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: VECTOR DISTRIBUTION AND TRANSMISSION RISK OF THE ZIKA VIRUS IN SOUTH AND CENTRAL AMERICA
Review round: 1
Reviewer: 3

Output:
Basic reporting: - L45-46: In the description of Zika disease (lines 45-46) it is unclear what the authors mean by “short Zika”. Is “short Zika” a synonym for Zika fever/disease or do they mean “Zika” is a short-hand term for the disease?

- L49-54: I understand the general idea is clear, however these sentences could be condensed and streamlined so they are not redundant.
-  L54: This is a styling preference. I would suggest substituting “But” with “However,” or a similar word.

- L64-65: Since ecological niche models are tools, I would suggest removing “tools of”.

- L66: Mismatch between noun and verb. Should read as “diseases are present”

- L67: Mismatch between noun (diseases) and possessive adjective (its). If the term is kept plural should read as “their potential distributions”

- L67: There are plenty of references that could be included here, please add some more. I would suggest looking up work developed by AT Peterson, DM Pigott, J Blackburn, among others.
- L70: Same comment as L67 regarding references

- L74: Since the authors have already introduced the abbreviation for ecological niche models (ENM) I would suggest using it in lieu of the full term.

- L81: This is a styling preference, however, the word “so-called” has two meanings which could lead to misinterpretations. I would suggest changing this word to something like “commonly called” to avoid confusion.

- L106:  There is a typo, quotations before GlobCover seem to be inverted.

- L120-121: The software note corresponding to the Maxent version implemented should be cited. “Steven J. Phillips, Robert P. Anderson, Miroslav Dudík, Robert E. Schapire, Mary Blair. 2017. Opening the black box: an open-source release of Maxent. In Ecography”

- L137-138: The sources for population density and GDP data are not referenced.

- L149: Typo. There is an extra comma after the CDC website citation
- Overall inconsistencies in the way references are cited in line. For example, sometimes the authors will cite a reference as “Following methods developed by Smith et al. (year)….”, while other times they will cite “Following methods developed by (Smith et al. year)”.

- L166-168: I think it would be very beneficial for the reader if the ECM classes proposed by Brad et al. (2012) and assigned numbers were presented in a table.
Experimental design: - L81-86: It is not clear how the temperature variables mentioned were included in the analysis. I would assume this variable is already incorporated in the ENMs of both vector species, however, from the wording it seems like temperature was accounted for after these models were built. Likewise, clarification is needed to explain how these socioeconomic factors were related to risk of infection and if this is another step in the modeling.

- L90: Please add a brief explanation on why that particular methodology was chosen.
-  L96-99: While I think it is wonderful that the authors include socio-economic variables to estimate risk of transmission, it is unclear why temperature of the warmest quarter is used to estimate risk. It seems like this variable would already be included in the vector distribution models. If there is a reason to do so, please provide a more elaborate explanation.

- L109: I think it would be beneficial to the reader if the authors could include a table of which land cover classes were selected for the study as well as a brief explanation as to why they were.

- L101-112:  Though it is not explicitly stated, I understand the authors implemented a PCA to reduce model overfitting by reducing the dimensionality of predictor variables (Anderson & Gonzalez (2011) Ecol. Model. 222: 2796– 2811; Radosavljevic & Anderson (2014). J. Biogeo. 41(4), 629-643). However, this must be done with caution as results derived from a model using PCs are more difficult to interpret ecologically. An alternative way to deal with this problem is by only choosing environmental variables known to be ecologically relevant to the species at hand. This topic has been discussed at length by several authors (for example, Anderson (2013) Annals of the New York Academy of Sciences). The number of variables can be further reduced by using the categorical land cover raster instead of the 20 derived percentage land cover class layers that the authors used. Maxent can handle combinations of categorical and continuous variables, as the authors are aware since they use both types of variables to build the ZIKV models. Therefore, I am slightly confused as to why they didn’t use the same approach for the vector models.

- L122: The total number of mosquito occurrence records used for the vector models is not reported, nor are the total number of background/pseudoabsence points. Likewise, the authors fail to mention how the study region was delimited (i.e. from which background points will be selected for model calibration). The inclusion of areas where the species is absent despite being environmentally suitable for the species could lead to biased modeling results (Barve et al. (2011) Ecol. Model., Anderson & Raza (2013) J. Biogeog.). This is why many studies choose to delimit the study region using methods as the minimum convex hull.

- L132-142: I find the implementation of ENM to model transmission risk of infectious diseases very interesting, however, I believe justification as to why the authors believe this is an appropriate method to do so is warranted. Though I agree that mean temperature of the warmest month is likely very relevant for mosquito-borne disease transmission, I can’t help but ask whether this is because of the variable’s effect on vector biology (and was included in the vector models as well). Does temperature affect virus distribution directly or indirectly? See Anderson (2013) Annals NYAS.

- L124: I imagine the reason why only one record per grid cell was used for model construction is to reduce spatial biases, however this is not explicitly stated (See Aiello-Lammens et al. 2015 Ecograhy). Likewise, given the biology of mosquitoes and the nature of disease transmission, it is unclear why the authors chose a spatial resolution of 5 arc minutes when finer resolutions are available in Worldclim.

- L132-141: Same as L132-142

 - L182-190: I appreciate that the authors attempted to lay out their hypothesized relationships between ZIKV transmission risk and each predictor variable. However, I would have liked to see the reasoning behind these assumptions to be a little more fleshed out.

- L194-199: Many studies have addressed the issue of using default Maxent settings since modeling results may be greatly affected by the selection of regularization multipliers that penalize model complexity (See Merow et al. (2013) Ecography; Elith et al. (2010) Methods Ecol. Evol). Methods for model tuning to select appropriate regularization multipliers and feature classes that optimize balance between goodness-of-fit and model complexity (i.e. model tuning) have been proposed and are widely available (See Muscarella et al. (2014) Methods Ecol Evol) and should by now be common-practice in any implementation of ENM. Furthermore, model performance can be affected by the partitioning method used in model calibration, particularly when dealing with large geographic extents (see Radosavljevic, A., & Anderson, R. P. (2014) J. Biogeog).
Validity of the findings: - L215-225: Interpretation of response curves may be a little tricky. I noticed that most of the response curves were truncated which generally means that the background was not sampled enough to actually give you a unimodal response.

- L223-236: Please be mindful that the results of variable jack-knifing only reveals which variables contributed to the model more heavily. Ecological interpretations of these results must be done with extreme caution.

- L203-236: Metrics of model performance (e.g. AUC, AICc, Omission rates) were not reported.
Additional comments: This article addresses a very relevant and current issue and proposes an interesting approach to modeling the risk of disease transmission via ecological niche modeling.

Unfortunately, there are many fundamental flaws in the methodology that must be addressed before considering this article for publication.

I do believe this article has great potential and have strived to provide comments that will be helpful in development of a revised version.

Best of luck.


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: VECTOR DISTRIBUTION AND TRANSMISSION RISK OF THE ZIKA VIRUS IN SOUTH AND CENTRAL AMERICA
Review round: 2
Reviewer: 1

Output:
Basic reporting: -
Experimental design: Original comment:
One major criticism of this work is the lack of detail given on the modelling approach. The authors appear to have used the MaxEnt software without any customization to this specific application. The statement that it has previous been used for other species distribution modelling examples is not sufficient given the unique nature of the Zika datasets which were collected in an international public health emergency and I cannot see any adjustment of the datasets used to consider their specific nuances in this analysis. A big concern here would be the highly variable reporting practices for Zika that vary across space and time (particularly early in the outbreak). No attempt has been made to adjust the model to account for this or assess sensitivity to such biases.
I couldn’t find any information on how background points were generated- this is key in assessing how observation bias was included.

Response:
We now provide more details on the specific settings we used (paragraph “Software” L226). Briefly, Maxent was used with the default settings using only LQP features to get smoother and continuously differentiable niche functions and to avoid overfitting. Background points were sampled according to the default settings.
The high variability in space and time during outbreaks is typical for emerging infectious diseases like Zika and we certainly agree that there is likely sampling bias in the data. We added another few sentences on this aspect in the discussion (L403ff). We also added a paragraph on previous modelling approaches in the Introduction (L75ff).

Re-review comment:
I see the inability or unwillingness of the authors to assess the sensitivity of their findings to their chosen method, analysis steps and parameterisations as a fatal flaw in what is primarily a modelling paper. All three reviewers have highlighted a range of analysis steps that could substantially alter the findings of these studies and I do not believe any of these have been adequately addressed by new analyses in this resubmission (particularly the comments by reviewer # 3 which contains some responses that are just plain incorrect (see reviewer 3 validity of findings section)).

