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: RESPONSE OF BACTERIAL COMMUNITY STRUCTURE TO DIFFERENT ECOLOGICAL NICHES AND THEIR FUNCTIONS IN KOREAN PINE FORESTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors aim to analyse the bacterial community structure of rhizosphere and root endosphere of Korean pine trees. They want to reveal differences in response to forest age and seasonal changes. However, the manuscript suffers from several shortcomings. I understand the intention of the authors, but the paper is exhausting to read and often formulated contradictorily.
The cited literature partly do not fit/prove to the statements and the data analysis seems not to be up to date.
Experimental design: My main concern is about the experimental design. The authors compared five forest plots but they did not use any replicates. Moreover, there are several other inconsistencies in the data analysis (see below).
Validity of the findings: Based on the experimental design and the inconsistencies in the data analysis (see below), the meaningfulness of the findings is doubtful.
I also do not think that the study is currently able to answer the four hypotheses.
Additional comments: - l. 64. Clarify the hypothesis and move to the other ones. The fourth hypothesis (l. 120) is incomprehensible.
- l. 50, 106. The references do not prove the given statements.
- l. 124. Please rephrase, clarify and shorten the whole section 2.1
- l. 166 “Composite…” Why did the authors not analyse the four plots separately??
- Please specify sampling of the rhizosphere.
- l. 186. The chosen primers do not exclude cp and mt 16S rRNA genes. What about the percentage in the root samples?
- The authors should think about using a ASVs pipeline instead of the traditional OTU approach. Further, they applied outdated databases (e.g. RDP release 11 instead of the current release 18). A confidence threshold of 0.5 is very unusual. Why did the authors use this low confidence value (in contrast to 80%)? This influences decisively the community structure especially at the genus level.
- l. 212 The subsampling should be specified in Material and Methods (not in the Results).
- Difference between Bray-Curtis and UniFrac should be revised and clarified.
- “p < 0.01 was considered extremely statistically significant.” Please rephrase.
- The first paragraph of the Results section is very confusing. First, I do not understand “we generated 20 gross samples from 1,000 subsamples”. Then you provided the total number of sequences (420,000) and in the next sentence again with 690,000… Further, following your subsampling procedure (minimum 26,088/0.75 * 20), you should have much more sequence reads. And the last sentence seems not to make any sense in this context.
- In the next paragraph, the authors mentioned results of a PCA but in M&M a PCoA is described. Further, it should be revised to show a result not a list of sampling points. The differences should be tested for significance by ANOSIM, MRPP or a similar procedure. Please also mention if there was an impact of plant age and the season on the community structure. I understand that this was your main topic.
- The alpha diversity indices were provided with a SD. However, the authors did not study replicates!
- l. 532 The given pipeline in M&M does not allow the assignment at the species level.
I want to stop here as I think it already suggests that the complete story should be clarified and revised.


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: RESPONSE OF BACTERIAL COMMUNITY STRUCTURE TO DIFFERENT ECOLOGICAL NICHES AND THEIR FUNCTIONS IN KOREAN PINE FORESTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author has carefully revised the all sections according to the Reviewers’ suggestions.  Taken altogether, the paper has met the basic requirements for publication. It is suggested that this MS need further language editing before the publication.
Experimental design: The authors have carefully revised the Materials and Methods part according to suggestions of the reviewer, in particular the Study sites and experimental design, and Sampling and processing of the root tips and rhizospheric soil.
Validity of the findings: This MS analyzed the composition of bacterial communities and their affecting factors in the rhizospheric soil and root tips of Korean pine forests with different ages, which is helpful to improve soil nutrient management in artificial Korean pine forests.
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: RESPONSE OF BACTERIAL COMMUNITY STRUCTURE TO DIFFERENT ECOLOGICAL NICHES AND THEIR FUNCTIONS IN KOREAN PINE FORESTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: First, I want to reply to the answers of the authors:
I understand and appreciate that the authors studied five different forest plots. However, I disagree that the two similar plots can be used as replicates. The basis of any statistical analysis is the comparison of within and between-group variability. In view of this, the four sample areas per plot should not have been pooled! It’s a pity and limits the meaningfulness of the paper. As a result, you have only one observation per plot and you cannot analyze statistical differences for the alpha or beta diversity (Table 1 without SD and statement of significance; pCoA but without a statement of significance, e.g. using PERMANOVA or ANOSIM). Please be careful with conclusions for the bacterial community for the different forest plots. The respective statements in Abstract, Results and Discussion should be revised.

Further, Figure 1-3 just show the difference between root and rhizosphere microbiome. These differences between both habitats are well known and have been studied for several years.
The results shown in Fig. 4, 5 and Table 1 do not substantiate differences between the forest plots and fit to the pCoA ordination plot. There is no clear difference and without any knowledge about the variation within the plots, the authors cannot conclude unambiguous results. (BTW, please avoid the word “significantly” in context with the 5 forest plots, as you did not analyze significant differences.)
Figure 6 contains error bars. Without any replicates, I wonder about the basis for the calculation.

All in all, I suggest a complete revision as stated above.
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: BIOMASS DISTRIBUTION PATTERN AND STOICHIOMETRIC CHARACTERISTICS IN MAIN SHRUB ECOSYSTEMS IN CENTRAL YUNNAN, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: Precipitation and temperature serve as important data for the paper，But not found it in the paper, whether it can explain the situation ？In addition, only the average annual rainfall and temperature to analyze the sample data once, the analysis results are not convincing？
Additional comments: 1，The sampling point Q1-Q23, is not clearly annotated in Figure 2
2.In Table 2, the standard deviation of the data is too large, such as "0.70±10.38" .Can you explain these standard deviations?


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: BIOMASS DISTRIBUTION PATTERN AND STOICHIOMETRIC CHARACTERISTICS IN MAIN SHRUB ECOSYSTEMS IN CENTRAL YUNNAN, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: I commend the authors for their extensive data set, compiled over large number detailed ﬁeldwork. The results are interesting and useful to future readers. However, the manuscript need further modification, especially for the section of the results.
1.	The most important issue.
The results should be rewritten. The most important results (such as biomass pattern, stoichiometric characteristics, and their relationship with MAP and MAT).
2.	The next most important item
The language should be edited in the entire manuscript. Many sentences are difficult to understand. Some examples where the language could be improved include Lines 8-10, 13, 16-18, 38-39, 65-67, …….
I strongly suggest you have a colleague who is proﬁcient in English and familiar with the subject matter review your entire manuscript, or contact a professional editing service.
3.	The third important points.
The part of MATERIALS & METHODS should be rewritten. The section of Site description and Experimental design are too repetitious.
4.	The fourth important points
Previous studies about the shrub land in the study sites should be added in the introduction.
5. The fifth important points
   Too many figures and tables.  Delete or combine some figures and tables.  Just show the key resuls.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Other point
1. Check the Latin scientific names of animals, plants and microorganisms in the text (subject to the latest authoritative reference book), legal unit of measurement symbols, etc;
2. Detailed information needs to be supplemented. What is the basis, representativeness and the main shrub type?
3. How to collect root, stem and leaf samples of shrub layer?
4. The text is rough, many places are not smooth, the abstract is not concise, and the writing and terminology are not standardized. The decimal places in the chart are not uniform and need to be corrected;
6. The length of the article is too long. Please reduce the length appropriately. The total number of characters shall not exceed 12000 words (including spaces), and the total page number of word documents shall not exceed 10 pages (including charts).

Some other suggestions and comments are edited in the manuscript.


