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: RETHINKING THE USE OF FINITE ELEMENT SIMULATIONS IN COMPARATIVE BIOMECHANICS RESEARCH
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript is very-well written, with no grammatical typos and clear, easy-to-follow language. It is structured in a standard, professional manner and crucial data is contained within the supplementary data. As the article now stands, the relevant background literature is cited, although some additional references may be needed - please see my comments below.

Overall goal of the manuscript is clearly stated in the paragraph starting Line 47.

The study is mostly self-contained although some important data (included in the two previous studies from which data for the meta-analysis are taken) should be included here, please see further comments.

A few minor suggestions for grammatical changes are made in the attached annotated PDF.
Experimental design: As noted in Part 1, the overall research question and how this study fills an important knowledge gaps are clearly stated in the Introduction.

Generally, the methodology applied is sound. The author makes use of finite element models from two previous studies on which they were an author (Prybyla et al 2018 and Perez-Ramos et al 2020). The selection of these models is well-supported - they were analysed using the same FE software (Strand7), muscle forces were calculated using the dry skull method, applied with Boneload and similar percentages used for the working and balancing sides, similar constraints were applied and the selected output (ME and SE) were scaled to account for differences in sizes. One minor thing missing is material properties applied, as the elastic moduli used in the two studies varied slightly (18 vs 20 GPa) - please specify what was used here.

Furthermore, the author is to be commended for clearly discussing assumptions that meta-analyses make of the data (Line 153).

However, there is some information missing in the methods section. First, Prybyla et al 2018 included 21 taxa and Perez-Ramos et al 2020 included 12 taxa yet the current study makes use of 27 taxa - why were the others excluded? Although full information on the taxa used is in the supplementary table, this should be noted, as well as whether the taxa analysed here were extinct or fossil (both were analysed in the earlier studies).

In the supplementary table "eco-dataset" there is no key for the number coding for dietary breadth or trophic level. Please include some key with this supplementary table - do not make readers have to look this up in PanTHERIA.

I definitely feel that the crucial information contained within the supplementary table "FE dataset" is important enough to be a table within the main text, rather than supplementary data.

My biggest concern with experimental design and interpretation of results involves the output variables/performance metrics considered. Both are measures of structural efficiency (in terms of conversion of muscle force to bite force and strain energy) that are then associated to ecological variables and phylogeny. There are two points to be made here:

1. It is not explained in the text HOW these variables are expected to vary with (and therefore help identify) different diets or ecologies. Why use these metrics? Do we expect herbivores to have more efficient skulls than carnivores, for example? I realise the author covered this to some extent in a previous paper, Tseng and Flynn 2015, but a brief explanation is needed here. Additionally, why were two bite points tested? What do differences in results between these bite points signify? Again, in Perez-Ramos et al 2020 it is stated that larger differences in results between the two bite points suggests higher functional differentiation along the tooth row and therefore more restrictive diets. Such explanations - even briefly - would be useful here, otherwise it is unclear why these metrics are used.

2. One of the wonderful and tricky things about FEA is the sheer amount and diversity of data that is produced. Most FE studies only consider a small subset of output to analyse, usually targeted to the hypothesis being tested. In this case, the author chooses two measures of efficiency. However, it is very important to note that efficiency is not the only performance metric linked to ecology and diet. For example, some taxa with inefficient jaw systems (for example, crocodilians) still produce extremely high (relative to body size) bite forces which strongly influence ecology. Other important outputs include peak stress/strain magnitudes - I will note that great care must be taken when extracting and interpreting such values as validation studies have shown FEA is not 100% accurate in predicting such values compared to experimental data. Nonetheless, relative comparisons of peak stress/strain between scaled models is an important indicator of structural strength. Also important are more qualitative outputs such as von Mises stress distribution (areas of high vs low stress) and how the skull deforms under loads (torsion, bending, etc.).

I am certainly NOT saying that the author should consider all of these performance metrics in the current study, which would make it substantially longer and more complicated. However, I think it must be noted somewhere in the main text that other outputs strongly linked with diet and ecology are not being analysed and that this study only considers a small (but important) subset of performance metrics available.

A few additional and minor notes. How does the quite unequal distribution of dietary breadth categories (for example, one each in types 4 and 5 and none in type 2) and trophic level (predominantly type 2, with few from type 1) impact statistical analyses?

Given that Fig 1A is used to illustrate the increased application of FEA in biosciences and that the present analysis focuses on the skull, the first paragraph of the Survey Methodology could be substantially trimmed. Similarly, it would be useful to know the number of studies focused on the skull illustrated in Fig 1B.
Validity of the findings: Overall the results of this study are very interesting and I think will prove useful in designing future studies using FEA. The main point is that smaller data sets produce stronger correlations between FE results and ecology/phylogeny than increasingly larger datasets. It will be interesting to see whether this trend holds true for other clades/anatomical regions/biomechanical techniques/FE performance metrics. Nonetheless, the results presented here are intriguing.

The author's comments on the importance of taxon sampling - and in particular the influence of outliers - are particularly fascinating. One question - do you have any evidence that demonstrates that the smaller samples tended to include a larger proportion of outliers? If so, are there any recommendations to identify prior to designing a study which taxa are outliers and may impact results (morphometrics?)?

I agree with the conclusion of the need to more carefully design FE studies by considering the taxa and metrics needed to address specific questions. Also interesting is the suggestion made that one possible solution is the use of theoretical modelling to eliminate outliers by providing a morphological/functional continuum.

A minor note - the opening lines of the first three Results paragraphs imply weak to no correlation between FE results and ecological traits/phylogeny for the full data set. Yet both previous studies from which these models are derived (Prybyla et al 2018 and Perez-Ramos et al 2020) did draw substantial correlations between these results and diet in fossil taxa (the sample sizes in those studies were smaller than the full data set here but still above the thresholds identified in the current study). Why did the same models produce more meaningful results in the previous studies but not here?
Additional comments: Figure 1: The X axis in part B would be easier to understand using ranges, i.e., 1 – 4, 4 – 7, etc. rather than the current notation using parentheses and brackets.


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: RETHINKING THE USE OF FINITE ELEMENT SIMULATIONS IN COMPARATIVE BIOMECHANICS RESEARCH
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is succinct with a clear and easy flow from Introduction through Conclusions.

The literature cited is appropriate and sufficient for the purposes of this study. The paper does a good job of articulating the primary issues and approaches associated with the use of FE analysis in a comparative framework.

The FE variables in the data file do not match the variables in the text. Changing CME and P4ME in the text to ACME and P4ME will solve that issue. For ease of reading, consider adding captions to Figure 2 (e.g., along the lines of, FEA results and feeding, FEA results and phylogeny, Feeding and phylogeny).
Experimental design: The approach of correlating dendrograms is clever and accompanied by appropriate implementation of bootstrapped distributions.

The methods are clearly described and can be replicated with the data and code provided. The only minor clarification that would be helpful is whether the phylogeny dendrogram included branch lengths. Branch lengths in the feeding and FEA dendrograms were equal. If the phylogeny dendrogram includes branch lengths, then consider adding a comment about the impact, or lack thereof, of correlating dendrograms with equal and unequal branch lengths.

Consider providing a brief description of how dietary breadth and trophic level are defined in PanTHERIA. Opinions about categorizing feeding ecology vary widely and briefly addressing the method will help readers assess their level of comfort with the data.

The list of papers included in the meta-analysis may be a useful resource for future studies. Consider including those data.
Validity of the findings: The results are directly relevant to the hypotheses and stand alone (and beg several interesting questions).

The study confirms that small sample size can lead to elevated correlations between feeding ecology and FE-based performance measures relative to the clade-level pattern.
Additional comments: The suggestion that clade-level analyses of FE-based performance variables focus on “theoretical morphological approaches of representing morphological disparity” is thoughtful and forward-thinking. As noted, several studies have already provided approaches to mapping FEA performance variables into theoretical morphospace. Some have concluded that there is no evidence of selection for FEA-based variables that were hypothesized to reflect performance in the early days of comparative FEA studies. From that perspective, some comparative FEA analyses are already rising to meet the challenge of scrutiny and analytical rigor that is called for in the concluding sentence. Meanwhile, most recent studies, even those with small sample sizes, acknowledge the need for broader taxonomic sampling refrain from claiming to have identified adaptations. There is a great deal of room for innovation in using applying FEA within comparative framework, but perhaps the current state of progress is not as bleak as it seems.