The AUCs (now visible in this resubmission) are adequate, but really should be higher given the high ratio of presence : randomly sampled background points. This strongly suggests various steps of model building, fitting and evaluation need to be revisited to optimize predictive performance. I also would still like to see how AUC (as well as the rider ROC curve if the authors insist on deviating from threshold based methods) changes based on different methods of background point sampling given the, acknowledged, sampling bias of the data.
Validity of the findings: -
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: VECTOR DISTRIBUTION AND TRANSMISSION RISK OF THE ZIKA VIRUS IN SOUTH AND CENTRAL AMERICA
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors have addressed all the comments that were notified before.
Experimental design: The authors have addressed all the comments that were notified before.
Validity of the findings: The authors have addressed all the comments that were notified before.
Additional comments: The authors have addressed all the comments that were notified before.


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: COMBINING DATA FROM DIFFERENT SAMPLING METHODS TO STUDY THE DEVELOPMENT OF AN ALIEN CRAB CHIONOECETES OPILIO INVASION IN THE REMOTE AND PRISTINE ARCTIC KARA SEA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Text is written in professional English, although some minor stylistic corrections are needed.

The paper is well structured. Some text should be narrowed down to Tables.

In some places text looks redundant and may be easily shortened (more comments provided in attached file)
Experimental design: no comment
Validity of the findings: Discussion may be better structured and shortened (some parts can be moved to Materials and Methods)
Additional comments: This is an interesting and useful paper. It requires some revision - more details are given in attached file


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: COMBINING DATA FROM DIFFERENT SAMPLING METHODS TO STUDY THE DEVELOPMENT OF AN ALIEN CRAB CHIONOECETES OPILIO INVASION IN THE REMOTE AND PRISTINE ARCTIC KARA SEA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basic reporting

Professional editing and cleaning of the language are necessary throughout the document before the publishing. Please foresee that e.g. the sentence (line 297-298) “Each video frame was visually inspected by A. Zalota and only frames with tolerable visibility were used” -> where both the person and the range of the “tolerance” is unknown and need explanations. Such “undefined” wordings and sentences need to be cleaned up throughout the document, and I have given some few (but not all) examples in the document.

Intro & background are showing the context well, but need to be divided into appropriate subchapters. Please see comments throughout the documents about moving the text to appropriate sections.

Please avoid using Institution names, Cruises, and Person names (see e.g. line 50-58) outside the “Material and Method” section, but only use appropriate references to what has been published from these Institutions, Cruises, and Persons.

Please use a consistent name of the snow crab. Several names are used throughout the manuscript as it is now.

I have not had the time to look through the Literature and referenced list, but have added some comments on the document on relevance.

The figure text in figure 3 and 4 are very similar .. could these two figures be merged?

Time limits prevented me from considering the Raw data supplied.
Experimental design: EXPERIMENTAL DESIGN

Time limitation made it difficult to carefully read the “Original primary research within the Scope of the journal” and evaluate if this publication falls within this scope. I hope the editor of the Journal can help here.

The research question is not well defined at the end of the Introduction. I have suggested a way to do this that I find relevant & meaningful. But it is up to the auditors to evaluate what they will like.

The research fills an identified knowledge gap: Because the snow crab only recently has been recorded in the Kara Sea (i.e. a new spreading species), this work is novel, important and timely.

Rigorous investigation performed to a high technical & ethical standard: The authors use three different sampling methods and draw conclusions across these methods. The conclusions are that the Sigsbee trawl with small mesh-size and Video sampling obtain information of both large and small crabs, while the large bottom trawls only on large crabs because of a large mesh-size. Trawl sampled individuals can be accurately measured, while Video sampled individuals only occasionally. The combined use of these gears is recommended by the auditors to provide a full data-scope of the existing size groups in a population.

I find that the 3 methods are described with sufficient detail & information to replicate.
Validity of the findings: VALIDITY OF THE FINDINGS

Knowing the propagule areas, the reproductive and spreading potential of the Kara Sea snow crab population will have an Impact on the forecast of the future of the Siberian Shelf ecosystems, and the options for resource management and biodiversity conservation.

Because few studies are made on the Kare Sea snow crab population due to the remoteness of this area. Combined with the fact that the spreading of the crab is ongoing, makes this paper novel.

Data are robust as far as possible, statistically sound, & controlled. But as the authors state: Three different methods are combined and evaluated as far as possible. No standardized sampling system exists in the remote Kara Sea, and this work has made a good attempt to compile all information from these different methods.

The Conclusion paragraph should be better stated, linked to the research question (that need to be clearly written in the end of the Introduction” & limited to supporting results.
Additional comments: Combining data from different sampling methods to study the development of an alien crab Chionoecetes opilio invasion in the remote and pristine Arctic Kara Sea, by Anna K Zalota Olga L Zimina Vassily A Spiridonov

Review based on Dr. Lis Lindal Jørgensen:

This work is a description of the spatial distribution of snow crabs in the Kara Sea, mainly based on the size and sex of the crab. Because the snow crab only recently has been recorded in the Kara Sea (i.e. a new spreading species), this work is novel, important and timely and should be published. As the authors correctly and timely states: it is critical to study the development of the snow crab population in the Kara Sea to forecast the future of the Siberian Shelf ecosystems, and the options for resource management and biodiversity conservation.

The authors use three different sampling methods and draw conclusions across these methods. The conclusions are that the Sigsbee trawl with small mesh-size and Video sampling obtain information of both large and small crabs, while the large bottom trawls only on large crabs because of a large mesh-size. Trawl sampled individuals can be accurately measured, while Video sampled individuals only occasionally. The combined use of these gears is recommended by the auditors to provide a full data-scope of the existing size groups in a population.

My opinion is, that while the title: “Combining data from different sampling methods to study the development of an alien crab Chionoecetes opilio invasion in the remote and pristine Arctic Kara Sea” and the paper is focusing on “sampling methodology”, I suggest turning the focus to study: “The development of an alien crab Chionoecetes opilio invasion in the remote and pristine Arctic Kara Sea” and therefore focus on 3 goals (see also line 138-140):

We will like to 1) identify from where the snow crab has entered the Kara Sea by population size, 2) identify brooding areas in the Kara Sea by measuring size distribution of snow crab populations, 3) to evaluate if the snow crab population in the Kara Sea is self-sustained by measuring the population size of mature, egg brooding females.

This should be clearly expressed in both the abstract, discussion and in the conclusion.


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

Input:
Title: GENOME-WIDE ANALYSIS OF TRANSCRIPTION FACTORS RELATED TO ANTHOCYANIN BIOSYNTHESIS IN CARMINE RADISH (RAPHANUS SATIVUS L.) FLESHY ROOTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1、The language should be improved by English expert.
2、I concern where the transcriptome data come from. Had these data been deposited in the public database?
3、The authors did not describe the data of miRNAs used in this paper clearly.
Experimental design: In my opinion, the transcriptme data used for the following analysis should be with at least three biological replicates. please describe this part in detail.
Validity of the findings: The authors had described the expression profiles of somes miRNAs and their corresponding target genes. Did these  miRNAs  cleavge their  target genes? could you validate this conclusion  by 5' RLM-RACE?
Additional comments: 1 、The language should be improved by English expert.
2、The title does not conform to the content of the paper exactly, which focused on the biosynthesis of anthocyanin.
3、Please use the abbreviations regularly. When the item appeared in the paper firstly, please use the style of full name (abbreviation). Then use the abbreviation after that.
4、Could you validate the target of miRNAd by 5' RLM-RACE?


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 ANALYSIS OF TRANSCRIPTION FACTORS RELATED TO ANTHOCYANIN BIOSYNTHESIS IN CARMINE RADISH (RAPHANUS SATIVUS L.) FLESHY ROOTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: BASIC REPORTING
In this manuscript, authors present a research about the identification of transcription factor families during the development of carmine radish (Raphanus sativus) roots. Besides, they show results about the expression miRNAs and their targets by RT-qPCR. They also relate the expression of TFs genes and miRNAs with the anthocyanin biosynthesis in roots. Finally, a model of the anthocyanin biosynthesis regulation mediated by miRNAs and their respective TFs targets is proposed. This research could be a good start point to understanding the anthocyanin biosynthesis in roots of carmine radish.
1.	The most important point of this manuscript is the focus and the obtained results. Authors should not confuse the development of the roots with the anthocyanin biosynthesis. The development concept is a broad term involving growth of root structures, between other physiological changes, while the anthocyanin biosynthesis is product of the secondary metabolism. I suggest relating the anthocyanin biosynthesis, their TFs and miRNAs related the most important topic, and other TFs without scientific evidence in the regulation of the flavonoids could be omitted.  Authors should improve the text writing of this point in the introduction, results and discussion.

