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

Input:
Title: THE INFLUENCE OF ECOLOGICAL INFRASTRUCTURES ADJACENT TO CROPS ON THEIR CARABID ASSEMBLAGES IN INTENSIVE AGROECOSYSTEMS
Review round: 2
Reviewer: 3

Output:
Basic reporting: This paper addresses the effect of perennial ecological infrastructures on conservation of carabid species and its functional traits, often related to pest and weed control. Specifically, they compare carabidae assemblages between  grassy strips, hedges and annual strips. They found a clear distinction between carabid assemblages occupying crops and ecological infrastructures (e.g. flower and grassy strips, hedges). Moreover, assemblages in ecological infrastructures were mostly dominated by generalist species and an unexpected result of low diversity and activity was found at hedges. The paper reads well and is well written, the literature used is sufficient. However, authors need to double check the whole text carefully since many mistakes are found along the paper, such as many spaces between lines, additional space between references, linked words (such as line 93 "withinthe", etc.

The parts that worries me most (described below) is regarding the sampling design, low replication and applied stats. Even though authors corrected for the problems in stats, I'm not sure it it will be enough for publication, especially due to low replication of the study.
Experimental design: There are some issues regarding sampling design and stats that concerns me. Moreover, the few replications of the study design must have implications in the discussed results and authors must acknowledge that.

Some main points that concerns me:

1- Scale of analysis:
Lines 117-118: within radii of 50 and 500 meters, distances known to influence carabid assemblages (Aviron et al., 2005). Can authors explain better? Because there is a huge difference between 50 and 500m. How does both scales affect carabid assemblages? Moreover, it is not clear what scale was used in the end (50 or 500)?

2- Functional analysis
Line 164: Functional traits were used to analyse the structure of carabid assemblages.  Explain the differences and details of functional indexes. Moreover, the link between traits and service is weak.

3- Sampling independency.
*10m for independency between sampling sites* -
For me this is an important issue because not only the whole study has few replicates, but basically the samplings within sites are pseudo-replicates.

4- Adjacent crop
This is another important issue because the adjacent crop was not controlled and it will absolutely affect the carabidae assemblages. I think that the crop type must be included as predictor variable as well. Even though it was not their question, unfortunately it should have been controlled.

5 - Random effects
This is a huge problem of the paper because authors are using the Study sites (N=3) as random effects in the models, and it violates the main assumption of using random effects in mixed models, regarding the number of levels required to obtain variability (see Bolker, B. (2015). Linear and generalized mixed models. In: Ecological Statistics: contemporary theory and application. Edited by Fox, G.A., Negrete-Yankelevich, S.,  Sosa, V.J. Oxford University Press,  United Kingdom, Pages 309-333.) Thus, study site MUST be included as fixed factor as well, otherwise it wont't be right.

6 - Temporal sampling
"Traps were simultaneously open for seven days during the second week of May,  June, July and at the end of September - Not clear either. How many times each site was sampled? and when?
Validity of the findings: The low replication of the study and the lack of relationship with carabidae assemblages and ecological infrastructures might be just a sample effect due to the low replication of the study. Moreover, the analysis need to be redone, taking into account the issues I pointed before. Moreover, it is important that authors discuss the limitations of its results especially regarding the weak replication and study design.
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: IDENTIFYING MODEL VIOLATIONS UNDER THE MULTISPECIES COALESCENT MODEL USING P2C2M.SNAPP
Review round: 1
Reviewer: 1

Output:
Basic reporting: I enjoyed reading this manuscript, it is well-written, succinct, and clearly describes some new, important tools that were developed for assessing the reliability of phylogenetic inferences under coalescent models.
Experimental design: The methods are well documented and suited to addressing the questions presented here.

Line 91: A minor point, but would it be possible to add an option for users to sample uniformly from the posterior? This might be preferred in some cases to reduce sample autocorrelation.

As the authors point out, poor performance of the Fst summary statistic is unfortunate because its calculation only requires the use of the raw datasets, and thus may be more computationally approachable for some users. Although it’s not necessary, calculating several other population genetics summary statistics from the posterior and posterior predictive datasets seems like a relatively straightforward extension, and if any were found to be useful, I would guess that the tests may be more widely applied. Another option that comes to mind would be to develop a test focused around concordance factors calculated from the SNP datasets.
Validity of the findings: no comment
Additional comments: This manuscript documents an important area of research, detecting model violations in empirical data is foundational to accurate phylogenetic inference. Generally, I think the manuscript is in great shape, though I’ll provide a few suggestions for the authors consideration:

The extensive focus on gene flow as a violation of the MSCM in the manuscript felt limited in scope. While I recognize that was the focus of the simulation testing in the manuscript, in theory, the test statistics identified here could be useful in detecting poor fit between the model and a dataset, regardless of the processes that produce this. Some discussion of this issue would be nice.

I’d imagine the poor performance of many of the statistics that were evaluated was somewhat unsatisfying to the authors as well. Some further discussion of this may be warranted, especially for those test statistics with high false positive rates, as posterior predictive checks are often thought to be highly conservative. Do the authors have any idea why the MLSD is so useful for detecting poor fit in this scenario compared to the others that are evaluated? Could it be related to the specific simulation conditions that were considered? Although quite a bit of work has been done recently developing methods for assessing model fit in phylogenetics, less work has been directed towards identifying when and why some test statistics work better than others. Though outside the scope of this manuscript, I’m sure potential users of these tools and other workers in the field would appreciate any ideas about this the authors have gleaned from their work.

Finally, I think some further presentation of the results would be useful. For example, the manuscript doesn’t report the performance of the summary statistics under different levels of gene flow, despite the simulations being done under a very large range. One might expect high rates of gene flow to be more problematic for phylogenetic inference and easier to detect using tests of model fit. Was there any correlation between the migration rates under which the data was simulated and the test statistic values? If there were, Fig. 2 might warrant some modification to demonstrate this.


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: IDENTIFYING MODEL VIOLATIONS UNDER THE MULTISPECIES COALESCENT MODEL USING P2C2M.SNAPP
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written, clear and concise.

General Comments:
1). This is personal preference, but I find figure 2 really hectic and lacking in detail. Since the SNAPP parts of the analyses aren't talked about in the manuscript at all, and aren't controlled by the R package in review, perhaps minimizing those parts of the figure, and expanding the "grey box" portion to add more detail in what happens in each step would be a more clear way to show the work flow?

Minor Comments:

Line 44: occurs should be occur
Experimental design: General Comments:

1). The package doesn't seem to install with R version >3.6. That should be listed in the manuscript someplace as minimum system requirement, or perhaps is a bug in the current CRAN archive? If it's intended, the manuscript should formally define those system requirements at some point.
Validity of the findings: 1.) The findings of which test statistics have a propensity to report false negatives is quite interesting. This is an area were PPS needs far more work. It would be helpful, almost necessary in some ways, for the package to include some type of effect size statistic. Without it, detecting model violation is a bit of a binary result. Yes there is model violation, or no there is not, without any information helping a researcher determine what the impact of that violation is on their analyses. One possible example is in the Brown et. al. paper the authors cite, though I'm not sure if it would be appropriate for this package, something similar would be very helpful.
Additional comments: Overall the work is solid and will add another needed piece to researchers using PPS to determine the model adequacy of their experimental design. Incorporating this package in an already available R package in a familiar framework will hopefully help users become more accustomed to doing this type of model checking as a natural part of their workflow.


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: IDENTIFYING MODEL VIOLATIONS UNDER THE MULTISPECIES COALESCENT MODEL USING P2C2M.SNAPP
Review round: 1
Reviewer: 3

Output:
Basic reporting: Overall, I find this manuscript well written and the present application useful for the community. As you will see in my comments, my main concerns regard the clarity of the manuscript. If found that it could have been more detailed in several parts.

General comments:
It would be very helpful if you could provide a better overview about the summary statistics and methods used. I'ld suggest to add a box with the brief definition of specific summary statistics (e.g. Fst, RF and KF tree distance).

The interactions of the user was not very clear. When does the user need to run an analysis manually (e.g., running SNAPP or computing summary stats) and when does this happen automatically? Would it be possible to insert a code or pseudo-code example with the steps a user has to take for the analysis pipeline to run?

Could you add a sketch showing the two models used in the simulation. I find it easier to see the gene-flow example instead of only reading the description.

What was the motivation to choose these specific summary statistics? Are there any other summary statistics in the literature that could be used too? How easy would it be to add new summary statistics?

It took me quite some time to wrap my head around Figure 2 and the results. Perhaps it would be better to split the results into two plots; one for each simulation setting. Some of the results are very surprising. Why are the two tree metrics (RF and KF) always rejecting one model? Why is it that a summary statistic can have so many false positives? I would love to see some insights here.

Specific comments:
What doesP2C2M actually stand for? Maybe you could provide the full name when you first use it (line 77).

