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: SACCADES AND HANDEDNESS INTERACT TO AFFECT SCENE MEMORY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Regarding references to the literature, I am uncomfortable with the authors' citation of Christman and Butler's (2005) unpublished conference presentation in support of the claim that "the benefits of SIRE...have been reported to impair the encoding but enhance the retrieval of episodic memories."  (Also note that the sentence in which this claim appears is less than eloquent--how can benefits of SIRE impair encoding?)  The claim is important and, while I respect the work of Christman and Butler, I feel the claim needs to be backed up with data that a reader can easily access.  I would encourage the authors to cite Brunye et al. (2009) instead of, or at least in addition to, Christman and Butler.  This will necessitate amending the claim.
Also regarding Brunye et al. (2009), the following description of their findings is unclear: "These...authors found that the eye movements were only beneficial when old-new recognition was compared to forced-choice recognition".
Experimental design: I think it would be helpful for the authors to report in the Subjects section how many subjects scored as left-handed using the handedness inventory.
Validity of the findings: No comment.
Additional comments: When reporting and discussing their findings regarding direction of laterality, I think the authors must acknowledge the small number of left-handers in their sample.  For example, the authors state that "when saccades occurred before the working memory task, working memory percent correct accuracy increased significantly as a function of direction of laterality."  Could it be that this was driven by the single very low performing left-hander represented by the red triangle in the lower left corner of Figure 3a?
In regard to the aforementioned finding, the authors state that "when saccades were made before encoding scenes in working memory, performance as measured by regression slopes relating overall percent correct with direction of handedness increased significantly positively (Fig 3a) with right-handers (+LQ) performing better than left-handers (-LQ)."  This makes it sound like there was a group-level difference between right- and left-handers, and I cannot help but see this as misleading.  There were, after all, only two left-handers.  Possibly the authors feel their characterization of their findings is defensible, but then I would like to hear their argument.
The authors also state that "recognition performance as measured by both overall percent correct and d-prime in the group of subjects who fixated after working memory and before recognition did increase significantly as a function of direction of handedness, with better performance as LQ increased indicating an advantage for right-handed subjects."   Here again the language suggests a group-level difference but there is only one left-handed individual.
In general, I find this version of the manuscript much improved over the original and I applaud the authors' efforts.  In my opinion, some revision is still necessary but I think the manuscript is much closer to warranting publication.


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

Input:
Title: SACCADES AND HANDEDNESS INTERACT TO AFFECT SCENE MEMORY
Review round: 2
Reviewer: 3

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: The revised manuscript satisfactorily addresses the concerns I raised in my initial review. I believe it now merits publication.


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

Input:
Title: EFFECTS OF SEX AND JOINT ACTION ON VOLUNTARY ACTIVATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: Please report additional references regarding the possibility that there are differences in motor unit firing rates between males and females. For example, Beck et al. (2005) reported that there were no differences in the patterns of response for global firing rates between males and females (assessed with mechanomyography). Also, that other potential differences in motor unit activation strategies were related more to absolute torque production than underlying mechanisms of neural control. Could the present study's findings be related to differences in torque production capabilities? For example, on average, men produces more torque than women.
Experimental design: Perhaps, to improve clarity and understanding of the stated aim (page 2, line 56), authors should define interaction. For example, instead of stating that an "interaction exists" the authors hypothesize that there is a "sex-dependent difference related to joint-action for VA%" or "VA% conditionally depends on both sex and joint-action". This suggestion is aimed to improve the clarity to the reader.

Concerns with the the 2 x 2 repeated measures ANOVA and its appropriateness for the given study. How was sex as a factor repeated? Would a mixed factorial ANOVA have been more appropriate?
Validity of the findings: Was the repeated measures ANOVA most appropriate model to examine the 2 (sex; women and men) x 2 (joint-action; knee extension and plantar flexion)? Are those both within factors? Or was this a mixed factorial ANOVA with sex being the between factor and joint-action being the within factor. I appreciate any and all details to help clear up my confusion.  Specifically, my confusions sits with the sex factor and how that was repeated as a within factor.

How did the authors break down the significant sex x joint-action interaction (page 7, line 130)? Was it broken down or was the main effect of sex just examined?

If this sex difference truly exists, how will this knowledge improve training studies/training investigations?

As aforementioned, to what degree do the differences in VA% depend on the generalization that men are stronger than women?
Additional comments: The manuscript was well written, however, I recommend that results section is expanded. Specifically, how the authors broke down their significant interaction. In addition, the aim and scope (page 2, lines 51-57) be improved. Specifically, remove statistical terms such as 'interaction' and use a common definition to promote clarity. In addition, specific hypotheses such as "Based on previous findings (refs; refs; refs) men will have a greater VA% at this joint-action." This recommendation is suggested because that is what the actual repeated measures ANOVA is examining (differences in the means).


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

Input:
Title: EFFECTS OF SEX AND JOINT ACTION ON VOLUNTARY ACTIVATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: 'no comment'
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: ABSTRACT

Line 21 – I wonder what the added value of this sentence is.  It should be clear that this is what happened based on the previously discussed findings.
23-24 – Be more precise with the conclusion. The results also revealed no sex differences in two of the tests. Do not solely focus on the positive effects.

INTRODUCTION

27 – A instead of THE
30 – Do you mean joint angle? Throughout the text the term joint action is used by isn’t defined anywhere.
37-38 – You assume a clear relationship between fiber type and %VA but provide no reference for it. This is quite a leap which requires a bare minimum of a few sentences showing that such a relationship does indeed exist.
40 – What does the following sentence “comprises mainly type I fibers even in men (Johnson et al., 1973) suggesting that any possible sex difference of the soleus fiber type composition will be small.” mean? The cited study provides no information about type 1 fiber distribution in females and you provide no citation showing that females and males have similar type 1 distribution.
Generally speaking, the set up for the question can be both clearer and stronger. First, a number of leaps were made without adequate citations. Mainly, the assumption about the relationship between fiber type and VA. Second, it is unclear why and how the proposed investigation “should promote better understanding of the sex dependency in training adaptation.” In what sense? You can considerably improve this part.

METHODS

Line 58 – Good job with calculating and reporting power analysis.
79 –Please add a picture of the set up for both sitting and lying positions.
109- How long was each contraction? How long of a break was provided between each one? When exactly were the twitches provides? 2 seconds into the MVC? When peak forces were visually observed on screen? Please provide exact details. Also, when exactly was the second twitch provided? Immediately post the MVC? Please clarify.
Overall, the methodology section is thin and should be expanded. Currently, if other scientists try to replicate your methodology it would be impossible for them as too many details are missing. Add more details so it would be easy for other to replicate.

STATISTICS

118 – So just to be clear, you conducted two different two-way ANOVA?
2 Gender x 2 muscle group
2 Gender x 2 joint angle
Please add Cohen’s d in addition to, or instead of partial η2, and provide the exact way it was calculated. Mainly, what the mean differences were divided by. This paper should be helpful.
https://www.frontiersin.org/articles/10.3389/fpsyg.2013.00863/full
127 – Please add an effect size measure to the differences such as Cohen’s d, % differences and also consider adding 95% confidence intervals. Avoid interpreting the results of your data solely based on p values. After you add effect size measures I recommend discussing the results in view of them as well. For example, “A small/medium/large magnitude, (non)statistically significant (ES = ; p =) main effect for condition was observed in which average VA% was X% higher in males (ABSOLUTE VALUE + SD) compared to the females (ABSOLUTE VALUE + SD).” This way of reporting is more informative and accounts for the magnitude of the effect.
Overall the results rely too heavily on p-values. I suggest moving the results into a table that includes p-values, 95% CI, Cohen’s d and absolute differences. It will be much easier to read and understand.

DISCUSSION

The first paragraph suggests that interpretation of the results was based solely on p-values. After redoing the stats section and including effect size measures, reinterpret the results in view of them as well and do so for the rest of the discussion as well.
163 – be careful not to give a reader the impression that results from other studies are the ones found in the present study. Make sure there is a clear distinction throughout the discussion as to when you are discussing results observed the present study and those reported elsewhere. Line 163, is an example of a confusing sentence that may give the wrong impression.
Overall I find the discussion section to be overly speculative, confusing, and indirect. It would be better if the authors systematically go over the findings one by one in a simpler and direct manner and in cases which the results were surprising to the authors I recommend stating that clearly. I also suggest avoiding overly speculative explanations. Finally, what is the added value of the results? How do they enrich the literature? Which gaps do the fill? What should be the next stage? What were the limitations?

CONCLUSION

The results, to my understanding, show no effect between genders other than with the knee position. This is not stated clearly in the conclusion.


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

Input:
Title: EFFECTS OF SEX AND JOINT ACTION ON VOLUNTARY ACTIVATION
Review round: 3
Reviewer: 1

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: The authors did a great job addressing the comments that I raised.

A few minor points:

Abstract

L.18  Consider adding some statistical information concerning the significant and non-significant effects.

L. 21. Same as above. Include some raw values and/or statistical information. Maybe distinguish between within/between comparisons for the ease of reading.


