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: REAL-TIME REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION DEVELOPMENT FOR RAPID DETECTION OF TOMATO BROWN RUGOSE FRUIT VIRUS AND COMPARISON WITH OTHER TECHNIQUES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article develops new qRT-PCR primers and probe to determine the presence of a tomato virus that recently affected the south of Italy. Because of the importance of this crop in this region I think that the possibility to detect this disease in a easier way is crucial. In my point of view, the most relevant and original section of this work is the fact that the author explored the possibility of manipulate in a lesser extend the samples. So, they offer an easy, cheap and sensitive way to detect the virus.
I consider very important to correct some aspects of this work previous of publishing.
In general the English writing must be check out in all the manuscript, I suggest to contact some expert in English writing.
Some examples of sentences that according with my point of view need to be corrected:
In Bacground: In Sicily, the ﬁrst outbreak occurred in 2018 in diﬀerent Sicilian provinces represents a serious threat for tomato crops.
Line 54: In Italy the tomato production is more located in Sicily, where is one of the most economically horticultural crops, with the yield of approximately 40% of the total Italian production in greenhouses (Agri ISTAT, 2017).
Line 67: instead of makes should say make.
Line 70: instead of subsequently should say subsequent.
Line 342: it should say sample, not samples.
Line 357: should say the most important tomato production, not productions
Check this sentence: So, with regard to this pathogen, to date the only two tools available are:
I think that the world cultivation is used in a wrong way in many sentences, please review this in all the text.
Experimental design: Some issues that on my point of view need to be address to improve the work:

In results, section Mechanical transmission, the authors said that they could infect with the virus tomato and pepper plants, but not eggplant. And they detected the virus by PCR. There is no reference to a Table or Figure where the results are shown. For example: percentage of the total infected plants with symptoms, positive or negative PCR result. I suggest perform a graph showing these results.

In results, section Primer, Taqman® MGB probe design and protocol optimization, the author claim that their designed 5 pairs of primers for qRT-PCR and showed the one with the highest sensibility in Table 2. What means highest sensibility? Lower Cq values? Earlier virus detection? Better primer efficiency. I think that if the section is named protocol optimization they should show all the primers sequences with their corresponding primer efficiency and R2 values. Also, they should show the parameter that they measured that helped them to decide for the best one. Also, I think that it is very important when a person optimize a qRT-PCR show the melting curves in a supplementary figure.

Supplementary Table 1 needs more information. It is not clear what means % or at what correspond the Ac. numbers, I mean if they are all of the analyzed. It is not an intuitive table and there is no extra information in Results.

In section Different method for sample preparation and comparison of different techniques
for ToBRFV detection:
I think this is the most interesting result of the paper, the comparison between different isolation techniques and virus determination in my opinion is the most applicable part of this paper. But, my concern is about the final conclusion. The author said that the qRT-PCR method is the most sensitive because can detect the virus even with crude tissue extracts. However, most of the Cqs obtained using this extracts as template are higher than 30. These high Cq in most of the cases are considered as noise. I think that it is necessary show that these are real viral amplifications showing for example qRT-PCR negative controls.

Material and Methods:
Line 117: Why do you use 1 mM of primer F and 1 uM primer reverse? Is this a mistake?

There is an excel file (supplementary information) that is not mentioned in the paper at all.
Validity of the findings: As I mentioned before, I think that the author have developed a novel way of virus examination for tomato samples. Compared with the usually used techniques in the field seems to be a cheaper and easy way to do it. That's the novelty of the paper.

However  and as I mention in the previous sections of this revision, I think that several issues need to be check out before to publish this work
Additional comments: I suggest a deeper revision of the English writing. Some sentences are not clear and not easy to follow.

Please, check out the tables, some of them need more details for a better interpretation of the results.

Please, add the information suggested before. Some results affirmations are not supported with 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: TRANSCRIPTOME ANALYSIS OF THE INDUCTION OF SOMATIC EMBRYOGENESIS IN COFFEA CANEPHORA AND THE PARTICIPATION OF ARF AND AUX/IAA GENES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors of the study analysed expression changes during SE in Coffea canephora by using rna-seq ad qPCR. Generally speaking it is a good study but there are some concerns needing to be addressed.
Experimental design: 1. line146 why to choose these days (14, 9, 0 DBI and 1, 2, 21 DAI) for RNA-seq DEG experiments? Besides, why to choose these 5 comparisons must be clearly stated. 14 and 21 likely stand for two and three weeks. What about the others? These experimental designs are essential to conclusions. Why were not DBI0 VS DAI2,14,21 analysed? They look to me to make sense because they are to compare between before induction and after induction. I'd like to know why not choosing these comparisons. Please correct me if I was wrong or overlooked it.
2. In figure 4, can the authors classify why 0DBI showed less DEGs than 9DBI? Because 0DBI stands for the later developmental stage I think 0DBI should have more DEGs compared to 14DBI.
3. DEGs in the study didn't consider the change of fold (line 176-177), which is typically standard in DE analysis. This perhaps leads to the high fraction of DEGs showed in the line241-245. I recommend the authors to carefully revise it. Or if the authors think it's fine not to set an arbitraty cutoff of fold change for DEs I'd like to know the reasons.
Validity of the findings: 1. The correlations between replicates for each range from 0.7 to 1.0 (line 174-177, fig. S1). However, 0.7 between replicates is not very high as compared to other studies. Is there any reason for that?
2. Why is there not an error bar shown in the qPCR figure 6? I do not think the authors have stated that there are replicates for qPCR experiments. If so why didn't the authors have any replicates for qpcr or simply because they were done but not indicated in the manuscript?
3. citations are needed to support the discussion at line332
Additional comments: 1. Figure 2 what are the values indicating? what is the shaded area in the right part of the figure?
2. what are the values in table 2 representing?
3. in table s2: at 1 times and > 1 times should be changed to uniquely aligned and multiply aligned reads
4. typos:
line121: this, the aim?
line 124-125: rephrase please
line276 lowly expressed
line277: in which it increases
382: showed to have


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: TRANSCRIPTOME ANALYSIS OF THE INDUCTION OF SOMATIC EMBRYOGENESIS IN COFFEA CANEPHORA AND THE PARTICIPATION OF ARF AND AUX/IAA GENES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The work is fairly well-written  and sheds light on the involvement , whose findings lead to a better understanding of the genes involved in auxin signaling pathway as well as their expression profiles during the somatic embryogenesis (SE) process in Coffea canephora.

Authors clearly indicate a knowledge gap in the field of study, establishing the context, background and/or importance of the topic.  It is established the desirability of the research, and listing the research questions and  hypotheses, and explaining the significance and validity of the study.
Experimental design: What is presented is  an original primary research pretty much in line with the scope of the Peer J.  The research question is well- defined, relevant and meaningful, and the findings do contribute to expand and advance the current knowledge on coffee SE. It is clearly stated how the research fills an identified the knowledge gap of SE in coffee.

As far as the methodology is concerned a rigorous investigation performed to a high technical and ethical standard, with methods described with sufficient detail and information to be replicated elsewhere.
Validity of the findings: Regarding the findings the research group is a leading team in the targeted topic and the data presented here are  robust, statistically sound, and well-controlled.  However, in Figure 6 there is no indication whatsoever of a statistical analysis to compare expression levels!

Remarkably, the  conclusions are   appropriately stated, pretty much connected to the original question investigated, and  limited to those supported by the results.
Additional comments: The work is fairly well-written  and sheds light on the involvement , whose findings lead to a better understanding of the genes involved in auxin signaling pathway as well as their expression profiles during the somatic embryogenesis (SE) process in Coffea canephora.

Authors clearly indicate a knowledge gap in the field of study, establishing the context, background and/or importance of the topic.  It is established the desirability of the research, and listing the research questions and  hypotheses, and explaining the significance and validity of the study.

However, it would be desired to offer a brief synopsis by mentioning the state-of-art of the application of the transcriptome approach to coffee, just mentioning some relevant previously literature:

Yuyama et al. (2016) Mol Genet Genomics,  291(1):323-36. doi: 10.1007/s00438-015-1111-x.
Cheng et al. (2017) Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts, GigaScience, Volume 6, Issue 11, November 2017, gix086, https://doi.org/10.1093/gigascience/gix086

Ivamoto et al. (2017). Transcriptome analysis of leaves, flowers and fruits perisperm of Coffea arabica L. reveals the differential expression of genes involved in raffinose biosynthesis. PLOS ONE, doi: 10.1371/journal.pone.0169595

- I would suggest to include ‘cellular totipotency’ in the Keywords.

- It is suggested that authors should add a reference to justify the choice of Cyclophilin as the reference gene, since it is not a commonly used gene;

- In line 146 describe better how these young leaves were sampled (how many and how much mass this represents);

- It is interesting to have the scale bars in Figure 1, at least for 1 B, 1C and 1E;

- In Figure 6 there is no indication whatsoever of a statistical analysis to compare expression levels.

Overall, the article should be accepted if the authors make some revisions, minor enough that I would NOT necessarily need to re-review it .


