Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE FUNGAL COMMUNITY IN NON-RHIZOSPHERE SOIL OF PANAX GINSENG ARE DRIVEN BY DIFFERENT CULTIVATION MODES AND INCREASED CULTIVATION PERIODS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This ms studied the impact of cultivation models, period and fallowing on fungal community composition in the non-rhizosphere compartment of ginseng soil. The current ms did not use the data effectively. Current result cannot support the objective of this study perfectly. Introduction, discussion and conclusions also need be improved. There are a lot of minor mistakes in current ms, the authors should be more careful.
My specific comments are as follows:
Title: present title is not appropriate. There are five treatments in your ms, which also include different cultivations and cultivation period. Only considering fallowing is not appropriate.

Abstract:
Lines 22-28 part of background is too long, please shorten them. Meanwhile, only fungal community composition cannot represent or reflect soil microbiome imbalance. The objective of measuring fungal community composition is not clear, reconsider it please.

Lines 28-31 Introduce your treatments more clearly, this can help readers understand your research quickly. (cultivation models, cultivation period; W15, W35, C2, C5, F10)

Lines 38-40 conclusion is not well written. I think that you cannot say fallowing is a practical and effective practice to restore healthy fungal community only according to the results of OTU richness and PD whole tree.

Introduction:
Lines 47-50 As you cited here (It has been reported that replantation of ginseng 50 may cause up to 75% of ginseng seedling death), continuous cropping obstacles is a limitation of yield and quality of Ginseng. Thus, soil microbial community imbalance is a factor of continuous cropping obstacles. For soil microbial community imbalance, the growth of pathogenic fungi is a main factor of yield decrease of Ginseng. I suggest that add some data of Ginseng yield and quality, and then do some functional prediction analysis using FUNGuild (http://www.stbates.org/guilds/app.php). Combination of the results of alpha diversity and functional analysis can represent soil microbial community imbalance effectively. These will improve this ms a lot.

Lines 57-60 All right, but you did not offer the result of bacteria in this ms.

Lines 69-74 Objective is not well written, reconsider and improve it please.

Materials and methods:
Line 78 As far as I known, you only collected soil samples for one time. So, why you chose this season? And in which day in this month (July 2016)? Make this more clear, please.

Line 79 Add the longitude and latitude here.

Lines 86-88 This is repeating Line 82.

Line 91 How do you prevent cross contamination of different soil samples by using PVC tube?

Lines 92-93 How much soil do you use for DNA extraction? Meanwhile, do you have negative control? See Schöler et al. (2017) and Vestergaard et al. (2017) in Biology and fertility of soils, please.

Line 103 QIIME1 or QIIME2? Make this clear, please. QIIME 1 is no longer supported at this time, as development and support effort for QIIME is now focused entirely on QIIME 2 (http://qiime.org/).

Line 114 Add the method of PCoA analysis and T test.

Results:
Lines 124-125 Delete, this is repeating Lines 69-71.

Lines 126-130 Delete, this is repeating Lines 80-83.

Line 130 Whole name for ITS should be used in Line 95.

Line 135 Add the whole name of PCoA here. Meanwhile. I suggest doing Adonis or anoism analysis combined with PCoA, this could give more information of your data.

Line 166 R2, revise it please.

Discussion is not well written, after revising your ms (especially data analysis, functional analysis and result part), improve discussion as well.

Conclusions
Conclusions are not well written. Current result cannot reflect fungal community imbalance as you said in abstract and introduction.

References
Lines 291-292 “…Study on fungi diversity of ginseng rhizosphere soil in northeastern China…” only capitalize the first letter of “Study”.

Lines 302-303 same as Lines 291-292

Line 337 …soil fungal global…

Lines 339-341 same as Lines 291-292

Lines 355-359 same as Lines 291-292

Table and Figures
Figure 1A The PCoA analysis is done based on OTU data or genus data? Clarify this please. Is there 0 value in your data? Was the data Hellinger transformed when you do PCoA analysis? And do adonis and anoism analysis to combined with PCoA analysis, this can give more information to readers.

Figure 1B where is F10 treatment in this Venn diagram.

Figure 1C Phylum level can give us little information. Thus, I suggest to use Class level to make this figure. Meanwhile, do the statistic (ANOVA or Kruskal-Wallist, it is up to your data) analysis for each taxa.

Figure 2 R2, not R2. Keep preciseness.

Table 1 Add the indication of W15, W35, C2, C5 and F10 in the note of Table. Use mean value of three replications and add SE or SD value. Then, do statistic analysis for five treatments. Meanwhile, did you do the normality and homogeneity of variance analysis of your data?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE FUNGAL COMMUNITY IN NON-RHIZOSPHERE SOIL OF PANAX GINSENG ARE DRIVEN BY DIFFERENT CULTIVATION MODES AND INCREASED CULTIVATION PERIODS
Review round: 2
Reviewer: 1

Output:
Basic reporting: After revised, the manuscript improved a lot, and is suitable for publishing in PeerJ.
Experimental design: well
Validity of the findings: no comments
Additional comments: no comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MULTIPLE FACTORS INFLUENCE LOCAL PERCEPTIONS OF SNOW LEOPARDS AND HIMALAYAN WOLVES IN THE CENTRAL HIMALAYAS, NEPAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: The strength of this study is it includes relevant results for further research on the conservation strategies of these carnivore species in the central Himalayas. Moreover, the introduction and background are sufficient in terms of placing the reader in the study context. Regarding the format, the manuscript is correctly structured, fulfills the journal standards, and contains all the sections needed. Overall, the manuscript is clearly written in a professional language. However, several improvements with regard to basic reporting are required.

Major comments:
1. With regard to the Introduction and background of the study, a relevant point to explain here is that this research constitutes a further step in a long-term study (if not, explain why). I recommend including a justification of the novelty of the current study in relation to your previous studies in this matter (Chetri 2018).
2. Some grammar errors can be found along the manuscript and paragraph structure should be improved by polishing edition, particularly within the Introduction and Methods sections. Moreover, I highly encourage you to improve the paragraph structure in the Introduction section as follows: Lines 49-80 one paragraph is too long. I think that this aspect can be managed by creating two different paragraphs for each species information, focusing on local tolerance and ecological aspects (before Line 67), and then one more paragraph explaining common information (from Line 67 to 80). Furthermore, I suggest putting Lines 92-99 in another paragraph, as a specific statement of the questions formulated for this study. Lines 98-99, the size of the study area fits better in the Study area subsection.
3. I have some doubts relative to the questionnaire design because of certain questions formulated were excluded from the analyses, such as livestock numbers of each species (instead of the total number of domestic animals owned), season, losses experienced (yes/no) and reported, habitat type, etc. Why did you exclude these data from the analyses and results sections? Please, justify this and include a statement clarifying these omissions.

Minor comments:
1.  (Line 62) Why the density estimates of wolves are still lacking? Is it because of the lack of recent DNA fecal study of wolves, or because this species is not easy to detect within the study area? How rare are the wolf species in the study area? Please, explain this and include this information if possible.
2. In general, in-text citations are well performed. Although they should be improved according to the Journal Instructions for Authors (check the Reference format section). A comma is required after the list of all author names and before the publication year, for example, Athreya et al., 2013. In line 41, remove the middle name of the second author (Cesar). In-Line 62, Chetri (2014) is not included in the Reference section. In line 306, add the publication year in the in-text citation. Moreover, the Reference Section’s guidelines recommend choosing an option to give the DOI on each reference. For example: DOI: 10.1016/j.jnc.2016.09.004. Please, apply these modifications along the manuscript.
3. According to PeerJ Ethic policies, an Ethics statement should be provided in the Materials and Methods section of the manuscript whenever the research was conducted on humans or human tissue; on animals or animal tissue. Please, include this statement related to Human participant's approval documentation obtained from the relevant approval body in the Material & Methods section (Line 147). If not being able to include it, please provide a statement explaining why it is not necessary.
4. In accordance with the PeerJ submission guidelines, all tables and figures titles should be in bold and with a colon after the figure or table name. Please check the format recommended and implement these changes along the manuscript but also in the figure and table files loaded. In more detail, Figure 1 requires more space at the map bottom to avoid cutting the map legend; the font of geographic coordinates of the map grid have to be increased to clear reading. If possible, try to reduce the white space inside the figure file loaded and cite map sources in the legend if you used anyone. In Figure 2, I recommend to define the VDC acronym in the legend but also to increase the font size in both axis titles and axis lines (and the same for Fig. 3). Table 1 can be improved as below: No. or number instead of No; “included or valid questionnaires” instead of “included respondents”; “invalid/excluded questionnaires” instead of “neutral responses”; all the units (i.e. years) should be placed in the row title in parentheses; all the acronyms and abbreviations defined in the footnote (VCD, ACA, MCA); all the footnote markers have to be referenced in the table; “proportions” should be changed by “percentage” or instead of that, specify what means here. Why are not included the answers relative to livestock losses and the loss numbers? Please, provide this information or explain why is not included. In Table 2, VDC would be defined in the legend (as well as in Table S1 and Table S2 in the Supplemental File), and selected models for each species highlighted in bold and this formatting explained in the legend. Moreover, you need to include the distance from the nearest conservation field office to the respondent household (DIST) as a predictor variable in the legend of Table 2 and Table S1, because it is included as a predictor variable in both cases.
5. Thank you for sharing the raw data and ensuring you follow our Data Sharing policy. However, supplemental files provided (peerj-48442-Raw_data_Snow_leopards.csv; peerj-48442-Raw_data_Himalayan_wolves.csv) require more descriptive column identifiers, including measurement units for each variable and acronyms or abbreviations definitions to easy reading. The file names provided in the “How are you submitting your raw data or code?” section do not correspond with the required ones. Please, correct it in this section.
Experimental design: The manuscript submitted is within the scope of this journal. The research aims sound rather clear and constitute relevant points for the study. In general, the research performance fulfills the basic technical and ethical standards (with the exception of minor comments made in the basic reporting). The methods section is rather detailed and contains relevant information to replicate the study. However, several improvements relative to the experimental design should be implemented, thus I would give some feedback relative to the Introduction and the Methods sections.