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: A TAXONOMIC REASSESSMENT OF PIRAMYS AUFFENBERGI, A NEGLECTED TURTLE FROM THE LATE MIOCENE OF PIRAM ISLAND, GUJARAT, INDIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a very clear and concisely written contribution on the taxonomic affinities of an isolated, and partially preserved turtle skull from the Miocene of Piram Island, India. The background and relevant literature are well covered. The authors re-studied the anatomy of the holotype skull concluding that it is a pleurodiran podocnemidid turtle, and not, as was originally proposed, a cryptodiran, i.e. a member of emydid turtles.
Experimental design: The authors use standard taxonomic methods to elucidate the status of the species. Their results are backed up by the data and by a number of support values to more confidently interpret their results. The primary research is also well within the scope of the journal and interesting to a broad audience of turtle workers.

As a large part of the anatomy of the specimen remains within sediment matrix, however, the reader is left wondering, whether additional preparation, CT scans, or even a simple X-ray image might not have revealed further anatomical features and thus added to the dataset used. The authors should thus at least include a sentence or two in the Materials and Methods section, why those additional steps were not undertaken.
Validity of the findings: Both the presented data in the main text as well as the supplementary file is deemed well presented and sound. The conclusions are well backed by the presented data.

The aspect on the absence of nasals and its implications needs to be expanded upon. For example in the "Abstract -Results section" (lines 22-23) it is stated that "absence of nasals" besides "the presence of a processus trochlearis pterygoidei" conclusively indicate pleurodiran affinities of the Piramys holotype skull. While I agree on the latter point, I am more cautious about the former - chelids, another prominent group of pleurodiran turtles, do have nasal bones, whereas most cryptodirans also lack nasals. This point thus needs to be refined here and in the discussion section.

In line 283, the statement "Given that all Asian taxa also form a clade..." needs to be refined, because they form a clade together with African taxa, as is later pointed out correctly in line 289.
Additional comments: I think this a very clear and concisely written contribution on the taxonomic affinities of an isolated, but only partially preserved turtle skull from the Miocene of Piram Island, India.
1) The authors should consider adding information to the Materials and Methods section as to why no further preparation, CT scanning or X-raying of the specimen was done to maximize the anatomical information that could be retrieved from the specimen.
2) The authors should consider revising the text at several part of the manuscript (Abstract, Results, Discussion) about the impact of the absence of nasals for their analysis.
3) I have added additional stylistic comments directly on the PDF.

I consider all my comments to be minor in nature.


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: A TAXONOMIC REASSESSMENT OF PIRAMYS AUFFENBERGI, A NEGLECTED TURTLE FROM THE LATE MIOCENE OF PIRAM ISLAND, GUJARAT, INDIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: All necessary data is sufficently documented and the relevant literature is provided. If there is any ways to precise the locality that would be a welcome addition.
Experimental design: No need to be improved.
Validity of the findings: The conclusions are supported by the data and are balanced - a big bonus. I think using Africa and Asia as biogeographic units in the cladograms actually masks a monophyletic Tethyian clade. The phylogeny and occurrences suggest that this clade was widespread in the Tethys during the Paleogene. Is that bytheway correct that the outgroups to Stereogenynini do not suggest an earlier presence of the group than the Oligocene? Can you doublecheck? I think it makes less sense to classify these species as African or Asian since they are marine and were all around the Tethys. Perhaps use Paleogene marine provinces instead.

In a paper of mine describing a Cretaceous bothremydid (Rabi et al. 2012), I discuss reversal of nearshore marine to freshwater lifestyle in pelomedusoid turtles - this is perhaps relevant to the manuscript of the authors. I no longer think that what I proposed were actual reversals - for the same reasons as what the authors pointed out in their ms (euryhalininty of nearshore marine forms and transition of environments).
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: A TAXONOMIC REASSESSMENT OF PIRAMYS AUFFENBERGI, A NEGLECTED TURTLE FROM THE LATE MIOCENE OF PIRAM ISLAND, GUJARAT, INDIA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is clearly written, with clear and unambiguous, professional English. It is well-organized, with precise information, clear and concise. The references and background is well documented. I made some minor comments in the attached PDF. Besides, in the SM2 it would be good to add the source you used to change the scorings of the taxa.
Experimental design: The work is well-executed and fits in the aims and scope of this journal. The research is rigorous and using the appropriated methodology.  The methodology is described in the way it can be reproduced.
Validity of the findings: The primary data (e.g., pictures, drawings, descriptions, phylogenetic analysis) is robust and clearly presented by the authors. Their findings are very interesting and bring to light some forgotten or poorly described taxa. The conclusions are well-supported by the data.
Additional comments: Nice job! Congratulations!


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: INTAKE OF SUPPLEMENTARY FOOD DURING PREGNANCY AND LACTATION AND ITS ASSOCIATION WITH CHILD NUTRITION IN TIMOR LESTE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Keeping in mind what is written in the following sections, there are aspects of the work that can be improved at the time of publication, as follows:
- In the summary, lines 52, 53 and 54, in the odds ratio values the corresponding confidence intervals should be placed, as has been done in lines 48 and 49.
- In material and methods, line 142, "and hig maternal mortality rates (citations)" should be added, in order to better understand the paragraph.
On line 156, a bibliographic citation must be entered involuntarily in the form (17).
- In line 168 the recommendations of the WHO are named, but the bibliographic citation should be included.
- In results, lines 243 and 244, the 95% confidence intervals should be included.
- The same on lines 260 and 262.
- In table 2 I think that confidence intervals should be placed for each OR and the values of p.
- The same in table 3.
- Finally figures 1, 2 and 3, should be done in a way that were more illustrative, because due to the large number of columns are difficult to understand with the naked eye. For example, and given the great similarity between the data of stunting, underweight and wasting, perhaps join the figures by type of supplementation and eliminate the complementary columns. Or put another way, place only those that took supplements and eliminate those that did not, in its different forms.
Experimental design: The experimental design is very well done, has a very strong statistical base and the number of participants makes the conclusions of the study and its applicability can be extended to the whole country.
Validity of the findings: I already highlighted in the previous paragraph that the results and conclusions drawn from the work I believe are very valid and can be extrapolated to the entire population, so its applicability can be very good when designing campaigns to prevent malnutrition states through the nutritional supplement in mothers and children.
Additional comments: The work is of a high quality in that sense and include:
The large number of the sample (female diada, children) analyzed.
The very idea of monitoring the state of nutrition and growth using the three variables analyzed in relation to a whole series of factors both maternal and children themselves.
The statistical study performed for each of the three variables considered as outcomes.
The consequences obtained from the work itself with respect to its future applicability, since with the data obtained, it is possible to influence the population at greatest risk, with policies aimed at achieving higher percentages of success in monitoring correct feeding during maternity.


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: INTAKE OF SUPPLEMENTARY FOOD DURING PREGNANCY AND LACTATION AND ITS ASSOCIATION WITH CHILD NUTRITION IN TIMOR LESTE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Line 222 the confidence interval of the mean shown in Table 1 should be added to the average age of mothers and children and withdraw these results from that table since it only reflects qualitative variables and appear below column% ..

Correct in table 1 the description of the BMI variable since it is wrong.
Experimental design: The authors acknowledge that there is no precise information on what type of supplementary diet was consumed, but the authors should indicate in the methodology section what is the usual diet of mothers in Timor Leste and what most mothers consider to be dietary supplements.
Validity of the findings: No comment
Additional comments: No comment


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

Input:
Title: INTAKE OF SUPPLEMENTARY FOOD DURING PREGNANCY AND LACTATION AND ITS ASSOCIATION WITH CHILD NUTRITION IN TIMOR LESTE
Review round: 1
Reviewer: 3

Output:
Basic reporting: Please see the section "General comments for the author".
Experimental design: Please see the section "General comments for the author".
Validity of the findings: Please see the section "General comments for the author".
Additional comments: Reviewer’s comments
Influence of supplementary foods and nutrients on the pregnancy and newborns have been well researched and documented. In the current manuscript, authors have analyzed data of “Timor  Leste Demographic and Health Survey (TLDHS)” conducted in 2009-10 to see the effects of supplementary foods (information of the types of supplements is missing) on the health of children. Authors conclude that odds of healthy children in women who take the supplementary foods during the pregnancy and lactation are higher. Manuscript is well written, and data is thoroughly analyzed. But, the manuscript does not provide any new knowledge in terms of contribution of supplementary foods on the health of the children. All  the interpretations have been extensively studied previously. I am afraid to say that the manuscript is not suitable to be accepted as research article in the PeerJ.


