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: GENOME-WIDE CHARACTERIZATION OF THE AUXIN RESPONSE FACTOR (ARF) GENE FAMILY OF LITCHI (LITCHI CHINENSIS SONN.): PHYLOGENETIC ANALYSIS, MIRNA REGULATION AND EXPRESSION CHANGES DURING FRUIT ABSCISSION
Review round: 1
Reviewer: 3

Output:
Basic reporting: no commen
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript has elaborated transcriptional analysis based on qRT-PCR of LcARF gene family. It predicts important roles of these LcARF genes in various tissues/organs/zones and hormone-treated conditions. The authors conducted an interesting investigation on a topic that is of interest to several plant biologists and hence shall invite a broad range of audience. The quality of work and illustrations are excellent. I recommend this for publication after the authors carry out some minor revisions raised by me. The revisions will improve the readability of the paper.
1.	Authors should provide the resource of Litchi genomic database. The detail of predicted protein sequences of LcARFs should also provide.
Authors also should indicate some report of characterization of ARF family in important crops such as rice, maize, soybean in introduction paragraph.
2.	Nomenclature for LcARFs should use no.1--> 39. The chromosome location of LcARFs should include in Table S1.
Gene names should be corrected in Italic in Figures 4,5, table S1 and main text of the manuscript.
3.	Authors should discuss more of the evolution as well as the tissue specific of the LcARFs to identify some potential genes for further analysis.
4.	Authors should include a conclusive table for the important genes and their function, observed in the transcriptome study in tissue/zone specific and hormone condition, that can be used for further functional validation.
5.	Author should be correct the English, format errors and missing of citation. For example, length of proteins (aa), molecular mass (Da) L151-154, italic format for the gene name.


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: GENOME-WIDE CHARACTERIZATION OF THE AUXIN RESPONSE FACTOR (ARF) GENE FAMILY OF LITCHI (LITCHI CHINENSIS SONN.): PHYLOGENETIC ANALYSIS, MIRNA REGULATION AND EXPRESSION CHANGES DURING FRUIT ABSCISSION
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment.
Experimental design: no comment.
Validity of the findings: no comment.
Additional comments: The authors have positively addressed my concerns and the revised manuscript has been well improved. I have no further 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: GENOME-WIDE CHARACTERIZATION OF THE AUXIN RESPONSE FACTOR (ARF) GENE FAMILY OF LITCHI (LITCHI CHINENSIS SONN.): PHYLOGENETIC ANALYSIS, MIRNA REGULATION AND EXPRESSION CHANGES DURING FRUIT ABSCISSION
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: all concerns have been addressed


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: MULTI-GENE PHYLOGENY AND DIVERGENCE ESTIMATIONS FOR EVANIIDAE (HYMENOPTERA)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The language of the article is sufficient, but the writing could be improved to make the article more concise. I am not a native English speaker and thus hesitate to make major corrections, but still suggest the authors check again for typos and aim to improve the writing. There are expressions such as "belongs for a group" which I at least have never heard before.
The taxonomic context is outlined in a very detailed fashion. However, I miss a few more sentences about the diversity and biology of the group, which would make the article more accessible for non-specialists. Context is missing altogether for the dating part, both considering the methodology and previous estimates for Hymenoptera and the evaniid fossil record. The abstract seems to have an overly long introduction and methods part, while the reported results are purely taxonomic, with no mention whatsoever of the dating results and a complete absence of anything resembling a discussion of the implications of this study for the understanding of evaniid evolution.
The authors should also make additional effort to improve figure readability (especially the phylogeny would profit from some colour), and the layout of the supplementary files needs to be improved, given that this will not be done by the journal.
I think you should move a (potentially shortened) list of taxa to the main article, as taxon sampling is so central to taxonomic and phylogenetic studies.
The sequence data has been uploaded on Genbank and input files for the various phylogenetic and dating analyses are available on a repository. However, the file names there are somewhat cryptic. Please add a ReadMe file or similar which explains the contents of the different files and add file extensions where missing.
Experimental design: The Evaniidae certainly could do with a more robust phylogenetic hypothesis than what has been available until now, and the rich fossil record does indeed call for a dating analysis – the work thus would certainly fill a gap. However, I have some major concerns about the execution of this study.
My first major concern is the large number of included specimens that have only been identified to genus. They appear in the tree and tables with numbers that obviously reflect extraction numbers (e.g., "Acanthinevania sp.240"). In fact, only a minority of the terminals have been identified to species, and it is entirely unclear if the remaining ones represent species not yet named, nor if they (within genus) all represent the same (morpho)species or not. Given that the focus of this paper is almost exclusively taxonomic, this is somewhat disconcerting. We know from experience that sequence data (and with it phylogenetic insights) tend to become meaningless if no species name can be attached to it, even if the depository of the voucher is reported in the paper. Is it really not possible to obtain better identifications of these specimens? Are there plans to describe the new species at some point in the near future?
My second issue is with the dating analysis, especially with the choice and interpretation of calibration fossils. You state that you used them "with each fossil assigned to the crown group for which they belonged" (line 240/241). Did you really place these calibrations on the MRCA of the respective group? How can you just assume that they belong to the crown group and are not stem-group representatives? I am not familiar with most of these fossils, but researched a bit on one example: Hyptia deansi (Jennings et al., 2012) has been associated with this genus based mostly on a reduced wing venation. In the original description, the authors state that the distinct notauli distinguished the species from most extant representatives of the genus – could that not be an indication that H. deansi would actually attach to the stem of the genus, instead of one of the crown group branches? Misrepresenting fossils as crown instead of stem groups is known to lead to sometimes massive overestimation of divergence times in molecular trees. If there is evidence (even unpublished) for these fossils to be crown group representatives, please explain it in detail in the supplementaries.
And besides, why did you not take the oldest representatives of each group, e.g., H. hennigi from Baltic amber to calibrate Hyptia?
line 245: what is a " 95% highest priority density interval"?
Validity of the findings: I disagree with people that suggest that few-gene analyses are not useful anymore in our time of phylogenomics - the robustness of the molecular data for phylogenetic inference seems to be sufficient here, judging from (most of) the support values. However, the data matrix is far from complete, with some markers only available for about half of the specimens. Please add information on coverage to the main text and not just supplementary material. Also point out clearly which markers were already used in Deans et al. (2006).
Some of these markers were also used in the Hymenoptera tree of life study (Klopfstein et al. 2013) – did you use the same gene portions here, especially for CAD? Also, it is great that you discuss the support in the individual gene trees for certain groupings. Why not add that information graphically to Figure 2 which would increase its value a lot?
Homogeneity tests: It is interesting that you identified significant heterogeneity in some markers, but this apparently did not have an impact on the phylogenetic estimate. Could you discuss that a bit more? Also, in the supplementary, the p values of the X2 test for nucleotide homogeneity are given as "p=0.00". How low were they really? And can a test be "falsified"?
Another point concerns the validity of the choice of calibration densities. This is, however, not only an issue in this paper, but has been discussed for the entire field of node dating for some time (maybe cite Warnock et al. (2011) when discussing sensitivity to node age priors). I like that the authors here perform a sensitivity analysis by using two different choices for the age priors, first a fixed maximum of 25 million years (or rather upper bound of the 95%) and second an approach in which fossils of a more inclusive group are chosen as maximum bounds. The way they then choose the former as the “better” option is however rather ad hoc: “It is likely that the normal analysis uses too broad a range, with the maximum bound being set too far away from the oldest known fossil for the crown lineage” (lines 325 ff.). Please discuss this in more detail. Also, provide a more in-depth justification why the 25-million-year assumption might be a good idea for the Evaniidae and not just for bees. Would a maximum derived from the maximum age of suitable hosts be an alternative for Evaniidae?
You seem to imply that you used a normal instead of a lognormal prior density on the calibrations in your second analysis (lines 318/19 and 321). Did I miss something here? Was it a truncated normal or does it mean you used soft minima also and not just soft maxima? Please make this clear in the MM section.
line 330/31: "consistent with dates for Evanioidea using total-evidence dating (Zhang et al., 2015)." – This reference only included a single (composite) representative of Evanoidea and thus could not possibly be used as a comparison to your estimate of the MRCA of this superfamily. In fact, the analysis that you seem to cite here (diversified sampling results, their Figure 7) was recovering the divergence between a representative of Evanoidea and one of Chalcidoidea as about 80-160 my, which would be in conflict with your (older) age of Evanoidea.
Table S4: why not put the posterior clade probability directly instead of shaded and unshaded "x"es?
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: MULTI-GENE PHYLOGENY AND DIVERGENCE ESTIMATIONS FOR EVANIIDAE (HYMENOPTERA)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is generally very clearly and concisely written, and well organized.  I found it very easy to look for answers to questions that popped up, as the use of subtitles/section headings was well designed.

