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: GENOTYPIC CHARACTERIZATION AND GENOME COMPARISON REVEAL INSIGHTS INTO POTENTIAL VACCINE COVERAGE AND GENEALOGY OF NEISSERIA MENINGITIDIS IN MILITARY CAMPS IN VIETNAM
Review round: 1
Reviewer: 1

Output:
Basic reporting: Clear presentation of the results, sufficient introduction provided, relevant references provided, the structure of the article is convenient, tables and figure are clear.
Experimental design: Methods are described with sufficient details and information to replicate.
Validity of the findings: New results of WGS of N. meningitidis in Vietnam are presented, conclusions are well stated.
Additional comments: Abstract, line 29:
I recommend to add the serogoup and the source of isolation for two additional N. meningitidis isolates.

Introduction – line 75:
I recommend using the whole name of the method before using the abbreviation WGS for the first time.

Introduction – lines 83-84:
I recommend to add the serogoup and the source of isolation for two additional N. meningitidis isolates.

Materials and Methods – line 98:
I recommend using Serogroup identification instead of Serogroup typing.

Results – lines 200-202:
It might be useful to add a reference to the source of information about these 108 isolates.

Results – lines 190-191 and 197-198:
I recommend to analyze these results with the gMATS method (Muzzi A. et al., 2019).

Discussion – lines 276-278:
I recommend to discuss the results with the gMATS method (Muzzi A. et al., 2019).


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: GENOTYPIC CHARACTERIZATION AND GENOME COMPARISON REVEAL INSIGHTS INTO POTENTIAL VACCINE COVERAGE AND GENEALOGY OF NEISSERIA MENINGITIDIS IN MILITARY CAMPS IN VIETNAM
Review round: 1
Reviewer: 2

Output:
Basic reporting: •	There are some minor instances throughout where there are slight issues with grammar, which should be corrected before publication.
•	There are also issues related to the discussion of genes versus proteins, which are covered in greater detail below. The authors must be clear in their writing in this regard throughout the manuscript.
•	There is good background regarding the increased risk for certain communities, which include university students and military units where people live in close proximity. These are well referenced.
•	There is good background regarding genomics and MLST for Neisseria meningitidis with appropriate reference to the literature and relevant URLs. This gives the reader sufficient background to understand the context of the work described here.
•	The structure of the manuscript needs some attention. For example, the Results includes quite a bit of information that is more appropriate in a Discussion. It might be warranted for the authors to consider creating a combined Results and Discussion, otherwise the more discursive portions of the Results need to be moved to the Discussion, such as in lines 144-145, in lines 159-161, in lines 190-191 (this isn’t clear whether antibody testing in a lab was actually done or this is bioinformatics – if so, it is not in the Methods, in fact even the bioinformatics-based methodology should be in the ), and lines 192-198. This isn’t exhaustive, it is also discursive toward the end of the Results and elsewhere. The manuscript would likely benefit from a combined Results and Discussion.
•	In Table 1, it is unclear to the reader what the numbers under each locus represent. It has bene assumed by the reviewer that these are the indicators from MLST, but it is not clear from just looking at the table itself. An appropriate footnote is needed for the reader to be able to understand the nature of this data, citing the PubMLST database.
•	In Table 2, the abbreviation ST (cc) should be defined for the reader, so that they are readily able to interpret what this data means in the table and its source. Also, if the antigenic profile is based on the protein, then the protein is properly written as PorA, for example, not PorA. If what has been analysed and indicated by the data in Table 2 is actually the gene information, then it should be porA, starting with a lower case letter, rather than PorA as written here. Again, the source of this data needs to be clarified for the reader with a footnote.
•	In Table 3, it would be easier for the general reader in the field to understand what has and has not been found in the isolates if the well-known gene names are included with the Locus information, as well as the Locus (which needs to have a footnote that this is from PubMLST) and Product information. For example, the first three appear to be rfbA, rfbA2, and ctrF. Having deciphered this, it then makes the reader wonder about the rest of the ctr genes in the capsule locus.
•	In Table 4, the source of the data that was not generated in this study needs to be indicated in a footnote.
•	In Figure 1, the legend should be expanded for the benefit of the reader. Include more detail on how many isolates are in each of the panels and the basis of their inclusion. Also, either remove the red lines or comment upon them in the figure legend. The same is true for the other labels on the trees – remove them or comment upon them and their significance in the legend.
•	Tables and Figures need to be able to be able to be understood as stand-alone entities without reference to the main text. Currently, they do not.
•	Table 4 is mentioned first in the manuscript (line 106). This should be rectified.
•	The data is appropriately deposited as a BioProject with NCBI.
Experimental design: •	This research is original, having investigated two isolates from a military unit that is in proximity to one from which N. meningitidis had previously been isolated and sequenced. This provided the authors with some geographic context, whilst expanding out the scope of the previous study. The analysis also included the comparison of their data to the world-wide data available in the PubMLST database and other sources. This is an excellent contribution to the field based on its originality and primary findings.
•	The various MLST analyses find that the three Vietnamese isolates cluster into their own separate clade apart from the rest of the network of previously defined N. meningitidis, which is and important result.
•	The research question is well defined and clearly presented to the reader.
•	There is a good selection of antibiotics that were assessed. It is unfortunate that azithromycin is not one of the antibiotics that was investigated. It is not something this reviewer would ask that the investigators go back to the laboratory and check – particularly in the current environment when so many labs are closed, but even if this were not the case. This is a choice that was made by the investigators and that is fine. Given the WHO recommendations for dual therapy with ceftriaxone and azithromycin, however, it might have been interesting to know. Perhaps the authors could look at the potential genomic features that may contribute to resistance or otherwise comment in the manuscript on azithromycin in the absence of this testing.
•	It must be clear in the use of language when the investigation has based its conclusions on genomic data and on experimental data. For example, in lines 180-181, the authors discuss expression of antigenic proteins. This cannot be known or determined from analysis of the genomic data. Unless there were experimental investigations undertaken using immunoassays that are not included in the Methods, this sentence and the presented information needs to be considerably re-worded and presented accurately to the readers. Possessing genetic sequences does not necessarily equate to expression of a protein. The authors must be clear when writing that use of the protein name, such a PorA, implies that they have investigated the protein. From the Methods, they have not. They have done a genomic analysis and therefore can comment only upon the sequence information about porA. Great care and attention needs to be paid to how bioinformatics investigations are written about and presented to the reader.
•	In the capsular cluster investigation, is cnl not the designation for the capsule null locus – as in the genomic location when there are no capsular genes, present in some isolates of N. meningitidis? This is not clear from the manuscript as written and should be made so for the reader. Indeed, mention of cnl could possibly actually be removed because the two isolates have capsule loci, therefore there is no need to even compare to the cnl. An appropriate comparison is therefore to capsular isolates.
•	Methods are described with sufficient detail either in this manuscript or in the references cited. The methods being used are appropriate for this investigation.
Validity of the findings: •	The novelty of the data has been well assessed, although there are some points that need to be clarified and written in a more robust manner, as pointed out in the other sections of this review.
•	The genomic data assessment on the general features are robust and correct that they align with the previous genomes and are typical. However, the authors should include a reference to previous literature for the benefit of readers. Reference to some of the early complete genome sequences for N. meningitidis and N. gonorrhoeae from mid-2000s would be sufficient.
•	It isn’t clear on what basis capsule switching is proposed (lines 259-260). Also, capsule switching as a process should be cited.
•	The conclusions are clearly and well stated and link directly to the findings of the research. They are supported by the data, especially because they include that the data predicts that the isolates are not covered by the serogroup B vaccines, since this is based on bioinformatics analysis.
Additional comments: •	The title is accurate, however it does not address the most striking finding of this paper, which is that the isolates that were sequenced from the Vietnamese military units were predicted to not be covered by either the Bexsero or Trumenba vaccines. This is a significant discovery that might be overlooked by researchers skimming the literature by title. The authors are urged to consider a title that reflects this finding and highlights it, therefore directing readers to their publication.
•	The term de novo, as first used in the Abstract (line 33), should be in italics as a non-English term.
•	The gene names should also be in italics, such as aroE (twice on line 155).
•	In line 222, ‘pseudo’ is not a word in itself. It should be hyphenated as pseudo-gene or written as pseudogene.
•	In line 268, Neisseria should be abbreviated. This is not the first instance of its use in the manuscript.
•	Line 278 has an undefined abbreviation ‘NmB’ that should be defined and clarified for the benefit of all readers.
•	Genus species names and gene names in the references should be italics.
•	The gene names in Table 1, gyrA, penA, and rpoB should be in italics.