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

Input:
Title: INTAKE OF SUPPLEMENTARY FOOD DURING PREGNANCY AND LACTATION AND ITS ASSOCIATION WITH CHILD NUTRITION IN TIMOR LESTE
Review round: 1
Reviewer: 4

Output:
Basic reporting: In general, the manuscript is well written and complies with the review criteria of PeerJ. The most important issue is how data is presented in the figures (see below), all other comments are minor issues.
Specific comments:
Line 89: There is a coma before the parenthesis.
Line 102: “… access to appropriate food, and diverse…”
Line 125: Please define “DHS”
Line 128: “… as there is no currently no research…”
Line 156: There is a “[17]” at the end.
Line 171: “… protein and energy, or frequent infection.”
Line 179: It says “… and not wasted”, it should say “… and no underweight”
Line 207: I suggest expressing the level of significance with the widely used and understood p-value (p<0.05) instead of a percentage.
Line 211: “Stud” should be “Study”.
Line 284: “absolutely” should be “absolute”
Line 297: “and” should be “of”
Line 308: “… in contrast to past evidences.”
Line 310: “… to reduce the the risk of …”
Line 312: “… during pregnancy on birthweight …”
Line 319: “… potential indication of poor maternal healt …”
Figures: Even though the figures are neatly constructed, they do not present the data in a manner easy to understand and interpret. The percentages shown are confusing because they do not relate to the total of children in each category (prevalence). For example, in Figure 1, it is shown that 77.1% of stunted children in urban houses come from mothers that took supplemental food during pregnancy and 22.9% come from mothers that did not (100% is all the stunted children in urban houses, but it should be all the children in urban houses, stunted and not stunted). Since the bars are taller for the ones that took supplements, it looks like there are a lot more stunted children from women that took supplemental food than from women that did not. I suggest presenting the data as percentages of the total of children in each category (prevalence). Also, variability of the data should be represented (standard deviation or error bars) and significant differences should be clearly indicated within the figure.
Tables 2 and 3: I suggest highlighting the significant differences instead of the not significant ones.
Throughout the text:
-	There is a missing space between the last word and the parenthesis of most references (it seems to be a problem of the references software used).
-	All abbreviations should be explained the first time used. Please define HFA, WFH, WFA, CIs, ORs, and others.
Experimental design: - I agree with the author in that the results may vary depending on the type of supplement women take during pregnancy and/or lactation, so it would be good to specify what was considered as “supplementary food”. Do you know if all women in the study took the same or similar supplements?
- In the methods section, it would be good to state if the dietary supplements are provided free of charge to all pregnant women in Timor Leste (to rule out accessibility as a variable). If so, maybe it is possible to know the type of supplement provided to the women in the study.
- How do you calculate prevalence? It looks like Figures are not representing prevalence as it is usually calculated (number of cases divided by total population).
Validity of the findings: In the discussion, it would be good to comment on the possible reasons of the findings, for example: it was clear from the study that women in urban areas are more likely to take supplements, could that be related to how the supplement is distributed? Maybe it is more difficult for women in rural areas to have access to the supplements, henceforth they are less likely to take them.
Additional comments: Overall the manuscript shows considerable promise, it is well written and the data is robust. However, the figures need to be modified to present the data in a manner easy to understand and interpret, according to the results highlighted in the text, as well as clearly indicate statistical differences. Also, there are some minor revisions that would improve the quality of the publication if fixed.

I recommend accepting this manuscript for publication IF the authors revise and improve the quality of the figures of the manuscript, considering the comments above.


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

Input:
Title: INTAKE OF SUPPLEMENTARY FOOD DURING PREGNANCY AND LACTATION AND ITS ASSOCIATION WITH CHILD NUTRITION IN TIMOR LESTE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have satisfactorily completed all the suggestions made by the reviewers, so I believe that the work is correct and can be published.
Experimental design: The authors have satisfactorily completed all the suggestions made by the reviewers, so I believe that the work is correct and can be published.
Validity of the findings: The authors have satisfactorily completed all the suggestions made by the reviewers, so I believe that the work is correct and can be published.
Additional comments: The authors have satisfactorily completed all the suggestions made by the reviewers, so I believe that the work is correct and can be published.


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: INTAKE OF SUPPLEMENTARY FOOD DURING PREGNANCY AND LACTATION AND ITS ASSOCIATION WITH CHILD NUTRITION IN TIMOR LESTE
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Authors have justified my previously raised issues. Improved manuscript is well suited for the acceptance.


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

Input:
Title: INTAKE OF SUPPLEMENTARY FOOD DURING PREGNANCY AND LACTATION AND ITS ASSOCIATION WITH CHILD NUTRITION IN TIMOR LESTE
Review round: 2
Reviewer: 3

Output:
Basic reporting: The manuscript is well written and has been further improved from its first version, I thank the authors for their hard work.

The figures look better, but they are still a little hard to interpret. I suggest adding the percentage scale in the Y axis.
Experimental design: No comments
Validity of the findings: No comments
Additional comments: No 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: DO MOTHERS ALSO “MANIPULATE” GRANDPARENTAL CARE?
Review round: 1
Reviewer: 1

Output:
Basic reporting: See below. No further comments.
Experimental design: See below. No further comments.
Validity of the findings: See below. No further comments.
Additional comments: I reviewed this manuscript previously for another journal and I am happy to see that this is an improved version of the already satisfactory original version that I saw before. In this study the authors put forward a controversial and most interesting hypothesis, the “manipulative mother hypothesis”, according to which mothers (compared to putative fathers) exploit the alloparenting environment (namely grandparental investment) by expressing biased resemblance descriptions. The hypothesis makes sense from an adaptive point of view and in turn fits with the well-accepted notion that paternity uncertainty modulates grandparental investments: Maternal grandmothers, who have higher certainties of genetic relatedness with grandchildren are predicted to invest most in grandparental care, compared to other grandparents, and especially compared to paternal grandfathers, whose grandpaternal genetic links are the least certain of the four grandparents. To test their hypothesis the authors gather data from two questionnaires filled by two populations of Norwegian respondents. The findings are most revealing: daughters more often and more intensely than sons voice their opinions about the resemblance between their parents and their grandchildren, and the results in the questionnaires point towards the idea that this conscious or unconscious manipulation may bias grandparental investment.

The paper is well written, the study has good (internal) controls, and the authors make a strong case to consider seriously the controversial hypothesis that is assessed. The hypothesis complements and expands the paternity uncertainty hypothesis, and by doing so this manuscript makes a meaningful contribution to the field that no doubt will attract attention by the scientific community. Whether the “manipulative mother hypothesis” remains valid after further tests aiming to falsify its predictions remains to be seen, but both the concept and these first results are worth publishing.

I only have a few comments and several minor suggestions:

1. The authors justify why they do not adjust for multiple probability estimates. While what they say is true I do not think the justification of big data applies specifically to this study. However, I agree that the focus should be in effect size rather than p values. Perhaps the authors would like to reformulate their justification.

2. Reported frequency of contact can be a proxy for investment, but frequency of contact also depends on the grandparents’ sons or daughters’ manipulation abilities and many other factors (e.g., social status, working status, and so on), and biases in frequency of contact also depend on whether there are interactions between these factors and the sex of the grandparent and that of his/her offspring (e.g., grandmothers could be more susceptible to being manipulated than grandfathers, and daughters could be better at manipulating grandmothers etc.). Discussing at length all these possibilities would perhaps enter the realms of going too far with speculation, but
acknowledging that these kind of modulations may further play a role could be useful. This is not a major issue and it should be left to the authors’ decision.

3. The study’s results are based on responses to questionnaires, and this may come with noise and uncertainty stemming from many factors. However, the authors make a strong case for the interpretations, ensuring that some of the potential confounding factors are kept at bay, and they further acknowledge some limitations and provide satisfactory arguments against them. Participants in Study 2 are all academics from a University. However, the authors acknowledge these limitations and show why they are not serious shortfalls. Moreover, this kind of studies necessarily comes with some of these limitations, as manipulative experiments on these questions in humans are not feasible or ethical.

4. The study has good controls overall. For instance, the same individual is at the same time a maternal and paternal grandparent. Also, each respondent grandparent is independent from any other grandparent. For future studies the authors could consider that having different grandparents for same offspring-grandoffspring (and controlling for non-independence) would be interesting as well from a different perspective, and would be a conservative control. For instance, both grandparents in a couple might contribute equally because of manipulative actions by one of the two grandparents (e.g., by the maternal grandmother upon the maternal grandfather). Likewise, if data were available such that investment into the same two focal grand-offspring (the grandson and the granddaughter) by all the actors involved (i.e., all the 4 grandparents) could be assessed, that would be informative. This is out of the scope of the present study but they could be the basis of useful avenues to further refine some of the findings in the present study. As before, this is a just a comment to the authors and requires no action in the present manuscript.

5. Other comments:
- Some references in the list may require attention. For instance, reference 31 is in capital letters.
- Please provide a citation for the statement that the bias of mothers ascribing higher resemblance of newborns to the mothers’ partner (putative father) than to themselves is exaggerated in the presence of the putative fathers and reduced in their absence (line 120). References are given before for maternal manipulation but a specific referral to the research providing the exaggeration of that bias, which is very revealing, would be welcome in this line.
- L517. fMRI acronym is not explained unless I missed it.