The supporting literature was very well documented - I especially appreciated the section on previous use of each of the genes used in the analysis, and on the characteristics of the new gene.

The manuscript would benefit from decreased use of the word "however" in the results/conclusions, as it tends to disrupt the flow of thought when a simple contrast would be more effective.
Experimental design: The paper used very well-justified and state of the art analytical methods.  Some might argue that using only 6 genes for such an analysis is somewhat minimalist in today's context, but the well-chosen genes appear to be very effective in estimating the phylogeny in a convincing manner.
Validity of the findings: I especially like the section where the authors have clearly proposed specific classificatory and nomenclatural changes based on the strong findings of the study - this is often not carried through upon in phylogenetic studies at this level.

I did not find any conclusions that were not supported by the results.
Additional comments: Very nice upgrade to the Deans et al. 2006 study.


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: MULTI-GENE PHYLOGENY AND DIVERGENCE ESTIMATIONS FOR EVANIIDAE (HYMENOPTERA)
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article is clear, professional and self-contained.  I had a couple of specific suggestions regarding wording that I will paste below.

Line 16: “Ensign wasps (Hymenoptera: Evaniidae), which develop as predators of cockroach eggs (Blattodea), are
distributed nearly worldwide and exhibit numerous interesting biological phenomena.” - > could you reconfigure this sentence so it wasn’t parenthetic?  Something like, ‘Ensign wasps (Hymenoptera: Evaniidae) develop as predators of cockroach eggs (Blattodea) and are distributed nearly worldwide.’
Line 20: “novel marker AM2” -> the marker is not novel, but it’s use in phylogeny estimation is.  I would suggest re-phrasing to reflect this.  Perhaps something like: “and a marker (gene AM2) used for the first time in phylogenetic reconstruction”.
Line 51: “and biologically compelling “ I would argue for removing this.  What taxon isn’t?
Line 59 – “also” is a strange way to start a paragraph.  Remove.
Line 254 “according to the authors of the program, they are unlikely to have an effect on the analysis” I’m uncertain if this is the desired form of reference for “pers com” in PeerJ.
Experimental design: The research question is well defined, relevant and meaningful.  The data and analyses clearly improve our understanding of Evaniidae systematics.  I have three small suggestions below for clarity of reporting.

Line 152 – “has been little explored for phylogenetic studies” – clarify here.  Is it little, or none?  I didn’t see any pop-sets in NCBI for AM2.  On line 336 you say it has never.  If never – great, but say it!.
Line 281 “observed notable differences in nucleotide composition across taxa for some genes” – refer here to your Supplemental table. .
Line 344 – “gel cuts” – define or describe here.  The specific term doesn’t appear in the Methods.
Validity of the findings: Data is robust, statistically sound and the conclusions are well and concisely stated.
Additional comments: I enjoyed the manuscript and think it will have a good home in PeerJ.  I have one general point that I think warrants consideration/alteration before publication.

General Point: COI deletions.  The Evania wasp COI here all have in frame 3 or 6 bp deletions.  This isn’t abnormal for Hymenoptera (see Hansson et al 2015 and Quicke et al 2012) but it should be noted – particularly in light of your use of molecular motifs such as this in other markers.  Also, the COI sequence for Zeuxevania_splendidula_voucher_312 (KY082487.1) has a string of 13 “?” within the sequence near the same region as the Evania deletions.  I’m not certain what to make of these “?”.  Are these ambiguities?  Are they hypothesised deletions?  If so – that they are out of frame nature needs to be commented upon.  Is this a COI pseudogene?

•	Hansson C, Smith MA, Janzen DH, Hallwachs W (2015) Integrative taxonomy of New World Euplectrus Westwood (Hymenoptera, Eulophidae), with focus on 55 new species from Area de Conservación Guanacaste, northwestern Costa Rica. ZooKeys 485: 1-236. https://doi.org/10.3897/zookeys.485.9124
•	QUICKE, D. L., ALEX SMITH, M. , JANZEN, D. H., HALLWACHS, W. , FERNANDEZ‐TRIANA, J. , LAURENNE, N. M., ZALDÍVAR‐RIVERÓN, A. , SHAW, M. R., BROAD, G. R., KLOPFSTEIN, S. , SHAW, S. R., HRCEK, J. , HEBERT, P. D., MILLER, S. E., RODRIGUEZ, J. J., WHITFIELD, J. B., SHARKEY, M. J., SHARANOWSKI, B. J., JUSSILA, R. , GAULD[DECEASED], I. D., CHESTERS, D. and VOGLER, A. P. (2012), Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): data release and new measure of taxonomic congruence. Molecular Ecology Resources, 12: 676-685. doi:10.1111/j.1755-0998.2012.03143.x


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: MULTI-GENE PHYLOGENY AND DIVERGENCE ESTIMATIONS FOR EVANIIDAE (HYMENOPTERA)
Review round: 2
Reviewer: 1

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: The authors have improved the manuscript considerably – I especially like the addition on the biology and the fossil record of the taxon. As for the phylogeny mostly including undescribed species, I still think this is unfortunate, but am of course aware of the scarcity of funding options for alpha taxonomy. I hope the authors will be able to describe these species formally in the future, in order to not further contribute to the gap between accumulating molecular data and proper species names as a reference system.
As to my main point about the setting of calibration points, I am still not entirely convinced that this was done correctly, so I have to get back to my point about crown group versus stem group. For each fossil, you very clearly list the synapomorphies that justify familial or generic placement – that is well done. But as far as I can see (feel free to correct me if I am wrong), this does not exclude the possibility that we are looking at stem group representatives. In some cases, such as the now abandoned Hyptia deansi, there was even indication (presumably plesiomorphic notauli character) that it was indeed a stem group representative. To justify crown group placement, you need to demonstrate that the fossil belongs to a species group WITHIN the genus (same as Archeopterix not being useful for calibrating the MRCA of extant birds, but rather of the ancestor of birds + crocodiles). So, either move (some of) your calibration points one node down or justify crown group placement for each of them.
Minor points:
-	Change the title to “divergence TIME estimations”? “Divergence” as such might be misunderstood to mean “sequence divergence”.
-	There are still some “to belong for a group” and similar expressions in the supplementary on fossil calibrations, please correct these.


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: PREHEMODIALYSIS ARTERIOVENOUS ACCESS CREATION IS ASSOCIATED WITH BETTER CARDIOVASCULAR OUTCOMES IN PATIENTS RECEIVING HEMODIALYSIS: A POPULATION-BASED COHORT STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: OK
Experimental design: OK
Validity of the findings: OK
Additional comments: The study is well designed and the analysis looks appropriate.


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: PREHEMODIALYSIS ARTERIOVENOUS ACCESS CREATION IS ASSOCIATED WITH BETTER CARDIOVASCULAR OUTCOMES IN PATIENTS RECEIVING HEMODIALYSIS: A POPULATION-BASED COHORT STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a potentially interesting observational study regarding the timing of AVA implant in dialysis patients, however, the study suffers from several limitations. The research question is very simplified. There seems to be evidence that the implant prior to 1 month from dialysis date has evidence for efficacy as reflected in guidelines which were not discussed in the introduction. There is strong selection bias which may not be attenuated by propensity matching, how about provider quality which may impact implant timing and mortality. Also, the study did not control relevant factors such as ACE/ARBs use, statins, time effect which could impact CVD mortality. I have included additional comments in relevant sections.