2.	A deep review of the English language is required.

3.	Some figures could be moved to supplementary information (pdf review).

4.	Bibliography: some cites into the text and the list references should be reviewed.
Experimental design: 1.	Question about the target genes: TFs constituting the MBW complex (MYB, bHLH and WD40) are the most important for the regulation of the anthocyanin biosynthesis, so, the authors should justify why the ERF and C2C2-Dof families were used for search of miRNA regulators.
2.	Material and Methods section:
2.1.	Information about the methods is lacking. For instance, more information is necessary to understand the expression analysis by RT-qPCR about the miRNAs. Please add all information.
2.2.	Some subheadings is not related with the description the method. For example: “Expression pattern analysis and regulatory pathway identification”.
2.3.	Information about the methods of anthocyanin levels quantification (Fig. S1) should be described.
2.4.	If you have data about the statistical significance, you should include it. Please, also to include number of biological and/or technical replicates for anthocyanin quantification and RT-qPCR analysis.
Validity of the findings: 1.	Statistical analysis should be showed for the expression analysis.
2.	Discussion should be improved. I recommend to focus in the possible implications of target TFs by miRNAs, and how it is related with the anthocyanin levels.
3.	Please, to add some general conclusions.
4.	The final model (Fig. 4) should be modified, considering that many experiments are necessary for clarify that the TFs that you are reporting are involved in the anthocyanin biosynthesis. Besides, you consider that some TFs that regulate organ polarity also regulate the anthocyanin biosynthesis.
Additional comments: Dear Gao et al.,

I read and and reviewed the manuscript entitled "Genome-wide analysis of transcription factors involved in development of carmine radish (Raphanus sativus L.) fleshy roots". It is a interesting research about the TFs and miRNAs regulating the anthocyanin biosynthesis, however, you should improve the focus, the methodology and methods information and the discussion. You can review these items in general comments and the attached pdf.

Best regards.


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 ANALYSIS OF TRANSCRIPTION FACTORS RELATED TO ANTHOCYANIN BIOSYNTHESIS IN CARMINE RADISH (RAPHANUS SATIVUS L.) FLESHY ROOTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The English should be improved in the entire manuscript, and there are some typographical  errors in this article. For example, line 106, 'six cultivars',line 195,  'hongxin1' should be 'Hongxin1'and line 245, the citation 'Yulong et al.2016' should not be italic.
Experimental design: The first part of 'Materials and methods' section is 'Experiment design and RNA isolation' ,however, the authors did not describe how to isolate the RNA in this part.
Validity of the findings: The author did not state the replication of the experiment.
Additional comments: In this study, the authors performed a genome-wide analysis of transcription factors during  carmine radish development  based on the transcriptom data and proposed a putative miRNA-target model in anthocyanin biosynthesis. However, the conclusion is stated according to the transcriptom data, online miRNAs and targets prediction and a little qRT-PCR analysis, lacking the solid experimental support. Otherwise, the development of carmine radish is a complex process including transformation of nutrition, cell expansion, secondary metabolism except for anthocyanin biosynthesis, etc.. Some TFs identified in this article such as WRKYs and ERFs may mainly participate in other process rather than anthocyanin biosynthesis. So, it is too arbitrary to say these TFs modulate anthocyanin biosynthesis when there is no direct empirical evidence support it.


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

Input:
Title: GENOME-WIDE ANALYSIS OF TRANSCRIPTION FACTORS RELATED TO ANTHOCYANIN BIOSYNTHESIS IN CARMINE RADISH (RAPHANUS SATIVUS L.) FLESHY ROOTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors considered the comments suggested in the first manuscript revision: Question 1, Q3, Q5-6, Q8, Q10, Q11 (according to ‘Response to reviewers’ file) are correct and well explained. However, I suggest that responses of Q4, Q7, Q9 and Q12 should be improved. Next, I indicate the main changes and several details in the text:

Q2. A deep review of the English language is required.
Response: We thank the reviewer for making this comment. We have polished the English of our manuscript carefully.
Reviewer response:  Please, Could you do the next changes?
•	Line 36: to remove “a”.
•	Line 53: “layse” by “lyase”.
•	Line 63-64: “recent researcher” by “Recently, researches…”
•	Line 69: change “which” by “these miRNAs have not been…” or similar.
•	Line 84: “Total” in lower case.
•	Line 103: Please, change “dynamics Anthocyanidin profiles” by “anthocyanin profile dynamics” or something like that.
•	Lina 139: “were identified obtained” by “were obtained”.
•	Line 172: “are designed” by “were designed”.
•	Line 173: “radish gene (Actin)” by “radish actin gene”. “standard control” by “reference gene” or “housekeeping gene”.
•	Line 210: “…43 members and…” by “43 members, respectively; and…”.
•	Line 211: to remove “respectively”.
•	Line 266: Please, to modify “were identified increased” by “were increased”, “increased” or something like that.

Q4. Bibliography: some cites into the text and the list references should be reviewed.
Response: Thanks for your suggestions, we have checked all cites in the list references and checked them thoroughly, and fixed them carefully following the queries of PEERJ article.
Reviewer response: Some additional references should be improved.
•	Line 56: ‘Anju Bajpai et al. 2017’. This cite is wrong wrote. Besides, the corresponding reference in the bibliography list has different write format of the others.
•	Line 195: Please, change it “Jian et al.(Jian et al. 2015)” by “Jian et al. (2015)”.
•	Line 300: ‘(WILLIAMS 2005)’. Please, change it by “(Williams 2005)”.
•	Line 328-329: “Kuhn et. al” and “(Kühn & Grof 2010)” are write differently.
•	Line 335-336: I think that “Gaifeng Yao et al.” should be written like “Yao et al.”

New comments for “BASIC REPORTING”:
• Please, write Raphanus sativus in italics.
- Lines 32, 88-89, 253, 277, 365:  Please, change “25 miRNAs family” by “25 miRNA families”.
•	Line 326: “D-fructose” by “D-fructose”
•	Line 189: change “RT-PCR” by “qRT-PCR”.
•	Please, change “anthocyanidin” by “anthocyanin” through the text.
Experimental design: Q7. Some subheadings is not related with the description the method. For example: “Expression pattern analysis and regulatory pathway identification”.
Response: Thanks for your good suggestions; we have fixed all the subheadings in the new modified.
Reviewer reponse: Thanks for consider this suggestion. I think that the new subheading ‘experiment design’ should be changed to “Quantification of anthocyanin levels” or similar.

Q9. If you have data about the statistical significance, you should include it. Please, also to include number of biological and/or technical replicates for anthocyanin quantification and RT-qPCR analysis.
Response: Thanks a lot, we have included the number of biological and/or technical replicates for anthocyanin quantification and RT-qPCR analysis in the new manuscript.
Reviewer reponse: Thanks. However, I can not find the number of replicates used for anthocyanin quantification. Please, add it.
Validity of the findings: Q12. Please, to add some general conclusions.
Response: Thanks a lot, we have added general conclusions in the new manuscript.
Reviewer reponse: I think that ‘conclusiones’ section can not be a copy of the abstract. Could you change it?

New comments for “VALIDITY OF THE FINDINGS”:
1.	Line 161: You indicate that “ten DETFs were used for qRT-PCR analysis. However, only 8 DETFs are showed in Figure 3. Please, explain this or change “ten” for “eight”.
2.	Line 280: miRNA5720 can not find in the proposed model.
Additional comments: Dear authors,

I reviewed the new manuscript version. I think that the article is better understood with your changes. But, I think that you should consider some minor changes.

Best regards.


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: CHRONIC TRACE METALS EFFECTS OF MINE TAILINGS ON ESTUARINE ASSEMBLAGES REVEALED BY ENVIRONMENTAL DNA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well writen and clear, and proposes the use of eDNA as indicator of meiofaunal community, in order to observe effects caused by metals related to mining tailings in an estuarine region. In general, the objective is well defined, the results are properly presented and the discussion is well organized and address the aspects that attend the objectives. Some details can be provided on the approach used, and some parts of the discussion can be improved, based on the results or on a better exploration of the literature.
Experimental design: The experimental design is mostly ok. Regarding the geochemistry, the use of HF (together with other acids) to digest the sediment samples can cause an overestimation of the contamination levels, because it includes elements from the crystallin matrix.
Validity of the findings: Most of the results are ok. Some details could be provided, as for example the influence on the grain size or TOM on the benthic diversity and metals. Some caution should be taken when interpreting the chemistry data (as commented above).
Besides, to my best knowledge, the Rio Doce river basin presents a history of contamination by metals and pesticides, thus the benthic community probably is influenced by such hystorical factor, together with the contamination associated with the mining tailings. This should be discussed in more detail and include the uncertainty on determining if the current benthic condition is due to the disaster or to a combination of different contamination processes.
I also would like to see a more detailed comparison between classic morphological based benthic diversity and that provided by eDNA. How congruent are they?
Additional comments: Specific comments
Line 47 and on: You could provide more details on these techniques
Lines 129-131: Acid digestion with HF causes the extraction of elements related to the crystallin matrix and consequently may produce overestimation of the concentrations of bioavailable metals.
This fact may have implications for the results' interpretation.
Line 138: which are the advantages and limitations of using the 18S SSU rRNA gene?
Lines 196-200: How did metals concentrarions correlate with sediment textural classes and TOM?
Since sediment grain size distribution and TOM are important factor to condition the distribution of benthic species and metals, knowing such correlations would be hepful.
Line 253 and on: One would like to see the relationship between eOTUs and some regular biotic variables, such as species richness and/or diversity. Have you tried to do such comparisons?
Line 291: Consider the river basin (and I guess, the estuary as well) was previously contaminated by metals (mainly from mining activities located along the river basin)
Lines 299-304: As I mentioned, the sediments from the river basin were previouly contaminated by metals, thus some hystorical adaptation/resistance could be expected in native organisms.
Lines 307-308: this is quite possible, especially regarding the As, since the acid digestion used HF.
Lines 311-312: Is Pb (and other elements mentioned) related with tailings composition?
Lines 312-315: However, it is widely known that acid volatile sulfides become predominant in hypoxic (or anoxic) sediments and they are efficient chelators of metals. I suggest the authors to search some literature on the AVS-SEM  ratios and their relationship with bioavailability and toxicity.
Line 316 and on: As mentioned, Fe occurs along the Rio Doce basin, prior to the disaster, possibly as a chronic consequence of the mining activities upstream. Additional amounts of Fe were brought to the system due to the mining tailings.  Therefore, it is not possible to affirm that metals were due to the tailings only; instead, a certain fact is that metal contamination is mainly due to mining exploration (chronic contamination by the mining activities plus the residues from the disaster)
Line 322 and on: I agree with you. However, since you have information on the taxonomic distribution based on both eDNA and classic morphological characteristics, you could use the comparison to justify or corroborate the choice of using eDNA to estimate biodiversity in the studied case.
Line 345: no funding agency? no institutional support? no other support?