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: DO MOTHERS ALSO “MANIPULATE” GRANDPARENTAL CARE?
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is very well written and very well referenced with respect to the literature. The statistical analysis is straightforward and easy to understand. The figures included are useful.
Experimental design: The experimental design is both good and novel. The problem is clearly stated and the statistical analysis is adequate.
Validity of the findings: While the sample sizes are generally small, some robust significant results of general interest were obtained. The authors discussion of their results in sound, supported logically, and is not overly speculative.
Additional comments: Comments on MS #30207: Do mothers also manipulate grandparental care?
In this manuscript, the authors use questionnaires to determine access of grandparents to grandchildren and to determine if the parents of grandchildren differ by sex in how they ascribe the resemblance of their children to the children’s grandparents. The authors argue that their results are not consistent with paternity uncertainty and posit that mothers attempt to manipulate children’s grandmothers to their own reproductive advantage. The use of personality as well as physical resemblance is nice.
The manuscript is very well written and very well referenced with respect to the literature. The statistical analysis is straightforward and easy to understand. The figures included are useful. I did find the results a little difficult to keep straight as there were many analyses pertaining to the questionnaires and it was not always apparent that a statistical test supported a statement. I suggest a figure for each questionnaire that is a flow chart showing the questions and other information relevant to each relative. Parts of each flow chart could be numbered to correspond to statistical tests that are then placed in tables. Thus, the results section would contain only statements about what was found (not test results) and readers could match statistical tests to parts of the questionnaires. Subheadings in the discussion section would also help readers follow arguments.
I agree that the uncertainty of paternity hypothesis fails to account for the data. This hypothesis would seem to predict that ascriptions of resemblance should be made especially to paternal grandparents and even made by the fathers of those grandchildren. The manipulative mother hypothesis seems reasonable but also does not account for the indifference of the fathers of the grandchildren. Perhaps, part of the explanation lies in the social structure of ancient societies. If a small number of males had harems, paternal grandparents could have many grandchildren relative to maternal grandparents, reducing their ability to invest in individual grandchildren. Males may then have evolved not to bother with appeals to their own parents in their children’s behalf. Maternal grandparents would often have fewer grandchildren and might, therefore, be better able to assist them. I admit that I may not have thought this through. The authors may consider this point if they so desire.
I noticed a few typographical errors. These are: (1) Line 153, add “s” to “material” and to “method”, (2) Line 228, change “do” to “does”, (3) Line 286, add subheadings to match those of experiment 1, (4) line 292, add “is” after “This”, (5) Line 373, change “were” to “was”, (6) Line 374, the use of “children” seems wrong, (7) Line 429, add an “s” to “suggest”, and (8) Line 454, change “believes” to “beliefs”.


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: ECOLOGICAL DIVERGENCE OF BURYING BEETLES INTO THE FOREST CANOPY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The reviewed manuscript takes a novel approach to the examination and discovery of foraging height preference in burying beetles of Ontario.  These authors provide data to suggest that Nicrophorus pustulatus prefers foraging in the forest canopy, thus allowing this species to coexist with other closely related species in the same time and space.  While this is not the first report of canopy foraging N. pustulatus, the data do provide further evidence in its northern range, as well as presence absence data for sympatric species.

The wording of the “traps being distinguished by predictors” is an odd objective.
In general, the data suggest a preference for a ground or canopy trap.  Determining a preference for either trap is important, thus it should be directly stated that these three species clearly have a preference.  To me this is the difference between "Predictors verses Observed data".
Experimental design: The first section of the methods should be moved to the Introduction and perhaps the discussion.
Validity of the findings: No Comment
Additional comments: Review of “Ecological divergence of burying beetles into the forest canopy”

Abstract
Line 25:  The wording of the “traps being distinguished by predictors” is an odd statement.
In general, the data suggest a preference for a ground or canopy trap.  Determining a preference for either trap is important, thus it should be directly stated that these species have a preference.

Line 27: delete Indeed

Methods
Line 101: Study Species: Discussion of the study family should be moved to the Introduction.  (Lines 102–111).
State the number of species known to be reported in the study area, and provide reference.  You may also provide pertinent information regarding N. pustulatus as this is the species of focus.

Line 114–124.  Remove from the methods.  These reports could be provided later in the discussion, if seasonality is discussed.

Line 131: State what bait is used here.

Line 140: basswood

Line 142: eastern white cedar

Line 144–145): red oak, etc…  be consistent with capitalization

Line 172: The species and sex identification section is unnecessary.  Please just state what resources were used for the identification of the study species.

Line 210 – indent paragragh

Line 243: Random Forest (be consistent either way stated)

Results
Line 270–271: First sentence is unnecessary as same results are stated in next sentence

Discussion:

The entire first paragraph of the discussion is repetitive from the results section, as if restating. Be brief and combine with second paragraph.

Line 304: delete different

Line 306: delete (Fig. 1,2) – don’t need to refer to figures in the discussion.

Line 319: provide four previously stated references here from the Introduction.

Line 321: awkward sentence

Line 323: Our study supports the findings of Dyer and Price (2013), suggesting that N. pustulatus can be common, but only within the forest canopy.

Line 328–344:  add Hocking et al. reference [Hocking, M. D., R. A. Ring, and T. E. Reimchen. 2006. Burying beetle Nicrophorus investigator reproduction on Pacific salmon carcasses. Ecological Entomology 31(1): 5–12.]. These authors found N. pustulatus on fish, and Dyer and Price (2013) suggest this as a possible resource, especially in areas of abundant raptor nests.
Literature Cited
Bold the authors, and Volume number.  Also use a – between pages for range, not a dash.
Figure 3: State why Log transformation was used. Readers need to be reminded of differing N values.
Table 1: Carrion beetles captured in ground and canopy traps at …


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: ECOLOGICAL DIVERGENCE OF BURYING BEETLES INTO THE FOREST CANOPY
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript is very well written with clear language and structure. I had no issues with the literature or background, and the results and discussion were directly relevant to the clearly stated hypotheses and predictions.
Experimental design: 1. The methods included some extraneous information (i.e., the description of how each species was identified -- this is in the key cited but should be moved to an appendix if the authors would like to include it) and a couple of places where more information is needed, detailed below.
2. Station should be included as a random effect in your analyses since each Station was sampled twice. It likely will not affect the overall conclusions, but currently n is being artificially inflated in the statistical analyses since collections from the same station are not independent.
Validity of the findings: The data seem adequate for the questions and analyses, and the conclusions the authors draw are justified (pending the station random effect noted above).
Additional comments: This study was really interesting and is a nice, concise blend of basic natural history and basic community ecology. The introduction is really well written. It flows smoothly, covers the relevant background well, and very quickly grabbed my interest. With a few (probably) minor changes to the statistical analyses, this article would be a good contribution to the body of literature on carrion beetles. Please find comments for particular line numbers below.

79-80: "...in only four studies" seems to imply that there have been many studies with baited elevated traps, but most were not successful in capturing N. pustulatus. Is this the intended meaning? Or rather that there have only been a few studies that used baited elevated traps?

91-99: Having the questions *and* predictions so explicitly listed here is very helpful.

160: "...hung 6m high in tree branches" -- could you clarify? Were there any guidelines for proximity to branches, distance from the branch holding the trap, etc?

177-203: This section seems unnecessary since this information is included in Anderson & Peck 1985 which you cited as your key.

208: Were there traps that did catch beetles that also showed evidence of disturbance?

210-222: I think you should include Station as a random effect in your model since each trap was sampled twice. It doesn't seem justified to assume that they're independent just because they are a month apart.

265: The 'n' in MuMIn should be italicized

304-317: Good, concise summary.

324: 21, 12, and 1 in how many traps? Is this a per-trap average? If not, that would probably be the most informative.

328: Doesn't the observation of larvae feeding on ringneck snake eggs mean that gray ratsnake eggs are *not* the only known breeding resource? One counterexample is all that is needed to show that 'only' is not reality. I recognize this is a bit nitpicky, but I think it's worth rewording to say either that this is a common (or historical?) assumption (despite the evidence laid out in the rest of the paragraph), or that they are thought to nearly exclusively reproduce on gray ratsnake eggs or similar.

Figure 3: Since random forests are still relatively uncommon in ecology, could you briefly explain the scale for relative accuracy in classification?

Figure 6: I think changing the y-axis to direct probability of presence rather than logit(prP)/2 would make this figure more effective. Constraining ylim(0,1) would then make the panels easier to compare. Also, what is the rug on the x-axis?

Table 1: For the 'Number of traps with each species present' column, could you add the corresponding % in parentheses?

Typo in 'round' description in Variable_descriptions.txt

All of your code ran with no issues and the results matched those reported in the manuscript. One minor suggestion for the future to help make your code easier to read is to follow the recommended style guide for R code: http://adv-r.had.co.nz/Style.html


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: ECOLOGICAL DIVERGENCE OF BURYING BEETLES INTO THE FOREST CANOPY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Upon review of the revised manuscript, I accept with minor revisions.  See Below.

Abstract

Line 28 – 29: Delete N. Pustulatus was the most common species in the canopy, and the only species that was more common in the 6m traps than on the ground.

This was repetitive

Line 30 – 31: but our results suggest it is uniquely common in canopy habitats [delete instead that N. pustulatus]
Line 32: [delete between N. pustulatus and other co-occurring burying beetles.]