It was not really clear to me that you were using both inference based and data based summary statistics. Perhaps you could make this more clear in the introduction (paragraph starting at line 66) and in the section called "Pipeline".

In lines 73 to 75 you are stating that there should should be little difference in the summary statistics if the model provides a good fit. This statements is technically not correct. Let us consider a hypothetical example as follows with two models A and B. Model A produces posterior predictive datasets where the summary statistics are very, very close to the ones computed from the empirical data, but always slightly larger. Thus, the posterior predictive p-value is 0 (rejected). Model B produces datasets with widely spread summary statistics (many of them not close to the empirical summary statistic), but half of the values are smaller and half of the values are larger than the empirical value. Thus, the p-value would be 0.5 (not rejected). So it is not (only) about closeness of the simulated datasets but more importantly that the empirical dataset is not unexpected because it lies in the simulated range of the model.

What do you mean by "samples at random" (line 91)? Wouldn't it be actually more efficient if you take every k-th sample because then you minimize the autocorrelation of MCMC samples (standard thinning)?

Please add a link to the tutorials in line 102.

Replace the "with" with "have" in line 109.

In your definition of p-values, what do you do when you have exactly the same value for the summary statistic? I believe this might happen very often for the RF tree distance. In our work, we specifically defined the lower p-value as samples being smaller or equal, thus using a conservative approach (see Höhna et al. 2018)

The sentence starting at line 144 can be removed; it is a repetition of line 120.

In line 165 you should provide the full link to the GitHub repository.

What is a gamma tree prior (line 165)? Commonly we use a birth-death process as a species tree prior, or the MSC as a gene tree prior. Did you mean a gamma prior on the population size?

What gamma rate prior do you mean (line 166)? On which rate is this prior used? Substitution rate, clock rate, among site rate variation?

What specifically do you mean by "the effect it could have" (line 235)? Could you provide an example what you would researchers suggest to write if they find model violations using P2C2M.SNAPP?
Experimental design: The experimental design is well suited. I have only some concerns about sufficient details about the methods, as provided above.
Validity of the findings: The results could be discussed a bit more. Overall, the results of the comparison between summary statistics was very brief and should be expanded. Clearly some results are surprising, and it would be nice to see what the next steps could be.
Additional comments: I reviewed the manuscript with a first year graduate student in my group. I've included her feedback in my evaluation. She strongly thought that the manuscript could be more precise with much more details about specific steps in the analysis pipeline. I agree that the present manuscript requires a good background knowledge in field and is hard to fully understand without. I leave it up to the authors if they prefer to refer to literature or expand the present manuscript to make it more accessible to young scientists.


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: IDENTIFYING MODEL VIOLATIONS UNDER THE MULTISPECIES COALESCENT MODEL USING P2C2M.SNAPP
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript reports progress on an important series of tools for detecting model violations in empirical data analyzed under the multispecies coalescent. I thank the authors for addressing my suggestions in my previous review of the study, and think that the manuscript (which was already in good shape) is clear, succinct, and a valuable contribution.

A couple minor comments that came up upon my reading that the authors may want to consider addressing in the manuscript:

Line 44: Should be “e.g.” not “i.e.”?

Line 99: Is there a justification or citation that can be provided for the minimum of 100 trees?

Fst outlier test: I am assuming users have the ability to control the parameters that determine the sensitivity of these tests to detecting outliers? Do the authors have any data (or even intuition) on how doing so might impact the performance of the posterior predictive test results?

Results: Did the authors qualitatively look at the effect of altering the p-value threshold (e.g., using 0.01 instead of 0.05) for model violations? I wonder if this would have any effect on the number of type 1 and type 2 errors for different tests.


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: MORPHOLOGICAL VARIATION OF LEAF TRAITS IN THE TERNSTROEMIA LINEATA SPECIES COMPLEX (ERICALES: PENTHAPHYLACACEAE) IN RESPONSE TO GEOGRAPHIC AND CLIMATIC VARIATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: Line 75, leaf size is also differed within a canopy with the top leaves being smaller and more thick. And in this paragraph, when authors talking about leaf size or "Smaller leaves are better adapted to hot or dry environments", does it refer to broad-leaf or even to conifer needles?

Line 75, it is hard to apart the cause due to precipitation/nutrient content from the cause due to different altitudes, normally precipitation also varied along a gradient. So should this sentence be "...with the increase in altitude because of the differences in precipitation and ?"?

Line 112-118, line 119-125 can be combined as one paragraph. And Line 119-125 should be mentioned before line 112-118 since it discussed the distribution of the species (more broad knowledge).

Line 129, the second objective is not a really objective, it is a discussion point. Unless authors conducted some meta-data analysis, this does not count as an objective.
Experimental design: Line 136-145, did authors measure those variables in the field or in the lab? If it was done in the lab, more details should be mentioned about how to preserve samples, fix samples on a white background, etc...Since authors used vernier to measure the size, I don't see any needs to collect leaves, they can just measure directly in the field.

Line 136, did authors record the locations of each sampled individuals using GPS, so later on they could map them?

Line 183, "ArcGIS"

In the Method section, for sentences using GIS, it might be better to attach a flowchart (for example if using a model builder), so readers would better understand the methods.
Validity of the findings: Line 217, no need to use "whereas", use "and". this is not a contrasting

Line 230, "Spatulated vs. elliptic leaves (DWLR)." this is not a complete sentence. Is this a subheading?

Line 249, I did not see any information of percent error in Table 4, how much is the minimum?

Line 259, typo "for de first"

Line 268, Were there any correlation between geography and climate in spatial? I think they are related. The reason that authors found climate is better indicate leaf shape than geography might be due to the small variance of climate (spatial) at this range. Right now, authors is comparing climate (seasonal/temporal) to geography (spatial).

Line 295, environmental factors due to gradients?

Line 298-302, those three sentences already appeared in the Result sections (line 230). Authors should not repeat the findings again but add more explains/linkage about environmental factors and leaves (spatulate vs. elliptic). Sentences in line 317 should be brought up here.

Line 350-354, was it necessary to conclude those methods in the Conclusion section? If those are new techniques that researchers have rarely applied to this area, it might be worth to mention. But I don't think interpolation map is.
Additional comments: In this study, authors measured 9 foliar traits from 270 individuals of Ternstroemia lineata complex, and related 19 environmental variables to variation in leaf morphology across a range in Mexico and north of Guatemala. I find this paper add some values to the society, however authors should reorganize the Discussion as the Discussion does not have to follow the order in result section. For example, it is better to group sentences in line 292-302 and in line 317-321 because they both talking about "spatulate leaf shape". Other comments please see 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: MORPHOLOGICAL VARIATION OF LEAF TRAITS IN THE TERNSTROEMIA LINEATA SPECIES COMPLEX (ERICALES: PENTHAPHYLACACEAE) IN RESPONSE TO GEOGRAPHIC AND CLIMATIC VARIATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a very interesting study that evaluated the intraspecific variation on leaf traits of Ternstroemia lineata in relation to climate and geographical variation. For this, the authors compared nine morphological leaf traits of 270 individuals of 32 populations from different regions of Mexico, delimiting groups and boundary zones of leaf morphology changes. Also, they evaluated which environmental variables influence more traits variability. I think this is a nice work with potential to be published, although it needs some improvements. The English grammar needs some revision. Some parts are not easy to follow and I found some words in Spanish. The whole text needs to be reviewed, especially on the results and discussion. The tables can be formatted to be more presentable and some figures needs to be redone.
Experimental design: I missed some information on the methods. There is no description regarding the environmental differences between the areas (provinces), so I do not know how different they are and I cannot associate them with the results. There is no information of how many samples per province were taken. I can find it in the supplementary material, but I think it should be described on the text. The Figure 1 is also not illustrative of how many samples per area they have. Looking at the supplementary material, I can see that the number of populations per area is not equal. It can influence on the results and should be clear on the text. I’m not sure if the use of three RDA analysis is necessary and brings additional information.
Validity of the findings: The results are interesting, but need to be better described and discussed. For example, there are nine areas that differed in leaf morphology, but there is no description of them. There is a description of the variation of the three traits selected (TL, WLR, DWLR), but I do not understood how these nine areas differ in leaf morphology. In the discussion, there is no information regarding the relation of each leaf characteristic with the environmental variables, for example, why leaves grow more on higher temperatures. The authors describe that larger leaves are related to higher temperatures, but do not say why it could be an important adaptation. Which are the adaptive advantages to have larger or shorter leaves, more spatulate leaves or elliptic leaves, in relation to the environmental variables analyzed? They briefly presented these relationship in the introduction, but it is not well explored. If the aim of the paper is to evaluate how traits plasticity in response to environmental characteristics can lead to adaptive evolution of species, it should be discussed. Also, there is no link between leaf traits with the subspecies. You discussed some things on the conclusions that you didn’t discussed before. Here you should summarize what are your main results, contributions of the study and which is still necessary to explore.
Additional comments: Line 34: ratio of the leave? You mean the ratio between the maximum width of the lamina and the lamina length (WLR)
Line 40-44: rewrite.
Line 61: What you mean with ‘current ecology’?
Line 68: you mean local climate?
Line 71: appreciate? Suggestion: to observe
Line 73: to the plant
Lines 78-79: This phrase is strange. And how does light adjust leaf shape?
Line 91: “…. key climatic factors to which it is related have been identified” I would remove ‘have been identified’.
Line 103: How they are correlated? Which biotic factors?
Lines 106-107: I think the transition of subject was very abrupt
Line 128: aim is better than objective
Line 151: “With these selected morphological... “ , here you should indicate which traits were chosen with the PCA, not in line 154.
Lines 155-158: I think that the explanation of what the ratios WLR e DWLR indicate should be together with the descriptions of the traits, on the earlier topic. This topic in more data analysis.
Line 224: visual inspection?
Lines 230-237: Rewrite this sentence, and follow a pattern to describe the results. It will be interesting if you remember the writer what means a higher or lower DWLR. Same thing for WLR.
Lines 245: It is better ‘discriminant analysis’. You don’t need to repeat that the nine groups are based on the three traits selected, because it is already explained.
Lines 252-254: rewrite this sentence. Suggestion: Based on iterative analysis we selected the environmental variables: ……
Lines 307-308: this phrase is confuse, I didn’t understand.
Lines 308-309: Most important variables for what?
Lines 314-315: clear correlation means positive or negative?
Lines 322-325: I didn’t understand.
Line 339: you didn’t mentioned before different levels of response
Line 342: appreciated?
You discussed some things on the conclusions that you didn’t discussed before. Here you should summarize what are your main results, contributions of the study and which is still necessary to explore.