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: RETHINKING THE USE OF FINITE ELEMENT SIMULATIONS IN COMPARATIVE BIOMECHANICS RESEARCH
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is a clear manuscript that identifies an issue which has yet to really emerge in FE studies, which is how low sample sizes can distort statistics. The reason that this issue hasn’t been identified before is that 1) very few studies have attempted to investigate more than (ballpark) five or so species at a time, and 2) even fewer have attempted to do any kind of quantitative analysis of the results, and mostly stop at visual comparison of contour plots. This is especially true of 3D models (although Marce-Nogue et al (2017: https://doi.org/10.7717/peerj.3793) have put forward some interesting methods to quantitatively compare 2D FE models using principal components analysis).

I think that this manuscript provides a useful warning for future FE studies as they grow in ambition and scope. However, I do have a broad question regarding the low correlations between FE-ecology, FE-phylogeny, and ecology-phylogeny, and why these correlations are so low in the full dataset. To an extent I would expect FE correlations to be low, because the metrics used in the analysis are themselves quite broad (e.g. total strain energy) and thus may not highlight the most ecologically or phylogenetically relevant differences between taxa (for example, one could argue that the total strain is not as important as whether/where that strain is concentrated). But the ecology-phylogeny one is surprising. Presumably there is a real relationship between ecology and phylogeny, and if you were to treat the ecological categories as tip traits and then test for a phylogenetic signal, you would find one? So it’s weird to me that as you add data, this correlation goes down. Can you explain why this is? If you can, does that explanation extend to the low FE correlation results too? If you can’t, does that mean that a cluster analysis isn’t appropriate for this type of data/question (I’ll admit that I don’t know much about cluster analyses, but presumably a cluster is less ‘constrained’ than a phylogeny because it doesn’t care about history? I may not be phrasing that correctly…). If you looked for a more traditional phylogenetic signal in your FE results (e.g. k, or lambda), would you find one that way?

Pushing it right to the edge, if those low correlations are real, what does that mean about our efforts more broadly to understand function from an evolutionary or ecological perspective? I realise these questions are somewhat tangential to your main point, which is that we need to think carefully and critically about what we’re measuring and why (I completely agree with this), but you’ve piqued my curiosity!

Minor adjustments:
L33: “covers”
L69: “The total number … was counted”
L217: The word ‘valid’ has a very specific meaning in FE studies, and implies that the model is producing realistic outputs. While context does indicate that you’re being more colloquial, a less loaded word (‘useful’?) would be more appropriate.

Code:
I’ve had all sorts of issues when packages stopped working because I was using the wrong version of R. I think it’s a good idea to comment which versions of R and the packages you used when you wrote the script, so that people can rollback if they need to.

The packages ‘datelife’ and ‘phylocurve’ don’t appear to be on CRAN at the moment. I was able to find versions of them on Github, but couldn’t install phylocurve because of an Rtools issue that I couldn’t be bothered to fix. Apparently, this doesn’t matter because everything ran without errors, which implies that phylocurve isn’t called anyway? Regardless, I’m not sure if these packages are going to go back on to CRAN at some point, but in the meantime I’d consider putting the Github addresses in for people.

Library function loads ape twice

code L22: .csv file extension missing


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

Input:
Title: RETHINKING THE USE OF FINITE ELEMENT SIMULATIONS IN COMPARATIVE BIOMECHANICS RESEARCH
Review round: 2
Reviewer: 1

Output:
Basic reporting: Again, this is a well-written and structured manuscript with all crucial data and methods as well as relevant background literature included, and study goals clearly stated.

The author has made all suggested minor grammatical changes in this revision.
Experimental design: I commend the author for clarifying what specimens were included (and why) from the two previous studies, including information on dietary breadth and trophic level within the manuscript (rather than referring readers to PanTHERIA) and for their thorough sensitivity analysis of the impact of slight differences in material properties between models taken from the two earlier studies - this addresses my concerns from the original version of the manuscript, thank you!

I am also satisfied with the author addressing the fact that while two key performance metrics (ME and SE) are analysed in this study, finite element modelling produces a diverse and enormous range of outputs that are beyond the aims of the study here, but nonetheless are very important. I also thank the reviewer for clearly describing why the two chosen metrics are important and what these outputs mean in terms of differentiating diet and ecology.
Validity of the findings: Again, the findings of this study are very interesting and will prove very useful in designing future FEA studies. Many thanks to the author for expanding the discussion on the impact of outliers on smaller sample sizes and their explanation for why more substantial correlations between FE outputs and diet in previous studies from which models were derived.
Additional comments: Once again, thank you for your substantial work on this revised version and your very clear point-by-point discussion of all issues raised in your rebuttal letter. I feel this manuscript is now ready for publication and look forward to seeing it in print!


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: COLOUR-EMOTION ASSOCIATIONS IN INDIVIDUALS WITH RED-GREEN COLOUR BLINDNESS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The aim of the study, which is to evaluate the association between colour and emotions, is absolutely interesting. The manuscript is clear and precise. In the introduction the current knowledge about the topic is well presented and exhaustive. I would recommend describing shortly in the introduction the different tests that can be used to assess red-green colour blindness (rather than only in the supplementary materials). I would also suggest adding also references to the use of behavioural tests to assess vision in the animal kingdom:
- Scholtyssek, C., Kelber, A., & Dehnhardt, G. (2015). Why do seals have cones? Behavioural evidence for colour-blindness in harbour seals. Animal cognition, 18(2), 551-560.
- Siniscalchi, M., d'Ingeo, S., Fornelli, S., & Quaranta, A. (2017). Are dogs red–green colour blind?. Royal Society open science, 4(11), 170869.
- Kelber, A., Vorobyev, M., & Osorio, D. (2003). Animal colour vision–behavioural tests and physiological concepts. Biological Reviews, 78(1), 81-118.
Experimental design: The methodology, as well as the results are clearly described and illustrated. However, light conditions of the testing room should be reported as well as the screen characteristics  (refresh rate, resolution, etc.).
Validity of the findings: The discussion is scientifically sound. I appreciated that Authors highlighted the limits (as well as strength) of the study. In my opinion, although recent literature demonstrates that there are similarities across cultures in the association, the influence of the culture of the participants should be taken into account and should be discussed (or eventually considered as a limit of the study). It could be possible, indeed, that social experiences might have produced an association between specific colour and emotional events. For instance, black is usually associated with death in the Western culture.
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: COLOUR-EMOTION ASSOCIATIONS IN INDIVIDUALS WITH RED-GREEN COLOUR BLINDNESS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors report an experiment in which they investigated the association between color (with both perceptual and verbal stimuli) and emotional labels in adults with deuteranopia compared to adults without color vision deficiency. Through several data analyses, the authors stated that the color-emotion association is quite similar for both groups for both semantic and perceptual tasks. It is a well-written paper. However, I suggest deepening some points.

Lines 39 to 47: the authors reported evidence about cross-cultural preferences between color and some associated attributes. However, there also some studies that show neither cross-cultural similarities (e.g., Taylor, Clifford & Franklin, 2013; Sorokowski, Sorokowska & Witzel, 2014) nor within a single culture (e.g., Taylor, Schloss, Palmer & Franklin, 2013).

Lines 52 to 56: the authors stated that the presentation mode does not affect the color-emotion association in different cultures. However, they reported a study in which exclusively Swiss people are tested (Jonauskaite et al., 2020b) in both perceptual and semantic tasks. Please soften the sentence so that it is relevant to the findings of  Jonauskaite et al. study. In other words, it should be made clear that those data are limited to the Swiss or at least to Western culture.
Furthermore, there is also experimental evidence on language development on color that should be discussed in relation to the universality issue (see for example Ozturk, Shayan, Liszkowski & Majid, 2013).

Overall, I would encourage authors to present and discuss conflicting results as well. The manuscript would benefit from this.

Finally, I was unable to access the data. Please share the data using an international repository (figshare, osf, Mendeley, and so on).

References
Taylor, C., Clifford, A., & Franklin, A. (2013). Color preferences are not universal. Journal of Experimental Psychology: General, 142(4), 1015.

Sorokowski, P., Sorokowska, A., & Witzel, C. (2014). Sex differences in color preferences transcend extreme differences in culture and ecology. Psychonomic bulletin & review, 21(5), 1195-1201.

Taylor, C., Schloss, K., Palmer, S. E., & Franklin, A. (2013). Color preferences in infants and adults are different. Psychonomic bulletin & review, 20(5), 916-922.