Major comments:
1. It is necessary to be more specific when defining the questions and justifying the need for this study in relation to the lack of knowledge about the problem analyzed (Lines 93-99). In Line 93, remove “in an area”.
2. I have found the questionnaire design used for data collection (Appendix S1) could be improved in order to answer the questions formulated. I believe that this issue can be solved if you justify the design provided in the Semi-structured questionnaire survey subsection and explain the reasons for excluding certain questions from the analyses in the data analysis subsection.
3. Why did you exclude the neutral respondents from the analyses? I believe that if you do not explain the exclusion reasons resembles a bias. Please, remove the neutral category from the answers because the response variable fits a binomial distribution (Line 155).
4. Change these two sentences (Lines 155-156) as follows: “We consider as invalid questionnaires when respondents did not want to answer or stated that they did not know about the species presence and conflict, thus they were excluded from the analyses” (see Appendix S1 comments). In Lines 158-159, change “neutral respondents” by “excluded or invalid questionnaires”.

Minor comments:
1. In Line 110, I believe that the preferred religion by the majority of the population is not relevant to the study. Please remove it, or instead of, please explain why the religion was not included as a factor in the analyses.
2. In the stud area subsection, there should be two different paragraphs between Lines 112-123 and Lines 123-128, or instead, try to summarize the information given in these lines.
3. In Lines 126-128, I have not found the link in this sentence to the rest of the paragraph, please remove it or create another paragraph to explain the distribution and ecological aspects of the study species.
4. In Line 167, are there any differences among the answers of individuals who have chosen the “others” option? It is possible to explain which answers were given as the “others” category and how did you manage this issue in the analyses.
Validity of the findings: I consider this study includes relevant findings for further research on the conservation strategies of these carnivore species in the central Himalayas. The statistical analyses seem well performed and the sample size used for the separated models is fairly balanced, and for both species, it allows a large number of factors and covariables to be included in model construction. Another good point is VDC was included as a random factor in both cases. Moreover, all the results were fully reported, and the figure design chosen to show the estimated effects is the most recommended. Most of the ideas argued in the Discussion section show a deep commitment to the labor of your team, and in general, most of the results are broadly supported. The conclusions highlight the most remarkable points of your study, but not all of them. To summarize, I believe the findings provided are rather robust and statistically sound, although certain clarifications in the Data analysis and the Results sections are required, as well as in the Discussion and the Conclusion sections remain open with respect to the background of the study.

Major comments:
1. The impact and the novelty of this research are not justified in the Introduction and Discussion sections. This manuscript will gain relevance if you improve these two aspects. For instance, which aspects of your research make a difference from what Kusi et al. (2019) observed?
2. I assumed that you performed a correlation test among predictor variables before the model construction; please confirm this doubt. In Line 28, how did you evaluate that the answer according to gender is independent of the number of losses? If possible, explain this point in the data analysis subsection. Moreover, I suggest you consider including the VDC as a nested factor of the number of losses variable.
3. According to Li et al. (2014), why did you not include religion as a predictive factor in both separated analyses? I suggest thinking about it particularly when you use this fact to give support in the Discussion section.

Minor comments:
1. Several points from the Discussion and the Conclusion sections remain open with respect to the background of the study. Between Lines 245-252, you suggested that all the commented cultural aspects are likely determining how have evolved local perceptions on snow leopards and Himalayan wolves. By contrast, you did not include religion as another factor in the analyses and you did not comment on the relevance of this aspect for the study species conservation in the introduction. Secondly, you suggested that the increasing tolerance for snow leopards could be linked with the continued efforts to increase awareness as part of the ongoing DNPWC conservation program (Line 266). However, you did not take into account for these measures in the data analysis and the introduction sections. Thirdly, as Caruso et al (2020) suggest (Lines 285-286), ecotourism development could be indirectly influencing local perceptions towards study species, though it was considered as the “other” category of occupation variable for the analyses. Lastly, the Oli et al. (1994) study reported that negative perceptions on wolves increased with the distances from conservation field offices, even so, you did not compare it when finding a weak effect of this variable (Lines 327-328). I encourage you to think about the ideas suggested and if possible, implement them in the new version of the manuscript.
2. The study concludes that the negative perceptions for wolves found in the study area are (Line 337: not is) probably due to fear and cultural bias as previously reported, although I also find interesting that this species suffers a scarcity in conservation awareness policies, and by contrast, the positive perception on snow leopards could be linked with higher conservation efforts. Apart from that, you have not controlled by this cultural bias in your analyses. Thus, I encourage you to implement these concluding remarks in the further version.
Additional comments: I really appreciate the study efforts during the data recording and the commitment of your team with the projects developed for both conservation species (ACA and MCA. I encourage you to improve this manuscript to provide the impact deserved of these study findings in order to promote further researches in conservation designing policies within the study area. I recommend you to apply the feedback provided in this review in order to get a new and improved version of the article for the second round of review.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MULTIPLE FACTORS INFLUENCE LOCAL PERCEPTIONS OF SNOW LEOPARDS AND HIMALAYAN WOLVES IN THE CENTRAL HIMALAYAS, NEPAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: I like to appreciate authors for conducting research in the world’s remotest area. It is a good research conducted focusing perception of people towards snow leopard and wolves. Definitely, the attitude of local people need to be understood for better conservation planning. Study has well speculated the perception of local people using generalized mixed effect model. However, the reasons behind the perception are not well discussed based on this study. I would like to suggest authors to focus rather on introduction and discussion while doing revision. I have pointed my comments line by line as follows.
Experimental design: No comment
Validity of the findings: Authors are suggested to support results with their own observation.  I suggest authors to give backup from their own findings. This study should find out the reasons behind negative or positive perception relying on their studied area.
Additional comments: Line 39 – for better clearance write “Human-carnivore conflict”

Line 62 – Two sentence are contradicting each other. One sentence is saying density has not been estimated and another is saying rare. In these regions, very less study have been done. That does not mean species is rare.

Line 68/69 – Depredation mortality is rather low than other causes of death. Then, why livestock depredation is big issue?

Line 70/72 –Better to talk about prey killing behavior of wolves? Author should justify why killing is brutal?

It is suggested to authors to talk about the situation of retaliatory killing and livestock depredation in relation to perception.

Line 94-why livestock depredation is main concern? author should justify the statement somewhere in introduction.

Line 116 – Author is suggested to change “abundant flat plain” to “abundant pasture land”

Line 135/136 – VDCs are no more administrative unit in Nepal since 2015.  VDC are changed to ward in most of cases and new rural municipalities have been established throughout the country. So, authors are suggested to review the study area accordingly.

Study area: Authors are suggested to touch briefly about human population and livestock numbers in study area. This will give readers idea about how human pressure and livestock pressure.

Line 159/160 – not clear. Authors are meant to say northwestern section of ACA and MCA or northwestern section of all studied settlements.

Line 162-172. In data analysis section; authors are suggested to justify “why your data fit to generalized mixed effect model” at the beginning and also suggested to include residual plot as supplementary information. As the model is mixed effect, it is good idea to plot by partially pooling. This will help to show relation with each group.

Line 174/175 –These two lines rather fit in methodology.

Discussion

Line 236-243 –Authors are suggested to support results with their own observation. Here in these lines, authors have supported their observation with other research. In discussion section, I found that findings of this research are justified by other research, for example in Line 252 to 260. I suggest authors to give backup from their own study. This study should find out the reasons behind negative or positive perception based on their studied area.

Line 247/249 – I think that traditional practice of grazing does not fit here. How are you relating this statement with your research finding?