Figure 1. It is not possible to see every point on the map, they overlap a lot. And the same thing happen to the ‘known distribution area’.
Figure 5. The canonical distribution graphic is too small.


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: MORPHOLOGICAL VARIATION OF LEAF TRAITS IN THE TERNSTROEMIA LINEATA SPECIES COMPLEX (ERICALES: PENTHAPHYLACACEAE) IN RESPONSE TO GEOGRAPHIC AND CLIMATIC VARIATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: The work is important and trying to understand relationship among species and climate a important subject in face of the warm up of the planet.

The article is quite well written, though it is not always clear and unambiguous. It would benefit from a thorough review of the English.

Abstract – it provides a complete abstract showing the importance of the study, however the results are spatially described by Mexico areas (Soconusco, Sierra Madre del Sur, Eje Volcanico province), rather than their spatial ecological gradient,  making it difficult for the reader to understand the main result (if they are not from Mexico).  Please check Hans ter Steege et al.  in 2006 (Nature paper) that found major gradients in Amazonia, for ideas on how to present your results in the abstract.

The Introduction introduces some of the main contextual issues but is not very well structured, with the narrative jumping between conceptual areas without very strong links. Also, the complexity of interactions that mould the relationship between leaf morphology and environmental conditions is not well explained, with no mention of the numerous trade-offs that can influence multiple aspects of a plant´s phenotype.

Also, there are a lot of debate about using “lat/long” as variable in this type of analyses, the introduction list some work that focus on this, but does not take a path in the argumentation.

Maybe it would be good to explain what this species T Lineata is an important species to be studied (see the work of Stropp at all 2017 in Oecologia)

It would also have been nice to have seen a synthesis of the methodological challenges of this type of study, such as how to deal with spatial autocorrelation and whether or not to control for phylogeny.

Finally, the article does not provide clear predictions for how leaf morphology in the study may change in relation to the environmental gradient. Why we think this study maybe bring new insights into the subject? Or new insights for a new ecosystem, etc.

The Figures are relevant, high quality, well labelled & described. The raw data is supplied
Experimental design: This represents original primary research that is clearly within Scope of the journal. However, the research question could be better defined (see above) and other than providing another example of phenotypic change over an environmental gradient it is not clear how the research is filling an important knowledge gap. On the positive side, the investigation appears to be performed to high technical and ethical standards and the methods were described with sufficient detail and information to replicate.

From the statistical perspective, it is not clear how the authors dealt with spatial autocorrelation and whether there was a need to control for the phylogenetic relationships between sub-populations within the species complex. Perhaps this information was not available?
Validity of the findings: Results start with “ the PCA explains” ……   I really wanted to find out more about your measurements, sizes, means, description of your data before we know about the results of the PCA.

The results are a bit difficult to interpret, maybe for this type of study would be good to have a clear hypothesis?  I understand that the new framing of research for big data, we do not need hypothesis to test, but  in this case, I think it might make the paper  more focused.

Given the large number of environmental variables and high sample size, maybe we could expect that some strong relationships with leaf traits would appear.  However, it would be nice to see some (convincing) adaptive explanations for why certain traits (e.g. leaf length) appear to have strong correlations with particular bioclimatic variables – while others do not.

The geographic variation in leaf morphology is fascinating and real, but it is still not clear that the research have i) identified the main drivers of this variation, and ii) excluded/controlled for the effects of phenotypic plasticity and phylogeny/biogeography.
Additional comments: This is a well-researched and detailed study that generates a large and interesting database. However, the research question could be better framed and the analysis might not be adequate to identify the key drivers of the observed geographic patterns of phenotypic variation in leaves.


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: MORPHOLOGICAL VARIATION OF LEAF TRAITS IN THE TERNSTROEMIA LINEATA SPECIES COMPLEX (ERICALES: PENTHAPHYLACACEAE) IN RESPONSE TO GEOGRAPHIC AND CLIMATIC VARIATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: None
Experimental design: Line 200, what is the linear correlation? Pearson correlation or Spearman?
Validity of the findings: None
Additional comments: I appreciated author's hardworking on revising the manuscript. New analysis was added in, and both Introduction and Discussion were improved a lot.


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: MORPHOLOGICAL VARIATION OF LEAF TRAITS IN THE TERNSTROEMIA LINEATA SPECIES COMPLEX (ERICALES: PENTHAPHYLACACEAE) IN RESPONSE TO GEOGRAPHIC AND CLIMATIC VARIATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors did a very nice work including all the reviewers’ suggestions and I indicate it for publication at PeerJ. I have just few considerations that are detailed below and correted some mistakes in the main text.

Line 74-75: For instance, leaf size has been shown to decrease with increasing altitude because of the differences in precipitation and nutrient content in the soil decrease
Suggestion: For instance, leaf size has been shown to decrease with increasing altitude because of the differences in precipitation and with the decrease of soil nutrient content.
Line 112: “cloudy conditions” is better
Line 118: suggestion: We analyzed how leaf morphology of the Ternstroemia lineata species complex vary in relation to climate variables across its geographic distribution to detect which environmental variables have influenced the leaf morphological differentiation in this species complex.
Line: 130: “… herbarium specimens identification?
Line 362 and 363: cloud or mist is better than fog
Line 364: transpiration is better than perspiration
Conclusions: You can make it more simple, going direct to the point and avoiding phrases like “in this study, we analyzed…..” or “our analysis showed…”
Graphics: Write the variable names in the correlation graphics, not the abbreviation. The number of the axis are too small.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: 16S RRNA METAGENOMIC ANALYSIS OF THE BACTERIAL COMMUNITY ASSOCIATED WITH TURF GRASS SEEDS FROM LOW MOISTURE AND HIGH MOISTURE CLIMATES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The work is very interesting from the point of view of microbial diversity in seeds, however the DNA of microorganisms that live on the surface and as endophytes of the seeds was generally obtained.
Which is very important because of the variable they are evaluating, because the abiotic factors modify the microbial diversity.
Experimental design: no comment'
Validity of the findings: In the discussion, enrich yourself with the effect of biotic factors on microbial diversity; as well as how it affects the development of diseases in low moisture and high moisture climates
Additional comments: I recommend that the authors mention in the discussion how the low
moisture and high moisture climates,  could affect the microorganisms on the surface of the seeds; in the same way to endophyte microorganisms


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: 16S RRNA METAGENOMIC ANALYSIS OF THE BACTERIAL COMMUNITY ASSOCIATED WITH TURF GRASS SEEDS FROM LOW MOISTURE AND HIGH MOISTURE CLIMATES
Review round: 2
Reviewer: 2

Output:
Basic reporting: Should improve figure 2 quality.
Experimental design: During the MS, the community studied in this work is the one associated to seeds. But the author uses the “bacterial communities on/in turf seeds”. I suggest rephrasing this to “bacterial communities associated to turf seeds” along the MS