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

Input:
Title: BIOMASS DISTRIBUTION PATTERN AND STOICHIOMETRIC CHARACTERISTICS IN MAIN SHRUB ECOSYSTEMS IN CENTRAL YUNNAN, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Shrub ecosystem plays vital roles in terrestrial ecosystems. Past studies mainly focused on community structure and biomass, or single plant of the shrub layer and shrub plants, but still lacked horizontal comparison of elements and the relationship between climatic factors. Guo et al. selected 12 main shrub types in the study area, and obtained soil and vegetation data. I have found the present manuscript is  interesting and has great application. The study is impressive in scale and appears to provide some interesting insight to the distribution relationship in the terrestrial shrub ecosystem and the relationship between climatic factors. Overall, the text of the manuscript is well-organized but there are some areas that require revision for clarity. I hope my comments are helpful to the authors in revising their manuscript. In addition, The English language should be improved to ensure that an international audience can clearly understand your text. I suggest you have a colleague who is proficient in English and familiar with the subject matter review your manuscript, or contact a professional editing service.
Lines 14-15 This sentence need to rewrite.
Lines 28-31 Do you have some more summary conclusions?
Lines 60-67 For this section, you can put forward several assumptions or questions.
Lines 70-31 “Surveys were conducted from June to September, 2019”, why not in a same time?
Line 132 There are so many results, and you need to divide them into different sections.
Line 234 Like results section, you need to divide them into different sections.
In addition, there are so many tables and figures, you need put some tables or figures in the appendixes.
Experimental design: This is an original primary research within aims and scope of the journal. You can put forward several assumptions or questions in Introduction section.
Validity of the findings: All underlying data have been provided, and  they are robust, statistically sound & controlled.
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: BIOMASS DISTRIBUTION PATTERN AND STOICHIOMETRIC CHARACTERISTICS IN MAIN SHRUB ECOSYSTEMS IN CENTRAL YUNNAN, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript has been modification.
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: DIVERSITY AND PATHOGENICITY OF ALTERNARIA SPECIES ASSOCIATED WITH THE INVASIVE PLANT AGERATINA ADENOPHORA AND LOCAL PLANTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: A bit more attention should be paid to the accuracy of sentences. The authors may choose to get the manuscript read by an external expert. Literature citation is adequate. Structure of article and hypothesis behind are OK.
Experimental design: Manuscript is within the scope of the journal. Research question can be better defined at the end of introduction. Methods are described and technically upto the standard. But, please refer to the detailed comments and address them.
Validity of the findings: Suggestions are provided at #4. Overall the rationale, adequacy of data and drawing conclusions are fine to me. A detailed response from the authors are needed if revision is submitted.
Additional comments: The study by Li et al. showed diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and native plants. Li et al. used multiple gene analysis/phylogenetic analysis to characterize the species composition of 107 isolates of Alternaria obtained from the invasive plant Ageratina adenophora and native plants from different provinces of China. Overall, the manuscript is well written, results supports the conclusion and the data presented in this report would be of interest to many readers.
Minor comments
Lines 62-64 Statement is unclear to me. The fitness of the invasive species is entirely depending on the following aspects: (I) the absence of competition and II) their responses in presence of different densities of intra- and inter-specific competitors, therefore, more references are needed to support the argument.
Lines 79-80 Few more examples with appropriate references are needed.
Lines 90-91 Alternaria spp. can also behave as asymptomatic endophytes in invasive species and also cause visible symptoms on co-occurring native plants.
Therefore, what kind of pathomorphological characteristics and disease diagnostic techniques have been employed?
How many days have been taken into account to determine plants are asymptomatic (absence of visible symptoms)?
Line 142 A detail regarding primer sequences should be mentioned.
Lines 187 and 229 Manuscript requires statistical analysis (PCA, Tuckey test for comparing different variables) to support conclusions derived from Figure 3 and Figure 4.
Some robust statistical analysis (PCA, Tuckey tests etc.) should be carried out to show convincingly the relationship between the degree of pathogen virulence and plant population (native/invasive). A table should also include that define the comparative analysis of parameters tested (percentage area with disease symptoms, relative virulence/abundance of fungal isolates/pathogens etc.) across plant species (invasive/local) tested.
Lines 206-208 In addition to geographical location, pathogen susceptibility and resistance strongly varied with environmental conditions such as temperature, heat, drought, salinity and humidity.  Do susceptibility of the isolates of Alternaria spp.  retrieved from A. adenophora varied with the geographical locations and/or under different environmental gradient?
Lines 230-235 For more clarity, a figure (main/supplemental) using appropriate statistics should be included to show the disease scoring such as infection area (in cm2) of native and invasive plant species inoculated with different A. alternata and A. gossypina/ longipes pathogen species.
Line 260 Host jump is an interesting phenomenon during the process of introduction of invasive plants to a particular geographical location. The authors are requested to add few sentences in the introduction and discussion section. Is it possible to determine host-jump phenomenon on community basis by comparing fungal pathogens/endophytes isolated from invasive plants in its native and invaded ranges?
Lines 289-291 Wide variations related to competitive ability, disease susceptibility and reduced growth and development have been observed in native plant species. Therefore, it is assumed that the difference in response of native plants to fungal infection and competition with an exotic/invasive plant species may suggest the differential response of native plant species to disease-mediated competition. Please elaborate more on this citing appropriate references.


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: DIVERSITY AND PATHOGENICITY OF ALTERNARIA SPECIES ASSOCIATED WITH THE INVASIVE PLANT AGERATINA ADENOPHORA AND LOCAL PLANTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: For accurate taxonomic identification of isolates suspected to be belonging to the Alternaria spp complex, authors are advised to refer to Table 4 of Woudenberg et al. (2015) (title: Alternaria section Alternaria: Species, formae speciales orpathotypes). In this Manuscript, the authors are inconclusive with respect to the identity of A. gossypina/ longipes, therefore, sequencing other genes/genomic regions (gapdh, OPA10-2, KOG1058) as suggested by Woudenberg et al. (2015) is required.
Validity of the findings: No comments
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: DIVERSITY AND PATHOGENICITY OF ALTERNARIA SPECIES ASSOCIATED WITH THE INVASIVE PLANT AGERATINA ADENOPHORA AND LOCAL PLANTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: See my previous report
Experimental design: See my previous report
Validity of the findings: See my previous report
Additional comments: Comments are addressed.


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: DIVERSITY AND PATHOGENICITY OF ALTERNARIA SPECIES ASSOCIATED WITH THE INVASIVE PLANT AGERATINA ADENOPHORA AND LOCAL PLANTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: Acceptable
Validity of the findings: Acceptable
Additional comments: The manuscript can be accepted in its present form.


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: GENOME-WIDE EVOLUTION AND EXPRESSION ANALYSIS OF THE MYB-CC GENE FAMILY IN BRASSICA SPP.
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript from Gu et al. Comprehensively analyzed MYB-CC gene family in Brassica species. MYB-CC family members, including PHR1, play significant roles in plant responses to low Pi stresses and other biological processes. The data in this manuscript will contribute to understand the evolutionary history of the MYB-CC gene family and their biological functions in Brassica species. I do have some minor concerns that I believe should be addressed prior to publication.
     1. In Fig. 5, two types of cis-elements (hormone-related and abiotic stress-related elements) should be provided the specific element sequences respectively in Results, such as the MeJA-responsive elements TGACG.
    2. Line 290-291, “methyl jasmonate (MeJA)-responsive elements (TGACG-motif and CGTCA-motif)” should be revised as “methyl jasmonate (MeJA)-responsive elements (TGACG)”.
    3. Line 325, “expression profiles of MYB-CC under Pi stresses” should be revised as “expression profiles of MYB-CC under low Pi stresses”.
    4. In Fig. 7, the inducible MYB-CCs by low Pi should be analyzed in detailed among B. napus, B. rapa and B, oleracea.
    5. Manuscript needs to be corrected by professional. There are some grammatical errors in current version.


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: GENOME-WIDE EVOLUTION AND EXPRESSION ANALYSIS OF THE MYB-CC GENE FAMILY IN BRASSICA SPP.
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript “Genome-wide identification and evolutionary analysis of MYB-CC gene family in two Brassica diploid species and their allotetraploid relative” (Ms ID: #61732v1) by Gu et al. presents a genome-wide identification and expression analysis of the PHR1 homolog genes in in Brassica rapa, Brassica oleracea and Brassica napus genomes. It is a survey study. The authors identified and investigated this gene family in these three genomes and did a bunch of bioinformatic analyses of the candidates. They also explored the expressions of the candidates in different tissues and under low Pi stresses. The reason to perform this study is convictive. The methods are relevant and well applied for most of the study. This type of study falls within the scope of Peerj. Overall, the contents and quality of this ms is suitable to be published in this journal. But, some points listed below should be corrected before it could be accepted for publication.

Major revision：
1. The title of this ms is a little long. It is better to compress it, such as “Genome-wide evolution and expression analysis of MYBCC gene family in Brassica rapa, Brassica oleracea and Brassica napus”.

2. In my opinion, it is worthy to discuss/check the nomenclature of this type of genes. They may be classified into the GARP-like gene family, which are often confused with MYB-related genes, because they contain a consensus sequence (SHLQKY) very similar to that of CCA1-like proteins (SHAQK(Y/F)F) at the C-terminal of the BD domain. However, they contain only 1 of the 3 regularly spaced Trp (W) residues found in the MYB domain of the typical MYB proteins (Du et al., 2013, DNA research).

3. “Abstract”, the contents in this section are poorly organized and wrote. The authors should focus on the main results of this study in this section, and state the results accurately to avoid confusion. For example, line 22-27, the background of this study is too long. Similarly, it is better to summarize the main results in a shorter length in line 29-34. The content in line 30 is not your result, it is just the background. So, it is better to delete it. In addition, line 34-36, the expression profile of this gene family is not clear. And the results related to the expressions under low Pi stresses were not showed here?

4. Line 51-53, the statement is confusing. The architecture of root system will be altered under which environmental condition? Low Pi stresses? Similar problems should be checked in the full text carefully.

5. Line 98, the statement is confusing as it should be named as sub-genome in B. napus. In addition, “It” should be “it”.

6. Line 112, “Chinese academy of agricultural sciences” should be “Chinese Academy of Agricultural Sciences”?

7. Line 113-123, as mentioned in the following text, the expression of candidate genes under low Pi stresses were analyzed based on the public RNA-Seq datasets acquired from NCBI? So, please re-write this part.