Several of the sentences are hard to read and some have grammatical errors.

Line 91 – are dates in the dataset, date-shifted? Date of service, day of first HD session or hospitalization are considered within the 18 HIPAA identifiers.

In the supplementary data, are admission/service and event dates, date-shifted? Service dates are considered personally identifiable information and should not be shared in a de-identified dataset or may be shared by date shifting with an unknown interval at least >45 days. Need to discuss with their local IRB.
Experimental design: Line 79-81 – there is threat of selection bias in this study. There could be other reasons that some patients received this service earlier on (higher income, went to a better provider, etc.) and which could impact their CVD event and mortality outcomes. The propensity method won’t attenuate selection bias due to non-observed confounders – it will only make the two groups comparable on the observed confounders.

Lines 104-105 – AVA implanted <1month prior to the index date of HD were excluded, this brings a very important point regarding the study design. It seems there is enough evidence as reflected by guidelines that AVA implant before 1 month from HD is efficacious. This was not included in the introduction. Also, it brings to the study question regarding when is the best timing to implant AVA. A better design would be to treat time as continuous with an indicator of pre and post dialysis, because the study design as in the current format, excluding this arm from the study leads to missing information. Also, what is the implications for practice – is it lack of knowledge from providers as to when they predict the patient to start dialysis or when to implant the AVA.

Line 110 – which definition of comorbidities did you use, the HCC or US CMS’s data warehouse, other?

Line 118 – why did you pick those medicines. How about statins, ACE/ARBs, or diabetes meds?  Statins, ACE/ARBS and diabetes meds may impact CVD events and mortality.

Events were observed only one year after index date – therefore, why conduct the study using data from earlier years, why not to extend the study to more recent years.

Consider using an alternative methods of propensity score matching, like inverse proportion, as to not exclude participants from the study, why doing 1 to 1 match? Did you include income in the propensity score matching?

Did you include time effects in the models since the management of CKD and dialysis has changes over time.

The statistical analysis section is very poorly described, consider adding better description about the actual statistical analysis tests and details about the models, which statistical tests were used and in which program.
Validity of the findings: The study suffers from several limitations described previously which would dampen enthusiasm about the findings.

Line 155, the use of the word obvious is ambiguous, use instead either statistically or clinically significant or not.
Additional comments: These are additional specific comments that I did not include in the previous sections.

When was the P4P program established, and what is the structure, is it incentive payment for nephrologists, primary care docs or medical teams/institutions?

Introduction

Line 54, this sentence is not clear, do you mean higher relative risk of 5-year mortality or higher percent 5-year mortality compared to which % in the general population?

Need to define what is AVA, and that AVA is arteriovenous shunt or fistula before using the terms interchangeably.

Line 71 – which other large-scale studies other than the USRDS study that was included?

Line 90 – what is the average insured payroll-related amount, is it what they pay for the insurance and indicator of the participant socioeconomic status?

The discussion section is a repetition of the results. It should be modified as to describe how the results may impact clinical practice and related to the guidelines they mentioned in the exclusion section. Also, what are the recommendations regarding the P4P program.

The issue around provider timing of AVA implant and why some providers do or do not implant by certain time is not well discussed, if it's only patient characteristics that impact timing or are there other provider or health system level factors?


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: DENSITY OF INTERTIDAL BARNACLES ALONG THEIR FULL ELEVATIONAL RANGE OF DISTRIBUTION CONFORMS TO THE ABUNDANT-CENTRE HYPOTHESIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Comments on the manuscript peerJ - #34082 “Remarkable fit of barnacle density data to the abundant-centre hypothesis and decoupling from body size data”.

1.	Basic Reporting

This article presents a test of the “Abundant Center Hypothesis” formulated by Brown in 1984 on a population of barnacles, focusing on the vertical distribution of the species and its upper and lower distribution limit. Authors have sampled a total 9  transects all located in the same bay in Canada. They analyzed how density and body size vary according to depth.

Regarding the form of this work, I’d say that the writing is good. Yet I think that the way authors cite literature references is quite odd, using 8 to 10 references at a time, which does not help to reader to understand which reference supports the point presented. Regarding the quality of the bibliography, while the biogeographic aspect seems appropriate, I feel that the scientific background on barnacle ecology could be weak (see my comment below). Data are shared through a figshare file with a DOI, and figures are of sufficient quality to be published.

I acknowledge that repeating experiment is a crucial step in ecology, and that this should be valorized and encouraged.
Experimental design: 2.	Experimental design

The research aims at testing the ACH, which has originally been conceived to explain biogeographical patterns. While I understand that such pattern can be detect at different spatial scale, authors only consider one population, which is not enough to discuss an ACH pattern. First, a single population cannot be representative of the general distribution pattern of a species, even on a very local scale when testing for vertical distribution. Addition of some other populations (even locally) would have helped to contextualize this result. Second, if authors want to discuss the ACH at a local scale (which is an interesting approach) they need to make it more explicit and add relevant literature on micro ecological variation and its impact on population characteristics. In particular, some authors have modified the ACH to formulated a ‘niche centre’ hypothesis in which traits (such as abundance) peak at the niche centre instead of the geographic centre (which can match or not the niche centre). Such literature could help to strengthen the reasoning.
Validity of the findings: 3.	Validity of the findings

As stated above, the finding do not bring insightful result to the biogeographical hypothesis tested, mainly due to the very limited sampling effort. Results could be more informative if presented in a context of population ecology instead of biogeography.

Additionally, despite I’m not a statistician, I think that the method to estimate body size trend is flawed. Actually, authors sampled the biggest animal of each quadrat to measure its size and estimate a trend across vertical distribution. This is wrong as extremes are not representatives of the mean of the population, and they are dependent of the variance of the trait considered. If, across a vertical distribution gradient, the mean body size of individuals remains constant BUT the variance increases, sampling the biggest individuals would ‘artificially’ lead authors to detect an increase in body size.
Such problem could be solved following two approaches :
-	randomly  sampling few individuals within each quadrat, and re-calculate the trend
-	re-writing the manuscript top make this point clear and state that this manuscript focuses on maximum size and is not representative of the global trend of barnacle size across vertical distribution.
Additional comments: 4. General comments

I have some additional concerns regarding the way authors discuss their findings and analyze their data in comparison with their previous publication.

First, I think that they need to better contextualize their study in the field of population ecology. As stated above, I think that this study does not relate directly to biogeography, and is more related to population ecology. Thus, while the biogeographical bibliography is sound, I feel like more emphasis should be put on the ecology of intertidal ecosystems. A huge amount of work has been produced on such systems that explore many aspects of variations in population densities, including trophic interactions, competition for space, and differential impact of ecological factors. Integrating such questions to the present paper could relevantly improve the discussion and feed the debate on the relative importance of abundance drivers across species range.

Thus, the interpretation (discussion) of the results is very supportive of the ACH, but I think that their results do not support their arguments. Therefore, I would advise authors to tone down their global message.

Below are some other comments on particular points of each section.

Introduction
Bibliographical references are not efficiently displaced within the text, and do not support the reasoning. There is no need to cite ~10 papers in a quote at the end of each paragraph : I would rather read few useful references cited at the end of each idea.

L66 : “ a well replicated study”
Please remain neutral when evocating your own work.

Material and methods
Methods need to be clarified as too few information are available to allow readers to clearly understand the sampling procedure. For example :
-	how distant are vertical transects from one another?
-	How did you place vertical transects within the bay (randomly, stratified…?)

