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: INCOMPLETE LINEAGE SORTING AND ANCIENT ADMIXTURE, AND SPECIATION WITHOUT MORPHOLOGICAL CHANGE IN GHOST-WORM CRYPTIC SPECIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors did a great job in addressing all the comments of the reviewers, not only mine. Well done. I am sure it will be an interesting paper for several readers.


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: INCOMPLETE LINEAGE SORTING AND ANCIENT ADMIXTURE, AND SPECIATION WITHOUT MORPHOLOGICAL CHANGE IN GHOST-WORM CRYPTIC SPECIES
Review round: 2
Reviewer: 2

Output:
Basic reporting: No further comments
Experimental design: No further comments
Validity of the findings: No further comments
Additional comments: I am very please with the response to my queries. No further comments.


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

Input:
Title: INCOMPLETE LINEAGE SORTING AND ANCIENT ADMIXTURE, AND SPECIATION WITHOUT MORPHOLOGICAL CHANGE IN GHOST-WORM CRYPTIC SPECIES
Review round: 2
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: There was considerable improvement to the manuscript in response to reviewers' concerns and I believe it is much better now. That said, the paper could benefit from revision of a few points. Here I start by making some comments that have been apparently overlooked during the first round of reviews and then I make a few suggestions based on the current version of the manuscript.
One of them was a problem already in the first version (model comparison by likelihoods), but the figure in the first version had an unlabelled axis and it was unclear whether this was the case. Now that it is clear, I suggest to use the likelihoods to calculate AIC instead of comparing models by likelihood directly. AIC scores should be comparable across models, but likelihood is not due to the different number of parameters. If anything, I believe this will make the main argument stronger, decreasing support for models including migration in relation to models with migration.

Before pointing out parts to be revised, I would like to commend the authors for the careful revision. While it is clear that great care was taken to address major comments, it seems some of minor issues that I pointed out in the first round were neglected, so I rephrase them here:

1 - I still do not understand why samples are split in A0 and A1 in Figure 2 if alleles are unphased. Whether an allele is marked as "0" or "1" is arbitrary because of the lack of phasing, and therefore grouping them this way makes no sense. I would think that a phylogeny based on the consensus sequence for each individual would be more appropriate.

2 - "Maps, Google" is still in the references. I would suggest reviewing references more broadly prior to publication. For example, there are two preprints cited and by now they might have been published already.

3 - "bad apple" is still mentioned in Supp. Table 2 but not defined in text. In the description of the method to minimize missing data one can guess these are the samples with >45% missing data that have been removed, but since the term "bad apples" is used in the supplement it should also be explicitly defined in the main text (or removed from the supplement).

In addition to those, I have a few comments on this version of the manuscript.

1 - Not sure if I am the one who failed here, but I could not find and download fastsimcoal files that should be in the supplement. Please make sure they are provided in the final version (e. g. together with code) to ensure reproducibility.

2 - While the authors disclosed the mutation rate used in the response to reviewers, it is not mentioned in the text. This is important, since the number of generations estimated and discussed depends on mutation rate. For example, the authors mention that species of Stygocapitella have one generation per year, which is as important as mutation rate to interpret how this relates to actual time scales. I would suggest adding it as a short sentence to methods, not only the supplement.

3 - While in the response authors mention not using a minimum allele frequency criterion for estimation of Tajima's D, it is not clear in the text when a maf was used or not. The only time maf is mentioned is in line 216, and it seems implicit that this criterion applies to all downstream analyses. If this is not the case (as seems to be from the response to reviewer's comments), it should be stated explicitly.

4 - Now that it is clear that the y axis in Figure 6 is likelihood, this reveals a problem. Model comparison in a likelihood framework needs to take into account the number of parameters, since a simpler model is preferable to a more complex one if they have the same likelihood. There are different ways of accounting for number of parameters, but the Akaike Information Criteria (AIC) is one of them and widely used in the context of fastsimcoal. AIC = 2*k - 2*L, where k is the number of free parameters (i. e. the number of parameters in the *.est file of fastsimcoal) and L is the log-likelihood. After calculating the AIC for each model, these can be directly compared and the best model should have the lower AIC. There are several tutorials available, I found one of them here, for example:https://speciationgenomics.github.io/fastsimcoal2/
I suspect that after comparing models by the AIC the model with no migration will be favored in relation to others, making the argument in the paper stronger.

5 - line 280, "module as asymmetric" should be "modelled as asymmetric".

6 - There are weird characters following numbers in the paragraph starting in line 294


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: IS THERE A LINK BETWEEN PRE-EXISTING ANTIBODIES ACQUIRED DUE TO CHILDHOOD VACCINATIONS OR PAST INFECTIONS AND COVID-19? A CASE CONTROL STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. The language used is precise, clear and without any ambiguities. Background information is succinct and covers the hypothesis generation well.
2. Tables contain all relevant information necessary to make conclusions.
3. Line 124, please correct 0,50 units to 0.50 units
Experimental design: 1. Line 91 mentions that the demographic characteristics of the volunteers were questioned. Please elaborate on this.
2. Rest of the methods section is well described and all ethical standards have been followed to obtain and assess samples.
Validity of the findings: no comment
Additional comments: 1. In the background, please give information about the vaccination status in the country where the sample patients and healthy volunteers were from.
2. in the discussion section, please talk about the involvement of the immune system with the vaccination status and how that could play a possible role in the COVID-19 case severity. Provide valid references. This is especially important since low lymphocyte count has been reported.
3. In discussion, a mention of increased fibrinogen has been made on line 226-227. How is this linked to coagulopathy, mentioned on line 228?


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: IS THERE A LINK BETWEEN PRE-EXISTING ANTIBODIES ACQUIRED DUE TO CHILDHOOD VACCINATIONS OR PAST INFECTIONS AND COVID-19? A CASE CONTROL STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article should be edited by a native English speaker. There are many awkward sentences, too many to be cited all. I just provide examples from the introduction and the methods section:
Lines 65-67: this sentence can be cut into two sentences
Lines 68-72: this sentence can also be cut into two sentences
Same for 80-82
Line 91: it is not clear what is meant by “… demographic characteristics were questioned.” Please rephrase.
Line 101: replace -80 degrees by -80°C.
Line 123: “Level” should be in plural (Levels).
Line 129: this sentence is strange

Line 73: these are not “theories” but “hypotheses” at best

Line 100: what is meant by “centrifugation for 10 minutes at 2000 cycles”?
Lines 114-122 can be deleted, this is textbook knowledge
Lines 123 and 124: the repetition of “antibody units” is not necessary. It is sufficient to mention this once at the end for the last one (≥ 15 antibody units)

Line 146 and throughout the manuscript: these are not clinical parameters, but biological or biochemical parameters.

Lines 249-250: Blok et al speak about Tdap, containing an acellular pertussis vaccine, and show that Tdap augments immunity only very slightly and very briefly (in a matter of days). In Turkey probably people were vaccinated with whole-cell pertussis vaccine, thus this is reference is irrelevant here.

Lines 254-261: this is essentially a repetition of the results section. The authors do not really explain and discuss the significance of this, except to say that a combination of antibodies may protect. It would be important to expand this and be more precise as to what combination the authors think may protect.
Experimental design: In this case-control study 53 COVID patients were compared to 40 controls with respect to antibody titers to vaccine antigens. For rubella, pneumococci and pertussis these titers were lower in the case group than in the control group. This led the authors to conclude that childhood vaccination with these vaccines or past infections may protect against COVID through cross-reactivity by vaccine-induced antibodies.

Methods: it would be nice for the reader to know what the actual antigens really are. Are they purified antigens or whole bacterial lysates/viruses? This is particularly important for B. pertussis and for pneumococci.
Validity of the findings: A study to link unrelated antibodies to COVID is potentially useful, but the interpretation of the results is not really obvious. In order to be convinced one would like to see that these, so called pre-existing antibodies do indeed cross-react with SARS-CoV-2 antigens. This was not done in this study.
Instead of linking unrelated antibodies to protection against COVID, I think there may be another explanation that would be much more plausible, and that is the induction of innate immune training by viral and/or bacterial infections.
The fact that only low anti-rubella antibodies appear to correlate with disease or infection, but not anti-mumps and anti-measles antibodies, suggests that it may be a rubella infection, even as a silent infection, rather than the MMR vaccine that is linked to protection. Similarly, the fact that only low anti-B. pertussis antibodies correlate with disease or infection and not anti-diphtheria or anti-tetanus antibodies, given that all three vaccines are administered simultaneously and that anti-tetanus and anti-diphtheria antibodies are much longer lived than anti-B. pertussis antibodies, it is more likely that the effect seen is due to silent B. pertussis infection.
Live bacterial and viral infections are known to induce innate immune memory which in the case here is more likely to have contributed to the protection.
Thus the final conclusion (final sentence of the paper) is not supported by the data.