In line 95, there is no information regarding the seed’s treatment. The seeds were washed with water, alcohol or any other agent?
When reading results or supplemental material, it is said the sample n (LM: 4; HM: 19). As this is relevant data, should be clearly written in methods.
Primers listed in line 106 were previously used or designed in this work? Should cite previous work or make the reader know if it has not been previously used.
In line 150 the versions of the programs are required.
The information within the paragraph 181-186 lines, is in any table? If not, should be for smooth reading.
The more sequenced named in line 234, are statistical supported? In this case it may be said in the sentence.
Validity of the findings: The paragraph between lines 293-296 assures that HM sample is more diverse than LM sample. I don’t think that statement is correct given the unequal n samples. The n samples should be normalized to the same, should be 4 for both samples for statistical studies. Do not seem fair to compare 2 so different n samples in statistics.
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: 16S RRNA METAGENOMIC ANALYSIS OF THE BACTERIAL COMMUNITY ASSOCIATED WITH TURF GRASS SEEDS FROM LOW MOISTURE AND HIGH MOISTURE CLIMATES
Review round: 3
Reviewer: 1

Output:
Basic reporting: IIn general, the manuscript is well structured, so the methodology proposed is consistent with the objective of the research. As well as the research topic is of great interest, about the diversity of microorganisms associated with seeds and their role in tolerance to biotic and abiotic factors, so I recommend that it be accepted for publication
Experimental design: The authors mention in the discussion that the greater diversity of microorganisms can help to tolerate stress, however they do not refer to any specific genre, which is why I suggest enriching the discussion by relating the presence of bacterial genera with stress toleranc
Validity of the findings: No cmment
Additional comments: How can we differentiate which microorganisms are found on the surface of the seed from those that are endophytes?


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: 16S RRNA METAGENOMIC ANALYSIS OF THE BACTERIAL COMMUNITY ASSOCIATED WITH TURF GRASS SEEDS FROM LOW MOISTURE AND HIGH MOISTURE CLIMATES
Review round: 3
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have incorporated the suggestions that the reviewers have indicated.
The ease of reading the MS has improved, as the suggested changes had been added


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 PLANT GROWTH-PROMOTING RHIZOBACTERIA ON CO-INOCULATION WITH BRADYRHIZOBIUM IN SOYBEAN CROP: A META-ANALYSIS OF STUDIES FROM 1987 TO 2018
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall this was a useful study.  It integrates a wide range of data already present in the peer reviewed literature.  This kind of integration has clear value, although it can sometimes overlook important details, such as specific conditions where the inputs under investigation cause yield increases.
Experimental design: The papers on which the research was based were all peer reviewed and so very likely to have been based on research with appropriate experimental designs.  As to the meta-analysis, we do not have expertise in this area and so cannot attest to the appropriateness of this aspect of the work.
Validity of the findings: The findings, overall, appear to be valid and, from an agronomic/biological perspective, not entirely surprising.  Again, we worry that there might have been some important details that have been buried in the work.  However, that is not necessarily something that needs to be specifically addressed in this paper, although it would be good to provide some small comment/acknowledgement of this situation.
Additional comments: General comments:
1.	Overall:  It is very useful to have a meta-analysis across a wide range of published research data.  This provides a strong overall view of the utility of specific inputs.  However, it may be that an input is effective under specific conditions, and this could be lost in such an analysis.
2.	Line 21: This does seem to state the main problem; the authors give a quantification of other effects on the soybean crop, and yield, only for the field crops, and the reasons for this are clear.  In the end, there were no significant yield effects under overall field conditions.  Would there be yield effects under specific field conditions or with specific sets of microbe additions?
3.	Introduction: It might be good to add at least a brief comment on the environmental and economic benefits of this symbiosis.
4.	Introduction: A very short comment of the power and specific utility of meta-analysis would be useful.
5.	Introduction/Discussion: Some of the material in the Discussion is more of a background nature and could probably be moved to the Introduction.  This material could be replaced with a bit more consideration around the agronomic implications of the findings.
6.	Discussion:  It might be useful to have a bit more on the meta-analysis approach and how this one compares.
7.	Line 240: Is this because more nodules means more nitrogen fixation?
8.	Lines 282-284: This is the main agronomic finding.  Could some additional consideration regarding specific conditions or treatments be given.  If some treatments or conditions result in important improvements in yield, could this be indicated with at least a very rudimentary consideration of economic benefit?
9.	Lines 318-319: Perhaps this should be qualified, given the lack of yield effect.  Could some specific types of treatments be more promising?  Would such treatments, given the low cost of these kinds of inputs, be economically viable?
10.	Overall: From a biological perspective the pot studies may be of greater interest, while from an agronomics point of view, the fieldwork is clearly the most important part.  Were there key differences between the findings of two (aside from the obvious inability to collect yield data in the controlled environment work)?
11.	Language: In general the use of language was quite good.  However, we have marked some instances, on an accompanying PDF of the manuscript, that could be improved.


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

Input:
Title: EFFECTS OF PLANT GROWTH-PROMOTING RHIZOBACTERIA ON CO-INOCULATION WITH BRADYRHIZOBIUM IN SOYBEAN CROP: A META-ANALYSIS OF STUDIES FROM 1987 TO 2018
Review round: 1
Reviewer: 2

Output:
Basic reporting: The present study was aimed to provide a quantification of the effects of the co-inoculation of Bradyrhizobium and PGPR on the soybean crop using a meta-analysis approach.
The manuscript is well designed and written, so, I would like to support this manuscript to publish in PeerJ, with recommended MINOR revision. The co-inoculation of soybean with Bradyrhizobium and other plant growth-promoting rhizobacteria (PGPR) is considered a promising technology. However, there has been little quantitative analysis of the effects of this technique on yield parameters.
Experimental design: The bibliographic research and data collection was well planned and performed and it collects a series of measures on the different level of plant attributes. The experimental design was appropriate, and the Meta analysis was applied correctly. Authors used very progressive methods and protocols, and a total of 42 published articles were examined.
Validity of the findings: Overall, this manuscript represents good and new findings, however, some suggestions should be considered before publication.
Additional comments: Dear editor in chief of the PeerJ,

The present study was aimed to provide a quantification of the effects of the co-inoculation of Bradyrhizobium and PGPR on the soybean crop using a meta-analysis approach.
The manuscript is well designed and written, so, I would like to support this manuscript to publish in PeerJ, with recommended MINOR revision.
The co-inoculation of soybean with Bradyrhizobium and other plant growth-promoting rhizobacteria (PGPR) is considered a promising technology. However, there has been little quantitative analysis of the effects of this technique on yield parameters.
The topic of the research is coherent to the aims of the PeerJ. Abstract is clear, informative and precise.  The introduction is very clearly stated and comprehensive. The bibliographic research and data collection was well planned and performed and it collects a series of measures on the different level of plant attributes. The experimental design was appropriate, and the Meta analysis was applied correctly. Authors used very progressive methods and protocols, and a total of 42 published articles were examined.
Overall, this manuscript represents good and new findings, however, some suggestions should be considered before publication as follows:
-Line 35, "…were more pronounced under pot than under field conditions" should be changed to "… were more pronounced under pot than that of field conditions".
Line 36, "these studies outline that" should be changed to "this study summarize that"-
- Line 76-77, please check the writing style of "Hungria et al. (Hungria, 77 Nogueira & Araujo, 2013)"
- In materials and methods section (line 106), the authors should clarify why interaction data with biotic or abiotic stresses were not extracted from articles?
- Line 129, please include the reference of equation.
- The sentence in Line 232 (since the 95% CI of the moderator variables overlapped with zero) is not clear, please explain it precisely.
- Authors could add the new following references to develop discussion about coinoculation of bioinoculants to improve plant performance:
- Coinoculation of bioinoculants improve Acacia auriculiformis seedling growth and quality in a tropical Alfisol soil. J. For. Res., 2018, 29(3): 663-673.
- Leaf nitrogen and phosphorus resorption of woody species in response to climatic conditions and soil nutrients: a meta-analysis. J. For. Res., 2018, 29(4): 905-913.
- The description of the illustrations (in Figures) is insufficient, no explained all symbols and abbreviations used.
- The conclusion must be more defined without unnecessary discussion.


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 PLANT GROWTH-PROMOTING RHIZOBACTERIA ON CO-INOCULATION WITH BRADYRHIZOBIUM IN SOYBEAN CROP: A META-ANALYSIS OF STUDIES FROM 1987 TO 2018
Review round: 1
Reviewer: 3

Output:
Basic reporting: I think the ms is well-written and the results are mostly supported by the analyses; however, I have some concerns, stated below.
The language is clear, and the English style is fine, although I do not feel qualified to judge it.
Experimental design: The approach taken by the authors represents nowadays a very reliable way to compare and analyse a plethora of studies that sometimes have contradictions. This tool may be helpful for the scientific community and in my opinion, it should be more used, even in the elaboration of introduction sections and or other sections of actual manuscripts.
There are some concerns I would like to state here:

1.- Even the authors provide explanation in lines 131-136, I am not sure whether is good to compare pots vs field assays, even if you chose that meta-analyses approach. Did the authors of the meta-analysed papers involving pot assays reached production?