Line 251/252 – “Buddhist community did not kill wildlife”. It seems that they do kill wildlife now. Authors are suggested to change the structure of sentence.

Line 275/276 – As authors have studied perception and age. They are suggested to compare age vs perception to conclude in different perception of young and old people. As you have mentioned about religious belief. Possibly, old people are more religious and should be more positive towards snow leopard. You have also mentioned that the conservation practice in the region is quite old. I think that that program must have been focusing entire population (young people, old people, both male and female) of your study area without any bias

Line 289-292 – these sentences are suitable for conclusion or in concluding part of discussion.

Line 305/306 – Incomplete citation

Conclusion
Line 332 to 342: authors are suggested to include only their findings in conclusion.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MULTIPLE FACTORS INFLUENCE LOCAL PERCEPTIONS OF SNOW LEOPARDS AND HIMALAYAN WOLVES IN THE CENTRAL HIMALAYAS, NEPAL
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: The article is framed within the social sciences but with clear applicability in environmental sciences.

Given the scope of the journal I would recommend the authors to make brief recommendations for the conservation (or to foster tolerance) of these two species at the end of the manuscript

Methods are well described in general but I have doubts in the definition of the variable COMP (proportion of large stock). I interpret with this that only certain species (large ones) are considered for this variable, if so, which are they?
Validity of the findings: no comment
Additional comments: I have enjoyed reading this article which deals with the local perceptions of two large carnivores in the central Himalayas. As the authors said in the abstract " An understanding of local perceptions of carnivores is important for conservation and management planning" However, I believe that the article may benefit if the authors connect these perceptions with management planning by including a series of recommendations based on these results that may in some way favor co-existence in the area of study. I understand that they include a few sentences during the discussion but I think it would be useful to address this in further detail.

I don't know where it would fit better (introduction or discussion) but I think it would be good to include a small paragraph about the benefits (apex predator, ecotourism opportunities...) that these carnivores can bring in the area and not only focus on them as livestock predators.

I'm sorry, possibly  I have not understood well, throughout the text you mention two areas ACA and MCA. I understand that they differ in the type of species of livestock (among others characteristics I guess) but then I do not see that the analysis takes into account whether the respondents are from one area or another. Would it not be appropriate to include the regions in the analysis or the type of livestock they had?

Appendix S1 Questionnaire:
-Is there any relationship between having an encounter with the species (question 6 of the questionnaire) and the type of perception (positive/negative)?
-It would be interesting for the reader to have some more descriptive results from the questionnaire (for example questions 3, 4, 6 and 10)
-Questions 8 and 9: You ask why but I find no mention of these questions in the manuscript. Only just a suggestion, I find it interesting if the authors decide to analyze these questions. For example, a content analysis would be a good tool to determine which words could be associated with positive/negative perceptions of species.

I have other minor suggestions:

L31 future conservation projectS
L 64 ACA this acronym is not yet defined in the text
L66 Do you have any knowledge about the distribution ranges of these species that could be projected on the map?
L107 What kind of tourism? (mountaineering, or wildlife watching) Are there eco-tourism options for these species in the area?
L137 do you know  how these VDC (or differences between ACA and MCA) manage the attacks of the carnivores (legal hunting, lethal control, fences, aversive conditions...)
L236 Typo: This perception (without s)
L300 I think it should be "may have been"
L 304 some mistake by the reference manager.
L309 I think that “actually” it is not necessary here
L312 delete comma
L315-316 so why did you do not ask it in the questionnaire. I’m wondering if it also could be related with tolerance to snow leopard and wolves.
L327 “ perceptions of distant settlements ARE due to THE limited nature…”
L315-216 it would have been a good idea to include in the questionnaire some questions related to people's participation in conservation tasks
L335 “…perceptions for THE Wolf in our study area ARE probably…”


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: MULTIPLE FACTORS INFLUENCE LOCAL PERCEPTIONS OF SNOW LEOPARDS AND HIMALAYAN WOLVES IN THE CENTRAL HIMALAYAS, NEPAL
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript fulfills the general standards and all improvements suggested were effectively performed. I consider the introduction to have improved notably, and the background and the aims of the study are now sufficient to justify the novelty of the current research. The polishing edition is notable in the new version of the manuscript. However, some minor comments are included below for improving it.

Minor comments:

1. Thank you for including all the necessary corrections regarding the in-text citations and references section. In Line 42, please remove “de” before “Azevedo”. In Line 55, please remove the second dot in the last citation. In Line 82, I would suggest adding the reference citation (Chetri et al., 2019a), as an example of the background of the study. Please notice that parentheses () are not required after “et al.” in Line 194. In Lines 200, 252, and 304, a comma (,) is not required after the author names. In Line 512, Mijiddorj, Alexander and Samelius (2018) reference is not cited in the text. In Line 577, Zimmermann, Wabakken and Dötterer (2001) reference should be in a separate line. According to PeerJ submission guidelines, for three or fewer authors, you need to list all author names (e.g. Zimmermann, Wabakken and Dötterer, 2001). Please check the references section and in-text citations.

2. I appreciate all the improvements implemented in the introduction section. However, I believe that the question concerning the density of Himalayan wolves has not been resolved yet. I would suggest taking into account the following references “WWF (2015) Non-Invasive Genetic Population Survey of Snow Leopard and Wolf. Final report. WWF, Kathmandu, Nepal”; “Chetri et al. (2016) ZooKeys; and Chetri et al. (2017) PLoS ONE” and include them in Line 72. In Line 75, please consider removing “However” in the beginning, there is no opposition here.  Thank you for defining the acronyms in Lines 86-87. I would suggest adding the following specification: (ACA, hereafter) and (MCA, hereafter). In Line 101, I would recommend implementing the plural in “low livestock loss”.

3. I believe that the statement in the data analysis subsection helps to clarify the selection of the most appropriate predictors recorded through the semi-structured questionnaire. Thank you for including all the recommended predictors in the analysis, and all the changes needed in all tables and figures. Please consider including units (years) for “Mean age” and correct “parentheses” in the footnote of Table 1. Moreover, I recommend to add the definition of ownership predictor, and to replace “LIT1” with “LITyes”, and “AGE:LIT1” with “AGE:LITyES” in the legend of Figure 2 (please, check if the figure shown matches the selected model). Please, consider replacing “snow leopard” with “Himalayan wolf” when defining the LOSS predictor in the footnote of Table S2 (Supplemental files).
Experimental design: The study aims are well defined in the introduction section, and the novelty of the current research is well justified. Moreover, the research complies with technical and ethical requirements, and the methods section shows significant improvements, according to the comments received. Thank you for removing neutral respondents and for including a statement in the data analyses subsection in order to clarify the study design and model selection. However, I will provide some feedback in order to improve the manuscript.

Minor comments:

1. Thank you for improving the paragraph structure in the study area subsection. In Line 137, I recommend changing “Bos spp.” to the italic font.

2. In Line 176, I understand that the invalid questionnaires belong to respondents who gave neutral answers or ignored the presence of study species or conflicts with them. If that is correct, I would suggest including “(i.e., neutral responses)” after "conflict" for further clarification.

3. I agree with the reasons for excluding religion from the analyses. However, I would consider this explanation (or similar) to be included in Line 199: “we did not include religion as a predictive factor as all the locals residing in the region are Buddhist, only a few outsiders who are working as labor or teacher are non-Buddhist.”
Validity of the findings: The results of this study are widely supported. The findings are quite robust and statistically sound, with a significant application to future conservation plans for these large carnivore species in the Himalayan range. I would highlight the improvements made in the introduction as well as in the discussion and conclusion sections, which are now further strengthened in terms of the aims and background of this study. Thank you for including all the comments provided previously, particularly with reference to statistical analysis. However, I will provide some feedback to improve your manuscript.

Minor comments:

1. Results are rather strong and robust. However, I would suggest replacing “literate” with “being illiterate” in Line 231. Moreover, I would recommend checking if Figure 2 matches with the selected model. In this case, please consider adding "and ownership" after “sex” in Line 237.
2. Thank you for all your answers and changes implemented in the discussion section. In Line 266, I recommend adding “, to which most of our respondents belong,” after “Buddhist communities”. In Line 275, I would suggest replacing “dislike for” with “aversion to”. Please consider replacing “An other” with “another” in Line 313, and “perceived” with “perception of” in Line 314. In Line 353, please leave a space between “Theyneed”.

3. With regard to the impact of your findings, I suggest remarking which aspects are different from the study of Kusi et al. (2019). For example, your research was performed in a different study area. In Line 329, I would recommend comparing your results here in more detail (Fig. 3) in contrast to Kusi et al.