Lines 169 and 170: The dip in pertussis IgG in mild disease should be discussed;

Lines 246-249: I am not sure I can follow the argument of the authors. If most of the COVID patients are co-infected with S. peumoniae, there should be more anti-S. pneumoniae antibodies in the patients than in the controls.
Additional comments: A study to link unrelated antibodies to COVID is potentially useful, but the paper has to be edited by a native English speaker and the interpretation of the results has to be reviewed in a more in-depth manner. Please refer to my comments 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: IS THERE A LINK BETWEEN PRE-EXISTING ANTIBODIES ACQUIRED DUE TO CHILDHOOD VACCINATIONS OR PAST INFECTIONS AND COVID-19? A CASE CONTROL STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is well structured and written professionally.
Experimental design: no comment
Validity of the findings: More meaningful discussion will improve the manuscript.
Additional comments: Bilge Sümbül et al in the article “Is there a link between pre-existing antibodies acquired due to childhood vaccinations or past infections and COVID-19? A case control study" tried to find the correlation between existing antibodies with severity of COVID-19.
Overall, the study is well designed, thoughtfully carried out with precision. This study may have significant impact in understanding the immune response against SARS-CoV-2. Their studies showed that pre-existing antibodies acquired due to childhood vaccinations or past infections may play some role in controlling the severity of COVID-19. But in the study, they didn’t discuss extensively the possible reason for this less severity of COVID-19. This protection is mainly non-specific, as pre-existing antibodies were generated possible due to childhood vaccination or any other infection acquired over lifetime. Apart from the acquired antibodies, different innate immune cells like monocyte/macrophage or NK cells may play a role in this context. There are already enough studies being carried out regarding non-specific memory response (trained immunity) showed by innate immune cells. BCG vaccination and resultant non-specific protection against other diseases are one such specific example.
This study would have been more appealing and interesting if some of the role played by immune cells were shown experimentally or discussed properly.


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: IS THERE A LINK BETWEEN PRE-EXISTING ANTIBODIES ACQUIRED DUE TO CHILDHOOD VACCINATIONS OR PAST INFECTIONS AND COVID-19? A CASE CONTROL STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Nothing further to add
Experimental design: nothing further to add
Validity of the findings: nothing further to add
Additional comments: i comment the authors for having substantially improved the manuscript. The English was well revised and the paper is now clear overall, although there are still a few typos, but I hope they can be corrected by the editorial office.
The authors have also answered all my concerns to my satisfaction and have revised the manuscript accordingly.
Thank you very much.


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: IS THERE A LINK BETWEEN PRE-EXISTING ANTIBODIES ACQUIRED DUE TO CHILDHOOD VACCINATIONS OR PAST INFECTIONS AND COVID-19? A CASE CONTROL STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Bilge Sümbül et al revised their article “Is there a link between pre-existing antibodies acquired due to childhood vaccinations or past infections and COVID-19? A case control study" according to reviewers suggestion. The revised manuscript improved a lot from the previous version and it will be interesting read for the readers. The manuscript will enrich our knowledge about the possible link between childhood vaccination and it's non-specific effect on other diseases like COVID-19. I recommend this for publication in PeerJ.


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: RAPID CORAL REEF ASSESSMENT USING 3D MODELLING AND ACOUSTICS: ACOUSTIC INDICES CORRELATE TO FISH ABUNDANCE, DIVERSITY AND ENVIRONMENTAL INDICATORS IN WEST PAPUA, INDONESIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The paper submitted by Peck et al. reports an interesting research regarding the monitoring of coral reefs through acoustic methods. Coral reefs have an exceptional ecological value that urgently needs to be preserved so that efficient monitoring tools are necessary for a proper assessment at local and regional scales. The research conducted by the authors tests the possibility to employ low-cost equipment and rapid analyses that could be informative to policymakers for conservation. This effort is highly valuable. However, I have several comments listed below. Among them, the most important one concerns the estimation of fish diversity through the unique estimation of total abundance. I am a bit surprised that diversity could be summarized by a single variable that does not take into account neither species diversity, nor phylogenetic diversity, nor functional diversity. Because fish abundance is the main result of the research the authors should justify the choice of this unique variable and they should describe as well properly how it was estimated on videos. This point should also be mentioned in the discussion.

Introduction

+ l50-51: The authors start their introduction with an economic justification of the importance of Indonesia's coral reef fisheries. I understand this is important to show that such ecosystems have a monetary value when you discuss with policy makers but here the text is addressed mainly to a scientific audience. I would therefore suggest to start rather with an ecological justification and mention later in the introduction or in the discussion the economic side of it.
+ l89-91: please add a reference for "The coral reef environment has a unique soundscape..."
+ l107: "health" might not be the most appropriate word. I would suggest "ecological state".
+ l108-109: I would suggest to keep the same order (visual then audio) than in the text above. I would then suggest to write: "do habitat metrics and acoustic indices from underwater audio and video correlate to coral cover and fish abundance?"

M&M
+ l115-117: I am not used to such sampling so I was not sure to understand the meaning of replicates here. Could the author clarify?
+ l131-133: The estimation of fish abundance does not seem to be fully explained. How was it estimated? Which method was used? Did someone tagged the videos? Who did it? Was it double-checked by two observers? What do the authors mean here by abundance? Is it the total number of individuals seen? If so, I am not sure that raw abundance is a good estimator of local diversity. Could the authors estimate species richness?
+ l132: "between 5 and 6 minutes after" should be replaced with "from minutes 5-6" as written in the next paragraph.
+ l139-140: The authors very interestingly used two approaches: beta indices (cumulative spectral dissimilarity) and alpha indices (ADI, AEI, etc). However the authors did not use both index families exactly in the same way. The alpha indices were computed by separating the 100-1200 and 1200-11000 Hz frequency bands separately, which is fine, but the beta index was computed on the full spectrum range. I would actually be very interested in seeing the results of the cumulative spectral dissimilarity index on each frequency band. The index might be more discriminant when applied to low frequency band where most of the acoustic activity occurs.
+ l144: I guess that the package tuneR (or seewave) should be mentioned here as Soundecology does not process sound extraction. Soundecology does not seem either to frequency filters so that the 100-1200 and 1200-11000 Hz bands could be separated with it. Actually, how were the two frequency bands separated? Which Fourier parameters were used to compute the indices?
+ l152: "sound pressure levels": RMS and roughness are not sound pressure level measures. RMS is an amplitude measurement (that could be related to sound pressure level if the recording system is calibrated) and roughness estimates the irregularity of a numeric series.
+ l153: Seewave -> seewave
+ l163-164: the author mention visual tools to check the validity of the models but the authors also should mention which assumptions these plots check for (normality and homoscedasticity of the residuals).
+ l167-168: It is a good idea to cite RStudio but RStudio is only a GUI for R. It is therefore more important to cite the version of R (R Core Team).

RESULTS
+ l171-72: this first sentence sounds more like a comment than a result. This could be transferred to the discussion.
+ l173-174: It was not clear in the M&M (l112-114) that there were 2 sites and that they will be compared. Actually the authors do not use exactly the same geographical names in the M&M and in the Results. Please clarify.
+ l173-186: The statistics used are not mentioned and were not introduced in the M&M section. I have to admit I do not understand the way the authors report the results: "F; 1, 29 = 21.02, p < 0.001". Is F the ANOVA statistic, and 1, 29 the degrees of freedom? Please use standard way to report statistics and mention the test used.
+ l191-198: the dB-RDA should be computed separately on the low and high frequency bands as for the alpha indices. This might then reveal significant results.

FIGURES
+ It would be nice to add an illustration showing some raw data: a picture fo the coral reef, an example of the 3D model, a spectrogram and a spectrum of a typical recording showing the low and high frequency bands. This could also be accompanied with a video and an audio sample.
+ Figure 1: why is "Manokwari" in bold face?
+ Figure 2: the legend does not fit with the figure. This is the plot of figure 4.
+ Figure 2-4: explain what "Ratio" means here.

DISCUSSION
+ The authors seem to use the same word "community" in a context of conservation policy and community ecology. Please specify each time this word is used.
+ The authors need to discuss about the reliability of the abundance estimator. Other studies using acoustics estimated species richness.
+ l288-293: this is correct comment, this is why I suggest to compute the index by frequency band.
+ l348: "pattern in AEI" -> "pattern in ACI".

TABLE
+ Table 1: "(AEI 0hz – 1200 Hz / AEI 0Hz – 11000Hz)" and others coud be replaced by "AEI low / AEI High". If not, please check Hz with a capital and space are properly written everywhere.
+ Table 2: how were defined the classes LOW and HIGH for fish abundance? This does not seem to be explained in the M&M section.

Jerome Sueur


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: RAPID CORAL REEF ASSESSMENT USING 3D MODELLING AND ACOUSTICS: ACOUSTIC INDICES CORRELATE TO FISH ABUNDANCE, DIVERSITY AND ENVIRONMENTAL INDICATORS IN WEST PAPUA, INDONESIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: a.	Clear, unambiguous, professional English language has been used throughout the text.

b.	Intro & background show context only partially. Some concepts are well explained and sufficient literature/ background information are provided (e.g. coral reefs status, management requirements, habitat metrics based on visual data). Other concepts are lacking in both literature and of depth of the explanation, in particular when it comes to acoustic indexes and vocal communities. Adding on these concepts will strengthen the paper and help the authors to better focus the significance and novelty of their findings.

