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: ENSEMBLETAX: AN R PACKAGE FOR DETERMINATIONS OF ENSEMBLE TAXONOMIC ASSIGNMENTS OF PHYLOGENETICALLY-INFORMATIVE MARKER GENE SEQUENCES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The text is in general clear but as pointed out in 4 some areas near clarification.  Figures need to be improved (see 4).
Experimental design: No comment
Validity of the findings: No comment
Additional comments: # General comments
This paper presents a new R package aimed at reconciling taxonomic assignments of short sequences (metabarcodes) made using different algorithms (dada2 Bayesian assigner or DECIPHER TaxID) or different reference sequence databases (PR2, Silva, RDP) and computing an "ensemble" taxonomy.  This package should be useful as metabarcoding is becoming the method of choice for characterizing microbial communities both eukaryotic and prokaryotic.  The package has been published on CRAN which means that it has passed software tests successfully.  Unfortunately, I did not have the time to test it as extensively as I possibly would have liked. However I think that the package documentation and the paper should undergo a thorough revision in order to improve the package usability and the analyses provided in the paper itself.

* I found the on-line documentation quite minimal and a bit hard to follow.  I would suggest to show in  a vignette the whole process starting from a small metabarcode sequence dataset and providing the code for the assignement of sequences with dada2 and DECIPHER and then showing how to use the emsembleTax package and interpret the data.  I would also suggest that the vignette include plots comparing the output of the different assignments and of the "ensembleTax".
* The description of how the emsembleTax algorithm works should be explained in a separate vignette with examples.
* The description of the function "taxmapper" is not totally clear. Several examples should be given in a vignette. The sentence l. 206 to 208 should be clarified.
* I am not sure that the term "ensemble" taxonomy is really the most appropriate.  "ensemble" is in the name of the package which cannot be changed I guess but I would replace this term in the paper itself.  I would it rather call "consensus" taxonomy.
* The description of the ensembleTax function algorithm is a bit hard to follow and I would have liked to have an example (maybe in a vignette).  What is the "highest-frequency taxonomic assignement" (l. 252) ?  If there are only 2 tables, the each table counts for 1 (I understand that you can use the weights argument) ?
* The authors used a V9 dataset to demonstrate the use of the package and to show how it helps improving taxonomic assignement.  However I do not think that using V9 is best to demonstrate this as reference sequence databases such as PR2 have much less sequences covering the V9 region than the V4 region.  So it would be interesting to complement the analysis with a V4 dataset from the literature (e.g. OSD, Ocean Sampling Day) as well as a bacterial dataset.
* The analysis provided in Fig. 2 is very succinct (see also my comments on the readability of the figure).  I would like to understand better how the package improves really assignement, maybe by looking at specific taxonomic groups.  Also at least for PR2, the confidence values from DECIPHER are in general lower than the bootstrap values for dada2 assignements.  Therefore, this will contribute to the fact that less sequences are assigned with DECIPHER than with dada2 for a given bootstrap level. This may depend though on the way DECIPHER is trained (number of iterations and number of sequences per group)
* The term "misclassification" (l. 319) is a bit misleading.  For some taxonomic groups, one database maybe better than the other one, while this is the reverse for another group. None of the function parameters accounts for this, so rather than misclassified maybe use something "disagree with consensus"...

# Specific comments

* l. 239. Algaebase is protected by very strong copyright rules.  Does the authors secured an agreement from Algaebase to use the data ?
* Fig. 1 could be made clearer by adopting a more vertical structure...
* Fig. 2 is hard to read. Make bars wider.  Move the legend on the top so that the figure can be wider.  Explain in the legend what you mean by unassigned, is it anything that has a bootstrap value < 100 ? For panels C to F, it would be better to do cumulative bars for each of the taxonomy table since a given sequence falls into a single of the categories represented in the X axis.  Moreover as the panels C to F is shown now the order of the bars is different from the order of the legends... which makes things hard to visualize for color blind people.


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: ENSEMBLETAX: AN R PACKAGE FOR DETERMINATIONS OF ENSEMBLE TAXONOMIC ASSIGNMENTS OF PHYLOGENETICALLY-INFORMATIVE MARKER GENE SEQUENCES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript "ensembleTax: An R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences" is clearly written and provides the necessary references to support their statements and provide context. It is true that maybe the authors should make an effort to reduce the number of references as in some parts it is not necessary to provide multiple references to support a simple statement for example. The figures are correct, however, in figure two the order of the bar plots across the panels, and the legend are not always the same making it more difficult to follow.
Experimental design: It is not clear to me how the concepts of misclassification errors, overclassification errors, and underclassification errors have been defined. From my point of view, they can be only defined by using mock communities or by comparing against a tree built with the classified sequences and based on the tree annotated the taxonomic strings of the tree manually. So, the automatic annotation can be compared against the known mock community or a reliable curated tree, and consequently, the different errors in annotation can be reported. Otherwise, if their definition of the errors is based on the same automatic annotation I do not think they can be called errors, as the authors have not defined what would be the right classification.
Validity of the findings: Their initial premise is in general correct, there are some statements that I do not believe are true, so I would suggest modifying those. The proposed approach and the associated tools are very interesting and I think that part of it can benefit a lot the taxonomic identification of amplicon sequencing data. I find particularly useful the essembleTax part of the essembleTax package (I would like to mention that naming a part of the package as the whole package is somehow confusing, a different name would be helpful). Combining the results of different taxonomic annotation algorithms can be very helpful and I can see how I would use it for my own research. However, I am not so convinced about the taxmapper part. The implicit assumption for taxmapper is that all the reference databases present essentially the same taxonomy and the only real variation lies in the number of ranks. I have a lot of experience parsing and curating reference databases and comparing them and sadly that is not the case. The taxonomies differ, some are curated, some automatized, and when you compared them they can be very different, especially at the family, order, and class level. For certain groups these differences are substantial. So, if I understood how taxmapper works I believe that these divergences in the taxonomies will lead to errors in the annotation. Could the author clarify this (especially if I am wrong because I am not fully understanding what taxmapper is doing)?
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: ENSEMBLETAX: AN R PACKAGE FOR DETERMINATIONS OF ENSEMBLE TAXONOMIC ASSIGNMENTS OF PHYLOGENETICALLY-INFORMATIVE MARKER GENE SEQUENCES
Review round: 2
Reviewer: 1

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
Additional comments: I'm glad to see the manuscript is much improved. My comments have been satisfactorily address. Couple of errors I notice: line 186 "16S rRNA train set" still not corrected; line 297 "Callahah" should be "Callahan".


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: ENSEMBLETAX: AN R PACKAGE FOR DETERMINATIONS OF ENSEMBLE TAXONOMIC ASSIGNMENTS OF PHYLOGENETICALLY-INFORMATIVE MARKER GENE SEQUENCES
Review round: 2
Reviewer: 2

Output:
Basic reporting: OK
Experimental design: OK
Validity of the findings: OK
Additional comments: I did not have the time really to do a new full review of the paper as it has been substantially changed.  I think the authors tried in earnest to address all comments made by the 3 reviewers and I think the paper can now be published.  It will be complementary of the package and will be useful to its user.


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: HOW C: N: P STOICHIOMETRY IN SOILS AND CARBON DISTRIBUTION IN PLANTS RESPOND TO FOREST AGE IN A PINUS TABULIFORMIS PLANTATION IN THE MOUNTAINOUS AREA OF EASTERN LIAONING PROVINCE, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: correct
Validity of the findings: no comment
Additional comments: How C: N: P Stoichiometry in Soils and Carbon Distribution in Plants Respond to Forest Age in a Pinus tabuliformis Plantation were introduced in this paper. This is a subject of interest to researchers in related fields, but the paper needs a few minor changes before it can be accepted for publication. My detailed comments are as follows:
1. This paper studies the relationship between plant carbon distribution and soil C: N: P stoichiometry in Pinus tabuliformis plantation of five ages from young forest to over-mature forest. This idea is interesting, and the experimental methods adopted are very mature. And in this paper, some important conclusions were drawn, such as “the Pinus tabuliformis plantation had a good nitrogen fixation effect, and the carbon, nitrogen, and phosphorus content in the soil was adequate, and Soil nitrogen and phosphorus content had a significant effect on the fine roots and in forest management, the nitrogen and phosphorus content in soil should be controlled to avoid excessive application of nitrogen and phosphorus fertilizer” and so on.
2. Your result needs more detail. I suggest that you improve the description at lines 170- 172 to provide more justification for your study. And there is an incorrect word on line 212.
3. I suggest simplifying the units of the legend in Figure 2, 3, 4 and 6 to make the figure look cleaner.
4. In the discussion part of this paper, there are three words with dashes and one grammatical error in lines 272 to 277. I suggest you revise it carefully.
I commend the authors for their extensive data set, compiled over many years of detailed fieldwork. In addition, the manuscript is clearly written in professional, unambiguous language. If there is a weakness, it is as I have noted above which should be improved upon before 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: HOW C: N: P STOICHIOMETRY IN SOILS AND CARBON DISTRIBUTION IN PLANTS RESPOND TO FOREST AGE IN A PINUS TABULIFORMIS PLANTATION IN THE MOUNTAINOUS AREA OF EASTERN LIAONING PROVINCE, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment, see the general and specific comments.
Experimental design: No comment, see the general and specific comments.
Validity of the findings: No comment, see the general and specific comments.
Additional comments: This study deals with C:N:P stoichiometry in soil under five forest ages, those forests are in a Pinus tabuliformis plantation. The sampling site is a pretty good example for the study of ecological stoichiometry in the context of the plant-soil systems along the different forest ages. I have to say I like this study. And I am sure there might be interesting results in the data, howerve, the way the study is described leaves it unclear what the purpose of the data collection in the five forest ages was. In the Discussion section, I can see authors try to discuss and explain why their results are different from other studies, but the discussion needs references, not just mention that the influence is comprehensive or carbon synthesis strategy in leaves differs from those in branches without citation. Also, please do not repeat your results in the Discussion section.