The study organism is not well presented in the MS. Please :
-	Provide a map of its distribution
-	Add on the map the location of your sampling site
-	Bring information on its ecology (life duration, etc.). Are these animals mobile to some extent?

Results
Due to the very limited dataset, I think that the results are quite weak and do not bring insightful information to the question. The interesting point here would be the comparison of those new results with the one published some years ago. However, I don’t know if it is technically possible due to way field work was conceived…?

Discussion
Authors discuss their result in regard of their previous publication, which is an interesting approach. However, they highlight some changes in the ‘altitude’ where they observe highest local densities, but one cannot assess if this results from a true elevational shift, of if it’s an artefact due to different vertical extents of the two experiments. If authors have access to absolute elevational data of each quadrat (using a reference point common to the two studies) they could strengthen their reasoning and analyze both dataset conjointly.


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: DENSITY OF INTERTIDAL BARNACLES ALONG THEIR FULL ELEVATIONAL RANGE OF DISTRIBUTION CONFORMS TO THE ABUNDANT-CENTRE HYPOTHESIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is clear and unambiguous, and professional English used throughout. In addition, the writing style is excellent and the authors provide sufficient field context.
Experimental design: The research question is well defined and the investigation has been performed rigorously. I have just some comments on details needed in the statistical analysis section:

About the (generalised) additive model, I would suggest the authors including the information of how they checked for diagnostics of the analysis. The function gam.check() and plots of the component smooth functions (and residuals) on the linear predictor' scale would be useful here. In this line, how did the author determine what kind of model was the appropriate? I assume that a Gaussian model was used, but the type of data (i.e. density and body size) suggests that maybe other kinds of models would be needed. For instance, the range of density is, theoretically, [0, Inf[, and that of body size would be ]0, Inf[. According to those ranges, Gamma and maybe log-normal distributions would provide a good fit for densities and sizes, respectively (see Bolker 2008 – Ecological Models and Data in R, Princeton University Press, Princeton NJ). Please note that I am not saying that your models are wrong, I am asking for additional information on how the model’ error distribution was selected.

Some other details would be useful to provide; for instance, I would indicate the basis dimension (k) used for the smoothing parameter (elevation). The mgcv::gam function uses a default k = 10 (Wood, S.N. 2006), but there are only seven possible “steps” in the factor “elevation zone”. In addition, the estimated degrees of freedom of each fit would be useful to assess the strength and "curvature" of the smoothed trends.

Line 119: Using a \deltaAICc = 2 as threshold for selecting (or discarding) a given model. Please note that this is a rough rule of thumb (Burnham and Anderson, 2002) to assess the loss of information of a given model (in terms of Kullback-Leibler distance). The larger the delta, the less plausible it is that the fitted model is the best K-L model given the data. The range delta = [0, 2] would indicate that the candidate model (your null model in this case) has substantial level of empirical support; and values [4, 7] denote considerably less support (Burnham and Anderson, 2002; 2004). Indeed, Harrison et al. (2018) indicate that value of delta of 6 would be needed to discard uninformative models. Nevertheless, in this case in particular, the deltas were comparatively high (>10 units), which provides good support for the full models over the null model.

Burnham, K. P. and Anderson, D. R. 2002. Model Selection and Multi-Model Inference -Springer Verlag.

Burnham, K. P. and Anderson, D. R. 2004. Multimodel inference - understanding AIC and BIC in model selection. - Sociol Method Res 33: 261-304

Harrison, X. A., Donaldson, L., Correa-Cano, M. E., Evans, J., Fisher, D. N., Goodwin, C. E., Robinson, B. S., Hodgson, D. J. and Inger, R. 2018. A brief introduction to mixed effects modelling and multi-model inference in ecology. - Peerj 6.

Wood, S. N. 2006. Generalized Additive Models: An Introduction with R. - Taylor & Francis.
Validity of the findings: I believe this point will be fulfilled after the authors provide more details of model validation (please see previous points). This is by no means saying that the results are "invalid", but some more details are needed.
Additional comments: Some specific comments:

Line 42: Habitat conditions —are you referring to abiotic conditions or also to biotic factors? Biotic interactions can influence the abundance of species at local, but also regional spatial scales (e.g. Godsoe et al. 2017).

Line 55: Semibalanus balanoides as an exclusively marine intertidal sessile species. I think this is an important premise of this study, because it allows us to assume that the low intertidal or shallow subtidal represent “sub-optimal” environmental conditions for this species. You may want to provide a reference supporting this statement. Scrosati and Watts (2007) analysed intertidal, but not subtidal, habitats. Buschbaum (2002) may be useful here, albeit the work was conducted on European shores (intertidal and subitidal habitats). (Buschbaum, C. 2002. Predation on barnacles of intertidal and subtidal mussel beds in the Wadden Sea. - Helg Mar Res 56: 37-43.)

Line 78: What do you mean with ecological performance in this context? Competitive ability?

Line 143 – 144: I am not sure that density peaked with such a remarkable accuracy. Actually, the fit shows larger differences between predicted and observed values (residuals) in the middle of the range. I would suggest again checking if the gaussian was the more appropriate model here.

Line 144: OK, the information criteria was useful for selecting the K-S model in the set (actually one model against the null model). However, if all models are poor, AIC will still select the one estimated as the best (Burnham and Anderson, 2002). I would suggest the authors to include in the methods other model validation methods in addition with the explained deviance.

Line 155: Please note that the analyses of Sagarin and Gaines (2002) provided support for the ACH for only two species out of twelve in terms of mean densities, and one out of twelve in terms of maximum density. A similar case is that of Rivadeneira et al. (2010): the ACH was supported in a small proportion of the analysed species.

Line 157 (paragraph): I agree — explaining the differences between two points in time is very difficult.

Line 169-170: I do not understand this idea. Why is the prediction on body size more simplistic than on density?

Line 165 (paragraph): Body size. It is interesting that Rivadeneira et al. (2010) found no statistical fit of latitude with the body size of porcelain crabs, but a slight monotonic increase of the latter towards higher latitudes—which is similar in some degree to your result. Perhaps you may want to mention this in this section.


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: DENSITY OF INTERTIDAL BARNACLES ALONG THEIR FULL ELEVATIONAL RANGE OF DISTRIBUTION CONFORMS TO THE ABUNDANT-CENTRE HYPOTHESIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have made a compelling work including reviewers' suggestions.
Experimental design: No comments
Validity of the findings: The incorporation of model diagnostics allows now to validate of models.
Additional comments: I think the manuscript is ready to be published in PeerJ.


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

Input:
Title: ENVIRONMENTAL MODULATION OF THE PROTEOMIC PROFILES FROM CLOSELY PHYLOGENETICALLY RELATED POPULATIONS OF THE RED SEAWEED PLOCAMIUM BRASILIENSE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Authors have focused on studying proteomic profiles of P. brasiliense sampled at two geographically distinct sites at coastline of Brazil. Focus of this study was to see if there is any divergence of the P. brasiliense population due to adaptive process. Authors have chosen two different sites for investigation and they have used both genetic and proteomic approach for this study. Overall the writing of this manuscript was improved from previous version in terms of use of professional language. Authors need to check for spaces and over use of words in some sections. Major issues with the manuscript is the formats of the tree diagrams and labeling of some of the figures. Is this due to format issue from word to pdf or they are simply misrepresented? It is hard to tell what proteins the authors are looking at in Figure 4 due to format issues. Figure 1 legend looks like incomplete at the end. Literature work was improved from previous versions of the manuscript. Proteomic information studies on P. brasiliense is very encouraging however the interpretation of results is not so clear and conclusive.