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: CHRONIC TRACE METALS EFFECTS OF MINE TAILINGS ON ESTUARINE ASSEMBLAGES REVEALED BY ENVIRONMENTAL DNA
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This study investigated the effects of trace metals associated with mine tailings disaster in Rio Doce estuary area on the aquatic biodiversity using environmental metabarcoding (eDNA). Overall the manuscript is of great quality, well written, well structured and of interest. The main conclusion from the presented results is “We detected environmental filtering on the meiofaunal assemblages and multivariate analysis revealed strong influence of Fe contamination, supporting chronic impacts from mine tailing deposition in the estuary.” However, Fe is likely not the only one responsible for the observed environmental filtering, and all the other trace metals analysed and highly correlated with Fe should be considered in this result/phrasing, as some of those metals are much more toxic than Fe. As such, while it is understood that only Fe was used in the multivariate analysis, as the representative of the “same signal” and correlated with Al, Cd, Cr, Co, Cu, Mn and Zn, I advise the co-authors to rephrase the sentences when mentioning the effects of Fe by something like effects of Fe-group or Fe+other metals (?).
In addition, and as mentioned by the authors that there is a lack of environmental data for the Doce River, it is advised to present the concentrations of Al, Cd, Cr, Co, Cu, Mn and Zn per sampling site, adding on to table S1 for example.
The discussion could also benefit from a brief discussion on the concentration of metals found in this study and how they compare to non-impacted estuaries nearby, or to highly polluted areas, if such data exist… if not at least mention that fact, to give an idea to the reader whether the presented concentrations are much higher or not.

Throughout the manuscript, including table legends, the italics formatting is missing from p –values, r, or species names. Also superscript and lowerscript formatting is missing (e.g. lines 126, 130, 221, 224-226).
Line 178: Verify if reference Gabriel et al., in review is already published or remove it.
Line 196-198: This sentence is not necessary - The concentration of trace metals in the estuarine sediments also varied markedly along the studied area. - as the subsequent sentence says the same.
Line 332: The first sentence of the conclusion should directly state what in your results support your hypothesis that the impacts of tailings affect the benthic estuarine assemblages. Or a sentence similar to that in the abstract in lines 32-34 (but adding the other trace metals to Fe!).

I recommend the publication of this article in PeerJ, after addressing the minor revisions mentioned 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: EFFECTS OF AFFORESTATION ON WATER RESOURCE VARIATIONS IN THE INNER MONGOLIAN PLATEAU
Review round: 1
Reviewer: 1

Output:
Basic reporting: Most of the English expressions are clear and unambiguous, professional.
Literature was well referenced and relevant, and sufficient field background/context were provided.
Article structure should be more clearly arranged.
The result part should be well modified.
Experimental design: The manuscript is original primary research within Aims and Scope of the journal.
Research question well defined, relevant & meaningful.
Methods described should be with more sufficient detail & information to make it more clearly so that it can be replicated just by reading the methods part in this article.
Validity of the findings: Data is robust, statistically sound, & controlled.
Conclusion are not well stated, and should be modified or rewritten to be linked to original research question and supporting results.
Additional comments: 1. The language and format of this paper is fluent except for some few sentences, such as, line 35-37, line 84-86, sentences should be well arranged and some proprietary vocabularies should be corrected used.
please check the whole manuscript.
2. The abstract I think should be reorganized. Background sentences should be simplified or omitted. and the abstract should summarize the whole manuscript.
Here in the abstract, "This study uses GIS in order to determine the effects of forestation on water resource variations in the Inner Mongolian Plateau." I cannot find GIS method was described in the method part. I wonder what functions of GIS were used in the paper.
and "... this resource has generally exhibited a declining trend from 1980 to 2015, corresponding to the NDVI trend. " The resource decline? How? the quality or quantity?
the end part of the abstract should meet with the conclusion part of this manuscript.
3. Introduction
The introduction can be more logically narrated. Sufficient summery should be made to support the author's work, and in the end part of introduction, the work of this manuscript, maybe should be stated to show the significance.
4. figures should be referenced well in the text. see figure 1 and 2.
5. titles should not be followed by punctuations.
6. Line 141, Spatiotemporal analyses.
I cannot find Spatiotemporal analyses in the following statement. How Spatiotemporal analyses were carried out?
7. Line 164-167, should be placed in the results part.
8. Results.
More detailed analyses should be added in this part.
9. Discussion
Should be more closely related to the results of this study.
10. Conclusion
This part should be rewritten to conclude the main contribution of the authors. Some unrelated sentences at the beginning of the part could be omitted.


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 AFFORESTATION ON WATER RESOURCE VARIATIONS IN THE INNER MONGOLIAN PLATEAU
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.	The literatures in the manuscript were insufficient to introduce the background of the water resources studies in the introduction section, as well as to explain the knowledge gap in the discussion sections.

2.	The description of figures and table was also insufficient, more detail information is needed.
Experimental design: 1.	The manuscript need to more clearly define the research question and to explicitly indicate how the research fills the knowledge gap of water resources variation.

2.	The description of method and materials were also insufficient.
Validity of the findings: 1.	Some of findings and decisions are not supported by enough literatures.
Additional comments: Exploring the effect of afforestation on the water resources is of great important to under the ecohydrological processes in semiarid environment. This study combined Bodyko model with GIS to indicate the distribution of water resources and their change processes in Inner Mongolian Plateau. The scientific question of this study is very important for the evaluation of ecological restoration policies. The results obtained by the study are meaningful, i.e., water resources decreased significantly in the eastern section of Inner Mongolian Plateau. I think these findings could attract many researchers to concentrate on the water resources in semiarid environment. However, a major revision needs to be performed before acceptation.


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 AFFORESTATION ON WATER RESOURCE VARIATIONS IN THE INNER MONGOLIAN PLATEAU
Review round: 2
Reviewer: 1

Output:
Basic reporting: Clear and unambiguous, professional English used throughout
Experimental design: Original primary research within Aims and Scope of the journal
Validity of the findings: All underlying data have been provided
Additional comments: The authors have answered all thequestions and made enough correction. I
think it can be accepted as is.


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 AFFORESTATION ON WATER RESOURCE VARIATIONS IN THE INNER MONGOLIAN PLATEAU
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: this revised article meets the PeeJ criteria


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: SPATIAL GENETIC STRUCTURE IN PINUS CEMBROIDES ZUCC. AT POPULATION AND LANDSCAPE LEVELS IN CENTRAL AND NORTHERN MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: Dear Ph.D. Robert Winkler
Associate Editor

This study investigated the spatial genetic structure (SGS) in fine scale (within populations) and large scale (landscape) of five Pinus cembroides populations, using the dominant AFLP gene marker, aiming to establish guidelines for conservation and management of the species. The sample size ranged from 34 to 45 trees per population. The SGS analysis was carried out, using three different relatedness estimators between pairwise individuals and four different softwares. The results suggest low or no significant SGS within stands, but the pattern of gene dispersal of isolation by distance among stands.

The study is original, the results are discussed and paper fits the PeerJ scope. However, I have some suggestions and corrections to improve the paper.
Best regards,
The reviewer
Experimental design: The weak SGS in fine scale may an artifact of the low sample within the stands, as pointed also by authors, as well as due the fact that the study is based in samples of old individuals. To robust analysis based on 100 AFLP loci, samples of at least 150 individuals are recommended. The study is based on 283 loci, as recognize by authors, a higher sample size is necessary for SGS analysis (line 295), probably about 60 individuals. Old individuals may not be related due to many stochastic (random mortality, diseases, predation etc) and determinist factors (inbreeding depression, natural selection), decreasing SGS. However, SGS may occur in individuals of the younger classes. Thus, the results may only be valid for old trees. Alternatively, to overcome the problem of low sample size within populations, the intrapopulational SGS can be analyzed joint all individual and using shorter distance classes (for example 50, 75, 100, 150, 200, etc up to 700 m). Furthermore, more information about the populations is needed to understand the study, such as population density, origin of the population (natural or artificial and originate from plantation, probable age of the sampled trees).