Specific comments:

Line 67-85: Authors state “Two promising visual and audio approaches amenable to rapid and community-level data collection for coral reef monitoring including a) habitat metrics and b) use of acoustic indices as a proxy for vertebrate and invertebrate diversity”.
Although literature and context are well presented for the first method (a), the introduction lacks of context regarding acoustic indexes applied to marine environments (b). Only 2 literature references are provided here, one of which refers to terrestrial environments. A synoptic, more focused review of studies which have applied acoustic indexes to aquatic data, and of their findings, would surely strengthen the paper. For example, while some studies showed a correlation between taxonomic diversity and acoustic indexes, others showed that care should be taken when using acoustic indexes in different stages of their implementation, from calculation (dependence on settings, for example) to interpretation, at least for what concern marine data (e.g. which kind of acoustic information they detect? Abundances or diversity, or both? Are they sensitive to this ecologically relevant discrimination? etc). Adding a few lines in this sense would be beneficial. Also, it should be stated somewhere why indexes are getting so much attention, i.e. the allow the quick screening of large acoustic data without prior knowledge of the composition of the vocal community, on the contrary of manual analysis approach (which is extremely time consuming and requires skilled operators) or automated analysis based on sound type detection and recognition, e.g. Markov Chains (which requires previous knowledge on the target signals)

Suggested literature for indexes applied on aquatic data (mind that this list IS NOT exhaustive, but should provide a well-rounded picture)

	Davies, B. F., Attrill, M. J., Holmes, L., Rees, A., Witt, M. J., & Sheehan, E. V. (2020). Acoustic Complexity Index to assess benthic biodiversity of a partially protected area in the southwest of the UK. Ecological Indicators, 111, 106019.
	Elise, S., Urbina-Barreto, I., Pinel, R., Mahamadaly, V., Bureau, S., Penin, L., ... & Bruggemann, J. H. (2019). Assessing key ecosystem functions through soundscapes: A new perspective from coral reefs. Ecological Indicators, 107, 105623.
	Bolgan, M., Amorim, M. C. P., Fonseca, P. J., Di Iorio, L., & Parmentier, E. (2018). Acoustic Complexity of vocal fish communities: a field and controlled validation. Scientific reports, 8(1), 1-11.
	Bohnenstiehl, D., Lyon, R., Caretti, O., Ricci, S., & Eggleston, D. (2018). Investigating the utility of ecoacoustic metrics in marine soundscapes. J. Ecoacoustics, 2, R1156L.
	Elise, S., Bailly, A., Urbina-Barreto, I., Mou-Tham, G., Chiroleu, F., Vigliola, L., ... & Bruggemann, J. H. (2019). An optimised passive acoustic sampling scheme to discriminate among coral reefs’ ecological states. Ecological Indicators, 107, 105627.
	Bertucci, F., Parmentier, E., Lecellier, G., Hawkins, A. D., & Lecchini, D. (2016). Acoustic indices provide information on the status of coral reefs: an example from Moorea Island in the South Pacific. Scientific Reports, 6, 33326.
See also
	Desiderà, E., Guidetti, P., Panzalis, P., Navone, A., Valentini-Poirrier, C. A., Boissery, P., ... & Di Iorio, L. (2019). Acoustic fish communities: sound diversity of rocky habitats reflects fish species diversity. Marine Ecology Progress Series, 608, 183-197.

Line 93-94 The authors introduce the concept of acoustic communication in fish. No references are provided. Here, authors should provide references and expand their explanation.

Line 96-97 “biological community level acoustic indices as proxies for species richness and in tracking subtler habitat-dependent changes in community composition (Eldridge et al., 2018)”
Eldridge refers to avian communities, which are acoustically very different from aquatic communities. At line 102-103, on the other hand, there is no discussion about indexes limitations, which have been highlighted by other studies. I therefore refer the authors to my previous comment about acoustic indexes.

c.	Literature is well referenced & relevant but its completeness could be improved (e.g. acoustic indexes, aquatic vocal communities)

d.	Structure conforms to PeerJ standards
Experimental design: a.	The article presents original primary research within Scope of the journal.

b.	Research question are well defined, relevant & meaningful. However, the paper could be strengthened by adding a clearer explanation of how the research fills an identified knowledge gap.

c.	Rigorous investigation was partially performed to a high technical & ethical standard.
Acoustic data were extracted from the GOPRO microphone, which is not as sensitive, nor omnidirectional, as a dedicated underwater hydrophone. This might have resulted in an underestimation of the vocal community dynamics and complexity. Furthermore, it lacks of temporal resolution, as it provides short-term data, depending on the GOPRO battery, which runs out quite quickly (on the contrary of dedicated acoustic loggers, which can provide months of continuous data). The authors should clearly state this limitation, showing they are aware of it, especially because in the discussion it seems that this point is, for them, a “novel” aspect of this study (line 250-253). There is a reason for which people use dedicated acoustic dataloggers for similar kind of studies; although I appreciate the (obvious) advantage of using the authors’ approach, a more nuanced and balanced discussion in this sense is required, especially if tools are suggested for management. The approach used by the authors has surely a very nice potential, but it would not provide information on long-temporal dynamics, just out of example.

d.	Methods described with sufficient detail & information to replicate; partially.
The acoustic data lacks of important information, e.g. how many recordings were analysed? Why the authors chose to analyse only min 5-6 of a 10 min files? Which was the sample rate? And the Bit depth? In the analysis part… How was the mean frequency spectrum calculated, which FT size? Same applies to the calculation of indexes; which settings were used (e.g. temporal resolution? Frequency resolution?); RMS sound pressure levels were calibrated or not? Which was the unit of measurements (re dB or 1 dB re 1μPAa?) and so on.
Validity of the findings: a.	The findings are novel but, because some methodological aspects are lacking and some results are not presented, it is difficult to ascertain at which extent the interpretation given by the authors is coherent.  For example, at line 347-349 of the discussion, the authors state “the Acoustic Complexity Index ratio decreases with increase in fish abundance, also reflected in both frequency bands. Again, it may be reflecting anthrophony that correlates with higher fishing pressure or other anthropogenic impacts”. This is not clear because; a) the ACI “should” decrease in presence of anthropogenic noise, b) without knowing the settings used for its calculation, it is impossible to evaluate if the index was “tuned” at the best of its potential; c) there is mention to the vocal communities’ composition; e.g. how many sounds, how many sounds types, who were the species seen on site, do they belong to known vocal species? and so on

b.	Significant results have been presented, but the lack of some methodological details makes interpretation difficult.

c.	Conclusions are well stated, linked to original research question & limited to supporting results however they could benefit from wider comparison with other studies.

E.g. at line 388-390 the authors states “Acoustic indices offer insights to the status of biodiversity and function in reef environments, yet they remain rather blunt instruments”. They then suggest one alternative, but other alternatives have been suggested and should be mentioned/ considered (e.g. see Desidera’ et al. 2019 but there are others)
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: RAPID CORAL REEF ASSESSMENT USING 3D MODELLING AND ACOUSTICS: ACOUSTIC INDICES CORRELATE TO FISH ABUNDANCE, DIVERSITY AND ENVIRONMENTAL INDICATORS IN WEST PAPUA, INDONESIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author took into account all the remarks of my first review including those requiring extra work.
I would just suggest to revise Figure 5 which looks as a simple screenshot of Audacity with all buttons around... Not very easy to read.
Experimental design: OK
Validity of the findings: OK
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: RAPID CORAL REEF ASSESSMENT USING 3D MODELLING AND ACOUSTICS: ACOUSTIC INDICES CORRELATE TO FISH ABUNDANCE, DIVERSITY AND ENVIRONMENTAL INDICATORS IN WEST PAPUA, INDONESIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: •	Clear, unambiguous, professional English language used throughout the text.

•	Intro & background show context in an exhaustive way, although the introduction would be greatly improved by providing extra background information when presenting acoustic indices (see below).

•	Literature is well referenced but its completeness could be improved in the introduction section. Some works were incorrectly cited. Proper citations relating to coral reef soundscapes and tropical fish sound-producing species are needed (see below).

•	Structure conforms to PeerJ standards.

•	Figures are relevant and of high quality but may be improved (see below).

•	R code and data sets available.

Specific comments
Lines 49-50: Please add one or more references for “Indonesia’s coral reefs support exceptional biodiversity, providing food security and other important ecosystem services to many millions of people.”
E.g. In the most recent report by FAO (2018) it is stated that in Indonesia fish contributed ≥50 % of total animal protein intake in 2015. Indonesia is also among the main exporters of fish and fish products
FAO. 2018. The State of World Fisheries and Aquaculture 2018 - Meeting the sustainable development goals. Rome. Licence: CC BY-NC-SA 3.0 IGO.
Line 78: “The principle method” -> The principal
Lines 93-96: Mis-used citations of the works by Bolgan et al. (2018 & 2020) and by Desiderà et al. (2019), which are not about coral reef soundscapes and tropical marine fishes. Please replace them and add more appropriate references for "The coral reef environment has a unique soundscape..., and avoiding predators".
Lines 97-98: I agree that sounds may be produced by soniferous fish species during all the activities stated here but the authors should either expand the number of references provided or cite a more comprehensive tropical-based acoustic work. Two citations (Picciulin et al 2019,2020) are about Mediterranean fish species thus mis-used considering the tropical context of the study.

Figures
Figure 1: I don’t know if the image I am reviewing has been updated for the second submission of the manuscript but there is still "Manokwari" in bold face. Moreover, in the map there are only 4 survey locations indicated while in the M&M section you refer to 8 sites. Are there 4 main study locations and 2 survey sites within each location? If so, you should specify it in the legend and in the text. What was the distance between the 2 sites within each location? You should add this detail in the text.
Experimental design: •	The article presents original primary research within Scope of the journal.

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

•	Rigorous investigation performed to a high technical & ethical standard.

•	Methods described can be better detailed and explained so that the study can be replicated. At what time of the day were the surveys conducted? Were video and audio files recorded while SCUBA diving or free/skin diving? This would be crucial to know since SCUBA divers’ bubble noise would mask biological sounds. How many people were involved? In the discussion section (lines 296-298) you mentioned that “Each individual 10-minute replicate could be collected by 2 people in approximately 15 minutes, an important consideration if using SCUBA equipment that limits dive times” -> This detail (number of people involved) must be also mentioned in the M&M section. Were they always the same during data collection?