8. Line 128-130, please show the names of these three databases.

9. Line 158, please supplied the website of the “GSDS” online software.

10. Line 170-171, the content in this sentence is repeated with that in line 111-112?

11. The section of “Evolutionary analysis of MYB-CC transcription factor family”, the statement in this part is confusing. As the NJ tree was constructed based on the protein sequences, you should use “protein” instead of “gene” in the text. Accordingly, it is better to use the protein name in the text. Moreover, please state the reason/ criterion to classify the MYB-CC genes into nine distinct groups.

12. Line 217, please state the detail number of the MYB-CC genes, instead of using “several”.

13. Line 230-231, please delete the sentence of “Two genes linked together by a red line were collinear genes”.

14. Line 245-248, in general, the ratio of ka and ks of duplicated genes is <1. It is interesting that there are two gene pairs (BnaMYB-CC02/BnaMYB-CC06; BnaMYB-CC10/BnaMYB-CC13) were > 1. Please check the sequences of these two gene pairs to avoid genomic quality issues firstly.

15. Line 256, “and” needs not to be in italic.

16. Line 300-301, the authors stated that “It is worth noting that most cis-elements in the promoters of BnaMYB-CC genes were mainly 301 related to light response, but they were not shown in Fig. 5”.  Please state the reason why you did not show this result.

17. Line 348, “their expressing level is” should be “their expressing levels were”?

18. The contents in the section of “Conclusions” is a little long, it is better to compress it and summarize the main conclusion of this ms.

19. Table 1, please unify the decimal point digit in this table.

20. Figure 1, please supply the bootstrap value on the NJ tree for each group. And the names of the four species should be in italic in Figure 1B.

21. Figure 2, the quality of this figure should be improved. The font size is too small to see, and the layout of the B. napus chromosomes is not good as well.

22. Figure 3, there are some format problems in this figure. Please check it carefully.

23. Figure 4, the quality of this figure is bad. The information in this figure is hard to see for the readers. And the spatial arrangement of each figure is not good. Please improve the quality of this figure, carefully. Similar problem was observed in Figure 5 and 6.

24. Figure 7, please state the meanings of “R” and “S” in the names of the samples. Moreover, “heat map” should be heatmap”.

25. The writing needs to be thoroughly checked and substantially improved. There are many typos and some inaccuracies that should be corrected. I strongly recommend language editing for this paper.
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: COMPARATIVE TRANSCRIPTOME ANALYSIS OF MIRNA IN HYDRONEPHROSIS MALE CHILDREN CAUSED BY URETEROPELVIC JUNCTION OBSTRUCTION WITH OR WITHOUT RENAL FUNCTIONAL INJURY
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a clearly written manuscript that focuses on the molecular biology of pediatric obstructive uropathy which is a relatively common condition that impacts approximately 1:500-1,500 live births. Understanding the spectrum of underlying biomarkers (in the case of the present paper it is miRNAs) may have prognostic significance in determining which patients may progress to chronic kidney disease or end-stage renal disease and which will not.

The construction of the citations in the text and the reference section is confusing. The citations in the text use authors and year. Citations in the reference section are numerical and not in alphabetical order. It would appear that this manuscript has been revised from a version submitted to another journal previously. It is very difficult to ascribe a point made in the text with the appropriate cited literature.

The Figures are fine but the raw data is unreadable. The key animal and IRB compliance documents are in chinese characters and the supplemental data, a critical aspect of the review, is locked and unaccessible.
Experimental design: Well-defined research question and within the scope of the Journal. How to distinguish between children with and without kidney functional deficits as a result of ureteropelvic junction obstruction has significant clinical ramifications.

Methodology is nicely described and the statistical treatment of the data appropriate. The correct databases were utilized for predictive assessments of target genes.

Since the key compliance documents involving approval of animal studies and obtaining human tissue for research are in chinese characters, it is impossible for this reviewer to assess the ethical standards involved.
Validity of the findings: There are several issues outstanding that need to be addressed in a revised manuscript.
The lack of information regarding the miRNA target genes is a significant deficit. There were only 1499 genes that were identified as targets of the resolved miRNAs. They should be listed in a supplemental Excel file. It would be critically important to also indicate if these specific targets are shared in the human vs. rat obstructive diseases.

The paragraph beginning on line 288 is confusing and is of suspect relevance. This section of the discussion mixes KEGG pathway data on tumors with fibrosis and the linkages are not at all clear. The relationship to EMT is appreciated but not well described and while epithelial EMT may (and this is questionable) relate to tubular recovery it does not contribute to interstitial fibrosis which is driven almost exclusively by infiltrating pericytes (papers for Ben Humphreys lab). The purpose of much the the Discussion is muddled and off the issue.
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 TRANSCRIPTOME ANALYSIS OF MIRNA IN HYDRONEPHROSIS MALE CHILDREN CAUSED BY URETEROPELVIC JUNCTION OBSTRUCTION WITH OR WITHOUT RENAL FUNCTIONAL INJURY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article titled “Comparative transcriptome analysis of miRNA in hydronephrosis children caused by ureteropelvic junction obstruction with or without renal functional injury” (#57453) by Liu G et al., emphasizes miRNA regulation and its possible role in renal injury in pediatric subjects diagnosed with congenital hydronephrosis.

Overall, the findings were of interest to the peers working in congenital obstructive nephropathy but there were several areas that need authors attention to detail. I have the below comments and concerns regarding the article.
Experimental design: The study design justifies the rationale of this work. As a reviewer from a reader’s point of view the below comments were made to improve the overall reach of this work.
Validity of the findings: The findings are of interest to the specific field
Additional comments: As a reviewer from a reader’s point of view the below comments were made to improve the overall reach of this work.
Major:
1.	The introduction is very short, and it is not adequately providing the background of the disease and the significance of the work. The authors may think of providing more information on several aspects relevant to this work like hydronephrosis affects which age group, gender differences if exist, factors leading to or effecting the disease, other miRNA work on renal diseases and UPJO, statistics/number of people affected worldwide, number leading to CKD and deaths etc.
2.	Line 62: What is the rationale behind choosing children younger than 6 months, is there any gender bias exist, how many male and how many female subjects participated in this study and if there is gender bias, rationale for the same need to be provided
3.	Line 187: Why miR-212-5P is excluded? Is the data in the figure 3a and 3B not significant?
4.	Line 195: What about miR-142-5P, it is not mentioned in the results?
5.	In Figure 2 legend, more information about the figure need to be provided
Minor:
1.	Line 1: Delete space before “Comparative”
2.	Line 2: Delete space before “Children”
3.	Line 19: Add space before parentheses
4.	Line 30: delete “of”
5.	Line 34: Correct to “in vivo” and make it italics
6.	Change in vitro and in vivo to italics font throughout the manuscript
7.	Change to “up regulation and down regulation” throughout the manuscript to main uniformity
8.	Line 44: add space before parentheses
9.	Line 46: delete space before and after “/” and change to “renal dysfunction”
10.	Line 56: Elaborate “DRF” in the first appearance of the manuscript
11.	Line 63: Children below 6 months were addressed as research “OBJECTS” which is ethically not correct. Change to “subjects”
12.	Line 63: Correct to “diagnosis”
13.	Line 70: Is there a procedural name to collect the kidney parenchyma? If so, mention
14.	Line 71: delete comma
15.	Line 72: Delete space in the parentheses (before No. and after K)
16.	Line 74: Elaborate UUO at its first appearance in the text
17.	Line 75: Add space after “18”
18.	Line 84: Correct “Anesthesia”
19.	Line 90: Change to “Frozen in liquid nitrogen”
20.	Line 91-93: The sentence does not read well. Try to amend this by “in order to reduce the pain or suffering”
21.	Line 102 and 103: Add space between numbers and Hours. For e.g.: 24 h
22.	Line 107: Correct to amplified
23.	Lines 116, 117 and 118: delete space before and after the website links that are in the parentheses
24.	Line 121: delete space before and after “GO”
25.	Line 125: Change was to were
26.	Line 130: Correct to instructions and add space between 1 and µg
27.	Line 134: Correct 20 ul to 20 µl
28.	Line 144: Correct to significant
29.	Line 159: Correct to Hierarchical
30.	Line 158-159: 5 miRNA up regulated and 17 miRNA down regulated but in which group? And list those miRNAs in the results
31.	Line 163: delete space before and after the website link that is in the parentheses
32.	Line 166-173: Discuss the different N and S groups genes that are differentially regulated and name those miRNAs from the data here in the results
33.	Line 179: name the 4 and 8 differentially regulated miRNAs from the data here in the results
34.	Line 180-181: Move the 3 miRNAs names in parentheses next to the number 3 in line 180
35.	Line 186: Correct to Statistically
36.	Line 191: Change to “analyzed”
37.	Line 191: change to “levels of”
38.	Line 191: Add commas next to different miRNAs and remove the special character that is inserted instead of comma. Add “and” next to miR-21-5p
39.	Line 195: Delete extra space in the parentheses
40.	Line 199 and 201: in vitro to italics font
41.	Line 202 and 204: add space between 72 and hours and 144 and hours
42.	Line 208: Correct to Obstructive
43.	Line 221: Correct to “Progression” and add “and” before inflammatory diseases
44.	Line 226: Add space before However
45.	Line 234: Correct “Object” to “subjects”
46.	Line 236: Correct to “groups”
47.	Line 238: Add space after species
48.	Line 248: Add “the” before rat
49.	Line 249: Change to “Previously”
50.	Line 250: Chevalier RL et al., which year? Mention it here
51.	Line 253: Add space before parentheses
52.	Line 254: Add et al., after Chevalier RL
53.	Line 263: Delete comma after UUO
54.	Line 276-277: Add space before parentheses; before “Treatment” and add space after fibrosis
55.	Line 278: correct to TGF-β1 and in vitro in italics
56.	Line 279: Add space after 72 hours and correct TGF-β
57.	Line 283: correct to 144 h
58.	Line 286-287: Italics to in vitro and in vivo
59.	Line 291: Correct to Functional
60.	Line 302: Correct to Researchers and change have to has
61.	Line 310: Add space before parentheses
62.	Line 313: Correct to “it”
63.	Table 1: Line 3: Delete space before “fold” and after 0.01 in the parentheses
64.	Table 2: Line 1: Correct to “Human”
65.	Table 2: Why few residues were colored in “red”?  this needs to be mentioned in the legend
66.	Figure 1 Legend: Correct to “Hierarchical”; add space in between heatmap; delete space before and after fold change values in the parentheses
67.	Figure 1 Legend: Add “and” before differentially
68.	Figure 1 Legend: Change up-expression and under-expression to Up and down regulation, consistent with the text.
69.	Figure 1 Legend: (A) the “nodiff” color in the figure is not mentioned in the legend
70.	Figure 2: legend need more details. There is no adequate information about the figure
71.	Figure 3 legend: Delete space after “UUO 2d” and “;”
72.	Figure 3 legend: invitro in italics
73.	Figure 3D: Correct “Control” spelling in the figure


