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

Input:
Title: A DE NOVO ASSEMBLY OF THE SWEET CHERRY (PRUNUS AVIUM CV. TIETON) GENOME USING LINKED-READ SEQUENCING TECHNOLOGY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper: A new de novo assembly of sweet cherry (Prunus avium) improves genome coverage and completeness by the authors: Jiawei Wang, Weizhen Liu, Dongzi Zhu, Xiang Zhou, Po Hong, Hongjun Zhao, Yue Tan, Xin Chen, Xiaojuan Zong, Li Xu, Lisi Zhang, Hairong Wei and Qingzhong Liu prsent data for a new sweet cherry sequencing using the "Tieton" variety. I belive that the authors need to improve the introduction of the manuscript. There are few paper that should be considered, for instance: 1) Prunus genetics and applications after denovo genome sequencing: achievements and prospects by Aranzana et al. Horticulture Research ( 2019)6 :58; Also is important to add info about organel sequencing: The complete mitochondrial genome sequence of sweet cherry (Prunus avium
cv. ‘summit’) by Yang et aL., MITOCHONDRIAL DNA PART B 2019, VOL. 4, NO. 1, 1996–1997 AMONG OTHERS. The figures and tables need to be adreess in a more wide aspect.
Experimental design: The paper present a new sweet cherry genome sequencing using two powerful tools that allow to improve the sequencing, however no much information is given for those methods: linked-read sequencing technology and the Supernova genome assembler. These tewchniques are very important for genome sequencing in plants and should be highlighted.

The research question is well defined but I stated previously it need to considerer more publication on the field.
Validity of the findings: The results are good however they should discuss and compare their results with the previos seet cherry sequencing (Shirasawa et al., 2017). This will allow to present more robust conclusions for this sequencing. Most of the genome sequencing papers in these do a deep genome sequencing wth the same species or relates, for instance: peach; sweet cherry and apple.

Anoter concern is why the do not use the supplementary data through the manuscript?
Additional comments: The english need some improvement in the manuscript and supplementary data.


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

Input:
Title: A DE NOVO ASSEMBLY OF THE SWEET CHERRY (PRUNUS AVIUM CV. TIETON) GENOME USING LINKED-READ SEQUENCING TECHNOLOGY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors submitted a new version with a new tittle: “A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology”. I would like to thanks the authors because in this new version they considered the majority of my concerns nevertheless still they are some issues with the presentation of tables and figures.
The authors need to expand their arguments in the presentation of figures and tables otherwise when they refer to a table and/or figure in the manuscript is not clear what have to be seeing.
Lane 280: “Genomic analysis using D-GENIES showed a high contig-level synteny of the Tieton genome compared to the Satonishiki genome before 196.2 Mb”. The author should review all tables and figures. All of them should say: ….of the sweet cherry cv Tieton genome compared to the sweet cherry cv Satonishiki genome….” Tieton and Satonishiki are varieties, no species. In the same lane it is difficult to understand the meaning of “before 196.2 Mb”.
Table 1, tittle: “Summary statistics of sequence data”. A tittle in a Table has to be self-explanatory. In this case: What sequence data? Of what? Then in the column of samples, How the error date can be a sample? The tables need to be more concise.
Table 2, tittle: “Comparison of sweet cherry (Prunus avium) genome assembly between cv. Tieton in the current study and cv. Satonishiki in previous study”. Should be: “Comparison of sweet cherry (Prunus avium) genome assembly cv. Tieton and cv. Satonishiki” (the authors already gave info about both genomes). The in the foot table explain the abbreviation used!
Table 3, tittle: “Distribution of repeats and unique sequences”. It not clear the tittle. What is the meaning of LINE, SINE?? Why is a – in the table?
Table 4, tittle: “Summary of the none-coding RNA analysis”. None-coding and gene number?
Table 5, tittle: “Summary statistics for protein-coding gene prediction”. Foot note: add bp; the symbol * is refer to two software??? It is not clear. One software a* and the other a + or something like that.
Table 6, tittle: “Summary statistics for functional annotation”. What is the meaning of the star??
Table 7, tittle: “Summary statistics for orthogroups analysis between annotations of Tieton and Satonishiki”. Change the tittle based in my former commentary. Also need a foot note explaining the meaning of NCBI and original (give the references).
Figure 1, tittle: “Pseudomolecule construction of sweet cherry by assigning scaffolds to seven genetic maps KS, CP, CK, AC, VG, JWF, and JWF1 are the genetic maps reported in Calle et al. 2018; Guajardo et al. 2015 ; Klagges et al. 2013 ; Peace et al. 2012 ; Shirasawa et al. 2017 ; Wang et al. 2015” . This tittle has to be changed!!! Also the order of the publications and the names should be the same.
Figure 2, tittle: “Species tree and gene family expansion analysis. A species tree were also constructed by using STRIDE , as part of OrthoFinder. A comparison was conducted using CAFÉ (version 4.2) . Compared with other plant genomes, 1,012 gene families had expanded and 3,642 gene families had contracted in sweet cherry genome”. Has to be changed!!! It is confuse. What is the meaning of the colors in the figure??
Figure 3, tittle: “Synteny analysis between the Tieton genome and Satonishiki genome Left is the draft assembly comparison and right is pseudomolecules comparison. X- and Y axes are sequences of Tieton and Satonishiki. Sequence similarity is indicated by colors”. Also need to be changed based in my former comments. Which similarity of the colors?? Nothing is explained in the text!!
It will be more informative if the authors discuss more each figure and table through the manuscript. At the moment is one phrase and in parenthesis the number of the figure and/or table.
The same arguments are valid for the supplementary data. The authors do not use that through the manuscript; only they cite them but no discussion or presentation of the data. This need to be improved, otherwise better not to add supplementary data that cannot be understood. In my former review I corrected some of them, for example the names of species always in italic. Table S2 still the same!!
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: Still, some minor issues with the English. For example lane 168: “OrthoFinder (version 2.2.7) was used to identify the orthologous genes from the thirteen plant genomes (Emms & Kelly, 2015) of the sweet cherry cv. ………”. Whys is that reference there? That reference that no describe 13 genomes!!! I will recommend to the authors to include the 13 references in the reference section of the manuscript.


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

Input:
Title: NEBULIZED DEXMEDETOMIDINE IMPROVES PULMONARY SHUNT AND LUNG MECHANICS DURING ONE-LUNG VENTILATION: A RANDOMIZED CLINICAL CONTROLLED TRIAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: Clear and unambiguous, professional English used throughout?
I checked that language is relatively clear, but some words are odd. The manuscript would benefit from language editing by either a native English speaker or a professional editor.

Literature references, sufficient field background/context provided?
Yes, I think the background section is okay.

Professional article structure, figures, tables. Raw data shared?
I consider that article structure is okay. The data, however, contain very limited information. The authors need to provide not only the outcomes, but the other related data like intraoperative crystalloid infusion doses, colloid doses, and urine output, etc.

Self-contained with relevant results to hypotheses?
I think the results are appropriate.
Experimental design: Original primary research within Aims and Scope of the journal?
Yes, I think the study is an original primary research within Aims and Scope of the journal.

Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap?
Yes.

Rigorous investigation performed to a high technical & ethical standard?
Some improvement needs to be done before acceptance.

Methods described with sufficient detail & information to replicate?
Methods are somewhat hard to understand, especially the timing of administration of dexmedetomidine.
Validity of the findings: Impact and novelty not assessed.
Negative/inconclusive results accepted.
Meaningful replication encouraged where rationale & benefit to literature is clearly stated.
Okay.

All underlying data have been provided; they are robust, statistically sound, & controlled?
No, the authors need to provide not only the outcomes, but the other related data like intraoperative crystalloid infusion doses, colloid doses, and urine output, etc.

Conclusions are well stated, linked to original research question & limited to supporting results?
The authors need to remove “safe” from the conclusion. The sample size is not large enough to evaluate side effects.

Speculation is welcome, but should be identified as such?
Yes.
Additional comments: I’d like to thank the editor giving me this opportunity of reviewing Manuscript 39127v1. The authors evaluated the effects of nebulized dexmedetomidine on oxygenation during one lung ventilation. This is a well-done study and I think the results are interesting. I have, however, several concerns.

Major concerns
1. What’s the primary outcome? What is the clinically significant difference of primary outcome used in sample size calculation (Page 10, Line 107)?

2. The timing of drug administration or outcome measuring is unclear. A figure of protocol may help readers understand the protocol.

3. The authors gave intervention before initiation of one-lung ventilation. Why PaO2 values at TLV15min are not different?

4. The authors cited Groeben’s study. The study shows that intravenous dexmedetomidine dilated the airway. Inhalational dexmedetomidine constricted the airway. The authors need to discuss about this study (Anesthesiology 2004: 100; 359–63)

5. Why the authors used inspiration pressure of 20 cmH2O instead of tidal volume of 4-6 mL/kg? I prefer tidal volume of 4-6 mL/kg (Can J Anaesth. 2014: 61; 1103-21).

6. Randomization, blinding, or generalizability are not properly stated. Please revise. (Supplemental Files 3)

7. Raw

Minor concerns
1. Inclusion criteria are odd. Is the criteria determined before initiation of study?

2. The authors need to show actual P value.

3. The discrimination of the adverse events is poor.

4. The data, however, contain very limited information. The authors need to provide not only the outcomes, but the other related data like intraoperative crystalloid infusion doses, colloid doses, and urine output, etc.