Specific comments
Lines 122-123: Which kind of management measures are in place in the protected reef systems? Is there any scientific evidence (report/study/paper) about the effectiveness of such protection measures and the greater ecological/conservation status of the protected reefs? Clarifying this may further support the statement you make later in the discussion section (Lines 400-403): “Soniferous fish are generally thought … in the healthier reef systems sampled.” (Assuming that these “healthier systems” are the protected reefs of Waisai and Mansuar).
Lines 124: Does South Manokwari coincide with Manokwari Seletan? If so, please be consistent with the name of survey sites/locations throughout the manuscript.
Line 125: You provided the overall number of collected replicates (34) but how many replicates did you collect within each of the 8 reef sites?
Line 133: “Corner of the transect” or corner of each of the 2m×2m quadrats? The term “transect” has not been defined earlier in the M&M section. Does it indicate the linear path at the same depth along which you deployed the replicates?
Line 144: How did you estimate the lengths of individual fish (>30 cm) from video frames?
Validity of the findings: •	The findings are novel and significant.

•	As far as I can see, all underlying data have been provided; they are robust, statistically sound, & controlled.

•	Conclusions are well stated, linked to original research question & limited to supporting results.

Specific comments
Line 273: however -> with (?)
Line 296: quadrants -> quadrats
Line 304: specify that these are rapid short-term assessments -> “to support short-term reef assessments”
Lines 359-362: “It is worth noting… communities”. I have to admit that I find this sentence very long and I had to read it multiple times to get the point. Could you please clarify/rephrase?
Line 389: vocalizationS (?)
Line 402: increasing vocalizationS (?)
“healthier” -> more protected or pristine?
Lines 454-458: Honestly, I do not find this part very comprehensible, but it may be my fault. Would not be “develop” better than “development” in the sentence: “Data might be enhanced…. directly to components of reef function (Elise et al., 2019c).”? If so, please rephrase/clarify.
Additional comments: The research by Peck et al. is valuable as it investigates the use of low-cost technologies to provide rapid and key indications about the ecological status of coral reef ecosystems, whose study and conservation is of major importance nowadays. Moreover, I much appreciate the fact that the use of such technologies enables to archive material that can be re-analysed. I also consider very interesting the anecdotal evidence collected from local ecological knowledge about the use of snapping shrimps sounds as indicators of good fishing grounds (Lines 381-383).
Please find a few comments to improve the clarity of the paper.


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 OF SNPS ASSOCIATED WITH MAGNESIUM AND SODIUM UPTAKE AND THE EFFECT OF THEIR ACCUMULATION ON MICRO AND MACRO NUTRIENT LEVELS IN VITIS VINIFERA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript “Identification of SNPs associated with magnesium and sodium uptake and the effect of their accumulation on micro and macro nutrient levels in Vitis vinifera” by Naegele, Londo and Cousins (PeerJ id: 40548) reports the identification of a series of SNPs associated with magnesium and sodium levels in grapevine detected by association mapping in a ‘Verdejo’ x ‘Gewürztraminer’ offspring of 249 offsprings.

This work results novel and interesting, as not much information of the genetic basis of micro/macro nutrients accumulation in grapevine is available. The manuscript is nicely written, with clear and professional English language. Introduction is clear and it provides a nice of overview of the issues shown in the manuscript, and the number of references used is adequeate. Figures and tables are relevant, and appropriate for an adequate discussion.
Experimental design: The research shown in the manuscript is original, and it fits with the Aims and Scope of the Journal. Research questions are well defined to fill an identified knowledge gap, and authors carry out a nice investigation to answer it.

Nevertheless, I found authors should explain some of the methodological decisions taken during their investigation:

-	My main criticism deals with the mapping approach used, since their experimental approach (the genetic analysis of a biparental cross) seems more adequate to perform a classical QTL mapping study (via linkage map construction and QTL analysis) than the MLM method used in this work. Authors should discuss the reason of this choice, and how this method might have affected the results shown in the manuscript. Ideally, authors should perform a classical QTL mapping analysis to compare if their approach is equivalent to the one shown in the manuscript.

-	The second issue I would like to remark is the use of two genomes for reads alignment. Although the advantage is clear (and it is stated in lines 254-256), it is not clear if authors compared and merged the SNPs detected with these genomes (to construct a consensus dataset with common and specific SNPs), or if they conducted MLM association tests with both datasets in an independent way, which in turn will cause some redundancy in the results shown in the manuscript (see Tables 4 and 5). If that is the case, authors should show the number of common SNPs detected using both genomes, which should be high according to the findings of Genova et al., 2014 and Patel et al., 2018.

-	Related to the previous comment, did authors discard SNPs mapped the ChrUnk for MLM association tests? (they are not present in the Manhattan plot figure).

-	Also related to the previous comment, authors should discuss the different number of SNPs detected in the VxT progeny when using PN40024 or Thompson Seedless genomes for alignment.

-	An important point is the low number of markers obtained after GBS. Authors report the detection of “only” 10K/4K SNPs in a Vitis vinifera x Vitis vinifera progeny of 249 offsprings. Recent works report denser datasets. As an example, Tello et al. 2019 report the detection of an average of 17K SNPs in a series of progenies of 60 individuals. Do authors have any reason for such low efficacy? Did authors include Verdejo and Traminer in the GBS approach?

-	Some other detected issues include:

o	Abstract, line 21. Substitute Vitis for Vitis vinifera L. It applies to the rest of the document.
o	The term GWAS should be avoided in the document, as it is used for the genetic analysis of core collections or diversity panels (see line 213, as an example).
o	Line 361: genic “deserts”. Do authors mean intergenic regions?
o	Lines 378-380. Verdejo Blanco is not the grandson of Traminer. Verdejo Blanco is a direct offspring of Traminer (Castellana Blanca x Traminer). See: http://www.vivc.de/index.php?r=passport%2Fview&id=12949
o	Table 1. Authors found higher concentration levels for most nutrients than the expected “normal” range. Although it can be due to transgressive segregation, did authors analyse nutrients concentration in Verdejo and Traminer?
o	Tables 4 and 5. The likely role of these genes on the associated trait should be further discussed in the manuscript.
Validity of the findings: GBS are not available and bioinformatic scripts have not been provided (at least, it is not indicated in the manuscript). Authors should solve this issue.
Additional comments: No additional comments


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

Input:
Title: IDENTIFICATION OF SNPS ASSOCIATED WITH MAGNESIUM AND SODIUM UPTAKE AND THE EFFECT OF THEIR ACCUMULATION ON MICRO AND MACRO NUTRIENT LEVELS IN VITIS VINIFERA
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: Sounds very good.
Validity of the findings: No comments
Additional comments: Manuscript from Naegele et al. uses GWAS and identifies SNPs associated with magnesium and sodium uptake and the effect of their accumulation on micro and macronutrient levels in Vitis vinifera. It is a well-written manuscript and presents some useful data for the grape breeding and genetics community so I suggest it should be accepted for publication. However, before its acceptance authors should address some concerns.

I did not find a strong rationale for selecting some micro and macronutrients in the study. I would have loved to see authors talking about it from a biofortification perspective. The authors should focus little more to explain why they selected these 4-5 micro/macronutrients.

These variations in the correlation between the data collected from two different years. For example authors  reported “ Foliar symptoms were consistent (≥ 90%) between years and correlated with changes in nutrient concentrations of magnesium (r = 0.65 and r = 0.38 in 2015 and 2016,respectively), aluminum (r = 0.24 and r = 0.49), iron (r = 0.21 and r = 0.49), and sodium (r= 0.32 and r = 0.21)”. I see huge variations in the correlation data between the years. How do authors explain these variations?

Authors have used terms such as Sodium-associated SNPs, I am very critical of such descriptions. Authors should at least mention whether or not these SNPs are associated with higher or lower sodium / or another micro/macronutrient concentrations. It will provide a smooth reading to their audiences.


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 OF SNPS ASSOCIATED WITH MAGNESIUM AND SODIUM UPTAKE AND THE EFFECT OF THEIR ACCUMULATION ON MICRO AND MACRO NUTRIENT LEVELS IN VITIS VINIFERA
Review round: 1
Reviewer: 3

Output:
Basic reporting: This manuscript reports a genome-wide phenotype-genotype association study for traits related to plant mineral nutrition in a bi-parental population of cultivated grapevine. Provided that ion measurement protocol is valid (which I cannot assess because I am not a physiologist), this study is sound, producing a large amount of simultaneous results on the genetic variation and determinism of several ions content, with rigorous analyses and interpretation of results. However, it suffers from some weaknesses, which are listed below. Therefore, I recommend major changes to be made before acceptance.

On the whole, the manuscript is written in a clear, unambiguous, professional English language, but it still has to be double-checked to correct some small errors (e.g. lines 224 : 2015 written twice ; 236 : one genes ; 237 : which are a class ; 264 : on chromosome 3, 4, etc).

The context is well described in the Introduction. However, the reporting of previous QTL studies lacks precision:
Lines 88-91, formulation is unclear (“approximately” should be “up to”, important precisions such as “inter-specific cross”, “as rootstock” and “under chlorosing conditions” should be added, and many more small QTLs were found than stated).
Line 94: should be “Henderson et al 2018” and “the author characterized the proteins encoded by 4 alleles of a gene”.
Lines 87-98: all three studies were on inter-specific crosses, which should be stated.