2.- The authors said that they compared a final amount of 42 papers from 1987 to 2018; surprisingly, in the supplementary data S1, there are only 41 papers….is this a mistake? Moreover, some of these papers only contains 2 comparable data (Teixeira Filho et al 2017 and Galindo et al 2018). I was wondering if it is a good idea to include them or not in the study.

3.-One factor that was not contemplated by the authors is the inoculation method, regarding to how the inocula was added to the plant/soil (liquid, solid, with/without carrier, pelleted seeds…). I think that this is one of the key points in the success of an inoculum.

4.- It will be nice to read a little bit more discussion about the reasons of why the inoculated plants did not show significant increases in yield/production. This fact leads to the question of the success of isolates that are great in controlled conditions and then in soils are not, due to a bunch of reasons. I am aware that the authors include a paragraph (301-310) discussing some of the reasons, but I think they should develop the topic further.

More comments:

Lines 53-55. Valid species of the genus Bradyrhizobium are published in official journal, such as IJSEM, and/or validated in the Validation list. NCBI is not the best database for retrieving data on bacterial species. Please, check IJSEM or LSPN database. Also, in line 53, please add the complete reference of who described first the genus Bradyrhizobium

Lines 75-88. This paragraph is about the co-inoculation of Bradyrhizobium and Azospirillum; however, a co-inoculation with B. subtilis appears somehow. It is not clear if this is a mistake or the authors wanted to explain other co-inoculation assay.

Line 100-101 If the main criteria is that the evaluated papers should be written in English, Portuguese or Spanish, please, add this information in the supplementary data S1. Even I recognise there might be excellent works written in Portuguese and Spanish, I think only English-written papers should be evaluated.
Validity of the findings: The manuscript presented by Zeffa et al showed that meta-analyses approach might be an excellent approach for comparing really diverse data form many publications. Conclusions are well supported by the results of the analyses. I just have some comments that make me recommend to authors performing Minor Revisions.
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: NEW MAMMALIAN AND AVIAN RECORDS FROM THE LATE EOCENE LA MESETA AND SUBMESETA FORMATIONS OF SEYMOUR ISLAND, ANTARCTICA
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: See my main comments.
Additional comments: Dear Editor, dear Authors,

I had the pleasure to review the manuscript (MS) titled New mammalian and avian records from the late Eocene La Meseta Formation of Seymour Island, Antarctica. It encloses the description of original material that potentially has extremely important consequences on our understanding of the evolution and biogeography of the clades in question. Indeed, vertebrate fossils from the Eocene of Antarctica are extremely rare. I therefore strongly believe that this manuscript will translate into an important paper with crucial data that have to be published. Nevertheless, I have to express my doubts regarding the attribution of the mammalian specimen to a sloth, as performed in the MS. I was not convinced by the arguments in favor of this attribution, neither was I convinced by the arguments used to discard an attribution to other potential clades. Personally, I do not think that I would be able to give a definitive attribution for the specimen under study, and would be more tentative about the conclusions that can be drawn from it. But again, I consider that the material is worth publishing, and hence strongly encourage the publication of the manuscript, after having considered the concern I detail below.
	I have to make it clear that I am not qualified to review the parts of the manuscript that deal with the avian remains, so my comments only concern the mammal specimen. In addition to the comments given below, I am providing a pdf document showing tracked changes as well as an annotated figure at the end.

Introduction

Appropriate and well written.

Results
Major comments

1.		The proportion of the metapodial (“short and broad”) is the main argument for its attribution to a sloth. I do not think that this is sufficient, as many other clades have metapodials with similar proportions. It would therefore be great to corroborate this with other arguments, such as the disposition of the articular facets and processes. The authors do discuss those, but I believe that strong differences remain with known folivorans. Moreover, I don’t agree with the identification of structures. A first problem comes from the fact that there is necessarily a mistake in the bone orientation, as figured in Fig. 2: if the bone is indeed a left McII, and the facet for the McIII correctly identified, then Fig. 2C should be a dorsal view (and 2D a palmar view), contrary to what the figure legend states. However, I would tend to agree with the fact that 2C is a palmar/plantar view (and 2D a dorsal view)…which means that the bone is not a Mc II and/or that the facet for the McIII is not correctly identified.
	It is hard to be sure, but given the pictures and 3D model I have at hand, I would say that the view defined as the dorsal one (Fig. 2D) shows three contiguous facets. The whole facet that extends on the medial side of the bone is labelled as for the mcc. Again, hard to be sure, but given the angulation seen in dorsal view, I’d say that two bones articulate there, in addition to the proximal articular surface. I have annotated the Fig. 2 to illustrate this hypothesis.
	The definition of the facet for the mcc is not entirely clear to me. Is it the entire proximal face of the bone that is assumed to articulate with the mcc? Based on the proximal view, I would assume (again it is hard to be sure of that) that two facets for distinct bones are visible (see my annotation on the figure). The text refers to a facet for the trapezoid, but it was not directly clear to me to what part of the bone it is referred to. It should be labelled on the Fig. 2E.
2.		The trapezoid facet is described as “sub-planar, similar to that of Scelidotherium […].” But the disposition is completely different in Scelidotherium, in which the lateral part of the proximal articular surface articulates with the magnum. So the proximal surface as a whole is not sub-planar, as it is roughly the case in the specimen under study.
	All in all, I am not convinced by the attribution to a sloth. The most resembling sloth metapodial I could find is the Mc III of Eucholeops (size seem to roughly match as well), but differences are still precluding me from taking a definitive stand (please note that I did not observe Eucholeops Mc II first hand, my assessment is based on the work of De Iuliis et al. 2014). The most important difference concerns the shape of the distal end of the diaphysis: in all the sloths I could think of, including Eucholeops, this end is dorsopalmarly deeper than mediolaterally wide, to accommodate well-developed dorsopalmar keel on the distal epiphysis. This argument could actually be used to rule out a folivoran affinity, because the preserved distal end of the metapodial under study is wider than deep. Such a morphology might indicate that the distal epiphysis was not keeled. Instead, it could have either accommodated a simple condyle, as in astrapotheres for instance, or a saddle-shaped articulation, like in glyptodonts. Note that I do consider that the overall morphology and size could fit that of the latter (see for instance figs 33 and 41 of Glyptotherium: Gillette and Ray 1981). One important difference remains, though, as the proximal (trapezoid?) facet is clearly concave in Glyptotherium, and flat in the new metapodial. I would not be able to completely rule out an armadillo metapodial either.

3.		The section is concluded with the statement that the morphology of other mammals from the Formation, namely Astrapotheria, Gondwanatheria (note typo in the MS), and Litopterna, differ markedly from the specimen under study. I think it is important to expand this, as I am myself not entirely convinced. Keeping in mind that the distal end of the bone is missing, the bone is actually very reminiscent of the Mc II of ?Parastrapotherium as drawn in Scott (1909). Contrary to Glyptotherium, I would expect for the proximal facet of ?Parastrapotherium to be flat as well (I never studied first hand specimens of that taxon), as in the metapodial under study.
	It is also unclear to me why a comparison with other xenarthrans was not performed.

More minor comments:

4.	The authors seem to assume that there is necessarily a metacarpal-carpal complex (mcc) in sloths, but that’s not the case (e.g., Mionothropus, ;De Iuliis et al. 2011). Furthermore, the mcc can comprise different bones depending on the taxon. For instance, in Eremotherium, it includes the trapezoid (De Iuliis and Cartelle 1994), which seems to be assumed to be separate here. I would recommend to clarify the issue.
5.		The comparison ends with a sentence about “the width of the new metacarpal relative to dorsopalmar length” referring to observation about “Paleogene sloth material” of Amson et al. (2017). I am puzzled by this sentence, because 1) Amson et al. (2017) referred to a different ratio fo McII, proximodistal length to dorsopalmar depth (character 20 therein); 2) there is no Paleogene taxa studied therein. I actually am not aware of any Paleogene record of sloth Mc II.
6.	The MS states that the metacarpal is “missing its distal epiphysis” and that “due to the worn nature of the fossil we cannot rule out the possibility of belonging to a juvenile.” I would like the authors to be more accurate regarding this. Do they consider that the distal epiphysis is unfused and missing (which would suggest an immature ontogenetic stage), or just broken off? I am not entirely sure, but to me the distal end seems ‘crenelated’ and showing the texture of unfused bone surface. So I’d tend to interpret it as an unfused distal epiphysis (hence an immature individual).

Discussion [about the mammalian specimen]

7.	The discussion gives a good account of the history of Paleogene specimens that could potentially represent xenarthrans. However, given my assessment of the metapodial affiliation, I cannot agree with the definitive conclusions that are taken here.