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 TRANSCRIPTOME ANALYSIS OF MIRNA IN HYDRONEPHROSIS MALE CHILDREN CAUSED BY URETEROPELVIC JUNCTION OBSTRUCTION WITH OR WITHOUT RENAL FUNCTIONAL INJURY
Review round: 2
Reviewer: 1

Output:
Basic reporting: This manuscript has been adequately revised in accord with my previous suggestions. Acceptance is recommended.
Experimental design: This manuscript has been adequately revised in accord with my previous suggestions. Acceptance is recommended.
Validity of the findings: This manuscript has been adequately revised in accord with my previous suggestions. Acceptance is recommended.
Additional comments: This manuscript has been adequately revised in accord with my previous suggestions. Acceptance is recommended.


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: APPLICATIONS AND LIMITATIONS OF CURRENT MARKERLESS MOTION CAPTURE METHODS FOR CLINICAL GAIT BIOMECHANICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written, clear, and unambiguous.
Experimental design: The manuscript presents a study well designed (scoping review).
Validity of the findings: Conclusions are well stated and linked to the original research question.
Additional comments: The manuscript presents a scoping review that discusses the applications and limitations of markerless motion capture. The authors should be commended for their insightful and well drafted manuscript. I only have a few minor comments that are mainly to help improve some sentences.

The only other point beyond typos is whether the authors should consider using the PRISMA extension for scoping reviews?
Tricco, AC, Lillie, E, Zarin, W, O'Brien, KK, Colquhoun, H, Levac, D, Moher, D, Peters, MD, Horsley, T, Weeks, L, Hempel, S et al. PRISMA extension for scoping reviews (PRISMA-ScR): checklist and explanation. Ann Intern Med. 2018,169(7):467-473

Abstract (line 28): should read ‘that are relevant’ rather than ‘that a relevant’.
Line 95: just for clarity, are these averages across various joints of the body/lower limb? Perhaps clarify for the reader.
Line 142-143: should this read ‘provided sufficient image resolution’ rather than ‘providing sufficient image resolution’?
Figure 4 caption: just a small type here with ‘estimation’ as ‘estimate4ion’.
Line 233: reword ‘outline’ to ‘outlined’.
Line 269: reword ‘as high has 20 cm’ to ‘as high as 20 cm’.
Line 415: remove the word ‘of’.
Line 514: here you mention IMU systems – I wonder if this should be mentioned earlier as another area of ‘markerless’ motion capture for clinical use? IMUs and other wearables are also increasingly being used for clinical use, and I know it is beyond the scope of this review, but may be worth a mention earlier on.


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: APPLICATIONS AND LIMITATIONS OF CURRENT MARKERLESS MOTION CAPTURE METHODS FOR CLINICAL GAIT BIOMECHANICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are some areas that could be improved. Please see my additional comments.
Experimental design: N/A
Validity of the findings: no comment
Additional comments: The authors present an interesting and relevant review that is reasonably broad in scope. In general I enjoyed reading the work, but there are many cases where the wording is ambiguous and could be improved. This is important because the manuscript is currently difficult to read in places, which detracts from an otherwise interesting and timely paper. Specific suggestions are given below. Please keep in mind that I have been deliberately pedantic- these comments should not be interpreted as criticism, but rather as my attempt to help you improve what is already a solid piece of work, and one that is clearly worthy of publication.

Abstract, lines 20-1: “…this review explores how practical applications of this technology are being applied in clinical and rehabilitation settings” (double use of apply). I suggest re-wording to something like “this review explores how markerless approaches are being applied in clinical and rehabilitation settings”

27-29: “…and determine what gaps in the knowledge exist that a relevant to the
future directions and limitations of this developing technology”. I suggest simplifying: “and identify gaps in our knowledge that are relevant to future developments in this area”, or something similar.

29-30: “Markerless methods provide improved versatility of the data, enabling datasets to be re-analyzed using updated pose estimation algorithms”. How about “Markerless
methods increase data versatility, enabling datasets to be re-analyzed using updated pose estimation algorithms”.

31-4: “While it appears that markerless temporospatial measures generally appear to be equivalent to marker-based motion capture, joint center locations and joint angles are not yet sufficiently accurate. Current pose estimation algorithms appear to be approaching similar error rates of marker-based motion capture”. I think the flow here could be improved. For example, instead of the sentence starting “Current…”, could you instead state that it seems that error rates are improving quickly, resulting in progressively smaller errors between methods. You might also want to revise the double use of ‘appear’.

101-2: “an assumption that markers on the skin represent movement of the bone, leading to soft tissue artefact errors as muscle, fat and skin move beneath markers”. Could this be expressed more clearly? I think the assumption is that markers on the skin represent the position of the underlying bone. In addition, the problem is that the marker stays stationary on the skin, but that the skin moves relative to the underlying bone.

112: Markers-based should be marker-based

135: Reference instead of references

166-7: “…require increased lighting demands”. Suggest rephrasing

177 / Software: I leave it up to you, but it might be beneficial to introduce the concepts of supervised learning (first few paragraphs) and transfer learning (when introducing Deeplabcut) in this section.

201 (legend to fig 4): Remove ‘is’. Please also correct the spelling of ‘estimation’ in l203.

233: Outlined instead of outline

288-90: Could the authors expand on what they mean here? Specifically the ‘fundamental lack of data’ comment.

318: “Slower movements performed better” and “faster jumping and throwing movements were 20-40mm”. It’s obvious what is meant but I suggest revising this sentence- the movement itself cannot perform better.

330: Either remove ‘occurred’ or change to ‘occurring’.

330-2: I think this is a valid point, but why would the hip be the least accurate? If the problem were just poor labelling in general, then the errors for different body parts should be approximately the same. Could it be that the hip is more difficult to accurately identify just on the basis of an image (as opposed to physically palpating for the joint as you would in the lab), perhaps because it is (almost) always covered in images, whereas other body parts (e.g. ankle, wrist) may be easier to ‘see’ in an image?

339-40: “Another commercial system … recorded multiple movements … and then was processed”. Suggest revising.

363-75 / Practical applications: Here the different studies are introduced inconsistently. For some (Moro, Shin), the main findings are briefly summarised, whereas for others it is simply stated what was done. It would be good to use the former approach for all studies in my opinion- a brief sentence stating the key finding is sufficient, as done for the Moro/Shin studies.

393: Remove ‘be’

409: Please be more specific- greatly improve the efficiency of data collection? Or the ease?

415: “Therefore, markerless joint angle variability of may be similar to marker-based data collected on multiple days (inter-session). Remove ‘of’, but I also suggest revising. I think you mean that joint angle variability across multiple testing days may be similar between the two methods.

424: ‘this’ should presumably be ‘that’

483: ‘be’ instead of ‘are’?