Other point to be considered. Why did you use different methods to investigate the SGS in fine scale? Please, justify. I did not find any advantage in this strategy to analyses the data. I suggest use only Fij, implemented in Spagedi and to estimate the Sp-statistic for compare with other studies.
Validity of the findings: no comment
Additional comments: Manuscript ID: Peerj 39338-v0

Title: Spatial genetic structure in Pinus cembroides Zucc. at population and landscape levels in central and northern México

Dear Ph.D. Robert Winkler
Associate Editor

This study investigated the spatial genetic structure (SGS) in fine scale (within populations) and large scale (landscape) of five Pinus cembroides populations, using the dominant AFLP gene marker, aiming to establish guidelines for conservation and management of the species. The sample size ranged from 34 to 45 trees per population. The SGS analysis was carried out, using three different relatedness estimators between pairwise individuals and four different softwares. The results suggest low or no significant SGS within stands, but the pattern of gene dispersal of isolation by distance among stands.

The study is original, the results are discussed and paper fits the PeerJ scope. However, I have some suggestions and corrections to improve the paper. The weak SGS in fine scale may an artifact of the low sample within the stands, as pointed also by authors, as well as due the fact that the study is based in samples of old individuals. To robust analysis based on 100 AFLP loci, samples of at least 150 individuals are recommended. The study is based on 283 loci, as recognize by authors, a higher sample size is necessary for SGS analysis (line 295), probably about 60 individuals. Old individuals may not be related due to many stochastic (random mortality, diseases, predation etc) and determinist factors (inbreeding depression, natural selection), decreasing SGS. However, SGS may occur in individuals of the younger classes. Thus, the results may only be valid for old trees. Alternatively, to overcome the problem of low sample size within populations, the intrapopulational SGS can be analyzed joint all individual and using shorter distance classes (for example 50, 75, 100, 150, 200, etc up to 700 m). Furthermore, more information about the populations is needed to understand the study, such as population density, origin of the population (natural or artificial and originate from plantation, probable age of the sampled trees).

Other point to be considered. Why did you use different methods to investigate the SGS in fine scale? Please, justify. I did not find any advantage in this strategy to analyses the data. I suggest use only Fij, implemented in Spagedi and to estimate the Sp-statistic for compare with other studies.

Best regards,
The reviewer

Minor comments
Line 55. Where you read … isolation by distance …. I suggest ….. isolation by distance gene dispersal …

Lines 56-57. This sentence needs a citation.

Line 77. Where you read … thus providing few loci such as allozyme …. I suggest ….. thus, gene markers such as allozymes, which provide few loci are not adequate.

Line 105. Where you read … isolation by distance among…. I suggest ….. isolation by distance gene dispersal among…

Lines 107 and 118. Where you read … Pinus cembroides …. I suggest ….. P. cembroides …

Line 113. Please, delete “Add your introduction here.”

Lines 118-125. More information about populations is needed to understand the study, such as population density. In addition, Wehenkel et al. (2015) is written in German and not everyone can read to understand their study.

Line 222. The species name must be in italic (P. cembroides).

Line 244. Where you read … (4.4 % and 3.1 %) …. I suggest ….. (4.4 and 3.1%) …

Line 308. I suggest changing the term conclusions to conservation guidelines because the results continue to be discussed.


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: SPATIAL GENETIC STRUCTURE IN PINUS CEMBROIDES ZUCC. AT POPULATION AND LANDSCAPE LEVELS IN CENTRAL AND NORTHERN MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall accepted text clarity and structure.
Experimental design: Acceptable two-levels of sampling scales. OK DNA marker techniques.
Validity of the findings: Findings supported by data.
Additional comments: Main Coomments:

(1) Discussion is needed to be expanded about possible explanations of  the lack of small-scale SGS. Perhaps be more explicit about your possible explanation. Say perhaps that the fact that trees sampled were only on “trees in each stand which were adult, dominant and occurred in the older age group”. Perhaps if other (younger) age classes were sampled, SGS could be revealed, at it happened for Cecropia obtusifolia (Epperson & Alvarez‐Buylla, 1997)

(2) About conclusions: Are you sure that is worth to be engaged in a network of so close seed stands, distant less to 6 km, and use the seeds in a radius of only 3 km? Is it not exaggeratedly narrow and restrictive managing strategy, especially when, as you say, based on adaptive genetic variation, scale of differences likely would be much larger? Your forest management/conservation strategy seems to me not justified and if put in place (which I doubt), too expensive with dubious positive cost/benefit balance. Consider more about the reality of forest management.

(3) Conclusions are too long. Specially the  first paragraph: too much references and too few facts based on your results. Make something more synthetic, describing your more important findings, based directly on your results.

Specific comments.
45-46. What do you mean with?: “these stands should have a minimum width of at least 110 m to product seed” Do you mean to produce seeds?

56-67. Reference needed to support that.

72. Explain briefly wjay you mean with “a mixed sampling strategy”. Sampling at different intensities, e.g. sampling plots at small and a large scale, such as, say, every 50 m combined with plots every 50 km??

96 . Luna-cavazos -> Luna-Cavazos.

113. “Add your introduction here.” (¿???????????)

222. Pinus cembroidesin italics.

237. No so clear what you mean with “At the seed stand level”. Perhaps: “at the large-scale  -landscape- level (among seed stands, 6 to 168 km distance)..”

255. “..also detected no to weak SGS..” (?) Or “..also detected no too weak SGS..”?

267-270. About the lack of small-scale SGS. Perhaps be more explicit about your possible explanation. Say perhaps that the fact that trees sampled were only on “trees in each stand which were adult, dominant and occurred in the older age group”. Perhaps if other (younger) age classes were sampled, SGS could be revealed, at it happened for Cecropia obtusifolia (Epperson & Alvarez‐Buylla, 1997).

319. “to product seed” ¿? Or “to produce seeds”

325 “a maximum distance of 6 km” or you meant “a minimum  distance of 6 km” ??

325-326. Are you sure that is worth to be engaged in a network of so close seed stands, distant less to 6 km, and use the seeds in a radius of only 3 km? Is it not exaggeratedly narrow and restrictive managing strategy, specially when, as you say, based on adaptive genetic variation, scale of differences likely would be much larger? Your forest management/conservation strategy seems to me not justified and if put in place (which I doubt), too expensive with dubious positive cost/benefit balance. Consider more about the reality of forest management.

Figure 1. Panel of Mexico has too low resolution.


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: SPATIAL GENETIC STRUCTURE IN PINUS CEMBROIDES ZUCC. AT POPULATION AND LANDSCAPE LEVELS IN CENTRAL AND NORTHERN MEXICO
Review round: 2
Reviewer: 1

Output:
Basic reporting: I quickly reviewed the new version of the manuscript and realized that all my suggestions were accepted. Thus, in my opinion, the manuscript can be published in the present form.
Experimental design: Nothing to comment.
Validity of the findings: Nothing to comment.
Additional comments: Nothing to 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: SPATIAL GENETIC STRUCTURE IN PINUS CEMBROIDES ZUCC. AT POPULATION AND LANDSCAPE LEVELS IN CENTRAL AND NORTHERN MEXICO
Review round: 2
Reviewer: 2

Output:
Basic reporting: Overall acceptable manuscript
Experimental design: ALthough (as allways) a more intensive sampling of younger trees would be desirable, with the sampling that they did, results are supported and sicussion apply well for adult/older trees, as pointed out by the other reviewer. Thus, it is acceptable.
Validity of the findings: Results and conclusions supported, although I do not fully agree with so much restrictions of seed movement.
Additional comments: Auhtors responded in an acceptable way to my own comments and seems to me the responses to the other reviewer are reasonable.
Paper can be accepte in its present form.


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: ENFORCED SYMMETRY: THE NECESSITY OF SYMMETRIC WAXING AND WANING
Review round: 1
Reviewer: 1

Output:
Basic reporting: see General comments for the author
Experimental design: see General comments for the author
Validity of the findings: see General comments for the author
Additional comments: I read with interest the manuscript by Hohmann and Jarochowska, who describe how the use of diversity (or abundance) trajectories from the fossil record is affected by intrinsic biases. Essentially their findings show that regardless of the generating process, the trajectories averaged across multiple taxa are expected to show a symmetric wax and wane trend, which is therefore not necessarily informative of an underlying biological process.

I think the finding of this paper are interesting and as far as I can tell well justified mathematically. It is certainly useful to point out the limitations of using diversity trajectories, which is similar to what phylogenetists have come to realize in recent years for lineages-through-time plots. At the same time, I think the authors should do a better job at acknowledging that there are many alternative methods to make inferences about the processes underlying diversity trajectories, which are commonly used in (paleo)biology studies.