Authors mentioned in line 85 about the difference in secondary metabolites of P. brasiliense due to different geographical areas and In the next sentence they speculate whether proteomics of close populations vary due to environmental conditions. Are these studies were done based on the secondary metabolite context? This is a very loose concept. Moreover, Vasconcelos et al group only studied about monoterpenes but they have not done extensive characterization of several other secondary metabolites such as flavonoids, alkaloids, phenols etc.
Experimental design: Authors have chosen both genetic and proteomic approaches for this particular study. Sampling site and the method of collection were properly described. Maximum likelihood approach to determine the species that are tested using Cox1 was well explained. As mentioned above the figure representations are not formatted appropriately and need to be corrected. Internal transcribed spacer (ITS) has been widely used as marker for molecular phylogeny, especially due to its high variabilities between closely related species. Did the authors considered this approach to identify the populations between both sites?

Authors used proteomic approach to identify the spices in Sites P1 and P2 using Mascot searches against NCBInr databases. It is clear that most of the population belong to Rhodophyta based on Figure 3. Authors are encouraged to cut short the results section for this part as they can simply write that they observed higher percentages of Rhodophyta species at each site. There is no need to explain all the results with other species. Consider this as an minor comment. They can easily use this extra space to give more comprehensive results of the particular proteins identified based on P. brasiliense. Authors are encouraged to show the SDS-PAGE gel pictures for the proteomic data of P. Brasiliense specimens collected at P1 and P2 sites with markers for reference figures in supplemental data. Did the authors performed techniques such as 2D gel electrophoresis and Iso electric focusing for determination of proteins. This is will be one more verification step to confirm the findings.
Validity of the findings: Authors focused on proteomic profiles of phylogenetically related populations of the red seaweed Plocamium Brasiliense to verify if there is any divergence due to abiotic conditions. For this they have chosen two particular sites with varied climatic condition such as temperature, upwelling, depth, etc., Genetic profiles of the populations in the two sites indicate they are identical and belong to P. Brasiliense. This result is in accordance to their initial hypothesis.

To further investigate the population they have used proteomic approaches to see if there is any divergence or changes in response to abiotic conditions. The presence of increased levels Rubisco (photosynthesis related protein) is not any of significant find. Of course, these algae are autotrophic and they require photosynthesis apparatus for survival. Authors also showed the presence of photosynthetic proteins, phycobiliproteins.
In results section authors mentioned there is significantly more abundance of ATP synthase in P1 than P2 site but Table 1 shows there is not so much difference in the percentages (5,59 (48) in P1 and 13, 01 (54) in P2). Please clarify if there something that reviewers are missing any other supporting data.  Authors also failed to explain why there is more phycocyanin in P1than P2 site (Figure 4). Authors mentioned  in line 333 that phycobiliproteins are more abundant in P1, at the same time in line 353 and 354 they mention that higher temperatures conditions upregulate phycobiliproteins which suggests P2 as it has higher temperature. They are contradictory as one example they say P1 has more phycobiliproteins and in other they say its P2. Authors are encouraged to explain this. As per figure 2 there is a slight increase of phycobiliproteins in P1 rather than P2. Authors also mentioned in line 352 that P2 has lower protein levels and at the same time in line 354 they say higher temperatures upregulate phycobiliproteins. This is confusing aspect from this study.

If the whole goal of this study is to learn about the proteomic profiles of red seaweed from field samples, this manuscript is important for future research. However there is still a lack of clarity if there is any huge divergence between the genetically closely related species due to environmental modulations at proteomic level. Indeed there is some difference in some proteins especially phycocyanin, actin, heat sock protein etc., based on Table 1 but authors need to explain why they see these differences.
Additional comments: Manuscript reports on studying environmental effects on proteomes of phylogenetically related Plocamium brasiliense. Authors have improved the writing part of the manuscript and also they have used professional language. However work needs to be done on some spaces, over use of terms, representation and labelling (format) of figures. Discussion part need to be in-depth.

Authors have successfully used proteomic approach to provide information of key proteins of the populations from both sites that have varying conditions in terms of temperature, upwelling, depth etc., Major weakness of this study is lack of depth in interpretation the results. Some of the proteins does not have huge variation between two sites and the ones that have significant variation were not discussed in detail of why this kind of variation in expression. Temperature might be one of the factor but it looks like more work needs to be done to address other potential causes.
It will be very Interesting to increase the number of sites and sample size and do in depth analysis of these populations.


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: ENVIRONMENTAL MODULATION OF THE PROTEOMIC PROFILES FROM CLOSELY PHYLOGENETICALLY RELATED POPULATIONS OF THE RED SEAWEED PLOCAMIUM BRASILIENSE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is written in English but it needs some corrections, to make some passages clearer. In which concerns the background presented in introduction section I make some recommendations that I think essential to understand the importance of the study. For example, although the authors aim to examine the genetic profiles of Plocamium specimens through genetic markers they do not present the characteristics of these markers in terms of rate of evolution. It might be clear to phycologists, but it is not obvious to everyone else. For example, Cytochrome oxidase has enough variations to distinguish many metazoans species, however, it is very conserved to corals and sponges. Besides, they do not explain why they did not examine ITS sequences, since the literature show ITS are one of the most variable markers even to Plocamium species (Yano et al, 2006), and then, should fit better to (genetically and geographically) close populations.
(Yano, T., Kamiya, M., Murakami, A., Sasaki, H., & Kawai, H. (2006). BIOCHEMICAL PHENOTYPES CORRESPONDING TO MOLECULAR PHYLOGENY OF THE RED ALGAE PLOCAMIUM (PLOCAMIALES, RHODOPHYTA): IMPLICATIONS OF INCONGRUENCE WITH THE CONVENTIONAL TAXONOMY1. Journal of Phycology, 42(1), 155–169. doi:10.1111/j.1529-8817.2006.00178.x)
The article structure partially conforms the format. I suggest some parts should be relocated to better fit the format. (It is detailed further).
Not all figures and tables seem relevant. The horizontal axis of figure 4 is illegible and the information can be easily placed in the text. Also, it is not clear that differences between bars are statistically significant or not. Several proteins listed in Table 1 are not mentioned or discussed in the text.
Experimental design: The article meets the aims and scope of the journal and present a well-defined question.  However, I do not consider the methods applied the best to test the hypothesis. If the sequences of molecular markers were all identical it not means than all specimens genomes are identical because different parts of genome are under different evolutionary forces. The similarity between DNA markers only allows to state that there is no evidence that population are different species, or they are populations with any level of differentiation.
Why ITS marker was not included, and other phylogenetic methods was not examined? How did the authors select the model of nucleotide substitution to each marker and what test was done to verify if the concatenated markers would result in a reliable phylogenetic signal?
In many parts of the text the authors affirm that populations are not structured, however, the methods and the number of samples hamper such analyses. To verify the level of population structure, population genetics offers many options of clustering analyses, which have more appropriate statistics that better fit to such purpose than phylogenetic inference.
Validity of the findings: The study shows original results on proteomics of Plocamium specimens from Brazilian coast. Plocamium specimens living in shallow water show more clorophyll a than those living at 10m depth. It is related to RuBisCO enzyme that needs more energy in desiccation stress and for that uses more clorophyl to CO2 fixation. It seems to be the main finding of the article. However, no data was provided about desiccation, such: how long it lasts and how frequent it occurs.
The table 1 presents a list of protein identified in proteome profiles. Although some of them are significant different expressed nothing is discussed about them, for example: Haloalkane dehalogenase.
The conclusions on population structure are not appropriate stated since the methods and statistics applied do not allow such conclusions. Phylogenetic signal of variable markers can, indeed, suggest differentiation of populations, cryptic species and genetic isolation. However, such evolutionary phenomena must be tested with appropriate statistics and population genetics methods, for example, clustering or network analysis (Greenbaum et al. 2016 – doi: 10.1534/genetics.115.182626). The data only allow not discard the null-hypothesis of non-differentiation between populations.
Additional comments: Here I present more detailed comments:

Line 87: “the proteome of closely related populations of the same species respond to different environmental conditions” the authors mean: the genome respond to different environment conditions generating different proteome profiles?

Lines 101-103: It fits better on Introduction, particularly in the paragraph that explain the importance of Plocamium.