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

Input:
Title: TRANSCRIPTOME ANALYSIS OF THE INDUCTION OF SOMATIC EMBRYOGENESIS IN COFFEA CANEPHORA AND THE PARTICIPATION OF ARF AND AUX/IAA GENES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript "Transcriptome analysis of ARF and Aux/IAA expression during the induction of somatic embryogenesis in Coffea canephora" by Quintana-Escobar et al. ((#36035) is a very interesting work concerning a transcriptomic analysis of somatic embryo induction and development in an economically relevant crop, Coffea canephora. The work is well designed and adequately developed. The authors have made use of up-to-date bioinformatic tools to obtain significant results about the implication of auxin signaling in the induction of somatic embryos in this species. Nonetheless, to my understanding, some changes should be made to publish it, as well as I would appreciate some questions to be clarified.
- English language: the text should be checked to change some incorrect English grammar expressions, some sentences that are not clear, as well as several typos and punctuation marks. I will give some examples below:
  > English grammar expressions:
    - The  simple past of the verb "show" (showed) should be used instead of "show" or "shown". Examples can be found in Lines 203, 217, 222.
    - Correct correlation between subject and verb. Line 278: "The expression changes of the gene correlates...".
    - Adjectives have no plural: Line 163: "raws".
  > Sentences that must be corrected or re-written:
    - Line 68: "knowing in depth...". Line 215: "The recovery sequence rate...". Line 249: "...to the functional annotation as putative encodes to proteins involved...". Lines 404-405: the sentence should be rewritten.
  > Typos and punctuation marks:
    - Typos: Line 121: "This". Line 271: "ARAF6". Line 346:"AGAMUS". Line 398: "...in the account". Line 239: it should say "(14 DBI vs 21 DAI)".
    - Punctuation marks: many commas are found in the text that should not be there, as well as they are missing in other positions. Besides, particles are also missing throughout the text. Just a couple of examples: Line 87: " The PGR mainly used are auxins, alone or in combination with other regulators, and...". Line 116: "Using a RNA-seq approach, it has been...".

- Scientific comments. Please consider the following suggestions:
  - Expression of several genes is measured both with the RNA-seq data and with RT-PCR, but there is a lack of correlation between the values found. Were the same samples used for the two experiments? This should be addressed or clarified. For example, for the gene ARF18 the results are strikingly different in Fig 3, Fig 6 and Table 2. This should be explained. Indeed, the relative level of expression found for this gene with RT-PCR is extraordinary big for a transcription factor.
  - Some interesting results are not discussed. Though the paper is focused on ARF and Aux/IAA genes, the identification of other genes relevant for the process is not discussed, and I think that they should be at least outlined in the Discussion. Particularly for the NAC protein, mitogen-activated kinase and the ABC transporter.
 - At some points the Discussion lacks proper referencing. Examples can be found in Lines 330-335, 344-347 and 359-365.
- Lines 203-208: Do all the embryos generated successfully develop into a seedling?
 - Discussion about ARF genes should be focused on the orthologs of the genes analyzed in this work, rather than a generalist discussion about ARFs.
- Line 105: I think that the genomic resources are characterized rather than generated.
- Lines 117-121: Do the species that are mentioned correspond to the references that follow?
- Some Figure legends are too brief, it would be interesting if they included more information.
- Why was the cyclophilin gene chosen as a reference gene for the RT-PCR experiments?
- Lines 376-379: It should say that those expression data are for SE in Arabidopsis.

In conclusion, this is a very interesting work, but some English language editing is needed. On the other hand, a discussion more focused on the results and a proper referencing would help increase the quality of the manuscript.
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: TRANSCRIPTOME ANALYSIS OF THE INDUCTION OF SOMATIC EMBRYOGENESIS IN COFFEA CANEPHORA AND THE PARTICIPATION OF ARF AND AUX/IAA GENES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors did good revisions. However there are still several problems awaiting further clarification.
1. For the 1st question in last revision, it's nice that a new figure has been inserted and there were a few clarifications. But, why 9DBI, 1DAI, 2DAI, and 21DAI were chosen needs more rationales.
2. For the 2nd question, the authors replied in the letter "the most dramatic changes in gene expression occurred during the first days after placing the explants in a new culture media with a different composition to begin the induction of SE". They also cited Cao et al. 2007 in the revised manuscript to support their argument. However, if i didn't misundertand it, did 9DBI relate to the main purpose of the study? If the main focus is to study gene expression change after explants were placed in new media, then there should be more transcriptome samples during the first few days, ie. between 14DBI and 9DBI? Otherwise 9DBI may not be necessary to the study. Please clarify that this point (also relates to the above question in terms of selection of the days of sampling).
3. For the 3rd question, the authors said they forgot this important criterion in the original version of the manuscript. As so there should be original results with p-values and fold change in the supplementary materials or by online links.
Experimental design: 1. For the 1st question, i think 0.7 was reported as the minimum correlation coefficient between rna-seq and microarray in Sekhon et al. (2013). For Mukaka et al. (2012) I don't think it relates to rna-seq sample replicates directly. so I still am not convinced by the authors that their correlation between technical replicates is sufficient.
Validity of the findings: good
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: TRANSCRIPTOME ANALYSIS OF THE INDUCTION OF SOMATIC EMBRYOGENESIS IN COFFEA CANEPHORA AND THE PARTICIPATION OF ARF AND AUX/IAA GENES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have made several changes to the manuscript that greatly improve its quality. The have carefully answered all reviewer´s suggestions, taking them into account to upgrade this research article. Furthermore, they have included a new Figure for clarity purposes. I believe that with these changes the work is significantly improved.

Minor comments or typos:
- Line 179: RStudio.
- Line 343: identified.
- Line 440: PGR.
- LIne 451: mitogen-activated protein kinase...
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: LEAD ISOTOPE TRENDS AND SOURCES IN THE ATMOSPHERE AT THE ARTIFICIAL WETLAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please, see "General comments for author".
Experimental design: Please, see "General comments for author".
Validity of the findings: Please, see "General comments for author".
Additional comments: The article deals with the seasonal occurrence of lead (Pb) in total suspended particulate mater (TSP) in the Cuihu Wetland in Beijing (China) and the identification of possible Pb sources using stable Pb isotopes, 206Pb, 207Pb, 208Pb and 204Pb.
The main result is that the occurrence of Pb in the atmosphere of the Cuihu Wetland is seasonally variable and the main source of lead is coal burning together with traffic emissions.
I can conclude that the manuscript is original, although not fully novel. On the other hand, this type of research is still interesting, an of high importance, because still a huge number of articles dealt with this topic appear in peer-reviewed literature, mainly in highly impacted journals.
I can imagine that the article may be published in PeerJ, however, some revisions of this manuscript version are urgently needed.
My main comments on the manuscript are the following:
1. I could not find in „Materials and methods“ section no quality control/quality assurrance of the method used for the determination of isotopic Pb composition of TSP samples. It is one of the essential steps to provide precision, accurracy and reliability of analyses performed, especially, in the case of special isotopic analyses.
2. Lines 118 – 132 – You state here that as a reference element, Al was used. However, no information is given in „Materials and methods“ how Al was measured in your TSP samples. It would be also useful to provide the measured concentrations of Al in TSP samples in the main text. Additionally, you write here that as a background value for Al, Al concentration in Chinese soil in 1990 was used for the calculation of EFs, however, it is not clear why Al concentration in Chinese soil in 1990 was used as the background concentration. What was Al concentration? What is Chinese soil in 1990? This is not clear at all. Also, it would be very useful to add what value of Pb background concentration was used. Please, provide better explanation for this and provide it in the text.
3. Lines 209 – 215 – you write here very controversial conclusions. In Lines 155 – 157, a potential reader can read that Pb concentrations in TSP samples are not high because of self-purification ability of the Cuihu Wetland and its distance from pollution sources. However, here, one can read something about high concentrations of Pb and about close proximity of the Cuihu Wetland to some pollution sources, such as road and sand mining plant. Therefore, my question is „What is real situation?“. This must be clarified. Additionally (Lines 219 – 225), you state that different sources of Pb in TSP exist in summer and winter, however, Pb isotopic ratios seem to be not significantly different between summer and winter. Why then do you write about different sources of Pb in TSP of the Cuihu Wetland? Yes, I agree that the coal burning appears to be the main source. Is the coal used as energy source in the close vicinity of the Cuihu Wetland?