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: QUANTIFYING UNCERTAINTY IN ANNUAL RUNOFF DUE TO MISSING DATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Dear Authors
I have with great pleasure been reviewing your manuscript entitled ‘Quantifying uncertainty in annual runoﬀ due to missing data’ and find that your manuscript includes some very important scientific findings that are useful for all hydrologists and water quality scientists and managers.
Your language is very clear and a professional English language is used throughout the manuscript.
You have good and relevant references to the literature but I miss maybe references to the literature on uncertainty in load calculations for sediment and nutrients, which are very important for water managers. The uncertainty linked to e.g. daily flows during gap filling, might at high flows, be crucial for such load calculations.
Your structure conforms to PeerJ standards as far as I am aware and your Figures are relevant but could be improved for the readers to better see the results – e.g. Figure 4 and 5 – insert normal labelled axis – not logarithmic.
Raw data is also supplied as Supplementary Material.
Experimental design: Your results are clearly within the Scope of the journal. Moreover, your research questions are well deﬁned and you have conducted a rigorous sampling and statistics to a high scientific standard. The methods used are described with suﬃcient detail and information to be replicated by others – e.g. for larger streams and rivers.
Validity of the findings: Your detailed analysis of gaps in hydrographs and impact of gap filling methods on runoff in a small stream is novel and give important inputs to hydrological science.
The only thing I am a little curious to know more about is the bias of runoff that you find in your assessments – as this might be of even greater concern than the uncertainty measured as the standard deviation in Figure 5. I would find that you should include an assessment of the bias in gap filling in your manuscript.
Additional comments: In conclusion, I find that you need to revise your very nice manuscript according to the few proposals mentioned above.


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: QUANTIFYING UNCERTAINTY IN ANNUAL RUNOFF DUE TO MISSING DATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: A minor point, but Figures 2 and 3 units are inconsistent with the other figures.
Experimental design: I have noted in my general comments a few places where methods need clarification.
Validity of the findings: No comment.
Additional comments: This is a well-conceived study on a method for infilling high-frequency streamflow data for small catchments and estimating the associated uncertainty. The analytical approach is sound and reproducible, and the results are interpreted logically. I have only minor suggestions for improving the paper, by line number below.

Table 1. Why not indicate which of these 6 watersheds is the actual reference watershed where you are testing the infilling?

Line 38. "weir blockages" could be clarified and generalized to "debris on the control". Although weirs, with a restrictive geometric control, are highly prone to catch debris, most stream gages are not weirs.

71. Sentence beginning this line does not stand alone.

73. Capitalize “v” in V-notch as above.

77. “stage-discharge” is more conventional than “height-discharge”.

Figure 1 caption: I do not understand “in the model”, perhaps you mean “used in the model”? The left figure contains actual data, correct? Also, the inset technically shows all the data, not just the upper 2%.

95.  Make clear the bin size is 1%. Maybe you intend this to be clear by “Percentile” but since you do discuss the 0.5 and 99.5% Qs, it could stand clarification.

95-97. Since the watershed sizes vary over a factor of 4, was there any thought about testing time-lagged regressions?

Figures 2 and 3. Units should also be in mm/hr for consistency and comparison to other plots.

128-130. I think you need to restate. I think you are performing 1000 sums, not summing 1000 values. But it needs further clarification – if you have 1000 error estimates for each gap and an average of 22 gaps per year it’s not clear how you come up with 1000 error estimates. And is there an averaging step?

133.  It would be helpful to know the median gap length.

Figure 4. y-axis is runoff, not flow.

164-170. This paragraph would fit better as the next to last in the Discussion -after a more direct discussion of your results.

185. Homoscedasticity misspelled.

197. You could emphasize here, as you did in Intro, that stream discharge records often need to be complete; there is a stronger impetus for gapfilling than with most other environmental data series.


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

Input:
Title: THE REGULATORY GENOME CONSTRAINS PROTEIN SEQUENCE EVOLUTION: IMPLICATIONS FOR THE SEARCH FOR DISEASE-ASSOCIATED GENES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Really solid supplementary data reporting. Only a few notes: Supp Table 3 appears to be a “.tsv” not “.xlsx” (my computer had trouble opening it so just double check that it’s format is corrected). I also feel that it would be a pretty hefty table but a similar .tsv file for each gene that includes the mean, median, and variance in expression for all 53 tissues would be really nice to have too.

Should provide R code used in analysis or a link to it.

Missing some important references with regard to the tissue-specificity in the evolutionary rate/expression relationship. Lots of folks have looked at / questioned this issue of tissue specificity and think the authors could better characterize what is known up to this point. See, for instance:

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131673
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r142
https://link.springer.com/article/10.1186/1471-2148-10-241
https://www.pnas.org/content/104/8/2779
Experimental design: Overall a well defined and well researched paper. Methods section is very well written and it is clear that the authors have a firm understanding of the statistics and statistical issues.
Validity of the findings: Well written throughout and all conclusions are within the bounds of what the authors specifically show. Great job overall.
Additional comments: Summary:
In this manuscript, Evans et al. leverage a large resource of tissue-specific gene expression to investigate the determinants of evolutionary rate variation within humans. Overall, I found the research to be interesting and well-performed, and by and large found the manuscript to be well written. Most of my below points are fairly minor in scope but I’ll nevertheless dump them here for the authors to do with as they see fit.

First the figures: I found these to be a little bit messy overall. I can’t say that any of this stuff *needs* to be addressed prior to publication but in my opinion it could really be cleaned up. Some labels are really tiny/bordering on illegible (legend in 1B, axes and ticks in 2C). Some of the images look a bit fuzzy too, but this could just be a formatting thing at this stage. Figures follow a range of styles, even directly next to each other. See for instance the labels in 2B vs 2C or 4A vs 4B (in terms of whether to bold axes labels, and 4C actually uses a mixture of both). In 3B the “tree depth label” is just kind of hanging there awkwardly. In 4B there should be a legend saying what the two colors are or at least mention these in the caption. Finally, an opinion of mine is that I think the manuscript could be strengthened with some example data in Fig. 1. The data presented throughout is kind of abstracted from the basic level of essentially comparing scatterplots/correlations between variables. I feel that two example scatterplots for like the strongest and weakest rho tissues could help to show what these relationships actually look like rather than just always thinking of them as rho’s and p-values. Clearly can’t/shouldn’t do it for everything but examples always help with interpretation.

Line 47 – “A second engine of protein evolution, fixation of new mutations depends upon effect on fitness, genetic drift, and population size.” – probably better stated as something along the lines of “depends upon the fitness effect of the relevant mutations and the balance between selection and genetic drift, which is in part mediated by effective population size.”

Line 52 – Authors note that the assumption of dS being fully neutral is likely violated, think I would just draw a bit more attention to it with some references. But state that the reality is that in spite of the over-simplification of dN/dS it’s still one of the most commonly used and “acceptable” frameworks. I also feel like this paragraph is better suited to the discussion section, especially since dN/dS is so commonly used and the authors aren’t actually performing their own evolutionary analyses and rather are using the values from biomart. At very least think this section of the intro could be cut down as we’re in nitty-gritty protein evolution methods territory quickly before really getting to the actual problem the authors want to address.

Line 57 – Looks like the period is red.

Line 60 – Feel like there should be a lead in / discussion more about single-celled organisms. A lot of early protein evolution work was done on single-celled yeasts and bacteria. But the presence of tissues with unique expression profiles makes studying similar processes difficult in multi-cellular eukaryotes, a discussion of which would lead well in to this paragraph.

Line 68 – I really like this paragraph. But also think it’s another opportunity to better frame the research by questioning what “expression level” means for multi-cellular/multi-tissue organisms with long-lifespans and developmental processes (in contrast to, again single-celled organisms). As is obvious by this point, this is what I see as the big outstanding question that this paper really seems to be addressing without ever really explicitly stating it.

Line 343 – The beginning of this results section is really jarring and feels tacked on by a previous review or something. The first line there just kind of jumps out and I think the readability of the manuscript would be much improved with a brief re-iteration of what the major points of the analysis are here. My guess is that ~1% of the readership of the paper will likely read through the methods so throughout the results section I’d encourage the authors to write as if that were the case by re-iterating basic steps of the analysis at a high level to help readers follow the logic. i.e.:
“We compiled RNA-seq samples for 53 human tissues to estimate the range of expression patterns experienced for each gene (the number of samples for each tissue can be found in Supplementary Table 1). To assess evolutionary conservation, for each orthologous gene we estimated dN/dS rates by comparing human sequences separately with chimpanzee and mouse sequences. The human-chimp comparison may be more…”

Line 348 – “Rate…”=> “The rate…”

Line 349 (and 351, 352, 353) – It’s a bit unclear what the p-value there is, is it a meta-p-value for all 53 tissues? Or the p-value for the strongest or weakest correlation? This appears throughout when the authors are presenting a range of values and I think an explanation should just appear in that first one.

Line 350 – “with (mean? median?) expression level in all 53…”

Line 535 – This is a really nice section that you often wouldn’t find in similar work.


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

Input:
Title: THE REGULATORY GENOME CONSTRAINS PROTEIN SEQUENCE EVOLUTION: IMPLICATIONS FOR THE SEARCH FOR DISEASE-ASSOCIATED GENES
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment.
Experimental design: no comment.
Validity of the findings: no comment.
Additional comments: The authors performed a GTEx transcriptome analysis across multiple tissues to assess the effect of the transcriptome in protein sequence evolution. They analysed several expression-based models of protein evolution across tissues, examined the potential of this approach to be used to identify disease-related genes, and discussed the methodological implications for transcriptome-wide association studies of disease. The authors propose a tissue-based model of protein sequence evolution, where the correlation between gene expression levels and evolutionary rate varies significantly by tissue.