Structure conforms to PeerJ standards, except that “Materials and Methods” section has “Methods” as title, there is no “Conclusions” section, and no separate “Funding statement” section.

Main figures are relevant and high quality, but Figure 2 is not cited in the text and its legend lacks some precisions (remove “foliar” and define the horizontal line). Add “vinifera” to the legends of both figures. Supplemental Figures are not very well explained. Supplemental Figure 1 does not show the same list of ions as mentioned in the text lines 197-198. Supplemental Figure 2 has no legend at all. For marker-trait associations, Manhattan plots should be provided for all traits analysed as Supplemental Figures, for both genomes, in addition to Figure 2.

Raw data are not supplied.
Experimental design: This manuscript reports original primary research within the scope of the journal.

The research question (genome regions associated with variation in grapevine leaf micronutrient content) is well defined, relevant, and meaningful. Correlation between nutrients and deficiency symptoms is extensively discussed, therefore it should also appear in the research question. How this research fills a knowledge gap (on joint genetic variation and determinism of several nutrients in grapevine) should be more clearly stated in the introduction.

Rigorous investigation was performed to a high technical and ethical standard (as far as genotyping and statistical analyses are concerned). The authors chose to detect QTLs with GWAS instead of interval mapping, as usually done in bi-parental populations. This interesting strategy is made possible by the high marker density reached by next generation sequencing methods. It requires no preliminary genetic mapping, and therefore makes it more straightforward to detect correlations with SNPs found with different reference genome sequences. The advantages of this strategy could be emphasized in the manuscript, and its potential limits (uneven marker genome coverage) discussed.
A few minor issues on methods are:
Line 139: Pearson’s correlations on raw or transformed variables? If on raw variables, then rather use Spearman, since raw distributions were not normal.
Line 151: why was read length trimmed at 20 bp? This seems very short compared to usual read length (100-150 bp).
Line 157: a depth threshold of 5 is very small for a heterozygous species such as grapevine; it could lead to inflated genotyping error rates. This should at least be discussed as a potential limit of the study, since no genetic mapping was performed, which would allow to remove markers with genotyping problems.

At many places, methods are not described with sufficient detail:
Lines 119-120: the time and way these nutrients were applied should be described in more details, according to what is stated lines 44-46.
Line 122-123: it is not clear here whether symptoms were measured separately or combined (it is clear only later, at lines 134-135).
Line 124: more details are needed on the number of leaves taken per vine and their development stage, according to what is stated at lines 291-292. In particular, was leaf sampling done exactly the same way in both years?
Line 125: it is not clear here if on the 249 offsprings or on the subsets described in the preceding sentence.
Line 125: air dried: at which temperature and how long?
Line 126: the methods used to quantify each ion are not given here, whereas it is a key point for this study. Please detail, or at least give method names and references. In addition, please explicit whether there were any controls and/or replicates.
Line 133: the statistical method used for testing normality should be given.
Line 134: precise what effect was tested in ANOVA.
Line 137: differences in nutrient concentrations between what?
Line 139: Ward method: which software, version and parameters?
Lines 140-142: not clear at all (“mean square values across years”); please give the page referred to in Fehr 1987, and explicit the formula used for calculating heritability.
Line 148: which enzyme?
Lines 148-149: give a reference for the protocol.
Line 153: replace “Pinot noir” by “PN40024” throughout the text.
Lines 159-161: was association with SNPs tested for all ions measured? It is not clear because distribution and correlation results are given for all 13 ions (Supplemental Table 1), but QTL results are given only for Mg and Na (Supplemental Table 3). Please state here explicitly and complement results and discussion if need be.
Line 156: “using a reference genome”: not clear; do you mean “between reference genomes”?
Line 160: give Tassel version.
Line 166: give Blast2GO version and NCBI database versions.
Validity of the findings: All analysis results underlying conclusions have been provided. Many valuable results are shown. However, additional results of interest could easily been shown and a few points have to be made concerning results presentation.
- Plots and correlations between years are not shown.
- Authors could also easily estimate BLUPs of genotypic values for all offsprings, after fitting a mixed linear model with genotype as random effect and year as fixed effect (phenotype = genotype + year + error). This would allow them to study genetic correlations between traits.
- Raw distributions of traits should be given as supplementary figures and commented.
Lines 158-159: only the total number of SNPs is given. Since no genetic map is produced, the physical distribution of these markers along the genome should be shown, for the reader to assess genome coverage quality.
Line 191-192: it is not clear why heritability is not estimable for these ions? Given the experimental design, heritability should be estimable for all ions quantified.
Lines 197-210: correspondence between text and Tables should be double-checked in this paragragraph:
- Line 199: r up to 0.6146 and 0.4805, not >=
- Lines 199-200: no for Al, OK for Mg
- Line 206: in 2015, not 2016
- Line 207: S P K in 2015, not in 2016
- Line 208: not true in 2016
- Lines 208-210: P/K not in Supplemental Table 2; also comment other ratios
For marker-trait associations, please give in text the total number of significant SNPs for each trait from the start (e.g. line 225: 21 SNPs), and try to more clearly highlight overlaps between years and between genomes (Manhattan plots, as required, would be helpful).
Lines 251-268: not very clear; more clearly separate results on stunting vs combined, and on significant SNPs vs significant SNPs in genes.

Conclusions given are generally well stated, linked to original research question and limited to supporting results. However, a few issues should be addressed and several additional points should be discussed, given the results:
- Discuss differences between years both in ion concentrations, correlations, and SNPs associated (more in 2016): could they partly be due to differences in nutrient supply between years? And/or to genotype x year interactions?
- Discuss low heritability values: could they partly be due to methods (leaf sampling, precision of ion quantification methods)?
- Present results have been obtained in a pure V. vinifera population; discuss what differences this may make with previous works on inter-specific crosses? What is the impact on mineral nutrition of studying offsprings as seedlings/cuttings vs as rootstocks?
- Line 295: the results of Bates and Wolf 2008 are used as reference by the authors; please discuss to what extent they are comparable to your own data (plant management? Sampling procedure? Measurement method?).
- Lines 349-350: results were compared with other GWASs but allele frequencies are not comparable between bi-parental populations and diversity panels
- Line 369: year effect might be due not only to age, but also to environment or genotype x year interactions.
- Line 374: in bi-parental populations, confidence intervals are large due to large extent of linkage disequilibrium, and therefore they harbor many candidate genes.
- Line 381-382: not clear; segregation distortion could easily be tested along the genome (physical positions) for this population.
- Line 384-385: to clarify relationships between symptoms and nutrients, binary regression of symptoms on nutrients could be performed. PCA of nutrient contents (in each year and/or with inter-year genotypic BLUPs) may also help clarifying the relationships between these traits.
Additional comments: Miscellanous:
In the abstract: add main methods (GBS and GWAS) and the range of QTL effects (% variance explained by SNPs)
Table legends: often incomplete to be self-sufficient (e.g. for Tables 2 and 3, “in a Vitis vinifera F1 population” should be added)
Replace “Thompson” by “Thompson seedless” throughout
Lines 44-49 should be moved to line 75, and V. vinifera should be presented as the cultivated species at line 75
Line 145: replace “progeny” with “offspring”
Line 247: “similar replications” between years?
Line 254: replace potential by total
Line 265: “significant SNPs” in genes?
Line 307: >95%?
Line 347: give reference just after “previous work”
Table 1: replace “Normal range” by “Reference range”
Table 3: why is Ca in this Table and not only in Supplemental Table, since it is not correlated with symptoms in both years? Replace “Multivariate analysis of correlation” by “Correlations”, since only 2-way correlations were tested.
Table 3 and Supplementary Table 1: highlight strong correlations (r > 0.3) for ease of reading.
Table 5 is cited before Table 4 in text.
Table 5 line 7: add “and NCBI”
Supplemental Table 3: why are there negative R2 values?


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 OF SNPS ASSOCIATED WITH MAGNESIUM AND SODIUM UPTAKE AND THE EFFECT OF THEIR ACCUMULATION ON MICRO AND MACRO NUTRIENT LEVELS IN VITIS VINIFERA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The reviewed manuscript “Identification of SNPs associated with magnesium and sodium uptake and the effect of their accumulation on micro and macro nutrient levels in Vitis vinifera” by Naegele et al.  (ID: peerj-40548-2) reports the identification of some SNPs associated with magnesium and sodium levels in grapevine detected by association mapping in a ‘Verdejo’ x ‘Gewürztraminer’ offspring of 249 individuals. I appreciate the answer given by the authors to all my suggestions, and the effort done to improve the quality of their manuscript. Therefore, I only have some minor suggestions.