496-8: “While Needham and colleagues (Needham et al. 2021b) demonstrated that OpenPose had a greater difference on average between 16-48 mm, joint center location differences could be as high as 80 mm or even higher for some joints during running”. This sentence lacks context. For example, ‘had a greater difference’ is not informative. I think you are referring to differences between OpenPose and a marker-based estimate, but this should be made clearer.

543-4: “While it appears that markerless temporospatial measures generally appear…”. Same comment as for the abstract- I suggest being a bit more assertive and avoiding the double use of ‘appear’, e.g. “While it appears that markerless temporospatial measures are generally equivalent…”


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: APPLICATIONS AND LIMITATIONS OF CURRENT MARKERLESS MOTION CAPTURE METHODS FOR CLINICAL GAIT BIOMECHANICS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This manuscript presents a scoping review of the markerless motion capture literature as it relates to clinical gait biomechanics. Overall, I find it to be a thorough, current, and balanced review of the state-of-the-art of markerless motion capture, which would be of interest for readers engaged with the topics of motion capture technology, clinical gait analysis, injury prevention and rehabilitation, and those pursuing clinical adoption of biomechanical measures.

The manuscript is written in clear and professional English and provides sufficient background/context and referencing of the literature. The review was clear with respect to its scope, and responsibly identified areas that were not within the scope but have been discussed elsewhere and directed readers to those works where appropriate. While the field of markerless motion capture has been reviewed previously, this scoping review provides an updated view of the literature from a clinical biomechanics perspective that will be accessible to a wide audience of biomechanics researchers.
Experimental design: The manuscript is within the aims and scope of the journal and meets the definition of a scoping review described in Munn et al. (2018). The description of the survey methodology includes the literature databases that were searched, the search terms that were used, and the publication date restrictions (none). This survey methodology meets the broader inclusion process of scoping reviews, and there were no apparent omissions of literature. Sources are cited and appropriately paraphrased. The structure of the article is logical, and the included figures effectively serve to illustrate the concepts discussed within the review.
Validity of the findings: This manuscript does not assess impact nor novelty. The methodology is sufficiently described to allow replication of this scoping review, and replication of existing works that may benefit the literature is encouraged through the discussion and conclusions (i.e. improving and expanding biomechanically-oriented image training datasets). Conclusions are appropriately drawn from the review of existing literature and identify areas for continued investigation and improvement by the field.
Additional comments: Overall, this scoping review provides a useful clarification of the state-of-the-art of markerless motion capture in the context of clinical biomechanics and effectively identifies gaps in the knowledge and literature that require further exploration. Conclusions are drawn from the reviewed literature and provide clear direction for future research.

Additional minor comments and suggested revisions have been added to the manuscript pdf and attached to this review.


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

Input:
Title: APPLICATIONS AND LIMITATIONS OF CURRENT MARKERLESS MOTION CAPTURE METHODS FOR CLINICAL GAIT BIOMECHANICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is well written, clear, and unambiguous.
Experimental design: The manuscript presents a study well designed (scoping review).
Validity of the findings: Conclusions are well stated and linked to the original research question.
Additional comments: The authors have responded well to all comments from reviewers. I have no further comments to make - the authors should be commended for this interesting and timely scoping review.


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

Input:
Title: APPLICATIONS AND LIMITATIONS OF CURRENT MARKERLESS MOTION CAPTURE METHODS FOR CLINICAL GAIT BIOMECHANICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I thanks the authors for their revision. In general I am satisfied that the clarity has improved and that the paper is suitable 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: APPLICATIONS AND LIMITATIONS OF CURRENT MARKERLESS MOTION CAPTURE METHODS FOR CLINICAL GAIT BIOMECHANICS
Review round: 2
Reviewer: 3

Output:
Basic reporting: The revised manuscript improves upon the original submission with several corrections and clarifications to the language and grammar used. The writing is clear and unambiguous, and I have no issues with the reporting.

This review follows a logical structure and order, and the topic is adequately introduced. The scope of the article is clear and topics that are related but outside the scope are identified as such. The writing is consistent and should be understandable by the target audience.
Experimental design: The manuscript is rigorous and performed to a high technical and ethical standard, maintaining objectivity. The review covers all relevant topics and points readers to additional materials for further detail on related subjects where appropriate.
Validity of the findings: The conclusions and main future directions are well-founded, clear, and supported by referenced works and findings. Work towards closing the identified knowledge gaps and unresolved questions is encouraged and appropriate suggestions are provided for improvements in these areas.
Additional comments: Overall, I find this review to be well-written and provide a clear overview of the current state of markerless motion capture for clinical gait biomechanics. Besides the following very minor points, I have no suggested changes.

‘Pose’ is clarified as the combination of position and orientation in several places (lines 63, 117, 220) – only the first time is required.

Line 414: “…or may not” is not necessary, and missing apostrophe from “a pose estimation algorithm’s ability”.

Line 456: References to datasets “[55-58, 102]” appear to be in a difference style.


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: PROFILES OF ANEMIA IN ADOLESCENT STUDENTS WITH SPORTS CLUB MEMBERSHIP IN AN OUTPATIENT CLINIC SETTING: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: It seems that the files that are uploaded are in the Edit format, meaning that the version that was submitted had all changes on so it was a bit hard to read the tables. Nevertheless I managed to turn that off even though I do not think that it is Ok to submit this kind of files as final version.
Experimental design: The design is clear and easy to follow. What we lack is the frequency and intensity and volume of their weekly engagement in sport
Validity of the findings: Basically i think that it is a bit of a novel approach and that many relevant factors were included as predictors. i think that the article lacks  a physiology parts in discussion. Discussion mainly fokus on repeating the findings with no discussion about the physiology mechanisms of for example B12 and excercise etc...
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: PROFILES OF ANEMIA IN ADOLESCENT STUDENTS WITH SPORTS CLUB MEMBERSHIP IN AN OUTPATIENT CLINIC SETTING: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: In general, the English writing is easy to read but there is still some errors in the text. For instance, on line 77, "...were reported as was 2-29% and 3-7%....." in which "as was" might be a typo. The  recheck the English grammar throughout the paper.

The paper structure, content and references are finely written.

The hypothesis of the paper is well defined.
Experimental design: The experimental design is clearly described.
The methods is scientific and logical.
Validity of the findings: The study findings are relevant to the current knowledge and well answered to the study questions.
Additional comments: None


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: COMPARING DIFFERENT FARMING HABITATS FOR MID-WATER ROPE NURSERIES TO ADVANCE CORAL RESTORATION EFFORTS IN THE MALDIVES
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper describes a straightforward study articulating performance of coral fragments of two taxa in coral nurseries in two habitats.  The results show, somewhat expectantly, contrasting performance of the two taxa in the two habitats.  The study also includes more extensive quantification of ecological interactions (predation, disease, algal overgrowth, guard crabs) than is common in nursery studies.
Experimental design: These results thus do indeed provide some helpful basis for planning additional coral gardening activities in the region.  However, I would say that the appropriate guidance derived from this study is greatly limited by the lack of any information on the post-outplant performance of these gardened fragments.  In the end, the survival and growth of the frags on the actual reef is what we care about, and other studies have shown that this may or may not be closely predicted by the frags’ performance in the nursery setting.  The authors acknowledge this point very briefly in the discussion, but the usefulness of the current results is greatly limited by its lack.
Validity of the findings: No comments
Additional comments: Two other points I would suggest substantive revision; the first is semantic.  Although the term ‘nursery’ refers to a wide range of settings related to infant or juvenile organisms, the term ‘nursing’, at least in US English, is used primarily to refer to breastfeeding of human infants.  Therefore, I suggest to remove the term ‘nursing’, ‘nursing period’, ‘nursing environment’, ‘nursing performance’ etc. from the paper. (‘nursery’ can be replaced in most cases).
The second relates to a general expectation about corals and habitat performance.  Existing best-practice for coral gardening suggests there is probably benefit in matching the nursery habitat to 1) the habitat from which corals are provenance and/or 2) the habitat that is intended to be restored.  In fact, there is also benefit from sourcing restoration genotypes from across a diverse habitat range (to incorporate as much adaptive genetic variability as possible – see Baums et al. 2019 Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic.  Ecol Appl. 29:e01978 https://doi.org/10.1002/eap.1978) and this provides an important framing for testing habitat-specific nursery performance as addressed in the current paper.  However, the authors discuss and analyze the effects of ‘colony origin’ in the results, by which they mean the prior nursery culture location of the colonies.  If there is a local habitat adaptation in these populations, the actual origin of the genotypes (i.e. what reef habitat were they originally collected from) may be important.  Where were these genotypes originally from? And what effect might this actual (collection) origin have on differential performance between habitats.
Minor corrections:
Ln 31: the different descriptions of number of fragments seem inconsistent throughout.  Here in the abstract, it says ‘eight fragment replicates from the same donor colony (N=20) in each group’.  This sounds like 32 fragments were made from each donor colony, but then what does ‘N=20’ mean?