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: NEBULIZED DEXMEDETOMIDINE IMPROVES PULMONARY SHUNT AND LUNG MECHANICS DURING ONE-LUNG VENTILATION: A RANDOMIZED CLINICAL CONTROLLED TRIAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: 'no comment'
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: I would have liked them to work on graphs and not just tables, since it is a more illustrative way of showing the results.

The authors present an interesting study with immediate clinical applications.
The hazgos are relevant and very interesting from the clinical point of view, but also in the basic sciences.
It would be interesting to be able to know the mechanisms involved in reducing the dose of propofol, due to the serious problems of reperfusion after a general anesthesia.


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: NEBULIZED DEXMEDETOMIDINE IMPROVES PULMONARY SHUNT AND LUNG MECHANICS DURING ONE-LUNG VENTILATION: A RANDOMIZED CLINICAL CONTROLLED TRIAL
Review round: 2
Reviewer: 1

Output:
Basic reporting: Double check figures and tables
I checked that figures and tables have been appropriately manipulated.

Open the raw data
The authors improved data. But, I think adding data of tidal volume helps the readers to understand the data.

English language check
The authors improved language.

1. Basic Reporting
Clear and unambiguous, professional English used throughout?
The authors improved language.

Literature references, sufficient field background/context provided?
Yes.

Professional article structure, figures, tables. Raw data shared?
I consider that article structure is okay.

Self-contained with relevant results to hypotheses?
I think the results are appropriate.
Experimental design: 2. Experimental design
Original primary research within Aims and Scope of the journal?
Yes, I think the study is an original primary research within Aims and Scope of the journal.

Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap?
Yes.

Rigorous investigation performed to a high technical & ethical standard?
Some improvement needs to be done before acceptance.

Methods described with sufficient detail & information to replicate?
Yes.
Validity of the findings: 3. Validity of the findings
Impact and novelty not assessed.
Negative/inconclusive results accepted.
Meaningful replication encouraged where rationale & benefit to literature is clearly stated.
Okay.

All underlying data have been provided; they are robust, statistically sound, & controlled?
The authors improved data. But, I think adding data of tidal volume helps the readers to understand the data.

Conclusions are well stated, linked to original research question & limited to supporting results?
Yes.

Speculation is welcome, but should be identified as such?
Yes.
Additional comments: 4. General comments
The authors evaluated the effects of nebulized dexmedetomidine on oxygenation during one lung ventilation. This is a well-done study and I think the results are interesting. I think some improvement need to be done. The actual P values need to be reported.

Major concerns
None.

Minor concerns
1. What is the clinically significant difference of PaO2 used in sample size calculation (Page 11, Line 138)?

2. I think adding data of tidal volume helps the readers to understand the data.

3. I do not understand the sentence “150 patients with were undergoing elective thoracoscopic surgery”.

4. The actual P values need to be reported (Page 11, Line 153- Page 12, Line 154).

5. I do not understand the sentence “Vibrating mesh nebulizer unit before the already anesthetized patient” (Page 23, Figure 2).


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: TRANSITIONAL EVOLUTIONARY FORMS IN CHASMOSAURINE CERATOPSID DINOSAURS: EVIDENCE FROM THE CAMPANIAN OF NEW MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: I very much enjoyed reading the authors’ paper describing new chasmosaurine taxa from the Campanian of New Mexico, and stratigraphic trends in chasmosaurine clades over time, and applaud the authors' hard work and efforts. The new taxa are stratigraphically and morphologically intermediate to Pentaceratops and Anchiceratops, and the authors make a compelling argument that this represents morphological evolution over time. This paper contributes greatly to our understanding of chasmosaurines in Laramidia and provides several new avenues of research. The paper is well-written, organized, and illustrated, and it was an absolute pleasure of mine to review it.

I do have some minor critiques, which should be addressed before acceptance. I have included an annotated version of the manuscript, showing my comments in yellow sticky-notes. I also have some additional comments on the supplementary material (see below).

My general critique is that the stratigraphic trends outlined by the authors for chasmosaurines in the Dinosaur Park Formation (Chasmosaurus belli, C. russelli, and Vagaceratops irvinensis) are too simplified, and do not reflect the stratigraphic positions of specimens as given in Campbell et al. (2016, 2019). In Campbell et al. (2019), I assign two specimens (YPM 2016 and TMP 2009.034.0009) as basal members of the Vagaceratops lineage, and these specimens lie stratigraphically below some or all C. belli specimens (ROM 843 and CMN 2245), indicating that these two taxa arose via cladogenesis, not anagenesis as the authors propose. Also, the gradual lateral expansion of the epiparietal 1 locus moving from C. russelli to C. belli, as proposed by the authors, is not supported by the stratigraphy of specimens, as CMN 2245 (C. belli) has a modest-sized, unadorned epiparietal 1 locus, and occurs stratigraphically above ROM 843 (C. belli), which has a laterally-expanded epiparietal 1 locus. I agree with the authors that C. russelli, C. belli, and V. irvinensis are all closely-related , but the stratigraphic data suggests a cladogenetic (not anagenetic) origin for these taxa.

Below are my comments for the supplemental material.

Figs. S10, S13, S14:
“sealyi” should read “sealeyi”

Fig. S11:
“BMNH 4948” should read “NHMUK R4948”

Fig. S16:
“NMC 491” should read “CMN 491”

Fig. S18:
 	I agree with the authors’ interpretation (Supp. Info. 1 file) that the epiparietal on the posterolateral corner of the parietal in specimens that have more than 3 epiparietals (e.g., epiparietal 5 in Vagaceratops, YPM 2016, and Kosmoceratops) is most likely evolutionarily derived from the epiparietal 3 seen in more basal taxa that only have 3 epiparietals; and that the only reason why the posterolateral corner epiparietal in Vagaceratops and YPM 2016 is referred to as “epiparietal 5” and not “epiparietal 3” is simply because additional epiparietals have subsequently appeared between it and the midline of the parietal. In light of this, I understand the authors’ point-of-view in wanting to designate “epiparietal 3” as the epiparietal that occupies the posterolateral corner of the frill, regardless of how many epiparietals are visible on a given specimen.
 	I can also understand the authors’ point-of-view that these two additional epiparietals may have emerged via the elongation of the epiparietal 1 locus, as some C. belli specimens (e.g., CMN 491, ROM 843) have what appears to be a laterally extensive epiparietal 1 locus. However, looking at the stratigraphy of only C. belli specimens (see Campbell et al., 2016), the epiparietal 1 locus does not increase laterally over time, as ROM 843 occurs below CMN 2245, the latter of which has only a modest-sized, unadorned epiparietal 1 locus (see Fig. 16 of Campbell et al., 2016). Also, the stratigraphic trend proposed by the authors, wherein C. belli is replaced stratigraphically with V. irvinensis, is not supported by the stratigraphic data presented in Campbell et al. (2016, 2019). YPM 2016 and TMP 2009.034.0049 – specimens identified by Campbell et al. (2019) as being basal members of the Vagaceratops lineage – occur below either all C. belli specimens (in the case of YPM 2016) or some C. belli specimens (in the case of TMP 2009.034.0009). As the authors point out in Supp. Info 1 file, there is some uncertainty over the stratigraphic position of YPM 2016. This uncertainty is addressed by Campbell et al. (2019), who say that the Bearpaw Formation (and Lethbridge Coal Zone) are not exposed anywhere near the site that yielded YPM 2016, so the specimen’s purportedly close stratigraphic position below those horizons (as written in the original field notes) appear somewhat dubious; instead, Campbell et al. (2019) consider the quarry identified in the 1930’s (which is located in a geographic location consistent with the original field notes) as being the YPM 2016 site, which occurs much lower in section. But, apart from YPM 2016, the stratigraphic overlap of C. belli and the Vagaceratops lineage is further supported by the relatively low stratigraphic position of TMP 2009.034.0009 relative to the C. belli specimen CMN 2245.
	I confess that I haven’t seen Kosmoceratops skulls in-person, so I can’t comment on the location of the parietal-squamosal suture. However, I think that the authors’ placement of this suture (i.e., such that each side of the parietal has 5 epiparietals and not 3, as originally proposed by Sampson et al., 2010) is much more convincing than that described by Sampson et al. (2010), who concluded that the squamosal wrapped around the back of the frill, which I’ve always had trouble believing.
 	As for the origin of the two additional epiparietals in Vagaceratops, YPM 2016, and Kosmoceratops, the loci underlying the epiparietals in these specimens are admittedly obscured, making it difficult to say whether the medialmost 3 epiparietals rest on separate loci, or one continuous, elongated epiparietal 1 locus. I believe that AMNH 5402 can shed some light on this. In this specimen, three epiparietals are present on each side, occupying homologous positions as epiparietals 1, 4 and 5 in Vagaceratops (Campbell et al., 2019). Epiparietal 1 in this specimen sits on its own, low-relief, comparatively-sized locus, and between epiparietals 1 and 4 lie two additional, low-relief loci, occupying homologous positions as epiparietals 2 and 3 in Vagaceratops. So, if AMNH 5402 represents a basal member of the Vagaceratops lineage (as I interpret in Campbell et al., 2019), this would indicate that the 3 medialmost epiparietals in Vagaceratops are attached to their own, separate loci.