Ozturk, O., Shayan, S., Liszkowski, U., & Majid, A. (2013). Language is not necessary for color categories. Developmental Science, 16(1), 111-115.
Experimental design: I appreciate the study design, but some detailed specifications are needed in the method section.

Line 150: Authors should report the number of participants for each condition within the text.
Line 170: Authors should include table S 2 in the text.

Color blindness index: I wonder why you used PCA instead of factorial analysis. PCA is best suited for exploratory data analysis. In your case, I believe you want to detect the latent construct of "color blindness" and factorial analysis should be preferred.

Data analyses

Overall, I appreciate how the data analyses were conducted but found it difficult to follow through as there are too many references to supplemental materials (and maybe the reader too). I suggest including the most relevant tables in the main text and moving some sections away from the main text to supplementary materials (e.g., Color naming). Additionally, the article would benefit from a more detailed graphical representation of the results.

I would recommend the authors to consider re-running the analysis with the multilevel logistic regression model instead of the logistic regression and Bayesian model, including both participants
Validity of the findings: As noted above, the authors should address the issue of conflicting findings on cross-cultural evidence. Furthermore, I found the strength points of the research very clear, but the limitations are not well discussed.
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: COLOUR-EMOTION ASSOCIATIONS IN INDIVIDUALS WITH RED-GREEN COLOUR BLINDNESS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The present manuscript has been improved according to the main comments provided by the reviewers and the Editors. However, as suggested before, I would recommend to add some references and literature on the behavioural tests used to evaluate red-green color blindness in the animal kingdom. I understand the reasons behind the authors decision but I strongly believe that a deeper background would significantly improve the manuscript. It would not be necessary to illustrate the tests in details or the reasons why authors preferred the use of a specific test among all the ones described; but I think it could be interesting to report the different methodologies employed, just mentioning them. It could provide a more comprehensive background for the readers.
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: INJURIES AND MOLTING INTERFERENCE IN A TRILOBITE FROM THE CAMBRIAN (FURONGIAN) OF SOUTH CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Zong presents a new malformed trilobite and discusses possible interpretation of the fossil. I have reviewed this text previously for another journal and find it much improved from the previous version.

However, there are many stylistic errors I have highlighted in the text that need to be addressed before acceptance. Furthermore, the English is in places convoluted and hard to follow, making an interpretation of the material harder. This needs to be improved

There are a selection of citations that are missing and should be considered to help improve the scope and use of the text.

The structure of the text is fine and it is self contained.
Experimental design: The topic is well defined, and the consideration of the fossil and the material is acceptable
Validity of the findings: The findings are valid (this is a single malformed specimen, nothing wrong with that). It is the conclusion that lacks support.

Zong campions the notion that radiodonts, likely Anomalocaris, produced the injury. This is an outdated perspective on Cambrian ecology. Indeed, in the 80s and 90s this view was accepted, but now we know there are groups like Redlichia rex; large trilobites with effective structures for shell crushing. Furthermore, Zong fails to have understood how gnathobasic feeding works. If the author considers that serially arranged appendages with gnathobases were used in feeding (as we see in trilobites and horseshoe crabs) then the injuries—2 V-shaped indentations next to each other—can easily be explained by such feeding. Put differently, more than one leg can be used in mastication and can therefore make multiple injuries on the same side of the carapace. Further to this, there so is no evidence for radiodonts in the deposit, but there are groups that have gnathobasic like structures, like Mollisonia-like arthropods. I think this speaks volumes that the author is supporting the wrong notion here.

I believe that if the author is able to demonstrate the presence of a radiodont in the deposit to support the notion, then there is evidence for their claim. At this point, however; there is, in my perspective, too much evidence for the theory presented by myself and not enough to thoroughly support the view of the author
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: INJURIES AND MOLTING INTERFERENCE IN A TRILOBITE FROM THE CAMBRIAN (FURONGIAN) OF SOUTH CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: As the author points out, in vitae damage to paleo specimens is a hot topic at the moment. Food webs in the Cambrian were already complex, with a variety of predators attacking a variety of prey (although I would omit fish line 42. This is the Cambrian). Which predators attacking which prey is the question. The author very nicely reasons out a probable answer to this first question.
   Unfortunately the paper falls apart when the author tries to decide if the injury interfered with moulting, a reasonable question that, if answered well, moves knowledge of the Cambrian forward. Some sections are irritatingly repetitive, the same thing (I assume) said in exactly the same words. Had the author recast some of the repetitive statements, I might have been able to discern what the author was attempting to explain. For example, what is meant by the phrase “dragged forward the old exuvia (sic)”?  24, 157, 175
   A line editor can insert the plethora of definite and indefinite articles that this paper lacks (at least 3 in the abstract alone). Perhaps the line editor, if feeling magnanimous at the moment, might correct such misuses as most superior (102) and larger (21, 43, 50). But the major flaws in English expression must be addressed by the author, preferably, please, with the guidance of a native English speaker. Examples include 132-134, 151-154, 163-165, which are not clear.
Experimental design: No problem. The analysis of the specimen was good. It could easily be replicated by observing the original specimen.
   All the references given in the bibleography are cited in text, and no citations lack a reference.
Validity of the findings: No problem here either
Additional comments: [please send along the comments up in 1, Basic Reporting]


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: INJURIES AND MOLTING INTERFERENCE IN A TRILOBITE FROM THE CAMBRIAN (FURONGIAN) OF SOUTH CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article is well written in clear English.
On the whole it is well referenced, but I have suggested areas where additional references would allow the author to expand on topics of interest and broaden the discussion.
The article is self contained, and the data presented professionally.
Experimental design: The article presents new data, a single specimen with repaired injuries to one side.
Validity of the findings: The findings are in three parts.
The first, that the specimen represents a trilobite with healed injuries, I agree with.
The second is that the injury was caused by a radiodont, I find more problematic and in need of much more discussion (see detailed comments in next section). At the very least, this should be identified as speculation, as per PeerJ guidelines.
The third, that the injury caused a problem during moulting which the trilobite overcame, I find also problematic and in need of much more discussion to support it. The author notes that this is speculative, however it needs a fuller discussion of alternative causes, and the variation observed in trilobite moulting behaviours, to be sound (see detailed comments in next section).
Additional comments: It is always nice to read a paper considering trilobite malformations, it is a topic I find very interesting. Thank you for working on this project, and I hope you find the points I have raised useful in your revisions.
I have uploaded a .pdf file, with suggestions organised by line number.
These are suggestions of where to expand the discussion through the incorporation of references which may be of interest. It is not necessary to include all the references I suggest in the final manuscript, I include them for completeness.
I also have outlined points you may wish to consider, to make the arguments around the potential predator which caused the injury, and the potential issues with moulting, more comprehensive.


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: INJURIES AND MOLTING INTERFERENCE IN A TRILOBITE FROM THE CAMBRIAN (FURONGIAN) OF SOUTH CHINA
Review round: 1
Reviewer: 4

Output:
Basic reporting: All good, my only suggestions for additional references are in the comments on the MS.
Experimental design: No comment.
Validity of the findings: Overall, looks good, but I had three areas in which, as a reader, I wanted to be more convinced. I've noted some of this in my comments on the MS but some additional points added  here:

1) The author raises amplectobeluids among anomalocaridids as possessing among the most predatorially-adapted frontal appendages but says that their structure doesn't match the wounds, preferring Anomalocaris-like frontal appendage morphology as more likely. This might be worth revisiting. I still see Amplectobelua's frontal appendages as compatible and, also considering Daley and Bergstrom's (2012) work regarding anomalocaridid oral cones, I remain skeptical about Anomalocaris or something with a similar frontal appendage being the predator.

2) I think ruling out taphonomic effects more is still important. The break to the 7th thoracic segment looks pretty sharp and jagged (at least in Fig. 2B), compared to that of segments 3 and 4, which seem pretty clearly healed. Also, there is a (compaction?) crack in the left anterior pygidium that appears to continue anteriorly across the 8th thoracic segment and lines up with the break in the 7th. This appears to line up with bends but not breaks in thoracic segments 6 and 5 as well. The possibility that the missing portion of the 7th segment is a taphonomic effect related to that crack should be ruled out, especially given the depth of the lost portion of 7 and the apparent lack of damage to the 6th and 8th segments.

3) Finally, after point 2 is covered but I suppose before getting into 1, I think more should be presented on why the wounds were necessarily caused at the same time. I don't necessarily see a reason why they couldn't have been but I'm not entirely convinced that they were either.
Additional comments: Nice illustrations, clearly written over all.