Ln 173: here in the methods it would be nice to give a bit more info on ‘predation’ and ‘associated organisms’.  There is more info given in the discussion, but as a reader, I was curious what evidence and source of predation you were scoring (scars,  bite marks, active feeding?)

Ln 221-222: Clarification: This sentence says that all but 3 of these fragments suffered more than 50% mortality – I think this is not correct(?).  Also, delete redundant ‘in’

Ln 251: Temporarily should be Temporary

Ln 280-281: Mh appears for the first time.  Should be defined in the Methods.  Also, the term ‘longest linear extension’ is ambiguous.  I think you mean simply ‘colony diameter or ‘colony dimension’ either of which would be less ambiguous terms.  (Other studies use the term ‘total linear extension’ to indicate the total branch length in a branching colony, rather than the colony dimension)

Ln 336: I believe that Moriarty is missing from the Refs cited section.

Ln 340: Save should be safe

Ln 402: extend should be extent

Ln 418: the meaning of the phrase ‘was placed offsite resort activities’ is unclear.  Does this just mean the placement of the nursery was further distant and not affected by resort activities? Should be re-phrased.

Discussion/Conclusion sections: generally, could be tightened/shortened.  These sections completely recapitulate all the results and are at times repetitive.


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: COMPARING DIFFERENT FARMING HABITATS FOR MID-WATER ROPE NURSERIES TO ADVANCE CORAL RESTORATION EFFORTS IN THE MALDIVES
Review round: 1
Reviewer: 2

Output:
Basic reporting: In general, the study demonstrate the application of mid-water rope coral nurseries in Maldives and found both habitats (lagoon nursery and reef nursery) are suitable for coral restoration using the proposed method. The manuscript is easy to understand. However, there are several modification need to be done before accepting the manuscript as indicated in attached notes.
Experimental design: Author provide a well defined research and within the scope of the journal. Require minor modification by adding some details related to the location of the study, sample collection method, etc. See details in attached document.
Validity of the findings: No major comment. See details in attached document.
Additional comments: Even though the mid-water rope coral nurseries have been applied in other places, this study conducted a preliminary test on different reef habitat to seek efficacy of the method for coral restoration. However, several details need to be added (as indicated in attached document) to improve the quality of the manuscript. The study is suggested for publication due to the important of coral restoration in tackling the coral reefs degradation.


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: COMPARING DIFFERENT FARMING HABITATS FOR MID-WATER ROPE NURSERIES TO ADVANCE CORAL RESTORATION EFFORTS IN THE MALDIVES
Review round: 2
Reviewer: 1

Output:
Basic reporting: This revision is indeed improved.  Although the new paragraph (~Ln 159-168) adds information, it is still difficult to understand the history of the colonies used in the experiment and the potential effect of the natal habitat.  As I understand it, Pocillopora colonies were collected in 2018 from two separate sites. One (off-island) collection site populated the LN and one the RN (what kind of ‘artificial structure’ were they collected from?).  Then, two years later, these colonies were reciprocally mixed between the two nursery habitats such that there were equal colonies from both ‘collection habitats’ in each ‘nursery habitat’ treatment in the study reported here.  Thus, the conclusion that the RN ‘nursery habitat’ treatment had higher growth rates (clearly an interesting result) includes genotypes that were originally collected from two separate (natal) habitats that were subsequently cultured for two years in different habitats.  Is this correct? Was there any difference in the performance of the genotypes from the two different (natal) habitat origins? Perhaps a supplemental figure depicting the steps in the history of the experimental colonies would be helpful?
The language is also still cumbersome in places.  Example (Ln 430-432) “Yet, we found that reef farmed donor fragments outperformed fragments from lagoon reared donor corals in growth rate in nearly all cases, even though stocking size was controlled for.”  I believe that ‘reef-farmed’ and ‘lagoon-reared’ should be hyphenated in this construction, but it would perhaps be much simpler to say ‘Fragments previously cultured in the RN outperformed those previously reared in the LN even after controlling for initial fragment size.’  Also, I think that ‘initial size’ is a better term than ‘stocking size’ . . .
Example (Ln 441) “ . . Structure over-growing algae were found in both habitats . . “  would be clearer to say ‘Algae were observed fouling (or growing over) the nursery structures in both habitats’            Example (Ln 504) “the newly adapted, streamlined design of the reef rope nursery passed its test in a current and fish rich environment”  Clearer to say: “Our streamlined rope nursery design withstood the high currents and fish abundance in the outer reef environment . . .”

Ln 496:  This is where better acknowledgement of the consideration of the destination (outplanting) habitat is needed. It is premature to recommend prioritizing shallower depths for nursery culture unless and until performance in appropriate outplanting destinations is demonstrated.  If shallow outplanting sites are intended, this is probably true, but may not be true if deeper outplanting is intended.
Moriarty et al. is still obscured in the refs section
Fig 1 A seems to have 3 separate scales (though only one is given) and it should be articulated what is represented in depiction of the atoll (I assume gray is land and white is ocean? What is the black region?)
Fig 6: Easier to interpret by placing p-value on the figure over each pair of bars (not in the legend)
Experimental design: As above, still challenging to understand the origin of the colonies involved and potential influence of genotype origin
Validity of the findings: Fine
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: COMPARING DIFFERENT FARMING HABITATS FOR MID-WATER ROPE NURSERIES TO ADVANCE CORAL RESTORATION EFFORTS IN THE MALDIVES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The author follow all the comments suggested by the reviewers by providing a clear and meaningful explanation on the comments stated previously.  Language used is clear and much easier to understand by reader. The authors also add details on literate review regarding the coal reefs status in Maldives and several successful coral restoration program to support certain statement. Figures were improved by adding photos which will help readers to understand more on the situation of the study. The authors also issued on positive and negative implications of coral farming environments and their specific challenges, which is important consideration for future study.
Experimental design: The study following the aims and scope of the journal which is appropriate in the Biological Sciences and Environmental Sciences section.  The research question is well defined, relevant and meaningful for coral restoration program, particularly in Maldivian coral reefs as the research related to coral restoration is still scarce in the region. Description in the method was improved and provide sufficient information on the study area and coral restoration technique applied in the study.
Validity of the findings: The mid-water coral nursery have been applied as part of the reef management strategy to overcome the coral degradation. Even though the research on the coral restoration using the mid-water rope have been well described in other studies, the present research will add value to the literature and helps the reef managers to understand and plan the coral restoration strategy for conservation purposes. The findings presented in the manuscript are statistically tested and well explained. Conclusion is well described with some recommendation for future studies.
Additional comments: Overall, the authors followed all the recommendation and suggestion by the reviewers which improved the quality of the manuscript in line with PEERJ standard. As a second reviewer, I'm satisfied with all the changes made in the manuscript and the authors answered all the comments appropriately.


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: ANIMAL TRAIT VARIATION AT THE WITHIN-INDIVIDUAL LEVEL: ERYTHROCYTE SIZE VARIATION AND MALARIA INFECTION IN A TROPICAL LIZARD
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written and is clear and concise on an interesting and clearly understudied topic. The introduction and background provide an important foundation for the reason for the manuscript, and clearly explain why it may be important to study the topic of “within individual variation” in animals. Please see my comment in the “General Comments” on where it may include more background. Overall, the manuscript fits PeerJ’s standards as well as scope. The attached figures, code, and data are high quality, easy to understand, and very clear.
Experimental design: The experimental design is straightforward and easy to understand. This combination means that the results make sense and the paper works well to answer the question they originally asked. The methods are regularly used, generally explained well, and are replicable. Please see “General Comments” for questions about the methodology.
Validity of the findings: The authors asked an interesting and important question, and this is particularly evident in the findings. Any information found using their solid techniques would be both interesting and move the field forward (due to an extreme lack of WIV examples in vertebrates). The underlying data and code are provided, including statistical modelling code. The authors make sure to explain their findings and give several reasons as to why the data are the way they are.
Additional comments: Overall, I thought this was a well written and interesting paper on a topic that is rarely studied, especially outside of humans. While Plasmodium infection is relatively well studied, this manuscript does two important things: looks at how within individual variation may be related to Plasmodium infection and introduces within individual variation into the animal literature. Please see my comments below on how it can be improved and clarified.