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: TRANSITIONAL EVOLUTIONARY FORMS IN CHASMOSAURINE CERATOPSID DINOSAURS: EVIDENCE FROM THE CAMPANIAN OF NEW MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper is generally well-written, using clear language throughout, although I have numerous grammatical suggestions (and other considerations) that are given in the attached ms markup. Covering as much ground as it does (naming of two new species, chasmosaurine taxonomy and phylogeny, heterochrony, and biogeography), the paper is really quite long, and although I typically appreciate more detail than less, I found it a difficult read because I was not always able to follow all of the different threads of discussion through the manuscript. Since the two newly erected species have bearing on the authors' proposed anagenetic lineage from Pentaceratops to Anchiceratops, my strongest suggestion might be that the authors focus on this topic, rather than trying to address every detail of chasmosaurine phylogeny and biogeography, which are better saved for a separate paper.
The manuscript also suffers from not being current with the literature (likely a result of fact that this paper stems from a dissertation written some years ago). A few omissions stand out: (1) James Campbell's recent work on the Chasmosaurus belli-irvinensis transition, which contradicts the hypothesis of anagenesis between these species (Campbell et al. 2019. Vertebrate Anatomy Morphology Palaeontology 7:83-100); (2) my own work on the status of Pentaceratops "aquilonius" (Mallon et al. 2016. PLOS ONE 11:e0154218); (3) a couple of recent papers on ontogeny in non-Triceratops chasmosaurines (Mallon et al. 2015. Zoological Journal of the Linnean Society 175: 910-929; Currie et al. Journal of Vertebrate Paleontology 36:e1048348). I would also strongly discourage Fowler and Freedman-Fowler from citing the Longrich F1000 manuscript. This is an online pre-print that was never formally published because it did not pass peer review. As such, the taxa named therein (and repeated here; e.g., Chasmosaurus "priscus") are invalid.
Experimental design: I think the most serious issues with this manuscript are with the experimental design.
First, I am uncertain about the application of geometric morphometrics here. The authors have decided a priori that the most interesting variation is in the parietal embayment and epiparietal orientation (something I don't necessarily disagree with). Therefore, they design their analysis to capture strictly these sources of variation and find that... their specimens differ in those very features they chose to look at. This approach seems almost tautological to me, unless I am missing something, in which case, I hope the authors will clarify. I think simply illustrating the frills in stratigraphic succession is enough to make the authors' point re: the linked changes in frill morphology. The abstraction of (half) frill shape through landmarks unnecessarily confuses the matter.
A still bigger issue is with the phylogenetic analysis. It's really obvious from the outset that Fowler and Freedman-Fowler have decided a priori on their phylogeny of choice, which is one divided into clades leading to Kosmoceratops, Anchiceratops, and Triceratops. And yet, when their phylogenetic analysis rejects their preferred topology (contrary to what they state in lines 877-879, but consistent with what they state in lines 1115-1116), the authors effectively ignore the results and blame the working matrix for being inadequate. To be sure, I agree that there are issues with the current working matrix, but if the authors are going to basically ignore the outcome of their analysis because it does not support their pet hypothesis, then I don't see the point of doing a cladistic analysis at all.
A couple of other issues with the cladistic analysis: If the authors are going to go there, I would be curious to know the CI and RI statistics and how these compare with published analyses. It is also disappointing to see that some taxa (e.g., Regaliceratops, Spiclypeus) were not coded into the cladistic analysis. These are both based on relatively complete skulls, and were published a few years ago now. I would love to know how they fit into the authors' preferred phylogenetic scheme, since I'm not sure they fit comfortably into any of their three envisioned clades.
Lastly, Fowler and Freedman-Fowler make the case that many of the medialmost epiparietals in Vagaceratops and Kosmoceratops are outgrowths of the ep1 locus, as evidenced by Chasmosaurus belli YPM 2016. However, this specimen was recently described by Campbell et al. (cited above), and they identify discrete epiossifications along the parietal, rather than simply "an elongate ridge" in the ep1 position. The authors need to address this disagreement because, as they note, it affects the coding of 17 characters in their cladistic analysis, which throws the whole exercise into question.
Validity of the findings: Strictly speaking, the conclusions do not follow from the results because the authors' preferred set of relationships among chasmosaurines does not follow from their own cladistic analysis. However, I'm generally on board with what the authors are trying to do, here. I accept that they have found new species. I applaud their otherwise taxonomically conservative approach. I find the hypothesis that there exists a lineage from Pentaceratops to Anchiceratops, where the parietal embayment gradually closes, intriguing. I just don't think their methodological approach is justified.
It's hard to know where to go from here. If Fowler and Freedman-Fowler think the anagenetic relationships they propose are better than the topology(-ies) returned by recent cladistic analyses, perhaps they could use cladistic modeling to determine how many more steps it would take to recover their preferred topology, and to identify which problematic characters (I'm sure there are many) are leading chasmosaurine researchers astray. Perhaps we should be weighting frill characters over, say, horncore characters? I think these approaches would be much more informative than simply running an updated working matrix and then ignoring the results.
Additional comments: I anticipate that implementing even some of my comments will require a lot of re-writing, but I think the gist of what Fowler and Freedman-Fowler are trying to do is warranted, and will help invigorate systematic investigations of Chasmosaurinae again. For this reason, I recommend publication pending major revisions.


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: TRANSITIONAL EVOLUTIONARY FORMS IN CHASMOSAURINE CERATOPSID DINOSAURS: EVIDENCE FROM THE CAMPANIAN OF NEW MEXICO
Review round: 1
Reviewer: 3

Output:
Basic reporting: Flawless.
Experimental design: Perfectly acceptable.
Validity of the findings: No comment
Additional comments: I recommend acceptance of this manuscript for publication in PeerJ as is.  This paper adds greatly to the discussion of chasmosaurine radiation and morphological evolution and will be welcomed by the ceratopsid working community, the paleontology community in general and the general public.  I do not agree with everything the authors propose, but this paper will further discussions regarding taxonomic validity and provincialism.  As far as grammar, anatomical nomenclature, figures and captions, I have never reviewed a paper that is this flawless in its first iteration.  The authors are to be commended.  In summary, I think this is a great paper that will generate a lot of interest in the ceratopsian worker community.


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

Input:
Title: TRANSITIONAL EVOLUTIONARY FORMS IN CHASMOSAURINE CERATOPSID DINOSAURS: EVIDENCE FROM THE CAMPANIAN OF NEW MEXICO
Review round: 2
Reviewer: 1

Output:
Basic reporting: Clear and unambiguous, professional English used throughout. Literature references, sufficient field background/context provided. Professional article structure, figures, tables. Raw data shared. Self-contained with relevant results to hypotheses.
Experimental design: Original primary research within Aims and Scope of the journal. Research question well defined, relevant and meaningful. It is stated how research fills an identified knowledge gap. Rigorous investigation performed to a high technical and ethical standard. Methods described with sufficient detail and information to replicate.
Validity of the findings: All underlying data have been provided; they are robust, statistically sound, and controlled. Conclusions are well stated, linked to original research question and limited to supporting results.
Additional comments: I appreciate the changes the authors made to acknowledge differing interpretations of anatomy and stratigraphic positions of specimens, including those presented in Campbell et al. (2016, 2019). Not to belabour the opinion presented in Campbell et al. (2019), but the quarry which they believed to have yielded YPM 2016 doesn’t directly contradict the original field notes for this specimen, as the geographic location of the supposed quarry is consistent with the geographic location given in the field notes, and in that broad area of badlands the Bearpaw Formation is not exposed at all, making it most likely that YPM 2016 wasn’t collected near the base of that unit; anyways though, I’m happy to agree to disagree about the stratigraphic position of this specimen.

 	I also appreciate that the authors don’t rule out the possibility of cladogenesis amongst chasmosaurines from the Dinosaur Park Formation, due to possible stratigraphic overlap between different taxa. Like the authors, I believe it’s possible that a population of “C. russelli” (i.e., excluding C. russelli holotype) could give rise to C. belli, and C. belli to C. irvinensis, and possibly even C. irvinensis to Kosmoceratops richardsoni (given the new squamosal/parietal interpretation given by the authors for the latter), but given that there appears to be some stratigraphic overlap between these taxa, cladogenesis can’t be ruled out for these taxa. As the authors say, regardless of whether these taxa arose via cladogenesis or anagenesis, this doesn’t change the overall morphological changes that occur over geological time. As the authors say, more specimens are needed to better understand the stratigraphic and evolutionary relationships of these taxa.

 	In my first review of this paper, my understanding was that the authors suggest that the parietal locus underlying epiparietal 1 (in Chasmosaurus specimens with three epiparietals on each side of the frill) expands laterally over evolutionary time, and that two additional epiparietals appear on this ridge, for a total of five epiparietals on each side of the frill (as in Vagaceratops, YPM 2016, and AMNH 5402, and likely Kosmoceratops too as the authors suggest). In my first review, I sided with the authors’ interpretation that the large epiparietal on the posterolateral corner of taxa/specimens with five epiparietals (i.e., “epiparietal 5”) is most likely derived from the large epiparietal on the posterolateral corner of Chasmosaurus specimens with three epiparietals (i.e., “epiparietal 3”); for these reasons, I understand the authors’ interpretation of these corner epiparietals as being evolutionary homologous elements. I think this is a reasonable explanation. As the authors say, demonstrating the homology of particular epiparietals between basal chasmosaurines (e.g., Chasmosaurus) and triceratopsins is more difficult, given that the epiparietals in the latter (e.g., Triceratops) are fairly uniform in size and shape, that there is no distinct posterolateral corner of the frill (e.g., Triceratops), and there’s a median epiparietal (as in Triceratops and Regaliceratops) – perhaps this epiparietal arose from the conjoining of the medialmost pair of epiparietals?