Minor comments and notes
- I found different style for reference citation in the main text, chronollogicaly as well as alphabetically. Please, use one style, meet requirements of the journal.
Line 68 – use „...difficult to make a...“
Lines 105-106 – use „Then, 8 mL of nitric acid (6%, v/v) and 2 mL of hydrogen peroxide were added to the vessel.“
Line 118 – „the origin of the heavy elements?; better would be „...the origin of lead...“
Line 122 – „the folume?“. What is it? You mean likely „The value of...“
Line 130 – „the crustal soil?“ Do you think seriously? Please, revise. You mean likely „parent rock“ or „underlying rock“
Line 135 – this should be „Figure 3“ because „Figure 2“ shows TSP concentrations. Please, replace figures in the way that „Figure 2“ will show Pb concentrations in TSP and „Figure 3“ will show TSP concentrations and cite them in the text.
Line 141 and Line 144 – in Line 141 – from 0.55 ng/m3 but in Line 144 you start with lower numbers. Please, revise this carefully.
Line 150 – use „...comparison...“; not „comparson“ and „...related to...“
Line 151 – use „...in the Cuihu Wetland were enough low...“. Please, check the whole manuscript, and use only one form of the wetland name. I prefer using „the Cuihu Wetland“ as in Abstract.
Line 156 – delete „due to the“
Line 166 – use „...is inversely proportional...“
Line 171 – use „For example, it is shown that...“
Line 193 – use „...in studying...“
Line 216 – use „...are reported to vary widely...“
Line 217 – use „...are enough low, while they are high in...“
Line 218 – use „This may be...“
Line 229 – use „Studies have also shown...“
Line 235 – use „...of lead in the samples.“
Lines 261 – use „...important factor...“
Figure 4 – it is not clear what numbers were potted on x-axis. Why Figure 4 is not made as Figures 2 and 3, where x-axis are seasons? Please, explain this or revise Figure 4.


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: LEAD ISOTOPE TRENDS AND SOURCES IN THE ATMOSPHERE AT THE ARTIFICIAL WETLAND
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. English of this manuscript needs as many sentences are unformal. What's more, the format of reference citation requires greatly improvment.
Experimental design: More information on the analytic methods should be added in the text.
Validity of the findings: no commnet
Additional comments: please find in the attachment


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: LEAD ISOTOPE TRENDS AND SOURCES IN THE ATMOSPHERE AT THE ARTIFICIAL WETLAND
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors improved significantly their original manuscript.
Experimental design: No comment.
Validity of the findings: The authors used stable isotopic analysis of Pb that was able to characterize the sources of lead in air.
Additional comments: The authors improved significantly their original manuscript. However, despite the improvement of the original version of the manuscript after the first round of review, some additional changes must be done before accepting it.
All my comments and changes that should be done are included directly in pdf-version of the revised manuscript. The majority of the comments is of formal character. My main concern is about the calculation of EF values because the background concentration of Al seems to me to be unreally low, only 6.22 mg/kg!!!. Normal Al concentrations in soils are in a range of thousands up to ten thousands mg/kg.
Please, request the editor for pdf-copy with comments that are highlighted by yellow color.


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: LEAD ISOTOPE TRENDS AND SOURCES IN THE ATMOSPHERE AT THE ARTIFICIAL WETLAND
Review round: 2
Reviewer: 2

Output:
Basic reporting: The English and referce format of this version have been improved. The figures and tables are neccessary and understandable.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: FULL GENOME SEQUENCE ANALYSIS OF A 1-7-4-LIKE PRRSV STRAIN IN FUJIAN PROVINCE, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Authors report the molecular characterization of an PRRSV isolate named  FJ0908 in Fujian Province, China. I recommend major changes to accept the manuscript. Although the methodological approach is correct, the authors should indicate what is the difference between FJ0908 with the strain LNWK130 previously reported and characterized by Zhang et al., 2018.  LNWK130 is an emergent strain from sublineage 1.5 and derived from the recombination of 1-7-4 isolates which were isolated in the United States. LNWK130 was identified in Liaoning Province and for the first time in China (Zhang et al., 2018: Emergence of novel porcine reproductive and respiratory syndrome viruses (ORF5 RFLP 1-7-4 viruses) in China. Vet Microbiol. 222:105-108).
If both strains (FJ0908 and LNWK130) have the same recombination pattern, this work, in the way it is proposed, does not have great originality. The important point would be that this emerging strain was found for the first time in Funjian province, clarifying the differences with the strain LNWK130 (if there are any).


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: FULL GENOME SEQUENCE ANALYSIS OF A 1-7-4-LIKE PRRSV STRAIN IN FUJIAN PROVINCE, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. Figure 2 is too small to see clearly. Need to redesign/reorganize this figure so it's readable when printed on a paper.
2. In Table 1, LNWK96 was isolated in China, not USA. This should be corrected. Other isolates should be double checked as the reviewer cannot check for you one by one.
3. Line 59, "more than ten open read frames", but line 60 only listed 10 ORFs. Either remove the "more than" on line 59 or list more than 10 ORFs.
4. Line 71, 1-7-4 should not be called a lineage here, especially lineages, 1, 3, 4.1, 8.7 were just introduced in the same paragraph. Calling 1-7-4 in this context may mislead the readers to think 1-7-4 is a true lineage in parallel to them, while actually it belongs to lineage 1 sublineage 1.5.
5. Remove the period on line 84.
6. Lines 123-124, "four proven antigenic regions were proven"? should the first proven be changed to "predicted"?
7. Line 169, add "is" between "It" and "hard".
Experimental design: 1. The previous study by Zhang et al. and the isolate LNWK130 should be compared and discussed more in the current study. Due credit should be given to the previous study, as many of the analyses (including the PCR method) are either very similar to the Zhang et al. study or used the method in Zhang et al.
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: FULL GENOME SEQUENCE ANALYSIS OF A 1-7-4-LIKE PRRSV STRAIN IN FUJIAN PROVINCE, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: see general comments
Validity of the findings: see general comments
Additional comments: The corrections made in the manuscript are not enough to show the differences between LNWK130 and FJ0908. I think that the central point of this article is to focus on the comparison of these two strains since LNWK130 was identified for the first time in Liaoning Province China and shared a high sequence identity with FJ0908. Authors sould highlight that this emergent strain now also circulates in another province of China, Fujian Province.
To improve this point, authors should:
  -Deepen the information provided in table 2 regarding the nucleotide changes between FJ0908 and LNW130.For example, focus on changes in the recombination zone.
-Replace the analysis of figure 2 by amino acid comparison between FJ0908 and LNW130.
-Perform  the recombination study for LNWK130 with the same methodology and the same sequences used for the study of FJ0908 and compare the recombination breakpoints. This can be shown in a complementary figure.
Minor comments:
Eliminate figure 1, it is not necessary since the same information is published in Zhang et al. 2018
Show the recombination zone in gray in Figure 4 as it was in the previous version.
Problem with spaces between words in the new PDF version 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: FULL GENOME SEQUENCE ANALYSIS OF A 1-7-4-LIKE PRRSV STRAIN IN FUJIAN PROVINCE, CHINA
Review round: 4
Reviewer: 1

Output:
Basic reporting: see general comments
Experimental design: see general comments
Validity of the findings: see general comments
Additional comments: The manuscript is ready to publish correcting some minor points: It is very important that LNWK130 appear in the analysis of figure 1 but it does not have to appear in the recombination study (Figure 2b and 2c). This brings confusion and suggests that it is the same type of recombinant. Others recombinant strains should not be included in a recombination analysis. However, the comparison is neccesary since LNWK130 is a previously identified recombinant strain in China that has a high similarity with the strain identified in this work.  In line 165 authors should emphasize that LNWK130 is a recombinant strain too but is something different to FJ0908 and then compare the breakpoints. Authors must indicate the reference or put "data not shown" if they performed the analysis.

I don't understand what the authors wanted to put in the conclusión: In conclusion, 1-7-4-like PRRSV was also detected in Fujian Province of China except  Liaoning Province. Except?


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: INTEGUMENTARY STRUCTURE AND COMPOSITION IN AN EXCEPTIONALLY WELL-PRESERVED HADROSAUR (DINOSAURIA: ORNITHISCHIA)
Review round: 1
Reviewer: 1

Output:
Basic reporting: Additional citations are needed, please see attached review for suggestions.
Experimental design: Tthis paper could benefit from additional experiments conducting a baseline study using the same methodology on taphonomically altered extant skin, and unaltered, desiccated skin.  See description in review.
Validity of the findings: The findings are valid, but could be expanded.  See attached
Additional comments: Review of “Integumentary structure and composition in an exceptionally well-preserved
hadrosaur (Dinosauria: Ornithischia)” by Barbi et al.

These authors use SEM, optical microscopy (OM) and various synchrotron techniques to examine the composition of Late Cretaceous hadrosaur skin recovered from Alberta Canada.

This paper is carefully written and goes to great lengths not to overstate the data presented.  That is much appreciated.

The following is a line-by-line commentary on the paper, with conclusions at the end.