4. Thank you for emphasizing the difference in perceptions of wolves and snow leopards in the introduction and the discussion sections. However, I recommend adding “an issue to be considered in future conservation plans in ACA and MCA” at the end of Line 279. In Line 339, after “conservation issues”, please consider adding “with particular efforts to the Himalayan wolf”.
Additional comments: I really appreciate all the improvements implemented in the current version of the manuscript. I would highlight the research efforts and the commitment of your research group with the projects developed for both conservation species in ACA and MCA. I highly encourage you to improve this manuscript and give these results the impact they deserve, with the ultimate goal of getting more funding for monitoring these two carnivore species and promoting future conservation and management strategies in remote settlements, particularly focused on the Himalayan wolf. I recommend you to apply the feedback provided in this review in order to get a more polished version of the article before publication.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONFLICTING PHYLOGENETIC SIGNALS IN PLASTOMES OF THE TRIBE LAUREAE (LAURACEAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Following are my comments on manuscript #49532 entitled “Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)” by Xiao and coworkers.

Note that special formatting (e.g., italics) may not be preserved in this online review.

Line 42		The authors fail to include one major biological factor that has the potential to introduce artifacts to phylogenies. This is natural selection, especially positive selection, of protein coding sequences. Selection is well-documented for plastid genes and has the potential to bias phylogenies (e.g., see Piot et al., 2018; Saarela et al. 2018).

Lines 52-53	The phrase: “…biparental inheritance and heteroplasmy…has been reported…” should be “…biparental inheritance and heteroplasmy…have been reported…”

Lines 72-73, 330-332	A recent paper, in which the impact of noncoding partitions in the plastomes of Poaceae were investigated, is Saarela et al. (2018). The authors should cite this relevant paper and compare their methods and results with those of Saarela et al. (2018).

Lines 99-100	The phrase: “…Neolitsea sericea is a constructive species …” is unclear and should be reworded. Perhaps the intended meaning was that N. sericea is a source of lumber used for construction.

Line 124	The phrase: “…we now report 12 new plastomes…” should be “…we now report 12 newly sequenced plastomes…”

Lines 232-233	This sentence regarding model selection may be more appropriate in the “Methods” section of the manuscript.

Line 362	The phrase: “…cause alternate but conflicting topologies…” should be “…cause alternate, but conflicting topologies…” (insert comma).

Lines 273-275	When small subsets of genes have a “decisive role” in the inference of phylogenies (line 274), the possibility exists that selection in one or two genes (in this case, ycf2 and psaB) may bias the result creating false phylogenetic signal. The authors should acknowledge this possibility.

The original release date for the paper by Duvall et al. was 2019. However, the paper wasn’t officially published in Botanical Journal of the Linnean Society until 2020. The date of the citations (lines 62, 180, 361, 363) and the reference (line 456) should probably be changed to 2020.

I am unable to find legends for supplemental figures S1-S8.

This paper is clearly written, well-organized, generally well-researched, and uses contemporary methods to examine the plastome phylogenomics of Laureae. The influence of different data partitions on the phylogeny is explored including subsets of coding and noncoding regions and gapped positions introduced by the alignment.

One factor that is overlooked in this otherwise thorough study is the possibility of selection bias. Selection, and the potential impact of positive selection artifacts on phylogenetic results, would ideally be measured for the protein coding sequences, but at least should be discussed.

Literature cited:

Piot, A., Hackel, J., Christin, P.A. and Besnard, G., 2018. One-third of the plastid genes evolved under selection in PACMAD grasses. Planta, 247(1): 255-266.

Saarela, Jeffery M., et al. A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions. PeerJ 6 (2018): e4299.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONFLICTING PHYLOGENETIC SIGNALS IN PLASTOMES OF THE TRIBE LAUREAE (LAURACEAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript was a pleasure to read, with clear, easily understood English throughout. The study was well placed in the broader context of the field, and, as a result, the purpose of the study is well defined. The raw data are available from GenBank, and the results of each analysis in the study are available either in the main text or the supplement. I have only minor suggestions for additional reporting.

The figure captions could be more complete by describing the phylogenetic trees in full. The ML trees should mention the program that they were inferred with. The ASTRAL tree should mention that ASTRAL the tree was inferred using a multispecies coalescent approach in ASTRAL. Given that many trees were inferred in the study, the reason for presenting those two particular trees in the main text should be justified.

The authors point out that: “By contrast, relatively few studies have focused on tree conflicts among plastid genes”, and “Aside from biological factors, non-biological factors (e.g., outlier genes, uninformative loci, and gaps) may cause conflict as well.” These are good points, and the authors have cited several of the few recent studies that address conflict among plastid genes. However, an additional, relevant citation would be: Foster et al. (2018) Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea), Molecular Phylogenetics and Evolution, 127: 156-167. In Foster et al. (2018), a topology-clustering approach was used, finding discordance among chloroplast gene trees. The discordance was then investigated with respect to strength of selection (dN/dS), tree length, and GC content. These are useful biological reasons for discordance among chloroplast genes that should be mentioned in the present study.

I found the following sentence a little confusing: “The sum of absolute ΔlnL of T1 was higher than that of T2 and T3 (Fig. 4), suggesting that our data support the topology of T1 rather than T2 or T3.” If it could be rephrased to better explain the rationale behind justifying T1 as better based on likelihood ratios, that would be beneficial.

Finally, it should be mentioned in the discussion that, at deep timescales, non-coding genes are often discarded for being uninformative, or for being misleading due to saturation.
Experimental design: The research is original and within the scope of PeerJ. The objectives of the study are well defined, and represent clear advances on previous work. The Methods are generally described well, with the exception of a few queries.

The authors describe six main, initial data sets for phylogenetic analysis: “(1) complete plastome (cp), (2) coding regions (CDS), (3) non-coding regions (non-CDS), (4) large single copy region (LSC), (5) small single copy region (SSC), and (6) inverted repeat region (IR)”.  As the name of the IR implies, it contains two copies of its constituent genes. I’m assuming that only one copy of each gene was used for phylogenetic analysis, but this should be made explicit in the manuscript.

All sequences for each data set were aligned, then analysed using RAxML-NG to estimate trees. A key part of multilocus phylogenetic analysis is partitioning of the data, but there is no mention of partitioning in the manuscript. For example, the CDS data set could/should have been partitioned by gene and by codon position, with appropriate nucleotide substitution models applied to each partition.

Was any partitioning carried out? If yes, please report it in the manuscript. If not, why not? Given the impact of adequate partitioning on topology inference, it’s an important omission.
Validity of the findings: By and large, the findings are valid and well justified, and the conclusions are appropriate given the results of the study. The only minor concern I have about the validity of the findings relates to my query in the experimental design feedback section about partitioning. Depending on how the authors respond to my queries, these concerns may not be important.
Additional comments: Congratulations on a great study.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONFLICTING PHYLOGENETIC SIGNALS IN PLASTOMES OF THE TRIBE LAUREAE (LAURACEAE)
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: In this revision of manuscript #49532 by Xiao and coworkers, the suggestions on the previous draft of the manuscript have been satisfactorily addressed.

No further revisions are needed.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CONFLICTING PHYLOGENETIC SIGNALS IN PLASTOMES OF THE TRIBE LAUREAE (LAURACEAE)
Review round: 2
Reviewer: 2

Output:
Basic reporting: In my previous review, I noted that the manuscript was well written. This feedback still stands, but I have these additional minor comments based on new text:

59: change “gene evolutionary rate” to “a proxy for evolutionary rate:

186: personal preference, but change “cp” to “CP” here (and henceforth). This would also require changing “cp-reduced” to “CP-reduced”. I feel capitalising the data set name helps to delimit the abbreviation in the text, rather than having it look like a typo.

194–195: change to “the CP dataset”

196: Change to “the optimal partitioning schemes for each dataset”.

197: change “the best partition schemes and models for each partition“ to “the optimal partitioning schemes, and nucleotide substitution models for each partition,”

212: change “paml” to “PAML”

293: change “confirmed” to “supported”

295–296: change “indicating that partitioning did not affect our tree topology.” to “indicating that our results were robust to different partitioning schemes”.

293–302: instead of having three one-sentence paragraphs, merge all into one paragraph. The following sentence also needs to be reworded for clarity: “LRT showed that the dN/dS ratios of labeled lineages (subclades I, II and III) were not significantly different from background (p > 0.05), of which dN/dS ratios were less than one (Table S4), suggesting that there was no positive selection on the plastid genes.” I suggest something like:

“Additionally, a likelihood ratio test showed that the dN/dS ratios of labeled lineages (subclades I, II and III) were not significantly different from background (p > 0.05), of which dN/dS ratios were less than one (Table S4), suggesting that there was no positive selection on the plastid genes.”

Please also note my reservations that I have about the selection analyses (including the way they are reported), outlined in the next section of the review.
Experimental design: I’m pleased the authors conducted further analyses using different partitioning schemes and investigating signatures of selection in the protein-coding genes. However, I am not convinced that the selection analyses were conducted properly.

212–215: The explanation of the tests for selection is very confusing: “To statistically test for positive selection, we compared the performance of two branch models (M0 and M2) for each gene. Three foreground branches were labeled on the unpartitioned CDS ML tree. Likelihood ratio tests (LRT) were performed using pchisq function in R 3.6.2 (R Core Team, 2018).”