This study delivers a very sound approach to better assess and quantify the effect of gene expression on protein sequence evolution, with implications for the prediction of disease-associated genes. I just recommend clarifying the below-mentioned issues before publication.

As a general comment, throughout the manuscript, you use two types of divergence without any explanation of why you use one or the other (except for disease-associated genes). For most of the analyses, you use the human-mouse divergence data, but it’s unclear why.

Minor comments:
Introduction:
Lines 47-48: unclear sentence, I propose to rephrase it as: “The fixation of new mutations depends on its fitness effect, (…)”.

Lines 54-56: This sentence needs to be clarified. Using the dN/dS ratio is a conservative approach because it only provides an average of the substitution rate across a certain number of sites. Since most of the amino-acid mutations are either neutral or deleterious, dN/dS will generally be lower than 1, hence potentially overlooking positions under positive selection.

Methods:
Line 93: Were the inter-individual variability analyses performed on human individuals? If so, how many? This is not clear in the text.

Line 99: define “LCLs” here, you have it only in the results section.

Line 107: define “PEER” here, you have it only in the results section.

Line 208: by correlation in gene expression, you mean genes that belong to the same gene network?

Lines 221-223: if I understood correctly, you mean here that you use the GLS to account for the non-independence of genes in a gene network, like in a phylogenetic statistical approach, is that right? If so, it needs to be better clarified. It may not be straightforward for the reader to understand this.

Lines 284-285: this sentence is unclear to me. What do you mean by modifying the germline genetic profile? I thought that the software only provided a prediction for the association with a disease trait.

Results
Lines 348-354: If I understood correctly, you estimated the mean dN and dN/dS across genes in a tissue. Why not use the median here? Were these estimates corrected for the number of genes expressed in each tissue? Just for a sanity check, you could perform the same analyses by randomly downsampling the same number of genes in each tissue (say 100 times) and then estimate the mean value dN and dN/dS of the bootstrap replicates.

Lines 376-378: This sentence could be simplified. You could say something like, “The tissue patterns of the correlation of gene expression with synonymous divergence differ from that with non-synonymous divergence”.

Lines 381-384: Not very clear. Do you mean that the correlation between expression levels with the synonymous substitution rate for each tissue is stronger when using the human-mouse divergence?

Line 397: population structure between which populations?

Line 399: what do you mean by the impact of batch effects?

Lines 425-428: I don’t understand how the Kruskal-Wallis test was performed here. Which groups are you comparing? And what do you mean by associated with the evolutionary rate? Do “MaxTissues” have genes with higher evolutionary rates in general?

Line 434: I would remove “namely” from the brackets to make it clearer.

Lines 434-436: confusing, do you mean significant variance in dN/dS between genes in a MaxTissue? 100 of what? Do you mean the 100 genes with the highest expression variance?

Line 493: I would replace “that capture” with “of” to simplify the sentence.

Lines 497-500: I would split this sentence after “heritable component”, and start “For many genes (…)”.

Line 573: how was this estimated?

Discussion
Line 636: missing the direction of the correlation (positive).

Line 708: “the use”.

Figures
The figures are quite hard to see as the quality is not very good. I recommend improving this issue before publication.

Figure 1A: which divergence did you use in this plot, human-chimp or human-mouse?
Figure 3A: which statistical test was used?
Figure 4B: what do the colours represent?


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: PREDICTION OF HUMAN FETAL–MATERNAL BLOOD CONCENTRATION RATIO OF CHEMICALS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors have reported to develop a first valid quantitative structure-activity relationship (QSAR) model following OECD guidelines based on multiple linear regression to improve prediction of in vivo human fetal-maternal blood concentration ratio (logFM) of chemicals.
This study is overall well designed and the manuscript is well written.There are a few items that need to be addressed in order to further improve the quality of the paper.

1.	All the abbreviations such as OECD, AATSC1c should be defined at the first instance of using them.
2.	line 107-108, please explain the biological reason the rule of the feature selection:  2) more than or equal to 50% zero values (scarcity), and 3) small variation (less than 8 unique values).
3.	Please give the reference of Eq. 1.
4.	line 146, Eq. 2. should be interpreted with the biological reason such as what the meaning of negative-valued in the prediction model.
5.	line 156, background of y-randomization test should be given to explain why using it to test the model?
6.	line 175-179, the authors should explain the 3 exclusion rules were selected to exclude chemicals out of AD. For example, 3 corresponding chemicals (Mifepristone, Didanosine, Diazepam) were identified to be out in training dataset while 3 compounds (chloroquine, didanosine, and DDE) were considered outliers because they have more than two of the standardized residuals (Takaku, T. etc. 2015).
Experimental design: To clarify the importance of the features used in multiple linear regression analysis, the standard partial regression coefficients should be calculated.
Validity of the findings: Any limitations to use this model needs to be discussed.
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: PREDICTION OF HUMAN FETAL–MATERNAL BLOOD CONCENTRATION RATIO OF CHEMICALS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written in general.
A few suggestions:
1) cite original data source of the in vivo fetal-maternal blood ratio of 55 chemicals.
2) Add legends to figures (e.g. color label, Y/N meaning).
3) Include a supplementary table for all the original 1444 descriptors.
Experimental design: 1) Correlation coefficients of descriptors should be checked to avoid the multicollinearity before feature selection.
2) It's not clear if the authors did Feature Scaling? if so, which method used? Feature Scaling is important for linear regression. With feature scaling, the first 3 steps of feature selection may not necessary to apply.
Validity of the findings: 1) Could the authors give some explanations/discussions  on why the two descriptors (AATSC1c and ZMIC1) are informative, any biological significance behind them?
2) Since the current study used the same dataset and algorithm for predicting the same biological question (DOI: 10.1248/bpb.b14-00883), the author should discuss more about how and why the predicting performance improved.
3) Previous research identified MW, Hmax and TopoPSA as the best descriptors. Did these three descriptors identified as well in the original 1444 descriptor set? why they are not been picked up after feature selection?
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: THE EFFECTS OF “FANGCANG, HUOSHENSHAN, AND LEISHENSHAN” HOSPITALS AND ENVIRONMENTAL FACTORS ON THE MORTALITY OF COVID-19
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	This paper requires proof-reading from a native speaker. Specific comments are listed below:
Line 18/19 – split sentence
Line 20 – of data --> be more specific
Line 20 – either the “China National Health..” or the Chinese
Line 21 – “standard forms” --> be more specific
Line 27 – define U
Line 31 – significantly correlated: it should be pointed out that it is a negative correlation, the warmer the temperature, the lower the mortality rates. Otherwise, this implies that it is a positive correlation.
Line 34 – here patients is better than cases
Line 42 – delete additional space
Lines 43/44 – delete “that”
Line 46 – add comma after Wuhan
Line 49 – further compressed instead of would then further compress
Line 49 – options instead of space
Lines 54/55 – better: we assumed that differences in AT in different regions might have contributed to the unbalanced mortality rate
Lines 57/58 – better: the first three makeshift hospitals (MSHs) …. had been put into operation starting 5th of February 2020
Line 59 – hospital or hospitals?
Line 62 – build on the spot instead of can rush to the scene
Line 63 – investigate rather than research
Line 65 - patients instead of cases
Line 69 – missing: 2020
Line 69 - each day’s….--> better: daily total number of confirmed cases by nucleic acid testing, the daily numbers of severe cases and deaths in Wuhan city …were independently collected by two authors.
Line 72 - of the National…
Line 75 - better: the daily mortality rate…
Line 78 - from the Chinese Weather Net
Line 80 – be more specific, how many cities? Is average or median better?
Line 88 – had a skewed distribution instead of was skewed distribution
Line 101 – daily number of confirmed cases…
Line 103 – had a skewed distribution
Lines 107/109/110 – in contrast
Line 113 – are shown
Line 116 – split sentence
Line 123 – sentence is not clear, please restructure
Lines 125/126 – the growth rate of confirmed cases was not significantly correlating with AT in Wuhan or the Hubei region
Line 128 – point out negative correlation also in the written text
Lines 127/128 – sentence is not clear, please restructure
Line 130 – this means that
Line 135 – patients not cases
Line 135 – was significantly decreased in contrast to a non-Hubei region
Line 137 – patients not cases
Line 138 – patients with mild symptoms instead of light patients
Line 140 – rescue patients with severe symptoms
Line 141 – through which MSHs worked
Line 144 – however, this difference became also significant in a non-Hubei region
Line 148 – this means that SARS-CoV2 with weak virulence
Line 148 – split sentence
Line 153 – define common?; cases instead of patients
Line 154 – the first deaths that occurred were mainly
Line 158 – exposure coincided with
Line 161 – patients instead of cases
Lines 162-164 – please restructure sentence
Line 166 – when the climate was relatively cold and dry
Line 169 – might have been instead of was
Line 170 – rises instead of gets higher
Line 176 – please delete “as far as we are concerned”
Line  179 – to future research
Lines 170-185 – please move them to the discussion and do not leave in the conclusion part
Line 188 – infectivity of SARS-CoV2
Line 189 – please restructure, not clearly written
Table 1 –heading: daily instead of each day; cross “daily” in the sub-heading
Table 2/3 – please use a different title which refers to the data being analyzed; difference of what?
Fig. 2 – Regions instead of Rejions