I think many studies (e.g. Quental and Marshall 2013 Science) do not actually average multiple trajectories but look at individual clades, do the concerns raised by the authors affect these studies too?

Also, while it is true that several studies used trajectories to make ecological/evolutionary inferences, many others attempt to infer the the underlying processes without looking at the trajectory per se. For example, Liow and Finarelli 2014 (Proc B) used presence/absence data to infer diversification dynamics; Silvestro et al. 2015 (PNAS) used birth-death models to estimate the processes underlying the wax and wane of different carnivore clades; Hagen et al. 2017 (Syst Biol) developed a model to estimate age dependent extinction. I think the Discussion should mention that these (and other) methods are alternative ways to test hypotheses from fossil data, going beyond the use of trajectories, and ideally discuss whether these methods solve the problems of “necessary symmetry”.

As part of better placing this manuscript in the context previous literature, I think the authors should refer to the paper by Budd and Mann 2018 (Evolution), which is discussing the “push of the past” bias derived from conditioning on clades to be large. This seems quite tightly related with the “Symmetry by conditioning” bias shown on p. 5 of this manuscript.

It is worth noting that there are many clades that do not show symmetric wax and wane, for example ammonites, mammalian carnivores, most plant clades (e.g. angiosperms families) and all clades that survived (and recovered from) a mass extinction.

I think the description of the non-parametric approach developed by the authors should be given in the main text rather than in the appendix. Right now the method is only mentioned twice (Introduction and Discussion) in the main text, and without reading the appendix it is hard to tell what it is really about.

 The data displayed in Fig. 1 should be explained: what are the “trajectories of individual taxa” referring to? Are taxa species, genera, families? Do their trajectories quantify diversity or abundance through time? Additional information is available in the Appendix, but I think the reader should be given the information to understand it based on the caption and the main text.

Minor points

A figure schematically showing the procedure described on p. 3 (way the data are processed) would be useful.

The word “data” is plural so I would replace “The Way Data is Processed” with “The Way Data are Processed”

Line 176 “it *is* time reversible”

Line 180: “…same, independent whether they are plotted” rephrase, e.g. “independently of whether”

Fig. 1 I think adding a plot of the actual trajectories would be very useful here. Also, I suggest replacing the large red and blue circles with dashed vertical lines.


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: ENFORCED SYMMETRY: THE NECESSITY OF SYMMETRIC WAXING AND WANING
Review round: 1
Reviewer: 2

Output:
Basic reporting: See comments to authors.
Experimental design: See comments to authors.
Validity of the findings: See comments to authors.
Additional comments: In 2007, a few papers were published showing that various measures of the "footprint" of species and genera rise and fall symmetrically, on average, over the lifespan of taxa. The important caveat is "on average." Hohmann and Jarochowska show that several mathematical factors lead to exaggerated symmetry even if individual taxon patterns are not symmetric. It's an important result, because a number of studies following the original 2007 papers modeled individual species histories as if they were symmetric. For example, the assumption is part of the original implementation of the PyRate method for estimating evolutionary rates (Silvestro et al. 2014, Systematic Biology 63:349). But, beyond showing that symmetry may be an artifact, the authors contribute a new measure of symmetry for individual taxa. I have not tested this measure, but it seems reasonable. My reading of the manuscript is that the authors are not questioning the tendency for individual taxa to expand and contract but are arguing that symmetry may be an artifact and that processes producing the rise and fall pattern are difficult if not impossible to infer from the average trajectories. (For example, I was surprised to find in my 2007 Paleobiology paper that the average trajectory of species richness, conditioned on extinction of the higher taxon, is expected to be symmetrical even if speciation and extinction rates are not equal.)

As one of the people guilty of promoting the idea of symmetry, I'm delighted to see this paper.

As far as I can tell, what the authors present is all sound. My main concern is that it is not always clear which elements of what they present are new and which are inherent in earlier work. For example, they cite my 2014 paper for the idea that a bounded random walk on average will yield a symmetric rise and fall (and I'm sure that idea was not original with me). But isn't that exactly what their Figure 2 is showing? More broadly, I think it would put the new work in a clearer context if the authors distinguished previous claims that average trajectories rise and fall symmetrically from claims that individual taxa do so. I also think that symmetry of individual taxa may not always be a bad approximation. For example, Tietje and Kiessling (2013) showed that the time of extinction of a genus could be reasonably well predicted based on the time it reached its maximal geographic range.

But these are really small suggestions that I think will increase the impact of the paper; they do not reflect the analytical quality of the work. I think minor changes to the text are all that are needed, and I look forward to seeing this paper published.

--Michael Foote


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: ENFORCED SYMMETRY: THE NECESSITY OF SYMMETRIC WAXING AND WANING
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: As I mentioned in my previous review there are lots of methods that estimate macroevolutionary parameters without averaging, which I think deserve being mentioned here. In particular, most of the methods to estimate origination and extinction rates are *not* based on the procedure described in the section of the paper titled: “The Way Data are Processed”. That procedure has indeed been used to describe rise and fall of species and occasionally the rise and fall of clades. However, most methods to infer diversification dynamics do not rely on such procedure: e.g. Alroy 2014 Paleobiology, Foote 2001 Paleobiology, Silvestro et al. 2014 Syst Biol, Sakamoto et al. 2016 PNAS, Liow and Finarelli 2014 Proc B. I think the author should better acknowledge this in the paper, and clarify that the procedure they describe has been mostly used to describe abundancy or occupancy of taxa throughout their lifespan.

On line 285: the authors mention that in paleobiology “origination and extinction times of taxa are known”. With few exceptions of extremely well-preserved taxa, origination and extinction times are typically not known and several methods exist to estimate them.

I find that the point of the paragraph “Predicting Extinction Risk” is unclear. I suggest clarify how this links to the previous and following paragraphs.

Lines 36-46: While the PyRate method includes a hat-shaped model, the model is used to estimate the origination and extinction times of each taxon, and not to estimate origination and extinction rates, which are instead estimated under skyline model (i.e. not based on waxing and waning).


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: ENFORCED SYMMETRY: THE NECESSITY OF SYMMETRIC WAXING AND WANING
Review round: 3
Reviewer: 1

Output:
Basic reporting: I thank the authors for revising their manuscript, which I am happy to recommend for publication. If you have the chance, I would suggest that you replace the PyRate reference with a newer article that shows more clearly the effects of assuming a hat-shaped model of preservation on the estimation of species longevity as well as the skyline alternative models: DOI: 10.1017/pab.2019.23

Congratulations on the very interesting contribution.
Best regards,
Daniele Silvestro
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: L-CYSTEINE TRANSPORTER-PCR TO DETECT HYDROGEN SULFIDE-PRODUCING CAMPYLOBACTER FETUS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors developed a new molecular method using PCR to characterize Campylobacter fetus strains based on a previously reported deletion that could be associated to the production of H2S, hence affecting this phenotype that is widely used to type C. fetus subspecies using biochemical tests. The manuscript is well-structured, self-contained and literature is correctly cited. Despite I think this is a relevant work to its specific field and deserves publication, I feel that some improvements in the experimental approach and the discussion would provide more robustness and validity to these findings.
Experimental design: Major comments:

- From the 38 strains included in the study, only 4 out of them were Cfv (10%). I think authors should include more Cfv strains to avoid this bias.

- To provide a more extensive evaluation of this novel method, authors can benefit from the large collection of publicly available whole-genome sequences of C. fetus (>200). For example, screening the L-Cys transporter polymorphism among these genomes that represent an international collection of strains from different parts of the world and isolated from bovine, ovine and human hosts, would improve the robustness of the proposed PCR assay.

-  The authors focused on Cff/Cfv that are mammal-associated C. fetus subspecies. There is a third suspecies, C. fetus subsp. testudinum, that is found in humans and reptiles. Despite this represents a distant phylogenetic lineage to Cff/Cfv, the manuscript should include a comment if this L-Cys transporter polymorphism is present or not in Cft. This can be easily achieved by screening several publicly available Cft genomes.
Validity of the findings: Major comments:

- I think this study represents a valid alternative or complement to C. fetus phenotyping based on biochemical tests. However, recent studies have questioned the clinical relevance and validity of biochemical phenotyping of C. fetus subspecies. In particular, van der Graaf-van Bloois et al. (2014, 10.1128/JCM.01837-14) first describe an inconsistency of biochemical and genomic characterization in C. fetus. In this work, they revealed two main phylogenetic lineages and that strains that were phenotypically classified as
Cfv and Cfvi belonged to a single lineage, but the phenotypically classified Cff strains were dispersed among both genome clusters. I would like to see in the revised version of this manuscript, a more in-depth discussion including these aspects, specifically discussing why today biochemical tests are useful in the analysis of C. fetus epidemiology.
Additional comments: Minor comments:

- Sequencing and assembly statistics of C. fetus genomes sequenced during this study would be more clear if presented in a table or supplementary table than in the main 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: L-CYSTEINE TRANSPORTER-PCR TO DETECT HYDROGEN SULFIDE-PRODUCING CAMPYLOBACTER FETUS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Well written, clear figures, clear tables.
Missing reads in the SRA. should be made available
Experimental design: Sufficient detail. Perhaps the PCR should be tested in more labs to validate the outcome.
Validity of the findings: no comment
Additional comments: The paper by Farace et al describes the development and validation of a PCR to replace the biochemical H2S test that distinguishes C. fetus venerealis from C. fetus venerealis biovar intermedius and C. fetus fetus. The manuscript is well written, but the usefulness of a test that distinguishes two pathogenic variants of C. fetus from each other is somewhat limited, although one could arque that a negative test would immediately identify the isolate as the pathogenic subspecies venerealis instead of the presumed less pathogenic C. fetus fetus subspecies. Unfortunately the prevalence of the H2S positive C. fetus venerealis biovar intermedius is quite high in Argentina.