Line 52: It would be helpful to note that of these only synchrotron takes these analyses beyond morphology, and then note the limitations of synchrotron in determining the nature and source of the material studied.
Line 62.  How do you know that this integument was displaced? The skin, in Fig 1, appears to overlay a rib (patch 2), and patch one appears to originate from the dorsal surface?  I am not sure why the assumption of displacement? Also, there is an abbreviation (Ra) on the diagram that is not listed in the figure legend. Additionally, “close-up” is not a technical term, better to use “higher magnification”.  Even though “precise mapping” (line 77-78) is impossible, it looks like the specimen is somewhat disarticulated and displaced before the rock falls occurred, thus probably before internment.  This seems to suggest the specimen was exposed for some time at the surface before burial. How might this affect your interpretation?
Line 107, was this material studied embedded in a resin before sectioning? Polymers such as these should be compensated for, as they react strongly in vibrational mode analyses. Was the same analysis under the same parameters conducted on a sample of the resin only?
Line 121, please define “pristine skin”.  How was this collected?  Were gloves worn in the field to prevent transfer of human compounds such as sweat, skin flakes or keratin?
Line 124, a “…section was manufactured…” Standard petrographic sections require that the material be embedded in a polymer resin of some type.  What resin was used, under what conditions, and did this resin undergo the same analyses as the skin sample?
Line 130-“pristine piece….embedded in matrix…” if the skin was embedded it was chemically treated, thus no longer “pristine”, and was the matrix in which it was embedded sediment or polymer?
Line 136, please include molarity (or normal) values for HCL used? These authors may have better luck using HF on such skin samples (see Pan et al 2019).
Line 139, please provide more detail? What type of water? What temperature? How were the flakes collected from the water bath?
Line 154-55, how were these parameters determined? Is this standard use? If so, please cite.
Line 168-69, please provide a citation for the use of threshold masking.
Line 181-185, please label the area of sediment in figure 2A using a thin line. In fig 2C, can you outline a ‘scale’ using dashes? Is this a scale with a hinge region as in extant ‘reptiles’? or is the ‘scale’ inferred by the undulating and layered nature of the dark regions?
Line 201-202.  There is experimental and other evidence for the role of clays and preservation of fossil components.  See McMahon et al 2016, and references therein.
Line 206, fig 4A. this image is blurry (in reviewer copy) and it is hard to detect the “chain of substructures” mentioned in the legend.
Line 215 and figure 5 legend needs citations for these values.
Line 219-220 needs a citation.
Line 223, what “other peaks” of the alcohol group are not present? Please give example and citation.
Line 224 needs a citation, also line 227, 230, 231, 235.
Line 238, please clarify.  If thet sample was embedded in polymer to  section to required thickness that is a LOT of chemical manipulation.
Line 240, ‘more intriguing’ is your opinion.  ‘suggestive’ may be a better choice.
Table 1, citations should be provided for these reference data.
Line 241. Please expand the legend for figure 7.
Line 247 needs a citation, and please clarify why ‘in this case’ the peak at 1789 “would correspond to….”  If this peak tends to shift, or change in interpretation, please clarify this.
Line 251, the use of a microtome implies it was embedded in a resin.  Please state how the vibrational effects of the resin were compensated for.
Line 254-258, this discussion is a bit confusing, as proteins, lipids and polysaccharides are very different biomolecules, but all are organic.  Yet, there was only a “single organic carbon spectrum”?
Line 260-261 need citations for these values and their subsequent assignments.
Line 261-162, I don't think you can rule this out completely using this one method, particularly when these spectra are not compared to biomolecules altered through diagenesis, or through actualistic experiments. A good control would be to also analyses check humics complexed to proteins, or heat treated samples (as a supposed proxy for time)? Baseline data of extant archosaur skin subjected to taphonomic alteration would be a good control.
Line 263-65, is there a precedence for this approach? Please cite.
Line 282-83 needs a citation
Line 310-312, please explain how Fe III and Fe II can coexist in the samples measured here can co-exist, given that one requires oxidizing conditions; the other reducing? Particularly as in Fig 12 B and C, the Fe II and Fe III signals map to the same small fragment at the bottom of the image? What environmental conditions lead to this co-localization of this species?  Also, can you please go into more detail as to the meaning of the “featureless spectra”? how is this informative?
Line 319, again please state if these were embedded samples and how interference of resin signal was accounted for.  Are these the structures later referred to as “subcircular substructures resembling cells”?  How were iron microcrystals ruled out as a source?
Line 332-334, I think that fig 14 and 15 could easily be combined. Figure 15B needs a scale bar.
Line 338, “resembling cells” these structures are too small to be vertebrate cells, and they are the wrong shape to be skin cells. They may, however, be remnants of microbial cells, but the methods employed herein would not allow differentiation.
Line 354, the authors eliminate ‘reandom processes induced by diagenetic modifications” to explain these round substructures.  Please specify which “random processes” these might be, and how you are able to eliminate these.  If these are remnants of microbial growth on degrading skin, this would be part of diagenesis per se.  And, if microbial overgrowth occurred, it is possible that this preserved at some level the skin architecture, even if in replication by biofilm.
Line 359, these substructures are not consistent with skin cells.  Again, if they are about 2 micrometers in diameter, this is too small, as most skin cells are quite a bit larger, no matter the taxon.  Furthermore, the outer skin layers are dominated by squamous cells fused by tight junctions.  These cells are greatly flattened, not subcircular.  I agree with the authors in line 357 that these materials are likely associated with the diagenetic processes that led to preservation.
Line 361 should be ‘implicated’
Line 365-66 please support this statement with a citation; also the following.
Line 381-82, there is abundant literature on the correlation between clays and delayed degradation; in part due to the small grain size and high charge of clay particles inactivating bacterial degradative enzymes.  This might be helpful to cite.

Supplemental:
Please expand the legends for fig S7 and S8 to indicate to what each color refers.  Additionally, in the legend for S8, it is stated that there is an “absence of any remarkable peaks….between 1500 and 1800 cm-1, but to me there appears to be many peaks at 1500 that are significantly above baseline. More explanation is needed for these legends.

General comments
In general, I applaud the authors on the thorough analyses and the use of multiple unrelated techniques to support the general ‘story’ of preservation,—even though these methods did not, in the long run, shed light on the nature of the ‘organic rich layer’, its source (endogenous or exogenous), or ultimately, taphonomic processes to which these materials were exposed. Although this study demonstrates the capabilities of the methods employed, I am not sure exactly what the take-away points are.  Is the skin ‘organic’?  Apparently this is supported through the identification and localization of carbonyls, but further information is needed to determine the nature of this layer.

This paper is interesting and has potential for the study of originally soft tissues in the fossil record, but it appears incomplete.  It would be greatly strengthened by adding a baseline study on experimentally altered extant skin (e.g. high heat, pressure, desiccation, buried in sediments infiltrated with carbonate-saturated waters, to name a few) for comparison. It would also be aided by a similar study on extant unaltered skin (e.g. shed skin from a lizard?).

To the authors’ great credit, they were cautious in interpretation, and did not overstate the data, which is rare.

I recommend publication if the above issues are addressed.


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

Input:
Title: INTEGUMENTARY STRUCTURE AND COMPOSITION IN AN EXCEPTIONALLY WELL-PRESERVED HADROSAUR (DINOSAURIA: ORNITHISCHIA)
Review round: 1
Reviewer: 2

Output:
Basic reporting: In my opinion, the study satisfies the criteria for basic reporting.

The paper uses very clear and moderated language, without superlatives or hyperbole.
Experimental design: This is a welcome contribution to advanced analytical techniques applied to paleontological material. The research question is well defined and states a clear knowledge gap.

My expertise is in synchrotron radiation applied to paleontological material, but I am not too familiar with the particular synchrotron experiments used here. Nevertheless, the methods are described with a clarity and confidence with the appropriate information required for synchrotron based experiments.

The set of experiments are complimentary and support each other nicely.
Validity of the findings: It was refreshing to read a study where the conclusions were not over inflated.
The suite of techniques used is novel and corroborating.

In fact there is almost no speculation whatsoever, but this is ok as I believe that the results would not support them.
Additional comments: Line 45: Edwards et al. 2011 applied IR and synchrotron radiation techniques to 50 mya squamate skin from the Green River Formation, but this study is not referenced and probably should be.

Line 191 main text and section 2 of the SI:
I am skeptical of suggesting specific minerals based elemental analysis as many minerals have similar elemental components but different stoichiometry. While these minerals are the most likely candidates and an educated guess based on the authors knowledge of the sample and its geological context, it is misleading to suggest mineral identification this way. Corroborating petrographic or X-ray diffraction for example is far more definitive. Barite is pretty diagnostic from its elemental composition and is lucky that the authors have areas of almost pure barite. Most samples will be more heterogenous and the elemental peaks convolved.

Figure 7 and S7:
IR measurements support the mineralogical assignments made earlier from the elemental analysis. However, there are still some potential ambiguities here and I would really like to see a petrographic/crystallographic analysis done to confirm these minerals. It is not so much the identification of the specific minerals that I care about really, it’s the speculative assignment based on the data presented.

Figure S7 is not really useful and is just a great mess of spectra. Maybe splitting these up into groups would be more useful, plus identifying where each spectrum came from. Maybe you could do a cluster for each horizontal line of the map. I can see at least 3 if not 4 different spectral groups here that would be good so see more clearly.

I am not too familiar with the techniques in the following section so it is not appropriate for me to comment here

Finally, how were the samples handled and stored after sampling in the field? Sterile scalpels, foil envelopes, sealed viles etc. This information should be added.