 	In the original draft of the authors’ paper, my understanding was that the authors were proposing that the epiparietal 1 locus expands laterally over evolutionary time, and that additional epiparietals (i.e., “epiparietals 2 and 3” in taxa/specimens with five epiparietals) subsequently develop on top of it. In my first review, I presented a counter-argument that there appear to be separate loci for “epiparietals 2 and 3” in AMNH 5402 (Chasmosaurus sp., a specimen which Campbell et al. 2019 interpret as having loci for five epiparietals). I made this counter-argument to show that the three medialmost epiparietals (i.e., “epiparietals 1, 2, and 3”) in taxa/specimens with five epiparietals may not necessarily be borne on a single, elongate locus – which the authors were proposing. In the authors’ rebuttal letter though, the authors’ say that it doesn’t matter whether the three medialmost epiparietals are borne on a single elongate locus or on separate loci, and that the take-home part of their hypothesis is that the two additional epiparietals seen in Vagaceratops, YPM 2016, AMNH 5402, and Kosmoceratops likely developed along the part of the parietal between the midline and “epiparietal 2” of Chasmosaurus. I understand now that the authors aren’t wedded to the idea that the three medialmost epiparietals are necessarily borne on a single elongated locus, but they weren’t explicit about this in the original draft of their paper, so their “frustration” with my (and Reviewer 2’s) misunderstanding of this is a bit unfair. Anyways, I thank the authors for clarifying their stance on this.

 	I’m happy with the changes made by the authors, and recommend the paper for acceptance, after the following changes are made. These are all very small fixes that will improve the consistency and clarity of the paper. Points 11 through 17 are points that I made in my first review which weren’t implemented but should be.

1) “and” needs to be added to the list of authors for the following references in the references section: Currie et al. (2016), Holmes et al. (2020), Mallon et al. (2016).

2) Line 172: change “indet..” to “indet.”. Also change “sp..” to “sp.” in lines 994 and 1073.

3) Line 251: space needed within “C.russelli”.

4) Line 624: change “Figures” to “Figs.”, since in brackets. Same thing on Line 943. Also, change “Figure” to “Fig.” in lines 998, 1011, 1076, and 1132.

5) Line 954: “Anchiceratops” should be italicized.

6) Line 1242: add comma after “However”.

7) Line 1311: add comma after “Consequently”.

8) Line 1327: change “ie.” to “i.e.”

9) Line 1356: change “fenstrae” to “fenestrae”.

10) In the paragraph before the Discussion section, “Campbell (2015)” should be added to the list of references of newly described chasmosaurine taxa, since Judiceratops is rediagnosed in that paper.

11) Descriptors like “upper” “late”, etc. preceding stages (e.g., Campanian) should be lower case. Some were fixed, but not all of them.

12) Under “Institutional Abbreviations”, states/provinces are given in some cases but not in these – need to be consistent.

13) “Campbell et al. (2016)” is cited in text but needs to be added to the references section. Conversely, “Campbell et al. (2013)” appears in the references section but isn’t cited in text (please remove from references section). Also, “Campbell (2015)” needs to be added to the references section.

14) In the “Locality and Stratigraphy” section of “Navahoceratops sullivani”, still need to say that the “uppermost local coal” is the uppermost coal bed of the Nehnahnezad Member. Also, in “Diagnosis”, still need to specify which specimens you’re referring to that have parietal posterior bar angles of 87 or 88.

15) Some changes still need to be made to Figure 1. The river names are difficult to read – the font should be changed from blue to black. The rivers are also hard to see – a thicker, darker blue line would be easier to see. Also, a white square should be placed underneath the state map in the bottom left corner so that it’s distinct from the rest of the map; the state map is particularly confusing where it is since a river flows through it. Also, “Denazin” appears in the caption and the legend, yet this member is spelled “De-na-zin” elsewhere in the paper.

16) A lithology legend still needs to be added to Figure 2. Abbreviations for members also need to be included in the caption; alternatively, to save space, maybe these member names can be added to the figure itself by connecting an arrow between the stratigraphic interval and the full name beside it?

17) In Figure 10, “Bearpaw Shale” still needs to be changed to Bearpaw Fm”.

I congratulate the authors on all of their hard work and I look forward to seeing the final published version. I think this paper will generate good discussion amongst other researchers in the field, and will advance our understanding of the morphological evolution of chasmosaurines. I also thank the authors for the opportunity for me to review it.

Sincerely,

James Campbell


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: TRANSITIONAL EVOLUTIONARY FORMS IN CHASMOSAURINE CERATOPSID DINOSAURS: EVIDENCE FROM THE CAMPANIAN OF NEW MEXICO
Review round: 2
Reviewer: 2

Output:
Basic reporting: See General Comments.
Experimental design: See General Comments.
Validity of the findings: See General Comments.
Additional comments: I'm generally satisfied with the changes that the authors made, although these pertain mainly to my minor concerns. I still have to respectfully (but strongly) disagree with the authors about not re-focusing their manuscript on that lineage containing the two new taxa they are describing (Pentaceratops --> Anchiceratops). The authors argue that reviewing chasmosaurine relationships more broadly provides better context, but I really think it does so at the expense of comprehension (causing the reader to miss the forest for the trees). I think that, where specific character coding issues have broader implications for chasmosaurine cladistics, those might be pointed out in the Discussion, but the reevaluation of the Chasmosaurus lineage is best explored in another focused paper (like the planned paper on the Oldman Fm Chasmosaurus). I suspect this is an issue on which we'll have to agree to disagree, and the editor and authors can do with my suggestion what they wish.

Re: the landmark analysis (which I still think isn't very helpful, but will concede the point), I did not mean to imply that the authors re-do the analysis using entire (rather than half) frills. Rather, I think it would be helpful if, instead of illustrating half frills in their Fig. 8 warp grids, the entire frill could be shown. Is this possible? Maybe using outline drawings? The grids themselves are very difficult to interpret, and could be relegated to the Appendix.

Drs. Fowler and Fowler-Freedman disagree with me about the support that their cladistic analyses offer their hypothesized relationships (Penta --> Navajo --> Termino --> Anchi), stating:
"The only part of the phylogenetic analysis that doesn't fit the lineage hypothesis is that Coahuila, Penta & Utah form their own clade, rather than forming stem taxa leading up to Navajo, Termino, and Anchi + Triceratopsini. So it's not perfect, but then the results of phylogenetic analysis are phylogenetic hypotheses:  A cladogram is not data, and if it does not match specimen data (stratigraphy, ontogeny or morphology) then it can be treated as suspect."
I agree with them that a cladogram is not data. But a cladogram is based on data (in this case, morphological data), and these data most parsimoniously unite Pentaceratops with Coahuilaceratops, Bravoceratops, and Utahceratops; not on the branch leading to Anchiceratops and beyond. The common ancestor of Penta + Anchi may well have had an embayed parietal, and this might have eventually given rise to the condition seen in Anchi. But the morphological data (ALL of the data, not just a select few frill characters) do not support a direct line of relationship between Pentaceratops and Anchiceratops. This needs to be addressed.
For what it's worth, I do think that the idea that the 'butterfly' ep1s of Anchiceratops resulted from the 'zipping up' of the parietal embayment of something like Pentaceratops is an intriguing idea worth publishing.

Since he has taken up the mantle, I will leave the issues with coding Chasmosaurus epiparietals in the capable hands of fellow reviewer James Campbell.

Since, to my mind, my major concerns still stand, I can't help but stick with my original assessment of 'major revisions' (sorry to be a spoil sport). I'll leave it with our dear editor to decide on the validity of my arguments. If I'm deemed out to lunch, I promise not to throw a fit.


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: TRANSITIONAL EVOLUTIONARY FORMS IN CHASMOSAURINE CERATOPSID DINOSAURS: EVIDENCE FROM THE CAMPANIAN OF NEW MEXICO
Review round: 3
Reviewer: 1

Output:
Basic reporting: See general comments.
Experimental design: See general comments.
Validity of the findings: See general comments.
Additional comments: I thank the authors for incorporating my revisions. The only remaining item I would like them to do is to change "Campbell (2014)" to "Campbell (2015)". This paper (Judiceratops re-evaluation) was first published online in 2014, but was eventually placed into the 2015 volume (volume 52). Please update.

I thank the editor and authors for the opportunity to review this paper. I congratulate the authors on all of their hard work and look forward to the final published version.

Sincerely,

James Campbell


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

Input:
Title: ASSESSMENT OF METHODS USED FOR 3-DIMENSIONAL SUPERIMPOSITION OF CRANIOFACIAL SKELETAL STRUCTURES: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: •	The article is well-written; all sections of the article are clearly written, and the message to the reader is direct. English language is professional and fluent.
•	The “Title” is short, accurate and provides the reader with a direct message of what to expect.
•	The literature is well referenced and relevant.
•	Figures and Tables are relevant, well-designed, of high quality, well labelled and described.
•	The supplemental Materials (“Appendix_1”, “PRISMA_Checklist” and “Rational_for_the_study” file) are informative and support the validity of the article.
•	Please spell out numbers at the start of sentences [e.g. line 176: Twenty-four instead of 24, line 190, line 200, etc.]. It would be better to add an introductory word or phrase, or even rephrase the sentence, so that you can avoid spelling out a large number [e.g. line 174: “2’540 studies…].
•	Maybe the term “Bibliography” could be replaced by the term “References” concerning the corresponding section.
Experimental design: •	The research question is well-defined. The “inclusion/exclusion criteria” are well-established. All key components prior to starting the review have been decided and rigorously cited (i.e. studies included, study sample, types of participants, type of intervention, primary outcome, comparator/control group etc.). Methods were described with sufficient detail and information to replicate.
Validity of the findings: •	All underlying data have been provided, they are informative and support the validity of the results.
•	The development and run of the electronic searches are meticulously described in the “Appendix_1” file. A comprehensive list of the key terms, related to each key component is present, ensuring that all relevant trials were identified.
•	The selected databases were screened by two authors, and discussed between all authors until a consensus was reached, thus establishing inter-rater reliability.
•	Thorough analysis and interpretation of the results was conducted.
•	The conclusions are well-stated, they are linked to the original research question and summarize the outcomes of the study.
Additional comments: No additional comments