2.	Please refer to difference of mild and severe cases in the introduction
3.	Please define the difference of mortality rate vs. mortality rate of severe cases
4.	Please explain also important parameters in the introduction e.g. growth rate
5.	Please define non-Hubei regions. Are these far away from the Hubei region or close     to it?
6.	Please add a summary sentence after each result section.
Experimental design: 1.	It is not clear whether the data is only derived from the three MSHs or also from regular hospitals. This difference should be made in order to promote that MSHs reduced growth rate / mortality rates.
2.	The rational for 8 days and 16 days before/after MSHs is not clear and the number of 32 days included in the study is rather small. Thus, including more timepoints also in the graphs, especially after the set-up of MSHs, would increase the power of the study. This should then be presented in a combined figure over time.
3.	Only AT was considered for this study. How about humidity?
4.	It would help a lot if lines 75-78 are presented as equations
5.	It is not clear which non-Hubei regions were chosen and its distance to the Hubei region. This should be specified.
6.	In order to point of that MSHs make a significant difference, data derived from single non-Hubei regions (closer and more distant to the Hubei region) should be included in the study.
7.	The present study would gain a lot when the authors point out differences in mortality / growth curve to AT among patients of different age or with pre-existing diseases. Is there a trend that AT is not relevant for younger COVID-19 patients compared to older patients?
Validity of the findings: 1.	Please add a short overview of the underlying analyses in the Figure legend so that they are self-explanatory
2.	Please contact a bioinformatician whether median and then showing box plots is more informative.
3.	Remove the lines in the figures 1 and 2 as there is no connection between the data sets
4.	It is not clear which data sets are used for the p-value analyses
5.	Please plot the R values also for Fig. 3A and B and make a correlation also for the non-Hubei regions in respect to temperature
Additional comments: 1.	The authors claim that the MSHs have a clear effect on mortality rates, yet analysis of non-Hubei regions without MSHs showed that reduction in growth rates and mortality rates are similar after 16 days, regardless where the cases originated. Thus, their statement “The positive results of our analysis would be of great significance to the current anti-epidemic work and would provide much guidance to the future researches.“ is not convincing.
2.	Please discuss other factors that might influence decrease in mortality rates
3.	Please discuss more papers that have studied environmental factors on the SARS pandemic:

e.g.
Lin K1, Yee-Tak Fong D, Zhu B, Karlberg J. Epidemiol Infect. 2006 Apr;134(2):223-30. Environmental factors on the SARS epidemic: air temperature, passage of time and multiplicative effect of hospital infection.
Bi P1, Wang J, Hiller JE. Intern Med J. 2007 Aug;37(8):550-4. Epub 2007 Apr 16. Weather: driving force behind the transmission of severe acute respiratory syndrome in China?
Tan J, Mu L, Huang J, Yu S, Chen B, Yin J. J Epidemiol Community Health. 2005 Mar;59(3):186-92. An initial investigation of the association between the SARS outbreak and weather: with the view of the environmental temperature and its variation.
Yip C, Chang WL, Yeung KH, Yu IT. J Environ Health. 2007 Oct;70(3):39-46. Possible meteorological influence on the severe acute respiratory syndrome (SARS) community outbreak at Amoy Gardens, Hong Kong.


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

Input:
Title: THE EFFECTS OF “FANGCANG, HUOSHENSHAN, AND LEISHENSHAN” HOSPITALS AND ENVIRONMENTAL FACTORS ON THE MORTALITY OF COVID-19
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well-writing, clear and unambiguous with relevant results.
References are fair.
There is only an inconsistency in the phrase "The growth rate of confirmed cases was
106 significantly decreased both in Wuhan (U = 27, P = 0.023) and Hubei (U = 23, P =
107 0.012), but in non-Hubei regions, as a contrast, changes were also significant (U = 3, P
108 < 0.001).", because non-Hubei regions also had significant p-value, so the "but" and "as a contrast" are ambiguous.
Experimental design: Aims and scope are well-defined.
There are some observations about the methods.
First, the normalization of ratings needs to adjust values measured on different scales to a notionally common scale, Although, for instance, authors may have break the cummulative growth of the data by the way they calculate it "Growth 74 rate of confirmed cases was calculated by dividing the new confirmed cases by the total 75 confirmed cases on the previous day.", the variance does not have a standard for all the range, so authors could use t-tests.
The author also should be aware of outliers in data, so they could hand it, because the data is too small and cannot support outliers.
After all, the violation of Independent samples/groups may be considered. For instance, the group "before" can influence the group "after", since the infected subjects can transmit to other subjects. In this case, a paired t-test may be used.
Validity of the findings: There are relevants impacts with conclusive results and meaningful replication. All underlying data have been provided.
Additional comments: It is an important article, reasonably well written and with findings of interest to public health policy makers. However, the methods need to be 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: THE EFFECTS OF “FANGCANG, HUOSHENSHAN, AND LEISHENSHAN” HOSPITALS AND ENVIRONMENTAL FACTORS ON THE MORTALITY OF COVID-19
Review round: 2
Reviewer: 1

Output:
Basic reporting: Although the English has improved, this manuscript still requires final editing by a native speaker. Incomplete sentences, weird phrases as well as punctuation mistakes are often found throughout the improved manuscript. Lines 181-183 should refer to AQI and not RH, which is stated as not significant in lines 174-178. Line 272 - please be more specific what "many other factors" are.
Experimental design: no comment
Validity of the findings: The figure legends have improved, yet please add more detail to the figure legends - they are still not self-explained.
Please add in Figures 4-6 the correlation of growth rate / mortality to  AT, RT, AQI for data derived from the non-Hubei region.
Additional comments: The authors have significantly improved their manuscript and taken into account the suggestions made after the first submission. Minor changes should still be included prior to accepting this manuscript 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: THE EFFECTS OF “FANGCANG, HUOSHENSHAN, AND LEISHENSHAN” HOSPITALS AND ENVIRONMENTAL FACTORS ON THE MORTALITY OF COVID-19
Review round: 2
Reviewer: 2

Output:
Basic reporting: Basic reporting adjusted.
Experimental design: I agree with the authors about the paired t-test as pointed out in their rebuttal letter: "the paired t-test is used to compare two sample means where there is a one-to-one correspondence (or pairing) between the samples. While in our study, although the group “before” might affect the group “after”, the specific impact was unclear; this means that there might be no one-to-one correspondence between group “before” and group “after”. In addition, when we tried to compare the difference 16 days before and 8 days after the use of MSHs, the sample sizes of the two groups were not equal. " I would like to thank the authors for considering it.
Validity of the findings: The paper is in accordance with journal standards.
Additional comments: Congratulations to the authors.
All my comments for review were considered by the authors.
I am pleased with the results. The paper was improved above my expectations.


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: IDENTIFICATION AND EXPRESSION PATTERN OF CHEMOSENSORY GENES IN THE TRANSCRIPTOME OF PROPSILOCERUS AKAMUSI
Review round: 1
Reviewer: 1

Output:
Basic reporting: The Background part need to be improved. The latest progress of all olfactory genes should be added.
Experimental design: The tissues used to qPCR analysis is quite few.
Validity of the findings: Obtain some novel olfactory genes in the Propsilocerus akamusi. However, the number is quite low.
Additional comments: Major concerns,
1.	The phylogenetic trees should be constructed, adding some flies and mosquitos, and then the newly identified gene functions can be inferred.
2.	The olfactory gene numbers are remarkably lower than other mosquitos. Why?
Minors,
1.	Line 31, Give the full name of CDS
2.	Line 37, Change “feet” to “leg.” Revise the whole MS.
3.	Line 46, The blank should be added between the reference and the text. Revise the whole MS.
4.	Lines 67-82, should add some lastest progress in these genes.
5.	Lines 102-104, Did all tissues collect from male adults? And which days after eclosion? Should clarify.
6.	Line 186, which dipteran species did you select? Should state the Blast parameters.
7.	Line 199, why did you select tubulin as the reference gene? Is it stable across tissues?
8.	Line 200, which one-way ANOVA test did you use?
9.	Line 280, according to the nomenclature rule, the chemosensory genes in insects should be named PakaOBPs, PakaORs, etc.
10.	Line 286, not “interestingly,” many OBPs are expressed only in antennae.