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: INJURIES AND MOLTING INTERFERENCE IN A TRILOBITE FROM THE CAMBRIAN (FURONGIAN) OF SOUTH CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: In reviewing this paper again, I find it much improved linguistically. I have made points in an annotated PDF attached, but overall, it is much easier to follow and I commend the author for putting in this work
Experimental design: More than fine. One specimen, well described. There are a few points, like the use of the word somite, which is rather specific and segment would be better employed. But otherwise fine.
Validity of the findings: The consideration on the molting theory is still a bit convoluted, and the fact that there are two possible explanations makes me wonder which is the more parsimonious of the two. But, I will leave that to the author
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: INJURIES AND MOLTING INTERFERENCE IN A TRILOBITE FROM THE CAMBRIAN (FURONGIAN) OF SOUTH CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Good
Experimental design: Good
Validity of the findings: Good
Additional comments: I am impressed with the quality of the revision and recommend publication. I commend the author on a good job and also a willingness to improve the content and articulation.

There are a few small nits I might pick, all of them mere line edits.
Line 135, ‘maybe’ should be two words, ‘may be’
179, ‘lead’ should be ‘led’; I do not fault the author, because Pb is spelled ‘lead’ which sounds exactly like ‘led’, which…dang, English is confusing.
And there is a lack of definite and indefinite articles toward the end. I trust a line editor will stick some in.
All in all, an excellent job. Thank you!


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: INJURIES AND MOLTING INTERFERENCE IN A TRILOBITE FROM THE CAMBRIAN (FURONGIAN) OF SOUTH CHINA
Review round: 2
Reviewer: 3

Output:
Basic reporting: Fine, no additional comment
Experimental design: Fine, no additional comment
Validity of the findings: See  below.
Additional comments: A few edits on the MS including one sentence starting on line 145 that I can't make any sense of -- the first "clause" is itself a complete sentence so I'm not sure how the next three parts are intended to go together.

I'm still not entirely convinced that the 7th thoracic segment break is necessarily an injury and not related to the crack that propagates from the pygidium through T8 and lines up with the T7 break. That the T7 break "looks pretty sharp and jagged" I agree with and is precisely why I worry it is possibly not an injury -- if it showed clear healing like T3-T4 that would be different. But that is for readership to decide and ultimately I may be in the minority in my caution, so this is not a major issue. Over all looks 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: EXTENSIVE MICROBIAL DIVERSITY WITHIN THE CHICKEN GUT MICROBIOME REVEALED BY METAGENOMICS AND CULTURE
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a worthwhile contribution that reports new metagenomes and representative genomes that, very likely, will be used by others in the future. However, I felt that in most lines of research that the paper presented, the reported results fell a bit short of what could be accomplished. Please see below for more details.
Experimental design: This is good overall but I felt the paper did not reach the expectation set by its title. Please see below for more details.
Validity of the findings: The methods are well executed; the results are valid overall.
Additional comments: This is a worthwhile contribution that reports new metagenomes and representative genomes that, very likely, will be used by others in the future. However, I felt that in most lines of research that the paper presented, the reported results fell a bit short of what could be accomplished. For instance, the paper claims to report a gene catalogue of the chicken microbiome but the gene sequences released lack functional annotations and metadata, and there was no discussion of what are the key, core functions that characterize this microbiome, and distinguish it from that of other animals. The paper attempts to name several new species recovered by isolates and metagenomes but the taxa descriptions are really minimum (too “shallow” in my view) as they do not include any ecological or functional characteristics (or diagnostic phenotypes) of the newly proposed taxa. So, I am not sure this is a good practice (seems more like “stamp collection” that could possibly prevent future, more detailed taxonomic descriptions). See also specific examples below. Further, I have an issue with the title because the results reported do not really represent much of a global analysis (this was very limited). That said, the methods are well described and robust. The data reported will be valuable to the scientific community, which is quite large for this specific area.

Abstract: the authors seem to focus on the taxonomic novelty of the members of the chicken microbiome but, given its title, I was also expecting to read about variation among chicken individuals and functions characterizing the chicken vs. other animal microbiomes.

Line 179. It is good that the authors released the gene catalogue and the sequences but the information is not useful without functional predictions and other metadata. Seems like only the fasta file with unique identifiers were included in Figshare.

Lines 218-222. The second approach for defining genomospecies (or de-replicating MAGs) is more straightforward than the first one reported just above. How consistent its results were compared to approach 1? Later in Results, it is reported that the approach 1 found seven new genomospecies, but how abundant and prevalent these were, how many genomospecies the second method found that the approach #1 did not, and what is the evidence that the uniquely found 7 are not chimeric, were not provided.

Lines 340-342. Can you define presence? If it was a couple reads in one sample, I would not call it a core member of the chicken microbiome and hence, these findings carry less weight. This applies to other parts of the study. In general, presence and prevalence should be clearly defined and what is core, or almost core, members should also be clearly outlined in order for the whole paper to read more clear.

Lines 348-350. Is it possible that these reads represent close relatives of E. coli as opposed to E. coli, e.g. what is the threshold for Bracken to assign a read to a genome (if the relatives are missing from the database -as it is likely the case here- Bracken/Kracken will assign reads to the closest available relative, if close enough)? Also was the underlying analysis done in a read competitive manner with all reference genomes?

Lines 418-420. I have an issue with the title because I would argue that some of the previous studies represent the global chicken microbiome much more than the present study which is focused on ~50 fecal samples form a single site in Great Brittan and two chicken lines.

Line 437. I think it is important to mention the prevalence of these species in the chicken samples and probably why the other approach (95% ANI de-replication of MAGs), which is much more popular, missed them. See also Rodriguez-R et al, Env. Microbiol. 2020, for some useful definitions of presence, prevalence etc., based on metagenomic data.

Line 445-450. I think this could be reported better (more quantitively) in terms of gains in phylogenetic diversity by the new MAGs. And to report these gains in terms of (or against) i) named species (isolates and Candidatus) and ii) all available MAG in GTDB.

Line 454-457. I think it is important to mention the prevalence of these species in the chicken samples, e.g., do they represent “spurious matches” in a couple samples or a truly prevalent and core members of the chicken microbiome?

Line 489-490. I am not sure this effort to name all novel taxa in the chicken microbiome does a good service to science. I like the approach to create names and I believe it solves a significant problem we have in the field, but I would prefer we name the taxa we care (not necessarily all extant taxa), and study the taxa in more depth their function or ecology and not just trying to put our stamp on each genomospecies recovered. For instance, what if it is proven that a species named here is much more abundant in other birds than chicken and by chance only was found in the chicken samples? The proposed names would not be successful in such case, and the existence of the names will deter other people for proposing new, most successful names, I believe.

Line 542-545. I think this is an important topic to expand upon.

Line 556. Several punctuation marks are missing like here; or a comma is in place of a period. But text is overall very good.


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: EXTENSIVE MICROBIAL DIVERSITY WITHIN THE CHICKEN GUT MICROBIOME REVEALED BY METAGENOMICS AND CULTURE
Review round: 1
Reviewer: 2

Output:
Basic reporting: A few figures require minor attention:

FIG 3 Unfortunately, this figure was not legible in the reviewer PDF. The symbols called out (triangles, hallow symbols, or stars) can’t be seen. Not sure if this is something the authors could have fixed or a problem with the PeerJ submission system, just be sure in the final print the image can be increased for the reader.

FIG S2a Please include more details regarding this panel legend. It is not abundantly clear what the inset graph is representing. I believe the information is already in the figure legend, it should just be labeled more distinctly.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This paper represents an exhaustive look into the chicken gut microbiome. The manuscript was highly detailed in its description and justification for the experimental design, as well as included extraordinarily detailed and thorough descriptions of the methods employed. This manuscript is a great example of the utility of combining metagenomics and culture techniques to gain deep insight into microbial communities.


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: ASSESSMENT OF ACTIVITIES OF DAILY LIVING IN PATIENTS POST COVID-19: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is well written.
2-But These suggestions may help readers to better understand the article.
3-The conclusion in the abstract is vague. It is not your article's conclusion.
4- Introduction is well written, but it is too long.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 5- some of your references are old Like (Weber-Carstens, 2011).
6- in covid-19 do we have muscle weakness or we have myalgia. Please explain what will happen in covid-19 in line 19-21.
7- please in conclusion explain about the differences between ADL in hospitalized patients and Before hospitalization and at discharge patients.