Introduction
Line 47: Delete comma after Knollenberg
Line 52: same as above
Line 53: delete comma after Peck
Line 63-64: oviparous snake eggs in general; this idea was supported by an …
Line 65: insert comma after Beresford
Line 66 insert comma after Beresford
Line 74: Further studies have reported N. pustulatus to be more common in the
Line 84: delete that
Line 84: delete their
Line 85: only 1 individual [ not individuals]
Line 100-101: in southeastern Ontario, Canada.  [and compared beetles trapped on the ground verses in the canopy]

Methods
Line 120: delete comma after Knollenberg
Line 123-124: Silphidae that were caught during our study
Line 133: birds, plants and insects
Line 141: Additional trapping locations at our study site
Line 149: At each trap location, we set two concurrent traps and collected them after…
Line 156-157: ripening and suspended above the saline preservative.
Line 160: Canopy traps were hung 6m high in tree branches; the exact distance between the paired ground and canopy traps …
Line 163: paired ground and canopy traps with the largest distance being within 20m).
Line 226: the Random Forest model provided an overall…
Line 236-238: We omitted traps when no beetles were caught, regardless of trap distance, because traps with zero beetles provided…

Results:
Line 274: trap being on the ground increased as abundance of both species increased (Fig. 6).
Line 275: add individuals after Nicrophorus pustulatus
Line 288: delete that

Discussion:
Line 294: Ground traps captured more species and more individuals of burying beetles than canopy traps
Line 295-296: The number of individuals and species increased as the season progressed from May to June, for both ground and canopy traps, indicating there is a greater abundance
Line 297: delete – (July) compared to early in the season (May)
Line 300: classification accuracy), indicating there were repeatable …
Line 302: replace number with abundance
Line 303: delete that
Line 304: replace number with abundance
Line 320: we successfully baited N. pustulatus using chicken, and it has been reported in the laboratory setting, N. pustulatus will behave like
Line 339: Furthermore, the breeding season of vertebrates in the …
Line 348: and their use of canopy resources suggests vertical height is another important…

Literature Cited:
Line 372 replace dash with –
Line 389: Journal should be italicized
Line 397: The Coleopterists Bulletin
Line 430: replace dash with –
Experimental design: The experimental design was relevant and repeatable.
Validity of the findings: Meaningful results were produced.
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: ECOLOGICAL DIVERGENCE OF BURYING BEETLES INTO THE FOREST CANOPY
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have adequately addressed my concerns on the previous draft. The adjusted analysis uses mixed effects models to account for non-independence among samples, and the results are similar but more robust. The additional discussion of Random Forests and potential limitations is also helpful. Please see below for a few very minor suggestions.

Minor comments:
87: change to '1 individual' instead of '1 individuals'

92: change to "fewer than 4%"

293: I'm curious why you used log(abundance + 3) instead of log(abundance + 1). I don't recall seeing that before, since the reason is to avoid log(0). The legend for Figure 4 states 'Log(number of beetle per trap + 1)', so one of these might be a typo?

239-240: Perhaps change 'to improve the fit of the models' to 'to meet the assumptions of the models' or similar. This would clarify that rounding was done because of the assumption that errors are poisson distributed, and not as part of some odd fishing expedition for 'more significant' results.


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

Input:
Title: CHARACTERISTICS OF THE COMPLETE MITOCHONDRIAL GENOME OF SUHPALACSA LONGIALATA (NEUROPTERA, ASCALAPHIDAE) AND ITS PHYLOGENETIC IMPLICATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study has sequenced and examined the mitochondrial genome of the owlfly Suhpalacsa longialata Yang, 1992 (Neuroptera, Ascalaphidae). The genomic structure, organization and composition was compared with published mitochondrial genomes of other species from the same family. Additionally, the authors performed a phylogenetic analysis within Neuroptera, based on 13 protein-coding genes of mitochondria. They used 43 Neuroptera species and an outgroup of four Megaloptera species. In general, the manuscript is well written. Yet, some parts of the text can be reformulated and better explored. I also believe that there are some misinterpretations that need to be rethinking. The figures also need to be improved. Some of the figures and tables could be combined or moved to Supplementary Materials without significantly impacting the manuscript. Please, see detailed comments below.
Experimental design: The research is original and adds to the growing body of knowledge about the mitochondrial genome of insects, as well on the evolutionary relationships within Neuroptera (Insecta). The description of the methods needs to be improved with more detail and clarity. Yet, the method used is in accordance with the objective of the study.
Validity of the findings: The manuscript is very straightforward, and the authors make good use of their data to address questions. However, the manuscript needs to be improved in some aspects, especially with regard to the interpretation of phylogenies. Some of the decisions taken need to be better justified.
Additional comments: My detailed comments are listed below by section, and line number when necessary.

    1. TITLE: All the comments regarding the title are just suggestions. First of all, I will suggest adding the name of the order and the family in the title, after the name of the species: “Suhpalacsa longialata (Neuroptera, Ascalaphidae)”. This will make it easier for people to recognize the group to which the species belongs. A second suggestion is to change the reference to phylogeny in the title. As it stands (“… and its phylogeny”), it may imply that it will be a phylogeny only of the species S. longialata, when in fact it is a phylogeny of Neuroptera. My suggestion is something like: “… and its phylogenetic implications”, “… and a phylogeny of Neuroptera”, or “… and with mitochondrial genome phylogeny of Neuroptera”.

    2. ABSTRACT: It can be improved to present all sections of the manuscript: background, objectives, results and discussion, and conclusion. PeerJ allows an abstract with no more than approx. 500 words. You have only approx. 95 words. It is important to write a complete but concise abstract to entice potential readers into obtaining a copy of the full paper.

    3. INTRODUCTION:
        3.1. Species names and the citation of authors: According to the International Code of Zoological Nomenclature, the citation of the author's name of any species is optional (Article 51.1). The norms of PeerJ also do not have instruction on the citation of the author. In this sense, you are free to cite or not. However, I recommend that you cite the original author and date for each species mentioned in the text, from the introduction onwards. You just need to cite the author at the first time the species name appears in the text. This can be important in distinguishing between homonyms and in identifying species-group names.
        3.2. Line 53 to 55: I do not understand the reason for relating the word “widespread” to the fact that the pattern of the gene order is found in Drosophila yakuba. I suggest that you remove the reference to Drosophila yakuba. Although not wrong, arrangement is more commonly used than “order”. You could write without losing the meaning: “The most widespread gene arrangement in insect mtDNAs is hypothesized to be ancestral for the entire class Insecta”
        3.3. Line 55 to 56: Actually, rearrangements in insects can define clades at a variety of taxonomic scales below the ordinal level. I believe you can make this clear in this sentence, since it is not just for families or orders. I suggest you look at the following article - Cameron, Stephen L. "Insect mitochondrial genomics: implications for evolution and phylogeny." Annual review of entomology 59 (2014): 95-117.
        3.4. Line 58 to 59: The statement “mtDNAs are likely to be superior to nuclear DNAs to reconstruct phylogenetic relationships...” is a mistake. Undoubtedly, mtDNAs has many uses, as being important markers for phylogenetics. However, it is neither better nor worse than other sources of data, such as nuclear DNA, morphology and so on. It is a data source like others, with problems and qualities, and that needed to be used and analyzed according to what you want to answer, as well the approach at hand. I suggest you improve this sentence.
        3.5. Line 79 to 81: Please, be careful about using the term “basal” or “primitive”. Surely, it is possible to infer the characteristics of extinct ancestral species or genes. However, it is misleading to speak of any species as ‘‘older’’ just based on a tree. I suggest you rethink the use of “basal” and “primitive”, as well rewrite this sentence. Please, see the comment 5.6 for more suggestions on this issue.
        3.6. Line 83: At first glance the sentence seems to be incomplete (“Hence, the present study has taken a first step to”). A first step to what? Is the sentence incomplete or left this way intentionally?

    4. MATERIALS AND METHODS
        4.1. Sample origin and DNA extraction: I missed some additional information. How the sample was collected? Was the sample preserved in ethanol or was it fresh? Was it stored in a freezer? Was the specimen placed in any scientific collection? Are there any considerations about species identification? Is there any relevant information about removal of the leg from the specimen body? Have you made any modifications to the extraction protocol or was it done according to the manufacturer's protocol?
        4.2. PCR amplification and sequencing of S. longialata mtDNA: I suggest that you improve the description at lines 95-97 to be reproducible. It is not clear to me how exactly the primers were used in the amplifications. It needs more detail. Did you do exactly as Zhang et al. (2008) did with the amplifications? If yes, it's not entirely clear. It is also unclear how and for what universal, conserved and specific primers were used. Is there any difference between the universal primers and the conserved primers?
        4.3. Line 97: Please, cite the manufacturer/developer of Primer Premier 5.0.
        4.4. Line 105: The citation of MITOS is not correct. To cite MITOS: M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Pütz, M. Middendorf, P. F. Stadler MITOS: Improved de novo Metazoan Mitochondrial Genome Annotation Molecular Phylogenetics and Evolution 2013, 69(2):313-319.
        4.5. Line 127: “Consequently, we discovered 9 subsets”. I believe that this sentence is a result obtained from the analysis with PartionFinder 1.1.1. Because of that, it should be described in the results section and not in the methods.
        4.6. Line 131 to 133:  About the long branch attraction, I also believe that this sentence is a result. It should be described in the results section.