Conclusion [about the mammalian specimen]

8.	I find the conclusion appropriately more careful about the metapodial attribution. I would recommend to use such a conditional tense for the Discussion as well.

General comments:

9.	The mammalian specimen is referred to “Xenarthra” in the abstract, and figure legend, but to a folivoran in the Results, Discussion and Conclusion. That’s misleading, I think. I would recommend to refer to the precise attribution throughout the MS.

Figures

Fig. 1.
•	I’d recommend to add a scale and locate North.
•	Text refers to two locations/sites. Fig. legend to “the locality”. Are the two sites too close at that scale to be figured separately?
Fig. 2.
•	The bone is very nice pictured. I would only recommend adding a label for the trapezoid facet, if that interpretation is kept.
•	As stated above, something must be wrong with the specimen’s orientation.

Cited references:

De Iuliis, G., & Cartelle, C. (1994). The medial carpal and metacarpal elements of Eremotherium and Megatherium (Xenarthra: Mammalia). Journal of Vertebrate Paleontology, 13(4), 525–533.
De Iuliis, G., Gaudin, T. J., & Vicars, M. J. (2011). A new genus and species of nothrotheriid sloth (Xenarthra, Tardigrada, Nothrotheriidae) from the Late Miocene (Huayquerian) of Peru. Palaeontology, 54(1), 171–205.
De Iuliis, G., Pujos, F., Toledo, N., Bargo, M. S., & Vizcaíno, S. F. (2014). Eucholoeops Ameghino, 1887 (Xenarthra, Tardigrada, Megalonychidae) from the Santa Cruz Formation, Argentine Patagonia: implications for the systematics of Santacrucian sloths. Geodiversitas, 36(2), 205–255.
Scott, W. B. (1909). Mammalia of the Santa Cruz beds. Part IV. Astrapotheria. Reports of the Princeton University Expeditions to Patagonia., 6, 301–351.

Sincerely,
Eli Amson


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: NEW MAMMALIAN AND AVIAN RECORDS FROM THE LATE EOCENE LA MESETA AND SUBMESETA FORMATIONS OF SEYMOUR ISLAND, ANTARCTICA
Review round: 1
Reviewer: 2

Output:
Basic reporting: References to previous works including fossil reports and stratigraphical context need an update.
The figure of penguins is unnecessary. Materials are not convincing and the authors cannot assign them in any of the cases. The situation is different regarding the metacarpal assigned to Xenarthra, I propose the inclusion of comparative material in this plate.
Experimental design: The Xenarthra is important enough and deserves to be published. However, it receives a deficient treatment.
What this record imply?
The author should compare the metacarpal with other mammals frequent in the Seymour Island levels (e.g. marsupials).

Background is also deficient. Marsupials are not even mentioned.
Validity of the findings: It fails in the backsground and comparisons, see the comments below
Additional comments: Particular comments are below, indicating the line number and the sentence of reference:

58 come from the Upper Eocene La Meseta Formation

The stratigraphy of Seymour Island was carefully studied during years. As a result, a detailed map was made by researchers from Spain and Argentina (Montes et al., 2013).
The Upper Eocene corresponds to Submeseta Formation, see Montes et al. (2013). The authors need to update it.

Montes, M., Nozal, F., Santillana, S., Marenssi, S., & Olivero, E. (2013). Mapa Geológico de la isla Marambio (Seymour) Escala 1: 20.000. Serie Cartográfica Geocientífica Antártica.

64 penguins, including some of the tallest penguins that ever lived

The tallest penguins are described in Acosta Hospitaleche 2014

Acosta Hospitaleche, C.  (2014). New giant penguin bones from Antarctica: systematic and paleobiological significance. Comptes Rendus Palevol, 13(7), 555-560.

68 gondwanathere, ungulate, cetacean, and other eutherian mammals (see reviews by Marenssi

You should make a reference of the Dryolestida MLP-91-II-4-3 reported in: MARTINELLI A, CHORNOGUBSKY L, ABELLO A, et al. 2014. The first non-therian dryolestoid from Antarctica. 2014 SCAR Open Science Conference, Auckland, New Zealand, Volume: Abstracts Volume. doi: 10.13140/2.1.2770.8805.

70 Gelfo et al. 2017) as well as non-penguin birds (e.g., Tambussi and Acosta Hospitaleche, 2007;
71 Jadwiszczak et al., 2008; Tambussi and Degrange, 2013; Acosta-Hostpitaleche and Gelfo, 2017)

These references are not the best examples, various relevant contributions are missing, please update.
check also the spelling of: "Hospitaleche and Jadwiszczak along the manuscript"

77 The fossils here described were collected from the Upper Eocene Submeseta Allomember

Now, Submeseta Formation (Montes et al., 2013)

78 (Telm 6/7) of the La Meseta Formation on Seymour Island (Fig. 1).

Take care with this. The authors need to update the stratigraphic scheme. The complete island was mapped, they could assign the place, without hesitations, to Submeseta Allomember II or III.

Fig. 1
This draw is too schematic. As a map, it needs improvement, I dont think it meets the standars of the journal. See comments in the figure.

85 The Submeseta Allomember

again

86 (Priabonian) between 34.96 and 35.13 Ma (Marenssi et al., 1998; Marenssi, 2006).

Many new references! with an update stratigraphic scheme

90 level on the northeastern section of the island (Fig. 1)

I cannot see the locality in this map

95 Geosciences Vertebrate Paleontology Laboratory, Austin, Texas, USA

USA.

102 PILOSA Flower, 1883
103 FOLIVORA Delsuc, Catzefilis, Stanhope, and Douzery, 2001

Please specify the characters that justify this assignment

107 Material – TMM 44190-1, left metacarpal II.

this is an important report, you should make a better comparison (pictures and descriptions)

109 Formation/Age – Submeseta Allomember (Telm 6/7), La Meseta Formation, late Eocene

update!

123 for the metacarpal-carpal complex. TMM 44190-1 is morphologically most consistent with those
124 of Xenarthra (anteaters, armadillos, sloths), especially sloths

The morphology is consistent, therefore it is assigned to a Xenarthra? or it is most consistent?
not the same

140 The majority of mammal fossils from the Eocene of Seymour Island comprise teeth of
141 Astrapotheria (Bond et al., 2011),

This is not true, most of the mammals are marsupials. By the way, considering the importarce of the marsupial record, you should at least mention it. You could also compare the new fossil with marsupials.
See:  Goin, F. J., Vieytes C. E., Gelfo, J. N., Chornogubsky, L., Zimicz, A. N. and Reguero, M. A. (2018) New metatherian mammal from the Eocene of Antartida. Journal of Mammalian Evolution

see also Reguero, M., Goin, F., Hospitaleche, C. A., Marenssi, S., & Dutra, T. (2013). West Antarctica: tectonics and paleogeography. In Late Cretaceous/Paleogene West Antarctica terrestrial biota and its intercontinental affinities (pp. 9-17). Springer, Dordrecht.

142 Litopterna (Bond et al., 2006; Gelfo et al., 2015

The authors should also mention the phalanx MLP 13-I-25-2 described in:  Gelfo et al., 2015

154 Locality – Seymour Island, Antarctic Peninsula.

This is a complete island, not a locality!

155 Formation/Age – Submeseta Allomember (Telm 6/7), La Meseta Formation, late Eocene.

update

156 Description — TMM 44189-2 preserves

what features support th assignment to Gruiformes?

175 TMM 44189-2 exhibits a combination of character states most similar to those observed
176 in Gruiformes

is this combination unique for these order?

209 Gen. et sp. indet. A

Species from Seymour Island were described from tarsometarsi, why the authors do not assign these materials?

278 represent a juvenile specimen of P. gunnari or a new species within Palaeeudyptes

Juveniles are just a little smaller than adults, the author can evaluate the ontogenetic stage comparing the ossification degree, the end morphology and the textural ageing.

283 Material – TMM 44187-1, partial mandible with associated caudal fragments

fragments of what?

284 Locality – Seymour Island

locality!

300 195, IB/P/B-0653; Jadwiszczak 2006; Acosta Hospitaleche and Haidr, 2011)

update! papers including comparable materials were posteriorly published

316 preservation, TMM 44187-1 is not considered referable to any known Eocene taxa at this time.

A single Eocene species (Anthropornis grandis) from Seympur Island has  cranium, mandible and postcranial associated elements (Acosta Hospitaleche et al., 2019). Therefore, mandibles can only be assigned to A.grandis, all the other known mandibles are isolated.

324 penecontemporaneous fossil discoveries from Patagonia (see Reguero et al., 2002; 2014).

avian references from Chile and Argentina are missing, where the same Antarctic species were reported

see:

Yury-Yáñez, R. E., Otero, R. A., Soto-Acuña, S., Suárez, M. E., Rubilar-Rogers, D., & Sallaberry, M. (2012). First bird remains from the Eocene of Algarrobo, central Chile. Andean Geology, 39(3), 548-557.