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: ASSESSMENT OF ACTIVITIES OF DAILY LIVING IN PATIENTS POST COVID-19: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.	In table2, the time of measurements should be more specific. Please specify if the at admission/discharge means admission/discharge of hospital or rehabilitation facility.
2.	In page 13 line 1-2, the reference should be inserted regarding on the statement of ‘In COVID-19 patients, delirium was found to be prevalent and was associated with poor functional outcomes.’
Experimental design: 1.	Most of the studies included in this paper were using different instruments to measure the ADLs, thus it is suggested that the authors should add some descriptions about these measurements, for example, what is the focus of each instruments and the differences among these instruments? What is the criteria of being ‘good’ or ‘bad’?
2.	In page 11 line 15, the authors stated that one of the studies ‘reported 67% of patients with <60 points and 45.6% of patients who were bedridden’. However, the measurements should be more clearly stated. The authors stated that the measures in this study were carried out at both admission and discharge; can the authors provide the information about when these scores were measured? Are these percent changes or raw percentages?
3.	In page 11 line 18, the authors wrote ‘the direct rehabilitation group was significantly older, had more intubated individuals, and had worse scores at baseline and discharge’, however, the reference group should be specified. Otherwise it is not clear why the authors would like to report the data of direct rehabilitation group and how does this relate to the impact of COVID-19 on ADL performance. In addition, the authors mentioned that the Sakai et al. study measured the BI scores at discharge, however in line 20, the authors reported the results both at baseline and discharge, this is a little confusing.
Validity of the findings: 1.	In page 15 line 3, since the conclusions are not consistent between the studies, can the authors comment on the possible reasons/factors that could possibly affect the results?
2.	The severity of COVID might have impacts on the ADL performance, can the authors provide more information on the severity of disease for each of the studies included?
3.	The heterogeneity of these included studies is large. The studies were using different measurements and each of the instruments were measured at different times based on different populations, which might weaken the conclusions. Thus, the authors should discuss more about the possible impacts on these differences, and why they could be combined together.
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: ASSESSMENT OF ACTIVITIES OF DAILY LIVING IN PATIENTS POST COVID-19: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 3

Output:
Basic reporting: COVID-19 has caused global health and economic crisis. This paper investigated the impact of the disease on activities of daily living (ADL) performance of COVID-19 infection by a systematic review, which will interest a wide variety of readers.  However, from the introduction, it is unclear the gap of current knowledge and how a systematic review can fill the gap.  In some parts, the statement is ambiguous. For example lines 97-102, to my understanding, “the great challenge” is “a variable number of subjects” can finish the tests, but how a “further analysis” can overcome this challenge?
Experimental design: In the results part, the authors searched, evaluated, and selected the available studies. Line 217, “a total of 1465 patients were studied in the articles included”. However, if the authors could not integrate information from different studies, they failed to reach high statistical power and robust results by large numbers of patients.
Line 243-244, do the bedridden patients have a worse score?
Line 246 to 248, different rehabilitation groups have different scores. Is that because more severe patients need rehabilitation? Can rehabilitation improve a patient’s score?
Line 254-259, the two studies accessed the ADL scores at a different timeline. Do they have different findings?
Line 264-265, “the evaluation was carried out at discharge and six weeks later,” Did the score improve six weeks later compared to at discharge?
Line 321-323, what is the underlying reason that rehabilitation can not improve ADL?
Validity of the findings: The conclusion for most result part is missing or unclear.
COVID19 is mainly a respiratory disease. How impaired respiratory function affect the ADL of the patients?
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: ASSESSMENT OF ACTIVITIES OF DAILY LIVING IN PATIENTS POST COVID-19: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 4

Output:
Basic reporting: The article deals with a very topical issue. The literature produced so far has partially investigated the impact of the disease on the activities of daily life.
About 1500 patients were investigated, with articles from all over the world; during the selected research period the articles to be considered were those highlighted by the authors.
Tablel 1: setting is “inpatient” in Belli et al's article. Not outpatients. Rehabilitation Clinic transformed in acute setting without ICU for positive patients.
Experimental design: The proposed review is in accordance with the journal's aim and scope.
Research question is defined
The survey was conducted correctly according to correct methods of investigation.
The methodology of the research was carried out according to a correct qualitative method (National Heart, Lung and Blood Institute’s study assessment tools).
.
Validity of the findings: The following work can help the reader to quickly overview what has been achieved so far.
I would advise authors to introduce a part of suggestions for further investigation at the end of the discussion. What is the best evaluation tool to use? What should be the rationale for further evaluating ADLs? What could be the future research fields? How can we do a deeper analysis of ADLs?
As this is a systematic review, is it necessary to provide additional data to support that covid has a negative impact on daily life?
This work underline an heterogeneity of the methodologies used for the evaluation of ADLs. which is the best one?
We still know little about the impact of the disease on younger patients still of working age. Can we use the same tools?
Additional comments: Interesting argument that further underlines the impact of covid-19 during daily life activities.
1-On the basis of the articles highlighted, do the authors consider the literature so far produced to be exhaustive?
2-"The data collected to date in this systematic review is a useful starting point for further studies" :the authors could suggest the best strategies to follow for future research.
3-the strengths are contained in the chapter "limtations"; it may be useful to split them or rename the chapter "Limitations and Strengths"


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: ASSESSMENT OF ACTIVITIES OF DAILY LIVING IN PATIENTS POST COVID-19: A SYSTEMATIC REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thanks for addressing my questions. The article looks great.


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: ASSESSMENT OF ACTIVITIES OF DAILY LIVING IN PATIENTS POST COVID-19: A SYSTEMATIC REVIEW
Review round: 2
Reviewer: 2

Output:
Basic reporting: The comments were properly addressed.
Experimental design: The comments were properly addressed.
Validity of the findings: The comments were properly addressed.
Additional comments: Thank you for properly addressing the 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: QUANTITATIVE STUDY OF THE BEHAVIOR OF TWO BROADCAST SPAWNERS, THE SEA URCHINS STRONGYLOCENTROTUS INTERMEDIUS AND MESOCENTROTUS NUDUS, DURING MASS SPAWNING EVENTS IN SITU
Review round: 1
Reviewer: 1

Output:
Basic reporting: No major issues
Experimental design: No major issues
Validity of the findings: No major issues
Additional comments: This is an interesting and informative study of patterns of behavior and gamete release in two species of sea urchins.  Although there are many papers that report patterns of natural spawning, few report long-term quantitative data.  As such this will be a welcome addition to the literature on spawning in broadcast spawning invertebrates.

There are only a few things that the authors might consider in a revision.
1.	The control for behavior appears to be the period prior to spawning.  Why not take a parallel data set from time periods picked at random on days in which no spawning was observed?
2.	The data on spawning duration appears to be video frames in which gametes are noted on the aboral surface.  Gametes often pool on the surface of sea urchins and the duration they remain on the surface is likely influenced by water flow (advection and turbulence).  Is there any information on whether gametes tend to remain on the aboral surface was influenced by flow and whether eggs and sperm respond to flow in a similar manner?
3.	Figure 1 suggests that males generally do initiate spawning prior to females.  At the end of the event the males and females appear to stop spawning at around the same time (males might be active for slightly longer).  It might be useful to test to see the asynchrony (males more likely to spawn) is symmetrical (female spawning is centered at the mean male spawning time) or if the overlap in spawning time between sexes is shifted to the end of the spawning time (both sexes tend to stop at around the same time).
4.	The authors are very thorough on incorporating the literature on spawning.  I would suggest they consider an often overlooked paper by Hamel and Mercer (1996 Beche-de-mer inf. Bull. 8:34-40).  This is a very detailed and quantitative investigation of the temporal pattern of spawning.  There is also a pretty extensive literature on spawning observations of sessile invertebrates (e.g. corals).  If the authors thought this was too much to cover, they might simply refer to this literature in a more general way so that readers are aware of the quantitative assessment of this group of (often) broadcast spawners.
5.	The spawning seasons of these two species overlap, it might be good to add a few sentences on the degree to which they did (or did not) both species spawned synchronously.  In other studies, Strongylocentrotus and Mesocentrotus were observed to spawn together.