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: IDENTIFICATION AND EXPRESSION PATTERN OF CHEMOSENSORY GENES IN THE TRANSCRIPTOME OF PROPSILOCERUS AKAMUSI
Review round: 1
Reviewer: 2

Output:
Basic reporting: The author carried out a transcriptome sequencing of P. akamusi. This is interesting study because of the ecology and environmental importance of this insect species.  These are clearly introduced. After went through the MS, I believe the MS failed to meet PeerJ standards and decided not to check the literature reference (see below).
        English needs to be improved throughout the MS to ensure that an international can clearly understand your text.  Some examples are given below.
        Figures are not very clear. The legend of Figure 2 is completely wrong, which is completely unacceptable because it demonstrates the authors do not read their MS carefully and professionally before submitting to PeerJ.
Experimental design: The experimental design is interesting. The authors started with the mating behavioural study and demonstrated an interesting result; males rather than females exhibit the attraction to females which are insensitive to males.  This is another strengthen of this MS. The authors decided to sequencing the transcriptome of male olfactory tissues. Unfortunately, the authors missed out the importance of control experiments. First, the analysis of female tissues should be included along with the male tissues. Second, a non-olfactory tissue should be included for the analysis of gene expression with 2-ΔΔCt method correctly. These make the authors the biological aspect of the data, and the possible correlations between the behavioural results and the transcriptome analysis.
         The relative expression levels are presented in all RT-qPCR results as ratio of target gene expression /reference gene expression. This is not correct. In the 2-ΔΔCt method, a reference (1st delta) to normalise the expression of a target gene and non-olfactory tissue (2nd delta) to calculate relative expression as fold change.    As the main experimental technique of the current study is the real-time qPCR, I would strongly urge the authors to reanalyse the data by using two reference genes and to study the commonly accepted MIQE guidelines on minimum information for the publication of quantitative real-time PCR experimental data (Bustin et al. (2009) Clin Chem 55,611).
Validity of the findings: The presence of chemiosensory genes in the genomes of Dipterans is not surprising.  The identification of them in P. akamusi is expected and not novel. The knowledge gap that this study provides in more such genes and their expression in olfactory tissues is makes the MS becomes another descriptive transcriptome sequencing MS, and provides no advance in olfaction research.
Additional comments: The description of Methods such as cDNA synthesis, bioinformatics analyses is too generalized. More details related to this insect species and experimental conditions are needed. Some examples are given below.
For above reasons, I would not recommend for the MS to be accepted for the publication in PeerJ.

Other points are listed below.
Line 32. “gene analysis showed little difference …in the three types of tissues”. However, DEG analysis shows > 1500 differential expression. This is not little difference.
Line 37. “17 odorant receptor (head 4; antennae 5)…”. The number in () does not match the total number.
Line 47. What dose “their high species richness” means?
Line 103. I suggest include another non-olfactory tissue for RT-qPCR analysis correctly.
Line 108. Change “fly” to “flies”. Please check all grammar mistakes in the MS.
Line 116. Please check grammar mistake.
Line 116. Experimental design. How to keep a live insect in an arm to attract another insect.
Line 134. “cDNA was synthesized …”. Please give more detail.
Line 135. “short fragments were purified…”. Please give details how they are purified and under what condition.
Line 138. Please give more details on quantification and qualification of the libraries.
Line 147. what does "low quality reads, defined as those in which >20% of the base had a quality <15” mean?
Line 150-154. Please do not explain how Trinity works if you have no idea how it exactly works.
Line 155-156. So the outcome of your Trinity assembly is a list of unigenes with either CL or unigene as their prefix. Is it true?
Line 161. How did you use BLAST to annotate unigenes into COG and GO databases? Please all websites of the software you used.
Line 165-166. This not the way to define CDS of a gene.
Line 168. what is the rational for this analysis? Do SSRs involved in insect olfaction?
Line 198. a reference gene (1st delta) and non-olfactory tissue (2nd delta) should be used. In this method, a reference (1st delta) to normalise the expression of a target gene and non-olfactory tissue (2nd delta) to calculate relative expression as fold change.
Line 199. Two reference genes should be used.
Line 205. Please check English in “To test the mate selection behavior reaction of individual male insects”
Line 232. What do you mean by “the distribution of annotated species is statisticed”
Line 262-263. An interesting result on SSRS but what do they implicate? any olfactory function.
Line 268. The feet are also sensory organ as you stated in the Introduction so it is better to compare with a non-olfactory tissue.
Line 279-280. What criteria to define “34 transcripts that encoded candidate OBPs”
Line 248. “with five expressed higher in the antennae” relative to which tissue?  Please check other sentences.
Line 298. Please change “transcriptomes” to transcripts.
Line 311. I would be more interested in the comparison between these three SMNPs with those of mosquitoes and Drosophila.
Line 335. incomplete discussion, which PaOBP is homologous to AmelOBP21?
Line 387-388. All transcriptoe sequences and unigene sequences should be deposited into a GenBank database.
Table 1, Table 2 and Table 3. What do “A, B, C2” stand for?
Figure legends need more detail description.
Figure 2 has a wrong legend.
Figure 6. It is not clear what comparison the Figure displays. The DEGs are relative.
Figure 7-11 (all RT-qPCR results). Relative expression of a gene should be fold change between target tissue and reference tissue after the normalization with the expression of the reference gene.


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: IDENTIFICATION AND EXPRESSION PATTERN OF CHEMOSENSORY GENES IN THE TRANSCRIPTOME OF PROPSILOCERUS AKAMUSI
Review round: 1
Reviewer: 3

Output:
Basic reporting: Please see the "General comments for the author"
Experimental design: Please see the "General comments for the author"
Validity of the findings: Please see the "General comments for the author"
Additional comments: The manuscript by Yan and colleagues surveys a transcriptome assembly generated with Illumina HiSeq platform of P. akamusi, which obtained 27,609 unigenes, 20,379 CDSs. In addition, they also identified some candidate olfactory-related genes and their relative abundances in the three tissues (antennae, head and feet). The organism is important and the goals of the study are sound. Although I feel that there is some value to this study, there are some methodological and analytical shortcomings that the authors must address before a decision can be made about the suitability of this manuscript for publication. My comments are below.

1.	The abstract does not tell the reader anything about mate selection behavioral test which is the first part of your results. It should be concerned in the abstract.
2.	Some titles in the “Materials & Methods” section are the same as the titles of the “results”, such as “2.2. Mate selection behavior test” and “3.1. Mate selection behavioral test”.
3.	The authors must state here how many individuals were subjected to the RNA preparation and cDNA library construction.
4.	The integrity of the RNA samples (e.g. RIN) is not given. This becomes crucial in the results as there are concerns about RNA integrity.
5.	What is “clean reads” (line 222) ? Please clarify.
6.	No software version numbers or parameters are given for the de novo assembly the downstream clustering with tgicl. More details on the specific run-time parameters used should be given in all instances.
7.	It is recommended to unify the expression of “leg”, in some sentence the author used “foot”.
8.	Please recheck the comments of Fig.2 and Fig.3.


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: IDENTIFICATION AND EXPRESSION PATTERN OF CHEMOSENSORY GENES IN THE TRANSCRIPTOME OF PROPSILOCERUS AKAMUSI
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have made a lot of changes and improvements. It is suggested to accept.
Experimental design: no problem.
Validity of the findings: The authors have made a lot of changes and improvements. It is suggested to accept.
Additional comments: The authors have made a lot of changes and improvements. It is suggested to accept.


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: RDRP MUTATIONS ARE ASSOCIATED WITH SARS-COV-2 GENOME EVOLUTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is mostly well written and referenced. I have some suggestions of modifications to be made on text, tables and figure presentations (explained below, at the general comments for the author)
Experimental design: The research theme is very actual, relevant and interesting. The experimental design seems rigorous enough and is also described with sufficient details for understanding and replication.
Validity of the findings: It seems to me that the authors performed an honest and robust analysis and that their fundamental conclusions are consistently based on the generated results.
Additional comments: I consider that the manuscript entitled “RdRp mutations are associated with SARS-CoV-2 genome evolution” contains important and relevant new information, which will have impact on the understating of SRS-CoV-2 worldwide spreading, evolving and adapting. The authors made good and extensive use of public available sequence data on SARS-CoV-2, constructed an interesting hypothesis on the relationship between occurrence of RdRp mutations and overall virus mutation rate and also performed a consistent and robust statistical analysis in order test it.
I have some observations regarding main text structure and results presentation which, I believe, will collaborate to improve the readability of the manuscript.

1. As, by the final of results/conclusion section, the authors make interesting considerations about emergence and spreading of SARS-Cov-2 mutations, I recommend the inclusion of information regarding time and origin of the reference viral genome sequence (NC_045512.2), as it is important as a referential point to this analysis.
2. I believe it would be very interesting and visually informative if the authors could transform the textual time/geographic information about SARS-Cov-2 mutations seen on the final paragraphs in a third figure, containing a map of the globe, dates and supposed directions of spreading between continents.  It is just a suggestion, but I think it would make a nice ending to the manuscript.
3. Figure 1. The information regarding gene names and colors is already present below the X axis. So, it is not necessary at all for it to appear in a legend.
4. Tables 1 and 2 have very important data, but it is somewhat difficult to discern the relationship between presented values, as there are a lot of columns and numbers. As it seems that the percentage values are more important to interpret the data, I suggest the authors to adjust the presentation of theses tables by displaying values of percentage with sample size within parentheses.
Thus, data in the first row would appear this way:
    38.4 (3905)       27.7 (2888)        37.4 (4193)
This way it will be easier to the reader to compare the values and understand the table.

Next, I present a list of comments, remarks and suggestions that, I hope, will improve the understanding of the text.

Row 65: You probably means " (...) not yet fully known".

Row 87: The end of this sentence is confusing. I think it means "(...) multiple forms of virus, varying on their mutation rate across the globe", or something similar.

Row 91: Consider changing "a" for "with".