1.	The statistics are valid and easily reviewed with the provided code. I think the authors need to do a better job at explaining why they did the stats though. This is because there are plausible ways to do very different analyses. For example, the current analysis is based on the hypothesis that within individual variation will predict Plasmodium infection (prediction based off the plant literature). The introduction explains a human example where within individual variation is caused by a disease though, and that could mean you could switch the model such that Plasmodium infection would predict within individual variation. The authors should make the argument stronger for why they are doing the model based on the plant hypothesis, and this may be improved using the literature brought up in the second comment below.
2.	The authors should include more examples of within individual variation in animals. This could include examples that is well studied in the literature, such as sickle cell anemia in humans. This particular example should be included because it is both relevant to the topic of within individual variation and Plasmodium infection (i.e. humans with sickle cell trait show high within individual variation of erythrocytes and this lowers Plasmodium infections). Including this will also provide a stronger biological reason for your hypotheses and predictions (i.e. the hypothesis that higher within individual variation would be associated with lower infection).
3.	Is Plasmodium infection related to BCI in the lizards in this study? Despite there being debate about this in the literature, this should be included in the manuscript, rather than simply citing Sanchez et al. 2018. This is because the authors are saying high WIV may be related to fitness via BCI. But if infection is not related to BCI at all, why would you test if WIV could be a proxy for fitness/infection? Particularly it would be important to note because on line 200, the authors state that there is a small negative effect size (according to Sanchez et al. 2018), so it would be good to know what it is in this study.
4.	There is some confusion about how lizards were assigned to be infected or not infected. Starting on line 119, the manuscript states “We considered a lizard infected if we detected through microscopy at least one cell invaded by P. azurophilum, and PCR positively amplified Plasmodium. We considered a lizard non-infected if we could not visually detect an invaded cell using microscopy and the PCR did not amplified [sic] Plasmodium.” This phrasing makes it sound as if to be identified as positively infected, a lizard had to have Plasmodium visually seen AND PCR had to amplify the parasite DNA (not OR). If it was one or the other, but not both, the lizard would be marked as non-infected. Later, on line 143, the authors state “PCR complemented diagnosis by helping avoid false negatives resulting from individuals with low parasitemia that may be missed by the slides”. It is unclear if the authors meant to say positively infected individuals could be found either through visual inspection or PCR.
5.	In the Discussion section, there are several lines that are very similar and can be condensed to be less repetitive and clearer. Lines 255-257 are very similar to 265-267.
6.	Small typographic error on line 260 (no space after period), and a small grammatical error on line 122.


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: ANIMAL TRAIT VARIATION AT THE WITHIN-INDIVIDUAL LEVEL: ERYTHROCYTE SIZE VARIATION AND MALARIA INFECTION IN A TROPICAL LIZARD
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study submitted to PeerJ addresses the hypothesis that a high within-individual variation (WIV) in reiterative components increases the individual fitness by mediating ecological interactions. The novelty of the study is its application to animal systems, a matter so far poorly studied. Authors investigated whether the area of reiterative components (i.e., erythrocytes) can mediate and reduce successful infections by Plasmodium azurophilum in the lizard host Anolis gundlachi.
Experimental design: The hypothesis is based on the idea that tight co-evolutionary histories obligate parasites to be highly specialized and, thus, encountering target components with a high variability reduces the parasite’s capability of infection and increases host's fitness. This is an interesting approach although I find (in page 118 of Sam R. Telford, Jr.’s 2009 book “Hemoparasites of the Reptilia: Color atlas and text”, CRC Press, Taylor and Francis Group, Boca Raton, FL) that Plasmodium azurophilum is not a specific parasite of A. gundlachi, and actually is a generalist known to infect 20 different species of Anolis which probably vary in their erythrocyte area. As it is known that close related lizards vary in their erythrocyte area depending on e.g. environmental conditions. All this said makes me think that this may not be a good model to test your hypothesis.

Besides this issue, I also think that the infection by Plasmodium, and first reproduction cycles, take place first in the liver (already damaging it and producing a negative impact) during the preerythrocytic phase. Thus, although hosts had a high WIV concerning their erythrocyte size I do not find how this could reduce the infection process and the negative impact on the liver. Maybe this could reduce, at some point, during the Plasmodium cycle, the invasion of erythrocytes and subsequent transmission to a new feeding mosquito. However, following the results achieved it neither seems to be the case because, contrary to predictions, WIV was higher in infected individuals.

In addition to these two major issues, I suggest calculating BCI for all the data together and not splitting the calculus for sex and season. You are interested to compare whether individuals are above or below the sample mean, if you split the calculus of BCI by group there is no point in comparing the values of BCI because you are making the subsamples independent (which also makes no sense including sex and season in the analysis, because you are already removing their effect).
Validity of the findings: I am afraid I cannot be more positive. The results concerning erythrocyte size are good but the approach of the study and the hypothesis should be reformulated. I have to mention that I agree with the interpretation of the results: WIV is higher in infected individuals probably due to the higher cell replacement rate.

The results concerning BCI should be recalculated based on my prior comments.
Additional comments: I think that the study could be refocused to tell a different story because you got a lot of data and I know that screening smears and DNA samples is a lot of work. I find very interesting your results suggesting that parasites destroy erythrocytes, which we already know that this happens, and lizards have to compensate the destruction of cells by replacing them (with the added cost). Maybe, refocusing this study, you can test the cost of the replacement of the destroyed cells comparing the ratio of immature erythrocytes against BCI (after you recalculate BCI for the entire sample).

I find Peig and Green (2009, calculation of SMI) in References but not in the text. Probably to be deleted.


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: ANIMAL TRAIT VARIATION AT THE WITHIN-INDIVIDUAL LEVEL: ERYTHROCYTE SIZE VARIATION AND MALARIA INFECTION IN A TROPICAL LIZARD
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors provide a complete revised version. I appreciate their effort. However, I still have some few comments before I can recommend publication.

Line 31. I would rather write ‘the host may respond by increase production’. I don’t think that the immune system is responsible in any way of producing erythrocytes.
Line 204. You did not really quantified fitness but a proxy of it. I would rather write here ‘We modelled body condition…’, and remove the first part of the phrase, which was already explained in Introduction.
Lines 212-214: This is redundant information ‘Therefor, while we calculate a pooled BCI we added sex and season as controlling variables in the linear model explaining the relationship between infection status and BCI.’
Line 215: The two references provided support the use of body condition indices as proxy to the ‘energetic state of animals’. However, I would prefer to have examples cited on lizards, or at least reptiles.
Line 219: You may prefer to cite something like: ‘Wilder, S. M., Raubenheimer, D., & Simpson, S. J. (2016). Moving beyond body condition indices as an estimate of fitness in ecological and evolutionary studies. Functional Ecology, 30(1), 108-115.’, rather than the message ‘see below’.
Lines 225: Please, remove ‘To test if individuals with higher WIV have improved fitness,’. This information might be better placed in Discussion.
Lines 280-282: an alternative hypothesis is that only lizards in better condition survived the infection. Indeed, the destruction of erythrocytes (and the need for replacement) is not a tolerance mechanism in any way, but rather a response mechanism to the infection demonstrating host vulnerability! I think that the following lines relating tolerance mechanisms should be shortened.
Line 298: This is a misconception. The immune system is not responsible in any way of erythropoiesis.
Line 315: Remove ‘host immune response to’.
Line 324: the authors provide no measure of fitness. Please, rephrase.
Figure 1. Could you provide a similar picture showing some infected erythrocytes?
Experimental design: no comment
Validity of the findings: I recommend revise some of the interpretations provided by the authors.
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: HOLOTHURIOPHILUS TRAPEZIFORMIS NAUCK, 1880 (DECAPODA: PINNOTHERIDAE) FROM THE PACIFIC COAST OF MEXICO: TAXONOMIC REVISION BASED ON INTEGRATIVE TAXONOMY
Review round: 1
Reviewer: 1

Output:
Basic reporting: -Cortés-Carrasco et al. studied and re-described Holothuriophilus trapeziformis from Mexico's Pacific coast, especially for the male. The morphology characteristics that the authors provided in this manuscript are essential and well described for future research of H. trapeziformis. I assume we need more studies to confirm the relationship between these species and their host (sea cucumbers). However, the population genetics part of this study is fragile, and it will not add much. The phylogenetic tree and the morphological characters are much better.

-Editing of the English language is needed for this manuscript.

-There is no map of the sampling locations.
Experimental design: -The genetic part needs a lot of rearrangements and corrections. The authors studied the population genetic structure based on one unspecific marker, a low number of samples, and populations in a small area. Additionally, it is hard to followup some parts, such as showing four populations in Table 1, but it shows only three populations in Figure 9 (which one is correct).  Also, it is not clear that they studied the genetics of sea cucumbers or no. Please delete the population genetic section from this study.

-The authors used a specific primer for the freshwater microcrustaceans (ZplankF1_t1 and ZplankR1_t1)
Validity of the findings: -The morphology characteristics that the authors provided in this manuscript are essential and well described for future research of H. trapeziformis.