Lines 129-132: I suggest create a paragraph in the introduction to explain the importance of chosen molecular markers and there, to explain the variability levels of the markers with examples of species that were distinguished by them, if it varies in different classes or orders of related algae.
Line 147: “the maximum likelihood (ML) approach and RAxML” Do you mean in RAxML?

Line 148: How do you choose GTR+Γ substitution model? Which software were used to determine the substitution model? This inference should be determined by the data (sequences used to constructo the tree). There are software that estimate the best model to each data set.

Lines 150-151: If substitution rates vary too much from each other may not be suitable to concatenate the sequences. It is important, before concatenation, to screen sequences for homogeneity of base substitution and other congruence parameters (Rampersad et al. 2014 – doi: 10.1186/2193-1801-3-614).

Lines 196-197: The phrase is not clear.

Line 203-204: “We used a combination of tools to overcome this hindrance.” With this statement I expected to find a discussion about it, but there is not. I consider this statement vague and I suggest explain better.

Line 239: Here and elsewhere in the text I find “groups”. It is not clear what is it about. Groups is applied to which taxonomic level? It refers to a specific clade in the phylogeny? Please, make it clear.

Line 247-249: It is confused. First it is stated that were used three genes in concatenated tree, then it is stated that individuals with two genes were also used. Please, make it clear.

Line 253-254: The methods do not allow to infer if population is or not structured. (Greenbaum et al. 2016 – doi: 10.1534/genetics.115.182626.)

Line 261/275: What do you mean with 27 specific types? Classes of proteins? Protein identities? Please, make it clear.

Lines 282-285: The data do not allow to state that populations are not structured.

Lines 288-304: This subsection presents information that should be introduced in Introduction section to explain from where comes the hypothesis that populations of Plocamium could be genetically distant. And in the Discussion section go back to the idea with literature examples contrasting and supporting the findings.

Lines 315-316: “slightly more abundant in P2 than in P1” – If this different is not statistically significant remove it. If it is statistically significant I suggest change slightly more abundant by significantly more abundant.

Lines 317-327: The order of the information does not help the reader to deduce the conclusion by himself. I suggest rewrite it.

Line 370: Metaproteome is not a term applied in this study since the protein analysed were only those from the Plocamium origin. The meta prefix is applied when you study a community.


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: ENVIRONMENTAL MODULATION OF THE PROTEOMIC PROFILES FROM CLOSELY PHYLOGENETICALLY RELATED POPULATIONS OF THE RED SEAWEED PLOCAMIUM BRASILIENSE
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have focused on studying genetic and proteomic profiles of P. brasiliense sampled at two geographically distinct sites at coastline of Brazil and to test if there is any divergence of the P. brasiliense population due to adaptive process.
The writing of the manuscript has been improved considerably from previous versions but they still need to address issues such as spacing in the text. Sometimes the words are written together which is a major issue in the manuscript.  Introduction part has been well trimmed and written well.  Discussion part has been improved with some minor issues still required to be addressed. I have given some minor comments and suggestions for the author comments section below.
Experimental design: Authors have not done any major changes in this methods section from previous version. No new methods have been included. However authors still did not provide details on why they did not consider the use of ITS marker for their study. Reviewer’s encourage to use such approach in the future experiments to test their first hypothesis.
Validity of the findings: Authors focused on proteomic profiles of phylogenetically related populations of the red seaweed Plocamium Brasiliense to verify if there is any divergence due to abiotic conditions. For this they have chosen two particular sites with varied climatic condition such as temperature, upwelling, depth, etc., Genetic profiles of the populations in the two sites indicate they are identical and belong to P. Brasiliense. This result is in accordance to their initial hypothesis.

To further investigate the population they have used proteomic approaches to see if there is any divergence or changes in response to abiotic conditions.
Authors mentioned  in line 354 that, “Specimens of P. brasiliense collected from the second site (P2) also express these proteins but at a lower level. This sentence has to be refrased. Authors either need to mention that they have found proteins at P1 and mention about the similarities in P2. They did not mention anything about finding proteins in P1. It is clear the some protein are more abundant at P1 then P2. Authors encouraged to mention this before talking about P2 site.

Authors mentioned in Line 361 about the presence of stress response proteins in P2. Can authors speculate the reason of these stress response proteins? Is it due the lower depth and higher temperatures and increased desiccation? Authors are encouraged to give future direction of this research. Marine microalgae has shown to have many defense mechanisms (chemical defence) against microbial species. Some of the upregulation of proteins can be part of defense mechanisms. Authors are encouraged to give any examples of such in P. brasiliense
Additional comments: Authors have done original work on analyzing the proteomic profiles of P. brasiliense. They have observed differences in sites (P1 and P2) from which they have collected the specimens and furture proteomic analysis. Authors have shown that difference in depth, temperature and desiccation might influence the proteomic profiles of the same species.

Authors need to check for spacing in the text. It might be due to formatting error. Please address.

Line 97-99: Authors can replace the sentence at line 67 as it is more suitable at the early introduction.
Below are some of the major and minor comments.
Figure 1 legend still looks incomplete at the end.
Table 1 legend still looks incomplete at the end.


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: ENVIRONMENTAL MODULATION OF THE PROTEOMIC PROFILES FROM CLOSELY PHYLOGENETICALLY RELATED POPULATIONS OF THE RED SEAWEED PLOCAMIUM BRASILIENSE
Review round: 2
Reviewer: 2

Output:
Basic reporting: The present work is a proteome analysis of Plocamium brasiliense, a seaweed occurring in part of Brazilian coast. The study shows upregulated expression of allophycocyanin in the environment with higher temperature and occurrence of desiccation in Plocamium brasiliense.
The article is written in English in conformity to professional standards. It includes sufficient background and literature references. The structure of the article is conforming the format of standard sections, except for the contents of lines 283-286 which are in Results section and I consider being part of Discussion/Conclusion. It is necessary to place space between words in several places throughout the text. Figure 3 seems irrelevant and the label of the table seems incomplete.
Experimental design: The article not successfully define its hypothesis and because of that it has a conceptual misinterpretation of the result (stating the null hypothesis, when it should be discarded or not). In fact, I recommend reading literature related to concept of null / alternative hypothesis and falsification of null (initial) hypothesis. (For example: Banerjee A, Chitnis UB, Jadhav SL, Bhawalkar JS, Chaudhury S. Hypothesis testing, type I and type II errors. Ind Psychiatry J. 2009;18(2):127-31.)
The collection location P2 do not correspond to coordinates. Geographical coordinates show a location called “Praia do Forno” at Arraial do Cabo, not at Buzios. It is distant about 8km from P1 (not 30km as appointed).
The phylogenetic reconstruction was made with GTR+Γ nucleotide substitution model, however it seems to be an excessively complex model to be used in COI phylogeny. The nucleotide substitution model must be estimated according to the data set, especially when genes with different rates of evolution are concatenated. Currently, there are many options of software capable to estimate the best fit model. I recommend reading the following literature: Arenas M. Trends in substitution models of molecular evolution. Front Genet. 2015; 6:319. Published 2015 Oct 26. doi:10.3389/fgene.2015.00319
Validity of the findings: The authors state the null hypothesis (lack of structuring of populations) when it can only be discarded or not. I suggest correcting that to meet the formal scientific speech. Also, it is important correcting the information of collection locations.
The authors affirm that Gst had low values suggesting lack of structuring of populations. However, Gst and other structuring indicators are relative values. It varies according to the molecular markers and to the organism examined. I recommend giving more emphasis to this part of the discussion, if possible, by giving more examples of studies that used the same markers and closely related organisms.
At one point in the discussion, the authors mention that the focus of the work includes a multispecies complex in addition to the seaweed proteome. However, no results were presented or discussed in relation to any species other than Plocamium brasiliense. Also, in the Conclusion paragraph it is stated that the study was a metaproteome. The meta prefix is generally used for studies that encompass a set of species, which does not occur in the present work.
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: REPRODUCTIVE BIOLOGY OF LITTLE TUNNY EUTHYNNUS ALLETTERATUS (RAFINESQUE, 1810) IN THE SOUTHWEST GULF OF MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment...
Experimental design: no comment...
Validity of the findings: no comment...
Additional comments: The manuscript provides some important parameters concerning with the fisheries management of E. alletteratus having a commercial value in Mexican fisheries industry. The article also has the powerful data set as well as the references. However, in terms of fisheries management of little tunny in Mexican waters, a final paragraph referring the importance of the study should be added to the end of the Conclusion section. After that, it 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: REPRODUCTIVE BIOLOGY OF LITTLE TUNNY EUTHYNNUS ALLETTERATUS (RAFINESQUE, 1810) IN THE SOUTHWEST GULF OF MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I reported my suggestions to authors on the text