L. 110. Material and Methods.
When transplanted, were the seedlings grafted or were they grafted on their own roots?
L. 152. The R package (and version) used for BLUP values calculation should be specified.
L. 178: Replace “principle components” by “principal components”.
L. 218. Authors found that: “Na, P, Cu, Mn, N, S, and Ca concentrations in 2015 or 2016 had no heritability”. Authors should discuss the power and precision of the reported QTLs in LGs 11, 12 and 18 for Na concentration considering that they suggest it as a non-heritable trait.
L. 225. Figure 2 does not show the correlation between symptoms and nutrients variation. Please, correct.
L. 229. How is this 22% value estimated?
L. 232. In my opinion, a correlation r=0.3 can not be considered as “strong”. In fact, in line 236 authors refer to correlations r= 0.2-0.4 as, low-moderate, which is more realistic.
L. 237. Why is copper shown in capitals?
L. 243. Replace “Significant positive associations” by “Significant associations”.
L. 245. Rewrite “Mg-related SNP effects were approximately 6%” by “SNPs associated with Mg levels explained ca. 6% of trait variation”, or something similar.
L. 256. “SNPs […] had both negative and positive effects” Per se, SNPs do not have positive nor negative effect on traits. Alleles do. Please, correct.
L. 258. “Two of the SNPs detected (S11_16152632 and S18_25745143) were detected in 2015 and 2016”. Please, rewrite.
L. 260. “Only a single SNP identified in 2016 (S11_11635675) was also 261 associated with a gene”. Do authors mean that only one SNP identified in 2016 was found in a gene region?
L. 261. “11 positive effect SNPs”. Please, correct as suggested for L.256 and check the whole document.
L. 290. Figure 2 is a PCA plot, not a Manhattan plot. Please correct and check the whole document for similar errors.
Table 5. “Pinot Noir 12x” Authors must avoid naming the reference genome as “Pinot Noir”, as it is not. The reference genome they refer to is the Vitis vinifera cv. PN40024, a nearly homozygous line derived from Pinot Noir. They should check the whole document.
Table 6. Replace “Thompson Sdls” by “Thompson Seedless”. Authors should check the whole document to harmonize the name of the Thompson Seedless cultivars, sometimes referred as “Thompson Seedless” and sometimes as “Thompson seedless”.
Figure 1. I think the symptomatic (stunted) stem internodes they refer to are shown in Figure 1B, not 1A. Please, correct. Besides, Figures 1C and 1D are not too clear.
Experimental design: no comment
Validity of the findings: Authors should discuss the power and precision of the reported QTLs in LGs 11, 12 and 18 for Na concentration considering that they suggest it as a non-heritable trait.
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: IDENTIFICATION OF SNPS ASSOCIATED WITH MAGNESIUM AND SODIUM UPTAKE AND THE EFFECT OF THEIR ACCUMULATION ON MICRO AND MACRO NUTRIENT LEVELS IN VITIS VINIFERA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Most points raised by the reviewers have been answered satisfactorily. However, revision is still needed for the following points.

I cannot see any indication that raw data are supplied in the beginning of the submission and I cannot see any " important announcement " section in the revised manuscript. If GBS data have been made available, this should be written in the text, with the corresponding links (I did not manage to find them in NCBI). Moreover, plant identifiers in the vcf file do not match plant identifiers in the phenotype file, thereby preventing duplicating the analysis. Please provide the correspondence between both identifier lists.

Some Table and Figure numbers have not been corrected in the revised text, please double-check numbering (e.g. Line 251 : replace " Suppl Table 3 " by " Suppl Table 2).

Figure 3 : is this Figure for symptoms (both stunting and chlorosis, as stated in Figure legend) or for stunting only as stated in the text ?

" We have however performed an additional PCA analysis of ions to demonstrate the weighting of Mg, Fe, and Al specifically along the vector where symptomatic plants occur. (Figure 2). " : this PCA is interesting (provided they are based on BLUPs of genotypic values), but symptomatic plants are not projected on it.

In supplemental Table 3, only the diagonal is of interest.

Line 275 : on chromosomes 11, 12, 13, and 18 (see Suppl Table 5). Please double-check consistency between Tables and text throughout.
Experimental design: The reasons why the authors chose to apply GWAS rather than QTL detection are not given in the discussion, unlike stated in the answer letter. Moreover, line 364 : Zou et al 2020 did not perform QTL detection, but only genetic mapping.

Several comments concerning BLUPs:
- Lines 163-165 : the authors have estimated BLUPs, but it is not clear at all what linear model they used, since it is not stated that they have included genotype effect as a random effect. The classical full model to use is : phenotype = genotype (random) + year (fixed) + error (random), where genotype is usally included but year is not always included, depending on the trait. Please clarify.
- All BLUP values do not need to be given as a Supplementary Table.
- " high correlation between average ion concentration and computed BLUPS indicate this method does not add much to the current analysis. " : BLUPs of genotypic values are more precise estimates of genetic values only when year effect is significant.
- " BLUPs have been calculated and are included as a supplemental file.  However, these results did not differ from our previous measures of correlations between ions and symptoms. " : correlations between BLUPs of the different traits (genetic correlations) are not shown.
- Line 166 : " the mean BLUPs " : not clear.

" Line 134: precise what effect was tested in ANOVA." : still not precised line 152.
Validity of the findings: Lines 375-376: Replace " However, correlations between years indicated that year x genotype played a substantial role in ion concentrations " by " However, low correlations between years indicated that year x genotype played a substantial role in ion concentrations "

" A depth threshold of 5 is very small for a heterozygous species such as grapevine; it could lead to inflated genotyping error rates. This should at least be discussed as a potential limit of the study, since no genetic mapping was performed, which would allow to remove markers with genotyping problems. " : All I can find in the discussion to answer this point is " Grape has a high level of heterozygosity, and separating genotype errors from minor alleles can be challenging (Hyma et al., 2015). " I insist that it should be explicitely stated that the combination of the low depth threshold and the absence of genetic mapping may result in genotyping errors, which is a limit of this study.

" Text has been updated to explicitly state that all ions were tested, but no QTL detected except for those described. " : I cannot see where it is stated that " no QTL were detected except for those described "

Lines 235-236 : still not clear : had null heritability ?

Lines 243-244 : still not exact : replace " In 2015 and 2016 concentrations of Mg (r = 0.6146) and Al (r = 0.4805) " by " In 2015 and 2016 concentrations of Mg (r <= 0.6146) and Al (r <= 0.4805) "

Lines 243-245 : replace " In 2015 and 2016 concentrations of Mg (r = 0.6146) and Al (r = 0.4805), respectively had the highest correlation with observed vineyard symptoms (Table 3) " by " Mg concentration in 2015 and Al concentration in 2016 had the highest correlation with observed vineyard symptoms (r = 0.6146 and 0.4805, respectively) (Table 4) "

Lines 255-257 : not clear which test was applied ; moreover, some ratios were consistently associated with symptoms in both years

For the points listed below, I can see no change in the v1 pdf version. Please check which version of Tables you included into the pdf.
- " Table 1: replace "Normal range" by "Reference range" - text has been adjusted "
- " Table 3: why is Ca in this Table and not only in Supplemental Table, since it is not correlated with symptoms in both years? Replace "Multivariate analysis of correlation" by "Correlations", since only 2-way correlations were tested. - Ca was deleted from Table 3 and title has been changed. ",
- "Table 3: highlight strong correlations (r > 0.3) for ease of reading. - Tables have been bolded."
- "Table 5 line 7: add "and NCBI" - text has been adjusted.

There were indeed negative R2 values in former Suppl Table 3 (for example, S3_5986778 had R2 value -0,054992312) but only for PN40024, but the equivalent for PN40024 of revised Suppl Table 5 is no more available in the revised version. In revised Suppl Table 5, what does " SNP effect " stand for ? Line 276 it is stated that " effects ranged from 8 to 13% of the observed variation ", but there are both positive and negative values in the " SNP effect " column.
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: ABNORMAL EXPRESSION OF HOXD11 PROMOTES THE MALIGNANT BEHAVIOR OF GLIOMA CELLS AND LEADS TO POOR PROGNOSIS OF GLIOMA PATIENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: As a reviewer I am not able to verify references for SVA technique used in line 133. Removing batch effects is important when working with multiple sources of data hence referencing this technique would be very useful to the future readers of this manuscript.

In line 134 & 270 authors have not stated what metric (ex: median) have been used to classify the expression levels of HOXD11 into high, low.

For figure 1b, 1c- authors have not stated what type of expression levels they have used. (ex: fpkm, log transformed, z scores etc). Please clarify this.

In line 254- is it age at sample collection or age at diagnosis – please clarify this variable description.

In line 376- can you reference/cite appropriate racial classification? As a reviewer I am not able to verify if there are any official race classifications (ex- yellow) as described here.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: ABNORMAL EXPRESSION OF HOXD11 PROMOTES THE MALIGNANT BEHAVIOR OF GLIOMA CELLS AND LEADS TO POOR PROGNOSIS OF GLIOMA PATIENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Writing style can be improved a little. Specific examples provided in comment below.
Experimental design: No comment
Validity of the findings: The findings appear valid and well-substantiated.
Additional comments: The authors have performed a thorough evaluation of the expression of HOXD11 in glioma across multiple cohorts. They used GSEA pathway-based analysis to establish the role of HOXD11 as an oncogene in glioma. They further validated the effect of HOXD11 on cell cycle experimentally using flow cytometry and western blotting.
While genes of the HOX family including HOXD11 are known to play a role in the development of a variety of cancers, the role of HOXD11 has not been specifically established in glioma.
Some comments below:
1.	The y-axis in figure 1a makes it tricky to see the expression patterns. Cutting off the y-axis to exclude extreme outliers would help more clearly focus on the expression patterns in individual tumor types.
2.	In the breakdown of expression by subtype (figure 2g), the x-axis legend is not clear. Detailed subtypes can be added in the legend.
3.	Are the survival analysis from CGGA (figure 3) adjusted for age, gender and tumor stage? Have the authors explored the association of HOXD11 with MGMT status?