Overall, the subject is relevant. A well-written article, albeit with many grammatical mistakes. I would highly recommend applying a professional language check to correct for many grammatical mistakes and terms used in an incorrect way as well as many articles missing and incorrect singular-plural use.


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: HOW C: N: P STOICHIOMETRY IN SOILS AND CARBON DISTRIBUTION IN PLANTS RESPOND TO FOREST AGE IN A PINUS TABULIFORMIS PLANTATION IN THE MOUNTAINOUS AREA OF EASTERN LIAONING PROVINCE, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Comments to the Authors

The paper by Wang L. et al. addresses the effects of soil C:N:P stoichiometry and plant carbon distribution respond to forest age in a Pinus tabuliformis plantation in the mountainous area. There are many points should be followed.

Abstract:
More numbers should be cited here, such as, you say “Carbon content was highest in the leaves of MAF and NMF and the trunks of YF, MF, and OMF, and was lowest in the branches over the entire life cycle of the aboveground components”. I want to know which is the highest or lowest value. “they had a significant effect on fine roots”…add some numbers will make the Abstract clear for readers if he/she do not see your full paper.

“In forest management, nitrogen and phosphorus content in the soil should be controlled to avoid excessive application of nitrogen and phosphorus fertilizer.” I do not suggest the sentence here, because it is not the major content. You did not summarize your study in the last sentence. I only see many results, but some conclusions should be put here.

Introduction

L41-44, add references.

L47, add point.

L49-52, add references.

L62-63, “and there are few studies on the eastern area of Liaoning Province”. The writing of this sentence is sudden. According to the first half sentence, you can describe the eastern area of Liaoning Province by using some climate attributive, such as temperate zone, etc.

L64, relationships

L64-68, I suggest that the passive sentence can be used here. The references should be put together.

L68 and 70, many studies? Where? List them. Check the whole manuscript.

L109, I suggest that delete the value in each plot, remain the average value in Table 1, while you can list them detailedly in the supplement materials.

Results

L151-180, You say many “there were significant differences between…”, “…showed significant differences”. However, readers need more clear information. If there is no figure, readers can access to information in the writing is important. If you want to express the result is significant, you may use p < 0.05 is OK.

L184, add SE or SD.

L220-221, delete

L227-228, delete

L232, 236, fig. 6

Figs. 5 & 6, I do not suggest the expression. Three point-line is unbelievable (R2= 0.999? 1? Really?). You can add a summary figure by using three colors (a trend line). In the section of materials, you say 360 soil samples? How to calculate? Detailedly. Maybe you can also use all data in the correlations.

Discussion

L287-288, add references.

In the section of 4.3, you should reorganize the data to indicate the conclusion.
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: HOW C: N: P STOICHIOMETRY IN SOILS AND CARBON DISTRIBUTION IN PLANTS RESPOND TO FOREST AGE IN A PINUS TABULIFORMIS PLANTATION IN THE MOUNTAINOUS AREA OF EASTERN LIAONING PROVINCE, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
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: HOW C: N: P STOICHIOMETRY IN SOILS AND CARBON DISTRIBUTION IN PLANTS RESPOND TO FOREST AGE IN A PINUS TABULIFORMIS PLANTATION IN THE MOUNTAINOUS AREA OF EASTERN LIAONING PROVINCE, CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: I believe the authors have provided reasonable responses to most of Reviewer 2's questions and concerns to some extent.
Experimental design: I still don’t understand why the authors collected 360 soil samples in 15 permanent sample plots, but mixed the soil sample in the same plot to make only one composite sample.
Validity of the findings: The work is interesting; however, the study scope is also quite narrowly defined.
Additional comments: General comments:
This is a re-review of the manuscript. I believe the authors have provided reasonable responses to most of Reviewer 2's questions and concerns to some extent. The work is interesting; however, the study scope is also quite narrowly defined. The major weakness of the study is the composite sample.

Specific comments:
L278, 281: Please use significantly instead of obviously, if the difference were statistically significant (p < 0.05).
L341, please add the value of “The soil TC: TN ratio in the present study area”.
L354, Add the value of “soil TC: TP ratio” as well as in L356.


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: HOW C: N: P STOICHIOMETRY IN SOILS AND CARBON DISTRIBUTION IN PLANTS RESPOND TO FOREST AGE IN A PINUS TABULIFORMIS PLANTATION IN THE MOUNTAINOUS AREA OF EASTERN LIAONING PROVINCE, CHINA
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
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: INTER-ETHNIC GENETIC VARIATIONS AND NOVEL VARIANT IDENTIFICATION IN THE PARTIAL SEQUENCES OF CYP2B6 GENE IN PAKISTANI POPULATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The work seems very important to me because it is an original article on different ethnic groups, which shows important contributions due to inter-ethnic differences in the same Pakistani population, showing the decrease in drug activity of two ethnic groups of the same population (Seraiki and Barochi); However, it is important that in the paragraphs where the activation and inactivation of drugs are mentioned, it is very important that they indicate which drugs (at least 3 to 5 drugs)
Experimental design: It is very important to clarify whether the informed consents obtained in the different ethnic groups were presented and obtained in the language of each ethnic group, given that in the same country not all their ethnic groups speak the same language.
Validity of the findings: Although the polymorphic differences of CYP450 cytochrome among the 5 Pakistani ethnic groups are evident, it is very important that they point out the differences in terms of the regions of the country where they live, customs, type of diet, habits, etc.
Additional comments: It is very important that you complete the responses to the previously suggested comments.
Respect work represents a valuable contribution


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: INTER-ETHNIC GENETIC VARIATIONS AND NOVEL VARIANT IDENTIFICATION IN THE PARTIAL SEQUENCES OF CYP2B6 GENE IN PAKISTANI POPULATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: I consider that the title of this work is very broad for the true scope of this research, since a study is not carried out on the complete CYP2B6 gene, only a region of it.

The background of the abstract is very ambiguous. I suggest targeting your reach directly to rs4803419 and rs3745274. Since in methods it is directly pointed out that a region containing these important SNPs is sequenced.

Introduction
- When referring to drugs metabolized by CYP2B6, it is necessary to include antiretrovirals (efavirenz).
- Paragraph of lines 67 to 69: there is a serious error in the wording, since it assumes that any SNPs in the CYP2B6 gene would affect the expression and/or activity of the enzyme.
- line 69: it should not refer to "races", it can speak of "ethnicities".
- line 71 and 76: improve the writing, consider that an allele is a variant of the gene.
- lines 81 to 82: it is not understood what it refers to.
- line 85: Please verify the indicated information, rs2279343 is not c.516G>T, but c.785A>G. For c.516G>T corresponds rs3745274.

It is necessary to add in the introduction the main characteristics of the ethnic groups of the Pakistani population. Since this is the main rationale for the research question.

Material and methods
- Informed consent is not just a written and signed document, it is a process.
- lines 112 to 113 should be moved to the introduction.
- line 131, you should improve the writing (twice "analysis")

Results

- In the PDF appear many: "Error! Reference source not found".
- Allele frequencies are better expressed as decimals not as a percentage (100% = 1.0)
- Table 2 is not referenced in the results.
- Verify that all supplementary figures or tables are referenced in the document.

Table 1

- For the position of the SNP, you must indicate which is the name of the sequence (for example: GRCh38.p12 chr 19)
- The information in the "Position" column is repetitive with the "Effects" column, since apparently only the reference sequence changes ...?
- On the other hand, information is repeated from the "REF" column and the "Effect" column (both indicate the nucleotide change ...?).
- At the bottom of the table include the meaning of REF and ALT.

The foot of table 1, seems to correspond to table 2.?

The wording needs to be improved.
Experimental design: Material and methods

The pattern observed in a 1% agarose gel allows to evaluate its quality (integrity), but does not allow to quantify the DNA (only a semi-quantification). Quantification should be by spectrophotometric or fluorescence methods.
Validity of the findings: A comparative analysis of the frequencies observed for this allele (*6) with other ethnic groups worldwide is necessary.