Acosta Hospitaleche, C., & Olivero, E. (2016). Re-evaluation of the fossil penguin Palaeeudyptes gunnari from the Eocene Leticia Formation, Argentina: additional material, systematics and palaeobiology. Alcheringa: An Australasian Journal of Palaeontology, 40(3), 373-382.

331 vertebra and tooth consistent with referral to a basilosaurid archaeocete and a previously
332 described ungulate species, respectively.

Please provide a picture, a more precise systematic reference and the material number. On the contrary, reader cannot identify these records.

360 (Tambussi and Acosta Hospitaleche, 2007),

update references! a decade of research and analysis is ignored here.

384 The penguin mandible described here is the largest and most complete from a spear-billed
385 penguin yet reported from the Eocene of Antarctica.

not true, see Acosta Hospitaleche et al., 2018 (abstract) and Acosta Hospitaleche et al., 2019 (paper)

399 and larger than other Eocene Antarctic spear-bills recovered (Acosta Hospitaleche and
400 Jadwiszczak, 2011).

see also Acosta Hospitaleche et al., 2019

404 from Seymour Island alone (Jadwiszczak, 2006; Ksepka and Clarke, 2010; Acosta Hospitaleche,
405 2013 and references therein).

it needs update. Acosta Hospitaleche et al., 2017 describe a new species, and other contributions of Jadwiszczak discuss the known diversity reporting new material that could belong to new species.

418 during the Eocene and support previously controversial reports of Gruiformes and Xenarthra. A
419 metacarpal is proposed to possibly represent the first record of Folivora and lends support to
420 previously reported xenarthran materials that have been subsequently questioned or lost.

It is assigned without doubts in the Systematic Paleontology

FIG1: The map needs some work. Please include coordinates, scale, reference points, north.
FIG.2: A comparative plate including other Pilosa and Vermilingua will be useful (something similar to Fig 3)
Fig. 4: Some materials are too fragmentary (e.g. E-F), considering that thousands of penguin remains are known from these units, it is not worth photographing this material.


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: NEW MAMMALIAN AND AVIAN RECORDS FROM THE LATE EOCENE LA MESETA AND SUBMESETA FORMATIONS OF SEYMOUR ISLAND, ANTARCTICA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Dear Editor, dear Authors,

I reviewed the revised manuscript titled New mammalian and avian records from the late Eocene La Meseta Formation of Seymour Island, Antarctica. The authors have carefully addressed all the concerns raised at the first round of reviews, so I strongly encourage publication of the manuscript, after consideration of minor issues I raise below:

The mammal specimen treatment was improved thanks to a more thorough comparison and a less decisive attribution. I might just suggest, given the revised comparison, to refer the specimen to ?XENARTHRA, to convey this more careful attribution.

228: typo in “Glyptotherium”

The reference referred to as Hatcher et al. (1903) (l.251 for instance) should be Scott (1903-1905)

250 “the facet also has a ridge located along the dorsal surface that is not seen in the new fossil”
	The ridge that I think the authors are referring to is a synostosis scar, of variable development (individually), so I would not consider it as an important character to mention.

265 but closer matches
	“but matches more closely”?

268: typo in “De Iuliis”

723: italicize “Anthropornis Grandis”

855: italicize “Neoglyptatelus”

859: typo for “Miocene”

912: Harcher: see above

969: “Pascual, R..” (double period)

1028: “Woodburne, MO..,” (double period)

References to doi not consistent (e.g., 826 and 883) and given just for a few refs.

Figure 2 caption: “mcc” could be replaced by “?mcc”, and reference to the fact that it could be the Mc I could be added there as well. Moreover, I’m not sure why the trapezoid facet is abbreviated including the word “facet” (which is not the case for the other facets).

Sincerely,
Eli Amson


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: ANALYSIS OF THE RNA VIROME OF BASAL HEXAPODS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The work of Rutar & Kordis is interesting  and timely. Analyzing viral diversity in different hosts is a very hot topic these days. I liked the manuscript and, in my opinion, it should be published after some modifications. I believe 3 ideas deserve to be discussed thoroughly:

1) Many of these viruses might infect not hexapods, but their parasites. Such examples have recently been reported by Fasel, Yurchenko & Beverley laboratories. In this sense, it may be necessary to cite some of their papers, e.g. Grybchuk et al PNAS USA and mBio, Akopyants et al, Genome Announc, etc This topic can also be discussed from the angle of HVT: it is easier to imagine this process via shared parasites.

2) Is author's approach sensitive enough? It may easily miss some divergent viruses - see  the case of Ostravirus in one of the above mentioned papers.

3) Can retroposon elements be identified in the vicinity of EVEs?

Minot comment:
Sentences on lines 90-94 appear redundant.
Experimental design: The experimental design is adequate. Methods are described with sufficient detail & information to allow replication.
Validity of the findings: The findings are scientifically sound.
Additional comments: I am also curios whether EVEs are integrated in some random genomic loci in different species or not. This, probably, goes beyond the scope of this manuscript, but authors might include this info, if it is available.


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: ANALYSIS OF THE RNA VIROME OF BASAL HEXAPODS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study identified a number of sequences of novel RNA viruses in the transcriptomes of 16 species of basal hexapods which belonged to 4 evolutionary divergent phyla, which were available Transcriptome Shotgun Assembly at NCBI. Also, a number of endogenous viral elements derived from RNA viruses of different clades were identified in the genomes of 6 sequenced basal hexapod species.

Basal hexapods are poorly characterised arthropods despite their ecological importance due to their role in decomposition of plant and animal remains, therefore identification of putative hexapod viruses could be basis of future work on basal hexapod biology and pathology.
Experimental design: The RNA virus sequences were identified  based on the amino acid homology with previously published RNA virus sequences (in particular  RdRp) using TBLASTN.
Validity of the findings: To my knowledge, this is the first systematic screening of the published basic hexapod transcriptomes  (and genomes) for the presence of RNA virus sequences. Identification of RNA-virus sequences was carried out using the appropriate approach.
Additional comments: The most important outcome of the analysis is the list of the newly identified virus sequences. Therefore the main text should include a table listing GenBank accession numbers for all 27 RNA virus sequences shown in “Supplementary Data: Nucleotide sequences of basal hexapod RNA viruses.”  This summary table should also provide additional data (e.g. source basal hexapod transcriptome, viral sequence length, GenBank accession of the previously published virus sequence showing highest homology with the new virus sequence with BLASTP E-value, and possibly %% of coverage in viral genome (sections)).

Throughout the text:  “RdRP” -> “RdRp”

Line 45:  ”…viruses, some of which are present as endogenous genomic copies” - these are not viruses but virus-derived sequences in genome - change to “endogenous viral elements derived from RNA viruses ”

In all figure legends showing phylogenetic trees specify that these are amino acid alignments.

Line 147: “…, we collected all RdRP proteins translated from the virus sequence collections described above.” -> “…, we used RdRp protein sequences”.

Lines 178-182. It should  be noted that the RNA virus sequences identified in the analysed transcriptomes of basal hexapods are their "putative" viruses and  specific experiments should be  carried out to prove that these viruses are indeed replicating in these arthropod species.

Lines 260-261 “Our analysis thus demonstrated that basal hexapods possess a diverse RNA virome that is richer than in numerous insect orders.”
Remove this claim, the number of RNA virus clades found in "Basal hexapods" is very similar to that of "Crustacea" and "Insects" (with all insect orders combined) - Fig. 4.  Note that different clades of basal hexapods are more diverse than orders within Insecta (Gao et al (2008) Zoological Science 25: 1139–1145  doi:10.2108/zsj.25.1139 ), it is more correct to compare diversity of viruses infecting all Insecta orders combined with that of basal hexapods.

Table 4. Specify that "Coleoptera-Lepidoptera...- to - Diptera" are "Insects"

Line 303-304. "...basal hexapod RNA virome differ from the rich arthropod RNA virome" -
Analysis of only 16 basal hexapod transcriptomes already resulted in identification of viruses which belong to 14 clades of 24 found in other arthropods. It could be a case that viruses belonging to oath clades could be found with wider screening. this is not excluding possibility of "basal hexapod-specific" virus clades.