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: QUANTITATIVE STUDY OF THE BEHAVIOR OF TWO BROADCAST SPAWNERS, THE SEA URCHINS STRONGYLOCENTROTUS INTERMEDIUS AND MESOCENTROTUS NUDUS, DURING MASS SPAWNING EVENTS IN SITU
Review round: 1
Reviewer: 2

Output:
Basic reporting: General Comments

The manuscript describes a series of observations based on video recordings during the spawning season of 2 species of sea urchins, Strongylocentrotus intermedius and Mesocentrotus nudus. The information provided is particularly useful to marine ecologist to get a better a understanding of spawning behavior of this species of sea urchins under natural conditions and also, could be useful to Aquaculturist to help. Them manipulate spawning of sea urchins in laboratory conditions. Considering the difficulties to get in situ observations of spawning of sea urchins, the results provided add to the existing information on the subject for those particular species. My main observations to the manuscript are the following:
1. The introduction is too long. I do not think is necessary to include a big number of references to support the text. Considering that the work is not a review, I consider would be enough to select few of them, maybe the ones that the authors think they are more relevant and more closely related to the species of sea urchins studied. Also, I do not think is necessary to include the spawning behavior of other classes of equinoderms different that sea urchins. There are several differences among them and from my point of view, these comparisons are not relevant for the study and only contribute to make a very long introductory section.
2.  The Discussion is a mixture of results already included (or  at least they should be included in the Results section) and material already mentioned in the Introduction (or  should be included if necessary), combined with a more proper Discussion.
I consider the authors should try to avoid to repeat introductory or results material and focus their Discussion in highlight the main findings of the study and contrasting to relevant literature. As in the Introduction, they have the tendency to used results that were already mention, to support their discussion. The following is an example to illustrate my point:

14. Lines 609-611. The authors don’t need to repeat information that already was mentioned in other sections (in this case Methods). The following text “In our study, sea urchin trajectories were traced at 1-min intervals for 3 h, and the changes in distances from the mass centers of females to males and non spawners were determined.” were already mention in methodology or should be included.
The same is true for the following text, already mentioned in the Results section. “The most significant changes in the distances between spawning and nonspawning S. intermedius and M. nudus sea urchins occurred during the first 50–60 min after the beginning of mass spawning (Fig. 7), and the ranges of these changes varied widely, as males/nonspawners both approached the females and moved away (Table 7). (Lines 614-617 in the original manuscript).

Finally, considering the difficulties and the logistics to capture the right moments of spawning of the species studied under their natural conditions in the ocean, the information provided I consider is very valuable; however, the authors did some manipulations of the natural conditions (moving organisms and providing food to set up the initial conditions on the sites), that maybe had an effect on the behavior of the species. I consider they at least, speculate in the Discussion if these handling of the species could have an impact in their spawning behavior or justify why they think this initial manipulation is irrelevant.
Detail comments about the particular sections of the manuscript are in the following paragraphs.

Basic Reporting

1. Lines 78-85. I do not think is necessary to use that many number of references in lines 78-85, to support their statements about environmental factors that influence spawning behavior in sea urchins. Chose the ones that consider most representative of the existing literature and I don’t think is necessary to elaborate about spawning behavior in other classes of echinoderms including ofiuroids, asteroids or holoturoids, considering that we know they are different from sea urchins in several ways.
Experimental design: 5. Lines 233-234. Is there a possibility that the spawning duration was longer?

6. Lines 267-271. Suggestion: This paragraph could be integrated with little changes to the proceeding one (Lines 262-266), considering that both ends with the same statistical analysis to both sets of data.

They also need to clarify in the Discussion if the initial manipulation of the organisms and the provision of food could alter their spawning behavior
Validity of the findings: 7. Line 317-322. Could you please indicate here in the text with more detail the interval of time at which mass spawning occurred during dusk or night and how many days before or after the new or full moon?

8. Lines 321-322. Did you performed any correlation analysis that support this phrase  “there was no evident link to any lunar phase” (Lines 321-322), considering that at the beginning of the paragraph is mentioned that “spawning events occurred close to new od full moon”

9. Lines 366-367. If you are talking about an “average”, it is not clear to me what measure of variation represents the “±” associated to the average. Please specify if it is a confident interval or Standard Deviation or Error, or any other measure of variability.

10. Lines 375-376. Be more direct to describe the findings. Instead of saying, “When watching video records, it was clearly seen that sea urchins of both species increased their movement” (We already know you were watching video records, that is the basis of the whole study). Directly say: “Our data show that sea urchins of both species increased their movement…”

11. Line 490. S franciscanus is now Mesocentrotus franciscanus

12. Lines 498-504. This whole paragraph belongs to the results section: “The last observation is clearly demonstrated by a video recording obtained by one of the cameras, which in 2018 (June 11–17) recorded 3 mass spawning events with the participation of 41 males of M. nudus. Another 27 males spawned during the intervals between mass spawning events. Taking into account that the total sea urchin number in the camera field of view during this week decreased from 41 to 34 individuals and that the female/male ratio was 1:1, one may calculate that each of the males spawned approximately 3 times during this period. The total duration of sperm release during this week decreased by 3 times, but this change was not significant (Mann–Whitney test, U = 15,P = 0.08).”
The authors don’t need to repeat what they already mention in the Results section. The only phrase they need here to support their second observation [(Text From the original manuscript, lines 497-498: “Second, males seem to be able to spawn several times during the spawning season (Zhadan, Vaschenko & Ryazanov, 2018; this study)]” is “The last observation is clearly demonstrated by our recording videos where several mass spawining of males were recorded (see results of the one in June 11-17, 2018).

13. Lines 537-540. The authors mention that “Considering that most mass spawning events in S. intermedius and M. nudus occurred at night and close to new or full moon phases, the night time and lunar phases may be additional environmental factors increasing the probability of mass spawning. However, in their Results section,  they mention that “there was no evident link to any lunar phase” (Lines 321-322 of the original mansucript). Could you please clarify this or elaborate according to your results. Maybe if they analyze the number of nights (before New or Full Moon), when the spawning occurs, they could find a possible pattern related to the phases of the moon. This has been well documented for example in many coral species.

14. Lines 609-611. The authors don’t need to repeat information that already was mentioned in other sections (in this case Methods). The following text “In our study, sea urchin trajectories were traced at 1-min intervals for 3 h, and the changes in distances from the mass centers of females to males and non spawners were determined.” were already mention in methodology or should be included.
The same is true for the following text, already mentioned in the Results section. “The most significant changes in the distances between spawning and nonspawning S. intermedius and M. nudus sea urchins occurred during the first 50–60 min after the beginning of mass spawning (Fig. 7), and the ranges of these changes varied widely, as males/nonspawners both approached the females and moved away (Table 7). (Lines 614-617 in the original manuscript).
Additional comments: General Comments

The manuscript describes a series of observations based on video recordings during the spawning season of 2 species of sea urchins, Strongylocentrotus intermedius and Mesocentrotus nudus. The information provided is particularly useful to marine ecologist to get a better a understanding of spawning behavior of this species of sea urchins under natural conditions and also, could be useful to Aquaculturist to help. Them manipulate spawning of sea urchins in laboratory conditions. Considering the difficulties to get in situ observations of spawning of sea urchins, the results provided add to the existing information on the subject for those particular species. My main observations to the manuscript are the following:
1. The introduction is too long. I do not think is necessary to include a big number of references to support the text. Considering that the work is not a review, I consider would be enough to select few of them, maybe the ones that the authors think they are more relevant and more closely related to the species of sea urchins studied. Also, I do not think is necessary to include the spawning behavior of other classes of equinoderms different that sea urchins. There are several differences among them and from my point of view, these comparisons are not relevant for the study and only contribute to make a very long introductory section.
2.  The Discussion is a mixture of results already included (or  at least they should be included in the Results section) and material already mentioned in the Introduction (or  should be included if necessary), combined with a more proper Discussion.
I consider the authors should try to avoid to repeat introductory or results material and focus their Discussion in highlight the main findings of the study and contrasting to relevant literature. As in the Introduction, they have the tendency to used results that were already mention, to support their discussion. The following is an example to illustrate my point:

14. Lines 609-611. The authors don’t need to repeat information that already was mentioned in other sections (in this case Methods). The following text “In our study, sea urchin trajectories were traced at 1-min intervals for 3 h, and the changes in distances from the mass centers of females to males and non spawners were determined.” were already mention in methodology or should be included.
The same is true for the following text, already mentioned in the Results section. “The most significant changes in the distances between spawning and nonspawning S. intermedius and M. nudus sea urchins occurred during the first 50–60 min after the beginning of mass spawning (Fig. 7), and the ranges of these changes varied widely, as males/nonspawners both approached the females and moved away (Table 7). (Lines 614-617 in the original manuscript).