The discussion and conclusions are quite adequate, however, they require better support from the introduction and the title of the paper.

On the other hand, I consider that the observation of a "new" SNP should be indicated in the title.
Additional comments: It would be very interesting to predict what percentage of the Pakistani population (or ethnic groups studied) would be poor metabolizers, based on the observed genotypes, and discuss their differences or similarities with other ethnic groups or populations globally.

I recommend seeking information on adherence to antiretroviral treatment with efevirez in the Pakistani population. It would be interesting to see how the rates of adverse events to this drug and/or discontinuation of therapy are. Then correlate with the observed frequencies for the *6 allele, compared to other ethnicities or populations.


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: INTER-ETHNIC GENETIC VARIATIONS AND NOVEL VARIANT IDENTIFICATION IN THE PARTIAL SEQUENCES OF CYP2B6 GENE IN PAKISTANI POPULATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: Clear and unambiguous, professional English used throughout

Literature references, sufficient field background/context provided.

Professional article structure, figures, tables. Raw data shared

Self-contained with relevant results to hypotheses
Experimental design: Original primary research within Aims and Scope of the journal.

Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.

Rigorous investigation performed to a high technical & ethical standard.

Methods described with sufficient detail & information to replicat
Validity of the findings: All underlying data have been provided; they are robust, statistically sound, & controlled.

Conclusions are well stated, linked to original research question & limited to supporting results
Additional comments: I found it to be an excellent job, very well prepared and developed


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: ASSESSING THE QUANTITATIVE RELATIONSHIPS BETWEEN THE IMPERVIOUS SURFACE AREA AND SURFACE HEAT ISLAND EFFECT DURING URBAN EXPANSION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English need further improve
Experimental design: no comment
Validity of the findings: The authors failed to collect basic data well in the study area, like the Population, land area, socioeconomic, consumption during 2002-2020 of Kunming City, As a result, the conclusion reached in the discussion is not supported by strong evidence.
Additional comments: Title: Assessing the quantitative relationships between the impervious surface area and heat island effect during urban expansion: a case study in Kunming, China
ID: #55463
Conclusion: Reject
Comments for authors:
Abstract:
(1)	Lack of presentation of key quantitative results, some important data need present.
Introduction:
(2) L37: An UHI not A UHI
(3) L71: Statistical yearbook no references
(4) Introduction should point out the situation of urban expansion during 2002-2020 years, and emphasize the importance of studying the UHI to Kunming City.
Materials & Methods
(5) Please added the area, population, and some basic information about Kunming City.
Results
(6) L240-247 should move to section of Materials & Methods
(7) Please add a distribution figure of Kunming City and clearly note the place name mentioned in your text, such as: First, second, and third Ring, Dianchi Lake, Yangzonghai, guandu, etc. Because readers not familiar with your study area.
(8) L321, where is the Fig A1?
(9) L460, where is [17]?
(10) Please add a regression figure to present the regression result.
Discussion
(11) L445-447, where is the reference or evidence for mentioned viewpoint?
(12) L481-495,The author admits that linear regression is flawed, why not use
nonlinear or multiple comparisons in current text? Present data completely satisfying the requirement of the method for nonlinear regression.
(13) The authors failed to collect basic data well in the study area, like the Population, land area, socioeconomic, consumption during 2002-2020 of Kunming City, As a result, the conclusion reached in the discussion is not supported by strong evidence. Such as L437-439, L457-459, L451-453, L518-530.
(14) L531-586, you mentioned 3 measures are irrelevant to your results in text.
Conclusion
(15) Rephrase
Overall, I think the manuscript should be rejected.


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: ASSESSING THE QUANTITATIVE RELATIONSHIPS BETWEEN THE IMPERVIOUS SURFACE AREA AND SURFACE HEAT ISLAND EFFECT DURING URBAN EXPANSION
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please refer to the general comments section.
Experimental design: Please refer to the general comments section.
Validity of the findings: Please refer to the general comments section.
Additional comments: The paper studies the relationship between LST and ISA in Kunming, China. The findings of the paper can be beneficial for the researchers in the field. However, the followings should be addressed.

There is a jump from the first to the second sentence of the abstract, without providing any information about the importance of doing this analysis on Kunming, China as a case study.
The abstract lacks cohesion and needs to be revised.
It is commonly known that there is a strong relationship between ISA and LST. So, the authors should specify how the findings of this paper will help urban planners and researchers.
The innovation of the research is not clearly specified.
Line 42: the sensitivity of LST to surface characteristics cannot be the reason for the current trend of studying UHI.
Line 243: 80% accuracy is not high. How does this satisfy the requirements?
Line 396: what does good represent here?
Line 419: “The heat island effect is related to the size of the city. The larger the scale is, the more obvious the heat island effect (that is, the greater the temperature difference between urban and rural areas)”. The statement needs reference.
Line 424: “that the urban atmospheric environment tends to be mild”. How can the results prove this statement while the research was done using LST?
Line 437: “Therefore, the background climate, the geographic location, the surrounding topography and even the collection times and seasons of different satellite data should be considered for different research areas.” How does this statement help the findings of this paper?
Line 481: “To analyze the quantitative relationships between impervious surfaces and LST, this article employs linear regression analysis. However, many scholars’ studies have shown that the quantitative relationships between impervious surfaces and LST are not simply linear.” If the literature already showed that the relationship between ISA and LST is not linear, why linear regression was used in this study?
Line 494: needs revision.
In the discussion part, the author mainly analyzed other works, while it is expected to justify the results of the current study with the results of other studies.
Figures and tables:
It is not clear what the right-hand section of Figure 1 shows.
The quality of the graphs should be increased.
The size of the figure 3 can be decreased. It would be easier for the reader to follow the trend if it was a linear graph.
The paper needs to be majorly revised in terms of grammar. Some of the examples that needs to be modified are listed below:
Line 15: Conjunctions were not used correctly.
Line 19: word “analysis” was used three times in a row.
Line 16: the sentence is very long and can be difficult for the reader to follow.
Line 61: “effect(Cheval & Dumitrescu 2015; Du et al. 2016)”. A space is required between the word “effect” and parenthesis. The same problem can be seen in line 63, 101, 192, …
Line 34: paragraph started without indentation while in line 48 the paragraph started with indentation.
Line 39: “boundary-layer heat islands and canopy-layer heat islands”; Unnecessary repetitions of words.
Line 72: “urban development, etc.”
Line 73: needs revision.
Line 71: a very long sentence.
Line 78: “the traditional methods cannot effective reflect”. grammatical error
Line 105: “this paper selects an impervious surface index”. Select might not be a suitable verb here.
Line 105: Very long sentence. Paper needs to be majorly revised in terms of the structure of sentences.
Line 114: “UHI effect for Kunming”. on Kunming?
Line 263: “revealing that the ISA in the main urban area of Kunming has been characterized by an overall increasing trend from 2002 to 2020”. needs revision.
Line 421: the sentence started with “However” while there is no contrast between the previous sentence and this sentence.
Line 423: conjunction was not used correctly.
Line 419: a very long sentence.


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: ASSESSING THE QUANTITATIVE RELATIONSHIPS BETWEEN THE IMPERVIOUS SURFACE AREA AND SURFACE HEAT ISLAND EFFECT DURING URBAN EXPANSION
Review round: 1
Reviewer: 3

Output:
Basic reporting: Please see 'General comments for the author'.
Experimental design: Please see 'General comments for the author'.
Validity of the findings: Please see 'General comments for the author'.
Additional comments: This study proposes the quantitative relationship between the impervious surface area and heat island effect during urban expansion in Kunming, China. While it has potentials to be published, there are some issues which need to be addressed before proceeding further.

•	Overall, the study lacks innovation.
•	English improvement is required as there are a lot of grammatical errors.
•	Lines 200 & 206: LC indices value ranges for different LC types should be indicated. See the paper below as an example:
“Remote sensing image-based analysis of the relationship between urban heat island and land use/cover changes”
•	Table 3: It is highly recommended to add the scatterplots of random samples to show the comparison clearly.
•	Figure 5: Using only one Landsat image every 6 years is not enough to explain the temporal variation of the SUHI over two decades. Now, Google Earth Engine platform enables RS researchers to process hundreds of images during long time periods to increase the accuracy of obtained results.
•	Line 340: Correlation between ISA and LST based on difference analysis
There are several places’ names in this part with unknown locations, which can make readers confused, like Chenggong University City, Xishan District, Airport New Area, Dianchi Lake, Yangzonghay ….
All places should be illustrated on a map. You can show them on the map used to show the study area (Figure 1)
•	Figure 1: The size of the border of Yunnan Province should be increased.
The map on the right side of this Fig and Table 1 are giving the same information. You do not need to have both.
•	Some statements need to be referenced. For examples:
‘Geospatial measurement analysis’: Profile analysis (Line 214), Difference analysis (Line 221), …
‘Discussion’: Line 419
•	There is no space between the words and in-text references. Fx:
Line 37: … overall livability of urban areas(Xie et al. 2011).
Line 43: … surface characteristics and human activities(Voogt 2002),…
Line 59: … the urban weather and location(Peng et al. 2005).
Spaces should be added.
•	Line 417:  The Discussion part should mainly discuss the results obtained in the study. The main purpose is to compare the results of a study with the literature and the implications of similarities and differences. But, in this study, the authors separated the discussion part from the results, and mainly reviewed the other similar works.