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

Input:
Title: INTEGUMENTARY STRUCTURE AND COMPOSITION IN AN EXCEPTIONALLY WELL-PRESERVED HADROSAUR (DINOSAURIA: ORNITHISCHIA)
Review round: 2
Reviewer: 1

Output:
Basic reporting: As per the original submission I find the basic reporting satisfactory.

The study satisfies the criteria for basic reporting.

The paper uses very clear and moderated language, without superlatives or hyperbole.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Thanks for adding the additional information as requested.

I still am not particularly happy with S7 and S8. There are many medium to small variations in these spectra that I would like to be able to see.

I am not suggesting to take these data out, only that they are not much use (in my opinion) in their current format. I suggest maybe breaking one figure into maybe 2-4 panels to help compartmentalize the spectra. Right now I do not feel the figures perform the function that the authors intended.

One last thing that I failed to catch last time a reference to the technical specifications of the beam lines used would be great (sorry if I missed it). This would avoid adding more detail in that regard into this paper such as flux etc.

The additional information the authors have added to the manuscript since the initial submission is welcome.


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

Input:
Title: COMPARISON BETWEEN TWO- AND THREE-DIMENSIONAL SCORING OF ZEBRAFISH RESPONSE TO PSYCHOACTIVE DRUGS: IDENTIFYING WHEN THREE-DIMENSIONAL ANALYSIS IS NEEDED
Review round: 1
Reviewer: 1

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: The manuscript describes the potential of 3D tracking of zebrafish locomotion for the analyses of two compounds. Several major and minor issues should be addressed:

Major issues:

1. Public availability of the 3D tracking sotware used is indispensable for an adequate evaluation of the manuscript, in terms of scientific transparency and possibilities of reproducibility of their findings. The authors state in this manuscript: "Images recorded from the high-resolution cameras were processed through an in-house developed tracking software, see (Butail et al. 2013) for a detailed description". A close inspection of the Butail et al, 2013 paper did not find that the 3D tracking sotware used is publicly available. Other papers of the same group mention it but does not include the public availability of the 3D tracking sotware used: Butail S, et al, PLOS ONE 2013 (10.1371/journal.pone.0076123); Ladu F, et al, Zebrafish. 2015 (10.1089/zeb.2014.1041); Macri S, et al, Sci Rep. 2017 (10.1038/s41598-017-01990-z). Without public availability of a working version of the 3D tracking sotware used, it is impossible for this reviewer and for other scientists to verify or replicate their findings.
2. An analysis of posible false positives and false negatives should have a different statistical approach.

Minor points:
-The titie should be modified, in order to have a better reflection of the actual findings of the study.
-"genetic and neuroanatomic isomorphism" should be revised
-"High-throughput behavioral experiments on zebrafish generally share the following methodological structure: administration of water-soluble drugs" should be revised, as it also involves other type of stimuli.
-"we aimed at prospectively investigating whether 3D scoring of zebrafish behavior may also benefit pharmacological research", should be revised, as alcohol is more related to toxicology.
-Authors should explain the reasons for use of "serotonin reuptake inhibitor citalopram". Citalopram is mainly used as an antidepressant in humans.
-Details of preliminary PCA analyses are better located in the Methods section.
-Authors should provide details of the "stress coat" used
-Authors should provide details of the Flea 3 high resolution cameras and associated videos
-Authors should highlight that some tanks for traditional 2D analyses restrict movement in one of the axes
-Authors should highlight that the "3D analysis" is also biased to restrict movements in one of the axes (width is only 8.5 cm)
-Authors should include details of statistical significance in figures.
-Authors should discuss the posible disadvantages or challenges of the proposed 3D tracking analysis


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

Input:
Title: COMPARISON BETWEEN TWO- AND THREE-DIMENSIONAL SCORING OF ZEBRAFISH RESPONSE TO PSYCHOACTIVE DRUGS: IDENTIFYING WHEN THREE-DIMENSIONAL ANALYSIS IS NEEDED
Review round: 1
Reviewer: 2

Output:
Basic reporting: -The title should be changed in order to describe clearly the study and its results
-The aims of the study should be described as clearer and more concise.
-Authors should explain why they used citalopram and ethanol
-The last part of the introduction, about PCA is redundant, this part is in statistical and in the results section.
-The legends of the figures should have more information for a better interpretation, for example, the statistical method used, P-value. In figure 1 is important to mention what software was used to the reconstruction of the trajectory.
Experimental design: -Authors should report of resolution of the cameras
-what was the distance between the camera in overhead and the bottom of the tank ?, and -what was the distance between the camera in the front and the bottom of the tank?
-The tracking software is available for anyone?
Validity of the findings: -In 3.1 section subtitle, authors should clarify that PCA was performed only for 3D analysis
-Authors should conclude and discuss clearly if the model was or not replicated, according to their proposed goals in the introduction. For example, in the introduction, they mentioned that one of the goals of this study was” to replicate existing findings indicating that ethanol (Pannia et al. 2014)”. However, in the discussion section, the authors no compared their results or discuss it with Pannia´s results.
-It is not clear how the authors determined the false positive and false negative, this should be described in the method section
Additional comments: No additional comments


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

Input:
Title: COMPARISON BETWEEN TWO- AND THREE-DIMENSIONAL SCORING OF ZEBRAFISH RESPONSE TO PSYCHOACTIVE DRUGS: IDENTIFYING WHEN THREE-DIMENSIONAL ANALYSIS IS NEEDED
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors incorporated the suggestions made by this reviewer. The revised manuscrip might be accepted 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: COMPARISON BETWEEN TWO- AND THREE-DIMENSIONAL SCORING OF ZEBRAFISH RESPONSE TO PSYCHOACTIVE DRUGS: IDENTIFYING WHEN THREE-DIMENSIONAL ANALYSIS IS NEEDED
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors made the suggested corrections
Experimental design: The authors made the suggested corrections
Validity of the findings: The authors made the suggested corrections
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: INFLUENCE OF PHYLOGENETIC STRUCTURE AND CLIMATE GRADIENTS ON GEOGRAPHICAL VARIATION IN THE MORPHOLOGY OF MEXICAN FLYCATCHER FORESTS ASSEMBLAGES (AVES: TYRANNIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is mostly clear in its presentation. Which is to say, the literature and background and figures and tables and such are all sufficient and acceptable. The English is pretty rough, though, and has quite a number of problems of subject-verb agreement and other grammatical problems. Which is to say, this manuscript needs a good, thorough editing pass by a native English speaker ... but this should not affect its consideration as a publishable contribution.
Experimental design: I have some major concerns about the design of the analysis... The major concern is the focus on the tyrannids OF MEXICO. That is, this is therefore explicitly a polyphyletic group. It is odd to develop such an analysis of a non-natural group, and there will be many biases and odd effects that will enter, because some of the lineages in the analysis will be lineages that are all included in the Mexican avifauna (e.g., Xenotriccus), and others for which one species has made it to Mexico, but 20 more have not (e.g., Platyrinchus or Zimmerius). I think that this design problem genuinely cripples the analysis, which is otherwise interesting and well executed.

How to fix this? The paper would benefit massively from either doing the hard work of expanding the dataset to a monophyletic group ... e.g., all of the tyrannids, or some major subclade ... which would therefore cross much of the Americas. OR one could pick a subclade that is endemic to some smaller area of analysis. This would reduce the number of species, but one would be analyzing a natural group.
Validity of the findings: See point 2 above...
Additional comments: The extent of the Los Tuxtlas highland area in Figure 1 is odd ... too extensive, and clearly including much lowland forest.

In Figure 3A, there are several places where a bright yellow dot is on top of a deep purple dot. This spatial coincidence of high and low phylostructure in the same place makes no sense at all.


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: INFLUENCE OF PHYLOGENETIC STRUCTURE AND CLIMATE GRADIENTS ON GEOGRAPHICAL VARIATION IN THE MORPHOLOGY OF MEXICAN FLYCATCHER FORESTS ASSEMBLAGES (AVES: TYRANNIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Line 27-28: The abstract needs to be clear an precise since this is what influences the reader’s decision of whether to read the full article or not. To me the first sentence is not clear enough. The structure suggests that the authors imply that evolutionary history of taxa varies across geography, though based on the remainder of the article they clearly mean morphological variation across geographical space. Since the second sentence also refers to geographic variation of morphology, I would suggest leaving out the second half of the first sentence (“, which in turn also vary in geography”) which will avoid confusion in the readers and generally reduce repetition.

Line 33: to make the point very clear I suggest changing this to “phylogenetic structure of flycatcher assemblages of each locality”

Line 35: This should be “Linear mixed-effects models”

Line 44: traits themselves (bill, wing etc) do not increase. This should be changed to “morphological trait values increased”

Line 59: It would be beneficial to include some more recent work as well to complement Losos & Miles (1994), since these studies are still relevant and more recent work also exists. Furthermore it shows good knowledge of the literature on the side of the authors. E.g. Seeholzer et al. 2017; Phillips et al. 2018; Dehling et al. 2014; Raposo do Amaral et al. 2009

Line 59: “the accumulation of morphological diversity”?