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

Input:
Title: ASSESSMENT OF METHODS USED FOR 3-DIMENSIONAL SUPERIMPOSITION OF CRANIOFACIAL SKELETAL STRUCTURES: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: - The authors have submitted an overall well written and well conducted systematic review.
- The literature review is sufficient and supports performing this review.
- Lines 58-60: Text needs to be revised here. The authors briefly mention the advantages of 3D over 2D but are emphasizing head positioning, which is less relevant to the topic of superimposition. The text here does not offer much to the manuscript.
- Lines 60-62: This text lacks citations to support what is stated. I am particularly referring to the sentence “Moreover, the handling and processing of these 3D data is more complex and expensive.” Please revise. My impression is that the authors are attempting to provide some background information on 3D imaging compared the 2D imaging. This part (lines 57-62) needs to be revised.
- Lines 65-66: Larger field of view means more radiation because anatomic structures that absorb higher amounts of radiation are included in the field of view. It would be better if this is mentioned and supported by a reference.
- Lines 66-68: The new methods that the authors are mentioning do not require a large field of few. This is indirectly related to the amount of radiation. The sentence implies that the new methods are directly related to less radiation.
- Line 74: What do the authors mean by “more comfortable” treatments?
- The authors have identified a gap in the literature and, thus, the rationale for conducting this systematic review is justified.
- Lines 147-149: Precision and sensitivity of a systematic search of the literature are by definition opposite, negatively correlated terms. Please revise wording.
Experimental design: - The research question is well defined and the search strategy is provided in detail as supplement.
- Line 97: Please replace “Pubmed” with “Medline (via Pubmed).
- The authors selected the databases recommended by the Cochrane Collaboration for systematic reviews of RCTs, in addition to Google Scholar, Grey literature and Unpublished literature. It has been suggested that the recall percentage of articles may increase by 3% if Web of Science is added to a systematic search, increasing however the NNR (number needed to read) (see: Wichor M. Bramer, Melissa L. Rethlefsen, Jos Kleijnen, Oscar H. Franco. Optimal database combinations for literature searches in systematic reviews: a prospective exploratory study. Syst Rev. 2017; 6: 245.  Published online 2017 Dec 6. doi: 10.1186/s13643-017-0644-y) Although their search strategy is very good, the authors may want to briefly discuss their selection of databases.
Validity of the findings: - The study is novel and provides very useful insights in the field of 3D  superimpositions, which are becoming increasingly relevant in clinical practice.
- The study results are thoroughly discussed and valuable implications for future research are made.
Additional comments: No additional comments


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

Input:
Title: ASSESSMENT OF METHODS USED FOR 3-DIMENSIONAL SUPERIMPOSITION OF CRANIOFACIAL SKELETAL STRUCTURES: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 3

Output:
Basic reporting: The introduction is nicely written. However does not really provide other insights compared to the systematic review done by Ponce-Garcia et al 2018.
line 52 the structural method. This is the golden standard for 2 D. So why do you mention it here? How could this be translated to 3D. What should be the golden standard for 3D? How does that compare to 2D?
I also miss a paragraph on what the problems are between non growing and growing persons.
You write that since in 3D one would not want to include for example sella because of the higher radiation dose. However you do not come back on this in your review. Did researchers find a way around it or is that why most research concentrates on the anterior cranial base.....
What would applicability include. This is something that returns often later in your manuscript. However you do not explain this.
Experimental design: The purpose of the review is really wide and it is actually logical that a previous systematic review researched mostly the anterior cranial base. See also your reference to the structural method by Björk. other areas maybe maxilla or mandible. In case you would want to do that specify. Furthermore in the systematic review you are expanding on growth versus non growth. However this was not covered in your aim.
I miss that you used the prisma reporting guidelines. Did you use them?
line 103: You are looking for evidence in a systematic review. Why would you want to include case reports opinions and other such things?
Line 105: why did you choose a study sample of 3 or more? Of course that is not an amount that you could do statistics on?
line 108: why did you choose serial craniofacial CT/CBCT? you do not write growth/non growth in your aim?
line 113 Actually in the 3 techniques you name it does mathematically not matter how you superimpose when you compare 3D distances or angles. The only way to really mathatically test whether a superimposition works is through distance kits and volume differences. So The primary outcome alone will provide a mixed bag of studeis.
line 117 I actually do not understand the comparator control group. Please make full sentences of what you mean here.
line 119 how do you now that the unit of analysis was the measured distance /angle? this excludes distance kits/tables or volumes.
line 121: this is also strange. You are also describing in your results section growth. For example Studies done in patients with craniofacial malformations should be excluded because they have a different  growth pattern.
142 heterogeneity as I understand this as done in and with the Quadas-2 tool. Please explain
146 bias as I understand this as done in and with the Quadas-2 tool. Please explain
line 162. You used the Quadas-2 tool. It requires that you make it specific to this systematic review. please explain that.
Line 166 you write  that it uses happy and sad smiles. What is in between? Does no moderate exist. What is the scale of that? Please also include that in the table (the legenda that is)
Validity of the findings: line 174 has a high ' ?
line 177 what does irrelevant mean? please explain
In the quality assessment you start now with a distinction between risk of bias and applicability concerns. Where did the heterogeneity go?
line 190 so what do you define as applicability concerns? please define
I miss any numbers in the quantitative synthesis. A statistically significant outcome maybe sub millimiter and the other way round.
I also do not understand what information I should get from these small summeries.
214 How can it be that you start out with 3 superimposition techniques while only 2 were left here (and in the Ponce-Garcia et al 2018 they did include one)
line 316 you do compare the different registration techniques but you present only 2 before hand and are reporting o 3 that is quite confusing.
Discussion.
 you refer to providing guidelines in the aim but that was probably not possible. so omit it from your aim.
line 363. Well this is logical to select the overall picture. You want to include maxilla and mandible in the systematic review as well but  I do not understand why you think that is comparable to the anterior cranial base. It depends on what part you want to focus on.
Again what are applicability concerns
Figure one. How can it be that you excluded records. You have no exclusion criteria according to your material and methods.
Table I. I do not find the explanation of reference standards or index tests. It is seen in risk og bias and applicabiliay concerns. What does it refer to? What does flow and timing mean/include?
Additional comments: I recommend that you focus your review on growing subjects or non growing subjects. When you use growing patients please distinguish between growth and result of treatment or a mixed bag.


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: IMMUNE PRIMING AGAINST BACTERIA IN SPIDERS AND SCORPIONS?
Review round: 1
Reviewer: 1

Output:
Basic reporting: Largely clear English although some areas where it could be improved to aid clarity. Suitable referencing and background.
Experimental design: Design is sound and analyses seem appropriate. Methods could do with more clearly pointing out sample size.
Validity of the findings: Useful results that help us understand how general the process of immune priming is.
Additional comments: Galvez et al provide an interesting study exploring whether there is evidence for immune priming in two different arachnids. This field is very excitign but also suffers from a large body of unreported negative results or challenging results, so I personally welcome stories that illustrate that it is complicated and may not always be there. By at large, I think the study is well conducted and should contribute to the field. I would say, that it can be tough to know why priming isn't seen, or why it isn't seen beyond the priming to wounding. I wonder, for instance, whether LPS is sufficent to induce priming in this system? Would heat inactivated bacterial challenge produce a stronger effect? But that is speculation on my part.

There are some places where writing could be tightened. eg. Sentences beginning intro (L38, L43. L59) which are a bit awkward.

I'm generally not a huge fan of titles as questions. But, that's stylistic, and the story isn't quite clear enough to definitively say yes or no.

Would like to have seen sample size more clearly in methods although it's in the figure legend and is good number of samples per treatment.

The effect of bacterial growth in media with hemolymph is a bit tougher to interpret. There are very small samples, and there might be a slight tendency for stronger inhibition in LPS and PBS injected scorpions but that's just eyeballing the data.

Generally pleased to have more data for different group of arthropods. The authors rightly point out that much of the work on priming is in insects. There are however papers on isopods, crustaceans, nematodes (which are mentioned in intro) but abstract does not suggest this (L15).

L62: wouldn't suggest that constitutive vs induced are an either or situation.

L77: (reviewed in FULL REF)
L79: bacteria at the midgut level -> bacteria in the midgut
L88: in terms of improved survival, we -> improved survival. We

L102-103: is nocturnality relevant?
L128 and around, would be good to see sample sizes here (or at least refer to fig for them?)
L137: N here too

I'm rarely in favor of tables, but here it may work. There are many contrasts with different test statistics etc. These might work a bit better as a table as it can get hard to follow.