In a study like this one, it would be useful to test whether there is evidence for selection in any of the protein-coding genes. Such an approach might show that (e.g.) most protein-coding genes are evolving under purifying selection, but a handful are evolving under positive selection. Most plastome studies take this approach. However, the authors in the present study chose to test foreground vs background lineages using branch models in CODEML. This approach is useful to determine whether particular lineage(s) are evolving under different regimes of selection, and can be interesting when there is an a priori explanation of why particular lineages might be expected to be evolving differently from others. To include the selection analyses in the manuscript, the authors need to either (a) justify why CODEML branch models were used, and what particular lineages were selected as foreground lineages and why (in the methods, not just results); or (b) use site models in CODEML to test for global signals of selection in genes based on multiple sequence alignments, rather than comparing particular lineages to a background.

I think the discrepancy in finding no genes under positive selection in the present study, compared to previous studies, might be because of the choice of tests conducted in CODEML.

Regardless of whether the authors take this advice into account, they really need to explain their analysis more carefully so it makes sense. Generally, the authors should also use “positive selection” instead of “natural selection”. It might also be worth mentioning the possibility of “relaxed selection”, since most protein-coding genes should be under purifying selection.
Validity of the findings: I am happy with the validity of the phylogenetic findings. However, I am not convinced of the validity of the selection tests findings (see previous section of review).
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: COLONIZATION OF NOVEL ALGAL HABITATS BY JUVENILES OF A MARINE TUBE-DWELLING AMPHIPOD
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is well written in general but can still use the help of a language editor. It aslo needs to update and broaden the literature cite. There is too much self citation.
Experimental design: The hypotheses make sense when the paper is read completely, but the experimental questions need to be stated more clearly.
I have no issues with the experimental design or analysis other than some clarifications requested. I find the number of figures and their clarity appropriate.
Validity of the findings: Only one of the conclusions (effects of adults) requires further discussion.  However, overall, the conclusion will be improved if they are placed in a broader context than just the amphipod or marine literature.
Additional comments: Review of Bueno et al. “Colonization of novel algal habitats…” PeerJ

General comments:
1)	Overall, this well written, but there are some slight mistakes in phrasing and the use of articles. A language editor should give this a reading.
2)	The authors are dealing with fundamental ecological issues such as the roles of dispersal and recruitment in population connectivity and community structure, age-related dispersal and other broader ecological questions. Most of the fundamental work on such questions has been done in terrestrial systems, especially with mammals and birds. It is surprising that so little of the relevant literature is cited. The manuscript will have broader appeal if the citations are less biased towards marine work in these fundamental issues.
3)	On a related issue, the literature cited is not current. For example, there are more recent reviews on the ecology of dispersal, including supply-side processes, than the ones cited here. In fact, all papers from 2015 on are from one of the coauthors. I think there is more recent relevant literature than this.
4)	Similarly, instances of repetitive citing should be avoided (see for example Mungia et al. 2007 in lines 97-99).

Specific comments:
Lines 46-48: the methods are just a repetition of the background, please rephrase one or the other. Also “settlement” invokes a specific type of movement. Please use colonization or recruitment as these amphipods are likely crawling, rather than swimming.
Line 113: Eliminate “known as”
Lines 131-145: The presentation of the hypotheses or experimental questions must be written more clearly. The authors use multiple vague statements and terms here that are not helpful (e.g., “the macroalgae-amphipod system”, “this early stage”). They also use several references when establishing their actual hypotheses, which is confusing. Are these hypotheses tested in those papers? The hypotheses and their justifications should be stated more directly.
Line 159: Deleted “the amphipod” and abbreviate the genus.
Line 163: “thalli” should not be in italics
Line 166: “Driven”, not “drove”
Lines 165-170: The experimental units are difficult to visualize so I recommend adding a picture or diagram as supplementary material. Also, it is unclear what the components of the unit are for. Please explain.
Line 172: Eliminate “of experiment”
Line 180-181: This sentence is unclear. What epibionts?
Line 184-194: Please eliminate superfluous details and explain more clearly. I am not sure what a replicate means from this
Lines 319-320: I am not sure what this means. All amphipods are capable of colonizing substrates pending on circumstances.
Lines 325-326: I am not convinced the presence of adults was irrelevant. The result of their analysis was borderline (p=0.055) and their replication was relatively low. The authors should comment on this.
Lines 366-368: I understand the trade-off but the role of juvenile mobility should be explained better in this context.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: COLONIZATION OF NOVEL ALGAL HABITATS BY JUVENILES OF A MARINE TUBE-DWELLING AMPHIPOD
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: 1- I have one comment on the statistics of the field experiment with the presence/absence of adults and its interpretation. There was a marginally-significant influence of adult male density and colonization rate (p=0.055); there was a 2-fold increase in juvenile recruits in cups with 8 adults relative to 0 adults (lines 306-309). The authors interpret this as no effect, but to me it is also possible, even likely, the experiment suffers from Type II error and low power. Id like the authors to mention this in either the results or Discussion. At the least, the Discussion should point out that the effect was marginally significant (e.g., paragraph starting line 392) - in fact, id suggest placing these results into a new figure. they are hard-fought data and deserve more attention.

I'd also recommend the authors try a couple of analyses to pull out this effect. Does the analysis treat the male density as ordinal levels, or does it ignore the increasing levels of male density? Also, you might want to treat the levels as presence / absence (i.e., group 4 and 8 males), since that likely increases your power.

2- a few issues with the artificial alga came to my head. Were artificial algae pre-treated in the water before any colonization experiments? If they were colonized by epibiota that can attract herbivorous amphipods (e.g., diatoms), then that would suggest they have both food and habitat quality.  Also, microbial biofilms can generally influence invertebrate habitat choices. Finally, plastic can leach chemicals that can either repel or harm marine organisms. What precautions did you take to prevent this?