Row 96: Consider changing sentence to "(...) under locus ID NC_045512.2".

Row 98: Consider changing sentence for " (...) which are not A, C, G, T, N, or -)".

Row 140: Please replace comma (,) for an end (.).

Row 144: Although it appears later in the text, it would be good to briefly explain here why this mutation is of interest.

Row 151: In order to improve the reading, I suggest to change this sentence to "Two of the top 50 sites were found (...)".

Rows 167-168 and 169: I suggest to list the nucleotides in crescent order.

Rows 190 to 192:  The structure of this sentence is somewhat strange. Please, consider to revise it.

Rows 208 - 210: The same as above. The structure of this sentence is also somewhat strange. Please, consider to revise it.

Row 236: Please insert reference for these studies.

Row 240: Seems to me improbable (but not impossible) that a single nucleotide position will modulate the interaction of viral genome with host factors. It would be more adequate to say that "It is possible that 15324C may be part of a DNA motif that modulates the interaction of viral genome and host factors", or something similar.

Rows 264 to 266: Please consider to revise sentence construction. I think it would be better if it reads "However, unless mechanistic insight arises that could explain how this particular mutation could lead to higher transmissibility, other explanations based on stochastic factors are equally possible.”.

Row 266: Insert "et al."

Row 272: Please insert the reference/code for the Italian isolate, as shown above for the Chinese one.

Row 277 - 278: The segment "(...), unless completely confined and eliminated," sounds strange and not related to the whole sentence. Please revise it to improve the understanding.

Row 286: Consider changing it to "Also, mutant RdRp may turn the virus more resistant to anti-viral drugs, such as the commonly used remdesivir.", as drug resistance is relative to the virus, not the polymerase.

Row 384: There is unnecessary redundancy of the world protein in this sentence. Consider changing it to “Bar graph of percent of isolates per region containing non-reference coding sequences for the envelope glycoprotein (E), membrane glycoprotein (M), and RdRp protein.

Finally, hoping that the authors will carefully consider my recommendations, I consider that the manuscript should be accepted for publication by Peer Journal with minor revisions and without need to re-review it. In the urgent context of Covid-19 pandemics, I think it is important that this information can be available to scientific community as soon as possible.


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: RDRP MUTATIONS ARE ASSOCIATED WITH SARS-COV-2 GENOME EVOLUTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors describe the importance of the mutations found in RNA-dependent RNA polymerase (RdRp) in relation to the genetic variation found in SARS-CoV-2. These are related to the evolution of virus variants according to mutation rates. The authors are also related to mutation rates found with regions of the world where the genome has been sequenced. The description of this molecular mechanism is essential to understand how SARS-CoV-2 is spreading around the world and opening perspectives on possible drug developments used. The professional language in English is consistent, as are the results presented through graphs and tables. The hypothesis discussed is in accordance with the data presented and with the literature provided in the manuscript.
Minor revision should be paid attention to the formatting of references, as some references that do not have the DOI number and in italic letter, are not all in the same pattern according to the journal. Throughout the text there are also grammatical errors in punctuation.
Experimental design: The research data is within the scope of the paper and defined in the materials and methods. Despite the research supplanting and adding interesting data in research related to SARS-CoV-2, with methodologies that can be replicated, there are some doubts. In figure 2, related to the percentage of isolates by region in relation to the studied targets and, according to table 2, the South America region has the highest percentage of mutants in RdRp, but have the lowest number of sequenced genomes. The authors should discuss more about this result, in which it remains valid, but qualitatively different from other regions. In addition, include in the materials and methods the number of sequenced genomes of each region, facilitating the reading and interpretation of the results.
Validity of the findings: There is no need to repeat the experiments, being well analyzed according to the existing literature. But, in some parts of the text, the actors associate genetic variations in SARS-CoV-2 with “epidemiological factors”, but do not quote and describe them. It is important to include these factors in the text, even if they are not addressed experimentally. The conclusions are in line with the discussion and linked to the central research of the work.
Additional comments: The work sent to PeerJ - the Journal of Life and Environmental Sciences addresses in a solid way the relationship of mutations in RdRp with the evolution of the SARS-CoV-2 genome. Despite a scarce literature, it is noted the importance of genomic studies and their aspects and relationships with the dispersion throughout the world of the COVID-19 virus. The text, despite small revisions to be made, manages to associate, discuss, and associate the analyzed results.


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: DETECTING THE OUTBREAK OF INFLUENZA BASED ON THE SHORTEST PATH OF DYNAMIC CITY NETWORK
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this paper, the authors proposed a method for identifying the dynamic network marker of influ outbreak. This is an important and challenging research topic. The number of the patients are not fully collected and some of the most important literature have not been cited. The prediction results are not clearly presented.
Experimental design: The experiments of building up a concept of dynamic network marker for influenza outbreak need be modified to de novo predictions. It is a time series and sequential data prediction. The sliding prediction with the time points need be implement to show the efficiency of the proposed method.
Validity of the findings: As claimed in the former comments, the validity of the results need be justified by more experiments. Moreover, the authors have cited some of the existing method. It is not clear what is the difference and improvement of this method compared to the other existing ones. For instance, the methods described in Ref. 14. Moreover, it is not clear the method listed in the other similar references Ref. 20-24.
Additional comments: In this paper, the authors developed a method for predicting the outbreak of influenza. This is an important topic for public health. Beyond the other comments listed above, I listed some comments here for consideration. First is about the network. The paper claimed the network model. However, it is not clear about the network property, such as the node and edge. The graph should be complete. The present graph is strange. What is the prediction? If only using the number of recorded patients, the traditional methods such as autoregression and many others in statistics can do this job. And the comparison with them is expected to show the necessity of building up a new method. Second is about the dynamics. In my understanding, the numbers of every hospital/city is dynamic and the movements of them and the linkage between the cities are also time dependent. It is not very clear how to include this important dynamics in this prediction. Third, the presentation need be improved. For instance, the discussion seems to be another result. The language need further polished before publication.


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

Input:
Title: DETECTING THE OUTBREAK OF INFLUENZA BASED ON THE SHORTEST PATH OF DYNAMIC CITY NETWORK
Review round: 1
Reviewer: 2

Output:
Basic reporting: In figure 3b, the columns may be mislabeled. Please carefully examine the column names.
Experimental design: no comments
Validity of the findings: no comments
Additional comments: The authors propose a new computational framework to forecast the outbreak of flu. It is interesting for the finding that changes of shorted paths between two points of a weighted city network are predictive of a flu outbreak. Two minor concerns should be further clarified before publication.

1. The significance of the finding should be further discussed. In particular, the authors should sufficiently discuss the advantage of the new finding over traditionally used metrics such as the incidence of flu.

2. "outbreak" can be further quantified, i.e., the quantitative relationship between the signals and the "outbreak" consequences can be further quantitatively evaluated.


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: DETECTING THE OUTBREAK OF INFLUENZA BASED ON THE SHORTEST PATH OF DYNAMIC CITY NETWORK
Review round: 1
Reviewer: 3

Output:
Basic reporting: In this study, the geographical districts/cities, Hokkaido and Tokyo, are in Japan. Please mention in the text that Hokkaido and Tokyo are located in Japan.

Line 38: Please revise “in the U.S.”

Line 166: Please revise “was based on”.

Lines 186-187:  It says: ”Both the two datasets have been normalized by dividing the number of wards in a region.” In Figure 1 (A), it says “Normalized by: data (t) = total hospitalization count / clinics count”. Please check and clarify the terms: “clinic count”, “clinic visits”, “hospitalization”, and “wards”. When speaking of health care systems with possible differences between various countries worldwide, are these “clinics” hospitals (specialized care: wards? outpatient clinics?) and/or primary care encounters (health care centers?) or what kind of clinics? Please consider describing briefly the Japanese health care system in terms of these “clinics”.

Lines 198-202: There are different paths to nodes (Kita-ku, Minato-ku, Suginami-ku, Katsushika-ku, Nerima-ku, Edogawa-ku, Adachi-ku, Setagaya-ku). Please consider using bold font or italics with these Japanese words.

Line 220: Please revise “seen in Figure 4 that”.

Lines 281 and 219: Please revise “based on”.

Line 339: Please revise “human lives”.

Both “clinic visits” and “clinics visits” are used in the text. Please choose “clinic visits”.

Figure 1: This Figure 1 seems to be in the end of the manuscript but Figure 1 is not mentioned in the text at all.

Figure 1, legend: It says: “covering 53 districts…”. However, in Figure 1 (A), there are 23 districts and 30 cities mentioned. Are these districts or cities? Please revise.

Figure 1 (A): A typo “peopele”. Please revise “people”.

Figure 1 (C): The text around the pattern is too small to be read.

Figure 3: The first line of the table B: The title of regions 13-23 seems to be wrong. Please change the order between “Region” and “Code”.

Figure 4: X axis seems to be in weeks. Please mention this in the figure legend.

Figure 4: X axis seems to end in week 55. Typically, the year ends in weeks 51-53. Please revise all X axises during 2010-2019 by checking that X axis ends in the exact week when the year ends.

Figure 4, legend: Please revise “on left/right side”.