Finally, considering the difficulties and the logistics to capture the right moments of spawning of the species studied under their natural conditions in the ocean, the information provided I consider is very valuable; however, the authors did some manipulations of the natural conditions (moving organisms and providing food to set up the initial conditions on the sites), that maybe had an effect on the behavior of the species. I consider they at least, speculate in the Discussion if these handling of the species could have an impact in their spawning behavior or justify why they think this initial manipulation is irrelevant.


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: QUANTITATIVE STUDY OF THE BEHAVIOR OF TWO BROADCAST SPAWNERS, THE SEA URCHINS STRONGYLOCENTROTUS INTERMEDIUS AND MESOCENTROTUS NUDUS, DURING MASS SPAWNING EVENTS IN SITU
Review round: 2
Reviewer: 1

Output:
Basic reporting: Agree with modifications provided by the authors in the revised version
Experimental design: Agree with modifications provided by the authors in the revised version
Validity of the findings: Agree with modifications provided by the authors in the revised version
Additional comments: I consider the additions and modifications provided in the revised version of the original manuscript clarify my comments to the original manuscript and consider the information provided by the authors a good contribution to get a better understanding of spawning behavior in sea urchins under natural conditions were always is a logistic challenge to get the information. I consider the manuscript ready to be published, after the final revision of format, if any, by the Journal.


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

Input:
Title: THE RELATIONSHIP BETWEEN THE FEMALE ATHLETE TRIAD AND INJURY RATES IN COLLEGIATE FEMALE ATHLETES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript should be reviewed for consistency, tense and grammar.
 The references are complete and appropriate. The introduction does not build a case for the purpose and hypothesis.  Both the Triad and REDs were introduced but there was no discussion of their differences or similarities. The main purpose was to use the Female  Athlete  Triad  Cumulative  Risk  Assessment but previous uses of the tool were not included and the reason to use this tool was not clear.  What are the instances of injury in  female athletes? Why would this tool help?
In lines 60-62; It seems that RED-S is a well established theoretical concept, when in fact it’s the opposite. Based on the DeSouza 2014b reference that they provided, which doesn’t (currently) support the use of RED-S as a well-established model, should include some a disclaimer or limitations as to how the IOC actually misinterprets or is lacking evidence behind their claims.
Raw data was shared in accordance with the Data Sharing policy.
The titles of the tables are incorrect for Tables Consistent terminology should be used for the tool Female  Athlete  Triad  Cumulative  Risk  Assessment.  The tables refer to the measure as female athlete triad coalition scoring category and triad risk categories, consistent terms are needed.
Experimental design: The main hypothesis of this work is interesting but is not supported by the current introduction.  The background of why this is important is unclear and how the current data will contribute to the knowledge gap.  The Introduction needs to be re-worked so the readers understand “why” this is an important topic and how these data will add to the knowledge gap in this area.
Medical Examinations: Who completed the examinations and attaching the questionnaire would be helpful. Was injury self report?
Anthropometry: Insufficient detail on all measures was given.
The ultrasound methods and estimation of energy deficiency should each have their own sections to explain how the data was collected. It is unclear what measures were collected from the ultrasound device and how BMD was determined from the standard measures of Speed of Sound (SOS) and broadband ultrasound attenuation (BUA) that are collected from these methods (REFS).
Ln 136 more information is needed on how the Z Scores from ultrasound measures were determined. Does the Female  Athlete  Triad  Cumulative  Risk  Assessment allow for measures of BMD other than from DXA measurements?
Ln 137 was the history of stress fracture self report or verified through medical records?  How was a stress fracture vs a trabecular stress fracture determined?
Ln 115-117 The triad is not  defined by the energy availability but one factor of the triad is low energy availability. More detail on the classifications in De Souza et al should be included as well as references to other studies that have utilized this method to determine energy availability. Furthermore, the limitations of this approach should be addressed.
Ln 118-119: low EA is not entirely defined as BMI <17.5 kg/m^2. Athletes may have low EA but a ‘normal’ BMI. Looking at other methods such as detailed food intake and energy expenditure can be used to determine this (DeSouza 2014a).
Injury Rate:
Were the injury data collected based on medical reports or by team/athlete physical  therapists during the season? How many physical therapists were reporting the data and how was consistency between therapists determined and verified?
Statistical analysis:
More detail on the statistical analysis is needed. Which comparisons are testing the hypothesis from the introduction, “  the  moderate  and  high-risk 93 groups  have  higher  injury  rates  than  the  low-risk  group  on  the  triad  risk assessment  score”. Also which statistical program was used.
Validity of the findings: Results:
Ln 157 Patients Characteristics, should not  be referred to  as patients but as participants or athletes.  Could information on their age or duration of sports participation be added to these results.
Ln 167 Title of this section does not clarify the results that are being addressed. Can the exact p values be included in the text or table not just the reference to p < 0.05.
Ln 162: These data should be from parts of Table 2 but it is unclear where these numbers are from.
Ln 171-172: indicate that a high  history of bone stress fracture was from the combined moderate and high risk.  Also reporting on the other factors of the triad may be interesting from table 2.
Ln 175 add “one” to the “since there was only one participant…”
Ln 178-179 please report exact p values for these 2 comparisons.
Ln 181-184 Is Table 4 needed and more detail on what Table 5 is illustrating.
Discussion:
The first paragraph of the discussion should highlight the main results on the data. Was the hypothesis supported? What was the main take away from these data.  The second paragraph of the discussion should be in the results section. Paragraph 5 addresses the primary hypothesis and should be addressed earlier in the discussion. The limitations say that injury rate could not be determined but the first paragraph  states “there  have  been  no  studies  of  the  relationship  between  the  triad  risk  assessment 190 score  and  sports  injury  rate.” Terminology and the use of injury risk  and injury rate need to be defined and clarified throughout the manuscript.
The conclusion states: “This  study  clarified  the  relationship  between  the  triad  risk  assessment  score  and  the  one year  sports  injury  rate  for  female  college  students  of  multiple  sports.”  It is not clear how the relationship has been clarified with the data presented. The discussion needs to convince the reader of this claim and in its current format the conclusion does not seem to be supported. In addition, the conclusion states “  This  was  not  a  prospective  survey,  but  its 255 results  suggest  that  athletes  with  RED-S  may  be  at  increased  risk of  injury. “ The authors used the Triad Cumulative Risk assessment so why is the conclusion focused on REDs? Both should be introduced and discussed in the manuscript, but should not be used interchangeably throughout the manuscript.
Additional comments: I am attaching a pdf with additional comments (footnotes) that can be. found on page 36.


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 THE FEMALE ATHLETE TRIAD AND INJURY RATES IN COLLEGIATE FEMALE ATHLETES
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basic reporting is satisfactory, however I would recommend further review of the literature with regards to classification and diagnostics of low energy availability and RED-S vs. female athlete triad.
Experimental design: Thank you for your submission. I find your broadening the scope of injury surveillance beyond bone stress injury interesting. I do however have strong methodological concerns regarding your choice of BMI as a sole marker of energy availability. I worry that this may influence the results of your paper. I would recommend further explanation in your methods regarding injury diagnosis.
Validity of the findings: Please see above statement.

Also please consider your statement in Line 200 that your athletes were "well managed". This statement is ambiguous and may be misinterpreted if not better explained.
Additional comments: Please see comments attached


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 THE FEMALE ATHLETE TRIAD AND INJURY RATES IN COLLEGIATE FEMALE ATHLETES
Review round: 2
Reviewer: 1

Output:
Basic reporting: For the Low BMD category:
In manuscript:
For low BMD, athletes with a Z139 score ≤−2 were scored 2, and those between −1 and −2 were scored 1; a score of 0 was given to
140 those over −1

But in Table 2: the low category is actually "good BMD"? At first glance it looks like there are a majority of athletes with low BMD. Maybe the title of the column could reiterate that Risk is (Low, Moderate, High).

The methods for the US need to be elaborated. How was BMD derived from SOS or BUA measurements. Is there a good correlation between US and DXA BMD measures?
Experimental design: No comment
Validity of the findings: no comment
Additional comments: My main concern is the use of BMD from and US measure. There seems to be some controversy in the literature and more detail in the Methods is needed and a comment in the limitations. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891842/#:~:text=A%20number%20of%20devices%20are,and%20quantitative%20CT%20(QCT).