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: ASSESSING THE QUANTITATIVE RELATIONSHIPS BETWEEN THE IMPERVIOUS SURFACE AREA AND SURFACE HEAT ISLAND EFFECT DURING URBAN EXPANSION
Review round: 2
Reviewer: 1

Output:
Basic reporting: Please refer to "general comments for the author".
Experimental design: Please refer to "general comments for the author".
Validity of the findings: Please refer to "general comments for the author".
Additional comments: The authors did make modifications.
As the abstract and conclusion parts are too long, it is highly recommended to revise these two parts.
Keywords are missing.


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: ASSESSING THE QUANTITATIVE RELATIONSHIPS BETWEEN THE IMPERVIOUS SURFACE AREA AND SURFACE HEAT ISLAND EFFECT DURING URBAN EXPANSION
Review round: 2
Reviewer: 2

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
Additional comments: The written English has been improved throughout the manuscript in the revised version.
As UHI and SUHI have different characteristics and in this manuscript LST has been explored, it is suggested to mention surface heat island rather heat island in the title.
Summarising the abstract is highly recommended, and then it would have the potential to be published in the journal.


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: EFFECTS OF STEP LENGTH AND CADENCE ON HIP MOMENT IMPULSE IN THE FRONTAL PLANE DURING THE STANCE PHASE
Review round: 1
Reviewer: 1

Output:
Basic reporting: I agree with the importance of research to prevent progression of hip OA. This paper is generally well organized and the figure is visually valid. However, the association between the risk factor in the progression of hip OA (hip adduction moment impulse) and this study is very weak. The author stated that the results of this study contribute to slowing the progression of hip OA, but this study was a rudimentary analysis of gait, and only presented imaginable results. Daily cumulative hip moment, risk factor for hip OA progression, is product of moment impulse and steps per day. So, increasing cadence alone does not reduce risk.
Experimental design: First, why did this study use healthy and young subjects? There is no reason not to experiment with patients with hip OA. Why the hip moment impulse was normalized with body mass and step length? Step length was also input as an independent variable. This analysis is not appropriate and may confuse the reader. Why did you choose only the hip adduction moment impulse in the frontal plane as a dependent variable? It is understandable to refer to the study of Tateuchi et al. 2017, it is inconclusive that hip adduction moment impulse is the only risk factor for hip OA. It is necessary to justify the sample size why this study required data for as many as 57 people.
Validity of the findings: It is obvious from the calculation process that the moment impulse is related to cadence, that is, stance time because moment impulse is a time-integrated value. It is also widely known that hip adduction moment has bimodal peaks. Unfortunately, I don’t feel any novelty, it’s just a very natural result. Increasing the step length was associated with decrease in the hip moment impulse, but why is that not emphasized?
Additional comments: Research subjects and analysis methods should be reconsidered. And above all, the results of this study do not appear to contribute to slowing the progression of hip OA.


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: EFFECTS OF STEP LENGTH AND CADENCE ON HIP MOMENT IMPULSE IN THE FRONTAL PLANE DURING THE STANCE PHASE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Introduction is relevant to the context.

Structure is clear.

English is clear and the paper is mostly very fluent.
Some detailed comments about language:
L26-28
Please write out this sentence without using the parentheses.
L35
I believe you don’t mean your data as this was public data but probably your findings?
L129-133
Again here I would recommend using full sentences instead of the parentheses to make it more reader friendly. Yes, the clarification is important but it can be written out.
L220
See my previous comment about data vs. findings.
Experimental design: This study is well justified and within the scope of the journal.

Research question is clear, relevant and meaningful.

Specific comments about methods:
Data processing:
Why use 15 of the 20 trials and not all?
Validity of the findings: The findings are well discussed and relevant literature is referenced.

In the conclusions, I would like to see more of an practical application of these findings. So if someone was to do an intervention with a population with hip OA, what kind of adjustments to walking speed and cadence should the clinician advice the patients to make?
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: EFFECTS OF STEP LENGTH AND CADENCE ON HIP MOMENT IMPULSE IN THE FRONTAL PLANE DURING THE STANCE PHASE
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is well structured and in accordance with a scientific article.
Experimental design: The manuscript used a public dataset that seems to be technically correct.
The statistical methods for the analysis also seems to be correct.
However, in my opinion the authors could explore more the data in to order to properly address their hypotheses.
The issue is that they are investigating the effects of step length and cadence on frontal hip moment without controlling for speed. I will point a possible problem with this approach on the next item.
Validity of the findings: The gait data analyzed are from subjects walking at self-selected speeds with no control of the step length and cadence. So, the gait speed covers a range of values. The authors regressed frontal hip moment with step length and cadence and they found that frontal hip moment is directly correlated with step length and inversely correlated with cadence.
The authors then concluded:
1. "...that a decrease in walking speed does not increase the hip moment impulse...".
Where are the regression results to support this statement?

2. "...a decrease in cadence (not step length) increases the hip moment impulse in the frontal plane."
I think it would be clearer if the authors simply stated the finding that an increase in step length increases the hip moment rather than negating the inverse of the finding.
Additional comments: I think the choice of step length as the focus to discuss the implications to frontal hip moment is somewhat arbitrary.
For example, the authors introduce the notion of cumulative hip moment (product of hip moment impulse in the frontal plane and mean number of steps per day).
So, the finding that an increase in step length leads to an increase in frontal hip moment may not have any implication for osteoarthritis, simply because a larger step length would imply a fewer number of step lengths for a same distance covered on a given day.
I would suggest to the authors to extend their analysis to include the following points:
1. Is frontal hip moment related to gait speed?
2. How much the cumulative hip moment for a hypothetical distance is affected by the increase in step length and speed?


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: EFFECTS OF STEP LENGTH AND CADENCE ON HIP MOMENT IMPULSE IN THE FRONTAL PLANE DURING THE STANCE PHASE
Review round: 2
Reviewer: 1

Output:
Basic reporting: I checked the resubmitted manuscript. Unfortunately, I couldn’t find enough revisions to my previous concerns. This study requires reconsideration of the data analysis and subjects. The results of this study (e.g., cadence was associated with the moment impulse) were self-evident and don’t update our knowledge of gait biomechanics. The publication of current manuscript can confuse and mislead readers. The reason is shown below.
Experimental design: Hip moment impulse was normalized by body weight and step length. Nevertheless, the step length was also input as an independent variable in multiple regression analysis for the hip moment impulse. This is clearly an error in the regression analysis. This was pointed out last time, but it hasn't improved.
The authors should include patients with hip OA if they hope that this study will have implications for the prevention of hip OA progression. Research using only the public data of healthy individuals without controlling gait speed will not be able to meet the wishes of the authors. I pointed out it last time; however, no improvement was found.
My previous comments included the following. However, it was not included in the response letter and was ignored.
“It is necessary to justify the sample size why this study required data for as many as 57 people.”
Validity of the findings: It is obvious from the calculation process that the moment impulse is associated with cadence, that is, stance time because moment impulse is a time-integrated value. The current result is naturally expected from the calculation process of the moment impulse. It is essential that the above revisions be made first.
Additional comments: Research subjects and analysis methods should be reconsidered. And above all, the results of this study do not appear to contribute to slowing the progression of hip OA. It’s unfortunate that the previous point wasn’t revised and some comment weren’t taken into account.


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: EFFECTS OF STEP LENGTH AND CADENCE ON HIP MOMENT IMPULSE IN THE FRONTAL PLANE DURING THE STANCE PHASE
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: My previous comments have been addressed adequately. I have no further 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: EFFECTS OF STEP LENGTH AND CADENCE ON HIP MOMENT IMPULSE IN THE FRONTAL PLANE DURING THE STANCE PHASE
Review round: 2
Reviewer: 3

Output:
Basic reporting: The authors have made substantial changes in the manuscript according to my comments. I endorse the publication.
Experimental design: Adequate.
Validity of the findings: Adequate.
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: DETECTION OF GENOMIC REGIONS ASSOCIATED MALFORMATIONS IN NEWBORN PIGLETS: A MACHINE-LEARNING APPROACH
Review round: 1
Reviewer: 1

Output:
Basic reporting: Paper is correctly written overall. Figures 2 and 3 are not clear.
Experimental design: This experiment is far too small for the purpose stated. It uses two separate populations that are apparently merged, inducing a stratification problem. Analyses by cluster adds some confusion here. How was sampling performed? It looks like incidence of malformations is very high.

Data are not enough, chosen nominal p-values are not stringent at all, p=0.01.
Validity of the findings: See above and below
Additional comments: This paper utilizes a gradient boosting machine to identify SNPs associated with malformations in piglets.