-Please add the accession numbers of the sequences provided by GeneBank.
Additional comments: Some minor corrections (not all):
-The manuscript needs English language editing. Some phrases, articles, and punctuations are not needed, and some sentences are unclear or hard to follow, for instance:
-Line 37: please remove the phrase "which is".
-Line 39: please remove the article "the" from "the females".
-Line 41-43: the sentence "Our goal ……." is hard to follow.
-Line 45-48: the sentence "We also….." is unclear and hard to follow. Also, remove "," after compared in line 45.
-Please reconstruct/rearrange the abstract and remove the unnecessary information. In the results section in Line 49, the authors started with the introduction and methods again in this part. Also, the authors' goal in Line 41 has the same meaning in Line 44; please describe the methods used to study morphology and DNA.
-Line 41 and Line 59-60: please rephrase "…..for the first time."
-Line 66-67: The number of known species is 16, not 13. Ng & Manning (2003) mentioned (P:901, last paragraph) that 16 species are known to be parasites of sea cucumbers; 13 of them occur in the Indo-West Pacific.
-Line 70: Add a reference to support this information.
-Line 87-88: "based on a single morphological character" could you please let the readers know what that single morphological character is?
-Line 94: Nauck (1880) made a great effort to record the information at that time. Therefore, please delete this sentence or rewrite it "did not designate a holotype…..".
-Line 193-194: It is hard to followup! Are the host sea cucumbers sequenced? If so, how many specimens?
-Line 204: Zooplankton primers (ZplankF1_t1 and ZplankR1_t1) are specific primers for freshwater microcrustaceans. Are these primers used for Holothuriophilus trapeziformis and sea cucumbers? I assume there many specific primer sets for marine microcrustaceans.
Line 222: Are COI sequences from other pinnotherids collected in America's Eastern Pacific coast were collected in this study? If no please add the reference.
-Line 227: please add the accession numbers of uploaded data on GeneBank.


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: HOLOTHURIOPHILUS TRAPEZIFORMIS NAUCK, 1880 (DECAPODA: PINNOTHERIDAE) FROM THE PACIFIC COAST OF MEXICO: TAXONOMIC REVISION BASED ON INTEGRATIVE TAXONOMY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Although this is a straightforward paper redescribing a single brachyuran species, Holothuriophilus trapeziformis Nauck, 1880, the manuscript is lengthy and difficult to trace what is the point of discussions.
Experimental design: The aims of the present study are not clearly stated, but if a part of them are redescription of the species and finding diagostic chracters from congeners, authors should be able to have enough dataset but not well presented.
Validity of the findings: Authors have good amount of data with good photographs and drawing.
Additional comments: Since authors have good amount of data and specimens, and it is important to redescribes the species in detailed, I encourage authors to revise the manuscript substantially and re-submit the ms to more specialized 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: HOLOTHURIOPHILUS TRAPEZIFORMIS NAUCK, 1880 (DECAPODA: PINNOTHERIDAE) FROM THE PACIFIC COAST OF MEXICO: TAXONOMIC REVISION BASED ON INTEGRATIVE TAXONOMY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Minor English editing such as:
-Line 117-122 long sentence, and it will lead to hard to follow.

-Adding comma in some sentences, for instance, before "and the male" line 87.

-Could you please check this reference (I think it is not cited in the text)? "Lefébure T, Douady CJ, Gouy M, Gibert J. 2006. Relationship between morphological and molecular divergence within Crustacea: Proposal of a molecular threshold to help species delimitation. Molecular Phylogenetics and Evolution 40(2006):435–447"
Experimental design: N/A
Validity of the findings: N/A
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: HOLOTHURIOPHILUS TRAPEZIFORMIS NAUCK, 1880 (DECAPODA: PINNOTHERIDAE) FROM THE PACIFIC COAST OF MEXICO: TAXONOMIC REVISION BASED ON INTEGRATIVE TAXONOMY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The current version of the manuscript is well modified from the previous version, but there is much room to improve it. See comments in the attached ms.
Experimental design: Although this is a simple re-description paper, targets and aims of comparisons are unclear. Are there any null-hypotheses that particular groupings (e.g. locality, carapace shape) may represent different species? Since points in questions are not well raised, it is very difficult to follow the flow.
Validity of the findings: Further justification may be needed, for example genetic comparison between "groups" (e.g. locality, carapace type).
Additional comments: See attached file for 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: SPATIAL PATTERNS IN THE CONTRIBUTION OF BIOTIC AND ABIOTIC FACTORS TO THE POPULATION DYNAMICS OF THREE FRESHWATER FISH SPECIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is adequately presented and clearly structured. While the methods section may be a bit long and on the more verbose side, it seems in this case justified given the complex statistical and modelling approach. No issues with language outside of small comments in passing. The figures and tables are also clear and nicely presented, although some edits are probably needed for figure 1 (see General Comments). Raw data is available for checking and is easily comprehensible.
Experimental design: I first commend the authors for the thorough and extensive analysis they conducted for this manuscript. Not only does it utilize an impressive dataset derived from a monitoring program spanning a large area, but it does so in a very clear and advanced modelling framework. The research question and framing of the introduction is well-crafted and perfectly sums up the background, theory and expected contribution behind this analysis, particularly the articulation of the three study species’ in relation to the abundant-centre / range-shifts hypotheses.

As written previously, the methods section is a bit long in comparison with the rest, but this is often warranted when complex modelling is involved, and it has here the merit of being clear and well presented. I am not especially well-experienced with Bayesian frameworks and I therefore won’t dive too much into the nitty-gritty of the statistics (although I would certainly be interested to read the comments of other reviewers), but the modelling approach itself was fitting and nicely presented. I am particularly appreciative of the elasticity analysis and its incorporation into testing the two biogeographic hypotheses. This brings a new and welcome layer of analysis as well as more caution to the discussion, which is something sadly too often left out from modelling studies.
Validity of the findings: The respective influences of biotic and abiotic factors on population dynamics is a widely studied (and debated) topic, but multi-populations or species comparisons integrating spatial elements are less commonly seen. Here, the authors use data from a long-term freshwater monitoring program to develop population dynamics modelling for three fish species with varying life histories and environmental preferences to quantify the relative importance of biotic and abiotic factors. In addition, the results are further used to evaluate spatial patterns in fish response to each factor following two (non-exclusive) ecological hypotheses. Studies on species distributional changes under shifting environmental conditions have been a key aspect of modern ecology, but freshwater ecosystems have been notoriously understudied and neglected in comparison to their marine counterparts. As such, this manuscript provides a welcome addition to a growing body of literature and provides interesting new perspectives on the influence of biotic / abiotic factors on freshwater fish dynamics, as well as encouraging further studies.

The discussion did a great job to provide a summary of the results and re-contextualize them with the research questions. A clear and concise conclusion is also provided at the end to summarize the key findings, encompassing both the modelling results on the factors driving population dynamics, and how they relate to the two mechanisms suspected to drive species distribution. Overall, this is a high-quality work.
I’d however be careful with some of the interpretations in the discussion. For example, the larger effects of density-dependent factors are here defined as a sign of stable populations near carrying capacity, and the authors therefore present several elements pointing toward a potential “resilience” of these fish populations to climate change. While it is true that density-dependence is often a significant control mechanism seen in larger and healthier populations, there is a growing body of evidence showing strong density-dependent effects appearing in disturbed populations past a certain threshold, especially when environmental changes are involved. Indeed, if external factors suddenly change the availability of resources (for example a long-term warming leading to a gradual mismatch between prey / predator peak recruitment season) an already disturbed population can become increasingly dependent on biotic control (either bottom up or top down) where the density-dependent effects will then limit its adaptability to further change.

In the manuscript there is a paragraph briefly touching on the potential factors not considered here behind the opposed effects of biotic / abiotic factors for some populations (lines 389 – 396), but I encourage the authors to be a bit more cautious on some of their conclusions as more and more evidence shows that these different factors often act synergistically in unexpected ways (see for example Morrongiello et al 2019, Synergistic effects of harvest and climate drive synchronous somatic growth within key New Zealand fisheries). For example, here the apparent contrast between a leading edge for chub predicted to shift upwards but a negative effect of climate change on high-latitude populations could very much indicate that the species is running out of optimal niche and is slowly forced to extend in potentially sub adequate environments.
Additional comments: Not an issue per se, but at times I got confused with the presentation of one of the two hypotheses (range-shift). While the results and discussion make it clearer further down the manuscript, the initial presentation of the range-shift hypothesis gave me the wrong impression that this study would be looking at latitudinal changes, i.e. poleward movement of freshwater species with abundances in the southern sites decreasing and those in northern sites increasing. This conflicted with the repeated use of “altitude” but because it wasn’t clearly stated that the range-shift hypothesis was here tested for altitudinal changes, it took me a re-read to correctly understand (though some may argue that these two are here not mutually exclusive). I think an extra sentence in passing in the methods could help to clarify.

Figure 1
In the caption, the word “raw” was wrongly used in place of the word “row”, this needs to be corrected. I think it would also be easier to read with annotated panels (say A to H). The panels are also rather small and difficult to read, in particular the smaller plots above. I’m not sure if the figure should be reorganized more vertically (3 rows instead of 2); be flipped in the published version; or if these elements should be made bigger.

Figure 4
Perhaps a minor comment, but consider changing the point colour palette from green/orange to something more contrasted like green/blue for those with colour eye deficiencies like colour-blindness.