3- there were substantial numbers of non-Cymadusa filosa juveniles in both field experiments. Were there any patterns between treatments in these other groups, or as a whole? If you know if any of these are competitors or predators, Id be particularly curious to know on this point, as it could help to explain the lack of field results.
Additional comments: This is a well-executed set of laboratory and field experiments exploring the ecology of juvenile colonization in a species of herbivorous amphipod. Overall, the experiments showed that these juveniles make explicit choice to colonize algal habitats over simple morphological structure, and that the effect of adult male presence on colonization rates was weaker. there was a marginally-significant increase in juvenile colonization in the field in the presence of adult males.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SPATIAL BENTHIC COMMUNITY ANALYSIS OF SHALLOW CORAL REEFS TO SUPPORT COASTAL MANAGEMENT IN CULEBRA ISLAND, PUERTO RICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: The writing needs some work and some of the references could be updated.
The manuscript is very long and could be considerably shortened. Analyses and results could be better tailored to objectives.
Experimental design: basic design is fine, and data is extensively analysed. Research questions could be better defined. Description of methods, particularly the statistical analyses needs to be clear and concise
Validity of the findings: replication is fine though this is a study looking at spatial differences, not temporal. Hence it is inappropriate to discuss findings with respect to change in benthos
Additional comments: This study assesses spatial variation in benthic reef communities within a bay subjected to recreational activity by tourists and terrestrial run-off. The authors show that there are spatial differences in the composition and diversity of benthic communities and relate these to indices of recreational activity, rugosity, distance from shore and urchin abundance. The analysis of data is extensive, though some clarification about statistical design, why analyses were performed and how they relate to study objectives is required. I also felt the results were very descriptive, somewhat repetitive and could be shortened considerably by focussing on the most relevant findings and deleting interpretive/ comparative text that references other studies and is better suited to the discussion.
The authors also need to be careful when interpreting their data which is from a single point in time. Hence it is difficult to know how these benthic communities may have looked in the past and what change these reefs have undergone. Finally, the manuscript needs to be carefully edited to remove ambiguous statements and correct grammar.  I have provided some guidance on the first page of the introduction but this needs to be done throughout the manuscript.
L24 why would reefs closer to recreational stressors have higher diversity and herbivory? Similarly, the statement about urchin propagation and restoration L35-37) is not supported by information presented in the abstract.
L50 the Riegl reference is >10 years old and mass bleaching events since this paper was published have caused widespread loss of coral reefs. See Hughes et al 2018 Science 359:80-83
L55 the Wernberg et al 2016 Science? reference relates more to temperate reefs and if anything an increase in tropical species (such as corals) at the expense of macroalgae. Note it is also not in the reference list.
L59 you probably need to be explicit about stressors form recreational activity e.g. breakage of corals from snorkellers?
L63 delete ‘through reef craters’. It is nor the craters that cause damage to corals. Or is it?
L74 management ‘is’ critical
L80 The combination ‘of’ local stressors
L111-117 this is a long sentence that covers several issues. I suggest breaking into multiple sentences
L127-128 without a temporal data set that records change in benthic assemblage over time it is difficult to determine if a regime shift has occurred.
L131 I think you need to be clear about what you are assessing when discussing vulnerability. Is this vulnerability to anthropogenic stressors in general, climate change, high turbidity and sedimentation, or tourist activities? The vulnerability of a benthic community will depend on the stressors that you are assessing it against, and appropriate indictors of these stressors should be chosen accordingly using information from the literature to support your decisions.
Perhaps it is best to keep objectives fairly simple and achievable ie describe benthic communities and assess how these vary with respect to distance from shore, tourist densities. Relationships between benthic composition and the other two variables: urchin densities and rugosity are difficult to interpret as its impossible to know if these factors influence the benthos or are a consequence of the benthos, especially rugosity
L132 this will facilitate the ‘identification of’ the major human activities….
L135-139 what is the basis for this expectation? Also how do you know that the interaction between stressors is synergistic. This paragraph does not add very much to the introduction and could be deleted.
L153 is there more recent rainfall data than 1938-1972?
L184 and 188 are transects randomly or haphazardly placed?
L196 is there a reference for this measure of coral health.
L197 how is coral recruitment measured. What do you consider a coral recruit?
L204 if one of the aims of the study is to assess vulnerability then I think the methods need to be clear about how this will be done rather than referring to other studies.
Methods
L215 why is rugosity tested with ANOVA and other variables tested using PERMANOVA
In general, there is unnecessary information in the methods describing what an analysis does (e.g. L245-251, though number of permutations is needed as this can vary among studies) but information on how it is applied for this study is lacking.
There are several statistical tests used (ANOVA, PERMANOVA, PCO, SIMPER, IDW) and I found it difficult to follow what the response variables and factors were for these analyses. For example I don’t know how urchin density, location, distance from shore, rugosity and recreation index can all be factors in a one or two way PERMANOVA? Are some of these co-variates or are these multiple analyses. I wondered if all of these analyses are necessary to address the aims and if the analytical approach could be consolidated to make the manuscript more succinct.
I also think it may be better to use urchin density, rugosity, recreational activity and distance from shore as continuous variables in analyses rather than categorical. The authors should also  clarify how distance from shore is measured. Is it distance to nearest shoreline, or the beach
Results
L296. This section is very long and I’m not sure that all subsections are necessary. For example, the section on overall benthic cover is very descriptive and it would be easier to just describe where there are significant differences in benthic variables, referring to figures as necessary. There are also sections when comparisons are made to published papers that are better suited to discussion e.g. L328—330
L357 is this dissimilarity between transects or locations?
L376 this opening sentence is awkwardly phrased. Perhaps better to say something like Species richness of benthic communities was not significantly influenced by rugosity, recreation….
More importantly, if there is a significant interaction between factors then the analysis should be interpreted at this level.
I’m also confused as to why there are interaction terms in Table 1 and 2 (which is labelled Table 1) and then terms that suggest a combination of two variables?
L440-514. This level of detail for correlations between benthic variables is very detailed and could be deleted, removed to supplementary files or shortened. Much of it is speculative, or contains text better suited to the discussion (e.g. L502-507) and does not add very much to what a description of the ordination in supp figure 6 would achieve. Indeed, this supp figure better summarises the data than fig 4 and 5 and could replace these in the main text.
L524-532 Fig 6 is a really nice summary of all the pertinent findings. However I don’t think this is the place to make suggestions about where restoration may be appropriate (L528).
L534-543 the description of the resilience index belongs in the methods, whilst interpretation of their findings is for the discussion. You should also explain how this aligns with your objectives in the methods.
Discussion
L550-555 the trends observed here are spatial not temporal. So it is inappropriate to suggest depletion of Acropora or trajectories through time based on a single assessment of benthic communities.
L584-586 Why would rugosity be positively correlated with macroalgal cover?
L592 has there been a loss of rugosity? The study shows spatial variation in rugosity
L613 here and elsewhere try to avoid overuse of emotive words or phrases like ‘alarming’ or ‘worrisome’.
L624 The presence of A palmata and A cerviconis skeletons certainly indicates that these corals were once present but without temporal data you con not really infer that there has been ‘expanding’ abundance of ephemeral corals and brown algae.
L651-654 This is a potentially important point. Though I’m not convinced that it is clearly illustrated in the results or analysis. If true it is somewhat lost in the other superfluous results and could be better presented.
L659-663 Its not clear to me how monitoring and analyses presented here would reduce sensitivity of benthic communities.
L690 I’m not sure the study characterised sediment plumes
L693 is this effluent or terrestrial run-off?
L705-707 agree that sedimentation and turbidly are stressors on some corals and can have a detrimental effect on their abundance/cover. But coral diversity is high close to shore (L703-4) which is somewhat inconsistent with this interpretation of findings?
L716-718 I’m not sure why the authors suggest some functional groups be omitted from future monitoring. Because these groups are low in abundance now does not mean they will be low in the future. This decision on which variables to included should be based on what are important indicators of benthic health and if they are sensitive to local stressors. Similarly, the basis for other recommendations for monitoring are not clear.
L725-728 the authors need to be careful when suggesting herbivory is low due to low abundance of urchins. As they note in the previous sentence there are other components of the faunal assemblage that are important for herbivory that have not been considered in this study.
L735 discussion about what locations are best suited to restoration is speculative, somewhat off-topic and could be reduced to a couple of sentences or deleted.
L747 similarly recommendations for making the bay a MPA are not well founded, off-topic and could be deleted
L805 what are these indicators? Are they synergistic? It could be argued the benthic community is less vulnerable if it has shifted towards coral species that are more tolerant of high turbidity and sediment loads.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SPATIAL BENTHIC COMMUNITY ANALYSIS OF SHALLOW CORAL REEFS TO SUPPORT COASTAL MANAGEMENT IN CULEBRA ISLAND, PUERTO RICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: Summary:

In this paper, the authors adopted a two-part approach to analyze the current status and future of coastal management practices in Culebra Island, Puerto Rico, the results of which can be applied to much of the Caribbean region. The authors conclude that reefs in Culebra Island are following the general trend seen in the greater Caribbean towards a degraded ecological state and a shift towards macroalgae-dominated and non-reef building coral-dominated benthic communities. Further, they list the critical state (and lack of recovery) of D. antillarum, reef flattening (a decrease in rugosity), and declines in coral cover as further threats facing Caribbean reefs of the future. These impacts leave reefs surrounding Culebra Island more vulnerable to anthropogenic and natural stressors such as tourism, pollution, hurricanes and sedimentation.

Following this analysis, the authors provide a detailed and interdisciplinary framework for how coastal management strategies can be improved to support conservation goals. These include specific strategies to integrate community stakeholders and local agencies into collaborative conservation efforts, such as the community-led enforcement of shallow-reef area No Take Zones to support herbivorous fish populations and build local economies. They recommend several key management actions that should be put into place to increase reef resilience, such as a citizen-science program to propagate D. antillarum and enhance the recovery of their populations.
Experimental design: The authors performed a thorough physical and biological characterization of shallow coral reefs neighboring a beach used heavily for tourism and recreational activities on Culebra Island to determine if different sites (moving from inshore to offshore) exhibited different characteristics. Photo-transects allowed for post hoc analysis of benthic community structure, including metrics such as reef rugosity, Diadema antillarum density, percent macroalgal and cyanobacterial cover, coral species richness and diversity, and substrate geomorphology. Across the eight reef sites, the authors found significant spatial variability in reef benthic community structure and composition. Specifically, shallow reefs closer to shore exhibited differences from reefs further offshore, which the authors associate with (at least in part) a decrease in anthropogenic stressors in the form of tourism and recreation moving further from the shore.
Validity of the findings: This paper is effective in that it provides a systematic analysis of the ecological status of a benthic coral reef ecosystem exposed to anthropogenic stressors and then uses this data to map out a series of management actions that can promote the recovery of coral reef ecosystems. The statistical analyses used to compare ecosystem characteristics at different sites were thorough and the resulting data support the authors’ conclusions. The literature is well-referenced and relevant. The authors do an impressive job at identifying relationships between variables and then predicting what ecological or natural process is responsible for driving them, such as the relationship between sea urchin populations and recreational human use. Finally, the authors provide informed predictions of the trajectory of coral reef health in the Caribbean and suggest revising the current system of monitoring by using novel health metrics that focus on location-specific resilience processes.

Overall, this study combines a characterization of a vulnerable and changing Caribbean coral reef environment with a novel perspective of how the environmental data can be used to inform and shape coastal management. This will be broadly useful to the field, helping to work towards a global “standard” for coral reef monitoring and the assessment of efficacy for conservation and coastal management strategies.