Main issues
- Population size is too small, and malformations may occur due to many independent diseases and therefore genes, assuming diseases is partly under genetic control.
- We do not know whether samples were collected in different farms with different incidences
- Disease is rare and so a case / control study is preferred, ie, collecting a large number of cases. This seems to be done but imperfectly as incidence of diseases is very high.
- The group congenital anomalies CA is a pool of different diseases and genetic causes
- Not clear how cross validation was performed, what % of data were left out for prediction? was it done stratified by breed and class?

Minor
- Quantify 'severe loss' , how important is it?
- Spell out and describe briefly GPS


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: DETECTION OF GENOMIC REGIONS ASSOCIATED MALFORMATIONS IN NEWBORN PIGLETS: A MACHINE-LEARNING APPROACH
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript detected genomic regions associated with congenital anomalie and piglet splay leg in newborn piglets using a machine-learning approach. The GWAS studies of congenital anomalie and piglet splay leg are interesting in pigs. The machine-learning approach was used to conduct GWAS is interesting. However, the manuscript did not consider the effect of sex to congenital anomalie and piglet splay leg in analysis model because it was reported that sex linked with piglet splay leg. In addition, the manuscript use “SNPs with positive relative importance” as significant criteria to generate top-associated SNPs. Is it feasible? If the number of significant SNPs is large, how to judge the most significant SNPs? The detailed comments list below.
Line 34 change “associated with congenital anomalies” to “associated with congenital anomalies and piglet splay leg”
Line 39 the sentence “complex genotypes associated with significant selection indicators of studied malformations and productive characteristics” is hard to understand. What is complex genotype? What is significant selection indicators?
Line 86 “We use the gradient boosting machine (GBM) approach since it is flexible and relatively easy to implement” The reason is not sufficient for using GBM. Why not use deep learning or random forest?
Line 178 and 182  the criteria value “p-value <10-2” is too low to judge the significance of SNP.
Line Table 1: Congenital Anomalies and Piglet Splay Leg were coded yes and no, respectively. They overlaped, to a certain extent. For examples, in landrace, 56 “no” of Congenital Anomalies contain 27 “yes” of Piglet Splay Leg. How to combine the overlapped part between Congenital Anomalies and Piglet Splay Leg?
Line figure 3: There is only the Manhattan plot of RRBLUP, Please show the Manhattan plot of Plink generated. In addition, please show the genes not SNPs on the Manhattan plot.


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: DETECTION OF GENOMIC REGIONS ASSOCIATED MALFORMATIONS IN NEWBORN PIGLETS: A MACHINE-LEARNING APPROACH
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: The sample size is not two small, and the case-control design should be clarified.
Validity of the findings: All underlying data have been provided.
Additional comments: using machine learning to detect regions associated with defect traits in pigs is a good option for small sample. The paper is good writing, while I have some comments as follows.

1.	L74. Hao et al. (Hao et al., 2017). --- Hao et al. (2017)
2, L108 saved – maintained
3.	Figure 2 dots and diamonds are not easy to be identified
4.	It is better to divide figure 3 into two figures to clearly illustrate the GWAS results.
5.	I am confused the sample size in this study, the authors mentioned 102 Landrace and 132 Large White were collected, while it is not consistent with the number in Table 1. And as to the case-control design, has the control no PSL and other congenital anomalies, are they the common control? Please clarify this as the sample size is very small for GWAS.
6.	I suggest the abbreviation of Landrace and Large White be used LL and YY like in most literatures.
7.	The authors used the high-density SNP chip to implement GWAS, as the linkage disequilibrium will deduce the dependent among SNPs and bring high false positive, the multiple test is usually taken into account, I suggest the authors to use it in this study.
8.	Machine learning and rrBLUP, Plink were implemented to identify regions or SNP related to PSL and other congenital anomalies, could the authors show the overlap of results from these three methods. Because the sample size in this study is too small, it is necessary to discuss the superiority of machine learning in such case.


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: DETECTION OF GENOMIC REGIONS ASSOCIATED MALFORMATIONS IN NEWBORN PIGLETS: A MACHINE-LEARNING APPROACH
Review round: 2
Reviewer: 1

Output:
Basic reporting: Some issues have been clearly addressed, although the main one, that of a small size, cannot be fixed. At least this should be acknowledged in the manuscript and a word of caution should be advised.
Experimental design: Fine with limitations.
Validity of the findings: Too small.
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: DETECTION OF GENOMIC REGIONS ASSOCIATED MALFORMATIONS IN NEWBORN PIGLETS: A MACHINE-LEARNING APPROACH
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript make some changes according to the reviewer’s comments.  The biggest problem of GBM algorithm is that can give a subsets of SNP with positive relative importance for a arbitrary SNP GWAS. Moreover,usually,the number of SNP with positive relative importance is large. Thus, it is necessary to give a critical value to judge the significance of SNP when the positive relative importance of SNP exceed the critical value. However, the manuscript doesn’t figure out the problem.


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: COMPARATIVE ANATOMY OF THE MIDDLE EAR IN SOME LIZARD SPECIES WITH COMMENTS ON THE EVOLUTIONARY CHANGES WITHIN SQUAMATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: I have made numerous comments on the manuscript and will direct the authors and the editors to the marked pdf copy of the manuscript for details.

However, to summarize, in terms of "Basic Reporting", the manuscript suffers from two current flaws:

1) The authors empirical observations are limited to 38 species from four major groups of squamates (iguanians, scincids, geckos and lacertoids = ~4000 species of extant squamates).  They did not sample snakes, anguimorphs, amphisbaenians, dibamids, xantusiids, etc., etc., but yet title their paper as "comparative anatomy" of "lizards".  This is simply not the case as a sample of all lizards (remember, snakes are lizards too), let alone all lizard groups/clades, was not done. The study is even more limited than just 38 species as 9 of them are all from a single iguanian genus, Anolis, which significantly narrows again the broad view of all lizards/squamates.  I hasten to point out that this is not a problem for the study, only for the manuscript, and it is easily remedied by rewriting the title to describe what the authors have actually done and outline those limitations when moving to their more broad conclusions.  This is a positive change as it indicates that substantial work remains but that preliminary findings show promising results.

2) The authors highlight very nicely the anatomy of the middle ear apparatus of "some lizards" and create 3 characters for phylogenetic analysis and subsequent character mapping to understand middle ear evolution.  Good.  However, the manuscript focuses on only two of those three characters - the columella and extracolumella.  The authors create a third character for the internal process, but devote only a handful of sentences to describing the morphology of literally 1/3 or 33% of their character complexes.  The internal process requires a great deal more description and highlighting in the body of their manuscript.  At the moment it is treated as an afterthought.  For example, in the Discussion, there are secondary headings for the Columella and Extracolumella, and literally nothing for the internal process. In the Discussion, the internal process merits 6 sentences, yet as I said, it is 33% of the characters analyzed.
Experimental design: The design is fine, but the conclusions and title of the paper need to reflect the small size of the sample - 38 species from ~10,000, with 1/4 of the data coming from a single genus.  I have no concerns with the methods as described and conducted.  The investigation is rigorous, but limited in scope.  There is still excellence in the work, but it needs to identify more precisely the limited scope.
Validity of the findings: All the data have been provided, they are robust, but need clarity in terms of limits relative to the scope of the project as written. All underlying data are provided.

Conclusions are more broad than the data allow, but this is easily remedied.  See marked pdf and opening and closing comments in this review.
Additional comments: I am recommending major revisions, and am happy to review a revised draft of the manuscript.  I do not think that the authors need to collect more data, nor change the way they have presented their results.  However, I think the manuscript needs a some work in terms of its title and the addition of descriptive text focused on the internal process.  If you have 3 characters, then there should be a corresponding amount of text describing the third character as you have devoted to the first two.  I do not think you need additional figures, analyses, etc.  You merely need to add text to the manuscript to give 1/3 of your character analysis the credit it deserves.  And finally, I would advise a title change to reflect the scale of your dataset - it is not all lizards.  it is some lizards, and a small sample at that.  There is nothing wrong with that limited dataset because we have collected is important and of value and deserves to be published in PEERJ.  The manuscript needs to be more specific about the limited data set and point out what is missing.  And finally, you use the words Squamate, Lizard and Lacertilia, as well as Serpentes, throughout the manuscript, and in a variable manner - I hasten to remind you that snakes are lizards and your own phylogenetic diagrams make that clear.  In any sense of lizard and squamate, they are thus the same thing, and in all cases, snakes are all three...squamates, lizards and lacertilians.  This is merely a pet peeve of mine and reflects a general problem in herpetology, not one that is specific to your collaboration nor this manuscript.

I am opposed to anonymity in the peer review process and identify myself as Michael Caldwell.