Figure 5: There are two terms “hospitalization” and “clinic visits”, included elsewhere in the text as well. Are these the same? Health care systems in different countries may vary, thus the terms need to be clarified. If the patient comes to a health care unit and is sent back home, is this a “clinic visit”?, and if the patient is taken into the hospital ward, is this “hospitalization”? Or are “clinic visit” and “hospitalization” the same thing?

In Figure 5, legend, and also elsewhere in the text: How do you determine “the number of clinic visits”? Are they the patients with influenza (or influenza-like illness) symptoms, and then a physician reports influenza diagnoses and/or laboratory positive findings of influenza A or B? Please clarify.

In Figure 5, please choose “blue bullet” instead of “blue circle”.
Experimental design: The research question is relevant and meaningful, although you may consider using the following to describe the purpose of your study: “The aim of this study was…” in the end of the Introduction and also in the Abstract.
Validity of the findings: This study has public health impact.
Additional comments: Thank you for having me to review this manuscript. This is a study on detecting the outbreak of influenza based on the shortest path of dynamic city network. My major revision requests include the terms related to the health care system.


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: DETECTING THE OUTBREAK OF INFLUENZA BASED ON THE SHORTEST PATH OF DYNAMIC CITY NETWORK
Review round: 1
Reviewer: 4

Output:
Basic reporting: The language of the paper is English and clear, unambiguous and technically correct text. The cited references in the paper are correct and sufficient enough to support the research background/context. The structure of the paper is possible to obey to the format, but I suggest that the figures and tables should be placed to be right for reading the paper.  The The relevant results are self-contained in the paper. And the discussion is  given between the results and conclusions. Therefore, I think that the paper is satisfied with the requirement of your journal.
Experimental design: The paper is within aims and scope of the journal.
The research question is clear, relevant and meaningful. The proposed method is detect the pre-outbreak state of influenza epidemics by monitoring the dynamical change of the shortest path in a city network to fill the gap. This method gives the sufficient detail and the experiments have done sufficiently.
Validity of the findings: The findings of the paper is valid. According to the figures and the tables, the underlying data have been provides.  The conclusions are given and are relevant to the results.
Additional comments: This paper proposed a computational method, the shortest-path-based  dynamical network marker (SP-DNM), to detect the pre-outbreak state of influenza epidemics by monitoring the dynamical change of the shortest path in a city network. The idea, structure and quality of the paper are acceptable and the authors did a high quality research on detecting the outbreak of influenza. There are some points before acceptance:
1.	In Figure 2, the terminal condition of algorithm is missing.
2.	The figures and tables should be the right place.
Before this paper is published, I would suggest that the wording, sentence structure and
grammatical structure of the article should be improved.
 I recommend that this paper is published in your 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: DETECTING THE OUTBREAK OF INFLUENZA BASED ON THE SHORTEST PATH OF DYNAMIC CITY NETWORK
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment.
Experimental design: no comment.
Validity of the findings: No comment.
Additional comments: I appreciate the responses to my former comments. I am concerning about how to use the identified markers in a real condition. For instance, in the city of Tokyo as reported. If you find some markers from the data, how to use it and end this transmission/outbreak of the disease. The authors need consider useful and specific application for these important findings that is important for this kind of research, especially in the pandemic of COVID-19.


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: DETECTING THE OUTBREAK OF INFLUENZA BASED ON THE SHORTEST PATH OF DYNAMIC CITY NETWORK
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is well written, with the whole story and related literature references clearly stated. The results are also self-contained.
Experimental design: The research question is well defined. Basically, this research adds a new dimension to forecast the outbreak of influenza in the increasing crowd city space.
Validity of the findings: The finding is interesting, which may also be applied to other infectious diseases given the related data. Particularly, with rapid global development, the results  are relevant to preventing and forecasting new outbreaks of infectious diseases.
Additional comments: The authors have addressed all my previous concerns.


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: DETECTING THE OUTBREAK OF INFLUENZA BASED ON THE SHORTEST PATH OF DYNAMIC CITY NETWORK
Review round: 2
Reviewer: 3

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
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: DETECTING THE OUTBREAK OF INFLUENZA BASED ON THE SHORTEST PATH OF DYNAMIC CITY NETWORK
Review round: 2
Reviewer: 4

Output:
Basic reporting: The article is clear and unambiguous,professional English used thoughout. The adopted references are enough. And the professional article structure,figures,tables,raw data are shared.
Experimental design: The content of the paper is within Aims and Scope of the journal.
Validity of the findings: The results of the paper are shown that the proposed method is novel and the conclusions are well stated.
Additional comments: This paper proposed a computational method, the shortestpath-based dynamical network marker (SP-DNM), to detect the pre-outbreak state of influenza epidemics by monitoring the dynamical change of the shortest path in a city network. The questions of last review are solved.
I agree that this paper will be published in Peer J.


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: QUANTIFYING LOCAL ECOLOGICAL KNOWLEDGE TO MODEL HISTORICAL ABUNDANCE OF LONG-LIVED, HEAVILY-EXPLOITED FAUNA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall well written. Could be streamlined. Figures and tables are clear. Specific suggestions in attached file.
Experimental design: Excellent experimental design for field work.

Analyses currently do not incorporate temporal auto-correlation, which they should. There is a good explanation of how to do this in Zuur 2009 (https://www.springer.com/gp/book/9780387874579)

Its not always clear which sample was used when and how sampling data from different sources was incorporated into analyses.

More comments in attachment.
Validity of the findings: Conclusions are well stated. There are additional topics which could be included in the discussion and the discussion could link more strongly to the results. See specific comments in attached file.
Additional comments: see attached file


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: QUANTIFYING LOCAL ECOLOGICAL KNOWLEDGE TO MODEL HISTORICAL ABUNDANCE OF LONG-LIVED, HEAVILY-EXPLOITED FAUNA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Pass. The writing is generally clear throughout the paper. Specific suggestions for reorganization of some information is suggested in comments and edits throughout the text to improve clarity and flow. Places where additional context and specific information would be helpful have been noted. Specific suggestions for text edits have also been included in the attached pdf. Suggestion to re-write the abstract in one concise paragraph which also highlights the significance of the work more clearly. As the authors are revising, suggestion for them to reduce redundancy wherever possible and really emphasize key points and significance of the research in strong topic sentences with good supporting points. Remove any unnecessary repetition of the same idea in different ways. Some of the appendices have minor editorial errors so should be checked for these before final publication.
Experimental design: Pass. Overall the paper is clear. Specific suggestions have been made in the paper to improve clarity in some sections. Part of the challenge is the iterative process of the method, such that some results are used to inform the methods following, therefore, there is some mixing of results within the methods, but for understandable reasons. In the revision, the authors should try to separate their methods and results as much as possible to be more clear. Figures 1 to 3 should specifically link more closely with the Phases of the methodology, and reference (i.e., names or titles or phases) to the phases should be used consistently in the manuscript. Places where more detail in methods or results would be helpful are included in the comments in the pdf.
Validity of the findings: Pass. Conclusions are generally well-stated and reasonable based on the information provided and analyses conducted. Raw databases have not been included presumably due to confidentiality of the data (following ethics guidelines). Specific suggestions are made in the article  to re-organize parts of the discussion to highlight important contributions and to be more clear in some sections. Suggestions have been made to move some content from results to discussion where the items actually belong because they are more speculation than direct results.
Additional comments: Overall, an important contribution for conservation science because a longer time-scale than that of contemporary scientific surveys is often required for more complete understanding of how social-ecological systems have changed over time, and how that affects assessment of species conservation status and ecosystem interactions. Some of the knowledge required to extend our time series of understanding is embedded in the communities that have been part of specific places over time. Knowledge of the people who use the resources in that place is an important and often unappreciated source of information for understanding long-term change. This paper presents an important approach and tools that could help bridge the gap between scientific surveys and local ecological knowledge, including indigenous knowledge.