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: IMMUNE PRIMING AGAINST BACTERIA IN SPIDERS AND SCORPIONS?
Review round: 1
Reviewer: 2

Output:
Basic reporting: The language throughout is precise and easy to follow. In some cases, prepositions are not correctly used (e.g. l51 and l53 should be “dependend on”) and there are a few typos (e.g. “ellicitor” in the abstract). The introduction gives a good background and cites the relevant literature. Maybe, some more information on the life history and lifestyle of the used arachnids could be given. Because they are non-model organisms many readers would probably need some more information. The overall structure is very clear, but the statistical results would be better presented in a table as they impede the reading. The figures are well presented. Figure 1 is missing labels at the two panels (A and B). The raw data seem to be missing. I was only able to find data for the dose response curve in the supplements.
Experimental design: The authors tested two non-model arachnids for within-generation immune priming for the first time and observed acquired immunity in scorpions but not in spiders. The experiments were thoroughly and well conducted and provide us with new insights into an underrepresented part of the field. Methods are described sufficiently.
Validity of the findings: The statistical analysis seems sound, but raw data are missing to confirm. The interpretation of the results makes sense and links back to the research question.
Additional comments: This is one of the first studies into a new field of research, i.e. priming in arachnids and therefore it is understandable that it is somewhat limited. However, I feel that the addition of a second pathogen might enable the authors to generalise their results. Furthermore, as I understand, the animals used here were individuals collected from the wild. The authors therefore do not know the animals' immunological history, i.e. the possibility of priming already happening before the experiment. Eventhough, it might not be possible to repeat experiments or to rear populations in the lab (especially given the currently ongoing pandemic), these issues should at least be mentioned in the discussion.


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

Input:
Title: IMMUNE PRIMING AGAINST BACTERIA IN SPIDERS AND SCORPIONS?
Review round: 2
Reviewer: 1

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
Additional comments: The authors have adressed all points. Everything looks good. I don't have anything to add.


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: COMPUTATIONAL ANALYSIS OF MICRORNA-MEDIATED INTERACTIONS IN SARS-COV-2 INFECTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this study, the authors have predicted through computational analyses several potential miRNAs, from SARS-COV2 that might play a role during infection.
A major concern relates to whether RNA viruses encode for miRNAs, which is a debated issue as also stated by the authors. This study should provide more support about this central point. For example, it would be useful to compare in Fig.1 the features for predicted SARS-COV2 miRNAs with those of known viral miRNAs from miRBase, in addition to the human ones. How the predictions would change by training the predictor using only features derived from the viral miRNAs ?
Some of the predicted miRNA should be experimentally validated.
Does any of the target gene of the predicted SARS-COV2 miRNAs participate to the recently characterized viral interactome (https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1), either directly or indirectly by participating to the same biological processes/pathways?
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: COMPUTATIONAL ANALYSIS OF MICRORNA-MEDIATED INTERACTIONS IN SARS-COV-2 INFECTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: Manuscript bring a set of predictions on SARS-CoV2 and human miRNAs and their targets. It is a good set of results and contribute to a yet not discussed point in the COVID-19 pandemic, but need to be much more explored in terms of mechanisms, results description, possible networks identified by epigenetic regulation. Authors should also discuss limitations on the use of antagomIRs as therapeutic "drugs".
Additional comments: The manuscript from Demirci and Adan describes a computational analysis of miRNAs mediated networks in SARS-CoV2 infection. Authors seek for viral miRNAs and correlate them with human mRNA targets. Moreover authors do the opposite, looking for  human miRNAs and their targets in viral genome.
It is a well written manuscript, with a good set of results that can only predict miRNAs interactions. It starts filling the gap in literatura about epigenetic regulation in COVID-19.
However there are some points:
1.	Abstract: the abstract is well written but it does not bring to readers the main findings of the manuscript. There is an example of STAT1 signaling but no further conclusion is presented. I suggest authors rewrite the abstract with this issue in mind.
2.	Line 41 – delete “there are”
3.	Introduction: authors make an extensively description of the origins of SARS viruses and pandemic COVI-19. This makes the introduction too long. Moreover, authors do not explore the theme “miRNAs and virus infections”. Introduction should be re-written.
4.	Methodology: it is not clear in this section, specifically “pre-miRNA prediction, the criteria used in the izMiR algorithm. Authors state they used 3 classifiers to generate scores and only 29 hairpins passed the threshold of 0.9. What does it mean? Which criteria? Why authors assume that virus miRNAs should have high similarity to human miRNAs?
5.	Results:
5.1.	30 mature miRNAs were identified in the first analysis. It would be important to show the list of these miRNAs.
5.2.	In lines 145-148 authors mention they were not able to identify similarities of the 30 selected mature viral miRNAs with human miRNAs. Maybe, it would be much more interesting if authors look for targets for these “possible viral miRNAs”. Maybe, there is no similarity with humans, but there is a correlation in sequence with mRNA targets. Indeed, authors say in line 154 that they were able to find about 1367 human targets for viral miRNAs. And they just show in table 1 some of them. What was the criteria to select only these targets? Why look at just for transcription regulators? How about control of immune response, cell signaling, etc.?
5.3.	Lines 152-154 – authors say that SARS-CoV2 ORF 1ab is the only one that might be targeted by miRNAs. Why? Has it been described elsewhere? Which result demonstrate this?
5.4.	Lines 165-168 – authors do not explore the results of figure 2 and 3. There is only a mention about them without describing the results properly.
6.	The set of results presented in this manuscript represent a good analysis of viral and human miRNAs and their targets. However, authors describe the results in a confused way. It is strongly recommended that authors reorganize results section in order to stablish two main points: (i) viral miRNAs and their targets and (ii) human miRNAs and their targets.
7.	Discussion:
7.1.	Lines 188-189 - Change the sentence “in this study, we elucidated miRNA-mediated regulation responsible for SRS-CoV2 infection...” Results presented here are much more the characterization of miRNAs and their targets related to SARS-CoV2.
7.2.	Line 191 – “…possible virulent genes…”What does virulent means?
8. Conclusion: authors should include limitation on the use o antagomIRs or miras agonists for therapeutics
Figure 2 and 3 are in low quality.
Table 2 title: predicted “viral” mRNA targets


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: COMPARATIVE STUDY OF GUT MICROBIOTA IN TIBETAN WILD ASSES (EQUUS KIANG) AND DOMESTIC DONKEYS (EQUUS ASINUS) ON THE QINGHAI-TIBET PLATEAU
Review round: 1
Reviewer: 1

Output:
Basic reporting: The quality of this manuscript is overall sound. The language is clear and well-organized, despite many trivial English which can be fixed. The Introduction and Discussion sections cited multiple literatures which are relevant to the topic to my point of view.
Experimental design: The research is original. The question is clearly defined. As authors indicated, this is the first study of TWA gut microbiome and it is helpful with the protection of this species. The Methods section contains sufficient details for readers to understand the entire protocol, though with some caveats as detailed below. The procedures are fair.
Validity of the findings: The authors shared the raw sequencing data (Fasta format). The results were sufficiently described. The conclusion was well stated based on their observations. However I have two major concerns of the validity of the results, which would require further clarification, as stated below.
Additional comments: This manuscript reports a study of the gut microbiome of Tibetan wild asses in comparison to that of domestic donkeys. The authors analyzed 16S rRNA V3-V4 sequencing data collected from fecal samples. They compared the taxonomic and functional profiles inferred from the DNA data. They found differential abundances and compositions. Based on the observations they proposed hypotheses to explain the differential physiological and ecological features of the two species, especially considering the ability of dry matter digestion.
The quality of this manuscript is overall sound. However I have the following concerns.
Two concerns are major and require the authors to carefully clarify: 1) Fig. 2B: What metric does the error bars represent (in this figure and other figures)? They look very small. However according to Fig. S3B, I doubt if they are this small, if they represent standard errors. It would also be great if the authors provide actual p-values instead of asterisks. The abundances are not very different, but the differences are significant according to the authors. The only explanation is that variance is low (as the error bars suggest).
2) Table 3: OTU118 Bromus tectorum is a plant, not a cyanobacterium. Is this a typo? Also see Line 219: “The relative abundance of Bacteroidetes, Firmicutes, Cyanobacteria, and Synergistetes ...” Either way, I want to ask the authors to double-check and clarify whether chloroplastic signals have been removed from the dataset. If not, this is a big problem because donkeys are herbivores and their fecal samples must have high plant contamination.
The following concerns are relatively minor but the authors still need to clarify seriously.
The first use of “TWA” and that of “4N HCL” in the abstract (line 21) are not explained.
The statement that “wild asses were superior to that of domestic donkeys in dry matter digestion, gut microbial community composition and function” (line 38) is not objective. One can’t assert that one microbiome is “superior” to another.
Line 143: Please state QIIME version and the main QIIME script / command used for filtering.
Line 149: Please state which SILVA release was used.
Line 155: Please state Tax2Fun version.
Line 156: Please state STAMP version.
Line 161: Please spell the full name of SE (standard error) at first usage.
Figure 1: alpha diversity: the authors should also try Faith’s PD, which is phylogenetic, since they used the phylogenetic metric UniFrac for beta diversity.
It appears to me that the distribution of alpha diversity is bimodal in both groups. What are the outliers at the low end? Why their microbiomes are so un diverse?
OTU filtering. Why the number of species can reach a few thousands? Can the authors explain?
Fig. 4B: What is “p-value (corrected)”? I guess it is FDR correction, but the authors need to clarify. In particular, which FDR-correction method was used and what was the population size (n)?
Table 1: “P valve” => “P value”
Table 3: “Unclassfied” => “Unclassified”
Line 210: “With regard to beta diversity, PCoA analysis showed that the two groups of bacterial communities differed significantly (Fig. S3A) (P < 0.05).” How was this p-value calculated? Sorry if I missed anything, but I did not see relevant description in the Methods section.
In the LEfSe analysis (line 238), all taxonomic units appear to be the same bug: Campylobacter. This is fine and I just want to note it.
Line 394: “lose” => “loss”
Line 314: “… we speculated that the lean body size of TWAs might be related to the high Bacteroidetes content in their intestinal microbiota.” This is a bold speculation, however it is not necessarily inconsistent with PeerJ’s peer-review guideline. Therefore I won’t complain but just note it to express my reservation.