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: COMPARATIVE ANATOMY OF THE MIDDLE EAR IN SOME LIZARD SPECIES WITH COMMENTS ON THE EVOLUTIONARY CHANGES WITHIN SQUAMATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors present the morphological description of the middle ear in lizards based on clear stained specimen (of 38 lizard species) and discuss a possible ancestral state condition for the lizard middle ear plotting the described characters on a phylogenetic analysis based on molecular data. The manuscript is overall well prepared and well-written. In few occasions the structure of the sentences need tweaking. The methods and results sections are well organized and the discussion is straight forward. 5 tables and 8 figures are provided to present the data and illustrate the findings.

As shown by the authors (literature used is sufficient) data on the morphological shape of the different elements of the lizard middle ear is limited and a majority of the descriptions that are available are from older studies (60ies and 70ies). A fresh view and new descriptions on especially the extracolumella with new findings is of general interest to the scientific community and should be considered to be published.

However, there are some things in the manuscript that need attention: 1) The abstract should include the major findings of the study, in its current state it very general (see my comments in the attached pdf), 2) all figure captions need more explanations (what does the reader see, which view is presented, etc.), they are all in all very short and should be written is full sentences, 3) only figure 1 has a scale, but it is not indicated if that scale is the same for all illustrations seen in figure 1, also the other figures need a scale, 4) some microscopic photos are very dark and somewhat blurry (Figure 4 A and C, 5 C).
Experimental design: The basic experimental frame of the study is overall ok, one thing I see that seems problematic is that in most cases only one specimen of a species (23 of 38) and sometimes two and more were used for the clear staining part of the study. I understand that it is a quite long process to clear stain and needs time, but with only one specimen it is hard to tell anything about the variation within a species (as mentioned by the authors themselves in the manuscript). It is clear that this is not the point of the study, but it is a weak point when for example a general pattern for the extracolumella of a species is established.

I am mostly ok with the analytical part (software and approach) of the ancestral state reconstruction. But I suggest to revise the way character states were chosen in terms of the extracolumella. The authors erected four character states of the extracolumella for the ancestral state reconstruction and describe the morphology in great detail, because this is the structure with the most variance in the lizard middle ear. However, the character states that were chosen can lead to difficulties in following the arguments in the discussion. And here is why:
- The four states chosen by the authors are “reduced” [character state 0], “expanded” [character state 1], “absent” [character state 2], and “extensive” [character state 4].
- 1) the order seems odd. Although it probably will not influence the conclusions, I suggest to rethink the order and wording. Why would the state “absent” be the third state and “reduced” be the first? It does not follow a logic frame. There is the basic rule to look for characters to be present (and if present how they look) or absent. So, in this manner “absent” should be last in line.
- 2) the difference between the states “expanded” and “extensive” is not really clear. Does it differentiate between numbers of processes, or does it describe the size of the processes? This needs clarification.
- 3) the word “reduced” is difficult in relation with a character state, because it already implies some kind of modification of a previously more complicated structure and therefore cannot be the ancestral state. To avoid this the authors could just say “simple”.
- 4) the terms used for the states if the structure is present should follow a logical order from simple to complicated (especially helping readers who are not familiar with the type of analysis). So, I suggest to rethink the character states and maybe use different terms. For example: simple [0], expanded [1], extensive [2], absent [3]

The last point I want to address is the discussion, which is well written and detailed in its presentation. But I would like to see some kind of comparison of the findings of the ancestral state that was reconstructed in this analysis with what is available from the fossil record. I am aware there is not much, but it is worth looking in to the chapter “The lepidosaurian ear: variations on a theme” by Susan Evans (Springer Handbook of Auditory Research, Volume 59) for a summary of the fossil evidence. It’s always good to back up a theoretical ancestral state with actual evidence.
Validity of the findings: Although the middle ear of lizards is a quite well investigated subject the presented study adds new information. The authors make clear what the new findings are and discuss them with the available data from previous work. However, their important new insights are not summarized in the abstract in its current state.

The data are made available in 5 tables (4 tables intended for supplement) and 8 figures. The analysis appears sound but as mentioned earlier, the defintion of the character states needs attention.

The conclusion section needs revision as its lacks the major findings of the study in terms of the ancestral state reconstruction (see my comments in the attached pdf). However, the discussion is well supported with literature and research questions addressed in the introduction were matched.
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: COMPARATIVE ANATOMY OF THE MIDDLE EAR IN SOME LIZARD SPECIES WITH COMMENTS ON THE EVOLUTIONARY CHANGES WITHIN SQUAMATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The language of the paper still needs revision for English grammar, syntax, etc. You will see in my marked copy that I tackled the abstract but realized swiftly that my role as reviewer was not to perform this editing function for the entire manuscript.

The references, background, structure, figures, etc., are all fine.
Experimental design: I have read through the authors rebuttals to my earlier critiques and find that they addressed or rebutted everything to my satisfaction.  The manuscript is retitled to reflect the experimental design, as are the explication of results and the discussion and conclusions.

As a second read, I find the manuscript in order on these points.
Validity of the findings: Same as above.
Additional comments: I would implore the authors to reread their manuscript in detail for English grammar, syntax, vocabulary, etc.

Other than that, the manuscript is scientifically sound.


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: COMPARATIVE ANATOMY OF THE MIDDLE EAR IN SOME LIZARD SPECIES WITH COMMENTS ON THE EVOLUTIONARY CHANGES WITHIN SQUAMATA
Review round: 2
Reviewer: 2

Output:
Basic reporting: This is the revised version of a previously submitted manuscript. The manuscript was revised and reworked and is in great condition. Methods and results sections are well organized and the discussion was extended significantly and the abstract was reworked completely. The authors made a great decision in revising their character states and added more information on the extracolumella. The figures were reworked according to the reviewer’s suggestions.
The manuscript now is in great condition and suitable for publication. I am happy with all changes that were made.
Experimental design: Experimental design was good from the beginning, but the authors made adjustments to the definition of their character states as suggested by the reviewer. Ancestral state reconstruction ok. The revised version is in great condition.
Validity of the findings: Expanding the discussion and reworking the abstract significantly helped the previous version of the manuscript. I am happy with all changes and have nothing to add.
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: CHANGE IN MENTAL HEALTH, PHYSICAL HEALTH, AND SOCIAL RELATIONSHIPS DURING HIGHLY RESTRICTIVE LOCKDOWN IN THE COVID-19 PANDEMIC: EVIDENCE FROM AUSTRALIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The basic reporting and the literature context is good. But it is tad long and mostly redundant. Usually Introductions are kept short and usually of three paragraphs... without any figures or Table to refer to.

Some contextual citations like sameer et al., 2020 is missing.

First paragraph of discussion is redundant. There are many portions of the paper which have been repeated either in introduction, results or discussion. .
Experimental design: It is well designed and implemented. The explanations are long and repetitive. It5 would be better to use figure an tables as supportive things to carry the message, rather to give description of everything..
Validity of the findings: The findings are robust and meaningful
Additional comments: Dear Authors,
The paper is well envisaged and robust in message. But is a bit tad long. And there are many redundancies in it.
Some of the papers or covid like Sameer et al., 2020 have not been cited.
I would recommend to shorten it and reduce the overlap of in the different sections of the paper.
Regards


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: CHANGE IN MENTAL HEALTH, PHYSICAL HEALTH, AND SOCIAL RELATIONSHIPS DURING HIGHLY RESTRICTIVE LOCKDOWN IN THE COVID-19 PANDEMIC: EVIDENCE FROM AUSTRALIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The author might avoid frequent compound sentences for clarity and easy readability.
Experimental design: Nil
Validity of the findings: Nil
Additional comments: The manuscript titled “Change in mental health, physical health, and social relationships during highly restrictive lockdown in the COVID-19 pandemic: Evidence from Australia" addresses an important public health issue which is highly relevant in the current global scenario.
Though the article has been written well in general, the author may address the following issues to improve the manuscript further.
1. Introduction is lengthy. The author could make it precise and concise narrowing down to the research problem.
2. Materials and methods: Under "Perceived impact of COVID19 lockdown on different aspects of life, and concerns about COVID19"- Interpretation of the overall score for impacts and concerns should be mentioned clearly for better understanding since each have different interpretation.
3. Results: Line 355, change "increases to increased"
Line 357, the cited figure number doesn't match with the results explained. (Figure 2 instead of Figure 4?)
Interpretation of the effect sizes should be reconsidered.
Line 396, spearman r value mentioned (0.63) and the value mentioned in the table (0.64) does not match
Line 394 and 395 - change participant to participants.
In general, the author may verify the values mentioned in the manuscript matches that with the tables and figures (rounding off the numbers)
Line 463, cite table 3 also
Line 466, Replace figure 7A with 7C
Line 466- 470, needs more clarity and may be broken down into simple sentences
Line 471, the author states "similar pattern is also evident". However the result interpretation was different for friends and coworkers. This statement needs more clarity.
Line 474, mentions "8% of the sample" which does not match the value given in the figure (6 %). Similar discrepancies in line 476, 478 and 479.
4. DIscussion: Line 495, replace increase with spread
Line 497, "our study examines a context where the public were largely not
498 experiencing direct adverse experiences from the virus". The authors may specify the % of participants who were COVID positive and those who recovered instead of "largely not".
Line 515, add the % of frequency of exercise to improve clarity.
Line 515, specify whether the author refers to emotional or physical wellbeing or both
Line 537, "Also, they reported quite a high proportion of their participants (70%) with prior lived
experience with a mental health diagnosis". Why was the prior history of mental illness not taken into account in the present study. Justify it. Is this another limitation of this study?
5. The conclusion sections appears too lengthy and repetitive and includes points that can be moved to the discussion.