I have a couple of comments:

1. Please make the reads available as well on the SRA
2. Discuss the (limited) use of the test in countries with high prevalence of Cfvi
3. In how many labs was the PCR tested? Should it be the subject of a ring test? Discuss


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: L-CYSTEINE TRANSPORTER-PCR TO DETECT HYDROGEN SULFIDE-PRODUCING CAMPYLOBACTER FETUS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Improved discussion. Well written
Experimental design: I like the addition of the in silico data. Although the test has some limitations (see below) in certain countries, it is still useful.
Validity of the findings: I would like to see the sentence "This might limit its use in countries where this biovar is present." Changed to "This will limit its use in countries where this biovar is prevalent", as that is the actual situation, it is not a hypothetical situation which may occur.
Additional comments: I have just one comment, see point 3, validity of 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: PREY SELECTIVITY AND THE EFFECT OF DIET ON GROWTH AND DEVELOPMENT OF A DRAGONFLY, SYMPETRUM SANGUINEUM
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment
Validity of the findings: No comment.
Additional comments: Comments to the Authors:
The authors investigate the effect of prey selectivity and diet on growth and survival in a dragonfly species. Two prey types were presented to the dragonfly larvae, Daphnia magna and Chironomus sp., in two separate trials. Dragonfly larvae consumed less chironomids across different combinations of prey availability. Moreover, metrics for approaches, attacking, capture, and handling were determined (but did not differ). The authors found that dragonflies had lowest mortality and greater mass on the mixed diet.

This study explores an interesting and relatively understudied line of questioning. Many comprehensive aspects of behavioral responses to diet have been explored in this study. My major concerns pertain to invoking perspectives from optimal foraging and ecological stoichiometry. The Introduction section presently offers substantial insight into dragonfly behavior and fairly great amount of effort is placed on outlining open areas for research. However, the section could also benefit from elucidating those nutritional frameworks. At least for a behavioral foraging study, although diets contain energy and elements it is worth noting that energy is a property of macronutrients and that most consumers’ sensory systems are tuned into macronutrients rather than elements (Raubenheimer et al. 2009 Functional Ecology). Further, elements and energy alone do not offer insight into digestibility (Wilder and Eubanks 2010 Ecology).

The nutritive composition of prey consumption in this paper is cited generally as “quality” (e.g. Lines 57-58, 317-320, 342-343). The authors speculate that their mortality and growth findings are driven by phosphorus (Lines 323-326), but this is rather weakly substantiated. The molar ratio of phosphorus was inferred to be twice as high in cladocerans than chironomids, but this could be confounded by the greater mass of chironomids (perhaps greater total magnitude phosphorus), if there were to be selective feeding on different prey parts by dragonflies, and perhaps other factors. The energetics of the consumed prey were incomplete, as only the initial prey mass was presented. To robustly refute any explanation of energetics (optimal foraging), elements (stoichiometry), or macronutrients (geometric framework) in these trials, a table of prey nutrients would be beneficial.

The scope of this study is limited to a single consumer species collected from a single small pond within a single season. In addition to potentially being of different nutritional composition, the prey also differed in one being collected from the field (Daphnia) and the other being purchased from a local supplier (Chironomus). Competing hypotheses of prey diet effects are so far limited to a relatively high mass low phosphorus prey (Chironomus) and low mass high phosphorus prey (Daphnia). It is possible that other prey-specific factors contributed to predator growth differences (e.g. relative digestible energy, protein, chitin, etc.), but the information on these are not yet available in this paper.

Specific Comments:
1. Line 57-58: The phrases “right quality” and “resource” in this paragraph should be more nutritionally explicit. That is, predators forage for prey containing different elements (particularly C, N, P), which form the macronutrients structures selected by consumer sensory systems and those macronutrients can also in turn be combusted for energy. The explicit nutrient is highly pertinent for disentangling behavioral and physiological responses to diet.
2. Lines 93-102: From this draft, the reader cannot yet determine if the prey is nutritionally balanced (i.e. prey composition) or what the nutritional demands of dragonflies are, which potentially weakens the proposed hypotheses.
3. Lines 103- : The Methods would be strengthened/condensed with a table for the prey composition (i.e. masses, element molar ratios, macronutrients, and energetics). At present, the only possible dietary comparison between the prey types from the Methods section is total dry mass.
4. Line 119: Fully randomized diet grouping was likely more effective than a lack of pre-determined scheme, but a sized-matched randomization scheme (i.e. aligning predator masses or lengths) could perhaps have more fully interspersed size-dependent variation across treatments.
5. Lines 168-170: Similar to the previous comment, it is not yet apparent that the variation in sizes and/or developmental stages of dragonfly larvae were interspersed between the treatment groups.
6. Lines 259-270: Pertaining to optimal foraging and energetics, besides mass it is also likely that the Daphnia magna contained a greater relative amount of energy than Chironomus (e.g. Cummins and Wuycheck 1971 Int. Ver. Theor. Angew. Limno. Verh.)
7. Lines 323-326: Given that the two prey types were effectively equivalent in most predation metrics following conditioning, the influence of nutrients seems to be particularly important in seeking explanations for long-term growth and mortality differences. The authors seem to be referencing the growth rate hypothesis (Elser et al. 1996 BioScience) when outlining the C:N:P of prey and this could explain growth differences between the Daphnia and Chironomus populations. However, this framework offers limited insight into predator growth without some understanding of the predator’s body composition and/or recycling.
8. Lines 326-328: This statement is broadly speculative. One aspect of predator fitness was investigated in this study (i.e. growth), but predictions of predator versus herbivore/prey nutrient composition have not yet been explicitly outlined (e.g. higher nitrogen composition). A series of counter-arguments against the frequently proposed predator composition/stoichiometry driving dietary selection paradigm were also provided in Wilder and Eubanks 2010 Ecology.


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: PREY SELECTIVITY AND THE EFFECT OF DIET ON GROWTH AND DEVELOPMENT OF A DRAGONFLY, SYMPETRUM SANGUINEUM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors investigate the links between short-term prey selectivity and long-term effects on fitness-related traits using S. sanguineum larvae.

The authors use clear, unambiguous, and professional language throughout while providing sufficient lit. references relative to the field and the study.
The authors results are relevant to the hypotheses; however, I have some confusion in how they interpret some of these results with regard to the prey selection experiment which should be addressed. I explain my confusion in more detail in later sections.
Experimental design: The research question is well defined. Experimental design is sound. It is stated how research fills an identified knowledge gap, especially with regards to blending short term prey selection studies and tracking the long-term effects of this diet selection. Overall, the methods described with sufficient detail, however, I have some additional questions that should be addressed:

Did you standardize the size or age of the prey? If so, explain. If not, state you did not.

Is it a selectivity index or electivity index? Both terms are used in text and on figures.

Line 172 calculated growth rate based on change in mass. Was this a dry weight on the different individuals or wet weights measured on the same individuals? You should state which is the case.

Fig. 2 The proportion of Chironomus larvae and Daphnia (the the x-axes) and different between Fig 2 A & B and Fig 2 C & D. Is the minimum proportion 0.0 or 0.2? The maximum proportion 0.8 or 1.0?

Fig. 3 how did you get dry mass of the prey consumed?

Could not find a reference to Fig. 3 in the text. If you don’t reference a figure in the text, is it important enough to be included in the main document? Perhaps in the supplementary material, or be sure to reference the figure.

Fig 4 & 5 post hoc analysis to show significant differences between treatment (labeled with letters above the data point on each figure) would be helpful in interpreting the results.
Validity of the findings: Conclusions are well stated, linked to original research questions and limited to supporting results. However, I am somewhat confused with how the authors are interpreting the prey selectivity results:

Line 195 The authors state S. sanguineum consumed more Daphnia and less Chironomus than expected based on prey availability referencing Figure 1. However, figure 2 A shows no difference in the number of Daphnia consumed between the two diet conditioning treatments. How can both of these be true? Again, the only significant results I can glean from figure 2 is that Chironomus conditioned S. sanguineum consume less Chironomus than S. sanguineum conditioned to Daphnia. Maybe I'm missing something, if so, the interpretation needs to be more clear.