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: REPRODUCTIVE BIOLOGY OF LITTLE TUNNY EUTHYNNUS ALLETTERATUS (RAFINESQUE, 1810) IN THE SOUTHWEST GULF OF MEXICO
Review round: 1
Reviewer: 3

Output:
Basic reporting: Given that I am not a native of English I will refrain from style or grammar comments. In terms of the effectiveness of communication, the message comes across without doubt. Writing is clear and technically correct. References are numerous, perhaps too many. Background is properly given. The article structure conforms professional and customary ways. Raw data are at disposal but I had some problems opening the Excel file. I got messages that the file had to be repaired. Once open the data base of the article can be seen. I missed in the Excel a glossary of abbreviations. Yes, you can find them in the text but it is easier for a reader to have them in the same file. I found a good correspondence between objectives, methods and results. Conclusions are correctly derived from observations plus analysis.
Experimental design: Methods used are standard. The histology analysis complemented well and was consistent with visual assessment of individual’s maturity. I miss, however, a clearer statement on up to which gonadal phase the individuals are considered mature (your Table 1). I have seen in literature that stages “post spawning” and “rest” are viewed as “not mature” despite of the fact that evidently such individuals area beyond their first sexual maturity.
Validity of the findings: The topic treated is interesting and valuable as criteria for management of the fish species concerned plus implications for the general biology of tropical fishes, for instance, the corroboration of extended but defined reproductive periods and environmental correlates, i.e., sea temperature. On the other hand, it would have been better to have sampled the population independently from the fishery because fishers operate in a directed manner and as it is of common knowledge, estimation of things like the first sexual maturity are strongly depend of the size range at hand. Nevertheless, the knowledge gained through the study is useful and relevant and I understand that in practice what a scientist can do in the field has a number of limitations, for instance, funding
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: COMPARISON OF SHALLOW-WATER SESTON AMONG BIOGENIC HABITATS ON TIDAL FLATS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, the manuscript was well written. A few areas, however, need to be rewritten to improve clarity and facilitate reader comprehension. Jargon throughout should be kept to a minimum, and definitions provided whenever terms are introduced that may not be universally known or agreed upon.

L36-39 - Please rephrase to improve clarity.

L45 – Please define foundation species.

L162 – “[…] within three hours.” – Of collection?

L310-311 – Please rephrase to improve clarity.

Figure 7a - Is the y-axis a log scale? Unclear given just two values, while most of the other figures have had log-scaled y axes.
Experimental design: The experimental design was largely adequate for the data. I do have a couple of questions that I would like the authors to address.

1) Why did you subset the data rather than use contrast statements? L188

2) Including tidal stage (ebb vs. flood) may help explain some of the variation in the data. Incoming tides are more directly interacting with the benthos than ebb tides. While water depth may partially address this, mid flood at 1-m depth has much more recently been close to the benthos than mid ebb at 1 m.

3) Including patch size as a random effect may also help identify habitat specific differences, and may be especially useful to identify changes in final/initial TSS and Chl, if they exist.
Validity of the findings: The data are robust and statistically sound. Pending how the authors address the questions about experimental design, some of the following comments may be moot.

1) You have made the assumption that bare tidal flats will be less effective at mitigating overlying TSS and Chl. Were these barren seascapes, that may be true, but the authors should also consider that tidal flats can support a large biomass of filter feeders (e.g., see https://doi.org/10.4319/lo.1987.32.1.0143), which may be as capable of removing seston as the oysters in the study, especially given the moderate biomasses recorded in the surveys. A few benthic grabs, both for sediment characteristics as noted by the authors, as well as infauna would have helped to address this.

2) In lines 270-272, you discuss how eel grass had higher initial TSS and Chl than the other habitats. Figure 4 demonstrates this, but the log-scaled y-axis doesn't make the assessment clear. I recommend including a bar plot (or equivalent) without a log-scaled y-axis to make this clearer.

3) The findings should be clearly stated throughout to apply to the surface waters in your study areas. Given that all sampling occurred within the top 0.3 m of the water column, and no measures of vertical mixing were taken, it is important to note that there may have been changes to the seston as it passed over the habitat patches, but that they weren't evident in the surface waters.

4) I'm not sure that I buy the argument in lines 320-322 that the higher Chl over eelgrass patches was because of mobilization of epiphytes. Most epiphytes have evolved to attach to their host, and in the low-wind conditions of your study, I'm not convinced that this is the best explanation. Please provide other support from the literature to support this speculation. The elevated Chl could also be more of the background water conditions at your sites. The oysters and infauna of bare patches can more directly interact with the overlying water column than the filter feeders below the eelgrass. There may be a slight decoupling of the filter feeders in eelgrass from the water column as local hydrodynamics within the overhead eelgrass dominate.
Additional comments: Overall, this is a good article with good data. There are some issues that need to be addressed, including the statistical analyses and subsequent interpretation. I'm looking forward to seeing the revisions, as I believe that the study was overall well-conceived and worthy of eventual 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: COMPARISON OF SHALLOW-WATER SESTON AMONG BIOGENIC HABITATS ON TIDAL FLATS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The reporting is clear, unambiguous, well-structured, and complete.
Experimental design: The research question is well defined, the methods are rigorous and well tested, and the analysis is well executed. Data are archived and openly available.
Validity of the findings: The conclusions are well supported by the results of the current and previous studies.
Additional comments: This is a brilliant, well designed and well executed study that advances our understanding of the role habitat-formers play in structuring their physical habitat properties and the habitats around them. The one and only [minor] question that comes to mind is where is the source of material? If oysters and eelgrass are seston-mobilizers, how is that material being deposited on these habitats in the first place? It may be worth speculating on this somewhere in the discussion. Maybe on windy days, which are difficult to sample with Lagrangian drifters? That goes against my expectation though.


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: COMPARISON OF SHALLOW-WATER SESTON AMONG BIOGENIC HABITATS ON TIDAL FLATS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The language of this article was professional and clear except a few minor comments:

Line 24: Instead of "During drifts" should this be "Across the eelgrass habitat..." Using "during drifts" implies (to me) that the drift changed the results and not the habitat.

Line 36-39: The article chose to put a list in parentheses here. I believe these are important for the article, especially the particulates, I would recommend taking this information out of parentheses.

Line 267-270 and 276-278: Both of these paragraphs start with "The conclusions...". I found this to be distracting from the flow and also the sentences. Especially 267-270, I had to re-read this sentence a couple of times to understand the meaning.

The background and context was quite clear to me. I'm not sure that we will find the genus change to Magallana from Crassostrea to be long-standing.

The figures and tables are clear and the raw data is shared. I might remove Figure 5 as the results are negative and explained within the text.
Experimental design: The article meets the PeerJ standards. I found the research questions to be well-defined and filling a meaningful gap in our understanding of the PNW oyster-eelgrass ecosystems.  This MS represents a rigorous investigation performed to a high technical and ethical standard. The methods were described in sufficient detail to replicate.
Validity of the findings: I can see that the study took sufficient effort, but I am wondering if the authors considered performing the same drifts over multiple seasons? If so, would you expect the results to be the same? It might be worth adding the potential effects of seasonality to the discussion.
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: COMPARISON OF SHALLOW-WATER SESTON AMONG BIOGENIC HABITATS ON TIDAL FLATS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have done an excellent job of addressing my previous questions and comments, and I have no further questions or concerns. The article is well written and easy to comprehend. I look forward to seeing it in 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: COMPARISON OF SHALLOW-WATER SESTON AMONG BIOGENIC HABITATS ON TIDAL FLATS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Thank you for your clarifications!