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: CHANGE IN MENTAL HEALTH, PHYSICAL HEALTH, AND SOCIAL RELATIONSHIPS DURING HIGHLY RESTRICTIVE LOCKDOWN IN THE COVID-19 PANDEMIC: EVIDENCE FROM AUSTRALIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have modified the manuscript as per the suggestions.
Experimental design: NA
Validity of the findings: NA
Additional comments: NA


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: CHANGE IN MENTAL HEALTH, PHYSICAL HEALTH, AND SOCIAL RELATIONSHIPS DURING HIGHLY RESTRICTIVE LOCKDOWN IN THE COVID-19 PANDEMIC: EVIDENCE FROM AUSTRALIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Thanks for the author for the substantial improvement in the manuscript.
However, I would like to point out a few points
1. Abstract section doesnt have conclusion. It has be clubbed together with results section
2. Though the author has made a significant effort in reducing the length of manuscript, the introduction section needs to be curtailed down considerably as most portions are still redundant. The authors could narrow down to the research problem and give background pertaining to those in a crisp way.
3. Limitations section needs to be curtailed
Experimental design: Nil
Validity of the findings: Nil
Additional comments: In general, the manuscript is way to lengthy for an original article. As pointed out by earlier reviews too, introduction and limitation section needs to be curtailed as its way too lengthy.


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: ALTERATIONS TO ARBUSCULAR MYCORRHIZAL FUNGAL COMMUNITY COMPOSITION IS DRIVEN BY WARMING AT SPECIFIC ELEVATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Yes
Experimental design: Yes
Validity of the findings: Yes
Additional comments: The manuscript titled “Community structure of arbuscular mycorrhiza fungi are influenced by elevation and the associated temperature changes ” by Yang et al studied the influence of warming and elevation on the community structure of arbuscular mycorrhizal fungi in Qinghai-Tibet Plateau. The results showed that warming increased AMF abundance increased from 57 to 70, but had no impact on AMF abundance. The present results sounds interesting and give the reader some new information on the response of AMF to elevation and global warming. However, the paper is in need of some major improvements before publication.

Firstly, The title should be changed. More description on experiment design should be added, such as, how long the warming time, the measurement of C, N, S, C_N. Warming and elevation were included in this study, the authors should consider the interactive effects, so that two-way ANOVA should be used to analysis the results. Moreover, some sentence in the result section should be moved to methods (eg. Line 243-245).

Secondly, both warming and elevation could affect soil temperature and moisture, which is helpful to understand the changes in AMF community structure, the authors should consider and discuss it. If possible, the author can add this results. Besides that warming and elevation might alter AMF community structure via affecting plant community, how about it in your study?

Thirdly, the author calculated the species composition (Shannon index, Simpson, ACE index, etc), and also analyzed the relative abundance, NDMS might be a good choice to understand changes in the community structure of AMF.

Fourthly, The English language should be improved to ensure that an international audience can clearly understand your text. Such as Lines, 86, 87, 225,

At last, there are some errors in the reference citation, such as, the misuse of author (Line 55-56), some words should be Italic or lower case.


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: ALTERATIONS TO ARBUSCULAR MYCORRHIZAL FUNGAL COMMUNITY COMPOSITION IS DRIVEN BY WARMING AT SPECIFIC ELEVATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors investigated the changes of AM fungal abundance and community structure on the Qinghai-Tibet Plateau (QTP) after a one year warming at 4 elevations (3000 m, 3500 m, 3800 m, and 4170 m). The results were interesting and have great contribution to the understanding of AMF distribution. However, the manuscript was not clearly written and some of it was hard to understand. Several basic information for the study sites were missing, e.g. the mineral nutrient level, the temperature, plant species. PLEASE, revise the manuscript in the introduction and discussion sections, piling up the description of others' researches does not does not validate data and opinion.
Experimental design: The experimental design was clearly stated, but several information were miss.
The measurement of soil proporty, the plant species, the change of soil temperatures was not written in the MM sectio.
Additionally, the repetitions per treatment was 3.
Validity of the findings: no comment.
Additional comments: Line 50-53, 56-58, 370-374, I recommended Keep all references together rather than declaring them separately.
Line 99-100, Please describe soil type and soil properties.
Line 166, Control check - > control check
Line 167, Your means AMF abundance only in CK and OTC, respectively?
Line 205-209, The rate of increase and decrease are confusion. You should write in more detail.
Line 253-254, the relative abundance of Unclassified is zero in CK but not zero in OTC.
Line 304, The description is error, change it.
Table 1-3, Family and genus names should be arranged on one line. I can not find the shared between CK and OTC.
Fig. 2-5, No lowercase letters above each column to indicate significant diffidence, and columns did not start at the origin.


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: ALTERATIONS TO ARBUSCULAR MYCORRHIZAL FUNGAL COMMUNITY COMPOSITION IS DRIVEN BY WARMING AT SPECIFIC ELEVATIONS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This work investigates modification of AMF communities upon rising temperatures through anin-situ manipulation experiment, using open top chambers, on an altitudinal gradient in the Qinghai-Tibet Plateau.
While the aims of the work and hypothesis made by authors are clear and the background is quickly discussed in the introduction section, results are not clearly presented and discussed. The work seems to suggest that warming can significantly change the AMF community structure, with different variations according to the altitude, it has no effects on AMF abundances.

1. Overall, one of the main issue is the English language which needs a deep revision: in many parts, sentences do not stand (e.g. lines 61-63) and oftentimes are too short and the subject is also omitted (see e.g. line 32).

2.The Introduction needs to include additional and up to date literature on AMF including proper references on their biology and on the induced resistance in plants.
Experimental design: 3. I’m really concerned on the data analysis step since data normalization has not been performed, at least as reported in the manuscript. Usually, amplicon sequence abundance data needs to be normalized accounting for sequencing depth. This can be primarily performed by rarefacting the OTU table, or better using rarefaction-free methods such as DESeq2 or other. Please include among methods section few more details on data analysis including downstream steps. As an example I did not understand why in Fig. 1 caption “n=3” is stated. If 3 biological replicates were considered it should be at least n=3 replicates *2 treatments*4 sampling altitudes. Please explain in detail what had been done.

4. I noticed in many parts of the work authors tended to confuse abundance with diversity. As an example, in the first Results paragraph they talk about abundances but shows and discuss the number of detected OTUs, which in microbial ecology are intended as diversity (together with the diversity indexes). I would restructure the Results section accordingly.
Similarly at line 242 the definition of Relative Abundance was completely wrong. I would encourage authors to include an expert microbial ecologist among authors list. Moreover, the effect of warming by OTC on Relative abundances needs to be statistically tested with a proper algorithm.

5. The meaning of “isolation” (from line 241) looks really obscure. Please detail what this parameter is and how it had been calculated since it is not commonly measured in microbial ecology and here is extensively discussed.

6. Overall, methods needs to be integrated in many parts. E.g. it is not clear where samples were harvested and which the features of the sampling site (vegetation cover, soil type, slope and so on..). All these information, including detailed coordinates for each point, should be reported in a supplementary table. Moreover, in many parts, proper references are missing: used methods, including software, primer pairs and databases used needs to be properly referenced. The number of replicates sequenced at each plot (altitude step) and the sampling season should also be clearly mentioned.
Validity of the findings: Unfortunately the statistics is almost fully lacking in a great part of the figures showed. A deep data re-analysis would be required to confirm the trends showed and discussed by authors.
Additional comments: - in the abstract authors stated that “AMF abundance increased from 57 to 70” (line 27). However, few lines below they also stated “But has no significantly effects on AMF abundance” (line 32). Please check.
- line 43: the words “assimilates” is not clear, please give more detail.
- line 57-58: here the citation is already occurring at the beginning of the sentence, please rephrase or add additional evidences rising from both these two papers.
- lines 75-77: this is not fully true, please see these papers: https://doi.org/10.3390/su12145617, https://doi.org/10.1371/journal.pone.0076447.
- lines 111-112: it is not clear here how temperatures were monitored through all the season.
- line 143: if demultiplexing has been performed “in house” the software used needs to be mentioned.
- figure 2 to 5 should be merged into a single one as they show basically the same thing. Moreover, even if in the caption of some of them it is mentioned, statistics is lacking.
- line 196: this sentence do not stand, what is 8? Is this a fold-change? Please give more details and possibily integrate methods section.
- line 226: please check “Maenwhile”