Line 249 I’m not sure you can say that the S. sanguineum conditioned to Chrionomus consistently preferred D. magna, as they ate the same amount of Daphnia as the S. sanguineum conditioned to Daphnia. S. sanguineum conditioned to Chrionomus simply just ate less Chironomus. Is this not what you show in Figure 2? -- # of Daphnia consumed is not different (Fig 2A); the Chironomus conditioned treatment eat less Chironomus (Fig 2B).
Additional comments: Abstract line 26. “no effect of experience” you mean diet here, correct? Maybe rephrase

Line 29 “performed significantly worse” Line 30 “performed the best” I would rephrase to had significantly lower growth and survival or the highest growth survival rather than “worst” or “best.” This may be a trivial point but the current language does not sound particularly scientific.

Line 42 – 46 is confusing, perhaps reword to something like, “Earlier research centred around the concept of optimal foraging theory (Emlen, 1966; MacArthur and Pianka, 1966; Stephens and Krebs, 1986) focused on the importance of energy gains on prey selectivity, positing that consumers should maximise their energy intake by selectively consuming the most profitable resource, i.e., a resource which provides the highest energy intake per unit of time.”

Line 150 Authors use “experience” and “diet conditioning” interchangeably throughout the paper, are these terms different? If not, choose one. I prefer diet conditioning as it is more descriptive.


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: PREY SELECTIVITY AND THE EFFECT OF DIET ON GROWTH AND DEVELOPMENT OF A DRAGONFLY, SYMPETRUM SANGUINEUM
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The authors appear to have contributed substantial revisions since the initial round of review. That is, the authors seemed to provide much greater insight into frameworks pertinent to foraging ecology (i.e. optimal foraging, ecological stoichiometry, and the geometric framework). Moreover, the authors appear to sufficiently address concerns pertaining to experimental design, such as the size matching schema.

Inferences on the mechanisms driving the differences in predator fitness (e.g. mortality and growth rate) are still limited to differences in prey species identity and mass. Elemental, micro/macro-nutritional, and/or energetic direct measures or estimates from the literature are not yet available in the manuscript. Revisions in the Discussion and Conclusion sections reflect this concern and highlight the significance of future research delving into these potential mechanistic drivers of predator diet mixing. Again, the authors have provided significant revisions to this interesting, potentially impactful paper and I look forward reading upcoming research further disentangling prey selection and dietary effects.


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: PREY SELECTIVITY AND THE EFFECT OF DIET ON GROWTH AND DEVELOPMENT OF A DRAGONFLY, SYMPETRUM SANGUINEUM
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have revised and addressed the concerns of both authors. Therefore I recommend accepting for publication.


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

Input:
Title: RECONSTRUCTING THE ARCHOSAUR RADIATION USING A MIDDLE TRIASSIC ARCHOSAURIFORM TOOTH ASSEMBLAGE FROM TANZANIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: I have reviewed the manuscript “Reconstructing the archosaur radiation using a Middle Triassic archosauriform tooth assemblage from Tanzania” by Devin Hoffman and collogues. This is an important contribution to the field of paleontology and outlines a significant method to quantify dental form as well as thorough descriptions of a diversity of Triassic dentitions from the Manda Beds in Tanzania. This research is appropriate for PeerJ and is an exciting contribution to the field of paleontology. This work also has exciting implications for paleoecological reconstruction in extinct reptiles and will hopefully open a novel, non-destructive avenue for dietary reconstruction.
Overall, the manuscript is well written, with only minor grammatical errors. It begins with an informative introduction, which clearly provides necessary background information and outlines the primary goals of the project. Aside from a few grammatical changes outlined in attached PDF, I would suggest adding a sentence on previous work that’s used quantitative methods to address tooth shape including work by D'Amore et al. (2019), Larson et al. (2016) (who is cited later), and my own 2019 work. Around line 82 may be a potential starting point.
As for other general requirements, the manuscript is largely in line with PeerJ standards. The manuscript is structured correctly and clearly. Unless I am mistaken, the references need to be reformatted to meet PeerJ guidelines. In fact, the section is misidentified as ‘Works Cited’ as opposed to ‘References’ as in other PeerJ publications. Additionally, some references in the Works Cited are not in the manuscript (e.g., Larson and Scanlon’s work, for instance). All figures are clear and necessary, adding important information to the manuscript. Minor edits are attached on the PDF. Finally, the authors make available the raw data used in the study, which is greatly appreciated.
Experimental design: My major concern with this paper is found in the experimental design. The first is that they may be biasing the total disparity investigated by only looking at teeth that look like those that belong to known archosauriforms. This is somewhat unavoidable for a study like this and does not negate the importance of the research, but it should be mentioned at some point in the paper.
The second concern is with how size is dealt with in the analyses. Figures 5 and 6 clearly show the primary axis of discrimination is size. The disparity measurements are log-transformed, but what about the linearly analyses? The reason I think this is an important distinction is that size is a part of what shape isn’t, which is slightly confusing, but by increasing size of something you’re not changing shape. So, when size is the primary driver in morphology studies you’re not really measuring shape, just size. To address this, you should normalize the data by size, including by adding additional measurement and dividing them by tooth height or something to that effect. Similarly, in the disparity analysis, Parringtonia is broken up into large and small groups, but if the data are log-transformed it should not need to be. Other taxa are not broken up and I think that if you’re going to present the data separated then it should also be figured as a complete dataset as well. The NMDS analysis addresses this by looking at only discrete traits and I think it would be beneficial to compare this result with a size-normalized linear result.
Aside from these worries, the experimental design is excellent. The research questions and goals are well defined. The methods are clear and thorough, and, to my knowledge, the analyses are performed to a high technical and ethical standard.
Validity of the findings: All findings are presented clearly and concisely, and this work will be an important contribution once revised. All data and results are presented, and when statistically significant, highlighted. Speculation on both ecology and evolutionary theory are done carefully and well within reason. Again, my concerns are with much of the analyses summarizing tooth size and not shape, but these worries can be taken care of if size is removed from the linear data. Additionally, the conclusions should mention adaptive radiation, as much of the introduction is based on exploring this topic using Triassic archosauriforms. Otherwise, this is a great paper!
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: RECONSTRUCTING THE ARCHOSAUR RADIATION USING A MIDDLE TRIASSIC ARCHOSAURIFORM TOOTH ASSEMBLAGE FROM TANZANIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: In general, basic reporting is sound. I have made one or two suggestions of adding additional references, but the article is well-cited overall. The structure of the article makes sense, and it is clearly self-contained. I would suggest increasing the number of citations to your figures substantially, particularly when describing the tooth morphology of each taxon and unknown morphotype. Additionally, please cite specimen numbers, especially when referring to individual teeth that deviate from the typical morphology.
Experimental design: The experimental methods are well-described, and the research question is very relevant and meaningful for paleontology. It is a difficult but important task to identify proxies for the taxonomy of isolated and fragmentary fossil specimens in the absence of unambiguous apomorphies, so projects like yours have the potential to add a lot to our understanding diversity in deep time. I also suggest that you make it clearer in your introduction how this archosauriform tooth assemblage relates to the early radiation of archosaurs.
Validity of the findings: In general, results and conclusions are well written and relevant to the theme of the paper; however, I would like to see you address the relative body sizes of your known taxa. I.e., how do we know that the discrete morphospaces you identify and depict in Figures 4-8 aren't simply related to body size? Additionally, it isn't clear to me why _Parringtonia_ is split in Figure 4 but not in subsequent figures.
Additional comments: Dear Devin, Hunter, Paul, and Sterling:

This is an important contribution, and as someone who also works on lots of fragmentary and isolated specimens, I am always excited to see new methods for tracking potential hidden taxonomic diversity in the fossil record.

A few other minor issues to correct that don't really fit in the above categories:
In Figures 4, 5, 6, and 7 "Morphotype B" is mis-spelled "Morphtype B."
All of your references are not formatted correctly for PeerJ (see: https://peerj.com/about/author-instructions/#reference-format).

In addition to the points above, I have made minor editorial comments and stylistic suggestions to your manuscript, so please see the PDF attached to my review.

I'm suggesting your article is accepted once you address the minor revisions I've suggested.

Good work, and thank you for the opportunity to review your paper!

Best,
Benn


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: RECONSTRUCTING THE ARCHOSAUR RADIATION USING A MIDDLE TRIASSIC ARCHOSAURIFORM TOOTH ASSEMBLAGE FROM TANZANIA
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 made all suggested changes and the paper is greatly improved. As it stands, I think the manuscript is ready for publication!


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

Input:
Title: RECONSTRUCTING THE ARCHOSAUR RADIATION USING A MIDDLE TRIASSIC ARCHOSAURIFORM TOOTH ASSEMBLAGE FROM TANZANIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment, see previous review. All concerns were addressed by the authors in their revisions.
Experimental design: No comment, see previous review. All concerns were addressed by the authors in their revisions.
Validity of the findings: No comment, see previous review. All concerns were addressed by the authors in their revisions.
Additional comments: Dear Devin, Hunter, Paul, and Sterling,

I think your revisions look good and am recommending your article for publication.

Good work, and thanks again for the opportunity to review this!

-Benn