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: PREVALENCE OF MALOCCLUSION AND OCCLUSAL TRAITS IN THE EARLY MIXED DENTITION IN SHANGHAI, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: there are many grammar and style issues, revise,

instead of 'maxillary crowing >2mm of anterior' revise to'anterior maxillary crowing >2mm'
deficient literature review, why you didnt use indices?

the title is misleading you need to change it to 'Prevalence of malocclusion in the early mixed dentition and selected severely deviated occlusal traits in Shanghai, China'

M&M, add subheadings for sample size calculation, study sample, the variables you measured, statistical analysis
results: you need to provide more information for the readers:

abstract needs revision, 'discussion' should change to' conclusion'

increased overjet (how did you define it?) (40.8%), anterior crossbite (10.5%), anterior edge to edge (confusing terminology, revise, how did you define it?) (8.1%), deep overbite >2/3 overlap (6.2%), class III (how did you define it?, what classification did you use, angle or British system(incisors)) (5.9%), open bite (4.3%), midline irregularity(what is this?) (36.1%), scissors or opposite scissors bite (very confusing, revise) (1.0%), posterior crossbite (2.0%), posterior edge to edge (0.6%), maxillary crowing >2mm of anterior (13.3%) and posterior teeth (0.2%), mandibular crowing >2mm of anterior (22.5%) and posterior teeth (1.0%), anterior spacing >4mm in maxilla (8.0%) and in mandible (3.0%).

what was the overall, prevalence in comparison to permanent detention(about 30%, Prog Orthod. 2011 Nov;12(2):132-42.;Eur J Paediatr Dent. 2009 Jun;10(2):69-74.)
Experimental design: fine
Validity of the findings: fine
Additional comments: revise the paper, look at similar papers and revise similarly


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: PREVALENCE OF MALOCCLUSION AND OCCLUSAL TRAITS IN THE EARLY MIXED DENTITION IN SHANGHAI, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1) Professional English needs to be improved, edit this paper by an expert in Scientific English language

2) Some references are too old, insert other epidemiological papers such as :
   - Prevalence of malocclusions, oral habits and orthodontic treatment need in a 7- to 15-year-old schoolchildren population in Tirana.
Laganà G, Masucci C, Fabi F, Bollero P, Cozza P.
Prog Orthod. 2013 Jun 14;14:12. doi: 10.1186/2196-1042-14-12.
    - Oral habits in a population of Albanian growing subjects.
Laganà G, Fabi F, Abazi Y, Beshiri Nastasi E, Vinjolli F, Cozza P.
Eur J Paediatr Dent. 2013 Dec;14(4):309-13.

3) Table 1 needs to be modified, remove the text, it is too much for a table

4) Seven tables are too many, you can represent more results in a single table
Experimental design: Clarify better the "consistency and reliability" of the five orthodontists
Validity of the findings: The results are important in the Chinese area, because of recent informations' lack
In Discussion section, Authors can discuss the results comparing with different countries
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: PREVALENCE OF MALOCCLUSION AND OCCLUSAL TRAITS IN THE EARLY MIXED DENTITION IN SHANGHAI, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The aim of the paper to evaluate the prevalence of malocclusion in the Chinese population is important, however there are several shortcomings: 1/ the modification of the  IOTN used is not explained; 2/ the calibration is not described; 3/ no effort was made to look at the pretreatment records of the "few" children who already had orthodontic treatment; 4/ the term "individual normal occlusion" was not explained; 5/ some of the significant results were not explained in the discussion, ie increase of overjet with age, increase in crowding in boys in comparison to girls etc .
Experimental design: 1/ The method used is "modified IOTN". It is not clear what kind of modification was preformed and  was it validated before it was used in this study?
2/ The calibration of the 5 dentists is not described.
3/ No effort was made to look at the pretreatment records of the "few" children who already had orthodontic treatment.
4/ The term "individual normal occlusion" guided the authors in their decision to treat or not to treat. However, this term in not explained in the text.
5/ Functional shift was not examined although it could possibly explain some of the results like "mixed" molar relationships.
Validity of the findings: 1/ Lack of validation of the modified IOTN may compromise the results.
Additional comments: In order to make a balanced review of the literature,  in the introduction section mention should be made also of malocclusions which do not have to be treated early (L Johnston, J Bowman and others).
There are significant findings whish are not discussed or explained.


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: PREVALENCE OF MALOCCLUSION AND OCCLUSAL TRAITS IN THE EARLY MIXED DENTITION IN SHANGHAI, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Good reading but needs edit proffing
Experimental design: Ok
Validity of the findings: Ok
Additional comments: Please revise the paper for grammar and style


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: PREVALENCE OF MALOCCLUSION AND OCCLUSAL TRAITS IN THE EARLY MIXED DENTITION IN SHANGHAI, CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: English has been corrected and improved
References now are correct
Tables are weel described
Experimental design: ok
Validity of the findings: ok
Additional comments: Authors' editing work on the paper was appreciated.


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: PREVALENCE OF MALOCCLUSION AND OCCLUSAL TRAITS IN THE EARLY MIXED DENTITION IN SHANGHAI, CHINA
Review round: 2
Reviewer: 3

Output:
Basic reporting: 1/Define "slightly more frequent" for line 156-7. The overjet in the early mixed dentition was found in 43.8% while in the primary stage in 33.9%. Is this a slight difference? Possible causes for this difference like the "ugly duckling stage" are not discussed.
2/ In Table 1: in the sagittal malocclusion only class III is mentioned. What about class II?
3/ In Table 3 the number of the footnotes in the table do not fit the  numbers at the bottom of the table.
4/ Table 4 refers to vertical problems but referes to midline displacement which is a transverse problem.
Experimental design: no comment
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: REVISION OF THE LATE JURASSIC DEEP-WATER TELEOSAUROID CROCODYLOMORPH TELEOSAURUS MEGARHINUS HULKE, 1871 AND EVIDENCE OF PELAGIC ADAPTATIONS IN TELEOSAUROIDEA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This MS describes an anterior end of a rostrum, a tooth, and 3 osteoderms of a teleosauroid crocodylomorph. Though this specimen is quite fragmentary, it possesses important overlapping elements with the type of ’Teleosaurus’ megarhinus described from the same stratigraphical horizon. English of the MS is clear, article structure is ok.
I think this is an important contribution to vertebrate paleontologists working with crocodiles and/or Mesozoic marine vertebrates, so, after some minor changes, I would be happy to see it published.
Experimental design: Research question is well defined, relevant & meaningful, methods are described with sufficient detail.
Validity of the findings: OK
Additional comments: 1) The authors refer the new specimen „DORCM G.05067i-v to ‘Teleosaurus’
megarhinus,” and say „that the species is indeed a valid taxon, and establish a new monotypic
genus, Bathysuchus.” I can accept this taxonomical interpretation but in this case, in the systematic paleontology section a differential diagnosis should be added where they conclude why the two Kimmeridge Bay and possibly the Quercy specimens are not Teleosaurus.

2) An important part of the work is the comparison of the new rostrum fragment with that of the Quercy specimen. So, I strongly suggest to add at least a photo from the French specimen, or, rather a comparative drawing of the narial end of the rostra of at least the three different specimens referred to Bathysuchus.

3) A locality map, as part of Figure 1, would be useful.

4) Citation-reference block is very incomplete! Many of the cited works are not in the Reference list, indicated in the annotated pdf (see attached).

5) Some minor comments and typos have been indicated in the annotated pdf.