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: ALTERATIONS TO ARBUSCULAR MYCORRHIZAL FUNGAL COMMUNITY COMPOSITION IS DRIVEN BY WARMING AT SPECIFIC ELEVATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The current version improved a lot and addressed all questions in the last version. The revised manuscript can meet the standards of PeerJ.
Experimental design: The experimental design is thoughtful, and the description is sufficient.
Validity of the findings: The results of this manuscript is very interesting, and which could give the reader some new insights on the effect of warming on soil microbes in Alpine grassland ecosystem.
Additional comments: The revised manuscript addressed the questions in the last version, the current version highly improved, which can be accepted for 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: ALTERATIONS TO ARBUSCULAR MYCORRHIZAL FUNGAL COMMUNITY COMPOSITION IS DRIVEN BY WARMING AT SPECIFIC ELEVATIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Since its first version the manuscript has been slightly improved incorporating almost all the comments raised from reviewers. However I still noticed that the language quality is really poor: iI feel like it should be deeply revised by a professional service or a native language speaker.
Moreover, even if many references on AMF were integrated in the introduction section, unfortunately they are mostly outdated. There are a plenty of new references available (see as an example those referenced in this review https://www.nature.com/articles/s41579-020-0402-3#Bib1).
Finally, the references related to primer pairs used to generate amplicon sequencing data are still missing.
Experimental design: Method section has been integrated with many missing information and statistics added. However, the pairwise statistic posthoc test performed after ANOVA should be cited also in Fig.2 caption. Moreover, even if analysis details have been added some further detail is missing. As an example it is not fully clear how reads were processed. Authors mentioned that reads were demultiplexed using bcl2fastq software which actually removes machine libraries barcodes, not sample barcode. However, at line 168, they mentioned that sample barcodes were recognized using FLASH, which however, as far as I known, does not have any demultiplexing options. Finally, the used sample barcodes are not mentioned anywhere.
Again, at lines 198-201, the methods used to perform the analysis mentioned, are not provided. Please integrate all this missing information.
Validity of the findings: no comment
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: PREDICTED DISTRIBUTION OF A RARE AND UNDERSTUDIED FOREST CARNIVORE: HUMBOLDT MARTEN (MARTES CAURINA HUMBOLDTENSIS)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors’ research effort was high but, despite being suitable for the aims and scope of PeerJ, I regret to say that in this form the ms. cannot be accepted for publication, needing to be deeply re-thought, revised and shortened for the sake of conciseness and clarity.
About shortening, in the attached PDF I have suggested the paragraphs that should be cut, because useless, repetitions or too speculative. This said, the authors need to put order in the methods and discussion sections, trying to be brief, which will result in being also straightforward and clearer. Below (General Comments) I suggest several changes which, in my intention, may help to revise the ms.
Experimental design: Although often difficult to follow, on the whole methods and analyses seem appropriate.
Models were run at 4 different scales (buffer radius), to test at which scale each variable was most strongly related to the species presence; anyway, in the results section, details about the predictive performance of the 4 best models are lacking.

Recent literature about HSMs for the pine marten should be included for comparing patterns
Validity of the findings: Lack of clarity throughout the ms makes it difficult to appreciate the soundness and impact of the research, but i believe that, when deeply revised, the ms will provide useful and interesting results
Additional comments: L46-49: this sentence disagrees with L500-503
L55-56: please see my comment at L124-25 and 536-60
L56-58: do you mean: “martens were recorded also in areas filed as unsuitable by the model”?
L50-51: is salal a shrub or a tree?
L68-94: this “incipit” let the reader think that your study will in some way overcome the described obstacles/bias, but this hope will not be satisfied. I suggest focusing on the need for detailed info about the distribution and habitat preference of elusive and low-density species such as H martens for conservation management.
L70-72: need rephrasing.
L95-97: need rephrasing.
L105-112: I suggest referring first to broad-scale attributes (large home range) and then to fine-scale ones.
L124-5: I would rather say that recent studies have highlighted that martens are more generalist than we believed. Also the pine marten had been associated to old and well-structured forests, but currently it has colonised small wood patches in lowland areas of SW Europe, where shrub cover sometimes becomes a major variable affecting its presence
L155: needs rephrasing.
L163: state clearly that you sampled all the 4 populations (if you did)
L191-2: need rephrasing.
L193: This 500 m cell has not been introduced before; you should state that you used a grid (UTM?)
L194: state here, rather than at L202, that you used only one location per cell.
L205: need rephrasing.
L237-8: repetition of L225-8
L239-40: lacking details or references, it is not clear in which way you obtained forest age.
L241 Canopy percent cover
L236-40: be more direct, for the sake of clarity: “We incorporated N biotic variable: 1,2,3,4. The first was assessed as …
L248: are these the min-max values within which the 12 diameter thresholds fall?
L252: please use “…” for variable names (e.g. “percent pine”) throughout the main text
L255-58: more simply: “because martens have been shown to occur in sparse pine woods growing on serpentine soils in the OCC” (right?)
L262: “overlap … areas”: unclear
L269: “which was the sum of the probabilities of both species occurrence” (?)
L290: basal area = cover?
L295: as for L236
L303-9: you may explain this var more clearly and briefly, e.g. “Using 4-km resolution available records from May through September 1996–2017 (NASA/NOAA Geostationary Environmental Satellite Imager measurements), “coastal low cloudiness” was satellite derived as described by Clemesha et al. (2016) and quantified as the yearly mean (± SD) percent of time that low clouds were present relative to the number of valid half-hourly, daily observations”.
L327: For clarity, before describing home ranges, state that the two largest radius were assessed from telemetry data. If these data have been already published, you may be briefer (L327-37).
L354-360: did you use Pearson or VIF? For the latter, usually a VIF>3 threshold is used to select variables
L399: “when… period” needs rewording.
L432-36: locations don’t seem evenly distributed (6, 37, 3, 54%)
L441-3: Both the medians and data distributions of all variables did not differ between the thinned sub-sample and the whole data set, except for…. Similarly, surveyed locations with no marten detections and random locations differed only for “salal”…
L450-1: based on what data/comparisons do you state this?
L452: I would say “suggesting that most variables… at the hr scale.”
L464-5. Comment to be moved to the discussion.
L472: line difficult to read and understand; do you mean: The predicted versus expected curve of our final model…?
L475: do you mean “the largest areas suitable to martens are in S Oregon and N California?”
Discussion: I suggest to start the discussion commenting biotic variables. Then, go on with lines 497-503 and add comments on abiotic variables
L484-5: but these abiotic variables may address conservation actions, e.g. providing protection areas including suitable (cool and wet) habitats
L:504-510: very confused and hard to understand
L512-13: “…related to increase canopy cover” but wasn’t the response of this variable quadratic (L506)?
L536-60: you should refer to the similar results that have been found for the pine marten in Mediterranean Europe (Spain, France, Italy), which suggest that martens are less forest-specialist than previously believed.
L597: here you tell us again about temp and rain, which had been commented at the start of the discussion!
L609-11: what do you mean?
L634-35: = L 479-81
Figure 3: I suggest showing response curves in order of variable importance for the model (i.e. start with salal and end with OGSi)


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: PREDICTED DISTRIBUTION OF A RARE AND UNDERSTUDIED FOREST CARNIVORE: HUMBOLDT MARTEN (MARTES CAURINA HUMBOLDTENSIS)
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an overall well-structured and clear manuscript, however, it is sometimes confusing and long in certain sections.
Experimental design: It is impressive the amount of data the authors are using to conduct the modeling presented here, which mostly relies on the collection of presence records and the derivation of environmental predictors used in modeling. However, the objective of the work or its main question is confusing: in the abstract, they refer to the historical distribution of the species, and this is later in the following sections not to be the case (including the Discussion). This is confusing overall.
Parts of the methods need to be reviewed to be clear (highlighted as specific comments in the PDF), for example, the meaning of some variables and specifications in the use of Maxent. Also, the accessibility area seems not to be completely adequate and should be carefully justified from a biogoegraphical point of view (see comments on PDF).
The Discussion is too long and repetitive at times. I suggest you organize by type of environmental predictor (e.g., biotic/abiotic) and then discuss how these variables are or could be interchanchagle surrogates. How this connects to Eltonian and Grinnellian niches may be also attractive.
Validity of the findings: All areas of the manuscript need to be reviewed and used as an opportunity to frame the problem and questions and then their results and discussion.
There are probably many conclusions throughout the Discussion that are probably lost because of the extensive length of this section. This should be reviewed and organized better. Overall, this sounds more like a really nice and modern natural history exercise improved by finely tuned ecological niche modeling methods. Also, try to clarify whether your work is about (or when is this the case to avoid confusion) a historic reconstruction of the distribution of martens or more on the ecology and natural history perse. It is obviously both or all of them, but better framing should help to improve transmitting the key findings.
Additional comments: Please, use the comments on the previous sections as a reference to general comments and also use the attached PDF to look at specific comments and areas where I believe your manuscript could see improvement.