The writing can be improved to enhance clarity and avoid redundancies. Some suggestions are below:
1.	In line number 26, clinical department of which institution? How many samples?
2.	It would be helpful if the authors could provide number of samples from each study in abstract or introduction to easily understand the scope – it is currently buried in methods section.
3.	The description of TCGA in lines 64-70 can be shortened as this is widely accepted across the field.
4.	There is a typo in line 74 – CGGA (as opposed to CCGA)
5.	Data description in lines 374-376 can improved.


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: ABNORMAL EXPRESSION OF HOXD11 PROMOTES THE MALIGNANT BEHAVIOR OF GLIOMA CELLS AND LEADS TO POOR PROGNOSIS OF GLIOMA PATIENTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1. The description of TCGA in line 64, 117 is redundant
2. There is a grammatical error in line 239
3. The Figure text is a little unreadable- can it be made a more clear.
4. The fig 5c is not very visible unless you zoom in- could that be modified?
5. For fig 6c, can the authors provide an uncropped image of the blot
Experimental design: The authors have conducted a thorough investigation of HOXD11 in glioma prognosis, very well utilizing the public datasets.

1. The authors used publicly available datasets to show the higher expression of HOXD11 in tumor vs. normal- were the datasets preprocessed before analysis. Did the authors consider any possible covariate in the dataset.
2. In fig 1b- a few samples from normal were in the range above the mean of tumor sample expression- what was different about these two samples?
3. In the survival analysis, the IDH wildtype does have significant difference between High and low HOXD11, however this difference seem to be minimal with IDH mutation without 1p19q codeletion. Did the authors consider to condition on the IDH mutation without 1p19q codeletion?
Validity of the findings: HOXD11 plays a significant role cancer, have the authors checked for literature describing a similar role in any other type of cancer.
Additional comments: The authors in the manuscript show the role of HOXD11 through bioinformatic analysis using publicly available datasets and through a series of experiments. The authors very efficiently use the available datasets to show the association of high expression of HOXD11 with age, WHO grade, chemotherapy status, histological type and 1p19q codeletion data and isocitrate dehydrogenase (IDH) mutation. They further validate the pathway predicted by GSEA with experiments proving knockdown HOXD11 inhibits proliferation, invasion and to prevent cell cycle progression.


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 OF A METABOLIC-RELATED GENE SIGNATURE PREDICTING THE OVERALL SURVIVAL FOR PATIENTS WITH STOMACH ADENOCARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: There are some minor grammatical errors, such as the lack of "of" in "expression mRNAn" on line 92, etc.
Experimental design: no comment
Validity of the findings: In the GEO cohort, compared with other clinical indicators, the "AUC" of "the risk score" is not very good. The author should discuss the possible reasons.
Additional comments: GSEA is used to analyze all possible KEGGs of genes in the model. It is recommended that the author add GO and KEGG analysis to the differential genes of "the high-risk group" and "the low-risk group".


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 OF A METABOLIC-RELATED GENE SIGNATURE PREDICTING THE OVERALL SURVIVAL FOR PATIENTS WITH STOMACH ADENOCARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript by Yuan Nie et al. demonstrates novel prognostic markers which help in early diagnosis in Stomach adenocarcinoma (STAD). Using databases from TCGA authors have established prognostic model systems and validated by GSE84437 cohort. Manuscript is properly referenced and data is professionally tabulated.  However, manuscript have grammatical and spelling mistakes at places. It would be useful if manuscript can be prrofread by a native speaker before resubmission
Experimental design: 1.	Authors have concluded their entire findings based on TCGA and GEO databases only. It would have been more tempting to include other cancer data repository e.g Oncomine ,Bioportal etc.

2.	In addition to univariate Cox regression author can also use survival trees (e.g.CART for survival data) analysis which will further support the finding.
Validity of the findings: No comments
Additional comments: The manuscript by Yuan Nie et al. demonstrates novel prognostic markers which help in early diagnosis in Stomach adenocarcinoma (STAD). Using databases from TCGA authors have established prognostic model systems and validated by GSE84437 cohort. I find manuscript  can be considered for publication in PeerJ with addressing a few following minor comments.

1.	The authors have concluded their entire findings based on TCGA and GEO databases only. It would have been more tempting to include other cancer data repository e.g Oncomine ,Bioportal etc.

2.	In addition to univariate Cox regression author can also use survival trees (e.g.CART for survival data) analysis which will further support the finding.

3.	Manuscript have grammatical and spelling mistakes at places. It would be useful if manuscript can be prrofread by a native speaker before resubmission.


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 OF A METABOLIC-RELATED GENE SIGNATURE PREDICTING THE OVERALL SURVIVAL FOR PATIENTS WITH STOMACH ADENOCARCINOMA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors proposed a bioinformatics study to identify a metabolic-related gene signature
predicting the overall survival of patients with stomach adenocarcinoma. Some efforts have been done, however, there are some major points that need to be improved:

- The use of English should be improved significantly. There are some grammatical errors and typos. It is better to be checked by a native speaker or an English editing service.

- Lacking literature review. The authors missed to mention and discuss a lot of related bioinformatics studies on stomach adenocarcinoma specifically.

- Quality of figures should be improved.
Experimental design: - Did the authors concern about the batch effect removal in their study?

- TCGA & GEO have been used in previous bioinformatics studies such as https://doi.org/10.1016/j.meomic.2020.100001 and https://doi.org/10.3390/jpm10030128. Therefore, the authors should mention more works to attract a broader readership.

- The authors should release source codes for replicating the methods.

- Why did the authors select median values as the cut-off for risk score?
Validity of the findings: - Performance results were not so good (about AUC of 0.57 in validation set)

- I cannot see the legends in the heatmap, it is important to improve the quality of figures.

- How did the authors calculate the risk-scores for four-gene signatures together? As I have known, it is easier to calculate risk-score for individual genes.

- ROC curve or AUC has been used in previous bioinformatics studies i.e., PMID: 31362508 and PMID: 31921391. It is suggested to refer to more works in this description.

- In Fig. 5, it is better to use the same color for the same characteristic among TCGA and GEO set. It is not easy to compare with different color use.

- In Fig. 5 also, why did GEO dataset have fewer characteristics (fewer lines) than TCGA?

- There is overfitting on the results (AUC of 0.696 and 0.574 in training and validation set). The authors should discuss how to deal with it.
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: IDENTIFICATION OF A METABOLIC-RELATED GENE SIGNATURE PREDICTING THE OVERALL SURVIVAL FOR PATIENTS WITH STOMACH ADENOCARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: No comment.


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

Input:
Title: IDENTIFICATION OF A METABOLIC-RELATED GENE SIGNATURE PREDICTING THE OVERALL SURVIVAL FOR PATIENTS WITH STOMACH ADENOCARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
Additional comments: Authors have provided a logical and satisfactory point-by-point explanation for the concerns raised during review process. I think that manuscript  has improved substantially and can be considered 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: IDENTIFICATION OF A METABOLIC-RELATED GENE SIGNATURE PREDICTING THE OVERALL SURVIVAL FOR PATIENTS WITH STOMACH ADENOCARCINOMA
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: My previous comments have been addressed satisfactorily.


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: STAGE 1 REGISTERED REPORT: SPATIOTEMPORAL PATTERNS OF THE COVID-19 EPIDEMIC IN MEXICO AT THE MUNICIPALITY LEVEL
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript describes the hypothesis and the methods used for making an spatio-temporal analysis of the COVID-19 spread on Mexico.
The manuscript is generally clear, although some corrections should be done in order to reach a higher level of clarity and professional English, specified below.
I find that the introduction lacks some references that may be key for the study. For example, I think that sero-prevalence studies should be cited (eg Pollan et al, The Lancet, doi:10.1016/S0140-6736(20)31483-5), to explain that the statistics typically reflect symptomatic patients, but there may be asymptomatic individuals that are infectious. There are also some studies considering the mobility between municipalities as the connection between them to fit the COVID-19 outbreaks (see Arenas et al, medRxiv, doi:10.1101/2020.03.21.20040022, Eguíluz et al, medRxiv, doi:10.1101/2020.05.03.20089623).
Experimental design: The experimental design is interesting. My main concern is the lack of a link between the clear and well-defined hypothesis and the listed methods, such that the author explains the role of each of the methods. For example, Moran's I index is introduced, but I am missing an explanation of the expected values, what they mean, and what these values will imply for the analysis.
Validity of the findings: For a Stage 1 Registered Report, the description of the hypothesis and the methods is relevant and clear.
Additional comments: I have some additional comments for the author that may help improve the manuscript:
-Abstract: as this is a Stage 1 Registered Report, I think that the abstract should not talk about something done (i.e. in past tense), but about something that will be done.
-L21: I suggest replacing the word region by continent.
-L25-31: which are the sources of this information? Citation needed.
-Additionally to the proposed networks connecting municipalities, is there available census data specifying people that commute (i.e., people that live in one location and work in another)? Two of the proposed references above use similar census data.
-L67-69: more detail is needed. Is this data individual-based, i.e. for each patient you have sex, age... or they are grouped at some aggregation level?
-L79: I think that contaminated is not the best technical word for this context.
-L95-97: first it is proposed to analyse the new number of cases and deaths in Mexico and then it will be compared with the cumulative data in other countries. I propose using the same information for comparing both.
-L138: Euclidean distance is proposed, but the Earth is approximately a sphere. Maybe it would be better to use the Haversine formula for calculating the distances between two points in the surface of a sphere.
-Fig. 1: the color code should be specified, either as a legend or in the caption. The caption states that the figure illustrates the distances, but I just see straight lines, maybe the numbers in km should be annotated next to each line. I also guess this figure does not represent whole Mexico, so 1) an illustration of the data (for example, cumulative cases or deaths) across the whole country would be very illustrative, and 2) it would be good to specify which zone of Mexico is represented in this figure.