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: COMPARATIVE STUDY OF GUT MICROBIOTA IN TIBETAN WILD ASSES (EQUUS KIANG) AND DOMESTIC DONKEYS (EQUUS ASINUS) ON THE QINGHAI-TIBET PLATEAU
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, the article is well-written. However, some aspects can be improved.
i) Abbreviations:
- Line 18: Add the TWAs abbreviation after “Tibetan Wild Asses”, since the abbreviation is used afterward in line 21.
- Line 220: Abbreviation used was “TWD”. Shouldn’t it be TWA?

ii) Some rephrasing
- Line 28: “the two dominant phyla of Bacteroidetes and Firmicutes”. The preposition “of” should not be used here. The whole sentence could be rewritten.
- Line 38, 79, 408 : The use of “were superior” is not suitable in the cases in which it was used. Sentences with “were superior” should be rewritten.
- Line 279: It is not clear why the word “Although” was used in this sentence.
- Lines 335 - 336: “Researchers have found that Akkermansia contains a single species”. Since more Akkermansia species may be identified in the future, it would be better if the sentence was: “Akkermansia currently contains a single known species”.

iii) Grammatical errors
- Line 25: “were” should be “was”.
- Line 31: add “in” after “higher than”.
- Line 275: “Firmicutes” was misspelled.

iv) Literature references
- Lines 309-315: Although Turnbaugh et al. 2006 found correlations in the decrease of Bacteroidetes and obesity, many recent studies have found controversial results. These controversies could be briefly addressed. The following review state many details about this theme: Castaner et al. The Gut Microbiome Profile in Obesity: A Systematic Review. Int J Endocrinol. 2018
Experimental design: - Line 119: The authors should add a reference or explanation for the use of the equation to measure Dry Matter Digestibility.
- Lines 165-177: positive/negative correlations should be explained here since it will be explored throughout the article.
- Lines 264-265: could have a brief reminder of what positive/negative correlation means.
Validity of the findings: - Lines 210-211: The PcoA analysis was based on what taxonomic rank (e.g. genus, family, phylum)? Considering the barplot based on phylum in Fig S3B, TWAs and NPDDs gut microbiota seem very similar.
- Figures 2B and 3B: It is curious that Spirochaetae and Treponema did not show significant differences between TWA and NPDD. I advise the authors to double-check this.
- In Supplemental files, the authors could add tables with mean abundances of TWAs and NPDDs taxonomic profiles, as was done for the metabolic pathways.
- Line 248: Some of the 18 gene families presented in Fig 4B don’t appear to be “remarkably different” between TWA and NPDD. In fact, some of these gene families were identified with less than 0,1% abundance (based on Table S2). Therefore, it would be good to use a minimum abundance threshold and measure the significance afterward.
- Line 332-334: The association of NPDDs having more abundance of Spirochaetes and being more likely to suffer from an intestinal disease is too speculative and should be removed.
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: COMPARATIVE STUDY OF GUT MICROBIOTA IN TIBETAN WILD ASSES (EQUUS KIANG) AND DOMESTIC DONKEYS (EQUUS ASINUS) ON THE QINGHAI-TIBET PLATEAU
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I appreciate that the authors have made dedicated point-to-point responses to my comments as well as the other reviewer’s. Both of my previous major concerns have been well-addressed. I have no more concerns and hereby recommend 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: COMPARATIVE STUDY OF GUT MICROBIOTA IN TIBETAN WILD ASSES (EQUUS KIANG) AND DOMESTIC DONKEYS (EQUUS ASINUS) ON THE QINGHAI-TIBET PLATEAU
Review round: 2
Reviewer: 2

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: I thank the authors for taking my comments and suggestions into account and I think the paper is now suitable for publication.

But I still found a few typos:

Line 235: "sinificant" -> "significant"
Line 267: "VIP" -> "P"
Line 328: "reagard" -> "regard"
Line 410: "53th" -> "53rd"
Line 418: "commubities" -> "communities"


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

Input:
Title: EVIDENCE OF OVERFISHING OF GEODUCK CLAM PANOPEA GLOBOSA FROM A LENGTH-BASED STOCK ASSESSMENT APPROACH
Review round: 1
Reviewer: 1

Output:
Basic reporting: a. Abstract line 38 – subject-verb agreement “the dynamics were (not was)” here and in other usage in the manuscript
b. Introduction line 79 - I assume that P. globosa are unable to survive initial excavation. Since the authors raise a minimum legal size here, I think it is important background information to explain how a minimum legal size would work if size cannot be determined prior to excavation.
c. Methods line 171 – I don’t understand what is meant by a “gnomonic interval”. The shortest amount of time possible to complete the stage?
d. General – can you make clear that the fishery (harvest) continued in 2013, even if the sampling program did not?
e. Results line 321 – I usually define a “harvest rate” as the amount harvested divided by the total biomass. It appears that you are reporting here a proportion that each size class represents in the total harvest amount. Or do you estimate you harvested up to half of an entire size class in one year? Please clarify.
f. Discussion line 359 – This sentence could be revised for clarity. It is unclear whether the second half of the sentence refers to geoduck or shrimp/squid.
g. Figure 6 – The reference lines in this figure correspond to 10% and 5% harvest rates. The introduction (line 80) refers to 1% and 0.5% harvest rates. Is one of them a typo?
Experimental design: a.	Methods line 144 – Can you give more detail about how sampling was randomized? Were the commercial fishers taking samples at the direction of the authors, or were the authors sampling from regular commercial harvest? Either way, how were locations, depths, etc. managed to ensure a random sample of the population and not one that follows the harvest choices of the fleet?
b.	Methods line 222 – I am confused by how the data collected were translated into measures of recruitment. Were many smaller individuals sampled in the field each year, or was recruitment back-calculated from adult growth and survival in the model, or was it reconstructed from aging? If recruitment to the fishery occurs over a range of size classes in the model, isn’t that the same as fishery selectivity of those size classes? In certain size classes, are some individuals assumed to be recruits and others not? Perhaps you can add explanation in plain language to this section to help me understand.
c.	Methods line 238 – I assume GRG stands for generalized reduced gradient (although please spell out all acronyms). I am not familiar with this method, and so my ignorance may be betrayed by my question. By using a non-linear fit in phases, is there a risk to “over-fitting” the model – so that RSS criterion is minimized but generalizability is also low? I am concerned that over-fitting could lead to large fluctuations in the output, which seems to be the case in your results.
Validity of the findings: a.	Results line 292 – I’m curious if any external validation or “ground-truthing” can be done for the estimates of biomass over time. Do you have any guess for the prefishing biomass for this area? Do the results reported (Table 3) correspond to harvest removed (2010 – 2012) and the natural mortality rate? I’m guessing they do not, given that the target harvest rates (introduction line 80) and natural mortality estimates reported are quite low, while the biomass is reduced by two-thirds in two years. Similarly, the biomass quadruples in two later years (2012-2014). That does not seem possible for a species like P. globosa – which casts doubt onto the methods used to estimate biomass. Or perhaps this expansion in biomass is due to additional harvest areas being identified?
b.	Discussion line 373 – Unfortunately I cannot evaluate the recruitment results because of my inability to understand how they were calculated. However, I enjoy the general discussion around recruitment in this genus.
c.	Discussion line 399 – I think this discussion could benefit from a clearer link between the results (harvest rate at shell length) and the conclusion that overfishing is occurring. What harvest rates at shell length would be indicative of sustainable harvest?
d.	Discussion line 410 – I don’t understand how a size limit is used in fishery management given that harvesters cannot tell size before excavation.
e.	Discussion line 453 - Given the variability in results, particularly in biomass, this line is particularly troubling “If fishers are moving the fishing effort along the latitudinal gradient and from shoreline to offshore areas, then the biomass and recruitment cannot be adequately quantified…”. I agree, and serial depletion is certainly a concern. Are fishers moving the effort or not? In particular, are the results from 2010-2012 and 2014-16 potentially different populations? If they are, does this not invalidate much of your attempt to estimate biomass using length frequencies? It seems from Figure 9 that harvest is shifting in space, but the discussion seems uncertain on this point. I also assume that moving off shore results in a deeper depth of harvest, which could have important implications, but I am not familiar with the bathymetry around Puerto Peñasco.
f.	Discussion line 462 – I like this idea of managing the high- and low-productivity regions separately.
Additional comments: This is an interesting and important study describing an attempt to detect overfishing in a data-limited, emerging fishery. I have concerns about the appropriate use of a length-based approach in a species that is long-lived and with slow and variable growth. Data on P. generosa show highly variable size with age, and I don't see evidence here that P. globosa would be much different. The length-distribution methods appear to detect large fluctuations in population biomass, which seem unlikely given the species’ life-history. A possible explanation for the results, a shift in harvest areas, is particularly concerning. It suggests that the population was not sampled randomly (although description of the methods is insufficient to tell) and that the methods may not be a good match for the conclusions. More detail and clearer explanation of the methods and their link to the conclusions will aid in evaluating this. There is certainly potential evidence that this population is being overfished or serially-depleted, and as such this could be an important contribution to science and fishery management. However, the manuscript could be re-worked substantially in order to make a clear case.