Line 61-63: Suggest rephrasing. Speculation is not needed here: morphological variation is known to reflect species’ responses to biotic and abiotic factors, as traits are closely related to specific ecological niche dimensions such as diet and foraging behaviour (Grant & Grant 2006; Jonsson et al 2012), aerial movement and dispersal distance (Calmaestra & Moreno 2000; Dawideit et al 2009) and bipedal locomotion (Fitzpatrick 1985).

Line 66-68: I would have liked more detail here. How has evolutionary history been shown to influence geographic gradients? How do morphological traits vary with climate? i.e. bill shape and size for temperature regulation (see Campbell-Tennant et al. 2015)

Line 80: I find “morphological traits related to ecology” to be a more accurate description. Lifestyle traits are often more broadly defined and often connected to breeding (e.g. Sibly et al. 2012), whereas in this area of research, wing and bill sizes are often referred to as ecomorphological traits due to their close association with the species’ ecological niche (foraging, aerial movement etc). Perhaps the authors should consider using the term “ecomorphology” here and in other parts of their manuscript.

Line 219: “Brownian evolution” While Brownian motion can be used as a model of trait evolution, there is no such thing as “Brownian evolution”. The authors should keep it precise by writing “evolution following a Brownian motion model” (or similar) and should check the remainder of the manuscript for similar discrepancies (e.g. line 402).

Lines 238-263: In my opinion hypotheses and assumptions generally fit contextually better in the introduction, where an overall hypothesis was originally stated. The methods are in themselves already very long, so the manuscript would benefit from this section being moved to the introduction.

Line 294: “Table S3” does not seem to be the right table (this provides the PC1 factor loadings) I believe this should be Table S4.

Line 379-380: It would be helpful to the reader (this reader) if the text also clarified from which analyses these results are, especially because the explanation of patterns in morphological variation here could be from either the mixed effects models or calculations of phylogenetic signal. I presume, because of the mention of Table 3, that these are results for the mixed-effects models, but it would be good to clarify this in the sentence.

Line 429-445: In my opinion this paragraph is not suited to the discussion. Rather it serves as a justification for why the study is of interest. It would be better placed in the introduction.

Table 2: Important references have been overlooked for wing length: e.g. for locomotion – wing length and shape are very important factors in migration, and many members of the Tyrannidae clade are migratory species. This should not escape mention in this table, as wing shape also directly influences dispersal ability and evasive movements against predators.  E.g. Winkler & Leisler 1992, Dawideit et al 2009; Förschler and Barlein 2011. Also, there is a stray bracket in the references for bill variation in this table. I suggest the authors proof read for similar editing errors.
Experimental design: Line 120-121: “Despite the obvious expectation…” I urge the authors to be careful about statements such as this. The statement of an “obvious expectation” will leave readers wondering why the authors would then expect something different. Since this is what the paper is investigating, I suggest the authors rephrase their statement to intrigue the readers as to why this relationship may behave differently than expected.

Line 137-139: A reference to the measuring method used is missing here. Did the authors follow the established techniques described in Eck et al. 2011, or another source? To allow reproducibility of each measurement on the specimens listed such a reference should be included.

Line 155: It is not clear to me why the authors seek to avoid morphological variations associated with sexual dimorphism, especially if as stated, variation between the sexes is lower than variation expected between species (Claramunt 2010). It is common practice to sample both male and females when analysing morphological differences between species, and in my opinion, the dataset would be more robust if these were included in the study. Furthermore, I am also missing details of how many specimens were measured per species. What was the distribution and the average number of specimens measured per species? At the moment these details are only available if they are pried painstakingly from the raw data, whereas they should be mentioned in the methods within the manuscript.

Line 162-164: I am concerned that through the transformation of bill values through a PCA they are no longer comparable with the wing length values which were not transformed with a PCA. My reasoning behind this is because I would assume that these values are no longer within the same scale. I would suggest instead creating a bill index as a single measure of bill shape; e.g. dividing bill height by bill length as a representation of diet and foraging behaviour (where bill height is considered to be one of the most informative variables e.g. Willson 1972; Grant & Grant 2006; Lederer 1975; Jonsson et al. 2012).

Line 176-179: I am not an expert in using climatic data. Do these methods provide enough detail to reproduce this aspect of the study?

Line 186: How were topographic variables related to morphological measurements? In linear regression models? More detail should be provided here…

Lines 232-234: Is there not sufficient occurrence data available for these species on public databases or in published research (e.g. GBIF data or range maps from the literature)? Why did the authors choose to use distributional hypotheses over actual observational data?

Line 277-298: This paragraph contains repetitions which could be removed. Since mixed-effects models are quite complex, the description should be crisp and clear. Shortening the paragraph and keeping statements precise and streamlined should help with this.
Validity of the findings: Line 453: I am surprised that the study conducted by Miller et al. (2013) is not mentioned here, or in the manuscript in general. It would be an interesting point of discussion considering the authors’ finding that climatic gradients explain variation in morphology, and finding a positive influence of phylogenetic membership in most communities, but with low phylogenetic signal. These results could suggest that these factors may also interact to influence morphological variation in assemblages. i.e. are morphological of more clustered assemblages more restricted in their climatic ranges? Miller et al. find that niche conservatism constrains honeyeater assemblages in arid regions.

Line 523-524: This to me suggests an interaction between temperature seasonality and phylogenetic structure on their influence on morphological variation, where phylogenetic structure modifies the effect of temperature seasonality on the morphological variation within assemblages. Did the authors test for such an interaction? If not, I would suggest that such a test should be done.
Additional comments: The article presents a well thought-out study with established and supported hypotheses and interesting, relevant objectives. In general I see this a publishable study relevant to the aims and scope of the journal. While the methods are presented with a good structure and with a lot of detail, I do have some concerns with some aspects methodology which I have outlined in the experimental design section.

The results have been described in detail and the authors paid attention to aiding the reader with their interpretation.

There were several places in the manuscript where grammar and syntax were incorrect (e.g. lines 76, 103-104, 317, and 384-385). In other areas of the manuscript, the sentences were very long and unnecessarily complicated (e.g. lines 48-51), or repeated aspects mentioned in previous sections (e.g. 302-305, which is described again in the methods of the actual experimental setup, and 277-298). Often these sentences could have been split in two and described a little simpler without a loss of detail. As a result I had trouble following many sentences. I think thorough copyediting and general proofreading is necessary throughout the article to correct grammar and reduce repetitions before resubmission.


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: INFLUENCE OF PHYLOGENETIC STRUCTURE AND CLIMATE GRADIENTS ON GEOGRAPHICAL VARIATION IN THE MORPHOLOGY OF MEXICAN FLYCATCHER FORESTS ASSEMBLAGES (AVES: TYRANNIDAE)
Review round: 2
Reviewer: 1

Output:
Basic reporting: I think that the presentation of this paper is now much improved. The analyses are clear and well-presented, and the arguments are effective.
Experimental design: See my concern about monophyly below.
Validity of the findings: I think that the paper now makes a clearer and more effective argument toward the points that it attempts to make. See my concern about monophyly below.
Additional comments: OK, so I raised this point in my first review... the group that is being analyzed is not monophyletic, and I do not like that. The authors responded that they are interested in the phylogenetic structure of the assemblage, and that their insights do not depend on monophyly. I think that an argument might be erected to the contrary, but let's accept the authors' proposition... in that case, then, why not expand the assemblage to include the entire set of species that seek arthropod food items while airborne ... some wood warblers, Tityra, and several other taxa should probably be included. Or maybe the entire field of phylogenetic structure of communities is OK with non-monophyly, and this concern should be ignored?

There is a misspelling in one of the in-text citations: (Wainwrigth & Reilly, 1994).


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: INFLUENCE OF PHYLOGENETIC STRUCTURE AND CLIMATE GRADIENTS ON GEOGRAPHICAL VARIATION IN THE MORPHOLOGY OF MEXICAN FLYCATCHER FORESTS ASSEMBLAGES (AVES: TYRANNIDAE)
Review round: 2
Reviewer: 2

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: I am satisfied with the authors' responses to my comments and changes made to the manuscript and am happy for it to be published as is.


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

Input:
Title: PLANT AND INSECT HERBIVORE COMMUNITY VARIATION ACROSS THE PALEOCENE–EOCENE BOUNDARY IN THE HANNA BASIN, SOUTHEASTERN WYOMING
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a well-researched study on the effects of rapid environmental change across the Paleocene-Eocene boundary on plants and plant-insect associations. Previous studies on the response of plants and insect herbivores during the PETM have mostly focused on the Bighorn Basin, Wyoming. This study focuses on floras from the Hanna Basin, Wyoming, which was likely wetter based on the abundance of coals. The data are analyzed in a variety of ways to look at how plant and insect damage type diversity changed before, during, and after the PETM, how community structure changed, and how this may have been affected by depositional environments. The study shows changes in plant communities during the late PETM, which did not return to pre-PETM composition after. Herbivore community structure, using insect damage as a proxy, also changed during the PETM but returned to pre-PETM structures afterwords. An unexpected finding was that the highest damage diversity occurred at sites with the lowest plant diversity.
Experimental design: The experimental design is appropriate for the questions posed.
Validity of the findings: The fossil localities in this study represent a variety of depositional environments. Are there differences in the quality of fossil plant preservation among the sites that could decrease the potential of damage being preserved at certain sites? I know that E was mentioned as having the best preservation.