This manuscript should be revised to fix the few spelling and grammar errors present, of which specific comments and suggestions are left below. Following these minor edits, I believe this paper to be ready for publication in PeerJ.
Additional comments: Line 80: should read “the combination of local stressors…”

Line 110: should read “the inherent complexity of these ecosystems…”

Line 121: due to its seamless capacity to integrate…

Line 361: Change “has” to “had”

Line 471: change “these” to “this”

Line 474: should read “stood out was at location C…”

Line 475: the wording in this sentence is confusing, consider revising.

Line 499: add in “Cyanobacteria was most abundant at inshore reef B…”

Line 536: change to “quantitative comparison”

Line 597: change “specially” to “especially”

Line 786: “repetitive assessment of the interests”


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: SPATIAL BENTHIC COMMUNITY ANALYSIS OF SHALLOW CORAL REEFS TO SUPPORT COASTAL MANAGEMENT IN CULEBRA ISLAND, PUERTO RICO
Review round: 2
Reviewer: 1

Output:
Basic reporting: ok
Experimental design: ok
Validity of the findings: ok
Additional comments: Dear Authors,

	I have not seen the original submission, but based on your responses, you have addressed all the major points brought up the reviewers. However, there still is room for improvement in orthography and sentence construction, i.e. English.

	I also think that the discussion is still a bit too long and should be more focused.  What are the principal risk factors? What is their relative contribution? What recommendation would you make to prevent further degradation, or to assure recovery. Although there might not be clear answers or easy solutions/recommendations, it is important to propose mitigation measures, if you want your study to have impact.

	Sincerely,


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ECOLOGICAL STOICHIOMETRY OF PLANT LEAVES, LITTER AND SOILS IN A SECONDARY FOREST ON CHINA’S LOESS PLATEAU
Review round: 1
Reviewer: 1

Output:
Basic reporting: see "General comments for the author"
Experimental design: see "General comments for the author"
Validity of the findings: see "General comments for the author"
Additional comments: The present ms. studied the C, N and P concentrations and their ratios in leaves, litter and soils in a temperate forest.
 The authors found that all these parameters varied among plant species and soil profiles. They also found that plant C/N/P were generally not correlated to soil nutrients.

Although the ms. is clear to follow and formulated, in my view the ms. in its present form suffers from some problems that should be thoroughly taken into account before acceptation.

My first comment is concerning the language, which needs to be substantially improved. I had problems understanding many statements. In many places, the ms. is poorly written in English – or what is otherwise known as Chinglish. For example, the wording ‘characteristics’ and 'area' in the title, if considering language only, shall be removed.  The wording ‘in dominant species of trees, bushes and grasses’ shall be also removed. The title may change to 'Ecological stoichiometry of plant leaves, litter and soils in a secondary forest on China's Loess Plateau'.

In the first opening sentence in the section of Abstract, ‘…interactions between soil, plants and their nutrient cycle’, although it is grammatically correct, this kind of English expression is weird and unusual. Also, in the 2nd sentence, ‘there is litter information…’ shall be corrected.  And more Chinglish, even grammar errors, could be found in this submission. I highly recommend that the manuscript is proof read by a native English speaking person before the reviewer process proceeds. The grammar could be improved in many places through the manuscript. It is, however, not only a matter of grammar; the ideas are sometimes difficult to follow, particularly in the Discussion section, where it is difficult to grasp what the authors mean because of the way data are presented.

Introduction: The introduction presents a number of ideas but lacks organization. Consequently, it is difficult to follow and pull out the justification and intent of the research.

The 1st paragraph talks about soil/ecosystem erosion, degradation and restoration. However, the data presented in this ms are not strongly associated to these terms and they are not adequately discussed in the section of Discussion.

M&M: The methods do not provide details of how the “six plant species” were selected. How many species are in the sites? Why only select 6 dominant species? Due to so many species in your sites, using averaging data of only 2 tree/shrub/grass species will lead to different results of statistical analysis and thus the discussion of growth form differences is largely speculative given the information presented.

Statistical analysis appears to be incorrect, or at least poorly justified. The authors need to present their statistical results of 2-way ANOVA. The authors must have misunderstood correlation and regression analysis (Table 5).

Three digitals are enough when reporting numbers.

All letters of R, P and n that are used to represent R square, probability and sample size shall be changed to be in italic.

Results: There are far too many graphs. I do not believe they are all necessary. Please think better about the exact message you want to make. I do not think you need to plot all leaf/litter/soil parameters against each other. Some pictures seem to tell the same story. Just present your most important points and some pictures can be presented in tables or moved to supplementary materials.

Figure 1 is repetitive compared to Table 5.

Discussion: I found the Discussion to repeat many of the concepts or arguments presented earlier and the logic often not particularly compelling. Overall, I felt this was the weakest section of the paper. Some of the statements in the Discussion are very speculative. Sometimes the authors seem to be making the same point but just in a slightly different way and they are urged to keep to the key issues. While it is important to compare results with other work, the discussion seems to compare results with all other work individually and in great detail, rather than giving a general overview of how this work fits in with previous findings (i.e. it reads too much like the first draft of a Ph.D. thesis in places!).


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ECOLOGICAL STOICHIOMETRY OF PLANT LEAVES, LITTER AND SOILS IN A SECONDARY FOREST ON CHINA’S LOESS PLATEAU
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper reports on an observational study of nutrient concentration and C:N:P stoichometry in three different plant communities growing on the loess plateau in china. All three communities may have originated from systematic ecosystem reconstruction initiated after severe soil erosion ensued post-deforestation. The paper showcases all differences between nutrient concentrations and stoichiometric ratios in fresh foliage, litter and various soil layers up to 1 m depth. The authors conclude that these tree communities – grassland, shrubland and forest – do indeed differ in plant tissue stoichiometry and this is reflected in the soil. The paper is fairly well written, although it would benefit from editorial review, there are some examples of potential improvement in the attached pdf.

This study is potentially interesting, however it needs substantial improvement if it is to be considered for publication. The main issues are lack of originality and poor description of methodology. These two issues must be addressed before the rest of the paper can be reviewed. For example, authors find that ‘soil sampling depth had an effect on nutrient concentration’ – this is not a novel finding, I believe we have known this for some time. Similarly, the paper would benefit from a much better description of the studies plant species and their community – species identity is one of the main drivers or its relation to the environment, including the nutrient cycle. In the discussion, the authors posit that ‘This is because shrub species was nitrogen-fixing plants, and their absorptions of N element are much greater than that the P element, resulting in a lack of P element in shrub specie.’ Well, obviously, but this information needs to be presented in Methodology so that the reader knows what to expect from each plant type.
Experimental design: This is an observational study analysing a single observation period, which is fine for a direct comparison of differences among plant types, but little further inference as to the ecology of these communities can be drawn. The sampling design is poorly described, it is not clear what is the replication rate. From the description available, it may well be that the underlying rate of replication is 1, severely reducing the scope of statistical analyses. It is not clear how many soil samples were collected, the authors mention an S-shaped sampling line, but no further detail is provided. Analytical methods are adequate for the task, however the use of a fairly strong acid to extract soil P is likely to provide an estimate of total P, most of which is not available to plants.
Validity of the findings: The findings and data reported in the paper are within expected range and probably describe the snapshot concentrations and ratios found on the day of the sampling fairly well. Beyond that, it is very difficult to assess the validity of the comparisons, mainly due to insufficient information on field sampling designs and on statistical analyses.
Additional comments: The authors need to improve their presentation of the objectives and the motivation for the paper, clarify methodology and statistical approach, shorten the results section (there is a lot of repetition between the text and the tables/figures), reduce the amount of figures by 2/3 and improve their clarity, reduce the length of the discussion and focus it on key findings only.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ECOLOGICAL STOICHIOMETRY OF PLANT LEAVES, LITTER AND SOILS IN A SECONDARY FOREST ON CHINA’S LOESS PLATEAU
Review round: 2
Reviewer: 1