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: QUANTIFYING LOCAL ECOLOGICAL KNOWLEDGE TO MODEL HISTORICAL ABUNDANCE OF LONG-LIVED, HEAVILY-EXPLOITED FAUNA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have greatly improved the clarity of their research.
Experimental design: The experimental design is excellent. The authors have greatly improved the communication of their experimental design.
Validity of the findings: No Comment
Additional comments: The authors did an excellent job of incorporating the comments from the first review. This is an excellent study, which is a strong contribution to our understanding of earlier sea turtle populations and the history of fisheries in Mexico. I have a few minor suggestions below. There are some minor formatting errors once the track changes are incorporated, so be sure to address those in the final draft.  Apologies, but the line numbers are wrong for comments 1-9. I was using the word version, which is different from the PDF.
1.	Line 1: Perhaps change “past” to “historical.” That is the more commonly used research term (e.g. historical ecology”) and might be better for search engines, etc.
2.	You might cite line 34, “building on previous work” to reference some of the work you are building on.
3.	Line 39: remove “only” and “already”
4.	I’d loose the last line of the abstract. The previous one is more powerful. Or can you change the focus of the sentence? Surely, the fact that other people can do research is not the biggest implication of your findings. You should end with that point (the biggest implication). Or flip the order of the last two sentences.
5.	Line 69 – formatting typo (line break)
6.	Line 96 - formatting typo (extra line break)
7.	Line 251-253 – bring the citations together, currently separated by reference to supplemental materials
8.	Line 281 move “(∼12 hours)” to after “fishing”
9.	Line 284 – Zar or Zurr – just checking
10.	Line 294 – long sentence. Could break after “consensus.  We used all ….” There is also a word missing in the middle of the sentence. Check for clarity.
11.	Line 308 “quantified data” of what? Say that explicitly.
12.	Line 309: fix “We chose oral content was chosen”
13.	Line 339: replace  “>63,” with “> 63:” And use the formatting for the numbers listed below too). Its better to not start sentences with numbers too
14.	Add a colon after “Topics included”
15.	Line 359: fix sentence “We used footnotes were to”
16.	Line 509 and 513: Great approaches to standardizing results
17.	Line 569: Reed 2008 (Biol Consv) Stakeholder participation for environmental management: A literature review provides a good review of this too
18.	The tables are very clear.
19.	The figures are great and support your descriptions of the processes
20.	Figure 6: remove extra space before “Collapse” in the legend


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

Input:
Title: THE IMPORTANCE OF OPEN SCIENCE FOR BIOLOGICAL ASSESSMENT OF AQUATIC ENVIRONMENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article presents a review of open science practices in ecological science. I found it to be well written and informative. I did however find the approach taken to be quite limited to ecological aquatic biological assessment. I understand within the field biological assessment is the correct term but given the scope of the journal, biological assessment could be expected to include other areas of biology such as medicine. Perhaps clear statement of ecological angle in the title would resolve this issue. I also thought the introduction would benefit from a more prominent mention of the failures in reliability that brought about the open science movement. In its current form, it seems to advocate standardisation as much as open practices (although I see the two are related). I also found the description of the principals of open science to be slightly narrower than I had expected (see below). I am not aware of a similar review having been recently published.
Experimental design: As stated above I found the coverage to be somewhat limited to ecological methodologies, but this is probably acceptable if the scope is clearer at the outset. More importantly, a major aspect of open science practice more broadly is the adoption of study pre-registration and registered reports. I thought the absence of a discussion of the impact of these practices was an omission. I would also suggest that were the authors to include a discussion of these practices it would be advisable to enlist the aid of someone with first-hand experience of implementing them. Adopting these practices is a major cultural shift in open science, which I don’t think can easily be left out (including them would certainly alter figures 1 and 2). Perhaps the distinction between confirmatory and exploratory research is not as relevant here as in other disciplines (e.g. neuroscience) and environmental science does not rely on hypothesis testing as much, in which case might that be noted? I also thought broader discussion of open access platforms and repositories (such as the osf.io) would benefit the reader.
Validity of the findings: The conclusions appear to be well supported and clearly made. My concerns here are centred upon the apparent omission of important aspects to open science practices, mentioned above.
Additional comments: I found this to be a manuscript of good quality. I did, however, feel a number of important open science practices, partially pre-registration, where not discussed and perhaps should have been. Perhaps the authors could consider narrowing the scope of the article and discussing open data and materials practices, rather than open science?


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

Input:
Title: THE IMPORTANCE OF OPEN SCIENCE FOR BIOLOGICAL ASSESSMENT OF AQUATIC ENVIRONMENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English is clear, unambiguous, and professional.
Although the Introduction and background show the context, there are some issues which need to be taken into account, including the absence of some relevant literature. Some comments to the Introduction are shown below.
-	Line 1: I would add ‘aquatic’ in the title, before ‘biological assessment’, since the authors focus mainly in that and this should be highlighted since the very beginning
-	Line 24: ‘Democratize science’, probably this is an opinion of the authors, and my response could be considered also as an opinion. As such, you can take it into account or not. I don’t like this expression, since it seems that the general scientific process is not democratic. However, in my opinion, is one of the most scrutinized human activities, since the moment in which scientists apply to public calls for projects and then publish the results either in open access or non-open access journals, since they are checked by editors and reviewers, trying to ensure replicability of the publications. Are open access principles more ‘democratic’? I disagree: they allow more interaction, more replicability, more transparent, more responses to new questions,… but I cannot see that as more ‘democratic’.
-	Lines 42-46: it is good to have some examples of the legislation driving monitoring and assessment in these three areas. However, there are many other countries/regions (e.g. China, South Africa, Australia, New Zealand, etc.), as well as other legislation (e.g. Oceans Act in several countries, Marine Strategy Framework Directive, international conventions, etc.), which deserve also to be cited. As this could be too long, I suggest you adding a citation here. To my best knowledge, although it has more than 10 years, the most complete review in this specific topic is this paper, collating the legislation around the world in monitoring and assessment: Borja, A., S. B. Bricker, D. M. Dauer, N. T. Demetriades, J. G. Ferreira, A. T. Forbes, P. Hutchings, X. Jia, R. Kenchington, J. C. Marques, C. Zhu, 2008. Overview of integrative tools and methods in assessing ecological integrity in estuarine and coastal systems worldwide. Marine Pollution Bulletin, 56: 1519-1537.
-	Lines 48-49: regarding marine waters, one of the co-authors of this manuscript has also a paper that can be cited here, since it constitutes a good review of the current methods availability: Borja, A., M. Elliott, J. H. Andersen, T. Berg, J. Carstensen, B. S. Halpern, A.-S. Heiskanen, S. Korpinen, J. S. S. Lowndes, G. Martin, N. Rodriguez-Ezpeleta, 2016. Overview of integrative assessment of marine systems: the Ecosystem Approach in practice. Frontiers in Marine Science, 3: doi: 10.3389/fmars.2016.00020.
-	Lines 72-85: regarding the use of open science in bioassessment, in relation to stakeholders, to my knowledge, this paper below is the single one dealing with that. The second one is dealing with the transparency issues. Both could be useful in this context.
o	Borja, A., J. M. Garmendia, I. Menchaca, A. Uriarte, Y. Sagarmínaga, 2019. Yes, We Can! Large-Scale Integrative Assessment of European Regional Seas, Using Open Access Databases. Frontiers in Marine Science, 6: 10.3389/fmars.2019.00019.
o	Essl, F., F. Courchamp, S. Dullinger, J. M. Jeschke, S. Schindler, 2020. Make Open Access Publishing Fair and Transparent! BioScience, 70: 201-204.

The structure is clear, and of broad and cross-disciplinary interest.
I don’t know any other recent review. However, one of the co-authors of this paper, is the first author or another paper on the topic (Lowndes et al., 2017), included in the references list. Probably, there are other papers around the topic, such as that abovementioned of Borja et al. (2019) and few others (e.g. van Oudenhoven, A. P. E., M. Schröter, R. de Groot, 2016. Open access to science on ecosystem services and biodiversity. International Journal of Biodiversity Science, Ecosystem Services & Management: 1-3).
Experimental design: The article content is within the Aims and Scope of the journal. Regarding the methods described, I think that they need more explanations:
-	Line 87: for the whole section, I cannot see later in the manuscript the results obtained from that search in Google Scholar. Why including this section, if there is no a section on the results? (maybe I have missed something).
-	Lines 104-107: a justification of the selection of these terms is necessary. There are many other possible that could expand the number of potential papers. Some few examples: ‘open databases’, ‘assessment’, ‘ecological status’, ‘health status assessment’, etc.
-	Lines 108-109: I agree that they are scarce, but an example that the terms used are insufficient is the fact that the first paper abovementioned was not found.
Although the review is organized logically, into coherent paragraphs/subsections, I cannot see why those subsections (what is the logic behind that organization, or what is the source to organize it in that way).
Validity of the findings: Some comments about the main text body.
-	Line 134: Figure 1: You should add the word ‘open’ in ‘publish data’ and ‘publish code’. In addition, in this conceptual workflow I think that something is wrong: after the publication in open access, you link the arrow with ‘conceptualize project’. However, if you are discussing about bioassessment, monitoring and taking decisions to improve aquatic systems, I think that, after publication, at least two boxes should be added: one on taking management measures, and another on recovery of the systems monitoring, which can lead to new ‘conceptualization of projects’. Otherwise, this figure is not useful, and endogamic for the research community.
-	Lines 167-170 and 188-196: an example of this are the metabarcoded databases of species (e.g. BOLD, GenBank,…).
-	Lines 253-255: there are also many taxonomical resources that can be mentioned e.g. WoRMs
-	Lines 400-417: you can mention also that in Europe any project supported by public funds must provide open access data and publish all papers in open access: https://ec.europa.eu/research/participants/docs/h2020-funding-guide/cross-cutting-issues/open-access-dissemination_en.htm. The same in Canada: https://www.ic.gc.ca/eic/site/063.nsf/eng/h_F6765465.html, and probably in many other countries/regions. Avoid being so local.
-	Line 424: spell out, in the legend of Figure 3, the abbreviation: TDML
The conclusions are coherent
Additional comments: The manuscript has some interest, but I have identified some weaknesses, regarding the lack of connection between the methodology presented and the absence of results associated to the search in Google Scholar. In addition, some references that I have included above could be of interest. The authors should present the applicability more global, not as local as California (although it can serve as example, I have given more examples in other areas)