comment. In general, you don’t need to add interpretations of the results to the figure caption, reserve this for the discussion. * Line 326: You did not mention in your statistical analysis that you assessed differences in percentage cover and biomass between the different sites. Please add this information. Furthermore, you should also provide a table with the model output. Referring to the figure only is not sufficient because the reader cannot judge based on a figure whether something is significant or not. Line 330 – 333: Sentence unclear and confusing. Line 336 – 337: Higher biomass is a result of warming, but warming is not determined by higher biomass. Please, rephrase this. Line 337: Figure S2 species-specific plots, are these plots in response to warming or in response to clipping or both? What does this figure add in comparison to figure 3? Line 343: Comma missing between ruprestis and Poa. Line 353: Using “suggest” here seems not fitting, rather use “show”. Line 356 – 357: This seems to be the same information than in the beginning of the paragraph just in other words. Consider to delete this? Line 358-359: Instead of “relationship” it would be better to use “effect” here. Also, not sure what you want to say here. Line 361: “though” may be the wrong word here. Line 362: Something is missing in this sentence, most ….? Line 365: There is no S4 figure in the supplement. Line 370: Do you mean increase or decrease? In the previous part of the sentence you write about a negative effect of clipping, so I assume it should be decrease. Again, it is confusing that you write clipping was not statistically significant but Fig.2 shows significant asterisks for the clipping treatment. Line 381ff: You describe panel a) but not panel b) in your figure. The meaning of “…than clipping” is unclear, could be removed? Discussion Line 392: In the results you say that clipping has NO significant effect! Line 394: Insert “increasing temperature” here, because OTCs are used to study effects of warming and not just temperature. Line 404: enhanced Line 405ff: Try to focus only on the warming treatment and not suddenly list discussion points related to the clipping treatment, since you will have a separate paragraph for it later. I suggest moving all discussions relevant to clipping treatment to the appropriate paragraph. Line 435 ff: I suggest moving all information related to warming to the previous paragraph. Otherwise, it's confusing to read about the ethnobotanical survey and then jump back to warming. Line 458: “… thus allowing natural selection to favor herbivores” does not sound right. Line 463 – 464: The sentence starting with “therefore” is unclear. Line 468: For consistency please decide whether you want to use AGB, aboveground biomass or biomass throughout the manuscript. If you use too many terms for the same variable, it becomes very confusing. Line 477 -479: Sentence unclear. Line 479 – 481: The reasoning here is unclear and not convincing. Your interaction shows that the positive warming effect is strongly reduced by clipping, so in my opinion you should discuss why grazing overrides the effect of warming. Line 485: Figure 2 does not show the information you are referring to. Figure S2 shows species specific responses, but it is unclear whether these are in response to the combination of warming and clipping. Please, clarify both the figure and the text! Line 501: What do you mean with indirect warming effects. Please explain in the text. Line 503 – 505: Sentence unclear. Line 511: Point missing before “Finally”. References Reference 29 and 31 are the same Reference 75 is not related to your topic and does not support the point of the sentence in which the reference is cited. Sometimes the references are reported in different styles e.g. number 54 includes editor names, number 74 has these lines | between names. Please check that the style of the references is consistent! Figures * Figure 1 Has improved, but there is still a confusing sense of scale, as the areas labeled "1m" are almost as large as the areas labeled 2.5m. Also was the species composition conducted in a hexagonal area or a square? Right now it looks inconsistent between the two treatments. What about the biomass extraction area, which is a weird shape? Where was the biomass extraction for the control and clipping-only plots? Figure 2 Please, put the correct amount of * to each treatment. For now, the model output, the text and the figure are not consistent regarding the significance of the treatments. Figure S2 The first graphs (a and b) are the same as Fig.2. Consider to delete these, because they take unnecessary space. Furthermore, it is unclear in the species-specific graphs whether these show responses to only one of the treatments or if the data are averages across all treatments. Figure S3 This does not have a clear message. Consider deleting it. Figure S4 Is missing, but referred to in the text. Tables Table 1 Good, but pay attention to consistent use of upper- and lower-case letters in the beginning of each word. Table S2 Good, though in the caption “specie” is supposed to be “species”. Table S4 Please see comment to line 240. ********** 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 [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. 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| Revision 3 |
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The Response of Culturally Important Plants to Experimental Warming and Clipping in Pakistan Himalayas PONE-D-20-21262R3 Dear Dr. Ali, 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, Abid Hussain Academic Editor PLOS ONE Additional Editor Comments (optional): Dear Authors, Thank you for addressing the concerns adequately. Reviewers' comments: |
| Formally Accepted |
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PONE-D-20-21262R3 The Response of Culturally Important Plants to Experimental Warming and Clipping in Pakistan Himalayas Dear Dr. Ali: 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. Abid Hussain Academic Editor PLOS ONE |
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