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 THE FEMALE ATHLETE TRIAD AND INJURY RATES IN COLLEGIATE FEMALE ATHLETES
Review round: 2
Reviewer: 2

Output:
Basic reporting: Basic Reporting

The authors appear to have addressed the previous reviewer comments to a good standard, there are a few issues within the introduction that would be useful to be addressed prior to publication.

The raw data is provided, although some coding descriptions, and replacing X/O with 0/1 would perhaps be beneficial to allow for other researchers to quickly perform counts of the data.

L64. You introduce “many studies” here that examine bone stress fractures and amenorrhea but fail to provide the references to these many studies. Could the authors include some evidence here (either a meta-analysis or some other high quality sources)?

L.67
You describe here a relationship between the menstrual cycle and injury risk, but I would suggest that this is unlikely and realistically the situation is more complex and nuanced than this.  A higher injury rate in female athletes is likely to be due to numerous factors and to simplify this down to menstrual cycle is too simple.  Some more clarification on this would be useful here.
Experimental design: The main hypothesis of this work is interesting as stated by previous reviewers, and the reworking of the introduction does provide this with more context in the literature.

The investigation is sound, however I have some concerns about the data analysis and the pre-registration of this study.  Was this study pre-registered? This is a requirement of research involving human participants and if this study was not pre-registered could the authors provide a justification as to why and I urge them to consider this approach in future.

The data presented here is quite superficial given what has been collected, and presented within the raw data file.  Some descriptive statistics about the population studied would be useful, as this would allow those who may wish to understand how the Triad may play a role in athletes that they work with (or themselves) to establish if this is a population similar to the one they work with.  This would also allow the reader to understand this study in comparison to the previous literature.

I would concur with previous reviewer on the value of Table 4, as I am unsure what it brings to the study, especially as this data is replicated in Table 5..  This information is presented within the raw data file, and feel the authors could refer to this in the manuscript as opposed to including within the manuscript.
Validity of the findings: The conclusions drawn from this study look robust,  and the combined with the request of the manuscript [and on conjunction with the previously requested amendments] have no concerns regarding this manuscript beyond those outlined above.
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: THE EFFECTS OF VEGETABLE PICKLING CONDITIONS ON THE DYNAMICS OF MICROBIOTA AND METABOLITES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The report is well presented and has the potentials to add more to the information already in the literature. However, some revisions are required as highlighted.

1. In line 48, where you stated "therefore, to avoid being the salinity too low,..", the statement is unclear. Kindly rephrase it for easy understanding by potential readers.
2. Similarly, in line 95, where you stated "Comparative analysis will be used to show that...", kindly consider replacing "will be" with "was".
3. The conclusion needs to be revised to completely reflect the title, the objectives of the study, the results, and recommendation (if any)
Experimental design: The experimental design appears to be reliable.

1. The full meaning of some of the acronyms need to be provided at the point they first appeared in the manuscript. For example, refer to line 85. Do so for other acronyms. Potential readers do not need to look out for the meaning from other sources.

2. The objective of the study is not clear enough, as seen in the last paragraph under introduction. Kindly make the objective more clear and specific.
Validity of the findings: The findings appear reliable. The conclusion needs revision as stated in number 3 under "Basic reporting"
Additional comments: Kindly go through the comments as highlighted. Minor revisions are required


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

Input:
Title: THE EFFECTS OF VEGETABLE PICKLING CONDITIONS ON THE DYNAMICS OF MICROBIOTA AND METABOLITES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The sentence in line 48 should be rearranged:
… therefore, to avoid the salinity being too low, pretreatment ….
Experimental design: In line 113-114, it was stated that the pickles were produced in 2017 and 2018. If possible, the months of production of the pickles should be stated.
Validity of the findings: i. Salt stock preparation process leads to increased production of BCAA via KARIs preference of NADH to NADPH; how would you account for general acceptability of this process to accommodate people on low-salt diet?

ii. In line 237-239, "The halophilic genera Halomonas and Halanaerobium constituted approximately 36% of the bacterial population, and Lactobacillus constituted approximately 15%." the sample group being described should be stated.
Additional comments: This is a very interesting paper on the effects of vegetable pickling conditions on the dynamics of microbiota and metabolites. The manuscript is well written, the experimental approach smart and sound, and the results are meaningfully and properly discussed. Thus, the manuscript certainly deserves publication in PeerJ. However, I would recommend the authors to address the issues raised before final acceptance of the manuscript.
Also, originality result (11%) using turnitin application is ok, however, it should be with no more than 1% from a source.


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

Input:
Title: THE EFFECTS OF VEGETABLE PICKLING CONDITIONS ON THE DYNAMICS OF MICROBIOTA AND METABOLITES
Review round: 1
Reviewer: 3

Output:
Basic reporting: Good
Experimental design: Perfect
Validity of the findings: Satisfactory
Additional comments: •	Provide point wise highlights for this article.
•	The abstract needs to be reframed with better inputs and novelty statement.
•	Summarize the aim of present work at the end of introduction.
•	All the abbreviations must be defined at the first place.
•	The discussion should discuss technical and scientific future directions and application in the area.
•	Paper should describe further research in the future.
•	Check the references throughout the manuscript.
•	Microbial isolates identified in this study (Using 16S rRNA sequencing) is submitted in publicly accessible culture collection or not and was the accession no. obtained??


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: PHYLOGENOMIC ANALYSES REVEAL A GONDWANAN ORIGIN AND REPEATED OUT OF INDIA COLONIZATIONS INTO ASIA BY TARANTULAS (ARANEAE: THERAPHOSIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript entitled “Phylogenomic analyses reveal a Gondwanan origin and repeated out of India colonizations into Asia by tarantulas (Araneae: Theraphosidae)” is clear and concise providing an easy reading. The introduction presents a clear background of the topic and the bibliography is well referenced and relevant. Figures and supplementary material are accurate and clear.

**One minor detail is in the supplementary material (Supp1_DEC+j_Probs and Supp2_BBMProbs) the different tones of red and blue on the square references can´t be distinguish in the nodes (circle references).
Experimental design: Despite that mygalomorph´s spiders are excellent models for biogeographic analyses, studies on this spider infraorder are scarce. This manuscript presents new insights on the evolution on the distribution of this group. The methodology used is suitable and concordant with other studies published. It is well described and well referenced.
Validity of the findings: Results obtained are robust and well represented in figures/tables. Discussion is well justified and is concordant with the results and previous studies. The authors propose a Gondwanan origin of Theraphosidae and a dual colonization from India to Asia. This manuscript contributes to the knowledge of the Mygalomorphae evolution providing new hypothesis for their current distribution (vicariance, continental rafting, geographic radiation).
Additional comments: Very nice manuscript.


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

Input:
Title: PHYLOGENOMIC ANALYSES REVEAL A GONDWANAN ORIGIN AND REPEATED OUT OF INDIA COLONIZATIONS INTO ASIA BY TARANTULAS (ARANEAE: THERAPHOSIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a nice study, whose findings do support their ideas.

#I was a reviewer on a previous version of this manuscript. I feel they have addressed most of my previous recommendations with regards to methodolgies (especially with regards to the available fossils for tarantulas and the use of secondary calibrations).
But I do have a few issues, once is critical (either needs to be explained or should be reevaluated due to potential issues).

See below for my explanations
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I am confused by the # of OGs. You had 743 and then say you had 125 after the RF metrics... you lost that many loci??? That seems really problematic.
Also, using the tree you previously generated (by using the same loci/type of dataset) seems circular and just produces potential bias.

not addressed from my previous review of this manuscript:
- why convert amino acids back to nucleotides and then use that for phylogeny inference? At this level of inference/investigation, why not just use amino acids?
- why start in BEAST, then switch to PhyloBayes?

line 169 - italicize Rosamygale grauvogely

Results
*SERIOUS* - The error bars in the dating analysis are incredibly small (tight)...something I don't feel like I've ever seen before, especially for a deep-time analysis like this across a divergent group of organisms. It just seems like something is wrong. Was this investigated?

The results are consistent with the “out of India” hypothesis, but why are you not discussing this VERY important radiation back into Africa (the Harpactirinae and the Stromatopelminae), from the Indian subcontinent?

"Tarantula radiations seem to occur with lifestyle switches" - I would say that this is a bit tough to say...given the sampling. This could definitely change if more lineages are included. I would be careful with the wording here.

I would also say that "habitat choices are maintained throughout radiations across large areas" is the equivalent of niche conservatism, no?