Line 342.  alfalfa mosaic virus ( plant virus) RNA could be a  present in ingested plant material infected with this virus. thesis definitely not a case of "horizontal virus transfer"


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: ANALYSIS OF THE RNA VIROME OF BASAL HEXAPODS
Review round: 2
Reviewer: 1

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


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

Input:
Title: A MULTIOMICS COMPARISON BETWEEN ENDOMETRIAL CANCER AND SEROUS OVARIAN CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: •	The study is an interesting topic, and the basic reporting is generally clear.
•	Minor grammatical editing is needed
•	To emphasize the research questions of interest, specifically state in abstract and intro that you compare the three cancer groups.  Initially it seems to be focused on just serous EC and OvCa, but the paper really describes comparisons of the three groups.
•	A bit more background on previous findings with TCGA would be helpful. How do these results differ from TCGA PanCancer analyses?  Was EC included in those papers? Have pathway analyses previously been performed on this data?
Experimental design: •	More detail should be provided on imputation of gene expression. How much data was missing?
•	Need more detail on how the mutation burden was calculated. Was it a sum of the mutations across all genes? Can you provide references if standard methods were used?
•	Provide some motivation for the use of single sample GSEA in the pathway analyses, as opposed to the traditional GSEA method used in the survival analysis.
•	How did you deal with potential batch effects in the RNAseq data? Presumably the two types of EC may have been sequenced at the same time, but OvCa was presumably done completely separately. This would confound any across cancer type comparisons, and has direct implications for the validity of the results below.
Validity of the findings: •	Many of the results seem very descriptive, and statements made comparing EC and OvCa are often made without formally testing or comparing the groups, such as the results displayed in Figure 1A and B.  In Figure 1B, if the serous-like EC points would be plotted last, it would be much easier to see how they group compared to the larger sample size endo EC and serouc OC types; the smaller number of serous EC points are hidden.
•	Again, the mutation burden results description of copy-number driven vs. mutation-driven cancers would be better supported with formal tests.
•	Line 181 in the pathway results says that the two ECs share common gene expression related to tumor progression, but this is not supported by Figure 3B, which shows different patterns.
•	Line 185-186: The statement ‘Consistent with gene expression, the two ECs share more common pathway profiles between each other than to the OvCa’ doesn’t seem to be supported by the figure, where the expression of all types seem distinct. Can you show a formal comparison of this?
•	Line 184 incorrectly refers to Figure 3B (should be Figure 3C). This figure needs a more descriptive legend of the heatmap. What is the dendogram representing?
•	In Figure 4 and the immune comparisons, were any direct statistical comparisons made or are all results descriptive? It seems that you should be comparing the hazard ratios across the cancer types.
•	Figure 4D: the survival relationship of DCTN6 is not similar between the two ECs, they go in opposite directions!
•	OvCa CD8 and survival associations disagree with prior reports of a strong association between higher CD8 TILs and better survival in high-grade serous ovarian cancer (Goode et al, JAMA Oncology, 2017).  This conflicts with what is shown in Figure 5C.
•	In the immune comparisons, were any direct statistical comparisons made or are all results descriptive? This isn’t clear in the methods section. Line 244 describes significantly higher levels for EC, but compared to what?
•	In general, the conclusions are over-generalized.
Additional comments: •	In general, the manuscript poses some interesting scientific questions, asking whether serous EC is molecularly more similar to endometrioid EC or serous OC.
•	Consider presenting copy number and mutation results under separate headings, since they are measuring different things
•	For survival associations, did you consider the fact that these cancers are treated differently (as alluded to in the text)?
•	Limitations to the study should be outlined.
•	Table 2 is helpful to summarize the findings


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 MULTIOMICS COMPARISON BETWEEN ENDOMETRIAL CANCER AND SEROUS OVARIAN CANCER
Review round: 1
Reviewer: 2

Output:
Basic reporting: - The manuscript uses, most of the time, clear and unambiguous, professional English, however, I would suggest to homogenize the use of acronyms throughout the paper, e.g., OvCa and OV are used in the same paragraph in the abstract to refer to Ovarian Carcinoma (Lines 17 and 19).

- If the main topic of the manuscript is the use of similar/different therapies for serous-like endometrial carcinoma and serous ovarian cancer, I would like to see more background/context about the current therapies for both cancer types. There is a relevant review which should be cited (Brasseur, K., Gévry, N. & Asselin, E. Chemoresistance and targeted therapies in ovarian and endometrial cancers. Oncotarget 8, 4008–4042 (2016)).

- The figures are clear, however, some of them are not vectorized figures. The authors shared their scripts in a GitHub repository, however, they did not share the raw data to run them and/or README files to be able to reproduce the figures.

- The authors were able to use TCGA data to compare the global somatic signatures and gene expression and immune infiltration profiles of serous-like endometrial cancer and ovarian cancer, however, these results are not conclusive to determine whether or not these two cancer types could share therapeutic targets.
Experimental design: - The manuscript contains a well structured methods section, however, the methods are not described with sufficient detail & information to replicate.

- In Fig 3B, the authors mention a set of uterus-specific and ovary-specific genes, however, I did not see them list in the manuscript. How many genes are in each set?
Validity of the findings: - The authors use TCGA data (clinical data, RNA expression, somatic copy number alterations and somatic mutation) to compare endometrial and ovarian cancers. The authors showed serous-like EC and serous OvCa have similar somatic CNA and somatic mutation signatures, but different global gene expression, survival signatures and immune infiltration profiles. They suggest endometrioid and serous-like EC "share several common bad and good prognostic genes", however, there did not perform a test to determine the statistical significance of the number of "common bad and good prognostic genes" and compare that to OvCa; also, the authors used DCTN6 as an example of "good indication of survival outcome for both ECs", but Fig 4D shows they have opposite prognostic effects in the two EC subtypes. I suggest a more strict approach when comparing the survival signatures between these three cancer subtypes.

- Using this molecular characterization, they concluded "against treating serous-like EC and serous ovarian OvCa as a simple "serous" cancer type". All the results combined showed similarities (CNV and somatic mutations) and differences (gene expression and immune infiltration) between serous-like EC and serous ovarian cancer, however, the authors did not address why the similarities found in these cancer types, are not important to be considered to have similar therapeutic targets.
Additional comments: Overall, the molecular characterization performed to compare serous-like endometrial cancer and serous ovarian cancer requires a more robust statistical framework.

The conclusion of arguing "against treating serous-like EC and serous ovarian OvCa as a simple "serous" cancer type" is not completely supported by the results, specifically the similarity of the somatic CNA and mutations signatures.


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 MULTIOMICS COMPARISON BETWEEN ENDOMETRIAL CANCER AND SEROUS OVARIAN CANCER
Review round: 2
Reviewer: 1

Output:
Basic reporting: For the most part, my comments were addressed.  There are still some minor grammatical issues. For example, in the introduction line 45 of the pdf 'income' should be 'outcome',
 and line 75 'ratiotherapy' should be 'radiotherapy'. I noticed some issues with the references. The survival R package was written by Terry Therneau (one person), not Terry and Therneau (two people), and the added reference in the discussion for the study of CD8 and survival and ovarian cancer (line 330) should be Goode et al, JAMA Oncology, not Leiber et al.
Experimental design: My previous comments were addressed. Although I believe some text regarding the possible batch effects should be added to the discussion in the limitations section.
Validity of the findings: My comments were adequately addressed, although I think some refinement is needed for discussion of the conflicting results regarding the CD8 survival association in OVCA. The Goode paper did not target specific types of CD8 cells, but total CD8+ T cells, as was done here. Rather, the difference in findings is likely due more to the first point the authors make regarding the tumor heterogeneity. The analyses we conducted in the Goode paper were restricted to epithelial cells, while the mRNA assessed here in TCGA would included stroma.  Differences could likely be due to stromal infiltration. In fact, when we look at CD8 gene expression from Nanostring data that was generated from a subset of the same subjects as assessed in the Goode et al paper, the association between CD8 and survival is much weaker.  I think differences with TCGA could also be a power issue, as the Goode paper include close to 5000 cases, where the TCGA analysis is only around 300.
Additional comments: No further comments


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

Input:
Title: A MULTIOMICS COMPARISON BETWEEN ENDOMETRIAL CANCER AND SEROUS OVARIAN CANCER
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors corrected homogenized most of the acronyms throughout the paper, but I think they missed some OvCa/OV in the abstract.

The authors have complemented the introduction/background with additional references relevant for providing the right context for this study.

The authors mentioned that they have uploaded the data matrices they used in this project to their GitHub repository, which is a very valuable aspect to reporting a study. They also included extra figures, and I recommend the authors make some changes to make sure all figures are large enough to visualize when printed, e.g., the boxplots in Figure 1C are too narrow and can get distorted when printed.

The authors have made changes that are beneficial for the understanding of the relevance of the results.
Experimental design: The authors have updated the methods section to "rephrase ambiguities" making the methods section clearer and more easy to replicate.

The authors provided additional supplementary information for a more clear understanding of all the datasets used.
Validity of the findings: The authors have updated the results/discussion sections to address discrepancies between the main conclusions and the results selected to support the conclusions. The authors now provide good evidence for the conclusions.
Additional comments: Bases on the previous revision, the authors have performed a more robust statistical comparison between the two cancer subtypes.

The authors have stressed the importance of showing the differences between the two cancer subtypes, which I agree, but now have rephrase the conclusions to make the more precise.