    5. RESULTS AND DISCUSSION
        5.1. Line 143 to 144: Please, be careful about using the term “basal” or “primitive”. Please, see the comment 3.5 and 5.6 for more suggestions on this issue. I suggest you change “basal ancestor” to “common ancestor”, or just “ancestor”.
        5.2. Line 153 to 156: The sentence about the transposition of contiguous genes is confusing. As it is written, it seems that you have empirical evidence to show that occurred a duplication followed by partial loss of genes. However, I belive that you are only suggesting a possible explanation for the pattern found. Beckenbach et al. (2008) just suggested a possible explanation for the reported rearrangement. I suggest that you improve this sentence to make it clear.
        5.3. Line 172: This sentence should be in the material and methods, not in the results. Please, remove from the results and add to the material and methods.
        5.4. Line 241 to 245: How did you infer that difference were caused mainly by long branch attraction? How did you come to the conclusion that the three species were unstable? I suggest you improve your discussion and provide justification for the long branch affirmation and the decision to remove all three species.
        5.5. Line 256 to 258: Describe the differences and similarities between the results of your phylogeny and that recovered by Wang et al. (2017).
        5.6. Line 258 to 259: There are two sentences in these lines, and I believe that each one contains misconceptions. You can not say that “Osmylidae is more primitive than Sisyridae” based on your phylogeny. This is a widespread misconception about what phylogenies can tell. A misinterpretation of phylogenies can be strongly influenced by many factors, which I will not discuss completely here. However, a misinterpretation of trees can occur when the species-poor sister group is thought of as “basal” or “early diverging” with respect to its species-rich sister. In this case, the species-poor sister group are mistakenly assumed to be “primitive” and to represent traits of the common ancestor. Since every branching in a tree is rotatable, if you change the position of the terminals just by rotating the nodes, which terminal would you consider as “primitive”? The term primitive is also problematic and should be avoided. It is misleading to speak of any species as ‘‘older’’ just based on a tree, especially without any information about time. If both lineages survive to the present, they continue to evolve at some rate at least for some characteristics throughout evolutionary history. I recommend three articles to read on the topic (listed below). These articles can help you interpret your phylogeny and rewrite this part of the discussion. I believe that there is also a misinterpretation in the sentence “Ascalaphidae branched earlier than the Myrmeleontidae”. According to the results, Ascalaphidae is not monophyletic in relation to Myrmeleontidae. In this sense, “Myrmeleontidae is inside Ascalaphidae”.
           Recommendation of articles
           Krell, Frank‐T., and Peter S. Cranston. "Which side of the tree is more basal?." Systematic Entomology 29.3 (2004): 279-281.
           Crisp, Michael D., and Lyn G. Cook. "Do early branching lineages signify ancestral traits?." Trends in Ecology & Evolution 20.3 (2005): 122-128.
           Omland, Kevin E., Lyn G. Cook, and Michael D. Crisp. "Tree thinking for all biology: the problem with reading phylogenies as ladders of progress." BioEssays 30.9 (2008): 854-867.

    6. CONCLUSION
        6.1. Line 266 to 267: I suggest you rewrite this sentence. You performed the analysis and you got a result. According to the results (the relationships recovered by the phylogenetic analysis), Ascalaphidae is not monophyletic.

    7. TABLES
        7.1. I would suggest rethinking the captions of all tables. The captions of the tables need to be well explained.
        7.2. Table 1: I suggest moving this table to the supplementary material. Although it is very important for other researchers to be able to repeat the work, I believe it is not relevant to be along with the text
        7.3. Table 2: You can consider moving this table to the supplementary material as well.
        7.4. Table 3: I consider it important to have this table along with the text. However, the dimensions of the table can be better adjusted
        7.5. Table 4: I believe that maybe this table is not needed along with the text. Perhaps the table can be moved to supplementary material. You barely use the information in this table for discussion in the text. Also, the table is too large. You need to write what is the abbreviation RSCU.

    8. FIGURES
        8.1. Figure 1: This is one of the most important figures of the work, however it needs to be improved. With the exception of color legend, all text outside the representation of the mitochondrial genome can be removed (Accession: unknown; Length: 15, 911 bp; and Suhpalacsa longialata complete genome). Color legend is too small, it is not possible to read what is written.
        8.2. Figure 2: I believe the description given in the text is probably enough, so it’s not necessary to include this figure.
        8.3. Figure 3: The caption of the figure needs to be better explained. What is the Y-axis? What is the X-axis?
        8.4. Figure 4: the dimensions of the figure can be better adjusted. Perhaps the figure can be moved to supplementary material.
        8.5. Figures 5 to 8: Maybe they can be combined. A figure with ML analysis and another figure with BI analysis. Or, a figure with ML and BI analysis of all species, and another figure with ML and BI analysis without the three “unstable species”.


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: CHARACTERISTICS OF THE COMPLETE MITOCHONDRIAL GENOME OF SUHPALACSA LONGIALATA (NEUROPTERA, ASCALAPHIDAE) AND ITS PHYLOGENETIC IMPLICATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: I think the work is very interesting, the Suhpalacsa longialata species is part of an under-represented family (Ascalaphidae) and part of an important Insecta order with unsolved phylogenetic questions (Neuroptera). In general, the manuscript is clearly written, the figures and tables are adequate. Only the Figure 6 is smaller than the other phylogenetic trees, so it is difficult to read the species names. In Table 4 caption lacks the initials for relative synonymous codon usage (RSCU) and in the Table 2 is a little difficult to understand to which family belong each species. I suggest put the name of the family aligned to the first species name for each group.
Lines 48-51: Lack reference about the conserved order of the genes in insect mitochondrial genomes.
Line 252: Lan et al. 2014 is not in the references, only Lan et al. 2016.

That being said, I would like to point some things that are not clear for me and give some suggestions that I think would improve the work:

The ideas in the first paragraph of the Introduction seem contradictory, it seems genes rearrangements are the main reason for the use of the mitochondrial molecule to solve phylogenetic questions, although the mitochondrial gene order is extremely conserved among the insects.
I think it is important to mention that most of rearrangements in the mitochondrial molecule are related to tRNAs or non-coding regions, and there are few cases that the morphology of the genome represents a synapomorphy, that is the case for the Neuroptera order, but not necessarily for the families in this group. Usually genomes rearrangements are not used as phylogenetic markers (Cameron et al 2006). The main usage of the mitochondrial molecule to solve phylogenetic questions is the use of the sequence to reconstruct the phylogenies and that was the approach used to answer the questions in this work. So, I think it could be better explained why the mitochondrial molecule is good as phylogenetic marker.
Also, in line 54, I did not understand why use the order present in fruit flies, that is a derivate group (Drosophila yakuba), as the example of the most spread gene order in insect mtDNAs. There are many works mentioning the ancestral insect gene order (pancrustacean) - Cameron et al 2006; Cook et al 2005 (DOI:10.1098/rspb.2004.3042), for example.
Experimental design: The research is within the scope of the journal and the methods are sufficient described. About the research question, one of the motivation to sequence the S. longialata genome was: “the other three published genomes show substantial gene rearrangements and it is unclear if the mitogenome of any of these species represents the basal condition in the Ascalaphidae”. What are these substantial rearrangements? Because the rearrangements cited in the references were the same found to other Neuroptera species. So, related to the morphology of the genome, all the species in this family are equal.
Validity of the findings: In the Results/Discussion of the Phylogenetic analysis, specifically in the lines 250 to 252, is not clear what was the previously controversial relationship between/within Myrmeleontidae that was solved in the present work. This is one of the most important results, so it could be more emphasized, better explained in the discussion or included in the background what was the issue. And it could be included a comparison with the other works that presented the controversial results.

Also, it is not clear why the increase in number of species included in the presented analysis resulted in different topologies related to Osmylidae, Sisyridae and Nevrorthidae found in Wang et al 2017 (lines 256-258). Mainly because the species included here were from the families: Myrmeleontidae, Chrysopidae and Ascalaphidae. Also, Wang et al 2017 mentioned the use of the heterogenous model (CAT-GTR) in the Bayesian inference as the only method able to recover Neuroptera as a monophyletic group. The differences found in this work would be due the different model used and not because of the species included here.
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: CHARACTERISTICS OF THE COMPLETE MITOCHONDRIAL GENOME OF SUHPALACSA LONGIALATA (NEUROPTERA, ASCALAPHIDAE) AND ITS PHYLOGENETIC IMPLICATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Please, refer to general comments to the author.
Experimental design: Please, refer to general comments to the author.
Validity of the findings: Please, refer to general comments to the author.
Additional comments: In my opinion, the authors have done a nice job. I believe that the authors have addressed my comments and suggestions appropriately. However, I have some minor suggestions below that I believe can improve the manuscript.

1. MATERIALS AND METHODS
1.1. Sample origin and DNA extraction:
*Line 87: You can remove the “an” before the name of the DNA extraction kit
*Line 109: I think the citation of MITOS is still not correct. The citation of the software should be after the name of the software. MITOS (Bernt et al., 2013). If you want to cite the webserver page, you can write MITOS (Bernt et al., 2013, available at http://mitos.bioinf.uni-leipzig.de/index.py).