The finding that insect damage diversity did not track plant diversity is interesting. In modern ecosystems, correlations between plant diversity and insect diversity has been suggested in multiple studies, and I think this discrepancy with findings in extant ecosystems should be should be discussed. Feeny's apparency hypothesis is mentioned as a possible explanation for the high damage diversity on Platanites raynoldsii at Level C (a level with low plant diversity). Is there a biological explanation for the low damage type diversity at sites with higher plant diversity or could this be a preservational issue? A recent paper that explores the correlation between plant and insect diversity is Schuldt et al. 2019. Multiple plant diversity components drive consumer communities across ecosystems. Nature Communications 10: 1460.https://www.nature.com/articles/s41467-019-09448-8. A number of other relevant studies are cited in this paper.

Regarding changes in damage type diversity through the studied interval – Locality D was difficult to collect and therefore has a low sample size compared to the other sites. Therefore, the results from this site are considered more tentative in the manuscript. If locality D was removed from the analyses, would your interpretation of the results change in any way? For example, without D, damage type diversity appears to track changes in mean annual temperature. I’m not advocating removing locality D, just curious how this poorly sampled level could be affecting your interpretations of the responses of plants and plant-insect associations to environmental change.

Line 339: The line mentions that the described form of skeletonization is characterized by thickening at the ends of the secondary veins. Do you have any pictures that illustrate this or, if it is depicted in Figure 9, could you add an arrow to mark the position of this character? Also, the paragraph mentions that the veins of the leaf have been eaten, which was noted as atypical. What orders of venation were consumed? I can see at least some of the secondary and tertiary veins intact.

Figure 9 caption – “damage believed to be caused by extant beetle family”. Is this type of damage exclusively made by chrysomelids today?
Additional comments: Line 33: “insect herbivore diversity” – “insect herbivore damage diversity” is probably more accurate.

Line 90-92: “If Paleogene plant and insect communities had the same basic needs as modern ones, Hanna Basin plant and insect communities would not have
 been limited by water.” – Can you justify this statement more or add citations? Water limitations can vary a lot by species, so I was wondering if you were referring to plants and insects that are part of a particular biome type.

Line 219-220: “Herbivore damage was quantified on all identifiable leaves, and damage morphotypes (DTs) were documented using Labandeira et al. (2007).” – This could be more specific, because there are a bunch of different ways to quantify herbivory (DT system, surface area measurements, percent of leaves damaged, etc.). I now see that this is clarified later, but the sentence could be rephrased slightly to let readers know the general method of damage quantification before getting into the details in a later paragraph.

Figure 5. In Fig. 5A, “number of plant species” should be “number of plant morphotypes” or “morphospecies”. In 5B and 5C axes, what is “individuals” referring to? Number of leaves?

Typos etc.
Here are a few little errors I noticed when reading the paper:
Line 54 – missing period
Line 478 – missing the word “increase” somewhere I think
Carefully check citations – some have DOIs and some don’t, some titles are capitalized when they shouldn’t be (line 561 and 595, for example), missing publication info (line 578), etc.
Figure 9 caption – “Chrysomelid” should say “Chrysomelidae”; add space between “raynoldsii” and “with”.
Appendix A.1, A.2, D – The first cell in each of these files says “ï»¿”.
Check spellings in Appendix B - For example, on the HB172 page, distinct and sharply; on HB178, symmetrical; HB183, Averrhoites; Platanites spelled wrong on Platanites page


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: PLANT AND INSECT HERBIVORE COMMUNITY VARIATION ACROSS THE PALEOCENE–EOCENE BOUNDARY IN THE HANNA BASIN, SOUTHEASTERN WYOMING
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper is very well written in clear, basic English. The structure conforms to normal scientific standard and the references cited are appropriate. The introduction and background information provide appropriate context. The figures are clear although there are perhaps more than necessary and few changes to improve the clarity of a couple of the figures are suggested in the general comments to the authors. Raw data is provided.
Experimental design: This paper documents original research, describing a new set of megafloral localities from the Hanna Basin of Wyoming. The authors construct the stratigraphic and depositional context of their localities and analyze floral composition as well as evidence of insect damage. The research question is stated in the first paragraph: to study how plant and insect herbivore communities change during times of disturbance. Their question is completely relevant to their samples, which span the Paleocene/Eocene Thermal Maximum (PETM), an interval of rapid global warming in deep time. The only other comparable terrestrial record of this interval is from a fluvial setting in the Bighorn Basin of Wyoming. This study complements similar previous studies of the Bighorn Basin plants and insect herbivores but in different (e.g., lacustrine) environments. The investigation is rigorous and the results documented and described in great detail. There are sufficient descriptions and data available to replicate the results.
Validity of the findings: The underlying data have been provided and are robust, although limited at the level of the greatest interest, the PETM. However, the authors are clear about the limitations of the sample at this level and the interpretation of results is tempered by the limitations. The main conclusions, as stated on lines 527-534, are appropriate with respect to the results described and link back to the original research question.
Additional comments: I greatly enjoyed reading this paper and was happy to see another terrestrial record of the Paleocene/Eocene boundary described. I appreciate the amount of work that went into this project and your clear description of methods. I have a few comments line-by-line and suggestions for simplicity and clarity, but no major changes seem warranted. Great work!

Lines 43-45. Need references to back up this statement.
Lines 45-48. The scale and magnitude of the PETM are not analogous to those of modern anthropogenic warming. Please be careful not to overstate the significance of this event for predicting change in our near future.
Lines 59-61. Need references to back up this statement.
Lines 61-66. You describe variation among regions after the bolide impact, but I do not see how this translates to instability across the Paleocene. Do we expect plant and insect diversity to always coincide? Apparently they don’t in this study.
Line 70. Energy “budge” – I assume you mean budget.
Line 79. Does the Hanna Basin really expand the geographic distribution of samples? Aren’t they all from this part of the country?
Lines 79-81. Not sure that you need a geologic map for figure 1a, which provides more detail than seems necessary. Might be better for context to make this part of the map a larger picture of western North America with the other PETM terrestrial sites located. This would demonstrate just how little is known about this interval and how much your study contributes to our understanding.
Lines 153-156. Can you put the radiometric ages onto figure 2 as they are described here? What is the significance, if any, for this study if the upper age limit is completely off? I don’t recall any other references to radiometric ages – perhaps the information about age calculations for the individual localities not relevant here?
Lines 167-213. I found it difficult to follow the localities and their placement with respect to the coal beds discussed here in figure 2. I’m also not sure that this detailed description is important. Could it be moved to the supplementary information and a briefer description of the sedimentology be provided?
Lines 193-203. This is a bit distressing. The most important of the samples for comparative purposes would be the D samples, as they are in the PETM. But they are the least well constrained stratigraphically and the least well preserved.
Lines 225-236. Is there any possibility of uneven sampling bias in the results of these equations? Please elaborate.
Lines 240-244. Why use two different diversity indices to assess the same influence? I found the discussion of the results of these a bit confusing and would suggest chosing one with a justification as to why it is the best.
Lines 245-246. Similarly, why use both Pielou’s J and rank-abundance curves?
Lines 264-266. Does this mean that some specialized herbivory is unrecognized, because it doesn’t look similar to what we know of modern specialized insect herbivory?
Lines 277-280. Please explain why LMAT appears to increase at level C before the PETM in your reconstructions in Table 1. This seems to me to be a major inconsistency with what is known of the interval.
Line 281. Not sure I understand this statement. It does seem the LMAT and MAP change considerably. Did you do an analysis of the statistical significance? Or do you mean that the errors overlap? How do your estimates compare with those for the Bighorn Basin? I think this should definitely be expanded.
Line 298. Floral “diversity richness” indices – do you mean one term or the other? I also assume you mean table 2 not table 1.
Lines 283-314. I found this discussion of results very confusing, constantly flipping between tables and back to figure 4. I would suggest simplifying this to describe each level in turn. I would also suggest using fewer indices, since it seems to me that you are basically describing floral richness and evenness. Jumping between levels and quarries using multiple indices that describe the same or similar aspects of the fauna and using multiple tables and figures makes this section needlessly complicated.
Lines 315-324. I don’t understand the difference between figures 5B, 5C and 6. Is figure 6 a subset of figure 5B? If so, why include figure 5B at all? I’m not sure what figure 6B demonstrates? I think figures 5 and 6 could be simplified and combined.
Lines 325-332. Just in terms of simplicity and spacing, it seems as though figures 7 and 8 could also be combined.
Lines 343-362. I find the legend in figure 10 confusing. I think you could simply have a green triangle indicating Paleocene, level A; a yellow triangle indicating Paleocene, level B; and so on. Somewhere, it needs to be clarified what these solid symbols mean. Are they the averages for each level? Maybe the x symbols could also be color-coded. Also, you explain in the text why some of the x symbols have labels but I would include this information in the figure caption. Those labels overlap and obscure many of the data points. I think it would be helpful to have a fuller description of what the axes mean.
Lines 446-448. I don’t see how the species:area relationship would add significantly to the depositional signal.
Lines 477-479. This sentence seems to be incomplete.