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: EVIDENCE OF OVERFISHING OF GEODUCK CLAM PANOPEA GLOBOSA FROM A LENGTH-BASED STOCK ASSESSMENT APPROACH
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: The interpretation of the analyses should be strengthened, with more explicit explanation of the evidence for overfishing.  Management recommendations should be clarified, citing the evidence presented.  The logical step at lines 456-460 needs elaboration, and specifically how the results of the presented analyses point to the rationale for rotational management needs to be clarified.
Additional comments: The manuscript presents valuable and compelling analyses of the Cortez geoduck fishery population dynamics at a specific locale in the northern Gulf of California, and conclude that overfishing has occurred at this locale.  If the authors consider the results as generalizable to the Cortez geoduck fishery, the case should be made more clearly. If they are specific to Puerto Peñasco, this information should be made explicit.
The title could be more accurate – e.g. the use of the length based stock assessment approach reveals overfishing in the species.
Introduction
Readability would be improved by reworking the paragraph at lines 94-111 as the first paragraph (more general info on stock assessments, then issues with sedentary/aggregator species as Orensanz et al outlined).  The introduction should be shorter—some of the information appears extraneous to the subject of the paper (e.g. lines 123-130, though this information could be relevant to Discussion), and some would fit better in the Discussion (e.g.
Lines 88-89—this is a good discussion point). It would serve the reader to include changes in management that have already occurred, e.g. the two species in Mexico were previously managed as one species (Aragon-Noriega et al 2012).

Subheadings in Methods and Results should be mirrored and in the same order, as appropriate, and should also be reflected in the abstract (if included there). For example, the abstract lists, in order: population changes, individual growth patterns, recruitment, selectivity, fishing mortality, and survival over time. Methods lists population dynamics, fishing mortality and selectivity, recruitment, parameter estimation, and management quantities. Results lists shell length structure, recruitment, total and vulnerable biomass, harvest rate, separable fishing mortality, and finally, selectivity.  It would greatly benefit the reader to be consistent with the organization of the manuscript.

Discussion
The first paragraph should clearly state the main finding of the work—present and interpret the evidence for overfishing of this population.  The first three paragraphs in the Discussion are about recruitment and recruitment failures, but the focus of the paper (based on the title, abstract, and introduction) is to show new evidence, from the length-based stock assessment approach, of overfishing.  The fourth paragraph of the Discussion should be expanded to include more discussion of fishing selectivity, and include criticisms of the 130 mm minimum size (Aragon-Noriega 2015; also the issue of fishery discards). Did the behavior of fishers with regard to sublegal size geoduck change over time, i.e. were they more compliant during 2010-2012 than in 2014-2016?  Were sublegal size geoduck discarded on the bottom and not reported? A comparison with other fisheries that are likewise vulnerable to serial depletion would be warranted here.  Management implications of the size limit, especially given that in some areas the modeled asymptotic size is below 130 mm, would also be valuable to include.

The Discussion paragraph on fishery management should closely follow the stated purpose of the study “is to analyze the effects of fishing pressure on the population of the geoduck clam, Panopea globosa, in the upper Gulf of California.”  While the shortcomings of the current management strategy are outlined (although it should also be noted that P. globosa and P. generosa were managed as a single species, Aragon-Noriega et al. 2012), the interpretation of specific information provided by the current study that sheds light on  management considerations should be made explicit--the sentence, “the ICSA model used in this study allowed us to estimate the changes in biomass, recruitment, and harvest rate along the shell length frequency distribution by year.” needs to be expanded to explicitly describe the interpretations that these estimations provide.

Discussion lines 441-458 are important, and should be more clearly devoted to the effect on the analyses of the new beds/areas that were exploited in 2016.  Figure 9 is key to understanding some of the results. The reader needs to better understand how the results that are interpreted as indications of overfishing may be confounded by the vagaries of serial depletion of sedentary, aggregating species.  Can the data be parsed to reveal specifically what occurred on tracts that were fished from 2011-2016? The new 2016 tracts in Figure 9, as the authors state, skew the information on overfishing when presented in aggregate.

Discussion lines 461-463—citations are needed re. low and high productivity areas.
Lines 464-466—there are extant examples of these strategies to cite for Panopea.


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 SEQUENCE IDENTIFICATION AND EXPRESSION ANALYSIS OF ARF FAMILY IN SUGAR BEET (BETA VULGARIS L.) UNDER SALINITY STRESSES
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: In this work, the authors identified 16 auxin response factor related genes using sugar beet genome sequence and gene annotations. Bioinformatics analyses, e.g., exon-intron structure, chromosomal locations, expression profiling, were conducted. Some BvARF genes in sugar beet were found to be up-regulated or down-regulated to varying degrees under salinity stress.
Generally, the work is lack of novelty. Some results can be searched by publically database of the genome and most of the manuscript is descriptive. More functional evidences of these genes need to be provided. Some suggestions:
1. There were no details for the salinity stress experiments, which should be added in the Method section.
2. Several control genes should be added. According to Fig. 9 and Fig. 10, I don't think the expressions showed large changes.
When genes were picked from another gene family, probably another gene set will have more remarkable response to salinity stress.
3. Any transgenic experiments of the BvARF into Arabidopsis to check the phenotypes with salinity stress?
4. The genes (ghtj, qzmp, hgze ...) seem to be named at will.


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 SEQUENCE IDENTIFICATION AND EXPRESSION ANALYSIS OF ARF FAMILY IN SUGAR BEET (BETA VULGARIS L.) UNDER SALINITY STRESSES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors of this manuscript describe the identification and analyses on the auxin response factor (BvARF) gene family in the sugar beet genome using a bioinformatics approach. Using a quantitative real-time PCR approach, they have also shown the changed levels of gene expression in many of these BvARFs when plant seedlings have been under salinity treatment. I believe this work would add to the understanding of the plant auxin response factors.

This manuscript is well organized. The figures and tables are clear and helpful.

In general, the English language should be improved to ensure that international readers can clearly understand the text. Some examples are given below in more detail.

The introduction requires more detail and accuracy.
•	For example, I suggest that the authors improve the description at lines 33- 36 to provide more details about what has been known on the ARFs of other plants and justification for your study.
•	At line 37, I suggest the authors check if the statement “Sugar beet is a biennial herb of Chenopodium” is true. I am not an expert in plant systemics, but I would think sugar beet belongs to a different genus.
•	At lines 39-40, more details required and reference needed for “In China, the sugar beet production area and the saline land overlap in a large area.” as this seems to be the only justification of the saline tolerance study.
Experimental design: The experimental design was clear enough. I can’t judge if the saline tolerance study design was adequate since it is not my area of expertise. But the treatment seems rather simplistic.

Some changes, additions, modifications would be suggested as follows:
1)	lines 53-55: It is not clear what the germination conditions (the settings for the incubator and culturing conditions). This should be clarified.
2)	lines 61-62: it is not clear which dataset(s), ie annotation or genomic, and which version were downloaded and searched. Please clarify.
3)	line 94: Please define ICDH.
4)	Line 103: It is considered untidy to start sentences with figures. Please either reword your sentence or write the number in full.
5)	Line 117: Should it be “…a total of 14 BvARF gene loci were obtained….”
6)	lines 126-127: Surely all genes can be located to a genome assembly, either in chromosomes or scaffolds. So it is incorrect to say “…The other three genes hgze, jrpi, orwr could not be located, …” Please clarify/
7)	lines 133-134: please specify “other plants” and provide background in the Introduction. The criteria for dividing into six categories need to be clarified.
8)	lines 149-151: what program was used for the motif analysis? Please justify why the expected number of motifs was set to 20.
Validity of the findings: The results are reasonable given the experiments. However, I suggest the authors moderate their claims in lines 246-248 that “…BvARF may play an important role in sugar beet response to salt stress…” purely based on different expression levels. A lot more supporting evidence is required for that claim.
Additional comments: It is a paper that would add more knowledge to the understanding of plant auxin response factors, even though similar studies have been published in other plant species.

Changes both with the English language and the text will be required to improve the current manuscript to the publication standards. Some examples have been given below.

The introduction requires more detail and accuracy.
•	For example, I suggest that the authors improve the description at lines 33- 36 to provide more details about what has been known on the ARFs of other plants and justification for your study.
•	At line 37, I suggest the authors check if the statement “Sugar beet is a biennial herb of Chenopodium” is true. I am not an expert in plant systemics, but I would think sugar beet belongs to a different genus.
•	At lines 39-40, more details required and reference needed for “In China, the sugar beet production area and the saline land overlap in a large area.” as this seems to be the only justification of the saline tolerance study.

Some changes, additions, modifications would be suggested:
•	lines 53-55: It is not clear what the germination conditions (the settings for the incubator and culturing conditions). This should be clarified.
•	lines 61-62: it is not clear which dataset(s), ie annotation or genomic, and which version were downloaded and searched. Please clarify.
•	line 94: Please define ICDH.
•	Line 103: It is considered untidy to start sentences with figures. Please either reword your sentence or write the number in full.
•	Line 117: Should it be “…a total of 14 BvARF gene loci were obtained….”
•	lines 126-127: Surely all genes can be located to a genome assembly, either in chromosomes or scaffolds. So it is incorrect to say “…The other three genes hgze, jrpi, orwr could not be located, …” Please clarify/
•	lines 133-134: please specify “other plants” and provide background in the Introduction. The criteria for dividing into six categories need to be clarified.
•	lines 149-151: what program was used for the motif analysis? Please justify why the expected number of motifs was set to 20.

I also suggest the authors moderate their claims in
lines 246-248 that “…BvARF may play an important role in sugar beet response to salt stress…” purely based on different expression levels. A lot more supporting evidence is required for that claim.


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 SEQUENCE IDENTIFICATION AND EXPRESSION ANALYSIS OF ARF FAMILY IN SUGAR BEET (BETA VULGARIS L.) UNDER SALINITY STRESSES
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The manuscript has been revised according to my suggestions. I'm satisfied with the revision.