2. RESULTS AND DISCUSSION
2.1. Mitogenome organization and structure:
*Line 149: change the word “commom” to “common”

2.2. Phylogenetic analyses: This section has been greatly improved. In the meantime, however, I have a some suggestions for minor clarifications.
*Line 253 to 254: I suggest you change “According to the opinion of Bergsten (2005)” to “According to Bergsten (2005)”. Remove the HYPERLINK from the text.
*Line 259: Please, be careful about using the term “basal” or “primitive”. I suggest removing the sentence or just saying that (Apochrysa matsumurae + Nothochrysa sp.) is a sister clade of (Nothancyla verreauxi + (Abachrysa eureka + (Chrysopa pallens + (Chrysoperla nipponensis + Chrysoperla externa)))).
*Line 263 to 264: I think it is best to change “supported” to “recovered” in this case. Another point: You did not fail to recover the monophyly. You got a result! Change “failed” to “did not recovered the monophyly of Ascalaphidae”.
*Line 267: Change “long-length attraction” to “long branch attraction”.
*Line 271: Again, be careful about using the term “basal” or “primitive”. Did you want to say that Osmylidae is sister clade of all other Neuroptera?
*Line 273: Change “supported” to “recovered”.
*Line 276: It's not clear what you mean by the phrase “were united with”. Do you want to say that they are sister clades? If yes, you need to make it clearer.
*Line 278 to 279: It's not clear what you want to say in this sentence. Do you mean that your results corroborated the results obtained by Wang et al. (2017) and Song et al. (2018)? If so, you need to make it clearer. However, it is important to note, your results did not recover the sister relationship of Myrmeleontidae and Ascalaphidae. Actually, Ascalaphidae is not monophyletic.
*Line 280 to 283: From the results and discussion of the manuscript, it does not seem that the relationship between/within Myrmeleontidae and Ascalaphidae is resolved. Futhermore, a different and/or higher sampling, as well the use of different data sources, may generate incongruent results. I suggest you reformulate this sentence to improve the discussion.
*Line 293 to 294: Again, you did not fail to recover the monophyly. You got a result! Change “failed” to “did not recovered the monophyly of Ascalaphidae”. Also, change “supported” to “recovered”. It is not clear what was also recovered by Wang et al. (2017) and Song et al. (2018). Did Wang et al. (2017) and Song et al. (2018) recovered the monophyly of Myrmeleontidae or did they not recover the monophyly of Ascalaphidae?
*Line 294: You can remove the phrase “Myrmeleontidae is inside Ascalaphidae in our results”. It is completely clear by the figures and by saying that Ascalaphidae is not monophyletic

3. CONCLUSION
*Line 302 to 304: I suggest you add the sentence that “you believe” that the cause of the differences is by the long branch attraction. I suggest this because at this moment, with the available data, the possibility of long branch attraction exists, but it is difficult to say with certainty. So, the phrase would be “From the results obtained in the present study, we believe the different topologies of phylogenetic relationships were caused mainly by long branch attraction of Coniopteryx sp., Dilar sp. and Semidalis aleyrodiformis”.

4. TABLES
*Table 1: It should be the table of Base composition of the mitochondrial genomes. However, it is presenting the species used in the work, which is the same table in the supplementary material (Table S2). Please, correct table 1.


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: CHARACTERISTICS OF THE COMPLETE MITOCHONDRIAL GENOME OF SUHPALACSA LONGIALATA (NEUROPTERA, ASCALAPHIDAE) AND ITS PHYLOGENETIC IMPLICATIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors made all the solicited changes and solved the important aspects that were not clear concerning the motivation of the study and the evolutionary questions of the group.
Much information was added to improve the manuscript, so I would like to point out some formatting details and some parts that are not totally clear for me yet:

Figures, tables and references
Table 1 is erroneously attached. Table 1 and Table S2 are the same.

Fig 4: Add in the caption (left) and (right) to ML and BI figures.
Change “The data is includes” to “The data include”.
Also, in the text is mentioned in the lines 246 and 284 the term BI 1, I believe it is the BI from figure 4, include this in the caption.

Fig 5: Add in the caption (left) and (right) to ML and BI figures.

Review references:
Ronquist et al. 2012 is not complete in the references.
Zhang et al. 2008: include a and b in the references and in the citation.

Lines 70 – 71: “These three published genomes (Ascalaphidae) show substantial gene rearrangements (Beckenbach et al., 2008; Negrisolo et al., 2011; Cheng et al., 2014)”.
How these 3 genomes show substantial gene rearrangements if they share the same arrangement as the other families of Neuroptera? (as mentioned in Lines 148 – 156)
Experimental design: Line 121: “For the first analysis that indicated Megaloptera as a sister clade to Neuroptera, as proposed by Engel et al. (2018) and Peters et al. (2014)”.
It seems a result and that Megaloptera as a sister clade of Neuroptera is a result only from the first approach.
Validity of the findings: Lines 241-246: the low support (ML29) found between Hemerobiidae and (Berothidae+Mantispidae) is being directly compared to the high support between Hemerobiidae and Chrysopidae. So, there are two different things being directly compared.
I would suggest, in the Fig. 4, to extend the red box until Matispidae (which includes the ML29) and let clear in the text the two results: 1- The change of the Hemerobiidae’s sister clade; 2- the high support found for both relations (Hemerobiidae+Chrysopidae) and ((Hemerobiidae+Chrysopidae) + (Berothidae+Mantispidae)) only in the BI analysis.

Lines 256 – 257: “In this situation, both the ML and BI phylogenetic trees showed identical topologies and high support values for most clades, except for the internal relations within the family Chrysopidae”. The outgroup is also different.

Lines 257-261: It is important to mention that in the ML (Apochrysa matsumurae + Nothochrysa sp.) is sister clade of (Nothochrysa sp. + (Nothancyla verreauxi + (Abachrysa eureka + (Chrysopa pallens + (Chrysoperla nipponensis + Chrysoperla externa))))) whereas in BI they are all part of the same clade.
The support is low to say the clade of (Apochrysa matsumurae +  Nothochrysa sp.) is the base clade of Chrysopidae. Also, in the text is not included Apochrysa matsumurae for the recovered BI analysis.

Lines 261 – 264: I would suggest change: “On the whole, this analysis highly supports the monophyly of Osmylidae, Sisyridae, Nevrorthidae, Berothidae, Mantispidae, Hemerobiidae, Chrysopidae, Psychopsidae, Nymphidae and Nemopteridae. But the monophyly of Ascalaphidae which was supported by Wang et al. (2017) failed to be supported in this study.” to something like: On the whole, this analysis supports the monophyly of all Neuroptera families except the Ascalaphidae, previously reported as monophyletic by wang et al 2017.

Lines 267-275:
Personally, I don’t think it is necessary include this deep discussion: “In the ML analysis long-length attraction existed with all families of Neuroptera (Fig. 4) and Coniopterygidae is recovered as sister clade to the remaining extant Neuroptera, which is consistent with the conclusions of Wang et al. (2017) and Winterton et al. (2010; 2018). By contrast, in the BI analysis (Fig. 4) Osmylidae is recovered as sister clade to (Coniopterygidae + (Sisyridae + Nevrorthidae). In the results of Haring and Aspӧck (2004) and Song et al. (2018), Osmylidae as the basal position of Neuroptera was supported whereas in the results of Wang et al. (2017), the relationship of (Osmylidae + (Sisyridae + Nevrorthidae)) is supported by ML and BI analyses with the homogenous GTR+I+G model. But when Wang et al. (2017) used the heterogenous CAT-GTR model in BI analysis, (Sisyridae + Nevrorthidae) + (Osmylidae + other Neuroptera) were recovered” for two reasons:
1-	It is related to Fig4 and the final trees you are considering are from Fig 5.
2-	These families of Neuroptera are not the focus of the study. The further discussion is more important and the reader can get lost in this part.
If this discussion will be maintained I would suggest changing it to before you start discuss fig 5 and try to summarize it.

Lines 291-294: “the monophyly of Myrmeleontidae was recovered again and is supported by Wang and Song”, but the monophyly of Myrmeleontidae is not supported by both (based on the introduction).
I would suggest to change this sentence and to make a conclusion based on the problem pointed out in the introduction (“Ascalaphidae as a sister clade of Myrmeleontidae is supported by Song et al. (2018), while Ascalaphidae within the clade of Myrmeleontidae is recovered by Wang et al. (2017)”.
Additional comments: Line 46: extra dot before the citation

Line 128: extra comma after Neuroptera

Line 133: correct the name of the program to PartitionFinder

Line 136: it lacks the citation for MrBayes 3.2

Line 156: correct 218 to 2018

Lines 164-165: “The greater length of the S. longialata mitogenome is due largely to 16 intergenic gaps ranging”
I would suggest change “gaps” to intergenic regions as you used in other topics.

Lines 220-221: “whereas the tRNA genes of Ascaloptynx appendiculatus almost displayed the typical cloverleaf secondary structure.”
What does it mean “almost” displayed the typical cloverleaf secondary structure?

Line 253 – 253: unformatted citation (“hyperlink…”)

Line 256: Change Figs. 5 to Fig 5.


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: INTEGRATION OF PHYLOGENOMICS AND MOLECULAR MODELING REVEALS LINEAGE-SPECIFIC DIVERSIFICATION OF TOXINS IN SCORPIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I enjoyed reading this manuscript. You did a good job of clearly outlining your goals, thoroughly explaining the methods and results, and putting the findings within a relevant broader context. I was particularly impressed with the extensive and rigorous methods. I think it is a creative approach for using genomic data to better understand the phylogenetic patterns in a group of organisms. The figures and tables are generally informative and look nice. The raw data is easily accessible. Nevertheless, I do have some suggestion that I think will improve the manuscript.

-	It would have been helpful to see more general background information on scorpion taxonomy in the introduction. How many species are there? You do a good job of referencing past phylogenetic work in scorpions, but there isn’t much context for statements about taxon sampling. Are 55 species a good representation?

-	In a few places in the introduction it is unclear if you are discussing toxins/venoms more generally or specific to scorpions. Line 55 is a good example of this. I assumed you were talking about scorpion venoms, but it’s not completely clear.

-	Figure 1: I think you should add divergence estimates on the tree. You make mention of some dates in the text, and it would be nice to reference these estimates and others across the group. Also, it’s not clear to me what the bars to the right of the tree indicate. Are they the number of genes in each taxon? Forgive me if I simply missed something in the caption.