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: DIFFERENCES IN TAIL FEATHER GROWTH RATE IN STORM-PETRELS BREEDING IN THE NORTHERN AND SOUTHERN HEMISPHERE: A PTILOCHRONOLOGICAL APPROACH
Review round: 1
Reviewer: 1

Output:
Basic reporting: Generally well-written and clear. Adequate introductory and background material. Figures relevant and of good quality. Raw data supplied. Experiments appear ethical and supported by the appropriate permits.
Experimental design: Seemingly within the scope of the journal, although the importance of the knowledge gap being filled is somewhat unclear. Methods are described in sufficient detail.
Validity of the findings: Raw data appear to be sound but I have some serious concerns regarding the statistical approaches used (see general comments).
Additional comments: This paper addresses the relationships between various feather growth parameters in 4 species of storm-petrel. Variation in these species is then compared to data from a wider sample of 164 bird species, and the results of this broader comparative analysis are then used to inform further assessment of variation within storm-petrels.

Overall this study is well written and I liked the attempt to link patterns of feather growth rate within storm-petrel species to variation across birds more generally. However, while I have less of an issue with the within-species component, I have serious concerns with aspects of the comparative analyses that must be addressed before going forward.

First, I have a number of issues with the methods used to compare Procellariform growth patterns to those of other avian species. Most importantly, I think the approach of ‘adjusting’ data points and then comparing the fit of resultant models is inappropriate and statistically flawed. In particular, to my knowledge it is entirely inappropriate to use a likelihood ratio test to compare goodness-of-fit for two models that are based on different data (L215-218). In this case, one model is based on untransformed data and the second is based on a dataset where Procellariformes or all outlier FGRs have been adjusted by a factor of 2. These two models are based on different data sets and therefore statements such as “It [the model] was significantly improved by both Procellariiformes adjustment…” (L246-248) and “Indeed, the improved fit of the Procellariiformes-adjusted model compared to the original model seems to confirm Langston and Rohwer’s (1996) suggestion” (L369-371) are invalid because you are comparing two different datasets.

Rather than a priori ‘adjusting’ data points to what you believe they should be based on a hypothesis, I think a much better way to approach this analysis would be to let the data speak for itself. Specifically, I think it would be much better to compare the fit of a model in which all species are described by a single intercept and slope, to one in which the Procellariform species are allowed to have their own intercept. In modelling terms, the first model would be FGR ~ FL (i.e. model A in Fig. 2) and the second model in which FGR ~ FL + Group, where Group is a variable distinguishing Procellariforms from non-Procellariforms (i.e. everything else). It would then be valid to compare these models using likelihood ratio tests to see if the ‘Group’ term significantly improved model fit (although achieving statistical significance may be difficult due to low sample size [n=4] for the Procellariform group).

Nevertheless, if your hunch about Procellariform growth bars is correct, then the ‘Group’ term in the model should indicate a different intercept for Procellariform species versus everything else. Moreover, using this approach it should then also be possible to derive estimates for the intercepts associated with these two groups, and if your hypothesis is correct then the Procellariform intercept should be half that of other birds (presumably because Procellariforms grow two bands per day rather than one). To my mind, this approach represents a more direct test of your hypotheses that is both statistically valid and avoids the need for forcing a pre-defined ‘adjustment’ onto some of your data points – the ‘adjustment’ is instead estimated as part of the model.

However, I should also note that if you use the same approach to test for different intercepts between outlier versus non-outlier data points (i.e. groups indicated in Fig. 2C) then you will automatically find that outliers have a significantly lower intercept, because that’s how the points were identified in the first place (i.e. they were chosen because they were lower than everything else). This raises the question of whether this ‘outlier’ analysis is useful or even warranted in the first place.

Second, and more minor but still important, in L193 the authors’ state that the performed a PGLS analysis using the corBrownian function. This approach assumes that your traits (or more accurately the residuals of the relationship between your traits) perfectly fit a Brownian motion model of trait evolution. This is rarely the case and therefore it is often better to run a PGLS analysis using Pagel’s lambda model, which is optimised to reflect the level of phylogenetic signal in the data. This can be easily done in the same framework as currently used by using the corPagel function instead of corBrownian.

Minor comments

L67-87 – This may be a naive question but isn’t part of the explanation that individuals use plumage signals to attract mates and maintain pair bonds during breeding, therefore should not moult such signals until after the breeding season? This explanation also implies a trade-off, but not in terms of energy allocation as is assumed throughout.

L69 – Should this read ‘temporally separated’ rather than ‘temporarily separated’?

L111-117 – I felt that there was perhaps a sentence or two missing here regarding why this is an important/useful thing to do. Can the authors expand upon the knowledge gap being filled, and why it is important?

L154-161 – does year (2017/18) explain any of the variation in measurements?

L182 – delete unnecessary ‘the’.
L219 – I don’t really follow what is being done in this analysis.


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: DIFFERENCES IN TAIL FEATHER GROWTH RATE IN STORM-PETRELS BREEDING IN THE NORTHERN AND SOUTHERN HEMISPHERE: A PTILOCHRONOLOGICAL APPROACH
Review round: 1
Reviewer: 2

Output:
Basic reporting: I only assessed other basic aspects of the manuscript (see general comments for authors)
Experimental design: I only assessed some basic aspects of the manuscript (see general comments for authors)
Validity of the findings: I only assessed some basic aspects of the manuscript (see general comments for authors)
Additional comments: In this manuscript Ausems and coauthors explore how growth rate of tail feathers (obtained from ptilochronology) varied between four storm petrel species differing in the degree of moult-breeding  overlap, i.e. two Northern hemisphere species typically showing this moult-breeding  overlap, and 2 Southern hemisphere species that do not show it. They also frame the values for these 4 storm petrel species within a larger database to infer “the nutritional condition of this species in relation to other species”. I think this approach could be useful to make some inferences on the way these storm petrels moult (feather growth rate can be a surrogate of moult speed, De la Hera et al. 2011) and whether one feather growth bar corresponds to a 24-h period. However, ptilochronology-based estimates of feather growth rate cannot be unequivocally considered estimates of nutritional condition (particularly when comparing between species), since growth bar width is also affected by other factors (e.g. birds grow their feathers relatively faster under temporal constraints; De la Hera et al. 2009, 2012). This raises the possibility that storm petrels differ in their feather growth rate by other innumerable reasons apart from the existence of a breeding-moult overlap.
This study assumes implicitly that sampled storm petrels from the Northern populations experienced a moult-breeding overlap during the growth of their tail feathers, but I have some doubts about this. Arroyo et al. (2004) show that there is overlap between primary moult and breeding, but the overlap with tail feather moult is very small in the Mediterranean populations of European Storm petrels, and is expected to be even smaller in Northern conespecific populations (such as in Faroe Islands, Arroyo et al. 2004). Additionally, the birds sampled in the Northern hemisphere by Ausem and coauthors were trapped using mistnets (not in the burrows), so they are likely to be sub-adult birds (floaters) that, in fact, could have never bred before. These two circumstances suggest that the tail feathers analysed by the authors for the Northern Hemisphere species were not necessarily produced during breeding which, in turn, suggests that the differences in feather growth rate between species could be caused by other factors apart from this breeding-moult overlap.
For previous reasons, I think the study cannot be so strongly framed in studying the effects of the moult-breeding overlap on feather growth rate and, consequently, should be completely reformulated. I also added below a few other important (non-exhaustive) comments that arouse from a first reading of the manuscript:
Line 105-110: this statement is not correct and I think authors misinterpreted the current evidence. The interspecies relationship between feather growth rate and feather length is perfectly linear, but this relationship is not isometric; it typically shows a negative allometry where birds with longer feathers grow those same feathers comparatively slower than birds with shorter feathers. There is also a linear relationship between feather mass and length that is isometric in this case (see Rohwer et al. 2009, De la Hera et al. 2012).
Line 154: Unlike small passerines, plucking full tail feathers from non-passerines (especially large ones) might damage the feather follicle, which might prevent the growth of a new tail feather in the future. Do you have information on whether storm petrels are able to regrow their tail feathers after a manual extraction? This would be relevant for future studies from an ethical and animal welfare point of view.
Line 168-170: Feathers tend to grow slower at the beginning and at the end of their development, so growth bars should be measured in homologous regions of the feather to avoid potential biases (Grubb, 2006).
Line 168: one spare “the”.
Line 172-173: Defining feather quality as a ratio between feather mass and length is not a good idea (see Peig and Green 2009, Oikos 118: 1883-1891). Why not to analyse and plot the relationship between feather mass and length, similarly to what was done in Figure 2 and 3 for feather growth rate and length.