Output:
Basic reporting: The presentation, layout of the document and language flow are much improved. The main message of the paper is now clearly visible.
Experimental design: Much better sampling design description, it is now possible to reproduce the study on the basis of the information presented in the paper.
Validity of the findings: Most of the findings presented in the paper are confirmatory, however stoichiometry of plant-soil systems is a developing field where additional observations from unusual systems are necessary to build a global picture.
Additional comments: A much improved version of the paper, I would like to thank the authors for taking our comments on board. There are some small editorial suggestions in the attached pdf, I am happy to recommend acceptance.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: QUANTILE-DEPENDENT EXPRESSIVITY OF PLASMA ADIPONECTIN CONCENTRATIONS MAY EXPLAIN ITS SEX-SPECIFIC HERITABILITY, GENE-ENVIRONMENT INTERACTIONS, AND GENOTYPE-SPECIFIC RESPONSE TO POSTPRANDIAL LIPEMIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The author has used clear and appropriate language throughout the manuscript. He has done a commendable job in communicating quite a complex concept "quantile-dependent expressivity" and provided many examples to illustrate how it influences plasma adiponectin concentrations. The available literature is sufficiently described and cited, and there are very few typographical errors in the manuscript. The manuscript is appropriately structured, and figures and tables are clear and illustrate the results in sufficient detail. Raw data has been shared, and the results are relevant to the hypotheses being tested.
In the introduction, could the author briefly speculate as to the factors that might have contributed to such a large range of heritability estimates for adiponectin concentrations?
Experimental design: The research question is well-defined, and the measurements and statistical analyses have been both described and performed satisfactorily. This paper is quite unique in that the statistical conclusion reached in the first dataset (Framingham) is subsequently applied to several examples in the literature (eg Kang et al, DeLuis et al) to illustrate the concept.
Overall the research is robust and very well-performed, and this has been one of the best manuscripts I have reviewed in some time.
Validity of the findings: As stated above, in addition to its robust methodology, the major strength of this manuscript was application of the concept to available examples in the literature.
I wondered aloud if there were any genetic studies published in which there is no evidence for "quartile-dependent expressivity". To his credit, the author has provided some examples in lines 431-436. I was also pleased to read about the potential for log-transformation of adiponectin concentrations to negatively influence GWAS results.
The conclusions are well-stated, but I was left wondering about the molecular machinery underlying quartile-dependent expressivity. Can the author elaborate (even briefly) on how a sex-dependent factor (such as testosterone) can not only reduce adiponectin concentrations AND reduce heritability? For example, is this likely due to occupation of an element upstream of ADIPOQ by the ligand-bound androgen receptor, which may subsequently suppress any other potential influences (like diet or inflammation) on adiponectin gene transcription? Are there prior examples in the literature, and has the molecular basis for these been described in any detail?
Additional comments: Your imaginative manuscript was presented to a very high standard, and as a researcher who has studied adiponectin polymorphisms and their influence on adiponectin concentrations, I really enjoyed reading about the concept of quartile-dependent expressivity and seeing it being applied to examples in the literature. I'm very happy to recommend acceptance for your manuscript.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: QUANTILE-DEPENDENT EXPRESSIVITY OF PLASMA ADIPONECTIN CONCENTRATIONS MAY EXPLAIN ITS SEX-SPECIFIC HERITABILITY, GENE-ENVIRONMENT INTERACTIONS, AND GENOTYPE-SPECIFIC RESPONSE TO POSTPRANDIAL LIPEMIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are several typos all over the manuscript, but in particular in the introduction.
To give to the reader a complete picture of adiponectin and its role in health and disease, the authors should not forget to cite the “adiponectin paradox”, describing the role of adiponectin on cardiovascular events and mortality (Menzaghi et al., Diabetes 2018). This is important in the light of heritability and its consequence. Could heritability of quantile-dependent expressivity of adiponectin be a possible explanation for the adiponectin paradox?
Experimental design: In the results section there is no mention at all for figures 5, 6 and 7. It is not really clear how the authors have revised several papers (Ref. 28-37) according to the “quantile-dependent expressivity” of adiponectin. Have they get raw data from the above cited papers’ authors in order to analyze data and produce figures? All this part needs to be accurately explained.
Validity of the findings: Most part of the discussion is a revision of previously published papers and are not really supported by the original results (see the above mentioned concern).
Additional comments: This report on the quantile-dipendent expressivity of adiponectin concentration could be interesting regarding the approach of using quantile expression of a trait and the results obtained are sound for sex specific heritability. Completely speculative are data on gene-envinromental interactions and genotype-specific response to postprandial lipemia, unsupported by data obtained in the cohorts analyzed for heritability.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ASSOCIATION OF PRE-PREGNANCY BODY MASS INDEX WITH ADVERSE PREGNANCY OUTCOME AMONG FIRST-TIME MOTHERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this manuscript, Li Li et al conducted a study on a total of 3,684 women who gave birth for the first time in south of China to investigate the associations of preterm birth (PTB), low birth weight (LBW) with pre-pregnancy Body Mass Index (BMI). Their study suggests that underweight women increase the risk of LBW.
Although their result is consistent with many others, there are several major concerns as outlined below:

1.	No big differences/advantages of this study are from the literatures (J Nutr. 2003 Nov;133(11):3449-55; BMC Pregnancy Childbirth. 2019 Mar 29;19(1):105....).

2.	This manuscript should be clearer, more succinct, and professional. For example: in Abstract, "Risks of PTB and LBW in the first subsequent pregnancy in women who had a abnomal BMI were compared with risks in women who had a ideal BMI.”

3.	It is better to show some data in Figure although the tables are accepted.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ASSOCIATION OF PRE-PREGNANCY BODY MASS INDEX WITH ADVERSE PREGNANCY OUTCOME AMONG FIRST-TIME MOTHERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study was designed to elucidate the association between maternal BMI and adverse pregnancy outcomes for first-time mothers in Southern China. The topic is valuable taking into account that obesity is increasing rapidly worldwide, particularly in rapid developing countries like China. However, I have some comments/concerns:

There have been many studies regarding the association of maternal BMI and offspring birth outcomes, in and out of China, such as Rahman MM, Abe SK, et al. 10.1111/obr.12293, Pan Y, Zhang S et al, 10.1136/bmjopen-2016-011227. The authors did not provide a comprehensive background in Introduction. Several latest published papers were not incorporated.

Moreover, the language is hard to follow. There are flaws and mistakes in written English. For ex, Introduction, line 58 “both” should be not capitalized; line 62, “is” should be “was”; Materials and methods, line 81 and 83, repeated “the control group”; Discussion Line 157, “showed” is in fact “showing”, line 158, “ruduced” should be “reduced”. It would be useful to have a native English speaker edit the manuscript for clarity and concise language.
Experimental design: 1) First, the meaning of this study is not well explained in Introduction. Given the many reports on this topic, the authors did not address clearly the importance and novelty for this study. Is it for Southern Chinese, or first-time mothers?

2) As the authors mentioned, preterm birth is related to a variety of factors. Gestational hypertension may be a mediator between maternal BMI and PTB or low birth weight. To simply adjust for gestational hypertension in the regression is not suitable.

3) Gestational diabetes, twin pregnancy, and gestational weight gain are also important factors influencing the association. Given your dataset, are you able to analyze the association taking into account these factors?

4) Birth weight is a key indicator for intrauterine environment. However, birth weight adjusted for gestational age would be more appropriate than birth weight itself.

5) Also, information on early and late PTB is useful for health professionals. It would be useful to examine the risk of PTB according to gestational age with maternal BMI strata.
Validity of the findings: 1) Table 2 and 3 are not well structured. In Results, the associations between overweight and obese mothers with offspring birth outcomes are not presented.
2) Please explain why this study did not find an association between high BMI and PTB.
3) The discussion part is not well organized and hard to follow.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ASSOCIATION OF PRE-PREGNANCY BODY MASS INDEX WITH ADVERSE PREGNANCY OUTCOME AMONG FIRST-TIME MOTHERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revision improved the paper as written.  There are several issues although the authors addressed most of concerns and suggestions in the revision.

1.	Word document of the revised manuscript is not the same version of the PDF
2.	One sentence is duplicated with the next one (line 221-222)
3.	Grammatical issues will need to be addressed.
        For example, line85-90; line131, line 132, line 162, line 178-179, line 212
Experimental design: What is the logical explanation for dividing newborns into six groups, not 8 groups? The authors divided gestational ages into four subtypes: extremely PTB (<28 gestational week), very PTB (28–31 gestational week), moderate PTB (32–36 gestational week) and normal (≧37 gestational week), and categorized newborn weight for gestational age into two groups: SGA and NSGA.
Validity of the findings: no comment
Additional comments: no comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: LONG NON-CODING RNA LINC01234 REGULATES PROLIFERATION, MIGRATION AND INVASION VIA HIF-2Α PATHWAYS IN CLEAR CELL RENAL CELL CARCINOMA CELLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is written in a clear and unambiguous technically English language throughout the paper. The article includes sufficient introduction but background references should be improved including most recent references. Overall article structures and figures sufficiently satisfy journal guideline. Raw data have been supplied. All results relevant for the hypothesis have been included
Experimental design: The present research is of interest for PeerJ and for PeerJ readers. The experimental design is properly described and conducted according to technical and ethical standard. Methods are sufficiently described to be replicated
Validity of the findings: Results are solid, consistent with hypothesis and clearly reported
Additional comments: 1)	Manuscript can be improved by the evaluation of  mRNA levels of genes reported in Figure 8 (not necessarily all)

2)	The article is well written and results are clearly described. However, it is not clear why authors are referring to HIF-2α pathways. They can generalize by referring to HIF-2α pathway. Moreover, it is not clear why authors focused on HIF-2α pathway, although also HIF-1α was modulated.

3)	Figure 8 can be improved. The quality of some western blot images is not satisfactory

4)	Figure 8 it is not mentioned in the relative Results section.