-	I don’t know if Figure 2 is necessary. It doesn’t seem to be adding any information that isn’t already in Figure 1. Perhaps it could be moved to the supplement?

-	The caption to Figure 4 doesn’t have an explanation of panels c and d.

-	In Lines 104-106, could you give a breakdown of the data you used? How many were your transcriptomes, complete scorpion genomes, and venom libraries? It’s in TableS1, but it would be nice to have just a few numbers here in the methods.

-	The manuscript is generally well written, but there are several typos and confusing/awkward phrases. I’ve made note of them in the additional comments below.
Experimental design: The experimental design, particularly the phylogenomic methods, seem solid to me. I have a few relatively minor comments:

-	Lines 119-120, 173: What were your parameters for MAFFT and trimAl?

-	Lines 142-143: I could not find the Bayesian dating results, even though you stated these were explored in this study. Perhaps you could add a dated Bayesian tree to the supplement?

-	Lines 160-161: Why did you only run PhyloBayes on Matrix 2? Computational time? I think it would be best to exclude this analysis from the paper altogether. It doesn’t add much other than to say “we did it.”
Validity of the findings: I thought the data and approach in this manuscript were very sound. The findings seem to be an important contribution to scorpion systematics and venom evolution more generally.

I do think the conclusion section can be expanded. As currently written, the conclusions focus only on molecular morphology as a synapomorphy for these particular groups of scorpions. However, this doesn’t exactly connect well with the abstract/introduction, which sets up the paper as addressing venom evolution. Basically, most of the paper seems to be moving towards using the scorpion phylogeny to understand the evolution of scorpion venom (see the first sentence of the abstract), but then concludes that you used scorpion venom to help resolve the scorpion phylogeny. I think you should add some conclusions and/or more discussion about how this phylogenetic hypothesis is important for our understanding of venom evolution. This would tie things nicely back to the intro.

I also have another comment regarding Figure 1. If the bars to the right of the tree are indeed the number of genes from each taxon (see above question), are you concerned that some taxa have so few genes? Some of less than 10. It’s also curious that so many taxa in Buthida are missing lots of genes. Any reason for this, and if so, perhaps devote space to this in the results and discussion?
Additional comments: Here are some additional minor comments, mostly related to typos and unclear sentences:

Line 24: say “phylogenomic relationships of scorpions” instead.

Line 39: Perhaps avoid using the word “fascinating” in consecutive sentences.

Lines 46-47 is worded awkwardly. I think the phrase “recruitment from housekeeping gene into venom” is confusing.

Line 69: say “contains” rather than “bears.”

Lines 80-81 and 84: I don’t think you need to say “taxonomic samping to…” Just say “limited to 25 species” and “limited to six species.”

Line 83. The term “non-overlap(ping) here and in the previous sentence is a little confusing. I understand what you’re saying, but I had to read it twice. Something like “focused on different species” and “used a different molecular dataset” would clarify things.

Line 105: “published” or “existing complete scorpion genomes…”

Line 121: “less than 50 amino acids…”

Line 147: What is “Matrix 1?” Maybe just say “our original matrix (Matrix 1).”

Line 150: “using a different number of species…”

Line 166: “well as from GenBank and…”

Line 278: “were represented by 52…”

Line 289-290: The sentence is a little awkward. Perhaps change to something like, “To detect the direction of selection acting on the codon…”

Line 291: No need for the “While” at the beginning of the sentence.

Line 365: should be “clades.”

Figure 6 caption: indicates greater or smaller p-value?

Figure 7 caption: “amino acid position in the multiple sequence alignment.”


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: INTEGRATION OF PHYLOGENOMICS AND MOLECULAR MODELING REVEALS LINEAGE-SPECIFIC DIVERSIFICATION OF TOXINS IN SCORPIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript is pretty solid and straightforward. The analyses are well-done and the manuscript as a whole is clear. While I am not an expert in toxins, the choice of analyses seems justified, are not difficult to understand or interpret, and the results are clear. The criteria for Basic Reporting, Experimental Design, and Validity of Findings are all met. The figures are clear and quite eye-catching. I feel this manuscript is acceptable for publication, given some minor edits, which I include below.

Minor comments and recommendations:

Line 104-105: “generated by us”. This is misleading since it seems that the vast majority of transcriptomes used were previously published by others. It seems only two transcriptomes were newly generated for this study. This should be clarified.

Line 147: “maximizing” to “maximize”

Line 150 and elsewhere: although “orthologues” is acceptable spelling, “orthologs” is more commonly used.

Line 265: “with previous hypothesis”. Which one? And it should be “with a previous hypothesis” or “with previous hypotheses”.

Line 272: I’ve never personally used phylobayes, but I hear about analyses failing to reach convergence with this program quite a bit. Honestly, I don’t think this analysis is even needed. Your other analyses are pretty well supported and congruent. It’s great that you want to report it, but it wouldn’t bother me to just cut out mentions of phylobayes.

Line 278: “were represented by 52”

Line 312: “Morphometric analysis of molecular”. Should this refer to Figure S3?

Figure 1. What are the numbers next to the phylogeny?

Figure 4. the axis labels could be bigger.


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: INTEGRATION OF PHYLOGENOMICS AND MOLECULAR MODELING REVEALS LINEAGE-SPECIFIC DIVERSIFICATION OF TOXINS IN SCORPIONS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is generally of a high standard, there are mostly just a few typos scattered across the text (listed below). Make sure that you present statistical results in full, it is not sufficient to just present P-values as is done throughout the results. Otherwise I would recommend the authors include their species tree on Figshare as well as the other resources available there. The authors have included the data needed to reconstruct this tree but it is fairly standard in the field to provide the tree as well as this enables readers to check details and replicate particular results without requiring the time-consuming step of building the tree again. Finally, the references are inconsistently formatted throughout in terms of issues such as capitalisation of article and journal titles, and the presence of a DOI. This should be standardised throughout. Part of the Coddington et al. reference seems to be missing and with the detail given I'm not sure what the Dongen reference is. There are also some issues with reference order, e.g. Santibanez-Lopez et al. (2017) is listed before Santibanez-Lopez et al. (2016), and Sharma et al. 2015 is listed before Sharma et al., 2016.

TYPOS AND SIMILAR MINOR ERRORS
ln 81 and 90 - Be careful about the use of 'significant' when not referring to statistical results as this can create confusion for readers.

ln 121 - 'less 50' should be 'less than 50'

ln 147 - maximizing should be maximize

ln 225-226 - the correct reference for phytools is Revell, L.J., 2012. phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3(2), pp.217-223

ln 245 - http://venom.space doesn't open for me, it just takes me to a login box with no option to create an account

ln 327 - 'conservative compared to what? The figures refered to here are open to subjective interpretation in support of this statement - for instance to me it looks like a reasonable amount of evolution has happened, so make sure you qualify this.

ln 346 - Fig. 6 doesn't need the reference to parts b and c

ln 350 - Reference to figure 7 has parts c and listed out of alphabetical order for some reason.

ln 365 - 'caldes' should be 'clades'

ln 375-378 - Nice point, but where your two libraries derived from different populations (if so where from)?

ln 395 - I think 'cysteine-rich like peptides' should just be 'cysteine-rich peptides'

ln 440 - 'retain' should be 'retains'

Figure 1 - what do the bars (and numbers) beside the phylogeny represent?

Figure 2 - 'Sensitive' should be 'sensitivity'. I'm also not sure from the descriptions and keys how the Navajo plots in Figures 1 and 2 actually differ other than in colour scheme - there are more plots in Figure 2 but those that overlap with the ones in Figure 1 seem identical (further adding to the confusion).

Figure 3 - Should the last sentence be structured with plurals (i.e. amino acids, their)?

Figure 4 - The legend refers only to parts a and b but the figures are labelled with a-d (I think a and b correspond to a in the legend and c and d correspond to b).

Figure 6 - 'color of the circle indicates greater correlation coefficient' could lose the word 'greater' and improve clarity, and 'size of the circle indicates greater P-value' should, I think, be 'increasing size of the circle indicates smaller P-values'

Figure 7 - 'date' should be 'dated', 'axe' should be 'axis'
Experimental design: Very well done throughout, in particular it is clear that careful attention has been paid to justifying analytical decisions.

The one exception is that at two points in the methods (ln 106 and 139-141) the authors refer to previous papers for details. Although this happens semi-regularly in the literature, I believe that readers should be able to understand what has been done in a paper without having to refer to several other papers to figure it out. Please give at least brief details here, and preferably a full account of methods.

I would also point out that the authors refer to "Matrix1" in ln 147 but don't actually explain what this is until the results section (ln 259-260).
Validity of the findings: Both data and results appear of high quality and the conclusions do not stray from what is justifiable from the results themselves. I might only suggest an idea to the authors, which they are free to ignore or incorporate depending on whether they think it has enough merit to be worth discussing. Your results seem to be consistent with the ancestral scorpion possessing an ICK toxin that is ancestral to both LKTx and calcins (which subsequently diversified into these groups in the two lineages originating from the basal split in scorpions). To me that would be a very interesting suggestion and might be one you want to make in the manuscript.
Additional comments: I would finally just like to congratulate the authors on an excellent piece of work that I greatly enjoyed reading. With only the minor issues above address, this paper is definitely worthy of publication.

Best wishes,
Kevin Arbuckle