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

Input:
Title: STAGE 1 REGISTERED REPORT: SPATIOTEMPORAL PATTERNS OF THE COVID-19 EPIDEMIC IN MEXICO AT THE MUNICIPALITY LEVEL
Review round: 1
Reviewer: 2

Output:
Basic reporting: Thank you for the opportunity to appraise this registered report which outlines steps that will be taken to identify local coronavirus 2019 (COVID-19) outbreaks in Mexico.
In this manuscript, the authors consider an outbreak detection algorithm–the scan statistic–to examine clusters of COVID-19 in Mexico. The use of scan statistics harmonises well with other approaches found in the literature, particularly papers from the United States of America e.g. Hohl et al. (DOI: 10.1016/j.sste.2020.100354) and Cordes and Castro (DOI: 10.1016/j.sste.2020.100355) who also use Moran’s I in their work.
I commend the authors for following current best scientific practices in submitting their registered research. It is good that authors provide a DOI to a repository where their data is located allowing for the reuse; it is my hope that they will also provide access to a repository with their analysis code. Authors should ensure colours used in figures are colour-blind friendly and are discernable when printed in black-and-white.
Experimental design: The following comments are highest priority and concern the methods used in the approach:
    1. (Line 77) My understanding, based on the description provided by the authors, is that the first (imported) case occurred on 28th February 2020. This would mean nearly 1/3 of the data is 0 counts. How does this affect the analysis? (Line 124) Would this mean the assumption of following a Poisson distribution is violated?
    2. (Line 92) Aggregating the data to weekly counts gives a time series of 32 observations of which eight-or-so are before the first case occurs. Is this a sufficient sample size for the authors to test their hypothesis of interest?
    3. (Line 49) Authors should provide more detail concerning how exactly they intend to test their hypotheses statistically. (Lines 124 and 125) To me it seems that authors are using a Neyman-Pearson decision-making framework rather than Fisher’s significance testing framework. If this is the case, they should specify their sample size, and pre-specified limits for type I and type II errors. (Line 126) Which values of the likelihood ratio would be considered significant?
    4. (Line 82) For reproducibility purposes, authors should note which versions of software and software packages they use
    5. (Lines 46-50) Authors should be aware that reporting standards do exist for registered reports that are not based on experiments. Authors should look at e.g. van den Akker et al. (DOI: 10.31234/osf.io/hvfmr)
    6. a. (Line 64) It is unclear to me why authors are using population projections rather than census data to obtain population counts. The Mexican national institute of statistics, geography, and information (INEGI) should have been conducting a nationwide population census in March of this year (censo2020.mx) so updated population counts should be available. b. Authors could consider using the United Nations World Population Projections as a sensitivity analysis, as these are constructed under a couple of different scenarios. However the UN projections may only exist at national level rather that subregional
    7. (Line 71) Since the analysis period covers a period of time when testing efforts may have been increased, this paragraph and its effect on the analysis should be discussed in more detail
    8. (Line 157) These considerations concerning large cities are captured in the gravity model approach (DOI: 10.1086/422341) and authors may wish to note that more explicitly
The following comments will hopefully provide more detail for the reader to understand the situation being studied:
    1. (Line 21) In the introduction I would suggest authors provide exact number of cases to support their point that the Americas are the most affected regions. If such information is sourced from the World Health Organization (WHO), I would further suggest authors use WHO regional terminology, which in this case the region would be WHO PAHO
    2. (Line 30-31) At the end of the second paragraph in the introduction it would be nice to have some more information about the situation in June, July, and August as the analysis also spans those months and the only policy information provided for the reader to understand the context concerns March to May
    3. (Line 61) Authors should note exactly which information they are using from the “Our World in Data” initiative to allow readers to access the same information, “country-based COVID-19 statistics” is vague
    4. (Line 138) Authors should motivate their choice of distances considered, it seems there may have been an additional option which was since removed
Validity of the findings: no comment - section will become relevant after IPA
Additional comments: The following comments are suggested minor changes to text:
    1. (Line 51) “COVID” should be “COVID-19”
    2. (Line 29) Anda-Jauregui used the term “Journada Nacional de Sana Distancia” (arXiv: 2006.11635) in their manuscript. I am not a Spanish speaker so I am not sure whether this is the correct term and “Sana distancia” is more colloquial
    3. (Line 107) Authors should note what n and x’s are
    4. (Line 109) Authors should explain that w_{ii} = 0 means a region cannot be adjacent to itself
    5. (Line 138) Authors should update numbering such that resistance distance is 3 and gravity model is 4
    6. (Line 152) Uppercase “K” should be lowercase “k” to match notation used in formula above
    7. (Line 152) Authors should note what d_{ij}^2 is
    8. (Lines 132, 152, and 169) Authors might wish to note why denominators cannot be zero
    9. (Line 172) Time is usually denoted t rather than w. This may avoid confusion with weights that are also denoted w


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: STAGE 1 REGISTERED REPORT: SPATIOTEMPORAL PATTERNS OF THE COVID-19 EPIDEMIC IN MEXICO AT THE MUNICIPALITY LEVEL
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thanks to the author for addressing our comments.
There are still two minor changes that I suggest:
-I proposed to provide examples of limit cases of Moran's index and explain what they mean, which could improve very much the understanding of the reader.
-Euclidean is not spelled right in the caption of Figure 1.
Probably the second point can be modified at the proof stage, and the first is just a remark, as I already mentioned that, but it seems that the author decided not to include it.
Experimental design: No new comments.
Validity of the findings: No new comments.
Additional comments: No additional comments


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

Input:
Title: STAGE 1 REGISTERED REPORT: SPATIOTEMPORAL PATTERNS OF THE COVID-19 EPIDEMIC IN MEXICO AT THE MUNICIPALITY LEVEL
Review round: 2
Reviewer: 2

Output:
Basic reporting: I believe the authors have addressed the points I raised in the previous review in a satisfactory manner and I have no further comments at this time. I look forward to seeing the results once the study has been conducted.
Experimental design: See previous comment
Validity of the findings: NA until after analysis conducted
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 RELATIONSHIP BETWEEN (SUB)TROPICAL CLIMATES AND THE INCIDENCE OF COVID-19
Review round: 1
Reviewer: 1

Output:
Basic reporting: However, I have some comments to improve the quality of the document
In the abstract, it is necessary a better description of materials and methods, as well as the most important results, the authors too much emphasis on justification, but not enough mention is made of the methodology.
The Authors write This study intends to corroborate with both laboratory experiments and real-world data to provide rationale for the adoption of public health policies. What laboratory experiments are they referring to? to covid tests? or maybe to statistical models?
This is not described in detail in the methodology
Introduction
Line 50, after 2019 space, the same for all documents
For editor,

Line 53, citations are not in the correct format, the same for all documents
Experimental design: In general, the methodology requires a more detailed description
Line 94: describe what the acronym INMET means
Validity of the findings: The results are tainted with arguments and assumptions
Line 124. Why do the authors report Spearman and Pearson correlation? should be one of the two based on the parametric distribution of the numerical data. In addition, the Spearman correlation between COVID incidence and mean temperature is negative (-0.08075), not positive.
Line 140-142, remove “The incubation period of COVID-19 combined with the delay of Sars-CoV-2 testing results necessitated a moving-average approach to account for the cumulative lag effect of temperature and relative humidity[7].” gives the impression of being discussion and not results

In table 1 you must put what T and RH and N (observation?) Mean
Figure two has poor resolution, it is impossible to read
Additional comments: The Study is relevant, mainly taking into consideration what was stated by the authors regarding that in tropical areas, people have greater contact with the external environment, the results of studies of this type, without a doubt, are of importance for decision-making and the implementation of local policies for infection prevention.


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 RELATIONSHIP BETWEEN (SUB)TROPICAL CLIMATES AND THE INCIDENCE OF COVID-19
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: The knowledge gap being investigated should be clearly mentioned and method should have been described in technical high standards.
Validity of the findings: The findings figure should have been simplified. In present form it contains lot of data and difficult understand from the layman's perspective. This is needed as today "covid-19" topic is related to every member of society. Authors can add/present their conclusive figure and in which their novelty aspect can be highlighted.
Additional comments: In all figures, there is overlapping of lot of data. Too much scattering of data is difficult to bring out the novelty or authors contribution in this work. I would suggest add one extra figure, it could be a schematic based highlighting the contribution.


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

Input:
Title: THE RELATIONSHIP BETWEEN (SUB)TROPICAL CLIMATES AND THE INCIDENCE OF COVID-19
Review round: 2
Reviewer: 1

Output:
Basic reporting: I can actually notice a great improvement over the first document
I just have a few little suggestions
In the abstract the wording was improved, however, the results still need to be better described, the results of the correlations can be described
Experimental design: A more detailed description of the methodology was made, Figure 2 helps to better understand the study design
Validity of the findings: In tables 2, 3, and 4 delete the columns, similar to table 1
In the figures in general the y-axis describe the incidence that is used (per 100k habitants?), Similarly in the X-axes, ° C should be added to T, that is, the units of measurements
Additional comments: I'm glad the necessary changes have been made


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 RELATIONSHIP BETWEEN (SUB)TROPICAL CLIMATES AND THE INCIDENCE OF COVID-19
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: Happy to see the revised text and the added figure 2.
Validity of the findings: No comment
Additional comments: No comment